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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] [MESH Headings] [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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Balaga RR, Itoh F, Chauhan S, Mandal M, Krishna PS, Suzuki I, Prakash JSS. Sll1252 Coordinates Electron Transport between Plastoquinone and Cytochrome b6/f Complex in Synechocystis PCC 6803. Genes (Basel) 2023; 14:2151. [PMID: 38136973 PMCID: PMC10743179 DOI: 10.3390/genes14122151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/13/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
A mutant, Δsll1252ins, was generated to functionally characterize Sll1252. Δsll1252ins exhibited a slow-growth phenotype at 70 µmol photons m-2 s-1 and glucose sensitivity. In Δsll1252ins, the rate of PSII activity was not affected, whereas the whole chain electron transport activity was reduced by 45%. The inactivation of sll1252 led to the upregulation of genes, which were earlier reported to be induced in DBMIB-treated wild-type, suggesting that Sll1252 may be involved in electron transfer from the reduced-PQ pool to Cyt b6/f. The inhibitory effect of DCMU on PSII activity was similar in both wild-type and Δsll1252ins. However, the concentration of DBMIB for 50% inhibition of whole chain electron transport activity was 140 nM for Δsll1252ins and 300 nM for wild-type, confirming the site of action of Sll1252. Moreover, the elevated level of the reduced-PQ pool in Δsll1252ins supports that Sll1252 functions between the PQ pool and Cyt b6/f. Interestingly, we noticed that Δsll1252ins reverted to wild-type phenotype by insertion of natural transposon, ISY523, at the disruption site. Δsll1252-Ntrn, expressing only the C-terminal region of Sll1252, exhibited a slow-growth phenotype and disorganized thylakoid structure compared to wild-type and Δsll1252-Ctrn (expressing only the N-terminal region). Collectively, our data suggest that Sll1252 regulates electron transfer between the PQ pool and the Cyt b6/f complex in the linear photosynthetic electron transport chain via coordinated function of both the N- and C-terminal regions of Sll1252.
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Affiliation(s)
- Radha Rani Balaga
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India;
| | - Fumihiro Itoh
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba 305-8572, Japan;
| | - Suraj Chauhan
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India; (S.C.); (M.M.); (P.S.K.)
| | - Mukulika Mandal
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India; (S.C.); (M.M.); (P.S.K.)
| | - Pilla Sankara Krishna
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India; (S.C.); (M.M.); (P.S.K.)
| | - Iwane Suzuki
- Institute of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba 305-8572, Japan;
| | - Jogadhenu S. S. Prakash
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India; (S.C.); (M.M.); (P.S.K.)
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Bantu L, Chauhan S, Srikumar A, Hirakawa Y, Suzuki I, Hagemann M, Prakash JSS. A membrane-bound cAMP receptor protein, SyCRP1 mediates inorganic carbon response in Synechocystis sp. PCC 6803. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194803. [PMID: 35272049 DOI: 10.1016/j.bbagrm.2022.194803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/24/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
The availability of inorganic carbon (Ci) as the source for photosynthesis is fluctuating in aquatic environments. Despite the involvement of transcriptional regulators CmpR and NdhR in regulating genes encoding Ci transporters at limiting CO2, the Ci-sensing mechanism is largely unknown among cyanobacteria. Here we report that a cAMP-dependent transcription factor SyCRP1 mediates Ci response in Synechocystis. The mutant ∆sycrp1 exhibited a slow-growth phenotype and reduced maximum rate of bicarbonate-dependent photosynthetic electron transport (Vmax) compared to wild-type at the scarcity of CO2. The number of carboxysomes was decreased significantly in the ∆sycrp1 at low CO2 consistent with its reduced Vmax. The DNA microarray analysis revealed the upregulation of genes encoding Ci transporters in ∆sycrp1. The membrane-localized SyCRP1 was released into the cytosol in wild-type cells shifted from low to high CO2 or upon cAMP treatment. Soluble His-tagged SyCRP1 was shown to target DNA-binding sites upstream of the Ci-regulated genes sbtA and ccmK3. In addition, cAMP enhanced the binding of SyCRP1 to its target sites. Our data collectively suggest that the Ci is sensed through the second messenger cAMP releasing membrane-bound SyCRP1 into cytoplasm under sufficient CO2 conditions. Hence, SyCRP1 is a possible regulator of carbon concentrating mechanism, and such a regulation might be mediated via sensing Ci levels through cAMP in Synechocystis.
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Affiliation(s)
- Lingaswamy Bantu
- From the Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Suraj Chauhan
- From the Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Afshan Srikumar
- From the Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Yoshihisa Hirakawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba 305-8572, Japan
| | - Iwane Suzuki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba 305-8572, Japan
| | - Martin Hagemann
- Plant Physiology Department, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany
| | - Jogadhenu S S Prakash
- From the Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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Ijaq J, Chandra D, Ray MK, Jagannadham MV. Investigating the Functional Role of Hypothetical Proteins From an Antarctic Bacterium Pseudomonas sp. Lz4W: Emphasis on Identifying Proteins Involved in Cold Adaptation. Front Genet 2022; 13:825269. [PMID: 35360867 PMCID: PMC8963723 DOI: 10.3389/fgene.2022.825269] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/07/2022] [Indexed: 11/28/2022] Open
Abstract
Exploring the molecular mechanisms behind bacterial adaptation to extreme temperatures has potential biotechnological applications. In the present study, Pseudomonas sp. Lz4W, a Gram-negative psychrophilic bacterium adapted to survive in Antarctica, was selected to decipher the molecular mechanism underlying the cold adaptation. Proteome analysis of the isolates grown at 4°C was performed to identify the proteins and pathways that are responsible for the adaptation. However, many proteins from the expressed proteome were found to be hypothetical proteins (HPs), whose function is unknown. Investigating the functional roles of these proteins may provide additional information in the biological understanding of the bacterial cold adaptation. Thus, our study aimed to assign functions to these HPs and understand their role at the molecular level. We used a structured insilico workflow combining different bioinformatics tools and databases for functional annotation. Pseudomonas sp. Lz4W genome (CP017432, version 1) contains 4493 genes and 4412 coding sequences (CDS), of which 743 CDS were annotated as HPs. Of these, from the proteome analysis, 61 HPs were found to be expressed consistently at the protein level. The amino acid sequences of these 61 HPs were submitted to our workflow and we could successfully assign a function to 18 HPs. Most of these proteins were predicted to be involved in biological mechanisms of cold adaptations such as peptidoglycan metabolism, cell wall organization, ATP hydrolysis, outer membrane fluidity, catalysis, and others. This study provided a better understanding of the functional significance of HPs in cold adaptation of Pseudomonas sp. Lz4W. Our approach emphasizes the importance of addressing the “hypothetical protein problem” for a thorough understanding of mechanisms at the cellular level, as well as, provided the assessment of integrating proteomics methods with various annotation and curation approaches to characterize hypothetical or uncharacterized protein data. The MS proteomics data generated from this study has been deposited to the ProteomeXchange through PRIDE with the dataset identifier–PXD029741.
