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Álvarez-Escribano I, Suárez-Murillo B, Brenes-Álvarez M, Vioque A, Muro-Pastor AM. Antisense RNA regulates glutamine synthetase in a heterocyst-forming cyanobacterium. PLANT PHYSIOLOGY 2024; 195:2911-2920. [PMID: 38708585 PMCID: PMC11288750 DOI: 10.1093/plphys/kiae263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/19/2024] [Accepted: 04/19/2024] [Indexed: 05/07/2024]
Abstract
Glutamine synthetase (GS) is a key enzyme involved in nitrogen assimilation and the maintenance of C/N balance, and it is strictly regulated in all bacteria. In cyanobacteria, GS expression is controlled by nitrogen control A (NtcA) transcription factor, which operates global nitrogen regulation in these photosynthetic organisms. Furthermore, posttranslational regulation of GS is operated by protein-protein interaction with GS inactivating factors (IFs). In this study, we describe an additional regulatory mechanism involving an antisense RNA. In Nostoc sp. PCC 7120, the gifA gene (encoding GS inactivating factor IF7) is transcribed downstream of the GS (glnA) gene, from the opposite strand, and the gifA mRNA extends into the glnA coding sequence in antisense orientation. Therefore, the dual RNA transcript that encodes gifA constitutes two functional regions: a 5' protein-coding region, encoding IF7, and a 3' untranslated region that acts as an antisense to glnA. By increasing the levels of such antisense RNA either in cis or in trans, we demonstrate that the amount of GS activity can be modulated by the presence of the antisense RNA. The tail-to-tail disposition of the glnA and gifA genes observed in many cyanobacterial strains from the Nostocales clade suggests the prevalence of such antisense RNA-mediated regulation of GS in this group of cyanobacteria.
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Affiliation(s)
- Isidro Álvarez-Escribano
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Sevilla, Spain
| | - Belén Suárez-Murillo
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Sevilla, Spain
| | - Manuel Brenes-Álvarez
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Agustín Vioque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Sevilla, Spain
| | - Alicia M Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Sevilla, Spain
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2
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Noell SE, Hellweger FL, Temperton B, Giovannoni SJ. A Reduction of Transcriptional Regulation in Aquatic Oligotrophic Microorganisms Enhances Fitness in Nutrient-Poor Environments. Microbiol Mol Biol Rev 2023; 87:e0012422. [PMID: 36995249 PMCID: PMC10304753 DOI: 10.1128/mmbr.00124-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
In this review, we consider the regulatory strategies of aquatic oligotrophs, microbial cells that are adapted to thrive under low-nutrient concentrations in oceans, lakes, and other aquatic ecosystems. Many reports have concluded that oligotrophs use less transcriptional regulation than copiotrophic cells, which are adapted to high nutrient concentrations and are far more common subjects for laboratory investigations of regulation. It is theorized that oligotrophs have retained alternate mechanisms of regulation, such as riboswitches, that provide shorter response times and smaller amplitude responses and require fewer cellular resources. We examine the accumulated evidence for distinctive regulatory strategies in oligotrophs. We explore differences in the selective pressures copiotrophs and oligotrophs encounter and ask why, although evolutionary history gives copiotrophs and oligotrophs access to the same regulatory mechanisms, they might exhibit distinctly different patterns in how these mechanisms are used. We discuss the implications of these findings for understanding broad patterns in the evolution of microbial regulatory networks and their relationships to environmental niche and life history strategy. We ask whether these observations, which have emerged from a decade of increased investigation of the cell biology of oligotrophs, might be relevant to recent discoveries of many microbial cell lineages in nature that share with oligotrophs the property of reduced genome size.
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Affiliation(s)
- Stephen E. Noell
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | | | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, United Kingdom
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3
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Baur ST, Poehlein A, Renz NJ, Hollitzer SK, Montoya Solano JD, Schiel-Bengelsdorf B, Daniel R, Dürre P. Modulation of sol mRNA expression by the long non-coding RNA Assolrna in Clostridium saccharoperbutylacetonicum affects solvent formation. Front Genet 2022; 13:966643. [PMID: 36035128 PMCID: PMC9402939 DOI: 10.3389/fgene.2022.966643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 07/11/2022] [Indexed: 12/01/2022] Open
Abstract
Solvents such as butanol are important platform chemicals and are often produced from petrochemical sources. Production of butanol and other compounds from renewable and sustainable resources can be achieved by solventogenic bacteria, such as the hyper-butanol producer Clostridium saccharoperbutylacetonicum. Its sol operon consists of the genes encoding butyraldehyde dehydrogenase, CoA transferase, and acetoacetate decarboxylase (bld, ctfA, ctfB, adc) and the gene products are involved in butanol and acetone formation. It is important to understand its regulation to further optimize the solvent production. In this study, a new long non-coding antisense transcript complementary to the complete sol operon, now called Assolrna, was identified by transcriptomic analysis and the regulatory mechanism of Assolrna was investigated. For this purpose, the promoter-exchange strain C. saccharoperbutylacetonicum ΔPasr::Pasr** was constructed. Additionally, Assolrna was expressed plasmid-based under control of the native Pasr promoter and the lactose-inducible PbgaL promoter in both the wild type and the promoter-exchange strain. Solvent formation was strongly decreased for all strains based on C. saccharoperbutylacetonicum ΔPasr::Pasr** and growth could not be restored by plasmid-based complementation of the exchanged promoter. Interestingly, very little sol mRNA expression was detected in the strain C. saccharoperbutylacetonicum ΔPasr::Pasr** lacking Assolrna expression. Butanol titers were further increased for the overexpression strain C. saccharoperbutylacetonicum [pMTL83151_asr_PbgaL] compared to the wild type. These results suggest that Assolrna has a positive effect on sol operon expression. Therefore, a possible stabilization mechanism of the sol mRNA by Assolrna under physiological concentrations is proposed.
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Affiliation(s)
- Saskia Tabea Baur
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
- *Correspondence: Saskia Tabea Baur,
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Niklas Jan Renz
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | | | | | | | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
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The Heterocyst-Specific Small RNA NsiR1 Regulates the Commitment to Differentiation in Nostoc. Microbiol Spectr 2022; 10:e0227421. [PMID: 35230129 PMCID: PMC9045159 DOI: 10.1128/spectrum.02274-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Heterocysts are specialized cells that filamentous cyanobacteria differentiate for the fixation of atmospheric nitrogen when other nitrogen sources are not available. Heterocyst differentiation at semiregular intervals along the filaments requires complex structural and metabolic changes that are under the control of the master transcriptional regulator HetR. NsiR1 (nitrogen stress-induced RNA 1) is a HetR-dependent noncoding RNA that is expressed from multiple chromosomal copies, some identical, some slightly divergent in sequence, specifically in heterocysts from very early stages of differentiation. We have previously shown that NsiR1 inhibits translation of the overlapping hetF mRNA by an antisense mechanism. Here, we identify alr3234, a hetP-like gene involved in the regulation of commitment (point of no return) to heterocyst differentiation, as a target of NsiR1. A strain overexpressing one of the identical copies of NsiR1 commits to heterocyst development earlier than the wild type. The posttranscriptional regulation exerted by NsiR1 on the expression of two genes involved in heterocyst differentiation and commitment, hetF and alr3234, adds a new level of complexity to the network of transcriptional regulation and protein-protein interactions that participate in heterocyst differentiation. IMPORTANCE Heterocysts are nitrogen-fixing specialized cells that appear at semiregular intervals along cyanobacterial filaments upon nitrogen starvation. The differentiation and patterning of heterocysts is a model for the study of cell differentiation in multicellular prokaryotes. The regulation of differentiation, which is only partially understood, includes transcriptional changes, factor diffusion between cells, and protein-protein interactions. This work describes the identification of a novel target for NsiR1, a small RNA (sRNA) encoded in multiple slightly divergent copies, and shows how different copies of “sibling” sRNAs regulate the expression of different targets involved in one of the few examples of a differentiation process in prokaryotes.
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5
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Li X, Xue C, Chen H, Zhang H, Wang Q. Small antisense RNA ThfR positively regulates Thf1 in Synechocystis sp. PCC 6803. JOURNAL OF PLANT PHYSIOLOGY 2022; 271:153642. [PMID: 35193088 DOI: 10.1016/j.jplph.2022.153642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Thylakoid formation1 (Thf1), encoded by sll1414 (thf1), is a multifunctional protein conserved in all photosynthetic organisms. thf1 expression is highly induced by high light in Synechocystis during photosynthesis-related stress. In this study, differential RNA sequencing analysis of the Synechocystis sp. PCC 6803 revealed a small antisense RNA (asRNA) gene located on the reverse-complementary strand of the thf1 gene. The full length of this asRNA (designated ThfR) was determined by 5' and 3' RACE analysis. The accumulation of thf1 mRNA was up-regulated synchronously with the ThfR level during survival after high-light stress or nitrogen starvation. Under nitrogen starvation or high-light stress, compared with the wild type, a ThfR overexpression mutant demonstrated relatively more Thf1 protein content, while a ThfR reduced-expression mutant accumulated less Thf1 protein. Furthermore, the overexpression of ThfR enhanced the electron transport rate and the proliferation of cyanobacteria under high-light stress. These results, which we confirmed further using an Escherichia coli sRNA expression platform, suggest that the thf1 gene is positively regulated by ThfR, possibly through protection of the RAUUW element at the RNase E cleavage site. This study represents the first report, to our knowledge, of a cis-transcript antisense RNA that targets thf1 in Synechocystis sp. PCC 6803 and provides evidence that ThfR regulates photosynthesis by positively modulating thf1 under high-light conditions.
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Affiliation(s)
- Xiang Li
- Hefei National Laboratory for Physical Sciences at Microscale, The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230026, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| | - Chunling Xue
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| | - Hui Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| | - Huafeng Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230026, China.
