New functions of pirin proteins and a 2-ketoglutarate: Ferredoxin oxidoreductase ortholog in Bacteroides fragilis metabolism and their impact on antimicrobial susceptibility to metronidazole and amixicile
Andrea M. Gough,
Anita C. Parker,
Patricia J. O'Bryan,
Terence R. Whitehead,
Sourav Roy,
Brandon L. Garcia,
Paul S. Hoffman,
C. Jeffrey Smith,
Edson R. Rocha,
Andrea M. Gough
Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
Contribution: Methodology, Investigation, Validation, Visualization, Formal analysis
Search for more papers by this authorAnita C. Parker
Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
Contribution: Methodology, Investigation, Validation, Visualization, Formal analysis
Search for more papers by this authorPatricia J. O'Bryan
USDA Agricultural Research Service, Peoria, Illinois, USA
Contribution: Methodology, Validation, Investigation, Formal analysis
Search for more papers by this authorTerence R. Whitehead
USDA Agricultural Research Service, Peoria, Illinois, USA
Contribution: Methodology, Validation, Investigation
Search for more papers by this authorSourav Roy
Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
Contribution: Writing - review & editing, Methodology, Validation, Visualization, Investigation, Formal analysis, Software
Search for more papers by this authorBrandon L. Garcia
Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
Contribution: Validation, Writing - review & editing, Methodology, Software, Visualization, Formal analysis, Investigation
Search for more papers by this authorPaul S. Hoffman
Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
Contribution: Writing - review & editing, Conceptualization, Formal analysis
Search for more papers by this authorC. Jeffrey Smith
Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
Contribution: Formal analysis, Writing - review & editing, Conceptualization
Search for more papers by this authorCorresponding Author
Edson R. Rocha
Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
Correspondence Edson R. Rocha, Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Biotech Bldg., Room 130, 600 Moye Blvd., Greenville, NC 27834, USA.
Email: [email protected]
Contribution: Writing - original draft, Investigation, Validation, Writing - review & editing, Project administration, Supervision, Conceptualization, Methodology, Formal analysis, Funding acquisition, Visualization
Search for more papers by this authorAndrea M. Gough,
Anita C. Parker,
Patricia J. O'Bryan,
Terence R. Whitehead,
Sourav Roy,
Brandon L. Garcia,
Paul S. Hoffman,
C. Jeffrey Smith,
Edson R. Rocha,
Andrea M. Gough
Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
Contribution: Methodology, Investigation, Validation, Visualization, Formal analysis
Search for more papers by this authorAnita C. Parker
Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
Contribution: Methodology, Investigation, Validation, Visualization, Formal analysis
Search for more papers by this authorPatricia J. O'Bryan
USDA Agricultural Research Service, Peoria, Illinois, USA
Contribution: Methodology, Validation, Investigation, Formal analysis
Search for more papers by this authorTerence R. Whitehead
USDA Agricultural Research Service, Peoria, Illinois, USA
Contribution: Methodology, Validation, Investigation
Search for more papers by this authorSourav Roy
Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
Contribution: Writing - review & editing, Methodology, Validation, Visualization, Investigation, Formal analysis, Software
Search for more papers by this authorBrandon L. Garcia
Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
Contribution: Validation, Writing - review & editing, Methodology, Software, Visualization, Formal analysis, Investigation
Search for more papers by this authorPaul S. Hoffman
Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
Contribution: Writing - review & editing, Conceptualization, Formal analysis
Search for more papers by this authorC. Jeffrey Smith
Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
Contribution: Formal analysis, Writing - review & editing, Conceptualization
Search for more papers by this authorCorresponding Author
Edson R. Rocha
Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
Correspondence Edson R. Rocha, Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Biotech Bldg., Room 130, 600 Moye Blvd., Greenville, NC 27834, USA.
Email: [email protected]
Contribution: Writing - original draft, Investigation, Validation, Writing - review & editing, Project administration, Supervision, Conceptualization, Methodology, Formal analysis, Funding acquisition, Visualization
Search for more papers by this authorAbstract
The understanding of how central metabolism and fermentation pathways regulate antimicrobial susceptibility in the anaerobic pathogen Bacteroides fragilis is still incomplete. Our study reveals that B. fragilis encodes two iron-dependent, redox-sensitive regulatory pirin protein genes, pir1 and pir2. The mRNA expression of these genes increases when exposed to oxygen and during growth in iron-limiting conditions. These proteins, Pir1 and Pir2, influence the production of short-chain fatty acids and modify the susceptibility to metronidazole and amixicile, a new inhibitor of pyruvate: ferredoxin oxidoreductase in anaerobes. We have demonstrated that Pir1 and Pir2 interact directly with this oxidoreductase, as confirmed by two-hybrid system assays. Furthermore, structural analysis using AlphaFold2 predicts that Pir1 and Pir2 interact stably with several central metabolism enzymes, including the 2-ketoglutarate:ferredoxin oxidoreductases Kor1AB and Kor2CDAEBG. We used a series of metabolic mutants and electron transport chain inhibitors to demonstrate the extensive impact of bacterial metabolism on metronidazole and amixicile susceptibility. We also show that amixicile is an effective antimicrobial against B. fragilis in an experimental model of intra-abdominal infection. Our investigation led to the discovery that the kor2AEBG genes are essential for growth and have dual functions, including the formation of 2-ketoglutarate via the reverse TCA cycle. However, the metabolic activity that bypasses the function of Kor2AEBG following the addition of phospholipids or fatty acids remains undefined. Overall, our study provides new insights into the central metabolism of B. fragilis and its regulation by pirin proteins, which could be exploited for the development of new narrow-spectrum antimicrobials in the future.
CONFLICT OF INTEREST STATEMENT
None declared.
Open Research
DATA AVAILABILITY STATEMENT
The data that supports the findings of this work are available at https://www.ncbi.nlm.nih.gov/gds/, GEO Datasets GSE241210 and GSE241676.
Supporting Information
| Filename | Description |
|---|---|
| mbo31429-sup-0001-Supplemental_File_S5.xlsx90.9 KB | Supporting information. |
| mbo31429-sup-0002-Supplemental_Files_in_PDF_format.pdf2.4 MB | Supporting information. |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
REFERENCES
- Agapakis, C. M., & Silver, P. A. (2010). Modular electron transfer circuits for synthetic biology: Insulation of an engineered biohydrogen pathway. Bioengineered Bugs, 1, 413–418. https://doi.org/10.4161/bbug.1.6.12462.
