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Loss of the Rhodobacter capsulatus Serine Acetyl Transferase Gene, cysE1, Impairs Gene Transfer by Gene Transfer Agents and Biofilm Phenotypes. Appl Environ Microbiol 2022; 88:e0094422. [PMID: 36098534 PMCID: PMC9552610 DOI: 10.1128/aem.00944-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biofilms are widespread in the environment, where they allow bacterial species to survive adverse conditions. Cells in biofilms are densely packed, and this proximity is likely to increase the frequency of horizontal gene transfer. Gene transfer agents (GTAs) are domesticated viruses with the potential to spread any gene between bacteria. GTA production is normally restricted to a small subpopulation of bacteria, and regulation of GTA loci is highly coordinated, but the environmental conditions that favor GTA production are poorly understood. Here, we identified a serine acetyltransferase gene, cysE1, in Rhodobacter capsulatus that is required for optimal receipt of GTA DNA, accumulation of extracellular polysaccharide, and biofilm formation. The cysE1 gene is directly downstream of the core Rhodobacter-like GTA (RcGTA) structural gene cluster and upregulated in an RcGTA overproducer strain, although it is expressed on a separate transcript. The data we present suggest that GTA production and biofilm are coregulated, which could have important implications for the study of rapid bacterial evolution and understanding the full impact of GTAs in the environment. IMPORTANCE Direct exchange of genes between bacteria leads to rapid evolution and is the major factor underlying the spread of antibiotic resistance. Gene transfer agents (GTAs) are an unusual but understudied mechanism for genetic exchange that are capable of transferring any gene from one bacterium to another, and therefore, GTAs are likely to be important factors in genome plasticity in the environment. Despite the potential impact of GTAs, our knowledge of their regulation is incomplete. In this paper, we present evidence that elements of the cysteine biosynthesis pathway are involved in coregulation of various phenotypes required for optimal biofilm formation by Rhodobacter capsulatus and successful infection by the archetypal RcGTA. Establishing the regulatory mechanisms controlling GTA-mediated gene transfer is a key stepping stone to allow a full understanding of their role in the environment and wider impact.
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Catalytic specificity of the Lactobacillus plantarum cystathionine γ-lyase presumed by the crystallographic analysis. Sci Rep 2020; 10:14886. [PMID: 32913258 PMCID: PMC7483736 DOI: 10.1038/s41598-020-71756-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/05/2020] [Indexed: 11/17/2022] Open
Abstract
The reverse transsulfuration pathway, which is composed of cystathionine β-synthase (CBS) and cystathionine γ-lyase (CGL), plays a role to synthesize l-cysteine using l-serine and the sulfur atom in l-methionine. A plant-derived lactic acid bacterium Lactobacillus plantarum SN35N has been previously found to harbor the gene cluster encoding the CBS- and CGL-like enzymes. In addition, it has been demonstrated that the L. plantarum CBS can synthesize cystathionine from O-acetyl-l-serine and l-homocysteine. The aim of this study is to characterize the enzymatic functions of the L. plantarum CGL. We have found that the enzyme has the high γ-lyase activity toward cystathionine to generate l-cysteine, together with the β-lyase activity toward l-cystine to generate l-cysteine persulfide. By the crystallographic analysis of the inactive CGL K194A mutant complexed with cystathionine, we have found the residues which recognize the distal amino and carboxyl groups of cystathionine or l-cystine. The PLP-bound substrates at the active site may take either the binding pose for the γ- or β-elimination reaction, with the former being the major reaction in the case of cystathionine.
