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Hou L, Zheng B, Jiang Z, Hu Y, Shi L, Dong Y, Jiang Y. The dmsEFABGH operon encodes an essential and modular electron transfer pathway for extracellular iodate reduction by Shewanella oneidensis MR-1. Microbiol Spectr 2024:e0051224. [PMID: 38916364 DOI: 10.1128/spectrum.00512-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Extracellular iodate reduction by Shewanella spp. contributes to iodide generation in the biogeochemical cycling of iodine. However, there is a disagreement on whether Shewanella spp. use different extracellular electron transfer pathways with dependence on electron donors in iodate reduction. In this study, a series of gene deletion mutants of Shewanella oneidensis MR-1 were created to investigate the roles of dmsEFABGH, mtrCAB, and so4357-so4362 operons in iodate reduction. The iodate-reducing activity of the mutants was tested with lactate, formate, and H2 as the sole electron donors, respectively. In the absence of single-dms gene, iodate reduction efficiency of the mutants was only 12.9%-84.0% with lactate at 24 hours, 22.1%-85.9% with formate at 20 hours, and 19.6%-57.7% with H2 at 42 hours in comparison to complete reduction by the wild type. Progressive inhibition of iodate reduction was observed when the dms homolog from the so4357-so4362 operon was deleted in the single-dms gene mutants. This result revealed complementation of dmsEFABGH by so4357-so4362 at the single-gene level, indicating modularity of the extracellular electron transfer pathway encoded by dmsEFABGH operon. Under the conditions of all electron donors, significant inhibition of iodate reduction and accumulation of H2O2 were detected for ΔmtrCAB. Collectively, these results demonstrated that the dmsEFABGH operon encodes an essential and modular iodate-reducing pathway without electron donor dependence in S. oneidensis MR-1. The mtrCAB operon was involved in H2O2 elimination with all electron donors. The findings in this study improved the understanding of molecular mechanisms underlying extracellular iodate reduction.IMPORTANCEIodine is an essential trace element for human and animals. Recent studies revealed the contribution of microbial extracellular reduction of iodate in biogeochemical cycling of iodine. Multiple reduced substances can be utilized by microorganisms as energy source for iodate reduction. However, varied electron transfer pathways were proposed for iodate reduction with different electron donors in the model strain Shewanella oneidensis MR-1. Here, through a series of gene deletion and iodate reduction experiments, we discovered that the dmsEFABGH operon was essential for iodate reduction with at least three electron donors, including lactate, formate, and H2. The so4357-so4362 operon was first demonstrated to be capable of complementing the function of dmsEFABGH at single-gene level.
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Affiliation(s)
- Lingyu Hou
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
| | - Beiling Zheng
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
| | - Zhou Jiang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
| | - Yidan Hu
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
| | - Liang Shi
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
| | - Yiran Dong
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
| | - Yongguang Jiang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
- Hubei Key Laboratory of Wetland Evolution & Eco-Restoration, Wuhan, Hubei, China
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Lo HH, Chang HC, Wu YJ, Liao CT, Hsiao YM. Functional characterization and transcriptional analysis of degQ of Xanthomonas campestris pathovar campestris. J Basic Microbiol 2024; 64:e2300441. [PMID: 38470163 DOI: 10.1002/jobm.202300441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/07/2024] [Accepted: 01/20/2024] [Indexed: 03/13/2024]
Abstract
High-temperature-requirement protein A (HtrA) family proteins play important roles in controlling protein quality and are recognized as virulence factors in numerous animal and human bacterial pathogens. The role of HtrA family proteins in plant pathogens remains largely unexplored. Here, we investigated the HtrA family protein, DegQ, in the crucifer black rot pathogen Xanthomonas campestris pathovar campestris (Xcc). DegQ is essential for bacterial attachment and full virulence of Xcc. Moreover, the degQ mutant strain showed increased sensitivity to heat treatment and sodium dodecyl sulfate. Expressing the intact degQ gene in trans in the degQ mutant could reverse the observed phenotypic changes. In addition, we demonstrated that the DegQ protein exhibited chaperone-like activity. Transcriptional analysis displayed that degQ expression was induced under heat treatment. Our results contribute to understanding the function and expression of DegQ of Xcc for the first time and provide a novel perspective about HtrA family proteins in plant pathogen.
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Affiliation(s)
- Hsueh-Hsia Lo
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, Taiwan
| | - Hsiao-Ching Chang
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, Taiwan
| | - Yi-Jyun Wu
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, Taiwan
| | - Chao-Tsai Liao
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, Taiwan
| | - Yi-Min Hsiao
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, Taiwan
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Ku RH, Li LH, Liu YF, Hu EW, Lin YT, Lu HF, Yang TC. Implication of the σ E Regulon Members OmpO and σ N in the Δ ompA299-356-Mediated Decrease of Oxidative Stress Tolerance in Stenotrophomonas maltophilia. Microbiol Spectr 2023; 11:e0108023. [PMID: 37284772 PMCID: PMC10433810 DOI: 10.1128/spectrum.01080-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/16/2023] [Indexed: 06/08/2023] Open
Abstract
Outer membrane protein A (OmpA) is the most abundant porin in bacterial outer membranes. KJΔOmpA299-356, an ompA C-terminal in-frame deletion mutant of Stenotrophomonas maltophilia KJ, exhibits pleiotropic defects, including decreased tolerance to menadione (MD)-mediated oxidative stress. Here, we elucidated the underlying mechanism of the decreased MD tolerance mediated by ΔompA299-356. The transcriptomes of wild-type S. maltophilia and the KJΔOmpA299-356 mutant strain were compared, focusing on 27 genes known to be associated with oxidative stress alleviation; however, no significant differences were identified. OmpO was the most downregulated gene in KJΔOmpA299-356. KJΔOmpA299-356 complementation with the chromosomally integrated ompO gene restored MD tolerance to the wild-type level, indicating the role of OmpO in MD tolerance. To further clarify the possible regulatory circuit involved in ompA defects and ompO downregulation, σ factor expression levels were examined based on the transcriptome results. The expression levels of three σ factors were significantly different (downregulated levels of rpoN and upregulated levels of rpoP and rpoE) in KJΔOmpA299-356. Next, the involvement of the three σ factors in the ΔompA299-356-mediated decrease in MD tolerance was evaluated using mutant strains and complementation assays. rpoN downregulation and rpoE upregulation contributed to the ΔompA299-356-mediated decrease in MD tolerance. OmpA C-terminal domain loss induced an envelope stress response. Activated σE decreased rpoN and ompO expression levels, in turn decreasing swimming motility and oxidative stress tolerance. Finally, we revealed both the ΔompA299-356-rpoE-ompO regulatory circuit and rpoE-rpoN cross regulation. IMPORTANCE The cell envelope is a morphological hallmark of Gram-negative bacteria. It consists of an inner membrane, a peptidoglycan layer, and an outer membrane. OmpA, an outer membrane protein, is characterized by an N-terminal β-barrel domain that is embedded in the outer membrane and a C-terminal globular domain that is suspended in the periplasmic space and connected to the peptidoglycan layer. OmpA is crucial for the maintenance of envelope integrity. Stress resulting from the destruction of envelope integrity is sensed by extracytoplasmic function (ECF) σ factors, which induce responses to various stressors. In this study, we revealed that loss of the OmpA-peptidoglycan (PG) interaction causes peptidoglycan and envelope stress while simultaneously upregulating σP and σE expression levels. The outcomes of σP and σE activation are different and are linked to β-lactam and oxidative stress tolerance, respectively. These findings establish that outer membrane proteins (OMPs) play a critical role in envelope integrity and stress tolerance.
