1
|
Thøgersen MS, Zervas A, Stougaard P, Ellegaard-Jensen L. Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland. Front Microbiol 2024; 15:1358787. [PMID: 38655082 PMCID: PMC11035741 DOI: 10.3389/fmicb.2024.1358787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/08/2024] [Indexed: 04/26/2024] Open
Abstract
The ikaite columns in the Ikka Fjord, SW Greenland, represent a permanently cold and alkaline environment known to contain a rich bacterial diversity. 16S and 18S rRNA gene amplicon and metagenomic sequencing was used to investigate the microbial diversity in the columns and for the first time, the eukaryotic and archaeal diversity in ikaite columns were analyzed. The results showed a rich prokaryotic diversity that varied across columns as well as within each column. Seven different archaeal phyla were documented in multiple locations inside the columns. The columns also contained a rich eukaryotic diversity with 27 phyla representing microalgae, protists, fungi, and small animals. Based on metagenomic sequencing, 25 high-quality MAGs were assembled and analyzed for the presence of genes involved in cycling of nitrogen, sulfur, and phosphorous as well as genes encoding carbohydrate-active enzymes (CAZymes), showing a potentially very bioactive microbial community.
Collapse
|
2
|
Peng C, Shi Y, Wang S, Zhang J, Wan X, Yin Y, Wang D, Wang W. Genetic and functional characterization of multiple thermophilic organosulfur-removal systems reveals desulfurization potentials for waste residue oil cleaning. JOURNAL OF HAZARDOUS MATERIALS 2023; 446:130706. [PMID: 36603426 DOI: 10.1016/j.jhazmat.2022.130706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/09/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
Heavy oil and petroleum refining residues usually contain high concentrations of recalcitrant hazardous organosulfur compounds, causing long-term serious global environmental pollution during leakage and combustion. Research conducted here identified a unique thermophilic bacterium Parageobacillus thermoglucosidasius W-36 with the notable ability of waste residue oil desulfurization, utilization and tolerance of multiplex hazardous organosulfur pollutants. Genome information mining revealed multiple desulfurization systems in three organosulfur-utilizing gene clusters. Enzymatic characterization, phylogenetic relationships, transcriptional performance and structural prediction indicated four novel key monooxygenases for diverse organosulfur removal. Importantly, all monooxygenases shared obvious commonalities in the predicted tertiary structure backbone and catalytic characteristics of C-S bond cleavage, implying the potential of genetic engineering for broad-spectrum hazardous organosulfur removal. Therefore, this work demonstrated the important application potential of thermophilic bacteria as a promising alternative biodesulfurization way for waste residue oil cleaning.
Collapse
Affiliation(s)
- Chenchen Peng
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China
| | - Yukun Shi
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China
| | - Shuo Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China
| | - Jingjing Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China
| | - Xuehua Wan
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China
| | - Yalin Yin
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China
| | - Dongxu Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China
| | - Wei Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China; Tianjin Key Laboratory of Microbial Functional Genomics, TEDA, Tianjin 300457, PR China.
| |
Collapse
|
3
|
Zhang W, Wu Y, Wu J, Zheng X, Chen Y. Enhanced removal of sulfur-containing organic pollutants from actual wastewater by biofilm reactor: Insights of sulfur transformation and bacterial metabolic traits. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 313:120187. [PMID: 36116571 DOI: 10.1016/j.envpol.2022.120187] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/06/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
Sulfur-containing organic pollutants in wastewater could threaten human health due to their high malodor and toxicity, and their conversion processes are more complex than inorganic sulfur compounds. Membrane aerated biofilm reactor (MABR), as a novel and environmentally-friendly biofilm-based technology, is able to remove inorganic sulfur in synthetic wastewater. However, it is unknown how sulfur-containing organic pollutants in actual wastewater are transformed in MABR system. This work demonstrated the feasibility of MABR to eliminate sulfur-containing organic pollutants in actual wastewater, and the removal efficiency could be reached at approximately 100%. Meanwhile, over 70% of sulfur-containing organic contaminants were transformed to SO42- during the long-term operation. Further analysis indicated that the functional bacteria that participated in sulfur transformation and carbohydrates degradation (e.g., Chujaibacter, Microscillaceaesp., and Thiobacillus) were evidently enriched when treating actual wastewater. Moreover, the critical metabolic pathways (e.g., sulfur metabolism, glycolysis metabolism, and pyruvate metabolism), and the corresponding genetic expressions (e.g., nrrA, tauA, tauC, sorA, and SUOX) were evidently up-regulated during long-term operation, which was beneficial for the transformation of sulfur-containing organic pollutants in actual wastewater by MABR. This work would expand the application of MABR for treating the actual sulfur-containing organic wastewater and provide an in-depth understanding of the organic sulfur transformation in MABR.
Collapse
Affiliation(s)
- Wei Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Yang Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Jing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Xiong Zheng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| |
Collapse
|
4
|
Méndez V, Holland S, Bhardwaj S, McDonald J, Khan S, O'Carroll D, Pickford R, Richards S, O'Farrell C, Coleman N, Lee M, Manefield MJ. Aerobic biotransformation of 6:2 fluorotelomer sulfonate by Dietzia aurantiaca J3 under sulfur-limiting conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154587. [PMID: 35306084 DOI: 10.1016/j.scitotenv.2022.154587] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 03/11/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
The polyfluorinated alkyl substance 6:2 fluorotelomer sulfonate (6:2 FTS) has been detected in diverse environments impacted by aqueous film-forming foams used for firefighting. In this study, a bacterial strain (J3) using 6:2 FTS as a sulfur source was isolated from landfill leachate previously exposed to polyfluoroalkyl substances in New South Wales, Australia. Strain J3 shares 99.9% similarity with the 16S rRNA gene of Dietzia aurantiaca CCUG 35676T. Genome sequencing yielded a draft genome sequence of 37 contigs with a G + C content of 69.7%. A gene cluster related to organic sulfur utilisation and assimilation was identified, that included an alkanesulfonate monooxygenase component B (ssuD), an alkanesulfonate permease protein (ssuC), an ABC transporter (ssuB), and an alkanesulfonate-binding protein (ssuA). Proteomic analyses comparing strain J3 cultures using sulfate and 6:2 FTS as sulfur source indicated that the ssu gene cluster was involved in 6:2 FTS biodegradation. Upregulated proteins included the SsuD monooxygenase, the SsuB transporter, the ABC transporter permease (SsuC), an alkanesulfonate-binding protein (SsuA), and a nitrilotriacetate monooxygenase component B. 6:2 Fluorotelomer carboxylic acid (6:2 FTCA) and 6:2 fluorotelomer unsaturated acid (6:2 FTUA) were detected as early degradation products in cultures (after 72 h) while 5:3 fluorotelomer acid (5:3 FTCA), perfluorohexanoic acid (PFHxA) and perfluoropentanoic acid (PFPeA) were detected as later degradation products (after 168 h). This work provides biochemical and metabolic insights into 6:2 FTS biodegradation by the Actinobacterium D. aurantiaca J3, informing the fate of PFAS in the environment.