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
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6
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Bolay P, Hemm L, Florencio FJ, Hess WR, Muro-Pastor MI, Klähn S. The sRNA NsiR4 fine-tunes arginine synthesis in the cyanobacterium Synechocystis sp. PCC 6803 by post-transcriptional regulation of PirA. RNA Biol 2022; 19:811-818. [PMID: 35678613 PMCID: PMC9196836 DOI: 10.1080/15476286.2022.2082147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
As the only oxygenic phototrophs among prokaryotes, cyanobacteria employ intricate mechanisms to regulate common metabolic pathways. These mechanisms include small protein inhibitors exerting their function by protein-protein interaction with key metabolic enzymes and regulatory small RNAs (sRNAs). Here we show that the sRNA NsiR4, which is highly expressed under nitrogen limiting conditions, interacts with the mRNA of the recently described small protein PirA in the model strain Synechocystis sp. PCC 6803. In particular, NsiR4 targets the pirA 5'UTR close to the ribosome binding site. Heterologous reporter assays confirmed that this interaction interferes with pirA translation. PirA negatively impacts arginine synthesis under ammonium excess by competing with the central carbon/nitrogen regulator PII that binds to and thereby activates the key enzyme of arginine synthesis, N-acetyl-L-glutamate-kinase (NAGK). Consistently, ectopic nsiR4 expression in Synechocystis resulted in lowered PirA accumulation in response to ammonium upshifts, which also affected intracellular arginine pools. As NsiR4 and PirA are inversely regulated by the global nitrogen transcriptional regulator NtcA, this regulatory axis enables fine tuning of arginine synthesis and conveys additional metabolic flexibility under highly fluctuating nitrogen regimes. Pairs of small protein inhibitors and of sRNAs that control the abundance of these enzyme effectors at the post-transcriptional level appear as fundamental building blocks in the regulation of primary metabolism in cyanobacteria.
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Affiliation(s)
- Paul Bolay
- Department of Solar Materials, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Luisa Hemm
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Francisco J Florencio
- de Sevilla, Instituto de Bioquímica Vegetal Y FotosíntesisCSIC-Universidad, Sevilla, Spain
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - M Isabel Muro-Pastor
- de Sevilla, Instituto de Bioquímica Vegetal Y FotosíntesisCSIC-Universidad, Sevilla, Spain
| | - Stephan Klähn
- Department of Solar Materials, Helmholtz Centre for Environmental Research, Leipzig, Germany
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Brenes-Álvarez M, Olmedo-Verd E, Vioque A, Muro-Pastor AM. A nitrogen stress-inducible small RNA regulates CO2 fixation in Nostoc. PLANT PHYSIOLOGY 2021; 187:787-798. [PMID: 34608966 PMCID: PMC8491059 DOI: 10.1093/plphys/kiab309] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/09/2021] [Indexed: 05/09/2023]
Abstract
In the absence of fixed nitrogen, some filamentous cyanobacteria differentiate heterocysts, specialized cells devoted to fixing atmospheric nitrogen (N2). This differentiation process is controlled by the global nitrogen regulator NtcA and involves extensive metabolic reprogramming, including shutdown of photosynthetic CO2 fixation in heterocysts, to provide a microaerobic environment suitable for N2 fixation. Small regulatory RNAs (sRNAs) are major post-transcriptional regulators of gene expression in bacteria. In cyanobacteria, responding to nitrogen deficiency involves transcribing several nitrogen-regulated sRNAs. Here, we describe the participation of nitrogen stress-inducible RNA 4 (NsiR4) in post-transcriptionally regulating the expression of two genes involved in CO2 fixation via the Calvin cycle: glpX, which encodes bifunctional sedoheptulose-1,7-bisphosphatase/fructose-1,6-bisphosphatase (SBPase), and pgk, which encodes phosphoglycerate kinase (PGK). Using a heterologous reporter assay in Escherichia coli, we show that NsiR4 interacts with the 5'-untranslated region (5'-UTR) of glpX and pgk mRNAs. Overexpressing NsiR4 in Nostoc sp. PCC 7120 resulted in a reduced amount of SBPase protein and reduced PGK activity, as well as reduced levels of both glpX and pgk mRNAs, further supporting that NsiR4 negatively regulates these two enzymes. In addition, using a gfp fusion to the nsiR4 promoter, we show stronger expression of NsiR4 in heterocysts than in vegetative cells, which could contribute to the heterocyst-specific shutdown of Calvin cycle flux. Post-transcriptional regulation of two Calvin cycle enzymes by NsiR4, a nitrogen-regulated sRNA, represents an additional link between nitrogen control and CO2 assimilation.
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Affiliation(s)
- Manuel Brenes-Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Seville E-41092, Spain
| | - Elvira Olmedo-Verd
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Seville E-41092, Spain
| | - Agustín Vioque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Seville E-41092, Spain
| | - Alicia M. Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Seville E-41092, Spain
- Author for communication:
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8
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Bolay P, Rozbeh R, Muro-Pastor MI, Timm S, Hagemann M, Florencio FJ, Forchhammer K, Klähn S. The Novel P II-Interacting Protein PirA Controls Flux into the Cyanobacterial Ornithine-Ammonia Cycle. mBio 2021; 12:e00229-21. [PMID: 33758091 PMCID: PMC8092223 DOI: 10.1128/mbio.00229-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/16/2021] [Indexed: 12/11/2022] Open
Abstract
Among prokaryotes, cyanobacteria have an exclusive position as they perform oxygenic photosynthesis. Cyanobacteria substantially differ from other bacteria in further aspects, e.g., they evolved a plethora of unique regulatory mechanisms to control primary metabolism. This is exemplified by the regulation of glutamine synthetase (GS) via small proteins termed inactivating factors (IFs). Here, we reveal another small protein, encoded by the ssr0692 gene in the model strain Synechocystis sp. PCC 6803, that regulates flux into the ornithine-ammonia cycle (OAC), the key hub of cyanobacterial nitrogen stockpiling and remobilization. This regulation is achieved by the interaction with the central carbon/nitrogen control protein PII, which commonly controls entry into the OAC by activating the key enzyme of arginine synthesis, N-acetyl-l-glutamate kinase (NAGK). In particular, the Ssr0692 protein competes with NAGK for PII binding and thereby prevents NAGK activation, which in turn lowers arginine synthesis. Accordingly, we termed it PII-interacting regulator of arginine synthesis (PirA). Similar to the GS IFs, PirA accumulates in response to ammonium upshift due to relief from repression by the global nitrogen control transcription factor NtcA. Consistent with this, the deletion of pirA affects the balance of metabolite pools of the OAC in response to ammonium shocks. Moreover, the PirA-PII interaction requires ADP and is prevented by PII mutations affecting the T-loop conformation, the major protein interaction surface of this signal processing protein. Thus, we propose that PirA is an integrator determining flux into N storage compounds not only depending on the N availability but also the energy state of the cell.IMPORTANCE Cyanobacteria contribute a significant portion to the annual oxygen yield and play important roles in biogeochemical cycles, e.g., as major primary producers. Due to their photosynthetic lifestyle, cyanobacteria also arouse interest as hosts for the sustainable production of fuel components and high-value chemicals. However, their broad application as microbial cell factories is hampered by limited knowledge about the regulation of metabolic fluxes in these organisms. Our research identified a novel regulatory protein that controls nitrogen flux, in particular arginine synthesis. Besides its role as a proteinogenic amino acid, arginine is a precursor for the cyanobacterial storage compound cyanophycin, which is of potential interest to biotechnology. Therefore, the obtained results will not only enhance our understanding of flux control in these organisms but also help to provide a scientific basis for targeted metabolic engineering and, hence, the design of photosynthesis-driven biotechnological applications.
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Affiliation(s)
- Paul Bolay
- Helmholtz Centre for Environmental Research, Department of Solar Materials, Leipzig, Germany
| | - Rokhsareh Rozbeh
- Interfaculty Institute for Microbiology and Infection Medicine, Organismic Interactions Department, Tübingen University, Tübingen, Germany
| | - M Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Stefan Timm
- Department of Plant Physiology, University of Rostock, Rostock, Germany
| | - Martin Hagemann
- Department of Plant Physiology, University of Rostock, Rostock, Germany
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Karl Forchhammer
- Interfaculty Institute for Microbiology and Infection Medicine, Organismic Interactions Department, Tübingen University, Tübingen, Germany
| | - Stephan Klähn
- Helmholtz Centre for Environmental Research, Department of Solar Materials, Leipzig, Germany
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Anand A, Pandi G. Noncoding RNA: An Insight into Chloroplast and Mitochondrial Gene Expressions. Life (Basel) 2021; 11:life11010049. [PMID: 33450961 PMCID: PMC7828403 DOI: 10.3390/life11010049] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/28/2020] [Accepted: 01/05/2021] [Indexed: 12/22/2022] Open
Abstract
Regulation of gene expression in any biological system is a complex process with many checkpoints at the transcriptional, post-transcriptional and translational levels. The control mechanism is mediated by various protein factors, secondary metabolites and a newly included regulatory member, i.e., noncoding RNAs (ncRNAs). It is known that ncRNAs modulate the mRNA or protein profiles of the cell depending on the degree of complementary and context of the microenvironment. In plants, ncRNAs are essential for growth and development in normal conditions by controlling various gene expressions and have emerged as a key player to guard plants during adverse conditions. In order to have smooth functioning of the plants under any environmental pressure, two very important DNA-harboring semi-autonomous organelles, namely, chloroplasts and mitochondria, are considered as main players. These organelles conduct the most crucial metabolic pathways that are required to maintain cell homeostasis. Thus, it is imperative to explore and envisage the molecular machineries responsible for gene regulation within the organelles and their coordination with nuclear transcripts. Therefore, the present review mainly focuses on ncRNAs origination and their gene regulation in chloroplasts and plant mitochondria.
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Affiliation(s)
- Asha Anand
- Correspondence: (A.A.); (G.P.); Tel.: +91-452-245-8230 (G.P.)
| | - Gopal Pandi
- Correspondence: (A.A.); (G.P.); Tel.: +91-452-245-8230 (G.P.)
