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.
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Introduction
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 molecules1,2,3,4. Such intercellular interactions were also implicated in regulation of major physiological processes including apoptosis, development, differentiation and maintenance of tissue homeostasis, as well as in human disease pathogeneses including familial zonular pulverulent cataracts, nonsyndromic and syndromic deafness, oculodentodigital dysplasia, peripheral neuropathy Charcot-Marie-Tooth disease and skin disorders erythorokeratoderma variabilis and Vohwinkel sydrome1,2,3,4. In terms of protein amino acid sequence features, the eutherian connexins were classified as 4TM α-helical transmembrane proteins including 4 transmembrane helices5,6,7,8,9. Morphologically, the gap junctions were described as “plaques” or “maculae” at intercellular interfaces including numerous intercellular channels that incorporated connexins10,11. Structurally, the eutherian connexins included 4 transmembrane α-helices traversing plasma membrane, cytoplasmic connexin regions including N-terminus, cytoplasmic loop that was positioned between second and third transmembrane helices and C-terminal domain, and, finally, extracellular connexin regions including two loops that were positioned between first and second transmembrane helices (region E1) and third and fourth transmembrane helices (region E2)10,11,12,13,14,15,16,17,18 (see Protein molecular evolution analysis below). The connexin hexamers (connexons or hemichannels) that were located in adjacent cells were implicated in formation of gap junction channel connexon pores and intercellular docking10,11,12,13,14,15,16,17,18. The homomeric connexons included single connexins, and heteromeric connexons included multiple connexins that were encoded by about 20 connexin genes among eutherians. For example, the analyses of connexin genes in human genome included either 20 connexin genes5,6,9,16,19,20,21,22,23,24 or 21 connexin genes2,4,8,25,26,27. The intercellular channels included either two identical connexons (homotypic junctions) or two different connexons (heterotypic junctions), and such combinatorial code contributed to functions of multiple cell types, tissues and organs expressing connexins19. 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 (gap junction), but conventional human connexin protein nomenclatures included connexin protein classifications according to predicted protein molecular mass calculated in kilodaltons and their naming using prefix CX2,4,5,6,8,9,16,19,20,21,22,23,24,25,26,27. For example, the human connexin CX31.1 was encoded by GJB5 gene. These conventional connexin gene and protein classifications could be regarded as unsuitable in descriptions of comprehensive human connexin gene data sets, due to numerous ambiguities and inconsistencies in connexin gene and protein nomenclatures6,22,23,25.
Importantly, one new era in biomedical research was ushered in by the public eutherian reference genomic sequence data sets28,29,30,31,32,33,34,35,36,37. For example, 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 diagnostics38. Nevertheless, future updates and revisions of human gene data sets were expected, due to the incompleteness of human reference genomic sequence assemblies38,39 and potential genomic sequence errors40. Specifically, the potential genomic sequence errors included Sanger DNA sequencing method errors (artefactual nucleotide deletions, insertions and substitutions), as well as analytical errors (erroneous gene annotations, genomic sequence misassemblies)38,39,40. For example, whereas the human initial integrated gene index included ≈32000 known and predicted protein coding genes38, recent analyses included ≈20000–21000 protein coding genes in human genome39,41,42. Furthermore, the eutherian reference genomic sequence assemblies including lower genomic sequence redundancies were more likely to include potential genomic sequence errors38,39,40,41,42,43,44,45,46 that could influence and bias phylogenetic analyses47,48. The eutherian comparative genomic analysis protocol RRID:SCR_014401 was established as one framework of eutherian gene descriptions49,50,51. 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. For example, the protocol was applicable in initial descriptions of human genes50,52. There was positive correlation between genomic sequence redundancies of 35 public eutherian reference genomic sequence data sets respectively and published complete coding sequence numbers50. Therefore, 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).