Collapse
Affiliation(s)
- Valentina Méndez
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - Sophie Holland
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - Shefali Bhardwaj
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - James McDonald
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - Stuart Khan
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - Denis O'Carroll
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - Russell Pickford
- UNSW Mark Wainwright Analytical Centre, UNSW, Sydney, NSW 2052, Australia
| | | | | | - Nicholas Coleman
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Matthew Lee
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - Michael J Manefield
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia.
| |
Collapse
|
5
|
Luenenschloss A, Ter Veld F, Albaum SP, Neddermann TM, Wendisch VF, Poetsch A. Functional Genomics Uncovers Pleiotropic Role of Rhomboids in Corynebacterium glutamicum. Front Microbiol 2022; 13:771968. [PMID: 35265054 PMCID: PMC8899591 DOI: 10.3389/fmicb.2022.771968] [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: 09/07/2021] [Accepted: 01/17/2022] [Indexed: 11/14/2022] Open
Abstract
The physiological role of ubiquitous rhomboid proteases, membrane-integral proteins that cleave their substrates inside the lipid bilayer, is still ill-defined in many prokaryotes. The two rhomboid genes cg0049 and cg2767 of Corynebacterium glutamicum were mutated and it was the aim of this study to investigate consequences in respect to growth phenotype, stress resistance, transcriptome, proteome, and lipidome composition. Albeit increased amount of Cg2767 upon heat stress, its absence did not change the growth behavior of C. glutamicum during exponential and stationary phase. Quantitative shotgun mass spectrometry was used to compare the rhomboid mutant with wild type strain and revealed that proteins covering diverse cellular functions were differentially abundant with more proteins affected in the stationary than in the exponential growth phase. An observation common to both growth phases was a decrease in ribosomal subunits and RNA polymerase, differences in iron uptake proteins, and abundance changes in lipid and mycolic acid biosynthesis enzymes that suggested a functional link of rhomboids to cell envelope lipid biosynthesis. The latter was substantiated by shotgun lipidomics in the stationary growth phase, where in a strain-dependent manner phosphatidylglycerol, phosphatidic acid, diacylglycerol and phosphatidylinositol increased irrespective of cultivation temperature.
Collapse
Affiliation(s)
| | - Frank Ter Veld
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Stefan P Albaum
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Tobias M Neddermann
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany.,Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Volker F Wendisch
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany.,Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Ansgar Poetsch
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany.,Department of Marine Biology, Ocean University of China, Qingdao, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| |
Collapse
|
6
|
Younus I, Kochkina S, Choi CC, Sun W, Ford RC. ATP-Binding Cassette Transporters: Snap-on Complexes? Subcell Biochem 2022; 99:35-82. [PMID: 36151373 DOI: 10.1007/978-3-031-00793-4_2] [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: 06/16/2023]
Abstract
ATP-binding cassette (ABC) transporters are one of the largest families of membrane proteins in prokaryotic organisms. Much is now understood about the structure of these transporters and many reviews have been written on that subject. In contrast, less has been written on the assembly of ABC transporter complexes and this will be a major focus of this book chapter. The complexes are formed from two cytoplasmic subunits that are highly conserved (in terms of their primary and three-dimensional structures) across the whole family. These ATP-binding subunits give rise to the name of the family. They must assemble with two transmembrane subunits that will typically form the permease component of the transporter. The transmembrane subunits have been found to be surprisingly diverse in structure when the whole family is examined, with seven distinct folds identified so far. Hence nucleotide-binding subunits appear to have been bolted on to a variety of transmembrane platforms during evolution, leading to a greater variety in function. Furthermore, many importers within the family utilise a further external substrate-binding component to trap scarce substrates and deliver them to the correct permease components. In this chapter, we will discuss whether assembly of the various ABC transporter subunits occurs with high fidelity within the crowded cellular environment and whether promiscuity in assembly of transmembrane and cytoplasmic components can occur. We also discuss the new AlphaFold protein structure prediction tool which predicts a new type of transmembrane domain fold within the ABC transporters that is associated with cation exporters of bacteria and plants.
