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Fu X, Zuo X, Zhao X, Zhang H, Zhang C, Lu W. Characterization and designing of an SAM riboswitch to establish a high-throughput screening platform for SAM overproduction in Saccharomyces cerevisiae. Biotechnol Bioeng 2023; 120:3622-3637. [PMID: 37691180 DOI: 10.1002/bit.28551] [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: 05/31/2023] [Revised: 08/20/2023] [Accepted: 08/29/2023] [Indexed: 09/12/2023]
Abstract
S-adenosyl- l-methionine (SAM) is a high-value compound widely used in the treatment of various diseases. SAM can be produced through fermentation, but further enhancing the microbial production of SAM requires novel high-throughput screening methods for rapid detection and screening of mutant libraries. In this work, an SAM-OFF riboswitch capable of responding to the SAM concentration was obtained and a high-throughput platform for screening SAM overproducers was established. SAM synthase was engineered by semirational design and directed evolution, which resulted in the SAM2S203F,W164R,T251S,Y285F,S365R mutant with almost twice higher catalytic activity than the parental enzyme. The best mutant was then introduced into Saccharomyces cerevisiae BY4741, and the resulting strain BSM8 produced a sevenfold higher SAM titer in shake-flask fermentation, reaching 1.25 g L-1 . This work provides a reference for designing biosensors to dynamically detect metabolite concentrations for high-throughput screening and the construction of effective microbial cell factories.
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Affiliation(s)
- Xiaomeng Fu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xiaoru Zuo
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xiaomeng Zhao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Huizhi Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Chuanbo Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, China
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, China
| | - Wenyu Lu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, China
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, China
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Veeramachineni VM, Ubayawardhana ST, Murkin AS. Kinetic characterization of methylthio-d-ribose-1-phosphate isomerase. Methods Enzymol 2023; 685:279-318. [PMID: 37245905 DOI: 10.1016/bs.mie.2023.03.015] [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: 05/30/2023]
Abstract
Methylthio-d-ribose-1-phosphate (MTR1P) isomerase (MtnA) catalyzes the reversible isomerization of the aldose MTR1P into the ketose methylthio-d-ribulose 1-phosphate. It serves as a member of the methionine salvage pathway that many organisms require for recycling methylthio-d-adenosine, a byproduct of S-adenosylmethionine metabolism, back to methionine. MtnA is of mechanistic interest because unlike most other aldose-ketose isomerases, its substrate exists as an anomeric phosphate ester and therefore cannot equilibrate with a ring-opened aldehyde that is otherwise required to promote isomerization. To investigate the mechanism of MtnA, it is necessary to establish reliable methods for determining the concentration of MTR1P and to measure enzyme activity in a continuous assay. This chapter describes several such protocols needed to perform steady-state kinetics measurements. It additionally outlines the preparation of [32P]MTR1P, its use in radioactively labeling the enzyme, and the characterization of the resulting phosphoryl adduct.
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Affiliation(s)
- Vamsee M Veeramachineni
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Subashi T Ubayawardhana
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Andrew S Murkin
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, United States.
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Veeramachineni VM, Ubayawardhana ST, Murkin AS. Covalent Adduct Formation in Methylthio-d-ribose-1-phosphate Isomerase: Reaction Intermediate or Artifact? Biochemistry 2022; 61:1124-1135. [PMID: 35580612 DOI: 10.1021/acs.biochem.2c00142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methylthio-d-ribose-1-phosphate (MTR1P) isomerase (MtnA) functions in the methionine salvage pathway by converting the cyclic aldose MTR1P to its open-chain ketose isomer methylthio-d-ribulose 1-phosphate (MTRu1P). What is particularly challenging for this enzyme is that the substrate's phosphate ester prevents facile equilibration to an aldehyde, which in other aldose-ketose isomerases is known to activate the α-hydrogen for proton or hydride transfer between adjacent carbons. We speculated that MtnA could use covalent catalysis via a phosphorylated residue to permit isomerization by one of the canonical mechanisms, followed by phosphoryl transfer back to form the product. In apparent support of this mechanism, [32P]MTR1P was found by SDS-PAGE and gel-filtration chromatography to radiolabel the enzyme. Susceptibility of this adduct to strongly acidic and basic pH and nucleophilic agents is consistent with an acyl phosphate. C160S and D240N, mutants of two conserved active-site residues, however, exhibited no difference in radiolabeling despite a reduction in activity of ∼107, leading to the conclusion that phosphorylation is unrelated to catalysis. Unexpectedly, prolonged incubations with C160S revealed up to 30% accumulation of radioactivity, which was identified by 31P and 13C NMR to be the result of a second adduct─a hemiketal formed between Ser160 and the carbonyl of MTRu1P. These results are interpreted as indirect support for a mechanism involving transfer of the proton from C-2 to C-1 by Cys160.
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Affiliation(s)
- Vamsee M Veeramachineni
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, United States
| | - Subashi T Ubayawardhana
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, United States
| | - Andrew S Murkin
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, United States
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Biodesulfurization Induces Reprogramming of Sulfur Metabolism in Rhodococcus qingshengii IGTS8: Proteomics and Untargeted Metabolomics. Microbiol Spectr 2021; 9:e0069221. [PMID: 34468196 PMCID: PMC8557817 DOI: 10.1128/spectrum.00692-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Sulfur metabolism in fuel-biodesulfurizing bacteria and the underlying physiological adaptations are not understood, which has impeded the development of a commercially viable bioprocess for fuel desulfurization. To fill these knowledge gaps, we performed comparative proteomics and untargeted metabolomics in cultures of the biodesulfurization reference strain Rhodococcus qingshengii IGTS8 grown on either inorganic sulfate or the diesel-borne organosulfur compound dibenzothiophene as a sole sulfur source. Dibenzothiophene significantly altered the biosynthesis of many sulfur metabolism proteins and metabolites in a growth phase-dependent manner, which enabled us to reconstruct the first experimental model for sulfur metabolism in a fuel-biodesulfurizing bacterium. All key pathways related to assimilatory sulfur metabolism were represented in the sulfur proteome, including uptake of the sulfur sources, sulfur acquisition, and assimilatory sulfate reduction, in addition to biosynthesis of key sulfur-containing metabolites such as S-adenosylmethionine, coenzyme A, biotin, thiamin, molybdenum cofactor, mycothiol, and ergothioneine (low-molecular weight thiols). Fifty-two proteins exhibited significantly different abundance during at least one growth phase. Sixteen proteins were uniquely detected and 47 proteins were significantly more abundant in the dibenzothiophene culture during at least one growth phase. The sulfate-free dibenzothiophene-containing culture reacted to sulfate starvation by restricting sulfur assimilation, enforcing sulfur-sparing, and maintaining redox homeostasis. Biodesulfurization triggered alternative pathways for sulfur assimilation different from those operating in the inorganic sulfate culture. Sulfur metabolism reprogramming and metabolic switches in the dibenzothiophene culture were manifested in limiting sulfite reduction and biosynthesis of cysteine, while boosting the production of methionine via the cobalamin-independent pathway, as well as the biosynthesis of the redox buffers mycothiol and ergothioneine. The omics data underscore the key role of sulfur metabolism in shaping the biodesulfurization phenotype and highlight potential targets for improving the biodesulfurization catalytic activity via metabolic engineering. IMPORTANCE For many decades, research on biodesulfurization of fossil fuels was conducted amid a large gap in knowledge of sulfur metabolism and its regulation in fuel-biodesulfurizing bacteria, which has impeded the development of a commercially viable bioprocess. In addition, lack of understanding of biodesulfurization-associated metabolic and physiological adaptations prohibited the development of efficient biodesulfurizers. Our integrated omics-based findings reveal the assimilatory sulfur metabolism in the biodesulfurization reference strain Rhodococcus qingshengii IGTS8 and show how sulfur metabolism and oxidative stress response were remodeled and orchestrated to shape the biodesulfurization phenotype. Our findings not only explain the frequently encountered low catalytic activity of native fuel-biodesulfurizing bacteria but also uncover unprecedented potential targets in sulfur metabolism that could be exploited via metabolic engineering to boost the biodesulfurization catalytic activity, a prerequisite for commercial application.
