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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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Wang J, Zhao X, Tao Y, Wang X, Yan L, Yu K, Hsu Y, Chen Y, Zhao J, Huang Y, Wei W. Biocompatible aggregation-induced emission active polyphosphate-manganese nanosheets with glutamine synthetase-like activity in excitotoxic nerve cells. Nat Commun 2024; 15:3534. [PMID: 38670989 PMCID: PMC11053040 DOI: 10.1038/s41467-024-47947-5] [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: 05/06/2023] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Glutamine synthetase (GS) is vital in maintaining ammonia and glutamate (Glu) homeostasis in living organisms. However, the natural enzyme relies on adenosine triphosphate (ATP) to activate Glu, resulting in impaired GS function during ATP-deficient neurotoxic events. To date, no reports demonstrate using artificial nanostructures to mimic GS function. In this study, we synthesize aggregation-induced emission active polyP-Mn nanosheets (STPE-PMNSs) based on end-labeled polyphosphate (polyP), exhibiting remarkable GS-like activity independent of ATP presence. Further investigation reveals polyP in STPE-PMNSs serves as phosphate source to activate Glu at low ATP levels. This self-feeding mechanism offers a significant advantage in regulating Glu homeostasis at reduced ATP levels in nerve cells during excitotoxic conditions. STPE-PMNSs can effectively promote the conversion of Glu to glutamine (Gln) in excitatory neurotoxic human neuroblastoma cells (SH-SY5Y) and alleviate Glu-induced neurotoxicity. Additionally, the fluorescence signal of nanosheets enables precise monitoring of the subcellular distribution of STPE-PMNSs. More importantly, the intracellular fluorescence signal is enhanced in a conversion-responsive manner, allowing real-time tracking of reaction progression. This study presents a self-sustaining strategy to address GS functional impairment caused by ATP deficiency in nerve cells during neurotoxic events. Furthermore, it offers a fresh perspective on the potential biological applications of polyP-based nanostructures.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, PR China
| | - Xinyang Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, PR China
| | - Yucheng Tao
- School of Life Sciences, Nanjing University, Nanjing, 210093, PR China
| | - Xiuxiu Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, PR China
| | - Li Yan
- Nanchuang (Jiangsu) Institute of Chemistry and Health, Sino-Danish Ecolife Science Industrial Incubator, Jiangbei New Area, Nanjing, 210000, PR China
| | - Kuang Yu
- Tsinghua-Berkeley Shenzhen Institute and Institute of Materials Research (iMR), Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, PR China
| | - Yi Hsu
- Taipei Wego Private Senior High School, Taipei, TWN, PR China
| | - Yuncong Chen
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, PR China.
- Nanchuang (Jiangsu) Institute of Chemistry and Health, Sino-Danish Ecolife Science Industrial Incubator, Jiangbei New Area, Nanjing, 210000, PR China.
| | - Jing Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, PR China.
- Nanchuang (Jiangsu) Institute of Chemistry and Health, Sino-Danish Ecolife Science Industrial Incubator, Jiangbei New Area, Nanjing, 210000, PR China.
- Shenzhen Research Institute, Nanjing University, Shenzhen, PR China.
| | - Yong Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, PR China.
| | - Wei Wei
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, PR China.
- School of Life Sciences, Nanjing University, Nanjing, 210093, PR China.
- Nanchuang (Jiangsu) Institute of Chemistry and Health, Sino-Danish Ecolife Science Industrial Incubator, Jiangbei New Area, Nanjing, 210000, PR China.
- Shenzhen Research Institute, Nanjing University, Shenzhen, PR China.