Collapse
Affiliation(s)
- Iqra Younus
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Sofia Kochkina
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Cheri C Choi
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Wenjuan Sun
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Robert C Ford
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK.
| |
Collapse
|
7
|
Wang J, Wang X, Liang Q, Li D, Li D, Guo Q. Transcriptome analysis of L-leucine-producing Corynebacterium glutamicum under the addition of trimethylglycine. Amino Acids 2021; 54:229-240. [PMID: 34837555 DOI: 10.1007/s00726-021-03105-5] [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] [Received: 05/07/2021] [Accepted: 11/14/2021] [Indexed: 11/30/2022]
Abstract
It has been widely reported that the addition of trimethylglycine (betaine) decreases osmotic pressure inhibition for cell growth, leading to increased production of amino acids. However, the underlying mechanism is unclear. To determine the global metabolic differences that occur under the addition of trimethylglycine, transcriptome analysis was performed. Transcriptome analysis of Corynebacterium glutamicum JL1211 revealed that 272 genes exhibited significant changes under trimethylglycine addition. We performed Gene Ontology (GO) and KEGG enrichment pathway analyses on these differentially expressed genes (DEGs). Significantly upregulated genes were mainly involved in the regulation of ABC transporters, especially phosphate transporters and sulfur metabolism. The three phosphate transporter genes pstC, pstA and pstB were upregulated by 13.06-fold, 29.80-fold and 30.49-fold, respectively. Notably, the transcriptional levels of the cysD, cysN, cysH and sir genes were upregulated by 81.5-fold, 57.3-fold, 77.6-fold and 125.4-fold, respectively, consistent with assimilatory sulfate reduction under the addition of trimethylglycine. The upregulation of ilvBN and leuD genes might result in increased L-leucine formation. The data indicated changes in the transcriptome of C. glutamicum with trimethylglycine treatment, thus providing a mechanism supporting the application of trimethylglycine in the production of L-leucine and other amino acids by C. glutamicum strains.
Collapse
Affiliation(s)
- Jian Wang
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China.
| | - Xuesong Wang
- College of Life Sciences, Jilin University, Changchun, China
| | - Qing Liang
- College of Life Sciences, Jilin University, Changchun, China
| | - Deheng Li
- Xinjiang Fufeng Biotechnologies Co., Urumqi, China
| | - Dawei Li
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Qunqun Guo
- Tianjin Dexiang Biotechnology Co., Ltd, Tianjin, China
| |
Collapse
|
8
|
Bottos EM, Al-Shabib EY, Shaw DMJ, McAmmond BM, Sharma A, Suchan DM, Cameron ADS, Van Hamme JD. Transcriptomic response of Gordonia sp. strain NB4-1Y when provided with 6:2 fluorotelomer sulfonamidoalkyl betaine or 6:2 fluorotelomer sulfonate as sole sulfur source. Biodegradation 2020; 31:407-422. [PMID: 33150552 PMCID: PMC7661421 DOI: 10.1007/s10532-020-09917-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/27/2020] [Indexed: 02/06/2023]
Abstract
Abstract Perfluoroalkyl and polyfluoroalkyl substances (PFAS) are environmental contaminants of concern. We previously described biodegradation of two PFAS that represent components and transformation products of aqueous film-forming foams (AFFF), 6:2 fluorotelomer sulfonamidoalkyl betaine (6:2 FTAB) and 6:2 fluorotelomer sulfonate (6:2 FTSA), by Gordonia sp. strain NB4-1Y. To identify genes involved in the breakdown of these compounds, the transcriptomic response of NB4-1Y was examined when grown on 6:2 FTAB, 6:2 FTSA, a non-fluorinated analog of 6:2 FTSA (1-octanesulfonate), or MgSO4, as sole sulfur source. Differentially expressed genes were identified as those with ± 1.5 log2-fold-differences (± 1.5 log2FD) in transcript abundances in pairwise comparisons. Transcriptomes of cells grown on 6:2 FTAB and 6:2 FTSA were most similar (7.9% of genes expressed ± 1.5 log2FD); however, several genes that were expressed in greater abundance in 6:2 FTAB treated cells compared to 6:2 FTSA treated cells were noted for their potential role in carbon–nitrogen bond cleavage in 6:2 FTAB. Responses to sulfur limitation were observed in 6:2 FTAB, 6:2 FTSA, and 1-octanesulfonate treatments, as 20 genes relating to global sulfate stress response were more highly expressed under these conditions compared to the MgSO4 treatment. More highly expressed oxygenase genes in 6:2 FTAB, 6:2 FTSA, and 1-octanesulfonate treatments were found to code for proteins with lower percent sulfur-containing amino acids compared to both the total proteome and to oxygenases showing decreased expression. This work identifies genetic targets for further characterization and will inform studies aimed at evaluating the biodegradation potential of environmental samples through applied genomics. Graphic Abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s10532-020-09917-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Eric M Bottos
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
| | - Ebtihal Y Al-Shabib
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
- Faculty of Science, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Dayton M J Shaw
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
| | - Breanne M McAmmond
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
| | - Aditi Sharma
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
- Faculty of Science, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Danae M Suchan
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
- Faculty of Science, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Andrew D S Cameron
- Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
- Faculty of Science, Institute for Microbial Systems and Society, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Jonathan D Van Hamme
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada.
| |
Collapse
|
9
|
Peng C, Huang D, Shi Y, Zhang B, Sun L, Li M, Deng X, Wang W. Comparative transcriptomic analysis revealed the key pathways responsible for organic sulfur removal by thermophilic bacterium Geobacillus thermoglucosidasius W-2. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 676:639-650. [PMID: 31051369 DOI: 10.1016/j.scitotenv.2019.04.328] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 04/20/2019] [Accepted: 04/22/2019] [Indexed: 06/09/2023]
Abstract
Biodesulfurization is a promising method to desulfurize sulfur-containing compounds in oil with its unique advantages, such as environment-friendly treatments and moderate reaction conditions. In this study, a thermophilic bacterium Geobacillus thermoglucosidasius W-2 was reported to show nearly 40% and 55% desulfurization rates on heavy oil with 2.81% and 0.46% initial total sulfur content, respectively. Subsequently, comparative transcriptome analysis indicated that several possible key desulfurization-related genes of this strain were found to be differentially up-regulated induced by benzothiophene and dibenzothiophene, respectively. These desulfurization-related genes were considered to conduct key step to convert organic sulfur to inorganic sulfur. Moreover, the characterization of thermophilic alkanesulfonate monooxygenase systems SsuD1/SsuE1 and SsuD2/SsuE2 revealed that the enzymes exhibit considerable thermal and pH stability and wide substrates applicability. These enzymes probably endowed the strain W-2 with the ability to desulfurize oil and eliminate the sulfur-containing surfactants. Thus, this study provides novel alkanesulfonate monooxygenase systems that have the application potential for heavy oil biodesulfurization, oil demulsification and other biocatalytic processes.
