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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 02 October 2012, Vol.109(40), pp.16306-11
    Description: The small RNA PcrZ (photosynthesis control RNA Z) of the facultative phototrophic bacterium Rhodobacter sphaeroides is induced upon a drop of oxygen tension with similar kinetics to those of genes for components of photosynthetic complexes. High expression of PcrZ depends on PrrA, the response regulator of the PrrB/PrrA two-component system with a central role in redox regulation in R. sphaeroides. In addition the FnrL protein, an activator of some photosynthesis genes at low oxygen tension, is involved in redox-dependent expression of this small (s)RNA. Overexpression of full-length PcrZ in R. sphaeroides affects expression of a small subset of genes, most of them with a function in photosynthesis. Some mRNAs from the photosynthetic gene cluster were predicted to be putative PcrZ targets and results from an in vivo reporter system support these predictions. Our data reveal a negative effect of PcrZ on expression of its target mRNAs. Thus, PcrZ counteracts the redox-dependent induction of photosynthesis genes, which is mediated by protein regulators. Because PrrA directly activates photosynthesis genes and at the same time PcrZ, which negatively affects photosynthesis gene expression, this is one of the rare cases of an incoherent feed-forward loop including an sRNA. Our data identified PcrZ as a trans acting sRNA with a direct regulatory function in formation of photosynthetic complexes and provide a model for the control of photosynthesis gene expression by a regulatory network consisting of proteins and a small noncoding RNA.
    Keywords: Models, Biological ; Bacterial Proteins -- Metabolism ; Gene Expression Regulation, Bacterial -- Physiology ; Photosynthesis -- Genetics ; RNA-Binding Proteins -- Metabolism ; Rhodobacter Sphaeroides -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 2012, Vol.109(40), pp.16306-16311
    Description: The small RNA PcrZ (photosynthesis control RNA Z) of the facultative phototrophic bacterium Rhodobacter sphaeroides is induced upon a drop of oxygen tension with similar kinetics to those of genes for components of photosynthetic complexes. High expression of PcrZ depends on PrrA, the response regulator of the PrrB/PrrA two-component system with a central role in redox regulation in R. sphaeroides . In addition the FnrL protein, an activator of some photosynthesis genes at low oxygen tension, is involved in redox-dependent expression of this small (s)RNA. Overexpression of full-length PcrZ in R. sphaeroides affects expression of a small subset of genes, most of them with a function in photosynthesis. Some mRNAs from the photosynthetic gene cluster were predicted to be putative PcrZ targets and results from an in vivo reporter system support these predictions. Our data reveal a negative effect of PcrZ on expression of its target mRNAs. Thus, PcrZ counteracts the redox-dependent induction of photosynthesis genes, which is mediated by protein regulators. Because PrrA directly activates photosynthesis genes and at the same time PcrZ, which negatively affects photosynthesis gene expression, this is one of the rare cases of an incoherent feed-forward loop including an sRNA. Our data identified PcrZ as a trans acting sRNA with a direct regulatory function in formation of photosynthetic complexes and provide a model for the control of photosynthesis gene expression by a regulatory network consisting of proteins and a small noncoding RNA. ; p. 16306-16311.
    Keywords: Models ; Photosynthesis ; Rhodobacter Sphaeroides ; Photosynthetic Bacteria ; Oxygen ; Messenger Rna ; Adverse Effects ; Non-Coding Rna ; Gene Overexpression ; Prediction ; Proteins ; Multigene Family
    ISSN: 0027-8424
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  • 3
    Language: English
    In: Molecular microbiology, June 2011, Vol.80(6), pp.1479-95
    Description: The photosynthetic alphaproteobacterium Rhodobacter sphaeroides has to cope with photooxidative stress that is caused by the bacteriochlorophyll a-mediated formation of singlet oxygen ((1)O(2)). Exposure to (1)O(2) induces the alternative sigma factors RpoE and RpoH(II) which then promote transcription of photooxidative stress-related genes, including small RNAs (sRNAs). The ubiquitous RNA chaperone Hfq is well established to interact with and facilitate the base-pairing of sRNAs and target mRNAs to influence mRNA stability and/or translation. Here we report on the pleiotropic phenotype of a Δhfq mutant of R. sphaeroides, which is less pigmented, produces minicells and is more sensitive to (1)O(2). The higher (1)O(2) sensitivity of the Δhfq mutant is paralleled by a reduced RpoE activity and a disordered induction of RpoH(II)-dependent genes. We used co-immunoprecipitation of FLAG-tagged Hfq combined with RNA-seq to identify association of at least 25 sRNAs and of mRNAs encoding cell division proteins and ribosomal proteins with Hfq. Remarkably, 〉 70% of the Hfq-bound sRNAs are (1)O(2)-affected. Proteomics analysis of the Hfq-deficient strain revealed an impact of Hfq on amino acid transport and metabolic functions. Our data demonstrate for the first time an involvement of Hfq in regulation of photosynthesis genes and in the photooxidative stress response.
