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Patyi G, Hódi B, Mallick I, Maróti G, Kós PB, Vass I. Investigation of singlet-oxygen-responsive genes in the cyanobacterium Synechocystis PCC 6803. PHYSIOLOGIA PLANTARUM 2024; 176:e14468. [PMID: 39140254 DOI: 10.1111/ppl.14468] [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: 10/04/2023] [Revised: 07/08/2024] [Accepted: 07/23/2024] [Indexed: 08/15/2024]
Abstract
Singlet oxygen (1O2) is an important reactive oxygen species whose formation by the type-II, light-dependent, photodynamic reaction is inevitable during photosynthetic processes. In the last decades, the recognition that 1O2 is not only a damaging agent, but can also affect gene expression and participates in signal transduction pathways has received increasing attention. However, contrary to several other taxa, 1O2-responsive genes have not been identified in the important cyanobacterial model organism Synechocystis PCC 6803. By using global transcript analysis we have identified a large set of Synechocystis genes, whose transcript levels were either enhanced or repressed in the presence of 1O2. Characteristic 1O2 responses were observed in several light-inducible genes of Synechocystis, especially in the hli (or scp) family encoding HLIP/SCP proteins involved in photoprotection. Other important 1O2-induced genes include components of the Photosystem II repair machinery (psbA2 and ftsH2, ftsH3), iron homeostasis genes isiA and idiA, the group 2 sigma factor sigD, some components of the transcriptomes induced by salt-, hyperosmotic and cold-stress, as well as several genes of unknown function. The most pronounced 1O2-induced upregulation was observed for the hliB and the co-transcribed lilA genes, whose deletion induced enhanced sensitivity against 1O2-mediated light damage. A bioreporter Synechocystis strain was created by fusing the hliB promoter to the bacterial luciferase (lux), which showed its utility for continuous monitoring of 1O2 concentrations inside the cell.
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Affiliation(s)
- Gábor Patyi
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
- Faculty of Science and Informatics, Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Barbara Hódi
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
- Faculty of Science and Informatics, Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | - Ivy Mallick
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Péter B Kós
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
- Department of Biotechnology, Faculty of Science and Informatics, University of Szeged, Hungary
| | - Imre Vass
- Institute of Plant Biology, HUN-REN Biological Research Centre, Szeged, Hungary
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Shahbazi M, Tohidfar M, Azimzadeh Irani M, Moheb Seraj RG. Functional annotation and evaluation of hypothetical proteins in cyanobacterium Synechocystis sp. PCC 6803. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2021.102246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Sun W, Alexander T, Man Z, Xiao F, Cui F, Qi X. Enhancing 2-Ketogluconate Production of Pseudomonas plecoglossicida JUIM01 by Maintaining the Carbon Catabolite Repression of 2-Ketogluconate Metabolism. Molecules 2018; 23:molecules23102629. [PMID: 30322137 PMCID: PMC6222622 DOI: 10.3390/molecules23102629] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/09/2018] [Accepted: 10/11/2018] [Indexed: 12/22/2022] Open
Abstract
2-Ketogluconate (2KGA) is an organic acid that is important for pharmaceutical, cosmetic, and environmental applications. Pseudomonas plecoglossicida JUIM01 strain is an important industrial 2KGA producer in China. In this paper, we found that P. plecoglossicida JUIM01 could convert glucose to 2KGA extracellularly, and the formed 2KGA was subsequently consumed after glucose was exhausted during the fermentation process. Experiments of glucose and 2KGA supplementation during fermentation process revealed that, only when glucose was exhausted, the strain started to consume the product 2KGA. Then, the mechanism of this phenomenon was investigated at transcription and protein levels, and the results indicated that P. plecoglossicida JUIM01 possesses carbon catabolite repression of 2KGA metabolism by glucose. Next, increasing the supply of glucose could attenuate 2KGA consumption and enhance the 2KGA yield from glucose. Finally, fed-batch fermentation of P. plecoglossicida JUIM01 resulted in 205.67 g/L of 2KGA with a productivity of 6.86 g/L/h and yield of 0.953 g/g glucose. These results can provide references for the industrial fermentation production of 2KGA and other fermentation products.
