Multi-Omic Analyses Reveal Habitat Adaptation of Marine Cyanobacterium Synechocystis sp. PCC 7338

Abstract

Cyanobacteria are considered as promising microbial cell factories producing a wide array of bio-products. Among them, Synechocystis sp. PCC 7338 has the advantage of growing in seawater, rather than requiring arable land or freshwater. Nonetheless, how this marine cyanobacterium grows under the high salt stress condition remains unknown. Here, we determined its complete genome sequence with the embedded regulatory elements and analyzed the transcriptional changes in response to a high-salt environment. Complete genome sequencing revealed a 3.70 mega base pair genome and three plasmids with a total of 3,589 genes annotated. Differential RNA-seq and Term-seq data aligned to the complete genome provided genome-wide information on genetic regulatory elements, including promoters, ribosome-binding sites, 5′- and 3′-untranslated regions, and terminators. Comparison with freshwater Synechocystis species revealed Synechocystis sp. PCC 7338 genome encodes additional genes, whose functions are related to ion channels to facilitate the adaptation to high salt and high osmotic pressure. Furthermore, a ferric uptake regulator binding motif was found in regulatory regions of various genes including SigF and the genes involved in energy metabolism, suggesting the iron-regulatory network is connected to not only the iron acquisition, but also response to high salt stress and photosynthesis. In addition, the transcriptomics analysis demonstrated a cyclic electron transport through photosystem I was actively used by the strain to satisfy the demand for ATP under high-salt environment. Our comprehensive analyses provide pivotal information to elucidate the genomic functions and regulations in Synechocystis sp. PCC 7338.

Interactors and effects of overexpressing YlxR/RpnM, a conserved RNA binding protein in cyanobacteria

“…Comparison of sequences from homologous loci in other Synechocystis strains revealed strong sequence and structure conservation ( Figure 3C ). These strains differ by several hundred genes from Synechocystis 6803 (51–53). Therefore, the conservation of the RNA fragment crosslinked to YlxR/Ssr1238 indicates its functional relevance.…”

“…Comparison of sequences from homologous loci in other Synechocystis strains revealed strong sequence and structure conservation ( Figure 3C ). These strains differ by several hundred genes from Synechocystis 6803 [33–35]. For instance, Synechocystis 6803 and Synechocystis 6714 share 2838 protein-coding genes, while 845 genes are unique for Synechocystis 6803 and 895 genes for Synechocystis 6714 [34].…”

“…Comparison of sequences from homologous loci in other Synechocystis strains revealed strong sequence and structure conservation (Figure 3C). These strains differ by several hundred genes from Synechocystis 6803 (51)(52)(53).…”

The high‐light‐induced protein SliP4 binds to NDH1 and photosystems facilitating cyclic electron transport and state transition in Synechocystis sp. PCC 6803

“…Although not annotated, further sliP4 homologs can be identified by TBLASTN searches in the genomes of Synechocystis sp. CACIAM 05 (GenBank accession CP019225), IPPAS B-1465 (Genbank accession CP028094), PCC 7338, and PCC 7339 (Jeong et al, 2021;and Genbank accessions CP054306 and CP063659). The corresponding SliP4 proteins are highly conserved in all Synechocystis spp.…”

Different Regulatory Modes of Synechocystis sp. PCC 6803 in Response to Photosynthesis Inhibitory Conditions

“…PCC 6803 in response to HL or LT stress conditions. Furthermore, we comprehensively analyzed the genome-scale data based on the genomic architecture, which includes the transcription unit (TU) architecture determined from the 5′- and 3′-end information obtained from differential transcriptome sequencing (dRNA-seq) and sequencing of 3′-ends (Term-seq) ( 31 , 32 ). By analyzing genomic architecture data alongside transcriptome and translatome data, we were able to investigate the posttranscriptional regulation in untranslated regions (UTRs) responsible for declining photosynthetic yield under stress conditions.…”