Tahira Riaz

• 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. Full text in Research Archive Show summary

  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.

• 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. Full text in Research Archive Show summary

  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.

• 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. Full text in Research Archive Show summary

  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.

• 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. Full text in Research Archive Show summary

  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.

• 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. Full text in Research Archive Show summary

  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.

• 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. Full text in Research Archive Show summary

  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

• 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. Full text in Research Archive Show summary

  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.

• 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. Full text in Research Archive Show summary

  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.

• Frye, Stephan Alfons; Beyene, Getachew Tesfaye; Namouchi, Amine; Munoz, Marta Gomez; Homberset, Håvard & Kalayou, Shewit [Show all 9 contributors for this article] (2017). The helicase DinG responds to stress due to DNA double strand breaks. PLOS ONE. 12:e0187900(11), p. 1–23. doi: 10.1371/journal.pone.0187900. Full text in Research Archive
• 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. Full text in Research Archive Show summary

  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.

• 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. Full text in Research Archive Show summary

  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.

• Riaz, Tahira; Sollid, Ludvig Magne; Olsen, Ingrid & Souza, Gustavo Antonio De (2016). Quantitative Proteomics of Gut-Derived Th1 and Th1/Th17 Clones Reveal the Presence of CD28+ NKG2D- Th1 Cytotoxic CD4+ T cells. Molecular & Cellular Proteomics. ISSN 1535-9476. 15(3), p. 1007–1016. doi: 10.1074/mcp.M115.050138. Full text in Research Archive
• Beyene, Getachew Tesfaye; Balasingham, Seetha; Frye, Stephan Alfons; Namouchi, Amine; Homberset, Håvard & Kalayou, Shewit [Show all 8 contributors for this article] (2016). Characterization of the Neisseria meningitidis Helicase RecG. PLOS ONE. 11:e0164588(10), p. 1–31. doi: 10.1371/journal.pone.0164588. Full text in Research Archive Show summary

  Neisseria meningitidis (Nm) is a Gram-negative oral commensal that opportunistically can cause septicaemia and/or meningitis. Here, we overexpressed, purified and characterized the Nm DNA repair/recombination helicase RecG (RecGNm) and examined its role during genotoxic stress. RecGNm possessed ATP-dependent DNA binding and unwinding activities in vitro on a variety of DNA model substrates including a Holliday junction (HJ). Database searching of the Nm genomes identified 49 single nucleotide polymorphisms (SNPs) in the recGNm including 37 non-synonymous SNPs (nsSNPs), and 7 of the nsSNPs were located in the codons for conserved active site residues of RecGNm. A transient reduction in transformation of DNA was observed in the Nm ΔrecG strain as compared to the wildtype. The gene encoding recGNm also contained an unusually high number of the DNA uptake sequence (DUS) that facilitate transformation in neisserial species. The differentially abundant protein profiles of the Nm wildtype and ΔrecG strains suggest that expression of RecGNm might be linked to expression of other proteins involved in DNA repair, recombination and replication, pilus biogenesis, glycan biosynthesis and ribosomal activity. This might explain the growth defect that was observed in the Nm ΔrecG null mutant.

• Bøhle, Liv Anette; Riaz, Tahira; Jacobsen, Wolfgang Mathias; Skaugen, Morten; Busk, Øyvind & Eijsink, Vincent [Show all 7 contributors for this article] (2011). Identification of surface proteins in Enterococcus faecalis V583. BMC Genomics. 12. doi: 10.1186/1471-2164-12-135. Full text in Research Archive Show summary

  Background Surface proteins are a key to a deeper understanding of the behaviour of Gram-positive bacteria interacting with the human gastro-intestinal tract. Such proteins contribute to cell wall synthesis and maintenance and are important for interactions between the bacterial cell and the human host. Since they are exposed and may play roles in pathogenicity, surface proteins are interesting targets for drug design. Results Using methods based on proteolytic "shaving" of bacterial cells and subsequent mass spectrometry-based protein identification, we have identified surface-located proteins in Enterococcus faecalis V583. In total 69 unique proteins were identified, few of which have been identified and characterized previously. 33 of these proteins are predicted to be cytoplasmic, whereas the other 36 are predicted to have surface locations (31) or to be secreted (5). Lipid-anchored proteins were the most dominant among the identified surface proteins. The seemingly most abundant surface proteins included a membrane protein with a potentially shedded extracellular sulfatase domain that could act on the sulfate groups in mucin and a lipid-anchored fumarate reductase that could contribute to generation of reactive oxygen species. Conclusions The present proteome analysis gives an experimental impression of the protein landscape on the cell surface of the pathogenic bacterium E. faecalis. The 36 identified secreted (5) and surface (31) proteins included several proteins involved in cell wall synthesis, pheromone-regulated processes, and transport of solutes, as well as proteins with unknown function. These proteins stand out as interesting targets for further investigation of the interaction between E. faecalis and its environment.

