Phylogenomics of Unusual Histone H2A Variants in Bdelloid Rotifers

Karine Van Doninck,Julien Guglielmini,William S Lane,Jae H Hur,Matthew Meselson,Morgan L Mandigo,Peter Wang,Michel C Milinkovitch,Harmit S Malik

doi:10.1371/journal.pgen.1000401

Abstract

Rotifers of Class Bdelloidea are remarkable in having evolved for millions of years, apparently without males and meiosis. In addition, they are unusually resistant to desiccation and ionizing radiation and are able to repair hundreds of radiation-induced DNA double-strand breaks per genome with little effect on viability or reproduction. Because specific histone H2A variants are involved in DSB repair and certain meiotic processes in other eukaryotes, we investigated the histone H2A genes and proteins of two bdelloid species. Genomic libraries were built and probed to identify histone H2A genes in Adineta vaga and Philodina roseola, species representing two different bdelloid families. The expressed H2A proteins were visualized on SDS-PAGE gels and identified by tandem mass spectrometry. We find that neither the core histone H2A, present in nearly all other eukaryotes, nor the H2AX variant, a ubiquitous component of the eukaryotic DSB repair machinery, are present in bdelloid rotifers. Instead, they are replaced by unusual histone H2A variants of higher mass. In contrast, a species of rotifer belonging to the facultatively sexual, desiccation- and radiation-intolerant sister class of bdelloid rotifers, the monogononts, contains a canonical core histone H2A and appears to lack the bdelloid H2A variant genes. Applying phylogenetic tools, we demonstrate that the bdelloid-specific H2A variants arose as distinct lineages from canonical H2A separate from those leading to the H2AX and H2AZ variants. The replacement of core H2A and H2AX in bdelloid rotifers by previously uncharacterized H2A variants with extended carboxy-terminal tails is further evidence for evolutionary diversity within this class of histone H2A genes and may represent adaptation to unusual features specific to bdelloid rotifers.

Highlights

Rotifers of Class Bdelloidea are freshwater invertebrates of widespread occurrence that have attracted particular interest because their apparent lack of both males and meiosis suggests they are ancient asexuals [1]
Bdelloid rotifers are microscopic animals common in ephemeral freshwater environments throughout the world. They are unusual because they have been reproducing without males for millions of years, and because they can survive long periods of complete desiccation at any life stage and exposure to levels of ionizing radiation that cause hundreds of DNA double strand breaks per genome
We find that bdelloids lack both H2A and H2AX, the absence of which is in contrast to their ubiquitous presence in other eukaryotes

Summary

Introduction

Rotifers of Class Bdelloidea are freshwater invertebrates of widespread occurrence that have attracted particular interest because their apparent lack of both males and meiosis suggests they are ancient asexuals [1]. The genes coding for the four canonical histones, H4, H3, H2B and H2A, which make up the nucleosome, are expressed during the S-phase of the cell cycle when the nuclear DNA is synthesized and are clustered in most metazoan genomes. These replication-dependent histone genes typically do not contain introns in animals and their mRNAs represent the only known cellular mRNAs that are not polyadenylated, ending instead in a highly conserved stem loop.

Methods

Results

Discussion

Conclusion