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Affiliation(s)
- Wenjing Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
- Parchn Sodium Isovitamin C Co. Ltd., Dexing, 334221, China.
| | - Tjahjasari Alexander
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Zaiwei Man
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Fangfang Xiao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Fengjie Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
- Parchn Sodium Isovitamin C Co. Ltd., Dexing, 334221, China.
| | - Xianghui Qi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
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Liu C, Mao L, Zheng X, Yuan J, Hu B, Cai Y, Xie H, Peng X, Ding X. Comparative proteomic analysis of Methanothermobacter thermautotrophicus reveals methane formation from H 2 and CO 2 under different temperature conditions. Microbiologyopen 2018; 8:e00715. [PMID: 30260585 PMCID: PMC6528648 DOI: 10.1002/mbo3.715] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 07/11/2018] [Accepted: 07/12/2018] [Indexed: 11/22/2022] Open
Abstract
The growth of all methanogens is limited to a specific temperature range. However, Methanothermobacter thermautotrophicus can be found in a variety of natural and artificial environments, the temperatures of which sometimes even exceed the temperature growth ranges of thermophiles. As a result, the extent to which methane production and survival are affected by temperature remains unclear. To investigate the mechanisms of methanogenesis that Archaea have evolved to cope with drastic temperature shifts, the responses of Methanothermobacter thermautotrophicus to temperature were investigated under a high temperature growth (71°C) and cold shock (4°C) using Isobaric tags for relative and absolute quantitation (iTRAQ). The results showed that methane formation is decreased and that protein folding and degradation are increased in both high‐ and low‐temperature treatments. In addition, proteins predicted to be involved in processing environmental information processing and in cell membrane/wall/envelope biogenesis may play key roles in affecting methane formation and enhancing the response of M. thermautotrophicus to temperature stress. Analysis of the genomic locations of the genes corresponding to these temperature‐dependent proteins predicted that 77 of the genes likely to form 32 gene clusters. Here, we assess the response of M. thermautotrophicus to different temperatures and provide a new level of understanding of methane formation and cellular putative adaptive responses.
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Affiliation(s)
- Cong Liu
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, Jiangxi, China
| | - Lihui Mao
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, Jiangxi, China
| | - Xiongmin Zheng
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, Jiangxi, China
| | - Jiangan Yuan
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, Jiangxi, China
| | - Beijuan Hu
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, Jiangxi, China
| | - Yaohui Cai
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Hongwei Xie
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Xiaojue Peng
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, Jiangxi, China
| | - Xia Ding
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, Jiangxi, China.,Biology Experimental Teaching Demonstration, Nanchang University, Nanchang, Jiangxi, China
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Pan L, Yang Z, Wang J, Wang P, Ma X, Zhou M, Li J, Gang N, Feng G, Zhao J, Zhang X. Comparative proteomic analyses reveal the proteome response to short-term drought in Italian ryegrass (Lolium multiflorum). PLoS One 2017; 12:e0184289. [PMID: 28910323 PMCID: PMC5598972 DOI: 10.1371/journal.pone.0184289] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 08/20/2017] [Indexed: 11/25/2022] Open
Abstract
Drought is a major abiotic stress that impairs growth and productivity of Italian ryegrass. Comparative analysis of drought responsive proteins will provide insight into molecular mechanism in Lolium multiflorum drought tolerance. Using the iTRAQ-based approach, proteomic changes in tolerant and susceptible lines were examined in response to drought condition. A total of 950 differentially accumulated proteins was found to be involved in carbohydrate metabolism, amino acid metabolism, biosynthesis of secondary metabolites, and signal transduction pathway, such as β-D-xylosidase, β-D-glucan glucohydrolase, glycerate dehydrogenase, Cobalamin-independent methionine synthase, glutamine synthetase 1a, Farnesyl pyrophosphate synthase, diacylglycerol, and inositol 1, 4, 5-trisphosphate, which might contributed to enhance drought tolerance or adaption in Lolium multiflorum. Interestingly, the two specific metabolic pathways, arachidonic acid and inositol phosphate metabolism including differentially accumulated proteins, were observed only in the tolerant lines. Cysteine protease cathepsin B, Cysteine proteinase, lipid transfer protein and Aquaporin were observed as drought-regulated proteins participating in hydrolysis and transmembrane transport. The activities of phospholipid hydroperoxide glutathione peroxidase, peroxiredoxin, dehydroascorbate reductase, peroxisomal ascorbate peroxidase and monodehydroascorbate reductase associated with alleviating the accumulation of reactive oxygen species in stress inducing environments. Our results showed that drought-responsive proteins were closely related to metabolic processes including signal transduction, antioxidant defenses, hydrolysis, and transmembrane transport.
