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Sengupta A, Liu D, Pakrasi HB. CRISPR-Cas mediated genome engineering of cyanobacteria. Methods Enzymol 2022; 676:403-432. [DOI: 10.1016/bs.mie.2022.07.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Brito LF, Irla M, Kalinowski J, Wendisch VF. Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA-seq technology. BMC Genomics 2017; 18:846. [PMID: 29100491 PMCID: PMC5670726 DOI: 10.1186/s12864-017-4235-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 10/23/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The plant growth promoting rhizobacterium Paenibacillus riograndensis SBR5 is a promising candidate to serve as crop inoculant. Despite its potential in providing environmental and economic benefits, the species P. riograndensis is poorly characterized. Here, we performed for the first time a detailed transcriptome analysis of P. riograndensis SBR5 using RNA-seq technology. RESULTS RNA was isolated from P. riograndensis SBR5 cultivated under 15 different growth conditions and combined together in order to analyze an RNA pool representing a large set of expressed genes. The resultant total RNA was used to generate 2 different libraries, one enriched in 5'-ends of the primary transcripts and the other representing the whole transcriptome. Both libraries were sequenced and analyzed to identify the conserved sequences of ribosome biding sites and translation start motifs, and to elucidate operon structures present in the transcriptome of P. riograndensis. Sequence analysis of the library enriched in 5'-ends of the primary transcripts was used to identify 1082 transcription start sites (TSS) belonging to novel transcripts and allowed us to determine a promoter consensus sequence and regulatory sequences in 5' untranslated regions including riboswitches. A putative thiamine pyrophosphate dependent riboswitch upstream of the thiamine biosynthesis gene thiC was characterized by translational fusion to a fluorescent reporter gene and shown to function in P. riograndensis SBR5. CONCLUSIONS Our RNA-seq analysis provides insight into the P. riograndensis SBR5 transcriptome at the systems level and will be a valuable basis for differential RNA-seq analysis of this bacterium.
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Affiliation(s)
- Luciana Fernandes Brito
- Department of Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany.,Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Marta Irla
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Volker F Wendisch
- Department of Genetics of Prokaryotes, Faculty of Biology, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany. .,Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
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Prasanna R, Pabby A, Saxena S, Singh PK. Modulation of pigment profiles of Calothrix elenkenii in response to environmental changes. JOURNAL OF PLANT PHYSIOLOGY 2004; 161:1125-1132. [PMID: 15535122 DOI: 10.1016/j.jplph.2003.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cyanobacteria are versatile tetrapyrrole synthesizers that can regulate their tetrapyrrole content and composition in response to environmental signals. The present investigation analyses the interplay between light and dark regimes (continuous light, light-dark cycles (16:8) and continuous darkness) and aerobic, air-tight, and anaerobic environments (argon-enriched), on the relative composition of various pigments and growth attributes of Calothrix elenkenii as a prelude to exploiting C. elenkenii's bioindustrial potential as a source of pigments. Incubation in an anaerobic environment stimulated hormogonia formation and induced colouration/thickening of cells. Aerobically grown cultures of Calothrix, under continuous illumination produced the maximum amount of total phycobiliproteins and sugars, although chlorophyll accumulation and nitrogenase activity were highest in the light-dark environment. However, the beta-carotene content was observed to vary under anaerobic conditions with different light-dark regimes. This C. elenkenii strain can be a valuable source of pigments under optimized environmental conditions.
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Affiliation(s)
- Radha Prasanna
- National Centre for Conservation and Utilization of Blue-Green Algae, Indian Agricultural Research Institute, New Delhi 110 012, India.
