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Jun JS, Jeong HE, Moon SY, Shin SH, Hong KW. Time-Course Transcriptome Analysis of Bacillus subtilis DB104 during Growth. Microorganisms 2023; 11:1928. [PMID: 37630488 PMCID: PMC10458515 DOI: 10.3390/microorganisms11081928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
Bacillus subtilis DB104, an extracellular protease-deficient derivative of B. subtilis 168, is widely used for recombinant protein expression. An understanding of the changes in gene expression during growth is essential for the commercial use of bacterial strains. Transcriptome and proteome analyses are ideal methods to study the genomic response of microorganisms. In this study, transcriptome analysis was performed to monitor changes in the gene expression level of B. subtilis DB104 while growing on a complete medium. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, K-mean cluster analysis, gene ontology (GO) enrichment analysis, and the function of sigma factors were used to divide 2122 differentially expressed genes (DEGs) into 10 clusters and identified gene functions according to expression patterns. The results of KEGG pathway analysis indicated that ABC transporter is down-regulated during exponential growth and metabolic changes occur at the transition point where sporulation starts. At this point, several stress response genes were also turned on. The genes involved in the lipid catabolic process were up-regulated briefly at 15 h as an outcome of the programmed cell death that postpones sporulation. The results suggest that changes in the gene expression of B. subtilis DB104 were dependent on the initiation of sporulation. However, the expression timing of the spore coat gene was only affected by the relevant sigma factor. This study can help to understand gene expression and regulatory mechanisms in B. subtilis species by providing an overall view of transcriptional changes during the growth of B. subtilis DB104.
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Affiliation(s)
| | | | | | | | - Kwang-Won Hong
- Department of Food Science and Biotechnology, College of Life Science and Biotechnology, Dongguk University, Goyang-si 10326, Republic of Korea; (J.-S.J.); (H.-E.J.); (S.-Y.M.); (S.-H.S.)
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McIntosh M, Eisenhardt K, Remes B, Konzer A, Klug G. Adaptation of the Alphaproteobacterium Rhodobacter sphaeroides to stationary phase. Environ Microbiol 2019; 21:4425-4445. [PMID: 31579997 DOI: 10.1111/1462-2920.14809] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 08/30/2019] [Accepted: 09/18/2019] [Indexed: 12/20/2022]
Abstract
Exhaustion of nutritional resources stimulates bacterial populations to adapt their growth behaviour. General mechanisms are known to facilitate this adaptation by sensing the environmental change and coordinating gene expression. However, the existence of such mechanisms among the Alphaproteobacteria remains unclear. This study focusses on global changes in transcript levels during growth under carbon-limiting conditions in a model Alphaproteobacterium, Rhodobacter sphaeroides, a metabolically diverse organism capable of multiple modes of growth including aerobic and anaerobic respiration, anaerobic anoxygenic photosynthesis and fermentation. We identified genes that showed changed transcript levels independently of oxygen levels during the adaptation to stationary phase. We selected a subset of these genes and subjected them to mutational analysis, including genes predicted to be involved in manganese uptake, polyhydroxybutyrate production and quorum sensing and an alternative sigma factor. Although these genes have not been previously associated with the adaptation to stationary phase, we found that all were important to varying degrees. We conclude that while R. sphaeroides appears to lack a rpoS-like master regulator of stationary phase adaptation, this adaptation is nonetheless enabled through the impact of multiple genes, each responding to environmental conditions and contributing to the adaptation to stationary phase.
