Phylogenetic Distribution and Diversity of Bacterial Pseudo-Orthocaspases Underline Their Putative Role in Photosynthesis.

Marina Klemenčič,Johannes Asplund-Samuelsson,Marko Dolinar,Christiane Funk

doi:10.3389/fpls.2019.00293

Abstract

Orthocaspases are prokaryotic caspase homologs – proteases, which cleave their substrates after positively charged residues using a conserved histidine – cysteine (HC) dyad situated in a catalytic p20 domain. However, in orthocaspases pseudo-variants have been identified, which instead of the catalytic HC residues contain tyrosine and serine, respectively. The presence and distribution of these presumably proteolytically inactive p20-containing enzymes has until now escaped attention. We have performed a detailed analysis of orthocaspases in all available prokaryotic genomes, focusing on pseudo-orthocaspases. Surprisingly we identified type I metacaspase homologs in filamentous cyanobacteria. While genes encoding pseudo-orthocaspases seem to be absent in Archaea, our results show conservation of these genes in organisms performing either anoxygenic photosynthesis (orders Rhizobiales, Rhodobacterales, and Rhodospirillales in Alphaproteobacteria) or oxygenic photosynthesis (all sequenced cyanobacteria, except Gloeobacter, Prochlorococcus, and Cyanobium). Contrary to earlier reports, we were able to detect pseudo-orthocaspases in all sequenced strains of the unicellular cyanobacteria Synechococcus and Synechocystis. In silico comparisons of the primary as well as tertiary structures of pseudo-p20 domains with their presumably proteolytically active homologs suggest that differences in their amino acid sequences have no influence on the overall structures. Mutations therefore affect most likely only the proteolytic activity. Our data provide an insight into diversification of pseudo-orthocaspases in Prokaryotes, their taxa-specific distribution, and allow suggestions on their taxa-specific function.

Highlights

Metazoan caspases, playing essential roles in programmed cell death, are synthesized as inactive zymogens, which for activation are cleaved into a catalytic, large (p20) and regulatory, small (p10) subunit (Earnshaw et al, 1999)
To better understand the distribution of pseudoorthocaspases, we performed a comprehensive in silico analysis on all prokaryotic caspase homologs with focus on variants, which instead of the conserved histidine – cysteine (HC) dyad harbor other amino acid residues. We show that these pseudo-enzymes are especially abundant in organisms performing oxygenic and to a lower extent in organisms executing anoxygenic photosynthesis (Cyanobacteria and Alphaproteobacteria, respectively)
Performing an hidden Markov model (HMM)-search in the most recent UniProt database, which contains 2,936,402 archaeal and 94,326,796 bacterial sequences, representing 4,042 and 94,934 organisms, respectively, we identified 11,208 protein sequences with homology to the p20 domain in prokaryotic organisms (Supplementary Table S1)

Summary

Introduction

Metazoan caspases (cysteine-aspartic proteases), playing essential roles in programmed cell death, are synthesized as inactive zymogens, which for activation are cleaved into a catalytic, large (p20) and regulatory, small (p10) subunit (Earnshaw et al, 1999). C14A, reviewed by Shalini et al, 2015) metacaspases (Minina et al, 2017), paracaspases (Jaworski and Thome, 2016) and orthocaspases (Klemencicand Funk, 2018a), classified as C14B and found in diverse organisms ranging from plants over slime molds and fungi to bacteria (Figure 1). Both subclasses contain active proteases, whose active sites contain catalytic histidine and cysteine residues (HC dyad). They are classified by lack of a p10 domain, but contain immunoglobulin-like (Ig) domains (Uren et al, 2000)

Methods

Results

Conclusion