|Chang, Perng Kuang
|WANG, BIN - South China University Of Technology
|HE, ZHU-MEI - Sun Yat-Sen University
|PAN, LI - South China University Of Technology
Submitted to: Austin Journal of Proteomics, Bioinformatics & Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/17/2014
Publication Date: 10/20/2014
Citation: Chang, P-K., Wang, B., He, Z-M., Yu, J., Pan, L. 2014. High temperature, differentiation, and endoplasmic reticulum stress decrease but epigenetic and antioxidative agents increase Aspergillus ribosomal protein gene expression. Austin Journal of Proteomics, Bioinformatics & Genomics. 1(1):6.
Interpretive Summary: Aspergillus flavus and Aspergillus oryzae are phylogenetically closely related, they are classified as separate species because of food safety and economic concerns. Genomes of both species have been sequenced. In the post-genomics era, RNA-Seq has been developed as the standard approach for profiling transcriptomes. Transcriptomic studies on fungi has been mostly focused on characterizing all transcript species, determining cellular protein genes differentially expressed, and elucidating pathogenicity or virulence. No other analyses on transcriptomic data have been attempted to evaluate ribosomal protein (RP) gene expression and its impact on general transcription and translation. In this study, we found that approximately half of the Aspergillus RP genes are highly expressed under normal growth conditions. Medium composition is a major determinant that affects the expressed RP gene population. The RP gene expression level is decreased by abiotic and biotic stress factors but elevated by relief of stress factors. These responses possibly are mediated via ER stress regulation. Transcriptomic analyses on RP gene expression profiles can contribute to fundamental knowledge regarding how general transcription and translation in fungi are shaped by their living environments.
Technical Abstract: Genome-wide gene expression assays using next-generation sequencing techniques have allowed the identification of transcriptomes in many species. Transcript abundance of ribosomal protein (RP) genes can serve as a proxy for the capacity of general transcription and synthesis of cellular proteins that provide molecular functions. We analyzed the species and expression levels of RP genes of four previous RNA-Seq datasets. These included studies on effects of temperature, developmental stages, and epigenetic and antioxidative agents on A. flavus, and culture type and endoplasmic reticulum (ER) stress on A. oryzae RP gene expression. Under normal growth conditions, 40 to 60% of total Aspergillus RP genes were highly expressed (defined as among the top 2% of the total genes). For the same experiment medium composition was the major determinant for the expressed RP gene populations. Stress factors such as high temperature and hyperoxidant state (differentiation) decreased RP gene expression levels and, to a much lesser extent, the expressed RP gene populations. In contrast, factors that relieve oxidative stress increased the expression levels. Both outcomes probably were mediated in part via ER stress regulation. Studies using RP gene profiling can provide new insights into general transcription and translation in fungi and how abiotic and biotic factors affect RP gene expression.