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Zha F, Pang R, Huang S, Zhang J, Wang J, Chen M, Xue L, Ye Q, Wu S, Yang M, Gu Q, Ding Y, Wu Q, Zhang H. Proteomic analysis reveals the non-coding small RNA Qrr5 influences autoaggregation and growth competition in Vibrio parahaemolyticus. J Proteomics 2023; 279:104866. [PMID: 36918054 DOI: 10.1016/j.jprot.2023.104866] [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: 10/25/2022] [Revised: 02/13/2023] [Accepted: 02/23/2023] [Indexed: 03/13/2023]
Abstract
Vibrio parahaemolyticus, a sea-born bacterial pathogen, is a primary inducement of food-borne gastroenteritis. Previous studies have shown that non-coding small RNA plays a vital role in the regulation of multiple biological processes in pathogenic bacteria, especially autoaggregation and growth competition. However, the inherent mechanisms have not yet to be fully understood. As important regulators in Vibrios, the involvement of Qrr sRNAs in V. parahaemolyticus is largely unknown. Here, we carried out the Qrr5 deletion mutant and utilized a proteomic method to describe global proteomic alterations in response to Qrr5 deletion. A total of 297 significantly expressed proteins were determined between the Qrr5 deletion mutant and wild-type strain, among which 137 proteins were upregulated and 160 proteins were downregulated. The upregulated proteins principally participated in membrane transporters and signal transcription, while the downregulated proteins participated in the two-component system and transcription factor binding. Notably, transcriptional regulator LysR, outer membrane protein OmpA, and conjugal transfer protein TraA-related proteins were upregulated, causing the promotion of autoaggregation ability and growth competition ability against E. coli. This study provides insights into the regulatory network of sRNA in this bacterium, which will facilitate further explorations of important biological processes in pathogenic bacteria. SIGNIFICANCE: sRNA Qrr5 is an important regulator involved in bacterial multiple physiological processes, including auto-aggregation and growth competition among food-borne pathogens Vibrio parahaemolyticus. Here, utilizing a TMT-labeling proteomic approach, we identified 137 proteins were upregulated and 160 proteins were downregulated between the Qrr5 deletion mutant and wild-type strain. The upregulated proteins were involved in membrane transporters and signal transcription, while downregulated proteins were involved in the two-component system and transcription factor binding. Moreover, the LysR, OmpA, and TraA proteins were significantly upregulated, causing the promotion of autoaggregation and commensal growth competition ability. The mechanism of how Qrr5 regulates the targeted genes remains unclarified and need great efforts to explore.
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Affiliation(s)
- Fei Zha
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Shixuan Huang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Juan Wang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Shi Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Meiyan Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Qihui Gu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Yu Ding
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Ministry of Agriculture and Rural Affairs, Key Laboratory of Agricultural Microbiomics and Precision Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, Guangdong, China.
| | - Hao Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China.
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Chen L, Wang Y, Miao J, Wang Q, Liu Z, Xie W, Liu X, Feng Z, Cheng S, Chi X, Ge Y. LysR-type transcriptional regulator FinR is required for phenazine and pyrrolnitrin biosynthesis in biocontrol Pseudomonas chlororaphis strain G05. Appl Microbiol Biotechnol 2021; 105:7825-7839. [PMID: 34562115 DOI: 10.1007/s00253-021-11600-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/10/2021] [Accepted: 09/14/2021] [Indexed: 11/30/2022]
Abstract
Phenazine-1-carboxylic acid and pyrrolnitrin, the two secondary metabolites produced by Pseudomonas chlororaphis G05, serve as biocontrol agents that mainly contribute to the growth repression of several fungal phytopathogens. Although some regulators of phenazine-1-carboxylic acid biosynthesis have been identified, the regulatory pathway involving phenazine-1-carboxylic acid synthesis is not fully understood. We isolated a white conjugant G05W03 on X-Gal-containing LB agar during our screening of novel regulator candidates using transposon mutagenesis with a fusion mutant G05Δphz::lacZ as a recipient. By cloning of DNA adjacent to the site of the transposon insertion, we revealed that a LysR-type transcriptional regulator (LTTR) gene, finR, was disrupted in the conjugant G05W03. To confirm the regulatory function of FinR, we constructed the finR-knockout mutant G05ΔfinR, G05Δphz::lacZΔfinR, and G05Δprn::lacZΔfinR, using the wild-type strain G05 and its fusion mutant derivatives as recipient strains, respectively. We found that the expressions of phz and prn operons were dramatically reduced in the finR-deleted mutant. With quantification of the production of antifungal metabolites biosynthesized by the finR-negative strain G05ΔfinR, it was shown that FinR deficiency also led to decreased yield of phenazine-1-carboxylic acid and pyrrolnitrin. In addition, the pathogen inhibition assay confirmed that the production of phenazine-1-carboxylic acid was severely reduced in the absence of FinR. Transcriptional fusions and qRT-PCR verified that FinR could positively govern the transcription of the phz and prn operons. Taken together, FinR is required for antifungal metabolite biosynthesis and crop protection against some fungal pathogens.Key points• A novel regulator FinR was identified by transposon mutagenesis.• FinR regulates antifungal metabolite production.• FinR regulates the phz and prn expression by binding to their promoter regions.
