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Zhu Z, Xu X, Huang J, Xu G, Liu S, Hong F, Chen Y, Yi X, Li H, Li J. Transcriptomic analysis of Vibrio alginolyticus challenged by Rhizoma coptidis reveals mechanisms of virulence genes. Gene 2024; 905:148188. [PMID: 38278336 DOI: 10.1016/j.gene.2024.148188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 01/28/2024]
Abstract
Rhizoma coptidis, a Chinese herbal medicine widely used to treat various bacterial infections, has the potential to develop antibiotic substitutes to overcome the drug resistance of Vibrio alginolyticus. To study the inhibitory effect of R. coptidis on V. alginolyticus, we sequenced the transcriptomes of three groups of samples of wild-type V. alginolyticus (CK) and V. alginolyticus, which were stressed by 5 mg/mL R. coptidis for 2 h (RC_2 h) and 4 h (RC_4 h). CK was compared with RC_2 h and RC_4 h, respectively, and a total of 1565 differentially expressed genes (DEGs) (988 up-regulated and 577 down-regulated) and 1737 DEGs (1152 up-regulated and 585 down-regulated) were identified. Comparing RC_2 h with RC_4 h, 156 DEGs (114 up-regulated and 42 down-regulated) were identified. The ability of biofilm formation and motility of V. alginolyticus altered upon with different concentrations of R. coptidis. Interestingly, relative expression patterns of virulence genes appeared statistically significantly varied, upon different concentrations of R. coptidis extract. DEGs were annotated to the Gene Ontology (GO) database for function enrichment analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the results showed that the main enriched pathways, was those related to the virulence of V. alginolyticus. This study provides a new perspective for understanding the complex pathogenic mechanism of V. alginolyticus. R. coptidis could potnetially be used as alternative or complimnetary to antibiotics to treat infections after further research.
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Affiliation(s)
- Zhiqin Zhu
- State Key Laboratory of Mariculture Breeding, Fisheries College, Jimei University, Xiamen, Fujian 361021, China, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Fujian Province, Xiamen 361021, China
| | - XiaoJin Xu
- State Key Laboratory of Mariculture Breeding, Fisheries College, Jimei University, Xiamen, Fujian 361021, China, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Fujian Province, Xiamen 361021, China; Fujian Province Key Laboratory of Special Aquatic Formula Feed (Fujian Tianma Science and Technology Group Co., Ltd, China.
| | - Jiangyuan Huang
- State Key Laboratory of Mariculture Breeding, Fisheries College, Jimei University, Xiamen, Fujian 361021, China, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Fujian Province, Xiamen 361021, China
| | - Genhuang Xu
- State Key Laboratory of Mariculture Breeding, Fisheries College, Jimei University, Xiamen, Fujian 361021, China, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Fujian Province, Xiamen 361021, China
| | - ShiChao Liu
- State Key Laboratory of Mariculture Breeding, Fisheries College, Jimei University, Xiamen, Fujian 361021, China, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Fujian Province, Xiamen 361021, China
| | - Fei Hong
- State Key Laboratory of Mariculture Breeding, Fisheries College, Jimei University, Xiamen, Fujian 361021, China, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Fujian Province, Xiamen 361021, China
| | - Yunong Chen
- State Key Laboratory of Mariculture Breeding, Fisheries College, Jimei University, Xiamen, Fujian 361021, China, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Fujian Province, Xiamen 361021, China
| | - Xin Yi
- State Key Laboratory of Mariculture Breeding, Fisheries College, Jimei University, Xiamen, Fujian 361021, China, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Fujian Province, Xiamen 361021, China
| | - Huiyao Li
- Fisheries Research Institute of Fujian, Xiamen 361013, China
| | - Jun Li
- State Key Laboratory of Mariculture Breeding, Fisheries College, Jimei University, Xiamen, Fujian 361021, China, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Fujian Province, Xiamen 361021, China.
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Snoeck S, Guidi C, De Mey M. "Metabolic burden" explained: stress symptoms and its related responses induced by (over)expression of (heterologous) proteins in Escherichia coli. Microb Cell Fact 2024; 23:96. [PMID: 38555441 PMCID: PMC10981312 DOI: 10.1186/s12934-024-02370-9] [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: 12/01/2023] [Accepted: 03/18/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Engineering bacterial strains to redirect the metabolism towards the production of a specific product has enabled the development of industrial biotechnology. However, rewiring the metabolism can have severe implications for a microorganism, rendering cells with stress symptoms such as a decreased growth rate, impaired protein synthesis, genetic instability and an aberrant cell size. On an industrial scale, this is reflected in processes that are not economically viable. MAIN TEXT In literature, most stress symptoms are attributed to "metabolic burden", however the actual triggers and stress mechanisms involved are poorly understood. Therefore, in this literature review, we aimed to get a better insight in how metabolic engineering affects Escherichia coli and link the observed stress symptoms to its cause. Understanding the possible implications that chosen engineering strategies have, will help to guide the reader towards optimising the envisioned process more efficiently. CONCLUSION This review addresses the gap in literature and discusses the triggers and effects of stress mechanisms that can be activated when (over)expressing (heterologous) proteins in Escherichia coli. It uncovers that the activation of the different stress mechanisms is complex and that many are interconnected. The reader is shown that care has to be taken when (over)expressing (heterologous) proteins as the cell's metabolism is tightly regulated.
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Affiliation(s)
- Sofie Snoeck
- Department of Biotechnology, Centre for Synthetic Biology, Coupure Links 653, Gent, 9000, Belgium
| | - Chiara Guidi
- Department of Biotechnology, Centre for Synthetic Biology, Coupure Links 653, Gent, 9000, Belgium
| | - Marjan De Mey
- Department of Biotechnology, Centre for Synthetic Biology, Coupure Links 653, Gent, 9000, Belgium.
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3
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Bouillet S, Bauer TS, Gottesman S. RpoS and the bacterial general stress response. Microbiol Mol Biol Rev 2024; 88:e0015122. [PMID: 38411096 PMCID: PMC10966952 DOI: 10.1128/mmbr.00151-22] [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] [Indexed: 02/28/2024] Open
Abstract
SUMMARYThe general stress response (GSR) is a widespread strategy developed by bacteria to adapt and respond to their changing environments. The GSR is induced by one or multiple simultaneous stresses, as well as during entry into stationary phase and leads to a global response that protects cells against multiple stresses. The alternative sigma factor RpoS is the central GSR regulator in E. coli and conserved in most γ-proteobacteria. In E. coli, RpoS is induced under conditions of nutrient deprivation and other stresses, primarily via the activation of RpoS translation and inhibition of RpoS proteolysis. This review includes recent advances in our understanding of how stresses lead to RpoS induction and a summary of the recent studies attempting to define RpoS-dependent genes and pathways.
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Affiliation(s)
- Sophie Bouillet
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
| | - Taran S. Bauer
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, Bethesda, Maryland, USA
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Zhang H, Shao C, Wang J, Chu Y, Xiao J, Kang Y, Zhang Z. Combined Study of Gene Expression and Chromosome Three-Dimensional Structure in Escherichia coli During Growth Process. Curr Microbiol 2024; 81:122. [PMID: 38530471 DOI: 10.1007/s00284-024-03640-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 02/13/2024] [Indexed: 03/28/2024]
Abstract
The chromosome structure of different bacteria has its unique organization pattern, which plays an important role in maintaining the spatial location relationship between genes and regulating gene expression. Conversely, transcription also plays a global role in regulating the three-dimensional structure of bacterial chromosomes. Therefore, we combine RNA-Seq and Hi-C technology to explore the relationship between chromosome structure changes and transcriptional regulation in E. coli at different growth stages. Transcriptome analysis indicates that E. coli synthesizes many ribosomes and peptidoglycan in the exponential phase. In contrast, E. coli undergoes more transcriptional regulation and catabolism during the stationary phase, reflecting its adaptability to changes in environmental conditions during growth. Analyzing the Hi-C data shows that E. coli has a higher frequency of global chromosomal interaction in the exponential phase and more defined chromosomal interaction domains (CIDs). Still, the long-distance interactions at the replication termination region are lower than in the stationary phase. Combining transcriptome and Hi-C data analysis, we conclude that highly expressed genes are more likely to be distributed in CID boundary regions during the exponential phase. At the same time, most high-expression genes distributed in the CID boundary regions are ribosomal gene clusters, forming clearer CID boundaries during the exponential phase. The three-dimensional structure of chromosome and expression pattern is altered during the growth of E. coli from the exponential phase to the stationary phase, clarifying the synergy between the two regulatory aspects.
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Affiliation(s)
- Hao Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changjun Shao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Jian Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Yanan Chu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Jingfa Xiao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Kang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
| | - Zhewen Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
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5
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McQuail J, Matera G, Gräfenhan T, Bischler T, Haberkant P, Stein F, Vogel J, Wigneshweraraj S. Global Hfq-mediated RNA interactome of nitrogen starved Escherichia coli uncovers a conserved post-transcriptional regulatory axis required for optimal growth recovery. Nucleic Acids Res 2024; 52:2323-2339. [PMID: 38142457 PMCID: PMC10954441 DOI: 10.1093/nar/gkad1211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/17/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023] Open
Abstract
The RNA binding protein Hfq has a central role in the post-transcription control of gene expression in many bacteria. Numerous studies have mapped the transcriptome-wide Hfq-mediated RNA-RNA interactions in growing bacteria or bacteria that have entered short-term growth-arrest. To what extent post-transcriptional regulation underpins gene expression in growth-arrested bacteria remains unknown. Here, we used nitrogen (N) starvation as a model to study the Hfq-mediated RNA interactome as Escherichia coli enter, experience, and exit long-term growth arrest. We observe that the Hfq-mediated RNA interactome undergoes extensive changes during N starvation, with the conserved SdsR sRNA making the most interactions with different mRNA targets exclusively in long-term N-starved E. coli. Taking a proteomics approach, we reveal that in growth-arrested cells SdsR influences gene expression far beyond its direct mRNA targets. We demonstrate that the absence of SdsR significantly compromises the ability of the mutant bacteria to recover growth competitively from the long-term N-starved state and uncover a conserved post-transcriptional regulatory axis which underpins this process.
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Affiliation(s)
- Josh McQuail
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Faculty of Medicine, Imperial College London, UK
| | - Gianluca Matera
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Tom Gräfenhan
- Core Unit Systems Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Thorsten Bischler
- Core Unit Systems Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, D-69117,Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, D-69117,Heidelberg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
- Institute for Molecular Infection Biology (IMIB), Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Sivaramesh Wigneshweraraj
- Section of Molecular Microbiology and Centre for Bacterial Resistance Biology, Faculty of Medicine, Imperial College London, UK
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Sui X, Wang J, Zhao Z, Liu B, Liu M, Liu M, Shi C, Feng X, Fu Y, Shi D, Li S, Qi Q, Xian M, Zhao G. Phenolic compounds induce ferroptosis-like death by promoting hydroxyl radical generation in the Fenton reaction. Commun Biol 2024; 7:199. [PMID: 38368473 PMCID: PMC10874397 DOI: 10.1038/s42003-024-05903-5] [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: 11/05/2023] [Accepted: 02/08/2024] [Indexed: 02/19/2024] Open
Abstract
Phenolic compounds are industrially versatile chemicals, also the most ubiquitous pollutants. Recently, biosynthesis and biodegradation of phenols has attracted increasing attention, while phenols' toxicity is a major issue. Here, we evolved phloroglucinol-tolerant Escherichia coli strains via adaptive evolution, and three mutations (ΔsodB, ΔclpX and fetAB overexpression) prove of great assistance in the tolerance improvement. We discover that phloroglucinol complexes with iron and promotes the generation of hydroxyl radicals in Fenton reaction, which leads to reducing power depletion, lipid peroxidation, and ferroptosis-like cell death of E. coli. Besides phloroglucinol, various phenols can trigger ferroptosis-like death in diverse organisms, from bacteria to mammalian cells. Furthermore, repressing this ferroptosis-like death improves phloroglucinol production and phenol degradation by corresponding strains respectively, showing great application potential in microbial degradation or production of desired phenolic compounds, and phloroglucinol-induced ferroptosis suppresses tumor growth in mice, indicating phloroglucinol as a promising drug for cancer treatment.
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Affiliation(s)
- Xinyue Sui
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jichao Wang
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Zhiqiang Zhao
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Miaomiao Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Min Liu
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Cong Shi
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Xinjun Feng
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Yingxin Fu
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Dayong Shi
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Shengying Li
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Mo Xian
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Guang Zhao
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China.
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.
