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Giner-Lamia J, Robles-Rengel R, Hernández-Prieto MA, Muro-Pastor MI, Florencio FJ, Futschik ME. Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803. Nucleic Acids Res 2017; 45:11800-11820. [PMID: 29036481 PMCID: PMC5714215 DOI: 10.1093/nar/gkx860] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 09/15/2017] [Indexed: 12/22/2022] Open
Abstract
In cyanobacteria, nitrogen homeostasis is maintained by an intricate regulatory network around transcription factor NtcA. Although mechanisms controlling NtcA activity appear to be well understood, its regulon remains poorly defined. To determine the NtcA regulon during the early stages of nitrogen starvation for the model cyanobacterium Synechocystis sp. PCC 6803, we performed chromatin immunoprecipitation, followed by sequencing (ChIP-seq), in parallel with transcriptome analysis (RNA-seq). Through combining these methods, we determined 51 genes activated and 28 repressed directly by NtcA. In addition to genes associated with nitrogen and carbon metabolism, a considerable number of genes without current functional annotation were among direct targets providing a rich reservoir for further studies. The NtcA regulon also included eight non-coding RNAs, of which Ncr1071, Syr6 and NsiR7 were experimentally validated, and their putative targets were computationally predicted. Surprisingly, we found substantial NtcA binding associated with delayed expression changes indicating that NtcA can reside in a poised state controlled by other factors. Indeed, a role of PipX as modulating factor in nitrogen regulation was confirmed for selected NtcA-targets. We suggest that the indicated poised state of NtcA enables a more differentiated response to nitrogen limitation and can be advantageous in native habitats of Synechocystis.
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Affiliation(s)
- Joaquín Giner-Lamia
- Systems Biology and Bioinformatics Laboratory, CBMR, University of Algarve, 8005-139 Faro, Portugal.,Laboratory of Intracellular Bacterial Pathogens, Department of Microbial Biotechnology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
| | - Rocío Robles-Rengel
- Instituto de Bioquímica Vegetal y Fotosíntesis. Universidad de Sevilla-CSIC, Av. Américo Vespucio 49, E-41092 Seville, Spain
| | - Miguel A Hernández-Prieto
- Systems Biology and Bioinformatics Laboratory, CBMR, University of Algarve, 8005-139 Faro, Portugal.,ARC Centre of Excellence for Translational Photosynthesis and School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - M Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis. Universidad de Sevilla-CSIC, Av. Américo Vespucio 49, E-41092 Seville, Spain
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis. Universidad de Sevilla-CSIC, Av. Américo Vespucio 49, E-41092 Seville, Spain
| | - Matthias E Futschik
- Systems Biology and Bioinformatics Laboratory, CBMR, University of Algarve, 8005-139 Faro, Portugal.,Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal.,School of Biomedical & Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth PL6 8BU, UK
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102
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Pervasive, Genome-Wide Transcription in the Organelle Genomes of Diverse Plastid-Bearing Protists. G3-GENES GENOMES GENETICS 2017; 7:3789-3796. [PMID: 28935754 PMCID: PMC5677165 DOI: 10.1534/g3.117.300290] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Organelle genomes are among the most sequenced kinds of chromosome. This is largely because they are small and widely used in molecular studies, but also because next-generation sequencing technologies made sequencing easier, faster, and cheaper. However, studies of organelle RNA have not kept pace with those of DNA, despite huge amounts of freely available eukaryotic RNA-sequencing (RNA-seq) data. Little is known about organelle transcription in nonmodel species, and most of the available eukaryotic RNA-seq data have not been mined for organelle transcripts. Here, we use publicly available RNA-seq experiments to investigate organelle transcription in 30 diverse plastid-bearing protists with varying organelle genomic architectures. Mapping RNA-seq data to organelle genomes revealed pervasive, genome-wide transcription, regardless of the taxonomic grouping, gene organization, or noncoding content. For every species analyzed, transcripts covered ≥85% of the mitochondrial and/or plastid genomes (all of which were ≤105 kb), indicating that most of the organelle DNA—coding and noncoding—is transcriptionally active. These results follow earlier studies of model species showing that organellar transcription is coupled and ubiquitous across the genome, requiring significant downstream processing of polycistronic transcripts. Our findings suggest that noncoding organelle DNA can be transcriptionally active, raising questions about the underlying function of these transcripts and underscoring the utility of publicly available RNA-seq data for recovering complete genome sequences. If pervasive transcription is also found in bigger organelle genomes (>105 kb) and across a broader range of eukaryotes, this could indicate that noncoding organelle RNAs are regulating fundamental processes within eukaryotic cells.
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103
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Ehira S, Shimmori Y, Watanabe S, Kato H, Yoshikawa H, Ohmori M. The nitrogen-regulated response regulator NrrA is a conserved regulator of glycogen catabolism in β-cyanobacteria. Microbiology (Reading) 2017; 163:1711-1719. [DOI: 10.1099/mic.0.000549] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Shigeki Ehira
- Department of Biological Science, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Yuka Shimmori
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Hiroaki Kato
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Hirofumi Yoshikawa
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Masayuki Ohmori
- Department of Biological Science, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
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104
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Lott SC, Wolfien M, Riege K, Bagnacani A, Wolkenhauer O, Hoffmann S, Hess WR. Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments. J Biotechnol 2017; 261:85-96. [DOI: 10.1016/j.jbiotec.2017.06.1203] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/22/2017] [Accepted: 06/26/2017] [Indexed: 12/14/2022]
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105
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Muro-Pastor AM, Brenes-Álvarez M, Vioque A. A combinatorial strategy of alternative promoter use during differentiation of a heterocystous cyanobacterium. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:449-458. [PMID: 28585763 DOI: 10.1111/1758-2229.12555] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/24/2017] [Accepted: 05/29/2017] [Indexed: 06/07/2023]
Abstract
Heterocystous cyanobacteria such as Nostoc sp. are filamentous photosynthetic organisms that, in response to nitrogen deficiency, undergo a differentiation process transforming certain, semi-regularly spaced cells into heterocysts, devoted to nitrogen fixation. During transition to a nitrogen-fixing regime, growth of most vegetative cells in the filament is temporarily arrested due to nutritional deprivation, but developing heterocysts require intense transcriptional activity. Therefore, the coexistence of arrested vegetative cells and actively developing prospective heterocysts relies on the simultaneous operation of somewhat opposite transcriptional programs. We have identified genes with multiple nitrogen-responsive transcriptional starts appearing in seemingly paradoxical combinations. For instance, sigA, encoding the RNA polymerase housekeeping sigma factor, is transcribed from one major nitrogen stress-repressed promoter and from a second, nitrogen stress-induced promoter. Here, we show that both promoters are expressed with complementary temporal dynamics. Using a gfp reporter we also show that transcription from the inducible promoter takes place exclusively in differentiating heterocysts and is already detected before any morphological or fluorescence signature of differentiation is observed. Tandem promoters with opposite dynamics could operate a compensatory mechanism in which repression of transcription from the major promoter operative in vegetative cells is offset by transcription from a new promoter only in developing heterocyst.
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Affiliation(s)
- Alicia M Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Sevilla, E-41092, Spain
| | - Manuel Brenes-Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Sevilla, E-41092, Spain
| | - Agustín Vioque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Sevilla, E-41092, Spain
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106
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Forcada-Nadal A, Palomino-Schätzlein M, Neira JL, Pineda-Lucena A, Rubio V. The PipX Protein, When Not Bound to Its Targets, Has Its Signaling C-Terminal Helix in a Flexed Conformation. Biochemistry 2017; 56:3211-3224. [PMID: 28581722 DOI: 10.1021/acs.biochem.7b00230] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PipX, an 89-residue protein, acts as a coactivator of the global nitrogen regulator NtcA in cyanobacteria. NtcA-PipX interactions are regulated by 2-oxoglutarate (2-OG), an inverse indicator of the ammonia abundance, and by PII, a protein that binds to PipX at low 2-OG concentrations. The structure of PipX, when bound to NtcA or PII, consists of an N-terminal, five-stranded β-sheet (conforming a Tudor-like domain), and two long α-helices. These helices adopt either a flexed conformation, where they are in close contact and in an antiparallel mutual orientation, also packing against the β-sheet, or an open conformation (observed only in the PII-PipX complex) where the last α-helix moves apart from the rest of the protein. The aim of this work was to study the structure and dynamics of isolated PipX in solution by NMR. The backbone chemical shifts, the hydrogen-exchange, and the NOE patterns indicated that the isolated, monomeric PipX structure was formed by an N-terminal five-stranded β-sheet and two C-terminal α-helices. Furthermore, the observed NOEs between the two helices, and of α-helix2 with β-strand2 suggested that PipX adopted a flexed conformation. The β-strands 1 and 5 were highly flexible, as shown by the lack of interstrand backbone-backbone NOEs; in addition, the 15N-dynamics indicated that the C terminus of β-strand4 and the following β-turn (Phe42-Thr47), and the C-cap of α-helix1 (Arg70-Asn71) were particularly mobile. These two regions could act as hinges, allowing PipX to interact with its partners, including PlmA in the newly recognized PII-PipX-PlmA ternary complex.
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Affiliation(s)
| | | | - José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , Elche (Alicante), Spain.,Instituto de Biocomputación y Física de Sistemas Complejos , Zaragoza, Spain
| | - Antonio Pineda-Lucena
- Centro de Investigación Príncipe Felipe , Valencia, Spain.,Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe , Valencia, Spain
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.,Group 739 of the CIBER de Enfermedades Raras (CIBERER-ISCIII) , Valencia, Spain
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107
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Shahmuradov IA, Mohamad Razali R, Bougouffa S, Radovanovic A, Bajic VB. bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli. Bioinformatics 2017; 33:334-340. [PMID: 27694198 PMCID: PMC5408793 DOI: 10.1093/bioinformatics/btw629] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/27/2016] [Indexed: 12/01/2022] Open
Abstract
Motivation The computational search for promoters in prokaryotes remains an attractive problem in bioinformatics. Despite the attention it has received for many years, the problem has not been addressed satisfactorily. In any bacterial genome, the transcription start site is chosen mostly by the sigma (σ) factor proteins, which control the gene activation. The majority of published bacterial promoter prediction tools target σ70 promoters in Escherichia coli. Moreover, no σ-specific classification of promoters is available for prokaryotes other than for E. coli. Results Here, we introduce bTSSfinder, a novel tool that predicts putative promoters for five classes of σ factors in Cyanobacteria (σA, σC, σH, σG and σF) and for five classes of sigma factors in E. coli (σ70, σ38, σ32, σ28 and σ24). Comparing to currently available tools, bTSSfinder achieves higher accuracy (MCC = 0.86, F1-score = 0.93) compared to the next best tool with MCC = 0.59, F1-score = 0.79) and covers multiple classes of promoters. Availability and Implementation bTSSfinder is available standalone and online at http://www.cbrc.kaust.edu.sa/btssfinder. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ilham Ayub Shahmuradov
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Rozaimi Mohamad Razali
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Salim Bougouffa
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Aleksandar Radovanovic
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Vladimir B Bajic
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
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108
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Prasse D, Förstner KU, Jäger D, Backofen R, Schmitz RA. sRNA 154 a newly identified regulator of nitrogen fixation in Methanosarcina mazei strain Gö1. RNA Biol 2017; 14:1544-1558. [PMID: 28296572 DOI: 10.1080/15476286.2017.1306170] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Trans-encoded sRNA154 is exclusively expressed under nitrogen (N)-deficiency in Methanosarcina mazei strain Gö1. The sRNA154 deletion strain showed a significant decrease in growth under N-limitation, pointing toward a regulatory role of sRNA154 in N-metabolism. Aiming to elucidate its regulatory function we characterized sRNA154 by means of biochemical and genetic approaches. 24 homologs of sRNA154 were identified in recently reported draft genomes of Methanosarcina strains, demonstrating high conservation in sequence and predicted secondary structure with two highly conserved single stranded loops. Transcriptome studies of sRNA154 deletion mutants by an RNA-seq approach uncovered nifH- and nrpA-mRNA, encoding the α-subunit of nitrogenase and the transcriptional activator of the nitrogen fixation (nif)-operon, as potential targets besides other components of the N-metabolism. Furthermore, results obtained from stability, complementation and western blot analysis, as well as in silico target predictions combined with electrophoretic mobility shift-assays, argue for a stabilizing effect of sRNA154 on the polycistronic nif-mRNA and nrpA-mRNA by binding with both loops. Further identified N-related targets were studied, which demonstrates that translation initiation of glnA2-mRNA, encoding glutamine synthetase2, appears to be affected by sRNA154 masking the ribosome binding site, whereas glnA1-mRNA appears to be stabilized by sRNA154. Overall, we propose that sRNA154 has a crucial regulatory role in N-metabolism in M. mazei by stabilizing the polycistronic mRNA encoding nitrogenase and glnA1-mRNA, as well as allowing a feed forward regulation of nif-gene expression by stabilizing nrpA-mRNA. Consequently, sRNA154 represents the first archaeal sRNA, for which a positive posttranscriptional regulation is demonstrated as well as inhibition of translation initiation.
