1
|
Arvizu-Gómez JL, Hernández-Morales A, Campos-Guillén J, González-Reyes C, Pacheco-Aguilar JR. Phaseolotoxin: Environmental Conditions and Regulatory Mechanisms Involved in Its Synthesis. Microorganisms 2024; 12:1300. [PMID: 39065068 PMCID: PMC11278893 DOI: 10.3390/microorganisms12071300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/12/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Phaseolotoxin is an antimetabolite toxin produced by diverse pathovars of Pseudomonas syringae which affects various plants, causing diseases of economic importance. Phaseolotoxin contributes to the systemic dissemination of the pathogen in the plant, therefore it is recognized as a major virulence factor. Genetic traits such as the Pht cluster, appear defining to the toxigenic strains phaseolotoxin producers. Extensive research has contributed to our knowledge concerning the regulation of phaseolotoxin revealing a complex regulatory network that involves processes at the transcriptional and posttranscriptional levels, in which specific and global regulators participate. Even more, significant advances in understanding how specific signals, including host metabolites, nutrient sources, and physical parameters such as the temperature, can affect phaseolotoxin production have been made. A general overview of the phaseolotoxin regulation, focusing on the chemical and physical cues, and regulatory pathways involved in the expression of this major virulence factor will be given in the present work.
Collapse
Affiliation(s)
- Jackeline Lizzeta Arvizu-Gómez
- Secretaría de Investigación y Posgrado, Centro Nayarita de Innovación y Transferencia de Tecnología (CENITT), Universidad Autónoma de Nayarit, Tepic 63000, Mexico
| | - Alejandro Hernández-Morales
- Facultad de Estudios Profesionales Zona Huasteca, Universidad Autónoma de San Luis Potosí, Ciudad Valles 79060, Mexico
| | - Juan Campos-Guillén
- Facultad de Química, Universidad Autónoma de Querétaro, Santiago de Querétaro 76010, Mexico; (J.C.-G.); (J.R.P.-A.)
| | - Christian González-Reyes
- Unidad Académica de Ciencias Químico Biológico y Farmacéuticas, Universidad Autónoma de Nayarit, Tepic 63000, Mexico;
| | - Juan Ramiro Pacheco-Aguilar
- Facultad de Química, Universidad Autónoma de Querétaro, Santiago de Querétaro 76010, Mexico; (J.C.-G.); (J.R.P.-A.)
| |
Collapse
|
2
|
Kretz J, Börner J, Friedrich T, McIntosh M, Procida-Kowalski T, Gerken F, Wilhelm J, Klug G. Function of the RNA-targeting class 2 type VI CRISPR Cas system of Rhodobacter capsulatus. Front Microbiol 2024; 15:1384543. [PMID: 38741736 PMCID: PMC11089165 DOI: 10.3389/fmicb.2024.1384543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Bacteria use CRISPR Cas systems to defend against invading foreign nucleic acids, e.g., phage genomes, plasmids or mobile genetic elements. Some CRISPR Cas systems were reported to have physiological importance under a variety of abiotic stress conditions. We used physiological tests under different stress conditions and RNA-seq analyses to address the possible function of the RNA-targeting class 2 type VI CRISPR Cas system of the facultative phototrophic α-proteobacterium Rhodobacter capsulatus. Expression of the system was low under exponential non-stress conditions and high during oxidative stress, membrane stress and in stationary phase. Induction of the CRISPR Cas system in presence of a target protospacer RNA resulted in a growth arrest of R. capsulatus. RNA-seq revealed a strong alteration of the R. capsulatus transcriptome when cas13a was induced in presence of a target protospacer. RNA 5' end mapping indicated that the CRISPR Cas-dependent transcriptome remodeling is accompanied by fragmentation of cellular RNAs, e.g., for mRNAs originating from a genomic locus which encodes multiple ribosomal proteins and the RNA polymerase subunits RpoA, RpoB and RpoC. The data suggest a function of this CRISPR Cas system in regulated growth arrest, which may prevent the spread of phages within the population.
Collapse
Affiliation(s)
- Jonas Kretz
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen, Germany
| | - Janek Börner
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen, Germany
| | - Tobias Friedrich
- Institute of Biochemistry, Justus-Liebig-University, Giessen, Germany
- Biomedical Informatics and Systems Medicine, Justus-Liebig-University, Giessen, Germany
| | - Matthew McIntosh
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen, Germany
| | | | - Florian Gerken
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen, Germany
| | - Jochen Wilhelm
- Institute for Lung Health, Justus-Liebig-University, Giessen, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University, Giessen, Germany
| |
Collapse
|
3
|
Börner J, Friedrich T, Klug G. RNase III participates in control of quorum sensing, pigmentation and oxidative stress resistance in Rhodobacter sphaeroides. Mol Microbiol 2023; 120:874-892. [PMID: 37823424 DOI: 10.1111/mmi.15181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023]
Abstract
RNase III is a dsRNA-specific endoribonuclease, highly conserved in bacteria and eukarya. In this study, we analysed the effects of inactivation of RNase III on the transcriptome and the phenotype of the facultative phototrophic α-proteobacterium Rhodobacter sphaeroides. RNA-seq revealed an unexpectedly high amount of genes with increased expression located directly downstream to the rRNA operons. Chromosomal insertion of additional transcription terminators restored wild type-like expression of the downstream genes, indicating that RNase III may modulate the rRNA transcription termination in R. sphaeroides. Furthermore, we identified RNase III as a major regulator of quorum-sensing autoinducer synthesis in R. sphaeroides. It negatively controls the expression of the autoinducer synthase CerI by reducing cerI mRNA stability. In addition, RNase III inactivation caused altered resistance against oxidative stress and impaired formation of photosynthetically active pigment-protein complexes. We also observed an increase in the CcsR small RNAs that were previously shown to promote resistance to oxidative stress. Taken together, our data present interesting insights into RNase III-mediated regulation and expand the knowledge on the function of this important enzyme in bacteria.
Collapse
Affiliation(s)
- Janek Börner
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Tobias Friedrich
- Biomedical Informatics and Systems Medicine, Justus-Liebig-University Giessen, Giessen, Germany
- Institute of Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Justus-Liebig-University Giessen, Giessen, Germany
| |
Collapse
|
4
|
Zhang J, Zheng M, Tang Z, Zhong S, Bu T, Li Q. The Regulatory Functions of the Multiple Alternative Sigma Factors RpoE, RpoHI, and RpoHII Depend on the Growth Phase in Rhodobacter sphaeroides. Microorganisms 2023; 11:2678. [PMID: 38004690 PMCID: PMC10673084 DOI: 10.3390/microorganisms11112678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Bacterial growth, under laboratory conditions or in a natural environment, goes through different growth phases. Some gene expressions are regulated with respect to the growth phase, which allows bacteria to adapt to changing conditions. Among them, many gene transcriptions are controlled by RpoHI or RpoHII in Rhodobacter sphaeroides. In a previous study, it was proven that the alternative sigma factors, RpoE, RpoHI, and RpoHII, are the major regulators of oxidative stress. Moreover, the growth of bacteria reached a stationary phase, and following the outgrowth, rpoE, rpoHI, and rpoHII mRNAs increased with respect to the growth phase. In this study, we demonstrated the regulatory function of alternative sigma factors in the rsp_0557 gene. The gene rsp_0557 is expressed with respect to the growth phase and belongs to the RpoHI/RpoHII regulons. Reporter assays showed that the antisigma factor ChrR turns on or over the RpoE activity to regulate rsp_0557 expression across the growth phase. In the exponential phase, RpoHII and sRNA Pos19 regulate the expression of rsp_0557 to an appropriate level under RpoE control. In the stationary phase, RpoHI and Pos19 stabilize the transcription of rsp_0557 at a high level. During outgrowth, RpoHI negatively regulates the transcription of rsp_0557. Taken together, our data indicate that these regulators are recruited by cells to adapt to or survive under different conditions throughout the growth phase. However, they still did not display all of the regulators involved in growth phase-dependent regulation. More research is still needed to learn more about the interaction between the regulators and the process of adapting to changed growth conditions and environments.
Collapse
Affiliation(s)
| | | | | | | | | | - Qingfeng Li
- College of Life Sciences, Sichuan Agricultural University, Ya’an 625014, China; (J.Z.); (M.Z.); (Z.T.); (S.Z.); (T.B.)
| |
Collapse
|
5
|
Kretz J, Israel V, McIntosh M. Design-Build-Test of Synthetic Promoters for Inducible Gene Regulation in Alphaproteobacteria. ACS Synth Biol 2023; 12:2663-2675. [PMID: 37561940 DOI: 10.1021/acssynbio.3c00251] [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] [Indexed: 08/12/2023]
Abstract
Inducible gene expression is useful for biotechnological applications and for studying gene regulation and function in bacteria. Many inducible systems that perform in model organisms such as the Gammaproteobacterium Escherichia coli do not perform well in other bacteria that are of biotechnological interest. Typical problems include weak or leaky expression. Here, we describe an invention named ACIT (Alphaproteobacteria chromosomally integrating transcription-control cassette) that is carried on a suicide plasmid to enable insertion into the chromosome of the host. ACIT consists of multiple DNA fragments specifically arranged in a cassette that allows tight transcription control over any gene or gene cluster of interest following homologous recombination. At the heart of the invention is the ability to modify or exchange parts, e.g., promoters, to suit particular bacteria and growth conditions, allowing for customized gene expression control. Furthermore, ACIT provides a basis for a design-build-test approach for controlling gene expression in less studied bacteria. We describe examples of its control over pigment and exopolysaccharide production, growth, cell form, and social behavior in various Alphaproteobacteria.