- Agarwal, G., Rajavel, M., Gopal, B., & Srinivasan, N. (2009). Structure-based phylogeny as a diagnostic for functional characterization of proteins with a cupin fold. PLoS One, 4:e5736. https://doi.org/10.1371/journal.pone.0005736.
- Ahsan, T., Shoily, S. S., Ahmed, T., & Sajib, A. A. (2023). Role of the redox state of the pirin-bound cofactor on interaction with the master regulators of inflammation and other pathways. PLoS One, 18:e0289158. https://doi.org/10.1371/journal.pone.0289158.
- Alauzet, C., Lozniewski, A., & Marchandin, H. (2019). Metronidazole resistance and nim genes in anaerobes: A review. Anaerobe, 55, 40–53. https://doi.org/10.1016/j.anaerobe.2018.10.004.
- Allison, M. J., & Robinson, I. M. (1970). Biosynthesis of α-Ketoglutarate by the reductive carboxylation of succinate inbacteroides ruminicola. Journal of Bacteriology, 104, 50–56. https://doi.org/10.1128/jb.104.1.50-56.1970.
- Allison, M. J., Robinson, I. M., & Baetz, A. L. (1979). Synthesis of alpha-ketoglutarate by reductive carboxylation of succinate in Veillonella, Selenomonas, and Bacteriodes species. Journal of Bacteriology, 140(3), 980–986. https://doi.org/10.1128/jb.140.3.980-986.1979.
- Alvaro, D., Cantafora, A., Attili, A. F., Ginanni Corradini, S., De Luca, C., Minervini, G., Di Blase, A., & Angelico, M. (1986). Relationships between bile salts hydrophilicity and phospholipid composition in bile of various animal species. Comparative Biochemistry and Physiology Part B: Comparative Biochemistry, 83, 551–554. https://doi.org/10.1016/0305-0491(86)90295-6.
- An, J., Sun, J., Yuan, Q., Tian, H., Qiu, W., Guo, W., & Zhao, F. (2004). Proteomics analysis of differentially expressed metastasis-associated proteins in adenoid cystic carcinoma cell lines of human salivary gland. Oral Oncology, 40, 400–408. https://doi.org/10.1016/j.oraloncology.2003.09.014.
- Baek, S. H., Li, A. H., & Sassetti, C. M. (2011). Metabolic regulation of mycobacterial growth and antibiotic sensitivity. PLoS Biology, 9, e1001065. https://doi.org/10.1371/journal.pbio.1001065.
- Ballard, T. E., Wang, X., Olekhnovich, I., Koerner, T., Seymour, C., Salamoun, J., Warthan, M., Hoffman, P. S., & Macdonald, T. L. (2011). Synthesis and antimicrobial evaluation of nitazoxanide-based analogues: Identification of selective and broad spectrum activity. ChemMedChem, 6, 362–377.
- Barman, A., & Hamelberg, D. (2016). Fe(II)/Fe(III) redox process can significantly modulate the conformational dynamics and electrostatics of pirin in NF-κB regulation. ACS Omega, 1, 837–842. https://doi.org/10.1021/acsomega.6b00231.
- Baughn, A. D., & Malamy, M. H. (2002). A mitochondrial-like aconitase in the bacterium Bacteroides fragilis: Implications for the evolution of the mitochondrial krebs cycle. Proceedings of the National Academy of Sciences, 99, 4662–4667. https://doi.org/10.1073/pnas.052710199.
- Baughn, A. D., & Malamy, M. H. (2003). The essential role of fumarate reductase in haem-dependent growth stimulation of Bacteroides fragilis. Microbiology, 149, 1551–1558. https://doi.org/10.1099/mic.0.26247-0. PMID: 12777495.
- Betteken, M. I., Rocha, E. R., & Smith, C. J. (2015). Dps and DpsL mediate survival in vitro and in vivo during the prolonged oxidative stress response in Bacteroides fragilis. Journal of Bacteriology, 197, 3329–3338. https://doi.org/10.1128/JB.00342-15
- Bock, A. K., Kunow, J., Glasemacher, J., & Schönheit, P. (1996). Catalytic properties, molecular composition and sequence alignments of pyruvate: ferredoxin oxidoreductase from the methanogenic archaeon Methanosarcina barkeri (strain Fusaro). European Journal of Biochemistry, 237, 35–44.
- Van Den Bossche, H., Verhoeven, H., Vanparijs, O., Lauwers, H., & Thienpont, D. (1979). Closantel, a new antiparasitic hydrogen ionophore. Archives Internationales de Physiologie et de Biochimie, 87, 851–853.
- Boyer, J. L. (2013). Bile formation and secretion. Comprehensive Physiology, 3, 1035–1078. https://doi.org/10.1002/cphy.c120027.
- Bunik, V. I., Tylicki, A., & Lukashev, N. V. (2013). Thiamin diphosphate-dependent enzymes: From enzymology to metabolic regulation, drug design and disease models. FEBS Journal, 280, 6412–6442. https://doi.org/10.1111/febs.12512.
- Butler, N. L., Ito, T., Foreman, S., Morgan, J. E., Zagorevsky, D., Malamy, M. H., Comstock, L. E., & Barquera, B. (2023). Bacteroides fragilis maintains concurrent capability for anaerobic and nanaerobic respiration. Journal of Bacteriology, 205, e0038922. https://doi.org/10.1128/jb.00389-22.
- Byun, J. H., Kim, M., Lee, Y., Lee, K., & Chong, Y. (2019). Antimicrobial susceptibility patterns of anaerobic bacterial clinical isolates from 2014 to 2016, including recently named or renamed species. Annals of Laboratory Medicine, 39, 190–199. https://doi.org/10.3343/alm.2019.39.2.190.
- Chen, M., & Wolin, M. J. (1981). Influence of heme and vitamin B12 on growth and fermentations of Bacteroides species. Journal of Bacteriology, 145, 466–471. https://doi.org/10.1128/jb.145.1.466-471.1981
- Chen, P. Y. T., Li, B., Drennan, C. L., & Elliott, S. J. (2019). A reverse TCA cycle 2-oxoacid:ferredoxin oxidoreductase that makes C-C bonds from CO2. Joule, 3, 595–611. https://doi.org/10.1016/j.joule.2018.12.006.
- Child, S. A., Rossi, V. P., & Bell, S. G. (2019). Selective ω-1 oxidation of fatty acids by CYP147G1 from Mycobacterium marinum. Biochimica et Biophysica Acta (BBA) - General Subjects, 1863, 408–417. https://doi.org/10.1016/j.bbagen.2018.11.013.
