scholarly journals Identification and in silico characterization of hemocyanin γ-type subunit protein in Vibrio harveyi infected freshwater prawn, Macrobrachium rosenbergii

2021 ◽  
Vol 42 (1) ◽  
pp. 14-23
Author(s):  
B.B. Patnaik ◽  
◽  
S. Baliarsingh ◽  
S. Sahoo ◽  
J.M. Chung ◽  
...  
Keyword(s):  
Amino Acid ◽  
In Silico ◽  
Vibrio Harveyi ◽  
Macrobrachium Rosenbergii ◽  
Full Length ◽  
Freshwater Prawn ◽  
Amino Acid Residues ◽  
Subunit Protein ◽  
In Silico Tools

Aim: Identification of full-length ORF of hemocyanin subunit-1 (Mr_HC_1) from the hepatopancreas transcriptome of freshwater prawn, Macrobrachium rosenbergii infected with Vibrio harveyi and characterization of its sequence and structure by in silico tools and softwares. Methodology: Illumina HiSeq and de novo assembled unigenes were scanned against PANM-DB to screen Mr_HC_1. FGENESH gene prediction and SMART programs were used to predict the ORF region. Subsequently, Clustal X2 and MEGA in-silico tools were used to understand the sequence relatedness and evolutionary status of Mr_HC_1. Structural prediction was performed by SWISS-MODEL and Ramachandran plot modeling programs Results: The full-length ORF was 1983 bp in length encoding a polypeptide of 661 amino acid residues. Mr_HC_1 showed a putative signal peptide of 21 amino acid residues at the N-terminus and three hemocyanin domains. Homology analysis of Mr_HC_1 amino acid sequence confirms maximum identity to M. nipponense hemocyanin subunit-1 (Mn_HC_1). Phylogenetic analysis showed that Mr_HC_1 is more closely related to the hemocyanin γ-type subunit of freshwater shrimps. Homology modeling of Mr_HC_1 showed homo-hexameric protein containing 12 copper ions. With a QMEAN score of -3.33 and model-template sequence identity of 59.15%, the predicted model of Mr_HC_1 is convincing Interpretation: This study characterizes the hemocyanin γ-type subunit protein of freshwater prawn, M. rosenbergii for future studies on host defense mechanisms.

scholarly journals In silico Identification and Comparative Analysis of Hevea brasiliensis COBRA Gene Family

2017 ◽  
Vol 1 ◽  
pp. 39-47
Author(s):  
Riza Arief Putranto ◽  
Irfan Martiansyah ◽  
Rizka Tamania Saptari
Keyword(s):  
Comparative Analysis ◽  
Amino Acid ◽  
Gene Family ◽  
In Silico ◽  
Rubber Tree ◽  
Protein Sequences ◽  
Full Length ◽  
Amino Acid Residues ◽  
Genes Encoding ◽  
Gene Subfamily

In this paper, the H. brasiliensis COBRA gene family, alleged to be involved in laticifer differentiation, was identified from the public rubber tree genome of Reyan 7-33-97 clone. A comparative analysis was carried out against A. thaliana genomic database. This analysis has resulted to the in silico validation of thirteen putative genes encoding glycophosphatidylinositol anchors (GPI) proteins harbored by nine Hevea genomic scaffolds. The sequence’s similarity of HbCOBL against AtCOBL genes were ranged from the threshold 50 to 81.58% covering 151 to 458 amino acid residues, respectively. Three partial and ten full-length protein sequences of HbCOBL genes were annotated. The partial protein sequences ranged from 89 to 184 amino acid residues as opposed to the full-length proteins ranging from 160 to 471 amino acid residues. Two types of COBRA domains (pfam04833 and cl04787) were found among HbCOBL genes. Phylogenetic analysis has clustered two subfamilies. Nine HbCOBL genes (HbCOBL-B, HbCOBL-J, HbCOBL-C, HbCOBL-H, HbCOBL-F, HbCOBL-I, HbCOBL-M, HBCOBL-A, and HbCOBL-N) were clustered as COBRA gene subfamily-I. By contrast, four genes (HbCOBL-O, HbCOBL-P, HbCOBL-E, and HbCOBL-L) were clustered as COBRA gene subfamily-II. The HbCOB subfamily-II was marked by the addition of 203 residues in C-terminal which is different with Arabidopsis. The gene HbCOBL-C was the putative ortholog to AtCOB carrying the unique COBRA domain cl04787 with 74 amino acid residues. Taken together, these results showed that Hevea and Arabidopsis COBRA genes might share similar functions while differ in gene structure.