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Affiliation(s)
- Johny Ijaq
- Metabolomics Facility, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Deepika Chandra
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Malay Kumar Ray
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - M. V. Jagannadham
- Metabolomics Facility, School of Life Sciences, University of Hyderabad, Hyderabad, India
- *Correspondence: M. V. Jagannadham,
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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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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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7
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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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Babele PK, Kumar J, Chaturvedi V. Proteomic De-Regulation in Cyanobacteria in Response to Abiotic Stresses. Front Microbiol 2019; 10:1315. [PMID: 31263458 PMCID: PMC6584798 DOI: 10.3389/fmicb.2019.01315] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 05/27/2019] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria are oxygenic photoautotrophs, exhibiting a cosmopolitan distribution in almost all possible environments and are significantly responsible for half of the global net primary productivity. They are well adapted to the diverse environments including harsh conditions by evolving a range of fascinating repertoires of unique biomolecules and secondary metabolites to support their growth and survival. These phototrophs are proved as excellent models for unraveling the mysteries of basic biochemical and physiological processes taking place in higher plants. Several known species of cyanobacteria have tremendous biotechnological applications in diverse fields such as biofuels, biopolymers, secondary metabolites and much more. Due to their potential biotechnological and commercial applications in various fields, there is an imperative need to engineer robust cyanobacteria in such a way that they can tolerate and acclimatize to ever-changing environmental conditions. Adaptations to stress are mainly governed by a precise gene regulation pathways resulting in the expression of novel protein/enzymes and metabolites. Despite the demand, till date few proteins/enzymes have been identified which play a potential role in improving tolerance against abiotic stresses. Therefore, it is utmost important to study environmental stress responses related to post-genomic investigations, including proteomic changes employing advanced proteomics, synthetic and structural biology workflows. In this respect, the study of stress proteomics offers exclusive advantages to scientists working on these aspects. Advancements on these fields could be helpful in dissecting, characterization and manipulation of physiological and metabolic systems of cyanobacteria to understand the stress induced proteomic responses. Till date, it remains ambiguous how cyanobacteria perceive changes in the ambient environment that lead to the stress-induced proteins thus metabolic deregulation. This review briefly describes the current major findings in the fields of proteome research on the cyanobacteria under various abiotic stresses. These findings may improve and advance the information on the role of different class of proteins associated with the mechanism(s) of stress mitigation in cyanobacteria under harsh environmental conditions.
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Affiliation(s)
- Piyoosh Kumar Babele
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Jay Kumar
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Venkatesh Chaturvedi
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
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Singh DK, Lingaswamy B, Koduru TN, Nagu PP, Jogadhenu PSS. A putative merR family transcription factor Slr0701 regulates mercury inducible expression of MerA in the cyanobacterium Synechocystis sp. PCC6803. Microbiologyopen 2019; 8:e00838. [PMID: 31094100 PMCID: PMC6741143 DOI: 10.1002/mbo3.838] [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] [Received: 12/18/2018] [Revised: 02/24/2019] [Accepted: 02/26/2019] [Indexed: 11/23/2022] Open
Abstract
In cyanobacteria, genes conferring mercury resistance are not organized as mer‐operon, unlike in other bacterial phyla. Synechocystis contains only a putative MerR regulator, Slr0701, and a mercury reductase, MerA, located aside from each other in the genome. The slr0701‐mutant showed reduction in photosynthetic activity and reduced tolerance to mercury compared to the wild‐type. The incubation of wild‐type cells with HgCl2 resulted in the upregulation of slr0701 and slr1849 genes whereas mercury‐induced expression was not observed in the slr0701‐mutant. Slr0701 binds to a conserved cis‐regulatory element located in the upstream of slr1849 and slr0701 ORFs. The same element was also identified in the upstream of other cyanobacterial homologs. Slr0701 binds to cis‐regulatory element with faster association and slower dissociation rates in the presence of HgCl2. Although these genes were constitutively expressed, the addition of HgCl2 enhanced their promoter activity suggesting that mercury‐bound Slr0701 triggers induced expression of these genes. The enhanced promoter activity could be attributed to the observed secondary structural changes in Slr0701 in the presence of HgCl2. For the first time, we demonstrated the mechanism of merA regulation in a cyanobacterium, Synechocystis. Although merA and merR genes are distantly located on the cyanobacterial genome and distinct from other bacterial mer‐operons, the transcriptional regulatory mechanism is conserved.