- Cook, G. M., Greening, C., Hards, K., & Berney, M. (2014). Energetics of pathogenic bacteria and opportunities for drug development. Advances in Microbial Physiology, 65, 1–62. https://doi.org/10.1016/bs.ampbs.2014.08.001.
- Delday, M., Mulder, I., Logan, E. T., & Grant, G. (2019). Bacteroides thetaiotaomicron ameliorates colon inflammation in preclinical models of Crohn's disease. Inflammatory Bowel Diseases, 25, 85–96. https://doi.org/10.1093/ibd/izy281.
- Dingsdag, S. A., & Hunter, N. (2018). Metronidazole: An update on metabolism, structure-cytotoxicity and resistance mechanisms. Journal of Antimicrobial Chemotherapy, 73, 265–279. https://doi.org/10.1093/jac/dkx351.
- Diniz, C. G. (2004). Differential gene expression in a Bacteroides fragilis metronidazole-resistant mutant. Journal of Antimicrobial Chemotherapy, 54, 100–108. https://doi.org/10.1093/jac/dkh256.
- Doucette, C. D., Schwab, D. J., Wingreen, N. S., & Rabinowitz, J. D. (2011). α-Ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition. Nature Chemical Biology, 7, 894–901. https://doi.org/10.1038/nchembio.685.
- Dörner, E., & Boll, M. (2002). Properties of 2-oxoglutarate: Ferredoxin oxidoreductase from Thauera aromatica and its role in enzymatic reduction of the aromatic ring. Journal of Bacteriology, 184, 3975–3983. https://doi.org/10.1128/JB.184.14.3975-3983.2002.
- Dunwell, J. M., Culham, A., Carter, C. E., Sosa-Aguirre, C. R., & Goodenough, P. W. (2001). Evolution of functional diversity in the cupin superfamily. Trends in Biochemical Sciences, 26, 740–746. https://doi.org/10.1016/s0968-0004(01)01981-8.
- Dunwell, J. M., Khuri, S., & Gane, P. J. (2000). Microbial relatives of the seed storage proteins of higher plants: Conservation of structure and diversification of function during evolution of the cupin superfamily. Microbiology and Molecular Biology Reviews, 64, 153–179. https://doi.org/10.1128/MMBR.64.1.153-179.2000.
- Dunwell, J. M., Purvis, A., & Khuri, S. (2004). Cupins: The most functionally diverse protein superfamily? Phytochemistry, 65(1), 7–17. https://doi.org/10.1016/j.phytochem.2003.08.016.
- Evans, R., O'Neill, M., Pritzel, A., Antropova, N., Senior, A., Green, T., Žídek, A., Bates, R., Blackwell, S., Yim, J., Ronneberger, O., Bodenstein, S., Zielinski, M., Bridgland, A., Potapenko, A., Cowie, A., Tunyasuvunakool, K., Jain, R., Clancy, E., Kohli, P., Jumper, J., & Hassabis, D. (2021). Protein complex prediction with alphafold-multimer. bioRxiv, 13, 463034. https://doi.org/10.1101/2021.10.04.463034
10.1101/2021.10.04.463034 Google Scholar
- Feng, X., Zhu, W., Schurig-Briccio, L. A., Lindert, S., Shoen, C., Hitchings, R., Li, J., Wang, Y., Baig, N., Zhou, T., Kim, B. K., Crick, D. C., Cynamon, M., McCammon, J. A., Gennis, R. B., & Oldfield, E. (2015). Antiinfectives targeting enzymes and the proton motive force. Proceedings of the National Academy of Sciences, 112, E7073–E7082. https://doi.org/10.1073/pnas.1521988112.
- Gatter, M., Förster, A., Bär, K., Winter, M., Otto, C., Petzsch, P., Ježková, M., Bahr, K., Pfeiffer, M., Matthäus, F., & Barth, G. (2014). A newly identified fatty alcohol oxidase gene is mainly responsible for the oxidation of long-chain ω-hydroxy fatty acids in Yarrowia lipolytica. FEMS Yeast Research, 14, 858–872. https://doi.org/10.1111/1567-1364.12176.
- Gauss, G. H., Reott, M. A., Rocha, E. R., Young, M. J., Douglas, T., Smith, C. J., & Lawrence, C. M. (2012). Characterization of the Bacteroides fragilis bfr gene product identifies a bacterial DPS-like protein and suggests evolutionary links in the ferritin superfamily. Journal of Bacteriology, 194, 15–27. https://doi.org/10.1128/JB.05260-11.
- Ghotaslou, R., Bannazadeh Baghi, H., Alizadeh, N., Yekani, M., Arbabi, S., & Memar, M. Y. (2018). Mechanisms of Bacteroides fragilis resistance to metronidazole. Infection, Genetics and Evolution, 64, 156–163. https://doi.org/10.1016/j.meegid.2018.06.020.
- Gibson, M. I., Chen, P. Y. T., & Drennan, C. L. (2016). A structural phylogeny for understanding 2-oxoacid oxidoreductase function. Current Opinion in Structural Biology, 41, 54–61. https://doi.org/10.1016/j.sbi.2016.05.011.
- Gil-Gil, T., Corona, F., Martínez, J. L., & Bernardini, A. (2020). The inactivation of enzymes belonging to the central carbon metabolism is a novel mechanism of developing antibiotic resistance. mSystems, 5(3), e00282–20. https://doi.org/10.1128/mSystems.00282-20.
- Gooyit, M., & Janda, K. D. (2016). Reprofiled anthelmintics abate hypervirulent stationary-phase Clostridium difficile. Scientific Reports, 6, 33642. https://doi.org/10.1038/srep33642.
- Gui, Q., Hoffman, P. S., & Lewis, J. P. (2019). Amixicile targets anaerobic bacteria within the oral microbiome. The Journal of Oral Biosciences, 61, 226–235. https://doi.org/10.1016/j.job.2019.10.004
- Gui, Q., Lyons, D. J., Deeb, J. G., Belvin, B. R., Hoffman, P. S., & Lewis, J. P. (2021). Non-human primate macaca mulatta as an animal model for testing efficacy of amixicile as a targeted anti-periodontitis therapy. Frontiers in Oral Health, 2, 752929. https://doi.org/10.3389/froh.2021.752929.
- Gui, Q., Ramsey, K. W., Hoffman, P. S., & Lewis, J. P. (2020). Amixicile depletes the ex vivo periodontal microbiome of anaerobic bacteria. Journal of Oral Biosciences, 62, 195–204. https://doi.org/10.1016/j.job.2020.03.004.