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Affiliation(s)
- Daniela Prasse
- a Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel , Am Botanischen Garten 1-9, Kiel , Germany
| | - Konrad U Förstner
- b Zentrum für Infektionsforschung , Universität Würzburg , Josef Schneider-Str. 2/ Bau D15, Würzburg
| | - Dominik Jäger
- a Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel , Am Botanischen Garten 1-9, Kiel , Germany
| | - Rolf Backofen
- c Institut für Informatik, Albert-Ludwigs-Universität zu Freiburg , Georges-Koehler-Allee, Freiburg , Germany
| | - Ruth A Schmitz
- a Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel , Am Botanischen Garten 1-9, Kiel , Germany
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109
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James K, Cockell SJ, Zenkin N. Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics. Methods 2017; 120:76-84. [PMID: 28434904 DOI: 10.1016/j.ymeth.2017.04.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 04/13/2017] [Accepted: 04/18/2017] [Indexed: 01/13/2023] Open
Abstract
The identification of the protein-coding regions of a genome is straightforward due to the universality of start and stop codons. However, the boundaries of the transcribed regions, conditional operon structures, non-coding RNAs and the dynamics of transcription, such as pausing of elongation, are non-trivial to identify, even in the comparatively simple genomes of prokaryotes. Traditional methods for the study of these areas, such as tiling arrays, are noisy, labour-intensive and lack the resolution required for densely-packed bacterial genomes. Recently, deep sequencing has become increasingly popular for the study of the transcriptome due to its lower costs, higher accuracy and single nucleotide resolution. These methods have revolutionised our understanding of prokaryotic transcriptional dynamics. Here, we review the deep sequencing and data analysis techniques that are available for the study of transcription in prokaryotes, and discuss the bioinformatic considerations of these analyses.
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Affiliation(s)
- Katherine James
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Bioscience, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle Upon Tyne NE2 4AX, UK.
| | - Simon J Cockell
- Bioinformatics Support Unit, Newcastle University, William Leech Building, Framlington Place, Newcastle Upon Tyne NE2 4HH, UK
| | - Nikolay Zenkin
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Bioscience, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle Upon Tyne NE2 4AX, UK
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110
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Kirti A, Kumar A, Rajaram H. Differential regulation of ssb genes in the nitrogen-fixing cyanobacterium, Anabaena sp. strain PCC7120 1. JOURNAL OF PHYCOLOGY 2017; 53:322-332. [PMID: 28000228 DOI: 10.1111/jpy.12500] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 09/23/2016] [Indexed: 06/06/2023]
Abstract
Anabaena sp. PCC7120 possesses three genes coding for single-stranded DNA-binding (SSB) protein, of which ssb1 was a single gene, and ssb2 and ssb3 are the first genes of their corresponding operons. Regulation of the truncated ssb genes, ssb1 (alr0088) and ssb2 (alr7559), was unaffected by N-status of growth. They were negatively regulated by the SOS-response regulatory protein LexA, as indicated by the (i) binding of Anabaena LexA to the LexA box of regulatory regions of ssb1 and ssb2, and (ii) decreased expression of the downstream gfp reporter gene in Escherichia coli upon co-expression of LexA. However, the full-length ssb gene, ssb3 (all4779), was regulated by the availability of Fe2+ and combined nitrogen, as indicated by (i) increase in the levels of SSB3 protein on Fe2+ -depletion and decrease under Fe2+ -excess conditions, and (ii) 1.5- to 1.6-fold decrease in activity under nitrogen-fixing conditions compared to nitrogen-supplemented conditions. The requirement of Fe2+ as a co-factor for repression by FurA and the increase in levels of FurA under nitrogen-deficient conditions in Anabaena (Lopez-Gomollon et al. 2007) indicated a possible regulation of ssb3 by FurA. This was substantiated by (i) the binding of FurA to the regulatory region of ssb3, (ii) repression of the expression of the downstream gfp reporter gene in E. coli upon co-expression of FurA, and (iii) negative regulation of ssb3 promoter activity by the upstream AT-rich region in Anabaena. This is the first report on possible role of FurA, an important protein for iron homeostasis, in DNA repair of cyanobacteria.
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Affiliation(s)
- Anurag Kirti
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Arvind Kumar
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Hema Rajaram
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
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111
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Pei G, Sun T, Chen S, Chen L, Zhang W. Systematic and functional identification of small non-coding RNAs associated with exogenous biofuel stress in cyanobacterium Synechocystis sp. PCC 6803. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:57. [PMID: 28286552 PMCID: PMC5341163 DOI: 10.1186/s13068-017-0743-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 02/28/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND The unicellular model cyanobacterium Synechocystis sp. PCC 6803 is considered a promising microbial chassis for biofuel production. However, its low tolerance to biofuel toxicity limits its potential application. Although recent studies showed that bacterial small RNAs (sRNAs) play important roles in regulating cellular processes in response to various stresses, the role of sRNAs in resisting exogenous biofuels is yet to be determined. RESULTS Based on genome-wide sRNA sequencing combined with systematic analysis of previous transcriptomic and proteomic data under the same biofuel or environmental perturbations, we report the identification of 133 trans-encoded sRNA transcripts with high-resolution mapping of sRNAs in Synechocystis, including 23 novel sRNAs identified for the first time. In addition, according to quantitative expression analysis and sRNA regulatory network prediction, sRNAs potentially involved in biofuel tolerance were identified and functionally confirmed by constructing sRNA overexpression or suppression strains of Synechocystis. Notably, overexpression of sRNA Nc117 revealed an improved tolerance to ethanol and butanol, while suppression of Nc117 led to increased sensitivity. CONCLUSIONS The study provided the first comprehensive responses to exogenous biofuels at the sRNA level in Synechocystis and opens an avenue to engineering sRNA regulatory elements for improved biofuel tolerance in the cyanobacterium Synechocystis.
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Affiliation(s)
- Guangsheng Pei
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072 People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, People’s Republic of China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072 People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, People’s Republic of China
| | - Shuo Chen
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, People’s Republic of China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072 People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, People’s Republic of China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, 300072 People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, People’s Republic of China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, People’s Republic of China
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112
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Hu J, Li T, Xu W, Zhan J, Chen H, He C, Wang Q. Small Antisense RNA RblR Positively Regulates RuBisCo in Synechocystis sp. PCC 6803. Front Microbiol 2017; 8:231. [PMID: 28261186 PMCID: PMC5306279 DOI: 10.3389/fmicb.2017.00231] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 02/01/2017] [Indexed: 11/21/2022] Open
Abstract
Small regulatory RNAs (sRNAs) function as transcriptional and post-transcriptional regulators of gene expression in organisms from all domains of life. Cyanobacteria are thought to have developed a complex RNA-based regulatory mechanism. In the current study, by genome-wide analysis of differentially expressed small RNAs in Synechocystis sp. PCC 6803 under high light conditions, we discovered an asRNA (RblR) that is 113nt in length and completely complementary to its target gene rbcL, which encodes the large chain of RuBisCO, the enzyme that catalyzes carbon fixation. Further analysis of the RblR(+)/(−) mutants revealed that RblR acts as a positive regulator of rbcL under various stress conditions; Suppressing RblR adversely affects carbon assimilation and thus the yield, and those phenotypes of both the wild type and the overexpressor could be downgraded to the suppressor level by carbonate depletion, indicated a regulatory role of RblR in CO2 assimilation. In addition, a real-time expression platform in Escherichia coli was setup and which confirmed that RblR promoted the translation of the rbcL mRNA into the RbcL protein. The present study is the first report of a regulatory RNA that targets RbcL in Synechocystis sp. PCC 6803, and provides strong evidence that RblR regulates photosynthesis by positively modulating rbcL expression in Synechocystis.
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Affiliation(s)
- Jinlu Hu
- School of Life Sciences, Northwestern Polytechnical University Xi'an, China
| | - Tianpei Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, the Chinese Academy of SciencesWuhan, China; University of the Chinese Academy of SciencesBeijing, China
| | - Wen Xu
- Crop Designing Centre, Henan Academy of Agricultural Sciences Zhengzhou, China
| | - Jiao Zhan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, the Chinese Academy of Sciences Wuhan, China
| | - Hui Chen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, the Chinese Academy of Sciences Wuhan, China
| | - Chenliu He
- Key Laboratory of Algal Biology, Institute of Hydrobiology, the Chinese Academy of Sciences Wuhan, China
| | - Qiang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Chinese Academy of Sciences Wuhan, China
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Colgan AM, Cameron AD, Kröger C. If it transcribes, we can sequence it: mining the complexities of host-pathogen-environment interactions using RNA-seq. Curr Opin Microbiol 2017; 36:37-46. [PMID: 28189909 DOI: 10.1016/j.mib.2017.01.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 02/07/2023]
Abstract
Host-pathogen interactions are exceedingly complex because they involve multiple host tissues, often occur in the context of normal microflora, and can span diverse microenvironments. Although decades of gene expression studies have provided detailed insights into infection processes, technical challenges have restricted experiments to single pathogenic species or host tissues. RNA-sequencing (RNA-seq) has revolutionized the study of gene expression because in addition to quantifying transcriptional output, it allows detection and characterization of all transcripts in a genome. Here, we review how refined approaches to RNA-seq are used to map the transcriptional networks that control host-pathogen interactions. These enhanced techniques include dRNA-seq and term-seq for the fine-scale mapping of transcriptional start and termination sites, and dual RNA-seq for simultaneous sequencing of host and bacterial pathogen transcriptomes. Dual RNA-seq experiments are currently limited to in vitro infection systems that do not fully reflect the complexities of the in vivo environment, thus a challenge is to develop in vivo model systems and experimental approaches that address the biological heterogeneity of host environments, followed by the integration of RNA-seq with other genome-scale datasets to identify the transcriptional networks that mediate host-pathogen interactions.
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Affiliation(s)
- Aoife M Colgan
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Andrew Ds Cameron
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | - Carsten Kröger
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland.