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Devi S, Tarique KF, Ali MF, Abdul Rehman SA, Gourinath S. Identification and characterization of Helicobacter pylori O-acetylserine-dependent cystathionine β-synthase, a distinct member of the PLP-II family. Mol Microbiol 2019; 112:718-739. [PMID: 31132312 DOI: 10.1111/mmi.14315] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2019] [Indexed: 02/02/2023]
Abstract
O-acetylserine sulfhydrylase (OASS) and cystathionine β-synthase (CBS) are members of the PLP-II family, and involved in L-cysteine production. OASS produces L-cysteine via a de novo pathway while CBS participates in the reverse transsulfuration pathway. O-acetylserine-dependent CBS (OCBS) was previously identified as a new member of the PLP-II family, which are predominantly seen in bacteria. The bacterium Helicobacter pylori possess only one OASS (hp0107) gene and we showed that the protein coded by this gene actually functions as an OCBS and utilizes L-homocysteine and O-acetylserine (OAS) to produce cystathionine. HpOCBS did not show CBS activity with the substrate L-serine and required OAS exclusively. The HpOCBS structure in complex with methionine showed a closed cleft state, explaining the initial mode of substrate binding. Sequence and structural analyses showed differences between the active sites of OCBS and CBS, and explain their different substrate preferences. We identified three hydrophobic residues near the active site of OCBS, corresponding to one serine and two tyrosine residues in CBSs. Mutational studies were performed on HpOCBS and Saccharomyces cerevisiae CBS. A ScCBS double mutant (Y158F/Y226V) did not display activity with L-serine, indicating indispensability of these polar residues for selecting substrate L-serine, however, did show activity with OAS.
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Affiliation(s)
- Suneeta Devi
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Khaja Faisal Tarique
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.,Public Health Research Institute, Rutgers, Newark, NJ, USA
| | - Mohammad Farhan Ali
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Syed Arif Abdul Rehman
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.,MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Samudrala Gourinath
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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Wüthrich D, Irmler S, Berthoud H, Guggenbühl B, Eugster E, Bruggmann R. Conversion of Methionine to Cysteine in Lactobacillus paracasei Depends on the Highly Mobile cysK-ctl-cysE Gene Cluster. Front Microbiol 2018; 9:2415. [PMID: 30386310 PMCID: PMC6200037 DOI: 10.3389/fmicb.2018.02415] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/20/2018] [Indexed: 11/23/2022] Open
Abstract
Milk and dairy products are rich in nutrients and are therefore habitats for various microbiomes. However, the composition of nutrients can be quite diverse, in particular among the sulfur containing amino acids. In milk, methionine is present in a 25-fold higher abundance than cysteine. Interestingly, a fraction of strains of the species L. paracasei – a flavor-enhancing adjunct culture species – can grow in medium with methionine as the sole sulfur source. In this study, we focus on genomic and evolutionary aspects of sulfur dependence in L. paracasei strains. From 24 selected L. paracasei strains, 16 strains can grow in medium with methionine as sole sulfur source. We sequenced these strains to perform gene-trait matching. We found that one gene cluster – consisting of a cysteine synthase, a cystathionine lyase, and a serine acetyltransferase – is present in all strains that grow in medium with methionine as sole sulfur source. In contrast, strains that depend on other sulfur sources do not have this gene cluster. We expanded the study and searched for this gene cluster in other species and detected it in the genomes of many bacteria species used in the food production. The comparison to these species showed that two different versions of the gene cluster exist in L. paracasei which were likely gained in two distinct events of horizontal gene transfer. Additionally, the comparison of 62 L. paracasei genomes and the two versions of the gene cluster revealed that this gene cluster is mobile within the species.