• Kozielski, Frank; Riaz, Tahira; DeBonis, Salvatore; Koehler, Christian; Panse, Isabel & Strozynski, Margarita Anna [Show all 9 contributors for this article] (2011). Proteome analysis of microtubule-associated proteins and their interacting partners from mammalian brain. Amino Acids. ISSN 0939-4451. 41(2), p. 363–385. doi: 10.1007/s00726-010-0649-5. Full text in Research Archive
• Kozielski, Frank; Riaz, Tahira; DeBonis, Salvatore; Koehler, Christian; Kröning, Mario & Panse, Isabel [Show all 9 contributors for this article] (2010). Proteome analysis of microtubule-associated proteins and their interacting partners from mammalian brain. Amino Acids. ISSN 0939-4451. doi: 10.1007/s00726-010-0649-5. Full text in Research Archive
• Yimer, Solomon Abebe; Godana, Alemayehu; Kalayou, Shewit; Riaz, Tahira; Zegeye, Ephrem Debebe & Beyene, Getachew Tesfaye [Show all 11 contributors for this article] (2010). 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. Full text in Research Archive Show summary

  In order to decipher the nature of the slowly growing Mycobacterium tuberculosis (M.tuberculosis) lineage 7, the differentially abundant proteins in strains of M. 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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• Støen, Mari; Riaz, Tahira & Tonjum, Tone (2024). Fra grunnforskning til innovasjon og startup bedrift. Full text in Research Archive
• Riaz, Tahira (2023). Comparative proteomics explain the mechanism of action of mycobacterial tolerance inhibitors. Full text in Research Archive
• Riaz, Tahira (2022). Fighting Antimicrobial Resistance – Education, Surveillance, Innovative therapeutics, Basic and Clinical research. Full text in Research Archive
• Riaz, Tahira (2022). Genome Dynamics in Infection Biology and Precision Medicine - The AMR paradigm: TB as a model example. Full text in Research Archive
• 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. Full text in Research Archive Show summary

  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.

• Riaz, Tahira (2022). Development of novel Mycobacterial Tolerance Inhibitors (MTIs) against MDR/XDR tuberculosis. Full text in Research Archive
• Riaz, Tahira; Tønjum, Tone; Støen, Mari; Berge, Tone; Sukenthirarasa, Pravina & Kai, Celina Ka Wai (2021). New Drugs to Combat AMR. Full text in Research Archive
• Riaz, Tahira (2021). JPIAMR Capacity Building Ideathon - Rapporteur. Full text in Research Archive
• Riaz, Tahira (2021). Development of novel Mycobacterial Tolerance Inhibitors (MTIs) against MDR/XDR tuberculosis. Full text in Research Archive
• Riaz, Tahira & Tonjum, Tone (2020). Resistance mechanisms and novel drug targets. Full text in Research Archive
• Riaz, Tahira (2020). Novel Mycobacterial Tolerance Inhibitors (MTIs) Against Multidrug-Resistant Tuberculosis. Full text in Research Archive
• 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. Full text in Research Archive
• Riaz, Tahira & Muñoz, Marta Gómez (2020). Genome dynamics in health and disease: Focus on AMR, TB and COVID-19. Full text in Research Archive
• Riaz, Tahira (2019). Proteome characterization of Mycobacterium tuberculosis. Full text in Research Archive
• 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. Full text in Research Archive
• Riaz, Tahira (2019). Proteomics studies to combat Tuberculosis. Full text in Research Archive
• Tonjum, Tone; Birhanu, Alemayehu Godana; Riaz, Tahira & Yimer, Solomon Abebe (2019). Abundance of post-translational modifications in Mycobacterium tuberculosis. Full text in Research Archive Show summary

  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.