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Khudyakov IY, Golden JW. Identification and inactivation of three group 2 sigma factor genes in Anabaena sp. strain PCC 7120. J Bacteriol 2001; 183:6667-75. [PMID: 11673438 PMCID: PMC95499 DOI: 10.1128/jb.183.22.6667-6675.2001] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Three new Anabaena sp. strain PCC 7120 genes encoding group 2 alternative sigma factors have been cloned and characterized. Insertional inactivation of sigD, sigE, and sigF genes did not affect growth on nitrate under standard laboratory conditions but did transiently impair the abilities of sigD and sigE mutant strains to establish diazotrophic growth. A sigD sigE double mutant, though proficient in growth on nitrate and still able to differentiate into distinct proheterocysts, was unable to grow diazotrophically due to extensive fragmentation of filaments upon nitrogen deprivation. This double mutant could be complemented by wild-type copies of sigD or sigE, indicating some degree of functional redundancy that can partially mask phenotypes of single gene mutants. However, the sigE gene was required for lysogenic development of the temperate cyanophage A-4L. Several other combinations of double mutations, especially sigE sigF, caused a transient defect in establishing diazotrophic growth, manifested as a strong and prolonged bleaching response to nitrogen deprivation. We found no evidence for developmental regulation of the sigma factor genes. luxAB reporter fusions with sigD, sigE, and sigF all showed slightly reduced expression after induction of heterocyst development by nitrogen stepdown. Phylogenetic analysis of cyanobacterial group 2 sigma factor sequences revealed that they fall into several subgroups. Three morphologically and physiologically distant strains, Anabaena sp. strain PCC 7120, Synechococcus sp. strain PCC 7002, and Synechocystis sp. strain PCC 6803 each contain representatives of four subgroups. Unlike unicellular strains, Anabaena sp. strain PCC 7120 has three additional group 2 sigma factors that cluster in subgroup 2.5b, which is perhaps specific for filamentous or heterocystous cyanobacteria.
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Affiliation(s)
- I Y Khudyakov
- Department of biology, Texas A & M University, College Station 77843-3258, USA
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Caslake LF, Gruber TM, Bryant DA. Expression of two alternative sigma factors of Synechococcus sp. strain PCC 7002 is modulated by carbon and nitrogen stress. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 12):3807-3818. [PMID: 9421905 DOI: 10.1099/00221287-143-12-3807] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The sigB and sigC genes, encoding two alternative sigma factors of the unicellular marine cyanobacterium Synechococcus sp. PCC 7002, were cloned and characterized. Strains in which the sigB and sigC genes were insertionally inactivated were viable under standard laboratory conditions, indicating that SigB and SigC are group 2 sigma factors. Starvation for either nitrogen or carbon caused an increase in sigB mRNA levels. Transcripts for the sigC gene initially increased but then decreased during nitrogen and carbon starvation. The SigC protein could not be identified in cyanobacterial extracts using antisera to Synechococcus sp. PCC 7002 SigA or RpoD from Bacillus subtilis. The ratio of the principal vegetative sigma factor, SigA, to SigB decreased during either nitrogen starvation or carbon starvation, and the levels of SigB also increased in the sigC mutant strain. These results imply that SigB and SigC play roles in modifying transcription in response to changes in carbon and nitrogen availability in this cyanobacterium.
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Affiliation(s)
| | - Tanja M Gruber
- Department of Biochemistry and Molecular Biology and Center for Biomolecular Structure and Function, The Pennsylvania State University, University Park,PA 16802,USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology and Center for Biomolecular Structure and Function, The Pennsylvania State University, University Park,PA 16802,USA
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Reyes JC, Muro-Pastor MI, Florencio FJ. Transcription of glutamine synthetase genes (glnA and glnN) from the cyanobacterium Synechocystis sp. strain PCC 6803 is differently regulated in response to nitrogen availability. J Bacteriol 1997; 179:2678-89. [PMID: 9098067 PMCID: PMC179018 DOI: 10.1128/jb.179.8.2678-2689.1997] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
In the cyanobacterium Synechocystis sp. strain PCC 6803 we have previously reported the presence of two different proteins with glutamine synthetase activity: GSI, encoded by the glnA gene, and GSIII, encoded by the glnN gene. In this work we show that expression of both the glnA and glnN genes is subjected to transcriptional regulation in response to changes in nitrogen availability. Northern blot experiments and transcriptional fusions demonstrated that the glnA gene is highly transcribed in nitrate- or ammonium-grown cells and exhibits two- to fourfold-higher expression in nitrogen-starved cells. In contrast, the glnN gene is highly expressed only under nitrogen deficiency. Half-lives of both mRNAs, calculated after addition of rifampin or ammonium to nitrogen-starved cells, were not significantly different (2.5 or 3.4 min, respectively, for glnA mRNA; 1.9 or 1.4 min, respectively, for glnN mRNA), suggesting that changes in transcript stability are not involved in the regulation of the expression of both genes. Deletions of the glnA and glnN upstream regions were used to delimit the promoter and the regulatory sequences of both genes. Primer extension analysis showed that structure of the glnA gene promoter resembles those of the NtcA-regulated promoters. In addition, mobility shift assays demonstrated that purified, Escherichia coli-expressed Synechocystis NtcA protein binds to the promoter of the glnA gene. Primer extension also revealed the existence of a sequence related to the NtcA binding site upstream from the glnN promoter. However, E. coli-expressed NtcA failed to bind to this site. These findings suggest that an additional modification of NtcA or an additional factor is required for the regulation of glnN gene expression.
