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Bilger R, Migur A, Wulf A, Steglich C, Urlaub H, Hess WR. A type III-Dv CRISPR-Cas system is controlled by the transcription factor RpaB and interacts with the DEAD-box RNA helicase CrhR. Cell Rep 2024; 43:114485. [PMID: 38996066 DOI: 10.1016/j.celrep.2024.114485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 05/26/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024] Open
Abstract
How CRISPR-Cas systems defend bacteria and archaea against invading genetic elements is well understood, but less is known about their regulation. In the cyanobacterium Synechocystis sp. PCC 6803, the expression of one of the three different CRISPR-Cas systems responds to changes in environmental conditions. The cas operon promoter of this system is controlled by the light- and redox-responsive transcription factor RpaB binding to an HLR1 motif, resulting in transcriptional activation at low light intensities. However, the strong promoter that drives transcription of the cognate repeat-spacer array is not controlled by RpaB. Instead, the leader transcript is bound by the redox-sensitive RNA helicase CrhR. Crosslinking coupled with mass spectrometry analysis and site-directed mutagenesis revealed six residues involved in the CrhR-RNA interaction, with C371 being critically important. Thus, the expression of a type III-Dv CRISPR-Cas system is linked to the redox status of the photosynthetic cell at the transcriptional and post-transcriptional levels.
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Affiliation(s)
- Raphael Bilger
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Angela Migur
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Alexander Wulf
- Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Centre, 37075 Göttingen, Germany; Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Claudia Steglich
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Henning Urlaub
- Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Centre, 37075 Göttingen, Germany; Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Wolfgang R Hess
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany.
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2
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Whitman BT, Wang Y, Murray CRA, Glover MJN, Owttrim GW. Liquid-Liquid Phase Separation of the DEAD-Box Cyanobacterial RNA Helicase Redox (CrhR) into Dynamic Membraneless Organelles in Synechocystis sp. Strain PCC 6803. Appl Environ Microbiol 2023; 89:e0001523. [PMID: 36920190 PMCID: PMC10132119 DOI: 10.1128/aem.00015-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/17/2023] [Indexed: 03/16/2023] Open
Abstract
Compartmentalization of macromolecules into discrete non-lipid-bound bodies by liquid-liquid phase separation (LLPS) is a well-characterized regulatory mechanism frequently associated with the cellular stress response in eukaryotes. In contrast, the formation and importance of similar complexes is just becoming evident in bacteria. Here, we identify LLPS as the mechanism by which the DEAD-box RNA helicase, cyanobacterial RNA helicase redox (CrhR), compartmentalizes into dynamic membraneless organelles in a temporal and spatial manner in response to abiotic stress in the cyanobacterium Synechocystis sp. strain PCC 6803. Stress conditions induced CrhR to form a single crescent localized exterior to the thylakoid membrane, indicating that this region is a crucial domain in the cyanobacterial stress response. These crescents rapidly dissipate upon alleviation of the stress conditions. Furthermore, CrhR aggregation was mediated by LLPS in an RNA-dependent reaction. We propose that dynamic CrhR condensation performs crucial roles in RNA metabolism, enabling rapid adaptation of the photosynthetic apparatus to environmental stresses. These results expand our understanding of the role that functional compartmentalization of RNA helicases and thus RNA processing in membraneless organelles by LLPS-mediated protein condensation performs in the bacterial response to environmental stress. IMPORTANCE Oxygen-evolving photosynthetic cyanobacteria evolved ~3 billion years ago, performing fundamental roles in the biogeochemical evolution of the early Earth and continue to perform fundamental roles in nutrient cycling and primary productivity today. The phylum consists of diverse species that flourish in heterogeneous environments. A prime driver for survival is the ability to alter photosynthetic performance in response to the shifting environmental conditions these organisms continuously encounter. This study demonstrated that diverse abiotic stresses elicit dramatic changes in localization and structural organization of the RNA helicase CrhR associated with the photosynthetic thylakoid membrane. These dynamic changes, mediated by a liquid-liquid phase separation (LLPS)-mediated mechanism, reveal a novel mechanism by which cyanobacteria can compartmentalize the activity of ribonucleoprotein complexes in membraneless organelles. The results have significant consequences for understanding bacterial adaptation and survival in response to changing environmental conditions.
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Affiliation(s)
- Brendan T. Whitman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Yixiong Wang
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Cameron R. A. Murray
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Mark J. N. Glover
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - George W. Owttrim
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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3
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Watanabe S, Stazic D, Georg J, Ohtake S, Sakamaki Y, Numakura M, Asayama M, Chibazakura T, Wilde A, Steglich C, Hess WR. Regulation of RNase E during the UV stress response in the cyanobacterium Synechocystis sp. PCC 6803. MLIFE 2023; 2:43-57. [PMID: 38818332 PMCID: PMC10989929 DOI: 10.1002/mlf2.12056] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 12/07/2022] [Accepted: 12/15/2022] [Indexed: 06/01/2024]
Abstract
Endoribonucleases govern the maturation and degradation of RNA and are indispensable in the posttranscriptional regulation of gene expression. A key endoribonuclease in Gram-negative bacteria is RNase E. To ensure an appropriate supply of RNase E, some bacteria, such as Escherichia coli, feedback-regulate RNase E expression via the rne 5'-untranslated region (5' UTR) in cis. However, the mechanisms involved in the control of RNase E in other bacteria largely remain unknown. Cyanobacteria rely on solar light as an energy source for photosynthesis, despite the inherent ultraviolet (UV) irradiation. In this study, we first investigated globally the changes in gene expression in the cyanobacterium Synechocystis sp. PCC 6803 after a brief exposure to UV. Among the 407 responding genes 2 h after UV exposure was a prominent upregulation of rne mRNA level. Moreover, the enzymatic activity of RNase E rapidly increased as well, although the protein stability decreased. This unique response was underpinned by the increased accumulation of full-length rne mRNA caused by the stabilization of its 5' UTR and suppression of premature transcriptional termination, but not by an increased transcription rate. Mapping of RNA 3' ends and in vitro cleavage assays revealed that RNase E cleaves within a stretch of six consecutive uridine residues within the rne 5' UTR, indicating autoregulation. These observations suggest that RNase E in cyanobacteria contributes to reshaping the transcriptome during the UV stress response and that its required activity level is secured at the RNA level despite the enhanced turnover of the protein.
