Transcriptome landscape of Synechococcus elongatus PCC 7942 for nitrogen starvation responses using RNA-seq

Choi, Sun Young; Park, Byeonghyeok; Choi, In Geol; Sim, Sang Jun; Lee, Sun Mi; Um, Youngsoon; Woo, Han Min

doi:10.1038/srep30584

Cited by 30 publications

(23 citation statements)

References 46 publications

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“…Based on re-analysis of published transcriptomic data (Table S2 from [ 49 ] and Table S1 from [ 50 ]), the transcript level of Synpcc7942_0905 was found to be most abundant among all protein-encoding genes of S. elongatus PCC 7942 under normal culture conditions (30 °C, 100 µmol photons/m 2 /s, CO 2 aeration) and significantly changed by the tested treatments. These transcriptional analyses showed that Synpcc7942_0905 is also a highly expressed and sensitive gene to environmental changes, similar to its homolog in S. elongatus UTEX 2973.…”

Section: Resultsmentioning

confidence: 99%

The primary transcriptome of the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973

Tan

Hou

Song

et al. 2018

Biotechnol Biofuels

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BackgroundCyanobacteria have shown promising potential for the production of various biofuels and chemical feedstocks. Synechococcus elongatus UTEX 2973 is a fast-growing strain with pronounced tolerance to high temperatures and illumination. Hence, this strain appears to be ideal for the development of photosynthetic biotechnology. However, molecular insights on how this strain can rapidly accumulate biomass and carbohydrates under high-light and high-temperature conditions are lacking.ResultsDifferential RNA-Sequencing (dRNA-Seq) enabled the genome-wide identification of 4808 transcription start sites (TSSs) in S. elongatus UTEX 2973 using a background reduction algorithm. High light promoted the transcription of genes associated with central metabolic pathways, whereas the highly induced small RNA (sRNA) PsrR1 likely contributed to the repression of phycobilisome genes and the accelerated glycogen accumulation rates measured under this condition. Darkness caused transcriptome remodeling with a decline in the expression of genes for carbon fixation and other major metabolic pathways and an increase in the expression of genes for glycogen catabolism and Calvin cycle inhibitor CP12. Two of the identified TSSs drive the transcription of highly abundant sRNAs in darkness. One of them is widely conserved throughout the cyanobacterial phylum. Its gene is fused to a protein-coding gene in some species, illustrating the evolutionary origin of sRNAs from an mRNA 3′-end.ConclusionsOur comprehensive set of genome-wide mapped TSSs, sRNAs and promoter activities will be valuable for projects requiring precise information about the control of transcription aimed at metabolic engineering and the elucidation of stress acclimation mechanisms in this promising strain.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1215-8) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

The primary transcriptome of the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973

Tan

Hou

Song

et al. 2018

Biotechnol Biofuels

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“…Accordingly, the cells rapidly adjust gene expression to various nutritional limitations (Krasikov et al, 2012;Ludwig and Bryant, 2012;Choi et al, 2016). In nitrogen-starved cells, these processes no longer serve as a major sink for products of this electron transfer chain and, thus, it is crucial to adjust the photosynthetic apparatus to the metabolic status of the cell to prevent possible damage associated with over reduction of the photosynthetic electron carriers.…”

Section: Immediate Response Of the Photosynthetic Apparatusmentioning

confidence: 99%

“…In nitrogen-starved cells, these processes no longer serve as a major sink for products of this electron transfer chain and, thus, it is crucial to adjust the photosynthetic apparatus to the metabolic status of the cell to prevent possible damage associated with over reduction of the photosynthetic electron carriers. Accordingly, the cells rapidly adjust gene expression to various nutritional limitations (Krasikov et al, 2012;Ludwig and Bryant, 2012;Choi et al, 2016).…”

Section: Immediate Response Of the Photosynthetic Apparatusmentioning

confidence: 99%

Nitrogen chlorosis in unicellular cyanobacteria – a developmental program for surviving nitrogen deprivation