Collapse
Affiliation(s)
- Jonas Kretz
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-Universität, 35292 Giessen, Germany
| | - Vera Israel
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-Universität, 35292 Giessen, Germany
| | - Matthew McIntosh
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-Universität, 35292 Giessen, Germany
| |
Collapse
|
6
|
Grützner J, Börner J, Jäger A, Klug G. The Small RNA-Binding Protein CcaF1 Promotes Formation of Photosynthetic Complexes in Rhodobacter sphaeroides. Int J Mol Sci 2023; 24:ijms24119515. [PMID: 37298460 DOI: 10.3390/ijms24119515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
In natural habitats, bacteria frequently need to adapt to changing environmental conditions. Regulation of transcription plays an important role in this process. However, riboregulation also contributes substantially to adaptation. Riboregulation often acts at the level of mRNA stability, which is determined by sRNAs, RNases, and RNA-binding proteins. We previously identified the small RNA-binding protein CcaF1, which is involved in sRNA maturation and RNA turnover in Rhodobacter sphaeroides. Rhodobacter is a facultative phototroph that can perform aerobic and anaerobic respiration, fermentation, and anoxygenic photosynthesis. Oxygen concentration and light conditions decide the pathway for ATP production. Here, we show that CcaF1 promotes the formation of photosynthetic complexes by increasing levels of mRNAs for pigment synthesis and for some pigment-binding proteins. Levels of mRNAs for transcriptional regulators of photosynthesis genes are not affected by CcaF1. RIP-Seq analysis compares the binding of CcaF1 to RNAs during microaerobic and photosynthetic growth. The stability of the pufBA mRNA for proteins of the light-harvesting I complex is increased by CcaF1 during phototrophic growth but decreased during microaerobic growth. This research underlines the importance of RNA-binding proteins in adaptation to different environments and demonstrates that an RNA-binding protein can differentially affect its binding partners in dependence upon growth conditions.
Collapse
Affiliation(s)
- Julian Grützner
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Janek Börner
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Andreas Jäger
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| |
Collapse
|
7
|
Spanka DT, Grützner J, Jäger A, Klug G. A Small RNA, UdsC, Interacts with the R poHII mRNA and Affects the Motility and Stress Resistance of Rhodobacter sphaeroides. Int J Mol Sci 2022; 23:ijms232415486. [PMID: 36555125 PMCID: PMC9779115 DOI: 10.3390/ijms232415486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
sRNAs have an important role in the regulation of bacterial gene expression. The sRNA, UdsC, of Rhodobacter sphaeroides is derived from the 3' UTR of the RSP_7527 mRNA, which encodes a hypothetical protein. Here, we showed the effect of UdsC on the resistance of Rhodobacter sphaeroides to hydrogen peroxide and on its motility. In vitro binding assays supported the direct interaction of UdsC with the 5' UTR of the rpoHII mRNA. RpoHII is an alternative sigma factor with an important role in stress responses in R. sphaeroides, including its response to hydrogen peroxide. We also demonstrated that RpoHII controls the expression of the torF gene, which encodes an important regulator of motility genes. This strongly suggested that the observed effect of UdsC on TorF expression is indirect and mediated by RpoHII.
Collapse
|
8
|
Karash S, Jiang T, Kwon YM. Genome-wide characterization of Salmonella Typhimurium genes required for the fitness under iron restriction. BMC Genom Data 2022; 23:55. [PMID: 35869435 PMCID: PMC9308263 DOI: 10.1186/s12863-022-01069-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 06/28/2022] [Indexed: 11/24/2022] Open
Abstract
Background Iron is a crucial element for bacterial survival and virulence. During Salmonella infection, the host utilizes a variety of mechanisms to starve the pathogen from iron. However, Salmonella activates distinctive defense mechanisms to acquire iron and survive in iron-restricted host environments. Yet, the comprehensive set of the conditionally essential genes that underpin Salmonella survival under iron-restricted niches has not been fully explored. Results Here, we employed transposon sequencing (Tn-seq) method for high-resolution elucidation of the genes in Salmonella Typhimurium (S. Typhimurium) 14028S strain required for the growth under the in vitro conditions with four different levels of iron restriction achieved by iron chelator 2,2′-dipyridyl (Dip): mild (100 and 150 μM), moderate (250 μM) and severe iron restriction (400 μM). We found that the fitness of the mutants reduced significantly for 28 genes, suggesting the importance of these genes for the growth under iron restriction. These genes include sufABCDSE, iron transport fepD, siderophore tonB, sigma factor E ropE, phosphate transport pstAB, and zinc exporter zntA. The siderophore gene tonB was required in mild and moderate iron-restricted conditions, but it became dispensable in severe iron-restricted conditions. Remarkably, rpoE was required in moderate and severe iron restrictions, leading to complete attenuation of the mutant under these conditions. We also identified 30 genes for which the deletion of the genes resulted in increased fitness under iron-restricted conditions. Conclusions The findings broaden our knowledge of how S. Typhimurium survives in iron-deficient environments, which could be utilized for the development of new therapeutic strategies targeting the pathways vital for iron metabolism, trafficking, and scavenging. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01069-3.
Collapse
|
9
|
Lee YR, Lee WH, Lee SY, Lee J, Kim MS, Moon M, Park GW, Kim HS, Kim JI, Lee JS, Lee S. Regulation of Reactive Oxygen Species Promotes Growth and Carotenoid Production Under Autotrophic Conditions in Rhodobacter sphaeroides. Front Microbiol 2022; 13:847757. [PMID: 35295297 PMCID: PMC8920488 DOI: 10.3389/fmicb.2022.847757] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/07/2022] [Indexed: 11/26/2022] Open
Abstract
Industrial demand for capture and utilization using microorganisms to reduce CO2, a major cause of global warming, is significantly increasing. Rhodobacter sphaeroides is a suitable strain for the process of converting CO2 into high-value materials because it can accept CO2 and has various metabolic pathways. However, it has been mainly studied for heterotrophic growth that uses sugars and organic acids as carbon sources, not autotrophic growth. Here, we report that the regulation of reactive oxygen species is critical for growth when using CO2 as a sole carbon source in R. sphaeroides. In general, the growth rate is much slower under autotrophic conditions compared to heterotrophic conditions. To improve this, we performed random mutagenesis using N-methyl-N’-nitro-N-nitrosoguanidine (NTG). As a result, we selected the YR-1 strain with a maximum specific growth rate (μ) 1.44 day–1 in the early growth phase, which has a 110% faster growth rate compared to the wild-type. Based on the transcriptome analysis, it was confirmed that the growth was more sensitive to reactive oxygen species under autotrophic conditions. In the YR-1 mutant, the endogenous contents of H2O2 levels and oxidative damage were reduced by 33.3 and 42.7% in the cells, respectively. Furthermore, we measured that concentrations of carotenoids, which are important antioxidants. The total carotenoid is produced 9.63 g/L in the YR-1 mutant, suggesting that the production is 1.7-fold higher than wild-type. Taken together, our observations indicate that controlling ROS promotes cell growth and carotenoid production under autotrophic conditions.
Collapse
Affiliation(s)
- Yu Rim Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju, South Korea
- Interdisciplinary Program of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Won-Heong Lee
- Interdisciplinary Program of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Soo Youn Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju, South Korea
| | - Jiye Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju, South Korea
| | - Min-Sik Kim
- Energy Resources Upcycling Research Laboratory, Korea Institute of Energy Research, Daejeon, South Korea
| | - Myounghoon Moon
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju, South Korea
| | - Gwon Woo Park
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju, South Korea
| | - Hui Su Kim
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju, South Korea
- Department of Advanced Chemicals and Engineering, Chonnam National University, Gwangju, South Korea
| | - Jeong-Il Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Jin-Suk Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju, South Korea
| | - Sangmin Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research, Gwangju, South Korea
- *Correspondence: Sangmin Lee,
| |
Collapse
|
10
|
Spanka DT, Klug G. Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions. Int J Mol Sci 2021; 22:ijms222212260. [PMID: 34830143 PMCID: PMC8625941 DOI: 10.3390/ijms222212260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/02/2021] [Accepted: 11/08/2021] [Indexed: 12/02/2022] Open
Abstract
Small regulatory RNAs play a major role in bacterial gene regulation by binding their target mRNAs, which mostly influences the stability or translation of the target. Expression levels of sRNAs are often regulated by their own promoters, but recent reports have highlighted the presence and importance of sRNAs that are derived from mRNA 3′ untranslated regions (UTRs). In this study, we investigated the maturation of 5′ and 3′ UTR-derived sRNAs on a global scale in the facultative phototrophic alphaproteobacterium Rhodobacter sphaeroides. Including some already known UTR-derived sRNAs like UpsM or CcsR1-4, 14 sRNAs are predicted to be located in 5 UTRs and 16 in 3′ UTRs. The involvement of different ribonucleases during maturation was predicted by a differential RNA 5′/3′ end analysis based on RNA next generation sequencing (NGS) data from the respective deletion strains. The results were validated in vivo and underline the importance of polynucleotide phosphorylase (PNPase) and ribonuclease E (RNase E) during processing and maturation. The abundances of some UTR-derived sRNAs changed when cultures were exposed to external stress conditions, such as oxidative stress and also during different growth phases. Promoter fusions revealed that this effect cannot be solely attributed to an altered transcription rate. Moreover, the RNase E dependent cleavage of several UTR-derived sRNAs varied significantly during the early stationary phase and under iron depletion conditions. We conclude that an alteration of ribonucleolytic processing influences the levels of UTR-derived sRNAs, and may thus indirectly affect their mRNA targets.
