Computational mining for terminator-like genes in soybean

Abstract

Plants and bacterial pathogens are in constant co-evolution to survive and sustain the next generation. Plants have two well-characterized levels of active defense -pathogens-associated molecular patterns (PAMPs)-triggered immunity (PTI) and effectors-triggered immunity (ETI). Some plants that are hosts for bacterial pathogens employing type three secretion system transcription activator-like (TAL) effectors have evolved a unique form of ETI, namely TAL effector-mediated ETI. TAL effectors induce expression of specific disease susceptibility (S) genes. Rice and pepper have evolved resistance genes termed terminator (T) genes, which have promoters that bind TAL effectors and, upon expression of the T gene, elicit a hypersensitive reaction (HR) and cell death. Only five T genes have been cloned, and the origin of most T genes is unknown. To determine the presence of candidate T genes in other plants species, a bioinformatics-based mining was designed. The basic approach utilized three structural features common to four terminator genes: a short trans-membrane domain, a secretion signal domain, and a length of <200 amino acid residues. Soybean was chosen as the test plant species, and 161 genes were retrieved that fulfilled the three parameters using R and Perl software programs. Further, functional annotation of candidate genes was conducted by comparisons to genes in public databases. Major classes of proteins found included unique and hypothetical, defense/stress/oxidative stress associated, DNA-binding, kinases, transferases, hydrolases, effector-related tRNA splicing, and F- box domain proteins. The potential T genes will serve as candidates for experimental validation and new resources for durable resistance strategies in crop species.