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Nabi B, Kumawat M, Ahlawat N, Ahlawat S. Molecular, Structural, and Functional Diversity of Universal Stress Proteins (USPs) in Bacteria, Plants, and Their Biotechnological Applications. Protein J 2024; 43:437-446. [PMID: 38492187 DOI: 10.1007/s10930-024-10192-2] [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] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
Universal stress proteins (USPs) are widely distributed and play crucial roles in cellular responses to biotic and abiotic stresses. These roles include regulating cell growth and development, cell motility, hypoxia responses, and ion sequestration. With the increasing frequency and intensity of extreme weather events due to climate change, pathogens have developed different strategies to withstand environmental stresses, in which USPs play a significant role in their survival and virulence. In this study, we analyzed the importance of USPs in various organisms, such as archaea, plants, and fungi, as a parameter that influences their survival. We discussed the different types Of USPs and their role, aiming to carry out fundamental research in this field to identify significant constraints for better understanding of USP functions at molecular level. Additionally, we discussed concepts and research techniques that could help overcome these hurdles and facilitate new molecular approaches to better understand and target USPs as important stress adaptation and survival regulators. Although the precise characteristics of USPs are still unclear, numerous innovative uses have already been developed, tested, and implemented. Complementary approaches to basic research and applications, as well as new technology and analytical techniques, may offer insights into the cryptic but crucial activities of USPs in various living systems.
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Affiliation(s)
- Bilkees Nabi
- Department of Biochemistry & Biochemical Engineering, SHUATS, Allahabad, 211007, India
| | - Manoj Kumawat
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, 462030, India.
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462066, Madhya Pradesh, India.
| | - Neeraj Ahlawat
- Department of Animal Husbandry and Dairying, SHUATS, Allahabad, 211007, India
| | - Sushma Ahlawat
- Department of Biochemistry & Biochemical Engineering, SHUATS, Allahabad, 211007, India.
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Yan T, Li M, Wang Q, Wang M, Liu L, Ma C, Xiang X, Zhou Q, Liu Z, Gong Z. Structures, functions, and regulatory networks of universal stress proteins in clinically relevant pathogenic Bacteria. Cell Signal 2024; 116:111032. [PMID: 38185228 DOI: 10.1016/j.cellsig.2023.111032] [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: 10/06/2023] [Revised: 12/14/2023] [Accepted: 12/30/2023] [Indexed: 01/09/2024]
Abstract
Universal stress proteins are a class of proteins widely present in bacteria, archaea, plants, and invertebrates, playing essential roles in bacterial adaptation to various environmental stresses. The functions of bacterial universal stress proteins are versatile, including resistance to oxidative stress, maintenance of cell wall integrity, DNA damage repair, regulation of cell division and growth, among others. When facing stresses such as temperature changes, pH shifts, fluctuations in oxygen concentration, and exposure to toxins, these proteins can bind to specific DNA sequences and rapidly adjust bacterial metabolic pathways and gene expression patterns to adapt to the new environment. In summary, bacterial universal stress proteins play a crucial role in bacterial adaptability and survival. A comprehensive understanding of bacterial stress response mechanisms and the development of new antibacterial strategies are of great significance. This review summarizes the research progress on the structure, function, and regulatory factors of universal stress proteins in clinically relevant bacteria, aiming to facilitate deeper investigations by clinicians and researchers into universal stress proteins.
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Affiliation(s)
- Tao Yan
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Min Li
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Qiuyan Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Meng Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lijuan Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Chengcheng Ma
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiaohong Xiang
- School of Pharmacy, Chongqing Medical and Pharmaceutical College, Chongqing, China
| | - Qiang Zhou
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhou Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.
| | - Zhen Gong
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.
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Song Y, Ma B, Feng X, Guo Q, Zhou L, Zhang X, Zhang C. Genome-Wide Analysis of the Universal Stress Protein Gene Family in Blueberry and Their Transcriptional Responses to UV-B Irradiation and Abscisic Acid. Int J Mol Sci 2023; 24:16819. [PMID: 38069138 PMCID: PMC10706445 DOI: 10.3390/ijms242316819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/16/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Universal stress proteins (USPs) play essential roles in plant development, hormonal regulation, and abiotic stress responses. However, the characteristics and functional divergence of USP family members have not been studied in blueberry (Vaccinium corymbosum). In this study, we identified 72 VcUSP genes from the Genome Database for Vaccinium. These VcUSPs could be divided into five groups based on their phylogenetic relationships. VcUSPs from groups Ⅰ, Ⅳ, and Ⅴ each possess one UspA domain; group Ⅰ proteins also contain an ATP-binding site that is not present in group Ⅳ and Ⅴ proteins. Groups Ⅱ and Ⅲ include more complex proteins possessing one to three UspA domains and UspE or UspF domains. Prediction of cis-regulatory elements in the upstream sequences of VcUSP genes indicated that their protein products are likely involved in phytohormone signaling pathways and abiotic stress responses. Analysis of RNA deep sequencing data showed that 21 and 7 VcUSP genes were differentially expressed in response to UV-B radiation and exogenous abscisic acid (ABA) treatments, respectively. VcUSP41 and VcUSP68 expressions responded to both treatments, and their encoded proteins may integrate the UV-B and ABA signaling pathways. Weighted gene co-expression network analysis revealed that VcUSP22, VcUSP26, VcUSP67, VcUSP68, and VcUSP41 were co-expressed with many transcription factor genes, most of which encode members of the MYB, WRKY, zinc finger, bHLH, and AP2 families, and may be involved in plant hormone signal transduction, circadian rhythms, the MAPK signaling pathway, and UV-B-induced flavonoid biosynthesis under UV-B and exogenous ABA treatments. Our study provides a useful reference for the further functional analysis of VcUSP genes and blueberry molecular breeding.
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Affiliation(s)
| | | | | | | | | | | | - Chunyu Zhang
- College of Plant Science, Jilin University, Changchun 130062, China
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Masamba P, Kappo AP. Parasite Survival and Disease Persistence in Cystic Fibrosis, Schistosomiasis and Pathogenic Bacterial Diseases: A Role for Universal Stress Proteins? Int J Mol Sci 2021; 22:10878. [PMID: 34639223 PMCID: PMC8509486 DOI: 10.3390/ijms221910878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/15/2021] [Accepted: 09/28/2021] [Indexed: 12/16/2022] Open
Abstract
Universal stress proteins (USPs) were originally discovered in Escherichia coli over two decades ago and since then their presence has been detected in various organisms that include plants, archaea, metazoans, and bacteria. As their name suggests, they function in a series of various cellular responses in both abiotic and biotic stressful conditions such as oxidative stress, exposure to DNA damaging agents, nutrient starvation, high temperature and acidic stress, among others. Although a highly conserved group of proteins, the molecular and biochemical aspects of their functions are largely evasive. This is concerning, as it was observed that USPs act as essential contributors to the survival/persistence of various infectious pathogens. Their ubiquitous nature in various organisms, as well as their augmentation during conditions of stress, is a clear indication of their direct or indirect importance in providing resilience against such conditions. This paper seeks to clarify what has already been reported in the literature on the proposed mechanism of action of USPs in pathogenic organisms.
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Affiliation(s)
- Priscilla Masamba
- Molecular Biophysics and Structural Biology (MBSB) Group, Department of Biochemistry, Kingsway Campus, University of Johannesburg, Auckland Park 2006, South Africa;
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Takenaka S, Kawashima T, Arita M. A sugar utilization phenotype contributes to the formation of genetic exchange communities in lactic acid bacteria. FEMS Microbiol Lett 2021; 368:6360976. [PMID: 34468734 PMCID: PMC8440127 DOI: 10.1093/femsle/fnab117] [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: 07/21/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
In prokaryotes, a major contributor to genomic evolution is the exchange of genes via horizontal gene transfer (HGT). Areas with a high density of HGT networks are defined as genetic exchange communities (GECs). Although some phenotypes associated with specific ecological niches are linked to GECs, little is known about the phenotypic influences on HGT in bacterial groups within a taxonomic family. Thanks to the published genome sequences and phenotype data of lactic acid bacteria (LAB), it is now possible to obtain more detailed information about the phenotypes that affect GECs. Here, we have investigated the relationship between HGT and internal and external environmental factors for 178 strains from 24 genera in the Lactobacillaceae family. We found a significant correlation between strains with high utilization of sugars and HGT bias. The result suggests that the phenotype of the utilization of a variety of sugars is key to the construction of GECs in this family. This feature is consistent with the fact that the Lactobacillaceae family contributes to the production of a wide variety of fermented foods by sharing niches such as those in vegetables, dairy products and brewing-related environments. This result provides the first evidence that phenotypes associated with ecological niches contribute to form GECs in the LAB family.
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Affiliation(s)
- Shinkuro Takenaka
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Takeshi Kawashima
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan.,National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Masanori Arita
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan.,National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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Burin R, Shah DH. Global transcriptional profiling of tyramine and d-glucuronic acid catabolism in Salmonella. Int J Med Microbiol 2020; 310:151452. [PMID: 33091748 DOI: 10.1016/j.ijmm.2020.151452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/13/2020] [Accepted: 09/25/2020] [Indexed: 11/17/2022] Open
Abstract
Salmonella has evolved various metabolic pathways to scavenge energy from the metabolic byproducts of the host gut microbiota, however, the precise metabolic byproducts and pathways utilized by Salmonella remain elusive. Previously we reported that Salmonella can proliferate by deriving energy from two metabolites that naturally occur in the host as gut microbial metabolic byproducts, namely, tyramine (TYR, an aromatic amine) and d-glucuronic acid (DGA, a hexuronic acid). Salmonella Pathogenicity Island 13 (SPI-13) plays a critical role in the ability of Salmonella to derive energy from TYR and DGA, however the catabolic pathways of these two micronutrients in Salmonella are poorly defined. The objective of this study was to identify the specific genetic components and construct the regulatory circuits for the TYR and DGA catabolic pathways in Salmonella. To accomplish this, we employed TYR and DGA-induced global transcriptional profiling and gene functional network analysis approaches. We report that TYR induced differential expression of 319 genes (172 up-regulated and 157 down-regulated) when Salmonella was grown in the presence of TYR as a sole energy source. These included the genes originally predicted to be involved in the classical TYR catabolic pathway. TYR also induced expression of majority of genes involved in the acetaldehyde degradation pathway and aided identification of a few new genes that are likely involved in alternative pathway for TYR catabolism. In contrast, DGA induced differential expression of 71 genes (58 up-regulated and 13 down-regulated) when Salmonella was grown in the presence of DGA as a sole energy source. These included the genes originally predicted to be involved in the classical pathway and a few new genes likely involved in the alternative pathway for DGA catabolism. Interestingly, DGA also induced expression of SPI-2 T3SS, suggesting that DGA may also influence nutritional virulence of Salmonella. In summary, this is the first report describing the global transcriptional profiling of TYR and DGA catabolic pathways of Salmonella. This study will contribute to the better understanding of the role of TYR and DGA in metabolic adaptation and virulence of Salmonella.