Results and Discussion
Gene annotations
Among 631 CXN potential coding sequences, the tests of reliability of eutherian public genomic sequences annotated, in aggregate, 349 CXN complete coding sequences that were deposited in European Nucleotide Archive under accession numbers LT990249-LT990597 (https://www.ebi.ac.uk/ena/data/view/LT990249-LT990597) (Fig. 1) (Supplementary Data File 1). The most comprehensive curated eutherian CXN gene data set described 21 CXN major gene clusters CXNA-CXNU, 4 of which included evidence of differential gene expansions (CXNH, CXNJ, CXNK and CXNP) (Fig. 1) (Supplementary Data File 2). Specifically, the major gene cluster CXNA included 18 GJB5 genes (Supplementary Data File 2A), major gene cluster CXNB included 18 GJB4 genes (Supplementary Data File 2B), major gene cluster CXNC included 18 GJB3 genes (Supplementary Data File 2C) and major gene cluster CXND included 15 GJB7 genes (Supplementary Data File 2D). For example, the CXND gene was annotated in rodent Ord’s kangaroo rat genome although it was not annotated in mouse and brown rat genomic sequence assemblies8,9. Whereas the major gene cluster CXNE included 19 GJB2 genes (Supplementary Data File 2E), major gene cluster CXNF included 17 GJB6 genes (Supplementary Data File 2F) and major gene cluster CXNG included 21 GJB1 genes (Supplementary Data File 2G). There were 18 GJA4 genes annotated in major gene cluster CXNH, including Otolemur garnettii CXNH1 paralogue (Supplementary Data File 2H). Whereas the major gene cluster CXNI included 20 GJA5 genes (Supplementary Data File 2I), there were 12 GJA3 genes annotated in major gene cluster CXNJ, including paralogues in little brown myotis and large flying fox genomes (Supplementary Data File 2J). Furthermore, there were 25 GJA1 genes annotated in major gene cluster CXNK including evidence of differential gene expansions (Supplementary Data File 2K). For example, the present analysis initially described human CXNK1 gene as complete coding sequence that disagreed with Fishman et al.53. Indeed, using eutherian CXNK orthologues and paralogues, the human CXNK1 and CXNK2 paralogues were annotated using indirect evidence of human gene annotations38,39,40,41,46. First, the pairwise nucleotide sequence identity between human paralogues CXNK1 and CXNK2 was a = 0,967 and pairwise nucleotide sequence identity between common chimpanzee paralogues CXNK1 and CXNK2 was a = 0,966. On the other hand, the pairwise nucleotide sequence identity between human CXNK1 and common chimpanzee CXNK1 was a = 0,988, and pairwise nucleotide sequence identity between human CXNK2 and common chimpanzee CXNK2 was a = 0,993. Furthermore, in agreement with Cruciani and Mikalsen21,22, the pairwise nucleotide sequence identity between mouse paralogues Cxnk1 and Cxnk2 was a = 0,52 and pairwise nucleotide sequence identity between brown rat paralogues Cxnk1 and Cxnk2 was a = 0,521 but pairwise nucleotide sequence identity between mouse Cxnk1 and brown rat Cxnk1 was a = 0,953 and pairwise nucleotide sequence identity between mouse Cxnk2 and brown rat Cxnk2 was a = 0,77. Third, the CXNK1 and CXNK2 paralogues were also annotated in horse, domestic dog, nine-banded armadillo and african bush elephant genomic sequences respectively. For example, the pairwise nucleotide sequence identity between horse paralogues CXNK1 and CXNK2 was a = 0,632 and pairwise nucleotide sequence identity between domestic dog paralogues CXNK1 and CXNK2 was a = 0,645 but pairwise nucleotide sequence identity between horse CXNK1 and domestic dog CXNK1 was a = 0,919 and pairwise nucleotide sequence identity between horse CXNK2 and domestic dog CXNK2 was a = 0,766. In addition, the pairwise nucleotide sequence identity between nine-banded armadillo paralogues CXNK1 and CXNK2 was a = 0,558 and pairwise nucleotide sequence identity between african bush elephant paralogues CXNK1 and CXNK2 was a = 0,696 but pairwise nucleotide sequence identity between nine-banded armadillo CXNK2 and african bush elephant CXNK1 was a = 0,911 and pairwise nucleotide sequence identity between nine-banded armadillo CXNK1 and african bush elephant CXNK2 was a = 0,679. Fourth, there were 4 eutherian CXN major gene clusters including evidence of differential gene expansions (CXNH, CXNJ, CXNK and CXNP), that was in agreement with analyses of differential gene expansions of vertebrate CXN genes of Hua et al.5 and Eastman et al.23. Fifth, Cruciani and Mikalsen22 indicated that positions of mutations in human CXNK1 and CXNK2 complete coding sequences were not randomly distributed, suggesting that human CXNK1 and CXNK2 complete coding sequences were bona fide paralogues.
