RNA-seq Profiling Reveals Novel Target Genes of LexA in the Cyanobacterium Synechocystis sp. PCC 6803

Kizawa, Ayumi; Kawahara, Akihito; Takimura, Yasushi; Nishiyama, Yoshitaka; Hihara, Yukako

doi:10.3389/fmicb.2016.00193

Cited by 36 publications

(55 citation statements)

References 59 publications

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“…The marine cyanobacteria of the genus Prochlorococcus and Synechococcus share a very similar lexA (clade C), while other strains possess a slightly different lexA (clade B), such as A. marina MBIC11017, and both Nostoc PCC7120 and Synechocystis PCC6803 (Li et al, 2010). Interestingly, the Synechocystis PCC6803 lexA gene appeared to regulate carbon assimilation (Domain et al, 2004) and cell motility (Kizawa et al, 2016), but not DNA recombination and repair (Domain et al, 2004). Furthermore, the Nostoc PCC7120 LexA protein has a RecA-independent autoproteolytic cleavage (Kumar et al, 2015).…”

Section: Resultsmentioning

confidence: 99%

“…While ruvB was found to operate in DNA-recombination, lexA appeared to regulate carbon assimilation (Domain et al, 2004) and cell motility (Kizawa et al, 2016) but not DNA repair (Domain et al, 2004). …”

Section: Resultsmentioning

confidence: 99%

“…90 lacks sulA, dinB, ogt, recBCD and umuCD . Synechocystis PCC6803 possesses lexA , but it does not regulate DNA repair genes; it controls carbon assimilation (Domain et al, 2004) and cell motility (Kizawa et al, 2016). Furthermore, the Synechocystis PCC6803 lexA and recA genes are not induced by UV-C as occur in E. coli , actually they are downregulated by UV-C (Domain et al, 2004) [ lexA is also negatively regulated by UV-B (Huang et al, 2002)].…”

Section: Resultsmentioning

confidence: 99%

“…The Synechocystis PCC6803 recA -null mutant was sensitive to UV-C and white light. The Synechocystis PCC6803 ruvB gene was found to operate in DNA-recombination, while lexA appeared to regulate carbon assimilation (Domain et al, 2004) and cell motility (Kizawa et al, 2016), but not DNA repair (Domain et al, 2004). We hope that this review will stimulate future studies of DNA recombination and repair in cyanobacteria so as to answer the following questions, among others.…”

Section: Resultsmentioning

confidence: 99%

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Comparative Genomics of DNA Recombination and Repair in Cyanobacteria: Biotechnological Implications

2016

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Cyanobacteria are fascinating photosynthetic prokaryotes that are regarded as the ancestors of the plant chloroplast; the purveyors of oxygen and biomass for the food chain; and promising cell factories for an environmentally friendly production of chemicals. In colonizing most waters and soils of our planet, cyanobacteria are inevitably challenged by environmental stresses that generate DNA damages. Furthermore, many strains engineered for biotechnological purposes can use DNA recombination to stop synthesizing the biotechnological product. Hence, it is important to study DNA recombination and repair in cyanobacteria for both basic and applied research. This review reports what is known in a few widely studied model cyanobacteria and what can be inferred by mining the sequenced genomes of morphologically and physiologically diverse strains. We show that cyanobacteria possess many E. coli-like DNA recombination and repair genes, and possibly other genes not yet identified. E. coli-homolog genes are unevenly distributed in cyanobacteria, in agreement with their wide genome diversity. Many genes are extremely well conserved in cyanobacteria (mutMS, radA, recA, recFO, recG, recN, ruvABC, ssb, and uvrABCD), even in small genomes, suggesting that they encode the core DNA repair process. In addition to these core genes, the marine Prochlorococcus and Synechococcus strains harbor recBCD (DNA recombination), umuCD (mutational DNA replication), as well as the key SOS genes lexA (regulation of the SOS system) and sulA (postponing of cell division until completion of DNA reparation). Hence, these strains could possess an E. coli-type SOS system. In contrast, several cyanobacteria endowed with larger genomes lack typical SOS genes. For examples, the two studied Gloeobacter strains lack alkB, lexA, and sulA; and Synechococcus PCC7942 has neither lexA nor recCD. Furthermore, the Synechocystis PCC6803 lexA product does not regulate DNA repair genes. Collectively, these findings indicate that not all cyanobacteria have an E. coli-type SOS system. Also interestingly, several cyanobacteria possess multiple copies of E. coli-like DNA repair genes, such as Acaryochloris marina MBIC11017 (2 alkB, 3 ogt, 7 recA, 3 recD, 2 ssb, 3 umuC, 4 umuD, and 8 xerC), Cyanothece ATCC51142 (2 lexA and 4 ruvC), and Nostoc PCC7120 (2 ssb and 3 xerC).