- Guiney, D. G., Hasegawa, P., & Davis, C. E. (1984). Plasmid transfer from Escherichia coli to Bacteroides fragilis: Differential expression of antibiotic resistance phenotypes. Proceedings of the National Academy of Sciences, 81, 7203–7206. https://doi.org/10.1073/pnas.81.22.7203.
- Hagedoorn, P. L., Hollmann, F., & Hanefeld, U. (2021). Novel oleate hydratases and potential biotechnological applications. Applied Microbiology and Biotechnology, 105, 6159–6172. https://doi.org/10.1007/s00253-021-11465-x.
- Haggoud, A., Reysset, G., Azeddoug, H., & Sebald, M. (1994). Nucleotide sequence analysis of two 5-nitroimidazole resistance determinants from Bacteroides strains and of a new insertion sequence upstream of the two genes. Antimicrobial Agents and Chemotherapy, 38, 1047–1051. https://doi.org/10.1128/AAC.38.5.1047.
- Hansen, G. Å., Ahmad, R., Hjerde, E., Fenton, C. G., Willassen, N. P., & Haugen, P. (2012). Expression profiling reveals Spot 42 small RNA as a key regulator in the central metabolism of Aliivibrio salmonicida. BMC Genomics, 13, 37. https://doi.org/10.1186/1471-2164-13-37.
- Harris, M. A., & Reddy, C. A. (1977). Hydrogenase activity and the H2-fumarate electron transport system in Bacteroides fragilis. Journal of Bacteriology, 131, 922–928. https://doi.org/10.1128/jb.131.3.922-928.1977.
- Hartmeyer, G. N., Sóki, J., Nagy, E., & Justesen, U. S. (2012). Multidrug-resistant Bacteroides fragilis group on the rise in Europe? Journal of Medical Microbiology, 61(Pt), 1784–1788. https://doi.org/10.1099/jmm.0.049825-0.
- Hihara, Y., Muramatsu, M., Nakamura, K., & Sonoike, K. (2004). A cyanobacterial gene encoding an ortholog of pirin is induced under stress conditions. FEBS Letters, 574, 101–105. https://doi.org/10.1016/j.febslet.2004.06.102.
- Hlasta, D. J., Demers, J. P., Foleno, B. D., Fraga-Spano, S. A., Guan, J., Hilliard, J. J., Macielag, M. J., Ohemeng, K. A., Sheppard, C. M., Sui, Z., Webb, G. C., Weidner-Wells, M. A., Werblood, H., & Barrett, J. F. (1998). Novel inhibitors of bacterial two-component systems with gram positive antibacterial activity: Pharmacophore identification based on the screening hit closantel. Bioorganic & Medicinal Chemistry Letters, 8(14), 1923–1928. https://doi.org/10.1016/s0960-894x(98)00326-6.
- Hoffman, P. S. (2020). Amixicile: A concept therapeutic for treatment of chronic anaerobic infections. British Journal of Gastroenterology, 2, 138–142. https://doi.org/10.31488/bjg.1000108.
- Hoffman, P. S., Bruce, A. M., Olekhnovich, I., Warren, C. A., Burgess, S. L., Hontecillas, R., Viladomiu, M., Bassaganya-Riera, J., Guerrant, R. L., & Macdonald, T. L. (2014). Preclinical studies of amixicile, a systemic therapeutic developed for treatment of Clostridium difficile infections that also shows efficacy against Helicobacter pylori. Antimicrobial Agents and Chemotherapy, 58, 4703–4712. https://doi.org/10.1128/AAC.03112-14.
- Hoffman, P. S., Sisson, G., Croxen, M. A., Welch, K., Harman, W. D., Cremades, N., & Morash, M. G. (2007). Antiparasitic drug nitazoxanide inhibits the pyruvate oxidoreductases of Helicobacter pylori, selected anaerobic bacteria and parasites, and Campylobacter jejuni. Antimicrobial Agents and Chemotherapy, 51, 868–876.
- Holdeman, L. V., Cato, E. P., & Moore, W. E. C. (1977). Anaerobe laboratory manual ( 4th ed.). Anaerobe Laboratory Virginia Polytechnic Institute and University.
- Hutcherson, J. A., Sinclair, K. M., Belvin, B. R., Gui, Q., Hoffman, P. S., & Lewis, J. P. (2017). Amixicile, a novel strategy for targeting oral anaerobic pathogens. Scientific Reports, 7, 10474.
- Ito, T., Gallegos, R., Matano, L. M., Butler, N. L., Hantman, N., Kaili, M., Coyne, M. J., Comstock, L. E., Malamy, M. H., & Barquera, B. (2020). Genetic and biochemical analysis of anaerobic respiration in Bacteroides fragilis and its importance. mBio, 11, e03238–19. https://doi.org/10.1128/mBio.03238-19.
- Jain, E., Zaenker, E. I., Hoffman, P. S., & Warren, C. A. (2022). In vitro activity of amixicile against T. vaginalis from clinical isolates. Parasitology Research, 121, 2453–2455. https://doi.org/10.1007/s00436-022-07567-8.
- Jasemi, S., Emaneini, M., Ahmadinejad, Z., Fazeli, M. S., Sechi, L. A., Sadeghpour Heravi, F., & Feizabadi, M. M. (2021). Antibiotic resistance pattern of Bacteroides fragilis isolated from clinical and colorectal specimens. Annals of Clinical Microbiology and Antimicrobials, 20, 27. https://doi.org/10.1186/s12941-021-00435-w.
- Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S. A. A., Ballard, A. J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., … Hassabis, D. (2021). Highly accurate protein structure prediction with AlphaFold. Nature, 596, 583–589. https://doi.org/10.1038/s41586-021-03819-2.
- Kang, W. R., Seo, M. J., Shin, K. C., Park, J. B., & Oh, D. K. (2017a). Comparison of biochemical properties of the original and newly identified oleate hydratases from Stenotrophomonas maltophilia. Applied and Environmental Microbiology, 83, e03351–16. https://doi.org/10.1128/AEM.03351-16.
- Kang, W. R., Seo, M. J., Shin, K. C., Park, J. B., & Oh, D. K. (2017b). Gene cloning of an efficiency oleate hydratase from Stenotrophomonas nitritireducens for polyunsaturated fatty acids and its application in the conversion of plant oils to 10-hydroxy fatty acids. Biotechnology and Bioengineering, 114(1), 74–82. https://doi.org/10.1002/bit.26058.