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3
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Battistuzzi M, Morlino MS, Cocola L, Trainotti L, Treu L, Campanaro S, Claudi R, Poletto L, La Rocca N. Transcriptomic and photosynthetic analyses of Synechocystis sp. PCC6803 and Chlorogloeopsis fritschii sp. PCC6912 exposed to an M-dwarf spectrum under an anoxic atmosphere. FRONTIERS IN PLANT SCIENCE 2024; 14:1322052. [PMID: 38304456 PMCID: PMC10830646 DOI: 10.3389/fpls.2023.1322052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/29/2023] [Indexed: 02/03/2024]
Abstract
Introduction Cyanobacteria appeared in the anoxic Archean Earth, evolving for the first time oxygenic photosynthesis and deeply changing the atmosphere by introducing oxygen. Starting possibly from UV-protected environments, characterized by low visible and far-red enriched light spectra, cyanobacteria spread everywhere on Earth thanks to their adaptation capabilities in light harvesting. In the last decade, few cyanobacteria species which can acclimate to far-red light through Far-Red Light Photoacclimation (FaRLiP) have been isolated. FaRLiP cyanobacteria were thus proposed as model organisms to study the origin of oxygenic photosynthesis as well as its possible functionality around stars with high far-red emission, the M-dwarfs. These stars are astrobiological targets, as their longevity could sustain life evolution and they demonstrated to host rocky terrestrial-like exoplanets within their Habitable Zone. Methods We studied the acclimation responses of the FaRLiP strain Chlorogloeopsis fritschii sp. PCC6912 and the non-FaRLiP strain Synechocystis sp. PCC6803 to the combination of three simulated light spectra (M-dwarf, solar and far-red) and two atmospheric compositions (oxic, anoxic). We first checked their growth, O2 production and pigment composition, then we studied their transcriptional responses by RNA sequencing under each combination of light spectrum and atmosphere conditions. Results and discussion PCC6803 did not show relevant differences in gene expression when comparing the responses to M-dwarf and solar-simulated lights, while far-red caused a variation in the transcriptional level of many genes. PCC6912 showed, on the contrary, different transcriptional responses to each light condition and activated the FaRLiP response under the M-dwarf simulated light. Surprisingly, the anoxic atmosphere did not impact the transcriptional profile of the 2 strains significantly. Results show that both cyanobacteria seem inherently prepared for anoxia and to harvest the photons emitted by a simulated M-dwarf star, whether they are only visible (PCC6803) or also far-red photons (PCC6912). They also show that visible photons in the simulated M-dwarf are sufficient to keep a similar metabolism with respect to solar-simulated light. Conclusion Results prove the adaptability of the cyanobacterial metabolism and enhance the plausibility of finding oxygenic biospheres on exoplanets orbiting M-dwarf stars.
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Affiliation(s)
- Mariano Battistuzzi
- National Council of Research of Italy, Institute for Photonics and Nanotechnologies (CNR-IFN), Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
- Center for Space Studies and Activities (CISAS), University of Padua, Padua, Italy
| | | | - Lorenzo Cocola
- National Council of Research of Italy, Institute for Photonics and Nanotechnologies (CNR-IFN), Padua, Italy
| | | | - Laura Treu
- Department of Biology, University of Padua, Padua, Italy
| | | | - Riccardo Claudi
- National Institute for Astrophysics, Astronomical Observatory of Padua (INAF-OAPD), Padua, Italy
- Department of Mathematics and Physics, University Roma Tre, Rome, Italy
| | - Luca Poletto
- National Council of Research of Italy, Institute for Photonics and Nanotechnologies (CNR-IFN), Padua, Italy
| | - Nicoletta La Rocca
- Department of Biology, University of Padua, Padua, Italy
- Center for Space Studies and Activities (CISAS), University of Padua, Padua, Italy
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4
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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.
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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
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5
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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.