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Affiliation(s)
- J C Reyes
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-CSIC, Seville, Spain
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Grossman AR, Schaefer MR, Chiang GG, Collier JL. The phycobilisome, a light-harvesting complex responsive to environmental conditions. Microbiol Rev 1993; 57:725-49. [PMID: 8246846 PMCID: PMC372933 DOI: 10.1128/mr.57.3.725-749.1993] [Citation(s) in RCA: 242] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Photosynthetic organisms can acclimate to their environment by changing many cellular processes, including the biosynthesis of the photosynthetic apparatus. In this article we discuss the phycobilisome, the light-harvesting apparatus of cyanobacteria and red algae. Unlike most light-harvesting antenna complexes, the phycobilisome is not an integral membrane complex but is attached to the surface of the photosynthetic membranes. It is composed of both the pigmented phycobiliproteins and the nonpigmented linker polypeptides; the former are important for absorbing light energy, while the latter are important for stability and assembly of the complex. The composition of the phycobilisome is very sensitive to a number of different environmental factors. Some of the filamentous cyanobacteria can alter the composition of the phycobilisome in response to the prevalent wavelengths of light in the environment. This process, called complementary chromatic adaptation, allows these organisms to efficiently utilize available light energy to drive photosynthetic electron transport and CO2 fixation. Under conditions of macronutrient limitation, many cyanobacteria degrade their phycobilisomes in a rapid and orderly fashion. Since the phycobilisome is an abundant component of the cell, its degradation may provide a substantial amount of nitrogen to nitrogen-limited cells. Furthermore, degradation of the phycobilisome during nutrient-limited growth may prevent photodamage that would occur if the cells were to absorb light under conditions of metabolic arrest. The interplay of various environmental parameters in determining the number of phycobilisomes and their structural characteristics and the ways in which these parameters control phycobilisome biosynthesis are fertile areas for investigation.
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Affiliation(s)
- A R Grossman
- Department of Plant Biology, Carnegie Institution of Washington, Stanford, California 94305
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Huckle JW, Morby AP, Turner JS, Robinson NJ. Isolation of a prokaryotic metallothionein locus and analysis of transcriptional control by trace metal ions. Mol Microbiol 1993; 7:177-87. [PMID: 8446025 DOI: 10.1111/j.1365-2958.1993.tb01109.x] [Citation(s) in RCA: 178] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In eukaryotes, metallothioneins (MTs) are involved in cellular responses to elevated concentrations of certain metal ions. We report the isolation and analysis of a prokaryotic MT locus from Synechococcus PCC 7942. The MT locus (smt) includes smtA, which encodes a class II MT, and a divergently transcribed gene, smtB. The sites of transcription initiation of both genes have been mapped and features within the smt operator-promoter region identified. Elevated concentrations of the ionic species of Cd, Co, Cr, Cu, Hg, Ni, Pb and Zn elicited an increase in the abundance of smtA transcripts. There was no detectable effect of elevated metal (Cd) on smtA transcript stability. Sequences upstream of smtA, fused to a promoterless lacZ gene, conferred metal-dependent beta-galactosidase activity in Synechococcus PCC 7942 (strain R2-PIM8). At maximum permissive concentrations, Zn was the most potent elicitor in vivo, followed by Cu and Cd with slight induction by Co and Ni. The deduced SmtB polypeptide has similarity to the ArsR and CadC proteins involved in resistance to arsenate/arsenite/antimonite and to Cd, contains a predicted helix-turn-helix DNA-binding motif and is shown to be a repressor of transcription from the smtA operator-promoter.