Collapse
Affiliation(s)
- Chenchen Peng
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China
| | - Di Huang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China
| | - Yukun Shi
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China
| | - Bingling Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China
| | - Linbo Sun
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China
| | - Mingchang Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China
| | - Xin Deng
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Wei Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China; Tianjin Key Laboratory of Microbial Functional Genomics, TEDA, Tianjin 300457, PR China.
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Driggers CM, Dayal PV, Ellis HR, Karplus PA. Crystal Structure of Escherichia coli SsuE: Defining a General Catalytic Cycle for FMN Reductases of the Flavodoxin-like Superfamily. Biochemistry 2014; 53:3509-19. [DOI: 10.1021/bi500314f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Camden M. Driggers
- Department
of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural
and Life Sciences Building, Corvallis, Oregon 97331, United States
| | - Paritosh V. Dayal
- Department
of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - Holly R. Ellis
- Department
of Chemistry and Biochemistry, Auburn University, 179 Chemistry Building, Auburn, Alabama 36849, United States
| | - P. Andrew Karplus
- Department
of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural
and Life Sciences Building, Corvallis, Oregon 97331, United States
| |
Collapse
|
12
|
Van Hamme JD, Bottos EM, Bilbey NJ, Brewer SE. Genomic and proteomic characterization of Gordonia sp. NB4-1Y in relation to 6 : 2 fluorotelomer sulfonate biodegradation. Microbiology (Reading) 2013; 159:1618-1628. [DOI: 10.1099/mic.0.068932-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jonathan D. Van Hamme
- Department of Biological Sciences, Thompson Rivers University, Kamloops, British Columbia, Canada V2C 0C8
| | - Eric M. Bottos
- Department of Biological Sciences, Thompson Rivers University, Kamloops, British Columbia, Canada V2C 0C8
| | - Nicholas J. Bilbey
- Department of Biological Sciences, Thompson Rivers University, Kamloops, British Columbia, Canada V2C 0C8
| | - Sharon E. Brewer
- Department of Chemical and Physical Sciences, Thompson Rivers University, Kamloops, British Columbia, Canada V2C 0C8
| |
Collapse
|
13
|
Ferrario V, Braiuca P, Tessaro P, Knapic L, Gruber C, Pleiss J, Ebert C, Eichhorn E, Gardossi L. Elucidating the structural and conformational factors responsible for the activity and substrate specificity of alkanesulfonate monooxygenase. J Biomol Struct Dyn 2012; 30:74-88. [PMID: 22571434 DOI: 10.1080/07391102.2012.674268] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The mechanism and substrate specificity of alkanesulfonate monooxygenase (SsuD) was investigated by combining molecular dynamics simulations, docking, and a comprehensive quantitative structure activity relationships (QSAR) analysis. The FMNH(2) dependent monooxygenase undergoes a dynamic conformational change of the active site, passing from a closed to an open state. As a consequence, substrates have access to the active site and the cofactor is then regenerated by the associated oxidoreductase FMN reductase SsuE.. Computational analysis of the interaction of SsuD with FMNH(2) based on molecular docking and multiple 20 ns molecular dynamics simulations pointed out that the conformational change is mainly driven by salt bridge formation between Arg297 and Glu20 or Asp111. A set of substrates accepted by SsuD were described by means of ALMOND chemical descriptors and a partial least square (PLS) mathematical model was constructed. The PLS model correlates the structure of substrates and enzyme activity, namely kinetic properties (k (cat)/K (M)). Therefore, information coming from the PLS analysis goes beyond the simple ability of the enzyme to recognize the substrate, but includes the factors that affect the capacity of the enzyme to reduce the activation energy of the rate determining step of the reaction. The two principal components of the model are able to describe both steric and electronic factors and, more importantly, their interactions. Indeed, interactions of factors appear to affect significantly the ability of SsuD of transforming efficiently a substrate.
Collapse
Affiliation(s)
- V Ferrario
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, P.le Europa 1, 34127, Trieste, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Trötschel C, Albaum SP, Wolff D, Schröder S, Goesmann A, Nattkemper TW, Poetsch A. Protein turnover quantification in a multilabeling approach: from data calculation to evaluation. Mol Cell Proteomics 2012; 11:512-26. [PMID: 22493176 DOI: 10.1074/mcp.m111.014134] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Liquid chromatography coupled to tandem mass spectrometry in combination with stable-isotope labeling is an established and widely spread method to measure gene expression on the protein level. However, it is often not considered that two opposing processes are responsible for the amount of a protein in a cell--the synthesis as well as the degradation. With this work, we provide an integrative, high-throughput method--from the experimental setup to the bioinformatics analysis--to measure synthesis and degradation rates of an organism's proteome. Applicability of the approach is demonstrated with an investigation of heat shock response, a well-understood regulatory mechanism in bacteria, on the biotechnologically relevant Corynebacterium glutamicum. Utilizing a multilabeling approach using both heavy stable nitrogen as well as carbon isotopes cells are metabolically labeled in a pulse-chase experiment to trace the labels' incorporation in newly synthesized proteins and its loss during protein degradation. Our work aims not only at the calculation of protein turnover rates but also at their statistical evaluation, including variance and hierarchical cluster analysis using the rich internet application QuPE.