Forchhammer

Schwarz

2018

Environmental Microbiology

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Summary Cyanobacteria evolved sophisticated mechanisms allowing them to cope with environmental depletion of combined nitrogen. Here, we describe progress in understanding the processes involved in acclimation of nondiazotrophic cyanobacteria to nitrogen shortage, known as nitrogen chlorosis. The process includes immediate metabolic changes and degradation of light harvesting complexes as well as long‐term acclimation responses. Consequently, quiescent cells substantially differing from vegetative cells are obtained. Thus, the process leading to these considerable metabolic and morphological changes is referred to as a developmental program. Current understanding of the relevant regulatory processes depicts an intricate mechanism involving modulation of transcription activators by proteinaceous interacting components, as well as by small metabolites reporting the energy status and carbon–nitrogen balance of the cell. In addition, we describe in detail the quiescent state characterizing cells under prolonged starvation and the process of recovery from this dormant chlorotic state. Accumulated data provide an in depth understanding of the mechanisms accompanying the cycling of cyanobacterial cells between vegetative growth, the quiescent‐state and the recovery program, allowing them to regain proliferative growth upon nutrient replenishment.

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“…The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment of DEGs ( Figure 3 c and Supplementary Table S4 ) showed that nine metabolic pathways were significantly affected by phosphate starvation, of which the three most enriched were ABC transporters, nitrogen metabolism, and cysteine and methionine metabolism. Similar responses were commonly implicated when organisms were exposed to adverse conditions [ 55 , 56 ].…”

Section: Resultsmentioning

confidence: 61%

Glyceroglycolipid Metabolism Regulations under Phosphate Starvation Revealed by Transcriptome Analysis in Synechococcus elongatus PCC 7942

Miao

2020

Marine Drugs

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Glyceroglycolipids, abundant in cyanobacteria’s photosynthetic membranes, present bioactivities and pharmacological activities, and can be widely used in the pharmaceutical industry. Environmental factors could alter the contents and compositions of cyanobacteria glyceroglycolipids, but the regulation mechanism remains unclear. Therefore, the glyceroglycolipids contents and the transcriptome in Synechococcus elongatus PCC 7942 were analyzed under phosphate starvation. Under phosphate starvation, the decrease of monogalactosyl diacylglycerol (MGDG) and increases of digalactosyl diacylglycerol (DGDG) and sulfoquinovosyl diacylglycerol (SQDG) led to a decrease in the MGDG/DGDG ratio, from 4:1 to 5:3, after 12 days of cultivation. However, UDP–sulfoquinovose synthase gene sqdB, and the SQDG synthase gene sqdX, were down-regulated, and the decreased MGDG/DGDG ratio was later increased back to 2:1 after 15 days of cultivation, suggesting the regulation of glyceroglycolipids on day 12 was based on the MGDG/DGDG ratio maintaining glyceroglycolipid homeostasis. There are 12 differentially expressed transcriptional regulators that could be potential candidates related to glyceroglycolipid regulation, according to the transcriptome analysis. The transcriptome analysis also suggested post-transcriptional or post-translational regulations in glyceroglycolipid synthesis. This study provides further insights into glyceroglycolipid metabolism, as well as the scientific basis for glyceroglycolipid synthesis optimization and cyanobacteria glyceroglycolipids utilization via metabolic engineering.

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Transcriptome landscape of Synechococcus elongatus PCC 7942 for nitrogen starvation responses using RNA-seq

Cited by 30 publications

References 46 publications

The primary transcriptome of the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973

The primary transcriptome of the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973

Nitrogen chlorosis in unicellular cyanobacteria – a developmental program for surviving nitrogen deprivation

Glyceroglycolipid Metabolism Regulations under Phosphate Starvation Revealed by Transcriptome Analysis in Synechococcus elongatus PCC 7942

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