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10
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Álvarez-Escribano I, Brenes-Álvarez M, Olmedo-Verd E, Georg J, Hess WR, Vioque A, Muro-Pastor AM. NsiR3, a nitrogen stress-inducible small RNA, regulates proline oxidase expression in the cyanobacterium Nostoc sp. PCC 7120. FEBS J 2020; 288:1614-1629. [PMID: 32799414 DOI: 10.1111/febs.15516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/17/2020] [Accepted: 08/10/2020] [Indexed: 11/30/2022]
Abstract
NsiR3 (nitrogen stress-inducible RNA 3) is a small noncoding RNA strongly conserved in heterocyst-forming cyanobacteria. In Nostoc sp. PCC 7120, transcription of NsiR3 is induced by nitrogen starvation and depends on the global nitrogen regulator NtcA. A conserved NtcA-binding site is centered around position -42.5 with respect to the transcription start site of NsiR3 homologs, and NtcA binds in vitro to a DNA fragment containing this sequence. In the absence of combined nitrogen, NsiR3 expression is induced in all cells along the Nostoc filament but much more strongly in heterocysts, differentiated cells devoted to nitrogen fixation. Co-expression analysis of transcriptomic data obtained from microarrays hybridized with RNA obtained from Nostoc wild-type or mutant strains grown in the presence of ammonium or in the absence of combined nitrogen revealed that the expression profile of gene putA (proline oxidase) correlates negatively with that of NsiR3. Using a heterologous system in Escherichia coli, we show that NsiR3 binds to the 5'-UTR of putA mRNA, resulting in reduced expression of a reporter gene. Overexpression of NsiR3 in Nostoc resulted in strong reduction of putA mRNA accumulation, further supporting the negative regulation of putA by NsiR3. The higher expression of NsiR3 in heterocysts versus vegetative cells of the N2 -fixing filament could contribute to the previously described absence of putA mRNA and of the catabolic pathway to produce glutamate from arginine via proline specifically in heterocysts. Post-transcriptional regulation by NsiR3 represents an indirect NtcA-operated regulatory mechanism of putA expression. DATABASE: Microarray data are available in GEO database under accession numbers GSE120377 and GSE150191.
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Affiliation(s)
- Isidro Álvarez-Escribano
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Sevilla, Spain
| | - 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
| | - Jens Georg
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - 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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11
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Brenes‐Álvarez M, Minguet M, Vioque A, Muro‐Pastor AM. NsiR1, a smallRNAwith multiple copies, modulates heterocyst differentiation in the cyanobacteriumNostocsp.PCC7120. Environ Microbiol 2020; 22:3325-3338. [DOI: 10.1111/1462-2920.15103] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Manuel Brenes‐Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis Consejo Superior de Investigaciones Científicas and Universidad de Sevilla Sevilla Spain
| | - Marina Minguet
- 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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12
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Castandet B, Germain A, Hotto AM, Stern DB. Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures. Nucleic Acids Res 2020; 47:11889-11905. [PMID: 31732725 PMCID: PMC7145512 DOI: 10.1093/nar/gkz1059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 10/02/2019] [Accepted: 11/05/2019] [Indexed: 12/23/2022] Open
Abstract
Chloroplast transcription requires numerous quality control steps to generate the complex but selective mixture of accumulating RNAs. To gain insight into how this RNA diversity is achieved and regulated, we systematically mapped transcript ends by developing a protocol called Terminome-seq. Using Arabidopsis thaliana as a model, we catalogued >215 primary 5′ ends corresponding to transcription start sites (TSS), as well as 1628 processed 5′ ends and 1299 3′ ends. While most termini were found in intergenic regions, numerous abundant termini were also found within coding regions and introns, including several major TSS at unexpected locations. A consistent feature was the clustering of both 5′ and 3′ ends, contrasting with the prevailing description of discrete 5′ termini, suggesting an imprecision of the transcription and/or RNA processing machinery. Numerous termini correlated with the extremities of small RNA footprints or predicted stem-loop structures, in agreement with the model of passive RNA protection. Terminome-seq was also implemented for pnp1–1, a mutant lacking the processing enzyme polynucleotide phosphorylase. Nearly 2000 termini were altered in pnp1–1, revealing a dominant role in shaping the transcriptome. In summary, Terminome-seq permits precise delineation of the roles and regulation of the many factors involved in organellar transcriptome quality control.
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Affiliation(s)
- Benoît Castandet
- Boyce Thompson Institute, Ithaca, NY 14853, USA.,Institut des Sciences des Plantes de Paris Saclay (IPS2), UEVE, INRA, CNRS, Univ. Paris Sud, Université Paris-Saclay, F-91192 Gif sur Yvette, France.,Université de Paris, IPS2, F-91192 Gif sur Yvette, France
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13
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Reimann V, Ziemann M, Li H, Zhu T, Behler J, Lu X, Hess WR. Specificities and functional coordination between the two Cas6 maturation endonucleases in Anabaena sp. PCC 7120 assign orphan CRISPR arrays to three groups. RNA Biol 2020; 17:1442-1453. [PMID: 32453626 DOI: 10.1080/15476286.2020.1774197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Many bacteria and archaea possess an RNA-guided adaptive and inheritable immune system that consists of clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. In most CRISPR-Cas systems, the maturation of CRISPR-derived small RNAs (crRNAs) is essential for functionality. Cas6 endonucleases function as the most frequent CRISPR RNA maturation enzymes. In the cyanobacterium Anabaena sp. PCC 7120, ten CRISPR loci are present, but only two cas gene cassettes plus a Tn7-associated eleventh array. In this study, we deleted the two cas6 genes alr1482 (Type III-D) or alr1566 (Type I-D) and tested the specificities of the two corresponding enzymes in the resulting mutant strains, as recombinant proteins and in a cell-free transcription-translation system. The results assign the direct repeats (DRs) to three different groups. While Alr1566 is specific for one group, Alr1482 has a higher preference for the DRs of the second group but can also cleave those of the first group. We found that this cross-recognition limits crRNA accumulation for the Type I-D system in vivo. We also show that the DR of the cas gene-free CRISPR array of cyanophage N-1 is processed by these enzymes, suggesting that it is fully competent in association with host-encoded Cas proteins. The data support the functionality of CRISPR arrays that frequently appear fragmented to multiple genomic loci in multicellular cyanobacteria and disfavour other possibilities, such as the nonfunctionality of these orphan repeat-spacer arrays. Our results show the functional coordination of Cas6 endonucleases with both neighbouring and remote repeat-spacer arrays in the CRISPR-Cas system of cyanobacteria.
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Affiliation(s)
- Viktoria Reimann
- Faculty of Biology, Institute of Biology III, University of Freiburg , Germany
| | - Marcus Ziemann
- Faculty of Biology, Institute of Biology III, University of Freiburg , Germany
| | - Hui Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences , Qingdao, China.,College of Life Sciences, University of Chinese Academy of Sciences , Beijing, China
| | - Tao Zhu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences , Qingdao, China
| | - Juliane Behler
- Faculty of Biology, Institute of Biology III, University of Freiburg , Germany
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences , Qingdao, China
| | - Wolfgang R Hess
- Faculty of Biology, Institute of Biology III, University of Freiburg , Germany
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14
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Álvarez-Escribano I, Brenes-Álvarez M, Olmedo-Verd E, Vioque A, Muro-Pastor AM. The Nitrogen Stress-Repressed sRNA NsrR1 Regulates Expression of all1871, a Gene Required for Diazotrophic Growth in Nostoc sp. PCC 7120. Life (Basel) 2020; 10:life10050054. [PMID: 32365616 PMCID: PMC7281752 DOI: 10.3390/life10050054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 12/14/2022] Open
Abstract
Small regulatory RNAs (sRNAs) are post-transcriptional regulators of bacterial gene expression. In cyanobacteria, the responses to nitrogen availability, that are mostly controlled at the transcriptional level by NtcA, involve also at least two small RNAs, namely NsiR4 (nitrogen stress-induced RNA 4) and NsrR1 (nitrogen stress-repressed RNA 1). Prediction of possible mRNA targets regulated by NsrR1 in Nostoc sp. PCC 7120 allowed, in addition to previously described nblA, the identification of all1871, a nitrogen-regulated gene encoding a protein of unknown function that we describe here as required for growth at the expense of atmospheric nitrogen (N2). We show that transcription of all1871 is induced upon nitrogen step-down independently of NtcA. All1871 accumulation is repressed by NsrR1 and its expression is stronger in heterocysts, specialized cells devoted to N2 fixation. We demonstrate specific interaction between NsrR1 and the 5′ untranslated region (UTR) of the all1871 mRNA, that leads to decreased expression of all1871. Because transcription of NsrR1 is partially repressed by NtcA, post-transcriptional regulation by NsrR1 would constitute an indirect way of NtcA-mediated regulation of all1871.
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15
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Lambrecht SJ, Steglich C, Hess WR. A minimum set of regulators to thrive in the ocean. FEMS Microbiol Rev 2020; 44:232-252. [DOI: 10.1093/femsre/fuaa005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/19/2020] [Indexed: 12/25/2022] Open
Abstract
ABSTRACT
Marine cyanobacteria of the genus Prochlorococcus thrive in high cell numbers throughout the euphotic zones of the world's subtropical and tropical oligotrophic oceans, making them some of the most ecologically relevant photosynthetic microorganisms on Earth. The ecological success of these free-living phototrophs suggests that they are equipped with a regulatory system competent to address many different stress situations. However, Prochlorococcus genomes are compact and streamlined, with the majority encoding only five different sigma factors, five to six two-component systems and eight types of other transcriptional regulators. Here, we summarize the existing information about the functions of these protein regulators, about transcriptomic responses to defined stress conditions, and discuss the current knowledge about riboswitches, RNA-based regulation and the roles of certain metabolites as co-regulators. We focus on the best-studied isolate, Prochlorococcus MED4, but extend to other strains and ecotypes when appropriate, and we include some information gained from metagenomic and metatranscriptomic analyses.
