Head of Department
Department of Microbiology-UiO
Member of
Contacts and network
- MiMa National RCN-funded research school Microbiology Matters
- Institute for Molecular Infection Biology (IMIB) / Zentrum für Infektgenetik (ZINF), Würzburg, Germany
Publications
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Özcan, Esma; Vagolu, Siva Krishna; Tamhaev, Rasoul; Lherbet, Christian; Mourey, Lionel & Tonjum, Tone
[Show all 8 contributors for this article]
(2025).
Isoniazid-Derived Hydrazones Featuring Piperazine/Piperidine Rings: Design, Synthesis, and Investigation of Antitubercular Activity.
Biomolecules.
15(9).
doi:
10.3390/biom15091305.
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Isoniazid (isonicotinic acid hydrazide, INH) is a key drug used to treat tuberculosis (TB), which continues to be the world’s most lethal infectious disease. Nevertheless, the efficacy of INH has diminished because of the emergence of Mycobacterium tuberculosis (Mtb) strains that are resistant to INH. Our goal in this study was to modify INH to reduce this significant resistance chemically. We synthesized INH-based hydrazones (IP1–IP13) through the reaction of INH with in-house obtained benzaldehydes carrying a piperidine or piperazine ring in refluxing ethanol. Upon confirmation of their proposed structures by various spectral techniques, IP1–IP13 were evaluated for their antimycobacterial capacity against Mtb H37Rv strain and INH-resistant clinical isolates with katG and inhA mutations using the Microplate Alamar Blue Assay (MABA). The compounds were additionally tested for their cytotoxicity. The obtained data indicated that the compounds with moderately increased lipophilicity compared to INH (IP7–IP13) were promising antitubercular drug candidates, exhibiting drug-like properties and negligible cytotoxicity. Out of these, IP11 (N′-(4-(4-cyclohexylpiperazin-1-yl)benzylidene)isonicotinohydrazide) emerged as the most promising derivative, demonstrating the lowest MIC values against all Mtb strains tested. Subsequently, the target molecules were evaluated for their capacity to inhibit enoyl acyl carrier protein reductase (InhA), the main target enzyme of INH. Except for IP11 demonstrating 81% InhA inhibition at a concentration of 50 μM, direct InhA inhibition was shown not to be the primary mechanism responsible for the antitubercular activity of the compounds. The binding mechanism of IP11 to InhA was analyzed through molecular docking and molecular dynamics simulations. Altogether, our research identified a novel approach to modify INH to address the challenges posed by the rising prevalence of drug-resistant Mtb strains.
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Tan, Oya Unsal; Vagolu, Siva Krishna; Tonjum, Tone; Kaplan, Ozan & Simsek, Rahime
(2025).
Promising Antimycobacterial Agents: Salicylidenehydrazines.
Archiv der Pharmazie.
ISSN 0365-6233.
358(7).
doi:
10.1002/ardp.70065.
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ABSTRACT Tuberculosis (TB) remains a major global health challenge, underscoring the urgent need for new therapeutic options. In this study, a series of salicylidenehydrazine derivatives were synthesized and characterized using spectroscopic techniques. Their antimycobacterial activity was assessed against Mycobacterium tuberculosis H37Rv. Among the 35 synthesized compounds, nine demonstrated significant inhibitory activity, with MIC values ranging from 0.78 to 50 μM. These active molecules were further evaluated against clinical isoniazid‐resistant (bearing inhA promoter and/or katG mutations) and multidrug‐resistant (MDR) M. tuberculosis strains. A particularly potent compound derived from 2‐bromo‐4‐nitrosalicylaldehyde exhibited an MIC of 0.78 μM against H37Rv and demonstrated low MIC values of 6.25, 1.56, and 1.56 μM against the inhA + , katG + , and MDR strains, respectively. Molecular docking studies were also conducted to investigate the interaction of active compounds with the target enzyme InhA. Overall, the results indicate that salicylidenehydrazine derivatives represent promising lead structures for the development of new anti‐TB agents effective against both drug‐sensitive and drug‐resistant M. tuberculosis strains.
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Boattini, Matteo; Aceti, Arianna; Bastos, Paulo; Mavromanolaki, Viktoria Eirini; Maraki, Sofia & Spiliopoulou, Anastasia
[Show all 50 contributors for this article]
(2025).
A European survey on anaerobes from paediatric blood cultures: a comparative analysis with adults.
European Journal of Clinical Microbiology and Infectious Diseases.
ISSN 0934-9723.
44(9),
p. 2207–2217.
doi:
10.1007/s10096-025-05185-7.
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Infections caused by anaerobes are common in children. However, limited data are available on bloodstream infections caused by these bacteria in Europe. A multicentre retrospective observational study was conducted over a 4-year period (2020–2023) across 44 European hospitals to analyze all anaerobes isolated from blood cultures. The study examined the epidemiology and antimicrobial resistance profiles of anaerobes identified in paediatric patients, comparing the findings with those observed in adults. Among the 14,527 total anaerobic isolates, 186 (1.3%) were detected from paediatric patients. These were predominantly Gram-positive (70%) and Gram-negative (22%) bacilli. The most prevalent species in paediatric patients were Cutibacterium acnes (24.7%), Schaalia odontolytica (9.7%), Actinomyces oris (8.1%), and Bacteroides fragilis (7.5%). Relative feature importance based on the mean SHAP (SHapley Additive exPlanations) values distinguished paediatric patients and adults based on their antibiotic resistance patterns with high accuracy. Compared to those from adult patients, Gram-positive bacilli detected in paediatric samples displayed higher resistance rates for meropenem (15% vs. 9%), metronidazole (52% vs. 24%), and vancomycin (27% vs. 6%), and lower resistance to benzylpenicillin (11% vs. 17%), amoxicillin/clavulanate (9% vs. 17%), and clindamycin (30% vs. 36%). Gram-negative bacilli in paediatric samples displayed lower resistance to benzylpenicillin (18% vs. 29%), piperacillin/tazobactam (26% vs. 33%), and clindamycin (20% vs. 27%), and they were highly susceptible to imipenem, meropenem, and metronidazole as those detected in adult patients. Bacteroides species detected in paediatric and adult patients displayed high resistance to piperacillin/tazobactam (33% vs. 39%) and clindamycin (38% vs. 29%), while they were highly susceptible to metronidazole. Compared to those from adult samples, Cutibacterium acnes in paediatric patients displayed lower resistance to benzylpenicillin (none vs. 15%) and clindamycin (17% vs. 29%). The comparison of species and susceptibility profiles of anaerobes detected in paediatric and adult patients highlighted the importance of reporting antimicrobial susceptibility surveillance data by age group
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Borgianni, Luisa; Cardinali, Gianluigi; Cassetti, Cristina; Cavalieri, Duccio; De Filippo, Carlotta & De Giuseppe, Rachele
[Show all 29 contributors for this article]
(2025).
The power of microbial life for the transformation towards a sustainable planet: key messages from the 2024 IUMS Congress in Florence, the city of the Renaissance.
microLife.
6.
doi:
10.1093/femsml/uqaf018.
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The 2024 International Union of Microbiological Societies Congress was held in Florence, the city of Renaissance. The theme was to increase the awareness of the power of microbial life, recognizing that it can lead the transformation towards a sustainable planet. The meeting gathered over 1400 experts from more than 90 countries and focused on the transformative potential of microbiology in addressing global challenges and aligning microbial science with the Sustainable Development Goals. Six roundtable discussions explored the pivotal role of microbiology in mitigating climate change, preparing for pandemics, producing sustainable energy, promoting a One Health approach, understanding microbiome dynamics, and developing data infrastructure. The discussions revealed that microbes are still overlooked agents in sustainable solutions. Expert panellists at the roundtables discussed microbial innovations in hydrogen and biofuel production, conversion of greenhouse gases, biomanufacturing, and soil restoration, the role of microbiome in immune health, the importance of cross-kingdom interactions, and the integration of food, environmental, and microbiomes under the One Health framework. Panels stressed the need for equitable access to vaccines, diagnostics, and data sharing, especially in the face of antimicrobial resistance. The importance of global collaboration, data repositories, and regulatory alignment, was repeatedly emphasized. The congress invited calls for the formation of an international microbiology coalition, need for interdisciplinary partnerships, increased investment in microbial technologies, updating of regulatory frameworks, and integration of microbiome science into public health and environmental policy. Microorganisms are the oldest architects of nature, able to build a sustainable future for the planet.
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Khose, Goraksha Machhindra; Vagolu, Siva Krishna; Aesoy, Reidun; Stefánsson, Ísak Máni; Ríkhardsson, Snorri Geir & Ísleifsdóttir, Dagmar
[Show all 12 contributors for this article]
(2025).
Functionalized regioisomers of the natural product phenazines myxin and iodinin as potent inhibitors of Mycobacterium tuberculosis and human acute myeloid leukemia cells.
European Journal of Medicinal Chemistry.
ISSN 0223-5234.
285.
doi:
10.1016/j.ejmech.2025.117244.
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The natural bioactive products myxin and iodinin are phenazine 5,10-dioxides possessing potent anti-bacterial and anti-cancer activity in vitro. This work describes the synthesis and derivatization of new myxin and iodinin regioisomers, developed from 1,3-dihydroxyphenazine 5,10-dioxide. Compounds were evaluated for activity towards M. tuberculosis (Mtb) strains, a human AML cell line (MOLM-13), and two non-cancerous mammalian cell lines (NRK and H9c2). Highly potent analogs were developed having IC50 values against MTB down to 20 nM and 1.4 μM for human AML cells. 1-OH-3-O-alkyl substituted derivatives demonstrated high efficacy against Mtb and low toxicity in normal cells. 2,3-substituted regioisomers of myxin and iodinin were shown to be inactive, highlighting the importance of oxygen substituent in position 1 of the scaffold. A strong positive correlation between anti-MTB and anti-AML activity was revealed, suggesting a common mechanism of action in bacteria and cancer cells. These findings demonstrate the therapeutic potential of 1,3-O-functionalized phenazine 5,10-dioxides in chemotherapy for Mtb and AML and contribute to the structure-activity understanding of phenazine 5,10-dioxides with respect to their biological activity.
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Karayavuz, Burcu; Vagolu, Siva Krishna; Kart, Didem; Tonjum, Tone & Unsal-Tan, Oya
(2024).
Synthesis, antimycobacterial and antifungal evaluation of new 4-(furan-2-ylmethyl)-6-methylpyridazin-3(2H)-ones.
Journal of the Serbian Chemical Society.
ISSN 0352-5139.
89(11),
p. 1423–1431.
doi:
10.2298/JSC230424040K.
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This study reports the synthesis and evaluation of a series of new pyridazin-3-ones with furan moieties 5a–j and 6a–f, to test for their antimycobacterial and antifungal activities. The structures of the target compounds were confirmed by elemental analysis and spectroscopic techniques (IR, mass, 1H-and 13C-NMR). Amongst the compounds tested, 5e, 5g, 5i and 6e exhibited highest activity against Mycobacterium tuberculosis, while 5h, 6d and 6f showed moderate in vitro antifungal activities against Candida albicans and Candida parapsilosis.
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Barouti, Angeliki; Herfindal, Lars; Vagolu, Siva Krishna; Homberset, Håvard; Tonjum, Tone & Kopplin, Georg
[Show all 7 contributors for this article]
(2024).
Evaluation of the cytotoxic and antimicrobial potential of epiphytic biomass obtained from Laminaria hyperborea biorefinery side-streams.
Frontiers in Marine Science.