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Eisenhardt KMH, Remes B, Grützner J, Spanka DT, Jäger A, Klug G. A Complex Network of Sigma Factors and sRNA StsR Regulates Stress Responses in R. sphaeroides. Int J Mol Sci 2021; 22:ijms22147557. [PMID: 34299177 PMCID: PMC8307010 DOI: 10.3390/ijms22147557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/01/2021] [Accepted: 07/09/2021] [Indexed: 11/16/2022] Open
Abstract
Adaptation of bacteria to a changing environment is often accompanied by remodeling of the transcriptome. In the facultative phototroph Rhodobacter sphaeroides the alternative sigma factors RpoE, RpoHI and RpoHII play an important role in a variety of stress responses, including heat, oxidative stress and nutrient limitation. Photooxidative stress caused by the simultaneous presence of chlorophylls, light and oxygen is a special challenge for phototrophic organisms. Like alternative sigma factors, several non-coding sRNAs have important roles in the defense against photooxidative stress. RNAseq-based transcriptome data pointed to an influence of the stationary phase-induced StsR sRNA on levels of mRNAs and sRNAs with a role in the photooxidative stress response. Furthermore, StsR also affects expression of photosynthesis genes and of genes for regulators of photosynthesis genes. In vivo and in vitro interaction studies revealed that StsR, that is under control of the RpoHI and RpoHII sigma factors, targets rpoE mRNA and affects its abundance by altering its stability. RpoE regulates expression of the rpoHII gene and, consequently, expression of stsR. These data provide new insights into a complex regulatory network of protein regulators and sRNAs involved in defense against photooxidative stress and the regulation of photosynthesis genes.
Collapse
|
13
|
Grützner J, Remes B, Eisenhardt KMH, Scheller D, Kretz J, Madhugiri R, McIntosh M, Klug G. sRNA-mediated RNA processing regulates bacterial cell division. Nucleic Acids Res 2021; 49:7035-7052. [PMID: 34125915 PMCID: PMC8266604 DOI: 10.1093/nar/gkab491] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/17/2021] [Accepted: 05/28/2021] [Indexed: 01/16/2023] Open
Abstract
Tight control of cell division is essential for survival of most organisms. For prokaryotes, the regulatory mechanisms involved in the control of cell division are mostly unknown. We show that the small non-coding sRNA StsR has an important role in controlling cell division and growth in the alpha-proteobacterium Rhodobacter sphaeroides. StsR is strongly induced by stress conditions and in stationary phase by the alternative sigma factors RpoHI/HII, thereby providing a regulatory link between cell division and environmental cues. Compared to the wild type, a mutant lacking StsR enters stationary phase later and more rapidly resumes growth after stationary phase. A target of StsR is UpsM, the most abundant sRNA in the exponential phase. It is derived from partial transcriptional termination within the 5' untranslated region of the mRNA of the division and cell wall (dcw) gene cluster. StsR binds to UpsM as well as to the 5' UTR of the dcw mRNA and the sRNA-sRNA and sRNA-mRNA interactions lead to a conformational change that triggers cleavage by the ribonuclease RNase E, affecting the level of dcw mRNAs and limiting growth. These findings provide interesting new insights into the role of sRNA-mediated regulation of cell division during the adaptation to environmental changes.
Collapse
Affiliation(s)
- Julian Grützner
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Bernhard Remes
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Katrin M H Eisenhardt
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Daniel Scheller
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Jonas Kretz
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Ramakanth Madhugiri
- Institute of Medical Virology, University of Giessen, Schubertstr. 81, D-35392 Giessen, Germany
| | - Matthew McIntosh
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| |
Collapse
|
14
|
Sen A, Imlay JA. How Microbes Defend Themselves From Incoming Hydrogen Peroxide. Front Immunol 2021; 12:667343. [PMID: 33995399 PMCID: PMC8115020 DOI: 10.3389/fimmu.2021.667343] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/19/2021] [Indexed: 12/02/2022] Open
Abstract
Microbes rely upon iron as a cofactor for many enzymes in their central metabolic processes. The reactive oxygen species (ROS) superoxide and hydrogen peroxide react rapidly with iron, and inside cells they can generate both enzyme and DNA damage. ROS are formed in some bacterial habitats by abiotic processes. The vulnerability of bacteria to ROS is also apparently exploited by ROS-generating host defense systems and bacterial competitors. Phagocyte-derived O 2 - can toxify captured bacteria by damaging unidentified biomolecules on the cell surface; it is unclear whether phagocytic H2O2, which can penetrate into the cell interior, also plays a role in suppressing bacterial invasion. Both pathogenic and free-living microbes activate defensive strategies to defend themselves against incoming H2O2. Most bacteria sense the H2O2via OxyR or PerR transcription factors, whereas yeast uses the Grx3/Yap1 system. In general these regulators induce enzymes that reduce cytoplasmic H2O2 concentrations, decrease the intracellular iron pools, and repair the H2O2-mediated damage. However, individual organisms have tailored these transcription factors and their regulons to suit their particular environmental niches. Some bacteria even contain both OxyR and PerR, raising the question as to why they need both systems. In lab experiments these regulators can also respond to nitric oxide and disulfide stress, although it is unclear whether the responses are physiologically relevant. The next step is to extend these studies to natural environments, so that we can better understand the circumstances in which these systems act. In particular, it is important to probe the role they may play in enabling host infection by microbial pathogens.
Collapse
Affiliation(s)
| | - James A. Imlay
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| |
Collapse
|
15
|
Grützner J, Billenkamp F, Spanka DT, Rick T, Monzon V, Förstner KU, Klug G. The small DUF1127 protein CcaF1 from Rhodobacter sphaeroides is an RNA-binding protein involved in sRNA maturation and RNA turnover. Nucleic Acids Res 2021; 49:3003-3019. [PMID: 33706375 PMCID: PMC8034643 DOI: 10.1093/nar/gkab146] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 02/10/2021] [Accepted: 02/26/2021] [Indexed: 12/16/2022] Open
Abstract
Many different protein domains are conserved among numerous species, but their function remains obscure. Proteins with DUF1127 domains number >17 000 in current databases, but a biological function has not yet been assigned to any of them. They are mostly found in alpha- and gammaproteobacteria, some of them plant and animal pathogens, symbionts or species used in industrial applications. Bioinformatic analyses revealed similarity of the DUF1127 domain of bacterial proteins to the RNA binding domain of eukaryotic Smaug proteins that are involved in RNA turnover and have a role in development from Drosophila to mammals. This study demonstrates that the 71 amino acid DUF1127 protein CcaF1 from the alphaproteobacterium Rhodobacter sphaeroides participates in maturation of the CcsR sRNAs that are processed from the 3' UTR of the ccaF mRNA and have a role in the oxidative stress defense. CcaF1 binds to many cellular RNAs of different type, several mRNAs with a function in cysteine / methionine / sulfur metabolism. It affects the stability of the CcsR RNAs and other non-coding RNAs and mRNAs. Thus, the widely distributed DUF1127 domain can mediate RNA-binding, affect stability of its binding partners and consequently modulate the bacterial transcriptome, thereby influencing different physiological processes.