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Tu Y, Kreinbring CA, Hill M, Liu C, Petsko GA, McCune CD, Berkowitz DB, Liu D, Ringe D. Crystal Structures of Cystathionine β-Synthase from Saccharomyces cerevisiae: One Enzymatic Step at a Time. Biochemistry 2018; 57:3134-3145. [PMID: 29630349 DOI: 10.1021/acs.biochem.8b00092] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cystathionine β-synthase (CBS) is a key regulator of sulfur amino acid metabolism, taking homocysteine from the methionine cycle to the biosynthesis of cysteine via the trans-sulfuration pathway. CBS is also a predominant source of H2S biogenesis. Roles for CBS have been reported for neuronal death pursuant to cerebral ischemia, promoting ovarian tumor growth, and maintaining drug-resistant phenotype by controlling redox behavior and regulating mitochondrial bioenergetics. The trans-sulfuration pathway is well-conserved in eukaryotes, but the analogous enzymes have different enzymatic behavior in different organisms. CBSs from the higher organisms contain a heme in an N-terminal domain. Though the presence of the heme, whose functions in CBSs have yet to be elucidated, is biochemically interesting, it hampers UV-vis absorption spectroscopy investigations of pyridoxal 5'-phosphate (PLP) species. CBS from Saccharomyces cerevisiae (yCBS) naturally lacks the heme-containing N-terminal domain, which makes it an ideal model for spectroscopic studies of the enzymological reaction catalyzed and allows structural studies of the basic yCBS catalytic core (yCBS-cc). Here we present the crystal structure of yCBS-cc, solved to 1.5 Å. Crystal structures of yCBS-cc in complex with enzymatic reaction intermediates have been captured, providing a structural basis for residues involved in catalysis. Finally, the structure of the yCBS-cc cofactor complex generated by incubation with an inhibitor shows apparent off-pathway chemistry not normally seen with CBS.
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Affiliation(s)
- Yupeng Tu
- Department of Biochemistry , Brandeis University , Waltham , Massachusetts 02454 , United States
| | - Cheryl A Kreinbring
- Department of Biochemistry , Brandeis University , Waltham , Massachusetts 02454 , United States
| | - Megan Hill
- Department of Biology , Brandeis University , Waltham , Massachusetts 02454 , United States
| | - Cynthia Liu
- Department of Biochemistry , Brandeis University , Waltham , Massachusetts 02454 , United States
| | - Gregory A Petsko
- Department of Neurology and Neuroscience , Weill Cornell Medical College , New York , New York 10021 , United States
| | - Christopher D McCune
- Department of Biochemistry , University of Nebraska , Lincoln , Nebraska 68588 , United States
| | - David B Berkowitz
- Department of Biochemistry , University of Nebraska , Lincoln , Nebraska 68588 , United States
| | - Dali Liu
- Department of Chemistry and Biochemistry , Loyola University Chicago , Chicago , Illinois 60660 , United States
| | - Dagmar Ringe
- Department of Biochemistry , Brandeis University , Waltham , Massachusetts 02454 , United States.,Department of Chemistry , Brandeis University , Waltham , Massachusetts 02454 , United States.,Rosenstiel Basic Medical Sciences Research Center , Brandeis University , Waltham , Massachusetts 02454 , United States
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Jeong DE, So Y, Park SY, Park SH, Choi SK. Random knock-in expression system for high yield production of heterologous protein in Bacillus subtilis. J Biotechnol 2017; 266:50-58. [PMID: 29229542 DOI: 10.1016/j.jbiotec.2017.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 12/07/2017] [Accepted: 12/07/2017] [Indexed: 10/18/2022]
Abstract
Chromosome-integrated recombinant protein expression in bacteria has advantages for the stable maintenance of genes without any use of antibiotics during large-scale fermentation. Even though different levels of gene expression were reported, depending upon their chromosomal position in bacterial species, only a limited number of integration sites have been used in B. subtilis. In this study, we randomly integrated the GFP and AprE expression cassettes into the B. subtilis genome to determine integration sites that can produce a high yield of heterologous protein expression. Our mariner transposon-based expression cassette integration system was able to find integration sites, which can produce up to 2.9-fold and 1.5-fold increased expression of intracellular GFP and extracellular AprE, respectively, compared to the common integration site amyE. By analyzing the location of integration sites, we observed an adjacent promoter effect, gene dosage effect, and gene knock-out effect all complexly contributing to the increased level of integrated gene expression. Besides obtaining a high yield of heterologous protein expression, our system can also provide a wide-range of expression to expand the systematic application for steady-state metabolic protein production.
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Affiliation(s)
- Da-Eun Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Younju So
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Soo-Young Park
- Genofocus Inc., 65 Techno 1-ro, Yuseong-gu, Daejeon 34014, Republic of Korea
| | - Seung-Hwan Park
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Soo-Keun Choi
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.
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Sannino F, Parrilli E, Apuzzo GA, de Pascale D, Tedesco P, Maida I, Perrin E, Fondi M, Fani R, Marino G, Tutino ML. Pseudoalteromonas haloplanktis produces methylamine, a volatile compound active against Burkholderia cepacia complex strains. N Biotechnol 2016; 35:13-18. [PMID: 27989956 DOI: 10.1016/j.nbt.2016.10.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 10/18/2016] [Accepted: 10/24/2016] [Indexed: 11/24/2022]
Abstract
The Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125 has been reported to produce several Volatile Organic Compounds (VOCs), which are able to inhibit the growth of Burkholderia cepacia complex (Bcc) strains, opportunistic pathogens responsible for the infection of immune-compromised patients. However, no specific antibacterial VOCs have been identified to date. The purpose of the present study was to identify specific VOCs that contribute to Bcc inhibition by the Antarctic strain. When grown on defined medium containing D-gluconate and L-glutamate as carbon, nitrogen and energy sources, P. haloplanktis TAC125 is unable to inhibit the growth of Bcc strains. However, single addition of several amino acids to the defined medium restores the P. haloplanktis TAC125 inhibition ability. With the aim of identifying specific volatile compound/s responsible for Bcc inhibition, we set up an apparatus for VOC capture, accumulation, and storage. P. haloplanktis TAC125 was grown in an automatic fermenter which was connected to a cooling system to condense VOCs present in the exhaust air outlet. Upon addition of methionine to the growth medium, the VOC methylamine was produced by P. haloplanktis TAC125. Methylamine was found to inhibit the growth of several Bcc strains in a dose-dependent way. Although it was reported that P. haloplanktis TAC125 produces VOCs endowed with antimicrobial activity, this is the first demonstration that methylamine probably contributes to the anti-Bcc activity of P. haloplanktis TAC125 VOCs.
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Affiliation(s)
- Filomena Sannino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126 Napoli, Italy.
| | - Ermenegilda Parrilli
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126 Napoli, Italy.
| | - Gennaro Antonio Apuzzo
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126 Napoli, Italy.
| | - Donatella de Pascale
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 111, 80126 Naples, Italy.
| | - Pietro Tedesco
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 111, 80126 Naples, Italy.
| | - Isabel Maida
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-50018, Sesto F.no, Florence, Italy.
| | - Elena Perrin
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-50018, Sesto F.no, Florence, Italy.
| | - Marco Fondi
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-50018, Sesto F.no, Florence, Italy.
| | - Renato Fani
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-50018, Sesto F.no, Florence, Italy.
| | - Gennaro Marino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126 Napoli, Italy.
| | - Maria Luisa Tutino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126 Napoli, Italy.
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A dual control mechanism synchronizes riboflavin and sulphur metabolism in Bacillus subtilis. Proc Natl Acad Sci U S A 2015; 112:14054-9. [PMID: 26494285 DOI: 10.1073/pnas.1515024112] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Flavin mononucleotide (FMN) riboswitches are genetic elements, which in many bacteria control genes responsible for biosynthesis and/or transport of riboflavin (rib genes). Cytoplasmic riboflavin is rapidly and almost completely converted to FMN by flavokinases. When cytoplasmic levels of FMN are sufficient ("high levels"), FMN binding to FMN riboswitches leads to a reduction of rib gene expression. We report here that the protein RibR counteracts the FMN-induced "turn-off" activities of both FMN riboswitches in Bacillus subtilis, allowing rib gene expression even in the presence of high levels of FMN. The reason for this secondary metabolic control by RibR is to couple sulfur metabolism with riboflavin metabolism.
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Jiang XW, Wang J, Gao Y, Chan LL, Lam PKS, Gu JD. Relationship of proteomic variation and toxin synthesis in the dinoflagellate Alexandrium tamarense CI01 under phosphorus and inorganic nitrogen limitation. ECOTOXICOLOGY (LONDON, ENGLAND) 2015; 24:1744-1753. [PMID: 26239440 DOI: 10.1007/s10646-015-1513-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/22/2015] [Indexed: 06/04/2023]
Abstract
Paralytic shellfish toxins (PSTs) are originated from cyanobacteria and dinoflagellates, including Alexandrium tamarense, the common dinoflagellate species. In this study, a toxic dinoflagellate strain of A. tamarense CI01 was selected for studying the PSTs' concentration and the related protein variation during the whole cell cycle under different nutrient conditions. High-performance liquid chromatography, 2-D DIGE and Western blotting were used collectively for protein profiling and identification. Results showed that the toxin content was suppressed under nitrogen limiting condition, but enhanced in phosphorous limiting medium. Based on the results of proteomics analysis, 7 proteins were discovered to be related to the PSTs biosynthesis of A. tamarense CI01, including S-adenosylhomocysteine hydrolase, ornithine cyclodeaminase, argininosuccinate synthase, methyluridine methyltransferase cystine ABC transporter, phosphoserine phosphatase, argininosuccinate synthase and acyl-CoA dehydrogenase, which corresponds to the metabolism of the methionine, cysteine, ornithine, arginine and proline. Moreover, some photosynthesis relating proteins also increased their expression during PST synthesis period in A. tamarense CI01, such as phosphoenolpyruvate carboxylase, chloroplast phosphoglycerate kinase, peridinin-chlorophyll α-binding protein, Mg(2+) transporter protein and chloroplast phosphoglycerate kinase. The above findings are in support of our hypothesis that these proteins are involved in toxin biosynthesis of A. tamarense CI01, but cause-and-effect mechanisms need to be investigated in further studies.