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Affiliation(s)
- S Joke Lambrecht
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Claudia Steglich
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
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16
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The Integrity of the Cell Wall and Its Remodeling during Heterocyst Differentiation Are Regulated by Phylogenetically Conserved Small RNA Yfr1 in Nostoc sp. Strain PCC 7120. mBio 2020; 11:mBio.02599-19. [PMID: 31964726 PMCID: PMC6974561 DOI: 10.1128/mbio.02599-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Bacterial small RNAs (sRNAs) are important players affecting the regulation of essentially every aspect of bacterial physiology. The cell wall is a highly dynamic structure that protects bacteria from their fluctuating environment. Cell envelope remodeling is particularly critical for bacteria that undergo differentiation processes, such as spore formation or differentiation of heterocysts. Heterocyst development involves the deposition of additional layers of glycolipids and polysaccharides outside the outer membrane. Here, we show that a cyanobacterial phylogenetically conserved small regulatory RNA, Yfr1, coordinates the expression of proteins involved in cell wall-related processes, including peptidoglycan metabolism and transport of different molecules, as well as expression of several proteins involved in heterocyst differentiation. Yfr1 is a strictly conserved small RNA in cyanobacteria. A bioinformatic prediction to identify possible interactions of Yfr1 with mRNAs was carried out by using the sequences of Yfr1 from several heterocyst-forming strains, including Nostoc sp. strain PCC 7120. The results of the prediction were enriched in genes encoding outer membrane proteins and enzymes related to peptidoglycan biosynthesis and turnover. Heterologous expression assays with Escherichia coli demonstrated direct interactions of Yfr1 with mRNAs of 11 of the candidate genes. The expression of 10 of them (alr2458, alr4550, murC, all4829, all2158, mraY, alr2269, alr0834, conR, patN) was repressed by interaction with Yfr1, whereas the expression of amiC2, encoding an amidase, was increased. The interactions between Yfr1 and the 11 mRNAs were confirmed by site-directed mutagenesis of Yfr1. Furthermore, a Nostoc strain with reduced levels of Yfr1 had larger amounts of mraY and murC mRNAs, supporting a role for Yfr1 in the regulation of those genes. Nostoc strains with either reduced or increased expression of Yfr1 showed anomalies in cell wall completion and were more sensitive to vancomycin than the wild-type strain. Furthermore, growth in the absence of combined nitrogen, which involves the differentiation of heterocysts, was compromised in the strain overexpressing Yfr1, and filaments were broken at the connections between vegetative cells and heterocysts. These results indicate that Yfr1 is an important regulator of cell wall homeostasis and correct cell wall remodeling during heterocyst differentiation.
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17
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Lambrecht SJ, Kanesaki Y, Fuss J, Huettel B, Reinhardt R, Steglich C. Interplay and Targetome of the Two Conserved Cyanobacterial sRNAs Yfr1 and Yfr2 in Prochlorococcus MED4. Sci Rep 2019; 9:14331. [PMID: 31586076 PMCID: PMC6778093 DOI: 10.1038/s41598-019-49881-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 09/02/2019] [Indexed: 01/22/2023] Open
Abstract
The sRNA Yfr1 and members of the Yfr2 sRNA family are almost universally present within cyanobacteria. The conserved motifs of these sRNAs are nearly complementary to each other, suggesting their ability to participate in crosstalk. The conserved motif of Yfr1 is shared by members of the Yfr10 sRNA family, members of which are otherwise less conserved in sequence, structure, and synteny compared to Yfr1. The different structural properties enable the discrimination of unique targets of Yfr1 and Yfr10. Unlike most studied regulatory sRNAs, Yfr1 gene expression only slightly changes under the tested stress conditions and is present at high levels at all times. In contrast, cellular levels of Yfr10 increase during the course of acclimation to darkness, and levels of Yfr2 increase when cells are shifted to high light or nitrogen limitation conditions. In this study, we investigated the targetomes of Yfr2, Yfr1, and Yfr10 in Prochlorococcus MED4, establishing CRAFD-Seq as a new method for identifying direct targets of these sRNAs that is applicable to all bacteria, including those that are not amenable to genetic modification. The results suggest that these sRNAs are integrated within a regulatory network of unprecedented complexity in the adjustment of carbon and nitrogen-related primary metabolism.
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Affiliation(s)
- S Joke Lambrecht
- University of Freiburg, Faculty of Biology, D-79104, Freiburg, Germany
| | - Yu Kanesaki
- NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan.,Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Janina Fuss
- Max Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, D-50829, Köln, Germany
| | - Bruno Huettel
- Max Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, D-50829, Köln, Germany
| | - Richard Reinhardt
- Max Planck-Genome-Centre Cologne, Max Planck Institute for Plant Breeding Research, D-50829, Köln, Germany
| | - Claudia Steglich
- University of Freiburg, Faculty of Biology, D-79104, Freiburg, Germany.
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18
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Klähn S, Bolay P, Wright PR, Atilho RM, Brewer KI, Hagemann M, Breaker RR, Hess WR. A glutamine riboswitch is a key element for the regulation of glutamine synthetase in cyanobacteria. Nucleic Acids Res 2019; 46:10082-10094. [PMID: 30085248 PMCID: PMC6212724 DOI: 10.1093/nar/gky709] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/25/2018] [Indexed: 12/19/2022] Open
Abstract
As the key enzyme of bacterial nitrogen assimilation, glutamine synthetase (GS) is tightly regulated. In cyanobacteria, GS activity is controlled by the interaction with inactivating protein factors IF7 and IF17 encoded by the genes gifA and gifB, respectively. We show that a glutamine-binding aptamer within the gifB 5′ UTR of Synechocystis sp. PCC 6803 is critical for the expression of IF17. Binding of glutamine induced structural re-arrangements in this RNA element leading to enhanced protein synthesis in vivo and characterizing it as a riboswitch. Mutagenesis showed the riboswitch mechanism to contribute at least as much to the control of gene expression as the promoter-mediated transcriptional regulation. We suggest this and a structurally related but distinct element, to be designated type 1 and type 2 glutamine riboswitches. Extended biocomputational searches revealed that glutamine riboswitches are exclusively but frequently found in cyanobacterial genomes, where they are primarily associated with gifB homologs. Hence, this RNA-based sensing mechanism is common in cyanobacteria and establishes a regulatory feedback loop that couples the IF17-mediated GS inactivation to the intracellular glutamine levels. Together with the previously described sRNA NsiR4, these results show that non-coding RNA is an indispensable component in the control of nitrogen assimilation in cyanobacteria.
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Affiliation(s)
- Stephan Klähn
- Genetics & Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Department of Solar Materials, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | - Paul Bolay
- Genetics & Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Patrick R Wright
- Bioinformatics, Technical Faculty, University of Freiburg, Freiburg, Germany
| | - Ruben M Atilho
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Kenneth I Brewer
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Martin Hagemann
- Department of Plant Physiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Ronald R Breaker
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
| | - Wolfgang R Hess
- Genetics & Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Freiburg Institute for Advanced Studies, University of Freiburg, Germany
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19
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Georg J, Rosana ARR, Chamot D, Migur A, Hess WR, Owttrim GW. Inactivation of the RNA helicase CrhR impacts a specific subset of the transcriptome in the cyanobacterium Synechocystis sp. PCC 6803. RNA Biol 2019; 16:1205-1214. [PMID: 31234711 PMCID: PMC6693541 DOI: 10.1080/15476286.2019.1621622] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
DEAD-box RNA-helicases catalyze the reorganization of structured RNAs and the formation of RNP complexes. The cyanobacterium Synechocystis sp. PCC 6803 encodes a single DEAD-box RNA helicase, CrhR (Slr0083), whose expression is regulated by abiotic stresses that alter the redox potential of the photosynthetic electron transport chain, including temperature downshift. Despite its proposed effect on RNA metabolism and its known relevance in cold-stress adaptation, the reported impact of a CrhR knockout on the cold adaption of the transcriptome only identified eight affected genes. Here, we utilized a custom designed microarray to assess the impact of the absence of CrhR RNA helicase activity on the transcriptome, independent of cold stress. CrhR truncation impacts an RNA subset comprising ~10% of the ncRNA and also ~10% of the mRNA transcripts. While equal numbers of mRNAs showed increased as well as decreased abundance, more than 90% of the ncRNAs showed enhanced expression in the absence of CrhR, indicative of a negative effect on ncRNA transcription or stability. We further tested the effect of CrhR on the stability of strongly responding RNAs that identify examples of post-transcriptional and transcriptional regulation. The data suggest that CrhR impacts multiple aspects of RNA metabolism in Synechocystis.
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Affiliation(s)
- Jens Georg
- a Faculty of Biology, University of Freiburg , Freiburg , Germany
| | | | - Danuta Chamot
- b Department of Biological Sciences, University of Alberta , Edmonton , AB , Canada
| | - Anzhela Migur
- a Faculty of Biology, University of Freiburg , Freiburg , Germany
| | - Wolfgang R Hess
- a Faculty of Biology, University of Freiburg , Freiburg , Germany.,c Freiburg Institute for Advanced Studies, University of Freiburg , Freiburg , Germany
| | - George W Owttrim
- b Department of Biological Sciences, University of Alberta , Edmonton , AB , Canada
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20
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Brenes‐Álvarez M, Mitschke J, Olmedo‐Verd E, Georg J, Hess WR, Vioque A, Muro‐Pastor AM. Elements of the heterocyst‐specific transcriptome unravelled by co‐expression analysis inNostocsp. PCC 7120. Environ Microbiol 2019; 21:2544-2558. [DOI: 10.1111/1462-2920.14647] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/06/2019] [Accepted: 05/01/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Manuel Brenes‐Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla E‐41092 Sevilla Spain
| | - Jan Mitschke
- Genetics and Experimental Bioinformatics, Faculty of BiologyUniversity of Freiburg D‐79104 Freiburg Germany
| | - Elvira Olmedo‐Verd
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla E‐41092 Sevilla Spain
| | - Jens Georg
- Genetics and Experimental Bioinformatics, Faculty of BiologyUniversity of Freiburg D‐79104 Freiburg Germany
| | - Wolfgang R. Hess
- Genetics and Experimental Bioinformatics, Faculty of BiologyUniversity of Freiburg D‐79104 Freiburg Germany
- Freiburg Institute for Advanced Studies, University of Freiburg D‐79104 Freiburg Germany
| | - Agustín Vioque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla E‐41092 Sevilla Spain
| | - Alicia M. Muro‐Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla E‐41092 Sevilla Spain
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21
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Hou S, Brenes-Álvarez M, Reimann V, Alkhnbashi OS, Backofen R, Muro-Pastor AM, Hess WR. CRISPR-Cas systems in multicellular cyanobacteria. RNA Biol 2019; 16:518-529. [PMID: 29995583 PMCID: PMC6546389 DOI: 10.1080/15476286.2018.1493330] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/01/2018] [Accepted: 06/19/2018] [Indexed: 01/12/2023] Open
Abstract
Novel CRISPR-Cas systems possess substantial potential for genome editing and manipulation of gene expression. The types and numbers of CRISPR-Cas systems vary substantially between different organisms. Some filamentous cyanobacteria harbor > 40 different putative CRISPR repeat-spacer cassettes, while the number of cas gene instances is much lower. Here we addressed the types and diversity of CRISPR-Cas systems and of CRISPR-like repeat-spacer arrays in 171 publicly available genomes of multicellular cyanobacteria. The number of 1328 repeat-spacer arrays exceeded the total of 391 encoded Cas1 proteins suggesting a tendency for fragmentation or the involvement of alternative adaptation factors. The model cyanobacterium Anabaena sp. PCC 7120 contains only three cas1 genes but hosts three Class 1, possibly one Class 2 and five orphan repeat-spacer arrays, all of which exhibit crRNA-typical expression patterns suggesting active transcription, maturation and incorporation into CRISPR complexes. The CRISPR-Cas system within the element interrupting the Anabaena sp. PCC 7120 fdxN gene, as well as analogous arrangements in other strains, occupy the genetic elements that become excised during the differentiation-related programmed site-specific recombination. This fact indicates the propensity of these elements for the integration of CRISPR-cas systems and points to a previously not recognized connection. The gene all3613 resembling a possible Class 2 effector protein is linked to a short repeat-spacer array and a single tRNA gene, similar to its homologs in other cyanobacteria. The diversity and presence of numerous CRISPR-Cas systems in DNA elements that are programmed for homologous recombination make filamentous cyanobacteria a prolific resource for their study. Abbreviations: Cas: CRISPR associated sequences; CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats; C2c: Class 2 candidate; SDR: small dispersed repeat; TSS: transcriptional start site; UTR: untranslated region.