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Affiliation(s)
- Satoru Watanabe
- Faculty of Biology, Genetics and Experimental BioinformaticsUniversity of FreiburgFreiburgGermany
| | - Damir Stazic
- Department of BioscienceTokyo University of AgricultureSetagaya‐kuTokyoJapan
- Present address:
NexxiotPrime Tower (Hardstrasse 201)ZurichSwitzerland
| | - Jens Georg
- Department of BioscienceTokyo University of AgricultureSetagaya‐kuTokyoJapan
| | - Shota Ohtake
- Faculty of Biology, Genetics and Experimental BioinformaticsUniversity of FreiburgFreiburgGermany
| | - Yutaka Sakamaki
- Faculty of Biology, Genetics and Experimental BioinformaticsUniversity of FreiburgFreiburgGermany
| | - Megumi Numakura
- Faculty of Biology, Genetics and Experimental BioinformaticsUniversity of FreiburgFreiburgGermany
| | - Munehiko Asayama
- School of Agriculture, Molecular GeneticsIbaraki UniversityIbarakiJapan
| | - Taku Chibazakura
- Faculty of Biology, Genetics and Experimental BioinformaticsUniversity of FreiburgFreiburgGermany
| | - Annegret Wilde
- Faculty of Biology, Molecular GeneticsUniversity of FreiburgFreiburgGermany
| | - Claudia Steglich
- Department of BioscienceTokyo University of AgricultureSetagaya‐kuTokyoJapan
| | - Wolfgang R. Hess
- Department of BioscienceTokyo University of AgricultureSetagaya‐kuTokyoJapan
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4
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Multiple Light-Dark Signals Regulate Expression of the DEAD-Box RNA Helicase CrhR in Synechocystis PCC 6803. Cells 2022; 11:cells11213397. [DOI: 10.3390/cells11213397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/16/2022] Open
Abstract
Since oxygenic photosynthesis evolved in the common ancestor of cyanobacteria during the Archean, a range of sensing and response strategies evolved to allow efficient acclimation to the fluctuating light conditions experienced in the diverse environments they inhabit. However, how these regulatory mechanisms are assimilated at the molecular level to coordinate individual gene expression is still being elucidated. Here, we demonstrate that integration of a series of three distinct light signals generate an unexpectedly complex network regulating expression of the sole DEAD-box RNA helicase, CrhR, encoded in Synechocystis sp. PCC 6803. The mechanisms function at the transcriptional, translational and post-translation levels, fine-tuning CrhR abundance to permit rapid acclimation to fluctuating light and temperature regimes. CrhR abundance is enhanced 15-fold by low temperature stress. We initially confirmed that the primary mechanism controlling crhR transcript accumulation at 20 °C requires a light quantity-driven reduction of the redox poise in the vicinity of the plastoquinone pool. Once transcribed, a specific light quality cue, a red light signal, was required for crhR translation, far-red reversal of which indicates a phytochrome-mediated mechanism. Examination of CrhR repression at 30 °C revealed that a redox- and light quality-independent light signal was required to initiate CrhR degradation. The crucial role of light was further revealed by the observation that dark conditions superseded the light signals required to initiate each of these regulatory processes. The findings reveal an unexpected complexity of light-dark sensing and signaling that regulate expression of an individual gene in cyanobacteria, an integrated mechanism of environmental perception not previously reported.
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5
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Whitman BT, Murray CRA, Whitford DS, Paul SS, Fahlman RP, Glover MJN, Owttrim GW. Degron-mediated proteolysis of CrhR-like DEAD-box RNA helicases in cyanobacteria. J Biol Chem 2022; 298:101925. [PMID: 35413287 PMCID: PMC9117542 DOI: 10.1016/j.jbc.2022.101925] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/01/2022] [Accepted: 04/02/2022] [Indexed: 11/18/2022] Open
Abstract
Conditional proteolytic degradation is an irreversible and highly regulated process that fulfills crucial regulatory functions in all organisms. As proteolytic targets tend to be critical metabolic or regulatory proteins, substrates are targeted for degradation only under appropriate conditions through the recognition of an amino acid sequence referred to as a “degron”. DEAD-box RNA helicases mediate all aspects of RNA metabolism, contributing to cellular fitness. However, the mechanism by which abiotic-stress modulation of protein stability regulates bacterial helicase abundance has not been extensively characterized. Here, we provide in vivo evidence that proteolytic degradation of the cyanobacterial DEAD-box RNA helicase CrhR is conditional, being initiated by a temperature upshift from 20 to 30 °C in the model cyanobacterium, Synechocystis sp. PCC 6803. We show degradation requires a unique, highly conserved, inherently bipartite degron located in the C-terminal extension found only in CrhR-related RNA helicases in the phylum Cyanobacteria. However, although necessary, the degron is not sufficient for proteolysis, as disruption of RNA helicase activity and/or translation inhibits degradation. These results suggest a positive feedback mechanism involving a role for CrhR in expression of a crucial factor required for degradation. Furthermore, AlphaFold structural prediction indicated the C-terminal extension is a homodimerization domain with homology to other bacterial RNA helicases, and mass photometry data confirmed that CrhR exists as a dimer in solution at 22 °C. These structural data suggest a model wherein the CrhR degron is occluded at the dimerization interface but could be exposed if dimerization was disrupted by nonpermissive conditions.
