1
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Kim JS, Liu L, Kant S, Orlicky DJ, Uppalapati S, Margolis A, Davenport BJ, Morrison TE, Matsuda J, McClelland M, Jones-Carson J, Vazquez-Torres A. Anaerobic respiration of host-derived methionine sulfoxide protects intracellular Salmonella from the phagocyte NADPH oxidase. Cell Host Microbe 2024; 32:411-424.e10. [PMID: 38307020 DOI: 10.1016/j.chom.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/06/2023] [Accepted: 01/10/2024] [Indexed: 02/04/2024]
Abstract
Intracellular Salmonella experiencing oxidative stress downregulates aerobic respiration. To maintain cellular energetics during periods of oxidative stress, intracellular Salmonella must utilize terminal electron acceptors of lower energetic value than molecular oxygen. We show here that intracellular Salmonella undergoes anaerobic respiration during adaptation to the respiratory burst of the phagocyte NADPH oxidase in macrophages and in mice. Reactive oxygen species generated by phagocytes oxidize methionine, generating methionine sulfoxide. Anaerobic Salmonella uses the molybdenum cofactor-containing DmsABC enzymatic complex to reduce methionine sulfoxide. The enzymatic activity of the methionine sulfoxide reductase DmsABC helps Salmonella maintain an alkaline cytoplasm that supports the synthesis of the antioxidant hydrogen sulfide via cysteine desulfuration while providing a source of methionine and fostering redox balancing by associated dehydrogenases. Our investigations demonstrate that nontyphoidal Salmonella responding to oxidative stress exploits the anaerobic metabolism associated with dmsABC gene products, a pathway that has accrued inactivating mutations in human-adapted typhoidal serovars.
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Affiliation(s)
- Ju-Sim Kim
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Lin Liu
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Sashi Kant
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - David J Orlicky
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Siva Uppalapati
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Alyssa Margolis
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Bennett J Davenport
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Thomas E Morrison
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | | | - Michael McClelland
- University of California Irvine School of Medicine, Department of Microbiology and Molecular Genetics, Irvine, CA, USA
| | - Jessica Jones-Carson
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Andres Vazquez-Torres
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Veterans Affairs, Eastern Colorado Health Care System, Aurora, CO 80045, USA.
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2
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Das M, Sreedharan S, Shee S, Malhotra N, Nandy M, Banerjee U, Kohli S, Rajmani RS, Chandra N, Seshasayee ASN, Laxman S, Singh A. Cysteine desulfurase (IscS)-mediated fine-tuning of bioenergetics and SUF expression prevents Mycobacterium tuberculosis hypervirulence. SCIENCE ADVANCES 2023; 9:eadh2858. [PMID: 38091389 PMCID: PMC10848736 DOI: 10.1126/sciadv.adh2858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023]
Abstract
Iron-sulfur (Fe-S) biogenesis requires multiprotein assembly systems, SUF and ISC, in most prokaryotes. M. tuberculosis (Mtb) encodes a complete SUF system, the depletion of which was bactericidal. The ISC operon is truncated to a single gene iscS (cysteine desulfurase), whose function remains uncertain. Here, we show that MtbΔiscS is bioenergetically deficient and hypersensitive to oxidative stress, antibiotics, and hypoxia. MtbΔiscS resisted killing by nitric oxide (NO). RNA sequencing indicates that IscS is important for expressing regulons of DosR and Fe-S-containing transcription factors, WhiB3 and SufR. Unlike wild-type Mtb, MtbΔiscS could not enter a stable persistent state, continued replicating in mice, and showed hypervirulence. The suf operon was overexpressed in MtbΔiscS during infection in a NO-dependent manner. Suppressing suf expression in MtbΔiscS either by CRISPR interference or upon infection in inducible NO-deficient mice arrests hypervirulence. Together, Mtb redesigned the ISC system to "fine-tune" the expression of SUF machinery for establishing persistence without causing detrimental disease in the host.
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Affiliation(s)
- Mayashree Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Sreesa Sreedharan
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore 560065, India
- School of Chemical and Biotechnology, (SASTRA)-Deemed to be University, Thanjavur 613401, India
| | - Somnath Shee
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Nitish Malhotra
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bangalore 560065, India
| | - Meghna Nandy
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bangalore 560065, India
| | - Ushashi Banerjee
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sakshi Kohli
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
| | - Raju S. Rajmani
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Aswin Sai Narain Seshasayee
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bangalore 560065, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore 560065, India
| | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore 560012, India
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3
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Elchennawi I, Carpentier P, Caux C, Ponge M, Ollagnier de Choudens S. Structural and Biochemical Characterization of Mycobacterium tuberculosis Zinc SufU-SufS Complex. Biomolecules 2023; 13:biom13050732. [PMID: 37238602 DOI: 10.3390/biom13050732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/28/2023] Open
Abstract
Iron-sulfur (Fe-S) clusters are inorganic prosthetic groups in proteins composed exclusively of iron and inorganic sulfide. These cofactors are required in a wide range of critical cellular pathways. Iron-sulfur clusters do not form spontaneously in vivo; several proteins are required to mobilize sulfur and iron, assemble and traffic-nascent clusters. Bacteria have developed several Fe-S assembly systems, such as the ISC, NIF, and SUF systems. Interestingly, in Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), the SUF machinery is the primary Fe-S biogenesis system. This operon is essential for the viability of Mtb under normal growth conditions, and the genes it contains are known to be vulnerable, revealing the Mtb SUF system as an interesting target in the fight against tuberculosis. In the present study, two proteins of the Mtb SUF system were characterized for the first time: Rv1464(sufS) and Rv1465(sufU). The results presented reveal how these two proteins work together and thus provide insights into Fe-S biogenesis/metabolism by this pathogen. Combining biochemistry and structural approaches, we showed that Rv1464 is a type II cysteine-desulfurase enzyme and that Rv1465 is a zinc-dependent protein interacting with Rv1464. Endowed with a sulfurtransferase activity, Rv1465 significantly enhances the cysteine-desulfurase activity of Rv1464 by transferring the sulfur atom from persulfide on Rv1464 to its conserved Cys40 residue. The zinc ion is important for the sulfur transfer reaction between SufS and SufU, and His354 in SufS plays an essential role in this reaction. Finally, we showed that Mtb SufS-SufU is more resistant to oxidative stress than E. coli SufS-SufE and that the presence of zinc in SufU is likely responsible for this improved resistance. This study on Rv1464 and Rv1465 will help guide the design of future anti-tuberculosis agents.
