1
|
Han Y, Ge H, Xu C, Zeng G, Li Z, Huang X, Zhang Y, Liu Z, Wang Y, Fang L. Glycosyltransferase Slr1064 regulates carbon metabolism by modulating the levels of UDP-GlcNAc in Synechocystis sp. PCC 6803. THE NEW PHYTOLOGIST 2024. [PMID: 38831647 DOI: 10.1111/nph.19872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/15/2024] [Indexed: 06/05/2024]
Abstract
Glycosyltransferases (GTs) are enzymes that transfer sugars to various targets. They play important roles in diverse biological processes, including photosynthesis, cell motility, exopolysaccharide biosynthesis, and lipid metabolism; however, their involvement in regulating carbon metabolism in Synechocystis sp. PCC 6803 has not been reported. We identified a novel GT protein, Slr1064, involved in carbon metabolism. The effect of slr1064 deletion on the growth of Synechocystis cells and functional mechanisms of Slr1064 on carbon metabolism were thoroughly investigated through physiological, biochemistry, proteomic, and metabolic analyses. We found that this GT, which is mainly distributed in the membrane compartment, is essential for the growth of Synechocystis under heterotrophic and mixotrophic conditions, but not under autotrophic conditions. The deletion of slr1064 hampers the turnover rate of Gap2 under mixotrophic conditions and disrupts the assembly of the PRK/GAPDH/CP12 complex under dark culture conditions. Additionally, UDP-GlcNAc, the pivotal metabolite responsible for the O-GlcNAc modification of GAPDH, is downregulated in the Δslr1064. Our work provides new insights into the role of GTs in carbon metabolism in Synechocystis and elucidate the mechanism by which carbon metabolism is regulated in this important model organism.
Collapse
Affiliation(s)
- Yuling Han
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Haitao Ge
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100049, China
| | - Congzhuo Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Gang Zeng
- Zunyi Normal College, Zunyi, 100049, China
| | - Zhen Li
- National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanya Zhang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhipeng Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100049, China
| | - Longfa Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| |
Collapse
|
2
|
Hoffmann UA, Lichtenberg E, Rogh SN, Bilger R, Reimann V, Heyl F, Backofen R, Steglich C, Hess WR, Wilde A. The role of the 5' sensing function of ribonuclease E in cyanobacteria. RNA Biol 2024; 21:1-18. [PMID: 38469716 PMCID: PMC10939160 DOI: 10.1080/15476286.2024.2328438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2024] [Indexed: 03/13/2024] Open
Abstract
RNA degradation is critical for synchronising gene expression with changing conditions in prokaryotic and eukaryotic organisms. In bacteria, the preference of the central ribonucleases RNase E, RNase J and RNase Y for 5'-monophosphorylated RNAs is considered important for RNA degradation. For RNase E, the underlying mechanism is termed 5' sensing, contrasting to the alternative 'direct entry' mode, which is independent of monophosphorylated 5' ends. Cyanobacteria, such as Synechocystis sp. PCC 6803 (Synechocystis), encode RNase E and RNase J homologues. Here, we constructed a Synechocystis strain lacking the 5' sensing function of RNase E and mapped on a transcriptome-wide level 283 5'-sensing-dependent cleavage sites. These included so far unknown targets such as mRNAs encoding proteins related to energy metabolism and carbon fixation. The 5' sensing function of cyanobacterial RNase E is important for the maturation of rRNA and several tRNAs, including tRNAGluUUC. This tRNA activates glutamate for tetrapyrrole biosynthesis in plant chloroplasts and in most prokaryotes. Furthermore, we found that increased RNase activities lead to a higher copy number of the major Synechocystis plasmids pSYSA and pSYSM. These results provide a first step towards understanding the importance of the different target mechanisms of RNase E outside Escherichia coli.
