Revising angiotensinogen from phylogenetic and genetic variants perspectives

Kumar, Abhishek; Sarde, Sandeep J.; Bhandari, Anita

doi:10.1016/j.bbrc.2014.02.139

Cited by 19 publications

(25 citation statements)

References 24 publications

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“…By comparing these syntenies with previous studies on syntenies analyses of vertebrate serpin groups (namely V1 11, 12, V2 6, 13, 14, V3 9, 14, V4 14, 15, V5 14, 5 and V6 14, 16), it is clear that there is no synteny relationship is shared among serpins of vertebrates and urochordates. Hence, this chromosomal mapping analysis supports that gene structure based six (U1-U6) groups as six groups maintained on six distinct chromosomal localizations and conserved in two urochordate genomes.…”

Section: Resultsmentioning

confidence: 79%

“…Similarly, groups V5 5 and V6 are also single member serpins possessing single members on the genomic loci. In the vertebrate's group V2 - two serpins namely angiotensinogen 6 and heparin cofactor 18, group V3 -- all five members 14, C1 inhibitor in the group V4 20, single group V5 5 and V6 16 have single serpin gene on one genomic loci. Group U4 member, Ci-Spn-5 is sharing two intron positions with vertebrate group V5 (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Serpins are single domain proteins with an average size: 350-400 amino acids and molecular weights of 40-60 kDa 2-4. These proteins are classified into two functional categories - inhibitory (majority) such as antithrombin III 5, while some of them are non-inhibitory, which adopt other function than inhibitory roles such as angiotensinogen, which lost inhibition during vertebrate evolution 6. Serpins are thought to have evolved through gene duplication and divergence events, giving rise to a large number of serpin genes within an organism, each encoding a protein with a unique reactive center region and physiological function(s) 7.…”

Section: Introductionmentioning

confidence: 99%

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

Kumar¹,

Bhandari²

2014

J. Genomics

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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.

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Section: Resultsmentioning

confidence: 79%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Kumar¹,

Bhandari²

2014

J. Genomics

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“…To date, this study also provides the largest report on the mutational hotspot analyses of any member of serpin superfamily, previously studied [44][45][46][47]. These mutational hotspots will be serving a major resource for understanding of the biology of HSP47, particularly how HSP47 regulates collagen maturations.…”

Section: Discussionmentioning

confidence: 90%

“…We unraveled the genetic variants of human HSP47 from different human populations available in the 1000 genomes project (phase 3, release 16) [9]. We assessed the impacts of missense variants on the human HSP47 protein using two widely accepted tools, SIFT [14] and PolyPhen V2 [15], as described previously [44][45][46][47].…”

Section: Characterization Of Genetic Variants Of Human Hsp47 Variantsmentioning

confidence: 99%

Mutational Hotspots and Protein Interactome Analyses of Collagen-Specific Chaperone—HSP47

Parveen¹,

Kumar²,

Tandon³

et al. 2018

Preprint

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Heat shock protein 47kDa (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 and protein network for human HSP47. Using five different human mutational databases, we deduced a comprehensive list of human HSP47 mutations and we found 24 67, 50, 43 and 2 deleterious mutations from the 1000 genomes data, gnomAD, COSMICv86, cBioPortal, and CanVar. 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 change as the predominant mutation. We also found that HSP47 is up-regulated and down-regulated in 11 and 4 of cancers types. Upon constructing protein interactome map of human HSP47, we found that a set of molecular chaperones is interaction partners of HSP47, which included two copies each of CREB binding proteins, HSP27, HSP40, HSP70, HSP90, ubiquitin proteins and one copy each of cartilage associated protein (CRTAP), HSPH1, HSBP1, FK506-binding protein B (FKBP), kruppel-like factor (KLF13), peptidyl-prolyl isomerase PIPB and Prolyl 4-hydroxylase beta subunit (P4HB). This suggested a cocktail of different chaperones interact with HSP47. These findings will assist in the evaluation of roles of HSP47 in human disease including different types of cancers.

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Angiotensinogen gene polymorphisms and progression of chronic kidney disease in ADPKD patients

et al. 2015

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Revising angiotensinogen from phylogenetic and genetic variants perspectives

Cited by 19 publications

References 24 publications

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

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

Mutational Hotspots and Protein Interactome Analyses of Collagen-Specific Chaperone—HSP47

Angiotensinogen gene polymorphisms and progression of chronic kidney disease in ADPKD patients

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Revising angiotensinogen from phylogenetic and genetic variants perspectives

Cited by 19 publications

References 24 publications

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

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

Mutational Hotspots and Protein Interactome Analyses of Collagen-Specific Chaperone&mdash;HSP47

Angiotensinogen gene polymorphisms and progression of chronic kidney disease in ADPKD patients

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Product

Resources

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Mutational Hotspots and Protein Interactome Analyses of Collagen-Specific Chaperone—HSP47