Zmat2 in mammals: conservation and diversification among genes and Pseudogenes

ZMAT2 in Humans and Other Primates: A Highly Conserved and Understudied Gene

Recent advances in genetics present unique opportunities for enhancing our understanding of human physiology and disease predisposition through detailed analysis of gene structure, expression, and population variation via examination of data in publicly accessible genome and gene expression repositories. Yet, the vast majority of human genes remain understudied. Here, we show the scope of these genomic and genetic resources by evaluating ZMAT2, a member of a 5-gene family that through May 2020 had been the focus of only 4 peer-reviewed scientific publications. Using analysis of information extracted from public databases, we show that human ZMAT2 is a 6-exon gene and find that it exhibits minimal genetic variation in human populations and in disease states, including cancer. We further demonstrate that the gene and its encoded protein are highly conserved among nonhuman primates and define a cohort of ZMAT2 pseudogenes in the marmoset genome. Collectively, our investigations illustrate how complementary use of genomic, gene expression, and population genetic resources can lead to new insights about human and mammalian biology and evolution, and when coupled with data supporting key roles for ZMAT2 in keratinocyte differentiation and pre-RNA splicing argue that this gene is worthy of further study.

The Zmat2 gene in non-mammalian vertebrates: Organizational simplicity within a divergent locus in fish

ZMAT2 is among the least-studied of mammalian proteins and genes, even though it is the ortholog of Snu23, a protein involved in pre-mRNA splicing in yeast. Here we have used data from genomic and gene expression repositories to examine the Zmat2 gene and locus in 8 terrestrial vertebrates, 10 ray-finned fish, and 1 lobe-finned fish representing > 500 million years of evolutionary diversification. The analyses revealed that vertebrate Zmat2 genes are similar to their mammalian counterparts, as in 16/19 species studied they contain 6 exons, and in 18/19 encode a single conserved protein. However, unlike in mammals, no Zmat2 pseudogenes were identified in these vertebrates, although an expressed Zmat2 paralog was characterized in flycatcher that resembled a DNA copy of a processed and retro-transposed mRNA, and thus could be a proto-pseudogene captured during its evolutionary journey from active to inert. The Zmat2 locus in terrestrial vertebrates, and in spotted gar and coelacanth, also shares additional genes with its mammalian counterparts, including Histidyl-tRNA synthetase (Hars), Hars2, and others, but these are absent from the Zmat2 locus in teleost fish, in which Stem-loop-binding protein 2 (Slbp2) and Lymphocyte cytosolic protein 2a (Lcp2a) are present instead. Taken together, these observations argue that a recognizable Zmat2 was present in the earliest vertebrate ancestors, and postulate that during chromosomal tetraploidization and subsequent re-diploidization during modern teleost evolution, the duplicated Zmat2 gene was retained and the original lost. This study also highlights how information from genomic resources can be leveraged to reveal new biologically significant insights.