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Affiliation(s)
- Ling Pan
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhongfu Yang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, United States of America
| | - Pengxi Wang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiao Ma
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Meiliang Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ji Li
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Nie Gang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Guangyan Feng
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Junming Zhao
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xinquan Zhang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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Dantas GC, Martins PMM, Martins DAB, Gomes E, Ferreira H. A protein expression system for tandem affinity purification in Xanthomonas citri subsp. citri. Braz J Microbiol 2016; 47:518-26. [PMID: 26991273 PMCID: PMC4874617 DOI: 10.1016/j.bjm.2016.01.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/23/2015] [Indexed: 11/30/2022] Open
Abstract
Citrus canker, caused by the Gram-negative bacterium Xanthomonas citri subsp. citri (Xac), is one of the most devastating diseases to affect citrus crops. There is no treatment for citrus canker; effective control against the spread of Xac is usually achieved by the elimination of affected plants along with that of asymptomatic neighbors. An in depth understanding of the pathogen is the keystone for understanding of the disease; to this effect we are committed to the development of strategies to ease the study of Xac. Genome sequencing and annotation of Xac revealed that ∼37% of the genome is composed of hypothetical ORFs. To start a systematic characterization of novel factors encoded by Xac, we constructed integrative-vectors for protein expression specific to this bacterium. The vectors allow for the production of TAP-tagged proteins in Xac under the regulation of the xylose promoter. In this study, we show that a TAP-expression vector, integrated into the amy locus of Xac, does not compromise its virulence. Furthermore, our results also demonstrate that the polypeptide TAP can be overproduced in Xac and purified from the soluble phase of cell extracts. Our results substantiate the use of our vectors for protein expression in Xac thus contributing a novel tool for the characterization of proteins and protein complexes generated by this bacterium in vivo.
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Affiliation(s)
- Giordanni C Dantas
- Depto. de Bioquimica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Paula M M Martins
- Depto. de Bioquimica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Daniela A B Martins
- Depto. de Bioquímica e Tecnologia Química, Instituto de Química, Universidade Estadual Paulista, Araraquara, SP, Brazil
| | - Eleni Gomes
- Depto. de Biologia, Universidade Estadual Paulista, São Jose do Rio Preto, SP, Brazil
| | - Henrique Ferreira
- Depto. de Bioquimica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil.
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Sinetova MA, Los DA. Systemic analysis of stress transcriptomics of Synechocystis reveals common stress genes and their universal triggers. MOLECULAR BIOSYSTEMS 2016; 12:3254-3258. [DOI: 10.1039/c6mb00551a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Systemic analysis of stress transcriptomics reveals that ROS and redox changes may universally trigger stress responses in Synechocystis (cyanobacteria).
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Affiliation(s)
- M. A. Sinetova
- Institute of Plant Physiology
- Russian Academy of Sciences
- Moscow
- Russia
| | - D. A. Los
- Institute of Plant Physiology
- Russian Academy of Sciences
- Moscow
- Russia
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8
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Gao L, Wang J, Ge H, Fang L, Zhang Y, Huang X, Wang Y. Toward the complete proteome of Synechocystis sp. PCC 6803. PHOTOSYNTHESIS RESEARCH 2015; 126:203-219. [PMID: 25862646 DOI: 10.1007/s11120-015-0140-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 04/02/2015] [Indexed: 06/04/2023]
Abstract
The proteome of the photosynthetic model organism Synechocystis sp. PCC 6803 has been extensively analyzed in the last 15 years for the purpose of identifying proteins specifically expressed in subcellular compartments or differentially expressed in different environmental or internal conditions. This review summarizes the progress achieved so far with the emphasis on the impact of different techniques, both in sample preparation and protein identification, on the increasing coverage of proteome identification. In addition, this review evaluates the current completeness of proteome identification, and provides insights on the potential factors that could affect the complete identification of the Synechocystis proteome.
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Affiliation(s)
- Liyan Gao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd, Beijing, 100101, China
| | - Jinlong Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd, Beijing, 100101, China
| | - Haitao Ge
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Longfa Fang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd, Beijing, 100101, China
| | - Yuanya Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd, Beijing, 100101, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd, Beijing, 100101, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd, Beijing, 100101, China.