Collapse
Affiliation(s)
- Ute A. Hoffmann
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, Freiburg, Germany
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Elisabeth Lichtenberg
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Said N. Rogh
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Raphael Bilger
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Viktoria Reimann
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Florian Heyl
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Claudia Steglich
- 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
| | - Annegret Wilde
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, Freiburg, Germany
| |
Collapse
|
3
|
Balaga RR, Itoh F, Chauhan S, Mandal M, Krishna PS, Suzuki I, Prakash JSS. Sll1252 Coordinates Electron Transport between Plastoquinone and Cytochrome b6/f Complex in Synechocystis PCC 6803. Genes (Basel) 2023; 14:2151. [PMID: 38136973 PMCID: PMC10743179 DOI: 10.3390/genes14122151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/13/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
A mutant, Δsll1252ins, was generated to functionally characterize Sll1252. Δsll1252ins exhibited a slow-growth phenotype at 70 µmol photons m-2 s-1 and glucose sensitivity. In Δsll1252ins, the rate of PSII activity was not affected, whereas the whole chain electron transport activity was reduced by 45%. The inactivation of sll1252 led to the upregulation of genes, which were earlier reported to be induced in DBMIB-treated wild-type, suggesting that Sll1252 may be involved in electron transfer from the reduced-PQ pool to Cyt b6/f. The inhibitory effect of DCMU on PSII activity was similar in both wild-type and Δsll1252ins. However, the concentration of DBMIB for 50% inhibition of whole chain electron transport activity was 140 nM for Δsll1252ins and 300 nM for wild-type, confirming the site of action of Sll1252. Moreover, the elevated level of the reduced-PQ pool in Δsll1252ins supports that Sll1252 functions between the PQ pool and Cyt b6/f. Interestingly, we noticed that Δsll1252ins reverted to wild-type phenotype by insertion of natural transposon, ISY523, at the disruption site. Δsll1252-Ntrn, expressing only the C-terminal region of Sll1252, exhibited a slow-growth phenotype and disorganized thylakoid structure compared to wild-type and Δsll1252-Ctrn (expressing only the N-terminal region). Collectively, our data suggest that Sll1252 regulates electron transfer between the PQ pool and the Cyt b6/f complex in the linear photosynthetic electron transport chain via coordinated function of both the N- and C-terminal regions of Sll1252.
Collapse
Affiliation(s)
- Radha Rani Balaga
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India;
| | - Fumihiro Itoh
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba 305-8572, Japan;
| | - Suraj Chauhan
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India; (S.C.); (M.M.); (P.S.K.)
| | - Mukulika Mandal
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India; (S.C.); (M.M.); (P.S.K.)
| | - Pilla Sankara Krishna
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India; (S.C.); (M.M.); (P.S.K.)
| | - Iwane Suzuki
- Institute of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba 305-8572, Japan;
| | - Jogadhenu S. S. Prakash
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India; (S.C.); (M.M.); (P.S.K.)
| |
Collapse
|
4
|
Opel F, Siebert NA, Klatt S, Tüllinghoff A, Hantke JG, Toepel J, Bühler B, Nürnberg DJ, Klähn S. Generation of Synthetic Shuttle Vectors Enabling Modular Genetic Engineering of Cyanobacteria. ACS Synth Biol 2022; 11:1758-1771. [PMID: 35405070 DOI: 10.1021/acssynbio.1c00605] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cyanobacteria have raised great interest in biotechnology due to their potential for a sustainable, photosynthesis-driven production of fuels and value-added chemicals. This has led to a concomitant development of molecular tools to engineer the metabolism of those organisms. In this regard, however, even cyanobacterial model strains lag behind compared to their heterotrophic counterparts. For instance, replicative shuttle vectors that allow gene transfer independent of recombination into host DNA are still scarce. Here, we introduce the pSOMA shuttle vector series comprising 10 synthetic plasmids for comprehensive genetic engineering of Synechocystis sp. PCC 6803. The series is based on the small endogenous plasmids pCA2.4 and pCB2.4, each combined with a replicon from Escherichia coli, different selection markers as well as features facilitating molecular cloning and the insulated introduction of gene expression cassettes. We made use of genes encoding green fluorescent protein (GFP) and a Baeyer-Villiger monooxygenase (BVMO) to demonstrate functional gene expression from the pSOMA plasmids in vivo. Moreover, we demonstrate the expression of distinct heterologous genes from individual plasmids maintained in the same strain and thereby confirmed compatibility between the two pSOMA subseries as well as with derivatives of the broad-host-range plasmid RSF1010. We also show that gene transfer into the filamentous model strain Anabaena sp. PCC 7120 is generally possible, which is encouraging to further explore the range of cyanobacterial host species that could be engineered via pSOMA plasmids. Altogether, the pSOMA shuttle vector series displays an attractive alternative to existing plasmid series and thus meets the current demand for the introduction of complex genetic setups and to perform extensive metabolic engineering of cyanobacteria.