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114
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Kumar A, Bansal M. Unveiling DNA structural features of promoters associated with various types of TSSs in prokaryotic transcriptomes and their role in gene expression. DNA Res 2017; 24:25-35. [PMID: 27803028 PMCID: PMC5381344 DOI: 10.1093/dnares/dsw045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/23/2016] [Indexed: 01/28/2023] Open
Abstract
Next-generation sequencing studies have revealed that a variety of transcripts are present in the prokaryotic transcriptome and a significant fraction of them are functional, being involved in various regulatory activities apart from coding for proteins. Identification of promoters associated with different transcripts is necessary for characterization of the transcriptome. Promoter regions have been shown to have unique structural features as compared with their flanking region, in organisms covering all domains of life. Here we report an in silico analysis of DNA sequence dependent structural properties like stability, bendability and curvature in the promoter region of six different prokaryotic transcriptomes. Using these structural features, we predicted promoters associated with different categories of transcripts (mRNA, internal, antisense and non-coding), which constitute the transcriptome. Promoter annotation using structural features is fairly accurate and reliable with about 50% of the primary promoters being characterized by all three structural properties while at least one property identifies 95%. We also studied the relative differences of these structural features in terms of gene expression and found that the features, viz. lower stability, lesser bendability and higher curvature are more prominent in the promoter regions which are associated with high gene expression as compared with low expression genes. Hence, promoters, which are associated with higher gene expression, get annotated well using DNA structural features as compared with those, which are linked to lower gene expression.
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Affiliation(s)
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012 Karnataka, India
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115
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Baumgartner D, Kopf M, Klähn S, Steglich C, Hess WR. Small proteins in cyanobacteria provide a paradigm for the functional analysis of the bacterial micro-proteome. BMC Microbiol 2016; 16:285. [PMID: 27894276 PMCID: PMC5126843 DOI: 10.1186/s12866-016-0896-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/14/2016] [Indexed: 12/21/2022] Open
Abstract
Background Despite their versatile functions in multimeric protein complexes, in the modification of enzymatic activities, intercellular communication or regulatory processes, proteins shorter than 80 amino acids (μ-proteins) are a systematically underestimated class of gene products in bacteria. Photosynthetic cyanobacteria provide a paradigm for small protein functions due to extensive work on the photosynthetic apparatus that led to the functional characterization of 19 small proteins of less than 50 amino acids. In analogy, previously unstudied small ORFs with similar degrees of conservation might encode small proteins of high relevance also in other functional contexts. Results Here we used comparative transcriptomic information available for two model cyanobacteria, Synechocystis sp. PCC 6803 and Synechocystis sp. PCC 6714 for the prediction of small ORFs. We found 293 transcriptional units containing candidate small ORFs ≤80 codons in Synechocystis sp. PCC 6803, also including the known mRNAs encoding small proteins of the photosynthetic apparatus. From these transcriptional units, 146 are shared between the two strains, 42 are shared with the higher plant Arabidopsis thaliana and 25 with E. coli. To verify the existence of the respective μ-proteins in vivo, we selected five genes as examples to which a FLAG tag sequence was added and re-introduced them into Synechocystis sp. PCC 6803. These were the previously annotated gene ssr1169, two newly defined genes norf1 and norf4, as well as nsiR6(nitrogen stress-induced RNA 6) and hliR1(high light-inducible RNA 1) , which originally were considered non-coding. Upon activation of expression via the Cu2+.responsive petE promoter or from the native promoters, all five proteins were detected in Western blot experiments. Conclusions The distribution and conservation of these five genes as well as their regulation of expression and the physico-chemical properties of the encoded proteins underline the likely great bandwidth of small protein functions in bacteria and makes them attractive candidates for functional studies.
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Affiliation(s)
- Desiree Baumgartner
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Matthias Kopf
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104, Freiburg, Germany.,Present Address: Molecular Health GmbH, Kurfürsten-Anlage 21, 69115, Heidelberg, Germany
| | - Stephan Klähn
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Claudia Steglich
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Wolfgang R Hess
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104, Freiburg, Germany.
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116
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The heterocyst regulatory protein HetP and its homologs modulate heterocyst commitment in Anabaena sp. strain PCC 7120. Proc Natl Acad Sci U S A 2016; 113:E6984-E6992. [PMID: 27791130 DOI: 10.1073/pnas.1610533113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The commitment of differentiating cells to a specialized fate is fundamental to the correct assembly of tissues within a multicellular organism. Because commitment is often irreversible, entry into and progression through this phase of development must be tightly regulated. Under nitrogen-limiting conditions, the multicellular cyanobacterium Anabaena sp. strain PCC 7120 terminally commits ∼10% of its cells to become specialized nitrogen-fixing heterocysts. Although commitment is known to occur 9-14 h after the induction of differentiation, the factors that regulate the initiation and duration of this phase have yet to be elucidated. Here, we report the identification of four genes that share a functional domain and modulate heterocyst commitment: hetP (alr2818), asl1930, alr2902, and alr3234 Epistatic relationships between all four genes relating to commitment were revealed by deleting them individually and in combination; asl1930 and alr3234 acted most upstream to delay commitment, alr2902 acted next in the pathway to inhibit development, and hetP acted most downstream to drive commitment forward. Possible protein-protein interactions between HetP, its homologs, and the heterocyst master regulator, HetR, were assessed, and interaction partners were defined. Finally, patterns of gene expression for each homolog, as determined by promoter fusions to gfp and reverse transcription-quantitative PCR, were distinct from that of hetP in both spatiotemporal organization and regulation. We posit that a dynamic succession of protein-protein interactions modulates the timing and efficiency of the commitment phase of development and note that this work highlights the utility of a multicellular cyanobacterium as a model for the study of developmental processes.
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117
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de Porcellinis AJ, Klähn S, Rosgaard L, Kirsch R, Gutekunst K, Georg J, Hess WR, Sakuragi Y. The Non-Coding RNA Ncr0700/PmgR1 is Required for Photomixotrophic Growth and the Regulation of Glycogen Accumulation in the Cyanobacterium Synechocystis sp. PCC 6803. PLANT & CELL PHYSIOLOGY 2016; 57:2091-2103. [PMID: 27440548 DOI: 10.1093/pcp/pcw128] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/12/2016] [Indexed: 06/06/2023]
Abstract
Carbohydrate metabolism is a tightly regulated process in photosynthetic organisms. In the cyanobacterium Synechocystis sp. PCC 6803, the photomixotrophic growth protein A (PmgA) is involved in the regulation of glucose and storage carbohydrate (i.e. glycogen) metabolism, while its biochemical activity and possible factors acting downstream of PmgA are unknown. Here, a genome-wide microarray analysis of a ΔpmgA strain identified the expression of 36 protein-coding genes and 42 non-coding transcripts as significantly altered. From these, the non-coding RNA Ncr0700 was identified as the transcript most strongly reduced in abundance. Ncr0700 is widely conserved among cyanobacteria. In Synechocystis its expression is inversely correlated with light intensity. Similarly to a ΔpmgA mutant, a Δncr0700 deletion strain showed an approximately 2-fold increase in glycogen content under photoautotrophic conditions and wild-type-like growth. Moreover, its growth was arrested by 38 h after a shift to photomixotrophic conditions. Ectopic expression of Ncr0700 in Δncr0700 and ΔpmgA restored the glycogen content and photomixotrophic growth to wild-type levels. These results indicate that Ncr0700 is required for photomixotrophic growth and the regulation of glycogen accumulation, and acts downstream of PmgA. Hence Ncr0700 is renamed here as PmgR1 for photomixotrophic growth RNA 1.
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Affiliation(s)
- Alice J de Porcellinis
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, DK-1871, Denmark
- These authors contributed equally to this work
| | - Stephan Klähn
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg, D-79104, Germany
- These authors contributed equally to this work
| | - Lisa Rosgaard
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, DK-1871, Denmark
- Present address: R&D Renescience Thermal Power, DONG Energy, Skærbæk-7000 Fredericia, Denmark
| | - Rebekka Kirsch
- Botanical Institute, Christian-Albrechts-University, Am Botanischen Garten 5, Kiel, D-24118, Germany
| | - Kirstin Gutekunst
- Botanical Institute, Christian-Albrechts-University, Am Botanischen Garten 5, Kiel, D-24118, Germany
| | - Jens Georg
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg, D-79104, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg, D-79104, Germany
| | - Yumiko Sakuragi
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, DK-1871, Denmark
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118
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The two Dps proteins, NpDps2 and NpDps5, are involved in light-induced oxidative stress tolerance in the N 2-fixing cyanobacterium Nostoc punctiforme. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1766-1776. [PMID: 27528559 DOI: 10.1016/j.bbabio.2016.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/09/2016] [Accepted: 08/11/2016] [Indexed: 11/23/2022]
Abstract
Cyanobacteria are photosynthetic prokaryotes that are considered biotechnologically prominent organisms for production of high-value compounds. Cyanobacteria are subject to high-light intensities, which is a challenge that needs to be addressed in design of efficient bio-engineered photosynthetic organisms. Dps proteins are members of the ferritin superfamily and are omnipresent in prokaryotes. They play a major role in oxidative stress protection and iron homeostasis. The filamentous, heterocyst-forming Nostoc punctiforme, has five Dps proteins. In this study we elucidated the role of these Dps proteins in acclimation to high light intensity, the gene loci organization and the transcriptional regulation of all five dps genes in N. punctiforme was revealed, and dps-deletion mutant strains were used in physiological characterization. Two mutants defective in Dps2 and Dps5 activity displayed a reduced fitness under increased illumination, as well as a differential Photosystem (PS) stoichiometry, with an elevated Photosystem II to Photosystem I ratio in the dps5 deletion strain. This work establishes a Dps-mediated link between light tolerance, H2O2 detoxification, and iron homeostasis, and provides further evidence on the non-redundant role of multiple Dps proteins in this multicellular cyanobacterium.
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119
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Shi C, Wang S, Xia EH, Jiang JJ, Zeng FC, Gao LZ. Full transcription of the chloroplast genome in photosynthetic eukaryotes. Sci Rep 2016; 6:30135. [PMID: 27456469 PMCID: PMC4960489 DOI: 10.1038/srep30135] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 06/28/2016] [Indexed: 11/09/2022] Open
Abstract
Prokaryotes possess a simple genome transcription system that is different from that of eukaryotes. In chloroplasts (plastids), it is believed that the prokaryotic gene transcription features govern genome transcription. However, the polycistronic operon transcription model cannot account for all the chloroplast genome (plastome) transcription products at whole-genome level, especially regarding various RNA isoforms. By systematically analyzing transcriptomes of plastids of algae and higher plants, and cyanobacteria, we find that the entire plastome is transcribed in photosynthetic green plants, and that this pattern originated from prokaryotic cyanobacteria - ancestor of the chloroplast genomes that diverged about 1 billion years ago. We propose a multiple arrangement transcription model that multiple transcription initiations and terminations combine haphazardly to accomplish the genome transcription followed by subsequent RNA processing events, which explains the full chloroplast genome transcription phenomenon and numerous functional and/or aberrant pre-RNAs. Our findings indicate a complex prokaryotic genome regulation when processing primary transcripts.