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9
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Gao L, Pei G, Chen L, Zhang W. A global network-based protocol for functional inference of hypothetical proteins in Synechocystis sp. PCC 6803. J Microbiol Methods 2015; 116:44-52. [DOI: 10.1016/j.mimet.2015.06.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 06/24/2015] [Accepted: 06/25/2015] [Indexed: 01/15/2023]
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Jaafar SNT, Coelho AV, Sheehan D. Redox proteomic analysis ofmytilus edulisgills: effects of the pharmaceutical diclofenac on a non-target organism. Drug Test Anal 2015; 7:957-66. [DOI: 10.1002/dta.1786] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/20/2015] [Accepted: 02/20/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Siti Nur Tahirah Jaafar
- Proteomics Research Group, School of Biochemistry and Cell Biology and Environmental Research Institute; University College Cork; Ireland
- Marine Biology Program, School of Marine Science and Environment; Universiti Malaysia Terengganu; Terengganu Malaysia
| | - Ana Varela Coelho
- Mass Spectrometry Laboratory, Analytical Services Unit, Institute of Chemical and Biological Technology (ITQB); New University of Lisbon; Avenida República - Quinta do Marquês 2784-505 Oeiras Portugal
| | - David Sheehan
- Proteomics Research Group, School of Biochemistry and Cell Biology and Environmental Research Institute; University College Cork; Ireland
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11
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Salt acclimation of cyanobacteria and their application in biotechnology. Life (Basel) 2014; 5:25-49. [PMID: 25551682 PMCID: PMC4390839 DOI: 10.3390/life5010025] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/19/2014] [Indexed: 12/25/2022] Open
Abstract
The long evolutionary history and photo-autotrophic lifestyle of cyanobacteria has allowed them to colonize almost all photic habitats on Earth, including environments with high or fluctuating salinity. Their basal salt acclimation strategy includes two principal reactions, the active export of ions and the accumulation of compatible solutes. Cyanobacterial salt acclimation has been characterized in much detail using selected model cyanobacteria, but their salt sensing and regulatory mechanisms are less well understood. Here, we briefly review recent advances in the identification of salt acclimation processes and the essential genes/proteins involved in acclimation to high salt. This knowledge is of increasing importance because the necessary mass cultivation of cyanobacteria for future use in biotechnology will be performed in sea water. In addition, cyanobacterial salt resistance genes also can be applied to improve the salt tolerance of salt sensitive organisms, such as crop plants.
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Coronado E, Roggo C, van der Meer JR. Identification of genes potentially involved in solute stress response in Sphingomonas wittichii RW1 by transposon mutant recovery. Front Microbiol 2014; 5:585. [PMID: 25408691 PMCID: PMC4219479 DOI: 10.3389/fmicb.2014.00585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 10/17/2014] [Indexed: 11/13/2022] Open
Abstract
The term water stress refers to the effects of low water availability on microbial growth and physiology. Water availability has been proposed as a major constraint for the use of microorganisms in contaminated sites with the purpose of bioremediation. Sphingomonas wittichii RW1 is a bacterium capable of degrading the xenobiotic compounds dibenzofuran and dibenzo-p-dioxin, and has potential to be used for targeted bioremediation. The aim of the current work was to identify genes implicated in water stress in RW1 by means of transposon mutagenesis and mutant growth experiments. Conditions of low water potential were mimicked by adding NaCl to the growth media. Three different mutant selection or separation method were tested which, however recovered different mutants. Recovered transposon mutants with poorer growth under salt-induced water stress carried insertions in genes involved in proline and glutamate biosynthesis, and further in a gene putatively involved in aromatic compound catabolism. Transposon mutants growing poorer on medium with lowered water potential also included ones that had insertions in genes involved in more general functions such as transcriptional regulation, elongation factor, cell division protein, RNA polymerase β or an aconitase.