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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
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6
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Buchholz HH, Bolaños LM, Bell AG, Michelsen ML, Allen MJ, Temperton B. A Novel and Ubiquitous Marine Methylophage Provides Insights into Viral-Host Coevolution and Possible Host-Range Expansion in Streamlined Marine Heterotrophic Bacteria. Appl Environ Microbiol 2022; 88:e0025522. [PMID: 35311512 PMCID: PMC9004378 DOI: 10.1128/aem.00255-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 11/25/2022] Open
Abstract
The methylotrophic OM43 clade are Gammaproteobacteria that comprise some of the smallest free-living cells known and have highly streamlined genomes. OM43 represents an important microbial link between marine primary production and remineralization of carbon back to the atmosphere. Bacteriophages shape microbial communities and are major drivers of mortality and global marine biogeochemistry. Recent cultivation efforts have brought the first viruses infecting members of the OM43 clade into culture. Here, we characterize a novel myophage infecting OM43 called Melnitz. Melnitz was isolated independently from water samples from a subtropical ocean gyre (Sargasso Sea) and temperate coastal (Western English Channel) systems. Metagenomic recruitment from global ocean viromes confirmed that Melnitz is globally ubiquitous, congruent with patterns of host abundance. Bacteria with streamlined genomes such as OM43 and the globally dominant SAR11 clade use riboswitches as an efficient method to regulate metabolism. Melnitz encodes a two-piece tmRNA (ssrA), controlled by a glutamine riboswitch, providing evidence that riboswitch use also occurs for regulation during phage infection of streamlined heterotrophs. Virally encoded tRNAs and ssrA found in Melnitz were phylogenetically more closely related to those found within the alphaproteobacterial SAR11 clade and their associated myophages than those within their gammaproteobacterial hosts. This suggests the possibility of an ancestral host transition event between SAR11 and OM43. Melnitz and a related myophage that infects SAR11 were unable to infect hosts of the SAR11 and OM43, respectively, suggesting host transition rather than a broadening of host range. IMPORTANCE Isolation and cultivation of viruses are the foundations on which the mechanistic understanding of virus-host interactions and parameterization of bioinformatic tools for viral ecology are based. This study isolated and characterized the first myophage known to infect the OM43 clade, expanding our knowledge of this understudied group of microbes. The nearly identical genomes of four strains of Melnitz isolated from different marine provinces and the global abundance estimations from metagenomic data suggest that this viral population is globally ubiquitous. Genome analysis revealed several unusual features in Melnitz and related genomes recovered from viromes, such as a curli operon and virally encoded tmRNA controlled by a glutamine riboswitch, neither of which are found in the host. Further phylogenetic analysis of shared genes indicates that this group of viruses infecting the gammaproteobacterial OM43 shares a recent common ancestor with viruses infecting the abundant alphaproteobacterial SAR11 clade. Host ranges are affected by compatible cell surface receptors, successful circumvention of superinfection exclusion systems, and the presence of required accessory proteins, which typically limits phages to singular narrow groups of closely related bacterial hosts. This study provides intriguing evidence that for streamlined heterotrophic bacteria, virus-host transitioning may not be necessarily restricted to phylogenetically related hosts but is a function of shared physical and biochemical properties of the cell.
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Affiliation(s)
| | | | | | | | - Michael J. Allen
- University of Exeter, School of Biosciences, Exeter, UK
- Plymouth Marine Laboratory, Plymouth, UK
| | - Ben Temperton
- University of Exeter, School of Biosciences, Exeter, UK
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7
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Hong KQ, Zhang J, Jin B, Chen T, Wang ZW. Development and characterization of a glycine biosensor system for fine-tuned metabolic regulation in Escherichia coli. Microb Cell Fact 2022; 21:56. [PMID: 35392910 PMCID: PMC8991567 DOI: 10.1186/s12934-022-01779-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/23/2022] [Indexed: 11/10/2022] Open
Abstract
Background In vivo biosensors have a wide range of applications, ranging from the detection of metabolites to the regulation of metabolic networks, providing versatile tools for synthetic biology and metabolic engineering. However, in view of the vast array of metabolite molecules, the existing number and performance of biosensors is far from sufficient, limiting their potential applications in metabolic engineering. Therefore, we developed the synthetic glycine-ON and -OFF riboswitches for metabolic regulation and directed evolution of enzyme in Escherichia coli. Results The results showed that a synthetic glycine-OFF riboswitch (glyOFF6) and an increased-detection-range synthetic glycine-ON riboswitch (glyON14) were successfully screened from a library based on the Bacillus subtilis glycine riboswitch using fluorescence-activated cell sorting (FACS) and tetA-based dual genetic selection. The two synthetic glycine riboswitches were successfully used in tunable regulation of lactate synthesis, dynamic regulation of serine synthesis and directed evolution of alanine-glyoxylate aminotransferase in Escherichia coli, respectively. Mutants AGXT22 and AGXT26 of alanine-glyoxylate aminotransferase with an increase of 58% and 73% enzyme activity were obtained by using a high-throughput screening platform based on the synthetic glycine-OFF riboswitch, and successfully used to increase the 5-aminolevulinic acid yield of engineered Escherichia coli. Conclusions A synthetic glycine-OFF riboswitch and an increased-detection-range synthetic glycine-ON riboswitch were successfully designed and screened. The developed riboswitches showed broad application in tunable regulation, dynamic regulation and directed evolution of enzyme in E. coli. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01779-4.
