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Jiao M, He W, Ouyang Z, Qin Q, Guo Y, Zhang J, Bai Y, Guo X, Yu Q, She J, Hwang PM, Zheng F, Wen Y. Mechanistic and structural insights into the bifunctional enzyme PaaY from Acinetobacter baumannii. Structure 2023; 31:935-947.e4. [PMID: 37329879 DOI: 10.1016/j.str.2023.05.015] [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: 12/01/2022] [Revised: 03/28/2023] [Accepted: 05/23/2023] [Indexed: 06/19/2023]
Abstract
PaaY is a thioesterase that enables toxic metabolites to be degraded through the bacterial phenylacetic acid (PA) pathway. The Acinetobacter baumannii gene FQU82_01591 encodes PaaY, which we demonstrate to possess γ-carbonic anhydrase activity in addition to thioesterase activity. The crystal structure of AbPaaY in complex with bicarbonate reveals a homotrimer with a canonical γ-carbonic anhydrase active site. Thioesterase activity assays demonstrate a preference for lauroyl-CoA as a substrate. The AbPaaY trimer structure shows a unique domain-swapped C-termini, which increases the stability of the enzyme in vitro and decreases its susceptibility to proteolysis in vivo. The domain-swapped C-termini impact thioesterase substrate specificity and enzyme efficacy without affecting carbonic anhydrase activity. AbPaaY knockout reduced the growth of Acinetobacter in media containing PA, decreased biofilm formation, and impaired hydrogen peroxide resistance. Collectively, AbPaaY is a bifunctional enzyme that plays a key role in the metabolism, growth, and stress response mechanisms of A. baumannii.
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Affiliation(s)
- Min Jiao
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Wenbo He
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Zhenlin Ouyang
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Qian Qin
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Yucheng Guo
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Jiaxin Zhang
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Yixin Bai
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Xiaolong Guo
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Qinyue Yu
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Junjun She
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Peter M Hwang
- Departments of Medicine and Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Fang Zheng
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Yurong Wen
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China; The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China.
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2
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Connor A, Wigham C, Bai Y, Rai M, Nassif S, Koffas M, Zha RH. Novel insights into construct toxicity, strain optimization, and primary sequence design for producing recombinant silk fibroin and elastin-like peptide in E. coli. Metab Eng Commun 2023; 16:e00219. [PMID: 36825067 PMCID: PMC9941211 DOI: 10.1016/j.mec.2023.e00219] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/06/2022] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Spider silk proteins (spidroins) are a remarkable class of biomaterials that exhibit a unique combination of high-value attributes and can be processed into numerous morphologies for targeted applications in diverse fields. Recombinant production of spidroins represents the most promising route towards establishing the industrial production of the material, however, recombinant spider silk production suffers from fundamental difficulties that includes low titers, plasmid instability, and translational inefficiencies. In this work, we sought to gain a deeper understanding of upstream bottlenecks that exist in the field through the production of a panel of systematically varied spidroin sequences in multiple E. coli strains. A restriction on basal expression and specific genetic mutations related to stress responses were identified as primary factors that facilitated higher titers of the recombinant silk constructs. Using these findings, a novel strain of E. coli was created that produces recombinant silk constructs at levels 4-33 times higher than standard BL21(DE3). However, these findings did not extend to a similar recombinant protein, an elastin-like peptide. It was found that the recombinant silk proteins, but not the elastin-like peptide, exert toxicity on the E. coli host system, possibly through their high degree of intrinsic disorder. Along with strain engineering, a bioprocess design that utilizes longer culturing times and attenuated induction was found to raise recombinant silk titers by seven-fold and mitigate toxicity. Targeted alteration to the primary sequence of the recombinant silk constructs was also found to mitigate toxicity. These findings identify multiple points of focus for future work seeking to further optimize the recombinant production of silk proteins and is the first work to identify the intrinsic disorder and subsequent toxicity of certain spidroin constructs as a primary factor related to the difficulties of production.
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Affiliation(s)
- Alexander Connor
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Caleb Wigham
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Yang Bai
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Manish Rai
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Sebastian Nassif
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Mattheos Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Corresponding author. Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
| | - R. Helen Zha
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA,Corresponding author. Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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3
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Nava-Ramírez T, Hansberg W. Chaperone activity of large-size subunit catalases. Free Radic Biol Med 2020; 156:99-106. [PMID: 32502516 DOI: 10.1016/j.freeradbiomed.2020.05.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/25/2020] [Accepted: 05/25/2020] [Indexed: 10/24/2022]
Abstract
Large-size subunit catalases (LSCs) have a C-terminal domain that is structurally similar to DJ-1 and Hsp31 proteins, which have well documented molecular chaperone activity. Like chaperones, LSCs are abundant proteins that are induced under stress conditions and during cell differentiation in different microorganisms. Here we document that the C-terminal domain of LSCs assist other proteins to preserve their active conformation. Heat, urea, or H2O2 denaturation of alcohol dehydrogenase was prevented by LSCs or the C-terminal domain of Catalase-3 (TDC3); in contrast, small-size subunit catalases (SSCs) or LSCs without the C-terminal domain (C3ΔTD or C63) did not have this effect. Similar results were obtained if the alcohol dehydrogenase was previously denatured by heat and then the different catalases or truncated enzymes were added. The TDC3 also protected both the C3ΔTD and the bovine liver catalase from heat denaturation. The chaperone activity of CAT-3 or the TDC3 increased survival of E. coli under different stress conditions whereas the C3ΔTD did not. It is concluded that the C-terminal domain of LSCs has a chaperone activity that is instrumental for cellular resistance to stress conditions, such as oxidative stress that leads to cell differentiation in filamentous fungi.
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Affiliation(s)
- Teresa Nava-Ramírez
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, UNAM, Mexico
| | - Wilhelm Hansberg
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, UNAM, Mexico.
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Ferdosh S, Banerjee S, Pathak BK, Sengupta J, Barat C. Hibernating ribosomes exhibit chaperoning activity but can resist unfolded protein-mediated subunit dissociation. FEBS J 2020; 288:1305-1324. [PMID: 32649051 DOI: 10.1111/febs.15479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/24/2020] [Accepted: 07/07/2020] [Indexed: 02/03/2023]
Abstract
Ribosome hibernation is a prominent cellular strategy to modulate protein synthesis during starvation and the stationary phase of bacterial cell growth. Translational suppression involves the formation of either factor-bound inactive 70S monomers or dimeric 100S hibernating ribosomal complexes, the biological significance of which is poorly understood. Here, we demonstrate that the Escherichia coli 70S ribosome associated with stationary phase factors hibernation promoting factor or protein Y or ribosome-associated inhibitor A and the 100S ribosome isolated from both Gram-negative and Gram-positive bacteria are resistant to unfolded protein-mediated subunit dissociation and subsequent degradation by cellular ribonucleases. Considering that the increase in cellular stress is accompanied by accumulation of unfolded proteins, such resistance of hibernating ribosomes towards dissociation might contribute to their maintenance during the stationary phase. Analysis of existing structures provided clues on the mechanism of inhibition of the unfolded protein-mediated disassembly in case of hibernating factor-bound ribosome. Further, the factor-bound 70S and 100S ribosomes can suppress protein aggregation and assist in protein folding. The chaperoning activity of these ribosomes is the first evidence of a potential biological activity of the hibernating ribosome that might be crucial for cell survival under stress conditions.