• Riaz, Tahira (2018). Proteomics of selected microbes and man. Full text in Research Archive
• Riaz, Tahira (2016). Th1 og Th1/Th17-cellekloner i tarmbiopsier fra pasienter med Crohns sykdom. BestPractice Gastroenterologi. ISSN 1903-6590. Full text in Research Archive
• 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. Full text in Research Archive Show summary

  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

• Tonjum, Tone; Riaz, Tahira; Lillenes, Meryl Sønderby; Detlie, Trond Espen & Jensen, Helge Leander B. (2016). The Brain-Gut axis: Differential expression of DNA repair in human brain and mucosal gut tissue. Full text in Research Archive Show summary

  The biology of the neurological and gastrointestinal systems are tightly interconnected, interacting with and influencing each other through multiple bidirectional signaling pathways. The human microbiome strongly influences the physiology of all organs including the central nervous system (CNS), and the CNS in turn modulates gut function, beyond the effects of the vagal nerve. Therefore, imbalance in the brain-gut axis could correlate with incipient pathology in the CNS and/or the gastrointestinal tract. We asked if and how the gut microbiome modulates susceptibility to progressive neurodegenerative Alzheimer’s disease (AD). The primary hypothesis we are testing is that imbalance in the brain-gut axis promotes neurodegeneration or gastrointestinal dysfunction, or both. The proteomic expression profile was tested in post-mortem human brain tissue and gut mucosal biopsies. In terms of DNA repair, predominant base excision repair (BER) was expressed in brain tissue, while nucleotide excision repair (NER) was more highly expressed in the gut mucosa. This differential expression pattern reflects local stress and organ environments, both the nature of non-replicating versus replicating cells as well as the state of a sterile organ versus that of an organ with a rich microbiome. Different DNA repair responses were evident in the prodromal versus late stages of AD and in IBD. We have previously shown that signature reactions in BER patterns in brain appear before AD pathology is evident and may represent a response to increased oxidative stress. These studies extend our findings on DNA repair and bioenergetics in AD and IBD, and will also address the contribution of the gut microbiome.

• Birhanu, Alemayehu Godana; Yimer, Solomon Abebe; Riaz, Tahira & Tonjum, Tone (2016). Proteomic Analysis of Mycobacterium tuberculosis Membrane Vesicles. Full text in Research Archive
• Birhanu, Alemayehu Godana; Yimer, Solomon Abebe; Riaz, Tahira & Tonjum, Tone (2016). Proteomic Analysis of Mycobacterium tuberculosis Membrane Vesicles. Full text in Research Archive Show summary

