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Paluszak Z, Kanarek P, Gryń G, Breza-Boruta B. Deodorizing bacterial consortium: community analysis of biofilms and leachate water collected from an air biofiltration system in a piggery. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:18993-19001. [PMID: 38353818 DOI: 10.1007/s11356-024-32223-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/23/2024] [Indexed: 03/09/2024]
Abstract
Intensive livestock production is a source of water, soil, and air contamination. The first aspect that negatively affects the quality of life of residents in the vicinity of piggeries is malodorous aerosols, which are not only responsible for discomfort but can be an etiological factor in the development of various diseases during prolonged exposure. One of the proven and efficient ways to counteract odor emissions is the usage of air biofiltration. The purpose of this study was to qualitatively analyze the bacterial community colonizing the biofilm of a biofilter operating at an industrial piggery in Switzerland. The study material consisted of biofilm and leachate water samples. The microbiological analysis consisted of DNA isolation, amplification of the bacterial 16S rRNA gene fragment (V3-V4), preparation of a library for high-throughput sequencing, high-throughput NGS sequencing, filtering of the obtained sequencing reads, and evaluation of the species composition in the studied samples. The investigation revealed the presence of the following bacterial genera: Pseudochelatococcus, Methyloversatilis, Flexilinea, Deviosia, Chryseobacterium, Kribbia, Leadbetterella, Corynebacterium, Flavobacterium, Xantobacter, Tessaracoccus, Staphylococcus, Thiobacillus, Enhydrobacter, Proteiniclasticum, and Giesbergeria. Analysis of the microbial composition of biofilters provides the opportunity to improve the biofiltration process.
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Affiliation(s)
- Zbigniew Paluszak
- Department of Microbiology and Food Technology, Faculty of Agriculture and Biotechnology, Bydgoszcz University of Science and Technology, 6 Bernardyńska Street, 85-029, Bydgoszcz, Poland
| | - Piotr Kanarek
- Department of Microbiology and Food Technology, Faculty of Agriculture and Biotechnology, Bydgoszcz University of Science and Technology, 6 Bernardyńska Street, 85-029, Bydgoszcz, Poland.
| | - Grzegorz Gryń
- Plant Breeding and Acclimatization Institute - National Research Institute, Al. Powstańców Wlkp. 10, 85-090, Bydgoszcz, Poland
| | - Barbara Breza-Boruta
- Department of Microbiology and Food Technology, Faculty of Agriculture and Biotechnology, Bydgoszcz University of Science and Technology, 6 Bernardyńska Street, 85-029, Bydgoszcz, Poland
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Du H, Qi Y, Qiao J, Li L, Wei L, Xu N, Shao L, Liu J. Transcription factor OxyR regulates sulfane sulfur removal and L-cysteine biosynthesis in Corynebacterium glutamicum. Appl Environ Microbiol 2023; 89:e0090423. [PMID: 37768042 PMCID: PMC10537588 DOI: 10.1128/aem.00904-23] [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] [Accepted: 07/09/2023] [Indexed: 09/29/2023] Open
Abstract
Sulfane sulfur, a collective term for hydrogen polysulfide and organic persulfide, often damages cells at high concentrations. Cells can regulate intracellular sulfane sulfur levels through specific mechanisms, but these mechanisms are unclear in Corynebacterium glutamicum. OxyR is a transcription factor capable of sensing oxidative stress and is also responsive to sulfane sulfur. In this study, we found that OxyR functioned directly in regulating sulfane sulfur in C. glutamicum. OxyR binds to the promoter of katA and nrdH and regulates its expression, as revealed via in vitro electrophoretic mobility shift assay analysis, real-time quantitative PCR, and reporting systems. Overexpression of katA and nrdH reduced intracellular sulfane sulfur levels by over 30% and 20% in C. glutamicum, respectively. RNA-sequencing analysis showed that the lack of OxyR downregulated the expression of sulfur assimilation pathway genes and/or sulfur transcription factors, which may reduce the rate of sulfur assimilation. In addition, OxyR also affected the biosynthesis of L-cysteine in C. glutamicum. OxyR overexpression strain Cg-2 accumulated 183 mg/L of L-cysteine, increased by approximately 30% compared with the control (142 mg/L). In summary, OxyR not only regulated sulfane sulfur levels by controlling the expression of katA and nrdH in C. glutamicum but also facilitated the sulfur assimilation and L-cysteine synthesis pathways, providing a potential target for constructing robust cell factories of sulfur-containing amino acids and their derivatives. IMPORTANCE C. glutamicum is an important industrial microorganism used to produce various amino acids. In the production of sulfur-containing amino acids, cells inevitably accumulate a large amount of sulfane sulfur. However, few studies have focused on sulfane sulfur removal in C. glutamicum. In this study, we not only revealed the regulatory mechanism of OxyR on intracellular sulfane sulfur removal but also explored the effects of OxyR on the sulfur assimilation and L-cysteine synthesis pathways in C. glutamicum. This is the first study on the removal of sulfane sulfur in C. glutamicum. These results contribute to the understanding of sulfur regulatory mechanisms and may aid in the future optimization of C. glutamicum for biosynthesis of sulfur-containing amino acids.
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Affiliation(s)
- Huanmin Du
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuting Qi
- Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Jinfang Qiao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Lingcong Li
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liang Wei
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ning Xu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Li Shao
- Department of Microbiology and Biotechnology, College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Jun Liu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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Park S, Kim I, Chhetri G, So Y, Jung Y, Woo H, Seo T. Alteromonas gilva sp. nov. and Erythrobacter fulvus sp. nov., isolated from a tidal mudflat. Int J Syst Evol Microbiol 2023; 73. [PMID: 37676705 DOI: 10.1099/ijsem.0.006032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023] Open
Abstract
Strains chi3T and sf7T were collected from a tidal mudflat around Dongmak beach in Ganghwa, Republic of Korea. Both strains were Gram-stain-negative, aerobic or facultatively anaerobic, and rod-shaped. Results of phylogenetic tree analysis based on 16S rRNA and whole-genome sequences suggested that strains chi3T and sf7T belong to the genera Alteromonas and Erythrobacter, respectively. The cells of strain chi3T were non-motile and grew at 15-45 °C (optimum, 38 °C), at pH 6.0-10.0 (optimum, pH 8.0) and in the presence of 0-9.0 % (w/v) NaCl (optimum, 2.0 %). The cells of strain sf7T were motile as they had flagella and grew at 20-48 °C (optimum, 38 °C), at pH 6.0-10.0 (optimum, pH 9.0) and in the presence of 0-5.0 % (w/v) NaCl (optimum, 1.0 %). Strains chi3T and sf7T have average nucleotide identity values (70.0-70.4% and 78.9-81.7 %) and digital DNA-DNA hybridization values (21.8-22.3% and 21.0-25.6 %) with reference strains in the genera Alteromonas and Erythrobacter, respectively. Data from digital DNA-DNA hybridization, as well as phylogenetic, biochemical and physiological analyses, indicated the distinction of the two strains from the genera Alteromonas and Erythrobacter, respectively, and we thus propose the names Alteromonas gilva sp. nov. (type strain chi3T=KACC 22866T=TBRC 16612T) and Erythrobacter fulvus sp. nov. (type strain sf7T=KACC 22865T=TBRC 16611T).
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Affiliation(s)
- Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Haejin Woo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
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Tran TH, Roberts AQ, Escapa IF, Gao W, Segre JA, Kong HH, Conlan S, Kelly MS, Lemon KP. Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543719. [PMID: 37333201 PMCID: PMC10274666 DOI: 10.1101/2023.06.05.543719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum, C. pseudodiphtheriticum, C. accolens, and C. tuberculostearicum. Based on the prevalence of these species, at least two likely coexist in the nasal microbiota of 82% of adults. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the functional protein repertoire and metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the U.S. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution across Africa and North America. All four species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent (core) compared to the accessory genome of each species indicating limited strain-level variability in metabolic capacity. Moreover, core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the U.S. clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in the Botswanan clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.
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Affiliation(s)
- Tommy H. Tran
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Ari Q. Roberts
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Isabel F. Escapa
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Wei Gao
- The Forsyth Institute (Microbiology), Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Julie A. Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Heidi H. Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Matthew S. Kelly
- Division of Pediatric Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Katherine P. Lemon
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Division of Infectious Diseases, Texas Children’s Hospital, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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Yang HD, Jeong H, Kim Y, Lee HS. The cysS gene (ncgl0127) of Corynebacterium glutamicum is required for sulfur assimilation and affects oxidative stress-responsive cysteine import. Res Microbiol 2022; 173:103983. [PMID: 35931248 DOI: 10.1016/j.resmic.2022.103983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022]
Abstract
The OsnR protein functions as a transcriptional repressor of genes involved in redox-dependent stress responses. Here, we studied Corynebacterium glutamicum ORF ncgl0127 (referred to as cysS in this study), one of the target genes of OsnR, to reveal its role in osnR-mediated stress responses. The ΔcysS strain was found to be a cysteine auxotroph, and the transcription levels of the sulfur assimilatory genes and cysR, the master regulatory gene for sulfur assimilation, were low in this strain. Complementation of the strain with cysR transformed the strain into a cysteine prototroph. Cells challenged with oxidants or cysteine showed transcriptional stimulation of the cysS gene and decreased transcription of the ncgl2463 gene, which encodes a cysteine/cystine importer. The transcription of the ncgl2463 gene was increased in the ΔcysS strain and further stimulated by cysteine. Unlike the wild-type strain, ΔcysS cells grown with an excess amount of cysteine showed an oxidant- and alkylating agent-resistant phenotype, suggesting deregulated cysteine import. Collectively, our data suggest that the cysS gene plays a positive role in sulfur assimilation and a negative role in cysteine import, in particular in cells under oxidative stress.
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Affiliation(s)
- Han-Deul Yang
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, Republic of Korea.
| | - Haeri Jeong
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea.
| | - Younhee Kim
- Department of Korean Medicine, Semyung University, Jecheon, Chungbuk 27136, Republic of Korea.
| | - Heung-Shick Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, Republic of Korea.