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Affiliation(s)
- J W Huckle
- Department of Biological Sciences, University of Durham, UK
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Tandeau de Marsac N, Houmard J. Adaptation of cyanobacteria to environmental stimuli: new steps towards molecular mechanisms. FEMS Microbiol Lett 1993. [DOI: 10.1111/j.1574-6968.1993.tb05866.x] [Citation(s) in RCA: 270] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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Braun-Howland EB, Nierzwicki-Bauer SA. Occurrence of the 32-kDa QB-binding protein of photosystem II in vegetative cells, heterocysts and akinetes ofAzolla carotiniana cyanobionts. PLANTA 1990; 180:361-371. [PMID: 24202015 DOI: 10.1007/bf01160391] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/1989] [Accepted: 10/10/1989] [Indexed: 06/02/2023]
Abstract
Transmission electron microscopy and immunocytological labeling were used to localize the 32-kilodalton (kDa) protein (DI polypeptide) of photosystem II in different cell types of the cyanobionts within leaf cavities ofAzolla caroliniana Willd. The 32-kDa protein binds the secondary electron acceptor QB, and is highly conserved between plants and cyanobacteria. Three antisera, specific for different epitopes of the 32-kDa protein, were used as primary antibodies. Immunologically recognizable 32-kDa protein was localized on membranes ofAzolla chloroplasts, vegetative cyanobacterial cells, akinetes, and heterocysts that were at all stages of the differentiation process. The 32-kDa protein was not detected in nonphotosynthetic endosymbiotic bacteria found within leaf cavities. The amount of the 32-kDa protein observed in different cyanobacterial cell types was dependent upon the primary antiserum used and membrane orientation within a cell with respect to the plane of sectioning. Therefore, although 32-kDa protein was present in all three cyanobacterial cell types and clear trends in labeling patterns could be elucidated, it was not possible to quantitate the amounts of protein with respect to either cell type or leaf-cavity age.
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Affiliation(s)
- E B Braun-Howland
- Plant Research Group, Department of Biology, MRC 306, Rensselaer Polytechnic Institute, 12180-3590, Troy, NY, USA
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Allen MM, Law A, Evans EH. Control of photosynthesis during nitrogen depletion and recovery in a non-nitrogen-fixing cyanobacterium. Arch Microbiol 1990. [DOI: 10.1007/bf00248422] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Braun-Howland EB, Nierzwicki-Bauer SA. Occurrence of the 32-kDa QB-binding protein of photosystem II in vegetative cells, dheterocysts and akinetes of Azolla carotiniana cyanobionts. PLANTA 1990; 180:361-371. [PMID: 24202014 DOI: 10.1007/bf00198787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/1989] [Accepted: 10/10/1989] [Indexed: 06/02/2023]
Abstract
Transmission electron microscopy and immunocytological labeling were used to localize the 32-kilodalton (kDa) protein (DI polypeptide) of photosystem II in different cell types of the cyanobionts within leaf cavities of Azolla caroliniana Willd. The 32-kDa protein binds the secondary electron acceptor QB, and is highly conserved between plants and cyanobacteria. Three antisera, specific for different epitopes of the 32-kDa protein, were used as primary antibodies. Immunologically recognizable 32-kDa protein was localized on membranes of Azolla chloroplasts, vegetative cyanobacterial cells, akinetes, and heterocysts that were at all stages of the differentiation process. The 32-kDa protein was not detected in nonphotosynthetic endosymbiotic bacteria found within leaf cavities. The amount of the 32-kDa protein observed in different cyanobacterial cell types was dependent upon the primary antiserum used and membrane orientation within a cell with respect to the plane of sectioning. Therefore, although 32-kDa protein was present in all three cyanobacterial cell types and clear trends in labeling patterns could be elucidated, it was not possible to quantitate the amounts of protein with respect to either cell type or leaf-cavity age.
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Affiliation(s)
- E B Braun-Howland
- Plant Research Group, Department of Biology, MRC 306, Rensselaer Polytechnic Institute, 12180-3590, Troy, NY, USA
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