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Affiliation(s)
- Ingie Elchennawi
- CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 38000 Grenoble, France
| | - Philippe Carpentier
- CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 38000 Grenoble, France
- European Synchrotron Radiation Facility, 38000 Grenoble, France
| | - Christelle Caux
- CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 38000 Grenoble, France
| | - Marine Ponge
- CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Université Grenoble Alpes, 38000 Grenoble, France
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4
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Pang Y, Wang J, Gao X, Jiang M, Zhu L, Liang F, Liang M, Wu X, Xu X, Ren X, Xie T, Wang W, Sun Q, Xiong X, Lyu J, Li J, Tan G. Roles of conserved active site residues in the IscS cysteine desulfurase reaction. Front Microbiol 2023; 14:1084205. [PMID: 36876095 PMCID: PMC9978102 DOI: 10.3389/fmicb.2023.1084205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
Escherichia coli cysteine desulfurase (CD), IscS, modifies basal metabolism by transferring sulphur (S) from L-cysteine to numerous cellular pathways, whereas NFS1, a human CD, is active only in the formation of the [Acp]2:[ISD11]2:[NFS1]2 complex. Despite the accumulation of red-coloured IscS in E. coli cells as a result of the deficiency of accessible iron, as revealed in our previous studies, the mechanism of the potential enzymatic reaction remains unclear. In this study, the N-terminus of IscS was fused with the C-terminus of NFS1, which was reported to be almost fully active as IscS and exhibits a pyridoxal 5'-phosphate (PLP) absorption peak at 395 nm. Moreover, SUMO-EH-IscS exhibited significant growth recovery and NADH-dehydrogenase I activity in the iscS mutant cells. Furthermore, through in vitro and in vivo experiments combined with high-performance liquid chromatography and ultra-performance liquid chromatography-tandem mass spectrometry, it was shown that the new absorption peaks of the IscS H104Q, IscS Q183E, IscS K206A, and IscS K206A&C328S variants at 340 and 350 nm may correspond to the enzyme reaction intermediates, Cys-ketimine and Cys-aldimine, respectively. However, after mutation of the conserved active-site residues, additional absorption peaks at 420 and 430 nm were associated with PLP migration in the active-site pocket. Additionally, the corresponding absorption peaks of Cys-quinonoid, Ala-ketimine, and Ala-aldimine intermediates in IscS were 510, 325, and 345 nm, respectively, as determined by site-directed mutagenesis and substrate/product-binding analyses during the CD reaction process. Notably, red IscS formed in vitro by incubating IscS variants (Q183E and K206A) with excess L-alanine and sulphide under aerobic conditions produced an absorption peak similar to the wild-type IscS, at 510 nm. Interestingly, site-directed mutation of IscS with hydrogen bonds to PLP at Asp180 and Gln183 resulted in a loss of enzymatic activity followed by an absorption peak consistent with NFS1 (420 nm). Furthermore, mutations at Asp180 or Lys206 inhibited the reaction of IscS in vitro with L-cysteine (substrate) and L-alanine (product). These results suggest that the conserved active site residues (His104, Asp180, and Gln183) and their hydrogen bond with PLP in the N-terminus of IscS play a key role in determining whether the L-cysteine substrate can enter the active-site pocket and regulate the enzymatic reaction process. Therefore, our findings provide a framework for evaluating the roles of conserved active-site residues, motifs, and domains in CDs.
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Affiliation(s)
- Yilin Pang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Hunan Animal Pharmaceutical Company, Hunan Agricultural Group Company, Hunan Agricultural Development & Investment Group Company, Wangcheng Economic and Technological Development Zone, Changsha, Hunan, China
| | - Jing Wang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xueping Gao
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Mengyao Jiang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lifei Zhu
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Feng Liang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Mengxiang Liang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaolin Wu
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xianxian Xu
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaojun Ren
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Ting Xie
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Wu Wang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qianqian Sun
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaojun Xiong
- Hunan Animal Pharmaceutical Company, Hunan Agricultural Group Company, Hunan Agricultural Development & Investment Group Company, Wangcheng Economic and Technological Development Zone, Changsha, Hunan, China
| | - Jianxin Lyu
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Jianghui Li
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Guoqiang Tan
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
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5
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Lin L, Wang Y, Srinivasan R, Zhang L, Song H, Song Q, Wang G, Lin X. Quantitative Proteomics Reveals That the Protein Components of Outer Membrane Vesicles (OMVs) in Aeromonas hydrophila Play Protective Roles in Antibiotic Resistance. J Proteome Res 2022; 21:1707-1717. [PMID: 35674493 DOI: 10.1021/acs.jproteome.2c00114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In recent years, the intracellular mechanisms that contribute to antibiotic resistance have received increasing attention, and outer membrane vesicles (OMVs) have been reported to be related to antibiotic resistance in several Gram-negative bacterial species. However, the intrinsic molecular mechanisms and the form of such antibiotic resistance are still largely unknown. In this study, OMVs from an oxytetracycline (OXY) sensitive aquatic pathogen, Aeromonas hydrophila (OXY-S), were found with significantly increased OXY resistance. Interestingly, the OXY-resistant strain (OXY-R) had a more protective role in OXY resistance. Therefore, a DIA-based quantitative proteomics analysis was performed to compare the differential expression of OMV proteins between OXY-R (OMVsR) and OXY-S (OMVsS). The results showed that seven proteins increased and five proteins decreased in OMVsR vs OMVsS. A subsequent antibiotics susceptibility assay showed that the deletion of icd, rpsF, and iscS significantly increased OXY sensitivity. Moreover, the exogenous addition of the crude OMV fractions of overexpressed recombinant proteins in E. coli with rRpsF, rIcd, rIscS, rOmpA, rPepA, rFrdA, and rRplQ demonstrated that these proteins promoted the OXY resistance of A. hydrophila. Overall, our results indicate the important protective role of OMVs in antibiotic resistance in A. hydrophila and provide novel insights on bacterial antibiotic resistance mechanisms.
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Affiliation(s)
- Ling Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 350002, PR China
| | - Yuqian Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 350002, PR China
| | - Ramanathan Srinivasan
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 350002, PR China
| | - Lishan Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 350002, PR China
| | - Huanhuan Song
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 350002, PR China
| | - Qingli Song
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 350002, PR China
| | - Guibin Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 350002, PR China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, PR China
| | - Xiangmin Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China.,Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 350002, PR China.,Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, PR China
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6
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Bandyopadhyay P, Pramanick I, Biswas R, PS S, Sreedharan S, Singh S, Rajmani RS, Laxman S, Dutta S, Singh A. S-Adenosylmethionine-responsive cystathionine β-synthase modulates sulfur metabolism and redox balance in Mycobacterium tuberculosis. SCIENCE ADVANCES 2022; 8:eabo0097. [PMID: 35749503 PMCID: PMC9232105 DOI: 10.1126/sciadv.abo0097] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/09/2022] [Indexed: 05/10/2023]
Abstract
Methionine and cysteine metabolisms are important for the survival and pathogenesis of Mycobacterium tuberculosis (Mtb). The transsulfuration pathway converts methionine to cysteine and represents an important link between antioxidant and methylation metabolism in diverse organisms. Using a combination of biochemistry and cryo-electron microscopy, we characterized the first enzyme of the transsulfuration pathway, cystathionine β-synthase (MtbCbs) in Mtb. We demonstrated that MtbCbs is a heme-less, pyridoxal-5'-phosphate-containing enzyme, allosterically activated by S-adenosylmethionine (SAM). The atomic model of MtbCbs in its native and SAM-bound conformations revealed a unique mode of SAM-dependent allosteric activation. Further, SAM stabilized MtbCbs by sterically occluding proteasomal degradation, which was crucial for supporting methionine and redox metabolism in Mtb. Genetic deficiency of MtbCbs reduced Mtb survival upon homocysteine overload in vitro, inside macrophages, and in mice coinfected with HIV. Thus, the MtbCbs-SAM axis constitutes an important mechanism of coordinating sulfur metabolism in Mtb.