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Martínez-Ruiz EB, Cooper M, Barrero-Canosa J, Haryono MAS, Bessarab I, Williams RBH, Szewzyk U. Genome analysis of Pseudomonas sp. OF001 and Rubrivivax sp. A210 suggests multicopper oxidases catalyze manganese oxidation required for cylindrospermopsin transformation. BMC Genomics 2021; 22:464. [PMID: 34157973 PMCID: PMC8218464 DOI: 10.1186/s12864-021-07766-0] [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] [Received: 10/09/2020] [Accepted: 06/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cylindrospermopsin is a highly persistent cyanobacterial secondary metabolite toxic to humans and other living organisms. Strain OF001 and A210 are manganese-oxidizing bacteria (MOB) able to transform cylindrospermopsin during the oxidation of Mn2+. So far, the enzymes involved in manganese oxidation in strain OF001 and A210 are unknown. Therefore, we analyze the genomes of two cylindrospermopsin-transforming MOB, Pseudomonas sp. OF001 and Rubrivivax sp. A210, to identify enzymes that could catalyze the oxidation of Mn2+. We also investigated specific metabolic features related to pollutant degradation and explored the metabolic potential of these two MOB with respect to the role they may play in biotechnological applications and/or in the environment. RESULTS Strain OF001 encodes two multicopper oxidases and one haem peroxidase potentially involved in Mn2+ oxidation, with a high similarity to manganese-oxidizing enzymes described for Pseudomonas putida GB-1 (80, 83 and 42% respectively). Strain A210 encodes one multicopper oxidase potentially involved in Mn2+ oxidation, with a high similarity (59%) to the manganese-oxidizing multicopper oxidase in Leptothrix discophora SS-1. Strain OF001 and A210 have genes that might confer them the ability to remove aromatic compounds via the catechol meta- and ortho-cleavage pathway, respectively. Based on the genomic content, both strains may grow over a wide range of O2 concentrations, including microaerophilic conditions, fix nitrogen, and reduce nitrate and sulfate in an assimilatory fashion. Moreover, the strain A210 encodes genes which may convey the ability to reduce nitrate in a dissimilatory manner, and fix carbon via the Calvin cycle. Both MOB encode CRISPR-Cas systems, several predicted genomic islands, and phage proteins, which likely contribute to their genome plasticity. CONCLUSIONS The genomes of Pseudomonas sp. OF001 and Rubrivivax sp. A210 encode sequences with high similarity to already described MCOs which may catalyze manganese oxidation required for cylindrospermopsin transformation. Furthermore, the analysis of the general metabolism of two MOB strains may contribute to a better understanding of the niches of cylindrospermopsin-removing MOB in natural habitats and their implementation in biotechnological applications to treat water.
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Affiliation(s)
- Erika Berenice Martínez-Ruiz
- Chair of Environmental Microbiology, Technische Universität Berlin, Institute of Environmental Technology, Straße des 17. Juni 135, 10623, Berlin, Germany.
| | - Myriel Cooper
- Chair of Environmental Microbiology, Technische Universität Berlin, Institute of Environmental Technology, Straße des 17. Juni 135, 10623, Berlin, Germany.
| | - Jimena Barrero-Canosa
- Chair of Environmental Microbiology, Technische Universität Berlin, Institute of Environmental Technology, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Mindia A S Haryono
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 119077, Singapore
| | - Irina Bessarab
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 119077, Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, 119077, Singapore
| | - Ulrich Szewzyk
- Chair of Environmental Microbiology, Technische Universität Berlin, Institute of Environmental Technology, Straße des 17. Juni 135, 10623, Berlin, Germany
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Zhou L, Ou P, Zhao B, Zhang W, Yu K, Xie K, Zhuang WQ. Assimilatory and dissimilatory sulfate reduction in the bacterial diversity of biofoulant from a full-scale biofilm-membrane bioreactor for textile wastewater treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 772:145464. [PMID: 33571768 DOI: 10.1016/j.scitotenv.2021.145464] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/23/2021] [Accepted: 01/24/2021] [Indexed: 06/12/2023]
Abstract
Assimilatory and dissimilatory sulfate reduction (ASR and DSR) are the core bacterial sulfate-reducing pathways involved in wastewater treatment. It has been reported that sulfate-reducing activities could happen within biofoulants of membrane bioreactors during wastewater treatment. Biofoulants are mainly microbial products contributing membrane fouling and subsequent rising energy consumption in driving membrane filtration. Biofoulants from a full-scale biofilm-membrane bioreactor (biofilm-MBR) treating textile wastewater were investigated in this study. During a 10-month operation, sulfate concentrations in the effluent of the biofilm-MBR gradually decreased alongside with the creeping up sulfite concentrations when biofoulants were also building up on membrane modules. Sulfide had no apparent increases in the effluent during this period. Metagenomic analysis revealed diverse microbial communities residing in the biofoulants. Further analysis on their genetic traits revealed abundant ASR's and DSR's functional genes. A plethora of sulfate-reduction bacteria (SRB), including the well-known Desulfovibrio, Desulfainum, Desulfobacca, Desulfobulbus, Desulfococcus, Desulfonema, Desulfosarcina, Desulfobacter, Desulfobacula, Desulfofaba, Desulfotigum, Desulfatibacillum, Desulfatitalea, Desulfobacterium, were detected in the biofoulants. They were believed to play some important carbon and sulfur-cycling roles in our study. Based on metagenomic analysis, we also deduced that ASR was a functionally more important sulfate-reducing route because of the high abundance of assimilatory sulfate reductases detected. Also, the "AMP (adenosine monophosphate)→sulfite" step was a key reaction shared by both ASR and DSR in the biofoulant. This step might be responsible for the sulfite accumulation in the biofilm-MBR effluent. Overall, ASR functional genes in the biofoulants were more abundant. But the bacteria possessing complete DSR pathways caused the sulfide production in the biofilm-MBR.
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Affiliation(s)
- Lijie Zhou
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Pingxiang Ou
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Bikai Zhao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Wenyu Zhang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Ke Yu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Guangdong, Shenzhen 518055, China
| | - Kang Xie
- School of Civil Engineering and Architecture, University of Jinan, Jinan 250022, China
| | - Wei-Qin Zhuang
- Department of Civil and Environmental Engineering, University of Auckland, Auckland 1142, New Zealand
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Kumru S, Tekedar HC, Blom J, Lawrence ML, Karsi A. Genomic diversity in flavobacterial pathogens of aquatic origin. Microb Pathog 2020; 142:104053. [PMID: 32058022 DOI: 10.1016/j.micpath.2020.104053] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/07/2020] [Accepted: 02/07/2020] [Indexed: 12/15/2022]
Abstract
Flavobacterium species are considered important fish pathogens in wild and cultured fish throughout the world. They can cause acute, subacute, and chronic infections, which are mainly characterized by gill damage, skin lesions, and deep necrotic ulcerations. Primarily, three Flavobacterium species, F. branchiophilum, F. columnare, and F. psychrophilum, have been reported to cause substantial losses to freshwater fish. In this study, we evaluated genomes of 86 Flavobacterium species isolated from aquatic hosts (mainly fish) to identify their unique and shared genome features. Our results showed that F. columnare genomes cluster into four different genetic groups. In silico secretion system analysis identified that all genomes carry type I (T1SS) and type IX (T9SS) secretion systems, but the number of type I secretion system genes shows diversity between species. F. branchiophilum, F. araucananum, F. chilense, F. spartansii, and F. tructae genomes have full type VI secretion system (T6SS). F. columnare, F. hydatis, and F. plurextorum carry partial T6SS with some of the T6SS genes missing. F. columnare, F. araucananum, F. chilense, F. spartansii, F. araucananum, F. tructae, Flavobacterium sp., F. crassostreae, F. succinicans, F. hydatis, and F. plurextorum carry most of the type IV secretion system genes (T4SS). F. columnare genetic groups 1 and 2, Flavobacterium sp., and F. crassostreae encode the least number of antibiotic resistance elements. F. hydatis, F. chilense, and F. plurextorum encode the greatest number of antibiotic resistance genes. Additionally, F. spartansii, F. araucananum, and chilense encode the greatest number of virulence genes while Flavobacterium sp. and F. crassostreae encode the least number of virulence genes. In conclusion, comparative genomics of Flavobacterium species of aquatic origin will help our understanding of Flavobacterium pathogenesis.
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Affiliation(s)
- Salih Kumru
- Faculty of Fisheries, Recep Tayyip Erdogan University, Rize, Turkey
| | - Hasan C Tekedar
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Hesse, Germany
| | - Mark L Lawrence
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States
| | - Attila Karsi
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States.
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Joo YC, Ko YJ, You SK, Shin SK, Hyeon JE, Musaad AS, Han SO. Creating a New Pathway in Corynebacterium glutamicum for the Production of Taurine as a Food Additive. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:13454-13463. [PMID: 30516051 DOI: 10.1021/acs.jafc.8b05093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Taurine is a biologically and physiologically valuable food additive. However, commercial taurine production mainly relies on environmentally harmful chemical synthesis. Herein, for the first time in bacteria, we attempted to produce taurine in metabolically engineered Corynebacterium glutamicum. The taurine-producing strain was developed by introducing cs, cdo1, and csad genes. Interestingly, while the control strain could not produce taurine, the engineered strains successfully produced taurine via the newly introduced metabolic pathway. Furthermore, we investigated the effect of a deletion strain of the transcriptional repressor McbR gene on taurine production. As a result, sulfur accumulation and l-cysteine biosynthesis were reinforced by the McbR deletion strain, which further increased the taurine production by 2.3-fold. Taurine production of the final engineered strain Tau11 was higher than in other previously reported strains. This study demonstrated a potential approach for eco-friendly biosynthesis as an alternative to the chemical synthesis of a food additive.