11,
p. 1–13.
doi:
10.3389/fmars.2024.1384136.
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Harvested Laminaria hyperborea contributes to approximately 3.3 million tonnes of epiphytes discarded as waste despite containing organisms such as red algae and bryozoa, known to produce a range of high-value and bioactive compounds. Our research aim is to valorize epiphyte biomass by exploring the cytotoxic and antimicrobial potential in various extracts and optimized fractionation by flash chromatography. All extracts and fractions were tested for cytotoxicity towards cell lines derived from Acute Myeloid Leukemia (AML), prostate cancer (PC-3), and breast cancer (MCF-7), as well as non-tumorigenic cell lines from the kidney and heart using metabolic activity as a read-out. Antimicrobial activity was assessed using microplate based Alamar Blue assay and minimum inhibitory concentration (MIC) to determine the MIC against various human pathogens. Six extracts demonstrated significant cytotoxicity across all five cell lines (EC50 values below 46 µg/mL), while hexane extract selectively targeted AML cells with EC50 of 1.1 µg/mL. The hexane and ethyl acetate extracts displayed antimycobacterial and antifungal activity (MIC 100 µg/mL). A multistep flash fractionation of the methanolic extract revealed several cytotoxic and antimicrobial activities. The flash fractions displayed a selective activity pattern depending on the elution solvent. Nine fractions were cytotoxic towards all cell lines (EC50 below 72 µg/mL), and four were highly cytotoxic (EC50 below 5.4 µg/mL). Two non-polar fractions were selective for the AML cell line. These results highlight the potential for discovering anticancer and antimicrobial compounds in epiphytes from Laminaria, necessitating further research on their active compounds. Overall, this work underscores the environmental and scientific value of converting marine by-products into a valuable resource, aligning with sustainability and ethical goals.
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Cao, Dan; Jiang, Xiuzhi; Wu, Tiantian; Xiang, Yanghui; Liu, Jiaying & Li, Zhen
[Show all 12 contributors for this article]
(2024).
Identification of essential oils with strong activity against stationary phase Mycobacterium abscessus.
Heliyon.
10(5),
p. 1–8.
doi:
10.1016/j.heliyon.2024.e27073.
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Purpose To identify essential oils (EOs) active against non-growing stationary phase Mycobacterium abscessus and multidrug-resistant M. abscessus strains. Methods The activity of EOs against both stationary and log phase M. abscessus was evaluated by colony forming unit (CFU) assay and minimum inhibitory concentration (MIC) testing. Results We assessed the activity of 80 EOs against stationary phase M. abscessus and found 12 EOs (Cinnamon, Satureja montana, Palmarosa, Lemon eucalyptus, Honey myrtle, Combava, Health shield, Mandarin, Thyme, Rosewood, Valerian Root and Basil) at 0.5% concentration to be active against both growing and non-growing stationary phase M. abscessus. Among them, Satureja montana essential oil and Palmarosa essential oil could eliminate all stationary phase M. abscessus at 0.125% and Cinnamon essential oil could eliminate stationary phase bacteria at 0.063% after 1-day treatment. Interestingly, these EOs also exhibited promising activity against multidrug-resistant M. abscessus clinical strains. Conclusions Our study indicates that some EOs display outstanding effectiveness against both drug susceptible M. abscessus and multidrug-resistant M. abscessus isolates. These findings may be significant for the treatment of persistent M. abscessus infections.
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Cao, Dan; Yuan, Xin; Jiang, Xiuzhi; Wu, Tiantian; Xiang, Yanghui & Ji, Zhongkang
[Show all 12 contributors for this article]
(2024).
Antimicrobial and Antibiofilm Effects of Bithionol against Mycobacterium abscessus.
Antibiotics.
13(6),
p. 1–11.
doi:
10.3390/antibiotics13060529.
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Mycobacterium abscessus (M. abscessus) is a multidrug-resistant nontuberculous mycobacterium (NTM) that is responsible for a wide spectrum of infections in humans. The lack of effective bactericidal drugs and the formation of biofilm make its clinical treatment very difficult. The FDA-approved drug library containing 3048 marketed and pharmacopeial drugs or compounds was screened at 20 μM against M. abscessus type strain 19977 in 7H9 medium, and 62 hits with potential antimicrobial activity against M. abscessus were identified. Among them, bithionol, a clinically approved antiparasitic agent, showed excellent antibacterial activity and inhibited the growth of three different subtypes of M. abscessus from 0.625 μM to 2.5 μM. We confirmed the bactericidal activity of bithionol by the MBC/MIC ratio being ≤4 and the time–kill curve study and also electron microscopy study. Interestingly, it was found that at 128 μg/mL, bithionol could completely eliminate biofilms after 48h, demonstrating an outstanding antibiofilm capability compared to commonly used antibiotics. Additionally, bithionol could eliminate 99.9% of biofilm bacteria at 64 μg/mL, 99% at 32 μg/mL, and 90% at 16 μg/mL. Therefore, bithionol may be a potential candidate for the treatment of M. abscessus infections due to its significant antimicrobial and antibiofilm activities.
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Alkaltham, Manal Fahad; Almansour, Abdulrahman I.; Arumugam, Natarajan; Vagolu, Siva Krishna; Tonjum, Tone & Alaqeel, Shatha Ibrahim
[Show all 8 contributors for this article]
(2024).
Activity against Mycobacterium tuberculosis of a new class of spirooxindolopyrrolidine embedded chromanone hybrid heterocycles.
RSC Advances.
14(17),
p. 11604–11613.
doi:
10.1039/d4ra01501k.
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A new class of structurally intriguing heterocycles embedded with spiropyrrolidine, oxindole and chromanones was prepared by regio- and stereoselectively in quantitative yields using an intermolecular tandem cycloaddition protocol. The compounds synthesized were assayed for their anti-mycobacterial activity against Mycobacterium tuberculosis (Mtb) H37Rv and isoniazid-resistant (katG and inhA promoter mutations) clinical Mtb isolates. Four compounds exhibited significant antimycobacterial activity against Mtb strains tested. In particular, a compound possessing a fluorine substituted derivative displayed potent activity at 0.39 μg mL−1 against H37Rv, while it showed 0.09 μg mL−1 and 0.19 μg mL−1 activity against inhA promoter and katG mutation isolates, respectively. A molecular docking study was conducted with the potent compound, which showed results that were consistent with the in vitro experiments.
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Birhanu, Alemayehu Godana; Riaz, Tahira; Støen, Mari & Tonjum, Tone
(2024).
Differential Abundance of Protein Acylation in Mycobacterium tuberculosis Under Exposure to Nitrosative Stress.
PROTEOMICS - Clinical Applications.
ISSN 1862-8346.
18(6),
p. 1–15.
doi:
10.1002/prca.202300212.
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Background: Human macrophages generate antimicrobial reactive nitrogen species in response to infection by Mycobacterium tuberculosis (Mtb). Exposure to these redox-reactive compounds induces stress response in Mtb, which can affect posttranslational modifications (PTM). Methods: Here, we present the global analysis of the PTM acylation of Mtb proteins in response to a sublethal dose of nitrosative stress in the form of nitric oxide (NO) using label free quantification. Results: A total of 6437 acylation events were identified on 1496 Mtb proteins, and O-acylation accounted for 92.2% of the events identified, while 7.8% were N-acylation events. About 22% of the sites identified were found to be acylated by more than one acyl-group. Furthermore, the abundance of each acyl-group decreased as their molecular weight increased. Quantitative PTM analysis revealed differential abundance of acylation in proteins involved in stress response, iron ion homeostasis, growth, energy metabolism, and antimicrobial resistance (AMR) induced by nitrosative stress over time. Conclusions: The results reveal a potential role of Mtb protein acylation in the bacterial stress responses and AMR. To our knowledge, this is the first report on global O-acylation profile of Mtb in response to NO. This will significantly improve our understanding of the changes in Mtb acylation under nitrosative stress, highly relevant for global health.
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Sarkar, Souvik; Bridwell, Anne E. Mayer; Good, James A. D.; Wang, Erin R.; McKee, Samuel R. & Valenta, Joy
[Show all 18 contributors for this article]
(2023).
Design, Synthesis, and Evaluation of Novel Δ<sup>2</sup>-Thiazolino 2-Pyridone Derivatives That Potentiate Isoniazid Activity in an Isoniazid-Resistant Mycobacterium tuberculosis Mutant.
Journal of Medicinal Chemistry.
ISSN 0022-2623.
66(16),
p. 11056–11077.
doi:
10.1021/acs.jmedchem.3c00358.
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Mycobacterium tuberculosis (Mtb) drug resistance poses an alarming threat to global tuberculosis control. We previously reported that C10, a ring-fused thiazolo-2-pyridone, inhibits Mtb respiration, blocks biofilm formation, and restores the activity of the antibiotic isoniazid (INH) in INH-resistant Mtb isolates. This discovery revealed a new strategy to address INH resistance. Expanding upon this strategy, we identified C10 analogues with improved potency and drug-like properties. By exploring three heterocycle spacers (oxadiazole, 1,2,3-triazole, and isoxazole) on the ring-fused thiazolo-2-pyridone scaffold, we identified two novel isoxazoles, 17h and 17j. 17h and 17j inhibited Mtb respiration and biofilm formation more potently with a broader therapeutic window, were better potentiators of INH-mediated inhibition of an INH-resistant Mtb mutant, and more effectively inhibited intracellular Mtb replication than C10. The (−)17j enantiomer showed further enhanced activity compared to its enantiomer and the 17j racemic mixture. Our potent second-generation C10 analogues offer promise for therapeutic development against drug-resistant Mtb.
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Özcan, Esma; Vagolu, Siva Krishna; Gündüz, Miyase Gözde; Stevanovic, Milena; Kökbudak, Zülbiye & Tonjum, Tone
[Show all 9 contributors for this article]
(2023).
Novel Quinoline-Based Thiosemicarbazide Derivatives: Synthesis, DFT Calculations, and Investigation of Antitubercular, Antibacterial, and Antifungal Activities.
ACS Omega.
8(43),
p. 40140–40152.
doi:
10.1021/acsomega.3c03018.
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The discovery of new antimicrobial agents as a means of treating drug-resistant microbial pathogens is of utmost significance to overcome their immense risk to human well-being. The current investigation involves the development, synthesis, and assessment of the antimicrobial efficacy of novel quinoline derivatives incorporating a thiosemicarbazide functionality. To design the target compounds (QST1–QST14), we applied the molecular hybridization approach to link various thiosemicarbazides to the quinoline core with a sulfonyl group. Upon the synthesis and completion of structural characterization via spectroscopic techniques (1H NMR, 13C NMR, 15N NMR, IR, and HRMS), the title molecules were extensively evaluated for their potential antitubercular, antibacterial, and antifungal activities. N-(3-Chlorophenyl)-2-(quinolin-8-ylsulfonyl)hydrazine-1-carbothioamide (QST4), the most effective compound against Mycobacterium tuberculosis H37Rv, was also tested on isoniazid-resistant clinical isolates with katG and inhA promoter mutations. Based on molecular docking studies, QST4 was also likely to demonstrate its antimycobacterial activity through inhibition of the InhA enzyme. Furthermore, three derivatives (QST3, QST4, and QST10) with preferable antimicrobial and drug-like profiles were also shown to be nontoxic against human embryonic kidney (HEK) cells. All compounds were optimized by the density functional theory method using B3LYP with the 6-31+G(d,p) basis set. Structural analysis, natural bond orbital calculations of donor–acceptor interactions, molecular electrostatic potential analysis, and frontier molecular orbital analysis were carried out. Quantum chemical descriptors and charges on the atoms were determined to compare the strengths of the intramolecular hydrogen bonds formed and their stabilities. We determined that the sulfur atom forms a stronger intramolecular hydrogen bond than the nitrogen, oxygen, and fluorine atoms in these sulfonyl thiosemicarbazide derivatives.