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7
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Zhu M, Mu H, Dai X. Integrated control of bacterial growth and stress response by (p)ppGpp in Escherichia coli: A seesaw fashion. iScience 2024; 27:108818. [PMID: 38299113 PMCID: PMC10828813 DOI: 10.1016/j.isci.2024.108818] [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: 07/13/2023] [Revised: 12/02/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024] Open
Abstract
To thrive in nature, bacteria have to reproduce efficiently under favorable conditions and persist during stress. The global strategy that integrates the growth control and stress response remains to be explored. Here, we find that a moderate induction of (p)ppGpp reduces growth rate but significantly enhances the stress tolerance of E. coli, resulting from a global resource re-allocation from ribosome synthesis to the synthesis of stress-responsive proteins. Strikingly, the activation of stress response by (p)ppGpp is still largely retained in the absence of RpoS. In addition, (p)ppGpp induction could activate the catabolism of alanine and arginine, facilitating the adaption of bacteria to nutrient downshift. Our work demonstrates that the activation of stress response by (p)ppGpp could occur in an RpoS-independent manner and (p)ppGpp enables bacteria to integrate the control of growth and stress response in a seesaw fashion, thus acting as an important global regulator of the bacterial fitness landscape.
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Affiliation(s)
- Manlu Zhu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences & National Key Laboratory of Green Pesticides, Central China Normal University, Wuhan, China
| | - Haoyan Mu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences & National Key Laboratory of Green Pesticides, Central China Normal University, Wuhan, China
| | - Xiongfeng Dai
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences & National Key Laboratory of Green Pesticides, Central China Normal University, Wuhan, China
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8
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Espaillat A, Alvarez L, Torrens G, Ter Beek J, Miguel-Ruano V, Irazoki O, Gago F, Hermoso JA, Berntsson RPA, Cava F. A distinctive family of L,D-transpeptidases catalyzing L-Ala-mDAP crosslinks in Alpha- and Betaproteobacteria. Nat Commun 2024; 15:1343. [PMID: 38351082 PMCID: PMC10864386 DOI: 10.1038/s41467-024-45620-5] [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: 11/09/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
The bacterial cell-wall peptidoglycan is made of glycan strands crosslinked by short peptide stems. Crosslinks are catalyzed by DD-transpeptidases (4,3-crosslinks) and LD-transpeptidases (3,3-crosslinks). However, recent research on non-model species has revealed novel crosslink types, suggesting the existence of uncharacterized enzymes. Here, we identify an LD-transpeptidase, LDTGo, that generates 1,3-crosslinks in the acetic-acid bacterium Gluconobacter oxydans. LDTGo-like proteins are found in Alpha- and Betaproteobacteria lacking LD3,3-transpeptidases. In contrast with the strict specificity of typical LD- and DD-transpeptidases, LDTGo can use non-terminal amino acid moieties for crosslinking. A high-resolution crystal structure of LDTGo reveals unique features when compared to LD3,3-transpeptidases, including a proline-rich region that appears to limit substrate access, and a cavity accommodating both glycan chain and peptide stem from donor muropeptides. Finally, we show that DD-crosslink turnover is involved in supplying the necessary substrate for LD1,3-transpeptidation. This phenomenon underscores the interplay between distinct crosslinking mechanisms in maintaining cell wall integrity in G. oxydans.
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Affiliation(s)
- Akbar Espaillat
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
- Chr. Hansen A/S, Microbial Physiology, R&D, 2970, Hoersholm, Denmark
| | - Laura Alvarez
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
| | - Gabriel Torrens
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
| | - Josy Ter Beek
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Vega Miguel-Ruano
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Blas Cabrera", CSIC, Madrid, Spain
| | - Oihane Irazoki
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
| | - Federico Gago
- Department of Biomedical Sciences & IQM-CSIC Associate Unit, School of Medicine and Health Sciences, University of Alcalá, E-28805, Madrid, Alcalá de Henares, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Blas Cabrera", CSIC, Madrid, Spain
| | - Ronnie P-A Berntsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden.
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9
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Yang H, Zhang B, Wu Z, Pan J, Chen L, Xiu X, Cai X, Liu Z, Zheng Y. Synergistic application of atmospheric and room temperature plasma mutagenesis and adaptive laboratory evolution improves the tolerance of Escherichia coli to L-cysteine. Biotechnol J 2024; 19:e2300648. [PMID: 38403408 DOI: 10.1002/biot.202300648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/16/2024] [Accepted: 01/27/2024] [Indexed: 02/27/2024]
Abstract
L-Cysteine production through fermentation stands as a promising technology. However, excessive accumulation of L-cysteine poses a challenge due to the potential to inflict damage on cellular DNA. In this study, we employed a synergistic approach encompassing atmospheric and room temperature plasma mutagenesis (ARTP) and adaptive laboratory evolution (ALE) to improve L-cysteine tolerance in Escherichia coli. ARTP-treated populations obtained substantial enhancement in L-cysteine tolerance by ALE. Whole-genome sequencing, transcription analysis, and reverse engineering, revealed the pivotal role of an effective export mechanism mediated by gene eamB in augmenting L-cysteine resistance. The isolated tolerant strain, 60AP03/pTrc-cysEf , achieved a 2.2-fold increase in L-cysteine titer by overexpressing the critical gene cysEf during batch fermentation, underscoring its enormous potential for L-cysteine production. The production evaluations, supplemented with L-serine, further demonstrated the stability and superiority of tolerant strains in L-cysteine production. Overall, our work highlighted the substantial impact of the combined ARTP and ALE strategy in increasing the tolerance of E. coli to L-cysteine, providing valuable insights into improving L-cysteine overproduction, and further emphasized the potential of biotechnology in industrial production.
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Affiliation(s)
- Hui Yang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
| | - Bo Zhang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
| | - Zidan Wu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
| | - Jiayuan Pan
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
| | - Lifeng Chen
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
| | - Xiaoling Xiu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
| | - Xue Cai
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
| | - Zhiqiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
| | - Yuguo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China
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10
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Kaul M, Meher SK, Nallamotu KC, Reddy M. Glycan strand cleavage by a lytic transglycosylase, MltD contributes to the expansion of peptidoglycan in Escherichia coli. PLoS Genet 2024; 20:e1011161. [PMID: 38422114 DOI: 10.1371/journal.pgen.1011161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 03/12/2024] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Peptidoglycan (PG) is a protective sac-like exoskeleton present in most bacterial cell walls. It is a large, covalently crosslinked mesh-like polymer made up of many glycan strands cross-bridged to each other by short peptide chains. Because PG forms a continuous mesh around the bacterial cytoplasmic membrane, opening the mesh is critical to generate space for the incorporation of new material during its expansion. In Escherichia coli, the 'space-making activity' is known to be achieved by cleavage of crosslinks between the glycan strands by a set of redundant PG endopeptidases whose absence leads to rapid lysis and cell death. Here, we demonstrate a hitherto unknown role of glycan strand cleavage in cell wall expansion in E. coli. We find that overexpression of a membrane-bound lytic transglycosylase, MltD that cuts the glycan polymers of the PG sacculus rescues the cell lysis caused by the absence of essential crosslink-specific endopeptidases, MepS, MepM and MepH. We find that cellular MltD levels are stringently controlled by two independent regulatory pathways; at the step of post-translational stability by a periplasmic adaptor-protease complex, NlpI-Prc, and post-transcriptionally by RpoS, a stationary-phase specific sigma factor. Further detailed genetic and biochemical analysis implicated a role for MltD in cleaving the nascent uncrosslinked glycan strands generated during the expansion of PG. Overall, our results show that the combined activity of PG endopeptidases and lytic transglycosylases is necessary for successful expansion of the cell wall during growth of a bacterium.
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Affiliation(s)
- Moneca Kaul
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Suraj Kumar Meher
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Krishna Chaitanya Nallamotu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Manjula Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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11
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Jeong GJ, Khan F, Tabassum N, Kim YM. Cellular and physiological roles of sigma factors in Vibrio spp.: A comprehensive review. Int J Biol Macromol 2024; 254:127833. [PMID: 37918595 DOI: 10.1016/j.ijbiomac.2023.127833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
Vibrio species are motile gram-negative bacteria commonly found in aquatic environments. Vibrio species include pathogenic as well as non-pathogenic strains. Pathogenic Vibrio species have been reported in invertebrates and humans, whereas non-pathogenic strains are involved in symbiotic relationships with their eukaryotic hosts. These bacteria are also able to adapt to fluctuations in temperature, salinity, and pH, in addition to oxidative stress, and osmotic pressure in aquatic ecosystems. Moreover, they have also developed protective mechanisms against the immune systems of their hosts. Vibrio species accomplish adaptation to changing environments outside or inside the host by altering their gene expression profiles. To this end, several sigma factors specifically regulate gene expression, particularly under stressful environmental conditions. Moreover, other sigma factors are associated with biofilm formation and virulence as well. This review discusses different types of sigma and anti-sigma factors of Vibrio species involved in virulence and regulation of gene expression upon changes in environmental conditions. The evolutionary relationships between sigma factors with various physiological roles in Vibrio species are also discussed extensively.
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Affiliation(s)
- Geum-Jae Jeong
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Fazlurrahman Khan
- Institute of Fisheries Sciences, Pukyong National University, Busan 48513, Republic of Korea; Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea.
| | - Nazia Tabassum
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Young-Mog Kim
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea; Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea.
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12
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Tezuka T, Mitsuyama K, Date R, Ohnishi Y. A unique sigma/anti-sigma system in the actinomycete Actinoplanes missouriensis. Nat Commun 2023; 14:8483. [PMID: 38123564 PMCID: PMC10733313 DOI: 10.1038/s41467-023-44291-y] [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: 09/05/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
Bacteria of the genus Actinoplanes form sporangia that contain dormant sporangiospores which, upon contact with water, release motile spores (zoospores) through a process called sporangium dehiscence. Here, we set out to study the molecular mechanisms behind sporangium dehiscence in Actinoplanes missouriensis and discover a sigma/anti-sigma system with unique features. Protein σSsdA contains a functional sigma factor domain and an anti-sigma factor antagonist domain, while protein SipA contains an anti-sigma factor domain and an anti-sigma factor antagonist domain. Remarkably, the two proteins interact with each other via the anti-sigma factor antagonist domain of σSsdA and the anti-sigma factor domain of SipA. Although it remains unclear whether the SipA/σSsdA system plays direct roles in sporangium dehiscence, the system seems to modulate oxidative stress responses in zoospores. In addition, we identify a two-component regulatory system (RsdK-RsdR) that represses initiation of sporangium dehiscence.
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Affiliation(s)
- Takeaki Tezuka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Graduate School of Infection Control Sciences, Kitasato University, Minato-ku, Tokyo, Japan.
| | - Kyota Mitsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Risa Date
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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13
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Petrova O, Semenova E, Parfirova O, Tsers I, Gogoleva N, Gogolev Y, Nikolaichik Y, Gorshkov V. RpoS-Regulated Genes and Phenotypes in the Phytopathogenic Bacterium Pectobacterium atrosepticum. Int J Mol Sci 2023; 24:17348. [PMID: 38139177 PMCID: PMC10743746 DOI: 10.3390/ijms242417348] [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: 11/07/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The alternative sigma factor RpoS is considered to be one of the major regulators providing stress resistance and cross-protection in bacteria. In phytopathogenic bacteria, the effects of RpoS have not been analyzed with regard to cross-protection, and genes whose expression is directly or indirectly controlled by RpoS have not been determined at the whole-transcriptome level. Our study aimed to determine RpoS-regulated genes and phenotypes in the phytopathogenic bacterium Pectobacterium atrosepticum. Knockout of the rpoS gene in P. atrosepticum affected the long-term starvation response, cross-protection, and virulence toward plants with enhanced immune status. The whole-transcriptome profiles of the wild-type P. atrosepticum strain and its ΔrpoS mutant were compared under different experimental conditions, and functional gene groups whose expression was affected by RpoS were determined. The RpoS promoter motif was inferred within the promoter regions of the genes affected by rpoS deletion, and the P. atrosepticum RpoS regulon was predicted. Based on RpoS-controlled phenotypes, transcriptome profiles, and RpoS regulon composition, the regulatory role of RpoS in P. atrosepticum is discussed.
