Identification of microRNA-size sRNAs Related to Salt Tolerance in Spirulina platensis

Abstract

microRNAs (miRNAs) are endogenous noncoding small RNAs (sRNA) that play important regulatory functions in growth, development, and environmental stress response of eukaryotes. Currently, miRNA-size sRNA (msRNAs) was discovered in several prokaryotes through deep sequencing. However, no data are available on whether msRNAs exist in cyanobacteria and whether they regulate biological tolerance to salt stress. In this study, three small RNA libraries were constructed from control (0.02 M NaCl), medium-(0.3 M NaCl), and high-salt treatments (0.5 M NaCl) of Spirulina platensis. After sequencing using a high-throughput Illumina Solexa system, nine msRNAs with msRNA* were identified, and 21 candidate msRNAs showed significantly differential expression under saltstress conditions. Seven of the selected msRNAs presented the consistent expression trends when compared with their deep sequencing results as verified by quantitative real-time polymerase chain reaction (qRT-PCR), demonstrating that the expression analyses for msRNAs according to small RNA sequencing data were reliable. Through computational identification, 33 target genes were predicted for 12 msRNAs in S. platensis; Gene Ontology (GO) and KEGG enrichment analyses revealed that the putative target genes were grouped into the categories of proteolysis, protein homotrimerization, glycosylation, ubiquinone biosynthetic process, DNA restriction-modification system, and polysaccharide catabolic process. Using proteomic analysis, two target proteins (glyceraldehyde-3-phosphate dehydrogenase and forkhead-associated (FHA) domain-containing protein) were differentially expressed under salt-stress conditions, which might be regulated by msRNAs. Our study demonstrates that msRNAs exist in S. platensis, and these msRNAs may have an important role in salt-stress responses; however, their functional significance requires further investigation.

Effects of β-diketone antibiotics on F1-zebrafish (Danio rerio) based on high throughput miRNA sequencing under exposure to parents

“…The measurement of Fragment Per Kilobase of exon per Million fragments mapped (FPKM) was applied for determining expression patterns of miRNAs among different treatments. The fold-change between different treatment groups was calculated on the basis of the equation: fold-change ¼ log 2 (treat/control); a measure commonly used to quantify changes in the expression level of a gene (Zhao et al, 2015).…”

Transcriptome Analysis of Spirulina platensis sp. at Different Salinity and Nutrient Compositions for Sustainable Cultivation in Vietnam

“…As a defense mechanism against low temperature pressure, S. platensis up-regulated the proteins involved in gluconeogenesis, amino acid biosynthesis, and starch and sucrose metabolism, whereas the translation and down-regulated tricarboxylic acid (TCA) cycle were linked to reduced energy consumption. The transcriptomic study of S. platensis was conducted at varied salinity conditions (1.17‰, 17.55‰, and 29.25‰) [17]. Zhao et al [17] confirmed the existence of msRNA in S. platensis, and these msRNA play a significant role in salt-induced stress responses.…”

“…The transcriptomic study of S. platensis was conducted at varied salinity conditions (1.17‰, 17.55‰, and 29.25‰) [17]. Zhao et al [17] confirmed the existence of msRNA in S. platensis, and these msRNA play a significant role in salt-induced stress responses. The mechanism underlying the genes related to stress and salt tolerance has not yet been discovered.…”