Genome-wide analysis of putative peroxiredoxin in unicellular and filamentous cyanobacteria.

Hongli Cui,Yinchu Wang,Yipeng Wang,Song Qin

doi:10.1186/1471-2148-12-220

Abstract

BackgroundCyanobacteria are photoautotrophic prokaryotes with wide variations in genome sizes and ecological habitats. Peroxiredoxin (PRX) is an important protein that plays essential roles in protecting own cells against reactive oxygen species (ROS). PRXs have been identified from mammals, fungi and higher plants. However, knowledge on cyanobacterial PRXs still remains obscure. With the availability of 37 sequenced cyanobacterial genomes, we performed a comprehensive comparative analysis of PRXs and explored their diversity, distribution, domain structure and evolution.ResultsOverall 244 putative prx genes were identified, which were abundant in filamentous diazotrophic cyanobacteria, Acaryochloris marina MBIC 11017, and unicellular cyanobacteria inhabiting freshwater and hot-springs, while poor in all Prochlorococcus and marine Synechococcus strains. Among these putative genes, 25 open reading frames (ORFs) encoding hypothetical proteins were identified as prx gene family members and the others were already annotated as prx genes. All 244 putative PRXs were classified into five major subfamilies (1-Cys, 2-Cys, BCP, PRX5_like, and PRX-like) according to their domain structures. The catalytic motifs of the cyanobacterial PRXs were similar to those of eukaryotic PRXs and highly conserved in all but the PRX-like subfamily. Classical motif (CXXC) of thioredoxin was detected in protein sequences from the PRX-like subfamily. Phylogenetic tree constructed of catalytic domains coincided well with the domain structures of PRXs and the phylogenies based on 16s rRNA.ConclusionsThe distribution of genes encoding PRXs in different unicellular and filamentous cyanobacteria especially those sub-families like PRX-like or 1-Cys PRX correlate with the genome size, eco-physiology, and physiological properties of the organisms. Cyanobacterial and eukaryotic PRXs share similar conserved motifs, indicating that cyanobacteria adopt similar catalytic mechanisms as eukaryotes. All cyanobacterial PRX proteins share highly similar structures, implying that these genes may originate from a common ancestor. In this study, a general framework of the sequence-structure-function connections of the PRXs was revealed, which may facilitate functional investigations of PRXs in various organisms.

Highlights

Cyanobacteria are photoautotrophic prokaryotes with wide variations in genome sizes and ecological habitats
A total of 244 proteins were considered in this study and an additional table file shows this in more detail [see Additional file 1, Table S1 and S2], among which 79 were originally annotated as AhpC/thiol-specific antioxidant (TSA) or AhpC/TSA family members, 66 were originally annotated as bacterioferritin comigratory protein (BCP), 25 were originally annotated as peroxidases and 25 were originally annotated as peroxiredoxins
The remaining 49 proteins were accepted as PRX family members for this study, including 12 proteins annotated by other additional domains, 25 proteins annotated as hypothetical proteins, 8 proteins annotated as redoxins, and 4 proteins annotated as twin-arginine translocation pathway proteins

Summary

Introduction

Cyanobacteria are photoautotrophic prokaryotes with wide variations in genome sizes and ecological habitats. With the availability of 37 sequenced cyanobacterial genomes, we performed a comprehensive comparative analysis of PRXs and explored their diversity, distribution, domain structure and evolution. As a taxonomic unit characterized by the first photosynthetic organisms with an oxygenic type of photosynthesis [2,3], cyanobacteria comprise a large number of species with diverse genome sizes and ocean and possess the smallest genome size, is responsible for significant biomass and primary production in the marine biosphere [10]. Other unicellular species have larger genome sizes, including water bloom forming cyanobacteria The diazotrophic filamentous cyanobacteria have the largest genome sizes and include strains isolated from fresh water Platensis NIES-39), from a plant-cyanobacterial symbionsis (Nostoc punctiforme PCC29133), and from tropical and subtropical oceans (Trichodesmium erythraeum IMS101). The phylogeny of sequenced cyanobacterial organisms has been reported in previous studies [7,12,13]

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Discussion

Conclusion