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Birhanu, Alemayehu Godana; Munoz, Marta Gomez; Kalayou, Shewit; Riaz, Tahira; Lutter, Timo & Yimer, Solomon Abebe
[Show all 8 contributors for this article]
(2022).
Proteome Profiling of Mycobacterium tuberculosis Cells Exposed to Nitrosative Stress.
ACS Omega.
7(4),
p. 3470–3482.
doi:
10.1021/acsomega.1c05923.
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Reactive nitrogen species (RNS) are secreted by human cells in response to infection by Mycobacterium tuberculosis (Mtb). Although RNS can kill Mtb under some circumstances, Mtb can adapt and survive in the presence of RNS by a process that involves modulation of gene expression. Previous studies focused primarily on stress-related changes in the Mtb transcriptome. This study unveils changes in the Mtb proteome in response to a sub-lethal dose of nitric oxide (NO) over several hours of exposure. Proteins were identified using liquid chromatography coupled with electrospray ionization mass spectrometry (LC–MS/MS). A total of 2911 Mtb proteins were identified, of which 581 were differentially abundant (DA) after exposure to NO in at least one of the four time points (30 min, 2 h, 6 h, and 20 h). The proteomic response to NO was marked by two phases, with few DA proteins in the early phase and a multitude of DA proteins in the later phase. The efflux pump Rv1687 stood out as being the only protein more abundant at all the time points and might play a role in the early protection of Mtb against nitrosative stress. These changes appeared to be compensatory in nature, contributing to iron homeostasis, energy metabolism, and other stress responses. This study thereby provides new insights into the response of Mtb to NO at the level of proteomics.
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Aslan, Ebru Koçak; Han, Muhammed İhsan; Vagolu, Siva Krishna; Tamhaev, Rasoul; Dengiz, Cagatay & Doğan, Şengül Dilem
[Show all 10 contributors for this article]
(2022).
Isoniazid Linked to Sulfonate Esters via Hydrazone Functionality: Design, Synthesis, and Evaluation of Antitubercular Activity.
Pharmaceuticals.
15:1301(10),
p. 1–15.
doi:
10.3390/ph15101301.
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Isoniazid (INH) is one of the key molecules employed in the treatment of tuberculosis (TB), the most deadly infectious disease worldwide. However, the efficacy of this cornerstone drug has seriously decreased due to emerging INH-resistant strains of Mycobacterium tuberculosis (Mtb). In the present study, we aimed to chemically tailor INH to overcome this resistance. We obtained thirteen novel compounds by linking INH to in-house synthesized sulfonate esters via a hydrazone bridge (SIH1–SIH13). Following structural characterization by FTIR, 1H NMR, 13C NMR, and HRMS, all compounds were screened for their antitubercular activity against Mtb H37Rv strain and INH-resistant clinical isolates carrying katG and inhA mutations. Additionally, the cytotoxic effects of SIH1–SIH13 were assessed on three different healthy host cell lines; HEK293, IMR-90, and BEAS-2B. Based on the obtained data, the synthesized compounds appeared as attractive antimycobacterial drug candidates with low cytotoxicity. Moreover, the stability of the hydrazone moiety in the chemical structure of the final compounds was confirmed by using UV/Vis spectroscopy in both aqueous medium and DMSO. Subsequently, the compounds were tested for their inhibitory activities against enoyl acyl carrier protein reductase (InhA), the primary target enzyme of INH. Although most of the synthesized compounds are hosted by the InhA binding pocket, SIH1–SIH13 do not primarily show their antitubercular activities by direct InhA inhibition. Finally, in silico determination of important physicochemical parameters of the molecules showed that SIH1–SIH13 adhered to Lipinski’s rule of five. Overall, our study revealed a new strategy for modifying INH to cope with the emerging drug-resistant strains of Mtb.
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Welekidan, Letemichael Negash; Yimer, Solomon Abebe; Skjerve, Eystein; Dejene, Tsehaye Asmelash; Homberset, Håvard & Tonjum, Tone
[Show all 7 contributors for this article]
(2021).
Whole Genome Sequencing of Drug Resistant and Drug Susceptible Mycobacterium tuberculosis Isolates From Tigray Region, Ethiopia.
Frontiers in Microbiology.
12.
doi:
10.3389/fmicb.2021.743198.
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Background: Tuberculosis, mainly caused by Mycobacterium tuberculosis (Mtb), is an ancient human disease that gravely affects millions of people annually. We wanted to explore the genetic diversity and lineage-specific association of Mtb with drug resistance among pulmonary tuberculosis patients. Methods: Sputum samples were collected from pulmonary tuberculosis patients at six different healthcare institutions in Tigray, Ethiopia, between July 2018 and August 2019. DNA was extracted from 74 Mtb complex isolates for whole-genome sequencing (WGS). All genomes were typed and screened for mutations with known associations with antimicrobial resistance using in silico methods, and results were cross-verified with wet lab methods. Results: Lineage (L) 4 (55.8%) was predominant, followed by L3 (41.2%); L1 (1.5%) and L2 (1.5%) occurred rarely. The most frequently detected sublineage was CAS (38.2%), followed by Ural (29.4%), and Haarlem (11.8%). The recent transmission index (RTI) was relatively low. L4 and Ural strains were more resistant than the other strains to any anti-TB drug ( P &lt; 0.05). The most frequent mutations to RIF, INH, EMB, SM, PZA, ETH, FLQs, and 2nd-line injectable drugs occurred at rpoB S450L, katG S315T, embB M306I/V, rps L K43R, pncA V139A, ethA M1R, gyr A D94G, and rrs A1401G, respectively. Disputed rpoB mutations were also shown in four (16%) of RIF-resistant isolates. Conclusion: Our WGS analysis revealed the presence of diverse Mtb genotypes. The presence of a significant proportion of disputed rpoB mutations highlighted the need to establish a WGS facility at the regional level to monitor drug-resistant mutations. This will help control the transmission of DR-TB and ultimately contribute to the attainment of 100% DST coverage for TB patients as per the End TB strategy.
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Arenas, Jesús; Szabo, Zalan; Wal, Jelle van der; Maas, Coen; Riaz, Tahira & Tonjum, Tone
[Show all 7 contributors for this article]
(2021).
Serum proteases prevent bacterial biofilm formation: role of kallikrein and plasmin.
Virulence.
ISSN 2150-5594.
12(1),
p. 2902–2917.
doi:
10.1080/21505594.2021.2003115.
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Biofilm formation is a general strategy for bacterial pathogens to withstand host defense mechanisms. In this study, we found that serum proteases inhibit biofilm formation by Neisseria meningitidis, Neisseria gonorrhoeae, Haemophilus influenzae, and Bordetella pertussis. Confocal laser-scanning microscopy analysis revealed that these proteins reduce the biomass and alter the architecture of meningococcal biofilms. To understand the underlying mechanism, the serum was fractionated through size-exclusion chromatography and anion-exchange chromatography, and the composition of the fractions that retained anti-biofilm activity against N. meningitidis was analyzed by intensity-based absolute quantification mass spectrometry. Among the identified serum proteins, plasma kallikrein (PKLK), FXIIa, and plasmin were found to cleave neisserial heparin-binding antigen and the α-peptide of IgA protease on the meningococcal cell surface, resulting in the release of positively charged polypeptides implicated in biofilm formation by binding extracellular DNA. Further experiments also revealed that plasmin and PKLK inhibited biofilm formation of B. pertussis by cleaving filamentous hemagglutinin. We conclude that the proteolytic activity of serum proteases toward bacterial adhesins involved in biofilm formation could constitute a defense mechanism for the clearance of pathogens.
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Mekonnen, Daniel; Derbie, Awoke; Mihret, Adane; Yimer, Solomon Abebe; Tonjum, Tone & Gelaw, Baye
[Show all 10 contributors for this article]
(2021).
Lipid droplets and the transcriptome of Mycobacterium tuberculosis from direct sputa: a literature review.
Lipids in Health and Disease.
20:129(1),
p. 1–13.
doi:
10.1186/s12944-021-01550-5.
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Mycobacterium tuberculosis (Mtb), the main etiology of tuberculosis (TB), is predominantly an intracellular pathogen that has caused infection, disease and death in humans for centuries. Lipid droplets (LDs) are dynamic intracellular organelles that are found across the evolutionary tree of life. This review is an evaluation of the current state of knowledge regarding Mtb-LD formation and associated Mtb transcriptome directly from sputa. Based on the LD content, Mtb in sputum may be classified into three groups: LD positive, LD negative and LD borderline. However, the clinical and evolutionary importance of each state is not well elaborated. Mounting evidence supports the view that the presence of LD positive Mtb bacilli in sputum is a biomarker of slow growth, low energy state, towards lipid degradation, and drug tolerance. In Mtb, LD may serve as a source of chemical energy, scavenger of toxic compounds, prevent destruction of Mtb through autophagy, delay trafficking of lysosomes towards the phagosome, and contribute to Mtb persistence. It is suggest that LD is a key player in the induction of a spectrum of phenotypic and metabolic states of Mtb in the macrophage, granuloma and extracellular sputum microenvironment. Tuberculosis patients with high proportion of LD positive Mtb in pretreatment sputum was associated with higher rate of poor treatment outcome, indicating that LD may have a clinical application in predicting treatment outcome. The propensity for LD formation among Mtb lineages is largely unknown. The role of LD on Mtb transmission and disease phenotype (pulmonary TB vs extra-pulmonary TB) is not well understood. Thus, further studies are needed to understand the relationships between LD positivity and Mtb lineage, Mtb transmission and clinical types.
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Welekidan, Letemichael Negash; Skjerve, Eystein; Dejene, Tsehaye Asmelash; Gebremichael, Mengistu Welday; Brynildsrud, Ola Brønstad & Tonjum, Tone
[Show all 7 contributors for this article]
(2020).
Frequency and patterns of first- and second-line drug resistance-conferring mutations in Mycobacterium tuberculosis isolated from pulmonary tuberculosis patients in a cross-sectional study in Tigray Region, Ethiopia.
Journal of Global Antimicrobial Resistance.
ISSN 2213-7165.
24,
p. 6–13.
doi:
10.1016/j.jgar.2020.11.017.
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Objectives Tuberculosis (TB) is a preventable and treatable infectious disease, but the continuing emergence and spread of multidrug-resistant TB is threatening global TB control efforts. This study aimed to describe the frequency and patterns of drug resistance-conferring mutations of Mycobacterium tuberculosis (MTB) isolates detected from pulmonary TB patients in Tigray Region, Ethiopia. Methods A cross-sectional study design was employed to collect sputum samples from pulmonary TB patients between July 2018 to August 2019. Culture and identification tests were done at Tigray Health Research Institute (THRI). Mutations conferring rifampicin (RIF), isoniazid (INH) and fluoroquinolone (FQ) resistance were determined in 227 MTB isolates using GenoType MTBDRplus and GenoType MTBDRsl. Results Mutations conferring resistance to RIF, INH and FQs were detected in 40/227 (17.6%), 41/227 (18.1%) and 2/38 (5.3%) MTB isolates, respectively. The majority of mutations for RIF, INH and FQs occurred at codons rpoB S531L (70%), katG S315T (78%) and gyrA D94Y/N (100%), respectively. This study revealed a significant number of unknown mutations in the rpoB, katG and inhA genes. Conclusion High rates of mutations conferring resistance to RIF, INH and FQs were observed in this study. A large number of isolates showed unknown mutations, which require further DNA sequencing analysis. Periodic drug resistance surveillance and scaling-up of drug resistance testing facilities are imperative to prevent the transmission of drug-resistant TB in the community.
