Revising angiotensinogen from phylogenetic and genetic variants perspectives

From Living in Saltwater to a Scarcity of Salt and Water, and Then an Overabundance of Salt-The Biological Roller Coaster to Which the Renin-Angiotensin System Has Had to Adapt: An Editorial

Angiotensin II (Ang II) is a hormone with much more complex actions than is typical for other agonists with heterotrimeric G protein-coupled receptors (GPCRs) [...].

Computational analyses prioritize and reveal the deleterious nsSNPs in human angiotensinogen gene

Angiotensinogen (AGT) is a key component of renin-angiotensin-aldosterone system (RAAS), which plays central role in blood pressure homeostasis. Association of AGT polymorphisms have been investigated in different ethnic populations in variety of cardiovascular and non-cardiovascular conditions. In this study, 354 non-synonymous SNPs (nsSNPs) of AGT were evaluated to predict damaging and structurally important variants. Majority of the deleterious nsSNPs occurred in the evolutionary conserved regions. Several of these nsSNPs were found to affect post-translational modifications like methylation, glycosylation, phosphorylation, ubiquitination etc. Structural evaluations predicted 19 variants as destabilizing and some of them were also predicted to destabilize the renin-AGT interaction. Therefore, the present computational investigation predicted pathogenic and functionally important variants of human AGT gene. The study has also shown that AGT deregulation is associated with survival outcome in patients with gastric and breast cancer, using microarray gene expression profile. Furthermore, the computationally screened nsSNPs can be analyzed in population based genotyping studies and may help futuristic drug development in the area of AGT pharmacogenomics.

Mutational hotspots of HSP47 and its potential role in cancer and bone-disorders

Heat shock protein 47 kDa (HSP47) serves as a client-specific chaperone, essential for collagen biosynthesis and its folding and structural assembly. To date, there is no comprehensive study on mutational hotspots. Using five different human mutational databases, we deduced a comprehensive list of human HSP47 mutations with 24, 67, 50, 43 and 2 deleterious mutations from the 1000 genomes data, gnomAD, COSMICv86, cBioPortal, and CanVar, respectively. We identified thirteen top-ranked missense mutations of HSP47 with the stringent cut-off of CADD score (>25) and Grantham score (≥151) as Ser76Trp, Arg103Cys, Arg116Cys, Ser159Phe, Arg167Cys, Arg280Cys, Trp293Cys, Gly323Trp, Arg339Cys, Arg373Cys, Arg377Cys, Ser399Phe, and Arg405Cys with the arginine-cysteine changes as the predominant mutations. These findings will assist in the evaluation of roles of HSP47 in collagen misfolding and human diseases such as cancer and bone disorders.

Molecular and evolutionary perspectives of the renin-angiotensin system from lamprey

The recent advance and revision on the renin-angiotensin system in lamprey were summarized and we emphasized that presence of two types of angiotensins (Angs) in lamprey. Due to the parasitic nature on fish blood, teleost-type Angs were produced in their buccal gland and secreted into the lamphredin to evade the host immunorejection. A native lamprey angiotensinogen (AGT) was identified in genome and it retains serine-protease inhibitor activity for thrombin that regulates the blood coagulation pathway. The native lamprey angiotensin II (Lp-Ang II) is hypotensive instead of hypertensive, suggesting a functional divergence on cardiovascular regulation from the main vertebrate groups. The renin gene was absent from the lamprey genome so far, and the mutation on the renin-recognition site on lamprey AGT suggested that other proteases may have replaced the role of renin. Lp-Ang II was shown to bind to AT1 receptor and internalized, but the downstream signaling was still unknown. Molecular and phylogenetic evidence on invertebrate ACE-like proteins indicated that they were not homologous to those in vertebrates and could be acting on other native peptides. Although it was generally believed that the RAS was a well-conserved hormone system in vertebrates and invertebrates, revision by molecular data indicated that invertebrates lack homologous RAS components while lamprey possess an almost complete RAS. This suggests that the hormone cascade system was first evolved around cyclostome emergence and invertebrates could have taken up the RAS components from vertebrates through horizontal gene transfer.