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Affiliation(s)
- Chao Shi
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650204, China.,University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Shuo Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650093, China
| | - En-Hua Xia
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650204, China.,University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Jian-Jun Jiang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650093, China
| | - Fan-Chun Zeng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650093, China
| | - Li-Zhi Gao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650204, China.,Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650093, China
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120
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Galmozzi CV, Florencio FJ, Muro-Pastor MI. The Cyanobacterial Ribosomal-Associated Protein LrtA Is Involved in Post-Stress Survival in Synechocystis sp. PCC 6803. PLoS One 2016; 11:e0159346. [PMID: 27442126 PMCID: PMC4956104 DOI: 10.1371/journal.pone.0159346] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 06/30/2016] [Indexed: 02/06/2023] Open
Abstract
A light-repressed transcript encodes the LrtA protein in cyanobacteria. We show that half-life of lrtA transcript from Synechocystis sp. PCC 6803 is higher in dark-treated cells as compared to light-grown cells, suggesting post-transcriptional control of lrtA expression. The lrtA 5´ untranslated leader region is involved in that darkness-dependent regulation. We also found that Synechocystis sp. PCC 6803 LrtA is a ribosome-associated protein present in both 30S and 70S ribosomal particles. In order to investigate the function of this protein we have constructed a deletion mutant of the lrtA gene. Cells lacking LrtA (∆lrtA) had significantly lower amount of 70S particles and a greater amount of 30S and 50S particles, suggesting a role of LrtA in stabilizing 70S particles. Synechocystis strains with different amounts of LrtA protein: wild-type, ∆lrtA, and LrtAS (overexpressing lrtA) showed no differences in their growth rate under standard laboratory conditions. However, a clear LrtA dose-dependent effect was observed in the presence of the antibiotic tylosin, being the LrtAS strains the most sensitive. Similar results were obtained under hyperosmotic stress caused by sorbitol. Conversely, after prolonged periods of starvation, ∆lrtA strains were delayed in their growth with respect to the wild-type and the LrtAS strains. A positive role of LrtA protein in post-stress survival is proposed.
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Affiliation(s)
- Carla V. Galmozzi
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Francisco J. Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, Spain
| | - M. Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, Spain
- * E-mail:
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121
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Asplund-Samuelsson J, Sundh J, Dupont CL, Allen AE, McCrow JP, Celepli NA, Bergman B, Ininbergs K, Ekman M. Diversity and Expression of Bacterial Metacaspases in an Aquatic Ecosystem. Front Microbiol 2016; 7:1043. [PMID: 27458440 PMCID: PMC4933709 DOI: 10.3389/fmicb.2016.01043] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/22/2016] [Indexed: 11/13/2022] Open
Abstract
Metacaspases are distant homologs of metazoan caspase proteases, implicated in stress response, and programmed cell death (PCD) in bacteria and phytoplankton. While the few previous studies on metacaspases have relied on cultured organisms and sequenced genomes, no studies have focused on metacaspases in a natural setting. We here present data from the first microbial community-wide metacaspase survey; performed by querying metagenomic and metatranscriptomic datasets from the brackish Baltic Sea, a water body characterized by pronounced environmental gradients and periods of massive cyanobacterial blooms. Metacaspase genes were restricted to ~4% of the bacteria, taxonomically affiliated mainly to Bacteroidetes, Alpha- and Betaproteobacteria and Cyanobacteria. The gene abundance was significantly higher in larger or particle-associated bacteria (>0.8 μm), and filamentous Cyanobacteria dominated metacaspase gene expression throughout the bloom season. Distinct seasonal expression patterns were detected for the three metacaspase genes in Nodularia spumigena, one of the main bloom-formers. Clustering of normalized gene expression in combination with analyses of genomic and assembly data suggest functional diversification of these genes, and possible roles of the metacaspase genes related to stress responses, i.e., sulfur metabolism in connection to oxidative stress, and nutrient stress induced cellular differentiation. Co-expression of genes encoding metacaspases and nodularin toxin synthesis enzymes was also observed in Nodularia spumigena. The study shows that metacaspases represent an adaptation of potentially high importance for several key organisms in the Baltic Sea, most prominently Cyanobacteria, and open up for further exploration of their physiological roles in microbes and assessment of their ecological impact in aquatic habitats.
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Affiliation(s)
- Johannes Asplund-Samuelsson
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - John Sundh
- Science for Life Laboratory, Department of Biology and Environmental Science, Linnaeus UniversitySolna, Sweden
| | - Chris L. Dupont
- Microbial and Environmental Genomics, J. Craig Venter InstituteSan Diego, CA, USA
| | - Andrew E. Allen
- Microbial and Environmental Genomics, J. Craig Venter InstituteSan Diego, CA, USA
| | - John P. McCrow
- Microbial and Environmental Genomics, J. Craig Venter InstituteSan Diego, CA, USA
| | - Narin A. Celepli
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - Birgitta Bergman
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - Karolina Ininbergs
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - Martin Ekman
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
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122
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López-Igual R, Wilson A, Leverenz RL, Melnicki MR, Bourcier de Carbon C, Sutter M, Turmo A, Perreau F, Kerfeld CA, Kirilovsky D. Different Functions of the Paralogs to the N-Terminal Domain of the Orange Carotenoid Protein in the Cyanobacterium Anabaena sp. PCC 7120. PLANT PHYSIOLOGY 2016; 171:1852-66. [PMID: 27208286 PMCID: PMC4936580 DOI: 10.1104/pp.16.00502] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/11/2016] [Indexed: 05/16/2023]
Abstract
The photoactive Orange Carotenoid Protein (OCP) is involved in cyanobacterial photoprotection. Its N-terminal domain (NTD) is responsible for interaction with the antenna and induction of excitation energy quenching, while the C-terminal domain is the regulatory domain that senses light and induces photoactivation. In most nitrogen-fixing cyanobacterial strains, there are one to four paralogous genes coding for homologs to the NTD of the OCP. The functions of these proteins are unknown. Here, we study the expression, localization, and function of these genes in Anabaena sp. PCC 7120. We show that the four genes present in the genome are expressed in both vegetative cells and heterocysts but do not seem to have an essential role in heterocyst formation. This study establishes that all four Anabaena NTD-like proteins can bind a carotenoid and the different paralogs have distinct functions. Surprisingly, only one paralog (All4941) was able to interact with the antenna and to induce permanent thermal energy dissipation. Two of the other Anabaena paralogs (All3221 and Alr4783) were shown to be very good singlet oxygen quenchers. The fourth paralog (All1123) does not seem to be involved in photoprotection. Structural homology modeling allowed us to propose specific features responsible for the different functions of these soluble carotenoid-binding proteins.
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Affiliation(s)
- Rocío López-Igual
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);Institut de Biologie et Technologies de Saclay (iBiTec-S), Commissariat à l'Energie Atomique, 91191 Gif-sur-Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (R.L.L., M.S., A.T., C.A.K.);Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (M.R.M., C.A.K.);Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (M.R.M., M.S., C.A.K.); andINRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, F-78026 Versailles, France (F.P.)
| | - Adjélé Wilson
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);Institut de Biologie et Technologies de Saclay (iBiTec-S), Commissariat à l'Energie Atomique, 91191 Gif-sur-Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (R.L.L., M.S., A.T., C.A.K.);Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (M.R.M., C.A.K.);Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (M.R.M., M.S., C.A.K.); andINRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, F-78026 Versailles, France (F.P.)
| | - Ryan L Leverenz
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);Institut de Biologie et Technologies de Saclay (iBiTec-S), Commissariat à l'Energie Atomique, 91191 Gif-sur-Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (R.L.L., M.S., A.T., C.A.K.);Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (M.R.M., C.A.K.);Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (M.R.M., M.S., C.A.K.); andINRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, F-78026 Versailles, France (F.P.)
| | - Matthew R Melnicki
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);Institut de Biologie et Technologies de Saclay (iBiTec-S), Commissariat à l'Energie Atomique, 91191 Gif-sur-Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (R.L.L., M.S., A.T., C.A.K.);Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (M.R.M., C.A.K.);Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (M.R.M., M.S., C.A.K.); andINRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, F-78026 Versailles, France (F.P.)
| | - Céline Bourcier de Carbon
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);Institut de Biologie et Technologies de Saclay (iBiTec-S), Commissariat à l'Energie Atomique, 91191 Gif-sur-Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (R.L.L., M.S., A.T., C.A.K.);Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (M.R.M., C.A.K.);Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (M.R.M., M.S., C.A.K.); andINRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, F-78026 Versailles, France (F.P.)
| | - Markus Sutter
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);Institut de Biologie et Technologies de Saclay (iBiTec-S), Commissariat à l'Energie Atomique, 91191 Gif-sur-Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (R.L.L., M.S., A.T., C.A.K.);Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (M.R.M., C.A.K.);Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (M.R.M., M.S., C.A.K.); andINRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, F-78026 Versailles, France (F.P.)
| | - Aiko Turmo
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);Institut de Biologie et Technologies de Saclay (iBiTec-S), Commissariat à l'Energie Atomique, 91191 Gif-sur-Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (R.L.L., M.S., A.T., C.A.K.);Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (M.R.M., C.A.K.);Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (M.R.M., M.S., C.A.K.); andINRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, F-78026 Versailles, France (F.P.)
| | - François Perreau
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);Institut de Biologie et Technologies de Saclay (iBiTec-S), Commissariat à l'Energie Atomique, 91191 Gif-sur-Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (R.L.L., M.S., A.T., C.A.K.);Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (M.R.M., C.A.K.);Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (M.R.M., M.S., C.A.K.); andINRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, F-78026 Versailles, France (F.P.)
| | - Cheryl A Kerfeld
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);Institut de Biologie et Technologies de Saclay (iBiTec-S), Commissariat à l'Energie Atomique, 91191 Gif-sur-Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (R.L.L., M.S., A.T., C.A.K.);Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (M.R.M., C.A.K.);Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (M.R.M., M.S., C.A.K.); andINRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, F-78026 Versailles, France (F.P.)
| | - Diana Kirilovsky
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);Institut de Biologie et Technologies de Saclay (iBiTec-S), Commissariat à l'Energie Atomique, 91191 Gif-sur-Yvette, France (R.L.-I., A.W., C.B.d.C., D.K.);MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (R.L.L., M.S., A.T., C.A.K.);Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (M.R.M., C.A.K.);Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (M.R.M., M.S., C.A.K.); andINRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, F-78026 Versailles, France (F.P.)
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D'Arrigo I, Bojanovič K, Yang X, Holm Rau M, Long KS. Genome-wide mapping of transcription start sites yields novel insights into the primary transcriptome ofPseudomonas putida. Environ Microbiol 2016; 18:3466-3481. [DOI: 10.1111/1462-2920.13326] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/01/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Isotta D'Arrigo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Klara Bojanovič
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Xiaochen Yang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Martin Holm Rau
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Katherine S. Long
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
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Li X, Dreher TW, Li R. An overview of diversity, occurrence, genetics and toxin production of bloom-forming Dolichospermum (Anabaena) species. HARMFUL ALGAE 2016; 54:54-68. [PMID: 28073482 DOI: 10.1016/j.hal.2015.10.015] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 10/19/2015] [Accepted: 10/24/2015] [Indexed: 05/12/2023]
Abstract
The new genus name Dolichospermum, for most of the planktonic former members of the genus Anabaena, is one of the most ubiquitous bloom-forming cyanobacterial genera. Its dominance and persistence have increased in recent years, due to eutrophication from anthropogenic activities and global climate change. Blooms of Dolichospermum species, with their production of secondary metabolites that commonly include toxins, present a worldwide threat to environmental and public health. In this review, recent advances of the genus Dolichospermum are summarized, including taxonomy, genetics, bloom occurrence, and production of toxin and taste-and-odor compounds. The recent and continuing acquisition of genome sequences is ushering in new methods for monitoring and understanding the factors regulating bloom dynamics.
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Affiliation(s)
- Xiaochuang Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Theo W Dreher
- Department of Microbiology, Oregon State University, Corvallis, OR, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA
| | - Renhui Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China.
