Szabolcs Makai | Search bioRxiv

bioRxiv2015

PDMQ - Protein Digestion Multi Query software tool to perform in silico digestion of protein/peptide sequences

MotivationIn silico enzymatic digestion tools mostly can be used for digestion of single sequence query, which means a significant limitation in their utility when a number of sequences need to be processed. The other limitation of these applications is the selection options of restriction enzymes that are usually allow only simultaneous digestion. Non-conventional proteins such as cereal prolamins require multi-enzyme multi step digestion, and for cereal proteomics experts this type of application is missing.\n\nResultsPDMQ, Protein Digestion Multi Query application was developed having multi query and multi enzyme options and that way can be customized for any digestion protocol.\n\nAvailability and implementationPDMQ is implemented in C# using the .NET framework and can be downloaded from http://www.agrar.mta.hu/_user/browser/File/bioinformatics/ProteinDigestion_v0_0_0_15.rar

Bioinformatics↗

bioRxiv2014

Distinct regulatory modules identified in the promoters of wheat Glu-1 genes suggest different regulatory mechanisms

High molecular weight glutenin subunits of wheat are economically important seed storage proteins. They are coded by paralog pairs of the Glu-1 gene on each of the three genomes in the hexaploid wheat. Their expressions are under both temporal and spatial control. Many factors have been identified that influence the activity of Glu-1 genes, but the underlying regulatory mechanisms are still unclear. In order to identify motifs and motif clusters responsible for quantitative regulation of Glu-1 gene expressions, promoter profiles and transcription dynamics of the genes were analysed. It was found that promoter motif compositions of homoeolog Glu-1 genes are conserved. Our results demonstrated that while promoter profiles explain the differences of expression between homoeologs and between paralogs, it does not explain the variation of activity between alleles. Interestingly, our analyses revealed that the promoters of Glu-1 genes are divided into six cis-regulatory modules that are either locally overrepresented by binding sites belonging to unique but distinct transcription factor (TF) families or have conserved motif clusters. Moreover, our analyses demonstrated that the varying expression dynamics of TFs across genotypes is likely to be the primary contributor of the allelic variation of Glu-1 gene expressions. Thus, the six putative cis-regulatory modules in the Glu-1 gene promoters bound by the differentially expressed TFs are suggested to play a key role in the quantitative and tissue specific regulation of these genes.

Plant Biology↗