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Affiliation(s)
- Lijuan Chen
- Affiliated Hospital of Ludong University, Yantai, 264025, China.,The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China
| | - Yanhua Wang
- The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China
| | - Jing Miao
- The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China
| | - Qijun Wang
- The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China
| | - Zili Liu
- The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China
| | - Wenqi Xie
- The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China
| | - Xinsheng Liu
- Affiliated Hospital of Ludong University, Yantai, 264025, China.,The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China
| | - Zhibin Feng
- The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China.,Biological Fermentation and Separation Engineering Laboratory, School of Life Sciences, Ludong University, Yantai, 264025, China
| | - Shiwei Cheng
- The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China.,Biological Fermentation and Separation Engineering Laboratory, School of Life Sciences, Ludong University, Yantai, 264025, China
| | - Xiaoyan Chi
- The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China.
| | - Yihe Ge
- The Department of Applied and Environmental Microbiology, School of Life Sciences, Ludong University, Yantai, 264000, China. .,Biological Fermentation and Separation Engineering Laboratory, School of Life Sciences, Ludong University, Yantai, 264025, China.
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Robador A, Amend JP, Finkel SE. Nanocalorimetry Reveals the Growth Dynamics of Escherichia coli Cells Undergoing Adaptive Evolution during Long-Term Stationary Phase. Appl Environ Microbiol 2019; 85:e00968-19. [PMID: 31152016 PMCID: PMC6643242 DOI: 10.1128/aem.00968-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 05/24/2019] [Indexed: 11/20/2022] Open
Abstract
Bacterial populations in long-term stationary-phase (LTSP) laboratory cultures can provide insights into physiological and genetic adaptations to low-energy conditions and population dynamics in natural environments. While overall population density remains stable, these communities are very dynamic and are characterized by the rapid emergence and succession of distinct mutants expressing the growth advantage in stationary phase (GASP) phenotype, which can reflect an increased capacity to withstand energy limitations and environmental stress. Here, we characterize the metabolic heat signatures and growth dynamics of GASP mutants within an evolving population using isothermal calorimetry. We aged Escherichia coli in anaerobic batch cultures over 20 days inside an isothermal nanocalorimeter and observed distinct heat events related to the emergence of three mutant populations expressing the GASP phenotype after 1.5, 3, and 7 days. Given the heat produced by each population, the maximum number of GASP mutant cells was calculated, revealing abundances of ∼2.5 × 107, ∼7.5 × 106, and ∼9.9 × 106 cells in the populations, respectively. These data indicate that mutants capable of expressing the GASP phenotype can be acquired during the exponential growth phase and subsequently expressed in LTSP culture.IMPORTANCE The present study is innovative in that we have identified previously unknown growth dynamics related to the temporal expression of the growth advantage in stationary phase (GASP) phenotype that allow mutants in long-term stationary-phase cultures to capitalize on the decrease of energy over prolonged incubation periods. By remaining in an active, but growth-limited, metabolic state similar to that observed in GASP cells grown in vitro, natural microbial communities might be able to prevail over much longer time scales. We believe this report to be a remarkable methodological and conceptual breakthrough in the study of the long-term survival and evolution of bacteria.
