From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon

Abstract

Numerous genomes are sequenced and made available to the community through the NCBI portal. However, and, unlike what happens for gene function annotation, annotation of promoter sequences and the underlying prediction of regulatory associations is mostly unavailable, severely limiting the ability to interpret genome sequences in a functional genomics perspective. Here we present an approach where one can download a genome of interest from NCBI in the GenBank Flat File (.gbff) format and, with a minimum set of commands, have all the information parsed, organized and made available through the platform web interface. Also, the new genomes are compared with a given genome of reference in search of homologous genes, shared regulatory elements and predicted transcription associations. We present this approach within the context of Community YEASTRACT of the YEASTRACT + portal, thus benefiting from immediate access to all the comparative genomics queries offered in the YEASTRACT + portal. Besides the yeast community, other communities can install the platform independently, without any constraints. In this work, we exemplify the usefulness of the presented tool, within Community YEASTRACT, in constructing a dedicated database and analysing the genome of the highly promising oleaginous red yeast species Rhodotorula toruloides currently poorly studied at the genome and transcriptome levels and with limited genome editing tools. Regulatory prediction is based on the conservation of promoter sequences and available regulatory networks. The case-study examined is focused on the Haa1 transcription factor-a key regulator of yeast resistance to acetic acid, an important inhibitor of industrial bioconversion of lignocellulosic hydrolysates. The new tool described here led to the prediction of a RtHaa1 regulon with expected impact in the optimization of R. toruloides robustness for lignocellulosic and pectin-rich residue biorefinery processes.

Fig. 1

Relational database schema

Fig. 2

Promoter sequence nucleotide difference (using the Levenshtein distance), as a boxplot distribution, between S. cerevisiae S288C in comparison to all the species gathered in the YEASTRACT + platform, including the newly added R. toruloides NP11

Fig. 3

Fraction of common TF binding sites, relative to sites conserved only in S. cerevisiae, to all the species gathered in the YEASTRACT + platform, including the newly added R. toruloides NP11. For each species, the boxplot distribution of the fraction is presented

Fig. 4

Predicted putative networks for the RHTO_01077 gene—encoding the closest homolog of the Haa1 protein in R. toruloides—projected from the documented regulatory associations of S. cerevisiae, C. glabrata and Z. bailii

Fig. 5

Inferred Regulon Venn Diagram, of the Haa1p transcription factor targets, considering the documented regulatory associations in S. cerevisiae, C. glabrata and Z. bailii

Fig. 6

The RtHaa1 regulon in weak acid stress. A Predicted RtHaa1-regulon, based on the set of documented regulatory associations of S. cerevisiae, C. glabrata and Z. bailii under weak acid stress. B Inferred Regulon Venn Diagram, of the Haa1 transcription factor targets, considering the documented regulatory associations in S. cerevisiae, C. glabrata and Z. bailii under weak acid stress conditions