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Affiliation(s)
- Xi-Wen Jiang
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, People's Republic of China
| | - Jing Wang
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
- College of Marine Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, People's Republic of China
| | - Yue Gao
- State Key Laboratory of Marine Environmental Science/Environmental Science Research Center, Xiamen University, 182 Daxue Road, Xiamen, 361005, China
| | - Leo Lai Chan
- Shenzhen Key Laboratory for the Sustainable Use of Marine Biodiversity, Research Centre for the Oceans and Human Heath, City University OF HONG KONG Shenzhen Research Institute, Shenzhen, People's Republic of China
- State Key Laboratory in Marine Pollution and Department of Biomedical Sciences, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, People's Republic of China
| | - Paul Kwan Sing Lam
- State Key Laboratory in Marine Pollution and Department of Biomedical Sciences, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, People's Republic of China
- State Key Laboratory in Marine Pollution and Department of Chemistry and Biology, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, People's Republic of China
| | - Ji-Dong Gu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China.
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Chan CM, Danchin A, Marlière P, Sekowska A. Paralogous metabolism: S-alkyl-cysteine degradation in Bacillus subtilis. Environ Microbiol 2013; 16:101-17. [PMID: 23944997 DOI: 10.1111/1462-2920.12210] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 07/10/2013] [Indexed: 11/29/2022]
Abstract
Metabolism is prone to produce analogs of essential building blocks in the cell (here named paralogous metabolism). The variants result from lack of absolute accuracy in enzyme-templated reactions as well as from molecular aging. If variants were left to accumulate, the earth would be covered by chemical waste. The way bacteria cope with this situation is essentially unexplored. To gain a comprehensive understanding of Bacillus subtilis sulphur paralogous metabolism, we used expression profiling with DNA arrays to investigate the changes in gene expression in the presence of S-methyl-cysteine (SMeC) and its close analog, methionine, as sole sulphur source. Altogether, more than 200 genes whose relative strength of induction was significantly different depending on the sulphur source used were identified. This allowed us to pinpoint operon ytmItcyJKLMNytmO_ytnIJ_rbfK_ytnLM as controlling the pathway cycling SMeC directly to cysteine, without requiring sulphur oxygenation. Combining genetic and physiological experiments, we deciphered the corresponding pathway that begins with protection of the metabolite by acetylation. Oxygenation of the methyl group then follows, and after deprotection (deacetylation), N-formyl cysteine is produced. This molecule is deformylated by the second deformylase present in B. subtilis DefB, yielding cysteine. This pathway appears to be present in plant-associated microbes.
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Affiliation(s)
- Che-Man Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam Road, Hong Kong
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Huillet E, Tempelaars MH, André-Leroux G, Wanapaisan P, Bridoux L, Makhzami S, Panbangred W, Martin-Verstraete I, Abee T, Lereclus D. PlcRa, a new quorum-sensing regulator from Bacillus cereus, plays a role in oxidative stress responses and cysteine metabolism in stationary phase. PLoS One 2012; 7:e51047. [PMID: 23239999 PMCID: PMC3519770 DOI: 10.1371/journal.pone.0051047] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 10/29/2012] [Indexed: 12/31/2022] Open
Abstract
We characterized a new quorum-sensing regulator, PlcRa, which is present in various members of the B. cereus group and identified a signaling heptapeptide for PlcRa activity: PapRa7. We demonstrated that PlcRa is a 3D structural paralog of PlcR using sequence analysis and homology modeling. A comparison of the transcriptomes at the onset of stationary phase of a ΔplcRa mutant and the wild-type B. cereus ATCC 14579 strain showed that 68 genes were upregulated and 49 genes were downregulated in the ΔplcRa mutant strain (>3-fold change). Genes involved in the cysteine metabolism (putative CymR regulon) were downregulated in the ΔplcRa mutant strain. We focused on the gene with the largest difference in expression level between the two conditions, which encoded -AbrB2- a new regulator of the AbrB family. We demonstrated that purified PlcRa bound specifically to the abrB2 promoter in the presence of synthetic PapRa7, in an electrophoretic mobility shift assay. We further showed that the AbrB2 regulator controlled the expression of the yrrT operon involved in methionine to cysteine conversion. We found that the ΔplcRa mutant strain was more sensitive to hydrogen peroxide- and disulfide-induced stresses than the wild type. When cystine was added to the culture of the ΔplcRa mutant, challenged with hydrogen peroxide, growth inhibition was abolished. In conclusion, we identified a new RNPP transcriptional regulator in B. cereus that activated the oxidative stress response and cysteine metabolism in transition state cells.
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Affiliation(s)
- Eugénie Huillet
- INRA, UMR1319 Micalis, Génétique microbienne et Environnement, Guyancourt, France
- * E-mail: (EH); (DL)
| | - Marcel H. Tempelaars
- Wageningen University, Laboratory of Food Microbiology, Wageningen, The Netherlands
| | | | - Pagakrong Wanapaisan
- INRA, UMR1319 Micalis, Génétique microbienne et Environnement, Guyancourt, France
- Mahidol University, Department of Biotechnology, Faculty of Science, Bangkok, Thailand
| | - Ludovic Bridoux
- INRA, UMR1319 Micalis, Génétique microbienne et Environnement, Guyancourt, France
| | | | - Watanalai Panbangred
- Mahidol University, Department of Biotechnology, Faculty of Science, Bangkok, Thailand
| | - Isabelle Martin-Verstraete
- Institut Pasteur, Laboratoire de Pathogénèse des Bactéries Anaérobies, Paris, France
- Univ. Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Tjakko Abee
- Wageningen University, Laboratory of Food Microbiology, Wageningen, The Netherlands
| | - Didier Lereclus
- INRA, UMR1319 Micalis, Génétique microbienne et Environnement, Guyancourt, France
- * E-mail: (EH); (DL)
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12
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Glekas GD, Mulhern BJ, Kroc A, Duelfer KA, Lei V, Rao CV, Ordal GW. The Bacillus subtilis chemoreceptor McpC senses multiple ligands using two discrete mechanisms. J Biol Chem 2012; 287:39412-8. [PMID: 23038252 DOI: 10.1074/jbc.m112.413518] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacillus subtilis can perform chemotaxis toward all 20 L-amino acids normally found in proteins. Loss of a single chemoreceptor, McpC, was previously found to reduce chemotaxis to 19 of these amino acids. In this study, we investigated the amino acid-sensing mechanism of McpC. We show that McpC alone can support chemotaxis to 17 of these amino acids to varying degrees. Eleven amino acids were found to directly bind the amino-terminal sensing domain of McpC in vitro. Sequence analysis indicates that the McpC sensing domain exhibits a dual Per-Arnt-Sim (PAS) domain structure. Using this structure as a guide, we were able to isolate mutants that suggest that four amino acids (arginine, glutamine, lysine, and methionine) are sensed by an indirect mechanism. We identified four candidate binding lipoproteins associated with amino acid transporters that may function in indirect sensing: ArtP, GlnH, MetQ, and YckB. ArtP was found to bind arginine and lysine; GlnH, glutamine; MetQ, methionine; and YckB, tryptophan. In addition, we found that ArtP, MetQ, and YckB bind the sensing domain of McpC, suggesting that the three participate in the indirect sensing of arginine, lysine, methionine, and possibly tryptophan as well. Taken together, these results further our understanding of amino acid chemotaxis in B. subtilis and gain insight into how a single chemoreceptor is able to sense many amino acids.
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Affiliation(s)
- George D Glekas
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA
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13
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Wang T, Leyh TS. Three-stage assembly of the cysteine synthase complex from Escherichia coli. J Biol Chem 2011; 287:4360-7. [PMID: 22179612 DOI: 10.1074/jbc.m111.288423] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Control of sulfur metabolism in plants and bacteria is linked, in significant measure, to the behavior of the cysteine synthase complex (CSC). The complex is comprised of the two enzymes that catalyze the final steps in cysteine biosynthesis: serine O-acetyltransferase (SAT, EC 2.3.1.30), which produces O-acetyl-L-serine, and O-acetyl-L-serine sulfhydrylase (OASS, EC 2.5.1.47), which converts it to cysteine. SAT (a dimer of homotrimers) binds a maximum of two molecules of OASS (a dimer) in an interaction believed to involve docking of the C terminus from a protomer in an SAT trimer into an OASS active site. This interaction inactivates OASS catalysis and prevents further binding to the trimer; thus, the system exhibits a contact-induced inactivation of half of each biomolecule. To better understand the dynamics and energetics that underlie formation of the CSC, the interactions of OASS and SAT from Escherichia coli were studied at equilibrium and in the pre-steady state. Using an experimental strategy that initiates dissociation of the CSC at different points in the CSC-forming reaction, three stable forms of the complex were identified. Comparison of the binding behaviors of SAT and its C-terminal peptide supports a mechanism in which SAT interacts with OASS in a non-allosteric interaction involving its C terminus. This early docking event appears to fasten the proteins in close proximity and thus prepares the system to engage in a series of subsequent, energetically favorable isomerizations that inactivate OASS and produce the fully isomerized CSC.
