1
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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.
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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
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2
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Zhang J, Zheng M, Tang Z, Zhong S, Bu T, Li Q. The Regulatory Functions of the Multiple Alternative Sigma Factors RpoE, RpoHI, and RpoHII Depend on the Growth Phase in Rhodobacter sphaeroides. Microorganisms 2023; 11:2678. [PMID: 38004690 PMCID: PMC10673084 DOI: 10.3390/microorganisms11112678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Bacterial growth, under laboratory conditions or in a natural environment, goes through different growth phases. Some gene expressions are regulated with respect to the growth phase, which allows bacteria to adapt to changing conditions. Among them, many gene transcriptions are controlled by RpoHI or RpoHII in Rhodobacter sphaeroides. In a previous study, it was proven that the alternative sigma factors, RpoE, RpoHI, and RpoHII, are the major regulators of oxidative stress. Moreover, the growth of bacteria reached a stationary phase, and following the outgrowth, rpoE, rpoHI, and rpoHII mRNAs increased with respect to the growth phase. In this study, we demonstrated the regulatory function of alternative sigma factors in the rsp_0557 gene. The gene rsp_0557 is expressed with respect to the growth phase and belongs to the RpoHI/RpoHII regulons. Reporter assays showed that the antisigma factor ChrR turns on or over the RpoE activity to regulate rsp_0557 expression across the growth phase. In the exponential phase, RpoHII and sRNA Pos19 regulate the expression of rsp_0557 to an appropriate level under RpoE control. In the stationary phase, RpoHI and Pos19 stabilize the transcription of rsp_0557 at a high level. During outgrowth, RpoHI negatively regulates the transcription of rsp_0557. Taken together, our data indicate that these regulators are recruited by cells to adapt to or survive under different conditions throughout the growth phase. However, they still did not display all of the regulators involved in growth phase-dependent regulation. More research is still needed to learn more about the interaction between the regulators and the process of adapting to changed growth conditions and environments.
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Affiliation(s)
| | | | | | | | | | - Qingfeng Li
- College of Life Sciences, Sichuan Agricultural University, Ya’an 625014, China; (J.Z.); (M.Z.); (Z.T.); (S.Z.); (T.B.)
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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.
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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.
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McIntosh M, Köchling T, Latz A, Kretz J, Heinen S, Konzer A, Klug G. A major checkpoint for protein expression in Rhodobacter sphaeroides during heat stress response occurs at the level of translation. Environ Microbiol 2021; 23:6483-6502. [PMID: 34668288 DOI: 10.1111/1462-2920.15818] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 10/05/2021] [Indexed: 12/24/2022]
Abstract
Temperature above the physiological optimum is a stress condition frequently faced by bacteria in their natural environments. Here, we were interested in the correlation between levels of RNA and protein under heat stress. Changes in RNA and protein levels were documented in cultures of Rhodobacter sphaeroides using RNA sequencing, quantitative mass spectrometry, western blot analysis, in vivo [35 S] methionine-labelling and plasmid-borne reporter fusions. Changes in the transcriptome were extensive. Strikingly, the proteome remained unchanged except for very few proteins. Examples include a heat shock protein, a DUF1127 protein of unknown function and sigma factor proteins from leaderless transcripts. Insight from this study indicates that R. sphaeroides responds to heat stress by producing a broad range of transcripts while simultaneously preventing translation from nearly all of them, and that this selective production of protein depends on the untranslated region of the transcript. We conclude that measurements of transcript abundance are insufficient to understand gene regulation. Rather, translation can be an important checkpoint for protein expression under certain environmental conditions. Furthermore, during heat shock, regulation at the level of transcription might represent preparation for survival in an unpredictable environment while regulation at translation ensures production of only a few proteins.
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Affiliation(s)
- Matthew McIntosh
- Institute of Microbiology und Molecular Biology, IFZ, Justus-Liebig-Universität, 35292, Giessen, Germany
| | - Thorsten Köchling
- Institute of Microbiology und Molecular Biology, IFZ, Justus-Liebig-Universität, 35292, Giessen, Germany
| | - Anna Latz
- Institute of Microbiology und Molecular Biology, IFZ, Justus-Liebig-Universität, 35292, Giessen, Germany
| | - Jonas Kretz
- Institute of Microbiology und Molecular Biology, IFZ, Justus-Liebig-Universität, 35292, Giessen, Germany
| | - Sandra Heinen
- Institute of Microbiology und Molecular Biology, IFZ, Justus-Liebig-Universität, 35292, Giessen, Germany
| | - Anne Konzer
- Biomolecular Mass Spectrometry, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Gabriele Klug
- Institute of Microbiology und Molecular Biology, IFZ, Justus-Liebig-Universität, 35292, Giessen, Germany
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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.
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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.
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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
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8
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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.
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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
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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].
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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
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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.
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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.