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Affiliation(s)
- Young-Chul Joo
- Department of Biotechnology , Korea University , Seoul 02841 , Republic of Korea
| | - Young Jin Ko
- Department of Biotechnology , Korea University , Seoul 02841 , Republic of Korea
| | - Seung Kyou You
- Department of Biotechnology , Korea University , Seoul 02841 , Republic of Korea
| | - Sang Kyu Shin
- Department of Biotechnology , Korea University , Seoul 02841 , Republic of Korea
| | - Jeong Eun Hyeon
- Institute of Life Science and Natural Resources , Korea University , Seoul 02841 , Republic of Korea
| | | | - Sung Ok Han
- Department of Biotechnology , Korea University , Seoul 02841 , Republic of Korea
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10
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Stoeva MK, Coates JD. Specific inhibitors of respiratory sulfate reduction: towards a mechanistic understanding. MICROBIOLOGY-SGM 2018; 165:254-269. [PMID: 30556806 DOI: 10.1099/mic.0.000750] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Microbial sulfate reduction (SR) by sulfate-reducing micro-organisms (SRM) is a primary environmental mechanism of anaerobic organic matter mineralization, and as such influences carbon and sulfur cycling in many natural and engineered environments. In industrial systems, SR results in the generation of hydrogen sulfide, a toxic, corrosive gas with adverse human health effects and significant economic and environmental consequences. Therefore, there has been considerable interest in developing strategies for mitigating hydrogen sulfide production, and several specific inhibitors of SRM have been identified and characterized. Specific inhibitors are compounds that disrupt the metabolism of one group of organisms, with little or no effect on the rest of the community. Putative specific inhibitors of SRM have been used to control sulfidogenesis in industrial and engineered systems. Despite the value of these inhibitors, mechanistic and quantitative studies into the molecular mechanisms of their inhibition have been sparse and unsystematic. The insight garnered by such studies is essential if we are to have a more complete understanding of SR, including the past and current selective pressures acting upon it. Furthermore, the ability to reliably control sulfidogenesis - and potentially assimilatory sulfate pathways - relies on a thorough molecular understanding of inhibition. The scope of this review is to summarize the current state of the field: how we measure and understand inhibition, the targets of specific SR inhibitors and how SRM acclimatize and/or adapt to these stressors.
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Affiliation(s)
- Magdalena K Stoeva
- 1Energy Biosciences Institute, University of California - Berkeley, Berkeley, CA, USA
- 2Department of Plant and Microbial Biology, University of California - Berkeley, Berkeley, CA, USA
| | - John D Coates
- 2Department of Plant and Microbial Biology, University of California - Berkeley, Berkeley, CA, USA
- 1Energy Biosciences Institute, University of California - Berkeley, Berkeley, CA, USA
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Marietou A, Røy H, Jørgensen BB, Kjeldsen KU. Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis. Front Microbiol 2018; 9:309. [PMID: 29551997 PMCID: PMC5840216 DOI: 10.3389/fmicb.2018.00309] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 02/09/2018] [Indexed: 12/31/2022] Open
Abstract
The first step in the sulfate reduction pathway is the transport of sulfate across the cell membrane. This uptake has a major effect on sulfate reduction rates. Much of the information available on sulfate transport was obtained by studies on assimilatory sulfate reduction, where sulfate transporters were identified among several types of protein families. Despite our growing knowledge on the physiology of dissimilatory sulfate-reducing microorganisms (SRM) there are no studies identifying the proteins involved in sulfate uptake in members of this ecologically important group of anaerobes. We surveyed the complete genomes of 44 sulfate-reducing bacteria and archaea across six phyla and identified putative sulfate transporter encoding genes from four out of the five surveyed protein families based on homology. We did not find evidence that ABC-type transporters (SulT) are involved in the uptake of sulfate in SRM. We speculate that members of the CysP sulfate transporters could play a key role in the uptake of sulfate in thermophilic SRM. Putative CysZ-type sulfate transporters were present in all genomes examined suggesting that this overlooked group of sulfate transporters might play a role in sulfate transport in dissimilatory sulfate reducers alongside SulP. Our in silico analysis highlights several targets for further molecular studies in order to understand this key step in the metabolism of SRMs.
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Affiliation(s)
- Angeliki Marietou
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Hans Røy
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Bo B Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper U Kjeldsen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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Gren T, Ostash B, Babiy V, Rokytskyy I, Fedorenko V. Analysis of Streptomyces coelicolor M145 genes SCO4164 and SCO5854 encoding putative rhodaneses. Folia Microbiol (Praha) 2017; 63:197-201. [DOI: 10.1007/s12223-017-0551-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 09/18/2017] [Indexed: 01/08/2023]
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Joo YC, Hyeon JE, Han SO. Metabolic Design of Corynebacterium glutamicum for Production of l-Cysteine with Consideration of Sulfur-Supplemented Animal Feed. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:4698-4707. [PMID: 28560868 DOI: 10.1021/acs.jafc.7b01061] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
l-Cysteine is a valuable sulfur-containing amino acid widely used as a nutrition supplement in industrial food production, agriculture, and animal feed. However, this amino acid is mostly produced by acid hydrolysis and extraction from human or animal hairs. In this study, we constructed recombinant Corynebacterium glutamicum strains that overexpress combinatorial genes for l-cysteine production. The aims of this work were to investigate the effect of the combined overexpression of serine acetyltransferase (CysE), O-acetylserine sulfhydrylase (CysK), and the transcriptional regulator CysR on l-cysteine production. The CysR-overexpressing strain accumulated approximately 2.7-fold more intracellular sulfide than the control strain (empty pMT-tac vector). Moreover, in the resulting CysEKR recombinant strain, combinatorial overexpression of genes involved in l-cysteine production successfully enhanced its production by approximately 3.0-fold relative to that in the control strain. This study demonstrates a biotechnological model for the production of animal feed supplements such as l-cysteine using metabolically engineered C. glutamicum.
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Affiliation(s)
- Young-Chul Joo
- Department of Biotechnology, Korea University , Seoul 02841, Republic of Korea
| | - Jeong Eun Hyeon
- Department of Biotechnology, Korea University , Seoul 02841, Republic of Korea
- Department of Chemical and Biomolecular Engineering, University of Delaware , Newark, Delaware 19702, United States
| | - Sung Ok Han
- Department of Biotechnology, Korea University , Seoul 02841, Republic of Korea
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Tarpgaard IH, Jørgensen BB, Kjeldsen KU, Røy H. The marine sulfate reducer Desulfobacterium autotrophicum HRM2 can switch between low and high apparent half-saturation constants for dissimilatory sulfate reduction. FEMS Microbiol Ecol 2017; 93:2966865. [DOI: 10.1093/femsec/fix012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 02/01/2017] [Indexed: 12/22/2022] Open
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Limberg MH, Schulte J, Aryani T, Mahr R, Baumgart M, Bott M, Wiechert W, Oldiges M. Metabolic profile of 1,5-diaminopentane producing Corynebacterium glutamicum
under scale-down conditions: Blueprint for robustness to bioreactor inhomogeneities. Biotechnol Bioeng 2016; 114:560-575. [DOI: 10.1002/bit.26184] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/08/2016] [Accepted: 09/16/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Michael H. Limberg
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Julia Schulte
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Tita Aryani
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Regina Mahr
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Meike Baumgart
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Michael Bott
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Wolfgang Wiechert
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
| | - Marco Oldiges
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences; IBG-1: Biotechnology; Wilhelm-Johnen-Straße 52425 Jülich Germany
- Institute of Biotechnology; RWTH Aachen University; Aachen Germany
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Milse J, Petri K, Rückert C, Kalinowski J. Transcriptional response of Corynebacterium glutamicum ATCC 13032 to hydrogen peroxide stress and characterization of the OxyR regulon. J Biotechnol 2014; 190:40-54. [DOI: 10.1016/j.jbiotec.2014.07.452] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/22/2014] [Accepted: 07/29/2014] [Indexed: 11/26/2022]
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Zhang L, Jiang W, Nan J, Almqvist J, Huang Y. The Escherichia coli CysZ is a pH dependent sulfate transporter that can be inhibited by sulfite. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1809-16. [DOI: 10.1016/j.bbamem.2014.03.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 03/08/2014] [Accepted: 03/10/2014] [Indexed: 12/27/2022]
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Corynebacterium glutamicum sdhA encoding succinate dehydrogenase subunit A plays a role in cysR-mediated sulfur metabolism. Appl Microbiol Biotechnol 2014; 98:6751-9. [DOI: 10.1007/s00253-014-5823-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/08/2014] [Accepted: 05/10/2014] [Indexed: 10/25/2022]
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Role for ferredoxin:NAD(P)H oxidoreductase (FprA) in sulfate assimilation and siderophore biosynthesis in Pseudomonads. J Bacteriol 2013; 195:3876-87. [PMID: 23794620 DOI: 10.1128/jb.00528-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pyridine-2,6-bis(thiocarboxylate) (PDTC), produced by certain pseudomonads, is a sulfur-containing siderophore that binds iron, as well as a wide range of transition metals, and it affects the net hydrolysis of the environmental contaminant carbon tetrachloride. The pathway of PDTC biosynthesis has not been defined. Here, we performed a transposon screen of Pseudomonas putida DSM 3601 to identify genes necessary for PDTC production (Pdt phenotype). Transposon insertions within genes for sulfate assimilation (cysD, cysNC, and cysG [cobA2]) dominated the collection of Pdt mutations. In addition, two insertions were within the gene for the LysR-type transcriptional activator FinR (PP1637). Phenotypic characterization indicated that finR mutants were cysteine bradytrophs. The Pdt phenotype of finR mutants could be complemented by the known target of FinR regulation, fprA (encoding ferredoxin:NADP(+) oxidoreductase), or by Escherichia coli cysJI (encoding sulfite reductase). These data indicate that fprA is necessary for effective sulfate assimilation by P. putida and that the effect of finR mutation on PDTC production was due to deficient expression of fprA and sulfite reduction. fprA expression in both P. putida and P. aeruginosa was found to be regulated by FinR, but in a manner dependent upon reduced sulfur sources, implicating FinR in sulfur regulatory physiology. The genes and phenotypes identified in this study indicated a strong dependence upon intracellular reduced sulfur/cysteine for PDTC biosynthesis and that pseudomonads utilize sulfite reduction enzymology distinct from that of E. coli and possibly similar to that of chloroplasts and other proteobacteria.