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Andersson, Dan I.; Balaban, Nathalie Q.; Baquero, Fernando; Courvalin, Patrice; Glaser, Philippe & Gophna, Uri
[Show all 9 contributors for this article]
(2020).
Antibiotic resistance: turning evolutionary principles into clinical reality.
FEMS Microbiology Reviews.
ISSN 0168-6445.
44(2),
p. 171–188.
doi:
10.1093/femsre/fuaa001.
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Antibiotic resistance is one of the major challenges facing modern medicine worldwide. The past few decades have witnessed rapid progress in our understanding of the multiple factors that affect the emergence and spread of antibiotic resistance at the population level and the level of the individual patient. However, the process of translating this progress into health policy and clinical practice has been slow. Here, we attempt to consolidate current knowledge about the evolution and ecology of antibiotic resistance into a roadmap for future research as well as clinical and environmental control of antibiotic resistance. At the population level, we examine emergence, transmission and dissemination of antibiotic resistance, and at the patient level, we examine adaptation involving bacterial physiology and host resilience. Finally, we describe new approaches and technologies for improving diagnosis and treatment and minimizing the spread of resistance.
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Welekidan, Letemichael Negash; Skjerve, Eystein; Dejene, Tsehaye Asmelash; Gebremichael, Mengistu Welday; Brynildsrud, Ola Brønstad & Agdestein, Angelika
[Show all 9 contributors for this article]
(2020).
Characteristics of pulmonary multidrug-resistant tuberculosis patients in Tigray Region, Ethiopia: A cross-sectional study.
PLOS ONE.
15(8).
doi:
10.1371/journal.pone.0236362.
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Background: Tuberculosis (TB) is among the top 10 causes of mortality and the first killer among infectious diseases worldwide. One of the factors fuelling the TB epidemic is the global rise of multidrug resistant TB (MDR-TB). The aim of this study was to determine the magnitude and factors associated with MDR-TB in the Tigray Region, Ethiopia.
Method: This study employed a facility-based cross-sectional study design, which was conducted between July 2018 and August 2019. The inclusion criteria for the study participants were GeneXpert-positive who were not under treatment for TB, PTB patients' ≥15 years of age and who provided written informed consent. A total of 300 participants were enrolled in the study, with a structured questionnaire used to collect data on clinical, sociodemographic and behavioral factors. Sputum samples were collected and processed for acid-fast bacilli staining, culture and drug susceptibility testing. Drug susceptibility testing was performed using a line probe assay. Logistic regression was used to analyze associations between outcome and predictor variables.
Results: The overall proportion of MDR-TB was 16.7% (11.6% and 32.7% for new and previously treated patients, respectively). Of the total MDR-TB isolates, 5.3% were pre-XDR-TB. The proportion of MDR-TB/HIV co-infection was 21.1%. A previous history of TB treatment AOR 3.75; 95% CI (0.7-2.24), cigarette smoking AOR 6.09; CI (1.65-2.50) and patients who had an intermittent fever (AOR = 2.54, 95% CI = 1.21-5.4) were strongly associated with MDR-TB development.
Conclusions: The magnitude of MDR-TB observed among new and previously treated patients is very alarming, which calls for an urgent need for intervention. The high proportion of MDR-TB among newly diagnosed cases indicates ongoing transmission, which suggests the need for enhanced TB control program performance to interrupt transmission. The increased proportion of MDR-TB among previously treated cases indicates a need for better patient management to prevent the evolution of drug resistance. Assessing the TB control program performance gaps and an optimal implementation of the WHO recommended priority actions for the management of drug-resistant TB, is imperative to help reduce the current high MDR-TB burden in the study region.
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Navarro, José Fernández; Croteau, Deborah L; Jurek, Aleksandra; Andrusivova, Zaneta; Yang, Beimeng & Wang, Yue
[Show all 15 contributors for this article]
(2020).
Spatial Transcriptomics Reveals Genes Associated with Dysregulated Mitochondrial Functions and Stress Signaling in Alzheimer Disease.
iScience.
23:101556(10),
p. 1–19.
doi:
10.1016/j.isci.2020.101556.
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Alzheimer disease (AD) is a devastating neurological disease associated with progressive loss of mental skills and cognitive and physical functions whose etiology is not completely understood. Here, our goal was to simultaneously uncover novel and known molecular targets in the structured layers of the hippocampus and olfactory bulbs that may contribute to early hippocampal synaptic deficits and olfactory dysfunction in AD mice. Spatially resolved transcriptomics was used to identify high-confidence genes that were differentially regulated in AD mice relative to controls. A diverse set of genes that modulate stress responses and transcription were predominant in both hippocampi and olfactory bulbs. Notably, we identify Bok, implicated in mitochondrial physiology and cell death, as a spatially downregulated gene in the hippocampus of mouse and human AD brains. In summary, we provide a rich resource of spatially differentially expressed genes, which may contribute to understanding AD pathology.
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Yimer, Solomon Abebe; Kalayou, Shewit; Homberset, Håvard; Birhanu, Alemayehu Godana; Riaz, Tahira & Zegeye, Ephrem Debebe
[Show all 11 contributors for this article]
(2020).
Lineage-specific proteomic signatures in the Mycobacterium tuberculosis complex reveal differential abundance of proteins involved in virulence, DNA repair, CRISPR-Cas, bioenergetics and lipid metabolism.
Frontiers in Microbiology.
11.
doi:
10.3389/fmicb.2020.550760.
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Despite the discovery of the tubercle bacillus more than 130 years ago, its physiology and the mechanisms of virulence are still not fully understood. A comprehensive analysis of the proteomes of members of the human-adapted Mycobacterium tuberculosis complex (MTBC) lineages 3, 4, 5, and 7 was conducted to better understand the evolution of virulence and other physiological characteristics. Unique and shared proteomic signatures in these modern, pre-modern and ancient MTBC lineages, as deduced from quantitative bioinformatics analyses of high-resolution mass spectrometry data, were delineated. The main proteomic findings were verified by using immunoblotting. In addition, analysis of multiple genome alignment of members of the same lineages was performed. Label-free peptide quantification of whole cells from MTBC lineages 3, 4, 5, and 7 yielded a total of 38,346 unique peptides derived from 3092 proteins, representing 77% coverage of the predicted proteome. MTBC lineage-specific differential expression was observed for 539 proteins. Lineage 7 exhibited a markedly reduced abundance of proteins involved in DNA repair, type VII ESX-3 and ESX-1 secretion systems, lipid metabolism and inorganic phosphate uptake, and an increased abundance of proteins involved in alternative pathways of the TCA cycle and the CRISPR-Cas system as compared to the other lineages. Lineages 3 and 4 exhibited a higher abundance of proteins involved in virulence, DNA repair, drug resistance and other metabolic pathways. The high throughput analysis of the MTBC proteome by super-resolution mass spectrometry provided an insight into the differential expression of proteins between MTBC lineages 3, 4, 5, and 7 that may explain the slow growth and reduced virulence, metabolic flexibility, and the ability to survive under adverse growth conditions of lineage 7.
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Shi, Wanliang; Cui, Peng; Niu, Hongxia; Zhang, Shuo; Tonjum, Tone & Zhu, Bingdong
[Show all 7 contributors for this article]
(2019).
Introducing RpsA Point Mutations Δ438A and D123A into the Chromosome of Mycobacterium tuberculosis Confirms Their Role in Causing Resistance to Pyrazinamide.
Antimicrobial Agents and Chemotherapy.
ISSN 0066-4804.
63:e02681-18(6),
p. 1–6.
doi:
10.1128/AAC.02681-18.
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Pyrazinamide (PZA) is a unique frontline drug for shortening tuberculosis (TB) treatment, but its mechanisms of action are elusive. We previously found one PZA-resistant strain that harbors an alanine deletion at position 438 (Δ438A) in RpsA, a target of PZA associated with PZA resistance, but its role in causing PZA resistance has been inconclusive. Here, we introduced the RpsA Δ438A mutation along with the D123A mutation into the Mycobacterium tuberculosis chromosome and demonstrated that these RspA mutations are indeed responsible for PZA resistance.
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Mekonnen, Daniel; Derbie, Awoke; Chanie, Asmamaw; Shumet, Abebe; Biadglegne, Fantahun & Kassahun, Yonas
[Show all 14 contributors for this article]
(2019).
Molecular epidemiology of M. tuberculosis in Ethiopia: A systematic review and meta-analysis.
Tuberculosis.
ISSN 1472-9792.
118:101858,
p. 1–10.
doi:
10.1016/j.tube.2019.101858.
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The molecular epidemiology of Mycobacterium tuberculosis (M. tuberculosis, Mtb) is poorly documented in Ethiopia. The data that exists has not yet been collected in an overview metadata form. Thus, this review summarizes available literature on the genomic diversity, geospatial distribution and transmission patterns of Mtb lineages (L) and sublineages in Ethiopia. Spoligotyping and Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR) based articles were identified from MEDLINE via PubMed and Scopus. The last date of article search was done on 12th February 2019. Articles were selected following the PRISMA flow diagram. The proportion of (sub)lineages was summarized at national level and further disaggregated by region. Clustering and recent transmission index (RTI) were determined using metan command and random effect meta-analysis model. The meta-analysis was computed using Stata 14 (Stata Corp. College Station, TX, USA). Among 4371 clinical isolates, 99.5% were Mtb and 0.5% were M. bovis. Proportionally, L4, L3, L1 and L7 made up 62.3%, 21.7%, 7.9% and 3.4% of the total isolates, respectively. Among sublineages, L4.2. ETH/SIT149, L4.10/SIT53, L3. ETH1/SIT25 and L4.6/SIT37 were the leading clustered isolates accounting for 14.4%, 9.7%, 7.2% and 5.5%, respectively. Based on MIRU-VNTR, the rate of clustering was 41% and the secondary case rate from a single source case was estimated at 29%. Clustering and recent transmission index was higher in eastern and southwestern Ethiopia compared with the northwestern part of the country. High level of genetic diversity with a high rate of clustering was noted which collectively mirrored the phenomena of micro-epidemics and super-spreading. The largest set of clustered strains deserves special attention and further characterization using whole genome sequencing (WGS) to better understand the evolution, genomic diversity and transmission dynamics of Mtb.
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Birhanu, Alemayehu Godana; Solomon, Abebe Yimer; Kalayou, Shewit; Riaz, Tahira; Zegeye, Ephrem Debebe & Holm-Hansen, Carol J C
[Show all 10 contributors for this article]
(2019).
Ample glycosylation in membrane and cell envelope proteins may explain the phenotypic diversity and virulence in the Mycobacterium tuberculosis complex.
Scientific Reports.
9:2927(1),
p. 1–15.
doi:
10.1038/s41598-019-39654-9.