  Studies in the last decades have demonstrated the importance of secreted proteins in bacterial pathogenesis. Secreted membrane vesicles (MVs), in particular, have been suggested to serve as a vehicle for the selective packaging and release of virulence factors, such as toxins and immunomodulatory molecules (1-2). Previous studies on Mycobacterium tuberculosis (Mtb) pathogenesis have shown that phagocytosed dead bacilli with no secreted proteins lose their ability to hinder phagosome-lysosome fusion (3). Therefore, understanding the contents and mechanism of action of MV proteins will lead to deeper understanding of TB disease. The aim of this project is characterise the proteomic profile of Mtb MVs to unveil their role in host-pathogen interaction. Mtb H37Rv cells were cultured in minimal media (MM) at 37 °C to mid-log phase (OD600 = 0.8) and the filtered cell free supernatant was used as a source to isolate MVs by density gradient ultra-centrifugation (4). The purified membrane vesicles and cellular pellets were loaded on Bis-Tris Protein Gels (4-12%) for in-gel digestion and cleaned up using c-18 zip-tip columns (5) before injection into the Q-Exactive mass spectrometer (Thermo Scientific, Germany) in triplicates. MaxQuant software was used to define the amounts of the various peptides present and the data was analyzed using Perseus software. The functional categories for the differentially expressed proteins identified were grouped using the KEGG database. The concentration and size distribution of membrane vesicles isolated were measured using NanoSight and the size ranges from 70-400 nm in diameter. Next-generation mass spectrometry revealed that there is enriched packaging of virulence associated mycobacterial proteins in MVs. A total of 83 proteins were identified in Mtb MVs out of which 69 are shared with the cellular proteome and 14 found exclusively in MVs. The majority of the MV components detected were secreted proteins which are reported to be major virulence factors (antigen 85 complex, ESAT-6 and PE/PPE). Furthermore, 71 proteins have never been reported in Mtb membrane vesicles before (2, 4), and some of the proteins were uncharacterized. KEGG pathway enrichment analysis showed proteins involved in two-component systems, ABC transporters, amino acid and fatty acid metabolism, and catalytic and hydrolase activity. This study generated new knowledge on the proteomic profile of Mtb MVs and their surface-exposed antigens. We have characterized Mtb membrane vesicles, which are enriched with surface/secreted antigenic proteins and virulence factors. Further in-silico and in-vitro/in-vivo study is needed to investigate the clinical relevance of the MV proteins identified, including the newly discovered un-characterized proteins. References: 1. Kuehn MJ, Kesty NC. Bacterial outer membrane vesicles and the host–pathogen interaction. Genes & development. 2005 Nov 15;19(22):2645-55. 2. Lee J, Kim SH, Choi DS, Lee JS, Kim DK, Go G, Park SM, Kim SH, Shin JH, Chang CL, Gho YS. Proteomic analysis of extracellular vesicles derived from Mycobacterium tuberculosis. Proteomics. 2015 Oct 1;15(19):3331-7. 3. Russell DG, Purdy GE, Owens RM, Rohde KH, Yates RM. Mycobacterium tuberculosis and the four minute phagosome. ASM News. 2005;71:459–463. 4. Prados-Rosales R, Brown L, Casadevall A, Montalvo-Quirós S, Luque-Garcia JL. Isolation and identification of membrane vesicle-associated proteins in Gram-positive bacteria and mycobacteria. MethodsX. 2014 Dec 31;1:124-9 5. Wiśniewski JR, Zougman A, Mann M. Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J Proteome Res 8(12):5674-8, 2009.

• Yimer, Solomon Abebe; Birhanu, Alemayehu Godana; Shewit, Kalayou; Riaz, Tahira; Zegeye, Ephrem Debebe & Beyene, Getachew Tesfaye [Show all 11 contributors for this article] (2016). First proteomic analysis of Mycobacterium tuberculosis lineage 7 differentially expressed proteins involved for growth. Full text in Research Archive
• Birhanu, Alemayehu Godana; Yimer, Solomon Abebe; Riaz, Tahira & Tonjum, Tone (2016). Proteomic Analysis of Mycobacterium tuberculosis Membrane Vesicles. Full text in Research Archive Show summary

  Secreted membrane vesicles (MVs) are abundant in Mycobacterium tuberculosis (Mtb) and are suggested to have important roles in mycobacterial physiology and pathogenesis. MVs may contain varied cargo, including nucleic acids, toxins, lipoproteins and enzymes. In particular, MVs have been shown to serve as a vehicle for the selective packaging and release of virulence factors, such as toxins and immunomodulatory molecules. However, how and why MVs escape the thick cell walls of mycobacteria is still unknown. The aim of this project is characterize the proteomic profile of MVs from selected Mtb lineages and to unveil the role of MVs in mycobacterial adaptation to environmental factors. Mtb cells were cultured with and without oxidative and nitrosative stress. The Mtb cell free culture supernatant was used as a source to isolate enriched MVs by density gradient ultra-centrifugation. The purified membrane vesicles were investigated by mass spectrometry. The MaxQuant and Perseus softwares were used for peptide search, data analysis and quality control, respectively. The functional categories of the proteins identified were grouped using the KEGG pathway database. The mass spectrometry proteomic data revealed that MVs contain enriched packaging of virulence associated mycobacterial proteins. A total of 83 proteins were identified in Mtb MVs, out of which 69 were shared with the cellular proteome and 14 were found exclusively in MVs. The majority of the MV-specific components detected were secreted proteins which are reported to be major virulence factors (antigen-85 complexes, ESAT-6 and PE/PPE, etc). Based on the KEGG pathway functional analysis, the identified proteins were found to be involved in two-component systems, ABC transporters, amino acid and fatty acid metabolism, as well as catalytic and hydrolase activity and hypothetical proteins. Thereby, this study generated new knowledge on the proteomic profile of Mtb MVs. We have characterized Mtb membrane vesicles, which are enriched with surface/secreted antigenic proteins and virulence factors. Further in silico and in vitro/in-vivo studies are required to investigate the adaptive and clinical relevance of the MV proteins identified, including the newly discovered un-characterized proteins.