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Pátek M, Nešvera J. Promoters and Plasmid Vectors of Corynebacterium glutamicum. CORYNEBACTERIUM GLUTAMICUM 2013. [DOI: 10.1007/978-3-642-29857-8_2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Identification of pOENI-1 and related plasmids in Oenococcus oeni strains performing the malolactic fermentation in wine. PLoS One 2012; 7:e49082. [PMID: 23139835 PMCID: PMC3489775 DOI: 10.1371/journal.pone.0049082] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 10/04/2012] [Indexed: 12/22/2022] Open
Abstract
Plasmids in lactic acid bacteria occasionally confer adaptive advantages improving the growth and behaviour of their host cells. They are often associated to starter cultures used in the food industry and could be a signature of their superiority. Oenococcus oeni is the main lactic acid bacteria species encountered in wine. It performs the malolactic fermentation that occurs in most wines after alcoholic fermentation and contributes to their quality and stability. Industrial O. oeni starters may be used to better control malolactic fermentation. Starters are selected empirically by virtue of their fermentation kinetics and capacity to survive in wine. This study was initiated with the aim to determine whether O. oeni contains plasmids of technological interest. Screening of 11 starters and 33 laboratory strains revealed two closely related plasmids, named pOENI-1 (18.3-kb) and pOENI-1v2 (21.9-kb). Sequence analyses indicate that they use the theta mode of replication, carry genes of maintenance and replication and two genes possibly involved in wine adaptation encoding a predicted sulphite exporter (tauE) and a NADH:flavin oxidoreductase of the old yellow enzyme family (oye). Interestingly, pOENI-1 and pOENI-1v2 were detected only in four strains, but this included three industrial starters. PCR screenings also revealed that tauE is present in six of the 11 starters, being probably inserted in the chromosome of some strains. Microvinification assays performed using strains with and without plasmids did not disclose significant differences of survival in wine or fermentation kinetics. However, analyses of 95 wines at different phases of winemaking showed that strains carrying the plasmids or the genes tauE and oye were predominant during spontaneous malolactic fermentation. Taken together, the results revealed a family of related plasmids associated with industrial starters and indigenous strains performing spontaneous malolactic fermentation that possibly contribute to the technological performance of strains in wine.
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22
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Phenylacetic acid catabolism and its transcriptional regulation in Corynebacterium glutamicum. Appl Environ Microbiol 2012; 78:5796-804. [PMID: 22685150 DOI: 10.1128/aem.01588-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The industrially important organism Corynebacterium glutamicum has been characterized in recent years for its robust ability to assimilate aromatic compounds. In this study, C. glutamicum strain AS 1.542 was investigated for its ability to catabolize phenylacetic acid (PAA). The paa genes were identified; they are organized as a continuous paa gene cluster. The type strain of C. glutamicum, ATCC 13032, is not able to catabolize PAA, but the recombinant strain ATCC 13032/pEC-K18mob2::paa gained the ability to grow on PAA. The paaR gene, encoding a TetR family transcription regulator, was studied in detail. Disruption of paaR in strain AS 1.542 resulted in transcriptional increases of all paa genes. Transcription start sites and putative promoter regions were determined. An imperfect palindromic motif (5'-ACTNACCGNNCGNNCGGTNAGT-3'; 22 bp) was identified in the upstream regions of paa genes. Electrophoretic mobility shift assays (EMSA) demonstrated specific binding of PaaR to this motif, and phenylacetyl coenzyme A (PA-CoA) blocked binding. It was concluded that PaaR is the negative regulator of PAA degradation and that PA-CoA is the PaaR effector. In addition, GlxR binding sites were found, and binding to GlxR was confirmed. Therefore, PAA catabolism in C. glutamicum is regulated by the pathway-specific repressor PaaR, and also likely by the global transcription regulator GlxR. By comparative genomic analysis, we reconstructed orthologous PaaR regulons in 57 species, including species of Actinobacteria, Proteobacteria, and Flavobacteria, that carry PAA utilization genes and operate by conserved binding motifs, suggesting that PaaR-like regulation might commonly exist in these bacteria.
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Shlykov MA, Zheng WH, Chen JS, Saier MH. Bioinformatic characterization of the 4-Toluene Sulfonate Uptake Permease (TSUP) family of transmembrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:703-17. [PMID: 22192777 DOI: 10.1016/j.bbamem.2011.12.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 11/26/2011] [Accepted: 12/06/2011] [Indexed: 11/29/2022]
Abstract
The ubiquitous sequence diverse 4-Toluene Sulfonate Uptake Permease (TSUP) family contains few characterized members and is believed to catalyze the transport of several sulfur-based compounds. Prokaryotic members of the TSUP family outnumber the eukaryotic members substantially, and in prokaryotes, but not eukaryotes, extensive lateral gene transfer occurred during family evolution. Despite unequal representation, homologues from the three taxonomic domains of life share well-conserved motifs. We show that the prototypical eight TMS topology arose from an intragenic duplication of a four transmembrane segment (TMS) unit. Possibly, a two TMS α-helical hairpin structure was the precursor of the 4 TMS repeat unit. Genome context analyses confirmed the proposal of a sulfur-based compound transport role for many TSUP homologues, but functional outliers appear to be prevalent as well. Preliminary results suggest that the TSUP family is a member of a large novel superfamily that includes rhodopsins, integral membrane chaperone proteins, transmembrane electron flow carriers and several transporter families. All of these proteins probably arose via the same pathway: 2→4→8 TMSs followed by loss of a TMS either at the N- or C-terminus, depending on the family, to give the more frequent 7 TMS topology.
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Sigma factors and promoters in Corynebacterium glutamicum. J Biotechnol 2011; 154:101-13. [DOI: 10.1016/j.jbiotec.2011.01.017] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 01/05/2011] [Accepted: 01/18/2011] [Indexed: 11/19/2022]
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Novel genetic tools for diaminopimelic acid selection in virulence studies of Yersinia pestis. PLoS One 2011; 6:e17352. [PMID: 21399698 PMCID: PMC3047566 DOI: 10.1371/journal.pone.0017352] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 01/31/2011] [Indexed: 11/22/2022] Open
Abstract
Molecular studies of bacterial virulence are enhanced by expression of
recombinant DNA during infection to allow complementation of mutants and
expression of reporter proteins in vivo. For highly pathogenic
bacteria, such as Yersinia pestis, these studies are currently
limited because deliberate introduction of antibiotic resistance is restricted
to those few which are not human treatment options. In this work, we report the
development of alternatives to antibiotics as tools for host-pathogen research
during Yersinia pestis infections focusing on the
diaminopimelic acid (DAP) pathway, a requirement for cell wall synthesis in
eubacteria. We generated a mutation in the dapA-nlpB(dapX)
operon of Yersinia pestis KIM D27 and CO92 which eliminated the
expression of both genes. The resulting strains were auxotrophic for
diaminopimelic acid and this phenotype was complemented in
trans by expressing dapA in single and multi-copy.
In vivo, we found that plasmids derived from the p15a
replicon were cured without selection, while selection for DAP enhanced
stability without detectable loss of any of the three resident virulence
plasmids. The dapAX mutation rendered Y.
pestis avirulent in mouse models of bubonic and septicemic plague
which could be complemented when dapAX was inserted in single
or multi-copy, restoring development of disease that was indistinguishable from
the wild type parent strain. We further identified a high level, constitutive
promoter in Y. pestis that could be used to drive expression of
fluorescent reporters in dapAX strains that had minimal impact
to virulence in mouse models while enabling sensitive detection of bacteria
during infection. Thus, diaminopimelic acid selection for single or multi-copy
genetic systems in Yersinia pestis offers an improved
alternative to antibiotics for in vivo studies that causes
minimal disruption to virulence.
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Aguilar-Barajas E, Díaz-Pérez C, Ramírez-Díaz MI, Riveros-Rosas H, Cervantes C. Bacterial transport of sulfate, molybdate, and related oxyanions. Biometals 2011; 24:687-707. [PMID: 21301930 DOI: 10.1007/s10534-011-9421-x] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 01/26/2011] [Indexed: 12/29/2022]
Affiliation(s)
- Esther Aguilar-Barajas
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Edificio B-3, Ciudad Universitaria, 58030 Morelia, Michoacan, Mexico
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Forquin MP, Hébert A, Roux A, Aubert J, Proux C, Heilier JF, Landaud S, Junot C, Bonnarme P, Martin-Verstraete I. Global regulation of the response to sulfur availability in the cheese-related bacterium Brevibacterium aurantiacum. Appl Environ Microbiol 2011; 77:1449-59. [PMID: 21169450 PMCID: PMC3067248 DOI: 10.1128/aem.01708-10] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 12/05/2010] [Indexed: 11/20/2022] Open
Abstract
In this study, we combined metabolic reconstruction, growth assays, and metabolome and transcriptome analyses to obtain a global view of the sulfur metabolic network and of the response to sulfur availability in Brevibacterium aurantiacum. In agreement with the growth of B. aurantiacum in the presence of sulfate and cystine, the metabolic reconstruction showed the presence of a sulfate assimilation pathway, thiolation pathways that produce cysteine (cysE and cysK) or homocysteine (metX and metY) from sulfide, at least one gene of the transsulfuration pathway (aecD), and genes encoding three MetE-type methionine synthases. We also compared the expression profiles of B. aurantiacum ATCC 9175 during sulfur starvation or in the presence of sulfate. Under sulfur starvation, 690 genes, including 21 genes involved in sulfur metabolism and 29 genes encoding amino acids and peptide transporters, were differentially expressed. We also investigated changes in pools of sulfur-containing metabolites and in expression profiles after growth in the presence of sulfate, cystine, or methionine plus cystine. The expression of genes involved in sulfate assimilation and cysteine synthesis was repressed in the presence of cystine, whereas the expression of metX, metY, metE1, metE2, and BL613, encoding a probable cystathionine-γ-synthase, decreased in the presence of methionine. We identified three ABC transporters: two operons encoding transporters were transcribed more strongly during cysteine limitation, and one was transcribed more strongly during methionine depletion. Finally, the expression of genes encoding a methionine γ-lyase (BL929) and a methionine transporter (metPS) was induced in the presence of methionine in conjunction with a significant increase in volatile sulfur compound production.