Ancestry & molecular evolutionary analyses of heat shock protein 47 kDa (HSP47/SERPINH1)

HSP47/SERPINH1 is key-regulator for collagen biosynthesis and its structural assembly. To date, there is no comprehensive study on the phylogenetic history of HSP47. Herein we illustrate the evolutionary history of HSP47/SERPINH1 along with sequence, structural and syntenic traits for HSP47/SERPINH1. We have identified ancestral HSP47/SERPINH1 locus in Japanese lamprey (Lethenteron japonicum). This gene remains on the same or similar locus for ~500 million years (MY), but chromosomal duplication was observed in ray-finned fishes, leading into three sets of three sets (I-III) of HSP47/SERPINH1. Two novel introns were inserted at the positions 36b and 102b in the first exon of only HSP47_1 gene from the selected ray-finned fishes. On the evolutionary time scale, the events of HSP47 duplications took placed between 416–360 MY ago (MYA) while intron insertion dates back to 231–190 MYA after early divergence of ray-finned fishes.

Data on the evolutionary history of the V(D)J recombination-activating protein 1 - RAG1 coupled with sequence and variant analyses

RAG1 protein is one of the key component of RAG complex regulating the V(D)J recombination. There are only few studies for RAG1 concerning evolutionary history, detailed sequence and mutational hotspots. Herein, we present out datasets used for the recent comprehensive study of RAG1 based on sequence, phylogenetic and genetic variant analyses (Kumar et al., 2015) [1]. Protein sequence alignment helped in characterizing the conserved domains and regions of RAG1. It also aided in unraveling ancestral RAG1 in the sea urchin. Human genetic variant analyses revealed 751 mutational hotspots, located both in the coding and the non-coding regions. For further analysis and discussion, see (Kumar et al., 2015) [1].

Egg serpins: The chicken and/or the egg dilemma

Twenty-seven serpins belonging to clade A, B, C, D, E, F, G, H and I serpins are currently referenced in chicken genome databases. Phylogenetic analysis of chicken serpins revealed that ovalbumin (Serpinb14) and its paralogs ovalbumin-related protein Y (Serpinb14b) and ovalbumin-related protein X (Serpinb14c) are found in bird species. These clade B serpins are specifically expressed in reproductive tissues and exported in the egg where they constitute major protein components. These data suggest that these three paralogs have probably appeared in birds to face new environments and ensure the extra-uterine development of an embryo in a shell egg. Twelve other serpins have been identified in the newly produced egg, some of them having a specific distribution in the respective egg structures (eggshell, egg white, vitelline membrane and egg yolk). The physiological role of these egg serpins remain largely unexplored, but there is increasing evidence in literature or by homologies with their mammalian counterparts, that some of them participate in cell proliferation, tissue remodeling and/or angiogenesis associated with folliculogenesis and development of extraembryonic structures, eggshell biomineralization, egg defense and nutrition of the embryo. A better knowledge of the phylogenetic evolution of these 15 serpins in other oviparous species, on their egg distribution, on their regulation during embryonic development (activation/degradation/transfer) and on their functional specificity, is needed to better appreciate their role and their bird-specificity. These review shed light on the multiple possibilities that offer the avian egg model to study the role of serpins in reproduction and developmental biology.

Risk given by AGT polymorphisms in inducing susceptibility to essential hypertension among isolated populations from a remote region of China: A case-control study among the isolated populations

INTRODUCTION

Hypertension is a serious risk factor affecting up to 30% of the world's population with a heritability of more than 30-50%. The aim of this study was to investigate the contribution of the polymorphisms localized in the angiotensinogen (AGT) gene, a main component of the renin-angiotensin-aldosterone system, in inducing the susceptibility to essential hypertension (EH) among isolated populations (Yi and Hani minorities) with low prevalence rate from the remote region of Yunnan in China.

METHODS

A case-control association study was performed, and all subjects were genotyped for the seven single nucleotide polymorphisms localized in the AGT region by polymerase chain reaction-restriction fragment length polymorphism analysis.

RESULTS

Three polymorphisms, i.e. rs5046, rs5049, and rs2478544, were significantly associated with EH among the Hani minority. The associations, found in the Yi minority, did not reach a conclusive level of statistical significance. The polymorphisms of rs2478544 and rs5046 caused the transformations of exonic splicing enhancer sites and transcription factor binding sites, respectively, in the bioinformatic analyses. The haplotype-rs5046T, rs5049A, rs11568020G, rs3789679C, rs2478544C was susceptible for EH among the Hani minority.