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Affiliation(s)
- Kun-Qiang Hong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China.,Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Jing Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China.,Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Biao Jin
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China.,Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Tao Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China.,Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Zhi-Wen Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China. .,Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China.
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8
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Abstract
More than 55 distinct classes of riboswitches that respond to small metabolites or elemental ions have been experimentally validated to date. The ligands sensed by these riboswitches are biased in favor of fundamental compounds or ions that are likely to have been relevant to ancient forms of life, including those that might have populated the "RNA World", which is a proposed biochemical era that predates the evolutionary emergence of DNA and proteins. In the following text, I discuss the various types of ligands sensed by some of the most common riboswitches present in modern bacterial cells and consider implications for ancient biological processes centered on the proven capabilities of these RNA-based sensors. Although most major biochemical aspects of metabolism are represented by known riboswitch classes, there are striking sensory gaps in some key areas. These gaps could reveal weaknesses in the performance capabilities of RNA that might have hampered RNA World evolution, or these could highlight opportunities to discover additional riboswitch classes that sense essential metabolites.
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Affiliation(s)
- Ronald R. Breaker
- Corresponding Author: Ronald R. Breaker - Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, United States; Phone: 203-432-9389; , Twitter: @RonBreaker
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9
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Miyakoshi M, Morita T, Kobayashi A, Berger A, Takahashi H, Gotoh Y, Hayashi T, Tanaka K. Glutamine synthetase mRNA releases sRNA from its 3'UTR to regulate carbon/nitrogen metabolic balance in Enterobacteriaceae. eLife 2022; 11:82411. [PMID: 36440827 PMCID: PMC9731577 DOI: 10.7554/elife.82411] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/27/2022] [Indexed: 11/29/2022] Open
Abstract
Glutamine synthetase (GS) is the key enzyme of nitrogen assimilation induced under nitrogen limiting conditions. The carbon skeleton of glutamate and glutamine, 2-oxoglutarate, is supplied from the TCA cycle, but how this metabolic flow is controlled in response to nitrogen availability remains unknown. We show that the expression of the E1o component of 2-oxoglutarate dehydrogenase, SucA, is repressed under nitrogen limitation in Salmonella enterica and Escherichia coli. The repression is exerted at the post-transcriptional level by an Hfq-dependent sRNA GlnZ generated from the 3'UTR of the GS-encoding glnA mRNA. Enterobacterial GlnZ variants contain a conserved seed sequence and primarily regulate sucA through base-pairing far upstream of the translation initiation region. During growth on glutamine as the nitrogen source, the glnA 3'UTR deletion mutants expressed SucA at higher levels than the S. enterica and E. coli wild-type strains, respectively. In E. coli, the transcriptional regulator Nac also participates in the repression of sucA. Lastly, this study clarifies that the release of GlnZ from the glnA mRNA by RNase E is essential for the post-transcriptional regulation of sucA. Thus, the mRNA coordinates the two independent functions to balance the supply and demand of the fundamental metabolites.
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Affiliation(s)
- Masatoshi Miyakoshi
- Department of Infection Biology, Faculty of Medicine, University of TsukubaTsukubaJapan,Transborder Medical Research Center, University of TsukubaTsukubaJapan,International Joint Degree Master’s Program in Agro-Biomedical Science in Food and Health (GIP-TRIAD), University of TsukubaTsukubaJapan
| | - Teppei Morita
- Institute for Advanced Biosciences, Keio UniversityTsuruokaJapan,Graduate School of Media and Governance, Keio UniversityFujisawaJapan
| | - Asaki Kobayashi
- Transborder Medical Research Center, University of TsukubaTsukubaJapan
| | - Anna Berger
- International Joint Degree Master’s Program in Agro-Biomedical Science in Food and Health (GIP-TRIAD), University of TsukubaTsukubaJapan
| | | | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu UniversityFukuokaJapan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu UniversityFukuokaJapan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of TechnologyYokohamaJapan
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10
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The Molecular Toolset and Techniques Required to Build Cyanobacterial Cell Factories. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022. [DOI: 10.1007/10_2022_210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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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.