Collapse
Affiliation(s)
- Franz Opel
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Nina A. Siebert
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Sabine Klatt
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Adrian Tüllinghoff
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Janis G. Hantke
- Institute of Experimental Physics, Biochemistry and Biophysics of Photosynthetic Organisms, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jörg Toepel
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Dennis J. Nürnberg
- Institute of Experimental Physics, Biochemistry and Biophysics of Photosynthetic Organisms, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Stephan Klähn
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| |
Collapse
|
5
|
Hoffmann UA, Heyl F, Rogh SN, Wallner T, Backofen R, Hess WR, Steglich C, Wilde A. Transcriptome-wide in vivo mapping of cleavage sites for the compact cyanobacterial ribonuclease E reveals insights into its function and substrate recognition. Nucleic Acids Res 2021; 49:13075-13091. [PMID: 34871439 PMCID: PMC8682795 DOI: 10.1093/nar/gkab1161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/26/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022] Open
Abstract
Ribonucleases are crucial enzymes in RNA metabolism and post-transcriptional regulatory processes in bacteria. Cyanobacteria encode the two essential ribonucleases RNase E and RNase J. Cyanobacterial RNase E is shorter than homologues in other groups of bacteria and lacks both the chloroplast-specific N-terminal extension as well as the C-terminal domain typical for RNase E of enterobacteria. In order to investigate the function of RNase E in the model cyanobacterium Synechocystis sp. PCC 6803, we engineered a temperature-sensitive RNase E mutant by introducing two site-specific mutations, I65F and the spontaneously occurred V94A. This enabled us to perform RNA-seq after the transient inactivation of RNase E by a temperature shift (TIER-seq) and to map 1472 RNase-E-dependent cleavage sites. We inferred a dominating cleavage signature consisting of an adenine at the -3 and a uridine at the +2 position within a single-stranded segment of the RNA. The data identified mRNAs likely regulated jointly by RNase E and an sRNA and potential 3' end-derived sRNAs. Our findings substantiate the pivotal role of RNase E in post-transcriptional regulation and suggest the redundant or concerted action of RNase E and RNase J in cyanobacteria.
Collapse
Affiliation(s)
- Ute A Hoffmann
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany
| | - Florian Heyl
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany
| | - Said N Rogh
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Wallner
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Claudia Steglich
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Annegret Wilde
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
6
|
Oeser S, Wallner T, Schuergers N, Bučinská L, Sivabalasarma S, Bähre H, Albers SV, Wilde A. Minor pilins are involved in motility and natural competence in the cyanobacterium Synechocystis sp. PCC 6803. Mol Microbiol 2021; 116:743-765. [PMID: 34115422 DOI: 10.1111/mmi.14768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 11/28/2022]
Abstract
Cyanobacteria synthesize type IV pili, which are known to be essential for motility, adhesion and natural competence. They consist of long flexible fibers that are primarily composed of the major pilin PilA1 in Synechocystis sp. PCC 6803. In addition, Synechocystis encodes less abundant pilin-like proteins, which are known as minor pilins. In this study, we show that the minor pilin PilA5 is essential for natural transformation but is dispensable for motility and flocculation. In contrast, a set of minor pilins encoded by the pilA9-slr2019 transcriptional unit are necessary for motility but are dispensable for natural transformation. Neither pilA5-pilA6 nor pilA9-slr2019 are essential for pilus assembly as mutant strains showed type IV pili on the cell surface. Three further gene products with similarity to PilX-like minor pilins have a function in flocculation of Synechocystis. The results of our study indicate that different minor pilins facilitate distinct pilus functions. Further, our microarray analysis demonstrated that the transcription levels of the minor pilin genes change in response to surface contact. A total of 122 genes were determined to have altered transcription between planktonic and surface growth, including several plasmid genes which are involved exopolysaccharide synthesis and the formation of bloom-like aggregates.