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Multiple regulatory mechanisms including post-translational modifications (PTMs) confer complexity to the simpler genomes and proteomes of Mycobacterium tuberculosis (Mtb). PTMs such as glycosylation play a significant role in Mtb adaptive processes. The glycoproteomic patterns of clinical isolates of the Mycobacterium tuberculosis complex (MTBC) representing the lineages 3, 4, 5 and 7 were characterized by mass spectrometry. A total of 2944 glycosylation events were discovered in 1325 proteins. This data set represents the highest number of glycosylated proteins identified in Mtb to date. O-glycosylation constituted 83% of the events identified, while 17% of the sites were N-glycosylated. This is the first report on N-linked protein glycosylation in Mtb and in Gram-positive bacteria. Collectively, the bulk of Mtb glycoproteins are involved in cell envelope biosynthesis, fatty acid and lipid metabolism, two-component systems, and pathogen-host interaction that are either surface exposed or located in the cell wall. Quantitative glycoproteomic analysis revealed that 101 sites on 67 proteins involved in Mtb fitness and survival were differentially glycosylated between the four lineages, among which 64% were cell envelope and membrane proteins. The differential glycosylation pattern may contribute to phenotypic variabilities across Mtb lineages. The study identified several clinically important membrane-associated glycolipoproteins that are relevant for diagnostics as well as for drug and vaccine discovery
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Tonjum, Tone
(2019).
Molecular epidemiology of M. tuberculosis in Ethiopia: A systematic review and meta-analysis.
Tuberculosis.
ISSN 1472-9792.
118.
doi:
10.1016/j.tube.2019.101858.
Full text in Research Archive
Show summary
The molecular epidemiology of Mycobacterium tuberculosis (M. tuberculosis, Mtb) is poorly documented in Ethiopia. The data that exists has not yet been collected in an overview metadata form. Thus, this review summarizes available literature on the genomic diversity, geospatial distribution and transmission patterns of Mtb lineages (L) and sublineages in Ethiopia. Spoligotyping and Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR) based articles were identified from MEDLINE via PubMed and Scopus. The last date of article search was done on 12th February 2019. Articles were selected following the PRISMA flow diagram. The proportion of (sub)lineages was summarized at national level and further disaggregated by region. Clustering and recent transmission index (RTI) were determined using metan command and random effect meta-analysis model. The meta-analysis was computed using Stata 14 (Stata Corp. College Station, TX, USA). Among 4371 clinical isolates, 99.5% were Mtb and 0.5% were M. bovis. Proportionally, L4, L3, L1 and L7 made up 62.3%, 21.7%, 7.9% and 3.4% of the total isolates, respectively. Among sublineages, L4.2. ETH/SIT149, L4.10/SIT53, L3. ETH1/SIT25 and L4.6/SIT37 were the leading clustered isolates accounting for 14.4%, 9.7%, 7.2% and 5.5%, respectively. Based on MIRU-VNTR, the rate of clustering was 41% and the secondary case rate from a single source case was estimated at 29%. Clustering and recent transmission index was higher in eastern and southwestern Ethiopia compared with the northwestern part of the country. High level of genetic diversity with a high rate of clustering was noted which collectively mirrored the phenomena of micro-epidemics and super-spreading. The largest set of clustered strains deserves special attention and further characterization using whole genome sequencing (WGS) to better understand the evolution, genomic diversity and transmission dynamics of Mtb.
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Shi, Wanliang; Cui, Peng; Niu, Hongxia; Zhang, Shuo; Tonjum, Tone & Zhu, Bingdong
[Show all 7 contributors for this article]
(2019).
Introducing RpsA point mutations ∆438A and D123A into the chromosome of M. tuberculosis confirms their role in causing resistance to pyrazinamide.
Antimicrobial Agents and Chemotherapy.
ISSN 0066-4804.
63:e02681-18(6),
p. 1–6.
doi:
10.1128/AAC.02681-18.
Full text in Research Archive
Show summary
Pyrazinamide (PZA) is a unique frontline drug for shortening tuberculosis (TB) treatment, but its mechanisms of action are elusive. We previously found one PZA-resistant strain that harbors an alanine deletion at position 438 (Δ438A) in RpsA, a target of PZA associated with PZA resistance, but its role in causing PZA resistance has been inconclusive. Here, we introduced the RpsA Δ438A mutation along with the D123A mutation into the Mycobacterium tuberculosis chromosome and demonstrated that these RspA mutations are indeed responsible for PZA resistance.
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Alfsnes, Kristian; Frye, Stephan Alfons; Eriksson, Jens; Eldholm, Vegard; Brynildsrud, Ola Brønstad & Bohlin, Jon
[Show all 11 contributors for this article]
(2018).
A genomic view of experimental intraspecies and interspecies transformation of a rifampicin-resistance allele into Neisseria meningitidis.
Microbial Genomics.
4(11),
p. 1–14.
doi:
10.1099/mgen.0.000222.
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The spread of antibiotic resistance within and between different bacterial populations is a major health problem on a global scale. The identification of genetic transformation in genomic data from Neisseria meningitidis, the meningococcus (Mc), and other bacteria is problematic, since similar or even identical alleles may be involved. A particular challenge in naturally
transformable bacteria generally is to distinguish between common ancestry and true recombined sites in sampled genome
sequences. Furthermore, the identification of recombination following experimental transformation of homologous alleles
requires identifiable differences between donor and recipient, which in itself influences the propensity for homologous recombination (HR). This study identifies the distribution of HR events following intraspecies and interspecies Mc transformations of rpoB alleles encoding rifampicin resistance by whole-genome DNA sequencing and single nucleotide
variant analysis. The HR events analysed were confined to the genomic region surrounding the single nucleotide genetic
marker used for selection. An exponential length distribution of these recombined events was found, ranging from a few
nucleotides to about 72 kb stretches. The lengths of imported sequences were on average found to be longer following experimental transformation of the recipient with genomic DNA from an intraspecies versus an interspecies donor (P<0.001). The recombination events were generally observed to be mosaic, with donor sequences interspersed with recipient
sequence. Here, we present four models to explain these observations, by fragmentation of the transformed DNA, by
interruptions of the recombination mechanism, by secondary recombination of endogenous self-DNA, or by repair/replication mechanisms.
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Jensen, Helge Leander B.; Lillenes, Meryl Sønderby; Rabano, Alberto; Günther, Clara-Cecilie; Riaz, Tahira & Kalayou, Shewit
[Show all 9 contributors for this article]
(2018).
Expression of nucleotide excision repair in Alzheimer's disease is higher in brain tissue than in blood.
Neuroscience Letters.
ISSN 0304-3940.
672,
p. 53–58.
doi:
10.1016/j.neulet.2018.02.043.
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Age-related changes are increased in patients with Alzheimer's disease (AD), including oxidative stress and DNA damage. We propose that genotoxic stress and DNA repair responses influence neurodegeneration in the pathogenesis of AD. Here, we focus on nucleotide excision repair (NER). Real-time qPCR and mass spectrometry were employed to determine the expression levels of selected NER components. The mRNA levels of the genes encoding the NER proteins RAD23B, RPA1, ERCC1, PCNA and LIG3 as well as the NER-interacting base excision repair protein MPG in blood and brain tissue from four brain regions in patients with AD or mild cognitive impairment and healthy controls (HC), were assessed. NER mRNA levels were significantly higher in brain tissue than in blood. Further, LIG3 mRNA levels in the frontal cortex was higher in AD versus HC, while mRNA levels of MPG and LIG3 in entorhinal cortex and RPA1 in the cerebellum were lower in AD versus HC. In blood, RPA1 and ERCC1 mRNA levels were lower in AD patients than in HC. Alterations in gene expression of NER components between brain regions were associated with AD, connecting DNA repair to AD pathogenesis and suggesting a distinct role for NER in the brain.
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Birhanu, Alemayehu Godana; Solomon, Abebe Yimer; Holm-Hansen, Carol J C; Norheim, Gunnstein; Aseffa, Abraham & Abebe, Markose
[Show all 7 contributors for this article]
(2017).
Nε- and O-Acetylation in Mycobacterium tuberculosis Lineage 7 and Lineage 4 strains: Proteins Involved in Bioenergetics, Virulence and Antimicrobial Resistance are Acetylated.
Journal of Proteome Research.
ISSN 1535-3893.
16(11),
p. 4045–4059.
doi:
10.1021/acs.jproteome.7b00429.
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Increasing evidence demonstrates that lysine acetylation is involved in Mycobacterium tuberculosis (Mtb) virulence and pathogenesis. However, previous investigations in Mtb have only monitored acetylation at lysine residues using selected reference strains. We analyzed the global Nε- and O-acetylation of 3 Mtb isolates; 2 lineage 7 clinical isolates and the lineage 4 H37Rv reference strain. Quantitative acetylome analysis resulted in identification of 2490 class-I acetylation sites, among them 2349 O-acetylation and 141 Nε-acetylation sites, derived from 953 unique proteins. Mtb O-acetylation was thereby significantly more abundant than Nε-acetylation. The acetylated proteins were found to be involved in central metabolism, translation, stress responses and antimicrobial drug resistance. Notably, 261 acetylation sites on 165 proteins were differentially regulated between lineage 7 and lineage 4 strains. A total of 257 acetylation sites on 161 proteins were hypoacetylated in lineage 7 strains. These proteins are involved in Mtb growth, virulence, bioenergetics, host-pathogen interaction and stress responses. This study provides the first global analysis of O-acetylated proteins in Mtb. This quantitative acetylome data expand the current understanding regarding the nature and diversity of acetylated proteins in Mtb, and opens a new avenue of research for exploring the role of protein acetylation in Mtb physiology.
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Yimer, Solomon Abebe; Birhanu, Alemayehu Godana; Kalayou, Shewit; Riaz, Tahira; Zegeye, Ephrem Debebe & Beyene, Getachew Tesfaye
[Show all 11 contributors for this article]
(2017).
Comparative proteomic analysis of Mycobacterium tuberculosis lineage 7 and lineage 4 strains reveals differentially abundant proteins linked to slow growth and virulence.
Frontiers in Microbiology.
8:795,
p. 1–14.
doi:
10.3389/fmicb.2017.00795.
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In order to decipher the nature of the slowly growing Mycobacterium tuberculosis (M.tuberculosis) lineage 7, the differentially abundant proteins in strains ofM. tuberculosis
lineage 7 and lineage 4 were defined. Comparative proteomic analysis by mass spectrometry was employed to identify, quantitate and compare the protein profiles of
strains from the two M. tuberculosis lineages. Label-free peptide quantification of Whole cells from M. tuberculosis lineage 7 and 4 yielded the identification of 2825 and 2541
proteins, respectively. A combined total of 2867 protein groups covering 71% of the predicted M. tuberculosis proteome were identified. The abundance of 125 proteins in
M. tuberculosis lineage 7 and 4 strains was significantly altered. Notably, the analysis showed that a number of M. tuberculosis proteins involved in growth and virulence were
less abundant in lineage 7 strains compared to lineage 4. Five ABC transporter proteins, three phosphate binding proteins essential for inorganic phosphate uptake, and six
components of the type 7 secretion system ESX-3 involved in iron acquisition were less abundant in M. tuberculosis lineage 7. This proteogenomic analysis provided an insight
into the lineage 7-specific protein profile which may provide clues to understanding the differential properties of lineage 7 strains in terms of slow growth, survival fitness, and pathogenesis.
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Castañeda-García, Alfredo; Prieto, Anabel I.; Rodríguez-Beltrán, Jerónimo; Alonso, N.; Cantillon, Daire & Costas, Coloma
[Show all 17 contributors for this article]
(2017).
A non-canonical mismatch repair pathway in prokaryotes.
Nature Communications.
8:14246,
p. 1–10.
doi:
10.1038/ncomms14246.
