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McIntosh M, Köchling T, Latz A, Kretz J, Heinen S, Konzer A, Klug G. A major checkpoint for protein expression in Rhodobacter sphaeroides during heat stress response occurs at the level of translation. Environ Microbiol 2021; 23:6483-6502. [PMID: 34668288 DOI: 10.1111/1462-2920.15818] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 10/05/2021] [Indexed: 12/24/2022]
Abstract
Temperature above the physiological optimum is a stress condition frequently faced by bacteria in their natural environments. Here, we were interested in the correlation between levels of RNA and protein under heat stress. Changes in RNA and protein levels were documented in cultures of Rhodobacter sphaeroides using RNA sequencing, quantitative mass spectrometry, western blot analysis, in vivo [35 S] methionine-labelling and plasmid-borne reporter fusions. Changes in the transcriptome were extensive. Strikingly, the proteome remained unchanged except for very few proteins. Examples include a heat shock protein, a DUF1127 protein of unknown function and sigma factor proteins from leaderless transcripts. Insight from this study indicates that R. sphaeroides responds to heat stress by producing a broad range of transcripts while simultaneously preventing translation from nearly all of them, and that this selective production of protein depends on the untranslated region of the transcript. We conclude that measurements of transcript abundance are insufficient to understand gene regulation. Rather, translation can be an important checkpoint for protein expression under certain environmental conditions. Furthermore, during heat shock, regulation at the level of transcription might represent preparation for survival in an unpredictable environment while regulation at translation ensures production of only a few proteins.
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Affiliation(s)
- Matthew McIntosh
- Institute of Microbiology und Molecular Biology, IFZ, Justus-Liebig-Universität, 35292, Giessen, Germany
| | - Thorsten Köchling
- Institute of Microbiology und Molecular Biology, IFZ, Justus-Liebig-Universität, 35292, Giessen, Germany
| | - Anna Latz
- Institute of Microbiology und Molecular Biology, IFZ, Justus-Liebig-Universität, 35292, Giessen, Germany
| | - Jonas Kretz
- Institute of Microbiology und Molecular Biology, IFZ, Justus-Liebig-Universität, 35292, Giessen, Germany
| | - Sandra Heinen
- Institute of Microbiology und Molecular Biology, IFZ, Justus-Liebig-Universität, 35292, Giessen, Germany
| | - Anne Konzer
- Biomolecular Mass Spectrometry, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Gabriele Klug
- Institute of Microbiology und Molecular Biology, IFZ, Justus-Liebig-Universität, 35292, Giessen, Germany
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2
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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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3
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A proteomic analysis of salt stress response in seedlings of two African rice cultivars. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1570-8. [DOI: 10.1016/j.bbapap.2016.08.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/08/2016] [Accepted: 08/15/2016] [Indexed: 11/20/2022]
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4
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Cho H, Chou HH. Thermodynamically optimal whole-genome tiling microarray design and validation. BMC Res Notes 2016; 9:305. [PMID: 27295952 PMCID: PMC4906886 DOI: 10.1186/s13104-016-2113-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 06/01/2016] [Indexed: 11/10/2022] Open
Abstract
Background Microarray is an efficient apparatus to interrogate the whole transcriptome of species. Microarray can be designed according to annotated gene sets, but the resulted microarrays cannot be used to identify novel transcripts and this design method is not applicable to unannotated species. Alternatively, a whole-genome tiling microarray can be designed using only genomic sequences without gene annotations, and it can be used to detect novel RNA transcripts as well as known genes. The difficulty with tiling microarray design lies in the tradeoff between probe-specificity and coverage of the genome. Sequence comparison methods based on BLAST or similar software are commonly employed in microarray design, but they cannot precisely determine the subtle thermodynamic competition between probe targets and partially matched probe nontargets during hybridizations. Findings Using the whole-genome thermodynamic analysis software PICKY to design tiling microarrays, we can achieve maximum whole-genome coverage allowable under the thermodynamic constraints of each target genome. The resulted tiling microarrays are thermodynamically optimal in the sense that all selected probes share the same melting temperature separation range between their targets and closest nontargets, and no additional probes can be added without violating the specificity of the microarray to the target genome. Conclusions This new design method was used to create two whole-genome tiling microarrays for Escherichia coli MG1655 and Agrobacterium tumefaciens C58 and the experiment results validated the design. Electronic supplementary material The online version of this article (doi:10.1186/s13104-016-2113-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hyejin Cho
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Hui-Hsien Chou
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA. .,Department of Computer Science, Iowa State University, Ames, IA, 50011, USA.