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Affiliation(s)
- Sehnaz Ferdosh
- Department of Biotechnology, St. Xavier's College, Kolkata, India
| | - Senjuti Banerjee
- Department of Biotechnology, St. Xavier's College, Kolkata, India
| | - Bani K Pathak
- Structural Biology and Bio-Informatics Division, Indian Institute of Chemical Biology (Council of Scientific and Industrial Research), Kolkata, India
| | - Jayati Sengupta
- Structural Biology and Bio-Informatics Division, Indian Institute of Chemical Biology (Council of Scientific and Industrial Research), Kolkata, India
| | - Chandana Barat
- Department of Biotechnology, St. Xavier's College, Kolkata, India
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Nava Ramírez T, Hansberg W. Características comunes de las chaperonas pequeñas y diméricas. TIP REVISTA ESPECIALIZADA EN CIENCIAS QUÍMICO-BIOLÓGICAS 2020. [DOI: 10.22201/fesz.23958723e.2020.0.234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Las chaperonas moleculares constituyen un mecanismo importante para evitar la muerte celular provocada por la agregación de proteínas. Las chaperonas independientes del ATP son un grupo de proteínas de bajo peso molecular que pueden proteger y ayudar a alcanzar la estructura nativa de las proteínas desplegadas o mal plegadas sin necesidad de un gasto energético. Hemos encontrado que el dominio C-terminal de las catalasas de subunidad grande tiene actividad de chaperona. Por ello, en esta revisión analizamos las características más comunes de las chaperonas pequeñas y más estudiadas como: αB-cristalina, Hsp20, Spy, Hsp33 y Hsp31. En particular, se examina la participación de los aminoácidos hidrofóbicos y de los aminoácidos con carga en el reconocimiento de las proteínas sustrato, así como el papel que tiene la forma dimérica y su oligomerización en la actividad de chaperona. En cada una de esas chaperonas revisaremos la estructura de la proteína, su función, localización celular e importancia para la célula.
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Evolution of Predicted Acid Resistance Mechanisms in the Extremely Acidophilic Leptospirillum Genus. Genes (Basel) 2020; 11:genes11040389. [PMID: 32260256 PMCID: PMC7231039 DOI: 10.3390/genes11040389] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 02/01/2023] Open
Abstract
Organisms that thrive in extremely acidic environments (≤pH 3.5) are of widespread importance in industrial applications, environmental issues, and evolutionary studies. Leptospirillum spp. constitute the only extremely acidophilic microbes in the phylogenetically deep-rooted bacterial phylum Nitrospirae. Leptospirilli are Gram-negative, obligatory chemolithoautotrophic, aerobic, ferrous iron oxidizers. This paper predicts genes that Leptospirilli use to survive at low pH and infers their evolutionary trajectory. Phylogenetic and other bioinformatic approaches suggest that these genes can be classified into (i) "first line of defense", involved in the prevention of the entry of protons into the cell, and (ii) neutralization or expulsion of protons that enter the cell. The first line of defense includes potassium transporters, predicted to form an inside positive membrane potential, spermidines, hopanoids, and Slps (starvation-inducible outer membrane proteins). The "second line of defense" includes proton pumps and enzymes that consume protons. Maximum parsimony, clustering methods, and gene alignments are used to infer the evolutionary trajectory that potentially enabled the ancestral Leptospirillum to transition from a postulated circum-neutral pH environment to an extremely acidic one. The hypothesized trajectory includes gene gains/loss events driven extensively by horizontal gene transfer, gene duplications, gene mutations, and genomic rearrangements.
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Gawade P, Gunjal G, Sharma A, Ghosh P. Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome-wide data analysis. Genomics 2019; 112:1264-1272. [PMID: 31356968 DOI: 10.1016/j.ygeno.2019.07.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 11/29/2022]
Abstract
Fis (Factor for inversion stimulation) and H-NS (Histone-like nucleoid-structuring protein) are two well-known nucleoid-associated proteins (NAPs) in proteobacteria, which play crucial roles in genome organization and transcriptional regulation. We performed RNA-sequencing to identify genes regulated by these NAPs. Study reveals that Fis and H-NS affect expression of 462 and 88 genes respectively in Escherichia coli at mid-exponential growth phase. By integrating available ChIP-seq data, we identified direct and indirect regulons of Fis and H-NS proteins. Functional analysis reveals that Fis controls expression of genes involved in translation, oxidative phosphorylation, sugar metabolism and transport, amino acid metabolism, bacteriocin transport, cell division, two-component system, biofilm formation, pilus organization and lipopolysaccharide biosynthesis pathways. However, H-NS represses expression of genes in cell adhesion, recombination, biofilm formation and lipopolysaccharide biosynthesis pathways under mid-exponential growth condition. The current regulatory networks thus provide a global glimpse of coordinated regulatory roles for these two important NAPs.
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Affiliation(s)
- Priyanka Gawade
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India
| | - Gaurav Gunjal
- Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Anamika Sharma
- Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Payel Ghosh
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India.
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8
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Kim J, Choi D, Cha SY, Oh YM, Hwang E, Park C, Ryu KS. Zinc-mediated Reversible Multimerization of Hsp31 Enhances the Activity of Holding Chaperone. J Mol Biol 2018; 430:1760-1772. [PMID: 29709570 DOI: 10.1016/j.jmb.2018.04.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 04/10/2018] [Accepted: 04/20/2018] [Indexed: 10/17/2022]
Abstract
Hsp31 protein, belonging to the DJ-1/ThiJ/PfpI superfamily, increases the survival of Escherichia coli under various stresses. While it was reported as a holding chaperone, Hsp31 was also shown to exhibit the glyoxalase III activity in subsequent study. Here, we describe our finding that Hsp31 undergoes a Zn+2-mediated multimerization (HMWZinc), resulting in an enhanced chaperone activity. Furthermore, it was shown that the formation of HMWZinc is reversible such that the oligomer dissociates into the native dimer by EDTA incubation. We attempted to determine the structural change involving the transition between the native dimer and HMWZinc by adding Ni+2, which is Zn+2-mimetic, producing a potential intermediate structure. An analysis of this intermediate revealed a structure with hydrophobic interior exposed, due to an unfolding of the N-terminal loop and the C-terminal β-to-α region. A treatment with hydrogen peroxide accelerated HMWZinc formation, so that the Hsp31C185E mutant rendered the formation of HMWZinc even at 45 °C. However, the presence of Zn+2 in the catalytic site antagonizes the oxidation of C185, implying a negative role. Our results suggest an unprecedented mechanism of the enhancing chaperone activity by Hsp31, in which the reversible formation of HMWZinc occurs in the presence of heat and Zn+2 ion.
