Transcriptome Analysis of Gene Expression in Dermacoccus abyssi HZAU 226 under Lysozyme Stress

Abstract

Lysozyme acts as a kind of cationic antimicrobial protein and effectively hydrolyzes bacterial peptidoglycan to have a bactericidal effect, which also plays an important role in protecting eggs from microbial contamination. Dermacoccus abyssi HZAU 226, a Gram-positive bacterium isolated from spoiled eggs, has egg white and lysozyme tolerance, but its survival mechanism is unknown, especially from a transcriptomics point of view. In this study, the high lysozyme tolerance of D. abyssi HZAU 226 was characterized by three independent experiments, and then the Illumina RNA-seq was used to compare the transcriptional profiles of this strain in Luria–Bertani (LB) medium with and without 5 mg/mL lysozyme to identify differentially expressed genes (DEGs); 1024 DEGs were identified by expression analysis, including 544 up-regulated genes and 480 down-regulated genes in response to lysozyme treatment. The functional annotation analysis results of DEGs showed that these genes were mainly involved in glutathione biosynthesis and metabolism, ion transport, energy metabolism pathways, and peptidoglycan biosynthesis. This study is the first report of bacterial-related lysozyme RNA-seq, and our results help in understanding the lysozyme-tolerance mechanism of bacteria from a new perspective and provide transcriptome resources for subsequent research in related fields.

Gene Analysis of Listeria monocytogenes Suspended Aggregates Induced by Ralstonia insidiosa Cell-Free Supernatants under Nutrient-Poor Environments

“…RNA was extracted based on the method described by Zhang et al [22]. The main reagent used is TRIzol (Invitrogen, Carlsbad, CA, USA), which is a new total RNA extraction reagent that can directly extract total RNA from cells or tissues.…”

“…RNA-seq library preparations were built based on the manufacturer's manual, and the Ribo-Zero rRNA removal kit (Bacteria, Illumina, San Diego, CA, USA) was applied to the loss of ribosomal RNA. The construction of the RNA-seq library mainly refers to the method of Zhang et al [22]. The basic process includes RNA interruption, doublestranded cDNA synthesis, terminal repair, dA-tailing, splice, fragment sorting, digestion of dUTP-labeled double strand and PCR amplification.…”

sRNA23, a novel small RNA, regulates to the pathogenesis ofStreptococcus suisserotype 2

“…Expression of sRNA23 was downregulated under iron deprivation medium, which was consistent with the results of RNA-seq. In addition, like many sRNAs, sRNA23 expression was induced by oxidative and lysozyme stress [ 42 , 43 ]. These findings suggest that differential expression of sRNA23 to different environments may be beneficial for bacterial adaptation and pathogenesis.…”

Comparative Transcriptome Analysis Reveals the Molecular Mechanisms of Acetic Acid Reduction by Adding NaHSO3 in Actinobacillus succinogenes GXAS137

“…In recent years, RNA-seq is a transcriptome analysis technique commonly used to explore microorganisms’ tolerance mechanism and analyze differentially expressed genes (DEGs) in transcriptomes ( Mo et al 2019 ). Zhang et al (2020) revealed the lysozyme tolerance mechanism of Dermacoccus abyssi through RNA-seq, and their results showed that the tolerance mechanism of the strain is related to the gene expression of glutathione biosynthesis and metabolism, ion transport, energy metabolism pathway, and peptidoglycan synthesis. The metabolic rule of Ethanoligenens harbinense in ethanol-type fermentation of anaerobic acidogenesis at different pH was studied by RNA-seq, and the results showed that low initial pH resulted in down-regulated expression of genes related to cell growth and acidification.…”