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Affiliation(s)
- Shengwei Hou
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - Manuel Brenes-Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Seville, Spain
| | - Viktoria Reimann
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - Omer S. Alkhnbashi
- Bioinformatics group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Alicia M. Muro-Pastor
- Bioinformatics group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Wolfgang R. Hess
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
- Freiburg Institute for Advanced Studies,University of Freiburg, Freiburg, Germany
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22
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Lambrecht SJ, Wahlig JML, Steglich C. The GntR family transcriptional regulator PMM1637 regulates the highly conserved cyanobacterial sRNA Yfr2 in marine picocyanobacteria. DNA Res 2019; 25:489-497. [PMID: 29901694 PMCID: PMC6191309 DOI: 10.1093/dnares/dsy019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/14/2018] [Indexed: 11/21/2022] Open
Abstract
Prochlorococcus is a marine picocyanobacterium with a streamlined genome that is adapted to different ecological niches in the oligotrophic oceans. There are currently >20 regulatory small RNAs (sRNAs) that have been identified in the model strain Prochlorococcus MED4. While most of these sRNAs are ecotype-specific, sRNA homologs of Yfr1 and of the Yfr2 family are widely found throughout the cyanobacterial phylum. Although they were identified 13 yrs ago, the functions of Yfr1 and Yfr2 have remained unknown. We observed a strong induction of two Yfr2 sRNA homologs of Prochlorococcus MED4 during high light stress and nitrogen starvation. Several Prochlorococcus and marine Synechococcus yfr2 promoter regions contain a conserved motif we named CGRE1 (cyanobacterial GntR family transcriptional regulator responsive element 1). Using the conserved promoter region as bait in a DNA affinity pull-down assay we identified the GntR family transcriptional regulator PMM1637 as a binding partner. Similar to Yfr2, homologs of PMM1637 are universally and exclusively found in cyanobacteria. We suggest that PMM1637 governs the induction of gene expression of Yfr2 homologs containing CGRE1 in their promoters under nitrogen-depleted and high-light stress conditions.
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Affiliation(s)
- S Joke Lambrecht
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - J Mascha L Wahlig
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - Claudia Steglich
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
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23
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Bolay P, Muro-Pastor MI, Florencio FJ, Klähn S. The Distinctive Regulation of Cyanobacterial Glutamine Synthetase. Life (Basel) 2018; 8:E52. [PMID: 30373240 PMCID: PMC6316151 DOI: 10.3390/life8040052] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/23/2018] [Accepted: 10/25/2018] [Indexed: 12/02/2022] Open
Abstract
Glutamine synthetase (GS) features prominently in bacterial nitrogen assimilation as it catalyzes the entry of bioavailable nitrogen in form of ammonium into cellular metabolism. The classic example, the comprehensively characterized GS of enterobacteria, is subject to exquisite regulation at multiple levels, among them gene expression regulation to control GS abundance, as well as feedback inhibition and covalent modifications to control enzyme activity. Intriguingly, the GS of the ecologically important clade of cyanobacteria features fundamentally different regulatory systems to those of most prokaryotes. These include the interaction with small proteins, the so-called inactivating factors (IFs) that inhibit GS linearly with their abundance. In addition to this protein interaction-based regulation of GS activity, cyanobacteria use alternative elements to control the synthesis of GS and IFs at the transcriptional level. Moreover, cyanobacteria evolved unique RNA-based regulatory mechanisms such as glutamine riboswitches to tightly tune IF abundance. In this review, we aim to outline the current knowledge on the distinctive features of the cyanobacterial GS encompassing the overall control of its activity, sensing the nitrogen status, transcriptional and post-transcriptional regulation, as well as strain-specific differences.
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Affiliation(s)
- Paul Bolay
- Helmholtz Centre for Environmental Research, Department of Solar Materials, Permoserstrasse 15, D-04318 Leipzig, Germany.
| | - M Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Américo Vespucio 49, E-41092 Seville, Spain.
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Américo Vespucio 49, E-41092 Seville, Spain.
| | - Stephan Klähn
- Helmholtz Centre for Environmental Research, Department of Solar Materials, Permoserstrasse 15, D-04318 Leipzig, Germany.
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Abstract
As the transcriptional and post-transcriptional regulators of gene expression, small RNAs (sRNAs) play important roles in every domain of life in organisms. It has been discovered gradually that bacteria possess multiple means of gene regulation using RNAs. They have been continuously used as model organisms for photosynthesis, metabolism, biotechnology, evolution, and nitrogen fixation for many decades. Cyanobacteria, one of the most ancient life forms, constitute all kinds of photoautotrophic bacteria and exist in almost any environment on this planet. It is believed that a complex RNA-based regulatory mechanism functions in cyanobacteria to help them adapt to changes and stresses in diverse environments. Although lagging far behind other model microorganisms, such as yeast and Escherichia coli, more and more non-coding regulatory sRNAs have been recognized in cyanobacteria during the past decades. In this article, by focusing on cyanobacterial sRNAs, the approaches for detection and targeting of sRNAs will be summarized, four major mechanisms and regulatory functions will be generalized, eight types of cis-encoded sRNA and four types of trans-encoded sRNAs will be reviewed in detail, and their possible physiological functions will be further discussed.
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Affiliation(s)
- Jinlu Hu
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Qiang Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan, China.,University of the Chinese Academy of Sciences, Beijing, China
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25
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Álvarez-Escribano I, Vioque A, Muro-Pastor AM. NsrR1, a Nitrogen Stress-Repressed sRNA, Contributes to the Regulation of nblA in Nostoc sp. PCC 7120. Front Microbiol 2018; 9:2267. [PMID: 30319578 PMCID: PMC6166021 DOI: 10.3389/fmicb.2018.02267] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/05/2018] [Indexed: 12/13/2022] Open
Abstract
Small regulatory RNAs (sRNAs) are currently considered as major post-transcriptional regulators of gene expression in bacteria. The interplay between sRNAs and transcription factors leads to complex regulatory networks in which both transcription factors and sRNAs may appear as nodes. In cyanobacteria, the responses to nitrogen availability are controlled at the transcriptional level by NtcA, a CRP/FNR family regulator. In this study, we describe an NtcA-regulated sRNA in the cyanobacterium Nostoc sp. PCC 7120, that we have named NsrR1 (nitrogen stress repressed RNA1). We show sequence specific binding of NtcA to the promoter of NsrR1. Prediction of possible mRNA targets regulated by NsrR1 allowed the identification of nblA, encoding a protein adaptor for phycobilisome degradation under several stress conditions, including nitrogen deficiency. We demonstrate specific interaction between NsrR1 and the 5'-UTR of the nblA mRNA, that leads to decreased expression of nblA. Because both NsrR1 and NblA are under transcriptional control of NtcA, this regulatory circuit constitutes a coherent feed-forward loop, involving a transcription factor and an sRNA.
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Affiliation(s)
- Isidro Álvarez-Escribano
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Seville, Spain
| | - Agustín Vioque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Seville, Spain
| | - Alicia M Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Seville, Spain
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26
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Rübsam H, Kirsch F, Reimann V, Erban A, Kopka J, Hagemann M, Hess WR, Klähn S. The iron-stress activated RNA 1 (IsaR1) coordinates osmotic acclimation and iron starvation responses in the cyanobacterium Synechocystis sp. PCC 6803. Environ Microbiol 2018; 20:2757-2768. [PMID: 29468839 DOI: 10.1111/1462-2920.14079] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 02/18/2018] [Indexed: 11/28/2022]
Abstract
In nature, microorganisms are exposed to multiple stress factors in parallel. Here, we investigated the response of the model cyanobacterium Synechocystis sp. PCC 6803 to simultaneous iron limitation and osmotic stresses. Iron is a major limiting factor for bacterial and phytoplankton growth in most environments. Thus, bacterial iron homeostasis is tightly regulated. In Synechocystis, it is mediated mainly by the transcriptional regulator FurA and the iron-stress activated RNA 1 (IsaR1). IsaR1 is an important riboregulator that affects the acclimation of the photosynthetic apparatus to iron starvation in multiple ways. Upon increases in salinity, Synechocystis responds by accumulating the compatible solute glucosylglycerol (GG). We show that IsaR1 overexpression causes a reduction in the de novo GG synthesis rate upon salt shock. We verified the direct interaction between IsaR1 and the 5'UTR of the ggpS mRNA, which in turn drastically reduced the de novo synthesis of the key enzyme for GG synthesis, glucosylglycerol phosphate synthase (GgpS). Thus, IsaR1 specifically interferes with the salt acclimation process in Synechocystis, in addition to its primary regulatory function. Moreover, the salt-stimulated GgpS production became reduced under parallel iron limitation in WT - an effect which is, however, attenuated in an isaR1 deletion strain. Hence, IsaR1 is involved in the integration of the responses to different environmental perturbations and slows the osmotic adaptation process in cells suffering from parallel iron starvation.