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Affiliation(s)
- Matthew McIntosh
- Institut für Mikrobiologie und Molekularbiologie, IFZ, Justus-Liebig-Universität, 35392, Giessen, Germany
| | - Katrin Eisenhardt
- Institut für Mikrobiologie und Molekularbiologie, IFZ, Justus-Liebig-Universität, 35392, Giessen, Germany
| | - Bernhard Remes
- Institut für Mikrobiologie und Molekularbiologie, IFZ, Justus-Liebig-Universität, 35392, Giessen, Germany
| | - Anne Konzer
- Biomolecular Mass Spectrometry, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Gabriele Klug
- Institut für Mikrobiologie und Molekularbiologie, IFZ, Justus-Liebig-Universität, 35392, Giessen, Germany
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Han LL, Shao HH, Liu YC, Liu G, Xie CY, Cheng XJ, Wang HY, Tan XM, Feng H. Transcriptome profiling analysis reveals metabolic changes across various growth phases in Bacillus pumilus BA06. BMC Microbiol 2017; 17:156. [PMID: 28693413 PMCID: PMC5504735 DOI: 10.1186/s12866-017-1066-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/04/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Bacillus pumilus can secret abundant extracellular enzymes, and may be used as a potential host for the industrial production of enzymes. It is necessary to understand the metabolic processes during cellular growth. Here, an RNA-seq based transcriptome analysis was applied to examine B. pumilus BA06 across various growth stages to reveal metabolic changes under two conditions. RESULTS Based on the gene expression levels, changes to metabolism pathways that were specific to various growth phases were enriched by KEGG analysis. Upon entry into the transition from the exponential growth phase, striking changes were revealed that included down-regulation of the tricarboxylic acid cycle, oxidative phosphorylation, flagellar assembly, and chemotaxis signaling. In contrast, the expression of stress-responding genes was induced when entering the transition phase, suggesting that the cell may suffer from stress during this growth stage. As expected, up-regulation of sporulation-related genes was continuous during the stationary growth phase, which was consistent with the observed sporulation. However, the expression pattern of the various extracellular proteases was different, suggesting that the regulatory mechanism may be distinct for various proteases. In addition, two protein secretion pathways were enriched with genes responsive to the observed protein secretion in B. pumilus. However, the expression of some genes that encode sporulation-related proteins and extracellular proteases was delayed by the addition of gelatin to the minimal medium. CONCLUSIONS The transcriptome data depict global alterations in the genome-wide transcriptome across the various growth phases, which will enable an understanding of the physiology and phenotype of B. pumilus through gene expression.
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Affiliation(s)
- Lin-Li Han
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Huan-Huan Shao
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Yong-Cheng Liu
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Gang Liu
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Chao-Ying Xie
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Xiao-Jie Cheng
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Hai-Yan Wang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Xue-Mei Tan
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
| | - Hong Feng
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
- College of Life Sciences, Sichuan University, Chengdu, 610064 Sichuan People’s Republic of China
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Yang S, Du G, Chen J, Kang Z. Characterization and application of endogenous phase-dependent promoters in Bacillus subtilis. Appl Microbiol Biotechnol 2017; 101:4151-4161. [DOI: 10.1007/s00253-017-8142-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 01/05/2017] [Accepted: 01/20/2017] [Indexed: 01/01/2023]
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Hsieh YH, Zhang H, Jin J, Dai C, Jiang C, Wang B, Tai PC. Biphasic actions of SecA inhibitors on Prl/Sec suppressors: Possible physiological roles of SecA-only channels. Biochem Biophys Res Commun 2017; 482:296-300. [PMID: 27856243 DOI: 10.1016/j.bbrc.2016.11.057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 11/11/2016] [Indexed: 11/30/2022]
Abstract
SecA is an essential component in the bacterial Sec-dependent protein translocation process. We previously showed that in addition to the ubiquitous, high-affinity SecYEG-SecDF·YajC protein translocation channel, there is a low-affinity SecA-only channel that elicits ion channel activity and promotes protein translocation. The SecA-only channels are less efficient, and like Prl suppressors, lack signal peptide specificity; they function in the absence of signal peptides. The presence of SecYEG-SecDF·YajC alters the sensitivity of ATPase inhibitor Rose Bengal. In this study, we found that the suppressor membranes are much more resistant to inhibition by Rose Bengal. Similar results have been found for a SecA-specific inhibitor. Moreover, biphasic responses of inhibition of ion current and protein translocation activities were observed for many PrlA/SecY and PrlG/SecE suppressor membranes, with a low IC50 value similar to that of the SecA-only channels and a very high IC50. However, the suppressor strains are as sensitive to the inhibitor as the parental strain, suggesting that SecA-only channels have some essential physiological function(s) in the cells that are inhibited by the specific SecA inhibitor.