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Affiliation(s)
- Parijat Bandyopadhyay
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Ishika Pramanick
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Rupam Biswas
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Sabarinath PS
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka 560065, India
| | - Sreesa Sreedharan
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka 560065, India
| | - Shalini Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Raju S. Rajmani
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka 560065, India
| | - Somnath Dutta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, Karnataka 560012, India
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7
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Tripathi A, Anand K, Das M, O'Niel RA, P S S, Thakur C, R L RR, Rajmani RS, Chandra N, Laxman S, Singh A. Mycobacterium tuberculosis requires SufT for Fe-S cluster maturation, metabolism, and survival in vivo. PLoS Pathog 2022; 18:e1010475. [PMID: 35427399 PMCID: PMC9045647 DOI: 10.1371/journal.ppat.1010475] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 04/27/2022] [Accepted: 03/25/2022] [Indexed: 11/18/2022] Open
Abstract
Iron-sulfur (Fe-S) cluster proteins carry out essential cellular functions in diverse organisms, including the human pathogen Mycobacterium tuberculosis (Mtb). The mechanisms underlying Fe-S cluster biogenesis are poorly defined in Mtb. Here, we show that Mtb SufT (Rv1466), a DUF59 domain-containing essential protein, is required for the Fe-S cluster maturation. Mtb SufT homodimerizes and interacts with Fe-S cluster biogenesis proteins; SufS and SufU. SufT also interacts with the 4Fe-4S cluster containing proteins; aconitase and SufR. Importantly, a hyperactive cysteine in the DUF59 domain mediates interaction of SufT with SufS, SufU, aconitase, and SufR. We efficiently repressed the expression of SufT to generate a SufT knock-down strain in Mtb (SufT-KD) using CRISPR interference. Depleting SufT reduces aconitase's enzymatic activity under standard growth conditions and in response to oxidative stress and iron limitation. The SufT-KD strain exhibited defective growth and an altered pool of tricarboxylic acid cycle intermediates, amino acids, and sulfur metabolites. Using Seahorse Extracellular Flux analyzer, we demonstrated that SufT depletion diminishes glycolytic rate and oxidative phosphorylation in Mtb. The SufT-KD strain showed defective survival upon exposure to oxidative stress and nitric oxide. Lastly, SufT depletion reduced the survival of Mtb in macrophages and attenuated the ability of Mtb to persist in mice. Altogether, SufT assists in Fe-S cluster maturation and couples this process to bioenergetics of Mtb for survival under low and high demand for Fe-S clusters.
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Affiliation(s)
- Ashutosh Tripathi
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Kushi Anand
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Mayashree Das
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Ruchika Annie O'Niel
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
| | - Sabarinath P S
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
| | - Chandrani Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Raghunatha Reddy R L
- Regional Horticultural Research and Extension Centre (RHREK), GKVK, Bengaluru, India
| | - Raju S Rajmani
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
| | - Amit Singh
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
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8
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Anand K, Tripathi A, Shukla K, Malhotra N, Jamithireddy AK, Jha RK, Chaudhury SN, Rajmani RS, Ramesh A, Nagaraja V, Gopal B, Nagaraju G, Narain Seshayee AS, Singh A. Mycobacterium tuberculosis SufR responds to nitric oxide via its 4Fe-4S cluster and regulates Fe-S cluster biogenesis for persistence in mice. Redox Biol 2021; 46:102062. [PMID: 34392160 PMCID: PMC8371249 DOI: 10.1016/j.redox.2021.102062] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/21/2021] [Accepted: 06/29/2021] [Indexed: 12/13/2022] Open
Abstract
The persistence of Mycobacterium tuberculosis (Mtb) is a major problem in managing tuberculosis (TB). Host-generated nitric oxide (NO) is perceived as one of the signals by Mtb to reprogram metabolism and respiration for persistence. However, the mechanisms involved in NO sensing and reorganizing Mtb's physiology are not fully understood. Since NO damages iron-sulfur (Fe-S) clusters of essential enzymes, the mechanism(s) involved in regulating Fe-S cluster biogenesis could help Mtb persist in host tissues. Here, we show that a transcription factor SufR (Rv1460) senses NO via its 4Fe-4S cluster and promotes persistence of Mtb by mobilizing the Fe-S cluster biogenesis system; suf operon (Rv1460-Rv1466). Analysis of anaerobically purified SufR by UV-visible spectroscopy, circular dichroism, and iron-sulfide estimation confirms the presence of a 4Fe-4S cluster. Atmospheric O2 and H2O2 gradually degrade the 4Fe-4S cluster of SufR. Furthermore, electron paramagnetic resonance (EPR) analysis demonstrates that NO directly targets SufR 4Fe-4S cluster by forming a protein-bound dinitrosyl-iron-dithiol complex. DNase I footprinting, gel-shift, and in vitro transcription assays confirm that SufR directly regulates the expression of the suf operon in response to NO. Consistent with this, RNA-sequencing of MtbΔsufR demonstrates deregulation of the suf operon under NO stress. Strikingly, NO inflicted irreversible damage upon Fe-S clusters to exhaust respiratory and redox buffering capacity of MtbΔsufR. Lastly, MtbΔsufR failed to recover from a NO-induced non-growing state and displayed persistence defect inside immune-activated macrophages and murine lungs in a NO-dependent manner. Data suggest that SufR is a sensor of NO that supports persistence by reprogramming Fe-S cluster metabolism and bioenergetics.
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Affiliation(s)
- Kushi Anand
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Ashutosh Tripathi
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Kaustubh Shukla
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Nitish Malhotra
- National Centre for Biological Science, Bangalore, 560065, India
| | | | - Rajiv Kumar Jha
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | | | - Raju S Rajmani
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Arati Ramesh
- National Centre for Biological Science, Bangalore, 560065, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | | | - Ganesh Nagaraju
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | | | - Amit Singh
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India; Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India.
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9
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Das M, Dewan A, Shee S, Singh A. The Multifaceted Bacterial Cysteine Desulfurases: From Metabolism to Pathogenesis. Antioxidants (Basel) 2021; 10:antiox10070997. [PMID: 34201508 PMCID: PMC8300815 DOI: 10.3390/antiox10070997] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/01/2021] [Accepted: 05/06/2021] [Indexed: 12/02/2022] Open
Abstract
Living cells have developed a relay system to efficiently transfer sulfur (S) from cysteine to various thio-cofactors (iron-sulfur (Fe-S) clusters, thiamine, molybdopterin, lipoic acid, and biotin) and thiolated tRNA. The presence of such a transit route involves multiple protein components that allow the flux of S to be precisely regulated as a function of environmental cues to avoid the unnecessary accumulation of toxic concentrations of soluble sulfide (S2−). The first enzyme in this relay system is cysteine desulfurase (CSD). CSD catalyzes the release of sulfane S from L-cysteine by converting it to L-alanine by forming an enzyme-linked persulfide intermediate on its conserved cysteine residue. The persulfide S is then transferred to diverse acceptor proteins for its incorporation into the thio-cofactors. The thio-cofactor binding-proteins participate in essential and diverse cellular processes, including DNA repair, respiration, intermediary metabolism, gene regulation, and redox sensing. Additionally, CSD modulates pathogenesis, antibiotic susceptibility, metabolism, and survival of several pathogenic microbes within their hosts. In this review, we aim to comprehensively illustrate the impact of CSD on bacterial core metabolic processes and its requirement to combat redox stresses and antibiotics. Targeting CSD in human pathogens can be a potential therapy for better treatment outcomes.