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Affiliation(s)
- Jihong Kim
- Protein Structure Group, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do 28119, South Korea; Department of Biological Sciences, KAIST, 291 Daehak-Ro, Yuseong-Gu, Daejeon 34141, South Korea
| | - Dongwook Choi
- Protein Structure Group, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do 28119, South Korea; Department of Biological Sciences, KAIST, 291 Daehak-Ro, Yuseong-Gu, Daejeon 34141, South Korea
| | - So-Young Cha
- Protein Structure Group, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do 28119, South Korea
| | - Young-Mee Oh
- Department of Biological Sciences, KAIST, 291 Daehak-Ro, Yuseong-Gu, Daejeon 34141, South Korea
| | - Eunha Hwang
- Protein Structure Group, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do 28119, South Korea
| | - Chankyu Park
- Department of Biological Sciences, KAIST, 291 Daehak-Ro, Yuseong-Gu, Daejeon 34141, South Korea.
| | - Kyoung-Seok Ryu
- Protein Structure Group, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do 28119, South Korea; Department of Bio-Analytical Science, University of Science and Technology, Daejeon 34113, South Korea.
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Islam T, Ghosh A. Genome-wide dissection and expression profiling of unique glyoxalase III genes in soybean reveal the differential pattern of transcriptional regulation. Sci Rep 2018; 8:4848. [PMID: 29555947 PMCID: PMC5859077 DOI: 10.1038/s41598-018-23124-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 03/02/2018] [Indexed: 11/28/2022] Open
Abstract
Reactive carbonyl species, such as methylglyoxal and glyoxal are very toxic in nature and can inactivate various cellular macromolecules such as DNA, RNA, and protein by forming advanced glycation end products. Conventional glyoxalase pathway with two enzymes- glyoxalase I and glyoxalase II, detoxify MG into D-lactate with the help of reduced glutathione. However, DJ-1/PfpI domain(s) containing DJ-1/ Hsp31 proteins do the same in a single step, and thus termed as "glyoxalase III". A comprehensive genome-wide analysis of soybean identified eleven putative glyoxalase III proteins with DJ-1/PfpI domain encoded by seven genes. Most of these proteins are predicted to be mitochondria and chloroplast localized. In spite of similar function, a differential evolution pattern was observed between Hsp31 and DJ-1 proteins. Expression of GmDJ-1A, GmDJ-1B, and GmDJ-1D2 transcripts was found to be constitutive in different tissues and developmental stages. Transcript profiling revealed the strong substrate-specific upregulation of GmDJ-1 genes in response to exogenous methylglyoxal exposure. Out of seven genes, GmDJ-1D1 and GmDJ-1D2 showed maximum upregulation against salinity, dehydration, and oxidative stresses. Moreover, GmDJ-1D2 showed functional glyoxalase III enzyme activity by utilizing MG as a substrate. Overall, this study identifies some novel tissue-specific and abiotic stress-responsive GmDJ-1 genes that could be investigated further.
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Affiliation(s)
- Tahmina Islam
- Plant Breeding and Biotechnology Laboratory, Department of Botany, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh.
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Köln, 50829, Germany.
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Biran D, Rotem O, Rosen R, Ron EZ. Coping with High Temperature: A Unique Regulation in A. tumefaciens. Curr Top Microbiol Immunol 2018; 418:185-194. [PMID: 30182196 DOI: 10.1007/82_2018_119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Elevation of temperature is a frequent and considerable stress for mesophilic bacteria. Therefore, several molecular mechanisms have evolved to cope with high temperature. We have been studying the response of Agrobacterium tumefaciens to temperature stress, focusing on two aspects: the heat-shock response and the temperature-dependent regulation of methionine biosynthesis. The results indicate that the molecular mechanisms involved in A. tumefaciens control of growth at high temperature are unique and we are still missing important information essential for understanding how these bacteria cope with temperature stress.
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Affiliation(s)
- Dvora Biran
- School of Molecular Cell Biology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Or Rotem
- School of Molecular Cell Biology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Ran Rosen
- School of Molecular Cell Biology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Eliora Z Ron
- School of Molecular Cell Biology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel.
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Kim J, Choi D, Park C, Ryu KS. Backbone resonance assignments of the Escherichia coli 62 kDa protein, Hsp31. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:159-163. [PMID: 28258548 DOI: 10.1007/s12104-017-9739-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 02/24/2017] [Indexed: 06/06/2023]
Abstract
Dimeric Hsp31 protein was first characterized as a holding chaperone of Escherichia coli (E. coli), and has been suggested as having protease activity due to the presence of a potential catalytic triad, Cys185, His186, and Asp214. However, it has recently been reported that Hsp31 displays a relatively strong glyoxalase III activity that can decompose reactive carbonyl species (methylglyoxal and glyoxal) in the absence of additional cofactor. Hsp31 is a representative member of the DJ-1/ThiJ/PfpI protein superfamily, and the importance of DJ-1 protein in Parkinson's disease has been well known. The structural flexibility of the long loop region, which encompasses from the P- to the A-domain, is important for the chaperone activity of Hsp31. The backbone chemical shifts (CSs) would be useful for studying the structural changes of Hsp31 that are critical for the holding chaperone activity, and also for deciphering the switching mechanism between the glyoxalase III and the chaperone. Here, we report the backbone CSs (HN, N, CO, Cα, and Cβ) of the deuterated Hsp31 protein (62 kDa). The CS analysis showed that the predicted regions of secondary structures are in good agreement with those observed in the previous crystal structure of Hsp31.
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Affiliation(s)
- Jihong Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Protein Structure Group, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do, 28119, Republic of Korea
| | - Dongwook Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
- Protein Structure Group, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do, 28119, Republic of Korea
- New Drug Development Center, Osong Medical Innovation Foundation, 123 Osongsaengmyeong-Ro, Osong-Eup, Heungdeok-Gu, Cheongju-Si, Chungcheongbuk-Do, 28160, Republic of Korea
| | - Chankyu Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
| | - Kyoung-Seok Ryu
- Protein Structure Group, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do, 28119, Republic of Korea.
- Department of Bio-Analytical Science, University of Science and Technology, 217 Gajeong-Ro, Yuseong-Gu, Daejon, 34113, Republic of Korea.