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Affiliation(s)
- Henriette Rübsam
- Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, University of Freiburg, D-79104 Freiburg, Germany
| | - Friedrich Kirsch
- Plant Physiology department, A.-Einstein-Str. 3, University of Rostock, Institute of Biological Sciences, D-18059 Rostock, Germany
| | - Viktoria Reimann
- Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, University of Freiburg, D-79104 Freiburg, Germany
| | - Alexander Erban
- Department of Molecular Physiology: Applied Metabolome Analysis, Am Mühlenberg 1, Max-Planck-Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| | - Joachim Kopka
- Department of Molecular Physiology: Applied Metabolome Analysis, Am Mühlenberg 1, Max-Planck-Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| | - Martin Hagemann
- Plant Physiology department, A.-Einstein-Str. 3, University of Rostock, Institute of Biological Sciences, D-18059 Rostock, Germany
| | - Wolfgang R Hess
- Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, University of Freiburg, D-79104 Freiburg, Germany
| | - Stephan Klähn
- Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, University of Freiburg, D-79104 Freiburg, Germany
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27
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Domínguez-Martín MA, López-Lozano A, Clavería-Gimeno R, Velázquez-Campoy A, Seidel G, Burkovski A, Díez J, García-Fernández JM. Differential NtcA Responsiveness to 2-Oxoglutarate Underlies the Diversity of C/N Balance Regulation in Prochlorococcus. Front Microbiol 2018; 8:2641. [PMID: 29375510 PMCID: PMC5767323 DOI: 10.3389/fmicb.2017.02641] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/19/2017] [Indexed: 11/29/2022] Open
Abstract
Previous studies showed differences in the regulatory response to C/N balance in Prochlorococcus with respect to other cyanobacteria, but no information was available about its causes, or the ecological advantages conferred to thrive in oligotrophic environments. We addressed the changes in key enzymes (glutamine synthetase, isocitrate dehydrogenase) and the ntcA gene (the global nitrogen regulator) involved in C/N metabolism and its regulation, in three model Prochlorococcus strains: MED4, SS120, and MIT9313. We observed a remarkable level of diversity in their response to azaserine, a glutamate synthase inhibitor which increases the concentration of the key metabolite 2-oxoglutarate, used to sense the C/N balance by cyanobacteria. Besides, we studied the binding between the global nitrogen regulator (NtcA) and the promoter of the glnA gene in the same Prochlorococcus strains, and its dependence on the 2-oxoglutarate concentration, by using isothermal titration calorimetry, surface plasmon resonance, and electrophoretic mobility shift. Our results show a reduction in the responsiveness of NtcA to 2-oxoglutarate in Prochlorococcus, especially in the MED4 and SS120 strains. This suggests a trend to streamline the regulation of C/N metabolism in late-branching Prochlorococcus strains (MED4 and SS120), in adaptation to the rather stable conditions found in the oligotrophic ocean gyres where this microorganism is most abundant.
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Affiliation(s)
- María A Domínguez-Martín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Antonio López-Lozano
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - Rafael Clavería-Gimeno
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units BIFI-IQFR-CSIC and GBsC-BIFI-CSIC, Universidad de Zaragoza, Zaragoza, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain.,Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units BIFI-IQFR-CSIC and GBsC-BIFI-CSIC, Universidad de Zaragoza, Zaragoza, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain.,Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas, Barcelona, Spain.,Fundación ARAID, Gobierno de Aragón, Zaragoza, Spain
| | - Gerald Seidel
- Professur für Mikrobiologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Andreas Burkovski
- Professur für Mikrobiologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jesús Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
| | - José M García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CeiA3, Universidad de Córdoba, Córdoba, Spain
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28
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Nitrogen cost minimization is promoted by structural changes in the transcriptome of N-deprived Prochlorococcus cells. ISME JOURNAL 2017; 11:2267-2278. [PMID: 28585937 PMCID: PMC5607370 DOI: 10.1038/ismej.2017.88] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 04/20/2017] [Accepted: 04/28/2017] [Indexed: 01/17/2023]
Abstract
Prochlorococcus is a globally abundant marine cyanobacterium with many adaptations that reduce cellular nutrient requirements, facilitating growth in its nutrient-poor environment. One such genomic adaptation is the preferential utilization of amino acids containing fewer N-atoms, which minimizes cellular nitrogen requirements. We predicted that transcriptional regulation might further reduce cellular N budgets during transient N limitation. To explore this, we compared transcription start sites (TSSs) in Prochlorococcus MED4 under N-deprived and N-replete conditions. Of 64 genes with primary and internal TSSs in both conditions, N-deprived cells initiated transcription downstream of primary TSSs more frequently than N-replete cells. Additionally, 117 genes with only an internal TSS demonstrated increased internal transcription under N-deprivation. These shortened transcripts encode predicted proteins with an average of 21% less N content compared to full-length transcripts. We hypothesized that low translation rates, which afford greater control over protein abundances, would be beneficial to relatively slow-growing organisms like Prochlorococcus. Consistent with this idea, we found that Prochlorococcus exhibits greater usage of glycine–glycine motifs, which causes translational pausing, when compared to faster growing microbes. Our findings indicate that structural changes occur within the Prochlorococcus MED4 transcriptome during N-deprivation, potentially altering the size and structure of proteins expressed under nutrient limitation.
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29
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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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30
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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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31
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Abstract
SAR11 is a group of small, carbon-oxidizing bacteria that reach a global estimated population size of 2.4×1028 cells-approximately 25% of all plankton. They are found throughout the oceans but reach their largest numbers in stratified, oligotrophic gyres, which are an expanding habitat in the warming oceans. SAR11 likely had a Precambrian origin and, over geological time, evolved into the niche of harvesting labile, low-molecular-weight dissolved organic matter (DOM). SAR11 cells are minimal in size and complexity, a phenomenon known as streamlining that is thought to benefit them by lowering the material costs of replication and maximizing transport functions that are essential to competition at ultralow nutrient concentrations. One of the surprises in SAR11 metabolism is their ability to both oxidize and produce a variety of volatile organic compounds that can diffuse into the atmosphere. SAR11 cells divide slowly and lack many forms of regulation commonly used by bacterial cells to adjust to changing environmental conditions. As a result of genome reduction, they require an unusual range of nutrients, which leads to complex biochemical interactions with other plankton. The study of SAR11 is providing insight into the biogeochemistry of labile DOM and is affecting microbiology beyond marine science by providing a model for understanding the evolution and function of streamlined cells.
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32
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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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33
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Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus. mSystems 2016; 1:mSystems00065-16. [PMID: 27868089 PMCID: PMC5111396 DOI: 10.1128/msystems.00065-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 10/17/2016] [Indexed: 01/05/2023] Open
Abstract
Microbes are known to employ three basic strategies to compete for limiting elemental resources: (i) cell quotas may be adjusted by alterations to cell physiology or by substitution of a more plentiful resource, (ii) stressed cells may synthesize high-affinity transporters, and (iii) cells may access more costly sources from internal stores, by degradation, or by petitioning other microbes. In the case of phosphorus, a limiting resource in vast oceanic regions, the cosmopolitan cyanobacterium Prochlorococcus marinus thrives by adopting all three strategies and a fourth, previously unknown strategy. By generating a detailed model of its metabolism, we found that strain MED4 has evolved a way to reduce its dependence on phosphate by minimizing the number of enzymes involved in phosphate transformations, despite the stringency of nearly half of its metabolic genes being essential for survival. Relieving phosphorus limitation, both physiologically and throughout intermediate metabolism, substantially improves phosphorus-specific growth rates. Inorganic phosphorus is scarce in the eastern Mediterranean Sea, where the high-light-adapted ecotype HLI of the marine picocyanobacterium Prochlorococcus marinus thrives. Physiological and regulatory control of phosphorus acquisition and partitioning has been observed in HLI both in culture and in the field; however, the optimization of phosphorus metabolism and associated gains for its phosphorus-limited-growth (PLG) phenotype have not been studied. Here, we reconstructed a genome-scale metabolic network of the HLI axenic strain MED4 (iJC568), consisting of 568 metabolic genes in relation to 794 reactions involving 680 metabolites distributed in 6 subcellular locations. iJC568 was used to quantify metabolic fluxes under PLG conditions, and we observed a close correspondence between experimental and computed fluxes. We found that MED4 has minimized its dependence on intracellular phosphate, not only through drastic depletion of phosphorus-containing biomass components but also through network-wide reductions in phosphate-reaction participation and the loss of a key enzyme, succinate dehydrogenase. These alterations occur despite the stringency of having relatively few pathway redundancies and an extremely high proportion of essential metabolic genes (47%; defined as the percentage of lethal in silico gene knockouts). These strategies are examples of nutrient-controlled adaptive evolution and confer a dramatic growth rate advantage to MED4 in phosphorus-limited regions. IMPORTANCE Microbes are known to employ three basic strategies to compete for limiting elemental resources: (i) cell quotas may be adjusted by alterations to cell physiology or by substitution of a more plentiful resource, (ii) stressed cells may synthesize high-affinity transporters, and (iii) cells may access more costly sources from internal stores, by degradation, or by petitioning other microbes. In the case of phosphorus, a limiting resource in vast oceanic regions, the cosmopolitan cyanobacterium Prochlorococcus marinus thrives by adopting all three strategies and a fourth, previously unknown strategy. By generating a detailed model of its metabolism, we found that strain MED4 has evolved a way to reduce its dependence on phosphate by minimizing the number of enzymes involved in phosphate transformations, despite the stringency of nearly half of its metabolic genes being essential for survival. Relieving phosphorus limitation, both physiologically and throughout intermediate metabolism, substantially improves phosphorus-specific growth rates.