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Affiliation(s)
- Olga Petrova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Elizaveta Semenova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Olga Parfirova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Ivan Tsers
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Natalia Gogoleva
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Yuri Gogolev
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Yevgeny Nikolaichik
- Department of Molecular Biology, Belarusian State University, 220030 Minsk, Belarus;
| | - Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
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14
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Detert K, Währer J, Nieselt K, Schmidt H. Broad time-dependent transcriptional activity of metabolic genes of E. coli O104:H4 strain C227/11Φcu in a soil microenvironment at low temperature. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:582-596. [PMID: 37644642 PMCID: PMC10667640 DOI: 10.1111/1758-2229.13198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023]
Abstract
In the current study, metabolic genes and networks that influence the persistence of pathogenic Escherichia coli O104:H4 strain C227/11Φcu in agricultural soil microenvironments at low temperature were investigated. The strain was incubated in alluvial loam (AL) and total RNA was prepared from samples at time point 0, and after 1 and 4 weeks. Differential transcriptomic analysis was performed by RNA sequencing analysis and values obtained at weeks 1 and 4 were compared to those of time point 0. We found differential expression of more than 1500 genes for either time point comparison. The two lists of differentially expressed genes were then subjected to gene set enrichment of Gene Ontology terms. In total, 17 GO gene sets and 3 Pfam domains were found to be enriched after 1 week. After 4 weeks, 17 GO gene sets and 7 Pfam domains were statistically enriched. Especially stress response genes and genes of the primary metabolism were particularly affected at both time points. Genes and gene sets for uptake of carbohydrates, amino acids were strongly upregulated, indicating adjustment to a low nutrient environment. The results of this transcriptome analysis show that persistence of C227/11Φcu in soils is associated with a complex interplay of metabolic networks.
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Affiliation(s)
- Katharina Detert
- Department of Food Microbiology and Hygiene, Institute of Food Science and BiotechnologyUniversity of HohenheimStuttgartGermany
| | - Jonathan Währer
- Institute for Bioinformatics and Medical InformaticsUniversity of TübingenTübingenGermany
| | - Kay Nieselt
- Institute for Bioinformatics and Medical InformaticsUniversity of TübingenTübingenGermany
| | - Herbert Schmidt
- Department of Food Microbiology and Hygiene, Institute of Food Science and BiotechnologyUniversity of HohenheimStuttgartGermany
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15
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Brugger C, Schwartz J, Novick S, Tong S, Hoskins JR, Majdalani N, Kim R, Filipovski M, Wickner S, Gottesman S, Griffin PR, Deaconescu AM. Structure of phosphorylated-like RssB, the adaptor delivering σ s to the ClpXP proteolytic machinery, reveals an interface switch for activation. J Biol Chem 2023; 299:105440. [PMID: 37949227 PMCID: PMC10755785 DOI: 10.1016/j.jbc.2023.105440] [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: 08/07/2023] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 11/12/2023] Open
Abstract
In enterobacteria such as Escherichia coli, the general stress response is mediated by σs, the stationary phase dissociable promoter specificity subunit of RNA polymerase. σs is degraded by ClpXP during active growth in a process dependent on the RssB adaptor, which is thought to be stimulated by the phosphorylation of a conserved aspartate in its N-terminal receiver domain. Here we present the crystal structure of full-length RssB bound to a beryllofluoride phosphomimic. Compared to the structure of RssB bound to the IraD anti-adaptor, our new RssB structure with bound beryllofluoride reveals conformational differences and coil-to-helix transitions in the C-terminal region of the RssB receiver domain and in the interdomain segmented helical linker. These are accompanied by masking of the α4-β5-α5 (4-5-5) "signaling" face of the RssB receiver domain by its C-terminal domain. Critically, using hydrogen-deuterium exchange mass spectrometry, we identify σs-binding determinants on the 4-5-5 face, implying that this surface needs to be unmasked to effect an interdomain interface switch and enable full σs engagement and hand-off to ClpXP. In activated receiver domains, the 4-5-5 face is often the locus of intermolecular interactions, but its masking by intramolecular contacts upon phosphorylation is unusual, emphasizing that RssB is a response regulator that undergoes atypical regulation.
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Affiliation(s)
- Christiane Brugger
- Laboratories of Molecular Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Jacob Schwartz
- Laboratories of Molecular Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Scott Novick
- Department of Molecular Medicine, The Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, Jupiter, Florida, USA
| | - Song Tong
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Joel R Hoskins
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Nadim Majdalani
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rebecca Kim
- Laboratories of Molecular Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Martin Filipovski
- Laboratories of Molecular Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Sue Wickner
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, Jupiter, Florida, USA
| | - Alexandra M Deaconescu
- Laboratories of Molecular Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA.
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16
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Gladysheva-Azgari M, Sharko F, Evteeva M, Kuvyrchenkova A, Boulygina E, Tsygankova S, Slobodova N, Pustovoit K, Melkina O, Nedoluzhko A, Korzhenkov A, Kudryavtseva A, Utkina A, Manukhov I, Rastorguev S, Zavilgelsky G. ArdA genes from pKM101 and from B. bifidum chromosome have a different range of regulated genes. Heliyon 2023; 9:e22986. [PMID: 38144267 PMCID: PMC10746416 DOI: 10.1016/j.heliyon.2023.e22986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/18/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023] Open
Abstract
The ardA genes are present in a wide variety of conjugative plasmids and play an important role in overcoming the restriction barrier. To date, there is no information on the chromosomal ardA genes. It is still unclear whether they keep their antirestriction activity and why bacterial chromosomes contain these genes. In the present study, we confirmed the antirestriction function of the ardA gene from the Bifidobacterium bifidum chromosome. Transcriptome analysis in Escherichia coli showed that the range of regulated genes varies significantly for ardA from conjugative plasmid pKM101 and from the B. bifidum chromosome. Moreover, if the targets for both ardA genes match, they often show an opposite effect on regulated gene expression. The results obtained indicate two seemingly mutually exclusive conclusions. On the one hand, the pleiotropic effect of ardA genes was shown not only on restriction-modification system, but also on expression of a number of other genes. On the other hand, the range of affected genes varies significally for ardA genes from different sources, which indicates the specificity of ardA to inhibited targets. Author Summary. Conjugative plasmids, bacteriophages, as well as transposons, are capable to transfer various genes, including antibiotic resistance genes, among bacterial cells. However, many of those genes pose a threat to the bacterial cells, therefore bacterial cells have special restriction systems that limit such transfer. Antirestriction genes have previously been described as a part of conjugative plasmids, and bacteriophages and transposons. Those plasmids are able to overcome bacterial cell protection in the presence of antirestriction genes, which inhibit bacterial restriction systems. This work unveils the antirestriction mechanisms, which play an important role in the bacterial life cycle. Here, we clearly show that antirestriction genes, which are able to inhibit cell protection, exist not only in plasmids but also in the bacterial chromosomes themselves. Moreover, antirestrictases have not only an inhibitory function but also participate in the regulation of other bacterial genes. The regulatory function of plasmid antirestriction genes also helps them to overcome the bacterial cell protection against gene transfer, whereas the regulatory function of genomic antirestrictases has no such effect.
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Affiliation(s)
| | - F.S. Sharko
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - M.A. Evteeva
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | | | - E.S. Boulygina
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | - S.V. Tsygankova
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | - N.V. Slobodova
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | - K.S. Pustovoit
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center “Kurchatov Institute”, Moscow, Russia, 115454
| | - O.E. Melkina
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center “Kurchatov Institute”, Moscow, Russia, 115454
| | - A.V. Nedoluzhko
- European University at Saint Petersburg, 191187, Saint-Petersburg, Russia
| | - A.A. Korzhenkov
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | - A.A. Kudryavtseva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - A.A. Utkina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - I.V. Manukhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
- Faculty of Physics, HSE University, 109028, Moscow, Russia
- Laboratory for Microbiology, BIOTECH University, 125080, Moscow, Russia
| | - S.M. Rastorguev
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovityanova Str. 1, Moscow, 117997, Russia
| | - G.B. Zavilgelsky
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center “Kurchatov Institute”, Moscow, Russia, 115454
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17
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Zhao X, Xu D, Xia W, Hu M, Peng X, Liu X, Ran T, Wang W. Multicopy expression of sigma factor RpoH reduces prodigiosin biosynthesis in Serratia marcescens FS14. Antonie Van Leeuwenhoek 2023; 116:1197-1208. [PMID: 37728826 DOI: 10.1007/s10482-023-01875-4] [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: 05/22/2022] [Accepted: 08/22/2023] [Indexed: 09/21/2023]
Abstract
Regulation of prodigiosin biosynthesis is received wide attention due to the antimicrobial, immunosuppressive and anticancer activities of prodigiosin. Here, we constructed a transposon mutant library in S. marcescens FS14 to identify genes involved in the regulation of prodigiosin biosynthesis. 62 strains with apparently different colors were obtained. Identification of the transposon insertion sites revealed that they are classified into three groups: the coding region of cyaA and two component system eepS/R and the promoter region of rpoH. Since the effect of cyaA and eepS/R genes on prodigiosin was extensively investigated in Serratia marcescens, we chose the mutant of rpoH for further investigation. Further deletion mutation of rpoH gene showed no effect on prodigiosin production suggesting that the effect on prodigiosin production caused by transposon insertion is not due to the deletion of RpoH. We further demonstrated that multicopy expression of RpoH reduced prodigiosin biosynthesis indicating that transposon insertion caused RpoH enhanced expression. Previous results indicate that RpoS is the sigma factor for transcription of pig gene cluster in FS14, to test whether the enhanced expression of RpoH prevents prodigiosin by competing with RpoS, we found that multicopy expression of RpoS could alleviate the prodigiosin production inhibition by enhanced RpoH. We proposed that multicopy expressed RpoH competes with RpoS for core RNA polymerase (RNAP) resulting in decreased transcription of pig gene cluster and prodigiosin production reduction. We also demonstrated that RpoH is not directly involved in prodigiosin biosynthesis. Our results suggest that manipulating the transcription level of sigma factors may be applied to regulate the production of secondary metabolites.
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Affiliation(s)
- Xuezheng Zhao
- Department of Microbiology, College of Life Sciences,, Nanjing Agricultural University, Nanjing, China
| | - Dongqing Xu
- Department of Microbiology, College of Life Sciences,, Nanjing Agricultural University, Nanjing, China
| | - Wenxiao Xia
- Department of Microbiology, College of Life Sciences,, Nanjing Agricultural University, Nanjing, China
| | - Menghua Hu
- Department of Microbiology, College of Life Sciences,, Nanjing Agricultural University, Nanjing, China
| | - Xuede Peng
- Department of Microbiology, College of Life Sciences,, Nanjing Agricultural University, Nanjing, China
| | - Xia Liu
- Department of Microbiology, College of Life Sciences,, Nanjing Agricultural University, Nanjing, China
| | - Tingting Ran
- Department of Microbiology, College of Life Sciences,, Nanjing Agricultural University, Nanjing, China.
| | - Weiwu Wang
- Department of Microbiology, College of Life Sciences,, Nanjing Agricultural University, Nanjing, China.
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18
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Zhang J, Zheng M, Tang Z, Zhong S, Bu T, Li Q. The Regulatory Functions of the Multiple Alternative Sigma Factors RpoE, RpoHI, and RpoHII Depend on the Growth Phase in Rhodobacter sphaeroides. Microorganisms 2023; 11:2678. [PMID: 38004690 PMCID: PMC10673084 DOI: 10.3390/microorganisms11112678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Bacterial growth, under laboratory conditions or in a natural environment, goes through different growth phases. Some gene expressions are regulated with respect to the growth phase, which allows bacteria to adapt to changing conditions. Among them, many gene transcriptions are controlled by RpoHI or RpoHII in Rhodobacter sphaeroides. In a previous study, it was proven that the alternative sigma factors, RpoE, RpoHI, and RpoHII, are the major regulators of oxidative stress. Moreover, the growth of bacteria reached a stationary phase, and following the outgrowth, rpoE, rpoHI, and rpoHII mRNAs increased with respect to the growth phase. In this study, we demonstrated the regulatory function of alternative sigma factors in the rsp_0557 gene. The gene rsp_0557 is expressed with respect to the growth phase and belongs to the RpoHI/RpoHII regulons. Reporter assays showed that the antisigma factor ChrR turns on or over the RpoE activity to regulate rsp_0557 expression across the growth phase. In the exponential phase, RpoHII and sRNA Pos19 regulate the expression of rsp_0557 to an appropriate level under RpoE control. In the stationary phase, RpoHI and Pos19 stabilize the transcription of rsp_0557 at a high level. During outgrowth, RpoHI negatively regulates the transcription of rsp_0557. Taken together, our data indicate that these regulators are recruited by cells to adapt to or survive under different conditions throughout the growth phase. However, they still did not display all of the regulators involved in growth phase-dependent regulation. More research is still needed to learn more about the interaction between the regulators and the process of adapting to changed growth conditions and environments.
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Affiliation(s)
| | | | | | | | | | - Qingfeng Li
- College of Life Sciences, Sichuan Agricultural University, Ya’an 625014, China; (J.Z.); (M.Z.); (Z.T.); (S.Z.); (T.B.)