    Keywords: Gene Expression Regulation, Bacterial ; Oxidative Stress ; Protein Binding ; Bacterial Proteins -- Metabolism ; Host Factor 1 Protein -- Metabolism ; Rhodobacter Sphaeroides -- Metabolism
    ISSN: 0950382X
    E-ISSN: 1365-2958
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  • 4
    Language: English
    In: Journal of bacteriology, May 2015, Vol.197(10), pp.1839-52
    Description: In bacteria, regulatory RNAs play an important role in the regulation and balancing of many cellular processes and stress responses. Among these regulatory RNAs, trans-encoded small RNAs (sRNAs) are of particular interest since one sRNA can lead to the regulation of multiple target mRNAs. In the purple bacterium Rhodobacter sphaeroides, several sRNAs are induced by oxidative stress. In this study, we focused on the functional characterization of four homologous sRNAs that are cotranscribed with the gene for the conserved hypothetical protein RSP_6037, a genetic arrangement described for only a few sRNAs until now. Each of the four sRNAs is characterized by two stem-loops that carry CCUCCUCCC motifs in their loops. They are induced under oxidative stress, as well as by various other stress conditions, and were therefore renamed here sRNAs CcsR1 to CcsR4 (CcsR1-4) for conserved CCUCCUCCC motif stress-induced RNAs 1 to 4. Increased CcsR1-4 expression decreases the expression of genes involved in C1 metabolism or encoding components of the pyruvate dehydrogenase complex either directly by binding to their target mRNAs or indirectly. One of the CcsR1-4 target mRNAs encodes the transcriptional regulator FlhR, an activator of glutathione-dependent methanol/formaldehyde metabolism. Downregulation of this glutathione-dependent pathway increases the pool of glutathione, which helps to counteract oxidative stress. The FlhR-dependent downregulation of the pyruvate dehydrogenase complex reduces a primary target of reactive oxygen species and reduces aerobic electron transport, a main source of reactive oxygen species. Our findings reveal a previously unknown strategy used by bacteria to counteract oxidative stress. Phototrophic organisms have to cope with photo-oxidative stress due to the function of chlorophylls as photosensitizers for the formation of singlet oxygen. Our study assigns an important role in photo-oxidative stress resistance to a cluster of four homologous sRNAs in the anoxygenic phototrophic bacterium Rhodobacter sphaeroides. We reveal a function of these regulatory RNAs in the fine-tuning of C1 metabolism. A model that relates oxidative stress defense to C1 metabolism is presented.
    Keywords: Gene Expression Regulation, Bacterial ; Carbon -- Metabolism ; Pyruvate Dehydrogenase Complex -- Metabolism ; RNA, Small Untranslated -- Genetics ; Rhodobacter Sphaeroides -- Genetics
    ISSN: 00219193
    E-ISSN: 1098-5530
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  • 5
    Language: English
    In: Journal of Bacteriology, 2015, Vol.197(9-10), p.1839(14)
    Description: In bacteria, regulatory RNAs play an important role in the regulation and balancing of many cellular processes and stress responses. Among these regulatory RNAs,trans-encoded small RNAs (sRNAs) are of particular interest since one sRNA can lead to the regulation of multiple target mRNAs. In the purple bacterium Rhodobacter sphaeroides, several sRNAs are induced by oxidative stress. In this study, we focused on the functional characterization of four homologous sRNAs that are cotranscribed with the gene for the conserved hypothetical protein RSP_6037, a genetic arrangement described for only a few sRNAs until now. Each of the four sRNAs is characterized by two stem-loops that carry CCUCCUCCC motifs in their loops. They are induced under oxidative stress, as well as by various other stress conditions, and were therefore renamed here sRNAs CcsR1 to CcsR4 (CcsR1u4) for onserved CUCCUCCC motif tress-induced NAs 1 to 4. Increased CcsR1u4 expression decreases the expression of genes involved in C metabolism or encoding components of the pyruvate dehydrogenase complex either directly by binding to their target mRNAs or indirectly. One of the CcsR1u4 target mRNAs encodes the transcriptional regulator FlhR, an activator of glutathione-dependent methanol/formaldehyde metabolism. Downregulation of this glutathione-dependent pathway increases the pool of glutathione, which helps to counteract oxidative stress. The FlhR-dependent downregulation of the pyruvate dehydrogenase complex reduces a primary target of reactive oxygen species and reduces aerobic electron transport, a main source of reactive oxygen species. Our findings reveal a previously unknown strategy used by bacteria to counteract oxidative stress.
    Keywords: Oxidative Stress – Research ; Photosynthetic Bacteria – Genetic Aspects ; Photosynthetic Bacteria – Physiological Aspects ; Pyruvate Dehydrogenase Complex – Research ; RNA – Research
    ISSN: 0021-9193
    Source: Cengage Learning, Inc.