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34
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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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Burns AS, Bullock HA, Smith C, Huang Q, Whitman WB, Moran MA. Small RNAs expressed during dimethylsulfoniopropionate degradation by a model marine bacterium. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:763-773. [PMID: 27337503 DOI: 10.1111/1758-2229.12437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 06/02/2016] [Accepted: 06/06/2016] [Indexed: 06/06/2023]
Abstract
The fate of the sulfur moiety of dimethylsulfoniopropionate (DMSP) depends on the 'bacterial switch', a regulatory point between two metabolic pathways with different biogeochemical endpoints. Studies have focused on transcriptional patterns of known genes to determine physiological and environmental factors affecting this switch, but post-transcriptional regulation has been under-studied. Here we use a model bacterium containing both pathways to look for transcription of non-coding regulatory small RNAs (sRNAs) during DMSP metabolism. RNA-seq analysis of Ruegeria pomeroyi DSS-3 grown with DMSP, metabolic intermediates of DMSP degradation (MMPA or acetate), or methionine revealed 182 putative sRNAs, with 46 showing differential expression during growth on DMSP. A knockout mutant constructed for an upregulated sRNA had a phenotype that differed in its use of the two degradation pathways. Because transcription patterns of many differentially expressed sRNAs were not correlated with the transcription of their putative target gene, their effects on DMSP degradation would not be observable in the transcriptome. Overall, our results indicate that sRNAs are crucial but largely cryptic actors in regulating DMSP metabolism in this model marine bacterium and potentially other bacterial groups involved in the surface ocean sulfur cycle.
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Affiliation(s)
- Andrew S Burns
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Hannah A Bullock
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Christa Smith
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Qiuyuan Huang
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | | | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
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McClure RS, Overall CC, McDermott JE, Hill EA, Markillie LM, McCue LA, Taylor RC, Ludwig M, Bryant DA, Beliaev AS. Network analysis of transcriptomics expands regulatory landscapes in Synechococcus sp. PCC 7002. Nucleic Acids Res 2016; 44:8810-8825. [PMID: 27568004 PMCID: PMC5062996 DOI: 10.1093/nar/gkw737] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 08/05/2016] [Indexed: 12/29/2022] Open
Abstract
Cyanobacterial regulation of gene expression must contend with a genome organization that lacks apparent functional context, as the majority of cellular processes and metabolic pathways are encoded by genes found at disparate locations across the genome and relatively few transcription factors exist. In this study, global transcript abundance data from the model cyanobacterium Synechococcus sp. PCC 7002 grown under 42 different conditions was analyzed using Context-Likelihood of Relatedness (CLR). The resulting network, organized into 11 modules, provided insight into transcriptional network topology as well as grouping genes by function and linking their response to specific environmental variables. When used in conjunction with genome sequences, the network allowed identification and expansion of novel potential targets of both DNA binding proteins and sRNA regulators. These results offer a new perspective into the multi-level regulation that governs cellular adaptations of the fast-growing physiologically robust cyanobacterium Synechococcus sp. PCC 7002 to changing environmental variables. It also provides a methodological high-throughput approach to studying multi-scale regulatory mechanisms that operate in cyanobacteria. Finally, it provides valuable context for integrating systems-level data to enhance gene grouping based on annotated function, especially in organisms where traditional context analyses cannot be implemented due to lack of operon-based functional organization.
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Affiliation(s)
- Ryan S McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Christopher C Overall
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Eric A Hill
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Lye Meng Markillie
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Lee Ann McCue
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ronald C Taylor
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Marcus Ludwig
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA 16802, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA 16802, USA Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Alexander S Beliaev
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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Stazic D, Pekarski I, Kopf M, Lindell D, Steglich C. A Novel Strategy for Exploitation of Host RNase E Activity by a Marine Cyanophage. Genetics 2016; 203:1149-59. [PMID: 27182944 PMCID: PMC4937493 DOI: 10.1534/genetics.115.183475] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 05/04/2016] [Indexed: 11/18/2022] Open
Abstract
Previous studies have shown that infection of Prochlorococcus MED4 by the cyanophage P-SSP7 leads to increased transcript levels of host endoribonuclease (RNase) E. However, it has remained enigmatic whether this is part of a host defense mechanism to degrade phage messenger RNA (mRNA) or whether this single-strand RNA-specific RNase is utilized by the phage. Here we describe a hitherto unknown means through which this cyanophage increases expression of RNase E during phage infection and concomitantly protects its own RNA from degradation. We identified two functionally different RNase E mRNA variants, one of which is significantly induced during phage infection. This transcript lacks the 5' UTR, is considerably more stable than the other transcript, and is likely responsible for increased RNase E protein levels during infection. Furthermore, selective enrichment and in vivo analysis of double-stranded RNA (dsRNA) during infection revealed that phage antisense RNAs (asRNAs) sequester complementary mRNAs to form dsRNAs, such that the phage protein-coding transcriptome is nearly completely covered by asRNAs. In contrast, the host protein-coding transcriptome is only partially covered by asRNAs. These data suggest that P-SSP7 orchestrates degradation of host RNA by increasing RNase E expression while masking its own transcriptome from RNase E degradation in dsRNA complexes. We propose that this combination of strategies contributes significantly to phage progeny production.
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Affiliation(s)
- Damir Stazic
- Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Irena Pekarski
- Department of Biology, Technion Institute of Technology, Haifa 32000, Israel
| | - Matthias Kopf
- Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Debbie Lindell
- Department of Biology, Technion Institute of Technology, Haifa 32000, Israel
| | - Claudia Steglich
- Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
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Torn apart and reunited: impact of a heterotroph on the transcriptome of Prochlorococcus. ISME JOURNAL 2016; 10:2831-2843. [PMID: 27258949 DOI: 10.1038/ismej.2016.82] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 03/29/2016] [Accepted: 04/12/2016] [Indexed: 11/09/2022]
Abstract
Microbial interactions, whether direct or indirect, profoundly affect the physiology of individual cells and ultimately have the potential to shape the biogeochemistry of the Earth. For example, the growth of Prochlorococcus, the numerically dominant cyanobacterium in the oceans, can be improved by the activity of co-occurring heterotrophs. This effect has been largely attributed to the role of heterotrophs in detoxifying reactive oxygen species that Prochlorococcus, which lacks catalase, cannot. Here, we explore this phenomenon further by examining how the entire transcriptome of Prochlorococcus NATL2A changes in the presence of a naturally co-occurring heterotroph, Alteromonas macleodii MIT1002, with which it was co-cultured for years, separated and then reunited. Significant changes in the Prochlorococcus transcriptome were evident within 6 h of initiating co-culture, with groups of transcripts changing in different temporal waves. Many transcriptional changes persisted throughout the 48 h experiment, suggesting that the presence of the heterotroph affected a stable shift in Prochlorococcus physiology. These initial transcriptome changes largely corresponded to reduced stress conditions for Prochlorococcus, as inferred from the depletion of transcripts encoding DNA repair enzymes and many members of the 'high light inducible' family of stress-response proteins. Later, notable changes were seen in transcripts encoding components of the photosynthetic apparatus (particularly, an increase in PSI subunits and chlorophyll synthesis enzymes), ribosomal proteins and biosynthetic enzymes, suggesting that the introduction of the heterotroph may have induced increased production of reduced carbon compounds for export. Changes in secretion-related proteins and transporters also highlight the potential for metabolic exchange between the two strains.
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The Entner-Doudoroff pathway is an overlooked glycolytic route in cyanobacteria and plants. Proc Natl Acad Sci U S A 2016; 113:5441-6. [PMID: 27114545 DOI: 10.1073/pnas.1521916113] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Glucose degradation pathways are central for energy and carbon metabolism throughout all domains of life. They provide ATP, NAD(P)H, and biosynthetic precursors for amino acids, nucleotides, and fatty acids. It is general knowledge that cyanobacteria and plants oxidize carbohydrates via glycolysis [the Embden-Meyerhof-Parnas (EMP) pathway] and the oxidative pentose phosphate (OPP) pathway. However, we found that both possess a third, previously overlooked pathway of glucose breakdown: the Entner-Doudoroff (ED) pathway. Its key enzyme, 2-keto-3-deoxygluconate-6-phosphate (KDPG) aldolase, is widespread in cyanobacteria, moss, fern, algae, and plants and is even more common among cyanobacteria than phosphofructokinase (PFK), the key enzyme of the EMP pathway. Active KDPG aldolases from the cyanobacterium Synechocystis and the plant barley (Hordeum vulgare) were biochemically characterized in vitro. KDPG, a metabolite unique to the ED pathway, was detected in both in vivo, indicating an active ED pathway. Phylogenetic analyses revealed that photosynthetic eukaryotes acquired KDPG aldolase from the cyanobacterial ancestors of plastids via endosymbiotic gene transfer. Several Synechocystis mutants in which key enzymes of all three glucose degradation pathways were knocked out indicate that the ED pathway is physiologically significant, especially under mixotrophic conditions (light and glucose) and under autotrophic conditions in a day/night cycle, which is probably the most common condition encountered in nature. The ED pathway has lower protein costs and ATP yields than the EMP pathway, in line with the observation that oxygenic photosynthesizers are nutrient-limited, rather than ATP-limited. Furthermore, the ED pathway does not generate futile cycles in organisms that fix CO2 via the Calvin-Benson cycle.
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Rivers AR, Burns AS, Chan LK, Moran MA. Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3. Front Microbiol 2016; 7:380. [PMID: 27065955 PMCID: PMC4809877 DOI: 10.3389/fmicb.2016.00380] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/09/2016] [Indexed: 12/31/2022] Open
Abstract
In oligotrophic ocean waters where bacteria are often subjected to chronic nutrient limitation, community transcriptome sequencing has pointed to the presence of highly abundant small RNAs (sRNAs). The role of sRNAs in regulating response to nutrient stress was investigated in a model heterotrophic marine bacterium Ruegeria pomeroyi grown in continuous culture under carbon (C) and nitrogen (N) limitation. RNAseq analysis identified 99 putative sRNAs. Sixty-nine were cis-encoded and located antisense to a presumed target gene. Thirty were trans-encoded and initial target prediction was performed computationally. The most prevalent functional roles of genes anti-sense to the cis-sRNAs were transport, cell-cell interactions, signal transduction, and transcriptional regulation. Most sRNAs were transcribed equally under both C and N limitation, and may be involved in a general stress response. However, 14 were regulated differentially between the C and N treatments and may respond to specific nutrient limitations. A network analysis of the predicted target genes of the R. pomeroyi cis-sRNAs indicated that they average fewer connections than typical protein-encoding genes, and appear to be more important in peripheral or niche-defining functions encoded in the pan genome.