Collapse
Affiliation(s)
- Julian Grützner
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Heinrich-Buff-Ring 26–32, D-35292 Giessen, Germany
| | - Fabian Billenkamp
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Heinrich-Buff-Ring 26–32, D-35292 Giessen, Germany
- Institute of Animal Nutrition, Friedrich Loeffler Institute, Bundesalle 37, D-38116 Braunschweig, Germany
| | - Daniel-Timon Spanka
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Heinrich-Buff-Ring 26–32, D-35292 Giessen, Germany
| | - Tim Rick
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Heinrich-Buff-Ring 26–32, D-35292 Giessen, Germany
| | | | - Konrad U Förstner
- ZB MED-Information Center of Life Science, Germany
- Institute of Information Science, TH Köln, University of Applied Science, Gustav-Heinemann-Ufer 54, D-50968 Köln, Cologne, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Heinrich-Buff-Ring 26–32, D-35292 Giessen, Germany
| |
Collapse
|
16
|
Spanka DT, Reuscher CM, Klug G. Impact of PNPase on the transcriptome of Rhodobacter sphaeroides and its cooperation with RNase III and RNase E. BMC Genomics 2021; 22:106. [PMID: 33549057 PMCID: PMC7866481 DOI: 10.1186/s12864-021-07409-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/26/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The polynucleotide phosphorylase (PNPase) is conserved among both Gram-positive and Gram-negative bacteria. As a core part of the Escherichia coli degradosome, PNPase is involved in maintaining proper RNA levels within the bacterial cell. It plays a major role in RNA homeostasis and decay by acting as a 3'-to-5' exoribonuclease. Furthermore, PNPase can catalyze the reverse reaction by elongating RNA molecules in 5'-to-3' end direction which has a destabilizing effect on the prolonged RNA molecule. RNA degradation is often initiated by an endonucleolytic cleavage, followed by exoribonucleolytic decay from the new 3' end. RESULTS The PNPase mutant from the facultative phototrophic Rhodobacter sphaeroides exhibits several phenotypical characteristics, including diminished adaption to low temperature, reduced resistance to organic peroxide induced stress and altered growth behavior. The transcriptome composition differs in the pnp mutant strain, resulting in a decreased abundance of most tRNAs and rRNAs. In addition, PNPase has a major influence on the half-lives of several regulatory sRNAs and can have both a stabilizing or a destabilizing effect. Moreover, we globally identified and compared differential RNA 3' ends in RNA NGS sequencing data obtained from PNPase, RNase E and RNase III mutants for the first time in a Gram-negative organism. The genome wide RNA 3' end analysis revealed that 885 3' ends are degraded by PNPase. A fair percentage of these RNA 3' ends was also identified at the same genomic position in RNase E or RNase III mutant strains. CONCLUSION The PNPase has a major influence on RNA processing and maturation and thus modulates the transcriptome of R. sphaeroides. This includes sRNAs, emphasizing the role of PNPase in cellular homeostasis and its importance in regulatory networks. The global 3' end analysis indicates a sequential RNA processing: 5.9% of all RNase E-dependent and 9.7% of all RNase III-dependent RNA 3' ends are subsequently degraded by PNPase. Moreover, we provide a modular pipeline which greatly facilitates the identification of RNA 5'/3' ends. It is publicly available on GitHub and is distributed under ICS license.
Collapse
Affiliation(s)
- Daniel-Timon Spanka
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Giessen, Germany
| | - Carina Maria Reuscher
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Giessen, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, IFZ, Giessen, Germany.
| |
Collapse
|
17
|
Reuscher CM, Klug G. Antisense RNA asPcrL regulates expression of photosynthesis genes in Rhodobacter sphaeroides by promoting RNase III-dependent turn-over of puf mRNA. RNA Biol 2021; 18:1445-1457. [PMID: 33258405 DOI: 10.1080/15476286.2020.1857520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Anoxygenic photosynthesis is an important pathway for Rhodobacter sphaeroides to produce ATP under oxygen-limiting conditions. The expression of its photosynthesis genes is tightly regulated at transcriptional and post-transcriptional levels in response to light and oxygen signals, to avoid photooxidative stress by the simultaneous presence of pigments, light and oxygen. The puf operon encodes pigment-binding proteins of the light-harvesting complex I (genes pufB and pufA), of the reaction centre (genes pufL and pufM), a scaffold protein (gene pufX) and includes the gene for sRNA PcrX. Segmental differences in the stability of the pufBALMX-pcrX mRNA contribute to the stoichiometry of LHI to RC complexes. With asPcrL we identified the third sRNA and the first antisense RNA that is involved in balancing photosynthesis gene expression in R. sphaeroides. asPcrL influences the stability of the pufBALMX-pcrX mRNA but not of the pufBA mRNA and consequently the stoichiometry of photosynthetic complexes. By base pairing to the pufL region asPcrL promotes RNase III-dependent degradation of the pufBALMX-prcX mRNA. Since asPcrL is activated by the same protein regulators as the puf operon including PcrX it is part of an incoherent feed-forward loop that fine-tunes photosynthesis gene expression.[Figure: see text].
Collapse
Affiliation(s)
- Carina M Reuscher
- Institut Für Mikro- Und Molekularbiologie, Justus-Liebig-Universität Giessen, IFZ, Giessen, Germany
| | - Gabriele Klug
- Institut Für Mikro- Und Molekularbiologie, Justus-Liebig-Universität Giessen, IFZ, Giessen, Germany
| |
Collapse
|
18
|
Nie X, Jäger A, Börner J, Klug G. Interplay between formation of photosynthetic complexes and expression of genes for iron-sulfur cluster assembly in Rhodobacter sphaeroides? PHOTOSYNTHESIS RESEARCH 2021; 147:39-48. [PMID: 33064275 PMCID: PMC7728643 DOI: 10.1007/s11120-020-00789-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
Formation of photosynthetic complexes leads to a higher demand for Fe-S clusters. We hypothesized that in the facultative phototrophic alpha-proteobacterium Rhodobacter sphaeroides expression of the isc-suf operon for Fe-S cluster formation may be increased under conditions that promote formation of photosynthetic complexes and that, vice versa, lack of the IscR regulator may also affect photosynthesis gene expression. To test this hypothesis, we monitored the activities of the isc-suf sense and anti-sense promoters under different growth conditions and in mutants which are impaired in formation of photosynthetic complexes. We also tested expression of photosynthesis genes in a mutant lacking the IscR regulator. Our results are not in agreement with a co-regulation of the Isc-Suf system and the photosynthetic apparatus at level of transcription. We provide evidence that, coordination of the systems occurs at post-transcriptional levels. Increased levels of isc-suf mRNAs under conditions promoting formation of photosynthetic complexes are due to higher RNA stability.
Collapse
Affiliation(s)
- Xin Nie
- Institute of Microbiology and Molecular Biology, University of Giessen, IFZ, Heinrich-Buff-Ring, 26-32, Germany
- School of Basic Medical Sciences, Chengdu Medical College, Chengdu, 610500, China
| | - Andreas Jäger
- Institute of Microbiology and Molecular Biology, University of Giessen, IFZ, Heinrich-Buff-Ring, 26-32, Germany
| | - Janek Börner
- Institute of Microbiology and Molecular Biology, University of Giessen, IFZ, Heinrich-Buff-Ring, 26-32, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, University of Giessen, IFZ, Heinrich-Buff-Ring, 26-32, Germany.
| |
Collapse
|
19
|
Adaptation to Photooxidative Stress: Common and Special Strategies of the Alphaproteobacteria Rhodobacter sphaeroides and Rhodobacter capsulatus. Microorganisms 2020; 8:microorganisms8020283. [PMID: 32093084 PMCID: PMC7074977 DOI: 10.3390/microorganisms8020283] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/10/2020] [Accepted: 02/13/2020] [Indexed: 12/20/2022] Open
Abstract
Photosynthetic bacteria have to deal with the risk of photooxidative stress that occurs in presence of light and oxygen due to the photosensitizing activity of (bacterio-) chlorophylls. Facultative phototrophs of the genus Rhodobacter adapt the formation of photosynthetic complexes to oxygen and light conditions, but cannot completely avoid this stress if environmental conditions suddenly change. R. capsulatus has a stronger pigmentation and faster switches to phototrophic growth than R. sphaeroides. However, its photooxidative stress response has not been investigated. Here, we compare both species by transcriptomics and proteomics, revealing that proteins involved in oxidation-reduction processes, DNA, and protein damage repair play pivotal roles. These functions are likely universal to many phototrophs. Furthermore, the alternative sigma factors RpoE and RpoHII are induced in both species, even though the genetic localization of the rpoE gene, the RpoE protein itself, and probably its regulon, are different. Despite sharing the same habitats, our findings also suggest individual strategies. The crtIB-tspO operon, encoding proteins for biosynthesis of carotenoid precursors and a regulator of photosynthesis, and cbiX, encoding a putative ferrochelatase, are induced in R. capsulatus. This specific response might support adaptation by maintaining high carotenoid-to-bacteriochlorophyll ratios and preventing the accumulation of porphyrin-derived photosensitizers.
Collapse
|
20
|
Genetic and structural determinants on iron assimilation pathways in the plant pathogen Xanthomonas citri subsp. citri and Xanthomonas sp. Braz J Microbiol 2019; 51:1219-1231. [PMID: 31848911 DOI: 10.1007/s42770-019-00207-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 12/06/2019] [Indexed: 10/25/2022] Open
Abstract
Iron is a vital nutrient to bacteria, not only in the basal metabolism but also for virulent species in infection and pathogenicity at their hosts. Despite its relevance, the role of iron in Xanthomonas citri infection, the etiological agent of citrus canker disease, is poorly understood in contrast to other pathogens, including other members of the Xanthomonas genus. In this review, we present iron assimilation pathways in X. citri including the ones for siderophore production and siderophore-iron assimilation, proven to be key factors to virulence in many organisms like Escherichia coli and Xanthomonas campestris. Based on classical iron-related proteins previously characterized in E. coli, Pseudomonas aeruginosa, and also Xanthomonadaceae, we identified orthologs in X. citri and evaluated their sequences, structural characteristics such as functional motifs, and residues that support their putative functions. Among the identified proteins are TonB-dependent receptors, periplasmic-binding proteins, active transporters, efflux pumps, and cytoplasmic enzymes. The role of each protein for the bacterium was analyzed and complemented with proteomics data previously reported. The global view of different aspects of iron regulation and nutrition in X. citri virulence and pathogenesis may help guide future investigations aiming the development of new drug targets against this important phytopathogen.