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Kim J, Choi D, Park C, Ryu KS. Per-deuteration and NMR experiments for the backbone assignment of 62 kDa protein, Hsp31. JOURNAL OF THE KOREAN MAGNETIC RESONANCE SOCIETY 2015. [DOI: 10.6564/jkmrs.2015.19.3.112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Lee C, Lee J, Lee JY, Park C. Characterization of theEscherichia coliYajL, YhbO and ElbB glyoxalases. FEMS Microbiol Lett 2015; 363:fnv239. [DOI: 10.1093/femsle/fnv239] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2015] [Indexed: 01/07/2023] Open
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14
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Herbst FA, Danielsen HN, Wimmer R, Nielsen PH, Dueholm MS. Label-free quantification reveals major proteomic changes in Pseudomonas putida F1 during the exponential growth phase. Proteomics 2015; 15:3244-52. [PMID: 26122999 DOI: 10.1002/pmic.201400482] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 04/30/2015] [Accepted: 06/26/2015] [Indexed: 01/12/2023]
Abstract
The physiological adaptation to stationary growth by Pseudomonas putida F1, a model organism for the degradation of aromatic compounds, was investigated by proteome-wide label-free quantification.The data unveiled that entrance to the stationary phase did not involve an abrupt switch within the P. putida F1 proteome, but rather an ongoing adaptation that started already during the mid-exponential growth phase. The proteomic adaptations involved a clear increase in amino acid degradation capabilities and a loss of transcriptional as well as translational capacity. The final entrance to the stationary phase was accompanied by increased oxidative stress protection, although the stress and stationary sigma factor RpoS increased in abundance already during mid-exponential growth. The results show that it is important to consider significant sample variations when exponentially growing cultures are studied alone or compared across proteomic or transcriptomic literature. All MS data have been deposited in the ProteomeXchange with identifier PXD001219 (http://proteomecentral.proteomexchange.org/dataset/PXD001219).
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Affiliation(s)
- Florian-Alexander Herbst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Heidi Nolsøe Danielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Reinhard Wimmer
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjaer Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Simonsen Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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15
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Mihoub M, Abdallah J, Gontero B, Dairou J, Richarme G. The DJ-1 superfamily member Hsp31 repairs proteins from glycation by methylglyoxal and glyoxal. Biochem Biophys Res Commun 2015; 463:1305-10. [PMID: 26102038 DOI: 10.1016/j.bbrc.2015.06.111] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 06/17/2015] [Indexed: 01/25/2023]
Abstract
Hsp31 belongs to the PfpI/Hsp31/DJ-1 superfamily, and has been reported to display chaperone, peptidase and glutathione-independent glyoxalase activities. Here, we show that Hsp31 repairs glyoxal- and methylglyoxal-glycated amino acids and proteins and releases repaired proteins and lactate or glycolate, respectively. Hsp31 deglycates cysteine, arginine and lysine by acting on early glycation intermediates (hemithioacetals and aminocarbinols) and prevents the formation of Schiff bases and advanced glycation endproducts. Hsp31 repairs glycated serum albumin, glyceraldehyde-3-phosphate dehydrogenase, fructose biphosphate aldolase and aspartate aminotransferase. Moreover, we show that bacterial extracts from the hchA mutant display increased glycation levels and that the apparent glyoxalase activity of Hsp31 reflects its deglycase activity. Our results suggest that other Hsp31 members, previously characterized as glutathione-independent glyoxalases, likely function as protein deglycases.
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Affiliation(s)
- Mouadh Mihoub
- Stress Molecules, Institut Jacques Monod, Université Paris 7, CNRS UMR 7592, 15 Rue Hélène Brion, 75013 Paris, France
| | - Jad Abdallah
- Stress Molecules, Institut Jacques Monod, Université Paris 7, CNRS UMR 7592, 15 Rue Hélène Brion, 75013 Paris, France
| | | | - Julien Dairou
- Stress Molecules, Institut Jacques Monod, Université Paris 7, CNRS UMR 7592, 15 Rue Hélène Brion, 75013 Paris, France
| | - Gilbert Richarme
- Stress Molecules, Institut Jacques Monod, Université Paris 7, CNRS UMR 7592, 15 Rue Hélène Brion, 75013 Paris, France.
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16
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Martínez P, Huedo P, Martinez-Servat S, Planell R, Ferrer-Navarro M, Daura X, Yero D, Gibert I. Stenotrophomonas maltophilia responds to exogenous AHL signals through the LuxR solo SmoR (Smlt1839). Front Cell Infect Microbiol 2015; 5:41. [PMID: 26029670 PMCID: PMC4432800 DOI: 10.3389/fcimb.2015.00041] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/28/2015] [Indexed: 11/22/2022] Open
Abstract
Quorum Sensing (QS) mediated by Acyl Homoserine Lactone (AHL) molecules are probably the most widespread and studied among Gram-negative bacteria. Canonical AHL systems are composed by a synthase (LuxI family) and a regulator element (LuxR family), whose genes are usually adjacent in the genome. However, incomplete AHL-QS machinery lacking the synthase LuxI is frequently observed in Proteobacteria, and the regulator element is then referred as LuxR solo. It has been shown that certain LuxR solos participate in interspecific communication by detecting signals produced by different organisms. In the case of Stenotrophomonas maltophilia, a preliminary genome sequence analysis revealed numerous putative luxR genes, none of them associated to a luxI gene. From these, the hypothetical LuxR solo Smlt1839, here designated SmoR, presents a conserved AHL binding domain and a helix-turn-helix DNA binding motif. Its genomic organization—adjacent to hchA gene—indicate that SmoR belongs to the new family “LuxR regulator chaperone HchA-associated.” AHL-binding assays revealed that SmoR binds to AHLs in-vitro, at least to oxo-C8-homoserine lactone, and it regulates operon transcription, likely by recognizing a conserved palindromic regulatory box in the hchA upstream region. Supplementation with concentrated supernatants from Pseudomonas aeruginosa, which contain significant amounts of AHLs, promoted swarming motility in S. maltophilia. Contrarily, no swarming stimulation was observed when the P. aeruginosa supernatant was treated with the lactonase AiiA from Bacillus subtilis, confirming that AHL contributes to enhance the swarming ability of S. maltophilia. Finally, mutation of smoR resulted in a swarming alteration and an apparent insensitivity to the exogenous AHLs provided by P. aeruginosa. In conclusion, our results demonstrate that S. maltophilia senses AHLs produced by neighboring bacteria through the LuxR solo SmoR, regulating population behaviors such as swarming motility.