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Affiliation(s)
- Deepak Kumar Singh
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Bantu Lingaswamy
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Tejaswi Naidu Koduru
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Prakash Prabhu Nagu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
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Srikumar A, Krishna PS, Sivaramakrishna D, Kopfmann S, Hess WR, Swamy MJ, Lin-Chao S, Prakash JSS. The Ssl2245-Sll1130 Toxin-Antitoxin System Mediates Heat-induced Programmed Cell Death in Synechocystis sp. PCC6803. J Biol Chem 2017; 292:4222-4234. [PMID: 28104802 DOI: 10.1074/jbc.m116.748178] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 01/17/2017] [Indexed: 12/13/2022] Open
Abstract
Two putative heat-responsive genes, ssl2245 and sll1130, constitute an operon that also has characteristics of a toxin-antitoxin system, thus joining several enigmatic features. Closely related orthologs of Ssl2245 and Sll1130 exist in widely different bacteria, which thrive under environments with large fluctuations in temperature and salinity, among which some are thermo-epilithic biofilm-forming cyanobacteria. Transcriptome analyses revealed that the clustered regularly interspaced short palindromic repeats (CRISPR) genes as well as several hypothetical genes were commonly up-regulated in Δssl2245 and Δsll1130 mutants. Genes coding for heat shock proteins and pilins were also induced in Δsll1130 We observed that the majority of cells in a Δsll1130 mutant strain remained unicellular and viable after prolonged incubation at high temperature (50 °C). In contrast, the wild type formed large cell clumps of dead and live cells, indicating the attempt to form biofilms under harsh conditions. Furthermore, we observed that Sll1130 is a heat-stable ribonuclease whose activity was inhibited by Ssl2245 at optimal temperatures but not at high temperatures. In addition, we demonstrated that Ssl2245 is physically associated with Sll1130 by electrostatic interactions, thereby inhibiting its activity at optimal growth temperature. This association is lost upon exposure to heat, leaving Sll1130 to exhibit its ribonuclease activity. Thus, the activation of Sll1130 leads to the degradation of cellular RNA and thereby heat-induced programmed cell death that in turn supports the formation of a more resistant biofilm for the surviving cells. We suggest to designate Ssl2245 and Sll1130 as MazE and MazF, respectively.
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Affiliation(s)
- Afshan Srikumar
- From the Department of Biotechnology and Bioinformatics, School of Life Sciences and
| | - Pilla Sankara Krishna
- From the Department of Biotechnology and Bioinformatics, School of Life Sciences and
| | | | - Stefan Kopfmann
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany, and
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany, and
| | - Musti J Swamy
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Sue Lin-Chao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Jogadhenu S S Prakash
- From the Department of Biotechnology and Bioinformatics, School of Life Sciences and
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11
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Li Q, Chang R, Sun Y, Li B. iTRAQ-Based Quantitative Proteomic Analysis of Spirulina platensis in Response to Low Temperature Stress. PLoS One 2016; 11:e0166876. [PMID: 27902743 PMCID: PMC5130222 DOI: 10.1371/journal.pone.0166876] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 11/04/2016] [Indexed: 12/26/2022] Open
Abstract
Low temperature (LT) is one of the most important abiotic stresses that can significantly reduce crop yield. To gain insight into how Spirulina responds to LT stress, comprehensive physiological and proteomic analyses were conducted in this study. Significant decreases in growth and pigment levels as well as excessive accumulation of compatible osmolytes were observed in response to LT stress. An isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomics approach was used to identify changes in protein abundance in Spirulina under LT. A total of 3,782 proteins were identified, of which 1,062 showed differential expression. Bioinformatics analysis indicated that differentially expressed proteins that were enriched in photosynthesis, carbohydrate metabolism, amino acid biosynthesis, and translation are important for the maintenance of cellular homeostasis and metabolic balance in Spirulina when subjected to LT stress. The up-regulation of proteins involved in gluconeogenesis, starch and sucrose metabolism, and amino acid biosynthesis served as coping mechanisms of Spirulina in response to LT stress. Moreover, the down-regulated expression of proteins involved in glycolysis, TCA cycle, pentose phosphate pathway, photosynthesis, and translation were associated with reduced energy consumption. The findings of the present study allow a better understanding of the response of Spirulina to LT stress and may facilitate in the elucidation of mechanisms underlying LT tolerance.
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Affiliation(s)
- Qingye Li
- College of Biological Sciences and Technology, Beijing Forestry University, Haidian District, Beijing, China
| | - Rong Chang
- College of Biological Sciences and Technology, Beijing Forestry University, Haidian District, Beijing, China
| | - Yijun Sun
- College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Bosheng Li
- College of Biological Sciences and Technology, Beijing Forestry University, Haidian District, Beijing, China
- Institute of Spirulina Research, Beijing Forestry University, Beijing, China
- * E-mail:
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12
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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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13
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Wang Y, Chen L, Zhang W. Proteomic and metabolomic analyses reveal metabolic responses to 3-hydroxypropionic acid synthesized internally in cyanobacterium Synechocystis sp. PCC 6803. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:209. [PMID: 27757169 PMCID: PMC5053081 DOI: 10.1186/s13068-016-0627-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 09/27/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND 3-hydroxypropionic acid (3-HP) is an important platform chemical with a wide range of applications. In our previous study, the biosynthetic pathway of 3-HP was constructed and optimized in cyanobacterium Synechocystis sp. PCC 6803, which led to 3-HP production directly from CO2 at a level of 837.18 mg L-1 (348.8 mg/g dry cell weight). As the production and accumulation of 3-HP in cells affect cellular metabolism, a better understanding of cellular responses to 3-HP synthesized internally in Synechocystis will be important for further increasing 3-HP productivity in cyanobacterial chassis. RESULTS Using a engineered 3-HP-producing SM strain, in this study, the cellular responses to 3-HP internally produced were first determined using a quantitative iTRAQ-LC-MS/MS proteomics approach and a LC-MS-based targeted metabolomics. A total of 2264 unique proteins were identified, which represented about 63 % of all predicted protein in Synechocystis in the proteomic analysis; meanwhile intracellular abundance of 24 key metabolites was determined by a comparative metabolomic analysis of the 3-HP-producing strain SM and wild type. Among all identified proteins, 204 proteins were found up-regulated and 123 proteins were found down-regulated, respectively. The proteins related to oxidative phosphorylation, photosynthesis, ribosome, central carbon metabolism, two-component systems and ABC-type transporters were up-regulated, along with the abundance of 14 metabolites related to central metabolism. The results suggested that the supply of ATP and NADPH was increased significantly, and the precursor malonyl-CoA and acetyl-CoA may also be supplemented when 3-HP was produced at a high level in Synechocystis. Confirmation of proteomic and metabolomic results with RT-qPCR and gene-overexpression strains of selected genes was also conducted, and the overexpression of three transporter genes putatively involved in cobalt/nickel, manganese and phosphate transporting (i.e., sll0385, sll1598 and sll0679) could lead to an increased 3-HP production in Synechocystis. CONCLUSIONS The integrative analysis of up-regulated proteome and metabolome data showed that to ensure the high-efficient production of 3-HP and the normal growth of Synechocystis, multiple aspects of cells metabolism including energy, reducing power supply, central carbon metabolism, the stress responses and protein synthesis were enhanced in Synechocystis. The study provides an important basis for further engineering cyanobacteria for high 3-HP production.