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Affiliation(s)
- Ren-Hsuan Ku
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Li-Hua Li
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Yi-Fu Liu
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - En-Wei Hu
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Tsung Lin
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hsu-Feng Lu
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan
| | - Tsuey-Ching Yang
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
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Xia M, Yu D, Chen H, Dai J, Gao N, Li S, Bi X, Qiu D. An RpoN-dependent PEP-CTERM gene is involved in floc formation of an Aquincola tertiaricarbonis strain. BMC Microbiol 2023; 23:20. [PMID: 36658495 PMCID: PMC9850573 DOI: 10.1186/s12866-022-02745-1] [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: 01/18/2022] [Accepted: 12/21/2022] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The floc is a characteristic of microbial aggregate growth, displaying cloudy suspensions in water. Floc formation has been demonstrated in a series of bacteria and the floc-forming bacteria play a crucial role in activated sludge (AS) process widely used for municipal sewage and industrial wastewater treatment over a century. It has been demonstrated that some exopolysaccharide biosynthesis genes and the sigma factor (sigma54 or rpoN) were required for floc forming in some bacteria. However, the mechanism underlying the floc formation stills need to be elucidated. RESULTS In this study, we demonstrate that a TPR (Tetratricopeptide repeats) protein-encoding gene prsT is required for floc formation of Aquincola tertiaricarbonis RN12 and an upstream PEP-CTERM gene (designated pepA), regulated by RpoN1, is involved in its floc formation but not swarming motility and biofilm formation. Overexpression of PepA could rescue the floc-forming phenotype of the rpoN1 mutant by decreasing the released soluble exopolysaccharides and increasing the bound polymers. CONCLUSION Our results indicate that the wide-spread PEP-CTERM proteins play an important role in the self-flocculation of bacterial cells and may be a component of extracellular polymeric substances required for floc-formation.
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Affiliation(s)
- Ming Xia
- grid.411854.d0000 0001 0709 0000School of Life Sciences, Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Jianghan University, Wuhan, 430056 China ,grid.411854.d0000 0001 0709 0000Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, 430056 China
| | - Dianzhen Yu
- grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China ,grid.419092.70000 0004 0467 2285Institute for Nutritional Sciences, SIBS, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Han Chen
- grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China ,grid.429211.d0000 0004 1792 6029Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 Hubei Province China
| | - Jingcheng Dai
- grid.429211.d0000 0004 1792 6029Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 Hubei Province China
| | - Na Gao
- grid.469521.d0000 0004 1756 0127Fisheries Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Shuyang Li
- grid.429211.d0000 0004 1792 6029Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 Hubei Province China
| | - Xuezhi Bi
- grid.452198.30000 0004 0485 9218Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, 138668 Singapore
| | - Dongru Qiu
- grid.429211.d0000 0004 1792 6029Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 Hubei Province China
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The Interaction between Oxidative Stress Biomarkers and Gut Microbiota in the Antioxidant Effects of Extracts from Sonchus brachyotus DC. in Oxazolone-Induced Intestinal Oxidative Stress in Adult Zebrafish. Antioxidants (Basel) 2023; 12:antiox12010192. [PMID: 36671053 PMCID: PMC9854779 DOI: 10.3390/antiox12010192] [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: 12/06/2022] [Revised: 01/08/2023] [Accepted: 01/11/2023] [Indexed: 01/14/2023] Open
Abstract
Oxidative stress is a phenomenon caused by an imbalance between the production and accumulation of reactive oxygen species in cells and tissues that eventually leads to the production of various diseases. Here, we investigated the antioxidant effects of the extract from Sonchus brachyotus DC. (SBE) based on the 0.2% oxazolone-induced intestinal oxidative stress model of zebrafish. Compared to the model group, the treatment group alleviated oxazolone-induced intestinal tissue damage and reduced the contents of malondialdehyde, reactive oxygen species, IL-1β, and TNF-α and then increased the contents of superoxide dismutase, glutathione peroxidase, and IL-10. The 16s rDNA gene sequencing findings demonstrated that SBE could increase the relative abundance of Fusobacteriota, Actinobacteriota, and Firmicutes and decrease the relative abundance of Proteobacteria. Based on the correlation analysis between the oxidative stress biomarkers and intestinal flora, we found that the trends of oxidative stress biomarkers were significantly correlated with intestinal microorganisms, especially at the genus level. The correlations of MDA, IL-1β, and TNF-α were significantly negative with Shewanella, while SOD, GSH-Px, and IL-10 were significantly positive with Cetobacterium, Gemmobacter, and Flavobacterium. Consequently, we concluded that the antioxidant effect of SBE was realized through the interaction between oxidative stress biomarkers and gut microbiota.
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Genomic Landscape Highlights Molecular Mechanisms Involved in Silicate Solubilization, Stress Tolerance, and Potential Growth-Promoting Activity of Bacterium Enterobacter sp. LR6. Cells 2022; 11:cells11223622. [PMID: 36429050 PMCID: PMC9688052 DOI: 10.3390/cells11223622] [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: 08/30/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
Abstract
Silicon (Si) is gaining widespread attention due to its prophylactic activity to protect plants under stress conditions. Despite Si's abundance in the earth's crust, most soils do not have enough soluble Si for plants to absorb. In the present study, a silicate-solubilizing bacterium, Enterobacter sp. LR6, was isolated from the rhizospheric soil of rice and subsequently characterized through whole-genome sequencing. The size of the LR6 genome is 5.2 Mb with a GC content of 54.9% and 5182 protein-coding genes. In taxogenomic terms, it is similar to E. hormaechei subsp. xiangfangensis based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH). LR6 genomic data provided insight into potential genes involved in stress response, secondary metabolite production, and growth promotion. The LR6 genome contains two aquaporins, of which the aquaglyceroporin (GlpF) is responsible for the uptake of metalloids including arsenic (As) and antimony (Sb). The yeast survivability assay confirmed the metalloid transport activity of GlpF. As a biofertilizer, LR6 isolate has a great deal of tolerance to high temperatures (45 °C), salinity (7%), and acidic environments (pH 9). Most importantly, the present study provides an understanding of plant-growth-promoting activity of the silicate-solubilizing bacterium, its adaptation to various stresses, and its uptake of different metalloids including As, Ge, and Si.