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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
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12
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Yadav A, Maertens L, Meese T, Van Nieuwerburgh F, Mysara M, Leys N, Cuypers A, Janssen PJ. Genetic Responses of Metabolically Active Limnospira indica Strain PCC 8005 Exposed to γ-Radiation during Its Lifecycle. Microorganisms 2021; 9:1626. [PMID: 34442705 PMCID: PMC8400943 DOI: 10.3390/microorganisms9081626] [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] [Received: 06/24/2021] [Revised: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022] Open
Abstract
Two morphotypes of the cyanobacterial Limnospira indica (formerly Arthrospira sp.) strain PCC 8005, denoted as P2 (straight trichomes) and P6 (helical trichomes), were subjected to chronic gamma radiation from spent nuclear fuel (SNF) rods at a dose rate of ca. 80 Gy·h-1 for one mass doubling period (approximately 3 days) under continuous light with photoautotrophic metabolism fully active. Samples were taken for post-irradiation growth recovery and RNA-Seq transcriptional analysis at time intervals of 15, 40, and 71.5 h corresponding to cumulative doses of ca. 1450, 3200, and 5700 Gy, respectively. Both morphotypes, which were previously reported by us to display different antioxidant capacities and differ at the genomic level in 168 SNPs, 48 indels and 4 large insertions, recovered equally well from 1450 and 3200 Gy. However, while the P2 straight type recovered from 5700 Gy by regaining normal growth within 6 days, the P6 helical type took about 13 days to recover from this dose, indicating differences in their radiation tolerance and response. To investigate these differences, P2 and P6 cells exposed to the intermediate dose of gamma radiation (3200 Gy) were analyzed for differential gene expression by RNA-Seq analysis. Prior to batch normalization, a total of 1553 genes (887 and 666 of P2 and P6, respectively, with 352 genes in common) were selected based on a two-fold change in expression and a false discovery rate FDR smaller or equal to 0.05. About 85% of these 1553 genes encoded products of yet unknown function. Of the 229 remaining genes, 171 had a defined function while 58 genes were transcribed into non-coding RNA including 21 tRNAs (all downregulated). Batch normalization resulted in 660 differentially expressed genes with 98 having a function and 32 encoding RNA. From PCC 8005-P2 and PCC 8005-P6 expression patterns, it emerges that although the cellular routes used by the two substrains to cope with ionizing radiation do overlap to a large extent, both strains displayed a distinct preference of priorities.
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Affiliation(s)
- Anu Yadav
- Interdisciplinary Biosciences, Microbiology Unit, Belgian Nuclear Research Centre (SCKCEN), 2400 Mol, Belgium; (A.Y.); (L.M.); (M.M.); (N.L.)
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium;
| | - Laurens Maertens
- Interdisciplinary Biosciences, Microbiology Unit, Belgian Nuclear Research Centre (SCKCEN), 2400 Mol, Belgium; (A.Y.); (L.M.); (M.M.); (N.L.)
- Research Unit in Biology of Microorganisms (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium
| | - Tim Meese
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium; (T.M.); (F.V.N.)
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium; (T.M.); (F.V.N.)
| | - Mohamed Mysara
- Interdisciplinary Biosciences, Microbiology Unit, Belgian Nuclear Research Centre (SCKCEN), 2400 Mol, Belgium; (A.Y.); (L.M.); (M.M.); (N.L.)
| | - Natalie Leys
- Interdisciplinary Biosciences, Microbiology Unit, Belgian Nuclear Research Centre (SCKCEN), 2400 Mol, Belgium; (A.Y.); (L.M.); (M.M.); (N.L.)
| | - Ann Cuypers
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium;
| | - Paul Jaak Janssen
- Interdisciplinary Biosciences, Microbiology Unit, Belgian Nuclear Research Centre (SCKCEN), 2400 Mol, Belgium; (A.Y.); (L.M.); (M.M.); (N.L.)