Collapse
Affiliation(s)
- Sabrina Oeser
- Molecular Genetics, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Thomas Wallner
- Molecular Genetics, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Nils Schuergers
- Molecular Genetics, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Lenka Bučinská
- Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Trebon, Czech Republic
| | - Shamphavi Sivabalasarma
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Heike Bähre
- Research Core Unit Metabolomics, Medical School Hannover, Hannover, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Annegret Wilde
- Molecular Genetics, Institute of Biology III, University of Freiburg, Freiburg, Germany
| |
Collapse
|
7
|
Riediger M, Spät P, Bilger R, Voigt K, Maček B, Hess WR. Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq). THE PLANT CELL 2021; 33:248-269. [PMID: 33793824 PMCID: PMC8136920 DOI: 10.1093/plcell/koaa017] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/12/2020] [Indexed: 05/23/2023]
Abstract
Although regulatory small RNAs have been reported in photosynthetic cyanobacteria, the lack of clear RNA chaperones involved in their regulation poses a conundrum. Here, we analyzed the full complement of cellular RNAs and proteins using gradient profiling by sequencing (Grad-seq) in Synechocystis 6803. Complexes with overlapping subunits such as the CpcG1-type versus the CpcL-type phycobilisomes or the PsaK1 versus PsaK2 photosystem I pre(complexes) could be distinguished, supporting the high quality of this approach. Clustering of the in-gradient distribution profiles followed by several additional criteria yielded a short list of potential RNA chaperones that include an YlxR homolog and a cyanobacterial homolog of the KhpA/B complex. The data suggest previously undetected complexes between accessory proteins and CRISPR-Cas systems, such as a Csx1-Csm6 ribonucleolytic defense complex. Moreover, the exclusive association of either RpoZ or 6S RNA with the core RNA polymerase complex and the existence of a reservoir of inactive sigma-antisigma complexes is suggested. The Synechocystis Grad-seq resource is available online at https://sunshine.biologie.uni-freiburg.de/GradSeqExplorer/ providing a comprehensive resource for the functional assignment of RNA-protein complexes and multisubunit protein complexes in a photosynthetic organism.
Collapse
Affiliation(s)
- Matthias Riediger
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Philipp Spät
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Raphael Bilger
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Karsten Voigt
- IT Administration, Institute of Biology 3, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Boris Maček
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| |
Collapse
|
8
|
Over Expression of the Cyanobacterial Pgr5-Homologue Leads to Pseudoreversion in a Gene Coding for a Putative Esterase in Synechocystis 6803. Life (Basel) 2020; 10:life10090174. [PMID: 32899164 PMCID: PMC7555055 DOI: 10.3390/life10090174] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 01/13/2023] Open
Abstract
Pgr5 proteins play a major direct role in cyclic electron flow paths in plants and eukaryotic phytoplankton. The genomes of many cyanobacterial species code for Pgr5-like proteins but their function is still uncertain. Here, we present evidence that supports a link between the Synechocystis sp. PCC6803 Pgr5-like protein and the regulation of intracellular redox balance. The knockout strain, pgr5KO, did not display substantial phenotypic response under our experimental conditions, confirming results obtained in earlier studies. However, the overexpression strain, pgr5OE, accumulated 2.5-fold more chlorophyll than the wild type and displayed increased content of photosystems matching the chlorophyll increase. As a result, electron transfer rates through the photosynthetic apparatus of pgr5OE increased, as did the amount of energy stored as glycogen. While, under photoautotrophic conditions, this metabolic difference had only minor effects, under mixotrophic conditions, pgr5OE cultures collapsed. Interestingly, this specific phenotype of pgr5OE mutants displayed a tendency for reverting, and cultures which previously collapsed in the presence of glucose were now able to survive. DNA sequencing of a pgr5OE strain revealed a second site suppression mutation in slr1916, a putative esterase associated with redox regulation. The phenotype of the slr1916 knockout is very similar to that of the strain reported here and to that of the pmgA regulator knockout. These data demonstrate that, in Synechocystis 6803, there is strong selection against overexpression of the Pgr5-like protein. The pseudoreversion event in a gene involved in redox regulation suggests a connection of the Pgr5-like protein to this network.