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Affiliation(s)
- Marie-Pierre Forquin
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
| | - Agnès Hébert
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
| | - Aurélie Roux
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
| | - Julie Aubert
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
| | - Caroline Proux
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
| | - Jean-François Heilier
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
| | - Sophie Landaud
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
| | - Christophe Junot
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
| | - Pascal Bonnarme
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
| | - Isabelle Martin-Verstraete
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
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PigS and PigP regulate prodigiosin biosynthesis in Serratia via differential control of divergent operons, which include predicted transporters of sulfur-containing molecules. J Bacteriol 2010; 193:1076-85. [PMID: 21183667 DOI: 10.1128/jb.00352-10] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Serratia sp. strain ATCC 39006 produces the red-pigmented antibiotic prodigiosin. Regulation of prodigiosin biosynthesis involves a complex hierarchy, with PigP a master transcriptional regulator of multiple genes involved in prodigiosin production. The focus of this study was a member of the PigP regulon, pigS, which encodes an ArsR/SmtB family transcriptional repressor. Mutations in pigS reduced production of prodigiosin by decreasing the transcription of the biosynthetic operon. The pigS gene is the first in a four-gene operon, which also encodes three membrane proteins (pmpABC) of the COG2391 (DUF395; YedE/YeeE) and COG0730 (DUF81; TauE/SafE) families that we propose constitute transport components for sulfur-containing compounds. We provide the first experimental evidence confirming the membrane localization of a COG2391 protein, that of PmpB. Divergently transcribed from pigS-pmpABC is a bicistronic operon (blhA-orfY), which encodes a metallo-β-lactamase and a coenzyme A-disulfide reductase containing a rhodanese homology domain, both of which may participate in reactions with sulfur-containing compounds. The overproduction of the BlhA and OrfY enzymes and the PmpABC membrane proteins differentially affected pigmentation. We have dissected the contributions of these various proteins and determined their importance in the control of prodigiosin production. PigS-mediated control of prodigiosin occurred via binding directly to a short inverted repeat sequence in the intergenic region overlapping the predicted -10 regions of both pigS and blhA promoters and repressing transcription. PigP was required for the activation of these promoters, but only in the absence of PigS-mediated repression.
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Fränzel B, Trötschel C, Rückert C, Kalinowski J, Poetsch A, Wolters DA. Adaptation of Corynebacterium glutamicum to salt-stress conditions. Proteomics 2010; 10:445-57. [PMID: 19950167 DOI: 10.1002/pmic.200900482] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Corynebacterium glutamicum is one of the biotechnologically most important microorganisms because of its ability to enrich amino acids extracellularly. Hence, C. glutamicum requires effective adaptation strategies against both hypo- and hyperosmotic stress. We give a comprehensive and coherent outline about the quantitative dynamics of C. glutamicum during adaptation to hyperosmotic stress at the transcript and protein levels. The osmolyte carrier ProP, playing a pivotal role in hyperosmotic stress defence, exhibits the strongest up-regulation of all proteins. A conspicuously regulated group comprises proteins involved in lipid biosynthesis of the cell envelope. This is in accordance with our observation of a more viscous and stickier cell envelope, which is supported by the findings of an altered lipid composition. Together with our results, showing that several transporters were down-regulated, this membrane adaptation appears to be one of C. glutamicum's major protection strategies against hyperosmotic stress. In addition, we demonstrate that no oxidative stress and no iron limitation occur during salt stress contrary to former postulations. Ultimately, it is remarkable that various proteins with divergent mRNA-protein dynamics and regulation have been observed. This leads to the assumption that there are still unknown mechanisms in between the bacterial transcription, translation and post-translation and that these are waiting to be unravelled.
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Affiliation(s)
- Benjamin Fränzel
- Department of Analytical Chemistry, University of Bochum, Bochum, Germany
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30
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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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31
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Krejčík Z, Hollemeyer K, Smits THM, Cook AM. Isethionate formation from taurine in Chromohalobacter salexigens: purification of sulfoacetaldehyde reductase. MICROBIOLOGY-SGM 2010; 156:1547-1555. [PMID: 20133363 DOI: 10.1099/mic.0.036699-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacterial generation of isethionate (2-hydroxyethanesulfonate) from taurine (2-aminoethanesulfonate) by anaerobic gut bacteria was established in 1980. That phenomenon in pure culture was recognized as a pathway of assimilation of taurine-nitrogen. Based on the latter work, we predicted from genome-sequence data that the marine gammaproteobacterium Chromohalobacter salexigens DSM 3043 would exhibit this trait. Quantitative conversion of taurine to isethionate, identified by mass spectrometry, was confirmed, and the taurine-nitrogen was recovered as cell material. An eight-gene cluster was predicted to encode the inducible vectorial, scalar and regulatory enzymes involved, some of which were known from other taurine pathways. The genes (Csal_0153-Csal_0156) encoding a putative ATP-binding-cassette (ABC) transporter for taurine (TauAB(1)B(2)C) were shown to be inducibly transcribed by reverse transcription (RT-) PCR. An inducible taurine : 2-oxoglutarate aminotransferase [EC 2.6.1.55] was found (Csal_0158); the reaction yielded glutamate and sulfoacetaldehyde. The sulfoacetaldehyde was reduced to isethionate by NADPH-dependent sulfoacetaldehyde reductase (IsfD), a member of the short-chain alcohol dehydrogenase superfamily. The 27 kDa protein (SDS-PAGE) was identified by peptide-mass fingerprinting as the gene product of Csal_0161. The putative exporter of isethionate (IsfE) is encoded by Csal_0160; isfE was inducibly transcribed (RT-PCR). The presumed transcriptional regulator, TauR (Csal_0157), may autoregulate its own expression, typical of GntR-type regulators. Similar gene clusters were found in several marine and terrestrial gammaproteobacteria, which, in the gut canal, could be the source of not only mammalian, but also arachnid and cephalopod isethionate.
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Affiliation(s)
- Zdeněk Krejčík
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, CZ-16637 Prague, Czech Republic.,Department of Biology, The University, D-78457 Konstanz, Germany
| | - Klaus Hollemeyer
- Institute of Biochemical Engineering, Saarland University, Box 50 11 50, D-66041 Saarbrücken, Germany
| | - Theo H M Smits
- Agroscope Changins-Wädenswil ACW, Schloss, Postfach, CH-8820 Wädenswil, Switzerland.,Department of Biology, The University, D-78457 Konstanz, Germany
| | - Alasdair M Cook
- Department of Biology, The University, D-78457 Konstanz, Germany
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32
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Wittmann C. Analysis and engineering of metabolic pathway fluxes in Corynebacterium glutamicum. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2010; 120:21-49. [PMID: 20140657 DOI: 10.1007/10_2009_58] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The Gram-positive soil bacterium Corynebacterium glutamicum was discovered as a natural overproducer of glutamate about 50 years ago. Linked to the steadily increasing economical importance of this microorganism for production of glutamate and other amino acids, the quest for efficient production strains has been an intense area of research during the past few decades. Efficient production strains were created by applying classical mutagenesis and selection and especially metabolic engineering strategies with the advent of recombinant DNA technology. Hereby experimental and computational approaches have provided fascinating insights into the metabolism of this microorganism and directed strain engineering. Today, C. glutamicum is applied to the industrial production of more than 2 million tons of amino acids per year. The huge achievements in recent years, including the sequencing of the complete genome and efficient post genomic approaches, now provide the basis for a new, fascinating era of research - analysis of metabolic and regulatory properties of C. glutamicum on a global scale towards novel and superior bioprocesses.
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Affiliation(s)
- Christoph Wittmann
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Gaussstrasse 17, 38106, Braunschweig, Germany,
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33
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Haussmann U, Qi SW, Wolters D, Rögner M, Liu SJ, Poetsch A. Physiological adaptation of Corynebacterium glutamicum to benzoate as alternative carbon source - a membrane proteome-centric view. Proteomics 2009; 9:3635-51. [PMID: 19639586 DOI: 10.1002/pmic.200900025] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The ability of microorganisms to assimilate aromatic substances as alternative carbon sources is the basis of biodegradation of natural as well as industrial aromatic compounds. In this study, Corynebacterium glutamicum was grown on benzoate as sole carbon and energy source. To extend the scarce knowledge about physiological adaptation processes occurring in this cell compartment, the membrane proteome was investigated under quantitative and qualitative aspects by applying shotgun proteomics to reach a comprehensive survey. Membrane proteins were relatively quantified using an internal standard metabolically labeled with (15)N. Altogether, 40 proteins were found to change their abundance during growth on benzoate in comparison to glucose. A global adaptation was observed in the membrane of benzoate-grown cells, characterized by increased abundance of proteins of the respiratory chain, by a starvation response, and by changes in sulfur metabolism involving the regulator McbR. Additional to the relative quantification, stable isotope-labeled synthetic peptides were used for the absolute quantification of the two benzoate transporters of C. glutamicum, BenK and BenE. It was found that both transporters were expressed during growth on benzoate, suggesting that both contribute substantially to benzoate uptake.
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Affiliation(s)
- Ute Haussmann
- Plant Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
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34
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Dondrup M, Hüser AT, Mertens D, Goesmann A. An evaluation framework for statistical tests on microarray data. J Biotechnol 2009; 140:18-26. [PMID: 19297690 DOI: 10.1016/j.jbiotec.2009.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Microarray analysis has become a popular and routine method in functional genomics. It is typical for such experiments to involve a small number of replicates, which causes unreliable estimates of the sample variance. Microarrays have fostered the development of new statistical methods to analyze data resulting from experiments with small sample sizes. In this study, we tackle the problem of evaluating the performance of statistical tests for generating ranked gene lists from two-channel direct comparisons. We propose an evaluation method based on a oligonucleotide microarray with a large number of replicate spots yielding a maximum of 400 replicates per gene. We apply Spearman's rank correlation coefficient to ranked gene-lists generated by eight widely used microarray specific test statistics, which are applied to small random samples. We could show that variance stabilizing methods such as Cyber-T, SAM, and LIMMA can be beneficial for very small sample sizes and that SAM and the t-test provide stronger control of the type I error rate than the other methods. Specifically, we report that for four replicates all methods reach a high to very high correlation with our reference standard.
