Phylogenetic Evolutionary Study Of Functional Genes Relating To Transcriptional Regulation And Transport System In Streptomyces

Streptomyces is a group of Gram-positive bacteria with high G+C content. It is renowned for its complex biology in gene regulation, antibiotic production, morphological differentiation, secretion system and stress response. The genome of Streptomyces consists of a linear chromosome; some Streptomyces species also carry linear or circular plasmids. To date genome sequences from more than 40 strains of Streptomyces are in various stages of completion and are available in public databases.This study presents the results of a comprehensive analysis of the genomes of five model Streptomyces species with distinct phenotypes. These streptomycetes have a pan-genome comprised of 17,362 orthologous families which includes 3,096 components in the core genome,5,066 components in the dispensable genome, and 9,200 components that are uniquely present in only one species. The core genome contains important genes for Streptomyces biology and provides the significant evidence for the studying of Streptomyces minimal genome. It makes up about 33-45% of each genome repertoire, including 50 Streptomyces signature proteins. Abundant lineage-specific expansion (LSE) genes have been identified, with 4-11% of the whole genomes, suggesting that frequent gene duplication or lateral gene transfer events play a role in shaping the genome diversification within this genus. Two types of LSE gene families are present:lineage-unique LSE and typical LSE. Two patterns of expansion, single gene expansion and chromosome block expansion are observed, representing different scales of duplication. A better understanding of the LSE gene families will bring a wealth of new insights into the mechanisms underlying strain-specific phenotypes.The classification of sigma factors in 11 completely sequenced Streptomyces genomes was based on the presence and distribution of the sigma conserved regions. The number of sigma factors ranged from 35 to 65, with 0.52-0.72% of each genome. Among these sigma factors,68.6-83.1% were extra-cytoplasmic function (ECF) sigma factors, which coordinated cellular responses to external signals. Homology analysis identified 22 conserved sigma gene families. And the relationship of sigma factors in each group was identified by phylogenetic analysis. A comprehensive analysis of the protein-protein association networks involving the sigma factors in three Streptomyces genomes were performed using STRING database. The number of each sigma factor interacting proteins range from 42 to 263, accounting 3,234,2,042 and 1,780 proteins in each genome. Homologous sigma factors in three Streptomyces species have similar interaction networks. The study of sigma factor interaction networks would shed lights on the Streptomyces transcriptional regulatory networks.According to the transporter classification database (TCDB), the transporters in 11 completely sequenced Streptomyces genomes were identified and classified. Each genome contained 761-1258 transport proteins respectively, accounting for 10.2-13.7% of each whole genome, with seven transporter classes and 171 transporter families. These transporters have 0-24 transmembrane segments,34.7-41.5% of the transporters don't contain any transmembrane segment,9.5-16.0% of the transporter protein has six transmembrane segments, and 7.3-10.7% of the transporter protein contains 12 transmembrane segments. The transport protein system controls the uptake of nutrients, secretion of antibiotics and extracellular proteins. ABC superfamily and MFS superfamily are the most abundant transporter families in Streptomyces, accounting for 32.7-47.5% and 10.1-15.0% of all transporters, respectively. The transporters of these two superfamilies are involved in the nutrient uptake and substrate export process, especially the process of drug efflux. Studying the function of transporters will help to explore of the secretion mechanism in Streptomyces, and will provide evidence to improve the antibiotics secretion system.Streptomyces protein translocation systems are mainly consisting of the Tat translocation system and the Sec translocation system. Auxiliary protein SecDF of the Sec system can promote protein secretion. In Streptomyces genomes, secD/F homologs have secD-secF genes with fission type and secDF gene with fusion type. Molecular evolution analysis found that Streptomyces secDF gene was obtained by a horizontal gene transfer event, and was lost in some Streptomyces species due to lacking of selective pressure. Functional analysis of S. coelicolor secD/F homologs found that deletion of secD-secF genes could cause the reduced efficiency of protein secretion by Sec pathway, while deletion of secDF gene had no significant change. In the double-deletion mutant, the efficiency of secretion of the Xylanase A decreased more significantly than the secD-secF deletion mutant, indicating that in the condition of secD-secF genes deletion, secDF gene expression increased, and partly recovered the secD-secF gene function. Gene expression analysis showed that the expression of secD-secF genes was efficient and stable in various growth stages, but the expression of secDF was fairly low. Two sets of genes might potentially be associated with each other in function and expression. As one set of gene was deleted, another set of gene could increase its own expression to recover the loss of functionality. The study showed that the secD-secF genes were important components of Sec pathway, while the functional of secDF gene had a significant evolutionary decline.