Phylogenomic and comparative analysis of the distribution and regulatory patterns of TPP riboswitches in fungi

Sumit Mukherjee, Matan Drory Retwitzer, Danny Barash, Supratim Sengupta

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

Abstract

Riboswitches are metabolite or ion sensing cis-regulatory elements that regulate the expression of the associated genes involved in biosynthesis or transport of the corresponding metabolite. Among the nearly 40 different classes of riboswitches discovered in bacteria so far, only the TPP riboswitch has also been found in algae, plants, and in fungi where their presence has been experimentally validated in a few instances. We analyzed all the available complete fungal and related genomes and identified TPP riboswitch-based regulation systems in 138 fungi and 15 oomycetes. We find that TPP riboswitches are most abundant in Ascomycota and Basidiomycota where they regulate TPP biosynthesis and/or transporter genes. Many of these transporter genes were found to contain conserved domains consistent with nucleoside, urea and amino acid transporter gene families. The genomic location of TPP riboswitches when correlated with the intron structure of the regulated genes enabled prediction of the precise regulation mechanism employed by each riboswitch. Our comprehensive analysis of TPP riboswitches in fungi provides insights about the phylogenomic distribution, regulatory patterns and functioning mechanisms of TPP riboswitches across diverse fungal species and provides a useful resource that will enhance the understanding of RNA-based gene regulation in eukaryotes.

Original languageEnglish
Article number5563
JournalScientific Reports
Volume8
Issue number1
DOIs
StatePublished - 3 Apr 2018
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2018 The Author(s).

Funding

This work has been supported by the University Grants Commission (UGC grant No. 6-7/2014(IC)) and Israel Science Foundation (ISF grant No. 9/14) grant awarded under the India-Israel Joint Research Project 2014. SM and SS thanks to the Department of Computer Science, Ben-Gurion University for the hospitality extended to them during their visits.

FundersFunder number
Iowa Science Foundation
University Grants Commission6-7/2014(IC)
University Grants Committee6-7/2014
Israel Science Foundation9/14

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