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Affiliation(s)
- Raquel Burin
- Department of Veterinary Microbiology and Pathology, United States
| | - Devendra H Shah
- Department of Veterinary Microbiology and Pathology, United States; Paul Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, 99164-7040, United States.
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Memar MY, Yekani M, Celenza G, Poortahmasebi V, Naghili B, Bellio P, Baghi HB. The central role of the SOS DNA repair system in antibiotics resistance: A new target for a new infectious treatment strategy. Life Sci 2020; 262:118562. [PMID: 33038378 DOI: 10.1016/j.lfs.2020.118562] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/15/2020] [Accepted: 10/01/2020] [Indexed: 01/19/2023]
Abstract
Bacteria have a considerable ability and potential to acquire resistance against antimicrobial agents by acting diverse mechanisms such as target modification or overexpression, multidrug transporter systems, and acquisition of drug hydrolyzing enzymes. Studying the mechanisms of bacterial cell physiology is mandatory for the development of novel strategies to control the antimicrobial resistance phenomenon, as well as for the control of infections in clinics. The SOS response is a cellular DNA repair mechanism that has an essential role in the bacterial biologic process involved in resistance to antibiotics. The activation of the SOS network increases the resistance and tolerance of bacteria to stress and, as a consequence, to antimicrobial agents. Therefore, SOS can be an applicable target for the discovery of new antimicrobial drugs. In the present review, we focus on the central role of SOS response in bacterial resistance mechanisms and its potential as a new target for control of resistant pathogens.
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Affiliation(s)
- Mohammad Yousef Memar
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Students' Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mina Yekani
- Department of Microbiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy.
| | - Vahdat Poortahmasebi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Behrooz Naghili
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Sen S, Rai R, Chatterjee A, Rai S, Yadav S, Agrawal C, Rai LC. Molecular characterization of two novel proteins All1122 and Alr0750 of Anabaena PCC 7120 conferring tolerance to multiple abiotic stresses in Escherichia coli. Gene 2019; 685:230-241. [PMID: 30448320 DOI: 10.1016/j.gene.2018.11.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 09/28/2018] [Accepted: 11/08/2018] [Indexed: 11/19/2022]
Abstract
In- silico and functional genomics approaches have been used to determine cellular functions of two hypothetical proteins All1122 and Alr0750 of Anabaena sp. PCC 7120. Motif analysis and multiple sequence alignment predicted them as typical α/β ATP binding universal stress family protein-A (UspA) with G-(2×)-G-(9×)-G(S/T) as conserved motif. qRT-PCR data under UV-B, NaCl, heat, As, CdCl2, mannitol and methyl viologen registered approximately 1.4 to 4.3 fold induction of all1122 and alr0750 thus confirming their multiple abiotic stress tolerance potential. The recombinant E. coli (BL21) cells harboring All1122 and Alr0750 showed 12-41% and 23-41% better growth respectively over wild type control under said abiotic stresses thus revalidating their stress coping ability. Functional complementation on heterologous expression in UspA mutant E. coli strain LN29MG1655 (ΔuspA::Kan) attested their UspA family membership. This study tempted us to suggest that recombinant Anabaena PCC 7120 over expressing all1122 and alr0750 might contribute to the nitrogen economy in paddy fields experiencing array of abiotic stresses including drought and nutrient limitation.
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Affiliation(s)
- Sonia Sen
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Ruchi Rai
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Antra Chatterjee
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Shweta Rai
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Shivam Yadav
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Chhavi Agrawal
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - L C Rai
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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Wang Y, Jia B, Xu X, Zhang L, Wei C, Ou H, Cui Y, Shi C, Shi X. Comparative Genomic Analysis and Characterization of Two Salmonella enterica Serovar Enteritidis Isolates From Poultry With Notably Different Survival Abilities in Egg Whites. Front Microbiol 2018; 9:2111. [PMID: 30245675 PMCID: PMC6137255 DOI: 10.3389/fmicb.2018.02111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/20/2018] [Indexed: 12/13/2022] Open
Abstract
Salmonellaenterica serovar Enteritidis (Salmonella Enteritidis) is a globally important foodborne pathogen, and the contaminated chicken eggs are the major source of salmonellosis in humans. Salmonella Enteritidis strains are differentially susceptible to the hostile environment of egg whites. Strains with superior survival ability in egg whites are more likely to contaminate eggs and consequently infect humans. However, the genetic basis for this phenotype is unclear. We characterized two Salmonella Enteritidis strains isolated from chicken meat that had similar genetic backgrounds but large differences in survival ability in egg whites. Although genome comparisons indicated that the gene content and genomic synteny were highly conserved, variations including six insertions or deletions (INDELs) and 70 single nucleotide polymorphisms (SNPs) were observed between the two genomes. Of these, 38 variations including four INDELs and 34 non-synonymous SNPs (nsSNP) were annotated to result in amino acid substitutions or INDELs in coding proteins. These variations were located in 38 genes involved in lysozyme inhibition, vitamin biosynthesis, cell division and DNA damage response, osmotic and oxidative protection, iron-related functions, cell envelope maintenance, amino acid and carbohydrate metabolism, antimicrobial resistance, and type III secretion system. We carried out allelic replacements for two nsSNPs in bioC (biotin synthesis) and pliC (lysozyme inhibition), and two INDELs in ftsK and yqiJ (DNA damage response) by homologous recombination, and these replacements did not alter the bacterial survival ability in egg whites. However, the bacterial survival ability in egg whites was reduced when deletion mutation of the genes bioC and pliC occurred. This study provides initial correlations between observed genotypes and phenotypes and serves as an important caveat for further functional studies.
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Affiliation(s)
- Yanyan Wang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Ben Jia
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuebin Xu
- Department of Microbiology, Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Lida Zhang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Chaochun Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hongyu Ou
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Cui
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Chunlei Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xianming Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
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Krin E, Pierlé SA, Sismeiro O, Jagla B, Dillies MA, Varet H, Irazoki O, Campoy S, Rouy Z, Cruveiller S, Médigue C, Coppée JY, Mazel D. Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation. BMC Genomics 2018; 19:373. [PMID: 29783948 PMCID: PMC5963079 DOI: 10.1186/s12864-018-4716-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/23/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicting LexA binding box consensus and in vitro validation. Here, we perform whole transcriptome sequencing from Vibrio cholerae treated with mitomycin C as an SOS inducer to characterize the SOS regulon and other pathways affected by this treatment. RESULTS Comprehensive transcriptional profiling allowed us to define the full landscape of promoters and transcripts active in V. cholerae. We performed extensive transcription start site (TSS) mapping as well as detection/quantification of the coding and non-coding RNA (ncRNA) repertoire in strain N16961. To improve TSS detection, we developed a new technique to treat RNA extracted from cells grown in various conditions. This allowed for identification of 3078 TSSs with an average 5'UTR of 116 nucleotides, and peak distribution between 16 and 64 nucleotides; as well as 629 ncRNAs. Mitomycin C treatment induced transcription of 737 genes and 28 ncRNAs at least 2 fold, while it repressed 231 genes and 17 ncRNAs. Data analysis revealed that in addition to the core genes known to integrate the SOS regulon, several metabolic pathways were induced. This study allowed for expansion of the Vibrio SOS regulon, as twelve genes (ubiEJB, tatABC, smpA, cep, VC0091, VC1190, VC1369-1370) were found to be co-induced with their adjacent canonical SOS regulon gene(s), through transcriptional read-through. Characterization of UV and mitomycin C susceptibility for mutants of these newly identified SOS regulon genes and other highly induced genes and ncRNAs confirmed their role in DNA damage rescue and protection. CONCLUSIONS We show that genotoxic stress induces a pervasive transcriptional response, affecting almost 20% of the V. cholerae genes. We also demonstrate that the SOS regulon is larger than previously known, and its syntenic organization is conserved among Vibrio species. Furthermore, this specific co-localization is found in other γ-proteobacteria for genes recN-smpA and rmuC-tatABC, suggesting SOS regulon conservation in this phylum. Finally, we comment on the limitations of widespread NGS approaches for identification of all RNA species in bacteria.