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13
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New insights into the function of the proteins IsiC and IsiD from Synechocystis sp. PCC 6803 under iron limitation. Appl Microbiol Biotechnol 2021; 105:4693-4707. [PMID: 34019114 DOI: 10.1007/s00253-021-11347-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/30/2021] [Accepted: 05/09/2021] [Indexed: 10/25/2022]
Abstract
Iron is a common cofactor in biological processes such as respiration, photosynthesis, and nitrogen fixation. The genes isiC and isiD encode unknown proteins, and the growth of ΔisiC and ΔisiD mutants is inhibited under iron-deficient conditions. To study the regulatory mechanisms of IsiC and IsiD during iron starvation, we carried out transcriptome and metabolome sequencing. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the photosynthesis, nitrogen metabolism, and ABC transporter pathways play a vital role in regulating iron deficiency. Upon iron repletion, IsiC and IsiD also have a regulatory effect on these pathways. Additionally, KEGG analysis of the differential metabolites of wild type (WT) and mutants showed that they were all enriched in starch and sucrose metabolism after iron limitation. Weighted gene co-expression network analysis (WGCNA) constructed a co-expression network of differentially expressed genes with phenotypes and metabolites, and finally identified five modules. The turquoise module was positively correlated with iron deficiency. In contrast, the WT and blue module exhibited a negative correlation, and the mutants ΔisiC and ΔisiD were positively correlated with the gray and brown modules, respectively. WGCNA also analyzed the relationship between metabolites and phenotypes, and the green module was related to iron starvation. The co-expression network determined the hub genes and metabolites of each module. This study lays a foundation for a better understanding of cyanobacteria in response to iron deficiency. KEY POINTS: • Nitrogen metabolism and ABC transporters are involved in iron regulation. • Starch and sucrose metabolism is related to the regulation of iron deficiency. • WGCNA analyzes the correlation between genes and metabolites.
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14
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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.
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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
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15
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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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16
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Phycobilisome breakdown effector NblD is required to maintain the cellular amino acid composition during nitrogen starvation. J Bacteriol 2021; 204:JB0015821. [PMID: 34228497 PMCID: PMC8765419 DOI: 10.1128/jb.00158-21] [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] [Indexed: 11/20/2022] Open
Abstract
Small proteins are critically involved in the acclimation response of photosynthetic cyanobacteria to nitrogen starvation. NblD is the 66-amino-acid effector of nitrogen-limitation-induced phycobilisome breakdown, which is believed to replenish the cellular amino acid pools. To address the physiological functions of NblD, the concentrations of amino acids, intermediates of the arginine catabolism pathway and several organic acids were measured during the response to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803 wild type and in an nblD deletion strain. A characteristic signature of metabolite pool composition was identified, which shows that NblD-mediated phycobilisome degradation is required to maintain the cellular amino acid and organic acid pools during nitrogen starvation. Specific deviations from the wild type suggest wider-reaching effects that also affect such processes as redox homeostasis via glutathione and tetrapyrrole biosynthesis, both of which are linked to the strongly decreased glutamate pool, and transcriptional reprogramming via an enhanced concentration of 2-oxoglutarate, the metabolite co-regulator of the NtcA transcription factor. The essential role played by NblD in metabolic homeostasis is consistent with the widespread occurrence of NblD throughout the cyanobacterial radiation and the previously observed strong positive selection for the nblD gene under fluctuating nitrogen supply. Importance Cyanobacteria play important roles in the global carbon and nitrogen cycles. In their natural environment, these organisms are exposed to fluctuating nutrient conditions. Nitrogen starvation induces a coordinated nitrogen-saving program that includes the breakdown of nitrogen-rich photosynthetic pigments, particularly phycobiliproteins. The small protein NblD was recently identified as an effector of phycobilisome breakdown in cyanobacteria. In this study, we demonstrate that the NblD-mediated degradation of phycobiliproteins is needed to sustain cellular pools of soluble amino acids and other crucial metabolites. The essential role played by NblD in metabolic homeostasis explains why genes encoding this small protein are conserved in almost all members of cyanobacterial radiation.
