Comparative genome analysis of PHB gene family reveals deep evolutionary origins and diverse gene function

Chao Di,Wenying Xu,Joshua S Yuan,Zhen Su

doi:10.1186/1471-2105-11-s6-s22

Abstract

BackgroundPHB (Prohibitin) gene family is involved in a variety of functions important for different biological processes. PHB genes are ubiquitously present in divergent species from prokaryotes to eukaryotes. Human PHB genes have been found to be associated with various diseases. Recent studies by our group and others have shown diverse function of PHB genes in plants for development, senescence, defence, and others. Despite the importance of the PHB gene family, no comprehensive gene family analysis has been carried to evaluate the relatedness of PHB genes across different species. In order to better guide the gene function analysis and understand the evolution of the PHB gene family, we therefore carried out the comparative genome analysis of the PHB genes across different kingdoms.ResultsThe relatedness, motif distribution, and intron/exon distribution all indicated that PHB genes is a relatively conserved gene family. The PHB genes can be classified into 5 classes and each class have a very deep evolutionary origin. The PHB genes within the class maintained the same motif patterns during the evolution. With Arabidopsis as the model species, we found that PHB gene intron/exon structure and domains are also conserved during the evolution. Despite being a conserved gene family, various gene duplication events led to the expansion of the PHB genes. Both segmental and tandem gene duplication were involved in Arabidopsis PHB gene family expansion. However, segmental duplication is predominant in Arabidopsis. Moreover, most of the duplicated genes experienced neofunctionalization. The results highlighted that PHB genes might be involved in important functions so that the duplicated genes are under the evolutionary pressure to derive new function.ConclusionPHB gene family is a conserved gene family and accounts for diverse but important biological functions based on the similar molecular mechanisms. The highly diverse biological function indicated that more research needs to be carried out to dissect the PHB gene function. The conserved gene evolution indicated that the study in the model species can be translated to human and mammalian studies.

Highlights

PHB (Prohibitin) gene family is involved in a variety of functions important for different biological processes
PHB proteins have been proposed to directly or indirectly interact with mtDNA to regulate the oxidative phosphorylation (OXPHOS) system and reactive oxygen species (ROS) formation, which could lead to senescence phenotype in plants and C.elegans [21,22,23,24]
Band_7domain, SPFH domain and prohibitin domain all refers to the similar protein domain with different names

Summary

Introduction

PHB (Prohibitin) gene family is involved in a variety of functions important for different biological processes. PHB genes play important roles for various biological processes and are associated with different disease phenotypes. Despite the diverse biological functions, most of molecular level studies for PHB genes were focused on their roles in mitochondria. PHB complex could interact with m-AAA protease to regulate the degradation of membrane proteins in mitochondria [18]. PHB proteins have been proposed to directly or indirectly interact with mtDNA to regulate the oxidative phosphorylation (OXPHOS) system and reactive oxygen species (ROS) formation, which could lead to senescence phenotype in plants and C.elegans [21,22,23,24]. All of the aforementioned molecular studies suggested the regulatory function of PHB genes for cell proliferation [5,27]

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Conclusion