- Kennedy, A. J., Bruce, A. M., Gineste, C., Ballard, T. E., Olekhnovich, I. N., Macdonald, T. L., & Hoffman, P. S. (2016). Synthesis and antimicrobial evaluation of amixicile-based inhibitors of the pyruvate-ferredoxin oxidoreductases of anaerobic bacteria and epsilonproteobacteria. Antimicrobial Agents and Chemotherapy, 60, 3980–3987. https://doi.org/10.1128/AAC.00670-16.
- Khademian, M., & Imlay, J. A. (2020). Do reactive oxygen species or does oxygen itself confer obligate anaerobiosis? The case of Bacteroides thetaiotaomicron. Molecular Microbiology, 114, 333–347. https://doi.org/10.1111/mmi.14516.
- Koropatkin, N. M., Martens, E. C., Gordon, J. I., & Smith, T. J. (2008). Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. Structure, 16, 1105–1115. https://doi.org/10.1016/j.str.2008.03.017.
- Krissinel, E., & Henrick, K. (2007). Inference of macromolecular assemblies from crystalline state. Journal of Molecular Biology, 372, 774–797. https://doi.org/10.1016/j.jmb.2007.05.022.
- Lapik, Y. R., & Kaufman, L. S. (2003). The arabidopsis cupin domain protein AtPirin1 interacts with the G protein α-Subunit GPA1 and regulates seed germination and early seedling development. The Plant Cell, 15, 1578–1590. https://doi.org/10.1105/tpc.011890.
- Liu, F., Rehmani, I., Esaki, S., Fu, R., Chen, L., de Serrano, V., & Liu, A. (2013). Pirin is an iron-dependent redox regulator of NF-κB. Proceedings of the National Academy of Sciences, 110, 9722–9727. https://doi.org/10.1073/pnas.1221743110.
- Lobo, L. A., Jenkins, A. L., Jeffrey Smith, C., & Rocha, E. R. (2013). Expression of Bacteroides Fragilis hemolysins in vivo and role of HlyBA in an intra-abdominal infection model. MicrobiologyOpen, 2, 326–337. https://doi.org/10.1002/mbo3.76.
- Lu, Z., & Imlay, J. A. (2019). A conserved motif liganding the [4Fe-4S] cluster in [4Fe-4S] fumarases prevents irreversible inactivation of the enzyme during hydrogen peroxide stress. Redox Biology, 26, 101296. https://doi.org/10.1016/j.redox.2019.101296.
- Lu, Z., & Imlay, J. A. (2021). When anaerobes encounter oxygen: mechanisms of oxygen toxicity, tolerance and defence. Nature Reviews Microbiology, 19, 774–785. https://doi.org/10.1038/s41579-021-00583-y.
- Macy, J., Probst, I., & Gottschalk, G. (1975). Evidence for cytochrome involvement in fumarate reduction and adenosine 5’-triphosphate synthesis by Bacteroides fragilis grown in the presence of hemin. Journal of Bacteriology, 123, 436–442. https://doi.org/10.1128/jb.123.2.436-442.1975.
- Macy, J. M., Ljungdahl, L. G., & Gottschalk, G. (1978). Pathway of succinate and propionate formation in Bacteroides fragilis. Journal of Bacteriology, 134, 84–91. https://doi.org/10.1128/jb.134.1.84-91.1978.
- Mai, X., & Adams, M. W. (1996). Characterization of a fourth type of 2-keto acid-oxidizing enzyme from a hyperthermophilic archaeon: 2-ketoglutarate ferredoxin oxidoreductase from Thermococcus litoralis. Journal of Bacteriology, 178, 5890–5896. https://doi.org/10.1128/jb.178.20.5890-5896.1996.
- Martens, E. C., Chiang, H. C., & Gordon, J. I. (2008). Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host & Microbe, 4, 447–457. https://doi.org/10.1016/j.chom.2008.09.007.
- McMillan, D. G. G., Marritt, S. J., Firer-Sherwood, M. A., Shi, L., Richardson, D. J., Evans, S. D., Elliott, S. J., Butt, J. N., & Jeuken, L. J. C. (2013). Protein-protein interaction regulates the direction of catalysis and electron transfer in a redox enzyme complex. Journal of the American Chemical Society, 135, 10550–10556. https://doi.org/10.1021/ja405072z.
- Menon, S., & Ragsdale, S. W. (1997). Mechanism of the Clostridium thermoaceticum pyruvate:ferredoxin oxidoreductase: evidence for the common catalytic intermediacy of the hydroxyethylthiamine pyropyrosphate radical. Biochemistry, 36, 8484–8494. https://doi.org/10.1021/bi970403k.
- Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., & Steinegger, M. (2022). ColabFold: making protein folding accessible to all. Nature Methods, 19, 679–682. https://doi.org/10.1038/s41592-022-01488-1.
- Miura, Y. (2013). The biological significance of ω-oxidation of fatty acids. Proceedings of the Japan Academy, Series B, 89, 370–382. https://doi.org/10.2183/pjab.89.370.
- Miura, Y., & Fulco, A. J. 1974. (ω-2) hydroxylation of fatty acids by a soluble system from Bacillus megaterium. Journal of Biological Chemistry 249: 1880–1888.
- Miura, Y., & Fulco, A. J. (1975). ω-1, ω-2 and ω-3 hydroxylation of long-chain fatty acids, amides and alcohols by a soluble enzyme system from bacillus megatyerium. Biochimica et Biophysica Acta (BBA) - Lipids and Lipid Metabolism, 388, 305–317. https://doi.org/10.1016/0005-2760(75)90089-2.
- Murima, P., McKinney, J. D., & Pethe, K. (2014). Targeting bacterial central metabolism for drug development. Chemistry & Biology, 21, 1423–1432. https://doi.org/10.1016/j.chembiol.2014.08.020.
- Nagy, E., Urbán, E., & Nord, C. E. (2011). Antimicrobial susceptibility of bacteroides fragilis group isolates in Europe: 20 years of experience. Clinical Microbiology and Infection, 17, 371–379. https://doi.org/10.1111/j.1469-0691.2010.03256.x.
- National Research Council. (2011). Guide for the care and use of laboratory animals ( 8th ed.). National Academies Press.
- Noth, J., Krawietz, D., Hemschemeier, A., & Happe, T. (2013). Pyruvate: Ferredoxin oxidoreductase is coupled to light-independent hydrogen production in Chlamydomonas reinhardtii. Journal of Biological Chemistry, 288, 4368–4377. https://doi.org/10.1074/jbc.M112.429985.