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17
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Current processes and future challenges of photoautotrophic production of acetyl-CoA-derived solar fuels and chemicals in cyanobacteria. Curr Opin Chem Biol 2020; 59:69-76. [DOI: 10.1016/j.cbpa.2020.04.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 01/03/2023]
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18
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Brandenburg F, Klähn S. Small but Smart: On the Diverse Role of Small Proteins in the Regulation of Cyanobacterial Metabolism. Life (Basel) 2020; 10:E322. [PMID: 33271798 PMCID: PMC7760959 DOI: 10.3390/life10120322] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/17/2022] Open
Abstract
Over the past few decades, bioengineered cyanobacteria have become a major focus of research for the production of energy carriers and high value chemical compounds. Besides improvements in cultivation routines and reactor technology, the integral understanding of the regulation of metabolic fluxes is the key to designing production strains that are able to compete with established industrial processes. In cyanobacteria, many enzymes and metabolic pathways are regulated differently compared to other bacteria. For instance, while glutamine synthetase in proteobacteria is mainly regulated by covalent enzyme modifications, the same enzyme in cyanobacteria is controlled by the interaction with unique small proteins. Other prominent examples, such as the small protein CP12 which controls the Calvin-Benson cycle, indicate that the regulation of enzymes and/or pathways via the attachment of small proteins might be a widespread mechanism in cyanobacteria. Accordingly, this review highlights the diverse role of small proteins in the control of cyanobacterial metabolism, focusing on well-studied examples as well as those most recently described. Moreover, it will discuss their potential to implement metabolic engineering strategies in order to make cyanobacteria more definable for biotechnological applications.
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Affiliation(s)
| | - Stephan Klähn
- Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany;
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19
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Rachedi R, Foglino M, Latifi A. Stress Signaling in Cyanobacteria: A Mechanistic Overview. Life (Basel) 2020; 10:life10120312. [PMID: 33256109 PMCID: PMC7760821 DOI: 10.3390/life10120312] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/22/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022] Open
Abstract
Cyanobacteria are highly diverse, widely distributed photosynthetic bacteria inhabiting various environments ranging from deserts to the cryosphere. Throughout this range of niches, they have to cope with various stresses and kinds of deprivation which threaten their growth and viability. In order to adapt to these stresses and survive, they have developed several global adaptive responses which modulate the patterns of gene expression and the cellular functions at work. Sigma factors, two-component systems, transcriptional regulators and small regulatory RNAs acting either separately or collectively, for example, induce appropriate cyanobacterial stress responses. The aim of this review is to summarize our current knowledge about the diversity of the sensors and regulators involved in the perception and transduction of light, oxidative and thermal stresses, and nutrient starvation responses. The studies discussed here point to the fact that various stresses affecting the photosynthetic capacity are transduced by common mechanisms.
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20
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Forchhammer K, Selim KA. Carbon/nitrogen homeostasis control in cyanobacteria. FEMS Microbiol Rev 2020; 44:33-53. [PMID: 31617886 PMCID: PMC8042125 DOI: 10.1093/femsre/fuz025] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/14/2019] [Indexed: 02/06/2023] Open
Abstract
Carbon/nitrogen (C/N) balance sensing is a key requirement for the maintenance of cellular homeostasis. Therefore, cyanobacteria have evolved a sophisticated signal transduction network targeting the metabolite 2-oxoglutarate (2-OG), the carbon skeleton for nitrogen assimilation. It serves as a status reporter for the cellular C/N balance that is sensed by transcription factors NtcA and NdhR and the versatile PII-signaling protein. The PII protein acts as a multitasking signal-integrating regulator, combining the 2-OG signal with the energy state of the cell through adenyl-nucleotide binding. Depending on these integrated signals, PII orchestrates metabolic activities in response to environmental changes through binding to various targets. In addition to 2-OG, other status reporter metabolites have recently been discovered, mainly indicating the carbon status of the cells. One of them is cAMP, which is sensed by the PII-like protein SbtB. The present review focuses, with a main emphasis on unicellular model strains Synechoccus elongatus and Synechocystis sp. PCC 6803, on the physiological framework of these complex regulatory loops, the tight linkage to metabolism and the molecular mechanisms governing the signaling processes.