Phylogenetic analysis of eutherian connexin genes. The minimum evolution phylogenetic tree was calculated using maximum composite likelihood method. The bootstrap estimates higher than 50% were shown after 1000 replicates. The 21 major gene clusters CXNA-CXNU were indicated.
Furthermore, the major gene cluster CXNL included 20 GJA8 genes (Supplementary Data File 2L). The major gene cluster CXNM included 14 GJA9 genes (Supplementary Data File 2M) and major gene cluster CXNN included 15 GJA10 genes (Supplementary Data File 2N). For example, although it was not annotated in mouse and brown rat genomes8,9, the CXNM gene was annotated in rodent Ord’s kangaroo rat genomic sequence. There were 4 GJC2 genes included in major gene cluster CXNO (Supplementary Data File 2O), but major gene cluster CXNP included 23 GJC3 genes (Supplementary Data File 2P) and major gene cluster CXNQ included 17 GJC1 genes (Supplementary Data File 2Q). For example, the evidence of differential gene expansions in major gene cluster CXNP included 4 CXNP1-CXNP4 paralogues that were annotated in nine-banded armadillo genome. There were 8 GJD3 genes annotated in major gene cluster CXNR (Supplementary Data File 2R). The major gene cluster CXNS included 20 GJD2 genes (Supplementary Data File 2S). Finally, the major gene cluster CXNT included 14 GJD5 genes (Supplementary Data File 2T) and major gene cluster CXNU included 13 GJD4 genes (Supplementary Data File 2U). For example, the present eutherian CXNT gene annotations agreed with analyses of Goodenough and Paul2, Bosco et al.4, Beyer and Berthoud8, Söhl and Willecke25,26 and Iovine et al.27. However, they disagreed with analyses of Hua et al.5, Abascal and Zardoya6, Beyer and Berthoud9, Beyer et al.16, Willecke et al.19, Bruzzone20, Cruciani and Mikalsen21,22, Eastman et al.23 and Sonntag et al.24 that did not include major gene cluster CXNT (GJD5 genes). Therefore, among 21 eutherian CXN major gene clusters CXNA-CXNU, the present CXN gene annotations initially described human CXNK1 gene and annotated 22 human CXN genes. Yet, whereas the human CXN gene number estimates were likely complete, CXN gene number estimates in other 34 eutherian species were subject to future updates, due to incompleteness of eutherian reference genomic sequence assemblies and potential genomic sequence errors38,39,40,41,42,43,44,45,46,47,48 (Supplementary Data File 1).
Phylogenetic analysis
The present phylogenetic analysis classified 21 eutherian CXN major gene clusters CXNA-CXNU using minimum evolution phylogenetic tree calculations (Fig. 1) and calculations of pairwise nucleotide sequence identity patterns (Supplementary Data File 3). The minimum evolution phylogenetic tree calculations were comparable with published phylogenetic analyses of human, eutherian and vertebrate CXN genes4,5,6,20,21,22,23. First, the clustering of β-connexins or group I connexins including major gene clusters CXNA (GJB5, CX31.1), CXNB (GJB4, CX30.3), CXNC (GJB3, CX31), CXND (GJB7, CX25), CXNE (GJB2, CX26), CXNF (GJB6, CX30) and CXNG (GJB1, CX32) agreed with phylogenetic analyses of Bosco et al.4, Hua et al.5, Abascal and Zardoya6, Bruzzone20, Cruciani and Mikalsen21,22 and Eastman et al.23. For example, whereas Hua et al.5 described connexin clusters I (CXNE-CXNG) and II (CXNA-CXND), Cruciani and Mikalsen22 described group I connexin clades IA (CXNE-CXNG) and IB (CXNA-CXND). Second, the distribution of α-connexins or group II connexins including major gene clusters CXNH (GJA4, CX37), CXNI (GJA5, CX40), CXNJ (GJA3, CX46), CXNK (GJA1, CX43) and CXNL (GJA8, CX50) was not supported by higher bootstrap estimates, except that clustering of major gene clusters CXNI and CXNJ agreed with Eastman et al.23. Of note, the clustering of major gene clusters CXNM (GJA9, CX59) and CXNN (GJA10, CX62) disagreed with phylogenetic analyses of Bosco et al.4, Hua et al.5, Abascal and Zardoya6, Bruzzone20, Cruciani and Mikalsen21,22 and Eastman et al.23. Third, although the grouping of γ-connexins or group IIIb connexins including major gene clusters CXNO (GJC2, CX47), CXNP (GJC3, CX30.2, CX31.3) and CXNQ (GJC1, CX45) agreed with Bosco et al.4, Hua