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Affiliation(s)
- Yunpeng Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People’s Republic of China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People’s Republic of China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, People’s Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People’s Republic of China
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Role of Spermidine in Overwintering of Cyanobacteria. J Bacteriol 2015; 197:2325-34. [PMID: 25917915 DOI: 10.1128/jb.00153-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/24/2015] [Indexed: 12/13/2022] Open
Abstract
UNLABELLED Polyamines are found in all groups of cyanobacteria, but their role in environmental adaptation has been barely investigated. In Synechocystis sp. strain PCC 6803, inactivation of spermidine synthesis genes significantly reduced the survivability under chill (5°C)-light stress, and the survivability could be restored by addition of spermidine. To analyze the effects of spermidine on gene expression at 5°C, lacZ was expressed from the promoter of carboxy(nor)spermidine decarboxylase gene (CASDC) in Synechocystis. Synechocystis 6803::PCASDC-lacZ pretreated at 15°C showed a high level of LacZ activity for a long period of time at 5°C; without the pretreatment or with protein synthesis inhibited at 5°C, the enzyme activity gradually decreased. In a spermidine-minus mutant harboring PCASDC-lacZ, lacZ showed an expression pattern as if protein synthesis were inhibited at 5°C, even though the stability of its mRNA increased. Four other genes, including rpoA that encodes the α subunit of RNA polymerase, showed similar expression patterns. The chill-light stress led to a rapid increase of protein carbonylation in Synechocystis. The protein carbonylation then quickly returned to the background level in the wild type but continued to slowly increase in the spermidine-minus mutant. Our results indicate that spermidine promotes gene expression and replacement of damaged proteins in cyanobacteria under the chill-light stress in winter. IMPORTANCE Outbreak of cyanobacterial blooms in freshwater lakes is a worldwide environmental problem. In the annual cycle of bloom-forming cyanobacteria, overwintering is the least understood stage. Survival of Synechocystis sp. strain PCC 6803 under long-term chill (5°C)-light stress has been established as a model for molecular studies on overwintering of cyanobacteria. Here, we show that spermidine, the most common polyamine in cyanobacteria, promotes the survivability of Synechocystis under long-term chill-light stress and that the physiological function is based on its effects on gene expression and recovery from protein damage. This is the first report on the role of polyamines in survival of overwintering cyanobacteria. We also analyzed spermidine synthesis pathways in cyanobacteria on the basis of bioinformatic and experimental data.
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Allahverdiyeva Y, Isojärvi J, Zhang P, Aro EM. Cyanobacterial Oxygenic Photosynthesis is Protected by Flavodiiron Proteins. Life (Basel) 2015; 5:716-43. [PMID: 25761262 PMCID: PMC4390876 DOI: 10.3390/life5010716] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/04/2015] [Accepted: 02/25/2015] [Indexed: 12/13/2022] Open
Abstract
Flavodiiron proteins (FDPs, also called flavoproteins, Flvs) are modular enzymes widely present in Bacteria and Archaea. The evolution of cyanobacteria and oxygenic photosynthesis occurred in concert with the modulation of typical bacterial FDPs. Present cyanobacterial FDPs are composed of three domains, the β-lactamase-like, flavodoxin-like and flavin-reductase like domains. Cyanobacterial FDPs function as hetero- and homodimers and are involved in the regulation of photosynthetic electron transport. Whilst Flv2 and Flv4 proteins are limited to specific cyanobacterial species (β-cyanobacteria) and function in photoprotection of Photosystem II, Flv1 and Flv3 proteins, functioning in the "Mehler-like" reaction and safeguarding Photosystem I under fluctuating light conditions, occur in nearly all cyanobacteria and additionally in green algae, mosses and lycophytes. Filamentous cyanobacteria have additional FDPs in heterocyst cells, ensuring a microaerobic environment for the function of the nitrogenase enzyme under the light. Here, the evolution, occurrence and functional mechanisms of various FDPs in oxygenic photosynthetic organisms are discussed.
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Affiliation(s)
- Yagut Allahverdiyeva
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
| | - Janne Isojärvi
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
| | - Pengpeng Zhang
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland.