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Hemme D, Veyel D, Mühlhaus T, Sommer F, Jüppner J, Unger AK, Sandmann M, Fehrle I, Schönfelder S, Steup M, Geimer S, Kopka J, Giavalisco P, Schroda M. Systems-wide analysis of acclimation responses to long-term heat stress and recovery in the photosynthetic model organism Chlamydomonas reinhardtii. THE PLANT CELL 2014; 26:4270-97. [PMID: 25415976 PMCID: PMC4277220 DOI: 10.1105/tpc.114.130997] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/13/2014] [Accepted: 10/24/2014] [Indexed: 05/19/2023]
Abstract
We applied a top-down systems biology approach to understand how Chlamydomonas reinhardtii acclimates to long-term heat stress (HS) and recovers from it. For this, we shifted cells from 25 to 42°C for 24 h and back to 25°C for ≥8 h and monitored abundances of 1856 proteins/protein groups, 99 polar and 185 lipophilic metabolites, and cytological and photosynthesis parameters. Our data indicate that acclimation of Chlamydomonas to long-term HS consists of a temporally ordered, orchestrated implementation of response elements at various system levels. These comprise (1) cell cycle arrest; (2) catabolism of larger molecules to generate compounds with roles in stress protection; (3) accumulation of molecular chaperones to restore protein homeostasis together with compatible solutes; (4) redirection of photosynthetic energy and reducing power from the Calvin cycle to the de novo synthesis of saturated fatty acids to replace polyunsaturated ones in membrane lipids, which are deposited in lipid bodies; and (5) when sinks for photosynthetic energy and reducing power are depleted, resumption of Calvin cycle activity associated with increased photorespiration, accumulation of reactive oxygen species scavengers, and throttling of linear electron flow by antenna uncoupling. During recovery from HS, cells appear to focus on processes allowing rapid resumption of growth rather than restoring pre-HS conditions.
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Affiliation(s)
- Dorothea Hemme
- Molekulare Biotechnologie and Systembiologie, TU Kaiserslautern, D-67663 Kaiserslautern, Germany Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Daniel Veyel
- Molekulare Biotechnologie and Systembiologie, TU Kaiserslautern, D-67663 Kaiserslautern, Germany Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Timo Mühlhaus
- Molekulare Biotechnologie and Systembiologie, TU Kaiserslautern, D-67663 Kaiserslautern, Germany Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Frederik Sommer
- Molekulare Biotechnologie and Systembiologie, TU Kaiserslautern, D-67663 Kaiserslautern, Germany Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Jessica Jüppner
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Ann-Katrin Unger
- Zellbiologie/Elektronenmikroskopie, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Michael Sandmann
- Institut für Biochemie und Biologie, Universität Potsdam, D-14476 Potsdam-Golm, Germany
| | - Ines Fehrle
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Stephanie Schönfelder
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Martin Steup
- Institut für Biochemie und Biologie, Universität Potsdam, D-14476 Potsdam-Golm, Germany
| | - Stefan Geimer
- Zellbiologie/Elektronenmikroskopie, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Joachim Kopka
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Patrick Giavalisco
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
| | - Michael Schroda
- Molekulare Biotechnologie and Systembiologie, TU Kaiserslautern, D-67663 Kaiserslautern, Germany Max-Planck-Institut für Molekulare Pflanzenphysiologie, D-14476 Potsdam-Golm, Germany
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6
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Tsai YL, Chiang YR, Wu CF, Narberhaus F, Lai EM. One out of four: HspL but no other small heat shock protein of Agrobacterium tumefaciens acts as efficient virulence-promoting VirB8 chaperone. PLoS One 2012. [PMID: 23185409 PMCID: PMC3504140 DOI: 10.1371/journal.pone.0049685] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Alpha-crystallin-type small heat shock proteins (sHsps) are ubiquitously distributed in most eukaryotes and prokaryotes. Four sHsp genes named hspL, hspC, hspAT1, and hspAT2 were identified in Agrobacterium tumefaciens, a plant pathogenic bacterium capable of unique interkingdom DNA transfer via type IV secretion system (T4SS). HspL is highly expressed in virulence-induced growth condition and functions as a VirB8 chaperone to promote T4SS-mediated DNA transfer. Here, we used genetic and biochemical approaches to investigate the involvement of the other three sHsps in T4SS and discovered the molecular basis underlying the dominant function of HspL in promoting T4SS function. While single deletion of hspL but no other sHsp gene reduced T4SS-mediated DNA transfer and tumorigenesis efficiency, additional deletion of other sHsp genes in the hspL deletion background caused synergistic effects in the virulence phenotypes. This is correlated with the high induction of hspL and only modest