et al.5, Abascal and Zardoya6, Bruzzone20, Cruciani and Mikalsen21,22 and Eastman et al.23, clustering of major gene clusters CXNP and CXNQ disagreed with these analyses. In addition, the grouping of major gene clusters CXNO, CXNP and CXNQ disagreed with human CXN nomenclature that was proposed by Söhl and Willecke25. Fourth, the distribution of δ-connexins or group IIIa connexins including major gene clusters CXNR (GJD3, CX31.9), CXNS (GJD2, CX36), CXNT (GJD5, GJE1, CX23) and CXNU (GJD4, CX40.1) was not monophyletic or supported by higher bootstrap estimates, except that clustering of major gene clusters CXNT and CXNU disagreed with phylogenetic analyses of Bosco et al.4, Hua et al.5, Abascal and Zardoya6, Bruzzone20, Cruciani and Mikalsen21,22 and Eastman et al.23.
Furthermore, the calculations of pairwise nucleotide sequence identity patterns among 21 eutherian CXN major gene clusters confirmed their phylogenetic classification (Supplementary Data File 3). First, the eutherian CXN gene data set including 349 complete coding sequences included average pairwise nucleotide sequence identity ā = 0,325 (largest pairwise nucleotide sequence identity amax = 0,999, smallest pairwise nucleotide sequence identity amin = 0,037, average absolute deviation āad = 0,101). Second, among eutherian CXN major gene clusters including orthologues respectively, there were nucleotide sequence identity calculations typical in comparisons between eutherian orthologues (≈0,65–0,9)49,50,52. The exceptions were major gene clusters CXNG (GJB1, CX32) and CXNQ (GJC1, CX45) respectively including close orthologues (≈0,9–0,95), as well as major gene cluster CXNU (GJD4, CX40.1) including distant orthologues (≈0,45–0,65) agreeing with analyses of Abascal and Zardoya6 and Cruciani and Mikalsen22. Third, the present analysis discriminated between eutherian CXN major gene clusters including evidence of differential gene expansions (CXNH, CXNJ, CXNK and CXNP) and major gene clusters not including evidence of differential gene expansions. Specifically, the major gene clusters CXNH (GJA4, CX37) and CXNK (GJA1, CX43) respectively included close eutherian orthologues and paralogues (≈0,7–0,85)49,50,52, but major gene clusters CXNJ (GJA3, CX46) and CXNP (GJC3, CX30.2, CX31.3) respectively included typical eutherian orthologues and paralogues (≈0,45–0,7). Fourth, in comparisons between eutherian CXN major gene clusters, there were nucleotide sequence identity patterns of very close (>0,5), close (≈0,35–0,5), typical (≈0,25–0,35), distant (≈0,15–0,25) and very distant (<0,15) eutherian homologues49,50,52. For example, there were nucleotide sequence identity patterns of very close and close eutherian homologues in comparisons between major gene clusters CXNA (GJB5, CX31.1), CXNB (GJB4, CX30.3), CXNC (GJB3, CX31) and CXND (GJB7, CX25) respectively, and in comparisons between major gene clusters CXNE (GJB2, CX26), CXNF (GJB6, CX30) and CXNG (GJB1, CX32) respectively there were nucleotide sequence identity patterns of very close eutherian homologues5,22. There were nucleotide sequence identity patterns of close eutherian homologues in comparisons between major gene clusters CXNI (GJA5, CX40) and CXNJ (GJA3, CX46)23. In comparisons between major gene clusters CXNM (GJA9, CX59) and CXNN (GJA10, CX62) as well as in comparisons between major gene clusters CXNO (GJC2, CX47) and CXNQ (GJC1, CX45) there were nucleotide sequence identity patterns of close eutherian homologues agreeing with Bosco et al.4, Hua et al.5, Abascal and Zardoya6, Bruzzone20, Cruciani and Mikalsen21,22 and Eastman et al.23. Finally, in comparisons between major gene clusters CXNR (GJD3, CX31.9), CXNS (GJD2, CX36), CXNT (GJD5, GJE1, CX23) and CXNU (GJD4, CX40.1) respectively and other major gene clusters respectively, there were nucleotide sequence identity patterns of typical, distant and very distant eutherian homologues. Therefore, the present minimum evolution phylogenetic tree calculations (Fig. 1) and calculations of pairwise nucleotide sequence identity patterns (Supplementary Data File 3) proposed revised and updated phylogenetic classification of eutherian CXN genes.