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Affiliation(s)
- Ting Wang
- Department of Microbiology and Immunology, The Albert Einstein College of Medicine, Bronx, New York 10461, USA
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14
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GILBERT JAMESDJ, FAGAN WILLIAMF. Contrasting mechanisms of proteomic nitrogen thrift in Prochlorococcus. Mol Ecol 2010; 20:92-104. [DOI: 10.1111/j.1365-294x.2010.04914.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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15
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Exploring the low-pressure growth limit: evolution of Bacillus subtilis in the laboratory to enhanced growth at 5 kilopascals. Appl Environ Microbiol 2010; 76:7559-65. [PMID: 20889789 DOI: 10.1128/aem.01126-10] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Growth of Bacillus subtilis cells, normally adapted at Earth-normal atmospheric pressure (∼101.3 kPa), was progressively inhibited by lowering of pressure in liquid LB medium until growth essentially ceased at 2.5 kPa. Growth inhibition was immediately reversible upon return to 101.3 kPa, albeit at a slower rate. A population of B. subtilis cells was cultivated at the near-inhibitory pressure of 5 kPa for 1,000 generations, where a stepwise increase in growth was observed, as measured by the turbidity of 24-h cultures. An isolate from the 1,000-generation population was obtained that showed an increase in fitness at 5 kPa when compared to the ancestral strain or a strain obtained from a parallel population that evolved for 1,000 generations at 101.3 kPa. The results from this preliminary study have implications for understanding the ability of terrestrial microbes to grow in low-pressure environments such as Mars.
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16
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Three paralogous LysR-type transcriptional regulators control sulfur amino acid supply in Streptococcus mutans. J Bacteriol 2010; 192:3464-73. [PMID: 20418399 DOI: 10.1128/jb.00119-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome of Streptococcus mutans encodes 4 LysR-type transcriptional regulators (LTTRs), three of which, MetR, CysR (cysteine synthesis regulator), and HomR (homocysteine synthesis regulator), are phylogenetically related. MetR was previously shown to control methionine metabolic gene expression. Functional analysis of CysR and HomR was carried out by phenotypical studies and transcriptional analysis. CysR is required to activate the transcription of cysK encoding the cysteine biosynthesis enzyme, tcyABC and gshT genes encoding cysteine and glutathione transporter systems, and homR. HomR activates the transcription of metBC encoding methionine biosynthesis enzymes, tcyDEFGH involved in cysteine transport, and still uncharacterized thiosulfate assimilation genes. Control of HomR by CysR provides evidence of a cascade regulation for sulfur amino acid metabolism in S. mutans. Two conserved motifs were found in the promoter regions of CysR and HomR target genes, suggesting their role in the regulator binding recognition site. Both CysR and HomR require O-acetylserine to activate transcription. A global sulfur amino acid supply gene regulatory pathway is proposed for S. mutans, including the cascade regulation consequent to transcriptional activation of HomR by CysR. Phylogenetic study of MetR, CysR, and HomR homologues and comparison of their potential regulatory patterns among the Streptococcaceae suggest their rapid evolution.
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17
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Kocabaş P, Çalık P, Çalık G, Özdamar TH. Microarray Studies inBacillus subtilis. Biotechnol J 2009; 4:1012-27. [DOI: 10.1002/biot.200800330] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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18
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Transcriptional regulation of Corynebacterium glutamicum methionine biosynthesis genes in response to methionine supplementation under oxygen deprivation. Appl Microbiol Biotechnol 2008; 81:505-13. [DOI: 10.1007/s00253-008-1694-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Revised: 08/27/2008] [Accepted: 09/01/2008] [Indexed: 10/21/2022]
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19
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Tanous C, Soutourina O, Raynal B, Hullo MF, Mervelet P, Gilles AM, Noirot P, Danchin A, England P, Martin-Verstraete I. The CymR regulator in complex with the enzyme CysK controls cysteine metabolism in Bacillus subtilis. J Biol Chem 2008; 283:35551-60. [PMID: 18974048 DOI: 10.1074/jbc.m805951200] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Several enzymes have evolved as sensors in signal transduction pathways to control gene expression, thereby allowing bacteria to adapt efficiently to environmental changes. We recently identified the master regulator of cysteine metabolism in Bacillus subtilis, CymR, which belongs to the poorly characterized Rrf2 family of regulators. We now report that the signal transduction mechanism controlling CymR activity in response to cysteine availability involves the formation of a stable complex with CysK, a key enzyme for cysteine biosynthesis. We carried out a comprehensive quantitative characterization of this regulator-enzyme interaction by surface plasmon resonance and analytical ultracentrifugation. We also showed that O-acetylserine plays a dual role as a substrate of CysK and as an effector modulating the CymR-CysK complex formation. The ability of B. subtilis CysK to bind to CymR appears to be correlated to the loss of its capacity to form a cysteine synthase complex with CysE. We propose an original model, supported by the determination of the intracellular concentrations of the different partners, by which CysK positively regulates CymR in sensing the bacterial cysteine pool.
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Affiliation(s)
- Catherine Tanous
- Institut Pasteur, UnitédeGénétique des Génomes Bactériens, Plate-forme de Biophysique des Macromolécules et de leurs Interactions, 75724 Paris cedex 15, France
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20
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Mostertz J, Hochgräfe F, Jürgen B, Schweder T, Hecker M. The role of thioredoxin TrxA in Bacillus subtilis: a proteomics and transcriptomics approach. Proteomics 2008; 8:2676-90. [PMID: 18601268 DOI: 10.1002/pmic.200701015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Thiol-disulfide oxidoreductases of the thioredoxin superfamily are crucial for maintaining the thiol redox state in living organisms. For the bacterium Bacillus subtilis thioredoxin A (TrxA) was described as the product of an essential gene indicating a key role during growth. By means of mRNA profiling Smits et al. (J. Bacteriol. 2005, 187, 3921-3930) suggested a critical function for TrxA in sulfur utilization during stationary phase. We extended the analysis of TrxA to exponential growth and characterized a trxA conditional mutant by proteome analysis complemented by transcriptomics. After TrxA-depletion, the growth rate was dramatically decreased. The cells responded at mRNA and protein level by the increased expression of genes involved in the utilization of sulfur, which represents the most obvious response as visualized by gel-based proteomics. Furthermore, several genes of the antioxidant response were found at higher expression levels after TrxA-depletion. When sulfate was replaced by thiosulfate or methionine as sulfur source, the growth inhibition was abolished. In the presence of thiosulfate but in the absence of TrxA, the induction of the sulfur limitation response and the oxidative stress response was not observed. Our results show that the global change of gene expression is primarily caused by the interruption of the sulfate utilization after TrxA depletion. Thus, its function in sulfate assimilation renders TrxA an essential protein in growing B. subtilis cells.
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Affiliation(s)
- Jörg Mostertz
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany.
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21
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Wang JX, Breaker RR. Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine. Biochem Cell Biol 2008; 86:157-68. [PMID: 18443629 DOI: 10.1139/o08-008] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Numerous riboswitches have been discovered that specifically recognize metabolites and modulate gene expression. Each riboswitch class is defined either by the consensus sequence and structural features of its metabolite-binding aptamer domain, or by the distinct metabolite that the aptamer recognizes. Several distinct classes of riboswitches that respond to S-adenosylmethionine (SAM or AdoMet) have been discovered. Representatives of these classes have been shown to strongly discriminate against S-adenosylhomocystenine (SAH or AdoHcy), which is the metabolic byproduct produced when SAM is used as a cofactor for methylation reactions. However, a distinct class of riboswitches that selectively binds SAH, and strongly discriminates against SAM, also has been discovered. Herein we compare the features of SAM and SAH riboswitches, which help showcase the enormous structural diversity that RNA can harness to form precision genetic switches for compounds that are critical for fundamental metabolic processes.