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10
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von Rosen T, Keller LM, Weber-Ban E. Survival in Hostile Conditions: Pupylation and the Proteasome in Actinobacterial Stress Response Pathways. Front Mol Biosci 2021; 8:685757. [PMID: 34179091 PMCID: PMC8223512 DOI: 10.3389/fmolb.2021.685757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/04/2021] [Indexed: 12/31/2022] Open
Abstract
Bacteria employ a multitude of strategies to cope with the challenges they face in their natural surroundings, be it as pathogens, commensals or free-living species in rapidly changing environments like soil. Mycobacteria and other Actinobacteria acquired proteasomal genes and evolved a post-translational, ubiquitin-like modification pathway called pupylation to support their survival under rapidly changing conditions and under stress. The proteasomal 20S core particle (20S CP) interacts with ring-shaped activators like the hexameric ATPase Mpa that recruits pupylated substrates. The proteasomal subunits, Mpa and pupylation enzymes are encoded in the so-called Pup-proteasome system (PPS) gene locus. Genes in this locus become vital for bacteria to survive during periods of stress. In the successful human pathogen Mycobacterium tuberculosis, the 20S CP is essential for survival in host macrophages. Other members of the PPS and proteasomal interactors are crucial for cellular homeostasis, for example during the DNA damage response, iron and copper regulation, and heat shock. The multiple pathways that the proteasome is involved in during different stress responses suggest that the PPS plays a vital role in bacterial protein quality control and adaptation to diverse challenging environments.
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Affiliation(s)
- Tatjana von Rosen
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Lena Ml Keller
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Eilika Weber-Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
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11
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Tamuhla T, Joubert L, Willemse D, Williams MJ. SufT is required for growth of Mycobacterium smegmatis under iron limiting conditions. MICROBIOLOGY-SGM 2020; 166:296-305. [PMID: 31860439 DOI: 10.1099/mic.0.000881] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Iron-sulphur (FeS) clusters are versatile cofactors required for a range of biological processes within cells. Due to the reactive nature of the constituent molecules, assembly and delivery of these cofactors requires a multi-protein machinery in vivo. In prokaryotes, SufT homologues are proposed to function in the maturation and transfer of FeS clusters to apo-proteins. This study used targeted gene deletion to investigate the role of SufT in the physiology of mycobacteria, using Mycobacterium smegmatis as a model organism. Deletion of the sufT gene in M. smegmatis had no impact on growth under standard culture conditions and did not significantly alter activity of the FeS cluster dependent enzymes succinate dehydrogenase (SDH) and aconitase (ACN). Furthermore, the ΔsufT mutant was no more sensitive than the wild-type strain to the redox cycler 2,3-dimethoxy-1,4-naphthoquinone (DMNQ), or the anti-tuberculosis drugs isoniazid, clofazimine or rifampicin. In contrast, the ΔsufT mutant displayed a growth defect under iron limiting conditions, and an increased requirement for iron during biofilm formation. This data suggests that SufT is an accessory factor in FeS cluster biogenesis in mycobacteria which is required under conditions of iron limitation.
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Affiliation(s)
- Tsaone Tamuhla
- Present address: Department of Integrative Biomedical Sciences, Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Lydia Joubert
- Present address: Stanford-SLAC Cryo-EM Center, Stanford University, Stanford, USA.,Central Analytical Facilties, Microbiology Department, Stellenbosch University, Stellenbosch, South Africa
| | - Danicke Willemse
- Present address: Texas Biomedical Research Institute, 8715 West Military Drive, San Antonio, TX, USA.,DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Monique J Williams
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Present address: Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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12
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Abstract
Iron–sulfur (Fe–S) clusters are protein cofactors of a multitude of enzymes performing essential biological functions. Specialized multi-protein machineries present in all types of organisms support their biosynthesis. These machineries encompass a scaffold protein on which Fe–S clusters are assembled and a cysteine desulfurase that provides sulfur in the form of a persulfide. The sulfide ions are produced by reductive cleavage of the persulfide, which involves specific reductase systems. Several other components are required for Fe–S biosynthesis, including frataxin, a key protein of controversial function and accessory components for insertion of Fe–S clusters in client proteins. Fe–S cluster biosynthesis is thought to rely on concerted and carefully orchestrated processes. However, the elucidation of the mechanisms of their assembly has remained a challenging task due to the biochemical versatility of iron and sulfur and the relative instability of Fe–S clusters. Nonetheless, significant progresses have been achieved in the past years, using biochemical, spectroscopic and structural approaches with reconstituted system in vitro. In this paper, we review the most recent advances on the mechanism of assembly for the founding member of the Fe–S cluster family, the [2Fe2S] cluster that is the building block of all other Fe–S clusters. The aim is to provide a survey of the mechanisms of iron and sulfur insertion in the scaffold proteins by examining how these processes are coordinated, how sulfide is produced and how the dinuclear [2Fe2S] cluster is formed, keeping in mind the question of the physiological relevance of the reconstituted systems. We also cover the latest outcomes on the functional role of the controversial frataxin protein in Fe–S cluster biosynthesis.
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13
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Anand K, Tripathi A, Shukla K, Malhotra N, Jamithireddy A, Jha RK, Chaudhury SN, Rajmani RS, Ramesh A, Nagaraja V, Gopal B, Nagaraju G, Seshasayee ASN, Singh A. Mycobacterium tuberculosis SufR Responds to Nitric oxide via its 4Fe-4S cluster and Regulates Fe-S cluster Biogenesis for Persistence in Mice.. [DOI: 10.1101/2020.08.10.245365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
The persistence of Mycobacterium tuberculosis (Mtb) is a major problem in managing tuberculosis. Host–generated nitric oxide (NO) is perceived as one of the signals by Mtb to reprogram metabolism and respiration for persistence. However, the mechanisms involved in NO sensing and reorganizing Mtb′s physiology are not fully understood. Since NO damages iron–sulfur (Fe–S) clusters of essential enzymes, the mechanism(s) involved in regulating Fe–S cluster biogenesis could help Mtb persist in host tissues. Here, we show that a transcription factor SufR (Rv1460) senses NO via its 4Fe–4S cluster and promotes persistence of Mtb by mobilizing the Fe-S cluster biogenesis system; suf operon (Rv1460–Rv1466). Analysis of anaerobically purified SufR by UV-visible spectroscopy, circular dichroism, and iron-sulfide estimation confirms the presence of a 4Fe–4S cluster. Atmospheric O2 and H2O2 gradually degrade the 4Fe–4S cluster of SufR. Furthermore, electron paramagnetic resonance (EPR) analysis demonstrates that NO directly targets SufR 4Fe–4S cluster by forming a protein-bound dinitrosyl–iron–dithiol complex. DNase I footprinting, gel–shift, and in vitro transcription assays confirm that SufR directly regulates the expression of the suf operon in response to NO. Consistent with this, RNA–sequencing of Mtb ΔsufR demonstrates deregulation of the suf operon under NO stress. Strikingly, NO inflicted irreversible damage upon Fe–S clusters to exhaust respiratory and redox buffering capacity of MtbΔsufR. Lastly, Mtb ΔsufR failed to recover from a NO-induced non-growing state and displayed persistence defect inside immune–activated macrophages and murine lungs in a NO–dependent manner. Data suggest that SufR is a sensor of NO that supports persistence by reprogramming Fe–S cluster metabolism and bioenergetics.