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Affiliation(s)
- Michael Dondrup
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
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35
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Lee SM, Hwang BJ, Kim Y, Lee HS. The cmaR gene of Corynebacterium ammoniagenes performs a novel regulatory role in the metabolism of sulfur-containing amino acids. Microbiology (Reading) 2009; 155:1878-1889. [PMID: 19383689 DOI: 10.1099/mic.0.024976-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel regulatory gene, which performs an essential function in sulfur metabolism, has been identified inCorynebacterium ammoniagenesand was designatedcmaR(cysteine andmethionine regulator inC.ammoniagenes). ThecmaR-disrupted strain (ΔcmaR) lost the ability to grow on minimal medium, and was identified as a methionine and cysteine double auxotroph. The mutant strain proved unable to convert cysteine to methionine (and vice versa), and lost the ability to assimilate and reduce sulfate to sulfide. In the ΔcmaRstrain, the mRNAs of the methionine biosynthetic genesmetYX,metBandmetFEwere significantly reduced, and the activities of the methionine biosynthetic enzymes cystathionineγ-synthase,O-acetylhomoserine sulfhydrylase, and cystathionineβ-lyase were relatively low, thereby suggesting that thecmaRgene exerts a positive regulatory effect on methionine biosynthetic genes. In addition, with the exception ofcysK, reduced transcription levels of the sulfur-assimilatory genescysIXYZandcysHDNwere noted in thecmaR-disrupted strain, which suggests that sulfur assimilation is also under the positive control of thecmaRgene. Furthermore, the expression of thecmaRgene itself was strongly induced via the addition of cysteine or methionine alone, but not the introduction of both amino acids together to the growth medium. In addition, the expression of thecmaRgene was enhanced in anmcbR-disrupted strain, which suggests thatcmaRis under the negative control of McbR, which has been identified as a global regulator of sulfur metabolism. DNA binding of the purified CmaR protein to the promoter region of its target genes could be demonstratedin vitro. No metabolite effector was required for the protein to bind DNA. These results demonstrated that thecmaRgene ofC. ammoniagenesplays a role similar to but distinct from that of the functional homologuecysRofCorynebacterium glutamicum.
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Affiliation(s)
- Seok-Myung Lee
- Department of Biotechnology and Bioinformatics, Korea University, Jochiwon, Chungnam 339-700, Republic of Korea
| | - Byung-Joon Hwang
- R&D Center, Daesang Co. 125-8, Pyokyo-Ri, Majang-Myun, Ichon, Kyoungki 467-813, Republic of Korea
| | - Younhee Kim
- Department of Oriental Medicine, Semyung University, Checheon, Chungbuk 390-230, Republic of Korea
| | - Heung-Shick Lee
- Department of Biotechnology and Bioinformatics, Korea University, Jochiwon, Chungnam 339-700, Republic of Korea
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36
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Krömer JO, Bolten CJ, Heinzle E, Schröder H, Wittmann C. Physiological response of Corynebacterium glutamicum to oxidative stress induced by deletion of the transcriptional repressor McbR. Microbiology (Reading) 2008; 154:3917-3930. [DOI: 10.1099/mic.0.2008/021204-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jens O. Krömer
- Biochemical Engineering Institute, Saarland University, Saarbrücken, Germany
| | - Christoph J. Bolten
- Biochemical Engineering Institute, Saarland University, Saarbrücken, Germany
| | - Elmar Heinzle
- Biochemical Engineering Institute, Saarland University, Saarbrücken, Germany
| | | | - Christoph Wittmann
- Biochemical Engineering Institute, Saarland University, Saarbrücken, Germany
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37
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Rückert C, Milse J, Albersmeier A, Koch DJ, Pühler A, Kalinowski J. The dual transcriptional regulator CysR in Corynebacterium glutamicum ATCC 13032 controls a subset of genes of the McbR regulon in response to the availability of sulphide acceptor molecules. BMC Genomics 2008; 9:483. [PMID: 18854009 PMCID: PMC2580772 DOI: 10.1186/1471-2164-9-483] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 10/14/2008] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Regulation of sulphur metabolism in Corynebacterium glutamicum ATCC 13032 has been studied intensively in the last few years, due to its industrial as well as scientific importance. Previously, the gene cg0156 was shown to belong to the regulon of McbR, a global transcriptional repressor of sulphur metabolism in C. glutamicum. This gene encodes a putative ROK-type regulator, a paralogue of the activator of sulphonate utilisation, SsuR. Therefore, it is an interesting candidate for study to further the understanding of the regulation of sulphur metabolism in C. glutamicum. RESULTS Deletion of cg0156, now designated cysR, results in the inability of the mutant to utilise sulphate and aliphatic sulphonates. DNA microarray hybridisations revealed 49 genes with significantly increased and 48 with decreased transcript levels in presence of the native CysR compared to a cysR deletion mutant. Among the genes positively controlled by CysR were the gene cluster involved in sulphate reduction, fpr2 cysIXHDNYZ, and ssuR. Gel retardation experiments demonstrated that binding of CysR to DNA depends in vitro on the presence of either O-acetyl-L-serine or O-acetyl-L-homoserine. Mapping of the transcription start points of five transcription units helped to identify a 10 bp inverted repeat as the possible CysR binding site. Subsequent in vivo tests proved this motif to be necessary for CysR-dependent transcriptional regulation. CONCLUSION CysR acts as the functional analogue of the unrelated LysR-type regulator CysB from Escherichia coli, controlling sulphide production in response to acceptor availability. In both bacteria, gene duplication events seem to have taken place which resulted in the evolution of dedicated regulators for the control of sulphonate utilisation. The striking convergent evolution of network topology indicates the strong selective pressure to control the metabolism of the essential but often toxic sulphur-containing (bio-)molecules.
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Affiliation(s)
- Christian Rückert
- Institut für Systembiologie & Genomforschung, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld, Germany.
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Krejcík Z, Denger K, Weinitschke S, Hollemeyer K, Paces V, Cook AM, Smits THM. Sulfoacetate released during the assimilation of taurine-nitrogen by Neptuniibacter caesariensis: purification of sulfoacetaldehyde dehydrogenase. Arch Microbiol 2008; 190:159-68. [PMID: 18506422 DOI: 10.1007/s00203-008-0386-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Revised: 04/28/2008] [Accepted: 05/05/2008] [Indexed: 11/25/2022]
Abstract
Taurine (2-aminoethanesulfonate) is a widespread natural product whose nitrogen moiety was recently shown to be assimilated by bacteria, usually with excretion of an organosulfonate via undefined novel pathways; other data involve transcriptional regulator TauR in taurine metabolism. A screen of genome sequences for TauR with the BLAST algorithm allowed the hypothesis that the marine gammaproteobacterium Neptuniibacter caesariensis MED92 would inducibly assimilate taurine-nitrogen and excrete sulfoacetate. The pathway involved an ABC transporter (TauABC), taurine:pyruvate aminotransferase (Tpa), a novel sulfoacetaldehyde dehydrogenase (SafD) and exporter(s) of sulfoacetate (SafE) (DUF81). Ten candidate genes in two clusters involved three sets of paralogues (for TauR, Tpa and SafE). Inducible Tpa and SafD were detected in cell extracts. SafD was purified 600-fold to homogeneity in two steps. The monomer had a molecular mass of 50 kDa (SDS-PAGE); data from gel filtration chromatography indicated a tetrameric native protein. SafD was specific for sulfoacetaldehyde with a K (m)-value of 0.12 mM. The N-terminal amino acid sequence of SafD confirmed the identity of the safD gene. The eight pathway genes were transcribed inducibly, which indicated expression of the whole hypothetical pathway. We presume that this pathway is one source of sulfoacetate in nature, where this compound is dissimilated by many bacteria.
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Affiliation(s)
- Zdenĕk Krejcík
- Department of Biology, The University, 78457, Constance, Germany
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39
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Lu ZJ, Cao YQ, Long WJ, Long ZD, Chen G, Ma QS, Wu B. Isolation and characterization of an operon involved in sulfate and sulfite metabolism in Sinorhizobium fredii. FEMS Microbiol Lett 2008; 282:89-99. [PMID: 18336549 DOI: 10.1111/j.1574-6968.2008.01102.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A gene cluster ORFabcd from a Sinorhizobium fredii HN01 mutant strain HSMRalpha was isolated. We showed that it was an operon involved in sulfur metabolism. Functional studies revealed that, except for ORFb, the three genes ORFa, ORFc and ORFd were involved in sulfite reduction. ORFa and ORFc were similar to the cysG and cysI from Sinorhizobium meliloti 1021 and Rhizobium etli CFN 42, respectively. ORFd encodes a conserved hypothetical protein in other bacteria. We demonstrate here, for the first time, that it was a new locus involved in sulfate assimilation in S. fredii HN01 and we designated it as cysII.
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Affiliation(s)
- Zu-Jun Lu
- College of Life Science and Technology of Guangxi University, Nanning, Guangxi, China
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SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 2008; 452:741-4. [PMID: 18337719 DOI: 10.1038/nature06776] [Citation(s) in RCA: 226] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Accepted: 01/30/2008] [Indexed: 11/08/2022]
Abstract
Sulphur is a universally required cell nutrient found in two amino acids and other small organic molecules. All aerobic marine bacteria are known to use assimilatory sulphate reduction to supply sulphur for biosynthesis, although many can assimilate sulphur from organic compounds that contain reduced sulphur atoms. An analysis of three complete 'Candidatus Pelagibacter ubique' genomes, and public ocean metagenomic data sets, suggested that members of the ubiquitous and abundant SAR11 alphaproteobacterial clade are deficient in assimilatory sulphate reduction genes. Here we show that SAR11 requires exogenous sources of reduced sulphur, such as methionine or 3-dimethylsulphoniopropionate (DMSP) for growth. Titrations of the algal osmolyte DMSP in seawater medium containing all other macronutrients in excess showed that 1.5 x 10(8) SAR11 cells are produced per nanomole of DMSP. Although it has been shown that other marine alphaproteobacteria use sulphur from DMSP in preference to sulphate, our results indicate that 'Cand. P. ubique' relies exclusively on reduced sulphur compounds that originate from other plankton.