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Affiliation(s)
- Joy Xin Wang
- Department of Molecular, Cellular and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
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22
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Metabolism of Methionine in Plants and Phototrophic Bacteria. SULFUR METABOLISM IN PHOTOTROPHIC ORGANISMS 2008. [DOI: 10.1007/978-1-4020-6863-8_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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23
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Zolotarev AS, Unnikrishnan M, Shmukler BE, Clark JS, Vandorpe DH, Grigorieff N, Rubin EJ, Alper SL. Increased sulfate uptake by E. coli overexpressing the SLC26-related SulP protein Rv1739c from Mycobacterium tuberculosis. Comp Biochem Physiol A Mol Integr Physiol 2007; 149:255-66. [PMID: 18255326 DOI: 10.1016/j.cbpa.2007.12.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Revised: 12/13/2007] [Accepted: 12/14/2007] [Indexed: 12/21/2022]
Abstract
Growth and virulence of mycobacteria requires sulfur uptake. The Mycobacterium tuberculosis genome contains, in addition to the ABC sulfate permease cysTWA, three SLC26-related SulP genes of unknown function. We report that induction of Rv1739c expression in E. coli increased bacterial uptake of sulfate, but not Cl(-), formate, or oxalate. Uptake was time-dependent, maximal at pH 6.0, and exhibited a K(1/2) for sulfate of 4.0 muM. Na(+)-independent sulfate uptake was not reduced by bicarbonate, nitrate, or phosphate, but was inhibited by sulfite, selenate, thiosulfate, N-ethylmaleimide and carbonyl cyanide 3-chloro-phenylhydrazone. Sulfate uptake was also increased by overexpression of the Rv1739c transmembrane domain, but not of the cytoplasmic C-terminal STAS domain. Mutation to serine of the three cysteine residues of Rv1739c did not affect magnitude, pH-dependence, or pharmacology of sulfate uptake. Expression of Rv1739c in a M. bovis BCG strain lacking the ABC sulfate permease subunit CysA could not complement sulfate auxotrophy. Moreover, inducible expression of Rv1739c in an E. coli strain lacking CysA did not increase sulfate uptake by intact cells. Our data show that facilitation of bacterial sulfate uptake by Rv1739c requires CysA and its associated sulfate permease activity, and suggest that Rv1739c may be a CysTWA-dependent sulfate transporter.
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Affiliation(s)
- Alexander S Zolotarev
- Molecular and Vascular Medicine and Renal Divisions, Beth Israel Deaconess Medical Center, USA
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24
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Natural variability in S-adenosylmethionine (SAM)-dependent riboswitches: S-box elements in bacillus subtilis exhibit differential sensitivity to SAM In vivo and in vitro. J Bacteriol 2007; 190:823-33. [PMID: 18039762 DOI: 10.1128/jb.01034-07] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Riboswitches are regulatory systems in which changes in structural elements in the 5' region of the nascent RNA transcript (the "leader region") control expression of the downstream coding sequence in response to a regulatory signal in the absence of a trans-acting protein factor. The S-box riboswitch, found primarily in low-G+C gram-positive bacteria, is the paradigm for riboswitches that sense S-adenosylmethionine (SAM). Genes in the S-box family are involved in methionine metabolism, and their expression is induced in response to starvation for methionine. S-box genes exhibit conserved primary sequence and secondary structural elements in their leader regions. We previously demonstrated that SAM binds directly to S-box leader RNA, causing a structural rearrangement that results in premature termination of transcription at S-box leader region terminators. S-box genes have a variety of physiological roles, and natural variability in S-box structure and regulatory response could provide additional insight into the role of conserved S-box leader elements in SAM-directed transcription termination. In the current study, in vivo and in vitro assays were employed to analyze the differential regulation of S-box genes in response to SAM. A wide range of responses to SAM were observed for the 11 S-box-regulated transcriptional units in Bacillus subtilis, demonstrating that S-box riboswitches can be calibrated to different physiological requirements.
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25
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Tralau T, Vuilleumier S, Thibault C, Campbell BJ, Hart CA, Kertesz MA. Transcriptomic analysis of the sulfate starvation response of Pseudomonas aeruginosa. J Bacteriol 2007; 189:6743-50. [PMID: 17675390 PMCID: PMC2045191 DOI: 10.1128/jb.00889-07] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes a number of infections in humans, but is best known for its association with cystic fibrosis. It is able to use a wide range of sulfur compounds as sources of sulfur for growth. Gene expression in response to changes in sulfur supply was studied in P. aeruginosa E601, a cystic fibrosis isolate that displays mucin sulfatase activity, and in P. aeruginosa PAO1. A large family of genes was found to be upregulated by sulfate limitation in both isolates, encoding sulfatases and sulfonatases, transport systems, oxidative stress proteins, and a sulfate-regulated TonB/ExbBD complex. These genes were localized in five distinct islands on the genome and encoded proteins with a significantly reduced content of cysteine and methionine. Growth of P. aeruginosa E601 with mucin as the sulfur source led not only to a sulfate starvation response but also to induction of genes involved with type III secretion systems.
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Affiliation(s)
- Tewes Tralau
- Faculty of Life Sciences, University of Manchester, Michael Smith Bldg., Oxford Rd., Manchester M13 9PT, England
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26
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Sperandio B, Gautier C, McGovern S, Ehrlich DS, Renault P, Martin-Verstraete I, Guédon E. Control of methionine synthesis and uptake by MetR and homocysteine in Streptococcus mutans. J Bacteriol 2007; 189:7032-44. [PMID: 17675375 PMCID: PMC2045202 DOI: 10.1128/jb.00703-07] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
MetR (formerly Smu.1225), a regulator of the LysR family, controls key genes for methionine supply in Streptococcus mutans. An S. mutans metR mutant is unable to transport l-methionine and to grow in the absence of this amino acid. Accordingly, MetR activates transcription by binding to the promoter regions of two gene clusters and smu.1487, whose products are involved in methionine biosynthesis (MetEF and Smu.1487) and uptake (AtmBDE). Transcriptional activation by MetR requires the presence of a 17-bp palindromic sequence, the Met box. Base substitutions in the Met box hinder the formation of a MetR-DNA complex and abolish MetR-dependent activation, showing that Met boxes correspond to MetR recognition sites. Activation by MetR occurs in methionine-depleted medium and is rapidly triggered under nonactivating conditions by the addition of homocysteine. This intermediate of methionine biosynthesis increases the affinity of MetR for DNA in vitro and appears to be the MetR coeffector in vivo. Homocysteine plays a crucial role in methionine metabolic gene regulation by controlling MetR activity. A similar mechanism of homocysteine- and MetR-dependent control of methionine biosynthetic genes operates in S. thermophilus. These data suggest a common mechanism for the regulation of the methionine supply in streptococci. However, some streptococcal species are unable to synthesize the homocysteine coeffector. This intriguing feature is discussed in the light of comparative genomics and streptococcal ecology.
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Affiliation(s)
- Brice Sperandio
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, 78352 Jouy-en-Josas Cedex, France
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27
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Oh YK, Palsson BO, Park SM, Schilling CH, Mahadevan R. Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J Biol Chem 2007; 282:28791-28799. [PMID: 17573341 DOI: 10.1074/jbc.m703759200] [Citation(s) in RCA: 306] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In this report, a genome-scale reconstruction of Bacillus subtilis metabolism and its iterative development based on the combination of genomic, biochemical, and physiological information and high-throughput phenotyping experiments is presented. The initial reconstruction was converted into an in silico model and expanded in a four-step iterative fashion. First, network gap analysis was used to identify 48 missing reactions that are needed for growth but were not found in the genome annotation. Second, the computed growth rates under aerobic conditions were compared with high-throughput phenotypic screen data, and the initial in silico model could predict the outcomes qualitatively in 140 of 271 cases considered. Detailed analysis of the incorrect predictions resulted in the addition of 75 reactions to the initial reconstruction, and 200 of 271 cases were correctly computed. Third, in silico computations of the growth phenotypes of knock-out strains were found to be consistent with experimental observations in 720 of 766 cases evaluated. Fourth, the integrated analysis of the large-scale substrate utilization and gene essentiality data with the genome-scale metabolic model revealed the requirement of 80 specific enzymes (transport, 53; intracellular reactions, 27) that were not in the genome annotation. Subsequent sequence analysis resulted in the identification of genes that could be putatively assigned to 13 intracellular enzymes. The final reconstruction accounted for 844 open reading frames and consisted of 1020 metabolic reactions and 988 metabolites. Hence, the in silico model can be used to obtain experimentally verifiable hypothesis on the metabolic functions of various genes.
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Affiliation(s)
- You-Kwan Oh
- Department of Bioengineering, University of California at San Diego, La Jolla, California 92093-0412 and
| | - Bernhard O Palsson
- Department of Bioengineering, University of California at San Diego, La Jolla, California 92093-0412 and
| | - Sung M Park
- Genomatica, Inc., San Diego, California 92121
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28
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Cholet O, Hénaut A, Bonnarme P. Transcriptional analysis of L-methionine catabolism in Brevibacterium linens ATCC9175. Appl Microbiol Biotechnol 2007; 74:1320-32. [PMID: 17225104 DOI: 10.1007/s00253-006-0772-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2006] [Revised: 11/17/2006] [Accepted: 11/17/2006] [Indexed: 11/28/2022]
Abstract
The expression of genes possibly involved in L-methionine and lactate catabolic pathways were performed in Brevibacterium linens (ATCC9175) in the presence or absence of added L-methionine. The expression of 27 genes of 39 selected genes differed significantly in L-methionine-enriched cultures. The expression of the gene encoding L-methionine gamma-lyase (MGL) is high in L-methionine-enriched cultures and is accompanied by a dramatic increase in volatile sulfur compounds (VSC) biosynthesis. Several genes encoding alpha-ketoacid dehydrogenase and one gene encoding an acetolactate synthase were also up-regulated by L-methionine, and are probably involved in the catabolism of alpha-ketobutyrate, the primary degradation product of L-methionine to methanethiol. Gene expression profiles together with biochemical data were used to propose catabolic pathways for L-methionine in B. linens and their possible regulation by L-methionine.