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Affiliation(s)
- Paula Martínez
- Grup de Genètica Molecular i Patogènesi Bacteriana, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain ; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona Barcelona, Spain
| | - Pol Huedo
- Grup de Genètica Molecular i Patogènesi Bacteriana, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain ; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona Barcelona, Spain
| | - Sònia Martinez-Servat
- Grup de Genètica Molecular i Patogènesi Bacteriana, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain ; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona Barcelona, Spain
| | - Raquel Planell
- Grup de Genètica Molecular i Patogènesi Bacteriana, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain
| | - Mario Ferrer-Navarro
- Grup de Genètica Molecular i Patogènesi Bacteriana, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain
| | - Xavier Daura
- Grup de Genètica Molecular i Patogènesi Bacteriana, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain ; Catalan Institution for Research and Advanced Studies Barcelona, Spain
| | - Daniel Yero
- Grup de Genètica Molecular i Patogènesi Bacteriana, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain ; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona Barcelona, Spain
| | - Isidre Gibert
- Grup de Genètica Molecular i Patogènesi Bacteriana, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain ; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona Barcelona, Spain
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17
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Li J, Overall CC, Nakayasu ES, Kidwai AS, Jones MB, Johnson RC, Nguyen NT, McDermott JE, Ansong C, Heffron F, Cambronne ED, Adkins JN. Analysis of the Salmonella regulatory network suggests involvement of SsrB and H-NS in σ(E)-regulated SPI-2 gene expression. Front Microbiol 2015; 6:27. [PMID: 25713562 PMCID: PMC4322710 DOI: 10.3389/fmicb.2015.00027] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 01/08/2015] [Indexed: 02/04/2023] Open
Abstract
The extracytoplasmic functioning sigma factor σE is known to play an essential role for Salmonella enterica serovar Typhimurium to survive and proliferate in macrophages and mice. However, its regulatory network is not well-characterized, especially during infection. Here we used microarray to identify genes regulated by σE in Salmonella grown in three conditions: a nutrient-rich condition and two others that mimic early and late intracellular infection. We found that in each condition σE regulated different sets of genes, and notably, several global regulators. When comparing nutrient-rich and infection-like conditions, large changes were observed in the expression of genes involved in Salmonella pathogenesis island (SPI)-1 type-three secretion system (TTSS), SPI-2 TTSS, protein synthesis, and stress responses. In total, the expression of 58% of Salmonella genes was affected by σE in at least one of the three conditions. An important finding is that σE up-regulates SPI-2 genes, which are essential for Salmonella intracellular survival, by up-regulating SPI-2 activator ssrB expression at the early stage of infection and down-regulating SPI-2 repressor hns expression at a later stage. Moreover, σE is capable of countering the silencing of H-NS, releasing the expression of SPI-2 genes. This connection between σE and SPI-2 genes, combined with the global regulatory effect of σE, may account for the lethality of rpoE-deficient Salmonella in murine infection.
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Affiliation(s)
- Jie Li
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University Portland, OR, USA
| | - Christopher C Overall
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Afshan S Kidwai
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University Portland, OR, USA
| | - Marcus B Jones
- Department of Infectious Diseases, J. Craig Venter Institute Rockville, MD, USA
| | - Rudd C Johnson
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University Portland, OR, USA
| | - Nhu T Nguyen
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University Portland, OR, USA
| | - Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Fred Heffron
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University Portland, OR, USA
| | - Eric D Cambronne
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University Portland, OR, USA
| | - Joshua N Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
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18
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Zhao Q, Su Y, Wang Z, Chen C, Wu T, Huang Y. Identification of glutathione (GSH)-independent glyoxalase III from Schizosaccharomyces pombe. BMC Evol Biol 2014; 14:86. [PMID: 24758716 PMCID: PMC4021431 DOI: 10.1186/1471-2148-14-86] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 04/15/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reactive carbonyl species (RCS), such as methylglyoxal (MG) and glyoxal (GO), are synthesized as toxic metabolites in living systems. Mechanisms of RCS detoxification include the glutathione (GSH)-dependent system consisting of glyoxalase I (GLO1) and glyoxalase II (GLO2), and GSH-independent system involving glyoxalase III (GLO3). Hsp31 and DJ-1 proteins are weakly homologous to each other and belong to two different subfamilies of the DJ-1/Hsp31/PfpI superfamily. Recently, the Escherichia coli Hsp31 protein and the DJ-1 proteins from Arabidopsis thaliana and metazoans have been demonstrated to have GLO3 activity. RESULTS We performed a systematic survey of homologs of DJ-1 and Hsp31 in fungi. We found that DJ-1 proteins have a very limited distribution in fungi, whereas Hsp31 proteins are widely distributed among different fungal groups. Phylogenetic analysis revealed that fungal and metazoan DJ-1 proteins and bacterial YajL proteins are most closely related and together form a sister clade to bacterial and fungal Hsp31 proteins. We showed that two Schizosaccharomyces pombe Hsp31 proteins (Hsp3101 and Hsp3102) and one Saccharomyces cerevisiae Hsp31 protein (ScHsp31) displayed significantly higher in vitro GLO3 activity than S. pombe DJ-1 (SpDJ-1). Overexpression of hsp3101, hsp3102 and ScHSP31 could confer MG and GO resistance on either wild-type S. pombe cells or GLO1 deletion of S. pombe. S. pombe DJ-1 and Hsp31 proteins exhibit different patterns of subcellular localization. CONCLUSIONS Our results suggest that fungal Hsp31 proteins are the major GLO3 that may have some role in protecting cells from RCS toxicity in fungi. Our results also support the view that the GLO3 activity of Hsp31 proteins may have evolved independently from that of DJ-1 proteins.
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Affiliation(s)
| | | | | | | | | | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China.
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19
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Yeast DJ-1 superfamily members are required for diauxic-shift reprogramming and cell survival in stationary phase. Proc Natl Acad Sci U S A 2014; 111:7012-7. [PMID: 24706893 DOI: 10.1073/pnas.1319221111] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The yeast Hsp31 minifamily proteins (Hsp31, Hsp32, Hsp33, Hsp34) belong to the highly conserved DJ-1 superfamily. The human DJ-1 protein is associated with cancer and neurodegenerative disorders, such as Parkinson disease. However, the precise function of human and yeast DJ-1 proteins is unclear. Here we show that the yeast DJ-1 homologs have a role in diauxic-shift (DS), characterized by metabolic reprogramming because of glucose limitation. We find that the Hsp31 genes are strongly induced in DS and in stationary phase (SP), and that deletion of these genes reduces chronological lifespan, impairs transcriptional reprogramming at DS, and impairs the acquisition of several typical characteristics of SP, including autophagy induction. In addition, under carbon starvation, the HSP31 family gene-deletion strains display impaired autophagy, disrupted target of rapamycin complex 1 (TORC1) localization to P-bodies, and caused abnormal TORC1-mediated Atg13 phosphorylation. Repression of TORC1 by rapamycin in the gene-deletion strains completely reversed their sensitivity to heat shock. Taken together, our data indicate that Hsp31 minifamily is required for DS reprogramming and cell survival in SP, and plays a role upstream of TORC1. The enhanced understanding of the cellular function of these genes sheds light into the biological role of other members of the superfamily, including DJ-1, which is an attractive target for therapeutic intervention in cancer and in Parkinson disease.