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Affiliation(s)
- Evelyne Krin
- 0000 0001 2353 6535grid.428999.7Département Génomes et Génétique, Institut Pasteur, Unité de Plasticité du Génome Bactérien, Paris, France
- 0000 0001 2112 9282grid.4444.0CNRS, UMR 3525, Paris, France
| | - Sebastian Aguilar Pierlé
- 0000 0001 2353 6535grid.428999.7Département Génomes et Génétique, Institut Pasteur, Unité de Plasticité du Génome Bactérien, Paris, France
- 0000 0001 2112 9282grid.4444.0CNRS, UMR 3525, Paris, France
| | - Odile Sismeiro
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
| | - Bernd Jagla
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
- Present adress: Institut Pasteur, Biomarker Discovery Platform, UtechS CB and Hub Bioinformatique et Biostatistique – C3BI, USR 3756 IP CNRS, Paris, France
| | - Marie-Agnès Dillies
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
- Present adress: Institut Pasteur, Hub Bioinformatique et Biostatistique – C3BI, USR 3756 IP CNRS, Paris, France
| | - Hugo Varet
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
| | - Oihane Irazoki
- grid.7080.fDepartament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, Spain
| | - Susana Campoy
- grid.7080.fDepartament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, Spain
| | - Zoé Rouy
- 0000 0001 2180 5818grid.8390.2UMR 8030, CNRS, CEA, Institut de Biologie François Jacob - Genoscope, Laboratoire d’Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Evry-Val-d’Essonne, Evry, France
| | - Stéphane Cruveiller
- 0000 0001 2180 5818grid.8390.2UMR 8030, CNRS, CEA, Institut de Biologie François Jacob - Genoscope, Laboratoire d’Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Evry-Val-d’Essonne, Evry, France
| | - Claudine Médigue
- 0000 0001 2180 5818grid.8390.2UMR 8030, CNRS, CEA, Institut de Biologie François Jacob - Genoscope, Laboratoire d’Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Evry-Val-d’Essonne, Evry, France
| | - Jean-Yves Coppée
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
| | - Didier Mazel
- 0000 0001 2353 6535grid.428999.7Département Génomes et Génétique, Institut Pasteur, Unité de Plasticité du Génome Bactérien, Paris, France
- 0000 0001 2112 9282grid.4444.0CNRS, UMR 3525, Paris, France
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Melencion SMB, Chi YH, Pham TT, Paeng SK, Wi SD, Lee C, Ryu SW, Koo SS, Lee SY. RNA Chaperone Function of a Universal Stress Protein in Arabidopsis Confers Enhanced Cold Stress Tolerance in Plants. Int J Mol Sci 2017; 18:ijms18122546. [PMID: 29186920 PMCID: PMC5751149 DOI: 10.3390/ijms18122546] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/23/2017] [Accepted: 11/25/2017] [Indexed: 02/07/2023] Open
Abstract
The physiological function of Arabidopsis thaliana universal stress protein (AtUSP) in plant has remained unclear. Thus, we report here the functional role of the Arabidopsis universal stress protein, AtUSP (At3g53990). To determine how AtUSP affects physiological responses towards cold stress, AtUSP overexpression (AtUSP OE) and T-DNA insertion knock-out (atusp, SALK_146059) mutant lines were used. The results indicated that AtUSP OE enhanced plant tolerance to cold stress, whereas atusp did not. AtUSP is localized in the nucleus and cytoplasm, and cold stress significantly affects RNA metabolism such as by misfolding and secondary structure changes of RNA. Therefore, we investigated the relationship of AtUSP with RNA metabolism. We found that AtUSP can bind nucleic acids, including single- and double-stranded DNA and luciferase mRNA. AtUSP also displayed strong nucleic acid-melting activity. We expressed AtUSP in RL211 Escherichia coli, which contains a hairpin-loop RNA structure upstream of chloramphenicol acetyltransferase (CAT), and observed that AtUSP exhibited anti-termination activity that enabled CAT gene expression. AtUSP expression in the cold-sensitive Escherichia coli (E. coli) mutant BX04 complemented the cold sensitivity of the mutant cells. As these properties are typical characteristics of RNA chaperones, we conclude that AtUSP functions as a RNA chaperone under cold-shock conditions. Thus, the enhanced tolerance of AtUSP OE lines to cold stress is mediated by the RNA chaperone function of AtUSP.
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Affiliation(s)
- Sarah Mae Boyles Melencion
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Yong Hun Chi
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Thuy Thi Pham
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Seol Ki Paeng
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Seong Dong Wi
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Changyu Lee
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Seoung Woo Ryu
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Sung Sun Koo
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21+ Program), PMBBRC, Gyeongsang National University, Jinju 52828, Korea.
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12
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Xiong L, Liao D, Lu X, Yan H, Shi L, Mo Z. Proteomic analysis reveals that a global response is induced by subinhibitory concentrations of ampicillin. Bioengineered 2017; 8:732-741. [PMID: 28881168 DOI: 10.1080/21655979.2017.1373532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In this study, a recipient-donor co-culture system was used to research the effect of subinhibitory concentrations of antibiotics on horizontal transmission in bacteria and the influence of antibiotics on protein expression. We employed two-dimensional gel electrophoresis combined with mass spectrometry to compare the protein expression profiles in systems with or without 0.5 × the minimum inhibitory concentration of ampicillin. RT-PCR was used to assess the transcriptional levels of the differentially expressed genes. Fifty-seven different proteins were induced or suppressed. The upregulated proteins were involved in transcription and translation, cell wall synthesis, bacterial SOS response, and detoxifying functions, and the downregulated proteins were involved in metabolism. These results indicated that a global response was induced in the recipient-donor co-culture system by the subinhibitory concentration of ampicillin. Further analysis revealed that a global regulatory network based on key pathways was induced in the system in response to the antibiotic pressure. These findings provide a new, more comprehensive view for research on antibiotic-resistance mechanisms in recipient-donor co-culture.
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Affiliation(s)
- Lina Xiong
- a The First Affiliated Hospital of Guangzhou Medical University , Guangzhou Institute of Respiratory Disease, State Key Laboratory of Respiratory Disease , Guangzhou , China.,b Jinan University , Guangzhou , China.,c School of Food Sciences and Technology , South China University of Technology , Guangzhou , China
| | - Dongjiang Liao
- a The First Affiliated Hospital of Guangzhou Medical University , Guangzhou Institute of Respiratory Disease, State Key Laboratory of Respiratory Disease , Guangzhou , China
| | - Xinpeng Lu
- a The First Affiliated Hospital of Guangzhou Medical University , Guangzhou Institute of Respiratory Disease, State Key Laboratory of Respiratory Disease , Guangzhou , China
| | - He Yan
- c School of Food Sciences and Technology , South China University of Technology , Guangzhou , China
| | - Lei Shi
- b Jinan University , Guangzhou , China.,c School of Food Sciences and Technology , South China University of Technology , Guangzhou , China
| | - Ziyao Mo
- a The First Affiliated Hospital of Guangzhou Medical University , Guangzhou Institute of Respiratory Disease, State Key Laboratory of Respiratory Disease , Guangzhou , China
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13
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Budeyri Gokgoz N, Avci FG, Yoneten KK, Alaybeyoglu B, Ozkirimli E, Sayar NA, Kazan D, Sariyar Akbulut B. Response ofEscherichia colito Prolonged Berberine Exposure. Microb Drug Resist 2017; 23:531-544. [DOI: 10.1089/mdr.2016.0063] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Fatma Gizem Avci
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | | | - Begum Alaybeyoglu
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
| | - Elif Ozkirimli
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
| | | | - Dilek Kazan
- Department of Bioengineering, Marmara University, Istanbul, Turkey
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14
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Jia Q, Hu X, Shi D, Zhang Y, Sun M, Wang J, Mi K, Zhu G. Universal stress protein Rv2624c alters abundance of arginine and enhances intracellular survival by ATP binding in mycobacteria. Sci Rep 2016; 6:35462. [PMID: 27762279 PMCID: PMC5071874 DOI: 10.1038/srep35462] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/30/2016] [Indexed: 01/05/2023] Open
Abstract
The universal stress protein family is a family of stress-induced proteins. Universal stress proteins affect latency and antibiotic resistance in mycobacteria. Here, we showed that Mycobacterium smegmatis overexpressing M. tuberculosis universal stress protein Rv2624c exhibits increased survival in human monocyte THP-1 cells. Transcriptome analysis suggested that Rv2624c affects histidine metabolism, and arginine and proline metabolism. LC-MS/MS analysis showed that Rv2624c affects the abundance of arginine, a modulator of both mycobacteria and infected THP-1 cells. Biochemical analysis showed that Rv2624c is a nucleotide-binding universal stress protein, and an Rv2624c mutant incapable of binding ATP abrogated the growth advantage in THP-1 cells. Rv2624c may therefore modulate metabolic pathways in an ATP-dependent manner, changing the abundance of arginine and thus increasing survival in THP-1 cells.
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Affiliation(s)
- Qiong Jia
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xinling Hu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing 100101, China.,The Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Dawei Shi
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 100050, China
| | - Yan Zhang
- Zhangjiakou Center for Adverse Drug Reaction and Drug Abuse, Hebei 075000, China
| | - Meihao Sun
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang 321004, China
| | - Jianwei Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Kaixia Mi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing 100101, China
| | - Guofeng Zhu
- Shanghai Municipal Center for Disease Control &Prevention, Shanghai 200336, China
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15
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Beyene GT, Balasingham SV, Frye SA, Namouchi A, Homberset H, Kalayou S, Riaz T, Tønjum T. Characterization of the Neisseria meningitidis Helicase RecG. PLoS One 2016; 11:e0164588. [PMID: 27736945 PMCID: PMC5063381 DOI: 10.1371/journal.pone.0164588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 09/27/2016] [Indexed: 11/19/2022] Open
Abstract
Neisseria meningitidis (Nm) is a Gram-negative oral commensal that opportunistically can cause septicaemia and/or meningitis. Here, we overexpressed, purified and characterized the Nm DNA repair/recombination helicase RecG (RecGNm) and examined its role during genotoxic stress. RecGNm possessed ATP-dependent DNA binding and unwinding activities in vitro on a variety of DNA model substrates including a Holliday junction (HJ). Database searching of the Nm genomes identified 49 single nucleotide polymorphisms (SNPs) in the recGNm including 37 non-synonymous SNPs (nsSNPs), and 7 of the nsSNPs were located in the codons for conserved active site residues of RecGNm. A transient reduction in transformation of DNA was observed in the Nm ΔrecG strain as compared to the wildtype. The gene encoding recGNm also contained an unusually high number of the DNA uptake sequence (DUS) that facilitate transformation in neisserial species. The differentially abundant protein profiles of the Nm wildtype and ΔrecG strains suggest that expression of RecGNm might be linked to expression of other proteins involved in DNA repair, recombination and replication, pilus biogenesis, glycan biosynthesis and ribosomal activity. This might explain the growth defect that was observed in the Nm ΔrecG null mutant.