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Affiliation(s)
- Edith Coronado
- Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
| | - Clémence Roggo
- Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
| | - Jan R van der Meer
- Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
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Peña-Castillo L, Mercer RG, Gurinovich A, Callister SJ, Wright AT, Westbye AB, Beatty JT, Lang AS. Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides. BMC Genomics 2014; 15:730. [PMID: 25164283 PMCID: PMC4158056 DOI: 10.1186/1471-2164-15-730] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 08/21/2014] [Indexed: 01/05/2023] Open
Abstract
Background The genus Rhodobacter contains purple nonsulfur bacteria found mostly in freshwater environments. Representative strains of two Rhodobacter species, R. capsulatus and R. sphaeroides, have had their genomes fully sequenced and both have been the subject of transcriptional profiling studies. Gene co-expression networks can be used to identify modules of genes with similar expression profiles. Functional analysis of gene modules can then associate co-expressed genes with biological pathways, and network statistics can determine the degree of module preservation in related networks. In this paper, we constructed an R. capsulatus gene co-expression network, performed functional analysis of identified gene modules, and investigated preservation of these modules in R. capsulatus proteomics data and in R. sphaeroides transcriptomics data. Results The analysis identified 40 gene co-expression modules in R. capsulatus. Investigation of the module gene contents and expression profiles revealed patterns that were validated based on previous studies supporting the biological relevance of these modules. We identified two R. capsulatus gene modules preserved in the protein abundance data. We also identified several gene modules preserved between both Rhodobacter species, which indicate that these cellular processes are conserved between the species and are candidates for functional information transfer between species. Many gene modules were non-preserved, providing insight into processes that differentiate the two species. In addition, using Local Network Similarity (LNS), a recently proposed metric for expression divergence, we assessed the expression conservation of between-species pairs of orthologs, and within-species gene-protein expression profiles. Conclusions Our analyses provide new sources of information for functional annotation in R. capsulatus because uncharacterized genes in modules are now connected with groups of genes that constitute a joint functional annotation. We identified R. capsulatus modules enriched with genes for ribosomal proteins, porphyrin and bacteriochlorophyll anabolism, and biosynthesis of secondary metabolites to be preserved in R. sphaeroides whereas modules related to RcGTA production and signalling showed lack of preservation in R. sphaeroides. In addition, we demonstrated that network statistics may also be applied within-species to identify congruence between mRNA expression and protein abundance data for which simple correlation measurements have previously had mixed results. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-730) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lourdes Peña-Castillo
- Department of Biology, Memorial University of Newfoundland, St, John's, NL A1B 3X5, Canada.
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Ilyas S, Rehman A, Varela AC, Sheehan D. Redox proteomics changes in the fungal pathogen Trichosporon asahii on arsenic exposure: identification of protein responses to metal-induced oxidative stress in an environmentally-sampled isolate. PLoS One 2014; 9:e102340. [PMID: 25062082 PMCID: PMC4111368 DOI: 10.1371/journal.pone.0102340] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 06/18/2014] [Indexed: 01/25/2023] Open
Abstract
Trichosporon asahii is a yeast pathogen implicated in opportunistic infections. Cultures of an isolate collected from industrial wastewater were exposed for 2 days to 100 mg/L sodium arsenite (NaAsO2) and cadmium (CdCl2). Both metals reduced glutathione transferase (GST) activity but had no effect on superoxide dismutase or catalase. NaAsO2 exposure increased glutathione reductase activity while CdCl2 had no effect. Protein thiols were labeled with 5-iodoacetamido fluorescein followed by one dimensional electrophoresis which revealed extensive protein thiol oxidation in response to CdCl2 treatment but thiol reduction in response to NaAsO2. Two dimensional electrophoresis analyses showed that the intensity of some protein spots was enhanced on treatment as judged by SameSpots image analysis software. In addition, some spots showed decreased IAF fluorescence suggesting thiol oxidation. Selected spots were excised and tryptic digested for identification by MALDI-TOF/TOF MS. Twenty unique T. asahii proteins were identified of which the following proteins were up-regulated in response to NaAsO2: 3-isopropylmalate dehydrogenase, phospholipase B, alanine-glyoxylate aminotransferase, ATP synthase alpha chain, 20S proteasome beta-type subunit Pre3p and the hypothetical proteins A1Q1_08001, A1Q2_03020, A1Q1_06950, A1Q1_06913. In addition, the following showed decreased thiol-associated fluorescence consistent with thiol oxidation; aconitase; aldehyde reductase I; phosphoglycerate kinase; translation elongation factor 2; heat shock protein 70 and hypothetical protein A1Q2_04745. Some proteins showed both increase in abundance coupled with decrease in IAF fluorescence; 3-hydroxyisobutyryl- CoA hydrolase; homoserine dehydrogenase Hom6 and hypothetical proteins A1Q2_03020 and A1Q1_00754. Targets implicated in redox response included 10 unique metabolic enzymes, heat shock proteins, a component of the 20S proteasome and translation elongation factor 2. These data suggest extensive proteomic alterations in response to metal-induced oxidative stress in T. asahii. Amino acid metabolism, protein folding and degradation are principally affected.
