Identification of Small RNAs and Differential Gene Expression in Rhodobacter Sphaeroides under Gold Chloride Stress
Mendel, Jovinna Laryssa
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Small, regulatory RNAs (sRNA) play an important role in mediating transcriptional and translational processes within bacterial organisms. Understanding how these sRNAs play a role in heavy metal stress is of importance for bacteria involved in bioremediation. The following study aims to (i) identify novel sRNA sequences within Rhodobacter sphaeroides using RNAspace, a bioinformatic approach, (ii) validate a set of sRNAs expressed when the bacterium is grown under an aerobic and/or gold chloride stress condition, and (iii) analyze the gene expression profiles to identify specific target genes involved in the gold chloride stress condition. A total of 712 sRNAs were predicted within the genome of R. sphaeroides using the bioinformatic approach. R. sphaeroides growth characteristics were observed under different concentrations of gold chloride and were found to withstand up to a 1.0 µM concentration. Total RNA isolated from the untreated control group and the 1.0 µM AuCl3 treated group were selected for small RNA and total RNA sequencing. A total of three differentially expressed sRNA sequences were detected in the 1.0µM AuCl3 group, thus implying the role of these sRNAs in gold chloride stress. Additionally, targets were predicted for each sRNA utilizing the CopraRNA prediction program. A transcriptomic analysis was performed to identify differentially expressed genes between the control and 1.0 µM AuCl3 groups at lag/early-log and late-log/stationary growth phases. A total of 121 genes representing a wide variety of gene functions exhibited up- or down- gene regulation at the lag/early-log phase, while 604 genes were up-/down-regulated at the late-log/stationary phase. A majority of commonly differentially expressed genes were observed to be involved in membrane alteration, chemotactic response, energy production, and intracellular/extracellular transport across the membrane. Small RNAs that were detected by sRNA sequencing were predicted to additionally target differentially expressed genes observed within this comparison. A compiled list of identified sRNAs and their corresponding target genes were used to further elucidate the regulatory roles of these sRNAs under gold chloride stress.