CONCLUSION

Our findings suggested that the AGT polymorphisms have played a vital role in determining an individual's susceptibility to EH among the isolated population, which would be helpful for EH management in the remote mountainous region of Yunnan in China.

Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ∼500 MY

The serpin superfamily is characterized by proteins that fold into a conserved tertiary structure and exploits a sophisticated and irreversible suicide-mechanism of inhibition. Vertebrate serpins are classified into six groups (V1-V6), based on three independent biological features-genomic organization, diagnostic amino acid sites and rare indels. However, this classification system was based on the limited number of mammalian genomes available. In this study, several non-mammalian genomes are used to validate this classification system using the powerful Bayesian phylogenetic method. This method supports the intron and indel based vertebrate classification and proves that serpins have been maintained from lampreys to humans for about 500 MY. Lampreys have fewer than 10 serpins, which expand into 36 serpins in humans. The two expanding groups V1 and V2 have SERPINB1/SERPINB6 and SERPINA8/SERPIND1 as the ancestral serpins, respectively. Large clusters of serpins are formed by local duplications of these serpins in tetrapod genomes. Interestingly, the ancestral HCII/SERPIND1 locus (nested within PIK4CA) possesses group V4 serpin (A2APL1, homolog of α 2-AP/SERPINF2) of lampreys; hence, pointing to the fact that group V4 might have originated from group V2. Additionally in this study, details of the phylogenetic history and genomic characteristics of vertebrate serpins are revisited.

Urochordate serpins are Classified into Six Groups Encoded by Exon-Intron Structures, Microsynteny and Bayesian Phylogenetic Analyses

Members of serpin superfamily are involved in wide array of cellular processes to control proteolytic activities of eukaryotic organisms. Vertebrate serpins are extensively studied and reported to be classified into six groups (V1-V6) based on gene structures. However, there is no study conducted for serpins in urochordates (the closest living invertebrates related to vertebrates) to date. To unravel further the phylogenetic history of serpin genes, we characterized serpin genes from two urochordates (Ciona intestinalis and Ciona savignyi). There are 11 and 5 serpins in the C. intestinalis and C. savignyi, respectively. The exon/intron structures and genomic locus comparisons together with sequence phylogenetic analysis, suggested that urochordate serpins are classified into six groups (U1-U6), different from six groups (V1-V6) of vertebrate serpins. Human α1-antitrypsin shared lower sequence identities and similarities with urochordates serpins ranged from 14-29% and 30-49%, respectively. Based on protein sequences, genes and genomic architectures, we conclude that these two urochordates do not contain a single copy of genuine ortholog of the vertebrate serpins.

Genetic variants and evolutionary analyses of heparin cofactor II

Heparin cofactor II (HCII) belongs to serpin superfamily and it acts as a thrombin inhibitor in the coagulation cascade, in a glycosaminoglycan-dependent pathway using the release of a sequestered hirudin-like N-terminal tail for interaction with thrombin. This serpin belongs to multiple member group V2 of vertebrate serpin classification. However, there is no comprehensive study illustrating the exact phylogenetic history of HCII, to date. Herein, we explored phylogenetic traits of HCII genes. Structures of HCII gene from selected ray-finned fishes and lamprey varied in exon I and II with insertions of novel introns of which one in core domain for ray-finned fishes in exon II at the position 241c. We found HCII remain nested in the largest intron of phosphatidylinositol (PI) 4-kinase (PIK4CA) gene (genetic variants of this gene cause schizophrenia) at the origin of vertebrates, dated about 500MY old. We found that sequence features such as two acidic repeats (AR1-II), GAG-binding helix-D, three serpin motifs and inhibitory reactive center loop (RCL) of HCII protein are highly conserved in 55 vertebrates analyzed. We identified 985 HCII variants by analysis of 1092 human genomes with top three variation classes belongs to SNPs (84.3%), insertion (7.1%) and deletion (5.0%). We identified 37 deleterious mutations in the human HCII protein and we have described these mutations in relation to HCII sequence-structure-function relationships. These understandings may have clinical and medical importance as well.