- Orzaez, D., Jong, A. J., & Woltering, E. J. (2001). A tomato homologue of the human protein PIRIN is induced during programmed cell death. Plant Molecular Biology, 46, 459–468. https://doi.org/10.1023/a:1010618515051.
- Pan, N., & Imlay, J. A. (2001). How does oxygen inhibit central metabolism in the obligate anaerobe Bacteroides thetaiotaomicron. Molecular Microbiology, 39, 1562–1571. https://doi.org/10.1046/j.1365-2958.2001.02343.x.
- Pang, H., Bartlam, M., Zeng, Q., Miyatake, H., Hisano, T., Miki, K., Wong, L. L., Gao, G. F., & Rao, Z. (2004). Crystal structure of human pirin. Journal of Biological Chemistry, 279, 1491–1498. https://doi.org/10.1074/jbc.M310022200.
- Parker, A. C., Seals, N. L., Baccanale, C. L., & Rocha, E. R. (2022). Analysis of six tonb gene homologs in bacteroides fragilis revealed that tonB3 is essential for survival in experimental intestinal colonization and intra-abdominal infection. Infection and Immunity, 90):e0046921. https://doi.org/10.1128/IAI.00469-21.
- Paunkov, A., Gutenbrunner, K., Sóki, J., & Leitsch, D. (2022a). Haemin deprivation renders Bacteroides fragilis hypersusceptible to metronidazole and cancels high-level metronidazole resistance. Journal of Antimicrobial Chemotherapy, 77, 1027–1031. https://doi.org/10.1093/jac/dkab485.
- Paunkov, A., Hummel, K., Strasser, D., Sóki, J., & Leitsch, D. (2023). Proteomic analysis of metronidazole resistance in the human facultative pathogen Bacteroides fragilis. Frontiers in Microbiology, 14, 1158086. https://doi.org/10.3389/fmicb.2023.1158086.
- Paunkov, A., Sóki, J., & Leitsch, D. (2022b). Modulation of iron import and metronidazole resistance in Bacteroides fragilis Harboring a nimA gene. Frontiers in Microbiology, 13, 898453. https://doi.org/10.3389/fmicb.2022.898453.
- Pfaffl, M. W. (2001). A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Research, 29:e45. https://doi.org/10.1093/nar/29.9.e45.
- Prajapati, S., Rabe von Pappenheim, F., & Tittmann, K. (2022). Frontiers in the enzymology of thiamin diphosphate-dependent enzymes. Current Opinion in Structural Biology, 76, 102441. https://doi.org/10.1016/j.sbi.2022.102441.
- Privitera, G., Dublanchet, A., & Sebald, M. (1979). Transfer of multiple antibiotic resistance between subspecies of Bacteroides fragilis. Journal of Infectious Diseases, 139, 97–101. https://doi.org/10.1093/infdis/139.1.97.
- Ragsdale, S. W. (2003). Pyruvate ferredoxin oxidoreductase and its radical intermediate. Chemical Reviews, 103, 2333–2346. https://doi.org/10.1021/cr020423e.
- Rajamuthiah, R., Fuchs, B. B., Jayamani, E., Kim, Y., Larkins-Ford, J., Conery, A., Ausubel, F. M., & Mylonakis, E. (2014). Whole animal automated platform for drug discovery against multi-drug resistant Staphylococcus aureus. PLoS One, 9:e89189. https://doi.org/10.1371/journal.pone.0089189.
- Reed, G. H., Ragsdale, S. W., & Mansoorabadi, S. O. (2012). Radical reactions of thiamin pyrophosphate in 2-oxoacid oxidoreductases. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1824, 1291–1298. https://doi.org/10.1016/j.bbapap.2011.11.010.
- Reed, L. A., O'Bier, N. S., Oliver, L. D., Hoffman, P. S., & Marconi, R. T. (2018). Antimicrobial activity of amixicile against Treponema denticola and other oral spirochetes associated with periodontal disease. Journal of Periodontology, 89, 1467–1474. https://doi.org/10.1002/JPER.17-0185.
- Reott, M. A., Parker, A. C., Rocha, E. R., & Smith, C. J. (2009). Thioredoxins in redox maintenance and survival during oxidative stress of Bacteroides fragilis. Journal of Bacteriology, 191, 3384–3391. https://doi.org/10.1128/JB.01665-08.
- Rios-Covian, D., Sánchez, B., Salazar, N., Martínez, N., Redruello, B., Gueimonde, M., & de Los Reyes-Gavilán, C. G. (2015). Different metabolic features of Bacteroides fragilis growing in the presence of glucose and exopolysaccharides of bifidobacteria. Frontiers in Microbiology, 6, 825. https://doi.org/10.3389/fmicb.2015.00825.
- Robertson, K. P., Smith, C. J., Gough, A. M., & Rocha, E. R. (2006). Characterization of Bacteroides fragilis hemolysins and regulation and synergistic interactions of HlyA and HlyB. Infection and Immunity, 74, 2304–2316. https://doi.org/10.1128/IAI.74.4.2304-2316.2006.
- Rocha, E. R., Selby, T., Coleman, J. P., & Smith, C. J. (1996). Oxidative stress response in an anaerobe, Bacteroides fragilis: A role for catalase in protection against hydrogen peroxide. Journal of Bacteriology, 178, 6895–6903. https://doi.org/10.1128/jb.178.23.6895-6903.1996.
- Rocha, E. R., & Smith, C. J. (1995). Biochemical and genetic analyses of a catalase from the anaerobic bacterium Bacteroides fragilis. Journal of Bacteriology, 177, 3111–3119. https://doi.org/10.1128/jb.177.11.3111-3119.1995.
- Rocha, E. R., & Smith, C. J. (1997). Regulation of Bacteriodes fragilis katB mRNA by oxidative stress and carbon limitation. Journal of Bacteriology, 179, 7033–7039. https://doi.org/10.1128/jb.179.22.7033-7039.1997.
- Rocha, E. R., & Smith, C. J. (1998). Characterization of a peroxide-resistant mutant of the anaerobic bacterium Bacteroides fragilis. Journal of Bacteriology, 180, 5906–5912. https://doi.org/10.1128/JB.180.22.5906-5912.1998.
- Rocha, E. R., & Smith, C. J. (1999). Role of the alkyl hydroperoxide reductase (ahpCF) gene in oxidative stress defense of the obligate anaerobe Bacteroides fragilis. Journal of Bacteriology, 181, 5701–5710. https://doi.org/10.1128/JB.181.18.5701-5710.1999.