Collapse
Affiliation(s)
- Christian Trötschel
- Department of Plant Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany.
| | | | | | | | | | | | | |
Collapse
|
15
|
Haussmann U, Poetsch A. Global proteome survey of protocatechuate- and glucose-grown Corynebacterium glutamicum reveals multiple physiological differences. J Proteomics 2012; 75:2649-59. [PMID: 22450470 DOI: 10.1016/j.jprot.2012.03.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 02/21/2012] [Accepted: 03/10/2012] [Indexed: 12/16/2022]
Abstract
Corynebacterium glutamicum can utilize various monocyclic aromatic carbon sources, including protocatechuate, which is catabolized via the β-ketoadipate pathway. In order to obtain a global survey of occurring physiological adaptations on the proteome level, cytoplasmic and membrane fraction from cells grown on protocatechuate or glucose as sole carbon and energy source were compared. Shotgun proteomics and relative protein quantification with metabolic isotope labeling and spectral counting were employed. Altogether, 139 proteins were found to change their abundance during growth on protocatechuate. A general adaptation of energy metabolism to meet increased energy production by oxidative phosphorylation and a stress response occurred. Adjustments of carbon and amino acid metabolism in the cytoplasmic and membrane proteome were indicative of a starvation response. The different regulation of porins and cell wall biosynthesis proteins suggests a change in its architecture upon assimilation of the aromatic carbon source. Some of the observed changes could be explained by an involvement of the GlxR and McbR regulons.
Collapse
Affiliation(s)
- Ute Haussmann
- Lehrstuhl fuer Biochemie der Pflanzen, Ruhr Universitaet Bochum, Bochum, Germany
| | | |
Collapse
|
16
|
Arabitol metabolism of Corynebacterium glutamicum and its regulation by AtlR. J Bacteriol 2011; 194:941-55. [PMID: 22178972 DOI: 10.1128/jb.06064-11] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Expression profiling of Corynebacterium glutamicum in comparison to a derivative deficient in the transcriptional regulator AtlR (previously known as SucR or MtlR) revealed eight genes showing more than 4-fold higher mRNA levels in the mutant. Four of these genes are located in the direct vicinity of the atlR gene, i.e., xylB, rbtT, mtlD, and sixA, annotated as encoding xylulokinase, the ribitol transporter, mannitol 2-dehydrogenase, and phosphohistidine phosphatase, respectively. Transcriptional analysis indicated that atlR and the four genes are organized as atlR-xylB and rbtT-mtlD-sixA operons. Growth experiments with C. glutamicum and C. glutamicum ΔatlR, ΔxylB, ΔrbtT, ΔmtlD, and ΔsixA derivatives with sugar alcohols revealed that (i) wild-type C. glutamicum grows on D-arabitol but not on other sugar alcohols, (ii) growth in the presence of D-arabitol allows subsequent growth on D-mannitol, (iii) D-arabitol is cometabolized with glucose and preferentially utilized over D-mannitol, (iv) RbtT and XylB are involved in D-arabitol but not in D-mannitol metabolism, (v) MtlD is required for D-arabitol and D-mannitol metabolism, and (vi) SixA is not required for growth on any of the substrates tested. Furthermore, we show that MtlD confers D-arabitol and D-mannitol dehydrogenase activities, that the levels of these and also xylulokinase activities are generally high in the C. glutamicum ΔatlR mutant, whereas in the parental strain, they were high when cells were grown in the presence of D-arabitol and very low when cells were grown in its absence. Our results show that the XylB, RbtT, and MtlD proteins allow the growth of C. glutamicum on D-arabitol and that D-arabitol metabolism is subject to arabitol-dependent derepression by AtlR.
Collapse
|
17
|
Fränzel B, Wolters DA. Advanced MudPIT as a next step toward high proteome coverage. Proteomics 2011; 11:3651-6. [DOI: 10.1002/pmic.201100056] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 04/29/2011] [Accepted: 06/10/2011] [Indexed: 11/10/2022]
|
18
|
Sugawara M, Shah GR, Sadowsky MJ, Paliy O, Speck J, Vail AW, Gyaneshwar P. Expression and functional roles of Bradyrhizobium japonicum genes involved in the utilization of inorganic and organic sulfur compounds in free-living and symbiotic conditions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:451-7. [PMID: 21190435 DOI: 10.1094/mpmi-08-10-0184] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Strains of Bradyrhizobium spp. form nitrogen-fixing symbioses with many legumes, including soybean. Although inorganic sulfur is preferred by bacteria in laboratory conditions, sulfur in agricultural soil is mainly present as sulfonates and sulfur esters. Here, we show that Bradyrhizobium japonicum and B. elkanii strains were able to utilize sulfate, cysteine, sulfonates, and sulfur-ester compounds as sole sulfur sources for growth. Expression and functional analysis revealed that two sets of gene clusters (bll6449 to bll6455 or bll7007 to bll7011) are important for utilization of sulfonates sulfur source. The bll6451 or bll7010 genes are also expressed in the symbiotic nodules. However, B. japonicum mutants defective in either of the sulfonate utilization operons were not affected for symbiosis with soybean, indicating the functional redundancy or availability of other sulfur sources in planta. In accordance, B. japonicum bacteroids possessed significant sulfatase activity. These results indicate that strains of Bradyrhizobium spp. likely use organosulfur compounds for growth and survival in soils, as well as for legume nodulation and nitrogen fixation.