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16
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Lei H, Chen G, Wang Y, Ding Q, Wei D. Sll0528, a Site-2-Protease, Is Critically Involved in Cold, Salt and Hyperosmotic Stress Acclimation of Cyanobacterium Synechocystis sp. PCC 6803. Int J Mol Sci 2014; 15:22678-22693. [PMID: 25493476 PMCID: PMC4284730 DOI: 10.3390/ijms151222678] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/21/2014] [Accepted: 11/25/2014] [Indexed: 12/17/2022] Open
Abstract
Site-2-proteases (S2Ps) mediated proteolysis of transmembrane transcriptional regulators is a conserved mechanism to regulate transmembrane signaling. The universal presence of S2P homologs in different cyanobacterial genomes suggest conserved and fundamental functions, though limited data has been available. Here we provide the first evidence that Sll0528, a site-2-protease in Synechocystis sp. PCC 6803 is crucial for salt, cold and hyperosmotic stress acclimation. Remarkable induction of sll0528 gene expression was observed under salt, cold and hyperosmotic stress, much higher than induction of the other three S2Ps. Knock-out of sll0528 gene in wild type Synechocystis sp. PCC 6803 increased their sensitivity to salt, cold and hyperosmotic stress, as revealed by retarded growth, reduced pigments and disrupted photosystems. The sll0528 gene was induced to a much smaller extent by high light and mixotrophic growth with glucose. Similar growth responses of the sll0528 knockout mutant and wild type under high light and mixotrophic growth indicated that sll0528 was dispensable for these conditions. Recombinant Sll0528 protein could cleave beta-casein into smaller fragments. These results together suggest that the Sll0528 metalloprotease plays a role in the stress response and lays the foundation for further investigation of its mechanism, as well as providing hints for the functional analysis of other S2Ps in cyanobacteria.
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Affiliation(s)
- Haijin Lei
- College of Light Industry and Food Sciences, South China University of Technology, 381 Wushan Road, Guangzhou 510641, China.
| | - Gu Chen
- College of Light Industry and Food Sciences, South China University of Technology, 381 Wushan Road, Guangzhou 510641, China.
| | - Yuling Wang
- College of Light Industry and Food Sciences, South China University of Technology, 381 Wushan Road, Guangzhou 510641, China.
| | - Qinglong Ding
- College of Light Industry and Food Sciences, South China University of Technology, 381 Wushan Road, Guangzhou 510641, China.
| | - Dong Wei
- College of Light Industry and Food Sciences, South China University of Technology, 381 Wushan Road, Guangzhou 510641, China.
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17
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Mähler N, Cheregi O, Funk C, Netotea S, Hvidsten TR. Synergy: a web resource for exploring gene regulation in Synechocystis sp. PCC6803. PLoS One 2014; 9:e113496. [PMID: 25420108 PMCID: PMC4242644 DOI: 10.1371/journal.pone.0113496] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 10/24/2014] [Indexed: 12/22/2022] Open
Abstract
Despite being a highly studied model organism, most genes of the cyanobacterium Synechocystis sp. PCC 6803 encode proteins with completely unknown function. To facilitate studies of gene regulation in Synechocystis, we have developed Synergy (http://synergy.plantgenie.org), a web application integrating co-expression networks and regulatory motif analysis. Co-expression networks were inferred from publicly available microarray experiments, while regulatory motifs were identified using a phylogenetic footprinting approach. Automatically discovered motifs were shown to be enriched in the network neighborhoods of regulatory proteins much more often than in the neighborhoods of non-regulatory genes, showing that the data provide a sound starting point for studying gene regulation in Synechocystis. Concordantly, we provide several case studies demonstrating that Synergy can be used to find biologically relevant regulatory mechanisms in Synechocystis. Synergy can be used to interactively perform analyses such as gene/motif search, network visualization and motif/function enrichment. Considering the importance of Synechocystis for photosynthesis and biofuel research, we believe that Synergy will become a valuable resource to the research community.
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Affiliation(s)
- Niklas Mähler
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Christiane Funk
- Department of Chemistry, Umeå University, Umeå, Sweden
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Sergiu Netotea
- Department of Chemistry, Umeå University, Umeå, Sweden
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
- Computational Life Science Cluster, Umeå University, Umeå, Sweden
| | - Torgeir R. Hvidsten
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
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18
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Paz-Gómez D, Villanueva-Chimal E, Navarro RE. The DEAD Box RNA helicase VBH-1 is a new player in the stress response in C. elegans. PLoS One 2014; 9:e97924. [PMID: 24844228 PMCID: PMC4028217 DOI: 10.1371/journal.pone.0097924] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 04/25/2014] [Indexed: 12/29/2022] Open
Abstract
For several years, DEAD box RNA helicase Vasa (DDX4) has been used as a bona fide germline marker in different organisms. C. elegans VBH-1 is a close homolog of the Vasa protein, which plays an important role in gametogenesis, germ cell survival and embryonic development. Here, we show that VBH-1 protects nematodes from heat shock and oxidative stress. Using the germline-defective mutant glp-4(bn2) we found that a potential somatic expression of vbh-1 might be important for stress survival. We also show that the VBH-1 paralog LAF-1 is important for stress survival, although this protein is not redundant with its counterpart. Furthermore, we observed that the mRNAs of the heat shock proteins hsp-1 and sip-1 are downregulated when vbh-1 or laf-1 are silenced. Previously, we reported that in C. elegans, VBH-1 was primarily expressed in P granules of germ cells and in the cytoplasm of all blastomeres. Here we show that during stress, VBH-1 co-localizes with CGH-1 in large aggregates in the gonad core and oocytes; however, VBH-1 aggregates do not overlap with CGH-1 foci in early embryos under the same conditions. These data demonstrate that, in addition to the previously described role for this protein in the germline, VBH-1 plays an important role during the stress response in C. elegans through the potential direct or indirect regulation of stress response mRNAs.