increase of hspC, hspAT1, and hspAT2 at their mRNA and protein abundance in virulence-induced growth condition. Interestingly, overexpression of any single sHsp gene alone in the quadruple mutant caused increased T4SS-mediated DNA transfer and tumorigenesis. Thermal aggregation protecting assays in vitro indicated that all four sHsps exhibit chaperone activity for the model substrate citrate synthase but only HspL functions as efficient chaperone for VirB8. The higher VirB8 chaperone activity of HspL was also demonstrated in vivo, in which lower amounts of HspL than other sHsps were sufficient in maintaining VirB8 homeostasis in A. tumefaciens. Domain swapping between HspL and HspAT2 indicated that N-terminal, central alpha-crystallin, and C-terminal domains of HspL all contribute to HspL function as an efficient VirB8 chaperone. Taken together, we suggest that the dominant role of HspL in promoting T4SS function is based on its higher expression in virulence-induced condition and its more efficient VirB8 chaperone activity as compared to other sHsps.
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Affiliation(s)
- Yun-Long Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yin-Ru Chiang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chih-Feng Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Franz Narberhaus
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, Bochum, Germany
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- * E-mail:
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7
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Rosen R, Matthysse AG, Becher D, Biran D, Yura T, Hecker M, Ron EZ. Proteome analysis of plant-induced proteins of Agrobacterium tumefaciens. FEMS Microbiol Ecol 2012; 44:355-60. [PMID: 19719616 DOI: 10.1016/s0168-6496(03)00077-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Abstract A proteome study of Agrobacterium tumefaciens exposed to plant roots demonstrated the existence of a plant-dependent stimulon. This stimulon was induced by exposure to cut roots and consists of at least 30 soluble proteins (pI 4-7), including several proteins whose involvement in agrobacteria-host interactions has not been previously reported. Exposure of the bacteria to tomato roots also resulted in modification of the proteins: Ribosomal Protein L19, GroEL, AttM, and ChvE, indicating the significance of protein modifications in the interactions of agrobacteria with plants.
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Affiliation(s)
- Ran Rosen
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
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8
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Rosen R, Ron EZ. Proteomics of a plant pathogen: Agrobacterium tumefaciens. Proteomics 2011; 11:3134-42. [DOI: 10.1002/pmic.201100019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 03/13/2011] [Accepted: 03/14/2011] [Indexed: 12/31/2022]
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9
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Yang FL, Yang YL, Wu SH. Structure and function of glycolipids in thermophilic bacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 705:367-80. [PMID: 21618118 DOI: 10.1007/978-1-4419-7877-6_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Feng-Ling Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.
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10
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Tsai YL, Chiang YR, Narberhaus F, Baron C, Lai EM. The small heat-shock protein HspL is a VirB8 chaperone promoting type IV secretion-mediated DNA transfer. J Biol Chem 2010; 285:19757-66. [PMID: 20427270 DOI: 10.1074/jbc.m110.110296] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Agrobacterium tumefaciens is a plant pathogen that utilizes a type IV secretion system (T4SS) to transfer DNA and effector proteins into host cells. In this study we discovered that an alpha-crystallin type small heat-shock protein (alpha-Hsp), HspL, is a molecular chaperone for VirB8, a T4SS assembly factor. HspL is a typical alpha-Hsp capable of protecting the heat-labile model substrate citrate synthase from thermal aggregation. It forms oligomers in a concentration-dependent manner in vitro. Biochemical fractionation revealed that HspL is mainly localized in the inner membrane and formed large complexes with certain VirB protein subassemblies. Protein-protein interaction studies indicated that HspL interacts with VirB8, a bitopic integral inner membrane protein that is essential for T4SS assembly. Most importantly, HspL is able to prevent the aggregation of VirB8 fused with glutathione S-transferase in vitro, suggesting that it plays a role as VirB8 chaperone. The chaperone activity of two HspL variants with amino acid substitutions (F98A and G118A) for both citrate synthase and glutathione S-transferase-VirB8 was reduced and correlated with HspL functions in T4SS-mediated DNA transfer and virulence. This study directly links in vitro and in vivo functions of an alpha-Hsp and reveals a novel alpha-Hsp function in T4SS stability and bacterial virulence.