Protein molecular evolution analysis
The eutherian CXN major protein cluster amino acid sequence alignments (Supplementary Data File 4) used CXN protein primary structure features as major alignment landmarks, including cysteine amino acid residues and predicted N-glycosylation sites common to 21 CXN major protein clusters respectively (Fig. 2). First, the eutherian CXN major protein clusters respectively included between 7–14 common cysteine amino acid residues. For example, whereas the CXNJ major protein cluster included 7 common cysteine amino acid residues, CXNN major protein cluster included 14 common cysteine amino acid residues. The CXN amino acid signature common cysteine amino acid residues that were implicated in disulfide bonding were described in protein amino acid sequence motifs C-x(6)-C-x(3)-C or C-x(10)-C and C-x(4,5)-C-x(5)-C or C-x(12,13)-C that agreed with phylogenetic analyses of Hua et al.5, Abascal and Zardoya6, Cruciani and Mikalsen21,22 and Eastman et al.23. Second, although they were described as not glycosylated proteins4,10, there were between 0–3 common predicted N-glycosylation sites annotated among eutherian CXN major protein clusters. For example, there were 3 common predicted N-glycosylation sites that were annotated in CXNK major protein cluster.
Major landmarks in eutherian connexin protein sequence alignments. The black squares labelled common cysteine amino acid residues and white squares labelled common N-glycosylation sites. The connexin amino acid signature common cysteine amino acid residues that were implicated in disulfide bonding were labelled by stars. The numbers indicated numbers of amino acid residues. The human substitutions of common cysteine amino acid residues were also indicated.
Furthermore, using 349 CXN complete coding sequences (Supplementary Data File 4), the tests of protein molecular evolution first calculated relative synonymous codon usage statistics (R) of eutherian CXN gene data set, and described 22 amino acid codons with R ≤ 0.7 as not preferable amino acid codons (Fig. 3A). The tests of protein molecular evolution used human CXNA primary structure as reference protein amino acid sequence, using N-terminal and C-terminal boundaries of CXN transmembrane α-helices M1-M4, cytoplasmic CXN regions (N-terminus, cytoplasmic loop and C-terminal domain) and extracellular CXN regions E1 and E2 as reference points in analysis10,11,12,13,14,15,16,17,18 (Fig. 3B,C). For example, whereas the extracellular CXN regions E1 and E2 included average pairwise nucleotide sequence identity ā = 0,607 (amax = 1, amin = 0, āad = 0,081) and CXN transmembrane α-helices M1-M4 included average pairwise nucleotide sequence identity ā = 0,504 (amax = 1, amin = 0,048, āad = 0,104), cytoplasmic CXN regions included average pairwise nucleotide sequence identity ā = 0,177 (amax = 1, amin = 0,011, āad = 0,1) agreeing with analyses of Hua et al.5, Abascal and Zardoya6, Cruciani and Mikalsen21,22 and Eastman et al.23. Thus, among 273 human CXNA protein amino acid residues, the tests of protein molecular evolution using relative synonymous codon usage statistics described 15 invariant amino acid sites (M1, W3, F51, C53, C60, C64, W77, C86, P87, Y131, P154, C164, P168, C169 and C175) and 2 variant alignment positions that did not include not preferable amino acid codons named forward amino acid sites (W44, D66) (Fig. 3B,C) (Supplementary Data File 4). For example, the human CXNA amino acid site W3 that was invariant in eutherian major protein clusters CXNA-CXNO, CXNQ and CXNR was described as critical in CXN protein secondary, tertiary and quaternary structural features and interactions with cytoplasmic proteins16. Furthermore, the human CXNA invariant amino acid sites C53, C60 and C64 in region E1 corresponded to common cysteine amino acid residues that were implicated in disulfide bonding and described in protein amino acid sequence motif C-x(6)-C-x(3)-C, and human CXNA invariant amino acid sites C164, C169 and C175 in region E2 corresponded to common cysteine amino acid residues that were implicated in disulfide bonding and described in protein