Collapse
|
21
|
Nie X, Remes B, Klug G. Multiple Sense and Antisense Promoters Contribute to the Regulated Expression of the isc-suf Operon for Iron-Sulfur Cluster Assembly in Rhodobacter. Microorganisms 2019; 7:microorganisms7120671. [PMID: 31835540 PMCID: PMC6956336 DOI: 10.3390/microorganisms7120671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/02/2019] [Accepted: 12/04/2019] [Indexed: 11/16/2022] Open
Abstract
A multitude of biological functions relies on iron-sulfur clusters. The formation of photosynthetic complexes goes along with an additional demand for iron-sulfur clusters for bacteriochlorophyll synthesis and photosynthetic electron transport. However, photooxidative stress leads to the destruction of iron-sulfur clusters, and the released iron promotes the formation of further reactive oxygen species. A balanced regulation of iron-sulfur cluster synthesis is required to guarantee the supply of this cofactor, on the one hand, but also to limit stress, on the other hand. The phototrophic alpha-proteobacterium Rhodobacter sphaeroides harbors a large operon for iron-sulfur cluster assembly comprising the iscRS and suf genes. IscR (iron-sulfur cluster regulator) is an iron-dependent regulator of isc-suf genes and other genes with a role in iron metabolism. We applied reporter gene fusions to identify promoters of the isc-suf operon and studied their activity alone or in combination under different conditions. Gel-retardation assays showed the binding of regulatory proteins to individual promoters. Our results demonstrated that several promoters in a sense and antisense direction influenced isc-suf expression and the binding of the IscR, Irr, and OxyR regulatory proteins to individual promoters. These findings demonstrated a complex regulatory network of several promoters and regulatory proteins that helped to adjust iron-sulfur cluster assembly to changing conditions in Rhodobacter sphaeroides.
Collapse
|
22
|
McIntosh M, Eisenhardt K, Remes B, Konzer A, Klug G. Adaptation of the Alphaproteobacterium Rhodobacter sphaeroides to stationary phase. Environ Microbiol 2019; 21:4425-4445. [PMID: 31579997 DOI: 10.1111/1462-2920.14809] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 08/30/2019] [Accepted: 09/18/2019] [Indexed: 12/20/2022]
Abstract
Exhaustion of nutritional resources stimulates bacterial populations to adapt their growth behaviour. General mechanisms are known to facilitate this adaptation by sensing the environmental change and coordinating gene expression. However, the existence of such mechanisms among the Alphaproteobacteria remains unclear. This study focusses on global changes in transcript levels during growth under carbon-limiting conditions in a model Alphaproteobacterium, Rhodobacter sphaeroides, a metabolically diverse organism capable of multiple modes of growth including aerobic and anaerobic respiration, anaerobic anoxygenic photosynthesis and fermentation. We identified genes that showed changed transcript levels independently of oxygen levels during the adaptation to stationary phase. We selected a subset of these genes and subjected them to mutational analysis, including genes predicted to be involved in manganese uptake, polyhydroxybutyrate production and quorum sensing and an alternative sigma factor. Although these genes have not been previously associated with the adaptation to stationary phase, we found that all were important to varying degrees. We conclude that while R. sphaeroides appears to lack a rpoS-like master regulator of stationary phase adaptation, this adaptation is nonetheless enabled through the impact of multiple genes, each responding to environmental conditions and contributing to the adaptation to stationary phase.
Collapse
Affiliation(s)
- Matthew McIntosh
- Institut für Mikrobiologie und Molekularbiologie, IFZ, Justus-Liebig-Universität, 35392, Giessen, Germany
| | - Katrin Eisenhardt
- Institut für Mikrobiologie und Molekularbiologie, IFZ, Justus-Liebig-Universität, 35392, Giessen, Germany
| | - Bernhard Remes
- Institut für Mikrobiologie und Molekularbiologie, IFZ, Justus-Liebig-Universität, 35392, Giessen, Germany
| | - Anne Konzer
- Biomolecular Mass Spectrometry, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Gabriele Klug
- Institut für Mikrobiologie und Molekularbiologie, IFZ, Justus-Liebig-Universität, 35392, Giessen, Germany
| |
Collapse
|
23
|
Bathke J, Konzer A, Remes B, McIntosh M, Klug G. Comparative analyses of the variation of the transcriptome and proteome of Rhodobacter sphaeroides throughout growth. BMC Genomics 2019; 20:358. [PMID: 31072330 PMCID: PMC6509803 DOI: 10.1186/s12864-019-5749-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/29/2019] [Indexed: 02/08/2023] Open
Abstract
Background In natural environments, bacteria must frequently cope with extremely scarce nutrients. Most studies focus on bacterial growth in nutrient replete conditions, while less is known about the stationary phase. Here, we are interested in global gene expression throughout all growth phases, including the adjustment to deep stationary phase. Results We monitored both the transcriptome and the proteome in cultures of the alphaproteobacterium Rhodobacter sphaeroides, beginning with the transition to stationary phase and at different points of the stationary phase and finally during exit from stationary phase (outgrowth) following dilution with fresh medium. Correlation between the transcriptomic and proteomic changes was very low throughout the growth phases. Surprisingly, even in deep stationary phase, the abundance of many proteins continued to adjust, while the transcriptome analysis revealed fewer adjustments. This pattern was reversed during the first 90 min of outgrowth, although this depended upon the duration of the stationary phase. We provide a detailed analysis of proteomic changes based on the clustering of orthologous groups (COGs), and compare these with the transcriptome. Conclusions The low correlation between transcriptome and proteome supports the view that post-transcriptional processes play a major role in the adaptation to growth conditions. Our data revealed that many proteins with functions in transcription, energy production and conversion and the metabolism and transport of amino acids, carbohydrates, lipids, and secondary metabolites continually increased in deep stationary phase. Based on these findings, we conclude that the bacterium responds to sudden changes in environmental conditions by a radical and rapid reprogramming of the transcriptome in the first 90 min, while the proteome changes were modest. In response to gradually deteriorating conditions, however, the transcriptome remains mostly at a steady state while the bacterium continues to adjust its proteome. Even long after the population has entered stationary phase, cells are still actively adjusting their proteomes. Electronic supplementary material The online version of this article (10.1186/s12864-019-5749-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jochen Bathke
- Institute of Bioinformatics, University of Giessen, Giessen, Germany
| | - Anne Konzer
- Biomolecular Mass Spectrometry, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Bernhard Remes
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | - Matthew McIntosh
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany.
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| |
Collapse
|
24
|
Zhao Z, Peng T, Oh JI, Glaeser J, Weber L, Li Q, Klug G. A response regulator of the OmpR family is part of the regulatory network controlling the oxidative stress response of Rhodobacter sphaeroides. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:118-128. [PMID: 30451391 DOI: 10.1111/1758-2229.12718] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 11/12/2018] [Indexed: 06/09/2023]
Abstract
As a free-living bacterium Rhodobacter sphaeroides needs to respond to many environmental stresses. Oxidative stress, membrane stress or heat stress induce the ompR-1 gene encoding a protein of the OmpR family. Overexpression of OmpR-1 results in increased resistance to organic peroxides and diamide. Our data demonstrate that OmpR-1 positively affects expression of several sRNAs with an established role in R. sphaeroides stress defences and negatively affects the promoter of the rpoHI gene. The RpoHI sigma factor has a main role in the activation of many stress responses. Thus OmpR-1 has a balancing effect on the activation of the RpoHI regulon. We present a model with OmpR-1 as part of a regulatory network controlling stress defences in R. sphaeroides.
Collapse
Affiliation(s)
- Zhiping Zhao
- Institut für Mikrobiologie und Molekularbiologie, Interdiziplinäres Forschungszentrum, Justus-Liebig-Universität Giessen, Giessen, Germany
- Department of Pharmaceutical Engineering, Sichuan University of Science and Engineering, Zigong, China
| | | | - Jeong-Il Oh
- Department of Microbiology, Pusan National University, Busan, South Korea
| | - Jens Glaeser
- Institut für Mikrobiologie und Molekularbiologie, Interdiziplinäres Forschungszentrum, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Lennart Weber
- Institut für Mikrobiologie und Molekularbiologie, Interdiziplinäres Forschungszentrum, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Qingfeng Li
- Institut für Mikrobiologie und Molekularbiologie, Interdiziplinäres Forschungszentrum, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Gabriele Klug
- Institut für Mikrobiologie und Molekularbiologie, Interdiziplinäres Forschungszentrum, Justus-Liebig-Universität Giessen, Giessen, Germany
| |
Collapse
|
25
|
Abstract
The propagation of most flowering plant species is determined by the success of seed germination, which is of both economic and ecologic importance. Mitochondria are the energy resource and crucial organelles for plant seed germination. Studying the underlying mechanism is important for us to understand the basic principles of plant development and improve crop yields. Here we identify HSP24.7 as a central activator for temperature-dependent seed germination. HSP24.7 modulates cytochrome C/C1 production in the mitochondrial electron transport chain and induces the generation of reactive oxygen species, which accelerates seed germination. Our work provides a comprehensive framework of how mitochondria regulate seed germination in response to the dynamics of environmental temperature. Seed germination is an energy demanding process that requires functional mitochondria upon imbibition. However, how mitochondria fine tune seed germination, especially in response to the dynamics of environmental temperature, remains largely unknown at the molecular level. Here, we report a mitochondrial matrix-localized heat shock protein GhHSP24.7, that regulates seed germination in a temperature-dependent manner. Suppression of GhHSP24.7 renders the seed insensitive to temperature changes and delays germination. We show that GhHSP24.7 competes with GhCCMH to bind to the maturation subunit protein GhCcmFc to form cytochrome C/C1 (CytC/C1) in the mitochondrial electron transport chain. GhHSP24.7 modulates CytC/C1 production to induce reactive oxygen species (ROS) generation, which consequently accelerates endosperm rupture and promotes seed germination. Overexpression of GhHSP24.7’s homologous genes can accelerate seed germination in Arabidopsis and tomato, indicating its conserved function across plant species. Therefore, HSP24.7 is a critical factor that positively controls seed germination via temperature-dependent ROS generation.