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Affiliation(s)
- Karl Forchhammer
- Lehrstuhl für Mikrobiologie, Universität Tübingen, Auf der Morgenstelle 28, D-72076 Tübingen, Germany
| | - Khaled A Selim
- Lehrstuhl für Mikrobiologie, Universität Tübingen, Auf der Morgenstelle 28, D-72076 Tübingen, Germany
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21
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Huang L, Wang J, Watkins AM, Das R, Lilley DMJ. Structure and ligand binding of the glutamine-II riboswitch. Nucleic Acids Res 2019; 47:7666-7675. [PMID: 31216023 PMCID: PMC6698751 DOI: 10.1093/nar/gkz539] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/31/2019] [Accepted: 06/06/2019] [Indexed: 12/14/2022] Open
Abstract
We have determined the structure of the glutamine-II riboswitch ligand binding domain using X-ray crystallography. The structure was solved using a novel combination of homology modeling and molecular replacement. The structure comprises three coaxial helical domains, the central one of which is a pseudoknot with partial triplex character. The major groove of this helix provides the binding site for L-glutamine, which is extensively hydrogen bonded to the RNA. Atomic mutation of the RNA at the ligand binding site leads to loss of binding shown by isothermal titration calorimetry, explaining the specificity of the riboswitch. A metal ion also plays an important role in ligand binding. This is directly bonded to a glutamine carboxylate oxygen atom, and its remaining inner-sphere water molecules make hydrogen bonding interactions with the RNA.
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Affiliation(s)
- Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Jia Wang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Andrew M Watkins
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
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22
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Santos-Merino M, Singh AK, Ducat DC. New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering. Front Bioeng Biotechnol 2019; 7:33. [PMID: 30873404 PMCID: PMC6400836 DOI: 10.3389/fbioe.2019.00033] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/05/2019] [Indexed: 01/25/2023] Open
Abstract
Cyanobacteria are promising microorganisms for sustainable biotechnologies, yet unlocking their potential requires radical re-engineering and application of cutting-edge synthetic biology techniques. In recent years, the available devices and strategies for modifying cyanobacteria have been increasing, including advances in the design of genetic promoters, ribosome binding sites, riboswitches, reporter proteins, modular vector systems, and markerless selection systems. Because of these new toolkits, cyanobacteria have been successfully engineered to express heterologous pathways for the production of a wide variety of valuable compounds. Cyanobacterial strains with the potential to be used in real-world applications will require the refinement of genetic circuits used to express the heterologous pathways and development of accurate models that predict how these pathways can be best integrated into the larger cellular metabolic network. Herein, we review advances that have been made to translate synthetic biology tools into cyanobacterial model organisms and summarize experimental and in silico strategies that have been employed to increase their bioproduction potential. Despite the advances in synthetic biology and metabolic engineering during the last years, it is clear that still further improvements are required if cyanobacteria are to be competitive with heterotrophic microorganisms for the bioproduction of added-value compounds.
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Affiliation(s)
- María Santos-Merino
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Amit K. Singh
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Daniel C. Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
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23
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Zhang CC, Zhou CZ, Burnap RL, Peng L. Carbon/Nitrogen Metabolic Balance: Lessons from Cyanobacteria. TRENDS IN PLANT SCIENCE 2018; 23:1116-1130. [PMID: 30292707 DOI: 10.1016/j.tplants.2018.09.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 09/07/2018] [Accepted: 09/11/2018] [Indexed: 05/20/2023]
Abstract
Carbon and nitrogen are the two most abundant nutrient elements for all living organisms, and their metabolism is tightly coupled. What are the signaling mechanisms that cells use to sense and control the carbon/nitrogen (C/N) metabolic balance following environmental changes? Based on studies in cyanobacteria, it was found that 2-phosphoglycolate derived from the oxygenase activity of Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) and 2-oxoglutarate from the Krebs cycle act as the carbon- and nitrogen-starvation signals, respectively, and their concentration ratio likely reflects the status of the C/N metabolic balance. We will present and discuss the regulatory principles underlying the signaling mechanisms, which are likely to be conserved in other photosynthetic organisms. These concepts may also contribute to developments in the field of biofuel engineering or improvements in crop productivity.
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Affiliation(s)
- Cheng-Cai Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan, Hubei 430072, People's Republic of China; Aix-Marseille Université, CNRS, LCB, France.
| | - Cong-Zhao Zhou
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230027, People's Republic of China
| | - Robert L Burnap
- Department of Microbiology and Molecular Genetics, Henry Bellmon Research Center, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ling Peng
- Aix-Marseille Université, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, Equipe Labellisée Ligue Contre le Cancer, CINaM UMR 7325, 13288 Marseille, France
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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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