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Affiliation(s)
- Ying-Hsin Hsieh
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Hao Zhang
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Jinshan Jin
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Chaofeng Dai
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Chun Jiang
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Binghe Wang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Phang C Tai
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA.
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Ogura M, Asai K. Glucose Induces ECF Sigma Factor Genes, sigX and sigM, Independent of Cognate Anti-sigma Factors through Acetylation of CshA in Bacillus subtilis. Front Microbiol 2016; 7:1918. [PMID: 27965645 PMCID: PMC5126115 DOI: 10.3389/fmicb.2016.01918] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 11/15/2016] [Indexed: 12/23/2022] Open
Abstract
Extracytoplasmic function (ECF) σ factors have roles related to cell envelope and/or cell membrane functions, in addition to other cellular functions. Without cell-surface stresses, ECF σ factors are sequestered by the cognate anti-σ factor, leading to inactivation and the resultant repression of regulons due to the inhibition of transcription of their own genes. Bacillus subtilis has seven ECF σ factors including σX and σM that transcribe their own structural genes. Here, we report that glucose addition to the medium induced sigX and sigM transcription independent of their anti-σ factors. This induction was dependent on an intracellular acetyl-CoA pool. Transposon mutagenesis searching for the mutants showing no induction of sigX and sigM revealed that the cshA gene encoding DEAD-box RNA helicase is required for gene induction. Global analysis of the acetylome in B. subtilis showed CshA has two acetylated lysine residues. We found that in a cshA mutant with acetylation-abolishing K to R exchange mutations, glucose induction of sigX and sigM was abolished and that glucose addition stimulated acetylation of CshA in the wild type strain. Thus, we present a model wherein glucose addition results in a larger acetyl-CoA pool, probably leading to increased levels of acetylated CshA. CshA is known to associate with RNA polymerase (RNAP), and thus RNAP with acetylated CshA could stimulate the autoregulation of sigX and sigM. This is a unique model showing a functional link between nutritional signals and the basal transcription machinery.
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Affiliation(s)
- Mitsuo Ogura
- Institute of Oceanic Research and Development, Tokai University Shizuoka, Japan
| | - Kei Asai
- Department of Bioscience, Saitama University Saitama, Japan
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Resilience in the Face of Uncertainty: Sigma Factor B Fine-Tunes Gene Expression To Support Homeostasis in Gram-Positive Bacteria. Appl Environ Microbiol 2016; 82:4456-4469. [PMID: 27208112 DOI: 10.1128/aem.00714-16] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Gram-positive bacteria are ubiquitous and diverse microorganisms that can survive and sometimes even thrive in continuously changing environments. The key to such resilience is the ability of members of a population to respond and adjust to dynamic conditions in the environment. In bacteria, such responses and adjustments are mediated, at least in part, through appropriate changes in the bacterial transcriptome in response to the conditions encountered. Resilience is important for bacterial survival in diverse, complex, and rapidly changing environments and requires coordinated networks that integrate individual, mechanistic responses to environmental cues to enable overall metabolic homeostasis. In many Gram-positive bacteria, a key transcriptional regulator of the response to changing environmental conditions is the alternative sigma factor σ(B) σ(B) has been characterized in a subset of Gram-positive bacteria, including the genera Bacillus, Listeria, and Staphylococcus Recent insight from next-generation-sequencing results indicates that σ(B)-dependent regulation of gene expression contributes to resilience, i.e., the coordination of complex networks responsive to environmental changes. This review explores contributions of σ(B) to resilience in Bacillus, Listeria, and Staphylococcus and illustrates recently described regulatory functions of σ(B).
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