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Affiliation(s)
- Daniel Paz-Gómez
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Distrito Federal, México
| | - Emmanuel Villanueva-Chimal
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Distrito Federal, México
| | - Rosa E. Navarro
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, Distrito Federal, México
- * E-mail:
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A novel transcriptional regulator, Sll1130, negatively regulates heat-responsive genes in Synechocystis sp. PCC6803. Biochem J 2013; 449:751-60. [PMID: 23088579 DOI: 10.1042/bj20120928] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A conserved hypothetical protein, Sll1130, is a novel transcription factor that regulates the expression of major heat-responsive genes in Synechocystis sp. PCC6803. Synechocystis exhibited an increased thermotolerance due to disruption of sll1130. Δsll1130 cells recovered much faster than wild-type cells after they were subjected to heat shock (50°C) for 30 min followed by recovery at 34°C for 48 h. In Δsll1130 cultures, 70% of the cells were viable compared with the wild-type culture in which only 30% of the cells were viable. DNA microarray analysis revealed that in Δsll1130, expression of the heat-responsive genes such as htpG, hspA, isiA, isiB and several hypothetical genes were up-regulated. Sll1130 binds to a conserved inverted-repeat (GGCGATCGCC) located in the upstream region of the above genes. In addition, both the transcript and protein levels of sll1130 were immediately down-regulated upon shift of wild-type cells from 34 to 42°C. Collectively the results of the present study suggest that Sll1130 is a heat-responsive transcriptional regulator that represses the expression of certain heat-inducible genes at optimum growth temperatures. Upon heat shock, a quick drop in the Sll1130 levels leads to de-repression of the heat-shock genes and subsequent thermal acclimation. On the basis of the findings of the present study, we present a model which describes the heat-shock response involving Sll1130.
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20
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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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Schomburg D, Schomburg I. RNA helicase 3.6.4.13. CLASS 3.4–6 HYDROLASES, LYASES, ISOMERASES, LIGASES 2013. [PMCID: PMC7123474 DOI: 10.1007/978-3-642-36260-6_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
EC number 3.6.4.13 Systematic name ATP phosphohydrolase (RNA helix unwinding) Recommended name RNA helicase Synonyms 1a NTPase/helicase <16> [5] ATP/dATP-dependent RNA helicase <1,42> [32] ATPase <10,12> [1,36] ATPase/RNA helicase <1,42> [32] ATPase/helicase <10> [36,41] BMV 1a protein <16> [5] BmL3-helicase <1,42> [32] Brr2p <6> [50] DBP2 <24> [30] DDX17 <33> [12] DDX19 <43> [56] DDX25 <23,34,35> [12,21] DDX3 <25> [8] DDX3X <25> (<25> the gene is localized to the X chromosome [12]) [12] DDX3Y <29> (<29> the gene is localized to the Y chromosome [12]) [12] DDX4 <30> [12] DDX5 <32> [12] DEAD box RNA helicase <1,2,3> [32,45,52] DEAD box helicase <2> [45] DEAD-box RNA helicase <4,5,7,38,47,48> [9,14,16,25,53,55] DEAD-box protein DED1 <38> [11] DEAD-box rRNA helicase <5> [26] DEAH-box RNA helicase <24> [30] DEAH-box protein 2 <24> [30] DED1 <38> [11,14] DENV NS3H <10> [41] DEXD/H-box RNA helicase <43> [56] DEx(H/D)RNA helicase <12> [23] DHX9 <44> [58] DbpA <5> [10,25,26] Dhx9/RNA helicase A <13> [61] EhDEAD1 <7> [16] EhDEAD1 RNA helicase <7> [16] FRH <9> [54] FRQ-interacting RNA helicase <9> [54] GRTH <3> [57] GRTH/DDX25 <3,35> [21,51] HCV NS3 helicase <12> [48] KOKV helicase <27> [7] Mtr4p <31> [22] NPH-II <8> [18,28] NS3 <10,12,17,20,39,41> (<12,39> ambiguous [27,42,44]) [1,2,4,27,35,36,39, 42,44,46] NS3 ATPase/helicase <10> [41] NS3 NTPase/helicase <17> (<17> ambiguous [46]) [46] NS3 helicase <10,12,17> [15,44,46] NS3 protein <10,12,17,18> (<12> ambiguous [39]) [15,39,40,41,62] NTPase/helicase <12> (<12> ambiguous [37]) [37,39] RHA <6> [31,49] RNA helicase <2> [45] RNA helicase A <6,44> [31,49,58] RNA helicase CrhR <14> [59] RNA helicase DDX3 <25> [8] RNA helicase Ddx39 <47> [53] RNA helicase Hera <4> [9] RNA-dependent ATPase <37> [34] RNA-dependent NTPase/helicase <12> [1] RTPase <10> [36] RhlB <5> [43] SpolvlgA <48> [55] Supv3L1 <46> [64] TGBp1 NTPase/helicase domain <22,28> [24] Tk-DeaD <15> [47] VRH1 <26> [33] YxiN <2> [45] eIF4A <36> [20] eIF4A helicase <36> [20] eIF4AIII <37> [34] eukaryotic initiation factor eIF 4A <36> [20] gonadotropin-regulated testicular RNA helicase <3> [51,57] helicase <10> [41] helicase B <5> [43] helicase/nucleoside triphosphatase <10> [4] non structural protein 3 <12> (<12> ambiguous [37,38]) [37,38] non-structural 3 <10> [36] non-structural protein 3 <17> [46] non-structural protein 3 protein <18> [40] nonstructural protein 3 <12,17,20,39,40,41> (<12,17,39,40> ambiguous [6,27, 39,42,44,46]) [1,2,6,27,35,39,42,44,46] nucleoside 5’-triphosphatase <10> [4] nucleoside triphosphatase/RNA helicase and 5’-RNA triphosphatase <20> [2] nucleoside triphosphatase/helicase <16> [5] p54 RNA helicase <45> [60] p68 RNA helicase <3,6> [52,63] protein NS3 <12> (<12> ambiguous [38]) [38]
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Abstract
Similar to proteins, RNA molecules must fold into the correct conformation and associate with protein complexes in order to be functional within a cell. RNA helicases rearrange RNA secondary structure and RNA-protein interactions in an ATP-dependent reaction, performing crucial functions in all aspects of RNA metabolism. In prokaryotes, RNA helicase activity is associated with roles in housekeeping functions including RNA turnover, ribosome biogenesis, translation and small RNA metabolism. In addition, RNA helicase expression and/or activity are frequently altered during cellular response to abiotic stress, implying they perform defined roles during cellular adaptation to changes in the growth environment. Specifically, RNA helicases contribute to the formation of cold-adapted ribosomes and RNA degradosomes, implying a role in alleviation of RNA secondary structure stabilization at low temperature. A common emerging theme involves RNA helicases acting as scaffolds for protein-protein interaction and functioning as molecular clamps, holding RNA-protein complexes in specific conformations. This review highlights recent advances in DEAD-box RNA helicase association with cellular response to abiotic stress in prokaryotes.