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Affiliation(s)
- Brendan T Whitman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Cameron R A Murray
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Denise S Whitford
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Simanta S Paul
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Richard P Fahlman
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Mark J N Glover
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - George W Owttrim
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
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Zhang J, Hess WR, Zhang C. "Life is short, and art is long": RNA degradation in cyanobacteria and model bacteria. MLIFE 2022; 1:21-39. [PMID: 38818322 PMCID: PMC10989914 DOI: 10.1002/mlf2.12015] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 06/01/2024]
Abstract
RNA turnover plays critical roles in the regulation of gene expression and allows cells to respond rapidly to environmental changes. In bacteria, the mechanisms of RNA turnover have been extensively studied in the models Escherichia coli and Bacillus subtilis, but not much is known in other bacteria. Cyanobacteria are a diverse group of photosynthetic organisms that have great potential for the sustainable production of valuable products using CO2 and solar energy. A better understanding of the regulation of RNA decay is important for both basic and applied studies of cyanobacteria. Genomic analysis shows that cyanobacteria have more than 10 ribonucleases and related proteins in common with E. coli and B. subtilis, and only a limited number of them have been experimentally investigated. In this review, we summarize the current knowledge about these RNA-turnover-related proteins in cyanobacteria. Although many of them are biochemically similar to their counterparts in E. coli and B. subtilis, they appear to have distinct cellular functions, suggesting a different mechanism of RNA turnover regulation in cyanobacteria. The identification of new players involved in the regulation of RNA turnover and the elucidation of their biological functions are among the future challenges in this field.
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Affiliation(s)
- Ju‐Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of HydrobiologyChinese Academy of SciencesWuhanChina
| | - Wolfgang R. Hess
- Genetics and Experimental Bioinformatics, Faculty of BiologyUniversity of FreiburgFreiburgGermany
| | - Cheng‐Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of HydrobiologyChinese Academy of SciencesWuhanChina
- Institut WUT‐AMUAix‐Marseille University and Wuhan University of TechnologyWuhanChina
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7
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Migur A, Heyl F, Fuss J, Srikumar A, Huettel B, Steglich C, Prakash JSS, Reinhardt R, Backofen R, Owttrim GW, Hess WR. The temperature-regulated DEAD-box RNA helicase CrhR interactome: Autoregulation and photosynthesis-related transcripts. JOURNAL OF EXPERIMENTAL BOTANY 2021:erab416. [PMID: 34499142 DOI: 10.1093/jxb/erab416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Indexed: 06/13/2023]
Abstract
RNA helicases play crucial functions in RNA biology. In plants, RNA helicases are encoded by large gene families, performing roles in abiotic stress responses, development, the post-transcriptional regulation of gene expression as well as house-keeping functions. Several of these RNA helicases are targeted to the organelles, mitochondria and chloroplasts. Cyanobacteria are the direct evolutionary ancestors of plant chloroplasts. The cyanobacterium Synechocystis 6803 encodes a single DEAD-box RNA helicase, CrhR, that is induced by a range of abiotic stresses, including low temperature. Though the ΔcrhR mutant exhibits a severe cold-sensitive phenotype, the physiological function(s) performed by CrhR have not been described. To identify transcripts interacting with CrhR, we performed RNA co-immunoprecipitation with extracts from a Synechocystis crhR deletion mutant expressing the FLAG-tagged native CrhR or a K57A mutated version with an anticipated enhanced RNA binding. The composition of the interactome was strikingly biased towards photosynthesis-associated and redox-controlled transcripts. A transcript highly enriched in all experiments was the crhR mRNA, suggesting an auto-regulatory molecular mechanism. The identified interactome explains the described physiological role of CrhR in response to the redox poise of the photosynthetic electron transport chain and characterizes CrhR as an enzyme with a diverse range of transcripts as molecular targets.
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Affiliation(s)
- Anzhela Migur
- Faculty of Biology, University of Freiburg, Schänzlestr., Freiburg, Germany
| | - Florian Heyl
- Department of Computer Science, University of Freiburg, Georges-Koehler-Allee, Freiburg, Germany
| | - Janina Fuss
- Max Planck-Genome-Centre Cologne, Carl-von-Linné-Weg, Köln, Germany
| | - Afshan Srikumar
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Bruno Huettel
- Max Planck-Genome-Centre Cologne, Carl-von-Linné-Weg, Köln, Germany
| | - Claudia Steglich
- Faculty of Biology, University of Freiburg, Schänzlestr., Freiburg, Germany
| | - Jogadhenu S S Prakash
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | | | - Rolf Backofen
- Department of Computer Science, University of Freiburg, Georges-Koehler-Allee, Freiburg, Germany
| | - George W Owttrim
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Wolfgang R Hess
- Faculty of Biology, University of Freiburg, Schänzlestr., Freiburg, Germany
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8
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Whitford DS, Whitman BT, Owttrim GW. Genera specific distribution of DEAD-box RNA helicases in cyanobacteria. Microb Genom 2021; 7. [PMID: 33539277 PMCID: PMC8190605 DOI: 10.1099/mgen.0.000517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Although RNA helicases are essentially ubiquitous and perform roles in all stages of RNA metabolism, phylogenetic analysis of the DEAD (Asp-Glu-Ala-Asp)-box RNA helicase family in a single phylum has not been performed. Here, we performed a phylogenetic analysis on DEAD-box helicases from all currently available cyanobacterial genomes, comprising a total of 362 helicase protein sequences from 280 strains. DEAD-box helicases belonging to three distinct clades were observed. Two clades, the CsdA (cold shock DEAD-box A)-like and RhlE (RNA helicase E)-like helicases, cluster with the homologous proteins from Escherichia coli. The third clade, the CrhR (cyanobacterial RNA helicase Redox)-like helicases, is unique to cyanobacteria and characterized by a conserved sequence motif in the C-terminal extension. Restricted distribution is observed across cyanobacterial diversity with respect to both helicase type and strain. CrhR-like and CsdA-like helicases essentially never occur together, while RhlE always occurs with either a CrhR-like or CsdA-like helicase. CrhR-like and RhlE-like proteins occurred in filamentous cyanobacteria of the orders Nostocales, Oscillatoriales and Synechococcales. Similarly, CsdA- and RhlE-like proteins are restricted to unicellular cyanobacteria of the genera Cyanobium and Synechococcus. In addition, the unexpected occurrence of RhlE in two Synechococcus strains suggests recent acquisition and evolutionary divergence. This study, therefore, raises physiological and evolutionary questions as to why DEAD-box RNA helicases encoded in cyanobacterial lineages display restricted distributions, suggesting niches that require either CrhR or CsdA RNA helicase activity but not both. Extensive conservation of gene synteny surrounding the previously described rimO–crhR operon is also observed, indicating a role in the maintenance of photosynthesis. The analysis provides insights into the evolution, origin and dissemination of sequences within a single gene family to yield divergent functional roles.