• Yimer, Solomon Abebe; Namouchi, Amine; Riaz, Tahira; Zegeye, Ephrem Debebe; Godana, Alemayehu & Holm-Hansen, Carol J C [Show all 9 contributors for this article] (2015). Genomic and proteomic analysis of Mycobacterium tuberculosis lineage 7 strains from Ethiopia. Oral presentation at the 46th Union World Conference on Lung Health Cape Town, South Africa: 2 December - 6 December 2015. Full text in Research Archive Show summary

  Background: Understanding the various factors driving the tuberculosis (TB) pandemic is essential to achieve the Global Plan for TB control and elimination. Recently, a new phylogenetic M. tuberculosis (Mtb) lineage (lineage 7) has been identified in Ethiopia, which is associated with prolonged delay among patients and grows slowly in vitro compared to other lineages. Given the potential implications for pathogenesis and virulence of the bacteria, genomic and proteomic studies on Mtb are warranted. The aim of this study was to delineate the molecular characteristics of Mtb lineage 7 strains by analysing genomic and proteomic profiles. Methods: The BACTEC MGIT 960 culture system was used to cultivate 30 Mtb lineage 7 isolates. DNA was extracted and whole genome sequencing was performed using the Illumina Hiseq2000. Overall, after aligning the generated reads for each strain to the genome sequence of the Mtb H37Rv strain, the coverage rate was above 300 times. High resolution Q-Exactive mass spectrometer was used to achieve proteome characterization. MaxQuant software was used to define the amounts of the various proteins present, while post-translational modifications (PTMs) were identified by Proteome Discoverer and manual inspection. Results: More than 800 mutations or single nucleotide polymorphisms (SNPs) specific to Mtb lineage 7 strains were identified. Compared to other lineages, Mtb lineage 7 strains exhibited a high number of mutations in genes involved in carbohydrate transport and metabolism, transcription, energy production and conversion. Notably, low frequencies of mutations were observed in genes involved in amino acid, lipid and coenzyme transport and metabolism, post translational modification, protein turnover and chaperone. Several interesting proteins, such as transcription factors, membrane proteins and proteins involved in pathogenesis of the bacteria were identified in lineage 7 strains. We also identified novel site-specific PTMs. Conclusions: This study generated novel knowledge regarding the genomic and proteomic profile of Mtb lineage 7 strains. Further research is essential to understand the consequences of the differential frequencies of mutations observed in the main gene groups of lineage 7 strains. Taken together, these studies have generated significant novel knowledge on a new lineage of Mtb, which can elucidate how these strains can have fitness for survival despite their relatively slow growth.

• Mathiesen, Geir; Riaz, Tahira; Bøhle, Liv Anette; Skaugen, Morten; Busk, Øyvind & Jacobsen, Wolfgang Mathias [Show all 7 contributors for this article] (2011). Identification of surface proteins in Enterococcus faecalis V583. Full text in Research Archive
• Bøhle, Liv Anette; Riaz, Tahira; Egge-Jacobsen, Wolfgang; Skaugen, Morten; Busk, Øyvind & Eijsink, Vincent (2010). Direct LC-MS/MS-based identification of surface-associated proteins in Enterococcus faecalis V583. Full text in Research Archive
• Riaz, Tahira; Mathiesen, Geir; Busk, Øyvind; Skaugen, Morten; Bøhle, Liv Anette & Egge-Jacobsen, Wolfgang [Show all 7 contributors for this article] (2009). Identification of Enterococcus faecalisV583 surface-associated proteins. Full text in Research Archive
• 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. Full text in Research Archive Show summary

  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.

• Riaz, Tahira (2008). Proteome analysis of microtubule-associated proteins and S-trityl-L-cysteine-induced mitotic arrest and apoptosis. UMB. Full text in Research Archive

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