Collapse
|
26
|
Eisenhardt KMH, Reuscher CM, Klug G. PcrX, an sRNA derived from the 3'- UTR of the Rhodobacter sphaeroides puf operon modulates expression of puf genes encoding proteins of the bacterial photosynthetic apparatus. Mol Microbiol 2018; 110:325-334. [PMID: 29995316 DOI: 10.1111/mmi.14076] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2018] [Indexed: 11/30/2022]
Abstract
Facultative phototrophic bacteria like Rhodobacter sphaeroides can produce ATP by anoxygenic photosynthesis, which is of advantage under conditions with limiting oxygen. However, the simultaneous presence of pigments, light and oxygen leads to the generation of harmful singlet oxygen. In order to avoid this stress situation, the formation of photosynthetic complexes is tightly regulated by light and oxygen signals. In a complex regulatory network several regulatory proteins and the small non-coding RNA PcrZ contribute to the balanced expression of photosynthesis genes. With PcrX this study identifies a second sRNA that is part of this network. The puf operon encodes pigment binding proteins of the light-harvesting I complex (PufBA) and of the reaction center (PufLM), a protein regulating porphyrin flux (PufQ), and a scaffolding protein (PufX). The PcrX sRNA is derived from the 3' UTR of the puf operon mRNA by RNase E-mediated cleavage. It targets the pufX mRNA segment, reduces the half-life of the pufBALMX mRNA and as a consequence affects the level of photosynthetic complexes. By its action PcrX counteracts the increased expression of photosynthesis genes that is mediated by protein regulators and is thus involved in balancing the formation of photosynthetic complexes in response to external stimuli.
Collapse
Affiliation(s)
- Katrin M H Eisenhardt
- Institut für Mikrobiologie und Molekularbiologie, Justus Liebig Universität Giessen, IFZ, Giessen, Germany
| | - Carina M Reuscher
- Institut für Mikrobiologie und Molekularbiologie, Justus Liebig Universität Giessen, IFZ, Giessen, Germany
| | - Gabriele Klug
- Institut für Mikrobiologie und Molekularbiologie, Justus Liebig Universität Giessen, IFZ, Giessen, Germany
| |
Collapse
|
27
|
Förstner KU, Reuscher CM, Haberzettl K, Weber L, Klug G. RNase E cleavage shapes the transcriptome ofRhodobacter sphaeroidesand strongly impacts phototrophic growth. Life Sci Alliance 2018; 1:e201800080. [PMID: 30456366 PMCID: PMC6238624 DOI: 10.26508/lsa.201800080] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/13/2018] [Accepted: 07/13/2018] [Indexed: 11/24/2022] Open
Abstract
This study identifies the cleavage sites of the endoribonuclease RNase E in the Rhodobacter sphaeroides transcriptome and demonstrates its effect on oxidative stress resistance and phototrophic growth. Bacteria adapt to changing environmental conditions by rapid changes in their transcriptome. This is achieved not only by adjusting rates of transcription but also by processing and degradation of RNAs. We applied TIER-Seq (transiently inactivating an endoribonuclease followed by RNA-Seq) for the transcriptome-wide identification of RNase E cleavage sites and of 5′ RNA ends, which are enriched when RNase E activity is reduced in Rhodobacter sphaeroides. These results reveal the importance of RNase E for the maturation and turnover of mRNAs, rRNAs, and sRNAs in this guanine-cytosine-rich α-proteobacterium, some of the latter have well-described functions in the oxidative stress response. In agreement with this, a role of RNase E in the oxidative stress response is demonstrated. A remarkably strong phenotype of a mutant with reduced RNase E activity was observed regarding the formation of photosynthetic complexes and phototrophic growth, whereas there was no effect on chemotrophic growth.
Collapse
Affiliation(s)
- Konrad U Förstner
- German National Library of Medicine—Information Center for Life Sciences, Cologne, Germany
- Technical University of Cologne, Faculty for Information and Communication Sciences, Cologne, Germany
- Core Unit Systems Medicine, Institutes of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
- Correspondence:
| | - Carina M Reuscher
- Institut für Mikrobiologie und Molekularbiologie, Interdisciplinary Research Center for Biosystems, Universität Giessen, Giessen, Germany
| | - Kerstin Haberzettl
- Institut für Mikrobiologie und Molekularbiologie, Interdisciplinary Research Center for Biosystems, Universität Giessen, Giessen, Germany
| | - Lennart Weber
- Institut für Mikrobiologie und Molekularbiologie, Interdisciplinary Research Center for Biosystems, Universität Giessen, Giessen, Germany
| | - Gabriele Klug
- Institut für Mikrobiologie und Molekularbiologie, Interdisciplinary Research Center for Biosystems, Universität Giessen, Giessen, Germany
| |
Collapse
|
28
|
Hu S, Yu Y, Zhou D, Li R, Xiao X, Wu H. Global transcriptomic Acid Tolerance Response in Salmonella Enteritidis. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2018.02.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
29
|
The PhyR homolog RSP_1274 of Rhodobacter sphaeroides is involved in defense of membrane stress and has a moderate effect on RpoE (RSP_1092) activity. BMC Microbiol 2018; 18:18. [PMID: 29486719 PMCID: PMC5830050 DOI: 10.1186/s12866-018-1161-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 02/20/2018] [Indexed: 11/10/2022] Open
Abstract
Background A major role of the PhyR-NepR-σ(EcfG) cascade in the general stress response was demonstrated for some bacterial species and considered as conserved in Alphaproteobacteria. The σ(EcfG) factor activates its target genes in response to diverse stresses and NepR represents its anti-sigma factor. PhyR comprises a response regulator domain and a sigma factor domain and acts as anti-sigma factor antagonist. The facultative phototrophic alphaproteobacterium Rhodobacter sphaeroides harbours a PhyR homolog in the same genomic context as found in other members of this class. Results Our study reveals increased expression of the phyR gene in response to superoxide, singlet oxygen, and diamide and also an effect of PhyR on rpoE expression. RpoE has a central role in mounting the response to singlet oxygen in R. sphaeroides. Despite these findings a mutant lacking PhyR was not significantly impeded in resistance to oxidative stress, heat stress or osmotic stress. However a role of PhyR in membrane stress is demonstrated. Conclusion These results support the view that the effect of the PhyR-NepR-σ(EcfG) cascade on diverse stress responses varies among members of the Alphaproteobacteria. In the facultative phototroph Rhodobacter sphaeroides PhyR plays no major role in the general stress or the oxidative stress response but rather has a more specialized role in defense of membrane stress. Electronic supplementary material The online version of this article (10.1186/s12866-018-1161-4) contains supplementary material, which is available to authorized users.
Collapse
|
30
|
Elkina D, Weber L, Lechner M, Burenina O, Weisert A, Kubareva E, Hartmann RK, Klug G. 6S RNA in Rhodobacter sphaeroides: 6S RNA and pRNA transcript levels peak in late exponential phase and gene deletion causes a high salt stress phenotype. RNA Biol 2017; 14:1627-1637. [PMID: 28692405 DOI: 10.1080/15476286.2017.1342933] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The function of 6S RNA, a global regulator of transcription, was studied in the photosynthetic α-proteobacterium Rhodobacter sphaeroides. The cellular levels of R. sphaeroides 6S RNA peak toward the transition to stationary phase and strongly decrease during extended stationary phase. The synthesis of so-called product RNA transcripts (mainly 12-16-mers) on 6S RNA as template by RNA polymerase was found to be highest in late exponential phase. Product RNA ≥ 13-mers are expected to trigger the dissociation of 6S RNA:RNA polymerase complexes. A 6S RNA deletion in R. sphaeroides had no impact on growth under various metabolic and oxidative stress conditions (with the possible exception of tert-butyl hydroperoxide stress). However, the 6S RNA knockout resulted in a robust growth defect under high salt stress (0.25 M NaCl). Remarkably, the sspA gene encoding the putative salt stress-induced membrane protein SspA and located immediately downstream of the 6S RNA (ssrS) gene on the antisense strand was expressed at elevated levels in the ΔssrS strain when grown in the presence of 250 mM NaCl.