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Affiliation(s)
- Denise S Whitford
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Brendan T Whitman
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - George W Owttrim
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
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9
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Rosana ARR, Whitford DS, Migur A, Steglich C, Kujat-Choy SL, Hess WR, Owttrim GW. RNA helicase-regulated processing of the Synechocystis rimO-crhR operon results in differential cistron expression and accumulation of two sRNAs. J Biol Chem 2020; 295:6372-6386. [PMID: 32209657 DOI: 10.1074/jbc.ra120.013148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/19/2020] [Indexed: 12/21/2022] Open
Abstract
The arrangement of functionally-related genes in operons is a fundamental element of how genetic information is organized in prokaryotes. This organization ensures coordinated gene expression by co-transcription. Often, however, alternative genetic responses to specific stress conditions demand the discoordination of operon expression. During cold temperature stress, accumulation of the gene encoding the sole Asp-Glu-Ala-Asp (DEAD)-box RNA helicase in Synechocystis sp. PCC 6803, crhR (slr0083), increases 15-fold. Here, we show that crhR is expressed from a dicistronic operon with the methylthiotransferase rimO/miaB (slr0082) gene, followed by rapid processing of the operon transcript into two monocistronic mRNAs. This cleavage event is required for and results in destabilization of the rimO transcript. Results from secondary structure modeling and analysis of RNase E cleavage of the rimO-crhR transcript in vitro suggested that CrhR plays a role in enhancing the rate of the processing in an auto-regulatory manner. Moreover, two putative small RNAs are generated from additional processing, degradation, or both of the rimO transcript. These results suggest a role for the bacterial RNA helicase CrhR in RNase E-dependent mRNA processing in Synechocystis and expand the known range of organisms possessing small RNAs derived from processing of mRNA transcripts.
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Affiliation(s)
- Albert Remus R Rosana
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Denise S Whitford
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Anzhela Migur
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Claudia Steglich
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Sonya L Kujat-Choy
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Wolfgang R Hess
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany.,Freiburg Institute for Advanced Studies, University of Freiburg, Albertstrasse 19, D-79104 Freiburg, Germany
| | - George W Owttrim
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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10
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Salze M, Muller C, Bernay B, Hartke A, Clamens T, Lesouhaitier O, Rincé A. Study of key RNA metabolism proteins in Enterococcus faecalis. RNA Biol 2020; 17:794-804. [PMID: 32070211 DOI: 10.1080/15476286.2020.1728103] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The control of mRNA turnover is essential in bacteria to allow rapid adaptation, especially in opportunistic pathogen like Enterococcus faecalis. This mechanism involves RNase and DEAD-box helicases that are key elements in RNA processing and their associations form the degradosome with accessory proteins. In this study, we investigated the function of four RNases (J1, J2, Y and III) and three DEAD-box helicases (CshA, CshB, CshC) present in most Enterococci. The interactions of all these RNA metabolism actors were investigated in vitro, and the results are in accordance with a degradosome structure close to the one of Bacillus subtilis. At the physiological level, we showed that RNase J1 is essential, whereas RNases J2 and III have a role in cold, oxidative and bile salts stress response, and RNase Y in general fitness. Furthermore, RNases J2, Y and III mutants are affected in virulence in the Galleria mellonella infection model. Concerning DEAD-box helicases, all of them are involved in cold shock response. Since the ΔcshA mutant was the most stress impacted strain, we studied this DEAD-box helicase CshA in more detail. This showed that CshA autoregulates its own expression by binding to its mRNA 5'Unstranslated Region. Interestingly, CshC is also involved in the expression control of CshA by a hitherto unprecedented mechanism.