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Affiliation(s)
- Orianne Cholet
- Institut National de la Recherche Agronomique, UMR Génie et Microbiologie des Procédés Alimentaires, CBAI, 78850 Thiverval-Grignon, France
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29
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Hullo MF, Auger S, Soutourina O, Barzu O, Yvon M, Danchin A, Martin-Verstraete I. Conversion of methionine to cysteine in Bacillus subtilis and its regulation. J Bacteriol 2006; 189:187-97. [PMID: 17056751 PMCID: PMC1797209 DOI: 10.1128/jb.01273-06] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Bacillus subtilis can use methionine as the sole sulfur source, indicating an efficient conversion of methionine to cysteine. To characterize this pathway, the enzymatic activities of CysK, YrhA and YrhB purified in Escherichia coli were tested. Both CysK and YrhA have an O-acetylserine-thiol-lyase activity, but YrhA was 75-fold less active than CysK. An atypical cystathionine beta-synthase activity using O-acetylserine and homocysteine as substrates was observed for YrhA but not for CysK. The YrhB protein had both cystathionine lyase and homocysteine gamma-lyase activities in vitro. Due to their activity, we propose that YrhA and YrhB should be renamed MccA and MccB for methionine-to-cysteine conversion. Mutants inactivated for cysK or yrhB grew similarly to the wild-type strain in the presence of methionine. In contrast, the growth of an DeltayrhA mutant or a luxS mutant, inactivated for the S-ribosyl-homocysteinase step of the S-adenosylmethionine recycling pathway, was strongly reduced with methionine, whereas a DeltayrhA DeltacysK or cysE mutant did not grow at all under the same conditions. The yrhB and yrhA genes form an operon together with yrrT, mtnN, and yrhC. The expression of the yrrT operon was repressed in the presence of sulfate or cysteine. Both purified CysK and CymR, the global repressor of cysteine metabolism, were required to observe the formation of a protein-DNA complex with the yrrT promoter region in gel-shift experiments. The addition of O-acetyl-serine prevented the formation of this protein-DNA complex.
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Affiliation(s)
- Marie-Françoise Hullo
- Unité de Génétique des Génomes Bactériens, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
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30
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Choi SY, Reyes D, Leelakriangsak M, Zuber P. The global regulator Spx functions in the control of organosulfur metabolism in Bacillus subtilis. J Bacteriol 2006; 188:5741-51. [PMID: 16885442 PMCID: PMC1540065 DOI: 10.1128/jb.00443-06] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Spx is a global transcriptional regulator of the oxidative stress response in Bacillus subtilis. Its target is RNA polymerase, where it contacts the alpha subunit C-terminal domain. Recently, evidence was presented that Spx participates in sulfate-dependent control of organosulfur utilization operons, including the ytmI, yxeI, ssu, and yrrT operons. The yrrT operon includes the genes that function in cysteine synthesis from S-adenosylmethionine through intermediates S-adenosylhomocysteine, ribosylhomocysteine, homocysteine, and cystathionine. These operons are also negatively controlled by CymR, the repressor of cysteine biosynthesis operons. All of the operons are repressed in media containing cysteine or sulfate but are derepressed in medium containing the alternative sulfur source, methionine. Spx was found to negatively control the expression of these operons in sulfate medium, in part, by stimulating the expression of the cymR gene. In addition, microarray analysis, monitoring of yrrT-lacZ fusion expression, and in vitro transcription studies indicate that Spx directly activates yrrT operon expression during growth in medium containing methionine as sole sulfur source. These experiments have uncovered additional roles for Spx in the control of gene expression during unperturbed, steady-state growth.
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Affiliation(s)
- Soon-Yong Choi
- OGI School of Science and Engineering, Oregon Health and Science University, Beaverton, OR 97006, USA
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McDaniel BA, Grundy FJ, Kurlekar VP, Tomsic J, Henkin TM. Identification of a mutation in the Bacillus subtilis S-adenosylmethionine synthetase gene that results in derepression of S-box gene expression. J Bacteriol 2006; 188:3674-81. [PMID: 16672621 PMCID: PMC1482843 DOI: 10.1128/jb.188.10.3674-3681.2006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genes in the S-box family are regulated by binding of S-adenosylmethionine (SAM) to the 5' region of the mRNA of the regulated gene. SAM binding was previously shown to promote a rearrangement of the RNA structure that results in premature termination of transcription in vitro and repression of expression of the downstream coding sequence. The S-box RNA element therefore acts as a SAM-binding riboswitch in vitro. In an effort to identify factors other than SAM that could be involved in the S-box regulatory mechanism in vivo, we searched for trans-acting mutations in Bacillus subtilis that act to disrupt repression of S-box gene expression during growth under conditions where SAM pools are elevated. We identified a single mutant that proved to have one nucleotide substitution in the metK gene, encoding SAM synthetase. This mutation, designated metK10, resulted in a 15-fold decrease in SAM synthetase activity and a 4-fold decrease in SAM concentration in vivo. The metK10 mutation specifically affected S-box gene expression, and the increase in expression under repressing conditions was dependent on the presence of a functional transcriptional antiterminator element. The observation that the mutation identified in this search affects SAM production supports the model that the S-box RNAs directly monitor SAM in vivo, without a requirement for additional factors.
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Affiliation(s)
- Brooke A McDaniel
- Department of Microbiology, The Ohio State University, Columbus, 43210, USA
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Even S, Burguière P, Auger S, Soutourina O, Danchin A, Martin-Verstraete I. Global control of cysteine metabolism by CymR in Bacillus subtilis. J Bacteriol 2006; 188:2184-97. [PMID: 16513748 PMCID: PMC1428143 DOI: 10.1128/jb.188.6.2184-2197.2006] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
YrzC has previously been identified as a repressor controlling ytmI expression via its regulation of YtlI activator synthesis in Bacillus subtilis. We identified YrzC as a master regulator of sulfur metabolism. Gene expression profiles of B. subtilis delta yrzC mutant and wild-type strains grown in minimal medium with sulfate as the sole sulfur source were compared. In the mutant, increased expression was observed for 24 genes previously identified as repressed in the presence of sulfate. Since several genes involved in the pathways leading to cysteine formation were found, we propose to rename YrzC CymR, for "cysteine metabolism repressor." A CymR-dependent binding to the promoter region of the ytlI, ssuB, tcyP, yrrT, yxeK, cysK, or ydbM gene was demonstrated using gel shift experiments. A potential CymR target site, TAAWNCN2ANTWNAN3ATMGGAATTW, was found in the promoter region of these genes. In a DNase footprint experiment, the protected region in the ytlI promoter region contained this consensus sequence. Partial deletion or introduction of point mutations in this sequence confirmed its involvement in ytlI, yrrT, and yxeK regulation. The addition of O-acetylserine in gel shift experiments prevented CymR-dependent binding to DNA for all of the targets characterized. Transcriptome analysis of a delta cymR mutant and the wild-type strain also brought out significant changes in the expression level of a large set of genes related to stress response or to transition toward anaerobiosis.
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Affiliation(s)
- Sergine Even
- Unité de Génétique des Génomes Bactériens, Institut Pasteur, URA CNRS 2171, 75724 Paris Cedex 15, France
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Albanesi D, Mansilla MC, Schujman GE, de Mendoza D. Bacillus subtilis cysteine synthetase is a global regulator of the expression of genes involved in sulfur assimilation. J Bacteriol 2005; 187:7631-8. [PMID: 16267287 PMCID: PMC1280300 DOI: 10.1128/jb.187.22.7631-7638.2005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The synthesis of L-cysteine, the major mechanism by which sulfur is incorporated into organic compounds in microorganisms, occupies a significant fraction of bacterial metabolism. In Bacillus subtilis the cysH operon, encoding several proteins involved in cysteine biosynthesis, is induced by sulfur starvation and tightly repressed by cysteine. We show that a null mutation in the cysK gene encoding an O-acetylserine-(thiol)lyase, the enzyme that catalyzes the final step in cysteine biosynthesis, results in constitutive expression of the cysH operon. Using DNA microarrays we found that, in addition to cysH, almost all of the genes required for sulfate assimilation are constitutively expressed in cysK mutants. These results indicate that CysK, besides its enzymatic role in cysteine biosynthesis, is a global negative regulator of genes involved in sulfur metabolism.