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Affiliation(s)
- Yun-Long Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
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11
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Gelvin SB. Agrobacterium in the genomics age. PLANT PHYSIOLOGY 2009; 150:1665-76. [PMID: 19439569 PMCID: PMC2719113 DOI: 10.1104/pp.109.139873] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2009] [Accepted: 05/06/2009] [Indexed: 05/18/2023]
Affiliation(s)
- Stanton B Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA.
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12
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Tsai YL, Wang MH, Gao C, Klüsener S, Baron C, Narberhaus F, Lai EM. Small heat-shock protein HspL is induced by VirB protein(s) and promotes VirB/D4-mediated DNA transfer in Agrobacterium tumefaciens. MICROBIOLOGY-SGM 2009; 155:3270-3280. [PMID: 19556291 PMCID: PMC2885654 DOI: 10.1099/mic.0.030676-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Agrobacterium tumefaciens is a Gram-negative plant-pathogenic bacterium that causes crown gall disease by transferring and integrating its transferred DNA (T-DNA) into the host genome. We characterized the chromosomally encoded alpha-crystallin-type small heat-shock protein (alpha-Hsp) HspL, which was induced by the virulence (vir) gene inducer acetosyringone (AS). The transcription of hspL but not three other alpha-Hsp genes (hspC, hspAT1, hspAT2) was upregulated by AS. Further expression analysis in various vir mutants suggested that AS-induced hspL transcription is not directly activated by the VirG response regulator but rather depends on the expression of VirG-activated virB genes encoding components of the type IV secretion system (T4SS). Among the 11 virB genes encoded by the virB operon, HspL protein levels were reduced in strains with deletions of virB6, virB8 or virB11. VirB protein accumulation but not virB transcription levels were reduced in an hspL deletion mutant early after AS induction, implying that HspL may affect the stability of individual VirB proteins or of the T4S complex directly or indirectly. Tumorigenesis efficiency and the VirB/D4-mediated conjugal transfer of an IncQ plasmid RSF1010 derivative between A. tumefaciens strains were reduced in the absence of HspL. In conclusion, increased HspL abundance is triggered in response to certain VirB protein(s) and plays a role in optimal VirB protein accumulation, VirB/D4-mediated DNA transfer and tumorigenesis.
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Affiliation(s)
- Yun-Long Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ming-Hsuan Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chan Gao
- Biology Department, McMaster University, Hamilton, ON, Canada
| | - Sonja Klüsener
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, Bochum, Germany
| | - Christian Baron
- Département de Biochimie, Université de Montréal, Montréal, QC, Canada.,Biology Department, McMaster University, Hamilton, ON, Canada
| | - Franz Narberhaus
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, Bochum, Germany
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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Jin LH, Um HJ, Yin CJ, Kim YH, Lee JH. Proteomic analysis of curdlan-producing Agrobacterium sp. in response to pH downshift. J Biotechnol 2008; 138:80-7. [DOI: 10.1016/j.jbiotec.2008.08.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Revised: 07/01/2008] [Accepted: 08/10/2008] [Indexed: 10/21/2022]
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14
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Zhao B, Poh CL. Insights into environmental bioremediation by microorganisms through functional genomics and proteomics. Proteomics 2008; 8:874-81. [DOI: 10.1002/pmic.200701005] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Muller LAH, Craciun AR, Ruytinx J, Lambaerts M, Verbruggen N, Vangronsveld J, Colpaert JV. Gene expression profiling of a Zn-tolerant and a Zn-sensitive Suillus luteus isolate exposed to increased external zinc concentrations. MYCORRHIZA 2007; 17:571-580. [PMID: 17530303 DOI: 10.1007/s00572-007-0134-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Accepted: 04/27/2007] [Indexed: 05/15/2023]
Abstract
Complementary DNA (cDNA)-amplified fragment-length polymorphism (AFLP) was applied to analyze transcript profiles of a Zn-tolerant and a Zn-sensitive isolate of the ectomycorrhizal basidiomycete Suillus luteus, both cultured with and without increased external zinc concentrations. From the obtained transcript profiles that covered approximately 2% of the total expected complement of genes in S. luteus, 144 nonredundant, differentially expressed transcript-derived fragments (TDFs), falling in different classes of expression pattern, were isolated and sequenced. Thirty-six of the represented genes showed homology to function-known genes, whereas 6 matched unknown protein coding sequences, and 102 were possibly novel. Although relatively few TDFs were found to be responsive to the different zinc treatments, their modulated expression levels may suggest a different transcriptional response to zinc treatments in both isolates. Among the identified genes that could be related to heavy-metal detoxification or the tolerance trait were genes encoding for homologues of a heat-shock protein, a putative metal transporter, a hydrophobin, and several proteins involved in ubiquitin-dependent proteolysis.