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20
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Vidovic S, Korber DR. Escherichia coli O157: Insights into the adaptive stress physiology and the influence of stressors on epidemiology and ecology of this human pathogen. Crit Rev Microbiol 2014; 42:83-93. [PMID: 24601836 DOI: 10.3109/1040841x.2014.889654] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Escherichia coli O157, a foodborne pathogen of major concern for public health, has been associated with numerous outbreaks of haemorrhagic colitis and hemolytic uremic syndrome worldwide. Human infection with E. coli O157 has been primarily associated with the food-chain transmission route. This transmission route commonly elicits a multi-faceted adaptive stress response of E. coli O157 for an extended period of time prior to human infection. Several recent research articles have indicated that E. coli O157:H7 has evolved unique survival characteristics which can affect the epidemiology and ecology of this zoonotic pathogen. This review article summarizes the recent knowledge of the molecular responses of E. coli O157 to the most common stressors found within the human food chain, and further emphasizes the influence of these stressors on the epidemiology and ecology of E. coli O157.
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Affiliation(s)
- Sinisa Vidovic
- a Department of Food and Bioproducts Sciences , University of Saskatchewan , Saskatchewan , Canada
| | - Darren R Korber
- a Department of Food and Bioproducts Sciences , University of Saskatchewan , Saskatchewan , Canada
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21
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Su F, Ou HY, Tao F, Tang H, Xu P. PSP: rapid identification of orthologous coding genes under positive selection across multiple closely related prokaryotic genomes. BMC Genomics 2013; 14:924. [PMID: 24373418 PMCID: PMC3882776 DOI: 10.1186/1471-2164-14-924] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 12/26/2013] [Indexed: 11/10/2022] Open
Abstract
Background With genomic sequences of many closely related bacterial strains made available by deep sequencing, it is now possible to investigate trends in prokaryotic microevolution. Positive selection is a sub-process of microevolution, in which a particular mutation is favored, causing the allele frequency to continuously shift in one direction. Wide scanning of prokaryotic genomes has shown that positive selection at the molecular level is much more frequent than expected. Genes with significant positive selection may play key roles in bacterial adaption to different environmental pressures. However, selection pressure analyses are computationally intensive and awkward to configure. Results Here we describe an open access web server, which is designated as PSP (Positive Selection analysis for Prokaryotic genomes) for performing evolutionary analysis on orthologous coding genes, specially designed for rapid comparison of dozens of closely related prokaryotic genomes. Remarkably, PSP facilitates functional exploration at the multiple levels by assignments and enrichments of KO, GO or COG terms. To illustrate this user-friendly tool, we analyzed Escherichia coli and Bacillus cereus genomes and found that several genes, which play key roles in human infection and antibiotic resistance, show significant evidence of positive selection. PSP is freely available to all users without any login requirement at: http://db-mml.sjtu.edu.cn/PSP/. Conclusions PSP ultimately allows researchers to do genome-scale analysis for evolutionary selection across multiple prokaryotic genomes rapidly and easily, and identify the genes undergoing positive selection, which may play key roles in the interactions of host-pathogen and/or environmental adaptation.
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Affiliation(s)
| | | | | | | | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, P,R, China.
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22
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Choi D, Ryu KS, Park C. Structural alteration of Escherichia coli Hsp31 by thermal unfolding increases chaperone activity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012. [PMID: 23202248 DOI: 10.1016/j.bbapap.2012.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Escherichia coli Hsp31, encoded by hchA, is a heat-inducible molecular chaperone. We found that Hsp31 undergoes a conformational change via temperature-induced unfolding, generating a high molecular weight (HMW) form with enhanced chaperone activity. Although it has previously been reported that some subunits of the Hsp31 crystal structure show structural heterogeneity with increased hydrophobic surfaces, Hsp31 basically forms a dimer. We found that a C-terminal deletion (CΔ19) of Hsp31 exhibited structurally and functionally similar characteristics to that of the HMW form. Both the CΔ19 and HMW forms achieved a structure with considerably more β-sheets and less α-helices than the native dimeric form, exposing a portion of its hydrophobic surfaces. The structural alterations were determined from its spectral changes in circular dichroism, intrinsic fluorescence of tryptophan residues, and fluorescence of bis-ANS binding to a hydrophobic surface. Interestingly, during thermal transition, the dimeric Hsp31 undergoes a conformational change to the HMW species via the CΔ19 structure, as monitored with near-UV CD spectrum, implying that the CΔ19 resembles an intermediate state between the dimer and the HMW form. From these results, we propose that Hsp31 transforms itself into a fully functional chaperone by altering its tertiary and quaternary structures.
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Affiliation(s)
- Dongwook Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Gwahangno 335, Yuseong-Gu, Daejon 305-701, South Korea
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23
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Vidovic S, Mangalappalli-Illathu AK, Xiong H, Korber DR. Heat acclimation and the role of RpoS in prolonged heat shock of Escherichia coli O157. Food Microbiol 2012; 30:457-64. [PMID: 22365361 DOI: 10.1016/j.fm.2011.12.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 12/11/2011] [Accepted: 12/28/2011] [Indexed: 11/29/2022]
Abstract
Escherichia coli, a commensal mesophile that primarily inhabits the gastro-intestinal tract, responds to temperature up-shifts with transient expression of stress-response proteins. The goal of this study was to identify adaptive proteins of E. coli O157 crucial for growth resumption of this human pathogen after heat shock, with specific focus on the role of the RpoS sigma factor. Using the comparative proteomic analysis of hyper-thermally acclimatized wild-type strain B-1 and rpoS-mutant strain SV521, we identified 39 proteins that underwent significantly-different induction upon temperature shock at 45°C or rpoS mutation. All identified proteins of the heat post-acclimation stimulon fell into two large sub-groups: (i) stress proteins, including molecular chaperons, proteases, DNA/RNA stabilizing enzymes, and anti-oxidant proteins, and (ii) housekeeping proteins. It was found that in the heat stress stimulon RpoS has significantly (P=0.012) limited control over the key stress proteins involved in translation, translational elongation, protein folding and refolding. However, RpoS showed a significant (P=0.035) control over the cellular metabolic processes that included NADPH regeneration, pentose-phosphate shunt, nicotinamide nucleotide and NADP metabolic processes, reflecting its specific importance in promoting resource utilization (energy, protein synthesis etc.) during proliferation of hyperthermally-adapted cells. Pathogenic strains, like E. coli O157, have the ability to survive a variety of harsh stress conditions, leading to their entry into the food chain, and subsequent pathogenesis. This research offers insights into the physiological response of this pathogen during the critical period following adaptation to thermal stress and subsequent resumption of growth.
