Investigation of promoter regions, motifs, and CpG islands in the regulation of gene expression in Trametes hirsuta strain 072

Dinku Senbeta,Mulugeta Kebede

doi:10.1186/s43141-021-00261-9

Abstract

BackgroundIn silico analysis of transcription start sites, promoter regions, transcription factors and their binding sites, and CpG islands for the Trametes hirsuta strain 072 genome were performed to understand the regulation mechanisms of gene expression and its genetic variations in the genomes. Therefore, a computational survey was carried out for the Trametes hirsuta strain 072 genome with the open reading frames from the National Center for Biotechnology Information database. Seventeen functional sequences were used to analyze promoter regions and their regulatory elements. ResultThe present study revealed that 94% of Trametes hirsuta strain 072 genes contained more than two TSSs. Among these identified TSSs, a TSS with the highest predictive score was considered to determine a promoter region of the genes. Moreover, a total of five common candidate motifs such as MotI, MotII, MotIII, MotIV, and MotV were identified. Among these motifs, motif IV was investigated as the common promoter motif for 41.17% of genes that serve as binding sites for transcription factors (TFs) involved in the expression regulation of Trametes hirsuta strain 072 genes. Motif IV was also compared to registered motifs in publically available databases to see if they are similar to known regulatory motifs for TF using TOMTOM web server. Hence, it was revealed that MotIV might serve as the binding site mainly for the leucine zipper TF gene family to regulate a gene expression of Trametes hirsuta strain 072. Regarding CpG island determination, it was concluded that there is no CpG island in both promoter and gene body regions of the Trametes hirsuta strain 072 genome. ConclusionsThis study provides a better insight into further molecular characterization which aimed to efficiently exploit a white rot fungus, Trametes hirsuta strain 072, for several biotechnological applications aimed to revitalize a severely contaminated environment.

Highlights

In silico analysis of transcription start sites, promoter regions, transcription factors and their binding sites, and CpG islands for the Trametes hirsuta strain 072 genome were performed to understand the regulation mechanisms of gene expression and its genetic variations in the genomes
This study provides a better insight into further molecular characterization which aimed to efficiently exploit a white rot fungus, Trametes hirsuta strain 072, for several biotechnological applications aimed to revitalize a severely contaminated environment
This study revealed that 94% of Trametes hirsuta strain 072 genes contained more than two Transcription start site (TSS)

Summary

Introduction

In silico analysis of transcription start sites, promoter regions, transcription factors and their binding sites, and CpG islands for the Trametes hirsuta strain 072 genome were performed to understand the regulation mechanisms of gene expression and its genetic variations in the genomes. White rot fungi (WRF) are crucial components of several terrestrial ecosystems [1, 2] which are fundamentally important in carbon balance, soil formation, forest regeneration, and support the biodiversity of our planet [3, 4] They can degrade lignocellulose efficiently and make. White rot fungi are an excellent microorganism in degrading lignin and a wide range of complex organopollutants [12] This ability is mainly associated with nonspecific extracellular ligninolytic enzymes such as laccase (Lac), lignin peroxidase (LiP), manganese peroxidase (MnP), and several other peroxidases such as versatile peroxidase (VP) and humic acid peroxidases (HuP) [13, 14]. [22] revealed that Trametes hirsuta potentially produces a wide spectrum of laccase isozymes of high redox potential, an efficient lignin degrader

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