Collapse
|
9
|
Yao L, Shabestary K, Björk SM, Asplund-Samuelsson J, Joensson HN, Jahn M, Hudson EP. Pooled CRISPRi screening of the cyanobacterium Synechocystis sp PCC 6803 for enhanced industrial phenotypes. Nat Commun 2020; 11:1666. [PMID: 32245970 PMCID: PMC7125299 DOI: 10.1038/s41467-020-15491-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/13/2020] [Indexed: 11/09/2022] Open
Abstract
Cyanobacteria are model organisms for photosynthesis and are attractive for biotechnology applications. To aid investigation of genotype-phenotype relationships in cyanobacteria, we develop an inducible CRISPRi gene repression library in Synechocystis sp. PCC 6803, where we aim to target all genes for repression. We track the growth of all library members in multiple conditions and estimate gene fitness. The library reveals several clones with increased growth rates, and these have a common upregulation of genes related to cyclic electron flow. We challenge the library with 0.1 M L-lactate and find that repression of peroxiredoxin bcp2 increases growth rate by 49%. Transforming the library into an L-lactate-secreting Synechocystis strain and sorting top lactate producers enriches clones with sgRNAs targeting nutrient assimilation, central carbon metabolism, and cyclic electron flow. In many examples, productivity can be enhanced by repression of essential genes, which are difficult to access by transposon insertion.
Collapse
Affiliation(s)
- Lun Yao
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21, Stockholm, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Kiyan Shabestary
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21, Stockholm, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Sara M Björk
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21, Stockholm, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Johannes Asplund-Samuelsson
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21, Stockholm, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Haakan N Joensson
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21, Stockholm, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Michael Jahn
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21, Stockholm, Sweden.,Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Elton P Hudson
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21, Stockholm, Sweden. .,Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden.
| |
Collapse
|
10
|
He P, Cai X, Chen K, Fu X. Identification of small RNAs involved in nitrogen fixation in Anabaena sp. PCC 7120 based on RNA-seq under steady state conditions. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01557-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Abstract
Purpose
Anabaena sp. PCC7120 is a genetically tractable model organism for nitrogen fixation and photosynthesis research. The importance of small regulatory RNAs (sRNAs) as mediators of a number of cellular processes in bacteria has begun to be recognized. Bacterial sRNA binds to target genes through base pairing, and play a regulatory role. Many studies have shown that bacterial sRNA can regulate cell stress response, carbon and nitrogen fixation, and so on. However, little is known about sRNAs in Anabaena sp. PCC 7120 regarded to nitrogen fixation under later steady state.
Methods
To provide a comprehensive study of sRNAs in this model organism, the sRNA (< 200 nt) extracted from Anabaena sp. PCC 7120 under nitrogen step-down treatment of 12 days, together with the sRNA from the control, was analyzed using deep RNA sequencing. Possible target genes regulated by all identified putative sRNAs were predicted by IntaRNA and further analyzed for functional categorizations for biological pathways.
Result
Totally, 14,132 transcripts were produced from the de novo assembly. Among them, transcripts that are located either in the intergenic region or antisense strand were kept, which resulted in 1219 sRNA candidates, for further analysis. RPKM-based differential expression analysis showed that 418 sRNAs were significantly differentially expressed between the samples from control (nitrogen addition, N+) and nitrogen depletion, (N−). Among them, 303 sRNAs were significantly upregulated, whereas 115 sRNAs were significantly downregulated. RT-PCR of 18 randomly chosen sRNAs showed a similar pattern as RNA-seq result, which confirmed the reliability of the RNA-seq data. In addition, the possible target genes regulated by unique sRNAs of Anabaena sp. PCC 7120 under nitrogen addition (N+) condition or that under nitrogen depletion (N−) condition were analyzed for functional categorization and biological pathways, which provided the evidences that sRNAs were indeed involved in many different metabolic pathways.