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Affiliation(s)
- L A H Muller
- Environmental Biology Group, Centre for Environmental Sciences, Hasselt University, Agoralaan, Gebouw D, 3590, Diepenbeek, Belgium
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, DUMC Box 3020, Durham, NC, 27710, USA
| | - A R Craciun
- Laboratoire de Physiologie et de Génétique Moléculaire des Plantes, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - J Ruytinx
- Environmental Biology Group, Centre for Environmental Sciences, Hasselt University, Agoralaan, Gebouw D, 3590, Diepenbeek, Belgium
| | - M Lambaerts
- Environmental Biology Group, Centre for Environmental Sciences, Hasselt University, Agoralaan, Gebouw D, 3590, Diepenbeek, Belgium
| | - N Verbruggen
- Laboratoire de Physiologie et de Génétique Moléculaire des Plantes, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - J Vangronsveld
- Environmental Biology Group, Centre for Environmental Sciences, Hasselt University, Agoralaan, Gebouw D, 3590, Diepenbeek, Belgium
| | - J V Colpaert
- Environmental Biology Group, Centre for Environmental Sciences, Hasselt University, Agoralaan, Gebouw D, 3590, Diepenbeek, Belgium.
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16
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Zhao B, Yeo CC, Tan CL, Poh CL. Proteome analysis of heat shock protein expression inPseudomonas alcaligenes NCIMB 9867 in response to gentisate exposure and elevated growth temperature. Biotechnol Bioeng 2007; 97:506-14. [PMID: 17149773 DOI: 10.1002/bit.21253] [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: 11/08/2022]
Abstract
Pseudomonas alcaligenes NCIMB 9867 (strain P25X) degrades xylenols and cresols via the gentisate pathway. P25X expresses two isofunctional gentisate 1,2-dioxygenases (GDO I and GDO II). The expression of both GDOs was not detected when P25X cells were grown at 42 degrees C, even in the presence of gentisate. A total of 19 heat shock proteins (Hsps) belonging to the Hsp100, Hsp90, Hsp70, Hsp60, Hsp45, and small heat shock protein (sHsp) families were identified among the protein spots that were either newly detected or were expressed at levels of at least twofold higher when P25X cells were cultured at 32 or 42 degrees C in the presence and absence of gentisate. Among these, 16 Hsps were commonly expressed at 42 degrees C. Two additional Hsps (H5 and H13) from the Hsp90 and Hsp60 families, respectively, were expressed only when P25X cells were grown at 42 degrees C and in the presence of gentisate. A protein of the sHsp (H16) family was expressed only in the presence of gentisate at 32 degrees C but not at 42 degrees C. The GroEL chaperonins of the Hsp60 family comprised the largest group of Hsps identified and exhibited high level of expression at 42 degrees C following gentisate exposure.
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Affiliation(s)
- Bing Zhao
- Programme in Environmental Microbiology, Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Block MD4, 5 Science Drive 2, Singapore
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17
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Koide T, Vêncio RZN, Gomes SL. Global gene expression analysis of the heat shock response in the phytopathogen Xylella fastidiosa. J Bacteriol 2006; 188:5821-30. [PMID: 16885450 PMCID: PMC1540087 DOI: 10.1128/jb.00182-06] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xylella fastidiosa is a phytopathogenic bacterium that is responsible for diseases in many economically important crops. Although different strains have been studied, little is known about X. fastidiosa stress responses. One of the better characterized stress responses in bacteria is the heat shock response, which induces the expression of specific genes to prevent protein misfolding and aggregation and to promote degradation of the irreversibly denatured polypeptides. To investigate X. fastidiosa genes involved in the heat shock response, we performed a whole-genome microarray analysis in a time course experiment. Globally, 261 genes were induced (9.7%) and 222 genes were repressed (8.3%). The expression profiles of the differentially expressed genes were grouped, and their expression patterns were validated by quantitative reverse transcription-PCR experiments. We determined the transcription start sites of six heat shock-inducible genes and analyzed their promoter regions, which allowed us to propose a putative consensus for sigma(32) promoters in Xylella and to suggest additional genes as putative members of this regulon. Besides the induction of classical heat shock protein genes, we observed the up-regulation of virulence-associated genes such as vapD and of genes for hemagglutinins, hemolysin, and xylan-degrading enzymes, which may indicate the importance of heat stress to bacterial pathogenesis. In addition, we observed the repression of genes related to fimbriae, aerobic respiration, and protein biosynthesis and the induction of genes related to the extracytoplasmic stress response and some phage-related genes, revealing the complex network of genes that work together in response to heat shock.