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19
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Adams J, Hoang J, Petroni E, Ashby E, Hardin J, Stoebel DM. The timing of transcription of RpoS-dependent genes varies across multiple stresses in Escherichia coli K-12. mSystems 2023; 8:e0066323. [PMID: 37623321 PMCID: PMC10654073 DOI: 10.1128/msystems.00663-23] [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: 06/27/2023] [Accepted: 07/14/2023] [Indexed: 08/26/2023] Open
Abstract
IMPORTANCE Bacteria adapt to changing environments by altering the transcription of their genes. Specific proteins can regulate these changes. This study explored how a single protein called RpoS controls how many genes change expression during adaptation to three stresses. We found that: (i) RpoS is responsible for activating different genes in different stresses; (ii) that during a stress, the timing of gene activation depends on the what stress it is; and (iii) that how much RpoS a gene needs in order to be activated can predict when that gene will be activated during the stress of stationary phase.
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Affiliation(s)
- Josephine Adams
- Department of Biology, Harvey Mudd College, Claremont, California, USA
| | - Johnson Hoang
- Department of Biology, Harvey Mudd College, Claremont, California, USA
| | - Emily Petroni
- Department of Biology, Harvey Mudd College, Claremont, California, USA
| | - Ethan Ashby
- Department of Mathematics and Statistics, Pomona College, Claremont, California, USA
| | - Johanna Hardin
- Department of Mathematics and Statistics, Pomona College, Claremont, California, USA
| | - Daniel M. Stoebel
- Department of Biology, Harvey Mudd College, Claremont, California, USA
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20
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Taylor JE, Palur DSK, Zhang A, Gonzales JN, Arredondo A, Coulther TA, Lechner ABJ, Rodriguez EP, Fiehn O, Didzbalis J, Siegel JB, Atsumi S. Awakening the natural capability of psicose production in Escherichia coli. NPJ Sci Food 2023; 7:54. [PMID: 37838768 PMCID: PMC10576766 DOI: 10.1038/s41538-023-00231-0] [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: 08/06/2023] [Accepted: 10/02/2023] [Indexed: 10/16/2023] Open
Abstract
Due to the rampant rise in obesity and diabetes, consumers are desperately seeking for ways to reduce their sugar intake, but to date there are no options that are both accessible and without sacrifice of palatability. One of the most promising new ingredients in the food system as a non-nutritive sugar substitute with near perfect palatability is D-psicose. D-psicose is currently produced using an in vitro enzymatic isomerization of D-fructose, resulting in low yield and purity, and therefore requiring substantial downstream processing to obtain a high purity product. This has made adoption of D-psicose into products limited and results in significantly higher per unit costs, reducing accessibility to those most in need. Here, we found that Escherichia coli natively possesses a thermodynamically favorable pathway to produce D-psicose from D-glucose through a series of phosphorylation-epimerization-dephosphorylation steps. To increase carbon flux towards D-psicose production, we introduced a series of genetic modifications to pathway enzymes, central carbon metabolism, and competing metabolic pathways. In an attempt to maximize both cellular viability and D-psicose production, we implemented methods for the dynamic regulation of key genes including clustered regularly interspaced short palindromic repeats inhibition (CRISPRi) and stationary-phase promoters. The engineered strains achieved complete consumption of D-glucose and production of D-psicose, at a titer of 15.3 g L-1, productivity of 2 g L-1 h-1, and yield of 62% under test tube conditions. These results demonstrate the viability of whole-cell catalysis as a sustainable alternative to in vitro enzymatic synthesis for the accessible production of D-psicose.
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Affiliation(s)
- Jayce E Taylor
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | | | - Angela Zhang
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | - Jake N Gonzales
- Plant Biology Graduate Group, University of California, Davis, Davis, CA, 95616, USA
| | - Augustine Arredondo
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | | | | | - Elys P Rodriguez
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
- West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, Davis, CA, 95616, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, Davis, CA, 95616, USA
| | - John Didzbalis
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
| | - Justin B Siegel
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
- Genome Center, University of California, Davis, Davis, CA, 95616, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, CA, 95616, USA
| | - Shota Atsumi
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA.
- Plant Biology Graduate Group, University of California, Davis, Davis, CA, 95616, USA.
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21
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Zoheir AE, Sobol MS, Meisch L, Ordoñez-Rueda D, Kaster AK, Niemeyer CM, Rabe KS. A three-colour stress biosensor reveals multimodal response in single cells and spatiotemporal dynamics of biofilms. NPJ Biofilms Microbiomes 2023; 9:57. [PMID: 37604827 PMCID: PMC10442448 DOI: 10.1038/s41522-023-00424-1] [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: 01/14/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
The plethora of stress factors that can damage microbial cells has evolved sophisticated stress response mechanisms. While existing bioreporters can monitor individual responses, sensors for detecting multimodal stress responses in living microorganisms are still lacking. Orthogonally detectable red, green, and blue fluorescent proteins combined in a single plasmid, dubbed RGB-S reporter, enable simultaneous, independent, and real-time analysis of the transcriptional response of Escherichia coli using three promoters which report physiological stress (PosmY for RpoS), genotoxicity (PsulA for SOS), and cytotoxicity (PgrpE for RpoH). The bioreporter is compatible with standard analysis and Fluorescent Activated Cell Sorting (FACS) combined with subsequent transcriptome analysis. Various stressors, including the biotechnologically relevant 2-propanol, activate one, two, or all three stress responses, which can significantly impact non-stress-related metabolic pathways. Implemented in microfluidic cultivation with confocal fluorescence microscopy imaging, the RGB-S reporter enabled spatiotemporal analysis of live biofilms revealing stratified subpopulations of bacteria with heterogeneous stress responses.
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Affiliation(s)
- Ahmed E Zoheir
- Institute for Biological Interfaces 1 (IBG-1), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Department of Genetics and Cytology, National Research Centre (NRC), Cairo, Egypt
| | - Morgan S Sobol
- Institute for Biological Interfaces 5 (IBG-5), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Laura Meisch
- Institute for Biological Interfaces 1 (IBG-1), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Diana Ordoñez-Rueda
- European Molecular Biology Laboratory (EMBL), Flow Cytometry Core Facility, Heidelberg, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5 (IBG-5), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Institute for Biological Interfaces 1 (IBG-1), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Institute for Biological Interfaces 1 (IBG-1), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.
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22
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Callens M, Rose CJ, Finnegan M, Gatchitch F, Simon L, Hamet J, Pradier L, Dubois MP, Bedhomme S. Hypermutator emergence in experimental Escherichia coli populations is stress-type dependent. Evol Lett 2023; 7:252-261. [PMID: 37475751 PMCID: PMC10355175 DOI: 10.1093/evlett/qrad019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/04/2023] [Accepted: 04/21/2023] [Indexed: 07/22/2023] Open
Abstract
Genotypes exhibiting an increased mutation rate, called hypermutators, can propagate in microbial populations because they can have an advantage due to the higher supply of beneficial mutations needed for adaptation. Although this is a frequently observed phenomenon in natural and laboratory populations, little is known about the influence of parameters such as the degree of maladaptation, stress intensity, and the genetic architecture for adaptation on the emergence of hypermutators. To address this knowledge gap, we measured the emergence of hypermutators over ~1,000 generations in experimental Escherichia coli populations exposed to different levels of osmotic or antibiotic stress. Our stress types were chosen based on the assumption that the genetic architecture for adaptation differs between them. Indeed, we show that the size of the genetic basis for adaptation is larger for osmotic stress compared to antibiotic stress. During our experiment, we observed an increased emergence of hypermutators in populations exposed to osmotic stress but not in those exposed to antibiotic stress, indicating that hypermutator emergence rates are stress type dependent. These results support our hypothesis that hypermutator emergence is linked to the size of the genetic basis for adaptation. In addition, we identified other parameters that covaried with stress type (stress level and IS transposition rates) that might have contributed to an increased hypermutator provision and selection. Our results provide a first comparison of hypermutator emergence rates under varying stress conditions and point towards complex interactions of multiple stress-related factors on the evolution of mutation rates.
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Affiliation(s)
- Martijn Callens
- CEFE, CNRS, University of Montpellier, EPHE, IRD, Montpellier, France
- Animal Sciences Unit—Aquatic Environment and Quality, Flanders Research Institute for Agriculture, Fisheries and Food, Oostende, Belgium
| | - Caroline J Rose
- CEFE, CNRS, University of Montpellier, EPHE, IRD, Montpellier, France
| | - Michael Finnegan
- CEFE, CNRS, University of Montpellier, EPHE, IRD, Montpellier, France
| | | | - Léna Simon
- CEFE, CNRS, University of Montpellier, EPHE, IRD, Montpellier, France
- Université Clermont Auvergne, VetAgro Sup, Lempdes, France
| | - Jeanne Hamet
- CEFE, CNRS, University of Montpellier, EPHE, IRD, Montpellier, France
| | - Léa Pradier
- CEFE, CNRS, University of Montpellier, EPHE, IRD, Montpellier, France
| | | | - Stéphanie Bedhomme
- Corresponding author: CEFE, 1919 route de Mende, 34293 Montpellier, France.
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23
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Maharjan RP, Sullivan GJ, Adams F, Shah B, Hawkey J, Delgado N, Semenec L, Dinh H, Li L, Short F, Parkhill J, Paulsen I, Barquist L, Eijkelkamp B, Cain A. DksA is a conserved master regulator of stress response in Acinetobacter baumannii. Nucleic Acids Res 2023; 51:6101-6119. [PMID: 37158230 PMCID: PMC10325922 DOI: 10.1093/nar/gkad341] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 04/11/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023] Open
Abstract
Coordination of bacterial stress response mechanisms is critical for long-term survival in harsh environments for successful host infection. The general and specific stress responses of well-studied Gram-negative pathogens like Escherichia coli are controlled by alternative sigma factors, archetypically RpoS. The deadly hospital pathogen Acinetobacter baumannii is notoriously resistant to environmental stresses, yet it lacks RpoS, and the molecular mechanisms driving this incredible stress tolerance remain poorly defined. Here, using functional genomics, we identified the transcriptional regulator DksA as a master regulator for broad stress protection and virulence in A. baumannii. Transcriptomics, phenomics and in vivo animal studies revealed that DksA controls ribosomal protein expression, metabolism, mutation rates, desiccation, antibiotic resistance, and host colonization in a niche-specific manner. Phylogenetically, DksA was highly conserved and well-distributed across Gammaproteobacteria, with 96.6% containing DksA, spanning 88 families. This study lays the groundwork for understanding DksA as a major regulator of general stress response and virulence in this important pathogen.
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Affiliation(s)
- Ram P Maharjan
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Geraldine J Sullivan
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Felise G Adams
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Bhumika S Shah
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Victoria, Australia
| | - Natasha Delgado
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Lucie Semenec
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Hue Dinh
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Liping Li
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Francesca L Short
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080Würzburg, Germany
- Faculty of Medicine, University of Würzburg, 97080Würzburg, Germany
| | - Bart A Eijkelkamp
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Amy K Cain
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW2109, Australia
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24
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Ratti A, Fassi EMA, Forlani F, Mori M, Villa F, Cappitelli F, Sgrignani J, Roda G, Cavalli A, Villa S, Grazioso G. Mechanistic Insights into the Antibiofilm Mode of Action of Ellagic Acid. Pharmaceutics 2023; 15:1757. [PMID: 37376205 DOI: 10.3390/pharmaceutics15061757] [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: 05/11/2023] [Revised: 06/09/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Bacterial biofilm is a major contributor to the persistence of infection and the limited efficacy of antibiotics. Antibiofilm molecules that interfere with the biofilm lifestyle offer a valuable tool in fighting bacterial pathogens. Ellagic acid (EA) is a natural polyphenol that has shown attractive antibiofilm properties. However, its precise antibiofilm mode of action remains unknown. Experimental evidence links the NADH:quinone oxidoreductase enzyme WrbA to biofilm formation, stress response, and pathogen virulence. Moreover, WrbA has demonstrated interactions with antibiofilm molecules, suggesting its role in redox and biofilm modulation. This work aims to provide mechanistic insights into the antibiofilm mode of action of EA utilizing computational studies, biophysical measurements, enzyme inhibition studies on WrbA, and biofilm and reactive oxygen species assays exploiting a WrbA-deprived mutant strain of Escherichia coli. Our research efforts led us to propose that the antibiofilm mode of action of EA stems from its ability to perturb the bacterial redox homeostasis driven by WrbA. These findings shed new light on the antibiofilm properties of EA and could lead to the development of more effective treatments for biofilm-related infections.