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Affiliation(s)
| | | | - Stephan A. Frye
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | - Amine Namouchi
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | | | - Shewit Kalayou
- Department of Microbiology, University of Oslo, Oslo, Norway
| | - Tahira Riaz
- Department of Microbiology, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
- * E-mail:
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16
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Integrated transcriptomic and proteomic analysis of the bile stress response in probiotic Lactobacillus salivarius LI01. J Proteomics 2016; 150:216-229. [PMID: 27585996 DOI: 10.1016/j.jprot.2016.08.021] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/24/2016] [Accepted: 08/25/2016] [Indexed: 12/11/2022]
Abstract
Lactobacillus salivarius LI01, isolated from healthy humans, has demonstrated probiotic properties in the prevention and treatment of liver failure. Tolerance to bile stress is crucial to allow lactobacilli to survive in the gastrointestinal tract and exert their benefits. In this work, we used a Digital Gene Expression transcriptomic and iTRAQ LC-MS/MS proteomic approach to examine the characteristics of LI01 in response to bile stress. Using culture medium with or without 0.15% ox bile, 591 differentially transcribed genes and 347 differentially expressed proteins were detected in LI01. Overall, we found the bile resistance of LI01 to be based on a highly remodeled cell envelope and a reinforced bile efflux system rather than on the activity of bile salt hydrolases. Additionally, some differentially expressed genes related to regulatory systems, the general stress response and central metabolism processes, also play roles in stress sensing, bile-induced damage prevention and energy efficiency. Moreover, bile salts appear to enhance proteolysis and amino acid uptake (especially aromatic amino acids) by LI01, which may support the liver protection properties of this strain. Altogether, this study establishes a model of global response mechanism to bile stress in L. salivarius LI01. BIOLOGICAL SIGNIFICANCE L. salivarius strain LI01 exhibits not only antibacterial and antifungal properties but also exerts a good health-promoting effect in acute liver failure. As a potential probiotic strain, the bile-tolerance trait of strain LI01 is important, though this has not yet been explored. In this study, an analysis based on DGE and iTRAQ was performed to investigate the gene expression in strain LI01 under bile stress at the mRNA and protein levels, respectively. To our knowledge, this work also represents the first combined transcriptomic and proteomic analysis of the bile stress response mechanism in L. salivarius.
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17
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D'Agostino PM, Song X, Neilan BA, Moffitt MC. Proteogenomics of a saxitoxin-producing and non-toxic strain ofAnabaena circinalis(cyanobacteria) in response to extracellular NaCl and phosphate depletion. Environ Microbiol 2016; 18:461-76. [DOI: 10.1111/1462-2920.13131] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 11/10/2015] [Accepted: 11/10/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Paul M. D'Agostino
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; NSW 2052 Australia
- School of Science and Health; Western Sydney University; Campbelltown NSW 2560 Australia
| | - Xiaomin Song
- Australian Proteomics Analysis Facility; Macquarie University; Macquarie Park NSW 2109 Australia
| | - Brett A. Neilan
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; NSW 2052 Australia
| | - Michelle C. Moffitt
- School of Science and Health; Western Sydney University; Campbelltown NSW 2560 Australia
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18
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Moscoso JA, Schramke H, Zhang Y, Tosi T, Dehbi A, Jung K, Gründling A. Binding of Cyclic Di-AMP to the Staphylococcus aureus Sensor Kinase KdpD Occurs via the Universal Stress Protein Domain and Downregulates the Expression of the Kdp Potassium Transporter. J Bacteriol 2016; 198:98-110. [PMID: 26195599 PMCID: PMC4686210 DOI: 10.1128/jb.00480-15] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 07/14/2015] [Indexed: 02/06/2023] Open
Abstract
UNLABELLED Nucleotide signaling molecules are important intracellular messengers that regulate a wide range of biological functions. The human pathogen Staphylococcus aureus produces the signaling nucleotide cyclic di-AMP (c-di-AMP). This molecule is common among Gram-positive bacteria and in many organisms is essential for survival under standard laboratory growth conditions. In this study, we investigated the interaction of c-di-AMP with the S. aureus KdpD protein. The sensor kinase KdpD forms a two-component signaling system with the response regulator KdpE and regulates the expression of the kdpDE genes and the kdpFABC operon coding for the Kdp potassium transporter components. Here we show that the S. aureus KdpD protein binds c-di-AMP specifically and with an affinity in the micromolar range through its universal stress protein (USP) domain. This domain is located within the N-terminal cytoplasmic region of KdpD, and amino acids of a conserved SXS-X20-FTAXY motif are important for this binding. We further show that KdpD2, a second KdpD protein found in some S. aureus strains, also binds c-di-AMP, and our bioinformatics analysis indicates that a subclass of KdpD proteins in c-di-AMP-producing bacteria has evolved to bind this signaling nucleotide. Finally, we show that c-di-AMP binding to KdpD inhibits the upregulation of the kdpFABC operon under salt stress, thus indicating that c-di-AMP is a negative regulator of potassium uptake in S. aureus. IMPORTANCE Staphylococcus aureus is an important human pathogen and a major cause of food poisoning in Western countries. A common method for food preservation is the use of salt to drive dehydration. This study sheds light on the regulation of potassium uptake in Staphylococcus aureus, an important aspect of this bacterium's ability to tolerate high levels of salt. We show that the signaling nucleotide c-di-AMP binds to a regulatory component of the Kdp potassium uptake system and that this binding has an inhibitory effect on the expression of the kdp genes encoding a potassium transporter. c-di-AMP binds to the USP domain of KdpD, thus providing for the first time evidence for the ability of such a domain to bind a cyclic dinucleotide.
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Affiliation(s)
- Joana A Moscoso
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection (CMBI), Imperial College London, London, United Kingdom
| | - Hannah Schramke
- Center for Integrated Protein Science (CiPSM), Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Yong Zhang
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection (CMBI), Imperial College London, London, United Kingdom
| | - Tommaso Tosi
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection (CMBI), Imperial College London, London, United Kingdom
| | - Amina Dehbi
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection (CMBI), Imperial College London, London, United Kingdom
| | - Kirsten Jung
- Center for Integrated Protein Science (CiPSM), Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Angelika Gründling
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection (CMBI), Imperial College London, London, United Kingdom
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Su T, Wang Q, Yu L, Yu CA. Universal Stress Protein Regulates Electron Transfer and Superoxide Generation Activities of the Cytochrome bc1 Complex from Rhodobacter sphaeroides. Biochemistry 2015; 54:7313-9. [PMID: 26580083 DOI: 10.1021/acs.biochem.5b00658] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interactions between Rhodobacter sphaeroides cytochrome bc1 complex (Rsbc1) and soluble cytosolic proteins were studied by a precipitation pull-down technique. After being purified, detergent-dispersed Rsbc1 complex was incubated with soluble cytosolic fraction and then dialyzed in the absence of detergent; the interacting proteins were coprecipitated with Rsbc1 complex upon centrifugation. One of the cytosolic proteins pulled down by Rsbc1 complex was identified by liquid chromatography-coupled tandem mass spectrometry (LC/MS/MS) to be the reported R. sphaeroides universal stress protein (UspA). Incubating purified UspA with the detergent dispersed bc1 complex resulted in an increase in the Rsbc1 complex activity by 60% and a decrease in superoxide generation activity by the complex by more than 70%. These UspA effects were only observed with Rsbc1 complexes containing subunit IV and assayed under aerobic conditions. These results suggest that the interaction between UspA and Rsbc1 complex may play an important role in R. sphaeroides cells during oxidative stress. Using a biotin label transfer technique, cytochrome c1 of the Rsbc1 complex was identified as the interacting site for UspA.
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Affiliation(s)
- Ting Su
- Department of Biochemistry and Molecular Biology, Oklahoma State University , Stillwater, Oklahoma 74078, United States
| | - Qiyu Wang
- Department of Biochemistry and Molecular Biology, Oklahoma State University , Stillwater, Oklahoma 74078, United States
| | - Linda Yu
- Department of Biochemistry and Molecular Biology, Oklahoma State University , Stillwater, Oklahoma 74078, United States
| | - Chang-An Yu
- Department of Biochemistry and Molecular Biology, Oklahoma State University , Stillwater, Oklahoma 74078, United States
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Krivoshiev BV, Dardenne F, Blust R, Covaci A, Husson SJ. Elucidating toxicological mechanisms of current flame retardants using a bacterial gene profiling assay. Toxicol In Vitro 2015; 29:2124-32. [DOI: 10.1016/j.tiv.2015.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/31/2015] [Accepted: 09/01/2015] [Indexed: 11/24/2022]
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21
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Xu Y, Quan CS, Jin X, Jin X, Zhao J, Li X, Zheng W, Jin L, Liu D, Fan S, Ha NC. Crystallization and preliminary X-ray diffraction analysis of UspE from Escherichia coli. Acta Crystallogr F Struct Biol Commun 2014; 70:1640-2. [PMID: 25484216 PMCID: PMC4259230 DOI: 10.1107/s2053230x14023437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 10/23/2014] [Indexed: 11/10/2022] Open
Abstract
Universal stress proteins (Usps) are among the most highly induced genes when bacteria are subjected to several stress conditions such as heat shock, nutrient starvation or the presence of oxidants or other stress agents. Escherichia coli has five small Usps and one tandem-type Usp. UspE (or YdaA) is the tandem-type Usp and consists of two Usp domains arranged in tandem. To date, the structure of UspE remains to be elucidated. To contribute to the molecular understanding of the function of the tandem-type UspE, UspE from E. coli was overexpressed and the recombinant protein was purified using Ni-NTA affinity, Q anion-exchange and gel-filtration chromatography. Crystals of UspE were obtained by sitting-drop vapour diffusion. A diffraction data set was collected to a resolution of 3.2 Å from flash-cooled crystals. The crystals belonged to the tetragonal space group I4122 or I4322, with unit-cell parameters a = b = 121.1, c = 241.7 Å.