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Affiliation(s)
- Tie Koide
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, Brazil
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Ferreira S, Hjernø K, Larsen M, Wingsle G, Larsen P, Fey S, Roepstorff P, Salomé Pais M. Proteome profiling of Populus euphratica Oliv. upon heat stress. ANNALS OF BOTANY 2006; 98:361-77. [PMID: 16740589 PMCID: PMC2803470 DOI: 10.1093/aob/mcl106] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Populus euphratica is a light-demanding species ecologically characterized as a pioneer. It grows in shelter belts along riversides, being part of the natural desert forest ecosystems in China and Middle Eastern countries. It is able to survive extreme temperatures, drought and salt stress, marking itself out as an important plant species to study the mechanisms responsible for survival of woody plants under heat stress. METHODS Heat effects were evaluated through electrolyte leakage on leaf discs, and LT(50) was determined to occur above 50 degrees C. Protein accumulation profiles of leaves from young plants submitted to 42/37 degrees C for 3 d in a phytotron were determined through 2D-PAGE, and a total of 45 % of up- and downregulated proteins were detected. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF)/TOF analysis, combined with searches in different databases, enabled the identification of 82 % of the selected spots. KEY RESULTS Short-term upregulated proteins are related to membrane destabilization and cytoskeleton restructuring, sulfur assimilation, thiamine and hydrophobic amino acid biosynthesis, and protein stability. Long-term upregulated proteins are involved in redox homeostasis and photosynthesis. Late downregulated proteins are involved mainly in carbon metabolism. CONCLUSIONS Moderate heat response involves proteins related to lipid biogenesis, cytoskeleton structure, sulfate assimilation, thiamine and hydrophobic amino acid biosynthesis, and nuclear transport. Photostasis is achieved through carbon metabolism adjustment, a decrease of photosystem II (PSII) abundance and an increase of PSI contribution to photosynthetic linear electron flow. Thioredoxin h may have a special role in this process in P. euphratica upon moderate heat exposure.
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Affiliation(s)
- Sílvia Ferreira
- Unit of Molecular Biology and Plant Biotechnology, Institute of Applied Science and Technology, Science Faculty of Lisbon University, Campo Grande, 1749-016 Lisbon, Portugal.
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Lai EM, Shih HW, Wen SR, Cheng MW, Hwang HH, Chiu SH. Proteomic analysis ofAgrobacterium tumefaciens response to thevir gene inducer acetosyringone. Proteomics 2006; 6:4130-6. [PMID: 16791832 DOI: 10.1002/pmic.200600254] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Agrobacterium tumefaciens causes crown gall disease in a wide range of plants by transforming plants through the transfer and integration of its transferred DNA (T-DNA) into the host genome. In the present study, we used two-dimensional gel electrophoresis to examine the protein expression profiles of A. tumefaciens in response to the phenolic compound acetosyringone (AS), a known plant-released virulence (vir) gene inducer. Using mass spectrometry, we identified 11 proteins consisting of 9 known AS-induced Vir proteins and 2 newly discovered AS-induced proteins, an unknown protein Y4mC (Atu6162) and a small heat shock protein HspL (Atu3887). Further expression analysis revealed that the AS-induced expression of Y4mC and HspL is regulated by the VirA/VirG two-component system. This report presents the first proteomics study successfully identifying both known and new AS-induced proteins that are implicated in Agrobacterium virulence.