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14
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Zhu Z, Yang L, Yu P, Wang Y, Peng X, Chen L. Comparative Proteomics and Secretomics Revealed Virulence and Antibiotic Resistance-Associated Factors in Vibrio parahaemolyticus Recovered From Commonly Consumed Aquatic Products. Front Microbiol 2020; 11:1453. [PMID: 32765437 PMCID: PMC7381183 DOI: 10.3389/fmicb.2020.01453] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/04/2020] [Indexed: 01/01/2023] Open
Abstract
Vibrio parahaemolyticus is a seafoodborne pathogen that can cause severe gastroenteritis and septicemia diseases in humans and even death. The emergence of multidrug-resistant V. parahaemolyticus leads to difficulties and rising costs of medical treatment. The bacterium of environmental origins containing no major virulence genes (tdh and trh) has been reported to be associated with infectious diarrhea disease as well. Identification of risk factors in V. parahaemolyticus is imperative for assuming food safety. In this study, we obtained secretomic and proteomic profiles of V. parahaemolyticus isolated from 12 species of commonly consumed aquatic products and identified candidate protein spots by using two-dimensional gel electrophoresis and liquid chromatography tandem mass spectrometry techniques. A total of 11 common and 28 differential extracellular proteins were found from distinct secretomic profiles, including eight virulence-associated proteins: outer membrane channel TolC, maltoporin, elongation factor Tu, enolase, transaldolase, flagellin C, polar flagellin B/D, and superoxide dismutase, as well as five antimicrobial and/or heavy metal resistance-associated ABC transporter proteins. Comparison of proteomic profiles derived from the 12 V. parahaemolyticus isolates also revealed five intracellular virulence-related proteins, including aldehyde-alcohol dehydrogenase, outer membrane protein A, alkyl hydroperoxide reductase C, phosphoenolpyruvate-protein phosphotransferase, and phosphoglycerate kinase. Additionally, our data indicated that aquatic product matrices significantly altered proteomic profiles of the V. parahaemolyticus isolates with a number of differentially expressed proteins identified. The results in this study meet the increasing need for novel diagnosis candidates of the leading seafoodborne pathogen worldwide.
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Affiliation(s)
- Zhuoying Zhu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Lianzhi Yang
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Pan Yu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yongjie Wang
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Xu Peng
- Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
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15
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Structural Analysis of an l-Cysteine Desulfurase from an Ssp DNA Phosphorothioation System. mBio 2020; 11:mBio.00488-20. [PMID: 32345643 PMCID: PMC7188994 DOI: 10.1128/mbio.00488-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Apart from its roles in Fe-S cluster assembly, tRNA thiolation, and sulfur-containing cofactor biosynthesis, cysteine desulfurase serves as a sulfur donor in the DNA PT modification, in which a sulfur atom substitutes a nonbridging oxygen in the DNA phosphodiester backbone. The initial sulfur mobilization from l-cysteine is catalyzed by the SspA cysteine desulfurase in the SspABCD-mediated DNA PT modification system. By determining the crystal structure of SspA, the study presents the molecular mechanism that SspA employs to recognize its cysteine substrate and PLP cofactor. To overcome the long distance (8.9 Å) between the catalytic Cys314 and the cysteine substrate, a conformational change occurs to bring Cys314 to the vicinity of the substrate, allowing for nucleophilic attack. DNA phosphorothioate (PT) modification, in which the nonbridging oxygen in the sugar-phosphate backbone is substituted by sulfur, is catalyzed by DndABCDE or SspABCD in a double-stranded or single-stranded manner, respectively. In Dnd and Ssp systems, mobilization of sulfur in PT formation starts with the activation of the sulfur atom of cysteine catalyzed by the DndA and SspA cysteine desulfurases, respectively. Despite playing the same biochemical role, SspA cannot be functionally replaced by DndA, indicating its unique physiological properties. In this study, we solved the crystal structure of Vibrio cyclitrophicus SspA in complex with its natural substrate, cysteine, and cofactor, pyridoxal phosphate (PLP), at a resolution of 1.80 Å. Our solved structure revealed the molecular mechanism that SspA employs to recognize its cysteine substrate and PLP cofactor, suggesting a common binding mode shared by cysteine desulfurases. In addition, although the distance between the catalytic Cys314 and the substrate cysteine is 8.9 Å, which is too far for direct interaction, our structural modeling and biochemical analysis revealed a conformational change in the active site region toward the cysteine substrate to move them close to each other to facilitate the nucleophilic attack. Finally, the pulldown analysis showed that SspA could form a complex with SspD, an ATP pyrophosphatase, suggesting that SspD might potentially accept the activated sulfur atom directly from SspA, providing further insights into the biochemical pathway of Ssp-mediated PT modification.
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16
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Dunkle JA, Bruno MR, Frantom PA. Structural evidence for a latch mechanism regulating access to the active site of SufS-family cysteine desulfurases. Acta Crystallogr D Struct Biol 2020; 76:291-301. [PMID: 32133993 PMCID: PMC7057215 DOI: 10.1107/s2059798320000790] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 01/22/2020] [Indexed: 11/10/2022] Open
Abstract
Cysteine serves as the sulfur source for the biosynthesis of Fe-S clusters and thio-cofactors, molecules that are required for core metabolic processes in all organisms. Therefore, cysteine desulfurases, which mobilize sulfur for its incorporation into thio-cofactors by cleaving the Cα-S bond of cysteine, are ubiquitous in nature. SufS, a type 2 cysteine desulfurase that is present in plants and microorganisms, mobilizes sulfur from cysteine to the transpersulfurase SufE to initiate Fe-S biosynthesis. Here, a 1.5 Å resolution X-ray crystal structure of the Escherichia coli SufS homodimer is reported which adopts a state in which the two monomers are rotated relative to their resting state, displacing a β-hairpin from its typical position blocking transpersulfurase access to the SufS active site. A global structure and sequence analysis of SufS family members indicates that the active-site β-hairpin is likely to require adjacent structural elements to function as a β-latch regulating access to the SufS active site.
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Affiliation(s)
- Jack A. Dunkle
- Department of Chemistry and Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL 35401, USA
| | - Michael R. Bruno
- Department of Chemistry and Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL 35401, USA
| | - Patrick A. Frantom
- Department of Chemistry and Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL 35401, USA
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17
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The role of low molecular weight thiols in Mycobacterium tuberculosis. Tuberculosis (Edinb) 2019; 116:44-55. [PMID: 31153518 DOI: 10.1016/j.tube.2019.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 04/16/2019] [Accepted: 04/22/2019] [Indexed: 02/06/2023]
Abstract
Low molecular weight (LMW) thiols are molecules with a functional sulfhydryl group that enable them to detoxify reactive oxygen species, reactive nitrogen species and other free radicals. Their roles range from their ability to modulate the immune system to their ability to prevent damage of biological molecules such as DNA and proteins by protecting against oxidative, nitrosative and acidic stress. LMW thiols are synthesized and found in both eukaryotes and prokaryotes. Due to their beneficial role to both eukaryotes and prokaryotes, their specific functions need to be elucidated, most especially in pathogenic prokaryotes such as Mycobacterium tuberculosis (M.tb), in order to provide a rationale for targeting their biosynthesis for drug development. Ergothioneine (ERG), mycothiol (MSH) and gamma-glutamylcysteine (GGC) are LMW thiols that have been shown to interplay to protect M.tb against cellular stress. Though ERG, MSH and GGC seem to have overlapping functions, studies are gradually revealing their unique physiological roles. Understanding their unique physiological role during the course of tuberculosis (TB) infection, would pave the way for the development of drugs that target their biosynthetic pathway. This review identifies the knowledge gap in the unique physiological roles of LMW thiols and proposes their mechanistic roles based on previous studies. In addition, it gives an update on identified inhibitors of their biosynthetic enzymes.