Collapse
Affiliation(s)
- Masayuki Sugawara
- Department of Soil Water and Climate, University of Minnesota, St. Paul, USA
| | | | | | | | | | | | | |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
New Insights into Buffer-Ionic Salt Interactions: Solubilities, Transfer Gibbs Energies, and Transfer Molar Volumes of TAPS and TAPSO from Water to Aqueous Electrolyte Solutions. J SOLUTION CHEM 2010. [DOI: 10.1007/s10953-010-9611-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
|
21
|
Fränzel B, Poetsch A, Trötschel C, Persicke M, Kalinowski J, Wolters DA. Quantitative proteomic overview on the Corynebacterium glutamicum l-lysine producing strain DM1730. J Proteomics 2010; 73:2336-53. [DOI: 10.1016/j.jprot.2010.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 06/16/2010] [Accepted: 07/07/2010] [Indexed: 11/15/2022]
|
22
|
Schröder J, Tauch A. Transcriptional regulation of gene expression inCorynebacterium glutamicum: the role of global, master and local regulators in the modular and hierarchical gene regulatory network. FEMS Microbiol Rev 2010; 34:685-737. [DOI: 10.1111/j.1574-6976.2010.00228.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
|
23
|
Corynebacterium glutamicum exhibits a membrane-related response to a small ferrocene-conjugated antimicrobial peptide. J Biol Inorg Chem 2010; 15:1293-303. [PMID: 20658302 DOI: 10.1007/s00775-010-0689-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 07/06/2010] [Indexed: 10/19/2022]
Abstract
Multiresistant bacteria are becoming more and more widespread. It is therefore necessary to have new compound groups in hand, such as small cationic peptides, to cope with these challenges. In this work, we present a comprehensive approach by monitoring protein expression profiles in a gram-positive bacterium (Corynebacterium glutamicum) to investigate the cellular response to such a compound, a ferrocene-conjugated arginine- and tryptophan-rich pentapeptide. To achieve this, a proteomic outline was performed where the compound-treated sample was compared with an untreated control. This study comprises more than 900 protein identifications, including numerous integral membrane proteins, and among these 185 differential expressions. Surprisingly, unregulated catalase and no elevated H(2)O(2) levels demonstrate that no oxidative stress occurs after treatment with the iron-containing compound as a consequence of the potential Fenton reaction. A sufficient iron supply is evidenced by the iron-containing protein aconitase and SufB (the latter belongs to an iron-sulfur cluster assembly system) and decreased levels of ATP-binding-cassette-type cobalamin/Fe(3+) siderophore transporters. The organometallic peptide antibiotic targets the cell membrane, which is evident by decreased levels of various integral membrane proteins, such as peptide permeases and transporters, and an altered lipid composition. Conversion to a more rigid cell membrane seems to be a relevant protective strategy of C. glutamicum against the ferrocene-conjugated antimicrobial peptide compound.
Collapse
|
24
|
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.
Collapse
Affiliation(s)
- Benjamin Fränzel
- Department of Analytical Chemistry, University of Bochum, Bochum, Germany
| | | | | | | | | | | |
Collapse
|
25
|
Taha M, Lee MJ. Buffer interactions: Densities and solubilities of some selected biological buffers in water and in aqueous 1,4-dioxane solutions. Biochem Eng J 2009. [DOI: 10.1016/j.bej.2009.06.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
26
|
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.
Collapse
Affiliation(s)
- Ute Haussmann
- Plant Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | | | | | | | | | | |
Collapse
|
27
|
Fränzel B, Fischer F, Trötschel C, Poetsch A, Wolters D. The two-phase partitioning system--a powerful technique to purify integral membrane proteins of Corynebacterium glutamicum for quantitative shotgun analysis. Proteomics 2009; 9:2263-72. [PMID: 19322788 DOI: 10.1002/pmic.200800766] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We established a single consecutive strategy which assigned the most comprehensive number of integral membrane proteins from Gram-positive bacteria to date. For this purpose, we adapted a biphasic partitioning system for the biotechnologically intensively used Corynebacterium glutamicum and proved for the first time that such a system is well suited for quantitative comparison. 297 integral membrane proteins were identified by our integrated approach, which depletes stringently cytosolic proteins. In combination with our previously developed SIMPLE strategy, our data comprise 61% (374 integral membrane proteins) of the entire membrane proteome, which aims towards an almost comprehensive coverage. Wild type and a production strain of C. glutamicum were compared by (15)N metabolic labelling and quantitation was obtained by spectral counting and peak areas. Both quantification strategies display a consistent trend in up or downregulation of proteins. Nevertheless, spectral counting often provides results indicating a much stronger regulation compared to ProRata values. Either spectral counting seems to exaggerate protein regulation or ProRata tends to attenuate the information about the regulation level. We highlight some of the biologically relevant candidates, which prove that our approach helps to give a deeper quantitative insight towards the understanding of transport and other membrane associated processes, important for strain development of C. glutamicum.
Collapse
Affiliation(s)
- Benjamin Fränzel
- Department of Analytical Chemistry, Ruhr-University Bochum, Bochum, Germany
| | | | | | | | | |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Citrate utilization by Corynebacterium glutamicum is controlled by the CitAB two-component system through positive regulation of the citrate transport genes citH and tctCBA. J Bacteriol 2009; 191:3869-80. [PMID: 19376865 DOI: 10.1128/jb.00113-09] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this work, the molecular basis of aerobic citrate utilization by the gram-positive bacterium Corynebacterium glutamicum was studied. Genome analysis revealed the presence of two putative citrate transport systems. The permease encoded by citH belongs to the citrate-Mg(2+):H(+)/citrate-Ca(2+):H(+) symporter family, whereas the permease encoded by the tctCBA operon is a member of the tripartite tricarboxylate transporter family. The expression of citH or tctCBA in Escherichia coli enabled this species to utilize citrate aerobically, indicating that both CitH and TctABC are functional citrate transporters. Growth tests with the recombinant E. coli strains indicated that CitH is active with Ca(2+) or Sr(2+) but not with Mg(2+) and that TctABC is active with Ca(2+) or Mg(2+) but not with Sr(2+). We could subsequently show that, with 50 mM citrate as the sole carbon and energy source, the C. glutamicum wild type grew best when the minimal medium was supplemented with CaCl(2) but that MgCl(2) and SrCl(2) also supported growth. Each of the two transporters alone was sufficient for growth on citrate. The expression of citH and tctCBA was activated by citrate in the growth medium, independent of the presence or absence of glucose. This activation was dependent on the two-component signal transduction system CitAB, composed of the sensor kinase CitA and the response regulator CitB. CitAB belongs to the CitAB/DcuSR family of two-component systems, whose members control the expression of genes that are involved in the transport and catabolism of tricarboxylates or dicarboxylates. C. glutamicum CitAB is the first member of this family studied in Actinobacteria.