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Affiliation(s)
- Alessandro Ratti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy
| | - Enrico M A Fassi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy
| | - Fabio Forlani
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Via G. Celoria 2, 20133 Milano, Italy
| | - Matteo Mori
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy
| | - Federica Villa
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Via G. Celoria 2, 20133 Milano, Italy
| | - Francesca Cappitelli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Via G. Celoria 2, 20133 Milano, Italy
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI), Via Chiesa 5, 6500 Bellinzona, Switzerland
| | - Gabriella Roda
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy
| | - Andrea Cavalli
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI), Via Chiesa 5, 6500 Bellinzona, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Stefania Villa
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy
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25
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Jia YL, Li J, Nong FT, Yan CX, Ma W, Zhu XF, Zhang LH, Sun XM. Application of Adaptive Laboratory Evolution in Lipid and Terpenoid Production in Yeast and Microalgae. ACS Synth Biol 2023; 12:1396-1407. [PMID: 37084707 DOI: 10.1021/acssynbio.3c00179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
Abstract
Due to the complexity of metabolic and regulatory networks in microorganisms, it is difficult to obtain robust phenotypes through artificial rational design and genetic perturbation. Adaptive laboratory evolution (ALE) engineering plays an important role in the construction of stable microbial cell factories by simulating the natural evolution process and rapidly obtaining strains with stable traits through screening. This review summarizes the application of ALE technology in microbial breeding, describes the commonly used methods for ALE, and highlights the important applications of ALE technology in the production of lipids and terpenoids in yeast and microalgae. Overall, ALE technology provides a powerful tool for the construction of microbial cell factories, and it has been widely used in improving the level of target product synthesis, expanding the range of substrate utilization, and enhancing the tolerance of chassis cells. In addition, in order to improve the production of target compounds, ALE also employs environmental or nutritional stress strategies corresponding to the characteristics of different terpenoids, lipids, and strains.
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Affiliation(s)
- Yu-Lei Jia
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Jin Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Fang-Tong Nong
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Chun-Xiao Yan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Wang Ma
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Xiao-Feng Zhu
- College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Li-Hui Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
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26
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Yang H, Song H, Zhang J, Li W, Han Q, Zhang W. Proteomic analysis reveals the adaptation of Vibrio splendidus to an iron deprivation condition. Appl Microbiol Biotechnol 2023; 107:2533-2546. [PMID: 36922441 DOI: 10.1007/s00253-023-12460-0] [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: 01/13/2023] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/18/2023]
Abstract
Vibrio splendidus is a ubiquitous Gram-negative marine bacterium that causes diseases within a wide range of marine cultured animals. Since iron deprivation is the frequent situation that the bacteria usually encounter, we aimed to explore the effect of iron deprivation on the proteomic profile of V. splendidus in the present study. There were 425 differentially expressed proteins (DEPs) responded to the iron deprivation condition. When the cells were grown under iron deprivation condition, the oxidation‒reduction processes, single-organism metabolic processes, the catalytic activity, and binding activity were downregulated, while the transport process, membrane cell component, and ion binding activity were upregulated, apart from the iron uptake processes. Kyoto Encyclopedia of Genes and Genomes analysis showed that various metabolism pathways, biosynthesis pathways, energy generation pathways of tricarboxylic acid cycle, and oxidative phosphorylation were downregulated, while various degradation pathways and several special metabolism pathways were upregulated. The proteomic profiles of cells at a OD600 ≈ 0.4 grown under iron deprivation condition showed high similarity to that of the cells at a OD600 ≈ 0.8 grown without iron chelator 2,2'-bipyridine. Correspondingly, the protease activity, the activity of autoinducer 2 (AI-2), and indole content separately catalyzed by LuxS and TnaA, were measured to verify the proteomic data. Our present study gives basic information on the global protein profiles of V. splendidus grown under iron deprivation condition and suggests that the iron deprivation condition cause the cell growth enter a state of higher cell density earlier. KEY POINTS: • Adaptation of V. splendidus to iron deprivation was explored by proteomic analysis. • GO and KEGG of DEPs under different iron levels or cell densities were determined. • Iron deprivation caused the cell enter a state of higher cell density earlier.
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Affiliation(s)
- Huirong Yang
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Zhejiang Province, Ningbo, 315832, People's Republic of China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Beilun District, 169 Qixingnan RoadZhejiang Province, Ningbo, 315832, People's Republic of China
| | - Huimin Song
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Zhejiang Province, Ningbo, 315832, People's Republic of China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Beilun District, 169 Qixingnan RoadZhejiang Province, Ningbo, 315832, People's Republic of China
| | - Jinxia Zhang
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Zhejiang Province, Ningbo, 315832, People's Republic of China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Beilun District, 169 Qixingnan RoadZhejiang Province, Ningbo, 315832, People's Republic of China
| | - Weisheng Li
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Zhejiang Province, Ningbo, 315832, People's Republic of China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Beilun District, 169 Qixingnan RoadZhejiang Province, Ningbo, 315832, People's Republic of China
| | - Qingxi Han
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Zhejiang Province, Ningbo, 315832, People's Republic of China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Beilun District, 169 Qixingnan RoadZhejiang Province, Ningbo, 315832, People's Republic of China
| | - Weiwei Zhang
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Zhejiang Province, Ningbo, 315832, People's Republic of China.
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Beilun District, 169 Qixingnan RoadZhejiang Province, Ningbo, 315832, People's Republic of China.
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27
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Sazykin IS, Sazykina MA. The role of oxidative stress in genome destabilization and adaptive evolution of bacteria. Gene X 2023; 857:147170. [PMID: 36623672 DOI: 10.1016/j.gene.2023.147170] [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: 08/09/2022] [Revised: 12/14/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
The review is devoted to bacterial genome destabilization by oxidative stress. The article discusses the main groups of substances causing such stress. Stress regulons involved in destabilization of genetic material and mechanisms enhancing mutagenesis, bacterial genome rearrangements, and horizontal gene transfer, induced by oxidative damage to cell components are also considered. Based on the analysis of publications, it can be claimed that rapid development of new food substrates and ecological niches by microorganisms occurs due to acceleration of genetic changes induced by oxidative stress, mediated by several stress regulons (SOS, RpoS and RpoE) and under selective pressure. The authors conclude that non-lethal oxidative stress is probably-one of the fundamental processes that guide evolution of prokaryotes and a powerful universal trigger for adaptive destabilization of bacterial genome under changing environmental conditions.
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Affiliation(s)
- I S Sazykin
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation
| | - M A Sazykina
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation.
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28
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Jeje O, Ewunkem AJ, Jeffers-Francis LK, Graves JL. Serving Two Masters: Effect of Escherichia coli Dual Resistance on Antibiotic Susceptibility. Antibiotics (Basel) 2023; 12:antibiotics12030603. [PMID: 36978471 PMCID: PMC10044975 DOI: 10.3390/antibiotics12030603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The prevalence of multidrug-resistant bacteria and their increased pathogenicity has led to a growing interest in metallic antimicrobial materials and bacteriophages as potential alternatives to conventional antibiotics. This study examines how resistance to excess iron (III) influences the evolution of bacteriophage resistance in the bacterium Escherichia coli. We utilized experimental evolution in E. coli to test the effect of the evolution of phage T7 resistance on populations resistant to excess iron (III) and populations without excess iron resistance. Phage resistance evolved rapidly in both groups. Dual-resistant (iron (III)/phage) populations were compared to their controls (excess iron (III)-resistant, phage-resistant, no resistance to either) for their performance against each stressor, excess iron (III) and phage; and correlated resistances to excess iron (II), gallium (III), silver (I) and conventional antibiotics. Excess iron (III)/phage-resistant populations demonstrated superior 24 h growth compared to all other populations when exposed to increasing concentrations of iron (II, III), gallium (III), ampicillin, and tetracycline. No differences in 24 h growth were shown between excess iron (III)/phage-resistant and excess iron (III)-resistant populations in chloramphenicol, sulfonamide, and silver (I). The genomic analysis identified selective sweeps in the iron (III) resistant (rpoB, rpoC, yegB, yeaG), phage-resistant (clpX →/→ lon, uvaB, yeaG, fliR, gatT, ypjF, waaC, rpoC, pgi, and yjbH) and iron (III)/phage resistant populations (rcsA, hldE, rpoB, and waaC). E. coli selected for resistance to both excess iron (III) and T7 phage showed some evidence of a synergistic effect on various components of fitness. Dual selection resulted in correlated resistances to ionic metals {iron (II), gallium (III), and silver (I)} and several conventional antibiotics. There is a likelihood that this sort of combination antimicrobial treatment may result in bacterial variants with multiple resistances.
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Affiliation(s)
- Olusola Jeje
- Biology Department, North Carolina Agricultural and Technical State University, 1601 E Market Street, Greensboro, NC 27411, USA
| | - Akamu J Ewunkem
- Department of Biological Sciences, Winston Salem State University, 601 S Martin Luther King Jr Drive, Winston Salem, NC 27110, USA
| | - Liesl K Jeffers-Francis
- Biology Department, North Carolina Agricultural and Technical State University, 1601 E Market Street, Greensboro, NC 27411, USA
| | - Joseph L Graves
- Biology Department, North Carolina Agricultural and Technical State University, 1601 E Market Street, Greensboro, NC 27411, USA
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29
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Derdouri N, Ginet N, Denis Y, Ansaldi M, Battesti A. The prophage-encoded transcriptional regulator AppY has pleiotropic effects on E. coli physiology. PLoS Genet 2023; 19:e1010672. [PMID: 36930675 PMCID: PMC10057817 DOI: 10.1371/journal.pgen.1010672] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/29/2023] [Accepted: 02/18/2023] [Indexed: 03/18/2023] Open
Abstract
Bacterial genome diversity is influenced by prophages, which are viral genomes integrated into the bacterial chromosome. Most prophage genes are silent but those that are expressed can provide unexpected properties to their host. Using as a model E. coli K-12 that carries 9 defective prophages in its genome, we aimed at highlighting the impact of genes encoded by prophages on host physiology. We focused our work on AppY, a transcriptional regulator encoded on the DLP12 prophage. By performing RNA-Seq experiments, we showed that AppY production modulates the expression of more than 200 genes. Among them, 11 were identified by ChIP-Seq as direct AppY targets. AppY directly and positively regulates several genes involved in the acid stress response including the master regulator gene gadE but also nhaR and gadY, two genes important for biofilm formation. Moreover, AppY indirectly and negatively impacts bacterial motility by favoring the degradation of FlhDC, the master regulator of the flagella biosynthesis. As a consequence of these regulatory effects, AppY increases acid stress resistance and biofilm formation while also causing a strong defect in motility. Our research shed light on the importance to consider the genetic interactions occurring between prophages and bacteria to fully understand bacterial physiology. It also highlights how a prophage-encoded transcriptional regulator integrates in a complex manner into the host regulatory network and how it benefits its host, allowing it to cope with changing environmental conditions.
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Affiliation(s)
- Naoual Derdouri
- Aix Marseille Université, Centre National de la Recherche Scientifique, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Nicolas Ginet
- Aix Marseille Université, Centre National de la Recherche Scientifique, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Yann Denis
- Aix Marseille Université, Centre National de la Recherche Scientifique, Plateforme Transcriptome, Institut de Microbiologie de la Méditerranée-, Marseille, France
| | - Mireille Ansaldi
- Aix Marseille Université, Centre National de la Recherche Scientifique, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Aurélia Battesti
- Aix Marseille Université, Centre National de la Recherche Scientifique, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Marseille, France
- * E-mail:
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30
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Moreau PL. Regulation of phosphate starvation-specific responses in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36972330 DOI: 10.1099/mic.0.001312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Toxic agents added into the medium of rapidly growing Escherichia coli induce specific stress responses through the activation of specialized transcription factors. Each transcription factor and downstream regulon (e.g. SoxR) are linked to a unique stress (e.g. superoxide stress). Cells starved of phosphate induce several specific stress regulons during the transition to stationary phase when the growth rate is steadily declining. Whereas the regulatory cascades leading to the expression of specific stress regulons are well known in rapidly growing cells stressed by toxic products, they are poorly understood in cells starved of phosphate. The intent of this review is to both describe the unique mechanisms of activation of specialized transcription factors and discuss signalling cascades leading to the induction of specific stress regulons in phosphate-starved cells. Finally, I discuss unique defence mechanisms that could be induced in cells starved of ammonium and glucose.
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Affiliation(s)
- Patrice L Moreau
- Laboratoire Chimie Bactérienne, LCB-UMR 7283, Institut Microbiologie Méditerranée, CNRS/Université Aix-Marseille, Marseille, France
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31
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Systematic metabolic engineering of Escherichia coli for the enhanced production of cinnamaldehyde. Metab Eng 2023; 76:63-74. [PMID: 36639020 DOI: 10.1016/j.ymben.2023.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/16/2022] [Accepted: 01/09/2023] [Indexed: 01/12/2023]
Abstract
Cinnamaldehyde (CAD) derived from cinnamon bark has received much attention for its potential as a nematicide and food additive. Previously, we have succeeded in developing an Escherichia coli strain (YHP05) capable of synthesizing cinnamaldehyde; however, the production titer (75 mg/L) was not sufficient for commercialization. Herein, to develop an economical and sustainable production bioprocess, we further engineered the YHP05 strain for non-auxotrophic, antibiotic-free, inducer-free hyperproduction of CAD using systematic metabolic engineering. First, the conversion of trans-cinnamic acid (t-CA) to CAD was improved by the co-expression of carboxylic acid reductase and phosphopantetheinyl transferase (PPTase) genes. Second, to prevent the spontaneous conversion of CAD to cinnamyl alcohol, 10 endogenous reductase and dehydrogenase genes were deleted. Third, all expression cassettes were integrated into the chromosomal DNA using an auto-inducible system for antibiotic- and inducer-free production. Subsequently, to facilitate CAD production, available pools of cofactors (NADPH, CoA, and ATP) were increased, and acetate pathways were deleted. With the final antibiotic-, plasmid-, and inducer-free strain (H-11MPmR), fed-batch cultivations combined with in situ product recovery (ISPR) were performed, and the production titer of CAD as high as 3.8 g/L could be achieved with 49.1 mg/L/h productivity, which is the highest CAD titer ever reported.