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18
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Cysteine Desulfurase IscS2 Plays a Role in Oxygen Resistance in Clostridium difficile. Infect Immun 2018; 86:IAI.00326-18. [PMID: 29866903 DOI: 10.1128/iai.00326-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 05/25/2018] [Indexed: 11/20/2022] Open
Abstract
Clostridium difficile is an anaerobic, spore-forming bacterium capable of colonizing the gastrointestinal tract of humans following disruption of the normal microbiota, typically from antibiotic therapy for an unrelated infection. With approximately 500,000 confirmed infections leading to 29,000 deaths per year in the United States, C. difficile infection (CDI) is an urgent public health threat. We previously determined that C. difficile survives in up to 3% oxygen. Low levels of oxygen are present in the intestinal tract, with the higher concentrations being associated with the epithelial cell surface. Additionally, antibiotic treatment, the greatest risk factor for CDI, increases the intestinal oxygen concentration. Therefore, we hypothesized that the C. difficile genome encodes mechanisms for survival during oxidative stress. Previous data have shown that cysteine desulfurases involved in iron-sulfur cluster assembly are involved in protecting bacteria from oxidative stress. In this study, deletion of a putative cysteine desulfurase (Cd630_12790/IscS2) involved in the iron-sulfur cluster (Isc) system caused a severe growth defect in the presence of 2% oxygen. Additionally, this mutant delayed colonization in a conventional mouse model of CDI and failed to colonize in a germfree model, which has higher intestinal oxygen levels. These data imply an undefined role for this cysteine desulfurase in protecting C. difficile from low levels of oxygen in the gut.
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19
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Willemse D, Weber B, Masino L, Warren RM, Adinolfi S, Pastore A, Williams MJ. Rv1460, a SufR homologue, is a repressor of the suf operon in Mycobacterium tuberculosis. PLoS One 2018; 13:e0200145. [PMID: 29979728 PMCID: PMC6034842 DOI: 10.1371/journal.pone.0200145] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/20/2018] [Indexed: 11/19/2022] Open
Abstract
Iron–sulphur (Fe-S) clusters are ubiquitous co-factors which require multi-protein systems for their synthesis. In Mycobacterium tuberculosis, the Rv1460-Rv1461-Rv1462-Rv1463-csd-Rv1465-Rv1466 operon (suf operon) encodes the primary Fe-S cluster biogenesis system. The first gene in this operon, Rv1460, shares homology with the cyanobacterial SufR, which functions as a transcriptional repressor of the sufBCDS operon. Rv1460’s function in M. tuberculosis has however not been determined. In this study, we demonstrate that M. tuberculosis mutants lacking a functional Rv1460 protein are impaired for growth under standard culture conditions. Elevated expression of Rv1460 and Rv1461 was observed in the mutant, implicating Rv1460 in the regulation of the suf operon. Binding of an Fe-S cluster to purified recombinant Rv1460 was confirmed by UV-visible spectroscopy and circular dichroism. Furthermore, three conserved cysteine residues, C203, C216 and C244, proposed to provide ligands for the coordination of an Fe-S cluster, were shown to be required for the function of Rv1460 in M. tuberculosis. Rv1460 therefore seems to be functionally analogous to cyanobacterial SufR.
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Affiliation(s)
- Danicke Willemse
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Brandon Weber
- Electron Microscope Unit, University of Cape Town, Cape Town, South Africa
| | - Laura Masino
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Robin M. Warren
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Salvatore Adinolfi
- Pharmaceutical Science and Technology, University of Turin, Turin, Italy
| | - Annalisa Pastore
- Department of Basic and Clinical Neuroscience, Maurice Wohl Institute, King's College London, London, United Kingdom
| | - Monique J. Williams
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
- * E-mail:
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20
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Compounds with Potential Activity against Mycobacterium tuberculosis. Antimicrob Agents Chemother 2018; 62:AAC.02236-17. [PMID: 29437626 DOI: 10.1128/aac.02236-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/01/2018] [Indexed: 12/26/2022] Open
Abstract
The high acquisition rate of drug resistance by Mycobacterium tuberculosis necessitates the ongoing search for new drugs to be incorporated in the tuberculosis (TB) regimen. Compounds used for the treatment of other diseases have the potential to be repurposed for the treatment of TB. In this study, a high-throughput screening of compounds against thiol-deficient Mycobacterium smegmatis strains and subsequent validation with thiol-deficient M. tuberculosis strains revealed that ΔegtA and ΔmshA mutants had increased susceptibility to azaguanine (Aza) and sulfaguanidine (Su); ΔegtB and ΔegtE mutants had increased susceptibility to bacitracin (Ba); and ΔegtA, ΔmshA, and ΔegtB mutants had increased susceptibility to fusaric acid (Fu). Further analyses revealed that some of these compounds were able to modulate the levels of thiols and oxidative stress in M. tuberculosis This study reports the activities of Aza, Su, Fu, and Ba against M. tuberculosis and provides a rationale for further investigations.
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Reyes AM, Pedre B, De Armas MI, Tossounian MA, Radi R, Messens J, Trujillo M. Chemistry and Redox Biology of Mycothiol. Antioxid Redox Signal 2018; 28:487-504. [PMID: 28372502 DOI: 10.1089/ars.2017.7074] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
SIGNIFICANCE Mycothiol (MSH, AcCys-GlcN-Ins) is the main low-molecular weight (LMW) thiol of most Actinomycetes, including the human pathogen Mycobacterium tuberculosis that affects millions of people worldwide. Strains with decreased MSH content show increased susceptibilities to hydroperoxides and electrophilic compounds. In M. tuberculosis, MSH modulates the response to several antituberculosis drugs. Enzymatic routes involving MSH could provide clues for specific drug design. Recent Advances: Physicochemical data argue against a rapid, nonenzymatic reaction of MSH with oxidants, disulfides, or electrophiles. Moreover, exposure of the bacteria to high concentrations of two-electron oxidants resulted in protein mycothiolation. The recently described glutaredoxin-like protein mycoredoxin-1 (Mrx-1) provides a route for catalytic reduction of mycothiolated proteins, protecting critical cysteines from irreversible oxidation. The description of MSH/Mrx-1-dependent activities of peroxidases helped to explain the higher susceptibility to oxidants observed in Actinomycetes lacking MSH. Moreover, the first mycothiol-S-transferase, member of the DinB superfamily of proteins, was described. In Corynebacterium, both the MSH/Mrx-1 and the thioredoxin pathways reduce methionine sulfoxide reductase A. A novel tool for in vivo imaging of the MSH/mycothiol disulfide (MSSM) status allows following changes in the mycothiol redox state during macrophage infection and its relationship with antibiotic sensitivity. CRITICAL ISSUES Redundancy of MSH with other LMW thiols is starting to be unraveled and could help to rationalize the differences in the reported importance of MSH synthesis observed in vitro versus in animal infection models. FUTURE DIRECTIONS Future work should be directed to establish the structural bases of the specificity of MSH-dependent enzymes, thus facilitating drug developments. Antioxid. Redox Signal. 28, 487-504.