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  • 6
    Language: English
    In: Journal of Bacteriology, May, 2010, Vol.192(9-10), p.2613(11)
    Description: Organisms performing photosynthesis in the presence of oxygen have to cope with the formation of highly reactive singlet oxygen ([sup.1][O.sub.2]) and need to mount an adaptive response to photooxidative stress. Here we show that the alternative sigma factors [RpoH.sub.I] and [RpoH.sub.II] are both involved in the [sup.1][O.sub.2] response and in the heat stress response in Rhodobacter sphaeroides. We propose [RpoH.sub.II] to be the major player in the [sup.1][O.sub.2] response, whereas [RpoH.sub.I] is more important for the heat stress response. Mapping of the 5' ends of [RpoH.sub.II]- and also [RpoH.sub.I]/[RpoH.sub.II]-dependent transcripts revealed clear differences in the -10 regions of the putative promoter sequences. By using bioinformatic tools, we extended the [RpoH.sub.II] regulon, which includes genes induced by [sup.1][O.sub.2] exposure. These genes encode proteins which are, e.g., involved in methionine sulfoxide reduction and in maintaining the quinone pool. Furthermore, we identified small RNAs which depend on [RpoH.sub.I] and [RpoH.sub.II] and are likely to contribute to the defense against photooxidative stress and heat stress. doi: 10.1128/JB.01605-09
    Keywords: Active Oxygen -- Physiological Aspects ; Promoters (Genetics) -- Physiological Aspects ; Proteobacteria -- Genetic Aspects ; Proteobacteria -- Physiological Aspects
    ISSN: 0021-9193
    Source: Cengage Learning, Inc.
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  • 7
    In: The Journal of Bacteriology, 2010, Vol. 192(10), p.2613
    Description: Organisms performing photosynthesis in the presence of oxygen have to cope with the formation of highly reactive singlet oxygen (...) and need to mount an adaptive response to photooxidative stress. Here we show that the alternative sigma factors RpoH... and RpoH... are both involved in the... response and in the heat stress response in Rhodobacter sphaeroides. We propose RpoH...I to be the major player in the ... response, whereas RpoH... is more important for the heat stress response. Mapping of the 5' ends of RpoH...- and also RpoH.../RpoH...-dependent transcripts revealed clear differences in the -10 regions of the putative promoter sequences. By using bioinformatic tools, we extended the RpoH... regulon, which includes genes induced by ... exposure. These genes encode proteins which are, e.g., involved in methionine sulfoxide reduction and in maintaining the quinone pool. Furthermore, we identified small RNAs which depend on RpoH... and RpoH... and are likely to contribute to the defense against photooxidative stress and heat stress. (ProQuest: ... denotes formulae/symbols omitted.)
    Keywords: Bacteria ; Oxygen ; Photosynthesis ; Gene Expression ; Proteins ; Ribonucleic Acid–RNA ; Bacteriology;
    ISSN: 0021-9193
    ISSN: 00219193
    E-ISSN: 10985530
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  • 8
    In: Molecular Microbiology, March 2017, Vol.103(6), pp.1020-1033
    Description: Bacterial survival strategies involve phenotypic diversity which is generated by regulatory factors and noisy expression of effector proteins. The question of how bacteria exploit regulatory RNAs to make decisions between phenotypes is central to a general understanding of these universal regulators. We investigated the TisB/IstR‐1 toxin‐antitoxin system of to appreciate the role of the RNA antitoxin IstR‐1 in TisB‐dependent depolarization of the inner membrane and persister formation. Persisters are phenotypic variants that have become transiently drug‐tolerant by arresting growth. The RNA antitoxin IstR‐1 sets a threshold for TisB‐dependent depolarization under DNA‐damaging conditions, resulting in two sub‐populations: polarized and depolarized cells. Furthermore, our data indicate that an inhibitory 5′ UTR structure in the mRNA serves as a regulatory RNA element that delays TisB translation to avoid inappropriate depolarization when DNA damage is low. Investigation of the persister sub‐population further revealed that both regulatory RNA elements affect persister levels as well as persistence time. This work provides an intriguing example of how bacteria exploit regulatory RNAs to control phenotypic heterogeneity. In Escherichia coli, two regulatory RNA elements set a threshold for production of toxin TisB and, as a consequence, depolarization of the inner membrane upon DNA damage. Downstream generation of persister cells is considered as “primed” by DNA damage as environmental trigger. Deletion of both RNA elements renders persister formation “stochastic”, since no environmental trigger is needed for TisB production in the double deletion strain.
    Keywords: Antitoxins ; Decision Making ; Translation ; DNA Damage ; Inner Membranes ; Survival ; Stochasticity ; Toxins ; Escherichia Coli ; DNA Metabolism & Structure;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 9
    Language: German
    In: BIOspektrum, 2012, Vol.18(3), pp.340-340
    Keywords: Life Sciences ; Human Genetics ; Life Sciences, General ; Pharmacology/Toxicology ; Biochemistry, General ; Developmental Biology ; Microbiology ; Sciences (General);
    ISSN: 0947-0867
    E-ISSN: 1868-6249
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  • 10
    Language: English
    In: PLoS ONE, 01 January 2013, Vol.8(11), p.e79520
    Description: Singlet oxygen ((1)O2) is the main agent of photooxidative stress and is generated by photosensitizers as (bacterio)chlorophylls. It leads to the damage of cellular macromolecules and therefore photosynthetic organisms have to mount an adaptive...
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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