Conclusion
The information from the present study provides a valuable reference for understanding the sRNA-mediated regulation of the nitrogen fixation in Anabaena PCC 7120 under steady state conditions.
Collapse
|
11
|
Muro-Pastor AM, Hess WR. Regulatory RNA at the crossroads of carbon and nitrogen metabolism in photosynthetic cyanobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1863:194477. [PMID: 31884117 DOI: 10.1016/j.bbagrm.2019.194477] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 12/16/2019] [Accepted: 12/22/2019] [Indexed: 12/17/2022]
Abstract
Cyanobacteria are photosynthetic bacteria that populate widely different habitats. Accordingly, cyanobacteria exhibit a wide spectrum of lifestyles, physiologies, and morphologies and possess genome sizes and gene numbers which may vary by up to a factor of ten within the phylum. Consequently, large differences exist between individual species in the size and complexity of their regulatory networks. Several non-coding RNAs have been identified that play crucial roles in the acclimation responses of cyanobacteria to changes in the environment. Some of these regulatory RNAs are conserved throughout the cyanobacterial phylum, while others exist only in a few taxa. Here we give an overview on characterized regulatory RNAs in cyanobacteria, with a focus on regulators of photosynthesis, carbon and nitrogen metabolism. However, chances are high that these regulators represent just the tip of the iceberg.
Collapse
Affiliation(s)
- Alicia M Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, E-41092 Sevilla, Spain
| | - Wolfgang R Hess
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104 Freiburg, Germany; University of Freiburg, Freiburg Institute for Advanced Studies, Albertstr. 19, D-79104 Freiburg, Germany.
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Zer H, Margulis K, Georg J, Shotland Y, Kostova G, Sultan LD, Hess WR, Keren N. Resequencing of a mutant bearing an iron starvation recovery phenotype defines Slr1658 as a new player in the regulatory network of a model cyanobacterium. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:235-245. [PMID: 29161470 DOI: 10.1111/tpj.13770] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 10/26/2017] [Accepted: 10/30/2017] [Indexed: 06/07/2023]
Abstract
Photosynthetic microorganisms encounter an erratic nutrient environment characterized by periods of iron limitation and sufficiency. Surviving in such an environment requires mechanisms for handling these transitions. Our study identified a regulatory system involved in the process of recovery from iron limitation in cyanobacteria. We set out to study the role of bacterioferritin co-migratory proteins during transitions in iron bioavailability in the cyanobacterium Synechocystis sp. PCC 6803 using knockout strains coupled with physiological and biochemical measurements. One of the mutants displayed slow recovery from iron limitation. However, we discovered that the cause of the phenotype was not the intended knockout but rather the serendipitous selection of a mutation in an unrelated locus, slr1658. Bioinformatics analysis suggested similarities to two-component systems and a possible regulatory role. Transcriptomic analysis of the recovery from iron limitation showed that the slr1658 mutation had an extensive effect on the expression of genes encoding regulatory proteins, proteins involved in the remodeling and degradation of the photosynthetic apparatus and proteins modulating electron transport. Most significantly, expression of the cyanobacterial homologue of the cyclic electron transport protein PGR5 was upregulated 1000-fold in slr1658 disruption mutants. pgr5 transcripts in the Δslr1658 mutant retained these high levels under a range of stress and recovery conditions. The results suggest that slr1658 is part of a regulatory operon that, among other aspects, affects the regulation of alternative electron flow. Disruption of its function has deleterious results under oxidative stress promoting conditions.