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Affiliation(s)
- Aníbal M Reyes
- 1 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,2 Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Brandán Pedre
- 3 Center for Structural Biology , VIB, Brussels, Belgium .,4 Brussels Center for Redox Biology , Brussels, Belgium .,5 Structural Biology Brussels, Vrije Universiteit Brussel , Brussels, Belgium
| | - María Inés De Armas
- 1 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,2 Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Maria-Armineh Tossounian
- 3 Center for Structural Biology , VIB, Brussels, Belgium .,4 Brussels Center for Redox Biology , Brussels, Belgium .,5 Structural Biology Brussels, Vrije Universiteit Brussel , Brussels, Belgium
| | - Rafael Radi
- 1 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,2 Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
| | - Joris Messens
- 3 Center for Structural Biology , VIB, Brussels, Belgium .,4 Brussels Center for Redox Biology , Brussels, Belgium .,5 Structural Biology Brussels, Vrije Universiteit Brussel , Brussels, Belgium
| | - Madia Trujillo
- 1 Departamento de Bioquímica, Facultad de Medicina, Universidad de la República , Montevideo, Uruguay .,2 Center for Free Radical and Biomedical Research , Universidad de la República, Montevideo, Uruguay
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Sao Emani C, Williams M, Van Helden P, Taylor M, Wiid I, Baker B. Gamma-glutamylcysteine protects ergothioneine-deficient Mycobacterium tuberculosis mutants against oxidative and nitrosative stress. Biochem Biophys Res Commun 2018; 495:174-178. [DOI: 10.1016/j.bbrc.2017.10.163] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 10/29/2017] [Indexed: 11/15/2022]
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Tong Y, Zhai Q, Lu W, Tian F, Zhao J, Zhang H, Chen W. New insights in integrated response mechanism of Lactobacillus plantarum under excessive manganese stress. Food Res Int 2017; 102:323-332. [DOI: 10.1016/j.foodres.2017.10.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/07/2017] [Accepted: 10/09/2017] [Indexed: 10/18/2022]
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Wang Y, Liu Q, Zhou H, Chen X. Expression, purification and function of cysteine desulfurase from Sulfobacillus acidophilus TPY isolated from deep-sea hydrothermal vent. 3 Biotech 2017; 7:360. [PMID: 28979833 DOI: 10.1007/s13205-017-0995-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/23/2017] [Indexed: 11/25/2022] Open
Abstract
The cysteine desulfurase (SufS) gene of Sulfobacillus acidophilus TPY, a Gram-positive bacterium isolated from deep-sea hydrothermal vent, was cloned and over-expressed in E. coli BL21. The recombinant SufS protein was purified by one-step affinity chromatography. The TPY SufS contained a well conserved motif RXGHHCA as found in that of other microorganisms, suggesting that it belonged to group II of cysteine desulfurase family. The recombinant TPY SufS could catalyze the conversion of l-cysteine to l-alanine and produce persulfide, and the enzyme activity was 95 μ/μL of sulfur ion per minute. The growth of E. coli BL21 was promoted by over-expressing TPY SufS in vivo or by directly adding recombinant TPY SufS in the medium (4.3-4.5 × 108 cells/mL vs. 3.2-3.5 × 108 cells/mL). Furthermore, the highest cell density of E. coli BL21 when the TPY SufS was over-expressed was about 3.5 times that of the control groups in the presence of sodium thiosulfate. These results indicate that the SUF system as the only assembly system of iron-sulfur clusters not only has significant roles in survival of S. acidophilus TPY, but also might be important for combating with high content of sulfide.
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Affiliation(s)
- Yuguang Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005 People's Republic of China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, 361005 People's Republic of China
| | - Qian Liu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005 People's Republic of China
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083 People's Republic of China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083 People's Republic of China
| | - Xinhua Chen
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005 People's Republic of China
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002 People's Republic of China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, 361005 People's Republic of China
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Boniecki MT, Freibert SA, Mühlenhoff U, Lill R, Cygler M. Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex. Nat Commun 2017; 8:1287. [PMID: 29097656 PMCID: PMC5668364 DOI: 10.1038/s41467-017-01497-1] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/21/2017] [Indexed: 01/25/2023] Open
Abstract
Iron-sulfur (Fe/S) clusters are essential protein cofactors crucial for many cellular functions including DNA maintenance, protein translation, and energy conversion. De novo Fe/S cluster synthesis occurs on the mitochondrial scaffold protein ISCU and requires cysteine desulfurase NFS1, ferredoxin, frataxin, and the small factors ISD11 and ACP (acyl carrier protein). Both the mechanism of Fe/S cluster synthesis and function of ISD11-ACP are poorly understood. Here, we present crystal structures of three different NFS1-ISD11-ACP complexes with and without ISCU, and we use SAXS analyses to define the 3D architecture of the complete mitochondrial Fe/S cluster biosynthetic complex. Our structural and biochemical studies provide mechanistic insights into Fe/S cluster synthesis at the catalytic center defined by the active-site Cys of NFS1 and conserved Cys, Asp, and His residues of ISCU. We assign specific regulatory rather than catalytic roles to ISD11-ACP that link Fe/S cluster synthesis with mitochondrial lipid synthesis and cellular energy status.
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Affiliation(s)
- Michal T Boniecki
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, Canada, S7N 5E5
| | - Sven A Freibert
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Robert-Koch-Strasse 6, 35032, Marburg, Germany
| | - Ulrich Mühlenhoff
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Robert-Koch-Strasse 6, 35032, Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität, Robert-Koch-Strasse 6, 35032, Marburg, Germany.
- LOEWE Zentrum für Synthetische Mikrobiologie SynMikro, Hans-Meerwein-Strasse, 35043, Marburg, Germany.
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, Canada, S7N 5E5.
- Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, Canada, H3G 0B1.
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Hu YH, Sun L. The global regulatory effect of Edwardsiella tarda Fur on iron acquisition, stress resistance, and host infection: A proteomics-based interpretation. J Proteomics 2016; 140:100-10. [PMID: 27102497 DOI: 10.1016/j.jprot.2016.04.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/27/2016] [Accepted: 04/07/2016] [Indexed: 02/01/2023]
Abstract
UNLABELLED Ferric uptake regulator (Fur) is an important transcriptional regulator of Gram-negative bacteria. Edwardsiella tarda is a severe fish bacterial pathogen with a broad host range that includes humans. In this study, we examined the regulatory function of Fur in E. tarda via a proteomic approach. Compared to the wild type TX01, the fur mutant TX01Δfur exhibited (i) retarded growth, (ii) enhanced siderophore production, (iii) increased acid tolerance, which is in contrast to observations in other bacterial species, (iv) decreased survival against oxidative stress and host serum, (v) impaired ability to inhibit host immune response, (vi) attenuated tissue infectivity and overall virulence. The deficiency of TX01Δfur was rescued by introduction of an exogenous fur gene. iTRAQ-based comparative proteomic analysis of TX01Δfur and TX01 identified 89 differentially expressed proteins that cover a wide range of functional categories including those affected by fur mutation. In addition, 16 proteins were identified for the first time to be regulated by Fur in Gram-negative bacteria. These results provide the first protein-based interpretation of the global impact of Fur on the physiology and infectivity of E. tarda. SIGNIFICANCE This study demonstrates that in E. tarda, Fur controls multiple aspects of bacterial life, including growth, metabolism, iron acquisition, stress response, and host infection. In line with these observations, proteomics analysis identified a large amount of proteins affected in expression by Fur, which are involved in bacterial physiology and infectivity. Hence, these results link for the first time the pleiotropic effect of Fur with global protein expression and shed new light on the function and regulatory mechanism of Fur in pathogenic bacteria.