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Affiliation(s)
- Daniel Wüthrich
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | | | | | | | - Elisabeth Eugster
- School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
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Wüthrich D, Wenzel C, Bavan T, Bruggmann R, Berthoud H, Irmler S. Transcriptional Regulation of Cysteine and Methionine Metabolism in Lactobacillus paracasei FAM18149. Front Microbiol 2018; 9:1261. [PMID: 29942297 PMCID: PMC6004538 DOI: 10.3389/fmicb.2018.01261] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/24/2018] [Indexed: 11/13/2022] Open
Abstract
Lactobacillus paracasei is common in the non-starter lactic acid bacteria (LAB) community of raw milk cheeses. This species can significantly contribute to flavor formation through amino acid metabolism. In this study, the DNA and RNA of L. paracasei FAM18149 were sequenced using next-generation sequencing technologies to reconstruct the metabolism of the sulfur-containing amino acids cysteine and methionine. Twenty-three genes were found to be involved in cysteine biosynthesis, the conversion of cysteine to methionine and vice versa, the S-adenosylmethionine recycling pathway, and the transport of sulfur-containing amino acids. Additionally, six methionine-specific T-boxes and one cysteine-specific T-box were found. Five of these were located upstream of genes encoding transporter functions. RNA-seq analysis and reverse-transcription quantitative polymerase reaction assays showed that expression of genes located downstream of these T-boxes was affected by the absence of either cysteine or methionine. Remarkably, the cysK2-ctl1-cysE2 operon, which is associated with te methionine-to-cysteine conversion and is upregulated in the absence of cysteine, showed high read coverage in the 5′-untranslated region and an antisense-RNA in the 3′-untranslated region. This indicates that this operon is regulated by the combination of cis- and antisense-mediated regulation mechanisms. The results of this study may help in the selection of L. paracasei strains to control sulfuric flavor formation in cheese.
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Affiliation(s)
- Daniel Wüthrich
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | | | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
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Stefanovic E, Fitzgerald G, McAuliffe O. Advances in the genomics and metabolomics of dairy lactobacilli: A review. Food Microbiol 2017; 61:33-49. [DOI: 10.1016/j.fm.2016.08.009] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/26/2016] [Accepted: 08/27/2016] [Indexed: 01/21/2023]
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Fuchsmann P, Stern MT, Brügger YA, Breme K. Olfactometry Profiles and Quantitation of Volatile Sulfur Compounds of Swiss Tilsit Cheeses. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:7511-7521. [PMID: 26230142 DOI: 10.1021/acs.jafc.5b02536] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
To establish the odor profiles of three differently fabricated commercial Swiss Tilsit cheeses, analyses were conducted using headspace solid-phase microextraction gas chromatography-mass spectrometry/pulsed flame photometric detection and gas chromatography-olfactometry to identify and quantitate volatile compounds. In addition, odor quality and the impact of target sulfur compounds on the overall odor of the cheeses were investigated. The odor profile was found to be mainly influenced by buttery-cheesy and sulfury odor notes in all cheeses. Buttery-cheesy odor notes were attributed to three main molecules: butanoic acid, 3-methylbutanoic acid, and butane-2,3-dione. Over a dozen volatile sulfur compounds were detected at parts per billion levels, but only a few influenced the odor profile of the cheeses: methanethiol, dimethyl disulfide, bis(methylthio)methane, dimethyl trisulfide, 3-(methylthio)propanal, and 2-methyltetrahydrothiophen-3-one (tentative). In conclusion, the conducted analyses allowed differentiation of the cheeses, and gas chromatography-olfactometry results confirmed that partially thermized milk cheese has a more intense and more multifaceted overall flavor.
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Affiliation(s)
- Pascal Fuchsmann
- Agroscope, Institute for Food Sciences (IFS), Schwarzenburgstrasse 161, CH-3003 Berne, Switzerland
| | - Mireille Tena Stern
- Agroscope, Institute for Food Sciences (IFS), Schwarzenburgstrasse 161, CH-3003 Berne, Switzerland
| | - Yves-Alain Brügger
- Agroscope, Institute for Food Sciences (IFS), Schwarzenburgstrasse 161, CH-3003 Berne, Switzerland
| | - Katharina Breme
- Agroscope, Institute for Food Sciences (IFS), Schwarzenburgstrasse 161, CH-3003 Berne, Switzerland
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A preliminary study on the effect of Lactobacillus casei expressing cystathionine lyase1/cystathionine lyase2 on Cheddar cheese and the formation of sulphur-containing compounds. Int Dairy J 2013. [DOI: 10.1016/j.idairyj.2013.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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