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Lan Q, Cao Z, Yang X, Gu Z. Physiological and Proteomic Responses of Dairy Buffalo to Heat Stress Induced by Different Altitudes. Metabolites 2022; 12:metabo12100909. [PMID: 36295811 PMCID: PMC9609643 DOI: 10.3390/metabo12100909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 11/20/2022] Open
Abstract
Buffalo are mainly distributed in low-altitude (LA), medium-altitude (MA), and high-altitude (HA) regions characterised by different thermal and oxygen environments in Yunnan province, China. Due to black skin, sparse hair, and the low density of skin sweat glands, buffalo are more sensitive to heat stress. Here, we used data-independent acquisition (DIA) proteomics to reveal a broad spectrum of proteins that play roles in adaptation to the heat stress of buffalo raised at low altitude or hypoxia at high altitude. LA buffalo showed higher body temperatures than MA- and HA buffalo, and HA buffalo had higher levels of GSH and SOD and lower levels of ROS compared to LA and MA buffalo. In 33 samples, 8476 peptides corresponding to 666 high-confidence proteins were detected. The levels of circulating complement proteins in the immune pathways were lower in LA and MA buffalo than in HA buffalo. There were higher levels of alpha-1 acid glycoprotein in LA buffalo than in MA and HA buffalo. Relative to MA buffalo, levels of blood oxygen delivery proteins were higher in LA and HA buffalo. A higher abundance of apolipoproteins was detected in LA and MA buffalo than in HA buffalo. In summary, buffalo adopted similar adaptation strategies to oxidative stress induced by heat stress or hypoxia, including immunological enhancement, high efficiency of blood oxygen delivery, and the inhibition of lipid oxidation.
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Affiliation(s)
- Qin Lan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Zhiyong Cao
- Faculty of Big Data, Yunnan Agricultural University, Kunming 650201, China
| | - Xiujuan Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Kunming 650201, China
| | - Zhaobing Gu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science, Kunming 650201, China
- Correspondence: or
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Genomic Insights into Omega-3 Polyunsaturated Fatty Acid Producing Shewanella sp. N2AIL from Fish Gut. BIOLOGY 2022; 11:biology11050632. [PMID: 35625360 PMCID: PMC9138089 DOI: 10.3390/biology11050632] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022]
Abstract
The genus Shewanella is widely distributed in niches ranging from an aquatic environment to spoiled fish and is loaded with various ecologically and commercially important metabolites. Bacterial species under this genus find application in bioelectricity generation and bioremediation due to their capability to use pollutants as the terminal electron acceptor and could produce health-beneficial omega-3 fatty acids, particularly eicosapentaenoic acid (EPA). Here, the genome sequence of an EPA-producing bacterium, Shewanella sp. N2AIL, isolated from the gastrointestinal tract of Tilapia fish, is reported. The genome size of the strain was 4.8 Mb with a GC content of 46.3% containing 4385 protein-coding genes. Taxonogenomic analysis assigned this strain to the genus Shewanella on the basis of average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH), phylogenetically most closely related with S. baltica NCTC 10735T. The comparative genome analysis with the type strain of S. baltica revealed 693 unique genes in the strain N2AIL, highlighting the variation at the strain level. The genes associated with stress adaptation, secondary metabolite production, antibiotic resistance, and metal reduction were identified in the genome suggesting the potential of the bacterium to be explored as an industrially important strain. PUFA synthase gene cluster of size ~20.5 kb comprising all the essential domains for EPA biosynthesis arranged in five ORFs was also identified in the strain N2AIL. The study provides genomic insights into the diverse genes of Shewanella sp. N2AIL, which is particularly involved in adaptation strategies and prospecting secondary metabolite potential, specifically the biosynthesis of omega-3 polyunsaturated fatty acids.
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Lara P, Vega-Alvarado L, Sahonero-Canavesi DX, Koenen M, Villanueva L, Riveros-Mckay F, Morett E, Juárez K. Transcriptome Analysis Reveals Cr(VI) Adaptation Mechanisms in Klebsiella sp. Strain AqSCr. Front Microbiol 2021; 12:656589. [PMID: 34122372 PMCID: PMC8195247 DOI: 10.3389/fmicb.2021.656589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/13/2021] [Indexed: 11/19/2022] Open
Abstract
Klebsiella sp. strain AqSCr, isolated from Cr(VI)-polluted groundwater, reduces Cr(VI) both aerobically and anaerobically and resists up 34 mM Cr(VI); this resistance is independent of the ChrA efflux transporter. In this study, we report the whole genome sequence and the transcriptional profile by RNA-Seq of strain AqSCr under Cr(VI)-adapted conditions and found 255 upregulated and 240 downregulated genes compared to controls without Cr(VI) supplementation. Genes differentially transcribed were mostly associated with oxidative stress response, DNA repair and replication, sulfur starvation response, envelope-osmotic stress response, fatty acid (FA) metabolism, ribosomal subunits, and energy metabolism. Among them, genes not previously associated with chromium resistance, for example, cybB, encoding a putative superoxide oxidase (SOO), gltA2, encoding an alternative citrate synthase, and des, encoding a FA desaturase, were upregulated. The sodA gene encoding a manganese superoxide dismutase was upregulated in the presence of Cr(VI), whereas sodB encoding an iron superoxide dismutase was downregulated. Cr(VI) resistance mechanisms in strain AqSCr seem to be orchestrated by the alternative sigma factors fecl, rpoE, and rpoS (all of them upregulated). Membrane lipid analysis of the Cr(IV)-adapted strain showed a lower proportion of unsaturated lipids with respect to the control, which we hypothesized could result from unsaturated lipid peroxidation followed by degradation, together with de novo synthesis mediated by the upregulated FA desaturase-encoding gene, des. This report helps to elucidate both Cr(VI) toxicity targets and global bacterial response to Cr(VI).
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Affiliation(s)
- Paloma Lara
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Leticia Vega-Alvarado
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Diana X Sahonero-Canavesi
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands.,Faculty of Geosciences, Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Fernando Riveros-Mckay
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Enrique Morett
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Katy Juárez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Dissimilatory Nitrate Reduction to Ammonium (DNRA) and Denitrification Pathways Are Leveraged by Cyclic AMP Receptor Protein (CRP) Paralogues Based on Electron Donor/Acceptor Limitation in Shewanella loihica PV-4. Appl Environ Microbiol 2021; 87:AEM.01964-20. [PMID: 33158888 DOI: 10.1128/aem.01964-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
Under anoxic conditions, many bacteria, including Shewanella loihica strain PV-4, could use nitrate as an electron acceptor for dissimilatory nitrate reduction to ammonium (DNRA) and/or denitrification. Previous and current studies have shown that DNRA is favored under higher ambient carbon-to-nitrogen (C/N) ratios, whereas denitrification is upregulated under lower C/N ratios, which is consistent with our bioenergetics calculations. Interestingly, computational analyses indicate that the common cyclic AMP receptor protein (designated CRP1) and its paralogue CRP2 might both be involved in the regulation of two competing dissimilatory nitrate reduction pathways, DNRA and denitrification, in S. loihica PV-4 and several other denitrifying Shewanella species. To explore the regulatory mechanism underlying the dissimilatory nitrate reduction (DNR) pathways, nitrate reduction of a series of in-frame deletion mutants was analyzed under different C/N ratios. Deletion of crp1 could accelerate the reduction of nitrite to NO under both low and high C/N ratios. CRP1 is not required for denitrification and actually suppresses production of NO and N2O gases. Deletion of either of the NO-forming nitrite reductase genes nirK or crp2 blocked production of NO gas. Furthermore, real-time PCR and electrophoretic mobility shift assays (EMSAs) demonstrated that the transcription levels of DNRA-relevant genes such as nap-β (napDABGH), nrfA, and cymA were upregulated by CRP1, while nirK transcription was dependent on CRP2. There are tradeoffs between the different physiological roles of nitrate/lactate, as nitrogen nutrient/carbon source and electron acceptor/donor and CRPs may leverage dissimilatory nitrate reduction pathways for maximizing energy yield and bacterial survival under ambient environmental conditions.IMPORTANCE Some microbes utilize different dissimilatory nitrate reduction (DNR) pathways, including DNR to ammonia (DNRA) and denitrification pathways, for anaerobic respiration in response to ambient carbon/nitrogen ratio changes. Large-scale industrial nitrogen fixation and fertilizer application raise the concern of emission of N2O, a stable gas with potent global warming potential, as consequence of microbial respiration, thereby aggravating global warming and climate change. However, little is known about the molecular mechanism underlying the choice of two competing DNR pathways. We demonstrate that the global regulator CRP1, which is widely encoded in bacteria, is required for DNRA in S. loihica PV-4 strain, while the CRP2 paralogue is required for transcription of the nitrite reductase gene nirK for denitrification. Sufficient carbon source lead to the predominance of DNRA, while carbon source/electron donor deficiency may result in an incomplete denitrification process, raising the concern of high levels of N2O emission from nitrate-rich and carbon source-poor waters and soils.