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Affiliation(s)
- Marine Salze
- Normandie Univ, UNICAEN, Unité De Recherche Risques Microbiens U2RM , Caen, France
| | - Cécile Muller
- Normandie Univ, UNICAEN, Unité De Recherche Risques Microbiens U2RM , Caen, France
| | - Benoit Bernay
- Proteogen Platform, Normandie Univ, UNICAEN, SFR ICORE , Caen, France
| | - Axel Hartke
- Normandie Univ, UNICAEN, Unité De Recherche Risques Microbiens U2RM , Caen, France
| | - Thomas Clamens
- Laboratoire de Microbiologie Signaux et Microenvironnement LMSM, Normandie Univ, University of Rouen , Evreux, France
| | - Olivier Lesouhaitier
- Laboratoire de Microbiologie Signaux et Microenvironnement LMSM, Normandie Univ, University of Rouen , Evreux, France
| | - Alain Rincé
- Normandie Univ, UNICAEN, Unité De Recherche Risques Microbiens U2RM , Caen, France
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11
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Ritter SPA, Lewis AC, Vincent SL, Lo LL, Cunha APA, Chamot D, Ensminger I, Espie GS, Owttrim GW. Evidence for convergent sensing of multiple abiotic stresses in cyanobacteria. Biochim Biophys Acta Gen Subj 2019; 1864:129462. [PMID: 31669584 DOI: 10.1016/j.bbagen.2019.129462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Bacteria routinely utilize two-component signal transduction pathways to sense and alter gene expression in response to environmental cues. While cyanobacteria express numerous two-component systems, these pathways do not regulate all of the genes within many of the identified abiotic stress-induced regulons. METHODS Electron transport inhibitors combined with western analysis and measurement of chlorophyll a fluorescent yield, using pulse amplitude modulation fluorometry, were used to detect the effect of a diverse range of abiotic stresses on the redox status of the photosynthetic electron transport chain and the accumulation and degradation of the Synechocystis sp. PCC 6803 DEAD box RNA helicase, CrhR. RESULTS Alterations in CrhR abundance were tightly correlated with the redox poise of the electron transport chain between QA and cytochrome b6f, with reduction favoring CrhR accumulation. CONCLUSIONS The results provide evidence for an alternative, convergent sensing mechanism mediated through the redox poise of QB/PQH2 that senses multiple, divergent forms of abiotic stress and regulates accumulation of CrhR. The RNA helicase activity of CrhR could then function as a post-translational effector to regulate downstream gene expression. GENERAL SIGNIFICANCE The potential for a related system in Staphylococcus aureus and higher plant chloroplasts suggest convergent sensing mechanisms may be evolutionarily conserved and occur more widely than anticipated.
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Affiliation(s)
- Sean P A Ritter
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Allison C Lewis
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden 01307, Germany.
| | - Shelby L Vincent
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Li Ling Lo
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | | | - Danuta Chamot
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Ingo Ensminger
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - George S Espie
- Department of Cell and Systems Biology, University of Toronto, Mississauga, ON L5L 1C6, Canada
| | - George W Owttrim
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
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12
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Daas MS, Acedo JZ, Rosana ARR, Orata FD, Reiz B, Zheng J, Nateche F, Case RJ, Kebbouche-Gana S, Vederas JC. Bacillus amyloliquefaciens ssp. plantarum F11 isolated from Algerian salty lake as a source of biosurfactants and bioactive lipopeptides. FEMS Microbiol Lett 2019; 365:4654845. [PMID: 29186395 DOI: 10.1093/femsle/fnx248] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/22/2017] [Indexed: 12/29/2022] Open
Abstract
In this study, we identified a new Bacillus strain isolated from an Algerian salty lake that produces metabolites that are active against Gram-positive and Gram-negative bacteria, as well as fungal pathogens. The draft genome sequence of the strain is presented herein. Genome sequence analysis identified the strain to be B. amyloliquefaciens subspecies plantarum F11, and showed that the strain carries the gene clusters for the production of a number of bioactive and surface-active compounds. These include the lipopeptides surfactin and fengycin, antibacterial polyketides macrolactin and bacillaene, and a putative novel lanthipeptide, among others. Through an activity-guided purification method using hydrophobic interaction chromatographic techniques, we confirmed the ability of the strain to produce fengycin lipopeptides. The identities of the isolated fengycin homologs were ascertained through tandem mass spectrometry.
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Affiliation(s)
- Mohamed Seghir Daas
- Valcore Laboratory, Department of Biology, University M'Hamed Bougara of Boumerdès, 35000, Boumerdès, Algeria.,Food Technology Research Division, Institut National de la Recherche Agronomiqued' Algérie, 16200, El Harrach, Algiers, Algeria
| | - Jeella Z Acedo
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Alberta, Canada
| | - Albert Remus R Rosana
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Alberta, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, Alberta, Canada
| | - Fabini D Orata
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, Alberta, Canada
| | - Béla Reiz
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Alberta, Canada
| | - Jing Zheng
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Alberta, Canada
| | - Farida Nateche
- Microbiology Group, Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Science and Technology-Houari Boumediene, 16111, Bab Ezzouar, Algiers, Algeria
| | - Rebecca J Case
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9, Alberta, Canada
| | - Salima Kebbouche-Gana
- Valcore Laboratory, Department of Biology, University M'Hamed Bougara of Boumerdès, 35000, Boumerdès, Algeria
| | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Alberta, Canada
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13
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Georg J, Rosana ARR, Chamot D, Migur A, Hess WR, Owttrim GW. Inactivation of the RNA helicase CrhR impacts a specific subset of the transcriptome in the cyanobacterium Synechocystis sp. PCC 6803. RNA Biol 2019; 16:1205-1214. [PMID: 31234711 PMCID: PMC6693541 DOI: 10.1080/15476286.2019.1621622] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
DEAD-box RNA-helicases catalyze the reorganization of structured RNAs and the formation of RNP complexes. The cyanobacterium Synechocystis sp. PCC 6803 encodes a single DEAD-box RNA helicase, CrhR (Slr0083), whose expression is regulated by abiotic stresses that alter the redox potential of the photosynthetic electron transport chain, including temperature downshift. Despite its proposed effect on RNA metabolism and its known relevance in cold-stress adaptation, the reported impact of a CrhR knockout on the cold adaption of the transcriptome only identified eight affected genes. Here, we utilized a custom designed microarray to assess the impact of the absence of CrhR RNA helicase activity on the transcriptome, independent of cold stress. CrhR truncation impacts an RNA subset comprising ~10% of the ncRNA and also ~10% of the mRNA transcripts. While equal numbers of mRNAs showed increased as well as decreased abundance, more than 90% of the ncRNAs showed enhanced expression in the absence of CrhR, indicative of a negative effect on ncRNA transcription or stability. We further tested the effect of CrhR on the stability of strongly responding RNAs that identify examples of post-transcriptional and transcriptional regulation. The data suggest that CrhR impacts multiple aspects of RNA metabolism in Synechocystis.