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32
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Baek J, Yoon H. Cyclic di-GMP Modulates a Metabolic Flux for Carbon Utilization in Salmonella enterica Serovar Typhimurium. Microbiol Spectr 2023; 11:e0368522. [PMID: 36744926 PMCID: PMC10100716 DOI: 10.1128/spectrum.03685-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/16/2023] [Indexed: 02/07/2023] Open
Abstract
Salmonella enterica serovar Typhimurium is an enteric pathogen spreading via the fecal-oral route. Transmission across humans, animals, and environmental reservoirs has forced this pathogen to rapidly respond to changing environments and adapt to new environmental conditions. Cyclic di-GMP (c-di-GMP) is a second messenger that controls the transition between planktonic and sessile lifestyles, in response to environmental cues. Our study reveals the potential of c-di-GMP to alter the carbon metabolic pathways in S. Typhimurium. Cyclic di-GMP overproduction decreased the transcription of genes that encode components of three phosphoenolpyruvate (PEP):carbohydrate phosphotransferase systems (PTSs) allocated for the uptake of glucose (PTSGlc), mannose (PTSMan), and fructose (PTSFru). PTS gene downregulation by c-di-GMP was alleviated in the absence of the three regulators, SgrS, Mlc, and Cra, suggesting their intermediary roles between c-di-GMP and PTS regulation. Moreover, Cra was found to bind to the promoters of ptsG, manX, and fruB. In contrast, c-di-GMP increased the transcription of genes important for gluconeogenesis. However, this effect of c-di-GMP in gluconeogenesis disappeared in the absence of Cra, indicating that Cra is a pivotal regulator that coordinates the carbon flux between PTS-mediated sugar uptake and gluconeogenesis, in response to cellular c-di-GMP concentrations. Since gluconeogenesis supplies precursor sugars required for extracellular polysaccharide production, Salmonella may exploit c-di-GMP as a dual-purpose signal that rewires carbon flux from glycolysis to gluconeogenesis and promotes biofilm formation using the end products of gluconeogenesis. This study sheds light on a new role for c-di-GMP in modulating carbon flux, to coordinate bacterial behavior in response to hostile environments. IMPORTANCE Cyclic di-GMP is a central signaling molecule that determines the transition between motile and nonmotile lifestyles in many bacteria. It stimulates biofilm formation at high concentrations but leads to biofilm dispersal and planktonic status at low concentrations. This study provides new insights into the role of c-di-GMP in programming carbon metabolic pathways. An increase in c-di-GMP downregulated the expression of PTS genes important for sugar uptake, while simultaneously upregulating the transcription of genes important for bacterial gluconeogenesis. The directly opposing effects of c-di-GMP on sugar metabolism were mediated by Cra (catabolite repressor/activator), a dual transcriptional regulator that modulates the direction of carbon flow. Salmonella may potentially harness c-di-GMP to promote its survival and fitness in hostile environments via the coordination of carbon metabolic pathways and the induction of biofilm formation.
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Affiliation(s)
- Jiwon Baek
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Hyunjin Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, Republic of Korea
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Zhang Y, Liao X, Feng J, Liu D, Chen S, Ding T. Induction of viable but nonculturable Salmonella spp. in liquid eggs by mild heat and subsequent resuscitation. Food Microbiol 2023; 109:104127. [DOI: 10.1016/j.fm.2022.104127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 08/16/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022]
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Peptidoglycan Remodeling by an L,D-Transpeptidase, LdtD during Cold Shock in Escherichia coli. J Bacteriol 2023; 205:e0038222. [PMID: 36507682 PMCID: PMC9879098 DOI: 10.1128/jb.00382-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Peptidoglycan (PG) is a unique and essential component of the bacterial cell envelope. It is made up of several linear glycan polymers cross-linked through covalently attached stem peptides making it a fortified mesh-like sacculus around the bacterial cytosolic membrane. In most bacteria, including Escherichia coli, the stem peptide is made up of l-alanine (l-Ala1), d-glutamate (d-Glu2), meso-diaminopimelic acid (mDAP3), d-alanine (d-Ala4), and d-Ala5 with cross-links occurring either between d-ala4 and mDAP3 or between two mDAP3 residues. Of these, the cross-links of the 4-3 (d-Ala4-mDAP3) type are the most predominant and are formed by penicillin-binding D,D-transpeptidases, whereas the formation of less frequent 3-3 linkages (mDAP3-mDAP3) is catalyzed by L,D-transpeptidases. In this study, we found that the frequency of the 3-3 cross-linkages increased upon cold shock in exponentially growing E. coli and that the increase was mediated by an L,D-transpeptidase, LdtD. We found that a cold-inducible RNA helicase DeaD enhanced the cellular LdtD level by facilitating its translation resulting in an increased abundance of 3-3 cross-linkages during cold shock. However, DeaD was also required for optimal expression of LdtD during growth at ambient temperature. Overall, our study finds that E. coli undergoes PG remodeling during cold shock by altering the frequency of 3-3 cross-linkages, implying a role for these modifications in conferring fitness and survival advantage to bacteria growing in diverse environmental conditions. IMPORTANCE Most bacteria are surrounded by a protective exoskeleton called peptidoglycan (PG), an extensively cross-linked mesh-like macromolecule. In bacteria, such as Escherichia coli, the cross-links in the PG are of two types: a major fraction is of 4-3 type whereas a minor fraction is of 3-3 type. Here, we showed that E. coli exposed to cold shock had elevated levels of 3-3 cross-links due to the upregulation of an enzyme, LdtD, that catalyzed their formation. We showed that a cold-inducible RNA helicase DeaD enhanced the cellular LdtD level by facilitating its translation, resulting in increased 3-3 cross-links during cold shock. Our results suggest that PG remodeling contributes to the survival and fitness of bacteria growing in conditions of cold stress.
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Ma Z, Li S, Xu W, Chen Y, Lu Z, Fu R, He X, Zhang H. Effect of
rpoS
on the survival and gene expression of
Salmonella
Enteritidis in low water activity foods. J Food Saf 2023. [DOI: 10.1111/jfs.13039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Zhuolin Ma
- College of Biological and Pharmaceutical Science, Guangdong University of Technology Panyu District, Guangzhou China
| | - Shaoting Li
- College of Biological and Pharmaceutical Science, Guangdong University of Technology Panyu District, Guangzhou China
| | - Weiying Xu
- College of Biological and Pharmaceutical Science, Guangdong University of Technology Panyu District, Guangzhou China
| | - Yingqi Chen
- College of Biological and Pharmaceutical Science, Guangdong University of Technology Panyu District, Guangzhou China
| | - Ziying Lu
- College of Biological and Pharmaceutical Science, Guangdong University of Technology Panyu District, Guangzhou China
| | - Rong Fu
- College of Biological and Pharmaceutical Science, Guangdong University of Technology Panyu District, Guangzhou China
| | - Xinyi He
- College of Biological and Pharmaceutical Science, Guangdong University of Technology Panyu District, Guangzhou China
| | - Hongmei Zhang
- College of Biological and Pharmaceutical Science, Guangdong University of Technology Panyu District, Guangzhou China
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Abstract
The ability of bacteria to respond to changes in their environment is critical to their survival, allowing them to withstand stress, form complex communities, and induce virulence responses during host infection. A remarkable feature of many of these bacterial responses is that they are often variable across individual cells, despite occurring in an isogenic population exposed to a homogeneous environmental change, a phenomenon known as phenotypic heterogeneity. Phenotypic heterogeneity can enable bet-hedging or division of labor strategies that allow bacteria to survive fluctuating conditions. Investigating the significance of phenotypic heterogeneity in environmental transitions requires dynamic, single-cell data. Technical advances in quantitative single-cell measurements, imaging, and microfluidics have led to a surge of publications on this topic. Here, we review recent discoveries on single-cell bacterial responses to environmental transitions of various origins and complexities, from simple diauxic shifts to community behaviors in biofilm formation to virulence regulation during infection. We describe how these studies firmly establish that this form of heterogeneity is prevalent and a conserved mechanism by which bacteria cope with fluctuating conditions. We end with an outline of current challenges and future directions for the field. While it remains challenging to predict how an individual bacterium will respond to a given environmental input, we anticipate that capturing the dynamics of the process will begin to resolve this and facilitate rational perturbation of environmental responses for therapeutic and bioengineering purposes.
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Sarkar S, Kamke A, Ward K, Hartung E, Ran Q, Feehan B, Galliart M, Jumpponen A, Johnson L, Lee ST. Pseudomonas cultivated from Andropogon gerardii rhizosphere show functional potential for promoting plant host growth and drought resilience. BMC Genomics 2022; 23:784. [PMID: 36451103 PMCID: PMC9710129 DOI: 10.1186/s12864-022-09019-0] [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: 06/21/2022] [Accepted: 11/16/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Climate change will result in more frequent droughts that can impact soil-inhabiting microbiomes (rhizobiomes) in the agriculturally vital North American perennial grasslands. Rhizobiomes have contributed to enhancing drought resilience and stress resistance properties in plant hosts. In the predicted events of more future droughts, how the changing rhizobiome under environmental stress can impact the plant host resilience needs to be deciphered. There is also an urgent need to identify and recover candidate microorganisms along with their functions, involved in enhancing plant resilience, enabling the successful development of synthetic communities. RESULTS In this study, we used the combination of cultivation and high-resolution genomic sequencing of bacterial communities recovered from the rhizosphere of a tallgrass prairie foundation grass, Andropogon gerardii. We cultivated the plant host-associated microbes under artificial drought-induced conditions and identified the microbe(s) that might play a significant role in the rhizobiome of Andropogon gerardii under drought conditions. Phylogenetic analysis of the non-redundant metagenome-assembled genomes (MAGs) identified a bacterial genome of interest - MAG-Pseudomonas. Further metabolic pathway and pangenome analyses recovered genes and pathways related to stress responses including ACC deaminase; nitrogen transformation including assimilatory nitrate reductase in MAG-Pseudomonas, which might be associated with enhanced drought tolerance and growth for Andropogon gerardii. CONCLUSIONS Our data indicated that the metagenome-assembled MAG-Pseudomonas has the functional potential to contribute to the plant host's growth during stressful conditions. Our study also suggested the nitrogen transformation potential of MAG-Pseudomonas that could impact Andropogon gerardii growth in a positive way. The cultivation of MAG-Pseudomonas sets the foundation to construct a successful synthetic community for Andropogon gerardii. To conclude, stress resilience mediated through genes ACC deaminase, nitrogen transformation potential through assimilatory nitrate reductase in MAG-Pseudomonas could place this microorganism as an important candidate of the rhizobiome aiding the plant host resilience under environmental stress. This study, therefore, provided insights into the MAG-Pseudomonas and its potential to optimize plant productivity under ever-changing climatic patterns, especially in frequent drought conditions.