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Todor H, Osadnik H, Campbell EA, Myers KS, Li H, Donohue TJ, Gross CA. Rewiring the specificity of extracytoplasmic function sigma factors. Proc Natl Acad Sci U S A 2020; 117:33496-33506. [PMID: 33318184 PMCID: PMC7776599 DOI: 10.1073/pnas.2020204117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Bacterial genomes are being sequenced at an exponentially increasing rate, but our inability to decipher their transcriptional wiring limits our ability to derive new biology from these sequences. De novo determination of regulatory interactions requires accurate prediction of regulators' DNA binding and precise determination of biologically significant binding sites. Here we address these challenges by solving the DNA-specificity code of extracytoplasmic function sigma factors (ECF σs), a major family of bacterial regulators, and determining their putative regulons. We generated an aligned collection of ECF σs and their promoters by leveraging the autoregulatory nature of ECF σs as a means of promoter discovery and analyzed it to identify and characterize the conserved amino acid-nucleotide interactions that determine promoter specificity. This enabled de novo prediction of ECF σ specificity, which we combined with a statistically rigorous phylogenetic footprinting pipeline based on precomputed orthologs to predict the direct targets of ∼67% of ECF σs. This global survey indicated that some ECF σs are conserved global regulators controlling many genes throughout the genome, which are important under many conditions, while others are local regulators, controlling a few closely linked genes in response to specific stimuli in select species. This analysis reveals important organizing principles of bacterial gene regulation and presents a conceptual and computational framework for deciphering gene regulatory networks.
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Affiliation(s)
- Horia Todor
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158;
| | - Hendrik Osadnik
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065
| | - Kevin S Myers
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726
| | - Hao Li
- California Institute of Quantitative Biology, University of California, San Francisco, CA 94158
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Timothy J Donohue
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158;
- California Institute of Quantitative Biology, University of California, San Francisco, CA 94158
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94158
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12
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Dai J, Dong A, Xiong G, Liu Y, Hossain MS, Liu S, Gao N, Li S, Wang J, Qiu D. Production of Highly Active Extracellular Amylase and Cellulase From Bacillus subtilis ZIM3 and a Recombinant Strain With a Potential Application in Tobacco Fermentation. Front Microbiol 2020; 11:1539. [PMID: 32793132 PMCID: PMC7385192 DOI: 10.3389/fmicb.2020.01539] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/12/2020] [Indexed: 11/25/2022] Open
Abstract
In this study, a series of bacteria capable of degrading starch and cellulose were isolated from the aging flue-cured tobacco leaves. Remarkably, there was a thermophilic bacterium, Bacillus subtilis ZIM3, that can simultaneously degrade both starch and cellulose at a wide range of temperature and pH values. Genome sequencing, comparative genomics analyses, and enzymatic activity assays showed that the ZIM3 strain expressed a variety of highly active plant biomass-degrading enzymes, such as the amylase AmyE1 and cellulase CelE1. The in vitro and PhoA-fusion assays indicated that these enzymes degrading complex plant biomass into fermentable sugars were secreted into ambient environment to function. Besides, the amylase and cellulase activities were further increased by three- to five-folds by using overexpression. Furthermore, a fermentation strategy was developed and the biodegradation efficiency of the starch and cellulose in the tobacco leaves were improved by 30–48%. These results reveal that B. subtilis ZIM3 and the recombinant strain exhibited high amylase and cellulase activities for efficient biodegradation of starch and cellulose in tobacco and could potentially be applied for industrial tobacco fermentation.
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Affiliation(s)
- Jingcheng Dai
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Aijun Dong
- Technology Research Center of China Tobacco Hubei Industry Co., Ltd., Wuhan, China
| | - Guoxi Xiong
- Technology Research Center of China Tobacco Hubei Industry Co., Ltd., Wuhan, China
| | - Yaqi Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Md Shahdat Hossain
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China.,National Institute of Biotechnology, Dhaka, Bangladesh
| | - Shuangyuan Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Na Gao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shuyang Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jing Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Dongru Qiu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
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13
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Koga R, Matsumoto A, Kouzuma A, Watanabe K. Identification of an extracytoplasmic function sigma factor that facilitates
c
‐type cytochrome maturation and current generation under electrolyte‐flow conditions in
Shewanella oneidensis
MR
‐1. Environ Microbiol 2020; 22:3671-3684. [DOI: 10.1111/1462-2920.15131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/11/2020] [Accepted: 06/13/2020] [Indexed: 11/27/2022]
Affiliation(s)
- Ryota Koga
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences 1432‐1 Horinouchi, Hachioji Tokyo 192‐0392 Japan
| | - Akiho Matsumoto
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences 1432‐1 Horinouchi, Hachioji Tokyo 192‐0392 Japan
| | - Atsushi Kouzuma
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences 1432‐1 Horinouchi, Hachioji Tokyo 192‐0392 Japan
| | - Kazuya Watanabe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences 1432‐1 Horinouchi, Hachioji Tokyo 192‐0392 Japan
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14
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Kloska A, Cech GM, Sadowska M, Krause K, Szalewska-Pałasz A, Olszewski P. Adaptation of the Marine Bacterium Shewanella baltica to Low Temperature Stress. Int J Mol Sci 2020; 21:ijms21124338. [PMID: 32570789 PMCID: PMC7352654 DOI: 10.3390/ijms21124338] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 11/30/2022] Open
Abstract
Marine bacteria display significant versatility in adaptation to variations in the environment and stress conditions, including temperature shifts. Shewanella baltica plays a major role in denitrification and bioremediation in the marine environment, but is also identified to be responsible for spoilage of ice-stored seafood. We aimed to characterize transcriptional response of S. baltica to cold stress in order to achieve a better insight into mechanisms governing its adaptation. We exposed bacterial cells to 8 °C for 90 and 180 min, and assessed changes in the bacterial transcriptome with RNA sequencing validated with the RT-qPCR method. We found that S. baltica general response to cold stress is associated with massive downregulation of gene expression, which covered about 70% of differentially expressed genes. Enrichment analysis revealed upregulation of only few pathways, including aminoacyl-tRNA biosynthesis, sulfur metabolism and the flagellar assembly process. Downregulation was observed for fatty acid degradation, amino acid metabolism and a bacterial secretion system. We found that the entire type II secretion system was transcriptionally shut down at low temperatures. We also observed transcriptional reprogramming through the induction of RpoE and repression of RpoD sigma factors to mediate the cold stress response. Our study revealed how diverse and complex the cold stress response in S. baltica is.