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Affiliation(s)
- Sinisa Vidovic
- Department of Food and Bioproducts Sciences, University of Saskatchewan, Saskatoon SK S7N 5A8, Canada
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24
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Subedi KP, Choi D, Kim I, Min B, Park C. Hsp31 of Escherichia coli K-12 is glyoxalase III. Mol Microbiol 2011; 81:926-36. [DOI: 10.1111/j.1365-2958.2011.07736.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Abstract
DJ-1 is a member of the large and functionally diverse DJ-1/PfpI superfamily and has homologs in nearly all organisms. Because of its connection to parkinsonism and cancer, human DJ-1 has been intensely studied for over a decade. The current view is that DJ-1 is a multifunctional oxidative stress response protein that defends cells against reactive oxygen species and mitochondrial damage, although the details of its biochemical function remain unclear. A conserved cysteine residue in DJ-1 (Cys106) is both functionally essential and subject to oxidation to the cysteine-sulfinate and cysteine-sulfonate. Consequently, the oxidative modification of Cys106 has been proposed to allow DJ-1 to act as a sensor of cellular redox homeostasis and to participate in cytoprotective signaling pathways in the cell. This review explores the current evidence for the role of cysteine oxidation in DJ-1 function, with emphasis on emerging models for how oxidative modification may regulate DJ-1's protective function and also contribute to dysfunction and disease.
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Affiliation(s)
- Mark A Wilson
- Department of Biochemistry, Redox Biology Center, The University of Nebraska-Lincoln, 68588-0664, USA.
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26
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Brzuszkiewicz E, Weiner J, Wollherr A, Thürmer A, Hüpeden J, Lomholt HB, Kilian M, Gottschalk G, Daniel R, Mollenkopf HJ, Meyer TF, Brüggemann H. Comparative genomics and transcriptomics of Propionibacterium acnes. PLoS One 2011; 6:e21581. [PMID: 21738717 PMCID: PMC3124536 DOI: 10.1371/journal.pone.0021581] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 06/03/2011] [Indexed: 11/19/2022] Open
Abstract
The anaerobic gram-positive bacterium Propionibacterium acnes is a human skin commensal that is occasionally associated with inflammatory diseases. Recent work has indicated that evolutionary distinct lineages of P. acnes play etiologic roles in disease while others are associated with maintenance of skin homeostasis. To shed light on the molecular basis for differential strain properties, we carried out genomic and transcriptomic analysis of distinct P. acnes strains. We sequenced the genome of the P. acnes strain 266, a type I-1a strain. Comparative genome analysis of strain 266 and four other P. acnes strains revealed that overall genome plasticity is relatively low; however, a number of island-like genomic regions, encoding a variety of putative virulence-associated and fitness traits differ between phylotypes, as judged from PCR analysis of a collection of P. acnes strains. Comparative transcriptome analysis of strains KPA171202 (type I-2) and 266 during exponential growth revealed inter-strain differences in gene expression of transport systems and metabolic pathways. In addition, transcript levels of genes encoding possible virulence factors such as dermatan-sulphate adhesin, polyunsaturated fatty acid isomerase, iron acquisition protein HtaA and lipase GehA were upregulated in strain 266. We investigated differential gene expression during exponential and stationary growth phases. Genes encoding components of the energy-conserving respiratory chain as well as secreted and virulence-associated factors were transcribed during the exponential phase, while the stationary growth phase was characterized by upregulation of genes involved in stress responses and amino acid metabolism. Our data highlight the genomic basis for strain diversity and identify, for the first time, the actively transcribed part of the genome, underlining the important role growth status plays in the inflammation-inducing activity of P. acnes. We argue that the disease-causing potential of different P. acnes strains is not only determined by the phylotype-specific genome content but also by variable gene expression.
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Affiliation(s)
- Elzbieta Brzuszkiewicz
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - January Weiner
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Antje Wollherr
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Andrea Thürmer
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Jennifer Hüpeden
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Hans B. Lomholt
- Department of Medical Microbiology and Immunology, Aarhus University, Aarhus, Denmark
| | - Mogens Kilian
- Department of Medical Microbiology and Immunology, Aarhus University, Aarhus, Denmark
| | - Gerhard Gottschalk
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | | | - Thomas F. Meyer
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Holger Brüggemann
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
- * E-mail:
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27
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Moreira RN, Dressaire C, Domingues S, Arraiano CM. A new target for an old regulator: H-NS represses transcription of bolA morphogene by direct binding to both promoters. Biochem Biophys Res Commun 2011; 411:50-5. [PMID: 21708124 DOI: 10.1016/j.bbrc.2011.06.084] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 06/13/2011] [Indexed: 11/28/2022]
Abstract
The Escherichia coli bolA morphogene is very important in adaptation to stationary phase and stress response mechanisms. Genes of this family are widespread in gram negative bacteria and in eukaryotes. The expression of this gene is tightly regulated at transcriptional and post-transcriptional levels and its overexpression is known to induce round cellular morphology. The results presented in this report demonstrate that the H-NS protein, a pleiotropic regulator of gene expression, is a new transcriptional modulator of the bolA gene. In this work we show that and in vivo the levels of bolA are down-regulated by H-NS and in vitro this global regulator interacts directly with the bolA promoter region. Moreover, DNaseI foot-printing experiments mapped the interaction regions of H-NS and bolA and revealed that this global regulator binds not only one but both bolA promoters. We provide a new insight into the bolA regulation network demonstrating that H-NS represses the transcription of this important gene.
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Affiliation(s)
- Ricardo N Moreira
- Instituto de Tecnologia Química e Biológica/Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
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28
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Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P. In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements. Nucleic Acids Res 2011; 39:5338-55. [PMID: 21398637 PMCID: PMC3141248 DOI: 10.1093/nar/gkr129] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Specific promoter recognition by bacterial RNA polymerase is mediated by σ subunits, which assemble with RNA polymerase core enzyme (E) during transcription initiation. However, σ70 (the housekeeping σ subunit) and σS (an alternative σ subunit mostly active during slow growth) recognize almost identical promoter sequences, thus raising the question of how promoter selectivity is achieved in the bacterial cell. To identify novel sequence determinants for selective promoter recognition, we performed run-off/microarray (ROMA) experiments with RNA polymerase saturated either with σ70 (Eσ70) or with σS (EσS) using the whole Escherichia coli genome as DNA template. We found that Eσ70, in the absence of any additional transcription factor, preferentially transcribes genes associated with fast growth (e.g. ribosomal operons). In contrast, EσS efficiently transcribes genes involved in stress responses, secondary metabolism as well as RNAs from intergenic regions with yet-unknown function. Promoter sequence comparison suggests that, in addition to different conservation of the −35 sequence and of the UP element, selective promoter recognition by either form of RNA polymerase can be affected by the A/T content in the −10/+1 region. Indeed, site-directed mutagenesis experiments confirmed that an A/T bias in the −10/+1 region could improve promoter recognition by EσS.