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Affiliation(s)
- Yongbin Xu
- Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian 116600, People’s Republic of China
| | - Chun-Shan Quan
- Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian 116600, People’s Republic of China
| | - Xuanzhen Jin
- College of Engineering, Yanbian University, Jilin Yanji 133002, People’s Republic of China
| | - Xiaoling Jin
- Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian 116600, People’s Republic of China
| | - Jing Zhao
- Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian 116600, People’s Republic of China
| | - Xihui Li
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, People’s Republic of China
| | - Wei Zheng
- Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian 116600, People’s Republic of China
| | - Liming Jin
- Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian 116600, People’s Republic of China
| | - Dedi Liu
- School of Physics and Materials Engineering, Dalian Nationalities University, Dalian 116600, People’s Republic of China
| | - Shengdi Fan
- Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian 116600, People’s Republic of China
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
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Acinetobacter baumannii universal stress protein A plays a pivotal role in stress response and is essential for pneumonia and sepsis pathogenesis. Int J Med Microbiol 2014; 305:114-23. [PMID: 25466824 DOI: 10.1016/j.ijmm.2014.11.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 09/14/2014] [Accepted: 11/09/2014] [Indexed: 01/15/2023] Open
Abstract
Acinetobacter baumannii is one of the most significant threats to global public health. This threat is compounded by the fact that A. baumannii is rapidly becoming resistant to all relevant antimicrobials. Identifying key microbial factors through which A. baumannii resists hostile host environment is paramount to the development of novel antimicrobials targeting infections caused by this emerging pathogen. An attractive target could be a molecule that plays a role in the pathogenesis and stress response of A. baumannii. Accordingly, the universal stress protein A (UspA) was chosen to be fully investigated in this study. A platform of A. baumannii constructs, expressing various levels of the uspA gene ranging from zero to thirteen folds of wild-type level, and a recombinant E. coli strain, were employed to investigate the role of UspA in vitro stress and in vivo pathogenesis. The UspA protein plays a significant role in protecting A. baumannii from H(2)O(2), low pH, and the respiratory toxin 2,4-DNP. A. baumannii UspA protein plays an essential role in two of the deadliest types of infection caused by A. baumannii; pneumonia and sepsis. This distinguishes A. baumannii UspA from its closely related homolog, the Staphylococcus aureus Usp2, as well as from the less similar Burkholderia glumae Usps. Heterologous and overexpression experiments suggest that UspA mediates its role via an indirect mechanism. Our study highlights the role of UspA as an important contributor to the A. baumannii stress and virulence machineries, and polishes it as a plausible target for new therapeutics.
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Sorci L, Ruggieri S, Raffaelli N. NAD homeostasis in the bacterial response to DNA/RNA damage. DNA Repair (Amst) 2014; 23:17-26. [PMID: 25127744 DOI: 10.1016/j.dnarep.2014.07.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 07/21/2014] [Accepted: 07/25/2014] [Indexed: 12/12/2022]
Abstract
In mammals, NAD represents a nodal point for metabolic regulation, and its availability is critical to genome stability. Several NAD-consuming enzymes are induced in various stress conditions and the consequent NAD decline is generally accompanied by the activation of NAD biosynthetic pathways to guarantee NAD homeostasis. In the bacterial world a similar scenario has only recently begun to surface. Here we review the current knowledge on the involvement of NAD homeostasis in bacterial stress response mechanisms. In particular, we focus on the participation of both NAD-consuming enzymes (DNA ligase, mono(ADP-ribosyl) transferase, sirtuins, and RNA 2'-phosphotransferase) and NAD biosynthetic enzymes (both de novo, and recycling enzymes) in the response to DNA/RNA damage. As further supporting evidence for such a link, a genomic context analysis is presented showing several conserved associations between NAD homeostasis and stress responsive genes.
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Affiliation(s)
- Leonardo Sorci
- Department of Clinical Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Silverio Ruggieri
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Nadia Raffaelli
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy.
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Abstract
The ATP binding proteins exist as a hybrid of proteins with Walker A motif and universal stress proteins (USPs) having an alternative motif for binding ATP. There is an urgent need to find a reliable and comprehensive hybrid predictor for ATP binding proteins using whole sequence information. In this paper the open source LIBSVM toolbox was used to build a classifier at 10-fold cross-validation. The best hybrid model was the combination of amino acid and dipeptide composition with an accuracy of 84.57% and Mathews correlation coefficient (MCC) value of 0.693. This classifier proves to be better than many classical ATP binding protein predictors. The general trend observed is that combinations of descriptors performed better and improved the overall performances of individual descriptors, particularly when combined with amino acid composition. The work developed a comprehensive model for predicting ATP binding proteins irrespective of their functional motifs. This model provides a high probability of success for molecular biologists in predicting and selecting diverse groups of ATP binding proteins irrespective of their functional motifs.
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25
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Application of universal stress proteins in probing the dynamics of potent degraders in complex terephthalate metagenome. BIOMED RESEARCH INTERNATIONAL 2013; 2013:196409. [PMID: 24151583 PMCID: PMC3782759 DOI: 10.1155/2013/196409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 07/11/2013] [Indexed: 11/21/2022]
Abstract
The culture-independent strategies to study microbial diversity and function have led to a revolution in environmental genomics, enabling fundamental questions about the distribution of microbes and their influence on bioremediation to be addressed. In this research we used the expression of universal stress proteins as a probe to determine the changes in degrading microbial population from a highly toxic terephthalate wastewater to a less toxic activated sludge bioreactor. The impact of relative toxicities was significantly elaborated at the levels of genus and species. The results indicated that 23 similar prokaryotic phyla were represented in both metagenomes irrespective of their relative abundance. Furthermore, the following bacteria taxa Micromonosporaceae, Streptomyces, Cyanothece sp. PCC 7822, Alicyclobacillus acidocaldarius, Bacillus halodurans, Leuconostoc mesenteroides, Lactococcus garvieae, Brucellaceae, Ralstonia solanacearum, Verminephrobacter eiseniae, Azoarcus, Acidithiobacillus ferrooxidans, Francisella tularensis, Methanothermus fervidus, and Methanocorpusculum labreanum were represented only in the activated sludge bioreactor. These highly dynamic microbes could serve as taxonomic biomarkers for toxic thresholds related to terephthalate and its derivatives. This paper, highlights the application of universal stress proteins in metagenomics analysis. Dynamics of microbial consortium of this nature can have future in biotechnological applications in bioremediation of toxic chemicals and radionuclides.
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Ricaldi JN, Fouts DE, Selengut JD, Harkins DM, Patra KP, Moreno A, Lehmann JS, Purushe J, Sanka R, Torres M, Webster NJ, Vinetz JM, Matthias MA. Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity. PLoS Negl Trop Dis 2012; 6:e1853. [PMID: 23145189 PMCID: PMC3493377 DOI: 10.1371/journal.pntd.0001853] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 08/25/2012] [Indexed: 12/25/2022] Open
Abstract
The whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (Leptospira licerasiae strains VAR010 and MMD0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. Comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including L. licerasiae) that are likely to be pathogenicity-related. Comparisons of the functional content of the genomes suggests that L. licerasiae retains several proteins related to nitrogen, amino acid and carbohydrate metabolism which might help to explain why these Leptospira grow well in artificial media compared with pathogenic species. L. licerasiae strains VAR010T and MMD0835 possess two prophage elements. While one element is circular and shares homology with LE1 of L. biflexa, the second is cryptic and homologous to a previously identified but unnamed region in L. interrogans serovars Copenhageni and Lai. We also report a unique O-antigen locus in L. licerasiae comprised of a 6-gene cluster that is unexpectedly short compared with L. interrogans in which analogous regions may include >90 such genes. Sequence homology searches suggest that these genes were acquired by lateral gene transfer (LGT). Furthermore, seven putative genomic islands ranging in size from 5 to 36 kb are present also suggestive of antecedent LGT. How Leptospira become naturally competent remains to be determined, but considering the phylogenetic origins of the genes comprising the O-antigen cluster and other putative laterally transferred genes, L. licerasiae must be able to exchange genetic material with non-invasive environmental bacteria. The data presented here demonstrate that L. licerasiae is genetically more closely related to pathogenic than to saprophytic Leptospira and provide insight into the genomic bases for its infectiousness and its unique antigenic characteristics. Leptospirosis is one of the most common diseases transmitted by animals worldwide and is important because it is a major cause of febrile illness in tropical areas and also occurs in epidemic form associated with natural disasters and flooding. The mechanisms through which Leptospira cause disease are not well understood. In this study we have sequenced the genomes of two strains of Leptospira licerasiae isolated from a person and a marsupial in the Peruvian Amazon. These strains were thought to be able to cause only mild disease in humans. We have compared these genomes with other leptospires that can cause severe illness and death and another leptospire that does not infect humans or animals. These comparisons have allowed us to demonstrate similarities among the disease-causing Leptospira. Studying genes that are common among infectious strains will allow us to identify genetic factors necessary for infecting, causing disease and determining the severity of disease. We have also found that L. licerasiae seems to be able to uptake and incorporate genetic information from other bacteria found in the environment. This information will allow us to begin to understand how Leptospira species have evolved.
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Affiliation(s)
- Jessica N. Ricaldi
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Derrick E. Fouts
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Jeremy D. Selengut
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Derek M. Harkins
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Kailash P. Patra
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Angelo Moreno
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Jason S. Lehmann
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Janaki Purushe
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Ravi Sanka
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Michael Torres
- Departamento de Ciencias Celulares y Moleculares, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Nicholas J. Webster
- Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Joseph M. Vinetz
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
- Departamento de Ciencias Celulares y Moleculares, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, Lima, Peru
- * E-mail: (JMV); (MAM)
| | - Michael A. Matthias
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
- * E-mail: (JMV); (MAM)
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alr0882 encoding a hypothetical protein of Anabaena PCC7120 protects Escherichia coli from nutrient starvation and abiotic stresses. Gene 2012; 511:248-55. [PMID: 23006586 DOI: 10.1016/j.gene.2012.09.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 05/15/2012] [Accepted: 09/05/2012] [Indexed: 11/20/2022]
Abstract
This study is the first to demonstrate cloning of alr0882, a hypothetical protein gene of Anabaena PCC7120, its heterologous expression in Escherichia coli strain LN29MG1655 (∆uspA::Kan) and functional complementation of abiotic stress tolerance of E. coli UspA. The recombinant vector pGEX-5X-2-alr0882 was used to transform ∆uspA E. coli strain. The IPTG induced expression of a 56.6kDa GST fusion protein was visualized on SDS-PAGE and attested by immunoblotting. E. coli ∆uspA strain harboring pGEX-5X-2-alr0882 when grown under carbon, nitrogen, phosphorus and sulphur limitation and abiotic stresses e.g. nalidixic acid, cycloserine, CdCl(2), H(2)O(2), UV-B, phenazine methosulphate (PMS), dinitrophenol (DNP), NaCl, heat, carbofuron and CuCl(2) demonstrated about 22.6-51.6% increase in growth over the cells transformed with empty vector. Expression of alr0882 gene in mutant E. coli as measured by semi-quantitative RT-PCR at different time points under selected treatments reaffirmed its role in tolerance against stresses employed in this study. Thus the results of this study vividly demonstrated that the novel protein alr0882, although appreciably different from the known UspA of E. coli, offers tolerance to abiotic stresses hence holds potential for the development of transgenic cyanobacteria.