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Affiliation(s)
- Daniela Albanesi
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET) and Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Argentina
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Ojha S, Sirois M, Macinnes JI. Identification of Actinobacillus suis genes essential for the colonization of the upper respiratory tract of swine. Infect Immun 2005; 73:7032-9. [PMID: 16177387 PMCID: PMC1230937 DOI: 10.1128/iai.73.10.7032-7039.2005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Actinobacillus suis has emerged as an important opportunistic pathogen of high-health-status swine. A colonization challenge method was developed, and using PCR-based signature-tagged transposon mutagenesis, 13 genes belonging to 9 different functional classes were identified that were necessary for A. suis colonization of the upper respiratory tract of swine.
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Burguière P, Fert J, Guillouard I, Auger S, Danchin A, Martin-Verstraete I. Regulation of the Bacillus subtilis ytmI operon, involved in sulfur metabolism. J Bacteriol 2005; 187:6019-30. [PMID: 16109943 PMCID: PMC1196162 DOI: 10.1128/jb.187.17.6019-6030.2005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The YtlI regulator of Bacillus subtilis activates the transcription of the ytmI operon encoding an l-cystine ABC transporter, a riboflavin kinase, and proteins of unknown function. The expression of the ytlI gene and the ytmI operon was high with methionine and reduced with sulfate. Using deletions and site-directed mutagenesis, a cis-acting DNA sequence important for YtlI-dependent regulation was identified upstream from the -35 box of ytmI. Gel mobility shift assays confirmed that YtlI specifically interacted with this sequence. The replacement of the sulfur-regulated ytlI promoter by the xylA promoter led to constitutive expression of a ytmI'-lacZ fusion in a ytlI mutant, suggesting that the repression of ytmI expression by sulfate was mainly at the level of YtlI synthesis. We further showed that the YrzC regulator negatively controlled ytlI expression while this repressor also acted on ytmI expression via YtlI. The cascade of regulation observed in B. subtilis is conserved in Listeria spp. Both a YtlI-like regulator and a ytmI-type operon are present in Listeria spp. Indeed, the Lmo2352 protein from Listeria monocytogenes was able to replace YtlI for the activation of ytmI expression and a lmo2352'-lacZ fusion was repressed in the presence of sulfate via YrzC in B. subtilis. A common motif, AT(A/T)ATTCCTAT, was found in the promoter region of the ytlI and lmo2352 genes. Deletion of part of this motif or the introduction of point mutations in this sequence confirmed its involvement in ytlI regulation.
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Affiliation(s)
- Pierre Burguière
- Unité de Génétique des Génomes Bactériens, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
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Erwin KN, Nakano S, Zuber P. Sulfate-dependent repression of genes that function in organosulfur metabolism in Bacillus subtilis requires Spx. J Bacteriol 2005; 187:4042-9. [PMID: 15937167 PMCID: PMC1151713 DOI: 10.1128/jb.187.12.4042-4049.2005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oxidative stress in Bacillus subtilis results in the accumulation of Spx protein, which exerts both positive and negative transcriptional control over a genome-wide scale through its interaction with the RNA polymerase alpha subunit. Previous microarray transcriptome studies uncovered a unique class of genes that are controlled by Spx-RNA polymerase interaction under normal growth conditions that do not promote Spx overproduction. These genes were repressed by Spx when sulfate was present as a sole sulfur source. The genes include those of the ytmI, yxeI, and ssu operons, which encode products resembling proteins that function in the uptake and desulfurization of organic sulfur compounds. Primer extension and analysis of operon-lacZ fusion expression revealed that the operons are repressed by sulfate and cysteine; however, Spx functioned only in sulfate-dependent repression. Both the ytmI operon and the divergently transcribed ytlI, encoding a LysR-type regulator that positively controls ytmI operon transcription, are repressed by Spx in sulfate-containing media. The CXXC motif of Spx, which is necessary for redox sensitive control of Spx activity in response to oxidative stress, is not required for sulfate-dependent repression. The yxeL-lacZ and ssu-lacZ fusions were also repressed in an Spx-dependent manner in media containing sulfate as the sole sulfur source. This work uncovers a new role for Spx in the control of sulfur metabolism in a gram-positive bacterium under nonstressful growth conditions.
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Affiliation(s)
- Kyle N Erwin
- Department of Environmental & Biomolecular Systems, OGI School of Science & Engineering, Oregon Health & Science University, 20000 NW Walker Rd., Beaverton, OR 97006, USA
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37
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Sperandio B, Polard P, Ehrlich DS, Renault P, Guédon E. Sulfur amino acid metabolism and its control in Lactococcus lactis IL1403. J Bacteriol 2005; 187:3762-78. [PMID: 15901700 PMCID: PMC1112055 DOI: 10.1128/jb.187.11.3762-3778.2005] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cysteine and methionine availability influences many processes in the cell. In bacteria, transcription of the specific genes involved in the synthesis of these two amino acids is usually regulated by different mechanisms or regulators. Pathways for the synthesis of cysteine and methionine and their interconversion were experimentally determined for Lactococcus lactis, a lactic acid bacterium commonly found in food. A new gene, yhcE, was shown to be involved in methionine recycling to cysteine. Surprisingly, 18 genes, representing almost all genes of these pathways, are under the control of a LysR-type activator, FhuR, also named CmbR. DNA microarray experiments showed that FhuR targets are restricted to this set of 18 genes clustered in seven transcriptional units, while cysteine starvation modifies the transcription level of several other genes potentially involved in oxidoreduction processes. Purified FhuR binds a 13-bp box centered 46 to 53 bp upstream of the transcriptional starts from the seven regulated promoters, while a second box with the same consensus is present upstream of the first binding box, separated by 8 to 10 bp. O-Acetyl serine increases FhuR binding affinity to its binding boxes. The overall view of sulfur amino acid metabolism and its regulation in L. lactis indicates that CysE could be a master enzyme controlling the activity of FhuR by providing its effector, while other controls at the enzymatic level appear to be necessary to compensate the absence of differential regulation of the genes involved in the interconversion of methionine and cysteine and other biosynthesis genes.
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Affiliation(s)
- Brice Sperandio
- Génétique Microbienne, Institut National de la Recherche Agronomique, 78352 Jouy-en-Josas cedex, France
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38
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Solovieva IM, Kreneva RA, Errais Lopes L, Perumov DA. The riboflavin kinase encoding gene ribR of Bacillus subtilis is a part of a 10 kb operon, which is negatively regulated by the yrzC gene product. FEMS Microbiol Lett 2005; 243:51-8. [PMID: 15668000 DOI: 10.1016/j.femsle.2004.11.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2004] [Revised: 11/05/2004] [Accepted: 11/21/2004] [Indexed: 11/19/2022] Open
Abstract
The riboflavin kinase encoding gene ribR is situated within a 12 genes locus ytmI-ytnM of the Bacillus subtilis chromosome. Here we demonstrate that ribR is transcribed as part of a 10 kb ytmI-ytnM operon. The riboflavin overproduction phenotype of B. subtilis ribC mutant strains, which is a result of the strongly reduced flavokinase activity of the riboflavin kinase/FAD synthetase RibC, was suppressed by ribR expression. Analysis of mutations with an upregulated ribR gene revealed 2 different groups of mutants. One class of mutants contained base substitutions in an 8 nucleotide sequence of the promoter region of the ytmI-ytnM operon. A second class of mutants had single point mutations within the yrzC gene or in the RBS of this gene. Dot-blot analysis of ytmI-ytnM transcription and the results of in trans complementation experiments for the yrzC mutants confirmed a role of the yrzC gene product as a negative regulator for the ytmI-ytnM operon.
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Affiliation(s)
- Irina M Solovieva
- Molecular and Radiation Biophysics Division, St. Petersburg Nuclear Physics Institute of the Russian Academy of Sciences, Gatchina, Leningrad district 188350, Russia.
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Auger S, Gomez MP, Danchin A, Martin-Verstraete I. The PatB protein of Bacillus subtilis is a C-S-lyase. Biochimie 2005; 87:231-8. [PMID: 15760717 DOI: 10.1016/j.biochi.2004.09.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2004] [Accepted: 09/13/2004] [Indexed: 10/26/2022]
Abstract
The PatB protein of Bacillus subtilis had both cystathionine beta-lyase and cysteine desulfhydrase activities in vitro. The apparent K(m) value of the PatB protein for cystathionine was threefold higher than that of the MetC protein, the previously characterized cystathionine beta-lyase of B. subtilis. In the presence of cystathionine as sole sulfur source, the patB gene present on a multicopy plasmid restored the growth of a metC mutant. In addition, the patB metC double mutant was unable to grow in the presence of sulfate or cystine while the patB or metC single mutants grew similarly to the wild-type strains in the presence of the same sulfur sources. In a metC mutant, the PatB protein can replace the MetC enzyme in the methionine biosynthetic pathway.