Collapse
Affiliation(s)
- Hagit Zer
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Ketty Margulis
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Jens Georg
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Yoram Shotland
- Department of Chemical Engineering, Shamoon College of Engineering, Beer Sheva, 84100, Israel
| | - Gergana Kostova
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Laure D Sultan
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Wolfgang R Hess
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany
- Freiburg Institute for Advanced Studies, University of Freiburg, Albertstr. 19, D-79104, Freiburg, Germany
| | - Nir Keren
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| |
Collapse
|
15
|
6S RNA plays a role in recovery from nitrogen depletion in Synechocystis sp. PCC 6803. BMC Microbiol 2017; 17:229. [PMID: 29216826 PMCID: PMC5721685 DOI: 10.1186/s12866-017-1137-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 11/27/2017] [Indexed: 12/30/2022] Open
Abstract
Background The 6S RNA is a global transcriptional riboregulator, which is exceptionally widespread among most bacterial phyla. While its role is well-characterized in some heterotrophic bacteria, we subjected a cyanobacterial homolog to functional analysis, thereby extending the scope of 6S RNA action to the special challenges of photoautotrophic lifestyles. Results Physiological characterization of a 6S RNA deletion strain (ΔssaA) demonstrates a delay in the recovery from nitrogen starvation. Significantly decelerated phycobilisome reassembly and glycogen degradation are accompanied with reduced photosynthetic activity compared to the wild type. Transcriptome profiling further revealed that predominantly genes encoding photosystem components, ATP synthase, phycobilisomes and ribosomal proteins were negatively affected in ΔssaA. In vivo pull-down studies of the RNA polymerase complex indicated that the presence of 6S RNA promotes the recruitment of the cyanobacterial housekeeping σ factor SigA, concurrently supporting dissociation of group 2 σ factors during recovery from nitrogen starvation. Conclusions The combination of genetic, physiological and biochemical studies reveals the homologue of 6S RNA as an integral part of the cellular response of Synechocystis sp. PCC 6803 to changing nitrogen availability. According to these results, 6S RNA supports a rapid acclimation to changing nitrogen supply by accelerating the switch from group 2 σ factors SigB, SigC and SigE to SigA-dependent transcription. We therefore introduce the cyanobacterial 6S RNA as a novel candidate regulator of RNA polymerase sigma factor recruitment in Synechocystis sp. PCC 6803. Further studies on mechanistic features of the postulated interaction should shed additional light on the complexity of transcriptional regulation in cyanobacteria. Electronic supplementary material The online version of this article (10.1186/s12866-017-1137-9) contains supplementary material, which is available to authorized users.
Collapse
|
16
|
De Porcellinis A, Frigaard NU, Sakuragi Y. Determination of the Glycogen Content in Cyanobacteria. J Vis Exp 2017. [PMID: 28745633 DOI: 10.3791/56068] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cyanobacteria accumulate glycogen as a major intracellular carbon and energy storage during photosynthesis. Recent developments in research have highlighted complex mechanisms of glycogen metabolism, including the diel cycle of biosynthesis and catabolism, redox regulation, and the involvement of non-coding RNA. At the same time, efforts are being made to redirect carbon from glycogen to desirable products in genetically engineered cyanobacteria to enhance product yields. Several methods are used to determine the glycogen contents in cyanobacteria, with variable accuracies and technical complexities. Here, we provide a detailed protocol for the reliable determination of the glycogen content in cyanobacteria that can be performed in a standard life science laboratory. The protocol entails the selective precipitation of glycogen from the cell lysate and the enzymatic depolymerization of glycogen to generate glucose monomers, which are detected by a glucose oxidase-peroxidase (GOD-POD) enzyme coupled assay. The method has been applied to Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 7002, two model cyanobacterial species that are widely used in metabolic engineering. Moreover, the method successfully showed differences in the glycogen contents between the wildtype and mutants defective in regulatory elements or glycogen biosynthetic genes.