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Affiliation(s)
- Sidra Ilyas
- Dept. Of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Abdul Rehman
- Dept. Of Microbiology and Molecular Genetics, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Ana Coelho Varela
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - David Sheehan
- Environmental Research Institute and School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- * E-mail:
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Overexpression of sigma factor SigB improves temperature and butanol tolerance of Synechocystis sp. PCC6803. J Biotechnol 2014; 182-183:54-60. [DOI: 10.1016/j.jbiotec.2014.04.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 04/17/2014] [Accepted: 04/25/2014] [Indexed: 11/21/2022]
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16
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Hosoda K, Habuchi M, Suzuki S, Miyazaki M, Takikawa G, Sakurai T, Kashiwagi A, Sueyoshi M, Matsumoto Y, Kiuchi A, Mori K, Yomo T. Adaptation of a cyanobacterium to a biochemically rich environment in experimental evolution as an initial step toward a chloroplast-like state. PLoS One 2014; 9:e98337. [PMID: 24874568 PMCID: PMC4038495 DOI: 10.1371/journal.pone.0098337] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 05/01/2014] [Indexed: 11/29/2022] Open
Abstract
Chloroplasts originated from cyanobacteria through endosymbiosis. The original cyanobacterial endosymbiont evolved to adapt to the biochemically rich intracellular environment of the host cell while maintaining its photosynthetic function; however, no such process has been experimentally demonstrated. Here, we show the adaptation of a model cyanobacterium, Synechocystis sp. PCC 6803, to a biochemically rich environment by experimental evolution. Synechocystis sp. PCC 6803 does not grow in a biochemically rich, chemically defined medium because several amino acids are toxic to the cells at approximately 1 mM. We cultured the cyanobacteria in media with the toxic amino acids at 0.1 mM, then serially transferred the culture, gradually increasing the concentration of the toxic amino acids. The cells evolved to show approximately the same specific growth rate in media with 0 and 1 mM of the toxic amino acid in approximately 84 generations and evolved to grow faster in the media with 1 mM than in the media with 0 mM in approximately 181 generations. We did not detect a statistically significant decrease in the autotrophic growth of the evolved strain in an inorganic medium, indicating the maintenance of the photosynthetic function. Whole-genome resequencing revealed changes in the genes related to the cell membrane and the carboxysome. Moreover, we quantitatively analyzed the evolutionary changes by using simple mathematical models, which evaluated the evolution as an increase in the half-maximal inhibitory concentration (IC50) and estimated quantitative characteristics of the evolutionary process. Our results clearly demonstrate not only the potential of a model cyanobacterium to adapt to a biochemically rich environment without a significant decrease in photosynthetic function but also the properties of its evolutionary process, which sheds light of the evolution of chloroplasts at the initial stage.
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Affiliation(s)
- Kazufumi Hosoda
- Institute for Academic Initiatives, Osaka University, Suita, Osaka, Japan
| | - Masumi Habuchi
- Department of Frontier Biosciences, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Shingo Suzuki
- Quantitative Biology Center, RIKEN, Suita, Osaka, Japan
| | - Mikako Miyazaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Go Takikawa
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Takahiro Sakurai
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Akiko Kashiwagi
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
| | - Makoto Sueyoshi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Yusuke Matsumoto
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Ayako Kiuchi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Kotaro Mori
- Department of Frontier Biosciences, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Tetsuya Yomo
- Department of Frontier Biosciences, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
- Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Agency, Suita, Osaka, Japan
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Bharti RK, Srivastava S, Thakur IS. Proteomic analysis of carbon concentrating chemolithotrophic bacteria Serratia sp. for sequestration of carbon dioxide. PLoS One 2014; 9:e91300. [PMID: 24619032 PMCID: PMC3949746 DOI: 10.1371/journal.pone.0091300] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 02/08/2014] [Indexed: 11/19/2022] Open
Abstract
A chemolithotrophic bacterium enriched in the chemostat in presence of sodium bicarbonate as sole carbon source was identified as Serratia sp. by 16S rRNA sequencing. Carbon dioxide sequestering capacity of bacterium was detected by carbonic anhydrase enzyme and ribulose-1, 5- bisphosphate carboxylase/oxygenase (RuBisCO). The purified carbonic anhydrase showed molecular weight of 29 kDa. Molecular weight of RuBisCO was 550 kDa as determined by fast protein liquid chromatography (FPLC), however, sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) showed presence of two subunits whose molecular weights were 56 and 14 kDa. The Western blot analysis of the crude protein and purified sample cross reacted with RuBisCO large-subunit polypeptides antibodies showed strong band pattern at molecular weight around 56 kDa regions. Whole cell soluble proteins of Serratia sp. grown under autotrophic and heterotrophic conditions were resolved by two-dimensional gel electrophoresis and MALDI-TOF/MS for differential expression of proteins. In proteomic analysis of 63 protein spots, 48 spots were significantly up-regulated in the autotrophically grown cells; seven enzymes showed its utilization in autotrophic carbon fixation pathways and other metabolic activities of bacterium including lipid metabolisms indicated sequestration potency of carbon dioxide and production of biomaterials.
