Chlamydomonas proteases: classification, phylogeny, and molecular mechanisms.

Yong Zou,Peter V Bozhkov,Karl-Josef Dietz

doi:10.1093/jxb/erab383

Abstract

Proteases can regulate myriad biochemical pathways by digesting or processing target proteins. While up to 3% of eukaryotic genes encode proteases, only a tiny fraction of proteases are mechanistically understood. Furthermore, most of the current knowledge about proteases is derived from studies of a few model organisms, including Arabidopsis thaliana in the case of plants. Proteases in other plant model systems are largely unexplored territory, limiting our mechanistic comprehension of post-translational regulation in plants and hampering integrated understanding of how proteolysis evolved. We argue that the unicellular green alga Chlamydomonas reinhardtii has a number of technical and biological advantages for systematic studies of proteases, including reduced complexity of many protease families and ease of cell phenotyping. With this end in view, we share a genome-wide inventory of proteolytic enzymes in Chlamydomonas, compare the protease degradomes of Chlamydomonas and Arabidopsis, and consider the phylogenetic relatedness of Chlamydomonas proteases to major taxonomic groups. Finally, we summarize the current knowledge of the biochemical regulation and physiological roles of proteases in this algal model. We anticipate that our survey will promote and streamline future research on Chlamydomonas proteases, generating new insights into proteolytic mechanisms and the evolution of digestive and limited proteolysis.

Highlights

Proteolytic enzymes, or proteases, catalyse the cleavage of peptide or isopeptide bonds in proteins
We argue that the simple unicellular life cycle of Chlamydomonas, coupled with the ease of cell phenotyping and the above-mentioned genetic and technical advantages, provide a powerful paradigm for systematic studies of proteases and proteolytic pathways.Here,we share a genome-wide survey and classification of Chlamydomonas proteases, compare proteases in Chlamydomonas and in Arabidopsis by catalytic type, and classify Chlamydomonas proteases based on their relatedness to major taxonomic groups
Since these mechanisms and pathways involve proteolytic regulation, and many proteases of Chlamydomonas are encoded by single-copy genes, the value of this model organism for studying proteolysis is difficult to overestimate

Summary

Introduction

Proteolytic enzymes, or proteases, catalyse the cleavage of peptide or isopeptide bonds in proteins. Chlorophyte proteases are largely unknown territory, which limits our mechanistic comprehension of the role of proteolytic mechanisms in plant biology and hampers integrated understanding of how proteolysis evolved With these thoughts in mind, we turned our attention to proteolytic enzymes of Chlamydomonas reinhardtii (hereafter Chlamydomonas), an ancient unicellular model organism belonging to the Chlorophyta that shares ancestral traits with higher plants and with animals. While Arabidopsis has a singlecopy gene encoding Deg (for Degradation of periplasmic proteins) protease belonging to the Deg/HtrA (for High temperature requirement A) family (S1), its Chlamydomonas orthologue is represented by three copies (Schuhmann et al, 2012) Based on these facts, we conclude that most of the proteases in Chlamydomonas are encoded by single-copy genes, offering a valuable model for genetic studies.

A28 AD A22 PE T5

Findings

Concluding remarks