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Affiliation(s)
- Adam R Rivers
- United States Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | - Andrew S Burns
- Department of Marine Sciences, University of Georgia Athens, GA, USA
| | | | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia Athens, GA, USA
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41
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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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Ramey CJ, Barón-Sola Á, Aucoin HR, Boyle NR. Genome Engineering in Cyanobacteria: Where We Are and Where We Need To Go. ACS Synth Biol 2015; 4:1186-96. [PMID: 25985322 DOI: 10.1021/acssynbio.5b00043] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Genome engineering of cyanobacteria is a promising area of development in order to produce fuels, feedstocks, and value-added chemicals in a sustainable way. Unfortunately, the current state of genome engineering tools for cyanobacteria lags far behind those of model organisms such as Escherichia coli and Saccharomyces cerevisiae. In this review, we present the current state of synthetic biology tools for genome engineering efforts in the most widely used cyanobacteria strains and areas that need concerted research efforts to improve tool development. Cyanobacteria pose unique challenges to genome engineering efforts because their cellular biology differs significantly from other eubacteria; therefore, tools developed for other genera are not directly transferrable. Standardized parts, such as promoters and ribosome binding sites, which control gene expression, require characterization in cyanobacteria in order to have fully predictable results. The application of these tools to genome engineering efforts is also discussed; the ability to do genome-wide searching and to introduce multiple mutations simultaneously is an area that needs additional research in order to enable fast and efficient strain engineering.
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Affiliation(s)
- C. Josh Ramey
- Chemical and Biological Engineering
Department, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Ángel Barón-Sola
- Chemical and Biological Engineering
Department, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Hanna R. Aucoin
- Chemical and Biological Engineering
Department, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Nanette R. Boyle
- Chemical and Biological Engineering
Department, Colorado School of Mines, Golden, Colorado 80401, United States
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43
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Klähn S, Orf I, Schwarz D, Matthiessen JKF, Kopka J, Hess WR, Hagemann M. Integrated Transcriptomic and Metabolomic Characterization of the Low-Carbon Response Using an ndhR Mutant of Synechocystis sp. PCC 6803. PLANT PHYSIOLOGY 2015; 169:1540-56. [PMID: 25630438 PMCID: PMC4634042 DOI: 10.1104/pp.114.254045] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 01/27/2015] [Indexed: 05/17/2023]
Abstract
The acquisition and assimilation of inorganic carbon (Ci) represents the largest flux of inorganic matter in photosynthetic organisms; hence, this process is tightly regulated. We examined the Ci-dependent transcriptional and metabolic regulation in wild-type Synechocystis sp. PCC 6803 compared with a mutant defective in the main transcriptional repressor for Ci acquisition genes, the NAD(P)H dehydrogenase transcriptional regulator NdhR. The analysis revealed that many protein-coding transcripts that are normally repressed in the presence of high CO2 (HC) concentrations were strongly expressed in ∆ndhR, whereas other messenger RNAs were strongly down-regulated in mutant cells, suggesting a potential activating role for NdhR. A conserved NdhR-binding motif was identified in the promoters of derepressed genes. Interestingly, the expression of some NdhR-regulated genes remained further inducible under low-CO2 conditions, indicating the involvement of additional NdhR-independent Ci-regulatory mechanisms. Intriguingly, we also observed that the abundance of 52 antisense RNAs and 34 potential noncoding RNAs was affected by Ci supply, although most of these molecules were not regulated through NdhR. Thus, antisense and noncoding RNAs could contribute to NdhR-independent carbon regulation. In contrast to the transcriptome, the metabolome in ∆ndhR cells was similar to that of wild-type cells under HC conditions. This observation and the delayed metabolic responses to the low-CO2 shift in ∆ndhR, specifically the lack of transient increases in the photorespiratory pathway intermediates 2-phosphoglycolate, glycolate, and glycine, suggest that the deregulation of gene expression in the ΔndhR mutant successfully preacclimates cyanobacterial cells to lowered Ci supply under HC conditions.
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Affiliation(s)
- Stephan Klähn
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Isabel Orf
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Doreen Schwarz
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Jasper K F Matthiessen
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Joachim Kopka
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
| | - Martin Hagemann
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany (S.K., J.K.F.M., W.R.H.);Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, D-14476 Potsdam-Golm, Germany (I.O., J.K.); andPlant Physiology Department, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany (D.S., M.H.)
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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: 75] [Impact Index Per Article: 8.3] [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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Bagby SC, Chisholm SW. Response of Prochlorococcus to varying CO2:O2 ratios. THE ISME JOURNAL 2015; 9:2232-45. [PMID: 25848872 PMCID: PMC4579476 DOI: 10.1038/ismej.2015.36] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 02/06/2015] [Accepted: 02/12/2015] [Indexed: 11/08/2022]
Abstract
Carbon fixation has a central role in determining cellular redox poise, increasingly understood to be a key parameter in cyanobacterial physiology. In the cyanobacterium Prochlorococcus-the most abundant phototroph in the oligotrophic oceans-the carbon-concentrating mechanism is reduced to the bare essentials. Given the ability of Prochlorococcus populations to grow under a wide range of oxygen concentrations in the ocean, we wondered how carbon and oxygen physiology intersect in this minimal phototroph. Thus, we examined how CO2:O2 gas balance influenced growth and chlorophyll fluorescence in Prochlorococcus strain MED4. Under O2 limitation, per-cell chlorophyll fluorescence fell at all CO2 levels, but still permitted substantial growth at moderate and high CO2. Under CO2 limitation, we observed little growth at any O2 level, although per-cell chlorophyll fluorescence fell less sharply when O2 was available. We explored this pattern further by monitoring genome-wide transcription in cells shocked with acute limitation of CO2, O2 or both. O2 limitation produced much smaller transcriptional changes than the broad suppression seen under CO2 limitation and CO2/O2 co-limitation. Strikingly, both CO2 limitation conditions initially evoked a transcriptional response that resembled the pattern previously seen in high-light stress, but at later timepoints we observed O2-dependent recovery of photosynthesis-related transcripts. These results suggest that oxygen has a protective role in Prochlorococcus when carbon fixation is not a sufficient sink for light energy.
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Affiliation(s)
- Sarah C Bagby
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sallie W Chisholm
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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46
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Transcriptomic and Proteomic Profiling of Anabaena sp. Strain 90 under Inorganic Phosphorus Stress. Appl Environ Microbiol 2015; 81:5212-22. [PMID: 26025890 DOI: 10.1128/aem.01062-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 05/18/2015] [Indexed: 01/06/2023] Open
Abstract
Inorganic phosphorus (Pi) is one of the main growth-limiting factors of diazotrophic cyanobacteria. Due to human activity, the availability of Pi has increased in water bodies, resulting in eutrophication and the formation of massive cyanobacterial blooms. In this study, we examined the molecular responses of the cyanobacterium Anabaena sp. strain 90 to phosphorus deprivation, aiming at the identification of candidate genes to monitor the Pi status in cyanobacteria. Furthermore, this study increased the basic understanding of how phosphorus affects diazotrophic and bloom-forming cyanobacteria as a major growth-limiting factor. Based on RNA sequencing data, we identified 246 differentially expressed genes after phosphorus starvation and 823 differentially expressed genes after prolonged Pi limitation, most of them related to central metabolism and cellular growth. The transcripts of the genes related to phosphorus transport and assimilation (pho regulon) were most upregulated during phosphorus depletion. One of the most increased transcripts encodes a giant protein of 1,869 amino acid residues, which contains, among others, a phytase-like domain. Our findings predict its crucial role in phosphorus starvation, but future studies are still needed. Using two-dimensional difference in gel electrophoresis (2D-DIGE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), we found 43 proteins that were differentially expressed after prolonged phosphorus stress. However, correlation analysis unraveled an association only to some extent between the transcriptomic and proteomic abundances. Based on the present results, we suggest that the method used for monitoring the Pi status in cyanobacterial bloom should contain wider combinations of pho regulon genes (e.g., PstABCS transport systems) in addition to the commonly used alkaline phosphatase gene alone.
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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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Papenfort K, Vanderpool CK. Target activation by regulatory RNAs in bacteria. FEMS Microbiol Rev 2015; 39:362-78. [PMID: 25934124 DOI: 10.1093/femsre/fuv016] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2015] [Indexed: 12/15/2022] Open
Abstract
Bacterial small regulatory RNAs (sRNAs) are commonly known to repress gene expression by base pairing to target mRNAs. In many cases, sRNAs base pair with and sequester mRNA ribosome-binding sites, resulting in translational repression and accelerated transcript decay. In contrast, a growing number of examples of translational activation and mRNA stabilization by sRNAs have now been documented. A given sRNA often employs a conserved region to interact with and regulate both repressed and activated targets. However, the mechanisms underlying activation differ substantially from repression. Base pairing resulting in target activation can involve sRNA interactions with the 5(') untranslated region (UTR), the coding sequence or the 3(') UTR of the target mRNAs. Frequently, the activities of protein factors such as cellular ribonucleases and the RNA chaperone Hfq are required for activation. Bacterial sRNAs, including those that function as activators, frequently control stress response pathways or virulence-associated functions required for immediate responses to changing environments. This review aims to summarize recent advances in knowledge regarding target mRNA activation by bacterial sRNAs, highlighting the molecular mechanisms and biological relevance of regulation.
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Affiliation(s)
- Kai Papenfort
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA Department of Biology I, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany
| | - Carin K Vanderpool
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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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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Abstract
The concept of the minimal cell has fascinated scientists for a long time, from both fundamental and applied points of view. This broad concept encompasses extreme reductions of genomes, the last universal common ancestor (LUCA), the creation of semiartificial cells, and the design of protocells and chassis cells. Here we review these different areas of research and identify common and complementary aspects of each one. We focus on systems biology, a discipline that is greatly facilitating the classical top-down and bottom-up approaches toward minimal cells. In addition, we also review the so-called middle-out approach and its contributions to the field with mathematical and computational models. Owing to the advances in genomics technologies, much of the work in this area has been centered on minimal genomes, or rather minimal gene sets, required to sustain life. Nevertheless, a fundamental expansion has been taking place in the last few years wherein the minimal gene set is viewed as a backbone of a more complex system. Complementing genomics, progress is being made in understanding the system-wide properties at the levels of the transcriptome, proteome, and metabolome. Network modeling approaches are enabling the integration of these different omics data sets toward an understanding of the complex molecular pathways connecting genotype to phenotype. We review key concepts central to the mapping and modeling of this complexity, which is at the heart of research on minimal cells. Finally, we discuss the distinction between minimizing the number of cellular components and minimizing cellular complexity, toward an improved understanding and utilization of minimal and simpler cells.
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