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125
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Mutation of the murC and murB Genes Impairs Heterocyst Differentiation in Anabaena sp. Strain PCC 7120. J Bacteriol 2016; 198:1196-206. [PMID: 26811320 DOI: 10.1128/jb.01027-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 01/20/2016] [Indexed: 01/04/2023] Open
Abstract
UNLABELLED To stabilize cellular integrity in the face of environmental perturbations, most bacteria, including cyanobacteria, synthesize and maintain a strong, flexible, three-dimensional peptidoglycan lattice. Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium capable of differentiating morphologically distinct nitrogen-fixing heterocyst cells in a periodic pattern. While heterocyst development has been shown to require proper peptidoglycan remodeling, the role of peptidoglycan synthesis has remained unclear. Here we report the identification of two peptidoglycan synthesis genes, murC (alr5065) and murB (alr5066), as required for heterocyst development. The murC and murB genes are predicted to encode a UDP-N-acetylmuramate:L-alanine ligase and a UDP-N-acetylenolpyruvoylglucosamine reductase, respectively, and we confirm enzymatic function through complementation of Escherichia coli strains deficient for these enzymes. Cells depleted of either murC or murB expression failed to differentiate heterocysts under normally inducing conditions and displayed decreased filament integrity. To identify the stage(s) of development affected by murC or murB depletion, the spatial distribution of expression of the patterning marker gene, patS, was examined. Whereas murB depletion did not affect the pattern of patS expression, murC depletion led to aberrant expression of patS in all cells of the filament. Finally, expression of gfp controlled by the region of DNA immediately upstream of murC was enriched in differentiating cells and was repressed by the transcription factor NtcA. Collectively, the data in this work provide evidence for a direct link between peptidoglycan synthesis and the maintenance of a biological pattern in a multicellular organism. IMPORTANCE Multicellular organisms that differentiate specialized cells must regulate morphological changes such that both cellular integrity and the dissemination of developmental signals are preserved. Here we show that the multicellular bacterium Anabaena, which differentiates a periodic pattern of specialized heterocyst cells, requires peptidoglycan synthesis by the murine ligase genes murC (alr5065) and murB (alr5066) for maintenance of patterned gene expression, filament integrity, and overall development. This work highlights the significant influence that intracellular structure and intercellular connections can have on the execution of a developmental program.
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126
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Brenes-Álvarez M, Olmedo-Verd E, Vioque A, Muro-Pastor AM. Identification of Conserved and Potentially Regulatory Small RNAs in Heterocystous Cyanobacteria. Front Microbiol 2016; 7:48. [PMID: 26870012 PMCID: PMC4734099 DOI: 10.3389/fmicb.2016.00048] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/12/2016] [Indexed: 12/13/2022] Open
Abstract
Small RNAs (sRNAs) are a growing class of non-protein-coding transcripts that participate in the regulation of virtually every aspect of bacterial physiology. Heterocystous cyanobacteria are a group of photosynthetic organisms that exhibit multicellular behavior and developmental alternatives involving specific transcriptomes exclusive of a given physiological condition or even a cell type. In the context of our ongoing effort to understand developmental decisions in these organisms we have undertaken an approach to the global identification of sRNAs. Using differential RNA-Seq we have previously identified transcriptional start sites for the model heterocystous cyanobacterium Nostoc sp. PCC 7120. Here we combine this dataset with a prediction of Rho-independent transcriptional terminators and an analysis of phylogenetic conservation of potential sRNAs among 89 available cyanobacterial genomes. In contrast to predictive genome-wide approaches, the use of an experimental dataset comprising all active transcriptional start sites (differential RNA-Seq) facilitates the identification of bona fide sRNAs. The output of our approach is a dataset of predicted potential sRNAs in Nostoc sp. PCC 7120, with different degrees of phylogenetic conservation across the 89 cyanobacterial genomes analyzed. Previously described sRNAs appear among the predicted sRNAs, demonstrating the performance of the algorithm. In addition, new predicted sRNAs are now identified that can be involved in regulation of different aspects of cyanobacterial physiology, including adaptation to nitrogen stress, the condition that triggers differentiation of heterocysts (specialized nitrogen-fixing cells). Transcription of several predicted sRNAs that appear exclusively in the genomes of heterocystous cyanobacteria is experimentally verified by Northern blot. Cell-specific transcription of one of these sRNAs, NsiR8 (nitrogen stress-induced RNA 8), in developing heterocysts is also demonstrated.
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Affiliation(s)
- Manuel Brenes-Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla Sevilla, Spain
| | - Elvira Olmedo-Verd
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla Sevilla, Spain
| | - Agustín Vioque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla Sevilla, Spain
| | - Alicia M Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla Sevilla, Spain
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Higo A, Isu A, Fukaya Y, Hisabori T. Efficient Gene Induction and Endogenous Gene Repression Systems for the Filamentous Cyanobacterium Anabaena sp. PCC 7120. PLANT & CELL PHYSIOLOGY 2016; 57:387-396. [PMID: 26684202 DOI: 10.1093/pcp/pcv202] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/15/2015] [Indexed: 06/05/2023]
Abstract
In the last decade, many studies have been conducted to employ genetically engineered cyanobacteria in the production of various metabolites. However, the lack of a strict gene regulation system in cyanobacteria has hampered these attempts. The filamentous cyanobacterium Anabaena sp. PCC 7120 performs both nitrogen and carbon fixation and is, therefore, a good candidate organism for such production. To employ Anabaena cells for this purpose, we intended to develop artificial gene regulation systems to alter the cell metabolic pathways efficiently. We introduced into Anabaena a transcriptional repressor TetR, widely used in diverse organisms, and green fluorescent protein (GFP) as a reporter. We found that anhydrotetracycline (aTc) substantially induced GFP fluorescence in a concentration-dependent manner. By expressing tetR under the nitrate-specific promoter nirA, we successfully reduced the concentration of aTc required for the induction of gfp under nitrogen fixation conditions (to 10% of the concentration needed under nitrate-replete conditions). Further, we succeeded in the overexpression of GFP by depletion of nitrate without the inducer by means of promoter engineering of the nirA promoter. Moreover, we applied these gene regulation systems to a metabolic enzyme in Anabaena and successfully repressed glnA, the gene encoding glutamine synthetase that is essential for nitrogen assimilation in cyanobacteria, by expressing the small antisense RNA for glnA. Consequently, the ammonium production of an ammonium-excreting Anabaena mutant was significantly enhanced. We therefore conclude that the gene regulation systems developed in this study are useful tools for the regulation of metabolic enzymes and will help to increase the production of desired substances in Anabaena.
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Affiliation(s)
- Akiyoshi Higo
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-ku, Yokohama, 226-8503 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, 102-0075 Japan
| | - Atsuko Isu
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-ku, Yokohama, 226-8503 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, 102-0075 Japan
| | - Yuki Fukaya
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-ku, Yokohama, 226-8503 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, 102-0075 Japan
| | - Toru Hisabori
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-ku, Yokohama, 226-8503 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, 102-0075 Japan
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128
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Valladares A, Flores E, Herrero A. The heterocyst differentiation transcriptional regulator HetR of the filamentous cyanobacteriumAnabaenaforms tetramers and can be regulated by phosphorylation. Mol Microbiol 2015; 99:808-19. [DOI: 10.1111/mmi.13268] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Ana Valladares
- Instituto de Bioquímica Vegetal y Fotosíntesis; Consejo Superior de Investigaciones Científicas; Universidad de Sevilla; Américo Vespucio 49 E-41092 Seville Spain
| | - Enrique Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis; Consejo Superior de Investigaciones Científicas; Universidad de Sevilla; Américo Vespucio 49 E-41092 Seville Spain
| | - Antonia Herrero
- Instituto de Bioquímica Vegetal y Fotosíntesis; Consejo Superior de Investigaciones Científicas; Universidad de Sevilla; Américo Vespucio 49 E-41092 Seville Spain
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129
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Structural insights into HetR-PatS interaction involved in cyanobacterial pattern formation. Sci Rep 2015; 5:16470. [PMID: 26576507 PMCID: PMC4649674 DOI: 10.1038/srep16470] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/12/2015] [Indexed: 01/07/2023] Open
Abstract
The one-dimensional pattern of heterocyst in the model cyanobacterium Anabaena sp. PCC 7120 is coordinated by the transcription factor HetR and PatS peptide. Here we report the complex structures of HetR binding to DNA, and its hood domain (HetRHood) binding to a PatS-derived hexapeptide (PatS6) at 2.80 and 2.10 Å, respectively. The intertwined HetR dimer possesses a couple of novel HTH motifs, each of which consists of two canonical α-helices in the DNA-binding domain and an auxiliary α-helix from the flap domain of the neighboring subunit. Two PatS6 peptides bind to the lateral clefts of HetRHood, and trigger significant conformational changes of the flap domain, resulting in dissociation of the auxiliary α-helix and eventually release of HetR from the DNA major grove. These findings provide the structural insights into a prokaryotic example of Turing model.
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130
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The sRNA NsiR4 is involved in nitrogen assimilation control in cyanobacteria by targeting glutamine synthetase inactivating factor IF7. Proc Natl Acad Sci U S A 2015; 112:E6243-52. [PMID: 26494284 DOI: 10.1073/pnas.1508412112] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Glutamine synthetase (GS), a key enzyme in biological nitrogen assimilation, is regulated in multiple ways in response to varying nitrogen sources and levels. Here we show a small regulatory RNA, NsiR4 (nitrogen stress-induced RNA 4), which plays an important role in the regulation of GS in cyanobacteria. NsiR4 expression in the unicellular Synechocystis sp. PCC 6803 and in the filamentous, nitrogen-fixing Anabaena sp. PCC 7120 is stimulated through nitrogen limitation via NtcA, the global transcriptional regulator of genes involved in nitrogen metabolism. NsiR4 is widely conserved throughout the cyanobacterial phylum, suggesting a conserved function. In silico target prediction, transcriptome profiling on pulse overexpression, and site-directed mutagenesis experiments using a heterologous reporter system showed that NsiR4 interacts with the 5'UTR of gifA mRNA, which encodes glutamine synthetase inactivating factor (IF)7. In Synechocystis, we observed an inverse relationship between the levels of NsiR4 and the accumulation of IF7 in vivo. This NsiR4-dependent modulation of gifA (IF7) mRNA accumulation influenced the glutamine pool and thus [Formula: see text] assimilation via GS. As a second target, we identified ssr1528, a hitherto uncharacterized nitrogen-regulated gene. Competition experiments between WT and an ΔnsiR4 KO mutant showed that the lack of NsiR4 led to decreased acclimation capabilities of Synechocystis toward oscillating nitrogen levels. These results suggest a role for NsiR4 in the regulation of nitrogen metabolism in cyanobacteria, especially for the adaptation to rapid changes in available nitrogen sources and concentrations. NsiR4 is, to our knowledge, the first identified bacterial sRNA regulating the primary assimilation of a macronutrient.
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131
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Stazic D, Voß B. The complexity of bacterial transcriptomes. J Biotechnol 2015; 232:69-78. [PMID: 26450562 DOI: 10.1016/j.jbiotec.2015.09.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/07/2015] [Accepted: 09/29/2015] [Indexed: 01/09/2023]
Abstract
For eukaryotes there seems to be no doubt that differences on the trancriptomic level substantially contribute to the process of species diversification, whereas for bacteria this is thought to be less important. Recent years saw a significant increase in full transcriptome studies for bacteria, which provided deep insight into the architecture of bacterial transcriptomes. Most notably, it became evident that, in contrast to previous scientific consensus, bacterial transcriptomes are quite complex. There exist a large number of cis-antisense RNAs, non-coding RNAs, overlapping transcripts and RNA elements that regulate transcription, such as riboswitches. Furthermore, processing and degradation of RNA has gained interest, because it has a significant impact on the composition of the transcriptome. In this review, we summarize recent findings and put them into a broader context with respect to the complexity of bacterial transcriptomes and its putative biological meanings.
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Affiliation(s)
- D Stazic
- University of Freiburg, Faculty of Biology, Computational Transcriptomics, Schänzlestr. 1, 79104 Freiburg, Germany.
| | - B Voß
- University of Freiburg, Faculty of Biology, Computational Transcriptomics, Schänzlestr. 1, 79104 Freiburg, Germany.
