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Physicochemical characterization and functional site analysis of lactoferrin gene of Vechur cow.

ABSTRACT: The Bos indicus Vechur breed cow milk is known for its medicinal value and the breed is listed under the category of critically maintained breeds by the Food and Agriculture Organization. The lactoferrin protein in milk is known for its nutritional value. Gene polymorphisms have been reported for Bovine lactoferrin. Mutations in the evolutionarily conserved sites tend to impair protein function and are related with the physicochemical difference between the known variants with 11 SNPs within the wild type. Structural differences are located due to these SNPs that may lead to functional variations. The structural variation is seen primarily in the first 48 residues at 5' end in all the samples modelled. Out of 11 SNPs 5 amino acid variations fall under alpha helix and beta sheet region, this might be of functional significance. This result may provide evidence that the SNPs detected in lactoferrin gene might have potential effects on milk composition. Our result demonstrates one major domain that could be a common binding pocket to all the samples, and important as an active site common to all the breeds that could be utilized for effective drug designing. Moreover, at some SNP positions in Vechur breed, antimicrobial peptides were located indicating importance of those residues for enhanced antimicrobial activity in lactoferrin of Vechur breed. Second binding pocket found in N- lobe region with the three required residues aspartic acid, histidine and tyrosine for iron binding, was considered as major binding site.

SUBMITTER: Shashidharan A

PROVIDER: S-EPMC3124693 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Physicochemical characterization and functional site analysis of lactoferrin gene of Vechur cow.

Shashidharan Anisha A Singh Ruchi R Bhasker Salini S Mohankumar Chinnamma C

Bioinformation 20110623 7

The Bos indicus Vechur breed cow milk is known for its medicinal value and the breed is listed under the category of critically maintained breeds by the Food and Agriculture Organization. The lactoferrin protein in milk is known for its nutritional value. Gene polymorphisms have been reported for Bovine lactoferrin. Mutations in the evolutionarily conserved sites tend to impair protein function and are related with the physicochemical difference between the known variants with 11 SNPs within the ...[more]

PMID: 21738329

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Project description:BackgroundCarotenoids play important roles in photosynthesis, hormone signaling, and secondary metabolism. Phytoene synthase (PSY) catalyzes the first step of the carotenoid biosynthetic pathway. In this study, we aimed to characterize the PSY genes in tobacco and analyze their function.ResultsIn this study, we identified three groups of PSY genes, namely PSY1, PSY2, and PSY3, in four Nicotiana species; phylogenetic analysis indicated that these genes shared a high similarity with those in tomato but not with those in monocots such as rice and maize. The expression levels of PSY1 and PSY2 were observed to be highest in leaves compared to other tissues, and they could be elevated by treatment with certain phytohormones and exposure to strong light. No PSY3 expression was detected under these conditions. We constructed virus-induced PSY1 and PSY2 silencing in tobacco and found that the newly emerged leaves in these plants were characterized by severe bleaching and markedly decreased carotenoid and chlorophyll content. Thylakoid membrane protein complex levels in the gene-silenced plants were also less than those in the control plants. The chlorophyll fluorescence parameters such as Fv/Fm, ΦPSII, qP, and NPQ, which reflect photosynthetic system activities, of the gene-silenced plants were also significantly decreased. We further performed RNA-Seq and metabonomics analysis between gene-silenced tobacco and control plants. RNA-Seq results showed that abiotic stress, isoprenoid compounds, and amino acid catabolic processes were upregulated, whereas the biosynthesis of cell wall components was downregulated. Metabolic analysis results were consistent with the RNA-Seq. We also found the downstream genes in carotenoid biosynthesis pathways were upregulated, and putative transcription factors that regulate carotenoid biosynthesis were identified.ConclusionsOur results suggest that PSY can regulate carotenoid contents not only by controlling the first biosynthesis step but also by exerting effects on the expression of downstream genes, which would thereby affect photosynthetic activity. Meanwhile, PSY may affect other processes such as amino acid catabolism and cell wall organization. The information we report here may aid further research on PSY genes and carotenoid biosynthesis.

Dataset Information

Physicochemical characterization and functional site analysis of lactoferrin gene of Vechur cow.

Publications

Physicochemical characterization and functional site analysis of lactoferrin gene of Vechur cow.

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