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Kosaka T, Kato S, Shimoyama T, Ishii S, Abe T, Watanabe K. The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota. Genome Res 2008; 18:442-8. [PMID: 18218977 DOI: 10.1101/gr.7136508] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The anaerobic biodegradation of organic matter is accomplished by sequential syntrophic catabolism by microbes in different niches. Pelotomaculum thermopropionicum is a representative syntrophic bacterium that catalyzes the intermediate bottleneck step in the anaerobic-biodegradation process, whereby volatile fatty acids (VFAs) and alcohols produced by upstream fermenting bacteria are converted to acetate, hydrogen, and carbon dioxide (substrates for downstream methanogenic archaea). To reveal genomic features that contribute to our understanding of the ecological niche and evolution of P. thermopropionicum, we sequenced its 3,025,375-bp genome and performed comparative analyses with genomes of other community members available in the databases. In the genome, 2920 coding sequences (CDSs) were identified. These CDSs showed a distinct distribution pattern in the functional categories of the Clusters of Orthologous Groups database, which is considered to reflect the niche of this organism. P. thermopropionicum has simple catabolic pathways, in which the propionate-oxidizing methylmalonyl-CoA pathway constitutes the backbone and is linked to several peripheral pathways. Genes for most of the important catabolic enzymes are physically linked to those for PAS-domain-containing regulators, suggesting that the catabolic pathways are regulated in response to environmental conditions and/or global cellular situations rather than specific substrates. Comparative analyses of codon usages revealed close evolutionary relationships between P. thermopropionicum and other niche members, while it was distant from phylogenetically related sugar-fermenting bacteria. These analyses suggest that P. thermopropionicum has evolved as a syntrophy specialist by interacting with niche-associated microbes.
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Affiliation(s)
- Tomoyuki Kosaka
- Laboratory of Applied Microbiology, Marine Biotechnology Institute, Kamaishi, Iwate 026-0001, Japan
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Xu Z, Zhou Y, Li L, Zhou R, Xiao S, Wan Y, Zhang S, Wang K, Li W, Li L, Jin H, Kang M, Dalai B, Li T, Liu L, Cheng Y, Zhang L, Xu T, Zheng H, Pu S, Wang B, Gu W, Zhang XL, Zhu GF, Wang S, Zhao GP, Chen H. Genome biology of Actinobacillus pleuropneumoniae JL03, an isolate of serotype 3 prevalent in China. PLoS One 2008; 3:e1450. [PMID: 18197260 PMCID: PMC2175527 DOI: 10.1371/journal.pone.0001450] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Accepted: 12/19/2007] [Indexed: 11/19/2022] Open
Abstract
Actinobacillus pleuropneumoniae is the etiologic agent of porcine contagious pleuropneumonia, a cause of considerable world wide economic losses in the swine industry. We sequenced the complete genome of A. pleuropneumoniae, JL03, an isolate of serotype 3 prevalent in China. Its genome is a single chromosome of 2,242,062 base pairs containing 2,097 predicted protein-coding sequences, six ribosomal rRNA operons, and 63 tRNA genes. Preliminary analysis of the genomic sequence and the functions of the encoded proteins not only confirmed the present physiological and pathological knowledge but also offered new insights into the metabolic and virulence characteristics of this important pathogen. We identified a full spectrum of genes related to its characteristic chemoheterotrophic catabolism of fermentation and respiration with an incomplete TCA system for anabolism. In addition to confirming the lack of ApxI toxin, identification of a nonsense mutation in apxIVA and a 5'-proximal truncation of the flp operon deleting both its promoter and the flp1flp2tadV genes have provided convincing scenarios for the low virulence property of JL03. Comparative genomic analysis using the available sequences of other serotypes, probable strain (serotype)-specific genomic islands related to capsular polysaccharides and lipopolysaccharide O-antigen biosyntheses were identified in JL03, which provides a foundation for future research into the mechanisms of serotypic diversity of A. pleuropneumoniae.
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Affiliation(s)
- Zhuofei Xu
- Division of Animal Infectious Disease, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yan Zhou
- Shanghai - MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Science, Fudan University, Shanghai, China
| | - Liangjun Li
- Division of Animal Infectious Disease, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Rui Zhou
- Division of Animal Infectious Disease, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Shaobo Xiao
- Division of Animal Infectious Disease, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yun Wan
- Division of Animal Infectious Disease, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Sihua Zhang
- Division of Animal Infectious Disease, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Kai Wang
- Shanghai - MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Wei Li
- Division of Animal Infectious Disease, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Lu Li
- Division of Animal Infectious Disease, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Hui Jin
- Division of Animal Infectious Disease, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Mingsong Kang
- Division of Animal Infectious Disease, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Baolige Dalai
- Division of Animal Infectious Disease, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Tingting Li
- Division of Animal Infectious Disease, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Lei Liu
- Division of Animal Infectious Disease, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yangyi Cheng
- Shanghai - MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Lei Zhang
- Shanghai - MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Tao Xu
- Shanghai - MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Huajun Zheng
- Shanghai - MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Shiying Pu
- Shanghai - MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Bofei Wang
- Shanghai - MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Wenyi Gu
- Shanghai - MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Xiang-Lin Zhang
- Shanghai - MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Geng-Feng Zhu
- Shanghai - MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Shengyue Wang
- Shanghai - MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Science, Fudan University, Shanghai, China
| | - Guo-Ping Zhao
- Shanghai - MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Science, Fudan University, Shanghai, China
- National Engineering Center for Biochip Research at Shanghai, Shanghai, China
- Laboratory of Molecular Microbiology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Huanchun Chen
- Division of Animal Infectious Disease, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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Weinitschke S, Denger K, Cook AM, Smits THM. The DUF81 protein TauE in Cupriavidus necator H16, a sulfite exporter in the metabolism of C2 sulfonates. MICROBIOLOGY-SGM 2007; 153:3055-3060. [PMID: 17768248 DOI: 10.1099/mic.0.2007/009845-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The degradation of taurine, isethionate and sulfoacetate in Cupriavidus necator (Ralstonia eutropha) H16 was shown by enzyme assays to be inducible, and each pathway involved sulfoacetaldehyde, which was subject to phosphatolysis by a common sulfoacetaldehyde acetyltransferase (Xsc, H16_B1870) to yield acetyl phosphate and sulfite. The neighbouring genes encoded phosphate acetyltransferase (Pta, H16_B1871) and a hypothetical protein [domain of unknown function (DUF)81, H16_B1872], with eight derived transmembrane helices. RT-PCR showed inducible transcription of these three genes, and led to the hypothesis that H16_B1872 and orthologous proteins represent a sulfite exporter, which was named TauE.
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Affiliation(s)
| | - Karin Denger
- Department of Biology, The University, D-78457 Konstanz, Germany
| | - Alasdair M Cook
- Department of Biology, The University, D-78457 Konstanz, Germany
| | - Theo H M Smits
- Department of Biology, The University, D-78457 Konstanz, Germany
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Neuweger H, Baumbach J, Albaum S, Bekel T, Dondrup M, Hüser AT, Kalinowski J, Oehm S, Pühler A, Rahmann S, Weile J, Goesmann A. CoryneCenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data. BMC SYSTEMS BIOLOGY 2007; 1:55. [PMID: 18034885 PMCID: PMC2212648 DOI: 10.1186/1752-0509-1-55] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2007] [Accepted: 11/22/2007] [Indexed: 11/10/2022]
Abstract
BACKGROUND The introduction of high-throughput genome sequencing and post-genome analysis technologies, e.g. DNA microarray approaches, has created the potential to unravel and scrutinize complex gene-regulatory networks on a large scale. The discovery of transcriptional regulatory interactions has become a major topic in modern functional genomics. RESULTS To facilitate the analysis of gene-regulatory networks, we have developed CoryneCenter, a web-based resource for the systematic integration and analysis of genome, transcriptome, and gene regulatory information for prokaryotes, especially corynebacteria. For this purpose, we extended and combined the following systems into a common platform: (1) GenDB, an open source genome annotation system, (2) EMMA, a MAGE compliant application for high-throughput transcriptome data storage and analysis, and (3) CoryneRegNet, an ontology-based data warehouse designed to facilitate the reconstruction and analysis of gene regulatory interactions. We demonstrate the potential of CoryneCenter by means of an application example. Using microarray hybridization data, we compare the gene expression of Corynebacterium glutamicum under acetate and glucose feeding conditions: Known regulatory networks are confirmed, but moreover CoryneCenter points out additional regulatory interactions. CONCLUSION CoryneCenter provides more than the sum of its parts. Its novel analysis and visualization features significantly simplify the process of obtaining new biological insights into complex regulatory systems. Although the platform currently focusses on corynebacteria, the integrated tools are by no means restricted to these species, and the presented approach offers a general strategy for the analysis and verification of gene regulatory networks. CoryneCenter provides freely accessible projects with the underlying genome annotation, gene expression, and gene regulation data. The system is publicly available at http://www.CoryneCenter.de.
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Affiliation(s)
- Heiko Neuweger
- Computational Methods for Emerging Technologies group, Bielefeld University, Bielefeld, Germany.
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Hänssler E, Müller T, Jessberger N, Völzke A, Plassmeier J, Kalinowski J, Krämer R, Burkovski A. FarR, a putative regulator of amino acid metabolism in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2007; 76:625-32. [PMID: 17483938 DOI: 10.1007/s00253-007-0929-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Revised: 03/06/2007] [Accepted: 03/06/2007] [Indexed: 11/25/2022]
Abstract
With the publication of the Corynebacterium glutamicum genome sequence, a global characterization of genes controlled by functionally uncharacterized transcriptional regulators became possible. We used DNA microarrays in combination with gel retardation experiments to study gene regulation by FarR, a HutC/FarR-type regulator of the GntR family. Based on our results, FarR seems to be involved in the regulation of amino acid biosynthesis in C. glutamicum. Especially, transcript levels of the arg cluster and the gdh gene are influenced by deletion of farR.