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Affiliation(s)
- Alberto Robador
- Center for Dark Energy Biosphere Investigations (C-DEBI), University of Southern California, Los Angeles, California, USA
- Marine and Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Jan P Amend
- Center for Dark Energy Biosphere Investigations (C-DEBI), University of Southern California, Los Angeles, California, USA
- Marine and Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
| | - Steven E Finkel
- Center for Dark Energy Biosphere Investigations (C-DEBI), University of Southern California, Los Angeles, California, USA
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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Klebsiella and Providencia emerge as lone survivors following long-term starvation of oral microbiota. Proc Natl Acad Sci U S A 2019; 116:8499-8504. [PMID: 30975748 PMCID: PMC6486781 DOI: 10.1073/pnas.1820594116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is well-understood that many bacteria have evolved to survive catastrophic events using a variety of mechanisms, which include expression of stress-response genes, quiescence, necrotrophy, and metabolic advantages obtained through mutation. However, the dynamics of individuals leveraging these abilities to gain a competitive advantage in an ecologically complex setting remain unstudied. In this study, we observed the saliva microbiome throughout the ecological perturbation of long-term starvation, allowing only the species best equipped to access and use the limited resources to survive. During the first several days, the community underwent a death phase that resulted in a ∼50-100-fold reduction in the number of viable cells. Interestingly, after this death phase, only three species, Klebsiella pneumoniae, Klebsiella oxytoca, and Providencia alcalifaciens, all members of the family Enterobacteriaceae, appeared to be transcriptionally active and recoverable. Klebsiella are significant human pathogens, frequently resistant to multiple antibiotics, and recently, ectopic colonization of the gut by oral Klebsiella was documented to induce dysbiosis and inflammation. MetaOmics analyses provided several leads for further investigation regarding the ecological success of the Enterobacteriaceae. The isolates accumulated single nucleotide polymorphisms in known growth advantage in stationary phase alleles and produced natural products closely resembling antimicrobial cyclic depsipeptides. The results presented in this study suggest that pathogenic Enterobacteriaceae persist much longer than their more benign neighbors in the salivary microbiome when faced with starvation. This is particularly significant, given that hospital surfaces contaminated with oral fluids, especially sinks and drains, are well-established sources of outbreaks of drug-resistant Enterobacteriaceae.
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Genomewide Mutational Diversity in Escherichia coli Population Evolving in Prolonged Stationary Phase. mSphere 2017; 2:mSphere00059-17. [PMID: 28567442 PMCID: PMC5444009 DOI: 10.1128/msphere.00059-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 05/05/2017] [Indexed: 11/20/2022] Open
Abstract
Prolonged stationary phase in bacteria, contrary to its name, is highly dynamic, with extreme nutrient limitation as a predominant stress. Stationary-phase cultures adapt by rapidly selecting a mutation(s) that confers a growth advantage in stationary phase (GASP). The phenotypic diversity of starving E. coli populations has been studied in detail; however, only a few mutations that accumulate in prolonged stationary phase have been described. This study documented the spectrum of mutations appearing in Escherichia coli during 28 days of prolonged starvation. The genetic diversity of the population increases over time in stationary phase to an extent that cannot be explained by random, neutral drift. This suggests that prolonged stationary phase offers a great model system to study adaptive evolution by natural selection. Prolonged stationary phase is an approximation of natural environments presenting a range of stresses. Survival in prolonged stationary phase requires alternative metabolic pathways for survival. This study describes the repertoire of mutations accumulating in starving Escherichia coli populations in lysogeny broth. A wide range of mutations accumulates over the course of 1 month in stationary phase. Single nucleotide polymorphisms (SNPs) constitute 64% of all mutations. A majority of these mutations are nonsynonymous and are located at conserved loci. There is an increase in genetic diversity in the evolving populations over time. Computer simulations of evolution in stationary phase suggest that the maximum frequency of mutations observed in our experimental populations cannot be explained by neutral drift. Moreover, there is frequent genetic parallelism across populations, suggesting that these mutations are under positive selection. Finally, functional analysis of mutations suggests that regulatory mutations are frequent targets of selection. IMPORTANCE Prolonged stationary phase in bacteria, contrary to its name, is highly dynamic, with extreme nutrient limitation as a predominant stress. Stationary-phase cultures adapt by rapidly selecting a mutation(s) that confers a growth advantage in stationary phase (GASP). The phenotypic diversity of starving E. coli populations has been studied in detail; however, only a few mutations that accumulate in prolonged stationary phase have been described. This study documented the spectrum of mutations appearing in Escherichia coli during 28 days of prolonged starvation. The genetic diversity of the population increases over time in stationary phase to an extent that cannot be explained by random, neutral drift. This suggests that prolonged stationary phase offers a great model system to study adaptive evolution by natural selection.