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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
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12
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Hu Q, Zhou N, Rene ER, Wu D, Sun D, Qiu B. Stimulation of anaerobic biofilm development in the presence of low concentrations of toxic aromatic pollutants. BIORESOURCE TECHNOLOGY 2019; 281:26-30. [PMID: 30784999 DOI: 10.1016/j.biortech.2019.02.076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 06/09/2023]
Abstract
The main aim of this work was to stimulate biofilm formation in the presence of wastewater containing aromatic compounds with different toxicities (EC50). The results indicated that wastewater with an EC50 value >85% accelerates the attachment of bacteria onto the bio-carriers because the toxic wastewater stimulates the production of extracellular polymeric substances (EPS) from the seed sludge. In order to understand the role of EPS on biofilm development, experiments were conducted using the seed sludge, from which the soluble, loosely bound, and tightly bound EPS were removed. The soluble EPS fraction was determined to be crucial for biofilm development. Firmicutes bacterium and Clostridium chromoreductans survived and were enriched in the formed biofilms in our study, which can resist toxic aromatics.
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Affiliation(s)
- Qian Hu
- Beijing Key Laboratory for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Na Zhou
- Beijing Key Laboratory for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Eldon R Rene
- Department of Environmental Engineering and Water Technology, IHE - Delft Institute for Water Education, Westvest 7, 2601 DA Delft, The Netherlands
| | - Dexiu Wu
- Beijing Key Laboratory for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Dezhi Sun
- Beijing Key Laboratory for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
| | - Bin Qiu
- Beijing Key Laboratory for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China.
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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.
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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
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14
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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.
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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
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15
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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.
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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
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16
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Yu SH, Vogel J, Förstner KU. ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes. Gigascience 2018; 7:5087959. [PMID: 30169674 PMCID: PMC6123526 DOI: 10.1093/gigascience/giy096] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 08/23/2018] [Indexed: 11/13/2022] Open
Abstract
To understand the gene regulation of an organism of interest, a comprehensive genome annotation is essential. While some features, such as coding sequences, can be computationally predicted with high accuracy based purely on the genomic sequence, others, such as promoter elements or noncoding RNAs, are harder to detect. RNA sequencing (RNA-seq) has proven to be an efficient method to identify these genomic features and to improve genome annotations. However, processing and integrating RNA-seq data in order to generate high-resolution annotations is challenging, time consuming, and requires numerous steps. We have constructed a powerful and modular tool called ANNOgesic that provides the required analyses and simplifies RNA-seq-based bacterial and archaeal genome annotation. It can integrate data from conventional RNA-seq and differential RNA-seq and predicts and annotates numerous features, including small noncoding RNAs, with high precision. The software is available under an open source license (ISCL) at https://pypi.org/project/ANNOgesic/.
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Affiliation(s)
- Sung-Huan Yu
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Josef-Schneider-Straße 2, 97080 Würzburg Germany
| | - Konrad U Förstner
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany.,ZB MED - Information Center for Life Sciences, Informationservices, Gleueler Straße 60, 50931 Cologne (Köln), Germany.,Technical University of Cologne, Faculty for Information and Communication Sciences, Claudiusstraße 1, 50678 Cologne (Köln), Germany
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17
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Xiong C, Li X, Liu J, Zhao X, Xu S, Huang X. Identification and Characterization of a Cis Antisense RNA of the rpoH Gene of Salmonella enterica Serovar Typhi. Front Microbiol 2018; 9:978. [PMID: 29867881 PMCID: PMC5963218 DOI: 10.3389/fmicb.2018.00978] [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: 02/01/2018] [Accepted: 04/25/2018] [Indexed: 12/31/2022] Open
Abstract
Antisense RNAs from complementary strands of protein coding genes regulate the expression of genes involved in many cellular processes. Using deep sequencing analysis of the Salmonella enterica serovar Typhi (S. Typhi) transcriptome, a novel antisense RNA encoded on the strand complementary to the rpoH gene was revealed. In this study, the molecular features of this antisense RNA were assessed using northern blotting and rapid amplification of cDNA ends. The 3,508 nt sequence of RNA was identified as the antisense RNA of the rpoH gene and was named ArpH. ArpH was found to attenuate the invasion of HeLa cells by S. Typhi by regulating the expression of SPI-1 genes. In an rpoH mutant strain, the invasive capacity of S. Typhi was increased, whereas overexpression of ArpH positively regulates rpoH mRNA levels. Results of this study suggest that the cis-encoded antisense RNA ArpH is likely to affect the invasive capacity of S. Typhi by regulating the expression of rpoH.
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Affiliation(s)
- Changyan Xiong
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, China.,Department of Forensic Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xuejiao Li
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, China.,Department of Laboratory Diagnosis, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - Juanli Liu
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xin Zhao
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Shungao Xu
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xinxiang Huang
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, China
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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.
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