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Global effects of catecholamines on Actinobacillus pleuropneumoniae gene expression. PLoS One 2012; 7:e31121. [PMID: 22347439 PMCID: PMC3275570 DOI: 10.1371/journal.pone.0031121] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 01/03/2012] [Indexed: 11/26/2022] Open
Abstract
Bacteria can use mammalian hormones to modulate pathogenic processes that play essential roles in disease development. Actinobacillus pleuropneumoniae is an important porcine respiratory pathogen causing great economic losses in the pig industry globally. Stress is known to contribute to the outcome of A. pleuropneumoniae infection. To test whether A. pleuropneumoniae could respond to stress hormone catecholamines, gene expression profiles after epinephrine (Epi) and norepinephrine (NE) treatment were compared with those from untreated bacteria. The microarray results showed that 158 and 105 genes were differentially expressed in the presence of Epi and NE, respectively. These genes were assigned to various functional categories including many virulence factors. Only 18 genes were regulated by both hormones. These genes included apxIA (the ApxI toxin structural gene), pgaB (involved in biofilm formation), APL_0443 (an autotransporter adhesin) and genes encoding potential hormone receptors such as tyrP2, the ygiY-ygiX (qseC-qseB) operon and narQ-narP (involved in nitrate metabolism). Further investigations demonstrated that cytotoxic activity was enhanced by Epi but repressed by NE in accordance with apxIA gene expression changes. Biofilm formation was not affected by either of the two hormones despite pgaB expression being affected. Adhesion to host cells was induced by NE but not by Epi, suggesting that the hormones affect other putative adhesins in addition to APL_0443. This study revealed that A. pleuropneumoniae gene expression, including those encoding virulence factors, was altered in response to both catecholamines. The differential regulation of A. pleuropneumoniae gene expression by the two hormones suggests that this pathogen may have multiple responsive systems for the two catecholamines.
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Raspoet R, Gantois I, Devloo R, Martel A, Haesebrouck F, Pasmans F, Ducatelle R, Van Immerseel F. Salmonella Enteritidis universal stress protein (usp) gene expression is stimulated by egg white and supports oviduct colonization and egg contamination in laying hens. Vet Microbiol 2011; 153:186-90. [DOI: 10.1016/j.vetmic.2011.05.047] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 05/24/2011] [Accepted: 05/31/2011] [Indexed: 11/16/2022]
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Curiel JA, Rodríguez H, de las Rivas B, Anglade P, Baraige F, Zagorec M, Champomier-Vergès M, Muñoz R, de Felipe FL. Response of a Lactobacillus plantarum
human isolate to tannic acid challenge assessed by proteomic analyses. Mol Nutr Food Res 2011; 55:1454-65. [DOI: 10.1002/mnfr.201000621] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 03/15/2011] [Accepted: 03/24/2011] [Indexed: 12/27/2022]
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31
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Wu R, Zhang W, Sun T, Wu J, Yue X, Meng H, Zhang H. Proteomic analysis of responses of a new probiotic bacterium Lactobacillus casei Zhang to low acid stress. Int J Food Microbiol 2011; 147:181-7. [DOI: 10.1016/j.ijfoodmicro.2011.04.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 03/25/2011] [Accepted: 04/05/2011] [Indexed: 10/18/2022]
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32
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Persson Ö, Nyström T, Farewell A. UspB, a member of the sigma-S regulon, facilitates RuvC resolvase function. DNA Repair (Amst) 2010; 9:1162-9. [DOI: 10.1016/j.dnarep.2010.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 08/09/2010] [Accepted: 08/09/2010] [Indexed: 10/19/2022]
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Hingley-Wilson SM, Lougheed KEA, Ferguson K, Leiva S, Williams HD. Individual Mycobacterium tuberculosis universal stress protein homologues are dispensable in vitro. Tuberculosis (Edinb) 2010; 90:236-44. [PMID: 20541977 PMCID: PMC2914252 DOI: 10.1016/j.tube.2010.03.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 03/16/2010] [Accepted: 03/31/2010] [Indexed: 01/25/2023]
Abstract
Mycobacterium tuberculosis has 10 universal stress proteins, whose function is unknown. However, proteomic and transcriptomic analyses have shown that a number of usp genes are significantly upregulated under hypoxic conditions and in response to nitric oxide and carbon monoxide, as well as during M. tuberculosis infection of macrophage cell lines. Six of these USPs are part of the DosR regulon and this, along with their expression pattern and the phenotypes of usp mutants in other bacterial species, suggests a potential role in the persistence and/or intracellular survival of Mtb. Knock-out mutants of individual usp genes encoding the USPs Rv1996, Rv2005c, Rv2026c and Rv2028c were generated and their growth and survival under hypoxic and other stress conditions examined. Although the majority of usp genes are highly induced in hypoxic conditions, mutation did not affect the long term survival of Mtb under these conditions, or in response to a range of stress conditions chosen to represent the environmental onslaughts experienced by the bacillus during an infection, nor during infection of mouse and human - derived macrophage cell lines. The possibility remains that these USPs are functionally redundant in Mtb.
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Affiliation(s)
- S M Hingley-Wilson
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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34
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Shih CJ, Lai MC. Differentially expressed genes after hyper- and hypo-salt stress in the halophilic archaeonMethanohalophilus portucalensis. Can J Microbiol 2010; 56:295-307. [DOI: 10.1139/w10-008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Methanohalophilus portucalensis FDF1 can grow over a range of external NaCl concentrations, from 1.2 to 2.9 mol/L. Differential gene expression in response to long-term hyper-salt stress (3.1 mol/L of NaCl) and hypo-salt stress (0.9 mol/L of NaCl) were compared by differential display RT-PCR. Fourteen differentially expressed genes responding to long-term hyper- or hypo-salt stress were detected, cloned, and sequenced. Several of the differentially expressed genes were related to the unique energy-acquiring methanogenesis pathway in this organism, including the transmembrane protein MttP, cobalamin biosynthesis protein, methenyl-H4MPT cyclohydrolase and monomethylamine methyltransferase. One signal transduction histidine kinase was identified from the hyper-salt stress cultures. Moreover, 3 known stress-response gene homologues — the DNA mismatch repair protein, MutS, the universal stress protein, UspA, and a member of the protein-disaggregating multichaperone system, ClpB — were also detected. The transcriptional analysis of these long-term salt stress response and adaptation-related genes for cells immediately after salt stress indicated that the expression of the energy metabolism genes was arrested during hyper-salt shock, while the chaperone clpB gene was stimulated by both hypo- and hyper-salt shock.
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Affiliation(s)
- Chao-Jen Shih
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
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35
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Global change of gene expression and cell physiology in YidC-depleted Escherichia coli. J Bacteriol 2010; 192:2193-209. [PMID: 20061485 DOI: 10.1128/jb.00484-09] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
YidC depletion affects membrane protein insertion and leads to a defect in the growth of the Escherichia coli cell. We analyzed global changes in gene expression upon YidC depletion to determine the importance of YidC for cellular functions using a gene chip method to compare the transcriptomes of JS71 (control) and JS7131 (yidC depletion strain). Of the more than 4,300 genes identified, 163 were upregulated and 99 were downregulated upon YidC depletion, including genes which are responsible for DNA/RNA repair; energy metabolism; various transporters, proteases and chaperones; stress response; and translation and transcription functions. Real-time PCR was performed on selected genes to confirm the results. Specifically, we found upregulation of the genes encoding the energy transduction proteins F(1)F(o) ATP synthase and cytochrome bo(3) oxidase due to perturbation in assembly when YidC was depleted. We also determined that the high-level induction of the PspA stress protein under YidC depletion conditions is roughly 10-fold higher than the activation due to the addition of protonophore carbonyl cyanide m-chlorophenylhydrazone (CCCP), which dissipates the proton motive force. In addition, the gene chip data reveal the Cpx stress pathway is activated upon YidC depletion. The data show the broad physiological contribution of YidC to the bacterial cell and the considerable ramification to the cell when it is depleted.
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36
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Inactivation of PadR, the repressor of the phenolic acid stress response, by molecular interaction with Usp1, a universal stress protein from Lactobacillus plantarum, in Escherichia coli. Appl Environ Microbiol 2009; 75:5273-83. [PMID: 19542339 DOI: 10.1128/aem.00774-09] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The phenolic acid decarboxylase gene padA is involved in the phenolic acid stress response (PASR) in gram-positive bacteria. In Lactobacillus plantarum, the padR gene encodes the negative transcriptional regulator of padA and is cotranscribed with a downstream gene, usp1, which encodes a putative universal stress protein (USP), Usp1, of unknown function. The usp1 gene is overexpressed during the PASR. However, the role and the mechanism of action of the USPs are unknown in gram-positive bacteria. Therefore, to gain insights into the role of USPs in the PASR; (i) a usp1 deletion mutant was constructed; (ii) the two genes padR and usp1 were coexpressed with padA under its own promoter as a reporter gene in Escherichia coli; and (iii) molecular in vitro interactions between the PadR, Usp1, and the padA promoter were studied. Although the usp1 mutant strain retained phenolic acid-dependent PAD activity, it displayed a greater sensitivity to strong acidic conditions compared to that of the wild-type strain. PadR cannot be inactivated directly by phenolic acid in E. coli recombinant cultures but is inactivated by Usp1 when the two proteins are coexpressed in E. coli. The PadR inactivation observed in recombinant E. coli cells was supported by electrophoretic mobility shift assays. Although Usp1 seems not to be absolutely required for the PASR, its capacity to inactivate PadR indicates that it could serve as an important mediator in acid stress response mechanisms through its capacity to interact with transcriptional regulators.