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Mismatch repair (MMR) is a near ubiquitous pathway, essential for the maintenance of genome stability. Members of the MutS and MutL protein families perform key steps in mismatch correction. Despite the major importance of this repair pathway, MutS-MutL are absent in almost all Actinobacteria and many Archaea. However, these organisms exhibit rates and spectra of spontaneous mutations similar to MMR-bearing species, suggesting the existence of an alternative to the canonical MutS-MutL-based MMR. Here we report that Mycobacterium smegmatis NucS/EndoMS, a putative endonuclease with no structural homology to known MMR factors, is required for mutation avoidance and anti-recombination, hallmarks of the canonical MMR. Furthermore, phenotypic analysis of naturally occurring polymorphic NucS in a M. smegmatis surrogate model, suggests the existence of M. tuberculosis mutator strains. The phylogenetic analysis of NucS indicates a complex evolutionary process leading to a disperse distribution pattern in prokaryotes. Together, these findings indicate that distinct pathways for MMR have evolved at least twice in nature.
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Lillenes, Meryl Sønderby; Støen, Mari; Günther, Clara-Cecilie; Selnes, Per; Stenset, Vidar & Espeseth, Thomas
[Show all 9 contributors for this article]
(2017).
Mitochondrial transcription factor A (TFAM) rs1937 and AP endonuclease 1 (APE1) rs1130409 alleles are associated with reduced cognitive performance.
Neuroscience Letters.
ISSN 0304-3940.
645,
p. 46–52.
doi:
10.1016/j.neulet.2017.02.062.
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Mitochondrial dysfunction and DNA damage is intimately connected to ageing and neurodegeneration, including Alzheimer’s disease (AD). A particular culprit in this context is oxidative stress, which is a result of increased reactive oxygen species (ROS) due to hyperactive or dysfunctional mitochondria and/or reduced DNA repair capacity. Base excision repair (BER) is the major pathway for repairing oxidative damage events in chromosomal and mitochondrial DNA. Defects in BER have been detected in ageing and neurodegeneration. Mitochondrial transcription factor A (TFAM) plays an important role in the maintenance of mitochondrial DNA integrity. The present study investigated single nucleotide polymorphisms (SNPs) in the genes encoding the BER components MutYH, OGG1, APE1, PolB and PolG and the gene encoding mitochondrial TFAM in a cohort of 161 AD patients, 96 non-AD patient controls (PC) and 192 healthy controls (HC). Notably, the minor allele carriers of APE1 rs1130409 and the common allele carriers of TFAM rs1937 were associated with reduced mini-mental state examination score in AD patients, PC and HC, with no distinction of SNP frequencies in either of these sub-groups. Collectively, the results suggest an association between DNA maintenance and decline in cognitive function. These studies enlighten the normal brain aging process and point to potential new biomarkers for cognitive function and impairment.
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Hovland, Eirik; Beyene, Getachew Tesfaye; Frye, Stephan Alfons; Homberset, Håvard; Balasingham, Seetha & Munoz, Marta Gomez
[Show all 9 contributors for this article]
(2017).
DprA from Neisseria meningitidis: properties and role in natural competence for transformation.
Microbiology (Reading).
ISSN 1350-0872.
163(7),
p. 1016–1029.
doi:
10.1099/mic.0.000489.
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DNA processing chain A (DprA) is a DNA-binding protein that is ubiquitous in bacteria and expressed in some archaea. DprA is active in many bacterial species that are competent for transformation of DNA, but its role in Neisseriameningitidis (Nm) is not well characterized. An Nm mutant lacking DprA was constructed, and the phenotypes of the wild-type and ΔdprA mutant were compared. The salient feature of the phenotype of dprA null cells is the total lack of competence for genetic transformation shown by all of the donor DNA substrates tested in this study. Here, Nm wild-type and dprA null cells appeared to be equally resistant to genotoxic stress. The gene encoding DprANm was cloned and overexpressed, and the biological activities of DprANm were further investigated. DprANm binds ssDNA more strongly than dsDNA, but lacks DNA uptake sequence-specific DNA binding. DprANm dimerization and interaction with the C-terminal part of the single-stranded binding protein SSBNmwere demonstrated. dprA is co-expressed with smg, a downstream gene of unknown function, and the gene encoding topoisomerase 1, topA.
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Norheim, Gunnstein; Seterelv, Siri Schøyen; Arnesen, Trude Margrete; Mengshoel, Anne Torunn; Tonjum, Tone & Rønning, Janne Oseberg
[Show all 7 contributors for this article]
(2017).
Tuberculosis Outbreak in an Educational Institution in Norway.
Journal of Clinical Microbiology.
ISSN 0095-1137.
55(5),
p. 1327–1333.
doi:
10.1128/JCM.01152-16.
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Within 1 week in April 2013, three cases of pulmonary tuberculosis (TB) were reported among students attending training sessions at an educational institution in Oslo, Norway. By the end of October 2013, a total of nine epidemiologically linked cases had been reported. The outbreak encompassed a total of 24 cases from 2009 to 2014, among which all of the 22 Mycobacterium tuberculosis isolates available had identical mycobacterial interspersed repetitive-unit–variable-number tandem-repeat (MIRU-VNTR) profiles (MtbC15-9 code 10287-189) belonging to the Beijing lineage. Whole-genome sequencing (WGS) of the M. tuberculosis isolates revealed 20 variable nucleotide positions within the cluster, indicating a clonal outbreak. The most likely index case was identified and diagnosed in Norway in 2009 but was born in Asia. WGS analyses verified that all of the cases were indeed part of a single transmission chain. However, even when combining WGS and intensified contact tracing, we were unable to fully reconstruct the TB transmission events.
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Beyene, Getachew Tesfaye; Kalayou, Shewit; Riaz, Tahira & Tonjum, Tone
(2017).
Comparative proteomic analysis of Neisseria meningitidis wildtype and dprA null mutant strains links DNA processing to pilus biogenesis.
BMC Microbiology.
17:96,
p. 1–18.
doi:
10.1186/s12866-017-1004-8.
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Background: DNA processing chain A (DprA) is a DNA binding protein which is ubiquitous in bacteria, and is
required for DNA transformation to various extents among bacterial species. However, the interaction of DprA with
competence and recombination proteins is poorly understood. Therefore, the proteomes of whole Neisseria
meningitidis (Nm) wildtype and dprA mutant cells were compared. Such a comparative proteomic analysis increases
our understanding of the interactions of DprA with other Nm components and may elucidate its potential role
beyond DNA processing in transformation.
Results: Using label-free quantitative proteomics, a total of 1057 unique Nm proteins were identified, out of which
100 were quantified as differentially abundant (P ≤ 0.05 and fold change ≥ |2|) in the dprA null mutant. Proteins
involved in homologous recombination (RecA, UvrD and HolA), pilus biogenesis (PilG, PilT1, PilT2, PilM, PilO, PilQ,
PilF and PilE), cell division, including core energy metabolism, and response to oxidative stress were downregulated
in the Nm dprA null mutant. The mass spectrometry data are available via ProteomeXchange with identifier
PXD006121. Immunoblotting and co-immunoprecipitation were employed to validate the association of DprA with
PilG. The analysis revealed reduced amounts of PilG in the dprA null mutant and reduced amounts of DprA in the
Nm pilG null mutant. Moreover, a number of pilus biogenesis proteins were shown to interact with DprA and /or
PilG.
Conclusions: DprA interacts with proteins essential for Nm DNA recombination in transformation, pilus biogenesis,
and other functions associated with the inner membrane. Inverse downregulation of Nm DprA and PilG expression
in the corresponding mutants indicates a link between DNA processing and pilus biogenesis.
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Namouchi, Amine; Munoz, Marta Gomez; Frye, Stephan Alfons; Moen, Line Victoria; Rognes, Torbjørn & Tonjum, Tone
[Show all 7 contributors for this article]
(2016).
The Mycobacterium tuberculosis transcriptional landscape under genotoxic stress.
BMC Genomics.
17:791,
p. 1–13.
doi:
10.1186/s12864-016-3132-1.
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Background: As an intracellular human pathogen, Mycobacterium tuberculosis (Mtb) is facing multiple stressful
stimuli inside the macrophage and the granuloma. Understanding Mtb responses to stress is essential to identify
new virulence factors and pathways that play a role in the survival of the tubercle bacillus. The main goal of this
study was to map the regulatory networks of differentially expressed (DE) transcripts in Mtb upon various forms of
genotoxic stress. We exposed Mtb cells to oxidative (H2O2 or paraquat), nitrosative (DETA/NO), or alkylation (MNNG)
stress or mitomycin C, inducing double-strand breaks in the DNA. Total RNA was isolated from treated and
untreated cells and subjected to high-throughput deep sequencing. The data generated was analysed to identify
DE genes encoding mRNAs, non-coding RNAs (ncRNAs), and the genes potentially targeted by ncRNAs.
Results: The most significant transcriptomic alteration with more than 700 DE genes was seen under nitrosative
stress. In addition to genes that belong to the replication, recombination and repair (3R) group, mainly found under
mitomycin C stress, we identified DE genes important for bacterial virulence and survival, such as genes of the type
VII secretion system (T7SS) and the proline-glutamic acid/proline-proline-glutamic acid (PE/PPE) family. By predicting
the structures of hypothetical proteins (HPs) encoded by DE genes, we found that some of these HPs might be
involved in mycobacterial genome maintenance. We also applied a state-of-the-art method to predict potential
target genes of the identified ncRNAs and found that some of these could regulate several genes that might be
directly involved in the response to genotoxic stress.
Conclusions: Our study reflects the complexity of the response of Mtb in handling genotoxic stress. In addition to
genes involved in genome maintenance, other potential key players, such as the members of the T7SS and PE/PPE
gene family, were identified. This plethora of responses is detected not only at the level of DE genes encoding
mRNAs but also at the level of ncRNAs and their potential targets.
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Lillenes, Meryl Sønderby; Rabano, Alberto; Støen, Mari; Riaz, Tahira; Misaghian, Dorna & Møllersen, Linda
[Show all 12 contributors for this article]
(2016).
Altered DNA base excision repair profile in brain tissue and blood in Alzheimer’s disease.
Molecular Brain.
9:61,
p. 1–14.
doi:
10.1186/s13041-016-0237-z.
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Background:
Alzheimer’s disease (AD) is a progressive, multifactorial neurodegenerative disorder that is the main cause of dementia globally. AD is associated with increased oxidative stress, resulting from imbalance in production and clearance of reactive oxygen species (ROS). ROS can damage DNA and other macromolecules, leading to genome instability and disrupted cellular functions. Base excision repair (BER) plays a major role in repairing oxidative DNA lesions. Here, we compared the expression of BER components APE1, OGG1, PARP1 and Polβ in blood and postmortem brain tissue from patients with AD, mild cognitive impairment (MCI) and healthy controls (HC).
Results:
BER mRNA levels were correlated to clinical signs and cerebrospinal fluid biomarkers for AD. Notably, the expression of BER genes was higher in brain tissue than in blood samples. Polβ mRNA level was significantly higher in the cerebellum than in the other brain regions, more so in AD patients than in HC. Blood mRNA levels of OGG1 was low and PARP1 high in MCI and AD.
Conclusions:
These findings suggest that alteration in BER gene expression is an event preceding AD and reflect the oxidative stress-generating energy-consumption in the brain and the importance of BER in repairing these damage events. The results link DNA repair in brain and blood to the etiology of AD at the molecular level and can potentially serve in establishing novel biomarkers, particularly in the AD prodromal phase.
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Yimer, Solomon Abebe; Namouchi, Amine; Zegeye, Ephrem Debebe; Holm-Hansen, Carol J C; Norheim, Gunnstein & Abebe, Markos
[Show all 8 contributors for this article]
(2016).