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Affiliation(s)
- Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
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Chhabra SR, He Q, Huang KH, Gaucher SP, Alm EJ, He Z, Hadi MZ, Hazen TC, Wall JD, Zhou J, Arkin AP, Singh AK. Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough. J Bacteriol 2006; 188:1817-28. [PMID: 16484192 PMCID: PMC1426554 DOI: 10.1128/jb.188.5.1817-1828.2006] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Desulfovibrio vulgaris Hildenborough belongs to a class of sulfate-reducing bacteria (SRB) and is found ubiquitously in nature. Given the importance of SRB-mediated reduction for bioremediation of metal ion contaminants, ongoing research on D. vulgaris has been in the direction of elucidating regulatory mechanisms for this organism under a variety of stress conditions. This work presents a global view of this organism's response to elevated growth temperature using whole-cell transcriptomics and proteomics tools. Transcriptional response (1.7-fold change or greater; Z >/= 1.5) ranged from 1,135 genes at 15 min to 1,463 genes at 120 min for a temperature up-shift of 13 degrees C from a growth temperature of 37 degrees C for this organism and suggested both direct and indirect modes of heat sensing. Clusters of orthologous group categories that were significantly affected included posttranslational modifications; protein turnover and chaperones (up-regulated); energy production and conversion (down-regulated), nucleotide transport, metabolism (down-regulated), and translation; ribosomal structure; and biogenesis (down-regulated). Analysis of the genome sequence revealed the presence of features of both negative and positive regulation which included the CIRCE element and promoter sequences corresponding to the alternate sigma factors sigma(32) and sigma(54). While mechanisms of heat shock control for some genes appeared to coincide with those established for Escherichia coli and Bacillus subtilis, the presence of unique control schemes for several other genes was also evident. Analysis of protein expression levels using differential in-gel electrophoresis suggested good agreement with transcriptional profiles of several heat shock proteins, including DnaK (DVU0811), HtpG (DVU2643), HtrA (DVU1468), and AhpC (DVU2247). The proteomics study also suggested the possibility of posttranslational modifications in the chaperones DnaK, AhpC, GroES (DVU1977), and GroEL (DVU1976) and also several periplasmic ABC transporters.
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Affiliation(s)
- S R Chhabra
- Biosystems Research Department, Mailstop 9292, Sandia National Laboratory, 7011 East Ave., Livermore, CA 94550, USA
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Su S, Stephens BB, Alexandre G, Farrand SK. Lon protease of the α-proteobacterium Agrobacterium tumefaciens is required for normal growth, cellular morphology and full virulence. Microbiology (Reading) 2006; 152:1197-1207. [PMID: 16549682 DOI: 10.1099/mic.0.28657-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ATP-dependent Lon (La) protease is ubiquitous in nature and regulates a diverse set of physiological responses in bacteria. In this paper alonmutant of theα-proteobacteriumAgrobacterium tumefaciensC58 has been characterized. Unlikelonmutants ofEscherichia coli, thelonmutant ofA. tumefaciensgrows very slowly, is not filamentous and exhibits normal resistance to UV irradiation. The mutant retains motility and chemotaxis, produces apparently normal amounts of exopolysacchride, but displays severe defects in cell morphology, with 80 % of the mutant cells appearing Y-shaped. Lon protease ofA. tumefaciensshares high homology with its counterparts inE. coliand inSinorhizobium meliloti, and functionally complements anE. coli lonmutant for defects in morphology and RcsA-mediated regulation of capsular polysaccharide production. Mutations at sites of LonAtcorresponding to the ATP-binding site and the active site serine of theE. coliLon protease abolish complementation of phenotypes of theA. tumefaciensandE. coli lonmutants. The nucleotide sequence upstream ofA. tumefaciens loncontains an element similar to the consensusσ32heat-shock promoter ofE. coli. Northern and Western blot analyses indicated that expression oflonis induced by elevated temperature, albeit to a much lower level than that ofgroEL. Thelonmutant is highly attenuated for virulence, suggesting that Lon may be required for the proper expression, assembly or function of the VirB/D4-mediated T-DNA transfer system.