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Affiliation(s)
- Jens Georg
- a Faculty of Biology, University of Freiburg , Freiburg , Germany
| | | | - Danuta Chamot
- b Department of Biological Sciences, University of Alberta , Edmonton , AB , Canada
| | - Anzhela Migur
- a Faculty of Biology, University of Freiburg , Freiburg , Germany
| | - Wolfgang R Hess
- a Faculty of Biology, University of Freiburg , Freiburg , Germany.,c Freiburg Institute for Advanced Studies, University of Freiburg , Freiburg , Germany
| | - George W Owttrim
- b Department of Biological Sciences, University of Alberta , Edmonton , AB , Canada
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14
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Daas MS, Rosana ARR, Acedo JZ, Douzane M, Nateche F, Kebbouche-Gana S, Vederas JC. Insights into the draft genome sequence of bioactives-producing Bacillus thuringiensis DNG9 isolated from Algerian soil-oil slough. Stand Genomic Sci 2018; 13:25. [PMID: 30344888 PMCID: PMC6186030 DOI: 10.1186/s40793-018-0331-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 09/28/2018] [Indexed: 12/16/2022] Open
Abstract
Bacillus thuringiensis is widely used as a bioinsecticide due to its ability to form parasporal crystals containing proteinaceous toxins. It is a member of the Bacillus cereus sensu lato, a group with low genetic diversity but produces several promising antimicrobial compounds. B. thuringiensis DNG9, isolated from an oil-contaminated slough in Algeria, has strong antibacterial, antifungal and biosurfactant properties. Here, we report the 6.06 Mbp draft genome sequence of B. thuringiensis DNG9. The genome encodes several gene inventories for the biosynthesis of bioactive compounds such as zwittermycin A, petrobactin, insecticidal toxins, polyhydroxyalkanoates and multiple bacteriocins. We expect the genome information of strain DNG9 will provide another model system to study pathogenicity against insect pests, plant diseases, and antimicrobial compound mining and comparative phylogenesis among the Bacillus cereus sensu lato group.
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Affiliation(s)
- Mohamed Seghir Daas
- Valcore Laboratory, Department of Biology, University M’Hamed Bougara of Boumerdes, 35000 Boumerdes, Algeria
- Food Technology Research Division, Institut National de la Recherche Agronomique d’Algérie, 16200, El Harrach, Algiers, Algeria
| | | | - Jeella Z. Acedo
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2 Canada
| | - Malika Douzane
- Food Technology Research Division, Institut National de la Recherche Agronomique d’Algérie, 16200, El Harrach, Algiers, Algeria
| | - Farida Nateche
- Microbiology Group, Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Science and Technology–Houari Boumediene, 16111, Bab Ezzouar, Algiers, Algeria
| | - Salima Kebbouche-Gana
- Valcore Laboratory, Department of Biology, University M’Hamed Bougara of Boumerdes, 35000 Boumerdes, Algeria
| | - John C. Vederas
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2 Canada
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15
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Hayashi R, Sugita C, Sugita M. The 5' untranslated region of the rbp1 mRNA is required for translation of its mRNA under low temperatures in the cyanobacterium Synechococcus elongatus. Arch Microbiol 2016; 199:37-44. [PMID: 27449001 DOI: 10.1007/s00203-016-1270-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 04/03/2016] [Accepted: 07/14/2016] [Indexed: 11/29/2022]
Abstract
The unicellular cyanobacterium Synechococcus elongatus has three RNA-binding protein (Rbp) genes, rbp1, rbp2 and rbp3. The rbp1 gene was upregulated by cold treatment while rbp2 and rbp3 expression decreased remarkably after exposure to cold temperatures. To investigate the mechanism underlying cold-induced rbp1 expression, a series of rbp1-luxAB transcriptional fusion constructs were expressed in S. elongatus PCC 7942 under cold conditions. The results showed that the region from -33 to -3 of the transcription initiation site contains an essential sequence for basal transcription of the rbp1 gene and that the 120-bp region (-34 to -153) does not contain critical cis-elements required for cold-shock induction. In contrast, mutational analysis carrying the 5'-untranslated region (UTR) of rbp1-luxAB translational fusions indicated that the 5'-UTR of rbp1 plays an important role in cold induction of the rbp1 gene product. Taken together, we conclude that the cold induction of rbp1 may be regulated at a posttranscriptional level rather than at the transcriptional level.
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Affiliation(s)
- Rie Hayashi
- Center for Gene Research, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan
- Leica Microsystems K.K., Shirokane-takanawa Station Bldg., 1-27-6 Shirokane, Minato-ku, Tokyo, 108-0072, Japan
| | - Chieko Sugita
- Center for Gene Research, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Mamoru Sugita
- Center for Gene Research, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan.
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16
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Cyanobacterial RNA Helicase CrhR Localizes to the Thylakoid Membrane Region and Cosediments with Degradosome and Polysome Complexes in Synechocystis sp. Strain PCC 6803. J Bacteriol 2016; 198:2089-99. [PMID: 27215789 DOI: 10.1128/jb.00267-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 05/20/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The cyanobacterium Synechocystis sp. strain PCC 6803 encodes a single DEAD box RNA helicase, CrhR, whose expression is tightly autoregulated in response to cold stress. Subcellular localization and proteomic analysis results indicate that CrhR localizes to both the cytoplasmic and thylakoid membrane regions and cosediments with polysome and RNA degradosome components. Evidence is presented that either functional RNA helicase activity or a C-terminal localization signal was required for polysome but not thylakoid membrane localization. Polysome fractionation and runoff translation analysis results indicate that CrhR associates with actively translating polysomes. The data implicate a role for CrhR in translation or RNA degradation in the thylakoid region related to thylakoid biogenesis or stability, a role that is enhanced at low temperature. Furthermore, CrhR cosedimentation with polysome and RNA degradosome complexes links alteration of RNA secondary structure with a potential translation-RNA degradation complex in Synechocystis IMPORTANCE The interaction between mRNA translation and degradation is a major determinant controlling gene expression. Regulation of RNA function by alteration of secondary structure by RNA helicases performs crucial roles, not only in both of these processes but also in all aspects of RNA metabolism. Here, we provide evidence that the cyanobacterial RNA helicase CrhR localizes to both the cytoplasmic and thylakoid membrane regions and cosediments with actively translating polysomes and RNA degradosome components. These findings link RNA helicase alteration of RNA secondary structure with translation and RNA degradation in prokaryotic systems and contribute to the data supporting the idea of the existence of a macromolecular machine catalyzing these reactions in prokaryotic systems, an association hitherto recognized only in archaea and eukarya.