Collapse
|
30
|
Barreiro C, Nakunst D, Hüser AT, de Paz HD, Kalinowski J, Martín JF. Microarray studies reveal a ‘differential response’ to moderate or severe heat shock of the HrcA- and HspR-dependent systems in Corynebacterium glutamicum. Microbiology (Reading) 2009; 155:359-372. [DOI: 10.1099/mic.0.019299-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Genome-wide transcription profile analysis of the heat-shocked wild-type strain under moderate (40 °C) and severe heat stress (50 °C) revealed that a large number of genes are differentially expressed after heat shock. Of these, 358 genes were upregulated and 420 were downregulated in response to moderate heat shock (40 °C) inCorynebacterium glutamicum. Our results confirmed the HrcA/controlling inverted repeat of chaperone expression (CIRCE)-dependent and HspR/HspR-associated inverted repeat (HAIR)-dependent upregulation of chaperones following heat shock. Other genes, including clusters of orthologous groups (COG) related to macromolecule biosynthesis and several transcriptional regulators (COG class K), were upregulated, explaining the large number of genes affected by heat shock. Mutants having deletions in thehrcAorhspRregulators were constructed, which allowed the complete identification of the genes controlled by those systems. The up- or downregulation of several genes observed in the microarray experiments was validated by Northern blot analyses and quantitative (real-time) reverse-transcription PCR. These analyses showed a heat-shock intensity-dependent response (‘differential response’) in the HspR/HAIR system, in contrast to the non-differential response shown by the HrcA/CIRCE-regulated genes.
Collapse
Affiliation(s)
- Carlos Barreiro
- INBIOTEC (Instituto de Biotecnología de León), Parque Científico de León, Avda. Real, 1, 24006 León, Spain
| | - Diana Nakunst
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Andrea T. Hüser
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Héctor D. de Paz
- INBIOTEC (Instituto de Biotecnología de León), Parque Científico de León, Avda. Real, 1, 24006 León, Spain
| | - Jörn Kalinowski
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Juan F. Martín
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, Campus de Vegazana, s/n. 24071 León, Spain
- INBIOTEC (Instituto de Biotecnología de León), Parque Científico de León, Avda. Real, 1, 24006 León, Spain
| |
Collapse
|
31
|
Buchinger S, Strösser J, Rehm N, Hänssler E, Hans S, Bathe B, Schomburg D, Krämer R, Burkovski A. A combination of metabolome and transcriptome analyses reveals new targets of the Corynebacterium glutamicum nitrogen regulator AmtR. J Biotechnol 2008; 140:68-74. [PMID: 19041910 DOI: 10.1016/j.jbiotec.2008.10.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Revised: 09/30/2008] [Accepted: 10/21/2008] [Indexed: 10/21/2022]
Abstract
The effects of a deletion of the amtR gene, encoding the master regulator of nitrogen control in Corynebacterium glutamicum, were investigated by metabolome and transcriptome analyses. Compared to the wild type, different metabolite patterns were observed in respect to glycolysis, pentose phosphate pathway, citric acid cycle, and most amino acid pools. Not all of these alterations could be attributed to changes at the level of mRNA and must be caused by posttranscriptional regulatory processes. However, subsequently carried out transcriptome analyses, which were confirmed by gel retardation experiments, revealed two new targets of AmtR, the dapD gene, encoding succinylase involved in m-diaminopimelate synthesis, and the mez gene, coding for malic enzyme. The regulation of dapD connects the AmtR-dependent nitrogen control with l-lysine biosynthesis, the regulation of mez with carbon metabolism. An increased l-glutamine pool in the amtR mutant compared to the wild type was correlated with deregulated expression of the AmtR-regulated glnA gene and an increased glutamine synthetase activity. The glutamate pool was decreased in the mutant and also glutamate excretion was impaired.
Collapse
|
32
|
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.
Collapse
Affiliation(s)
- Christian Rückert
- Institut für Systembiologie & Genomforschung, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld, Germany.
| | | | | | | | | | | |
Collapse
|
33
|
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]
|
34
|
The alternative sigma factor SigB of Corynebacterium glutamicum modulates global gene expression during transition from exponential growth to stationary phase. BMC Genomics 2007; 8:4. [PMID: 17204139 PMCID: PMC1779776 DOI: 10.1186/1471-2164-8-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Accepted: 01/04/2007] [Indexed: 11/16/2022] Open
Abstract
Background Corynebacterium glutamicum is a gram-positive soil bacterium widely used for the industrial production of amino acids. There is great interest in the examination of the molecular mechanism of transcription control. One of these control mechanisms are sigma factors. C. glutamicum ATCC 13032 has seven putative sigma factor-encoding genes, including sigA and sigB. The sigA gene encodes the essential primary sigma factor of C. glutamicum and is responsible for promoter recognition of house-keeping genes. The sigB gene codes for the non-essential sigma factor SigB that has a proposed role in stress reponse. Results The sigB gene expression was highest at transition between exponential growth and stationary phase, when the amount of sigA mRNA was already decreasing. Genome-wide transcription profiles of the wild-type and the sigB mutant were recorded by comparative DNA microarray hybridizations. The data indicated that the mRNA levels of 111 genes are significantly changed in the sigB-proficient strain during the transition phase, whereas the expression profile of the sigB-deficient strain showed only minor changes (26 genes). The genes that are higher expressed during transition phase only in the sigB-proficient strain mainly belong to the functional categories amino acid metabolism, carbon metabolism, stress defense, membrane processes, and phosphorus metabolism. The transcription start points of six of these genes were determined and the deduced promoter sequences turned out to be indistinguishable from that of the consensus promoter recognized by SigA. Real-time reverse transcription PCR assays revealed that the expression profiles of these genes during growth were similar to that of the sigB gene itself. In the sigB mutant, however, the transcription profiles resembled that of the sigA gene encoding the house-keeping sigma factor. Conclusion During transition phase, the sigB gene showed an enhanced expression, while simultaneously the sigA mRNA decreased in abundance. This might cause a replacement of SigA by SigB at the RNA polymerase core enzyme and in turn results in increased expression of genes relevant for the transition and the stationary phase, either to cope with nutrient limitation or with the accompanying oxidative stress. The increased expression of genes encoding anti-oxidative or protection functions also prepares the cell for upcoming limitations and environmental stresses.