amino acid sequence motif C-x(4,5)-C-x(5)-C5,6,21,22,23 (Fig. 2). Finally, the human CXNA forward amino acid sites W44 and D66 were described in extracellular region E1 that was implicated in gap junction channel connexon pore lining and ion selectivity modulation11,13,14,15. For example, the human CXNA forward amino acid site W44 was calculated among 329 CXN complete coding sequences, and human CXNA forward amino acid site D66 was calculated among 347 CXN complete coding sequences (Supplementary Data File 4). Therefore, in reference human CXNA primary structure, the present protein molecular evolution analysis described amino acid residues implicated as critical in eutherian CXN protein secondary, tertiary and quaternary structural features.
Tests of protein molecular evolution of eutherian connexins. (A) Relative synonymous codon usage statistics of eutherian CXN gene data set. The not preferable amino acid codons were indicated by white letters on red backgrounds. Counts, observed amino acid codon counts; R, relative synonymous codon usage statistics; &, stop codons. (B) Reference human CXNA protein amino acid sequence. Using white letters on violet backgrounds, the 15 invariant amino acid sites were shown. The 2 forward amino acid sites were indicated by arrows and shown using white letters on red backgrounds. The connexin amino acid signature common cysteine amino acid residues that were implicated in disulfide bonding were labelled by stars. The N-terminal and C-terminal boundaries of transmembrane α-helices 1–4 were described according to Nicholson10 and Sosinsky and Nicholson11. (C) Distribution of invariant and forward amino acid sites in human CXNA protein regions. The 15 invariant amino acid sites were shown using violet squares, and 2 forward amino acid sites were shown using red squares. The common cysteine amino acid residues that were implicated in disulfide bonding were connected by lines. C, C-terminal domain; E1 and E2, extracellular connexin regions 1 and 2; L, cytoplasmic loop; M1–M4, transmembrane α-helices 1–4; N, N-terminus.
Conclusions
The conventional connexin gene and protein classifications could be regarded as unsuitable in descriptions of comprehensive eutherian CXN gene data sets, due to ambiguities and inconsistencies in CXN gene and protein nomenclatures6,22,23,25. Using eutherian comparative genomic analysis protocol and 35 public eutherian reference genomic sequence assemblies49,50,52, the present analysis attempted to update and revise comprehensive eutherian CXN gene data sets, and address and resolve major discrepancies in their descriptions. The advantages of eutherian reference genomic sequence data sets included well established phylogenetic framework28,31,33, as well as calibrated taxon sampling including genomic sequence redundancies that were applicable in tests of reliability of eutherian public genomic sequences29,30,32,38,39,40,41,43,44,46. Indeed, the tests of reliability of eutherian public genomic sequences annotated most comprehensive curated eutherian CXN gene data set including, in aggregate, 349 CXN complete coding sequences. There were 21 CXN major gene clusters CXNA-CXNU described, 4 of which included evidence of differential gene expansions (CXNH, CXNJ, CXNK and CXNP). In addition, the present CXN gene annotations initially described human CXNK1 gene and annotated 22 human CXN genes. The phylogenetic tree calculations and calculations of pairwise nucleotide sequence identity patterns proposed revised and updated phylogenetic classification of eutherian CXN genes. Finally, in reference human CXNA primary structure, the tests of protein molecular evolution using relative synonymous codon usage statistics described 15 invariant amino acid sites and 2 forward amino acid sites, including amino acid residues that were described as critical in CXN protein secondary, tertiary and quaternary structural features. In conclusion, the present comparative genomic analysis integrating gene annotations, phylogenetic analysis and protein molecular evolution analysis proposed new nomenclature of eutherian CXN genes and proteins.