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Affiliation(s)
- Anna Kloska
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
- Correspondence: (A.K.); (P.O.)
| | - Grzegorz M. Cech
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (G.M.C.); (M.S.); (K.K.); (A.S.-P.)
| | - Marta Sadowska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (G.M.C.); (M.S.); (K.K.); (A.S.-P.)
| | - Klaudyna Krause
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (G.M.C.); (M.S.); (K.K.); (A.S.-P.)
| | - Agnieszka Szalewska-Pałasz
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland; (G.M.C.); (M.S.); (K.K.); (A.S.-P.)
| | - Paweł Olszewski
- 3P Medicine Laboratory, International Research Agenda, Medical University of Gdańsk, Dębinki 7, 80-211 Gdańsk, Poland
- Correspondence: (A.K.); (P.O.)
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15
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Liang H, Zhang Y, Wang S, Gao H. Mutual interplay between ArcA and σ E orchestrates envelope stress response in Shewanella oneidensis. Environ Microbiol 2020; 23:652-668. [PMID: 32372525 DOI: 10.1111/1462-2920.15060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 05/03/2020] [Indexed: 01/15/2023]
Abstract
To survive and thrive in harsh and ever-changing environments, intricate mechanisms have evolved for bacterial cells to monitor perturbations impacting the integrity of their envelope and to mount an appropriate response to contain or repair the damage. In this study, we report in Shewanella oneidensis a previously undescribed mechanism for the envelope defect resulting from the loss of Arc, a two-component transcriptional regulatory system crucial for respiration. We uncovered σE , a master regulator establishing and maintaining the integrity of the cell envelope in γ-proteobacteria, as the determining factor for the cell envelope defect of the arcA mutant. When ArcA is depleted, σE activity is compromised by enhanced production of anti-σE protein RseA. Surprisingly, S. oneidensis σE is not essential for viability, but becomes so in the absence of ArcA. Furthermore, we demonstrated that there is an interplay between these two regulators as arcA expression is affected by availability of σE . Overall, our results underscore functional interplay of regulatory systems for envelope stress response: although each of the systems may respond to perturbation of particular components of the envelope, they are functionally intertwined, working together to form an interconnected safety net.
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Affiliation(s)
- Huihui Liang
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China
| | - Yongting Zhang
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China
| | - Sijing Wang
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China
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16
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Adaptation to Photooxidative Stress: Common and Special Strategies of the Alphaproteobacteria Rhodobacter sphaeroides and Rhodobacter capsulatus. Microorganisms 2020; 8:microorganisms8020283. [PMID: 32093084 PMCID: PMC7074977 DOI: 10.3390/microorganisms8020283] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/10/2020] [Accepted: 02/13/2020] [Indexed: 12/20/2022] Open
Abstract
Photosynthetic bacteria have to deal with the risk of photooxidative stress that occurs in presence of light and oxygen due to the photosensitizing activity of (bacterio-) chlorophylls. Facultative phototrophs of the genus Rhodobacter adapt the formation of photosynthetic complexes to oxygen and light conditions, but cannot completely avoid this stress if environmental conditions suddenly change. R. capsulatus has a stronger pigmentation and faster switches to phototrophic growth than R. sphaeroides. However, its photooxidative stress response has not been investigated. Here, we compare both species by transcriptomics and proteomics, revealing that proteins involved in oxidation-reduction processes, DNA, and protein damage repair play pivotal roles. These functions are likely universal to many phototrophs. Furthermore, the alternative sigma factors RpoE and RpoHII are induced in both species, even though the genetic localization of the rpoE gene, the RpoE protein itself, and probably its regulon, are different. Despite sharing the same habitats, our findings also suggest individual strategies. The crtIB-tspO operon, encoding proteins for biosynthesis of carotenoid precursors and a regulator of photosynthesis, and cbiX, encoding a putative ferrochelatase, are induced in R. capsulatus. This specific response might support adaptation by maintaining high carotenoid-to-bacteriochlorophyll ratios and preventing the accumulation of porphyrin-derived photosensitizers.
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17
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Roslan NN, Ngalimat MS, Leow ATC, Oslan SN, Baharum SN, Sabri S. Genomic and phenomic analysis of a marine bacterium, Photobacterium marinum J15. Microbiol Res 2020; 233:126410. [PMID: 31945517 DOI: 10.1016/j.micres.2020.126410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/29/2019] [Accepted: 01/09/2020] [Indexed: 11/18/2022]
Abstract
Photobacterium species are widely distributed in the marine environment. The overall metabolism of this genus remains largely unknown. In order to improve our knowledge on this bacterium, the relationship between the genome and phenome of the Photobacterium isolate was analyzed. The cream colored, Gram-negative, rod-shaped and motile bacterial strain, J15, was isolated from marine water of Tanjung Pelepas, Johor, Malaysia. The 5,684,538 bp genome of strain J15 comprised 3 contigs (2 chromosomes and 1 plasmid) with G + C content of 46.39 % and contained 4924 protein-coding genes including 180 tRNAs and 40 rRNAs. The phenotypic microarray (PM) as analyzed using BIOLOG showed the utilization of; i) 93 of the 190 carbon sources tested, where 61 compounds were used efficiently; ii) 41 of the 95 nitrogen sources tested, where 22 compounds were used efficiently; and iii) 3 of the 94 phosphorous and sulphur sources tested. Furthermore, high tolerance to osmotic stress, basic pH and toxic compounds as well as resistance to antibiotics of strain J15 were determined by BIOLOG PM. The ANI and kSNP analyses revealed that strain J15 to be the same species with Photobacterium marinum AK15 with ANI value of 96.93 % and bootstrapping value of 100 in kSNP. Based on the ANI and kSNP analyses, strain J15 was identified as P. marinum J15.