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132
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Yingping F, Lemeille S, González A, Risoul V, Denis Y, Richaud P, Lamrabet O, Fillat MF, Zhang CC, Latifi A. The Pkn22 Ser/Thr kinase in Nostoc PCC 7120: role of FurA and NtcA regulators and transcript profiling under nitrogen starvation and oxidative stress. BMC Genomics 2015. [PMID: 26220092 PMCID: PMC4518582 DOI: 10.1186/s12864-015-1703-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background The filamentous cyanobacterium Nostoc sp. strain PCC 7120 can fix N2 when combined nitrogen is not available. Furthermore, it has to cope with reactive oxygen species generated as byproducts of photosynthesis and respiration. We have previously demonstrated the synthesis of Ser/Thr kinase Pkn22 as an important survival response of Nostoc to oxidative damage. In this study we wished to investigate the possible involvement of this kinase in signalling peroxide stress and nitrogen deprivation. Results Quantitative RT-PCR experiments revealed that the pkn22 gene is induced in response to peroxide stress and to combined nitrogen starvation. Electrophoretic motility assays indicated that the pkn22 promoter is recognized by the global transcriptional regulators FurA and NtcA. Transcriptomic analysis comparing a pkn22-insertion mutant and the wild type strain indicated that this kinase regulates genes involved in important cellular functions such as photosynthesis, carbon metabolism and iron acquisition. Since metabolic changes may lead to oxidative stress, we investigated whether this is the case with nitrogen starvation. Our results rather invalidate this hypothesis thereby suggesting that the function of Pkn22 under nitrogen starvation is independent of its role in response to peroxide stress. Conclusions Our analyses have permitted a more complete functional description of Ser/Thr kinase in Nostoc. We have decrypted the transcriptional regulation of the pkn22 gene, and analysed the whole set of genes under the control of this kinase in response to the two environmental changes often encountered by cyanobacteria in their natural habitat: oxidative stress and nitrogen deprivation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1703-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fan Yingping
- Aix-Marseille University and CNRS, Laboratoire de Chimie Bactérienne - UMR7283, IMM, 31 Chemin Joseph Aiguier, 13402, Marseille cedex 20, France.
| | - Sylvain Lemeille
- Department of Microbiology and Molecular Medicine, CMU, Medical Faculty, University of Geneva, Genève, 1211, Switzerland.
| | - Andrés González
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009, Zaragoza, Spain.
| | - Véronique Risoul
- Aix-Marseille University and CNRS, Laboratoire de Chimie Bactérienne - UMR7283, IMM, 31 Chemin Joseph Aiguier, 13402, Marseille cedex 20, France.
| | - Yann Denis
- Plate-forme Transcriptome FR3479, IMM-CNRS, Marseille, France.
| | - Pierre Richaud
- CEA, DSV, IBEB, SBVME, Saint-Paul-lez-Durance, F-13108, France. .,CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France. .,Aix Marseille Université, BVME UMR7265, Marseille, F-13284, France.
| | - Otmane Lamrabet
- Aix-Marseille University and CNRS, Laboratoire de Chimie Bactérienne - UMR7283, IMM, 31 Chemin Joseph Aiguier, 13402, Marseille cedex 20, France.
| | - Maria F Fillat
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009, Zaragoza, Spain.
| | - Cheng-Cai Zhang
- Aix-Marseille University and CNRS, Laboratoire de Chimie Bactérienne - UMR7283, IMM, 31 Chemin Joseph Aiguier, 13402, Marseille cedex 20, France.
| | - Amel Latifi
- Aix-Marseille University and CNRS, Laboratoire de Chimie Bactérienne - UMR7283, IMM, 31 Chemin Joseph Aiguier, 13402, Marseille cedex 20, France.
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ABC Transporter Required for Intercellular Transfer of Developmental Signals in a Heterocystous Cyanobacterium. J Bacteriol 2015; 197:2685-93. [PMID: 26055115 DOI: 10.1128/jb.00304-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/03/2015] [Indexed: 01/20/2023] Open
Abstract
UNLABELLED In the filamentous cyanobacterium Anabaena, patS and hetN encode peptide-derived signals with many of the properties of morphogens. These signals regulate the formation of a periodic pattern of heterocysts by lateral inhibition of differentiation. Here we show that intercellular transfer of the patS- and hetN-dependent developmental signals from heterocysts to vegetative cells requires HetC, a predicted ATP-binding cassette transporter (ABC transporter). Relative to the wild type, in a hetC mutant differentiation resulted in a reduced number of heterocysts that were incapable of nitrogen fixation, but deletion of patS or hetN restored heterocyst number and function in a hetC background. These epistasis results suggest that HetC is necessary for conferring self-immunity to the inhibitors on differentiating cells. Nine hours after induction of differentiation, HetC was required for neither induction of transcription of patS nor intercellular transfer of the patS-encoded signal to neighboring cells. Conversely, in strains lacking HetC, the patS- and hetN-encoded signals were not transferred from heterocyst cells to adjacent vegetative cells. The results support a model in which the patS-dependent signal is initially transferred between vegetative cells in a HetC-independent fashion, but some time before morphological differentiation of heterocysts is complete, transfer of both signals transitions to a HetC-dependent process. IMPORTANCE How chemical cues that regulate pattern formation in multicellular organisms move from one cell to another is a central question in developmental biology. In this study, we show that an ABC transporter, HetC, is necessary for transport of two developmental signals between different types of cells in a filamentous cyanobacterium. ABC transporters are found in organisms as diverse as bacteria and humans and, as the name implies, are often involved in the transport of molecules across a cellular membrane. The activity of HetC was shown to be required for signaling between heterocysts, which supply fixed nitrogen to the organism, and other cells, as well as for conferring immunity to self-signaling on developing heterocysts.
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Singh PK, Shrivastava AK, Chatterjee A, Pandey S, Rai S, Singh S, Rai LC. Cadmium toxicity in diazotrophic Anabaena spp. adjudged by hasty up-accumulation of transporter and signaling and severe down-accumulation of nitrogen metabolism proteins. J Proteomics 2015; 127:134-46. [PMID: 26021478 DOI: 10.1016/j.jprot.2015.05.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/29/2015] [Accepted: 05/20/2015] [Indexed: 10/23/2022]
Abstract
Present study demonstrates interspecies variation in proteome and survival strategy of three Anabaena species i.e., Anabaena L31, Anabaena sp. PCC 7120 and Anabaena doliolum subjected to respective LC50 doses of Cd at 0, 1, 3, 5 and 7day intervals. The proteome coverage with 452 differentially accumulated proteins unveiled species and time specific expression and interaction network of proteins involved in important cellular functions. Statistical analysis of protein abundance across Cd-treated proteomes clustered their co-expression pattern into four groups viz., (i) early (days 1 and 3) accumulated proteins, (ii) proteins up-accumulated for longer duration, (iii) late (days 5 and 7) accumulated proteins, and (iv) mostly down-accumulated proteins. Appreciable growth of Cd treated A L31 over other two species may be ascribed to proteins contained in the first and second groups (belonging to energy and carbohydrate metabolism (TK, G6-PI, PGD, FBA, PPA, ATP synthase)), sulfur metabolism (GR, GST, PGDH, PAPS reductase, GDC-P, and SAM synthetase), fatty acid metabolism (AspD, PspA, SQD-1), phosphorous metabolism (PhoD, PstB and SQD1), molecular chaperones (Gro-EL, FKBP-type peptidylprolyl isomerase), and antioxidative defense enzymes (SOD-A, catalase). Anabaena sp. PCC 7120 harboring proteins largely from the third group qualified as a late accumulator and A. doliolum housing majority of proteins from the fourth group emerged as the most sensitive species. Thus early up-accumulation of transporter and signaling category proteins and drastic reduction of nitrogen assimilation proteins could be taken as a vital indicator of cadmium toxicity in Anabaena spp. This article is part of a Special Issue entitled: Proteomics in India.
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Affiliation(s)
- Prashant Kumar Singh
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Alok Kumar Shrivastava
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Antra Chatterjee
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Sarita Pandey
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Snigdha Rai
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Shilpi Singh
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - L C Rai
- Molecular Biology Section, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India.
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135
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Induction of the Nitrate Assimilation nirA Operon and Protein-Protein Interactions in the Maturation of Nitrate and Nitrite Reductases in the Cyanobacterium Anabaena sp. Strain PCC 7120. J Bacteriol 2015; 197:2442-52. [PMID: 25962912 DOI: 10.1128/jb.00198-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/05/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Nitrate is widely used as a nitrogen source by cyanobacteria, in which the nitrate assimilation structural genes frequently constitute the so-called nirA operon. This operon contains the genes encoding nitrite reductase (nirA), a nitrate/nitrite transporter (frequently an ABC-type transporter; nrtABCD), and nitrate reductase (narB). In the model filamentous cyanobacterium Anabaena sp. strain PCC 7120, which can fix N2 in specialized cells termed heterocysts, the nirA operon is expressed at high levels only in media containing nitrate or nitrite and lacking ammonium, a preferred nitrogen source. Here we examined the genes downstream of the nirA operon in Anabaena and found that a small open reading frame of unknown function, alr0613, can be cotranscribed with the operon. The next gene in the genome, alr0614 (narM), showed an expression pattern similar to that of the nirA operon, implying correlated expression of narM and the operon. A mutant of narM with an insertion mutation failed to produce nitrate reductase activity, consistent with the idea that NarM is required for the maturation of NarB. Both narM and narB mutants were impaired in the nitrate-dependent induction of the nirA operon, suggesting that nitrite is an inducer of the operon in Anabaena. It has previously been shown that the nitrite reductase protein NirA requires NirB, a protein likely involved in protein-protein interactions, to attain maximum activity. Bacterial two-hybrid analysis confirmed possible NirA-NirB and NarB-NarM interactions, suggesting that the development of both nitrite reductase and nitrate reductase activities in cyanobacteria involves physical interaction of the corresponding enzymes with their cognate partners, NirB and NarM, respectively. IMPORTANCE Nitrate is an important source of nitrogen for many microorganisms that is utilized through the nitrate assimilation system, which includes nitrate/nitrite membrane transporters and the nitrate and nitrite reductases. Many cyanobacteria assimilate nitrate, but regulation of the nitrate assimilation system varies in different cyanobacterial groups. In the N2-fixing, heterocyst-forming cyanobacteria, the nirA operon, which includes the structural genes for the nitrate assimilation system, is expressed in the presence of nitrate or nitrite if ammonium is not available to the cells. Here we studied the genes required for production of an active nitrate reductase, providing information on the nitrate-dependent induction of the operon, and found evidence for possible protein-protein interactions in the maturation of nitrate reductase and nitrite reductase.
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136
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Kopf M, Hess WR. Regulatory RNAs in photosynthetic cyanobacteria. FEMS Microbiol Rev 2015; 39:301-15. [PMID: 25934122 PMCID: PMC6596454 DOI: 10.1093/femsre/fuv017] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/06/2015] [Accepted: 03/10/2015] [Indexed: 12/02/2022] Open
Abstract
Regulatory RNAs play versatile roles in bacteria in the coordination of gene expression during various physiological processes, especially during stress adaptation. Photosynthetic bacteria use sunlight as their major energy source. Therefore, they are particularly vulnerable to the damaging effects of excess light or UV irradiation. In addition, like all bacteria, photosynthetic bacteria must adapt to limiting nutrient concentrations and abiotic and biotic stress factors. Transcriptome analyses have identified hundreds of potential regulatory small RNAs (sRNAs) in model cyanobacteria such as Synechocystis sp. PCC 6803 or Anabaena sp. PCC 7120, and in environmentally relevant genera such as Trichodesmium, Synechococcus and Prochlorococcus. Some sRNAs have been shown to actually contain μORFs and encode short proteins. Examples include the 40-amino-acid product of the sml0013 gene, which encodes the NdhP subunit of the NDH1 complex. In contrast, the functional characterization of the non-coding sRNA PsrR1 revealed that the 131 nt long sRNA controls photosynthetic functions by targeting multiple mRNAs, providing a paradigm for sRNA functions in photosynthetic bacteria. We suggest that actuatons comprise a new class of genetic elements in which an sRNA gene is inserted upstream of a coding region to modify or enable transcription of that region.