Methods
Eutherian comparative genomic analysis protocol
The eutherian comparative genomic analysis protocol RRID:SCR_014401 integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis with new genomics and protein molecular evolution tests into one framework of eutherian gene descriptions49,50,52.
Gene annotations
In eutherian CXN gene annotations, the protocol included gene identifications in 35 public genomic sequences (Supplementary Data File 1), tests of reliability of eutherian public genomic sequences and multiple pairwise genomic sequence alignments. First, the protocol used sequence alignment editor BioEdit 7.0.5.3 in analyses and manipulations of nucleotide and protein sequences (http://www.mbio.ncsu.edu/BioEdit/bioedit.html). In identifications of potential CXN coding sequences in 35 eutherian reference genomic sequence data sets, the protocol used National Center for Biotechnology Information’s (NCBI) BLAST Genomes35,36,54,55 (https://blast.ncbi.nlm.nih.gov/Blast.cgi) or Ensembl genome browser’s BLAST or BLAT37 (https://www.ensembl.org). Second, the potential CXN coding sequences were then used in tests of reliability of eutherian public genomic sequences. The first test steps analysed nucleotide sequence coverages of each potential CXN coding sequence, using BLASTN54,55 and processed public Sanger DNA sequencing reads or traces deposited in NCBI’s Trace Archive35 (https://www.ncbi.nlm.nih.gov/Traces/trace.cgi). The protocol described potential CXN coding sequences as complete CXN coding sequences only if consensus trace sequence coverages were available for every nucleotide. On the other hand, if consensus trace sequence coverages were not available for every nucleotide, the potential CXN coding sequences were described as putative CXN coding sequences that were not used in analyses. The protocol then deposited complete CXN coding sequences in European Nucleotide Archive as one curated eutherian gene data set56,57,58 (https://www.ebi.ac.uk/ena/about/tpa-policy). In updated human and eutherian CXN gene classification and nomenclature, the protocol used guidelines of human gene nomenclature59 (http://www.genenames.org/about/guidelines) and guidelines of mouse gene nomenclature (http://www.informatics.jax.org/mgihome/nomen/gene.shtml). Specifically, the present eutherian CXN gene name assignments used both phylogenetic analysis (Fig. 1) and genomic sequence information (Supplementary Data File 1). Third, the protocol used mVISTA’s program AVID in multiple pairwise genomic sequence alignments using default settings51,60 (http://genome.lbl.gov/vista/index.shtml). In pairwise alignments with base sequences (Homo sapiens), the cut-offs of detection of common genomic sequence regions were calculated a posteriori using analyses of 11 eutherian major gene data sets49,50,52 including 95% along 100 bp (Homo sapiens, Pan troglodytes, Gorilla gorilla), 90% along 100 bp (Pongo abelii, Nomascus leucogenys), 85% along 100 bp (Macaca mulatta, Papio hamadryas), 80% along 100 bp (Callithrix jacchus), 75% along 100 bp (Tarsius syrichta, Microcebus murinus, Otolemur garnettii), 65% along 100 bp (Rodentia) or 70% along 100 bp in other pairwise alignments. However, the exceptions were pairwise alignments between base sequences and Otolemur garnettii CXNH1, Myotis lucifugus CXNJ1 and CXNJ2, Pteropus vampyrus CXNJ1 and CXNJ2, Sorex araneus CXNJ1, Mus musculus Cxnk2, Rattus norvegicus Cxnk2, Equus caballus CXNK2, Canis lupus familiaris CXNK2, Felis catus CXNK1, Dasypus novemcinctus CXNK1, Loxodonta africana CXNK2, Oryctolagus cuniculus CXNP1, Dasypus novemcinctus CXNP1-CXNP4 and Choloepus hoffmanni CXNP1 respectively including 60% along 100 bp as empirically calculated cut-off of detection of common genomic sequence regions. In preparatory steps of multiple pairwise genomic sequence alignments, the protocol used RepeatMasker version open-4.0.6 in detection and masking of transposable elements in base sequences using default settings, except that simple repeats and low complexity elements were not masked (sensitive mode, cross_match version 1.080812, RepBase Update 20160829, RM database version 20160829) (http://www.repeatmasker.org/).