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6
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Mitri S, Foster KR. Pleiotropy and the low cost of individual traits promote cooperation. Evolution 2016; 70:488-94. [DOI: 10.1111/evo.12851] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/08/2015] [Accepted: 12/16/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Sara Mitri
- Department of Fundamental Microbiology; University of Lausanne; Lausanne Switzerland
| | - Kevin R. Foster
- Department of Zoology; University of Oxford; Oxford UK
- Oxford Centre for Integrative Systems Biology; University of Oxford; Oxford UK
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Chen H, Chen CY. Starvation induces phenotypic diversification and convergent evolution in Vibrio vulnificus. PLoS One 2014; 9:e88658. [PMID: 24551129 PMCID: PMC3923799 DOI: 10.1371/journal.pone.0088658] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 01/12/2014] [Indexed: 12/18/2022] Open
Abstract
Starvation is a common stress experienced by bacteria living in natural environments and the ability to adapt to and survive intense stress is of paramount importance for any bacterial population. A series of starvation experiments were conducted using V. vulnificus 93U204 in phosphate-buffered saline and seawater. The starved population entered the death phase during the first week and approximately 1% of cells survived. After that the population entered a long-term stationary phase, and could survive for years. Starvation-induced diversification (SID) of phenotypes was observed in starved populations and phenotypic variants (PVs) appeared in less than 8 days. The cell density, rather than the population size, had a major effect on the extent of SID. SID was also observed in strain YJ016, where it evolved at a faster pace. PVs appeared to emerge in a fixed order: PV with reduced motility, PV with reduced proteolytic activity, and PV with reduced hemolytic activity. All of the tested PVs had growth advantages in the stationary phase phenotypes and increased fitness compared with 93U204 cells in co-culture competition experiments, which indicates that they had adapted to starvation. We also found that SID occurred in natural seawater with a salinity of 1%–3%, so this mechanism may facilitate bacterial adaptation in natural environments.
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Affiliation(s)
- Hwajiun Chen
- Department of Life Science, Tzu-Chi University, Hualien, Taiwan
- Institute of Medical Sciences, Tzu-Chi University, Hualien, Taiwan
| | - Chun-Yao Chen
- Department of Life Science, Tzu-Chi University, Hualien, Taiwan
- Institute of Medical Sciences, Tzu-Chi University, Hualien, Taiwan
- * E-mail:
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Helmus RA, Liermann LJ, Brantley SL, Tien M. Growth advantage in stationary-phase (GASP) phenotype in long-term survival strains of Geobacter sulfurreducens. FEMS Microbiol Ecol 2012; 79:218-28. [PMID: 22029575 DOI: 10.1111/j.1574-6941.2011.01211.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
Geobacter sulfurreducens exists in the subsurface and has been identified in sites contaminated with radioactive metals, consistent with its ability to reduce metals under anaerobic conditions. The natural state of organisms in the environment is one that lacks access to high concentrations of nutrients, namely electron donors and terminal electron acceptors (TEAs). Most studies have investigated G. sulfurreducens under high-nutrient conditions or have enriched for it in environmental systems via acetate amendments. We replicated the starvation state through long-term batch culture of G. sulfurreducens, where both electron donor and TEA were scarce. The growth curve revealed lag, log, stationary, death, and survival phases using acetate as electron donor and either fumarate or iron(III) citrate as TEA. In survival phase, G. sulfurreducens persisted at a constant cell count for as long as 23 months without replenishment of growth medium. Geobacter sulfurreducens demonstrated an ability to acquire a growth advantage in stationary-phase phenotype (GASP), with strains derived from subpopulations from death- or survival phase being able to out-compete mid-log-phase populations when co-cultured. The molecular basis for GASP was not because of any detectable mutation in the rpoS gene (GSU1525) nor because of a mutation in a putative homolog to Escherichia coli lrp, GSU3370.