scholarly journals Characterization of prostanoid pathway and the control of its activity by the eyestalk optic ganglion in the female giant freshwater prawn, Macrobrachium rosenbergii

Heliyon ◽  
2021 ◽  
Vol 7 (1) ◽  
pp. e05898
Author(s):  
Tipsuda Thongbuakaew ◽  
Chanudporn Sumpownon ◽  
Attakorn Engsusophon ◽  
Napamanee Kornthong ◽  
Charoonroj Chotwiwatthanakun ◽  
...  
Keyword(s):  
Macrobrachium Rosenbergii ◽  
Freshwater Prawn ◽  
Giant Freshwater Prawn ◽  
Optic Ganglion

scholarly journals Identification and characterization of amphibian SLC26A5 using RNA-Seq

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zhongying Wang ◽  
Qixuan Wang ◽  
Hao Wu ◽  
Zhiwu Huang
Keyword(s):  
Amino Acid ◽  
Inner Ear ◽  
Hair Cells ◽  
Rana Catesbeiana ◽  
Site Directed Mutagenesis ◽  
Amino Acid Residues ◽  
Rna Seq ◽  
American Bullfrog ◽  
Frog Species

Abstract Background Prestin (SLC26A5) is responsible for acute sensitivity and frequency selectivity in the vertebrate auditory system. Limited knowledge of prestin is from experiments using site-directed mutagenesis or domain-swapping techniques after the amino acid residues were identified by comparing the sequence of prestin to those of its paralogs and orthologs. Frog prestin is the only representative in amphibian lineage and the studies of it were quite rare with only one species identified. Results Here we report a new coding sequence of SLC26A5 for a frog species, Rana catesbeiana (the American bullfrog). In our study, the SLC26A5 gene of Rana has been mapped, sequenced and cloned successively using RNA-Seq. We measured the nonlinear capacitance (NLC) of prestin both in the hair cells of Rana’s inner ear and HEK293T cells transfected with this new coding gene. HEK293T cells expressing Rana prestin showed electrophysiological features similar to that of hair cells from its inner ear. Comparative studies of zebrafish, chick, Rana and an ancient frog species showed that chick and zebrafish prestin lacked NLC. Ancient frog’s prestin was functionally different from Rana. Conclusions We mapped and sequenced the SLC26A5 of the Rana catesbeiana from its inner ear cDNA using RNA-Seq. The Rana SLC26A5 cDNA was 2292 bp long, encoding a polypeptide of 763 amino acid residues, with 40% identity to mammals. This new coding gene could encode a functionally active protein conferring NLC to both frog HCs and the mammalian cell line. While comparing to its orthologs, the amphibian prestin has been evolutionarily changing its function and becomes more advanced than avian and teleost prestin.

Determination of amino acid sequence and site of mRNA expression of four vitellins in the giant freshwater prawn,Macrobrachium rosenbergii

2000 ◽  
Vol 287 (6) ◽  
pp. 413-422 ◽  
Author(s):  
Wei-Jun Yang ◽  
Tsuyoshi Ohira ◽  
Naoaki Tsutsui ◽  
Thanumalayaperumal Subramoniam ◽  
Do Thi Thanh Huong ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Mrna Expression ◽  
Macrobrachium Rosenbergii ◽  
Freshwater Prawn ◽  
Giant Freshwater Prawn

scholarly journals Molecular Cloning and Characterization of Bifidobacterium bifidum 1,2-α-l-Fucosidase (AfcA), a Novel Inverting Glycosidase (Glycoside Hydrolase Family 95)

2004 ◽  
Vol 186 (15) ◽  
pp. 4885-4893 ◽  
Author(s):  
Takane Katayama ◽  
Akiko Sakuma ◽  
Takatoshi Kimura ◽  
Yutaka Makimura ◽  
Jun Hiratake ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genomic Library ◽  
Bifidobacterium Bifidum ◽  
Glycoside Hydrolases ◽  
Glycoside Hydrolase Family ◽  
Amino Acid Residues ◽  
Gene Encoding ◽  
Sugar Chain ◽  
Hydrolysis Of

ABSTRACT A genomic library of Bifidobacterium bifidum constructed in Escherichia coli was screened for the ability to hydrolyze the α-(1→2) linkage of 2′-fucosyllactose, and a gene encoding 1,2-α-l-fucosidase (AfcA) was isolated. The afcA gene was found to comprise 1,959 amino acid residues with a predicted molecular mass of 205 kDa and containing a signal peptide and a membrane anchor at the N and C termini, respectively. A domain responsible for fucosidase activity (the Fuc domain; amino acid residues 577 to 1474) was localized by deletion analysis and then purified as a hexahistidine-tagged protein. The recombinant Fuc domain specifically hydrolyzed the terminal α-(1→2)-fucosidic linkages of various oligosaccharides and a sugar chain of a glycoprotein. The stereochemical course of the hydrolysis of 2′-fucosyllactose was determined to be inversion by using 1H nuclear magnetic resonance. The primary structure of the Fuc domain exhibited no similarity to those of any glycoside hydrolases (GHs) but showed high similarity to those of several hypothetical proteins in a database. Thus, it was revealed that the AfcA protein constitutes a novel inverting GH family (GH family 95).

