Comparative genomic analysis of eutherian connexin genes

Marko Premzl

doi:10.1038/s41598-019-53458-x

Abstract

The eutherian connexins were characterized as protein constituents of gap junctions implicated in cell-cell communications between adjoining cells in multiple cell types, regulation of major physiological processes and disease pathogeneses. However, conventional connexin gene and protein classifications could be regarded as unsuitable in descriptions of comprehensive eutherian connexin gene data sets, due to ambiguities and inconsistencies in connexin gene and protein nomenclatures. Using eutherian comparative genomic analysis protocol and 35 public eutherian reference genomic sequence data sets, the present analysis attempted to update and revise comprehensive eutherian connexin gene data sets, and address and resolve major discrepancies in their descriptions. Among 631 potential coding sequences, the tests of reliability of eutherian public genomic sequences annotated, in aggregate, 349 connexin complete coding sequences. The most comprehensive curated eutherian connexin gene data set described 21 major gene clusters, 4 of which included evidence of differential gene expansions. For example, the present gene annotations initially described human CXNK1 gene and annotated 22 human connexin genes. Phylogenetic tree calculations and calculations of pairwise nucleotide sequence identity patterns proposed revised and updated phylogenetic classification of eutherian connexin genes. Therefore, the present study integrating gene annotations, phylogenetic analysis and protein molecular evolution analysis proposed new nomenclature of eutherian connexin genes and proteins.

Highlights

The eutherian connexins were characterized as protein constituents of gap junctions implicated in cellcell communications between adjoining cells in multiple cell types, regulation of major physiological processes and disease pathogeneses
The eutherian connexins were characterized as protein constituents of gap junctions that were implicated in cell-cell communications between adjoining cells in multiple cell types, tissues and organs by means of passage of ions and small molecules[1,2,3,4]
The conventional human connexin gene nomenclatures included phylogenetic classifications of connexin genes into several classes and subclasses, including α-connexins or group II connexins, β-connexins or group I connexins, γ-connexins or group IIIb connexins and δ-connexins or group IIIa connexins and their naming using prefix GJ, but conventional human connexin protein nomenclatures included connexin protein classifications according to predicted protein molecular mass calculated in kilodaltons and their naming using prefix CX2,4–6,8,9,16,19–27

Summary

Introduction

The eutherian connexins were characterized as protein constituents of gap junctions implicated in cellcell communications between adjoining cells in multiple cell types, regulation of major physiological processes and disease pathogeneses. One major aim of initial sequencing and analysis of human genome was to revise and update human gene data sets and uncover potential new drugs and drug targets, as well as molecular markers in medical diagnostics[38]. The protocol included new test of reliability of public eutherian genomic sequences using genomic sequence redundancies, as well as new protein molecular evolution test using relative synonymous codon usage statistics that were applicable in revisions and updates of 11 eutherian gene data sets implicated in major physiological and pathological processes, including 1504 published complete coding sequences. The present analysis made attempts to revise and update comprehensive eutherian connexin gene data sets (CXN genes according to present study) and address and resolve major discrepancies in their descriptions, using eutherian comparative genomic analysis protocol and 35 public eutherian reference genomic sequence data sets (Supplementary Data File 1)

Methods

Results

Conclusion