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Affiliation(s)
- Anna Maciag
- Department of Biomolecular Sciences and Biotechnology, Università degli Studi di Milano, Milan, Italy
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29
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Mukherjee J, Ow SY, Noirel J, Biggs CA. Quantitative protein expression and cell surface characteristics of Escherichia coli MG1655 biofilms. Proteomics 2011; 11:339-51. [PMID: 21268264 DOI: 10.1002/pmic.201000386] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 10/05/2010] [Accepted: 11/01/2010] [Indexed: 11/06/2022]
Abstract
Cell surface physicochemical characterization techniques were combined with quantitative changes in protein expression, to investigate the biological and biophysical changes of Escherichia coli MG1655 cells when grown as a biofilm (BIO). The overall surface charge of BIO cells was found to be less negative, highlighting the need for a lower electrophoretic mobility for attachment to occur. Comparison of the chemical functional groups on the cell surface showed similar profiles, with the absorbance intensity higher for proteins and carbohydrates in the BIO cells. Quantitative proteomic analysis demonstrated that 3 proteins were significantly increased, and 9 proteins significantly decreased in abundance, in cells grown as a BIO compared to their planktonic counterparts, with 7 of these total 12 proteins unique to this study. Proteins showing significant increased or decreased abundance include proteins involved in acid resistance, DNA protection and binding and ABC transporters. Further predictive analysis of the metabolic pathways showed an increased abundance of the amino acid metabolism and tricarboxylic acid (TCA) cycle, with a decrease in expression within the pentose phosphate and glycolysis pathways. It is therefore hypothesized that cells grown as a BIO are still energetically viable potentially using amino acids as an indirect carbon backbone source into the TCA cycle.
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Affiliation(s)
- Joy Mukherjee
- The ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
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30
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Continuous culture and proteomic analysis of Escherichia coli DH5α and its acetate-tolerant mutant DA19 under conditions of nitrogen source limitation. Bioprocess Biosyst Eng 2010; 34:179-87. [DOI: 10.1007/s00449-010-0459-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 07/30/2010] [Indexed: 10/19/2022]
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31
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Shenhar Y, Rasouly A, Biran D, Ron EZ. Adaptation ofEscherichi colito elevated temperatures involves a change in stability of heat shock gene transcripts. Environ Microbiol 2009; 11:2989-97. [DOI: 10.1111/j.1462-2920.2009.01993.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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32
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Sastry MSR, Zhou W, Baneyx F. Integrity of N- and C-termini is important for E. coli Hsp31 chaperone activity. Protein Sci 2009; 18:1439-47. [PMID: 19517531 DOI: 10.1002/pro.158] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Hsp31 is a stress-inducible molecular chaperone involved in the management of protein misfolding at high temperatures and in the development of acid resistance in starved E. coli. Each subunit of the Hsp31 homodimer consists of two structural domains connected by a flexible linker that sits atop a continuous tract of nonpolar residues adjacent to a hydrophobic bowl defined by the dimerization interface. Previously, we proposed that while the bowl serves as a binding site for partially folded species at physiological temperatures, chaperone function under heat shock conditions requires that folding intermediates further anneal to high-affinity binding sites that become uncovered upon thermally induced motion of the linker. In support of a mechanism requiring that client proteins first bind to the bowl, we show here that fusion of a 20-residue-long hexahistidine tag to the N-termini of Hsp31 abolishes chaperone activity at all temperatures by inducing reversible structural changes that interfere with substrate binding. We further demonstrate that extending the C-termini of Hsp31 with short His tags selectively suppresses chaperone function at high temperatures by interfering with linker movement. The structural and functional sensitivity of Hsp31 to lengthening is consistent with the high degree of conservation of class I Hsp31 orthologs and will serve as a cautionary tale on the implications of affinity tagging.
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Affiliation(s)
- M S R Sastry
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
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33
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Fang FC, Rimsky S. New insights into transcriptional regulation by H-NS. Curr Opin Microbiol 2008; 11:113-20. [PMID: 18387844 DOI: 10.1016/j.mib.2008.02.011] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2008] [Revised: 02/14/2008] [Accepted: 02/21/2008] [Indexed: 11/25/2022]
Abstract
H-NS, a nucleoid-associated DNA-binding protein of enteric bacteria, was discovered 35 years ago and subsequently found to exert widespread and highly pleiotropic effects on gene regulation. H-NS binds to high-affinity sites and spreads along adjacent AT-rich DNA to silence transcription. Preferential binding to sequences with higher AT-content than the resident genome allows H-NS to repress the expression of foreign DNA in a process known as 'xenogeneic silencing.' Counter-silencing by a variety of mechanisms facilitates the evolutionary acquisition of horizontally transferred genes and their integration into pre-existing regulatory networks. This review will highlight recent insights into the mechanism and biological importance of H-NS-DNA interactions.
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Affiliation(s)
- Ferric C Fang
- Department of Laboratory Medicine, University of Washington School of Medicine, 1959 NE Pacific Street, Box 357242, Seattle, WA 98195-7242 USA.
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34
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Rasouly A, Shenhar Y, Ron EZ. Thermoregulation of Escherichia coli hchA transcript stability. J Bacteriol 2007; 189:5779-81. [PMID: 17526696 PMCID: PMC1951820 DOI: 10.1128/jb.00453-07] [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: 11/20/2022] Open
Abstract
The conserved chaperone Hsp31 of Escherichia coli is transcribed at low temperatures by sigma(S) and repressed by H-NS, whereas at high temperature, transcription is by sigma70 independently of both sigma(S) and H-NS. Here we present evidence for an additional, novel, temperature-dependent control of Hsp31 expression by increased transcript stability.
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Affiliation(s)
- Aviram Rasouly
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel, 69978
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35
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Mujacic M, Baneyx F. Chaperone Hsp31 contributes to acid resistance in stationary-phase Escherichia coli. Appl Environ Microbiol 2006; 73:1014-8. [PMID: 17158627 PMCID: PMC1800746 DOI: 10.1128/aem.02429-06] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Hsp31, the product of the sigmaS - and sigmaD -dependent hchA gene, is a heat-inducible chaperone implicated in the management of protein misfolding at high temperatures. We show here that Hsp31 plays an important role in the acid resistance of starved Escherichia coli but that it has little influence on oxidative-stress survival.
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Affiliation(s)
- Mirna Mujacic
- Department of Bioengineering, University of Washington, Box 351750, Seattle, WA 98195-1750, USA
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