- Rocha, E. R., & Smith, C. J. (2004). Transcriptional regulation of the Bacteroides Fragilis ferritin gene (ftnA) by redox stress. Microbiology, 150, 2125–2134. https://doi.org/10.1099/mic.0.26948-0.
- Rocha, E. R., Tzianabos, A. O., & Smith, C. J. (2007). Thioredoxin reductase is essential for thiol/disulfide redox control and oxidative stress survival of the anaerobe Bacteroides fragilis. Journal of Bacteriology, 189(22), 8015–8023. https://doi.org/10.1128/JB.00714-07.
- Roy, A. A., Dhawanjewar, A. S., Sharma, P., Singh, G., & Madhusudhan, M. S. (2019). Protein interaction Z score assessment (PIZSA): An empirical scoring scheme for evaluation of protein-protein interactions. Nucleic Acids Research, 47, W331–W337. https://doi.org/10.1093/nar/gkz368.
- Ruettinger, R. T., Olson, S. T., Boyer, R. F., & Coon, M. J. (1974). Identification of the ω-hydroxylase of pseudomonas oleovorans as a nonheme iron protein requiring phospholipid for catalytic activity. Biochemical and Biophysical Research Communications, 57, 1011–1017. https://doi.org/10.1016/0006-291x(74)90797-9.
- Schofield, W. B., Zimmermann-Kogadeeva, M., Zimmermann, M., Barry, N. A., & Goodman, A. L. (2018). The stringent response determines the ability of a commensal bacterium to survive starvation and to persist in the gut. Cell Host & Microbe, 24:120-132.e6. https://doi.org/10.1016/j.chom.2018.06.002.
- Schuetz, A. N. (2014). Antimicrobial resistance and susceptibility testing of anaerobic bacteria. Clinical Infectious Diseases, 59, 698–705. https://doi.org/10.1093/cid/ciu395.
- Shafquat, Y., Jabeen, K., Farooqi, J., Mehmood, K., Irfan, S., Hasan, R., & Zafar, A. (2019). Antimicrobial susceptibility against metronidazole and carbapenem in clinical anaerobic isolates from Pakistan. Antimicrobial Resistance & Infection Control, 8, 99. https://doi.org/10.1186/s13756-019-0549-8.
- Shilnikova, I. I., & Dmitrieva, N. V. (2015). Evaluation of antibiotic susceptibility of Bacteroides, Prevotella and Fusobacterium species isolated from patients of the N. N. Blokhin Cancer Research Center, Moscow, russia. Anaerobe, 31, 15–18. https://doi.org/10.1016/j.anaerobe.2014.08.003.
- Shoun, H., Sudo, Y., & Beppu, T. (1985). Subterminal hydroxylation of fatty acids by a cytochrome P-450-dependent enzyme system from a fungus, Fusarium oxysporum. The Journal of Biochemistry, 97, 755–763. https://doi.org/10.1093/oxfordjournals.jbchem.a135115.
- Simon, R., Priefer, U., & Pühler, A. (1983). A broad host range mobilization system for in vivo genetic engineering: Transposon mutagenesis in gram negative bacteria. Bio/Technology, 1, 784–791. https://doi.org/10.1038/nbt1183-784
- Sisson, G., Jeong, J. Y., Goodwin, A., Bryden, L., Rossler, N., Lim-Morrison, S., Raudonikiene, A., Berg, D. E., & Hoffman, P. S. (2000). Metronidazole activation is mutagenic and causes DNA fragmentation in Helicobacter pylori and in Escherichia coli containing a cloned H. pylori RdxA(+) (Nitroreductase) gene. Journal of Bacteriology, 182, 5091–5096. https://doi.org/10.1128/JB.182.18.5091-5096.2000.
- Skuce, P. J., & Fairweather, I. (1990). The effect of the hydrogen ionophore closantel upon the pharmacology and ultrastructure of the adult liver fluke Fasciola hepatica. Parasitology Research, 76, 241–250. https://doi.org/10.1007/BF00930821.
- Smith, C. J., Rogers, M. B., & McKee, M. L. (1992). Heterologous gene expression in Bacteroides fragilis. Plasmid, 27, 141–154. https://doi.org/10.1016/0147-619X(92)90014-2.
- Smith, C. J., Rollins, L. A., & Parker, A. C. (1995). Nucleotide sequence determination and genetic analysis of the Bacteroides plasmid, pBI143. Plasmid, 34, 211–222. https://doi.org/10.1006/plas.1995.0007.
- Snydman, D. R., Jacobus, N. V., McDermott, L. A., Goldstein, E. J. C., Harrell, L., Jenkins, S. G., Newton, D., Patel, R., & Hecht, D. W. (2017). Trends in antimicrobial resistance among Bacteroides species and Parabacteroides species in the United States from 2010-2012 with comparison to 2008-2009. Anaerobe, 43, 21–26. https://doi.org/10.1016/j.anaerobe.2016.11.003.
- Soo, P. C., Horng, Y. T., Lai, M. J., Wei, J. R., Hsieh, S. C., Chang, Y. L., Tsai, Y. H., & Lai, H. C. (2007). Pirin regulates pyruvate catabolism by interacting with the pyruvate dehydrogenase E1 subunit and modulating pyruvate dehydrogenase activity. Journal of Bacteriology, 189, 109–118. https://doi.org/10.1128/JB.00710-06.
- Stephenson, K., Yamaguchi, Y., & Hoch, J. A. (2000). The mechanism of action of inhibitors of bacterial two-component signal transduction systems. Journal of Biological Chemistry, 275, 38900–38904. https://doi.org/10.1074/jbc.M006633200.
- Stokes, J. M., Lopatkin, A. J., Lobritz, M. A., & Collins, J. J. (2019). Bacterial metabolism and antibiotic efficacy. Cell Metabolism, 30, 251–259. https://doi.org/10.1016/j.cmet.2019.06.009.
- Sund, C. J., Rocha, E. R., Tzinabos, A. O., Wells, W. G., Gee, J. M., Reott, M. A., O'Rourke, D. P., & Smith, C. J. (2008). The Bacteroides fragilis transcriptome response to oxygen and H2O2: the role of OxyR and its effect on survival and virulence. Molecular Microbiology, 67, 129–142. https://doi.org/10.1111/j.1365-2958.2007.06031.x.
- Talà, A., Damiano, F., Gallo, G., Pinatel, E., Calcagnile, M., Testini, M., Fico, D., Rizzo, D., Sutera, A., Renzone, G., Scaloni, A., De Bellis, G., Siculella, L., De Benedetto, G. E., Puglia, A. M., Peano, C., & Alifano, P. (2018). Pirin: A novel redox-sensitive modulator of primary and secondary metabolism in Streptomyces. Metabolic Engineering, 48, 254–268. https://doi.org/10.1016/j.ymben.2018.06.008.