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Affiliation(s)
- Noordiyanah Nadhirah Roslan
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mohamad Syazwan Ngalimat
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Biochemistry, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Syarul Nataqain Baharum
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Suriana Sabri
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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18
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Dai J, Liu Y, Liu S, Li S, Gao N, Wang J, Zhou J, Qiu D. Differential gene content and gene expression for bacterial evolution and speciation of Shewanella in terms of biosynthesis of heme and heme-requiring proteins. BMC Microbiol 2019; 19:173. [PMID: 31362704 PMCID: PMC6664582 DOI: 10.1186/s12866-019-1549-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/19/2019] [Indexed: 01/31/2023] Open
Abstract
Background Most species of Shewanella harbor two ferrochelatase paralogues for the biosynthesis of c-type cytochromes, which are crucial for their respiratory versatility. In our previous study of the Shewanella loihica PV-4 strain, we found that the disruption of hemH1 but not hemH2 resulted in a significant accumulation of extracellular protoporphyrin IX (PPIX), but it is different in Shewanella oneidensis MR-1. Hence, the function and transcriptional regulation of two ferrochelatase genes, hemH1 and hemH2, are investigated in S. oneidensis MR-1. Result In the present study, deletion of either hemH1 or hemH2 in S. oneidensis MR-1 did not lead to overproduction of extracellular protoporphyrin IX (PPIX) as previously described in the hemH1 mutants of S. loihica PV-4. Moreover, supplement of exogenous hemins made it possible to generate the hemH1 and hemH2 double mutant in MR-1, but not in PV-4. Under aerobic condition, exogenous hemins were required for the growth of MR-1ΔhemH1ΔhemH2, which also overproduced extracellular PPIX. These results suggest that heme is essential for aerobic growth of Shewanella species and MR-1 could also uptake hemin for biosynthesis of essential cytochrome(s) and respiration. Besides, the exogenous hemin mediated CymA cytochrome maturation and the cellular KatB catalase activity. Both hemH paralogues were transcribed in wild-type MR-1, and the hemH2 transcription was remarkably up-regulated in MR-1ΔhemH1 mutant to compensate for the loss of hemH1. The periplasmic glutathione peroxidase gene pgpD, located in the same operon with hemH2, and a large gene cluster coding for iron, heme (hemin) uptake systems are absent in the PV-4 genome. Conclusion Our results indicate that the genetic divergence in gene content and gene expression between these Shewanella species, accounting for the phenotypic difference described here, might be due to their speciation and adaptation to the specific habitats (iron-rich deep-sea vent versus iron-poor freshwater) in which they evolved and the generated mutants could potentially be utilized for commercial production of PPIX. Electronic supplementary material The online version of this article (10.1186/s12866-019-1549-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingcheng Dai
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yaqi Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuangyuan Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuyang Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Na Gao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.,Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94270, USA
| | - Dongru Qiu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei Province, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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19
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Wang L, Jiang S, Deng Z, Dedon PC, Chen S. DNA phosphorothioate modification-a new multi-functional epigenetic system in bacteria. FEMS Microbiol Rev 2019; 43:109-122. [PMID: 30289455 PMCID: PMC6435447 DOI: 10.1093/femsre/fuy036] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/03/2018] [Indexed: 12/20/2022] Open
Abstract
Synthetic phosphorothioate (PT) internucleotide linkages, in which a nonbridging oxygen is replaced by a sulphur atom, share similar physical and chemical properties with phosphodiesters but confer enhanced nuclease tolerance on DNA/RNA, making PTs a valuable biochemical and pharmacological tool. Interestingly, PT modification was recently found to occur naturally in bacteria in a sequence-selective and RP configuration-specific manner. This oxygen-sulphur swap is catalysed by the gene products of dndABCDE, which constitute a defence barrier with DndFGH in some bacterial strains that can distinguish and attack non-PT-modified foreign DNA, resembling DNA methylation-based restriction-modification (R-M) systems. Despite their similar defensive mechanisms, PT- and methylation-based R-M systems have evolved to target different consensus contexts in the host cell because when they share the same recognition sequences, the protective function of each can be impeded. The redox and nucleophilic properties of PT sulphur render PT modification a versatile player in the maintenance of cellular redox homeostasis, epigenetic regulation and environmental fitness. The widespread presence of dnd systems is considered a consequence of extensive horizontal gene transfer, whereas the lability of PT during oxidative stress and the susceptibility of PT to PT-dependent endonucleases provide possible explanations for the ubiquitous but sporadic distribution of PT modification in the bacterial world.
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Affiliation(s)
- Lianrong Wang
- Zhongnan Hospital, Wuhan University, 169 Donghu Road, Wuhan 430071, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 185 Donghu Road, Wuhan 430071, China
| | - Susu Jiang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 185 Donghu Road, Wuhan 430071, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 185 Donghu Road, Wuhan 430071, China
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Masschusetts Avenue, Cambridge, Massachusetts, USA
| | - Shi Chen
- Zhongnan Hospital, Wuhan University, 169 Donghu Road, Wuhan 430071, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 185 Donghu Road, Wuhan 430071, China
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20
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Beblawy S, Bursac T, Paquete C, Louro R, Clarke TA, Gescher J. Extracellular reduction of solid electron acceptors by Shewanella oneidensis. Mol Microbiol 2018; 109:571-583. [PMID: 29995975 DOI: 10.1111/mmi.14067] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2018] [Indexed: 12/11/2022]
Abstract
Shewanella oneidensis is the best understood model organism for the study of dissimilatory iron reduction. This review focuses on the current state of our knowledge regarding this extracellular respiratory process and highlights its physiologic, regulatory and biochemical requirements. It seems that we have widely understood how respiratory electrons can reach the cell surface and what the minimal set of electron transport proteins to the cell surface is. Nevertheless, even after decades of work in different research groups around the globe there are still several important questions that were not answered yet. In particular, the physiology of this organism, the possible evolutionary benefit of some responses to anoxic conditions, as well as the exact mechanism of electron transfer onto solid electron acceptors are yet to be addressed. The elucidation of these questions will be a great challenge for future work and important for the application of extracellular respiration in biotechnological processes.
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Affiliation(s)
- Sebastian Beblawy
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (CS), Karlsruhe, Germany
| | - Thea Bursac
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (CS), Karlsruhe, Germany
| | - Catarina Paquete
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República-EAN, Oeiras, 2780-157, Portugal
| | - Ricardo Louro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República-EAN, Oeiras, 2780-157, Portugal
| | - Thomas A Clarke
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Johannes Gescher
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (CS), Karlsruhe, Germany.,Institute for Biological Interfaces, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
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21
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Gao N, Xia M, Dai J, Yu D, An W, Li S, Liu S, He P, Zhang L, Wu Z, Bi X, Chen S, Haft DH, Qiu D. Both widespread PEP-CTERM proteins and exopolysaccharides are required for floc formation of Zoogloea resiniphila and other activated sludge bacteria. Environ Microbiol 2018; 20:1677-1692. [PMID: 29473278 DOI: 10.1111/1462-2920.14080] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/12/2018] [Accepted: 02/19/2018] [Indexed: 12/28/2022]
Abstract
Bacterial floc formation plays a central role in the activated sludge (AS) process, which has been widely utilized for sewage and wastewater treatment. The formation of AS flocs has long been known to require exopolysaccharide biosynthesis. This study demonstrates an additional requirement for a PEP-CTERM protein in Zoogloea resiniphila, a dominant AS bacterium harboring a large exopolysaccharide biosynthesis gene cluster. Two members of a wide-spread family of high copy number-per-genome PEP-CTERM genes, transcriptionally regulated by the RpoN sigma factor and accessory PrsK-PrsR two-component system and at least one of these, pepA, must be expressed for Zoogloea to build the floc structures that allow gravitational sludge settling and recycling. Without PrsK or PrsR, Zoogloea cells were planktonic rather than flocculated and secreted exopolysaccharides were released into the growth broth in soluble form. Overexpression of PepA could circumvent the requirement of rpoN, prsK and prsR for the floc-forming phenotype by fixing the exopolysaccharides to bacterial cells. However, overexpression of PepA, which underwent post-translational modifications, could not rescue the long-rod morphology of the rpoN mutant. Consistently, PEP-CTERM genes and exopolysaccharide biosynthesis gene cluster are present in the genome of the floc-forming Nitrospira comammox and Mitsuaria strain as well as many other AS bacteria.