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Affiliation(s)
- George W Owttrim
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
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Tian X, Chen L, Wang J, Qiao J, Zhang W. Quantitative proteomics reveals dynamic responses of Synechocystis sp. PCC 6803 to next-generation biofuel butanol. J Proteomics 2012; 78:326-45. [PMID: 23079071 DOI: 10.1016/j.jprot.2012.10.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 10/01/2012] [Accepted: 10/04/2012] [Indexed: 01/04/2023]
Abstract
Butanol is a promising biofuel, and recent metabolic engineering efforts have demonstrated the use of photosynthetic cyanobacterial hosts for its production. However, cyanobacteria have very low tolerance to butanol, limiting the economic viability of butanol production from these renewable producing systems. The existing knowledge of molecular mechanism involved in butanol tolerance in cyanobacteria is very limited. To build a foundation necessary to engineer robust butanol-producing cyanobacterial hosts, in this study, the responses of Synechocystis PCC 6803 to butanol were investigated using a quantitative proteomics approach with iTRAQ - LC-MS/MS technologies. The resulting high-quality dataset consisted of 25,347 peptides corresponding to 1452 unique proteins, a coverage of approximately 40% of the predicted proteins in Synechocystis. Comparative quantification of protein abundances led to the identification of 303 differentially regulated proteins by butanol. Annotation and GO term enrichment analysis showed that multiple biological processes were regulated, suggesting that Synechocystis probably employed multiple and synergistic resistance mechanisms in dealing with butanol stress. Notably, the analysis revealed the induction of heat-shock protein and transporters, along with modification of cell membrane and envelope were the major protection mechanisms against butanol. A conceptual cellular model of Synechocystis PCC 6803 responses to butanol stress was constructed to illustrate the putative molecular mechanisms employed to defend against butanol stress.
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Affiliation(s)
- Xiaoxu Tian
- School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China
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Markkula A, Lindström M, Johansson P, Björkroth J, Korkeala H. Roles of four putative DEAD-box RNA helicase genes in growth of Listeria monocytogenes EGD-e under heat, pH, osmotic, ethanol, and oxidative stress conditions. Appl Environ Microbiol 2012; 78:6875-82. [PMID: 22820328 PMCID: PMC3457484 DOI: 10.1128/aem.01526-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 07/13/2012] [Indexed: 01/21/2023] Open
Abstract
To examine the role of the four putative DEAD-box RNA helicase genes of Listeria monocytogenes EGD-e in stress tolerance, the growth of the Δlmo0866, Δlmo1246, Δlmo1450, and Δlmo1722 deletion mutant strains at 42.5°C, at pH 5.6 or pH 9.4, in 6% NaCl, in 3.5% ethanol, and in 5 mM H(2)O(2) was studied. Restricted growth of the Δlmo0866 deletion mutant strain in 3.5% ethanol suggests that Lmo0866 contributes to ethanol stress tolerance of L. monocytogenes EGD-e. The Δlmo1450 mutant strain showed negligible growth at 42.5°C, at pH 9.4, and in 5 mM H(2)O(2) and a lower maximum growth temperature than the wild-type EGD-e, suggesting that Lmo1450 is involved in the tolerance of L. monocytogenes EGD-e to heat, alkali, and oxidative stresses. The altered stress tolerance of the Δlmo0866 and Δlmo1450 deletion mutant strains did not correlate with changes in relative expression levels of lmo0866 and lmo1450 genes under corresponding stresses, suggesting that Lmo0866- and Lmo1450-dependent tolerance to heat, alkali, ethanol, or oxidative stress is not regulated at the transcriptional level. Growth of the Δlmo1246 and Δlmo1722 deletion mutant strains did not differ from that of the wild-type EGD-e under any of the conditions tested, suggesting that Lmo1246 and Lmo1722 have no roles in the growth of L. monocytogenes EGD-e under heat, pH, osmotic, ethanol, or oxidative stress. This study shows that the putative DEAD-box RNA helicase genes lmo0866 and lmo1450 play important roles in tolerance of L. monocytogenes EGD-e to ethanol, heat, alkali, and oxidative stresses.