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Sinetova MA, Los DA. New insights in cyanobacterial cold stress responses: Genes, sensors, and molecular triggers. Biochim Biophys Acta Gen Subj 2016; 1860:2391-2403. [PMID: 27422804 DOI: 10.1016/j.bbagen.2016.07.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/16/2016] [Accepted: 07/09/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Cold stress strongly induces the expression of ~100 genes in cyanobacteria. Some of these genes are necessary to protect cellular functions by adjustment of membranes, as well as transcriptional and translational machineries. About a half of cold-induced genes are not functionally characterized. A part of cold-induced genes is under control of a two-component regulatory system, consisting of histidine kinase Hik33 and response regulator Rre26. The mechanism(s) that control another part of cold-inducible genes are still unknown. SCOPE OF REVIEW The aim of this review is to summarise the latest findings in cyanobacterial cold-stress responses including transcriptomics, cold sensing, and molecular triggers. MAJOR CONCLUSIONS A feedback loop between the membrane fluidity and transcription of genes for fatty acid desaturases operates via the transmembrane red-light-activated cold sensor Hik33, which perceives cold-induced membrane rigidification as a change in its thickness. The cold-induced kinase activity of Hik33 is facilitated by interaction with a small protein, Ssl3451 - the third contributor to a canonical two-component regulatory system, which may explain the ability of some cyanobacterial histidine kinases to interact with different response regulators under different stress conditions. Other regulatory systems that control cold-stress responses operate via Ser/Thr protein kinase, SpkE, and via temperature-dependent changes in DNA supercoiling. Transcriptomic analysis shows that universal triggers of stress responses are reactive oxygen species and changes in redox status of plastoquinone pool. GENERAL SIGNIFICANCE Deeper understanding of molecular mechanisms of temperature sensing and regulation of cold-stress responses in photosynthetic cells provide a background for generation of cold-resistant crops.
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Affiliation(s)
- Maria A Sinetova
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276 Moscow, Russian Federation
| | - Dmitry A Los
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276 Moscow, Russian Federation.
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18
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Varkey D, Mazard S, Ostrowski M, Tetu SG, Haynes P, Paulsen IT. Effects of low temperature on tropical and temperate isolates of marine Synechococcus. THE ISME JOURNAL 2016; 10:1252-63. [PMID: 26495993 PMCID: PMC5029218 DOI: 10.1038/ismej.2015.179] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 08/01/2015] [Accepted: 08/24/2015] [Indexed: 11/08/2022]
Abstract
Temperature is an important factor influencing the distribution of marine picocyanobacteria. However, molecular responses contributing to temperature preferences are poorly understood in these important primary producers. We compared the temperature acclimation of a tropical Synechococcus strain WH8102 with temperate strain BL107 at 18 °C relative to 22 °C and examined their global protein expression, growth patterns, photosynthetic efficiency and lipid composition. Global protein expression profiles demonstrate the partitioning of the proteome into major categories: photosynthesis (>40%), translation (10-15%) and membrane transport (2-8%) with distinct differences between and within strains grown at different temperatures. At low temperature, growth and photosynthesis of strain WH8102 was significantly decreased, while BL107 was largely unaffected. There was an increased abundance of proteins involved in protein biosynthesis at 18 °C for BL107. Each strain showed distinct differences in lipid composition with higher unsaturation in strain BL107. We hypothesize that differences in membrane fluidity, abundance of protein biosynthesis machinery and the maintenance of photosynthesis efficiency contribute to the acclimation of strain BL107 to low temperature. Additional proteins unique to BL107 may also contribute to this strain's improved fitness at low temperature. Such adaptive capacities are likely important factors favoring growth of temperate strains over tropical strains in high latitude niches.
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Affiliation(s)
- Deepa Varkey
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Sophie Mazard
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Martin Ostrowski
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Sasha G Tetu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Paul Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
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Khemici V, Linder P. RNA helicases in bacteria. Curr Opin Microbiol 2016; 30:58-66. [PMID: 26808656 DOI: 10.1016/j.mib.2016.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/06/2016] [Indexed: 11/18/2022]
Abstract
RNA plays a crucial role in the control of bacterial gene expression, either as carrier of information or as positive or negative regulators. Moreover, the machinery to decode the information, the ribosome, is a large ribonucleoprotein complex composed of rRNAs and many proteins. RNAs are normally single stranded but have the propensity to fold into secondary structures or anneal each other. In some instances these interactions are beneficial for the function of the RNA, but in other cases they may be deleterious. All cells have therefore developed proteins that act as chaperones or helicases to keep RNA metabolism alive.
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Affiliation(s)
- Vanessa Khemici
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, 1, rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Patrick Linder
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, 1, rue Michel Servet, 1211 Geneva 4, Switzerland.