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Affiliation(s)
- Soumyadev Sarkar
- grid.36567.310000 0001 0737 1259Division of Biology, Kansas State University, Manhattan, KS USA
| | - Abigail Kamke
- grid.36567.310000 0001 0737 1259Division of Biology, Kansas State University, Manhattan, KS USA
| | - Kaitlyn Ward
- grid.36567.310000 0001 0737 1259Division of Biology, Kansas State University, Manhattan, KS USA
| | - Eli Hartung
- grid.36567.310000 0001 0737 1259Division of Biology, Kansas State University, Manhattan, KS USA
| | - Qinghong Ran
- grid.36567.310000 0001 0737 1259Division of Biology, Kansas State University, Manhattan, KS USA
| | - Brandi Feehan
- grid.36567.310000 0001 0737 1259Division of Biology, Kansas State University, Manhattan, KS USA
| | - Matthew Galliart
- grid.256032.00000 0001 2285 6924Department of Biological Sciences, Fort Hays State University, Hays, KS USA
| | - Ari Jumpponen
- grid.36567.310000 0001 0737 1259Division of Biology, Kansas State University, Manhattan, KS USA
| | - Loretta Johnson
- grid.36567.310000 0001 0737 1259Division of Biology, Kansas State University, Manhattan, KS USA
| | - Sonny T.M. Lee
- grid.36567.310000 0001 0737 1259Division of Biology, Kansas State University, Manhattan, KS USA
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Bian Z, Liu W, Jin J, Hao Y, Jiang L, Xie Y, Zhang H. Rcs phosphorelay affects the sensitivity of Escherichia coli to plantaricin BM-1 by regulating biofilm formation. Front Microbiol 2022; 13:1071351. [PMID: 36504793 PMCID: PMC9729257 DOI: 10.3389/fmicb.2022.1071351] [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: 10/23/2022] [Accepted: 11/10/2022] [Indexed: 11/27/2022] Open
Abstract
Introduction: Plantaricin BM-1 is a class IIa bacteriocin produced by Lactobacillus plantarum BM-1 that exerts significant antibacterial activity against many foodborne bacteria. Studies have shown that class IIa bacteriocins inhibit Gram-positive bacteria via the mannose phosphotransferase system; however, their mechanism of action against Gram-negative bacteria remains unknown. In this study, we explored the mechanism through which the Rcs phosphorelay affects the sensitivity of Escherichia coli K12 cells to plantaricin BM-1. Methods and Results: The minimum inhibitory concentrations of plantaricin BM-1 against E. coli K12, E. coli JW5917 (rcsC mutant), E. coli JW2204 (rcsD mutant), and E. coli JW2205 (rcsB mutant) were 1.25, 0.59, 1.31, and 1.22 mg/ml, respectively. Growth curves showed that E. coli JW5917 sensitivity to plantaricin BM-1 increased to the same level as that of E. coli K12 after complementation. Meanwhile, scanning electron microscopy and transmission electron microscopy revealed that, under the action of plantaricin BM-1, the appearance of E. coli JW5917 cells did not significantly differ from that of E. coli K12 cells; however, cell contents were significantly reduced and plasmolysis and shrinkage were observed at both ends. Crystal violet staining and laser scanning confocal microscopy showed that biofilm formation was significantly reduced after rcsC mutation, while proteomic analysis identified 382 upregulated and 260 downregulated proteins in E. coli JW5917. In particular, rcsC mutation was found to affect the expression of proteins related to biofilm formation, with growth curve assays showing that the deletion of these proteins increased E. coli sensitivity to plantaricin BM-1. Discussion: Consequently, we speculated that the Rcs phosphorelay may regulate the sensitivity of E. coli to plantaricin BM-1 by affecting biofilm formation. This finding of class IIa bacteriocin against Gram-negative bacteria mechanism provides new insights.
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Affiliation(s)
- Zheng Bian
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, College of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
| | - Wenbo Liu
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, College of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
| | - Junhua Jin
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, College of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
| | - Yanling Hao
- Department of Nutrition and Health, Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Government, China Agricultural University, Beijing, China
| | - Linshu Jiang
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Yuanhong Xie
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, College of Food Science and Engineering, Beijing University of Agriculture, Beijing, China,*Correspondence: Yuanhong Xie, ; Hongxing Zhang,
| | - Hongxing Zhang
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, College of Food Science and Engineering, Beijing University of Agriculture, Beijing, China,*Correspondence: Yuanhong Xie, ; Hongxing Zhang,
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Gao X, Qian Q, Zhu Y, Chen Z, Xu J, Xu W, Jiang Q, Wang J, Zhang X. Transcriptomic and phenotype analysis revealed the role of rpoS in stress resistance and virulence of pathogenic Enterobacter cloacae from Macrobrachium rosenbergii. Front Microbiol 2022; 13:1030955. [PMID: 36439857 PMCID: PMC9684176 DOI: 10.3389/fmicb.2022.1030955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2023] Open
Abstract
Enterobacter cloacae is widely distributed in the aquatic environment, and has been determined as a novel pathogen of various aquatic animals recently. Our previous studies have indicated E. cloacae caused repeated infections in Macrobrachium rosenbergii, suggesting a high survival ability of the bacteria, and rpoS gene has been known to regulate stress response and virulence of many bacteria. In this study, the E. cloacae-rpoS RNAi strain was constructed by RNAi technology, and the regulation role of rpoS in stress resistance and virulence of E. cloacae was explored by transcriptomic and phenotype analysis. The transcriptome analysis showed a total of 488 differentially expressed genes (DEGs) were identified between rpoS-RNAi and wild-type strains, including 30 up-regulated genes and 458 down-regulated genes, and these down-regulated DEGs were mainly related to environmental response, biofilm formation, bacterial type II secretory system, flagellin, fimbrillin, and chemotactic protein which associated with bacterial survival and virulence. The phenotype changes also showed the E. cloacae-rpoS RNAi strain exhibited significantly decreasing abilities of survival in environmental stresses (starvation, salinity, low pH, and oxidative stress), biofilm production, movement, adhesion to cells, pathogenicity, and colonization to M. rosenbergii. These results reveal that rpoS plays an important regulatory role in environmental stress adaptation and virulence of E. cloacae.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xiaojun Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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40
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Schwarz J, Schumacher K, Brameyer S, Jung K. Bacterial battle against acidity. FEMS Microbiol Rev 2022; 46:6652135. [PMID: 35906711 DOI: 10.1093/femsre/fuac037] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/11/2022] [Accepted: 07/27/2022] [Indexed: 01/09/2023] Open
Abstract
The Earth is home to environments characterized by low pH, including the gastrointestinal tract of vertebrates and large areas of acidic soil. Most bacteria are neutralophiles, but can survive fluctuations in pH. Herein, we review how Escherichia, Salmonella, Helicobacter, Brucella, and other acid-resistant Gram-negative bacteria adapt to acidic environments. We discuss the constitutive and inducible defense mechanisms that promote survival, including proton-consuming or ammonia-producing processes, cellular remodeling affecting membranes and chaperones, and chemotaxis. We provide insights into how Gram-negative bacteria sense environmental acidity using membrane-integrated and cytosolic pH sensors. Finally, we address in more detail the powerful proton-consuming decarboxylase systems by examining the phylogeny of their regulatory components and their collective functionality in a population.
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Affiliation(s)
- Julia Schwarz
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Sophie Brameyer
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
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Khan Z, Elahi A, Bukhari DA, Rehman A. Cadmium sources, toxicity, resistance and removal by microorganisms-A potential strategy for cadmium eradication. JOURNAL OF SAUDI CHEMICAL SOCIETY 2022. [DOI: 10.1016/j.jscs.2022.101569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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42
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Du GF, Dong Y, Fan X, Yin A, Le YJ, Yang XY. Proteomic Investigation of the Antibacterial Mechanism of Cefiderocol against Escherichia coli. Microbiol Spectr 2022; 10:e0109322. [PMID: 35980225 PMCID: PMC9603102 DOI: 10.1128/spectrum.01093-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 08/01/2022] [Indexed: 12/30/2022] Open
Abstract
This study aimed to investigate the antibacterial mechanism of cefiderocol (CFDC) using data-independent acquisition quantitative proteomics combined with cellular and molecular biological assays. Numerous differentially expressed proteins related to the production of NADH, reduced cofactor flavin adenine dinucleotide (FADH2), NADPH and reactive oxygen species (ROS), iron-sulfur cluster binding, and iron ion homeostasis were found to be upregulated by CFDC. Furthermore, parallel reaction monitoring analysis validated these results. Meanwhile, we confirmed that the levels of NADH, ROS, H2O2, and iron ions were induced by CFDC, and the sensitivity of Escherichia coli to CFDC was inhibited by the antioxidant vitamin C, N-acetyl-l-cysteine, and deferoxamine. Moreover, deferoxamine also suppressed the H2O2 stress induced by CFDC. In addition, knockout of the NADH-quinone oxidoreductase genes (nuoA, nuoC, nuoE, nuoF, nuoG, nuoJ, nuoL, nuoM) in the respiratory chain attenuated the sensitivity of E. coli to CFDC far beyond the effects of cefepime and ceftazidime; in particular, the E. coli BW25113 ΔnuoJ strain produced 60-fold increases in MIC to CFDC compared to that of the wild-type E. coli BW25113 strain. The present study revealed that CFDC exerts its antibacterial effects by inducing ROS stress by elevating the levels of NADH and iron ions in E. coli. IMPORTANCE CFDC was the first FDA-approved siderophore cephalosporin antibiotic in 2019 and is known for its Trojan horse tactics and broad antimicrobial activity against Gram-negative bacteria. However, its antibacterial mechanism is not fully understood, and whether it has an impact on in vivo iron ion homeostasis remains unknown. To comprehensively reveal the antibacterial mechanisms of CFDC, data-independent acquisition quantitative proteomics combined with cellular and molecular biological assays were performed in this study. The findings will further facilitate our understanding of the antibacterial mechanism of CFDC and may provide a theoretical foundation for controlling CFDC resistance in the future.
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Affiliation(s)
- Gao-Fei Du
- Key Laboratory of Laboratory Diagnostics, Medical Technology School, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yu Dong
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaolu Fan
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, China
| | - Ankang Yin
- Key Laboratory of Laboratory Diagnostics, Medical Technology School, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yao-Jin Le
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, Guangdong, China
| | - Xiao-Yan Yang
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, Guangdong, China
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The Role of ptsH in Stress Adaptation and Virulence in Cronobacter sakazakii BAA-894. Foods 2022; 11:foods11172680. [PMID: 36076869 PMCID: PMC9455513 DOI: 10.3390/foods11172680] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/21/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
Cronobacter sakazakii, an emerging foodborne pathogen that was isolated primarily from powdered infant formula, poses an important issue in food safety due to its high stress tolerance and pathogenicity. The Hpr (encoded by ptsH gene) has been shown to regulate carbon metabolism as well as stress response and virulence. However, the functional properties of ptsH in C. sakzakii have not been investigated. In this study, we clarified the role of ptsH in the C. sakzakii stress response and virulence, and explored its possible regulatory mechanism by RNA-seq. Compared with wild-type, the ΔptsH mutant showed a slower growth rate in the log phase but no difference in the stationary phase. Moreover, the resistance to heat stress (65 °C, 55 °C), simulated gastric fluid (pH = 2.5), biofilm formation and adhesion to HT-29 cells of ΔptsH mutant were significantly decreased, whereas the oxidative resistance (1, 5, 10 mM H2O2), osmotic resistance (10%, 15%, 20% NaCl), and superoxide dismutase activity were enhanced. Finally, RNA-seq analysis revealed the sulfur metabolism pathway is significantly upregulated in the ΔptsH mutant, but the bacterial secretion system pathway is dramatically downregulated. The qRT-PCR assay further demonstrated that the ΔptsH mutant has elevated levels of genes that are related to oxidative and osmotic stress (sodA, rpoS, cpxA/R, osmY). This study provides a great understanding of the role of ptsH in diverse stress responses and virulence in C. sakazakii, and it contributes to our understanding of the genetic determinant of stress resistance and pathogenicity of this important foodborne pathogen.
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Giannakis S, Gupta A, Pulgarin C, Imlay J. Identifying the mediators of intracellular E. coli inactivation under UVA light: The (photo) Fenton process and singlet oxygen. WATER RESEARCH 2022; 221:118740. [PMID: 35717710 PMCID: PMC11136163 DOI: 10.1016/j.watres.2022.118740] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/29/2022] [Accepted: 06/11/2022] [Indexed: 06/15/2023]
Abstract
Solar disinfection (SODIS) was probed for its underlying mechanism. When Escherichia coli was exposed to UVA irradiation, the dominant solar fraction acting in SODIS process, cells exhibited a shoulder before death ensued. This profile resembles cell killing by hydrogen peroxide (H2O2). Indeed, the use of specialized strains revealed that UVA exposure triggers intracellular H2O2 formation. The resultant H2O2 stress was especially impactful because UVA also inactivated the processes that degrade H2O2-peroxidases through the suppression of metabolism, and catalases through direct enzyme damage. Cell killing was enhanced when water was replaced with D2O, suggesting that singlet oxygen plays a role, possibly as a precursor to H2O2 and/or as the mediator of catalase damage. UVA was especially toxic to mutants lacking miniferritin (dps) or recombinational DNA repair (recA) enzymes, indicating that reactions between ferrous iron and UVA-generated H2O2 lead to lethal DNA damage. Importantly, experiments showed that the intracellular accumulation of H2O2 alone is insufficient to kill cells; therefore, UVA must do something more to enable death. A possibility is that UVA stimulates the reduction of intracellular ferric iron to its ferrous form, either by stimulating O2•- formation or by generating photoexcited electron donors. These observations and methods open the door to follow-up experiments that can probe the mechanisms of H2O2 formation, catalase inactivation, and iron reduction. Of immediate utility, the data highlight the intracellular pathways formed under UVA light during SODIS, and that the presence of micromolar iron accelerates the rate at which radiation disinfects water.