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Affiliation(s)
- Na Gao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingcheng Dai
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Dianzhen Yu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Weixing An
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Shuyang Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Shuangyuan Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Penghui He
- College of Life Sciences, Hubei University, Wuhan 430070, China
| | - Liping Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhenbin Wu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xuezhi Bi
- Agency for Science, Technology and Research, Bioprocessing Technology Institute, Singapore 138668, Singapore
| | - Shouwen Chen
- College of Life Sciences, Hubei University, Wuhan 430070, China
| | - Daniel H Haft
- National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Dongru Qiu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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22
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Rowe SF, Le Gall G, Ainsworth EV, Davies JA, Lockwood CWJ, Shi L, Elliston A, Roberts IN, Waldron KW, Richardson DJ, Clarke TA, Jeuken LJC, Reisner E, Butt JN. Light-Driven H2 Evolution and C═C or C═O Bond Hydrogenation by Shewanella oneidensis: A Versatile Strategy for Photocatalysis by Nonphotosynthetic Microorganisms. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02736] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sam F. Rowe
- School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Gwénaëlle Le Gall
- Quadram
Institute for Bioscience, Norwich Research Park, Norwich NR4 7UA, U.K
| | - Emma V. Ainsworth
- School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Jonathan A. Davies
- School
of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Colin W. J. Lockwood
- School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Liang Shi
- Department
of Biological Sciences and Technology, China University of Geoscience in Wuhan, Wuhan 430074, People’s Republic of China
| | - Adam Elliston
- Quadram
Institute for Bioscience, Norwich Research Park, Norwich NR4 7UA, U.K
| | - Ian N. Roberts
- Quadram
Institute for Bioscience, Norwich Research Park, Norwich NR4 7UA, U.K
| | - Keith W. Waldron
- Quadram
Institute for Bioscience, Norwich Research Park, Norwich NR4 7UA, U.K
| | - David J. Richardson
- School
of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Thomas A. Clarke
- School
of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Lars J. C. Jeuken
- School
of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Erwin Reisner
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Julea N. Butt
- School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
- School
of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
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23
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RpoN (σ 54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola tertiaricarbonis Strain. Appl Environ Microbiol 2017; 83:AEM.00709-17. [PMID: 28500044 DOI: 10.1128/aem.00709-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 05/08/2017] [Indexed: 11/20/2022] Open
Abstract
Some bacteria are capable of forming flocs, in which bacterial cells become self-flocculated by secreted extracellular polysaccharides and other biopolymers. The floc-forming bacteria play a central role in activated sludge, which has been widely utilized for the treatment of municipal sewage and industrial wastewater. Here, we use a floc-forming bacterium, Aquincolatertiaricarbonis RN12, as a model to explore the biosynthesis of extracellular polysaccharides and the regulation of floc formation. A large gene cluster for exopolysaccharide biosynthesis and a gene encoding the alternative sigma factor RpoN1, one of the four paralogues, have been identified in floc formation-deficient mutants generated by transposon mutagenesis, and the gene functions have been further confirmed by genetic complementation analyses. Interestingly, the biosynthesis of exopolysaccharides remained in the rpoN1-disrupted flocculation-defective mutants, but most of the exopolysaccharides were secreted and released rather than bound to the cells. Furthermore, the expression of exopolysaccharide biosynthesis genes seemed not to be regulated by RpoN1. Taken together, our results indicate that RpoN1 may play a role in regulating the expression of a certain gene(s) involved in the self-flocculation of bacterial cells but not in the biosynthesis and secretion of exopolysaccharides required for floc formation.IMPORTANCE Floc formation confers bacterial resistance to predation of protozoa and plays a central role in the widely used activated sludge process. In this study, we not only identified a large gene cluster for biosynthesis of extracellular polysaccharides but also identified four rpoN paralogues, one of which (rpoN1) is required for floc formation in A. tertiaricarbonis RN12. In addition, this RpoN sigma factor regulates the transcription of genes involved in biofilm formation and swarming motility, as previously shown in other bacteria. However, this RpoN paralogue is not required for the biosynthesis of exopolysaccharides, which are released and dissolved into culture broth by the rpoN1 mutant rather than remaining tightly bound to cells, as observed during the flocculation of the wild-type strain. These results indicate that floc formation is a regulated complex process, and other yet-to-be identified RpoN1-dependent factors are involved in self-flocculation of bacterial cells via exopolysaccharides and/or other biopolymers.
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24
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Deletion of degQ gene enhances outer membrane vesicle production of Shewanella oneidensis cells. Arch Microbiol 2016; 199:415-423. [PMID: 27796471 DOI: 10.1007/s00203-016-1315-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 10/17/2016] [Accepted: 10/22/2016] [Indexed: 10/20/2022]
Abstract
Shewanella oneidensis is a Gram-negative facultative anaerobe that can use a wide variety of terminal electron acceptors for anaerobic respiration. In this study, S. oneidensis degQ gene, encoding a putative periplasmic serine protease, was cloned and expressed. The activity of purified DegQ was inhibited by diisopropyl fluorophosphate, a typical serine protease-specific inhibitor, indicating that DegQ is a serine protease. In-frame deletion and subsequent complementation of the degQ were carried out to examine the effect of envelope stress on the production of outer membrane vesicles (OMVs). Analysis of periplasmic proteins from the resulting S. oneidensis strain showed that deletion of degQ induced protein accumulation and resulted in a significant decrease in protease activity within the periplasmic space. OMVs from the wild-type and mutant strains were purified and observed by transmission electron microscopy. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of the OMVs showed a prominent band at ~37 kDa. Nanoliquid chromatography-tandem mass spectrometry analysis identified three outer membrane porins (SO3896, SO1821, and SO3545) as dominant components of the band, suggesting that these proteins could be used as indices for comparing OMV production by S. oneidensis strains. Quantitative evaluation showed that degQ-deficient cells had a fivefold increase in OMV production compared with wild-type cells. Thus, the increased OMV production following the deletion of DegQ in S. oneidensis may be responsible for the increase in envelope stress.