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Affiliation(s)
- Ruth A Helmus
- Center for Environmental Kinetics Analysis, Pennsylvania State University, University Park, PA 16802, USA
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Navarro Llorens JM, Tormo A, Martínez-García E. Stationary phase in gram-negative bacteria. FEMS Microbiol Rev 2010; 34:476-95. [PMID: 20236330 DOI: 10.1111/j.1574-6976.2010.00213.x] [Citation(s) in RCA: 301] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Conditions that sustain constant bacterial growth are seldom found in nature. Oligotrophic environments and competition among microorganisms force bacteria to be able to adapt quickly to rough and changing situations. A particular lifestyle composed of continuous cycles of growth and starvation is commonly referred to as feast and famine. Bacteria have developed many different mechanisms to survive in nutrient-depleted and harsh environments, varying from producing a more resistant vegetative cell to complex developmental programmes. As a consequence of prolonged starvation, certain bacterial species enter a dynamic nonproliferative state in which continuous cycles of growth and death occur until 'better times' come (restoration of favourable growth conditions). In the laboratory, microbiologists approach famine situations using batch culture conditions. The entrance to the stationary phase is a very regulated process governed by the alternative sigma factor RpoS. Induction of RpoS changes the gene expression pattern, aiming to produce a more resistant cell. The study of stationary phase revealed very interesting phenomena such as the growth advantage in stationary phase phenotype. This review focuses on some of the interesting responses of gram-negative bacteria when they enter the fascinating world of stationary phase.
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Schoonbeek HJ, Jacquat-Bovet AC, Mascher F, Métraux JP. Oxalate-degrading bacteria can protect Arabidopsis thaliana and crop plants against botrytis cinerea. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2007; 20:1535-44. [PMID: 17990961 DOI: 10.1094/mpmi-20-12-1535] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Botrytis cinerea and Sclerotinia sclerotiorum secrete oxalic acid as a pathogenicity factor with a broad action. Consequently, it should be possible to interfere with the infection process by degrading oxalic acid during the interaction of these pathogens with their hosts. We have evaluated the potential of oxalate-degrading bacteria to protect plants against pathogenic fungi. Such bacteria were isolated from agricultural soil and selected on agar plates with Ca-oxalate as the sole carbon source. Four strains were retained with a medium-to-strong protective activity on Arabidopsis thaliana leaves against B. cinerea and S. sclerotiorum. They can provide 30 to 70% protection against fungal infection in different pathosystems, including B. cinerea on A. thaliana, cucumber, grapevine, and tomato. The oxalate-degrading bacteria induced only some marker genes for common plant signaling pathways for defenses, but protective effects were slightly reduced in A. thaliana mutants impaired in the ethylene and jasmonic acid signaling pathways. More detailed studies on the protective mechanism were performed in ox-strain B, identified as Cupriavidus campinensis, by analysis of transposon-tagged mutants that have a reduced ability to degrade oxalic acid.
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Affiliation(s)
- Henk-jan Schoonbeek
- Institute of Plant Biology, Department of Biology, University of Fribourg, Switzerland
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Poritsanos N, Selin C, Fernando WGD, Nakkeeran S, de Kievit TR. A GacS deficiency does not affect Pseudomonas chlororaphis PA23 fitness when growing on canola, in aged batch culture or as a biofilm. Can J Microbiol 2007; 52:1177-88. [PMID: 17473887 DOI: 10.1139/w06-079] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pseudomonas chlororaphis PA23 is a biocontrol agent that protects against the fungal pathogen Sclerotinia sclerotiorum. Employing transposon mutagenesis, we isolated a gacS mutant that no longer exhibited antifungal activity. Pseudomonas chlororaphis PA23 was previously reported to produce the nonvolatile antibiotics phenazine 1-carboxylic acid and 2-hydroxyphenazine. We report here that PA23 produces additional compounds, including protease, lipase, hydrogen cyanide, and siderophores, that may contribute to its biocontrol ability. In the gacS mutant background, generation of these products was markedly reduced or delayed with the exception of siderophores, which were elevated. Not surprisingly, this mutant was unable to protect canola from disease incited by S. sclerotiorum. The gacS mutant was able to sustain itself in the canola phyllosphere, therefore, the loss of biocontrol activity can be attributed to a reduced production of antifungal compounds and not a declining population size. Competition assays between the mutant and wild type revealed equivalent fitness in aged batch culture; consequently, the gacS mutation did not impart a growth advantage in the stationary phase phenotype. Under minimal nutrient conditions, the gacS-deficient strain produced a tenfold less biofilm than the wild type. However, no difference was observed in the ability of the mutant biofilm to protect cells from lethal antibiotic challenge.