Deciphering the recent phylogenetic expansion of the originally deeply rooted Mycobacterium tuberculosis lineage 7.
BMC Evolutionary Biology.
16:146,
p. 1–10.
doi:
10.1186/s12862-016-0715-z.
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Background: A deeply rooted phylogenetic lineage of Mycobacterium tuberculosis (M. tuberculosis) termed lineage 7
was discovered in Ethiopia. Whole genome sequencing of 30 lineage 7 strains from patients in Ethiopia was
performed. Intra-lineage genome variation was defined and unique characteristics identified with a focus on
genes involved in DNA repair, recombination and replication (3R genes).
Results: More than 800 mutations specific to M. tuberculosis lineage 7 strains were identified. The proportion of
non-synonymous single nucleotide polymorphisms (nsSNPs) in 3R genes was higher after the recent expansion
of M. tuberculosis lineage 7 strain started. The proportion of nsSNPs in genes involved in inorganic ion transport
and metabolism was significantly higher before the expansion began. A total of 22346 bp deletions were observed.
Lineage 7 strains also exhibited a high number of mutations in genes involved in carbohydrate transport and
metabolism, transcription, energy production and conversion.
Conclusions: We have identified unique genomic signatures of the lineage 7 strains. The high frequency of
nsSNP in 3R genes after the phylogenetic expansion may have contributed to recent variability and adaptation.
The abundance of mutations in genes involved in inorganic ion transport and metabolism before the expansion
period may indicate an adaptive response of lineage 7 strains to enable survival, potentially under environmental
stress exposure. As lineage 7 strains originally were phylogenetically deeply rooted, this may indicate fundamental
adaptive genomic pathways affecting the fitness of M. tuberculosis as a species.
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Vogt, Yngve; Tonjum, Tone; Kaniusaitê, Milda; Rudberg, Rosa Jodalen & Støen, Mari
(2024).
Lager biodrivstoff fra tang og tare.
[Journal].
Teknisk Ukeblad.
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Vogt, Yngve; Tonjum, Tone; Kaniusaitê, Milda; Rudberg, Rosa Jodalen & Støen, Mari
(2024).
Lager biodrivstoff fra tang og tare.
[Journal].
Apollon : Forskningsmagasin for Universitetet i Oslo.
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Riaz, Tahira; Kubendraraj, Shivani; Sanjeevan, Sharuga; Tonjum, Tone; Støen, Mari & Vagolu, Siva Krishna
[Show all 7 contributors for this article]
(2022).
Nye forbindelser i bekjempelsen mot antibiotikaresistent tuberkulose.
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I dette prosjektet ble fire gramnegative bakterier (Pseudomonas aeruginosa, Acinetobacter baumannii, Enterobacter cloacae og Klebsiella pneumoniae), en laboratoriestamme av Mycobacterium tuberculosis (MTB), og to INH-resistente MTB stammer testet med 17 forbindelser og kontrollforbindelsen Ciprofloxacin. Dette ble gjort for å teste og finne nye forbindelser som hemmer MTB og de ulike gramnegative bakteriene. Diskdiffusjon og Microbroth Dilution ble benyttet for screening av de ulike gramnegative bakteriene med testforbindelser. MABA assay ble brukt til screening av H37Rv, MTB #1 med KatG mutert stamme, og MTB #7 med InhA mutert stamme. Samlet sett er kontrollstammen Ciprofloxacin den beste forbindelsen til eliminering av INH- resistent MTB. Av testforbindelsene ga forbindelse 3, 4, 5, 11, 15 og 16 tilstrekkelig hemming av bakterievekst ved at forbindelsene hadde en IC50 verdi lavere enn 50 μM. Av de nye testforbindelsene virket forbindelse 11 best mot laboratoriestammen, forbindelse 5 regnes som best mot MTB #1, og forbindelsene 3 og 5 virker best mot #7. Toksisiteten av forbindelsene mot HEK-293 celler ble målt ved bruk av MTT Assay. Betydelige feilkilder og mangel på replikater gjorde at gyldige konklusjoner om toksisiteten av forbindelser ikke kunne trekkes.
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Riaz, Tahira; Tønjum, Tone; Støen, Mari; Berge, Tone; Sukenthirarasa, Pravina & Kai, Celina Ka Wai
(2021).
New Drugs to Combat AMR.
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Tonjum, Tone
(2021).
Role of Post-translational Modifications in Antimicrobial Resistance.
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Background: The public health challenge of antimicrobial resistance (AMR) is escalating rapidly throughout the world, while the number of effective antimicrobial drugs continues to decrease. Numerous microbial DNA mutations and horizontal gene transfer events that directly cause or contribute to AMR have been identified and thoroughly characterized. Now we are discovering that additional mechanisms, such as macromolecular decorations of proteins, termed post-translational modifications (PTMs), also are implicated in AMR development.
Tuberculosis (TB) is one of the top 10 causes of death worldwide. This devastating infectious disease, caused by Mycobacterium tuberculosis (Mtb), was reported to be the cause of 10 million new cases. and 1.5 million deaths in 2019.
Methods: Mtb members of lineages 3, 4, 5 and 7 were investigated to better understand the evolution of virulence and AMR. Unique and shared proteomic signatures, as deduced from quantitative bioinformatics analyses of high-resolution mass spectrometry data, were delineated and related to phenotypic traits.
Results: The slow-growing Lineage 7 exhibited increased abundance of proteins involved in DNA repair, secretion and the CRISPR/Cas system as compared to the other lineages. MDR strains of lineage 2 had a reduced abundance of proteins involved in DNA repair and CRISPR/Cas. Notably, protein PTMs such as glycosylation and acetylation were found to play a significant role in Mtb adaptive processes and in AMR.
Discussion: The study identified several clinically important glycosylated and acetylated proteins that are applicable for diagnostics as well as for drug and vaccine discovery, highly relevant for improved global health in a next-generation setting.
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Kaniusaite, Milda; Riaz, Tahira; Lillenes, Meryl Sønderby; Detlie, Trond Espen; Alfredo, Rabano & Tonjum, Tone
(2020).
On the Brain-Gut axis: The gut microbiome affects the differential expression of DNA repair pathways in the human brain and mucosal gut tissue.
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Tonjum, Tone
(2019).
Tuberculosis and Machine learning.
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Antimicrobial resistance (AMR) represents a health threat that demands joint action globally. At TTA4, we will address bacterial physiology, metabolism, virulence and host adaptation, exemplified by Mycobacterium tuberculosis (Mtb), and how genome dynamics impact on Mtb fitness adaptation in changing environments and on antimicrobial resistance (AMR). The topics addressed will be relevant for mycobacterial pathogenesis and evolution, genome dynamics and AMR in general. Biochemical, genetic, live imaging and ultrastructural approaches are used to probe the interactions between proteins of these pathways. The objective of the meeting is to highlight recent progress, to reveal a more integrated understanding of the architecture of mycobacterial physiology, fitness for survival and AMR.
A main part of the meeting is dedicated to machine learning relevant for these topics. Infection biology and biomedicine are prime examples of research fields in swift development, not the least because of integrated approaches and multidisciplinary interactions between different segments of the life sciences. The increasing complexity of microbiological data and emergence of Big Data invigorates a need for deep learning, machine learning (ML) and artificial intelligence (AI).
All the new –omics data pave the way for ML and AI. Big Data has become too complex for humans to even try to understand their impact. That's what big data is: It's the realization that there exist piles of data beyond the capacity of the traditional human methods of analysis. ML is a field that combines systematic information, computer programming, and AI, all in one synergistic manner.
Big data and ML will have a tremendous influence on our society ahead. This presents a serious challenge and is a tremendous opportunity to apply automated techniques to help solve problems in infection biology in the 21st century.
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Lillenes, Meryl Sønderby; Riaz, Tahira; Støen, Mari; Kalayou, Shewit; Rabano, Alberto & Tonjum, Tone
(2019).
Proteomic Analysis of Brain Tissue from Patients with Alzheimer’s disease and Healthy Controls Reveals Differential Expression of Proteins Involved in Mitochondrial Dysfunction between Brain Domains.
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Kristiansen, Bjørn Erik & Tonjum, Tone
(2019).
Andre gramnegative bakterier.
In Rollag, Halvor; Müller, Fredrik & Tonjum, Tone (Ed.),
Medisinsk mikrobiologi.
Gyldendal Akademisk.
ISSN 9788205500983.
p. 233–245.
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Zegeye, Ephrem Debebe; Gómez-Muñoz, Marta; Namouchi, Amine; Balasingham, Seetha; Szpinda, Irena & Förstner, Konrad
[Show all 8 contributors for this article]
(2019).
A nutrient supplement promotes the rapid detection and improved sensitivity of mycobacteria in clinical samples via the differential regulation of dormancy genes and noncoding RNAs.
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Tonjum, Tone; Birhanu, Alemayehu Godana; Riaz, Tahira & Yimer, Solomon Abebe
(2019).
Abundance of post-translational modifications in Mycobacterium tuberculosis.
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Background
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB), one of the top 10 causes of death worldwide and the leading cause of death from infectious disease. Despite the discovery of a multitude of Mtb strains with a high degree of genetic conservation, only a few sub-groups cause extensive outbreaks and antimicrobial drug resistance (AMR), with different clinical presentations in terms of transmissibility, virulence and elicited immune responses.
Various regulatory mechanisms contribute to the complexity of the simpler genomes and proteomes of Mtb, and post-translational modifications (PTMs) play a significant role in this variability. PTMs allow bacteria to rapidly alter protein activity in response to host factors and have been implicated in Mtb virulence and AMR. Our aim is to characterize the global acetylome and glycoproteomic profile of different Mtb lineages, to unveil the role of these PTMs in mycobacterial adaptation, survival and AMR.
Materials/methods
The global acetylome and glycoproteomic patterns in five Mtb strains, four clinical isolates including the slow-growing lineage 7 and the reference strain H37Rv, were analyzed. Mtb cell lysates were subjected to in-gel trypsin digestion and injected into a Nano LC-MS/MS mass spectrometer (Thermo Scientific). The MaxQuant and Perseus softwares were used peptide search and PTM site identification. Poteins were searched for 57 different glycan residues. The findings on N-linked protein glycosylation were verified by manual inspection. The Cytoscape plug-in MCODE was used to develop protein-protein interaction networks.
Results
Our analysis resulted in the identification of 2944 glycosylation sites on 1325 proteins and 2490 acetylation sites on 953 proteins. Notably, we report 489 sites that were N-glycosylated at N residues (17% of the total glycosylation events). The study identified strain-specific qualitative and quantitative differences in PTM abundances on proteins involved in virulence, pathogenesis and AMR.
Conclusions
Notably, this study reports a vast abundance of PTMs in clinical Mtb strains and is the first report on N-linked glycosylation and O-acetylation in Mtb. These novel PTM data also explain the role of protein acetylation and glycosylation in creating phenotypic variability and fitness for survival among the genetically conserved lineages of Mtb.
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Tonjum, Tone; Homberset, Håvard; Eriksson, Jens & kussell, edo
(2018).
Update on neisserial transformation.