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Affiliation(s)
- Yong-Hua Hu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Li Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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27
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SufB intein of Mycobacterium tuberculosis as a sensor for oxidative and nitrosative stresses. Proc Natl Acad Sci U S A 2015; 112:10348-53. [PMID: 26240361 DOI: 10.1073/pnas.1512777112] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inteins are mobile genetic elements that self-splice at the protein level. Mycobacteria have inteins inserted into several important genes, including those corresponding to the iron-sulfur cluster assembly protein SufB. Curiously, the SufB inteins are found primarily in mycobacterial species that are potential human pathogens. Here we discovered an exceptional sensitivity of Mycobacterium tuberculosis SufB intein splicing to oxidative and nitrosative stresses when expressed in Escherichia coli. This effect results from predisposition of the intein's catalytic cysteine residues to oxidative and nitrosative modifications. Experiments with a fluorescent reporter system revealed that reactive oxygen species and reactive nitrogen species inhibit SufB extein ligation by forcing either precursor accumulation or N-terminal cleavage. We propose that splicing inhibition is an immediate, posttranslational regulatory response that can be either reversible, by inducing precursor accumulation, or irreversible, by inducing N-terminal cleavage, which may potentially channel mycobacteria into dormancy under extreme oxidative and nitrosative stresses.
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Espinoza-Valles I, Vora GJ, Lin B, Leekitcharoenphon P, González-Castillo A, Ussery D, Høj L, Gomez-Gil B. Unique and conserved genome regions in Vibrio harveyi and related species in comparison with the shrimp pathogen Vibrio harveyi CAIM 1792. MICROBIOLOGY-SGM 2015. [PMID: 26198743 DOI: 10.1099/mic.0.000141] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Vibrio harveyi CAIM 1792 is a marine bacterial strain that causes mortality in farmed shrimp in north-west Mexico, and the identification of virulence genes in this strain is important for understanding its pathogenicity. The aim of this work was to compare the V. harveyi CAIM 1792 genome with related genome sequences to determine their phylogenic relationship and explore unique regions in silico that differentiate this strain from other V. harveyi strains. Twenty-one newly sequenced genomes were compared in silico against the CAIM 1792 genome at nucleotidic and predicted proteome levels. The proteome of CAIM 1792 had higher similarity to those of other V. harveyi strains (78%) than to those of the other closely related species Vibrio owensii (67%), Vibrio rotiferianus (63%) and Vibrio campbellii (59%). Pan-genome ORFans trees showed the best fit with the accepted phylogeny based on DNA-DNA hybridization and multi-locus sequence analysis of 11 concatenated housekeeping genes. SNP analysis clustered 34/38 genomes within their accepted species. The pangenomic and SNP trees showed that V. harveyi is the most conserved of the four species studied and V. campbellii may be divided into at least three subspecies, supported by intergenomic distance analysis. blastp atlases were created to identify unique regions among the genomes most related to V. harveyi CAIM 1792; these regions included genes encoding glycosyltransferases, specific type restriction modification systems and a transcriptional regulator, LysR, reported to be involved in virulence, metabolism, quorum sensing and motility.
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Affiliation(s)
| | - Gary J Vora
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Baochuan Lin
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Pimlapas Leekitcharoenphon
- National Food Institute, Division for Epidemiology and Microbial Genomics, Technical University of Denmark, Kongens Lyngby, Denmark.,Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Dave Ussery
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark.,Comparative Genomics group, Biosciences Division, Oak Ridge National Labs, Oak Ridge, Tennessee, USA
| | - Lone Høj
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Bruno Gomez-Gil
- CIAD A.C., Mazatlán Unit for Aquaculture, Mazatlán, Sinaloa, Mexico
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29
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Rybniker J, Chen JM, Sala C, Hartkoorn RC, Vocat A, Benjak A, Boy-Röttger S, Zhang M, Székely R, Greff Z, Orfi L, Szabadkai I, Pató J, Kéri G, Cole ST. Anticytolytic screen identifies inhibitors of mycobacterial virulence protein secretion. Cell Host Microbe 2015; 16:538-48. [PMID: 25299337 DOI: 10.1016/j.chom.2014.09.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/20/2014] [Accepted: 09/17/2014] [Indexed: 11/18/2022]
Abstract
Mycobacterium tuberculosis (Mtb) requires protein secretion systems like ESX-1 for intracellular survival and virulence. The major virulence determinant and ESX-1 substrate, EsxA, arrests phagosome maturation and lyses cell membranes, resulting in tissue damage and necrosis that promotes pathogen spread. To identify inhibitors of Mtb protein secretion, we developed a fibroblast survival assay exploiting this phenotype and selected molecules that protect host cells from Mtb-induced lysis without being bactericidal in vitro. Hit compounds blocked EsxA secretion and promoted phagosome maturation in macrophages, thus reducing bacterial loads. Target identification studies led to the discovery of BTP15, a benzothiophene inhibitor of the histidine kinase MprB that indirectly regulates ESX-1, and BBH7, a benzyloxybenzylidene-hydrazine compound. BBH7 affects Mtb metal-ion homeostasis and revealed zinc stress as an activating signal for EsxA secretion. This screening approach extends the target spectrum of small molecule libraries and will help tackle the mounting problem of antibiotic-resistant mycobacteria.
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Affiliation(s)
- Jan Rybniker
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; 1(st) Department of Internal Medicine, University of Cologne, 50937 Cologne, Germany
| | - Jeffrey M Chen
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Claudia Sala
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Ruben C Hartkoorn
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Anthony Vocat
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Andrej Benjak
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Stefanie Boy-Röttger
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Ming Zhang
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Rita Székely
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Zoltán Greff
- Vichem Chemie Research Ltd., Herman Otto u. 15, 1022 Budapest, Hungary
| | - László Orfi
- Vichem Chemie Research Ltd., Herman Otto u. 15, 1022 Budapest, Hungary; Department of Pharmaceutical Chemistry, Semmelweis University, Hőgyes Endre u. 9, 1092 Budapest, Hungary
| | - István Szabadkai
- Vichem Chemie Research Ltd., Herman Otto u. 15, 1022 Budapest, Hungary
| | - János Pató
- Vichem Chemie Research Ltd., Herman Otto u. 15, 1022 Budapest, Hungary
| | - György Kéri
- Vichem Chemie Research Ltd., Herman Otto u. 15, 1022 Budapest, Hungary; MTA-SE Pathobiochemistry Research Group, Department of Medical Chemistry, Semmelweis University, 1094 Budapest, Hungary
| | - Stewart T Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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30
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Cui T, He ZG. Improved understanding of pathogenesis from protein interactions inMycobacteriumtuberculosis. Expert Rev Proteomics 2014; 11:745-55. [DOI: 10.1586/14789450.2014.971762] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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