Collapse
Affiliation(s)
- Daria Elkina
- a Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology , M.V. Lomonosov Moscow State University , Leninskie Gory 1, Moscow , Russia
| | - Lennart Weber
- b Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-University-Gießen, Heinrich-Buff-Ring 26-32 , Gießen , Germany
| | - Marcus Lechner
- c Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6 , Marburg , Germany ; Skolkovo Institute for Science and Technology , Skoltech, Moscow
| | - Olga Burenina
- a Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology , M.V. Lomonosov Moscow State University , Leninskie Gory 1, Moscow , Russia
| | - Andrea Weisert
- b Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-University-Gießen, Heinrich-Buff-Ring 26-32 , Gießen , Germany
| | - Elena Kubareva
- a Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology , M.V. Lomonosov Moscow State University , Leninskie Gory 1, Moscow , Russia
| | - Roland K Hartmann
- c Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6 , Marburg , Germany ; Skolkovo Institute for Science and Technology , Skoltech, Moscow
| | - Gabriele Klug
- b Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-University-Gießen, Heinrich-Buff-Ring 26-32 , Gießen , Germany
| |
Collapse
|
31
|
An RpoHI-Dependent Response Promotes Outgrowth after Extended Stationary Phase in the Alphaproteobacterium Rhodobacter sphaeroides. J Bacteriol 2017; 199:JB.00249-17. [PMID: 28507242 DOI: 10.1128/jb.00249-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 05/05/2017] [Indexed: 12/31/2022] Open
Abstract
Under unfavorable growth conditions, bacteria enter stationary phase and can maintain cell viability over prolonged periods with no increase in cell number. To obtain insights into the regulatory mechanisms that allow bacteria to resume growth when conditions become favorable again (outgrowth), we performed global transcriptome analyses at different stages of growth for the alphaproteobacterium Rhodobacter sphaeroides The majority of genes were not differentially expressed across growth phases. After a short stationary phase (about 20 h after growth starts to slow down), only 7% of the genes showed altered expression (fold change of >1.6 or less than -1.6, corresponding to a log2 fold change of >0.65 or less than -0.65, respectively) compared to expression at exponential phase. Outgrowth induced a distinct response in gene expression which was strongly influenced by the length of the preceding stationary phase. After a long stationary phase (about 64 h after growth starts to slow down), a much larger number of genes (15.1%) was induced in outgrowth than after a short stationary phase (1.7%). Many of those genes are known members of the RpoHI/RpoHII regulons and have established functions in stress responses. A main effect of RpoHI on the transcriptome in outgrowth after a long stationary phase was confirmed. Growth experiments with mutant strains further support an important function in outgrowth after prolonged stationary phase for the RpoHI and RpoHII sigma factors.IMPORTANCE In natural environments, the growth of bacteria is limited mostly by lack of nutrients or other unfavorable conditions. It is important for bacterial populations to efficiently resume growth after being in stationary phase, which may last for long periods. Most previous studies on growth-phase-dependent gene expression did not address outgrowth after stationary phase. This study on growth-phase-dependent gene regulation in a model alphaproteobacterium reveals, for the first time, that the length of the stationary phase strongly impacts the transcriptome during outgrowth. The alternative sigma factors RpoHI and RpoHII, which are important regulators of stress responses in alphaproteobacteria, play a major role during outgrowth following prolonged stationary phase. These findings provide the first insight into the regulatory mechanisms enabling efficient outgrowth.
Collapse
|
32
|
Gilyazeva AG, Toymentseva AA, Mardanova AM. Analysis of Genome Grimelysin-Containing Locus in the Genome of Serratia grimesii A2. BIONANOSCIENCE 2017. [DOI: 10.1007/s12668-016-0330-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
33
|
Vuorijoki L, Tiwari A, Kallio P, Aro EM. Inactivation of iron-sulfur cluster biogenesis regulator SufR in Synechocystis sp. PCC 6803 induces unique iron-dependent protein-level responses. Biochim Biophys Acta Gen Subj 2017; 1861:1085-1098. [PMID: 28216046 DOI: 10.1016/j.bbagen.2017.02.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/31/2017] [Accepted: 02/14/2017] [Indexed: 10/20/2022]
Abstract
BACKGROUND Iron-sulfur (Fe-S) clusters are protein-bound cofactors associated with cellular electron transport and redox sensing, with multiple specific functions in oxygen-evolving photosynthetic cyanobacteria. The aim here was to elucidate protein-level effects of the transcriptional repressor SufR involved in the regulation of Fe-S cluster biogenesis in the cyanobacterium Synechocystis sp. PCC 6803. METHODS The approach was to quantitate 94 pre-selected target proteins associated with various metabolic functions using SRM in Synechocystis. The evaluation was conducted in response to sufR deletion under different iron conditions, and complemented with EPR analysis on the functionality of the photosystems I and II as well as with RT-qPCR to verify the effects of SufR also on transcript level. RESULTS The results on both protein and transcript levels show that SufR acts not only as a repressor of the suf operon when iron is available but also has other direct and indirect functions in the cell, including maintenance of the expression of pyruvate:ferredoxin oxidoreductase NifJ and other Fe-S cluster proteins under iron sufficient conditions. Furthermore, the results imply that in the absence of iron the suf operon is repressed by some additional regulatory mechanism independent of SufR. CONCLUSIONS The study demonstrates that Fe-S cluster metabolism in Synechocystis is stringently regulated, and has complex interactions with multiple primary functions in the cell, including photosynthesis and central carbon metabolism. GENERAL SIGNIFICANCE The study provides new insight into the regulation of Fe-S cluster biogenesis via suf operon, and the associated wide-ranging protein-level changes in photosynthetic cyanobacteria.
Collapse
Affiliation(s)
- Linda Vuorijoki
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
| | - Arjun Tiwari
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
| | - Pauli Kallio
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
| |
Collapse
|
34
|
von Zadow A, Ignatz E, Pokorny R, Essen LO, Klug G. Rhodobacter sphaeroides CryB is a bacterial cryptochrome with (6-4) photolyase activity. FEBS J 2016; 283:4291-4309. [PMID: 27739235 DOI: 10.1111/febs.13924] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 09/20/2016] [Accepted: 10/11/2016] [Indexed: 11/30/2022]
Abstract
Photolyases are efficient DNA repair enzymes that specifically repair either cyclobutane pyrimidine dimers or (6-4) photoproducts in a light-dependent cleavage reaction. The closely related classical cryptochrome blue light photoreceptors do not repair DNA lesions; instead they are involved in regulatory processes. CryB of Rhodobacter sphaeroides was until now described as a cryptochrome that affects light-dependent and singlet oxygen-dependent gene expression and is unusual in terms of its cofactor composition. Here we present evidence for a repair activity of (6-4) photoproducts by CryB and suggest a dual character combining the functions of cryptochromes and photolyases. We investigated the effects of crucial amino acids involved in cofactor or DNA lesion binding on the light-dependent recovery of cells after UV light exposure (in vivo photoreactivation). Remarkably, impairment of one of the two light absorbing cofactors, FAD or 6,7-dimethyl-8-ribityllumazine, only marginally affected the final survival rate but strongly decelerated photoreactivation kinetics. The impairment of both of them together through mutagenesis decreased CryB-dependent photoreactivation to the level of the ∆cryB knockout strain. The third cofactor, a [4Fe4S] iron-sulfur cluster, is indispensable for the structural integrity of the protein. The reduction of FAD via the conserved tryptophan W338, which is crucial for in vitro reduction and consequently DNA repair, is not required for in vivo photoreactivation, suggesting that this reduction pathway to FAD is dispensable in the cellular environment. This demonstrates that in vitro experiments give only limited information on in vivo photolyase activity.
Collapse
Affiliation(s)
- Andrea von Zadow
- Institute of Microbiology and Molecular Biology, Giessen University, Germany
| | - Elisabeth Ignatz
- Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Germany
| | - Richard Pokorny
- Department of Plant Physiology and Photobiology, Faculty of Biology, Philipps University Marburg, Germany
| | - Lars-Oliver Essen
- Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Giessen University, Germany
| |
Collapse
|
35
|
Weber L, Thoelken C, Volk M, Remes B, Lechner M, Klug G. The Conserved Dcw Gene Cluster of R. sphaeroides Is Preceded by an Uncommonly Extended 5' Leader Featuring the sRNA UpsM. PLoS One 2016; 11:e0165694. [PMID: 27802301 PMCID: PMC5089854 DOI: 10.1371/journal.pone.0165694] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 10/17/2016] [Indexed: 11/18/2022] Open
Abstract
Cell division and cell wall synthesis mechanisms are similarly conserved among bacteria. Consequently some bacterial species have comparable sets of genes organized in the dcw (division andcellwall) gene cluster. Dcw genes, their regulation and their relative order within the cluster are outstandingly conserved among rod shaped and gram negative bacteria to ensure an efficient coordination of growth and division. A well studied representative is the dcw gene cluster of E. coli. The first promoter of the gene cluster (mraZ1p) gives rise to polycistronic transcripts containing a 38 nt long 5’ UTR followed by the first gene mraZ. Despite reported conservation we present evidence for a much longer 5’ UTR in the gram negative and rod shaped bacterium Rhodobacter sphaeroides and in the family of Rhodobacteraceae. This extended 268 nt long 5’ UTR comprises a Rho independent terminator, which in case of termination gives rise to a non-coding RNA (UpsM). This sRNA is conditionally cleaved by RNase E under stress conditions in an Hfq- and very likely target mRNA-dependent manner, implying its function in trans. These results raise the question for the regulatory function of this extended 5’ UTR. It might represent the rarely described case of a trans acting sRNA derived from a riboswitch with exclusive presence in the family of Rhodobacteraceae.