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Affiliation(s)
- Matthias Kopf
- Faculty of Biology, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany
| | - Wolfgang R Hess
- Faculty of Biology, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany
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137
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Innocenti N, Golumbeanu M, Fouquier d'Hérouël A, Lacoux C, Bonnin RA, Kennedy SP, Wessner F, Serror P, Bouloc P, Repoila F, Aurell E. Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis. RNA (NEW YORK, N.Y.) 2015; 21:1018-30. [PMID: 25737579 PMCID: PMC4408782 DOI: 10.1261/rna.048470.114] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/22/2014] [Indexed: 05/21/2023]
Abstract
Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first snapshot of transcriptional organizations in this bacterium, we used a modified RNA-seq approach enabling to discriminate primary from processed 5' RNA ends. We also validated our approach by confirming known features in Escherichia coli. We mapped 559 transcription start sites (TSSs) and 352 processing sites (PSSs) in E. faecalis. A blind motif search retrieved canonical features of SigA- and SigN-dependent promoters preceding transcription start sites mapped. We discovered 85 novel putative regulatory RNAs, small- and antisense RNAs, and 72 transcriptional antisense organizations. Presented data constitute a significant insight into bacterial RNA landscapes and a step toward the inference of regulatory processes at transcriptional and post-transcriptional levels in a comprehensive manner.
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Affiliation(s)
- Nicolas Innocenti
- Department of Computational Biology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
| | - Monica Golumbeanu
- Department of Biosystems Science and Engineering, ETH Zürich, CH-4058, Basel, Switzerland SIB Swiss Institute of Bioinformatics, University of Basel, CH-4056, Basel, Switzerland
| | - Aymeric Fouquier d'Hérouël
- Department of Computational Biology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
| | - Caroline Lacoux
- INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
| | - Rémy A Bonnin
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS, UMR8621, F-91405, Orsay, France
| | - Sean P Kennedy
- INRA, MetaGenoPolis US1367, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
| | - Françoise Wessner
- INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
| | - Pascale Serror
- INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
| | - Philippe Bouloc
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS, UMR8621, F-91405, Orsay, France
| | - Francis Repoila
- INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Domaine de Vilvert, F-78350, Jouy-en-Josas, France
| | - Erik Aurell
- Department of Computational Biology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden Department of Information and Computer Science, Aalto University, FI-02150 Espoo, Finland
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138
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Xu C, Huang R, Teng L, Jing X, Hu J, Cui G, Wang Y, Cui Q, Xu J. Cellulosome stoichiometry in Clostridium cellulolyticum is regulated by selective RNA processing and stabilization. Nat Commun 2015; 6:6900. [PMID: 25908225 PMCID: PMC4423207 DOI: 10.1038/ncomms7900] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 03/11/2015] [Indexed: 01/23/2023] Open
Abstract
The mechanism, physiological relevance and evolutionary implication of selective RNA processing and stabilization (SRPS) remain elusive. Here we report the genome-wide maps of transcriptional start sites (TSs) and post-transcriptional processed sites (PSs) for Clostridium cellulolyticum. The PS-associated genes are preferably associated with subunits of heteromultimeric protein complexes, and the intergenic PSs (iPSs) are enriched in operons exhibiting highly skewed transcript-abundance landscape. Stem-loop structures associated with those iPSs located at 3′ termini of highly transcribed genes exhibit folding free energy negatively correlated with transcript-abundance ratio of flanking genes. In the cellulosome-encoding cip-cel operon, iPSs and stem-loops precisely regulate structure and abundance of the subunit-encoding transcripts processed from a primary polycistronic RNA, quantitatively specifying cellulosome stoichiometry. Moreover, cellulosome evolution is shaped by the number, position and biophysical nature of TSs, iPSs and stem-loops. Our findings unveil a genome-wide RNA-encoded strategy controlling in vivo stoichiometry of protein complexes. Selective RNA processing and stabilization (SRPS) can regulate bacterial operons, but the process is not well understood. Here, the authors show that the stoichiometry of cellulosome, a 12-subunit protein complex expressed from an operon in Gram-positive Clostridium cellullolyticum, is regulated by SRPS.
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Affiliation(s)
- Chenggang Xu
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Ranran Huang
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Teng
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyan Jing
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Jianqiang Hu
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guzhen Cui
- CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Yilin Wang
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Jian Xu
- Single-Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.,CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
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139
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Kopf M, Klähn S, Scholz I, Hess WR, Voß B. Variations in the non-coding transcriptome as a driver of inter-strain divergence and physiological adaptation in bacteria. Sci Rep 2015; 5:9560. [PMID: 25902393 PMCID: PMC5386190 DOI: 10.1038/srep09560] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/05/2015] [Indexed: 12/16/2022] Open
Abstract
In all studied organisms, a substantial portion of the transcriptome consists of non-coding RNAs that frequently execute regulatory functions. Here, we have compared the primary transcriptomes of the cyanobacteria Synechocystis sp. PCC 6714 and PCC 6803 under 10 different conditions. These strains share 2854 protein-coding genes and a 16S rRNA identity of 99.4%, indicating their close relatedness. Conserved major transcriptional start sites (TSSs) give rise to non-coding transcripts within the sigB gene, from the 5′UTRs of cmpA and isiA, and 168 loci in antisense orientation. Distinct differences include single nucleotide polymorphisms rendering promoters inactive in one of the strains, e.g., for cmpR and for the asRNA PsbA2R. Based on the genome-wide mapped location, regulation and classification of TSSs, non-coding transcripts were identified as the most dynamic component of the transcriptome. We identified a class of mRNAs that originate by read-through from an sRNA that accumulates as a discrete and abundant transcript while also serving as the 5′UTR. Such an sRNA/mRNA structure, which we name ‘actuaton’, represents another way for bacteria to remodel their transcriptional network. Our findings support the hypothesis that variations in the non-coding transcriptome constitute a major evolutionary element of inter-strain divergence and capability for physiological adaptation.
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Affiliation(s)
- Matthias Kopf
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Stephan Klähn
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Ingeborg Scholz
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Björn Voß
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
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140
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Li J, Qi L, Guo Y, Yue L, Li Y, Ge W, Wu J, Shi W, Dong X. Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus. Sci Rep 2015; 5:9209. [PMID: 25784521 PMCID: PMC5378194 DOI: 10.1038/srep09209] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/23/2015] [Indexed: 11/12/2022] Open
Abstract
Psychrophilic methanogenic Archaea contribute significantly to global methane emissions, but archaeal cold adaptation mechanisms remain poorly understood. Hinted by that mRNA architecture determined secondary structure respond to cold more promptly than proteins, differential RNA-seq was used in this work to examine the genome-wide transcription start sites (TSSs) of the psychrophilic methanogen Methanolobus psychrophilus R15 and its response to cold. Unlike most prokaryotic mRNAs with short 5' untranslated regions (5' UTR, median lengths of 20-40 nt), 51% mRNAs of this methanogen have large 5' UTR (>50 nt). For 24% of the mRNAs, the 5' UTR is >150 nt. This implies that post-transcriptional regulation may be significance in the psychrophile. Remarkably, 219 (14%) genes possessed multiple gene TSSs (gTSSs), and 84 genes exhibited temperature-regulated gTSS selection to express alternative 5' UTR. Primer extension studies confirmed the temperature-dependent TSS selection and a stem-loop masking of ribosome binding sites was predicted from the longer 5' UTRs, suggesting alternative 5' UTRs-mediated translation regulation in the cold adaptation as well. In addition, 195 small RNAs (sRNAs) were detected, and Northern blots confirmed that many sRNAs were induced by cold. Thus, this study revealed an integrated transcriptional and post-transcriptional regulation for cold adaptation in a psychrophilic methanogen.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing 100101, People's Republic of China
| | - Lei Qi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing 100101, People's Republic of China
| | - Yang Guo
- Novogene Bioinformatics Institute, 21st Floor, Jinma building B area, Xueqing Road, Beijing 100083, People's Republic of China
| | - Lei Yue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing 100101, People's Republic of China
| | - Yanping Li
- Novogene Bioinformatics Institute, 21st Floor, Jinma building B area, Xueqing Road, Beijing 100083, People's Republic of China
| | - Weizhen Ge
- Novogene Bioinformatics Institute, 21st Floor, Jinma building B area, Xueqing Road, Beijing 100083, People's Republic of China
| | - Jun Wu
- Novogene Bioinformatics Institute, 21st Floor, Jinma building B area, Xueqing Road, Beijing 100083, People's Republic of China
| | - Wenyuan Shi
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 10833 Le Conte Avenue, Los Angeles, CA90095, USA
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing 100101, People's Republic of China
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141
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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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142
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Kopf M, Möke F, Bauwe H, Hess WR, Hagemann M. Expression profiling of the bloom-forming cyanobacterium Nodularia CCY9414 under light and oxidative stress conditions. ISME JOURNAL 2015; 9:2139-52. [PMID: 25689027 DOI: 10.1038/ismej.2015.16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 01/08/2015] [Indexed: 11/10/2022]
Abstract
Massive blooms of toxic cyanobacteria frequently occur in the central Baltic Sea during the summer. In the surface scum, cyanobacterial cells are exposed to high light (HL) intensity, high oxygen partial pressure and other stresses. To mimic these conditions, cultures of Nodularia spumigena CCY9414, which is a strain isolated from a cyanobacterial summer bloom in the Baltic Sea, were incubated at a HL intensity of 1200 μmol photons m(-2) s(-1) or a combination of HL and increased oxygen partial pressure. Using differential RNA sequencing, we compared the global primary transcriptomes of control and stressed cells. The combination of oxidative and light stresses induced the expression of twofold more genes compared with HL stress alone. In addition to the induction of known stress-responsive genes, such as psbA, ocp and sodB, Nodularia cells activated the expression of genes coding for many previously unknown light- and oxidative stress-related proteins. In addition, the expression of non-protein-coding RNAs was found to be stimulated by these stresses. Among them was an antisense RNA to the phycocyanin-encoding mRNA cpcBAC and the trans-encoded regulator of photosystem I, PsrR1. The large genome capacity allowed Nodularia to harbor more copies of stress-relevant genes such as psbA and small chlorophyll-binding protein genes, combined with the coordinated induction of these and many additional genes for stress acclimation. Our data provide a first insight on how N. spumigena became adapted to conditions relevant for a cyanobacterial bloom in the Baltic Sea.