- Tang, Y. P., Dallas, M. M., & Malamy, M. H. (1999). Characterization of the BatI (Bacteroides aerotolerance) operon in Bacteroides fragilis: Isolation of ab. fragilismutant with reduced aerotolerance and impaired growth inin vivomodel systems. Molecular Microbiology, 32, 139–149. https://doi.org/10.1046/j.1365-2958.1999.01337.x.
- Thorgersen, M. P., Schut, G. J., Poole, F. L.,, Haja, D. K., Putumbaka, S., Mycroft, H. I., de Vries, W. J., & Adams, M. W. W. (2022). Obligately aerobic human gut microbe expresses an oxygen resistant tungsten-containing oxidoreductase for detoxifying gut aldehydes. Frontiers in Microbiology, 13, 965625. https://doi.org/10.3389/fmicb.2022.965625.
- Tran, T. B., Cheah, S. E., Yu, H. H., Bergen, P. J., Nation, R. L., Creek, D. J., Purcell, A., Forrest, A., Doi, Y., Song, J., Velkov, T., & Li, J. (2016). Anthelmintic closantel enhances bacterial killing of polymyxin B against multidrug-resistant Acinetobacter baumannii. The Journal of antibiotics, 69, 415–421. https://doi.org/10.1038/ja.2015.127.
- Turrens, J. F., Newton, C. L., Zhong, L., Hernandez, F. R., Whitfield, J., & Docampo, R. (1999). Mercaptopyridine-N-oxide, an NADH-fumarate reductase inhibitor, blocks Trypanosoma cruzi growth in culture and in infected myoblasts. FEMS Microbiology Letters, 175, 217–221. https://doi.org/10.1111/j.1574-6968.1999.tb13623.x.
- Vanhanen, S., West, M., Kroon, J. T. M., Lindner, N., Casey, J., Cheng, Q., Elborough, K. M., & Slabas, A. R. (2000). A consensus sequence for long-chain fatty-acid alcohol oxidases from candida identifies a family of genes involved in lipid ω-Oxidation in yeast with homologues in plants and bacteria. Journal of Biological Chemistry, 275, 4445–4452. https://doi.org/10.1074/jbc.275.6.4445.
- Veeranagouda, Y., Husain, F., Boente, R., Moore, J., Smith, C. J., Rocha, E. R., Patrick, S., & Wexler, H. M. (2014). Deficiency of the ferrous iron transporter FeoAB is linked with metronidazole resistance in Bacteroides fragilis. Journal of Antimicrobial Chemotherapy, 69, 2634–2643. https://doi.org/10.1093/jac/dku219.
- Warren, C. A., van Opstal, E., Ballard, T. E., Kennedy, A., Wang, X., Riggins, M., Olekhnovich, I., Warthan, M., Kolling, G. L., Guerrant, R. L., Macdonald, T. L., & Hoffman, P. S. (2012). Amixicile, a novel inhibitor of pyruvate: Ferredoxin oxidoreductase, shows efficacy against Clostridium difficile in a mouse infection model. Antimicrobial Agents and Chemotherapy, 56, 4103–4111.
- Wendler, W. M. F., Kremmer, E., Förster, R., & Winnacker, E. L. (1997). Identification of pirin, a novel highly conserved nuclear protein. Journal of Biological Chemistry, 272, 8482–8489. https://doi.org/10.1074/jbc.272.13.8482.
- Williams, K., Lowe, P. N., & Leadlay, P. F. (1987). Purification and characterization of pyruvate: Ferredoxin oxidoreductase from the anaerobic protozoon Trichomonas vaginalis. Biochemical Journal, 246, 529–536. https://doi.org/10.1042/bj2460529.
- Williamson, R. L., & Metcalf, R. L. (1967). Salicylanilides: A new group of active uncouplers of oxidative phosphorylation. Science, 158, 1694–1695. https://doi.org/10.1126/science.158.3809.1694.
- Yamamoto, M., Arai, H., Ishii, M., & Igarashi, Y. (2006). Role of two 2-oxoglutarate: Ferredoxin oxidoreductases in Hydrogenobacter thermophilus under aerobic and anaerobic conditions. FEMS Microbiology Letters, 263, 189–193. https://doi.org/10.1111/j.1574-6968.2006.00415.x.
- Yamamoto, M., Ikeda, T., Arai, H., Ishii, M., & Igarashi, Y. (2010). Carboxylation reaction catalyzed by 2-oxoglutarate: Ferredoxin oxidoreductases from Hydrogenobacter thermophilus. Extremophiles, 14, 79–85. https://doi.org/10.1007/s00792-009-0289-4.
- Yoshikawa, R., Yanagi, H., Hashimoto-Tamaoki, T., Morinaga, T., Nakano, Y., Noda, M., Fujiwara, Y., Okamura, H., & Yamamura, T. (2004). Gene expression in response to anti-tumour intervention by polysaccharide-k (PSK) in colorectal carcinoma cells. Oncology Reports, 12, 1287–1293.
- Young, M., Chojnacki, M., Blanchard, C., Cao, X., Johnson, W. L., Flaherty, D., & Dunman, P. M. (2023). Genetic determinants of Acinetobacter baumannii serum-associated adaptive efflux-mediated antibiotic resistance. Antibiotics (USSR), 12, 1173. https://doi.org/10.3390/antibiotics12071173.
- Yun, N. R., Arai, H., Ishii, M., & Igarashi, Y. (2001). The genes for anabolic 2-oxoglutarate: Ferredoxin oxidoreductase from Hydrogenobacter thermophilus TK-6. Biochemical and Biophysical Research Communications, 282, 589–594. https://doi.org/10.1006/bbrc.2001.4542.
- Yun, N. R., Yamamoto, M., Arai, H., Ishii, M., & Igarashi, Y. (2002). A novel five-subunit-type 2-oxoglutalate: Ferredoxin oxidoreductases from Hydrogenobacter thermophilus TK-6. Biochemical and Biophysical Research Communications, 292, 280–286. https://doi.org/10.1006/bbrc.2002.6651.
- Zhang, G., Dai, J., Lu, Z., & Dunaway-Mariano, D. (2003). The phosphonopyruvate decarboxylase from Bacteroides fragilis. Journal of Biological Chemistry, 278(42), 41302–41308. https://doi.org/10.1074/jbc.M305976200.