Collapse
Affiliation(s)
- Lennart Weber
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-University Giessen, Giessen, Germany
| | - Clemens Thoelken
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Marcel Volk
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-University Giessen, Giessen, Germany
| | - Bernhard Remes
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-University Giessen, Giessen, Germany
| | - Marcus Lechner
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-University Giessen, Giessen, Germany
- * E-mail:
| |
Collapse
|
36
|
Müller KMH, Berghoff BA, Eisenhardt BD, Remes B, Klug G. Characteristics of Pos19 - A Small Coding RNA in the Oxidative Stress Response of Rhodobacter sphaeroides. PLoS One 2016; 11:e0163425. [PMID: 27669425 PMCID: PMC5036791 DOI: 10.1371/journal.pone.0163425] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/08/2016] [Indexed: 02/07/2023] Open
Abstract
The phototrophic bacterium Rhodobacter sphaeroides induces several small RNAs (sRNAs) when singlet oxygen (1O2) levels are elevated, a situation also referred to as photo-oxidative stress. An RNA-seq study identified the RSs0019 sRNA, which is renamed Pos19 (photo-oxidative stress induced sRNA 19). Pos19 is part of the RpoE regulon and consequently induced upon 1O2 and peroxide stress. The 219 nt long Pos19 transcript contains a small open reading frame (sORF) of 150 nt, which is translated in vivo. Over-expression of Pos19 results in reduced mRNA levels for several genes, of which numerous are involved in sulfur metabolism. The negative effect on the potential targets is maintained even when translation of the sORF is abolished, arguing that regulation is entailed by the sRNA itself. Reporter studies further revealed that regulation of the most affected mRNA, namely RSP_0557, by Pos19 is Hfq-dependent. Direct binding of Pos19 to Hfq was shown by co-immunoprecipitation. Physiological experiments indicated Pos19 to be involved in the balance of glutathione biosynthesis. Moreover, a lack of Pos19 leads to elevated reactive oxygen species levels. Taken together our data identify the sRNA Pos19 as a coding sRNA with a distinct expression pattern and potential role under oxidative stress in the phototrophic bacterium R. sphaeroides.
Collapse
Affiliation(s)
- Katrin M. H. Müller
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität, Heinrich-Buff-Ring 26, 35392, Giessen, Germany
| | - Bork A. Berghoff
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität, Heinrich-Buff-Ring 26, 35392, Giessen, Germany
| | - Benjamin D. Eisenhardt
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität, Heinrich-Buff-Ring 26, 35392, Giessen, Germany
| | - Bernhard Remes
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität, Heinrich-Buff-Ring 26, 35392, Giessen, Germany
| | - Gabriele Klug
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität, Heinrich-Buff-Ring 26, 35392, Giessen, Germany
- * E-mail:
| |
Collapse
|
37
|
Peng T, Berghoff BA, Oh JI, Weber L, Schirmer J, Schwarz J, Glaeser J, Klug G. Regulation of a polyamine transporter by the conserved 3' UTR-derived sRNA SorX confers resistance to singlet oxygen and organic hydroperoxides in Rhodobacter sphaeroides. RNA Biol 2016; 13:988-999. [PMID: 27420112 DOI: 10.1080/15476286.2016.1212152] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Singlet oxygen is generated by bacteriochlorophylls when light and oxygen are simultaneously present in Rhodobacter sphaeroides. Singlet oxygen triggers a specific response that is partly regulated by the alternative sigma factor RpoHI/HII. The sRNA RSs2461 has previously been identified as an RpoHI/HII-dependent sRNA and is derived from the 3' UTR of the mRNA for an OmpR-type transcriptional regulator. Similar to the RpoHI/HII-dependent CcsR and SorY sRNAs, RSs2461 affects the resistance of R. sphaeroides against singlet oxygen and was therefore renamed here SorX. Furthermore, SorX has a strong impact on resistance against organic hydroperoxides that usually occur as secondary damages downstream of singlet oxygen. The 75-nt SorX 3' fragment, which is generated by RNase E cleavage and highly conserved among related species, represents the functional entity. A target search identified potA mRNA, which encodes a subunit of a polyamine transporter, as a direct SorX target and stress resistance via SorX could be linked to potA. The PotABCD transporter is an uptake system for spermidine in E. coli. While spermidine is generally described as beneficial during oxidative stress, we observed significantly increased sensitivity of R. sphaeroides to organic hydroperoxides in the presence of spermidine. We therefore propose that the diminished import of spermidine, due to down-regulation of potA by SorX, counteracts oxidative stress. Together with results from other studies this underlines the importance of regulated transport to bacterial stress defense.
Collapse
Affiliation(s)
- Tao Peng
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
| | - Bork A Berghoff
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
| | - Jeong-Il Oh
- b Department of Microbiology , Pusan National University , Busan , Korea
| | - Lennart Weber
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
| | - Jasmin Schirmer
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
| | - Johannes Schwarz
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
| | - Jens Glaeser
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
| | - Gabriele Klug
- a Institut für Mikrobiologie und Molekularbiologie, IFZ, Universität Giessen , Giessen , Germany
| |
Collapse
|
38
|
Adnan F, Weber L, Klug G. The sRNA SorY confers resistance during photooxidative stress by affecting a metabolite transporter in Rhodobacter sphaeroides. RNA Biol 2016; 12:569-77. [PMID: 25833751 PMCID: PMC4615379 DOI: 10.1080/15476286.2015.1031948] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Exposure to oxygen and light generates photooxidative stress by the bacteriochlorophyll a mediated formation of singlet oxygen (1O2) in the facultative photosynthetic bacterium Rhodobacter sphaeroides. We have identified SorY as an sRNA, which is induced under several stress conditions and confers increased resistance against 1O2. SorY by direct interaction affects the takP mRNA, encoding a TRAP-T transporter. We present a model in which SorY reduces the metabolite flux into the tricarboxylic acid cycle (TCA cycle) by reducing malate import through TakP. It was previously shown that oxidative stress in bacteria leads to switch from glycolysis to the pentose phosphate pathway and to reduced activity of the TCA cycle. As a consequence the production of the prooxidant NADH is reduced and production of the protective NADPH is enhanced. In R. sphaeroides enzymes for glycolysis, pentose phosphate pathway, Entner–Doudoroff pathway and gluconeogenesis are induced in response to 1O2 by the alternative sigma factor RpoHII. The same is true for the sRNA SorY. By limiting malate import SorY thus contributes to the balance of the metabolic fluxes under photooxidative stress conditions. This assigns a so far unknown function to an sRNA in oxidative stress response.
Collapse
Affiliation(s)
- Fazal Adnan
- a Institute of Microbiology and Molecular Biology ; IFZ ; Giessen University ; Giessen , Germany
| | | | | |
Collapse
|
39
|
Remes B, Eisenhardt BD, Srinivasan V, Klug G. IscR of Rhodobacter sphaeroides functions as repressor of genes for iron-sulfur metabolism and represents a new type of iron-sulfur-binding protein. Microbiologyopen 2015; 4:790-802. [PMID: 26235649 PMCID: PMC4618611 DOI: 10.1002/mbo3.279] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 06/15/2015] [Accepted: 06/23/2015] [Indexed: 12/20/2022] Open
Abstract
IscR proteins are known as transcriptional regulators for Fe–S biogenesis. In the facultatively phototrophic bacterium, Rhodobacter sphaeroides IscR is the product of the first gene in the isc-suf operon. A major role of IscR in R. sphaeroides iron-dependent regulation was suggested in a bioinformatic study (Rodionov et al., PLoS Comput Biol 2:e163, 2006), which predicted a binding site in the upstream regions of several iron uptake genes, named Iron-Rhodo-box. Most known IscR proteins have Fe–S clusters featuring (Cys)3(His)1 ligation. However, IscR proteins from Rhodobacteraceae harbor only a single-Cys residue and it was considered unlikely that they can ligate an Fe–S cluster. In this study, the role of R. sphaeroides IscR as transcriptional regulator and sensor of the Fe–S cluster status of the cell was analyzed. A mutant lacking IscR is more impaired in growth under iron limitation than the wild-type and exhibits significantly increased ROS levels in iron-replete and iron-deplete conditions. Expression studies reveal that R. sphaeroides IscR in its cluster-bound form functions as transcriptional repressor of genes involved in iron metabolism by direct binding to the promoter region of genes preceded by the motif. A total of 110 genes are directly or indirectly affected by IscR. Furthermore, IscR possesses a unique Fe–S cluster ligation scheme with only a single cysteine involved.
Collapse
Affiliation(s)
- Bernhard Remes
- Institut für Mikrobiologie und Molekularbiologie, IFZ, Justus-Liebig-Universität, 35392, Giessen, Germany
| | - Benjamin D Eisenhardt
- Institut für Mikrobiologie und Molekularbiologie, IFZ, Justus-Liebig-Universität, 35392, Giessen, Germany
| | - Vasundara Srinivasan
- LOEWE-Zentrum für Synthetische Mikrobiologie, Philipps Universität Marburg, 35043, Marburg, Germany
| | - Gabriele Klug
- Institut für Mikrobiologie und Molekularbiologie, IFZ, Justus-Liebig-Universität, 35392, Giessen, Germany
| |
Collapse
|