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Affiliation(s)
- Matthias Kopf
- Albert-Ludwigs-Universität Freiburg, Fakultät für Biologie, Genetik und Experimentelle Bioinformatik, Freiburg, Germany
| | - Fred Möke
- Universität Rostock, Institut für Biowissenschaften, Pflanzenphysiologie, Rostock, Germany
| | - Hermann Bauwe
- Universität Rostock, Institut für Biowissenschaften, Pflanzenphysiologie, Rostock, Germany
| | - Wolfgang R Hess
- Albert-Ludwigs-Universität Freiburg, Fakultät für Biologie, Genetik und Experimentelle Bioinformatik, Freiburg, Germany
| | - Martin Hagemann
- Universität Rostock, Institut für Biowissenschaften, Pflanzenphysiologie, Rostock, Germany
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143
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Ehira S, Miyazaki S. Regulation of Genes Involved in Heterocyst Differentiation in the Cyanobacterium Anabaena sp. Strain PCC 7120 by a Group 2 Sigma Factor SigC. Life (Basel) 2015; 5:587-603. [PMID: 25692906 PMCID: PMC4390870 DOI: 10.3390/life5010587] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/06/2015] [Accepted: 02/11/2015] [Indexed: 11/17/2022] Open
Abstract
The filamentous cyanobacterium Anabaena sp. strain PCC 7120 differentiates specialized cells for nitrogen fixation called heterocysts upon limitation of combined nitrogen in the medium. During heterocyst differentiation, expression of approximately 500 genes is upregulated with spatiotemporal regulation. In the present study, we investigated the functions of sigma factors of RNA polymerase in the regulation of heterocyst differentiation. The transcript levels of sigC, sigE, and sigG were increased during heterocyst differentiation, while expression of sigJ was downregulated. We carried out DNA microarray analysis to identify genes regulated by SigC, SigE, and SigG. It was indicated that SigC regulated the expression of genes involved in heterocyst differentiation and functions. Moreover, genes regulated by SigC partially overlapped with those regulated by SigE, and deficiency of SigC was likely to be compensated by SigE.
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Affiliation(s)
- Shigeki Ehira
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan.
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan.
| | - Shogo Miyazaki
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan.
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144
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Role of RNA secondary structure and processing in stability of the nifH1 transcript in the cyanobacterium Anabaena variabilis. J Bacteriol 2015; 197:1408-22. [PMID: 25666132 DOI: 10.1128/jb.02609-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED In the cyanobacterium Anabaena variabilis ATCC 29413, aerobic nitrogen fixation occurs in micro-oxic cells called heterocysts. Synthesis of nitrogenase in heterocysts requires expression of the large nif1 gene cluster, which is primarily under the control of the promoter for the first gene, nifB1. Strong expression of nifH1 requires the nifB1 promoter but is also controlled by RNA processing, which leads to increased nifH1 transcript stability. The processing of the primary nifH1 transcript occurs at the base of a predicted stem-loop structure that is conserved in many heterocystous cyanobacteria. Mutations that changed the predicted secondary structure or changed the sequence of the stem-loop had detrimental effects on the amount of nifH1 transcript, with mutations that altered or destabilized the structure having the strongest effect. Just upstream from the transcriptional processing site for nifH1 was the promoter for a small antisense RNA, sava4870.1. This RNA was more strongly expressed in cells grown in the presence of fixed nitrogen and was downregulated in cells 24 h after nitrogen step down. A mutant strain lacking the promoter for sava4870.1 showed delayed nitrogen fixation; however, that phenotype might have resulted from an effect of the mutation on the processing of the nifH1 transcript. The nifH1 transcript was the most abundant and most stable nif1 transcript, while nifD1 and nifK1, just downstream of nifH1, were present in much smaller amounts and were less stable. The nifD1 and nifK1 transcripts were also processed at sites just upstream of nifD1 and nifK1. IMPORTANCE In the filamentous cyanobacterium Anabaena variabilis, the nif1 cluster, encoding the primary Mo nitrogenase, functions under aerobic growth conditions in specialized cells called heterocysts that develop in response to starvation for fixed nitrogen. The large cluster comprising more than a dozen nif1 genes is transcribed primarily from the promoter for the first gene, nifB1; however, this does not explain the large amount of transcript for the structural genes nifH1, nifD1, and nifK1, which are also under the control of the distant nifB1 promoter. Here, we demonstrate the importance of a predicted stem-loop structure upstream of nifH1 that controls the abundance of nifH1 transcript through transcript processing and stabilization and show that nifD1 and nifK1 transcripts are also controlled by transcript processing.
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145
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Li X, Sandh G, Nenninger A, Muro-Pastor AM, Stensjö K. Differential transcriptional regulation of orthologous dps genes from two closely related heterocyst-forming cyanobacteria. FEMS Microbiol Lett 2015; 362:fnv017. [PMID: 25663155 DOI: 10.1093/femsle/fnv017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
In cyanobacteria, DNA-binding proteins from starved cells (Dps) play an important role in the cellular response to oxidative and nutritional stresses. In this study, we have characterized the cell-type specificity and the promoter regions of two orthologous dps genes, Npun_R5799 in Nostoc punctiforme and alr3808 in Anabaena sp. PCC 7120. A transcriptional start site (TSS), identical in location to the previously identified proximal TSS of alr3808, was identified for Npun_R5799 under both combined nitrogen supplemented and N2-fixing growth conditions. However, only alr3808 was also transcribed from a second distal TSS. Sequence homologies suggest that the promoter region containing the distal TSS is not conserved upstream of orthologous genes among heterocyst-forming cyanobacteria. The analysis of promoter GFP-reporter strains showed a different role in governing cell-type specificity between the proximal and distal promoter of alr3808. We here confirmed the heterocyst specificity of the distal promoter of alr3808 and described a very early induction of its expression during proheterocyst differentiation. In contrast, the complete promoters of both genes were active in all cells. Even though Npun_R5799 and alr3808 are orthologs, the regulation of their respective expression differs, indicating distinctions in the function of these cyanobacterial Dps proteins depending on the strain and cell type.
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Affiliation(s)
- Xin Li
- Microbial Chemistry, Department of Chemistry - Ångström Laboratory, Science for Life Laboratory, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Gustaf Sandh
- Microbial Chemistry, Department of Chemistry - Ångström Laboratory, Science for Life Laboratory, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Anja Nenninger
- Microbial Chemistry, Department of Chemistry - Ångström Laboratory, Science for Life Laboratory, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Alicia M Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, E-41092 Seville, Spain
| | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry - Ångström Laboratory, Science for Life Laboratory, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
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146
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Burnap RL, Hagemann M, Kaplan A. Regulation of CO2 Concentrating Mechanism in Cyanobacteria. Life (Basel) 2015; 5:348-71. [PMID: 25636131 PMCID: PMC4390856 DOI: 10.3390/life5010348] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 01/15/2015] [Accepted: 01/21/2015] [Indexed: 12/31/2022] Open
Abstract
In this chapter, we mainly focus on the acclimation of cyanobacteria to the changing ambient CO2 and discuss mechanisms of inorganic carbon (Ci) uptake, photorespiration, and the regulation among the metabolic fluxes involved in photoautotrophic, photomixotrophic and heterotrophic growth. The structural components for several of the transport and uptake mechanisms are described and the progress towards elucidating their regulation is discussed in the context of studies, which have documented metabolomic changes in response to changes in Ci availability. Genes for several of the transport and uptake mechanisms are regulated by transcriptional regulators that are in the LysR-transcriptional regulator family and are known to act in concert with small molecule effectors, which appear to be well-known metabolites. Signals that trigger changes in gene expression and enzyme activity correspond to specific "regulatory metabolites" whose concentrations depend on the ambient Ci availability. Finally, emerging evidence for an additional layer of regulatory complexity involving small non-coding RNAs is discussed.
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Affiliation(s)
- Robert L Burnap
- Department of Microbiology and Molecular Genetics, Henry Bellmon Research Center, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Martin Hagemann
- Institute Biosciences, Department Plant Physiology, University of Rostock, Albert-Einstein-Straße 3, Rostock D-18059, Germany.
| | - Aaron Kaplan
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Givat Ram, Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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147
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148
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The HetR-binding site that activates expression of patA in vegetative cells is required for normal heterocyst patterning in Anabaena sp. PCC 7120. Sci Bull (Beijing) 2015. [DOI: 10.1007/s11434-014-0724-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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149
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Thiel T, Pratte BS. Regulation of Three Nitrogenase Gene Clusters in the Cyanobacterium Anabaena variabilis ATCC 29413. Life (Basel) 2014; 4:944-67. [PMID: 25513762 PMCID: PMC4284476 DOI: 10.3390/life4040944] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 11/21/2014] [Accepted: 12/04/2014] [Indexed: 11/16/2022] Open
Abstract
The filamentous cyanobacterium Anabaena variabilis ATCC 29413 fixes nitrogen under aerobic conditions in specialized cells called heterocysts that form in response to an environmental deficiency in combined nitrogen. Nitrogen fixation is mediated by the enzyme nitrogenase, which is very sensitive to oxygen. Heterocysts are microxic cells that allow nitrogenase to function in a filament comprised primarily of vegetative cells that produce oxygen by photosynthesis. A. variabilis is unique among well-characterized cyanobacteria in that it has three nitrogenase gene clusters that encode different nitrogenases, which function under different environmental conditions. The nif1 genes encode a Mo-nitrogenase that functions only in heterocysts, even in filaments grown anaerobically. The nif2 genes encode a different Mo-nitrogenase that functions in vegetative cells, but only in filaments grown under anoxic conditions. An alternative V-nitrogenase is encoded by vnf genes that are expressed only in heterocysts in an environment that is deficient in Mo. Thus, these three nitrogenases are expressed differentially in response to environmental conditions. The entire nif1 gene cluster, comprising at least 15 genes, is primarily under the control of the promoter for the first gene, nifB1. Transcriptional control of many of the downstream nif1 genes occurs by a combination of weak promoters within the coding regions of some downstream genes and by RNA processing, which is associated with increased transcript stability. The vnf genes show a similar pattern of transcriptional and post-transcriptional control of expression suggesting that the complex pattern of regulation of the nif1 cluster is conserved in other cyanobacterial nitrogenase gene clusters.
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Affiliation(s)
- Teresa Thiel
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA.
| | - Brenda S Pratte
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA.
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150
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Sandh G, Ramström M, Stensjö K. Analysis of the early heterocyst Cys-proteome in the multicellular cyanobacterium Nostoc punctiforme reveals novel insights into the division of labor within diazotrophic filaments. BMC Genomics 2014; 15:1064. [PMID: 25476978 PMCID: PMC4363197 DOI: 10.1186/1471-2164-15-1064] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 11/12/2014] [Indexed: 01/30/2023] Open
Abstract
Background In the filamentous cyanobacterium Nostoc punctiforme ATCC 29133, removal of combined nitrogen induces the differentiation of heterocysts, a cell-type specialized in N2 fixation. The differentiation involves genomic, structural and metabolic adaptations. In cyanobacteria, changes in the availability of carbon and nitrogen have also been linked to redox regulated posttranslational modifications of protein bound thiol groups. We have here employed a thiol targeting strategy to relatively quantify the putative redox proteome in heterocysts as compared to N2-fixing filaments, 24 hours after combined nitrogen depletion. The aim of the study was to expand the coverage of the cell-type specific proteome and metabolic landscape of heterocysts. Results Here we report the first cell-type specific proteome of newly formed heterocysts, compared to N2-fixing filaments, using the cysteine-specific selective ICAT methodology. The data set defined a good quantitative accuracy of the ICAT reagent in complex protein samples. The relative abundance levels of 511 proteins were determined and 74% showed a cell-type specific differential abundance. The majority of the identified proteins have not previously been quantified at the cell-type specific level. We have in addition analyzed the cell-type specific differential abundance of a large section of proteins quantified in both newly formed and steady-state diazotrophic cultures in N. punctiforme. The results describe a wide distribution of members of the putative redox regulated Cys-proteome in the central metabolism of both vegetative cells and heterocysts of N. punctiforme. Conclusions The data set broadens our understanding of heterocysts and describes novel proteins involved in heterocyst physiology, including signaling and regulatory proteins as well as a large number of proteins with unknown function. Significant differences in cell-type specific abundance levels were present in the cell-type specific proteomes of newly formed diazotrophic filaments as compared to steady-state cultures. Therefore we conclude that by using our approach we are able to analyze a synchronized fraction of newly formed heterocysts, which enabled a better detection of proteins involved in the heterocyst specific physiology. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1064) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry - Ångström Laboratory, Science for Life Laboratory, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden.
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