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Affiliation(s)
- Randhir K. Bharti
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shaili Srivastava
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
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18
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Du C, Liang JR, Chen DD, Xu B, Zhuo WH, Gao YH, Chen CP, Bowler C, Zhang W. iTRAQ-based proteomic analysis of the metabolism mechanism associated with silicon response in the marine diatom Thalassiosira pseudonana. J Proteome Res 2014; 13:720-34. [PMID: 24372006 DOI: 10.1021/pr400803w] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Silicon is a critical element for diatom growth; however our understanding of the molecular mechanisms involved in intracellular silicon responses are limited. In this study, an iTRAQ-LC-MS/MS quantitative proteomic approach was coupled with an established synchrony technique to reveal the global metabolic silicon-response in the model diatom Thalassiosira pseudonana subject to silicon starvation and readdition. Four samples, which corresponded to the time of silicon starvation, girdle band synthesis, valve formation, and right after daughter cell separation (0, 1, 5, 7 h), were collected for the proteomic analysis. The results indicated that a total of 1,831 proteins, representing 16% of the predicted proteins encoded by the T. pseudonana genome, could be identified. Of the identified proteins, 165 were defined as being differentially expressed proteins, and these proteins could be linked to multiple biochemical pathways. In particular, a number of proteins related to silicon transport, cell wall synthesis, and cell-cycle progress could be identified. In addition, other proteins that are potentially involved in amino acid synthesis, protein metabolism, and energy generation may have roles in the cellular response to silicon. Our findings provide a range of valuable information that will be of use for further studies of this important physiological response that is unique to diatoms.
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Affiliation(s)
- Chao Du
- School of Life Sciences, Xiamen University , Xiamen 361005, China
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19
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Chen L, Wu L, Wang J, Zhang W. Butanol tolerance regulated by a two-component response regulator Slr1037 in photosynthetic Synechocystis sp. PCC 6803. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:89. [PMID: 24932218 PMCID: PMC4057619 DOI: 10.1186/1754-6834-7-89] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 05/27/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Butanol production directly from CO2 in photosynthetic cyanobacteria is restricted by the high toxicity of butanol to the hosts. In previous studies, we have found that a few two-component signal transduction systems (TCSTSs) were differentially regulated in Synechocystis sp. PCC 6803 after butanol treatment. RESULTS To explore regulatory mechanisms of butanol tolerance, in this work, by constructing gene knockout mutants of the butanol-responsive TCSTS genes and conducting tolerance analysis, we uncovered that an orphan slr1037 gene encoding a novel response regulator was involved in butanol tolerance in Synechocystis. Interestingly, the ∆slr1037 mutant grew similarly to the wild type under several other stress conditions tested, which suggests that its regulation on butanol tolerance is specific. Using a quantitative iTRAQ LC-MS/MS proteomics approach coupled with real-time reverse transcription PCR, we further determined the possible butanol-tolerance regulon regulated by Slr1037. The results showed that, after slr1037 deletion, proteins involved in photosynthesis and glycolysis/gluconeogenesis of central metabolic processes, and glutaredoxin, peptide methionine sulfoxide reductase and glucosylglycerol-phosphate synthase with stress-responsive functions were down-regulated, suggesting that Slr1037 may exhibit regulation to a wide range of cellular functions in combating butanol stress. CONCLUSIONS The study provided a proteomic description of the putative butanol-tolerance regulon regulated by the slr1037 gene. As the first signal transduction protein identified directly related to butanol tolerance, response regulator Slr1037 could be a natural candidate for transcriptional engineering to improve butanol tolerance in Synechocystis.
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Affiliation(s)
- Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P.R. China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China
| | - Lina Wu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P.R. China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China
| | - Jiangxin Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P.R. China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, P.R. China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, P.R. China
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Keller R, Schneider D. Homologs of the yeast Tvp38 vesicle-associated protein are conserved in chloroplasts and cyanobacteria. FRONTIERS IN PLANT SCIENCE 2013; 4:467. [PMID: 24312110 PMCID: PMC3836016 DOI: 10.3389/fpls.2013.00467] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 10/29/2013] [Indexed: 05/21/2023]
Abstract
Vesicle transfer processes in eukaryotes depend on specific proteins, which mediate the selective packing of cargo molecules for subsequent release out of the cells after vesicle fusion to the plasma membrane. The protein Tvp38 is conserved in yeasts and higher eukaryotes and potentially involved in vesicle transfer processes at the Golgi membrane. Members of the so-called "SNARE-associated proteins of the Tvp38-family" have also been identified in prokaryotes and those belong to the DedA protein family. Tvp38/DedA proteins are also conserved in cyanobacteria and chloroplasts. While only a single member of this family appears to be present in chloroplasts, cyanobacterial genomes typically encode multiple homologous proteins. Mainly based on our understanding of the DedA-homologous proteins of Escherichia coli, it appears likely that the function of these proteins in chloroplast and cyanobacteria involves stabilizing and organizing the structure of internal membrane systems.