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Affiliation(s)
- Annukka Markkula
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
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Li W, Gao H, Yin C, Xu X. Identification of a novel thylakoid protein gene involved in cold acclimation in cyanobacteria. MICROBIOLOGY-SGM 2012; 158:2440-2449. [PMID: 22767544 DOI: 10.1099/mic.0.060038-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In cyanobacteria, genes involved in cold acclimation can be upregulated in response to cold stress with or without light. By inactivating 17 such genes in Synechocystis sp. PCC 6803, slr0815 (ccr2) was identified to be a novel gene required for survival at 15 °C. It was upregulated by cold stress in the light. Upon exposure to low temperature, a ccr2-null mutant showed greatly reduced photosynthetic and respiratory activities within 12 h relative to the wild-type. At 48 h, the photosystem (PS)II-mediated electron transport in the mutant was reduced to less than one-third of the wild-type level, and the duration of electron transfer from the Q(B) binding site of PSII to PSI was increased to about eight times the wild-type level, whereas the PSI-mediated electron transport remained unchanged. Using an antibody against GFP, a Ccr2-GFP fusion protein was localized to the thylakoid membrane rather than the cytoplasmic and outer membranes. Homologues to Ccr2 can be found in most cyanobacteria, algae and higher plants with sequenced genomes. Ccr2 is probably representative of a group of novel thylakoid proteins involved in acclimation to cold or other stresses.
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Affiliation(s)
- Weizhi Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China
| | - Hong Gao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China
| | - Chuntao Yin
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China
| | - Xudong Xu
- The State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China
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RNA helicase, CrhR is indispensable for the energy redistribution and the regulation of photosystem stoichiometry at low temperature in Synechocystis sp. PCC6803. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1525-36. [PMID: 22575444 DOI: 10.1016/j.bbabio.2012.04.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 04/28/2012] [Accepted: 04/30/2012] [Indexed: 11/21/2022]
Abstract
We investigated the role of a cold-inducible and redox-regulated RNA helicase, CrhR, in the energy redistribution and adjustment of stoichiometry between photosystem I (PSI) and photosystem II (PSII), at low temperature in Synechocystis sp. PCC 6803. The results suggest that during low temperature incubation, i.e., when cells are shifted from 34°C to 24°C, wild type cells exhibited light-induced state transitions, whereas the mutant deficient in CrhR failed to perform the same. At low temperature, wild type cells maintained the plastoquinone (PQ) pool in the reduced state due to enhanced respiratory electron flow to the PQ pool, whereas in ∆crhR mutant cells the PQ pool was in the oxidized state. Wild type cells were in state 2 and ∆crhR cells were locked in state 1 at low temperature. In both wild type and ∆crhR cells, a fraction of PSI trimers were changed to PSI monomers. However, in ∆crhR cells, the PSI trimer content was significantly decreased. Expression of photosystem I genes, especially the psaA and psaB, was strongly down-regulated due to oxidation of downstream components of PQ in ∆crhR cells at low temperature. We demonstrated that changes in the low temperature-induced energy redistribution and regulation of photosystem stoichiometry are acclimatization responses exerted by Synechocystis cells, essentially regulated by the RNA helicase, CrhR, at low temperature.
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Rowland JG, Simon WJ, Prakash JSS, Slabas AR. Proteomics Reveals a Role for the RNA Helicase crhR in the Modulation of Multiple Metabolic Pathways during Cold Acclimation of Synechocystis sp. PCC6803. J Proteome Res 2011; 10:3674-89. [DOI: 10.1021/pr200299t] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- John G. Rowland
- School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | - William J. Simon
- School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Jogadhenu S. S. Prakash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Antoni R. Slabas
- School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
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López-Ramírez V, Alcaraz LD, Moreno-Hagelsieb G, Olmedo-Álvarez G. Phylogenetic distribution and evolutionary history of bacterial DEAD-Box proteins. J Mol Evol 2011; 72:413-31. [PMID: 21437710 PMCID: PMC3093544 DOI: 10.1007/s00239-011-9441-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 03/04/2011] [Indexed: 01/24/2023]
Abstract
DEAD-box proteins are found in all domains of life and participate in almost all cellular processes that involve RNA. The presence of DEAD and Helicase_C conserved domains distinguish these proteins. DEAD-box proteins exhibit RNA-dependent ATPase activity in vitro, and several also show RNA helicase activity. In this study, we analyzed the distribution and architecture of DEAD-box proteins among bacterial genomes to gain insight into the evolutionary pathways that have shaped their history. We identified 1,848 unique DEAD-box proteins from 563 bacterial genomes. Bacterial genomes can possess a single copy DEAD-box gene, or up to 12 copies of the gene, such as in Shewanella. The alignment of 1,208 sequences allowed us to perform a robust analysis of the hallmark motifs of DEAD-box proteins and determine the residues that occur at high frequency, some of which were previously overlooked. Bacterial DEAD-box proteins do not generally contain a conserved C-terminal domain, with the exception of some members that possess a DbpA RNA-binding domain (RBD). Phylogenetic analysis showed a separation of DbpA-RBD-containing and DbpA-RBD-lacking sequences and revealed a group of DEAD-box protein genes that expanded mainly in the Proteobacteria. Analysis of DEAD-box proteins from Firmicutes and γ-Proteobacteria, was used to deduce orthologous relationships of the well-studied DEAD-box proteins from Escherichia coli and Bacillus subtilis. These analyses suggest that DbpA-RBD is an ancestral domain that most likely emerged as a specialized domain of the RNA-dependent ATPases. Moreover, these data revealed numerous events of gene family expansion and reduction following speciation.
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Affiliation(s)
- Varinia López-Ramírez
- Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León CP, 36821 Irapuato, Guanajuato Mexico
| | - Luis D. Alcaraz
- Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León CP, 36821 Irapuato, Guanajuato Mexico
- Present Address: Department of Genomics and Health, Centro Superior de Investigación en Salud Pública, Avda. Cataluña 21, Valencia, Spain
| | - Gabriel Moreno-Hagelsieb
- Department of Biology, Wilfrid Laurier University, 75 University Ave. W., Waterloo, ON N2L 3C5 Canada
| | - Gabriela Olmedo-Álvarez
- Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León CP, 36821 Irapuato, Guanajuato Mexico
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