Collapse
Affiliation(s)
| | | | - Yumiko Sakuragi
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen;
| |
Collapse
|
17
|
Sun T, Chen L, Zhang W. Quantitative Proteomics Reveals Potential Crosstalk between a Small RNA CoaR and a Two-Component Regulator Slr1037 in Synechocystis sp. PCC6803. J Proteome Res 2017; 16:2954-2963. [PMID: 28677390 DOI: 10.1021/acs.jproteome.7b00243] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Bacterial small RNAs (sRNAs) and two-component systems (TCSs) were two vital regulatory mechanisms employed by microorganisms to respond to environmental changes and stresses. As a promising "autotrophic cell factory", photosynthetic cyanobacteria have attracted a lot of attention these years. Although most studies focused on studying the roles of sRNAs or TCS regulators in stress response in photosynthetic cyanobacteria, limited work has elucidated their potential crosstalk. Our previous work has identified a negative sRNA regulator CoaR and a positive response regulator Slr1037 both related to 1-butanol stress regulation in Synechocystis sp. PCC6803. In this work, the potential crosstalk between CoaR and Slr1307 (i.e., the coregulated genes mediated by CoaR and Slr1037) was identified and validated through quantitative proteomics and quantitative real-time PCR (qRT-PCR), respectively. The results showed that the sensitive phenotype to 1-butanol of Δslr1037 could be rescued by suppressing coaR in Δslr1037, probably due to the fact that some target genes of Slr1037 could be reactivated by repression of CoaR. Twenty-eight coregulated proteins mediated by CoaR and Slr1037 were found through quantitative proteomics, and 10 of the annotated proteins were validated via qRT-PCR. This study proved the existence of crosstalk between sRNAs and response regulators and provided new insights into the coregulation of biofuel resistance in cyanobacteria.
Collapse
Affiliation(s)
- Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University , Tianjin 300072, P. R. China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University , Tianjin 300072, P. R. China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 300072, P. R. China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University , Tianjin 300072, P. R. China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University , Tianjin 300072, P. R. China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 300072, P. R. China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University , Tianjin 300072, P. R. China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University , Tianjin 300072, P. R. China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 300072, P. R. China.,Center for Biosafety Research and Strategy, Tianjin University , Tianjin 300072, P. R. China
| |
Collapse
|
18
|
Orf I, Schwarz D, Kaplan A, Kopka J, Hess WR, Hagemann M, Klähn S. CyAbrB2 Contributes to the Transcriptional Regulation of Low CO2 Acclimation in Synechocystis sp. PCC 6803. PLANT & CELL PHYSIOLOGY 2016; 57:2232-2243. [PMID: 27638927 DOI: 10.1093/pcp/pcw146] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/29/2016] [Indexed: 06/06/2023]
Abstract
Acclimation to low CO2 conditions in cyanobacteria involves the co-ordinated regulation of genes mainly encoding components of the carbon-concentrating mechanism (CCM). Making use of several independent microarray data sets, a core set of CO2-regulated genes was defined for the model strain Synechocystis sp. PCC 6803. On the transcriptional level, the CCM is mainly regulated by the well-characterized transcriptional regulators NdhR (= CcmR) and CmpR. However, the role of an additional regulatory protein, namely cyAbrB2 belonging to the widely distributed AbrB regulator family that was originally characterized in the genus Bacillus, is less defined. Here we present results of transcriptomic and metabolic profiling of the wild type and a ΔcyabrB2 mutant of Synechocystis sp. PCC 6803 after shifts from high CO2 (5% in air, HC) to low CO2 (0.04%, LC). Evaluation of the transcriptomic data revealed that cyAbrB2 is involved in the regulation of several CCM-related genes such as sbtA/B, ndhF3/ndhD3/cupA and cmpABCD under LC conditions, but apparently acts supplementary to NdhR and CmpR. Under HC conditions, cyAbrB2 deletion affects the transcript abundance of PSII subunits, light-harvesting components and Calvin-Benson-Bassham cycle enzymes. These changes are also reflected by down-regulation of primary metabolite pools. The data suggest a role for cyAbrB2 in adjusting primary carbon and nitrogen metabolism to photosynthetic activity under fluctuating environmental conditions. The findings were integrated into the current knowledge about the acquisition of inorganic carbon (Ci), the CCM and parts of its regulation on the transcriptional level.
Collapse
Affiliation(s)
- Isabel Orf
- Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, Potsdam-Golm, Germany
| | - Doreen Schwarz
- Plant Physiology Department, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Aaron Kaplan
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Joachim Kopka
- Max-Planck-Institute of Molecular Plant Physiology, Department of Molecular Physiology: Applied Metabolome Analysis, Potsdam-Golm, Germany
| | - Wolfgang R Hess
- Genetics & Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Martin Hagemann
- Plant Physiology Department, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Stephan Klähn
- Genetics & Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Freiburg, Germany
| |
Collapse
|