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Affiliation(s)
- Eva Hänssler
- Lehrstuhl für Mikrobiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
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McLean KJ, Dunford AJ, Neeli R, Driscoll MD, Munro AW. Structure, function and drug targeting in Mycobacterium tuberculosis cytochrome P450 systems. Arch Biochem Biophys 2007; 464:228-40. [PMID: 17482138 DOI: 10.1016/j.abb.2007.03.026] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Revised: 03/02/2007] [Accepted: 03/23/2007] [Indexed: 11/17/2022]
Abstract
The human pathogen Mycobacterium tuberculosis has made a dramatic resurgence in recent years. Drug resistant and multidrug resistant strains are prevalent, and novel antibiotic strategies are desperately needed to counter Mtb's global spread. The M. tuberculosis genome sequence revealed an unexpectedly high number of cytochrome P450 (P450) enzymes (20), and parallel studies indicated that P450-inhibiting azole drugs had potent anti-mycobacterial activity. This article reviews current knowledge of structure/function of P450s and redox partner systems in M. tuberculosis. Recent research has highlighted potential drug target Mtb P450s and provided evidence for roles of selected P450 isoforms in host lipid and sterol/steroid transformations. Structural analysis of key Mtb P450s has provided fundamental information on the nature of the heme binding site, P450 interactions with azole drugs, the biochemical nature of cytochrome P420, and novel mutational adaptations by which azole binding to P450s may be diminished to facilitate azole resistance.
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Affiliation(s)
- Kirsty J McLean
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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Kovaleva GY, Gelfand MS. Regulation of methionine/cysteine biosynthesis in Corynebacterium glutamicum and related organisms. Mol Biol 2007. [DOI: 10.1134/s0026893307010177] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Brockmann-Gretza O, Kalinowski J. Global gene expression during stringent response in Corynebacterium glutamicum in presence and absence of the rel gene encoding (p)ppGpp synthase. BMC Genomics 2006; 7:230. [PMID: 16961923 PMCID: PMC1578569 DOI: 10.1186/1471-2164-7-230] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2006] [Accepted: 09/08/2006] [Indexed: 12/01/2022] Open
Abstract
Background The stringent response is the initial reaction of microorganisms to nutritional stress. During stringent response the small nucleotides (p)ppGpp act as global regulators and reprogram bacterial transcription. In this work, the genetic network controlled by the stringent response was characterized in the amino acid-producing Corynebacterium glutamicum. Results The transcriptome of a C. glutamicum rel gene deletion mutant, unable to synthesize (p)ppGpp and to induce the stringent response, was compared with that of its rel-proficient parent strain by microarray analysis. A total of 357 genes were found to be transcribed differentially in the rel-deficient mutant strain. In a second experiment, the stringent response was induced by addition of DL-serine hydroxamate (SHX) in early exponential growth phase. The time point of the maximal effect on transcription was determined by real-time RT-PCR using the histidine and serine biosynthetic genes. Transcription of all of these genes reached a maximum at 10 minutes after SHX addition. Microarray experiments were performed comparing the transcriptomes of SHX-induced cultures of the rel-proficient strain and the rel mutant. The differentially expressed genes were grouped into three classes. Class A comprises genes which are differentially regulated only in the presence of an intact rel gene. This class includes the non-essential sigma factor gene sigB which was upregulated and a large number of genes involved in nitrogen metabolism which were downregulated. Class B comprises genes which were differentially regulated in response to SHX in both strains, independent of the rel gene. A large number of genes encoding ribosomal proteins fall into this class, all being downregulated. Class C comprises genes which were differentially regulated in response to SHX only in the rel mutant. This class includes genes encoding putative stress proteins and global transcriptional regulators that might be responsible for the complex transcriptional patterns detected in the rel mutant when compared directly with its rel-proficient parent strain. Conclusion In C. glutamicum the stringent response enfolds a fast answer to an induced amino acid starvation on the transcriptome level. It also showed some significant differences to the transcriptional reactions occuring in Escherichia coli and Bacillus subtilis. Notable are the rel-dependent regulation of the nitrogen metabolism genes and the rel-independent regulation of the genes encoding ribosomal proteins.
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Affiliation(s)
- Olaf Brockmann-Gretza
- Institut für Genomforschung, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Institut für Genomforschung, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany
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Mormann S, Lömker A, Rückert C, Gaigalat L, Tauch A, Pühler A, Kalinowski J. Random mutagenesis in Corynebacterium glutamicum ATCC 13032 using an IS6100-based transposon vector identified the last unknown gene in the histidine biosynthesis pathway. BMC Genomics 2006; 7:205. [PMID: 16901339 PMCID: PMC1590026 DOI: 10.1186/1471-2164-7-205] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Accepted: 08/10/2006] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Corynebacterium glutamicum, a Gram-positive bacterium of the class Actinobacteria, is an industrially relevant producer of amino acids. Several methods for the targeted genetic manipulation of this organism and rational strain improvement have been developed. An efficient transposon mutagenesis system for the completely sequenced type strain ATCC 13032 would significantly advance functional genome analysis in this bacterium. RESULTS A comprehensive transposon mutant library comprising 10,080 independent clones was constructed by electrotransformation of the restriction-deficient derivative of strain ATCC 13032, C. glutamicum RES167, with an IS6100-containing non-replicative plasmid. Transposon mutants had stable cointegrates between the transposon vector and the chromosome. Altogether 172 transposon integration sites have been determined by sequencing of the chromosomal inserts, revealing that each integration occurred at a different locus. Statistical target site analyses revealed an apparent absence of a target site preference. From the library, auxotrophic mutants were obtained with a frequency of 2.9%. By auxanography analyses nearly two thirds of the auxotrophs were further characterized, including mutants with single, double and alternative nutritional requirements. In most cases the nutritional requirement observed could be correlated to the annotation of the mutated gene involved in the biosynthesis of an amino acid, a nucleotide or a vitamin. One notable exception was a clone mutagenized by transposition into the gene cg0910, which exhibited an auxotrophy for histidine. The protein sequence deduced from cg0910 showed high sequence similarities to inositol-1(or 4)-monophosphatases (EC 3.1.3.25). Subsequent genetic deletion of cg0910 delivered the same histidine-auxotrophic phenotype. Genetic complementation of the mutants as well as supplementation by histidinol suggests that cg0910 encodes the hitherto unknown essential L-histidinol-phosphate phosphatase (EC 3.1.3.15) in C. glutamicum. The cg0910 gene, renamed hisN, and its encoded enzyme have putative orthologs in almost all Actinobacteria, including mycobacteria and streptomycetes. CONCLUSION The absence of regional and sequence preferences of IS6100-transposition demonstrate that the established system is suitable for efficient genome-scale random mutagenesis in the sequenced type strain C.glutamicum ATCC 13032. The identification of the hisN gene encoding histidinol-phosphate phosphatase in C. glutamicum closed the last gap in histidine synthesis in the Actinobacteria. The system might be a valuable genetic tool also in other bacteria due to the broad host-spectrum of IS6100.
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Affiliation(s)
- Sascha Mormann
- Institut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
- Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Alexander Lömker
- Institut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
- Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Christian Rückert
- Institut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
- Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Lars Gaigalat
- Institut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
- Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Andreas Tauch
- Institut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Alfred Pühler
- Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Jörn Kalinowski
- Institut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
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50
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Brune I, Werner H, Hüser AT, Kalinowski J, Pühler A, Tauch A. The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum. BMC Genomics 2006; 7:21. [PMID: 16469103 PMCID: PMC1382209 DOI: 10.1186/1471-2164-7-21] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Accepted: 02/09/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The knowledge about complete bacterial genome sequences opens the way to reconstruct the qualitative topology and global connectivity of transcriptional regulatory networks. Since iron is essential for a variety of cellular processes but also poses problems in biological systems due to its high toxicity, bacteria have evolved complex transcriptional regulatory networks to achieve an effective iron homeostasis. Here, we apply a combination of transcriptomics, bioinformatics, in vitro assays, and comparative genomics to decipher the regulatory network of the iron-dependent transcriptional regulator DtxR of Corynebacterium glutamicum. RESULTS A deletion of the dtxR gene of C. glutamicum ATCC 13032 led to the mutant strain C. glutamicum IB2103 that was able to grow in minimal medium only under low-iron conditions. By performing genome-wide DNA microarray hybridizations, differentially expressed genes involved in iron metabolism of C. glutamicum were detected in the dtxR mutant. Bioinformatics analysis of the genome sequence identified a common 19-bp motif within the upstream region of 31 genes, whose differential expression in C. glutamicum IB2103 was verified by real-time reverse transcription PCR. Binding of a His-tagged DtxR protein to oligonucleotides containing the 19-bp motifs was demonstrated in vitro by DNA band shift assays. At least 64 genes encoding a variety of physiological functions in iron transport and utilization, in central carbohydrate metabolism and in transcriptional regulation are controlled directly by the DtxR protein. A comparison with the bioinformatically predicted networks of C. efficiens, C. diphtheriae and C. jeikeium identified evolutionary conserved elements of the DtxR network. CONCLUSION This work adds considerably to our currrent understanding of the transcriptional regulatory network of C. glutamicum genes that are controlled by DtxR. The DtxR protein has a major role in controlling the expression of genes involved in iron metabolism and exerts a dual regulatory function as repressor of genes participating in iron uptake and utilization and as activator of genes responsible for iron storage and DNA protection. The data suggest that the DtxR protein acts as global regulator by controlling the expression of other regulatory proteins that might take care of an iron-dependent regulation of a broader transcriptional network of C. glutamicum genes.
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Affiliation(s)
- Iris Brune
- Institut für Genomforschung, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Hendrikje Werner
- Institut für Genomforschung, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Andrea T Hüser
- Institut für Genomforschung, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Institut für Genomforschung, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Alfred Pühler
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Andreas Tauch
- Institut für Genomforschung, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
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