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Affiliation(s)
- Shengchang Su
- Department of Microbiology, University of Illinois at Urbana-Champaign, B103 CLSL, 601 South Goodwin Avenue, Urbana, IL 61801, USA
| | - Bonnie B Stephens
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Gladys Alexandre
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Stephen K Farrand
- Department of Microbiology, University of Illinois at Urbana-Champaign, B103 CLSL, 601 South Goodwin Avenue, Urbana, IL 61801, USA
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Laskos L, Ryan CS, Fyfe JAM, Davies JK. The RpoH-mediated stress response in Neisseria gonorrhoeae is regulated at the level of activity. J Bacteriol 2005; 186:8443-52. [PMID: 15576794 PMCID: PMC532417 DOI: 10.1128/jb.186.24.8443-8452.2004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The general stress response in Neisseria gonorrhoeae was investigated. Transcriptional analyses of the genes encoding the molecular chaperones DnaK, DnaJ, and GrpE suggested that they are transcribed from sigma32 (RpoH)-dependent promoters upon exposure to stress. This was confirmed by mutational analysis of the sigma32 promoter of dnaK. The gene encoding the gonococcal RpoH sigma factor appears to be essential, as we could not isolate viable mutants. Deletion of an unusually long rpoH leader sequence resulted in elevated levels of transcription, suggesting that this region is involved in negative regulation of RpoH expression during normal growth. Transcriptional analyses and protein studies determined that regulation of the RpoH-mediated stress response is different from that observed in most other species, in which regulation occurs predominantly at the transcriptional and translational levels. We suggest that an increase in the activity of preformed RpoH is primarily responsible for induction of the stress response in N. gonorrhoeae.
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Affiliation(s)
- Lina Laskos
- Department of Microbiology, Monash University, Clayton Campus, Victoria 3800, Australia.
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Balsiger S, Ragaz C, Baron C, Narberhaus F. Replicon-specific regulation of small heat shock genes in Agrobacterium tumefaciens. J Bacteriol 2004; 186:6824-9. [PMID: 15466035 PMCID: PMC522190 DOI: 10.1128/jb.186.20.6824-6829.2004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Four genes coding for small heat shock proteins (sHsps) were identified in the genome sequence of Agrobacterium tumefaciens, one on the circular chromosome (hspC), one on the linear chromosome (hspL), and two on the pAT plasmid (hspAT1 and hspAT2). Induction of sHsps at elevated temperatures was revealed by immunoblot analyses. Primer extension experiments and translational lacZ fusions demonstrated that expression of the pAT-derived genes and hspL is controlled by temperature in a regulon-specific manner. While the sHsp gene on the linear chromosome turned out to be regulated by RpoH (sigma32), both copies on pAT were under the control of highly conserved ROSE (named for repression of heat shock gene expression) sequences in their 5' untranslated region. Secondary structure predictions of the corresponding mRNA strongly suggest that it represses translation at low temperatures by masking the Shine-Dalgarno sequence. The hspC gene was barely expressed (if at all) and not temperature responsive.
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Affiliation(s)
- Sylvia Balsiger
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule, Zürich, Switzerland
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Rosen R, Ron EZ. Proteome analysis in the study of the bacterial heat-shock response. MASS SPECTROMETRY REVIEWS 2002; 21:244-265. [PMID: 12533799 DOI: 10.1002/mas.10031] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In recent years, it has become clear that, in addition to the regulation of the expression of specific genes, there are global regulatory systems that control the simultaneous expression of a large number of genes in response to a variety of environmental stresses. The first of these global control systems, and of substantial importance, is the heat-shock response. The heat-shock response is characterized by the induction of a large set of proteins (heat-shock proteins-HSPs) upon shifts to higher temperature and upon exposure to conditions in which proteins are denatured (i.e., alcohols, heavy metals). The heat-shock response is universal and many of the heat-shock proteins are highly conserved among species. In bacteria, the heat-shock response has been studied extensively in several Gram-positive bacteria (Bacillus subtilis) and in the Gram-negative bacteria (i.e., Escherichia coli, Agrobacterium tumefaciens). The first recognition of the molecular abundance of the bacterial heat-shock proteins took place with the introduction of high-resolution two-dimensional polyacrylamide gels (2D gels) to analyze complex mixtures of cellular proteins. Two-dimensional gels, followed by mass spectrometry, were used to define the heat-shock stimulons in several bacteria, and to study the regulatory elements that control the heat-shock response. Here, we review the heat-shock response and its regulation in bacteria. The review will emphasize the use of proteome analysis in the study of this response, and will point out those open questions that can be investigated with proteomics, including mass spectrometry techniques.
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Affiliation(s)
- Ran Rosen
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
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D'Haeze W. Agrobacteriumheat-shock proteome. Genome Biol 2002. [DOI: 10.1186/gb-2002-3-6-reports0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2002. [PMCID: PMC2448432 DOI: 10.1002/cfg.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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