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Affiliation(s)
- Stefanos Giannakis
- Department of Microbiology, University of Illinois, 601 S. Goodwin Ave, Urbana, IL 61801, USA; School of Basic Sciences (SB), Group of Advanced Oxidation Processes (GPAO), École Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Science and Engineering (ISIC), Station 6, Lausanne CH-1015, Switzerland; E.T.S. de Ingenieros de Caminos, Canales y Puertos, Departamento de Ingeniería Civil: Hidráulica, Energía y Medio Ambiente, Unidad docente Ingeniería Sanitaria, Universidad Politécnica de Madrid (UPM), c/ Profesor Aranguren, s/n, Madrid ES-28040, Spain.
| | - Anshika Gupta
- Department of Microbiology, University of Illinois, 601 S. Goodwin Ave, Urbana, IL 61801, USA
| | - Cesar Pulgarin
- School of Basic Sciences (SB), Group of Advanced Oxidation Processes (GPAO), École Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Science and Engineering (ISIC), Station 6, Lausanne CH-1015, Switzerland; Colombian Academy of Exact, Physical and Natural Sciences, Carrera 28 A No. 39A-63, Bogotá, Colombia
| | - James Imlay
- Department of Microbiology, University of Illinois, 601 S. Goodwin Ave, Urbana, IL 61801, USA.
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Yu X, Meng C, Tan X, Su Y, Cao Z, Hwang TS, Li L. RsmA3 modulates RpoS through the RetS-Gac-Rsm signaling pathway in response to H 2 O 2 stress in the phytopathogen Pseudomonas syringae. Environ Microbiol 2022; 24:4755-4770. [PMID: 35837862 DOI: 10.1111/1462-2920.16132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 05/27/2022] [Accepted: 07/06/2022] [Indexed: 11/28/2022]
Abstract
Reactive oxygen species are a fatal challenge to the plant pathogenic bacterium Pseudomonas syringae. In this study, we reveal that the global regulatory protein RsmA3 from the RetS-Gac/Rsm signaling pathway modulates RpoS in the early-log growth phase in the P. syringae wild-type strain MB03, thereby regulating oxidative tolerance to H2 O2 and ultimately affecting pathogenicity to the host plant. Following increased H2 O2 by external addition or endogenous induction by menadione, the resistance of the mutant strain ΔretS to H2 O2 is significantly enhanced due to rapid increases in the transcription of Rsm-related non-coding small RNAs (nc sRNAs), a sigma factor RpoS, and H2 O2 -detoxifying enzymes. Moreover, the ΔretS mutant is significantly less pathogenic in cucumber leaves. Seven Rsm-related nc sRNAs (namely, rsmZ, rsmY, and rsmX1-5 ) show functional redundancy in the RetS-Gac-Rsm signaling pathway. External addition of H2 O2 stimulates increases in the transcription of both rsmY and rsmZ. Thus, we propose a regulatory model of the RetS-Gac-Rsm signaling pathway in P. syringae MB03 for the regulation of H2 O2 tolerance and phytopathogenicity in the host plant.
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Affiliation(s)
- Xun Yu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agriculture University, Wuhan, PR China
| | - Cui Meng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agriculture University, Wuhan, PR China
| | - Xiaocheng Tan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agriculture University, Wuhan, PR China
| | - Yuwei Su
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agriculture University, Wuhan, PR China
| | - Zhiping Cao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agriculture University, Wuhan, PR China
| | - Tzann-Shun Hwang
- Graduate Institute of Biotechnology, Chinese Culture University, Taipei, Taiwan
| | - Lin Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agriculture University, Wuhan, PR China
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Zeng L, Si Z, Zhao X, Feng P, Huang J, Long X, Yi Y. Metabolome analysis of the response and tolerance mechanisms of Saccharomyces cerevisiae to formic acid stress. Int J Biochem Cell Biol 2022; 148:106236. [PMID: 35688405 DOI: 10.1016/j.biocel.2022.106236] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/01/2022] [Accepted: 06/05/2022] [Indexed: 11/18/2022]
Abstract
Various inhibitors are produced during the hydrolysis of lignocellulosic biomass that can interfere with the growth of yeast cells and the production of bioethanol. Formic acid is a common weak acid inhibitor present in lignocellulosic hydrolysate that has toxic effects on yeast cells. However, the mechanism of the response of Saccharomyces cerevisiae to formic acid is not fully understood. In this study, liquid chromatography-mass spectrometry (LC-MS) was used to investigate the effects of formic acid treatment on cell metabolites of S. cerevisiae. Treatment with different concentrations of formic acid significantly inhibited the growth of yeast cells, reduced the yield of ethanol, prolonged the cell fermentation cycle, and increased the content of malondialdehyde. Principal component analysis and orthogonal partial least squares discriminant analysis showed that 55 metabolites were significantly altered in S. cerevisiae after formic acid treatment. The metabolic relevance of these compounds in the response of S. cerevisiae to formic acid stress was investigated. Formic acid can cause oxidative stress, inhibit protein synthesis, and damage DNA in S. cerevisiae, and these are possible reasons for the inhibition of S. cerevisiae cell growth. In addition, the levels of several aromatic amino acids identified in the cells of formic acid-treated yeast were increased; the biosynthesis of nucleotides was slowed, and energy consumption was reduced. These mechanisms may help to improve the tolerance of yeast cells to formic acid. The results described herein highlight our current understanding of the molecular mechanism of the response of S. cerevisiae to formic acid. The study will provide a theoretical basis for research on the tolerance mechanisms of S. cerevisiae.
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Affiliation(s)
- Lingjie Zeng
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No. 268, Donghuan Road, Liuzhou City 545006, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zaiyong Si
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No. 268, Donghuan Road, Liuzhou City 545006, China
| | - Xuemei Zhao
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No. 268, Donghuan Road, Liuzhou City 545006, China
| | - Pixue Feng
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No. 268, Donghuan Road, Liuzhou City 545006, China
| | - Jinxiang Huang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No. 268, Donghuan Road, Liuzhou City 545006, China
| | - Xiufeng Long
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No. 268, Donghuan Road, Liuzhou City 545006, China
| | - Yi Yi
- Guangxi Key Laboratory of Green Processing of Sugar Resources, College of Biological and Chemical Engineering, Guangxi University of Science and Technology, No. 268, Donghuan Road, Liuzhou City 545006, China.
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Shotgun Proteomics Revealed Preferential Degradation of Misfolded In Vivo Obligate GroE Substrates by Lon Protease in Escherichia coli. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123772. [PMID: 35744894 PMCID: PMC9228906 DOI: 10.3390/molecules27123772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 11/25/2022]
Abstract
The Escherichia coli chaperonin GroEL/ES (GroE) is one of the most extensively studied molecular chaperones. So far, ~80 proteins in E. coli are identified as GroE substrates that obligately require GroE for folding in vivo. In GroE-depleted cells, these substrates, when overexpressed, tend to form aggregates, whereas the GroE substrates expressed at low or endogenous levels are degraded, probably due to misfolded states. However, the protease(s) involved in the degradation process has not been identified. We conducted a mass-spectrometry-based proteomics approach to investigate the effects of three ATP-dependent proteases, Lon, ClpXP, and HslUV, on the E. coli proteomes under GroE-depleted conditions. A label-free quantitative proteomic method revealed that Lon protease is the dominant protease that degrades the obligate GroE substrates in the GroE-depleted cells. The deletion of DnaK/DnaJ, the other major E. coli chaperones, in the ∆lon strain did not cause major alterations in the expression or folding of the obligate GroE substrates, supporting the idea that the folding of these substrates is predominantly dependent on GroE.
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48
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Division of labor and collective functionality in Escherichia coli under acid stress. Commun Biol 2022; 5:327. [PMID: 35393532 PMCID: PMC8989999 DOI: 10.1038/s42003-022-03281-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/03/2022] [Indexed: 11/09/2022] Open
Abstract
The acid stress response is an important factor influencing the transmission of intestinal microbes such as the enterobacterium Escherichia coli. E. coli activates three inducible acid resistance systems - the glutamate decarboxylase, arginine decarboxylase, and lysine decarboxylase systems to counteract acid stress. Each system relies on the activity of a proton-consuming reaction catalyzed by a specific amino acid decarboxylase and a corresponding antiporter. Activation of these three systems is tightly regulated by a sophisticated interplay of membrane-integrated and soluble regulators. Using a fluorescent triple reporter strain, we quantitatively illuminated the cellular individuality during activation of each of the three acid resistance (AR) systems under consecutively increasing acid stress. Our studies highlight the advantages of E. coli in possessing three AR systems that enable division of labor in the population, which ensures survival over a wide range of low pH values.
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49
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Baptista ISC, Kandavalli V, Chauhan V, Bahrudeen MNM, Almeida BLB, Palma CSD, Dash S, Ribeiro AS. Sequence-dependent model of genes with dual σ factor preference. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194812. [PMID: 35338024 DOI: 10.1016/j.bbagrm.2022.194812] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 10/18/2022]
Abstract
Escherichia coli uses σ factors to quickly control large gene cohorts during stress conditions. While most of its genes respond to a single σ factor, approximately 5% of them have dual σ factor preference. The most common are those responsive to both σ70, which controls housekeeping genes, and σ38, which activates genes during stationary growth and stresses. Using RNA-seq and flow-cytometry measurements, we show that 'σ70+38 genes' are nearly as upregulated in stationary growth as 'σ38 genes'. Moreover, we find a clear quantitative relationship between their promoter sequence and their response strength to changes in σ38 levels. We then propose and validate a sequence dependent model of σ70+38 genes, with dual sensitivity to σ38 and σ70, that is applicable in the exponential and stationary growth phases, as well in the transient period in between. We further propose a general model, applicable to other stresses and σ factor combinations. Given this, promoters controlling σ70+38 genes (and variants) could become important building blocks of synthetic circuits with predictable, sequence-dependent sensitivity to transitions between the exponential and stationary growth phases.
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Affiliation(s)
- Ines S C Baptista
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Vinodh Kandavalli
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland; Department of Cell and Molecular Biology, Uppsala University, Uppsala 752 37, Sweden
| | - Vatsala Chauhan
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Mohamed N M Bahrudeen
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Bilena L B Almeida
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Cristina S D Palma
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Suchintak Dash
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Andre S Ribeiro
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland; Center of Technology and Systems (CTS-Uninova), NOVA University of Lisbon, 2829-516 Monte de Caparica, Portugal.
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50
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Zeng L, Chen H, Wang Y, Hicks D, Ke H, Pruneda-Paz J, Dehesh K. ORA47 is a transcriptional regulator of a general stress response hub. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:562-571. [PMID: 35092704 DOI: 10.1111/tpj.15688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/14/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Transcriptional regulators of the general stress response (GSR) reprogram the expression of selected genes to transduce informational signals into cellular events, ultimately manifested in a plant's ability to cope with environmental challenges. Identification of the core GSR regulatory proteins will uncover the principal modules and their mode of action in the establishment of adaptive responses. To define the GSR regulatory components, we employed a yeast-one-hybrid assay to identify the protein(s) binding to the previously established functional GSR motif, termed the rapid stress response element (RSRE). This led to the isolation of octadecanoid-responsive AP2/ERF-domain transcription factor 47 (ORA47), a methyl jasmonate inducible protein. Subsequently, ORA47 transcriptional activity was confirmed using the RSRE-driven luciferase (LUC) activity assay performed in the ORA47 loss- and gain-of-function lines introgressed into the 4xRSRE::Luc background. In addition, the prime contribution of CALMODULIN-BINDING TRANSCRIPTIONAL ACTIVATOR3 (CAMTA3) protein in the induction of RSRE was reaffirmed by genetic studies. Moreover, exogenous application of methyl jasmonate led to enhanced levels of ORA47 and CAMTA3 transcripts, as well as the induction of RSRE::LUC activity. Metabolic analyses illustrated the reciprocal functional inputs of ORA47 and CAMTA3 in increasing JA levels. Lastly, transient assays identified JASMONATE ZIM-domain1 (JAZ1) as a repressor of RSRE::LUC activity. Collectively, the present study provides fresh insight into the initial features of the mechanism that transduces informational signals into adaptive responses. This mechanism involves the functional interplay between the JA biosynthesis/signaling cascade and the transcriptional reprogramming that potentiates GSR. Furthermore, these findings offer a window into the role of intraorganellar communication in the establishment of adaptive responses.
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Affiliation(s)
- Liping Zeng
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521, USA
| | - Hao Chen
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521, USA
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yaqi Wang
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521, USA
| | - Derrick Hicks
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Haiyan Ke
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521, USA
| | - Jose Pruneda-Paz
- Section of Cell and Developmental Biology, University of California, La Jolla, CA, 92093, USA
| | - Katayoon Dehesh
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521, USA
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