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The pathogenic Neisseria species, N. meningitidis and N. gonorrhoeae are readily transformed in vitro by exogenous heterologous DNA, such as antibiotic resistance cassettes. The closely related and generally harmless commensal species N. lactamica (Nla) is less tolerant of DNA heterology and has previously not been described to be competent for natural transformation. A possible explanation for this observation is that Nla-specific restriction endonucleases limit the transformability of Nla. Here, we provide evidence to support this hypothesis, including bioinformatics data consistent with the presence of an abundance of restriction-modification (RM) systems in Nla. Bioinformatics studies also demonstrated an aberrantly low frequency of the restriction/modification site CATG in the Nla genome, which can be attributed to restriction site avoidance. Furthermore, inactivation of genes encoding selected endonucleases increased the efficiency of Nla transformation with heterologous DNA. These results suggest that engineered Nla strains in which one or more RM systems are inactivated could be useful tools for developing anti-microbial vaccines.
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Tonjum, Tone
(2018).
The Brain-Gut axis: Differential expression of DNA repair in human brain and mucosal gut tissue.
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Tonjum, Tone; Birhanu, Alemayehu Godana; Noer, Marie Therese & Szpinda, Irena
(2017).
Proteomic analysis of Mycobacterium tuberculosis
membrane vesicles under stress - EP 0415.
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Munoz, Marta Gomez; Namouchi, Amine; Balasingham, Seetha & Tonjum, Tone
(2016).
Identifiying ncRNAs expressed under genotoxic stress and dormancy in Mycobacterium tuberculosis.
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Mycobacterium tuberculosis (Mtb) is the intracellular pathogen that causes tuberculosis (TB), an infectious disease responsible for 1.5 million deaths worldwide in 2015. This bacterium is inhaled in aerosol droplets and once in the lung, it is engulfed by alveolar macrophages. Inside the activated macrophage, Mtb is exposed to a hostile environment, including reactive oxygen species (ROS) and reactive nitrogen species (RNS) that cause oxidation, deamination and alkylation of macromolecules. This condition is fatal to most bacterial pathogens, but Mtb has the ability to sense the host environment and eventually enter into a non-replicating, persistent state. The tubercle bacilli can remain in this latent stage for a lifetime without causing disease or, under certain conditions, it can awake resulting in TB disease. In this context, the aim of our study is to identify and characterize non-coding RNAs (ncRNAs) transcribed under genotoxic stress as well as during reactivation from the dormant stage.
Here, Mtb strain H37Rv was exposed to various forms of genotoxic stress (oxidative, nitrosative or alkylative stress or double strand DNA breaks) and defined culture supplements. Total RNA from treated and untreated H37Rv cells was isolated and subjected to high-throughput RNA-seq. ncRNAs were identified using Rockhopper. A subset of the ncRNAs detected was selected for a more detailed analysis, including validation by northern blot. The secondary structure of the ncRNAs under study was predicted using mfold and their potential gene targets were predicted using intaRNA and CopraRNA.
Ahead, we will combine our molecular and bioinformatics results with in vitro studies, including mapping 5’ and 3’ by RACE, establishing their secondary structure with SHAPE, and detecting sRNA-mRNA interactions by performing EMSA. The potential physiological role of the Mtb ncRNAs predicted will be tested by employing mutants or by repression, deletion or over-expression of the ncRNA of interest and measuring the potential phenotypic outcome by next-generation quantitative mass spectrometry.
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Frye, Stephan Alfons; Balasingham, Seetha; Beyene, Getachew Tesfaye; Homberset, Håvard; Namouchi, Amine & Tonjum, Tone
(2016).
Meningococcal DNA binding and unwinding proteins.
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Background: DNA helicases are a ubiquitous group of enzymes that use the energy of nucleoside triphosphate (dNTP) hydrolysis to catalyze the separation of double-stranded DNA (dsDNA). Helicases are involved in essentially every step in DNA metabolism, including replication, DNA repair, recombination, transcription, Holliday junction movement, and displacement of proteins from DNA. We investigated the DNA helicases RecG and DinG from Neisseria meningitidis (NmRecG and NmDinG) and their roles during genotoxic stress, including DNA damage. These helicases belong to superfamily 2, are ATP dependent and exert 5′to 3′ directionality. Our aim was to define the potential roles of NmRecG and NmDinG in DNA repair, recombination and replication (3R).
Methods and results: Cell lysates from Nm wildtype and recG and dinG null mutants (NmrecG and dinG) were assessed by quantitative mass spectrometry (MS). In the ∆recG mutant, 16 proteins were differentially expressed as compared to the Nm wildtype. RecN, Ssb and DnaX were upregulated in the Nm∆recG mutant, while the type 4 pilus structural subunit protein PilE as well as pilus biogenesis components (PilF, PilT and PilQ) were downregulated. Global proteomics analysis of Nm wildtype and ∆recG mutant strains thus revealed the most abundant differentially expressed proteins and linked RecG to DNA repair, recombination and replication, pilus biogenesis components and glycan biosynthesis. Notably, when NmdinG cells grown under mitomycin C (MMC) stress, 134 proteins were shown to be differentially abundant compared to the unstressed NmdinG. Most of them are involved in metabolic functions like carbon, amino acid and nucleotide synthesis. Among 3R proteins, polymerase III subunits and recombinational repair proteins RuvA, RuvB, RecB and RecD were significantly downregulated while TopA and SSB were upregulated under stress. Genotoxic stress analysis demonstrated that NmdinG was more sensitive to double-strand DNA breaks (DSB) induced MMC than the Nm wildtype, defining the role of neisserial DinG in DSB repair.
An unusually high number of DNA uptake sequences (DUS) that facilitate the transformation in neisserial species were identified in the Nm recG gene, signifying its importance.
The genes encoding NmRecG and NmDinG were cloned and overexpressed, the recombinant NmRecG and NmDinG proteins were purified to homogeneity and their enzymatic activity was characterized. NmRecG acts through its ability to process Holliday junction (HJ) intermediates and catalyse branch migration of complex DNA structures. NmRecG and NmDinG possess 5′to3′ directionality and prefer DNA substrates containing a 5′overhang. ATPase activity of NmRecG and NmDinG is strictly DNA-dependent, and DNA unwinding activity requires nucleoside triphosphate in addition to divalent metal cations. This study contributes to understand the overall role of RecG in neisserial genome maintenance and evolution.
Conclusions: This study gives new insight into the functional roles and interactions of the helicases RecG and DinG, elucidation their roles in meningococcal DNA repair and recombination, with a link of RecG to transformation also through pilus biogenesis.
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Lillenes, Meryl Sønderby; Riaz, Tahira; Rabano, Alberto; Fladby, Tormod & Tonjum, Tone
(2016).
Altered DNA base excision repair profile in brain tissue and blood in Alzheimer's disease.
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Alzheimer’s disease (AD) is the major contributor to cognitive decline and dementia worldwide. Considering the expanding numbers of elderly in our society, studies of health and disease in the aging population is increasingly important. In order to understand AD, one must understand normal aging. AD is preceded by mild cognitive impairment (MCI), and once MCI occurs, early diagnostics and therapies are urgently needed. MCI/AD is associated with increased oxidative stress, resulting from imbalance in production and clearance of reactive oxygen species (ROS). ROS can damage DNA and other macromolecules, leading to genome instability and disrupted cellular functions. To counteract the harmful effects of oxidative DNA damage, cells use the base excision repair (BER) pathway. We have monitored the expression of the DNA repair profile in human blood and post-mortem brain biopsies from AD and MCI patients and healthy aged individuals by transcriptional profiling and mass spectrometry. In this context, we have a particular a focus on selected BER components, to define if the expression profile varies between AD patients as compared to healthy controls. Notably, BER expression was significantly higher in brain tissue compared to blood. BER mRNA levels were correlated to clinical signs and cerebrospinal fluid biomarkers for AD. Blood mRNA levels of OGG1 was low and PARP1 high in MCI and AD. These findings suggest that alteration in BER gene expression is an event preceding AD and reflect the oxidative stress-generating energy-consumption in the brain and the importance of BER in repairing these damage events. Collectively, these studies provide new keys to understanding early events in the progression of AD and also expand the pool of potential biomarkers for pre-clinical AD
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Lillenes, Meryl Sønderby & Tonjum, Tone
(2016).
Altered DNA base excision repair profile in brain tissue and blood in Alzheimer's disease.
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Yimer, Solomon Abebe; Yimer, Solomon Abebe & Tonjum, Tone
(2016).
Current knowledge on Mycobacterium tuberculosis lineage 7: the paradox of slow growth and still success.
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Tonjum, Tone
(2016).
Utvikling av antibiotikaresistens hos Gramnegative og Grampositive bakterier: påvisning og ny behandling.
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Birhanu, Alemayehu Godana; Tonjum, Tone & Abebe, Markos
(2019).
Unveiling phenotypic differences among the genetically conserved Mycobacterium tuberculosis complex: Characterization of proteomes and post-translational modifications.
Universitetet i Oslo.
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Members of the genetically conserved Mycobacterium tuberculosis complex (MTBC) exhibit vast discrepancies in clinical outcome and epidemiological behaviour. Bacterial factors that contribute to these phenotypic variabilities remain elusive. We hypothesize that qualitative and quantitative differences in the abundance of proteins and their post-translational modifications (PTMs) may contribute to MTBC phenotypic diversity. The study analyzed the proteomic and PTM profiles (acetylation and glycosylation) among members of the MTBC using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). Comparative proteomic analysis of the MTBC lineages revealed significantly different abundances of proteins involved in virulence, growth and bioenergetics. The PTM study provides the first report on O-acetylation and N-glycosylation of MTBC proteins. The study presents a comprehensive proteomic and PTM map of MTBC and demonstrated the presence of significant differences among different lineages. These new discoveries will enable a better understanding of the pathogen with new potential for identification of novel drug targets and vaccine candidates, as well as efficient diagnostics for TB disease.
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Riaz, Tahira; Tonjum, Tone & Olsen, Ingrid
(2019).
Proteomic approaches to study CD4+ T cells and meningococci: New insight into life science and infection biology.
Universitetet i Oslo.
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The human mucosa in both the gut and the oropharynx is constantly under exposure to commensals and opportunists and are a key site of immune responses. Homoeostasis between mucosal components play a critical role in avoiding immune mediated diseases and fighting infections. This Thesis aims to delineate the comprehensive proteome analysis of two selected mucosal entities representing the host and a potential pathogen by use of high-throughput mass spectrometry analysis. In the first part of the Thesis (Papers I and II), the cellular composition of CD4+ T helper (Th) cells from the inflamed gut of Crohn’s disease patients were addressed. Paper I explored the phenotypic characteristics and molecular functions of Th cells by comparison of gut-derived Th cell phenotypes. Paper II addressed the relationship between the transcriptome and proteome upon activation of gut-derived cytotoxic Th cells. In the second part of the Thesis (Papers III and IV), DNA metabolic components from an oropharyngeal mucosal opportunist, the bacterium Neisseria meningitidis (Nm), were addressed. The aim was to understand which Nm proteins contribute to transformation of DNA (DprA, Paper III) and DNA repair/recombination (helicase RecG, Paper IV) by comparative analysis of Nm wildtype and deletion mutants. Thus, by investigating relatively homogenous cellular assemblies, the unique properties of the host cell clone and bacterial cultures studied were characterized. In Paper I, the homogenous primary Th cells analysis led to crucial findings on a novel phenotype of cytotoxic CD4+ T cells. In Paper II, the changes observed by 'omics' analysis upon activation of cytotoxic Th cell provided a deeper description of their complexity and molecular mechanisms. In Papers III and IV, Nm proved to be a relevant genetically amenable model for investigating DNA-related proteins and a good source for protein-protein interaction studies. Collectively, these results provided new insight into life science and infection biology, focused on the gut and oral mucosal surfaces.
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Published
Oct. 25, 2013 10:00 AM
- Last modified
Feb. 9, 2026 10:43 AM