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Hegde SR, Manimaran P, Mande SC. Dynamic changes in protein functional linkage networks revealed by integration with gene expression data. PLoS Comput Biol 2008; 4:e1000237. [PMID: 19043542 PMCID: PMC2580820 DOI: 10.1371/journal.pcbi.1000237] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Accepted: 10/20/2008] [Indexed: 12/12/2022] Open
Abstract
Response of cells to changing environmental conditions is governed by the dynamics of intricate biomolecular interactions. It may be reasonable to assume, proteins being the dominant macromolecules that carry out routine cellular functions, that understanding the dynamics of protein:protein interactions might yield useful insights into the cellular responses. The large-scale protein interaction data sets are, however, unable to capture the changes in the profile of protein:protein interactions. In order to understand how these interactions change dynamically, we have constructed conditional protein linkages for Escherichia coli by integrating functional linkages and gene expression information. As a case study, we have chosen to analyze UV exposure in wild-type and SOS deficient E. coli at 20 minutes post irradiation. The conditional networks exhibit similar topological properties. Although the global topological properties of the networks are similar, many subtle local changes are observed, which are suggestive of the cellular response to the perturbations. Some such changes correspond to differences in the path lengths among the nodes of carbohydrate metabolism correlating with its loss in efficiency in the UV treated cells. Similarly, expression of hubs under unique conditions reflects the importance of these genes. Various centrality measures applied to the networks indicate increased importance for replication, repair, and other stress proteins for the cells under UV treatment, as anticipated. We thus propose a novel approach for studying an organism at the systems level by integrating genome-wide functional linkages and the gene expression data.
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Affiliation(s)
- Shubhada R. Hegde
- Centre for DNA Fingerprinting and Diagnostics, Nacharam, Hyderabad, India
| | | | - Shekhar C. Mande
- Centre for DNA Fingerprinting and Diagnostics, Nacharam, Hyderabad, India
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38
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Nachin L, Brive L, Persson KC, Svensson P, Nyström T. Heterodimer formation within universal stress protein classes revealed by an in silico and experimental approach. J Mol Biol 2008; 380:340-50. [PMID: 18514734 DOI: 10.1016/j.jmb.2008.04.074] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 04/09/2008] [Accepted: 04/30/2008] [Indexed: 11/18/2022]
Abstract
Universal stress proteins (Usps) are found in all kingdoms of life and can be divided into four classes by phylogenic analysis. According to available structures, Usps exist as homodimers, and genetic studies show that their cellular assignments are extensive, including functions relating to stress resistance, carbon metabolism, cellular adhesion, motility, and bacterial virulence. We approached the question of how Usps can achieve such a variety of functions in a cell by using a new procedure for statistical analysis of multiple sequence alignments, based on physicochemically related values for each amino acid residue of Usp dimer interfaces. The results predicted that Usp proteins within a class may, in addition to forming homodimers, be able to form heterodimers. Using Escherichia coli Usps as model proteins, we confirmed the existence of such interactions. We especially focused on class I UspA and UspC and demonstrated that they are able to form homo- and heterodimers in vitro and in vivo. We suggest that this ability to form both homo- and heterodimers may allow for an expansion of the functional repertoire of Usps and explains why organisms usually contain multiple usp paralogues.
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Affiliation(s)
- Laurence Nachin
- Department of Cell and Molecular Biology, Microbiology, Molecular Biology, Göteborg University, Box 462, 40530 Göteborg, Sweden.
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Persson O, Valadi A, Nyström T, Farewell A. Metabolic control of the Escherichia coli universal stress protein response through fructose-6-phosphate. Mol Microbiol 2007; 65:968-78. [PMID: 17640273 DOI: 10.1111/j.1365-2958.2007.05838.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The universal stress protein (Usp) superfamily encompasses a conserved group of proteins involved in stress resistance, adaptation to energy deficiency, cell motility and adhesion, and is found in all kingdoms of life. The paradigm usp gene, uspA, of Escherichia coli is transcriptionally activated by a large variety of stresses, and the alarmone ppGpp is required for this activation. Here, we show that the uspA gene is also regulated by an intermediate of the glycolytic/gluconeogenic pathways. Specifically, mutations and conditions resulting in fructose-6-phosphate (F-6-P) accumulation elicit superinduction of uspA upon carbon starvation, whereas genetic manipulations reducing the pool size of F-6-P have the opposite effect. This metabolic control of uspA does not act via ppGpp. Other, but not all, usp genes of the usp superfamily are similarly affected by alterations in F-6-P levels. We suggest that alterations in the pool size of phosphorylated sugars of the upper glycolytic pathway may ensure accumulation of required survival proteins preceding the complete depletion of the external carbon source. Indeed, we show that uspA is, in fact, induced before the carbon source is depleted from the medium.
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Affiliation(s)
- Orjan Persson
- Department of Cell and Molecular Biology-Microbiology, Göteborg University, Box 462, 405 30 Göteborg, Sweden
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Jin H, Retallack DM, Stelman SJ, Hershberger CD, Ramseier T. Characterization of the SOS response of Pseudomonas fluorescens strain DC206 using whole-genome transcript analysis. FEMS Microbiol Lett 2007; 269:256-64. [PMID: 17250760 DOI: 10.1111/j.1574-6968.2007.00630.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
DNA microarray technology was used to survey changes in gene expression in Pseudomonas fluorescens after mitomycin C treatment. As expected, genes associated with the SOS response were upregulated, such as those encoding the recombination protein RecA, DNA repair protein RecN, excinuclease ABC subunit A UvrA, and the LexA repressor protein. Interestingly, expression of 33 clustered bacteriophage-like genes was upregulated, suggesting that mitomycin C (MMC) may induce a prophage resident in the P. fluorescens genome. However, no phage particles were detected in P. fluorescens strain DC206 that had been treated with MMC using transmission electron microscopy. The same preparation failed to produce phage plaques on lawns of any of 10 different Pseudomonas strains tested, indicating that the 33 bacteriophage-like gene cluster represents a defective prophage.
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Affiliation(s)
- Hongfan Jin
- The Dow Chemical Company, Oberlin Drive, San Diego, CA 92121, USA.
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Dardenne F, Nobels I, De Coen W, Blust R. Dose-response relationships and statistical performance of a battery of bacterial gene profiling assays. Appl Microbiol Biotechnol 2007; 75:223-34. [PMID: 17225096 DOI: 10.1007/s00253-006-0808-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Revised: 12/08/2006] [Accepted: 12/11/2006] [Indexed: 11/29/2022]
Abstract
Because of increasing awareness and legislative demands, there is a demand for the development and use of biological assays for the assessment of the toxicity of chemicals, environmental samples. Recently, a growing number of bacterial reporter assays have been developed and implemented. Nevertheless, little data is published on the performance of these assays in terms of analytical parameters. We present results on a battery of 14 transgenic Escherichia coli strains carrying different promoter::reporter fusions. Growth characteristics and basal expression levels were modeled and fitted, data show that growth curves should be taken into account during test development. Our study shows that the induction profiles reflect the mode of action, e.g., paraquat clearly induces the soxRS operon. The sensitivity of the assay compares well to that of whole organism tests, e.g., fish and Daphnia for polar organics. Metal toxicity is detected less efficiently, e.g., cadmium is detected near the LC50 of carp, considered a relatively insensitive species towards cadmium. The assay variability ranges from 10 to 40% depending on the strain, comparable to that of other bioassays. The variability was shown to be determined by the intrinsic traits of the promoter-strain combination, not by operating conditions.
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Affiliation(s)
- F Dardenne
- Department of Biology, Ecophysiology, Biochemistry and Toxicology Group, University of Antwerp, Groenenborgerlaan 171/U7, Antwerp, Belgium.
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Scrimgeour J, Eriksson E, Goksör M. Laser Surgery and Optical Trapping in a Laser Scanning Microscope. Methods Cell Biol 2007; 82:629-46. [PMID: 17586274 DOI: 10.1016/s0091-679x(06)82022-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Optical manipulation opens up many new possibilities for experiments in the field of microbiology and is a very powerful tool for investigating cellular structure. In this emerging field imaging retains an important role, and systems that combine advanced imaging techniques with optical manipulation tools, such as laser scalpels or optical tweezers, are an important starting point for researchers. We present a flexible experimental platform that contains both a laser scalpel and optical tweezers, in combination with confocal and multiphoton microscopy. A simple manipulation of the external optics is used to retain the three-dimensional imaging capabilities of the microscopes. Two applications of the system are presented. In the first, the laser scalpel is used to initiate diffusion of a fluorescent dye through Escherichia coli mutants, which exhibit abnormal cell division, forming filaments, or chains of bacteria. The diffusion assay is used to assess the potential for the exchange of cytoplasmic material between neighboring cells. The second application investigates the binding of endoplasmic reticulum (ER) to chloroplasts in Pisum sativum (garden pea). Individual plant protoplasts are ruptured using the laser scalpel, allowing individual chloroplasts to be trapped and manipulated. Strands of the ER which are attached to the chloroplast are identified. The magnitude and nature of the binding between the chloroplast and the ER are investigated.
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Affiliation(s)
- Jan Scrimgeour
- Department of Physics, Göteborg University, SE-412 96 Göteborg, Sweden
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Chen W, Honma K, Sharma A, Kuramitsu HK. A universal stress protein of Porphyromonas gingivalis is involved in stress responses and biofilm formation. FEMS Microbiol Lett 2006; 264:15-21. [PMID: 17020544 DOI: 10.1111/j.1574-6968.2006.00426.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Porphyromonas gingivalis is recognized as one of the major periodontal pathogens in subgingival plaque, which is implicated in the progression of chronic periodontal disease. We analyzed the role of upsA in P. gingivalis 381 and its uspA-deficient mutant CW301 under various stress conditions. In general, the uspA mutant was less tolerant to a variety of environmental stresses relative to the parental strain. In addition, gene expression of uspA is upregulated during biofilm formation. Biofilm formation of the uspA mutant was also less than that of strain 381. In conclusion, the uspA gene affecting the stress responses of P. gingivalis is required for optimal biofilm formation.
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Affiliation(s)
- Wen Chen
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, State University of New York, Buffalo, New York, NY 14214-3092, USA
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Liu WT, Karavolos MH, Bulmer DM, Allaoui A, Hormaeche RDCE, Lee JJ, Khan CMA. Role of the universal stress protein UspA of Salmonella in growth arrest, stress and virulence. Microb Pathog 2006; 42:2-10. [PMID: 17081727 DOI: 10.1016/j.micpath.2006.09.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Revised: 09/15/2006] [Accepted: 09/15/2006] [Indexed: 11/29/2022]
Abstract
Pathogenic bacteria employ a variety of mechanisms to resist a barrage of stresses they encounter during active growth in or outside the host as well as during growth stasis. An in silico screen of the Salmonella genome sequence revealed that Salmonella typhimurium LT2 possesses a homologue belonging to the universal stress protein A (UspA) family. We assessed the transcriptional profile of uspA in S. typhimurium C5 by constructing a lacZ fusion revealing that uspA is induced by metabolic, oxidative, and temperature stresses. The highest transcriptional levels occurred in cells entering stationary phase, an observation consistent with expression patterns in Escherichia coli. The protein was purified as a fusion with GST (UspA(F)) and antibodies raised against UspA(F) revealed elevated protein levels in stressed and growth-arrested cells. Inactivation of uspA in S. typhimurium C5, lead to increased susceptibility to stress conditions. Furthermore, UspA makes an important contribution to the in vivo virulence of Salmonella in mice thus highlighting the importance of stress resistance regulation in pathogenicity and survival within the host.