Phylogenetic analysis
In eutherian CXN gene data set phylogenetic analysis, the protocol included protein and nucleotide sequence alignments, calculations of phylogenetic trees, calculations of pairwise nucleotide sequence identities and analysis of differential gene expansions. First, the protocol translated complete CXN coding sequences using BioEdit 7.0.5.3, and aligned them at amino acid level using ClustalW that was implemented in BioEdit 7.0.5.3. The CXN protein primary sequence alignments were then manually corrected, and CXN nucleotide sequence alignments were prepared accordingly using BioEdit 7.0.5.3. Second, the protocol used MEGA 6.06 program61,62 in phylogenetic tree calculations, using minimum evolution method that was suitable in phylogenetic analysis of very close, close, typical, distant and very distant eutherian homologues (default settings, except gaps/missing data treatment = pairwise deletion and maximum composite likelihood method) (http://www.megasoftware.net/). Third, the pairwise nucleotide sequence identities of complete CXN coding sequences were calculated using BioEdit 7.0.5.3, and then used in statistical analyses (Microsoft Office Excel). More specifically, using CXN nucleotide sequence alignments, the protocol calculated average pairwise nucleotide sequence identities (ā) and their average absolute deviations (āad), as well as largest (amax) and smallest (amin) pairwise nucleotide sequence identities.
Protein molecular evolution analysis
In protein molecular evolution analysis, the protocol included analysis of CXN protein amino acid sequence features and tests of protein molecular evolution that integrated patterns of CXN nucleotide sequence similarities with CXN protein primary structures. First, among 21 eutherian CXN major protein clusters respectively, the common cysteine amino acid residues were annotated manually. Second, using protein amino acid sequence motif N-x-[ST], the common predicted N-glycosylation sites were also annotated manually among 21 eutherian CXN major protein clusters respectively. Third, in eutherian CXN protein primary structures, the N-terminal and C-terminal boundaries of transmembrane α-helices 1–4 were described according to Nicholson10 and Sosinsky and Nicholson11. In tests of protein molecular evolution, the protocol used entire CXN nucleotide sequence alignments including 349 CXN nucleotide sequences and 114138 codons. For example, the average number of codons among CXN nucleotide sequence was 327 codons. The MEGA 6.06 program61,62 calculated relative synonymous codon usage statistics as ratios between observed and expected amino acid codon counts (R = Counts / Expected counts). The protocol described 22 amino acid codons having R ≤ 0.7 as not preferable amino acid codons, viz: TTT, TTA, TTG, CTT, CTA, ATA, GTT, GTA, TCG, CCG, ACG, GCA, GCG, CAT, CAA, AAA, GAA, TGT, CGT, CGA, GGT and GGA (Fig. 3A). Accordingly, the protocol described reference human CXNA protein sequence amino acid sites as invariant amino acid sites (invariant alignment positions), forward amino acid sites (variant alignment positions that did not include amino acid codons with R ≤ 0.7) or compensatory amino acid sites (variant alignment positions that included amino acid codons with R ≤ 0.7).
Data availability
The original curated eutherian connexin gene data set included 349 complete coding sequences that were deposited in European Nucleotide Archive (accession numbers: LT990249-LT990597).
Change history
26 June 2020
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Acknowledgements
The author would like to express his gratitude to manuscript reviewers, as well as to data analysts, producers and providers of public eutherian reference genomic sequence data sets. The present analysis was undertaken under NCBI BioProject PRJNA453891 entitled “Curated eutherian third party data gene data sets” (https://www.ncbi.nlm.nih.gov/bioproject/453891) and Open Science Framework project entitled “Comparative genomic analysis of eutherian genes” (https://doi.org/10.17605/OSF.IO/AX3TS).
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Premzl, M. Comparative genomic analysis of eutherian connexin genes. Sci Rep 9, 16938 (2019). https://doi.org/10.1038/s41598-019-53458-x
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DOI: https://doi.org/10.1038/s41598-019-53458-x
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