Collapse
|
35
|
Koch DJ, Rückert C, Albersmeier A, Hüser AT, Tauch A, Pühler A, Kalinowski J. The transcriptional regulator SsuR activates expression of the Corynebacterium glutamicum sulphonate utilization genes in the absence of sulphate. Mol Microbiol 2005; 58:480-94. [PMID: 16194234 DOI: 10.1111/j.1365-2958.2005.04836.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In a recent study, the putative regulatory gene cg0012 was shown to belong to the regulon of McbR, a global transcriptional regulator of sulphur metabolism in Corynebacterium glutamicum ATCC 13032. A deletion of cg0012, now designated ssuR (sulphonate sulphur utilization regulator), led to the mutant strain C. glutamicum DK100, which was shown to be blocked in the utilization of sulphonates as sulphur sources. According to DNA microarray hybridizations, transcription of the ssu and seu genes, encoding the sulphonate utilization system of C. glutamicum, was considerably decreased in C. glutamicum DK100 when compared with the wild-type strain. Electrophoretic mobility shift assays with purified SsuR protein demonstrated that the upstream regions of ssuI, seuABC, ssuD2 and ssuD1CBA contain SsuR binding sites. A nucleotide sequence alignment of the four DNA fragments containing the SsuR binding sites revealed a common 21 bp motif consisting of T-, GC- and A-rich domains. Mapping of the transcriptional start sites in front of ssuI, seuABC, ssuD2 and ssuD1CBA indicated that the SsuR binding sites are located directly upstream of identified promoter sequences and that the ssu genes are expressed by leaderless transcripts. Binding of the SsuR protein to its operator was shown to be diminished in vitro by the effector substance sulphate and its direct assimilation products adenosine 5'-phosphosulphate, sulphite and sulphide. Real-time reverse transcription polymerase chain reaction experiments verified that the expression of the ssu and seu genes was also repressed in vivo by the presence of sulphate or sulphite. Therefore, the regulatory protein SsuR activates the expression of the ssu and seu genes in C. glutamicum in the absence of the preferred sulphur source sulphate.
Collapse
Affiliation(s)
- Daniel J Koch
- Institut für Genomforschung, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | | | | | | | | | | | | |
Collapse
|
36
|
Rückert C, Koch DJ, Rey DA, Albersmeier A, Mormann S, Pühler A, Kalinowski J. Functional genomics and expression analysis of the Corynebacterium glutamicum fpr2-cysIXHDNYZ gene cluster involved in assimilatory sulphate reduction. BMC Genomics 2005; 6:121. [PMID: 16159395 PMCID: PMC1266029 DOI: 10.1186/1471-2164-6-121] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2005] [Accepted: 09/13/2005] [Indexed: 11/11/2022] Open
Abstract
Background Corynebacterium glutamicum is a high-GC Gram-positive soil bacterium of great biotechnological importance for the production of amino acids. To facilitate the rational design of sulphur amino acid-producing strains, the pathway for assimilatory sulphate reduction providing the necessary reduced sulfur moieties has to be known. Although this pathway has been well studied in Gram-negative bacteria like Escherichia coli and low-GC Gram-positives like Bacillus subtilis, little is known for the Actinomycetales and other high-GC Gram-positive bacteria. Results The genome sequence of C. glutamicum was searched for genes involved in the assimilatory reduction of inorganic sulphur compounds. A cluster of eight candidate genes could be identified by combining sequence similarity searches with a subsequent synteny analysis between C. glutamicum and the closely related C. efficiens. Using mutational analysis, seven of the eight candidate genes, namely cysZ, cysY, cysN, cysD, cysH, cysX, and cysI, were demonstrated to be involved in the reduction of inorganic sulphur compounds. For three of the up to now unknown genes possible functions could be proposed: CysZ is likely to be the sulphate permease, while CysX and CysY are possibly involved in electron transfer and cofactor biosynthesis, respectively. Finally, the candidate gene designated fpr2 influences sulphur utilisation only weakly and might be involved in electron transport for the reduction of sulphite. Real-time RT-PCR experiments revealed that cysIXHDNYZ form an operon and that transcription of the extended cluster fpr2 cysIXHDNYZ is strongly influenced by the availability of inorganic sulphur, as well as L-cysteine. Mapping of the fpr2 and cysIXHDNYZ promoters using RACE-PCR indicated that both promoters overlap with binding-sites of the transcriptional repressor McbR, suggesting an involvement of McbR in the observed regulation. Comparative genomics revealed that large parts of the extended cluster are conserved in 11 of 17 completely sequenced members of the Actinomycetales. Conclusion The set of C. glutamicum genes involved in assimilatory sulphate reduction was identified and four novel genes involved in this pathway were found. The high degree of conservation of this cluster among the Actinomycetales supports the hypothesis that a different metabolic pathway for the reduction of inorganic sulphur compounds than that known from the well-studied model organisms E. coli and B. subtilis is used by members of this order, providing the basis for further biochemical studies.
Collapse
Affiliation(s)
- Christian Rückert
- International NRW Graduate School in Bioinformatics & Genome Research, Universität Bielefeld, D-33594 Bielefeld, Germany
- lnstitut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Daniel J Koch
- International NRW Graduate School in Bioinformatics & Genome Research, Universität Bielefeld, D-33594 Bielefeld, Germany
- lnstitut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Daniel A Rey
- lnstitut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Andreas Albersmeier
- lnstitut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Sascha Mormann
- lnstitut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Alfred Pühler
- Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Jörn Kalinowski
- lnstitut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
| |
Collapse
|