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Affiliation(s)
- N Poritsanos
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
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Bacun-Druzina V, Cagalj Z, Gjuracic K. The growth advantage in stationary-phase (GASP) phenomenon in mixed cultures of enterobacteria. FEMS Microbiol Lett 2007; 266:119-27. [PMID: 17233722 DOI: 10.1111/j.1574-6968.2006.00515.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Growth advantage in stationary phase (GASP) is the term used to describe the ability of mutants with an increased fitness from 10-day-old enterobacteria culture to out-compete 1-day-old cells of the same initial strain during a prolonged stationary phase, although the aged cells are introduced as a minority. We studied this bacterial trait in mixed cultures of two enterobacterial species, Escherichia coli and Salmonella enterica, wild type in addition to derived mutants from both strains that contain chromosomal-encoded resistance to either nalidixic acid or streptomycin. The strong GASP phenotype was obtained in mixed cultures with the aged mutant strains, but not when the isogenic antibiotic-sensitive strains were used. This phenomenon was associated with chromosomal rearrangements in 10-day-old bacterial antibiotic-resistant mutated cells.
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Affiliation(s)
- Visnja Bacun-Druzina
- Laboratory of Biology and Microbial Genetics, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia.
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Heurlier K, Dénervaud V, Haas D. Impact of quorum sensing on fitness of Pseudomonas aeruginosa. Int J Med Microbiol 2006; 296:93-102. [PMID: 16503417 DOI: 10.1016/j.ijmm.2006.01.043] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
In Pseudomonas aeruginosa, cell-cell communication based on N-acyl-homoserine lactone (AHL) signal molecules (termed quorum sensing) is known to control the production of extracellular virulence factors. Hence, in pathogenic interactions with host organisms, the quorum-sensing (QS) machinery can confer a selective advantage on P. aeruginosa. However, as shown by transcriptomic and proteomic studies, many intracellular metabolic functions are also regulated by quorum sensing. Some of these serve to regenerate the AHL precursors methionine and S-adenosyl-methionine and to degrade adenosine via inosine and hypoxanthine. The fact that a significant percentage of clinical and environmental isolates of P. aeruginosa is defective for QS because of mutation in the major QS regulatory gene lasR, raises the question of whether the QS machinery can have a negative impact on the organism's fitness. In vitro, lasR mutants have a higher probability to escape lytic death in stationary phase under alkaline conditions than has the QS-proficient wild type. Similar selective forces might also operate in natural environments.
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Affiliation(s)
- Karin Heurlier
- Institute of Infection, Immunity, and Inflammation, Centre for Biomolecular Sciences, Nottingham University, Nottingham NG7 2RD, UK
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Kassab DM, Roane TM. Differential responses of a mine tailings Pseudomonas isolate to cadmium and lead exposures. Biodegradation 2006; 17:379-87. [PMID: 16477362 DOI: 10.1007/s10532-005-9010-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2005] [Accepted: 08/04/2005] [Indexed: 10/25/2022]
Abstract
We examined cadmium and lead resistance in Pseudomonas sp. S8A, an isolate obtained from mine tailings-contaminated soil. Resistant to soluble metal concentrations up to 200 mg l(-1) cadmium and 300 mg l(-1) lead, S8A produced both exopolymer and biosurfactant. Upon growth, this pseudomonad diverged into two morphologically distinct colony subtypes; small and round or large and flat. In the presence of lead and in the no metal control the large morphotype appeared only in late stationary phase. With cadmium the large morphotype appeared immediately following exposure. Results show that the large morphotype produced greater amounts of surfactant than the small morphotype, suggesting a unique subpopulation response to cadmium toxicity. Results also indicate that an unidentified 28 kDa protein was expressed following exposure to >10 mg l(-1) cadmium. This study demonstrates new links between surfactant production, differential subpopulation response and metal exposure.
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Affiliation(s)
- Duried M Kassab
- Department of Biology, University of Colorado at Denver, Denver, USA
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