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20
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Tan B, Semple K, Foght J. Anaerobic alkane biodegradation by cultures enriched from oil sands tailings ponds involves multiple species capable of fumarate addition. FEMS Microbiol Ecol 2015; 91:fiv042. [PMID: 25873461 DOI: 10.1093/femsec/fiv042] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2015] [Indexed: 01/18/2023] Open
Abstract
A methanogenic short-chain alkane-degrading culture (SCADC) was enriched from oil sands tailings and transferred several times with a mixture of C6, C7, C8 and C10 n-alkanes as the predominant organic carbon source, plus 2-methylpentane, 3-methylpentane and methylcyclopentane as minor components. Cultures produced ∼40% of the maximum theoretical methane during 18 months incubation while depleting the n-alkanes, 2-methylpentane and methylcyclopentane. Substrate depletion correlated with detection of metabolites characteristic of fumarate activation of 2-methylpentane and methylcyclopentane, but not n-alkane metabolites. During active methanogenesis with the mixed alkanes, reverse-transcription PCR confirmed the expression of functional genes (assA and bssA) associated with hydrocarbon addition to fumarate. Pyrosequencing of 16S rRNA genes amplified during active alkane degradation revealed enrichment of Clostridia (particularly Peptococcaceae) and methanogenic Archaea (Methanosaetaceae and Methanomicrobiaceae). Methanogenic cultures transferred into medium containing sulphate produced sulphide, depleted n-alkanes and produced the corresponding succinylated alkane metabolites, but were slow to degrade 2-methylpentane and methylcyclopentane; these cultures were enriched in Deltaproteobacteria rather than Clostridia. 3-Methylpentane was not degraded by any cultures. Thus, nominally methanogenic oil sands tailings harbour dynamic and versatile hydrocarbon-degrading fermentative syntrophs and sulphate reducers capable of degrading n-, iso- and cyclo-alkanes by addition to fumarate.
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Affiliation(s)
- BoonFei Tan
- Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Kathleen Semple
- Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Julia Foght
- Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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21
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Conditional, temperature-induced proteolytic regulation of cyanobacterial RNA helicase expression. J Bacteriol 2014; 196:1560-8. [PMID: 24509313 DOI: 10.1128/jb.01362-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Conditional proteolysis is a crucial process regulating the abundance of key regulatory proteins associated with the cell cycle, differentiation pathways, or cellular response to abiotic stress in eukaryotic and prokaryotic organisms. We provide evidence that conditional proteolysis is involved in the rapid and dramatic reduction in abundance of the cyanobacterial RNA helicase, CrhR, in response to a temperature upshift from 20 to 30°C. The proteolytic activity is not a general protein degradation response, since proteolysis is only present and/or functional in cells grown at 30°C and is only transiently active at 30°C. Degradation is also autoregulatory, since the CrhR proteolytic target is required for activation of the degradation machinery. This suggests that an autoregulatory feedback loop exists in which the target of the proteolytic machinery, CrhR, is required for activation of the system. Inhibition of translation revealed that only elongation is required for induction of the temperature-regulated proteolysis, suggesting that translation of an activating factor was already initiated at 20°C. The results indicate that Synechocystis responds to a temperature shift via two independent pathways: a CrhR-independent sensing and signal transduction pathway that regulates induction of crhR expression at low temperature and a CrhR-dependent conditional proteolytic pathway at elevated temperature. The data link the potential for CrhR RNA helicase alteration of RNA secondary structure with the autoregulatory induction of conditional proteolysis in the response of Synechocystis to temperature upshift.
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Importance and determinants of induction of cold-induced DEAD RNA helicase in the hyperthermophilic archaeon Thermococcus kodakarensis. J Bacteriol 2013; 195:3442-50. [PMID: 23729644 DOI: 10.1128/jb.00332-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Thermococcus kodakarensis, which grows optimally at 85°C, expresses cold stress-inducible DEAD box RNA helicase (Tk-deaD) when shifted to 60°C. A DDA1 deletion (ΔTk-deaD) mutant exhibited decreased cell growth, and cells underwent lysis at 60°C in nutrient broth in the absence of elemental sulfur. In contrast, cells in medium containing elemental sulfur at 60°C did not undergo lysis, suggesting that Tk-deaD is necessary for cell growth in sulfur-free medium. To identify the element responsible for the cold response, a pTKR expression probe plasmid was constructed using thermostable catalase from Pyrobaculum calidifontis as a reporter. The plasmid pTKRD, which contained the transcription factor B recognition element, TATA region, and Shine-Dalgarno (SD) region, including the initiation codon of the Tk-deaD gene, exhibited cold inducibility. We also constructed a series of deletion and chimeric constructs with the glutamate dehydrogenase (gdh) promoter, whose expression is constitutive independent of culture temperatures and catalase expression. Reporter assay experiments indicated that the regulatory element is located in the region between the SD region and the initiation codon (ATG). Nucleotide sequences in the upstream regions of Tk-deaD and gdh were compared and revealed a five-adenosine (AAAAA) sequence between SD and ATG of Tk-deaD that was not present in gdh. Replacement of the repeated adenosine sequence with other sequences revealed that the AAAAA sequence is important for cold induction. This sequence-specific mechanism is unique and is one that has not been identified in other known cold-inducible genes.
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Bacterial helicases in post-transcriptional control. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:878-83. [PMID: 23291566 DOI: 10.1016/j.bbagrm.2012.12.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 12/17/2012] [Accepted: 12/20/2012] [Indexed: 12/25/2022]
Abstract
Among the five superfamilies of helicases involved in RNA and DNA metabolism, superfamily 2 and superfamily 5 include bacterial RNA-helicases. These enzymes have been shown to be involved in ribosome biogenesis and post-transcriptional gene regulation. Here, we focus on bacterial regulatory mechanisms that are mediated by RNA helicases belonging to superfamily 2, which includes DEAD-box and DEAH-box helicases. Some of these helicases are part of bacterial degradosomes and were shown to unwind RNA duplexes. We will review examples where these enzymes have been implicated in translatability and metabolic stability of bacterial transcripts. This article is part of a Special Issue entitled: The Biology of RNA helicases - Modulation for life.
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