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25
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An W, Guo F, Song Y, Gao N, Bai S, Dai J, Wei H, Zhang L, Yu D, Xia M, Yu Y, Qi M, Tian C, Chen H, Wu Z, Zhang T, Qiu D. Comparative genomics analyses on EPS biosynthesis genes required for floc formation of Zoogloea resiniphila and other activated sludge bacteria. WATER RESEARCH 2016; 102:494-504. [PMID: 27403872 DOI: 10.1016/j.watres.2016.06.058] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 06/27/2016] [Accepted: 06/27/2016] [Indexed: 06/06/2023]
Abstract
Activated sludge (AS) process has been widely utilized for municipal sewage and industrial wastewater treatment. Zoolgoea and its related floc-forming bacteria are required for formation of AS flocs which is the key to gravitational effluent-and-sludge separation and AS recycling. However, little is known about the genetics, biochemistry and physiology of Zoogloea and its related bacteria. This report deals with the comparative genomic analyses on two Zoogloea resiniphila draft genomes and the closely related proteobacterial species commonly found in AS. In particular, the metabolic processes involved in removal of organic matters, nitrogen and phosphorus were analyzed. Furthermore, it is revealed that a large gene cluster, encoding eight glycosyltransferases and other proteins involved in biosynthesis and export of extracellular polysaccharides (EPS), was required for floc formation. One of the two asparagine synthase paralogues, associated with this EPS biosynthesis gene cluster, was required for floc formation in Zoogloea. Similar EPS biosynthesis gene cluster(s) were identified in the genome of other AS proteobacteria including polyphosphate-accumulating Candidatus Accumulibacter phosphatis (CAP) and nitrifying Nitrosopira and Nitrosomonas bacteria, but the gene composition varies interspecifically and intraspecifically. Our results indicate that floc formation of desired AS bacteria, including CAP strains, facilitate their recruitment into AS and gradual enrichment via repeated AS settling and recycling processes.
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Affiliation(s)
- Weixing An
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Guo
- School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Yulong Song
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Gao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijie Bai
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Institute of Deep-sea Science and Technology, Chinese Academy of Sciences, Sanya 572000, China
| | - Jingcheng Dai
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Hehong Wei
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liping Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Dianzhen Yu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Yu
- Institute for Genetics and Development, Chinese Academy of Sciences, Beijing 100101, China
| | - Ming Qi
- Institute for Genetics and Development, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunyuan Tian
- School of Life Sciences and Technology, Hubei Engineering University, Xiaogan 43200, China
| | - Haofeng Chen
- Institute for Genetics and Development, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenbin Wu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong.
| | - Dongru Qiu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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26
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Regulation of Gene Expression in Shewanella oneidensis MR-1 during Electron Acceptor Limitation and Bacterial Nanowire Formation. Appl Environ Microbiol 2016; 82:5428-43. [PMID: 27342561 DOI: 10.1128/aem.01615-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 06/22/2016] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED In limiting oxygen as an electron acceptor, the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1 rapidly forms nanowires, extensions of its outer membrane containing the cytochromes MtrC and OmcA needed for extracellular electron transfer. RNA sequencing (RNA-Seq) analysis was employed to determine differential gene expression over time from triplicate chemostat cultures that were limited for oxygen. We identified 465 genes with decreased expression and 677 genes with increased expression. The coordinated increased expression of heme biosynthesis, cytochrome maturation, and transport pathways indicates that S. oneidensis MR-1 increases cytochrome production, including the transcription of genes encoding MtrA, MtrC, and OmcA, and transports these decaheme cytochromes across the cytoplasmic membrane during electron acceptor limitation and nanowire formation. In contrast, the expression of the mtrA and mtrC homologs mtrF and mtrD either remains unaffected or decreases under these conditions. The ompW gene, encoding a small outer membrane porin, has 40-fold higher expression during oxygen limitation, and it is proposed that OmpW plays a role in cation transport to maintain electrical neutrality during electron transfer. The genes encoding the anaerobic respiration regulator cyclic AMP receptor protein (CRP) and the extracytoplasmic function sigma factor RpoE are among the transcription factor genes with increased expression. RpoE might function by signaling the initial response to oxygen limitation. Our results show that RpoE activates transcription from promoters upstream of mtrC and omcA The transcriptome and mutant analyses of S. oneidensis MR-1 nanowire production are consistent with independent regulatory mechanisms for extending the outer membrane into tubular structures and for ensuring the electron transfer function of the nanowires. IMPORTANCE Shewanella oneidensis MR-1 has the capacity to transfer electrons to its external surface using extensions of the outer membrane called bacterial nanowires. These bacterial nanowires link the cell's respiratory chain to external surfaces, including oxidized metals important in bioremediation, and explain why S. oneidensis can be utilized as a component of microbial fuel cells, a form of renewable energy. In this work, we use differential gene expression analysis to focus on which genes function to produce the nanowires and promote extracellular electron transfer during oxygen limitation. Among the genes that are expressed at high levels are those encoding cytochrome proteins necessary for electron transfer. Shewanella coordinates the increased expression of regulators, metabolic pathways, and transport pathways to ensure that cytochromes efficiently transfer electrons along the nanowires.
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27
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Differential Regulation of the Two Ferrochelatase Paralogues in Shewanella loihica PV-4 in Response to Environmental Stresses. Appl Environ Microbiol 2016; 82:5077-88. [PMID: 27287322 DOI: 10.1128/aem.00203-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/06/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Determining the function and regulation of paralogues is important in understanding microbial functional genomics and environmental adaptation. Heme homeostasis is crucial for the survival of environmental microorganisms. Most Shewanella species encode two paralogues of ferrochelatase, the terminal enzyme in the heme biosynthesis pathway. The function and transcriptional regulation of two ferrochelatase genes, hemH1 and hemH2, were investigated in Shewanella loihica PV-4. The disruption of hemH1 but not hemH2 resulted in a significant accumulation of extracellular protoporphyrin IX (PPIX), the precursor to heme, and decreased intracellular heme levels. hemH1 was constitutively expressed, and the expression of hemH2 increased when hemH1 was disrupted. The transcription of hemH1 was regulated by the housekeeping sigma factor RpoD and potentially regulated by OxyR, while hemH2 appeared to be regulated by the oxidative stress-associated sigma factor RpoE2. When an oxidative stress condition was mimicked by adding H2O2 to the medium or exposing the culture to light, PPIX accumulation was suppressed in the ΔhemH1 mutant. Consistently, transcriptome analysis indicated enhanced iron uptake and suppressed heme synthesis in the ΔhemH1 mutant. These data indicate that the two paralogues are functional in the heme synthesis pathway but regulated by environmental conditions, providing insights into the understanding of bacterial response to environmental stresses and a great potential to commercially produce porphyrin compounds. IMPORTANCE Shewanella is capable of utilizing a variety of electron acceptors for anaerobic respiration because of the existence of multiple c-type cytochromes in which heme is an essential component. The cytochrome-mediated electron transfer across cellular membranes could potentially be used for biotechnological purposes, such as electricity generation in microbial fuel cells and dye decolorization. However, the mechanism underlying the regulation of biosynthesis of heme and cytochromes is poorly understood. Our study has demonstrated that two ferrochelatase genes involved in heme biosynthesis are differentially regulated in response to environmental stresses, including light and reactive oxygen species. This is an excellent example showing how bacteria have evolved to maintain cellular heme homeostasis. More interestingly, the high yields of extracellular protoporphyrin IX by the Shewanella loihica PV-4 mutants could be utilized for commercial production of this valuable chemical via bacterial fermentation.
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