scholarly journals Structure analysis of deleterious nsSNPs in human PALB2 protein for functional inference

2021 ◽  
Vol 17 (3) ◽  
pp. 424-438
Author(s):  
Noshin Nawar ◽  
Keyword(s):  
In Silico ◽  
General Outline ◽  
Recombination Repair ◽  
Functional Inference ◽  
Wd40 Domain ◽  
Project Data ◽  
Dbsnp Database ◽  
Comprehensive Characterization ◽  
In Silico Tools

Partner and Localizer of BRCA2 or PALB2 is a typical tumor suppressor protein, that responds to DNA double stranded breaks through homologous recombination repair. Heterozygous mutations in PALB2 are known to contribute to the susceptibility of breast and ovarian cancer. However, there is no comprehensive study characterizing the structural and functional impacts of SNPs located in the PALB2 gene.Therefore, it is of interest to document a comprehensive analysis of coding and non-coding SNPs located at the PALB2 loci using in silico tools. The data for 1455 non-synonymous SNPs (nsSNPs) located in the PALB2 loci were retrieved from the dbSNP database. Comprehensive characterization of the SNPs using a combination of in silico tools such as SIFT, PROVEAN, PolyPhen, PANTHER, PhDSNP, Pmut, MutPred 2.0 and SNAP-2, identified 28 functionally important SNPs. Among these, 16 nsSNPs were further selected for structural analysis using conservation profile and protein stability. The most deleterious nsSNPs were documented within the WD40 domain of PALB2. A general outline of the structural consequences of each variant was developed using the HOPE project data. These 16 mutant structures were further modelled using SWISS Model and three most damaging mutant models (rs78179744, rs180177123 and rs45525135) were identified. The non-coding SNPs in the 3’ UTR region of the PALB2 gene were analyzed for altered miRNA target sites. The comprehensive characterization of the coding and non-coding SNPs in the PALB2 locus has provided a list of damaging SNPs with potential disease association. Further validation through genetic association study will reveal their clinical significance.

scholarly journals Identification of a Gene Involved in Assembly ofActinomyces naeslundii T14V Type 2 Fimbriae

1998 ◽  
Vol 66 (4) ◽  
pp. 1482-1491 ◽  
Author(s):  
Maria K. Yeung ◽  
Jacob A. Donkersloot ◽  
John O. Cisar ◽  
Pamela A. Ragsdale
Keyword(s):  
Amino Acid ◽  
Kanamycin Resistance ◽  
Amino Acid Residues ◽  
Subunit Protein ◽  
Actinomyces Naeslundii ◽  
Cell Extracts ◽  
Acid Protein ◽  
Structural Subunit ◽  
Antipeptide Antibody

ABSTRACT The nucleotide sequence of the Actinomyces naeslundiiT14V type 2 fimbrial structural subunit gene, fimA, and the 3′ flanking DNA region was determined. The fimA gene encoded a 535-amino-acid precursor subunit protein (FimA) which included both N-terminal leader and C-terminal cell wall sorting sequences. A second gene, designated orf365, that encoded a 365-amino-acid protein which contained a putative transmembrane segment was identified immediately 3′ to fimA. Mutants in which either fimA or orf365 was replaced with a kanamycin resistance gene did not participate in type 2 fimbriae-mediated coaggregation with Streptococcus oralis34. Type 2 fimbrial antigen was not detected in cell extracts of thefimA mutant by Western blotting with anti-A. naeslundii type 2 fimbrial antibody, but the subunit protein was detected in extracts of the orf365 mutant. The subunit protein detected in this mutant also was immunostained by an antibody raised against a synthetic peptide representing the C-terminal 20 amino acid residues of the predicted FimA. The antipeptide antibody reacted with FimA isolated from the recombinant Escherichia coliclone containing fimA but did not react with purified type 2 fimbriae in extracts of the wild-type strain. These results indicate that synthesis of type 2 fimbriae in A. naeslundii T14V may involve posttranslational cleavage of both the N-terminal and C-terminal peptides of the precursor subunit and also the expression oforf365.

Sign in / Sign up

Export Citation Format

Share Document