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Affiliation(s)
- Wen-Tssann Liu
- Institute for Cell and Molecular Biosciences and School of Biomedical Sciences, The Medical School, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
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Yang Y, Fix D. Genetic analysis of the anti-mutagenic effect of genistein in Escherichia coli. Mutat Res 2006; 600:193-206. [PMID: 16872640 DOI: 10.1016/j.mrfmmm.2006.05.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2005] [Revised: 04/21/2006] [Accepted: 05/01/2006] [Indexed: 10/24/2022]
Abstract
Genistein, the main isoflavone in soy, has received considerable attention for its potential anti-carcinogenic properties. In a previous report, we investigated the possible role of genistein in anti-mutagenesis, using an Escherichia coli reversion assay system. Genistein reduced ENU-induced mutagenesis in a dose-dependent manner and the reduction of mutation frequency was differential among several categories of mutation. Most notable was a loss of transversion mutations, which require SOS functions. In this report, we further investigated the anti-mutagenic effect of genistein using a genetic approach. E. coli strains having alterations in genes involved in SOS-mutagenesis were examined, as were strains having defects in proteins that might serve as potential targets for genistein. The results showed that ENU-induced mutations produced in recA730 and lexA(Def) strains, both expressing a constitutive SOS response, were reduced by genistein to a lesser extent than in the wild-type strain. The effect of genistein was not entirely abolished, however. ENU mutagenesis in a umuC derivative, which reflects predominantly transition mutations, was unaffected by genistein. ENU-induced mutations in strains having defects in topA, gyrA, typA or uspA were not different than the wild-type, suggesting that these gene products were not involved in genistein's anti-mutagenic effect. In addition, we determined the distribution of genistein in various cellular fractions using HPLC. These studies revealed that genistein could be recovered from E. coli cells grown on agar media containing genistein; the intracellular concentration was similar to that in the agar plates. Further, most of the genistein recovered was associated with proteins in the cytosolic fraction and little partitioned in the membrane fraction. In vitro studies showed that genistein could be precipitated from a protein (BSA) containing solution. Finally, we examined the effect of genistein on formation of the RecA filament on ssDNA in vitro and observed an inhibition at high concentrations of genistein. In total, these results suggested that genistein may reduce SOS-dependent mutagenesis by reducing the interaction of RecA protein with ssDNA. As a consequence, genistein could cause a reduction in (1) the overall SOS response (confirmed using beta-galactosidase assays) and (2) trans-lesion DNA synthesis by DNA polymerase V.
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Affiliation(s)
- Yixin Yang
- Department of Microbiology, Southern Illinois University, Carbondale, IL 62901, United States
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Schreiber K, Boes N, Eschbach M, Jaensch L, Wehland J, Bjarnsholt T, Givskov M, Hentzer M, Schobert M. Anaerobic survival of Pseudomonas aeruginosa by pyruvate fermentation requires an Usp-type stress protein. J Bacteriol 2006; 188:659-68. [PMID: 16385055 PMCID: PMC1347276 DOI: 10.1128/jb.188.2.659-668.2006] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recently, we identified a pyruvate fermentation pathway in Pseudomonas aeruginosa sustaining anaerobic survival in the absence of alternative anaerobic respiratory and fermentative energy generation systems (M. Eschbach, K. Schreiber, K. Trunk, J. Buer, D. Jahn, and M. Schobert, J. Bacteriol. 186:4596-4604, 2004). Anaerobic long-term survival of P. aeruginosa might be essential for survival in deeper layers of a biofilm and the persistent infection of anaerobic mucus plaques in the cystic fibrosis lung. Proteome analysis of P. aeruginosa cells during a 7-day period of pyruvate fermentation revealed the induced synthesis of three enzymes involved in arginine fermentation, ArcA, ArcB, and ArcC, and the outer membrane protein OprL. Moreover, formation of two proteins of unknown function, PA3309 and PA4352, increased by factors of 72- and 22-fold, respectively. Both belong to the group of universal stress proteins (Usp). Long-term survival of a PA3309 knockout mutant by pyruvate fermentation was found drastically reduced. The oxygen-sensing regulator Anr controls expression of the PPA3309-lacZ reporter gene fusion after a shift to anaerobic conditions and further pyruvate fermentation. PA3309 expression was also found induced during the anaerobic and aerobic stationary phases. This aerobic stationary-phase induction is independent of the regulatory proteins Anr, RpoS, RelA, GacA, RhlR, and LasR, indicating a currently unknown mechanism of stationary-phase-dependent gene activation. PA3309 promoter activity was detected in the deeper layers of a P. aeruginosa biofilm using a PPA3309-gfp (green fluorescent protein gene) fusion and confocal laser-scanning microscopy. This is the first description of an Anr-dependent, anaerobically induced, and functional Usp-like protein in bacteria.
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Affiliation(s)
- Kerstin Schreiber
- Institute of Microbiology, Technical University Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany
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Siezen RJ, Renckens B, van Swam I, Peters S, van Kranenburg R, Kleerebezem M, de Vos WM. Complete sequences of four plasmids of Lactococcus lactis subsp. cremoris SK11 reveal extensive adaptation to the dairy environment. Appl Environ Microbiol 2006; 71:8371-82. [PMID: 16332824 PMCID: PMC1317451 DOI: 10.1128/aem.71.12.8371-8382.2005] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactococcus lactis strains are known to carry plasmids encoding industrially important traits. L. lactis subsp. cremoris SK11 is widely used by the dairy industry in cheese making. Its complete plasmid complement was sequenced and found to contain the plasmids pSK11A (10,372 bp), pSK11B (13,332 bp), pSK11L (47,165 bp), and pSK11P (75,814 bp). Six highly homologous repB-containing replicons were found, all belonging to the family of lactococcal theta-type replicons. Twenty-three complete insertion sequence elements segment the plasmids into numerous modules, many of which can be identified as functional units or containing functionally related genes. Plasmid-encoded functions previously known to reside on L. lactis SK11 plasmids were now mapped in detail, e.g., lactose utilization (lacR-lacABCDFEGX), the proteolytic system (prtM-prtP, pepO, pepF), and the oligopeptide permease system (oppDFBCA). Newly identified plasmid-encoded functions could facilitate the uptake of various cations, while the pabA and pabB genes could be essential for folate biosynthesis. A competitive advantage could be obtained by using the putative flavin adenine dinucleotide-dependent d-lactate dehydrogenase and oxalate:formate antiporter for enhanced ATP synthesis, while the activity of the predicted alpha-acetolactate decarboxylase may contribute to the formation of an additional electron sink. Various stress response proteins are plasmid encoded, which could enhance strain robustness. A substantial number of these "adaptation" genes have not been described before on L. lactis plasmids. Moreover, several genes were identified for the first time in L. lactis, possibly reflecting horizontal gene transfer.
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Affiliation(s)
- Roland J Siezen
- Centre for Molecular andBiomolecular Informatics, Radboud University, P.O. Box 9010, 6500GL Nijmegen, The Netherlands.
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Affiliation(s)
- Deborah A Siegele
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843-3258, USA.
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Trautinger BW, Jaktaji RP, Rusakova E, Lloyd RG. RNA polymerase modulators and DNA repair activities resolve conflicts between DNA replication and transcription. Mol Cell 2005; 19:247-58. [PMID: 16039593 DOI: 10.1016/j.molcel.2005.06.004] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2004] [Revised: 03/18/2005] [Accepted: 06/02/2005] [Indexed: 11/27/2022]
Abstract
Organisms rely on close interplay between DNA replication, recombination, and repair to secure transmission of the genome. In rapidly dividing cells, there is also great pressure for transcription, which may induce conflict with replication. We investigated the potential for conflict in bacterial cells, where there is no temporal separation of these processes. Eliminating the stringent response regulators ppGpp and DksA or the GreA and Mfd proteins, which revive or dislodge stalled transcription complexes, and especially combinations of these factors, is shown to severely reduce viability when DNA repair is also compromised. Both ppGpp and certain RNA polymerase (RNAP) mutations reduce accumulation of backed-up arrays of stalled transcription complexes. We propose these arrays are formidable obstacles to replication that are normally kept in check in wild-type cells by ppGpp, DksA, GreA, and Mfd. When arrays do obstruct replication, the consequences are resolved by one of the many pathways available to rescue stalled forks.
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Affiliation(s)
- Brigitte W Trautinger
- Institute of Genetics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK
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Nyström T. Growth versus maintenance: a trade-off dictated by RNA polymerase availability and sigma factor competition? Mol Microbiol 2005; 54:855-62. [PMID: 15522072 DOI: 10.1111/j.1365-2958.2004.04342.x] [Citation(s) in RCA: 166] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The regulatory design of higher organisms is proposed to comprise a trade-off between activities devoted to reproduction and those devoted to cellular maintenance and repair. Excessive reproduction will inevitably limit the organism's ability to resist stress whereas excessively devoted stress defence systems may increase lifespan but reduce Darwinian fitness. The trade-off is arguably a consequence of limited resources in any one organism but the nature and identity of such limiting resources are ambiguous. Analysis of global control of gene expression in Escherichia coli suggests that reproduction and maintenance activities are also at odds in bacteria and that this antagonism may be a consequence of a battle between transcription factors for limiting RNA polymerase. The outcome of this battle is regulated and depends on the nutritional status of the environment, the levels of the alarmone ppGpp, and RNA polymerase availability. This paper reviews how the concentration of RNA polymerase available for transcription initiation may vary upon shifts between growth and growth-arrest conditions and how this adjustment may differentially affect genes whose functions relate to reproduction and maintenance.
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Affiliation(s)
- Thomas Nyström
- Department of Cell and Molecular Biology - Microbiology, Göteborg University, Medicinaregatan 9C, 413 90 Göteborg, Sweden.
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