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Comparative Genomics of DNA Recombination and Repair in Cyanobacteria: Biotechnological Implications

2016

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“…We found that the transcription of over 500 genes was altered in various functional categories and the transcription of 63 genes altered twofold or more. Global transcriptomic studies have been carried out on Synechocystis using either microarrays or RNA-seq to examine the effects of various conditions (Anfelt, Hallstr€ om, Nielsen, Uhl en, & Hudson, 2013;Hern andez-Prieto et al, 2012;Hihara, Kamei, Kanehisa, Kaplan, & Ikeuchi, 2001;Huang, McCluskey, Ni, & Larossa, 2002;Kizawa, Kawahara, Takimura, Nishiyama, & Hihara, 2016;Kl€ ahn et al, 2015;Kopf et al, 2014;Lau, Foong, Kurihara, Sudesh, & Matsui, 2014;Wang, Postier, & Burnap, 2004;Zhang et al, 2008).…”

Section: Discussionmentioning

confidence: 99%

Ethylene causes transcriptomic changes in Synechocystis during phototaxis

et al. 2018

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Ethylene is well known as a plant hormone, but its role in bacteria is poorly studied.We recently showed that Synechocystis sp. Strain PCC 6803 has a functional receptor for ethylene, ethylene response 1 (Etr1), that is involved in various processes such as phototaxis in response to directional light and biofilm formation. Here, we use RNA sequencing to examine the changes in gene transcripts caused by ethylene under phototaxis conditions. Over 500 gene transcripts across many functional categories, of approximately 3700 protein-encoding genes, were altered by application of ethylene. In general, ethylene caused both up-and downregulation of genes within a functional category. However, the transcript levels of amino acid metabolism genes were mainly upregulated and cell envelope genes were mostly downregulated by ethylene. The changes in cell envelope genes correlate with our prior observation that ethylene affects cell surface properties to alter cell motility. Ethylene caused a twofold or more change in 62 transcripts with the largest category of upregulated genes annotated as transporters and the largest category of downregulated genes annotated as glycosyltransferases which sometimes are involved in changing the composition of sugars on the cell surface. Consistent with changes in cell envelope, glycosyltransferase, and transporter gene transcripts, application of ethylene altered the levels of specific sugar moieties on the surface of cells. Light signaling from Etr1 involves two proteins (Slr1213 and Slr1214) and a small, noncoding RNA, carbon stress-induced RNA1 (csiR1). Application of ethylene caused a rapid, but transient, decrease in the transcript levels of etr1, slr1213, and slr1214 and a rapid and prolonged decrease in csiR1 transcript. Deletion of Slr1214 caused a large increase in csiR1 transcript levels and ethylene lowered csiR1 transcript.These data combined with prior reports indicate that ethylene functions as a signal to affect a variety of processes altering the physiology of Synechocystis cells. K E Y W O R D Sethylene receptor, extracellular polymeric substances, RNA-seq, Synechocystis

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Regulation of RNase E during the UV stress response in the cyanobacterium Synechocystis sp. PCC 6803

Watanabe

Stazic

Georg

et al. 2023

mLife

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Endoribonucleases govern the maturation and degradation of RNA and are indispensable in the posttranscriptional regulation of gene expression. A key endoribonuclease in Gram-negative bacteria is RNase E. To ensure an appropriate supply of RNase E, some bacteria, such as Escherichia coli, feedback-regulate RNase E expression via the rne 5′-untranslated region (5′ UTR) in cis. However, the mechanisms involved in the control of RNase E in other bacteria largely remain unknown. Cyanobacteria rely on solar light as an energy source for photosynthesis, despite the inherent ultraviolet (UV) irradiation. In this study, we first investigated globally the changes in gene expression in the cyanobacterium Synechocystis sp. PCC 6803 after a brief exposure to UV. Among the 407 responding genes 2 h after UV exposure was a prominent upregulation of rne mRNA level. Moreover, the enzymatic activity of RNase E rapidly increased as well, although the protein stability decreased. This unique response was underpinned by the increased accumulation of full-length rne mRNA caused by the stabilization of its 5′ UTR and suppression of premature transcriptional termination, but not by an increased transcription rate. Mapping of RNA 3′ ends and in vitro cleavage assays revealed that RNase E cleaves within a stretch of six consecutive uridine residues within the rne 5′ UTR, indicating autoregulation. These observations suggest that RNase E in cyanobacteria contributes to reshaping the transcriptome during the UV stress response and that its required activity level is secured at the RNA level despite the enhanced turnover of the protein.

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RNA-seq Profiling Reveals Novel Target Genes of LexA in the Cyanobacterium Synechocystis sp. PCC 6803

Cited by 36 publications

References 59 publications

Comparative Genomics of DNA Recombination and Repair in Cyanobacteria: Biotechnological Implications

Comparative Genomics of DNA Recombination and Repair in Cyanobacteria: Biotechnological Implications

Ethylene causes transcriptomic changes in Synechocystis during phototaxis

Regulation of RNase E during the UV stress response in the cyanobacterium Synechocystis sp. PCC 6803

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