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Affiliation(s)
- S Auger
- Unité de Génétique des Génomes Bactériens, Institut Pasteur, URA CNRS 2171, 28, rue du Docteur Roux, 75724 Paris cedex 15, France
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40
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Burguière P, Auger S, Hullo MF, Danchin A, Martin-Verstraete I. Three different systems participate in L-cystine uptake in Bacillus subtilis. J Bacteriol 2004; 186:4875-84. [PMID: 15262924 PMCID: PMC451631 DOI: 10.1128/jb.186.15.4875-4884.2004] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The symporter YhcL and two ATP binding cassette transporters, YtmJKLMN and YckKJI, were shown to mediate L-cystine uptake in Bacillus subtilis. A triple DeltayhcL DeltaytmJKLMN DeltayckK mutant was unable to grow in the presence of L-cystine and to take up L-cystine. We propose that yhcL, ytmJKLMN, and yckKJI should be renamed tcyP, tcyJKLMN, and tcyABC, respectively. The L-cystine uptake by YhcL (K(m) = 0.6 microM) was strongly inhibited by seleno-DL-cystine, while the transport due to the YtmJKLMN system (K(m) = 2.5 microM) also drastically decreased in the presence of DL-cystathionine, L-djenkolic acid, or S-methyl-L-cysteine. Accordingly, a DeltaytmJKLMN mutant did not grow in the presence of 100 microM DL-cystathionine, 100 microM L-djenkolic acid, or 100 microM S-methyl-L-cysteine. The expression of the ytmI operon and the yhcL gene was regulated in response to sulfur availability, while the level of expression of the yckK gene remained low under all the conditions tested.
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Affiliation(s)
- Pierre Burguière
- Unité de Génétique des Génomes Bactériens, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.
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41
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Hullo MF, Auger S, Dassa E, Danchin A, Martin-Verstraete I. The metNPQ operon of Bacillus subtilis encodes an ABC permease transporting methionine sulfoxide, D- and L-methionine. Res Microbiol 2004; 155:80-6. [PMID: 14990259 DOI: 10.1016/j.resmic.2003.11.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2003] [Accepted: 11/04/2003] [Indexed: 11/22/2022]
Abstract
The Bacillus subtilis yusCBA operon, which encodes an ABC-type transporter, contains an S-box motif in its promoter region. We showed that the expression of these genes is repressed via the S-box system when methionine is available. The YusCB proteins are involved in the transport of both d- and l-methionine but also methionine sulfoxide. A yusCB mutant is unable to grow in the presence of 5 microM l-methionine or 100 microM methionine sulfoxide, while it grows similarly to the wild type with 100 microM l-methionine and 1 mM methionine sulfoxide. Other uptake systems are therefore present for these two compounds. In contrast, the Yus ABC transporter corresponds to the sole d-methionine uptake system. We propose to rename yusC, yusB and yusA as metN, metP and metQ, respectively.
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Affiliation(s)
- Marie-Françoise Hullo
- Unité de Génétique des Génomes Bactériens, Institut Pasteur, URA CNRS 2171, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
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42
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Mostertz J, Scharf C, Hecker M, Homuth G. Transcriptome and proteome analysis of Bacillus subtilis gene expression in response to superoxide and peroxide stress. MICROBIOLOGY-SGM 2004; 150:497-512. [PMID: 14766928 DOI: 10.1099/mic.0.26665-0] [Citation(s) in RCA: 202] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Gram-positive soil bacterium Bacillus subtilis responds to oxidative stress by the activation of different cellular defence mechanisms. These are composed of scavenging enzymes as well as protection and repair systems organized in highly sophisticated networks. In this study, the peroxide and the superoxide stress stimulons of B. subtilis were characterized by means of transcriptomics and proteomics. The results demonstrate that oxidative-stress-responsive genes can be classified into two groups. One group encompasses genes which show similar expression patterns in the presence of both reactive oxygen species. Examples are members of the PerR and the Fur regulon which were induced by peroxide and superoxide stress. Similarly, both kinds of stress stimulated the activation of the stringent response. The second group is composed of genes primarily responding to one stimulus, like the members of the SOS regulon which were particularly upregulated in the presence of peroxide, and many genes involved in sulfate assimilation and methionine biosynthesis which were only induced by superoxide. Several genes encoding proteins of unknown function could be assigned to one of these groups.
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Affiliation(s)
- Jörg Mostertz
- Institut für Mikrobiologie und Molekularbiologie, Ernst-Moritz-Arndt-Universität Greifswald, D-17487 Greifswald, Germany
| | - Christian Scharf
- Institut für Mikrobiologie und Molekularbiologie, Ernst-Moritz-Arndt-Universität Greifswald, D-17487 Greifswald, Germany
| | - Michael Hecker
- Institut für Mikrobiologie und Molekularbiologie, Ernst-Moritz-Arndt-Universität Greifswald, D-17487 Greifswald, Germany
| | - Georg Homuth
- Institut für Mikrobiologie und Molekularbiologie, Ernst-Moritz-Arndt-Universität Greifswald, D-17487 Greifswald, Germany
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Minami H, Suzuki H, Kumagai H. Gamma-glutamyltranspeptidase, but not YwrD, is important in utilization of extracellular glutathione as a sulfur source in Bacillus subtilis. J Bacteriol 2004; 186:1213-4. [PMID: 14762019 PMCID: PMC344223 DOI: 10.1128/jb.186.4.1213-1214.2004] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
gamma-Glutamyltranspeptidase (EC 2.3.2.2) of Bacillus subtilis, which is an extracellular enzyme, hydrolyzes the gamma-glutamyl linkage of glutathione. YwrD, which is homologous to gamma-glutamyltranspeptidase, was speculated to have a similar physiological role. It was shown that gamma-glutamyltranspeptidase, but not YwrD, is important in utilizing glutathione as the sole sulfur source in Bacillus subtilis.
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Affiliation(s)
- Hiromichi Minami
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
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44
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Perego M, Hoch JA, Barrett JF. Functional genomics of gram-positive microorganisms. J Bacteriol 2004; 186:903-9. [PMID: 14761984 PMCID: PMC344236 DOI: 10.1128/jb.186.4.903-909.2004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Marta Perego
- Division of Cellular Biology, Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA.
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45
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Epshtein V, Mironov AS, Nudler E. The riboswitch-mediated control of sulfur metabolism in bacteria. Proc Natl Acad Sci U S A 2003; 100:5052-6. [PMID: 12702767 PMCID: PMC154296 DOI: 10.1073/pnas.0531307100] [Citation(s) in RCA: 181] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many operons in Gram-positive bacteria that are involved in methionine (Met) and cysteine (Cys) biosynthesis possess an evolutionarily conserved regulatory leader sequence (S-box) that positively controls these genes in response to methionine starvation. Here, we demonstrate that a feed-back regulation mechanism utilizes S-adenosyl-methionine as an effector. S-adenosyl-methionine directly and specifically binds to the nascent S-box RNA, causing an intrinsic terminator to form and interrupt transcription prematurely. The S-box leader RNA thus expands the family of newly discovered riboswitches, i.e., natural regulatory RNA aptamers that seem to sense small molecules ranging from amino acid derivatives to vitamins.
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Affiliation(s)
- Vitaly Epshtein
- Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
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46
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Stanley NR, Britton RA, Grossman AD, Lazazzera BA. Identification of catabolite repression as a physiological regulator of biofilm formation by Bacillus subtilis by use of DNA microarrays. J Bacteriol 2003; 185:1951-7. [PMID: 12618459 PMCID: PMC150146 DOI: 10.1128/jb.185.6.1951-1957.2003] [Citation(s) in RCA: 185] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biofilms are structured communities of cells that are encased in a self-produced polymeric matrix and are adherent to a surface. Many biofilms have a significant impact in medical and industrial settings. The model gram-positive bacterium Bacillus subtilis has recently been shown to form biofilms. To gain insight into the genes involved in biofilm formation by this bacterium, we used DNA microarrays representing >99% of the annotated B. subtilis open reading frames to follow the temporal changes in gene expression that occurred as cells transitioned from a planktonic to a biofilm state. We identified 519 genes that were differentially expressed at one or more time points as cells transitioned to a biofilm. Approximately 6% of the genes of B. subtilis were differentially expressed at a time when 98% of the cells in the population were in a biofilm. These genes were involved in motility, phage-related functions, and metabolism. By comparing the genes differentially expressed during biofilm formation with those identified in other genomewide transcriptional-profiling studies, we were able to identify several transcription factors whose activities appeared to be altered during the transition from a planktonic state to a biofilm. Two of these transcription factors were Spo0A and sigma-H, which had previously been shown to affect biofilm formation by B. subtilis. A third signal that appeared to be affecting gene expression during biofilm formation was glucose depletion. Through quantitative biofilm assays and confocal scanning laser microscopy, we observed that glucose inhibited biofilm formation through the catabolite control protein CcpA.
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Affiliation(s)
- Nicola R Stanley
- Department of Microbiology, Immunology and Molecular Genetics, University of California-Los Angeles, Los Angeles, California 90095, USA
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47
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2003. [PMCID: PMC2447381 DOI: 10.1002/cfg.226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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