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Affiliation(s)
- Rebecca Keller
- Department of Pharmacy and Biochemistry, Johannes Gutenberg-UniversityMainz, Germany
| | - Dirk Schneider
- Department of Pharmacy and Biochemistry, Johannes Gutenberg-UniversityMainz, Germany
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21
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Qiao J, Huang S, Te R, Wang J, Chen L, Zhang W. Integrated proteomic and transcriptomic analysis reveals novel genes and regulatory mechanisms involved in salt stress responses in Synechocystis sp. PCC 6803. Appl Microbiol Biotechnol 2013; 97:8253-64. [PMID: 23925534 DOI: 10.1007/s00253-013-5139-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 07/15/2013] [Accepted: 07/15/2013] [Indexed: 11/30/2022]
Abstract
Salt stress is a common stress that limits growth and productivity of photosynthetic microbes in natural environments. Although cellular responses of a model cyanobacterium Synechocystis sp. PCC6803 to high and changing salt concentration have been studied, it remains undefined of the gene components and their regulation in the long-term salt acclimation networks. In this study, we performed an integrated study coupling a quantitative iTRAQ-LC-MS/MS proteomics and a next-generation sequencing-based RNA-seq transcriptomics on Synechocystis under salt stress for an extended period of time. Comparative quantification of protein abundances led to the identification of 68 and 108 proteins differentially regulated by salt treatment at 24 and 48 h, respectively. RNA-seq transcriptomic analysis showed that genes involved in energy metabolism and protein synthesis, and genes encoding hypothetical proteins responded to salt stress in a phase-dependent pattern. Notably, a gene encoding CO2-uptake-related protein (CupA) and three genes encoding hypothetical proteins were induced significantly at either transcript or protein level after long-term salt stress. Gene knockout and comparative growth analysis demonstrated that these four genes were involved in salt tolerance in Synechocystis. In addition, a complementary proteome and transcriptome analysis showed that concordance between protein abundances and their corresponding mRNAs varied significantly between various gene-protein pairs, indicating divergent regulation of transcriptional and post-transcriptional processes during salt stress adaptation in Synechocystis. The study provided new insights on genes and regulatory mechanism involved in salt stress response in Synechocystis.
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Affiliation(s)
- Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
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22
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Wang J, Wu G, Chen L, Zhang W. Cross-species transcriptional network analysis reveals conservation and variation in response to metal stress in cyanobacteria. BMC Genomics 2013; 14:112. [PMID: 23421563 PMCID: PMC3598940 DOI: 10.1186/1471-2164-14-112] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 02/13/2013] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND As one of the most dominant bacterial groups on Earth, cyanobacteria play a pivotal role in the global carbon cycling and the Earth atmosphere composition. Understanding their molecular responses to environmental perturbations has important scientific and environmental values. Since important biological processes or networks are often evolutionarily conserved, the cross-species transcriptional network analysis offers a useful strategy to decipher conserved and species-specific transcriptional mechanisms that cells utilize to deal with various biotic and abiotic disturbances, and it will eventually lead to a better understanding of associated adaptation and regulatory networks. RESULTS In this study, the Weighted Gene Co-expression Network Analysis (WGCNA) approach was used to establish transcriptional networks for four important cyanobacteria species under metal stress, including iron depletion and high copper conditions. Cross-species network comparison led to discovery of several core response modules and genes possibly essential to metal stress, as well as species-specific hub genes for metal stresses in different cyanobacteria species, shedding light on survival strategies of cyanobacteria responding to different environmental perturbations. CONCLUSIONS The WGCNA analysis demonstrated that the application of cross-species transcriptional network analysis will lead to novel insights to molecular response to environmental changes which will otherwise not be achieved by analyzing data from a single species.
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Affiliation(s)
- Jiangxin Wang
- School of Chemical Engineering & Technology, Tianjin University, 300072, Tianjin, People's Republic of China
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