Alternative splice variants of rhomboid proteins: In silico analysis of database entries for select model organisms

Rhomboid serine proteases are present in many species with Background: sequenced genomes, and are often encoded in each species by more than one predicted gene. Based on protein sequence comparisons, rhomboids can be differentiated into groups secretases, presenilin-like associated rhomboid-like (PARL) proteases, iRhoms, and “inactive” rhomboid proteins. Although these rhomboid groups are distinct, the different types can operate simultaneously. Studies in showed that the number of rhomboid proteins working Arabidopsis simultaneously can be further diversified by alternative splicing. This phenomenon was confirmed for the plastid rhomboid proteins Arabidopsis At1g25290 and At1g74130. Although alternative splicing was determined to be a significant mechanism for diversifying these two plastid Arabidopsis rhomboids, there has yet to be an assessment as to whether this mechanism extends to other rhomboids and to other species. We thus conducted a multi-year analysis of databases to determine Methods: if the alternative splicing mechanism observed for the two plastid Arabidopsis rhomboids was utilized in other species to expand the repertoire of rhomboid proteins. To help verify the findings, select splice variants from different in silico groups were tested for activity using transgenicand additive-based assays. These assays aimed to uncover evidence that the selected splice variants display capacities to influence processes like antimicrobial sensitivity. The multi-year assessment for six model experimental Results: in silico species (human, mouse, , , nematode, and yeast) Arabidopsis Drosophila revealed robust usage of alternative splicing to diversify rhomboid protein structure across the various motifs or regions, especially in human, mouse and . Subsequent validation studies uncover evidence that the splice Arabidopsis variants selected for testing displayed functionality in the different activity assays. The combined results support the hypothesis that alternative Conclusions: splicing is likely used to diversify and expand rhomboid protein functionality, and this potentially occurred across the various motifs or regions of the protein. Referee Status: AWAITING PEER REVIEW 01 Feb 2018, :139 (doi: ) First published: 7 10.12688/f1000research.13383.1 01 Feb 2018, :139 (doi: ) Latest published: 7 10.12688/f1000research.13383.1 v1 Page 1 of 22 F1000Research 2018, 7:139 Last updated: 02 FEB 2018