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2004

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Biochemistry, Biophysics, and Structural Biology

Vadim Gladyshev Publications

Articles 1 - 7 of 7

Full-Text Articles in Life Sciences

Identification And Characterization Of Phosphoseryl-Trna [Ser]Sec Kinase, Bradley A. Carlson, Xue-Ming Xu, Gregory V. Kryukov, Mahadev Rao, Marla J. Berry, Vadim N. Gladyshev, Dolph L. Hatfield Aug 2004

Identification And Characterization Of Phosphoseryl-Trna [Ser]Sec Kinase, Bradley A. Carlson, Xue-Ming Xu, Gregory V. Kryukov, Mahadev Rao, Marla J. Berry, Vadim N. Gladyshev, Dolph L. Hatfield

Vadim Gladyshev Publications

In 1970, a kinase activity that phosphorylated a minor species of seryl-tRNA to form phosphoseryl-tRNA was found in rooster liver [Maenpaa, P. H. & Bernfield, M. R. (1970) Proc. Natl. Acad. Sci. USA 67, 688–695], and a minor seryl-tRNA that decoded the nonsense UGA was detected in bovine liver. The phosphoseryl-tRNA and the minor UGA-decoding seryl-tRNA were subsequently identified as selenocysteine (Sec) tRNA [Ser]Sec, but the kinase activity remained elusive. Herein, by using a comparative genomics approach that searched completely sequenced archaeal genomes for a kinase-like protein with a pattern of occurrence similar to that of components of Sec ...


The Prokaryotic Selenoproteome, Gregory V. Kryukov, Vadim N. Gladyshev May 2004

The Prokaryotic Selenoproteome, Gregory V. Kryukov, Vadim N. Gladyshev

Vadim Gladyshev Publications

In the genetic code, the UGA codon has a dual function as it encodes selenocysteine (Sec) and serves as a stop signal. However, only the translation terminator function is used in gene annotation programs, resulting in misannotation of selenoprotein genes. Here, we applied two independent bioinformatics approaches to characterize a selenoprotein set in prokaryotic genomes. One method searched for selenoprotein genes by identifying RNA stem–loop structures, selenocysteine insertion sequence elements; the second approach identified Sec/Cys pairs in homologous sequences. These analyses identified all or almost all selenoproteins in completely sequenced bacterial and archaeal genomes and provided a view ...


Specific Excision Of The Selenocysteine Trna [Ser]Sec (Trsp) Gene In Mouse Liver Demonstrates An Essential Role Of Selenoproteins In Liver Function, Bradley A. Carlson, Sergey V. Novoselov, Easwari Kumaraswamy, Byeong Jae Lee, Miriam R. Anver, Vadim N. Gladyshev, Dolph L. Hatfield Feb 2004

Specific Excision Of The Selenocysteine Trna [Ser]Sec (Trsp) Gene In Mouse Liver Demonstrates An Essential Role Of Selenoproteins In Liver Function, Bradley A. Carlson, Sergey V. Novoselov, Easwari Kumaraswamy, Byeong Jae Lee, Miriam R. Anver, Vadim N. Gladyshev, Dolph L. Hatfield

Vadim Gladyshev Publications

Selenium is essential in mammalian embryonic development. However, in adults, selenoprotein levels in several organs including liver can be substantially reduced by selenium deficiency without any apparent change in phenotype. To address the role of selenoproteins in liver function, mice homozygous for a floxed allele encoding the selenocysteine (Sec) tRNA [Ser]Sec gene were crossed with transgenic mice carrying the Cre recombinase under the control of the albumin promoter that expresses the recombinase specifically in liver. Recombination was nearly complete in mice 3 weeks of age, whereas liver selenoprotein synthesis was virtually absent, which correlated with the loss of Sec ...


Methionine Sulfoxide Reduction In Mammals: Characterization Of Methionine-R-Sulfoxide Reductases, Hwa-Young Kim, Vadim Gladyshev Feb 2004

Methionine Sulfoxide Reduction In Mammals: Characterization Of Methionine-R-Sulfoxide Reductases, Hwa-Young Kim, Vadim Gladyshev

Vadim Gladyshev Publications

Methionine residues in proteins are susceptible to oxidation by reactive oxygen species, but can be repaired via reduction of the resulting methionine sulfoxides by methionine-S-sulfoxide reductase (MsrA) and methionine-R-sulfoxide reductase (MsrB). However, the identity of all methionine sulfoxide reductases involved, their cellular locations and relative contributions to the overall pathway are poorly understood. Here, we describe a methionine-R-sulfoxide reduction system in mammals, in which two MsrB homologues were previously described. We found that human and mouse genomes possess three MsrB genes and characterized their protein products, designated MsrB1, MsrB2, and MsrB3. MsrB1 (Selenoprotein R) was present in the cytosol and ...


Reconsidering The Evolution Of Eukaryotic Selenoproteins: A Novel Nonmammalian Family With Scattered Phylogenetic Distribution, Sergi Castellano, Sergey V. Novoselov, Gregory V. Kryukov, Alain Lescure, Enrique Blanco, Alain Krol, Vadim N. Gladyshev, Roderic Guigo Jan 2004

Reconsidering The Evolution Of Eukaryotic Selenoproteins: A Novel Nonmammalian Family With Scattered Phylogenetic Distribution, Sergi Castellano, Sergey V. Novoselov, Gregory V. Kryukov, Alain Lescure, Enrique Blanco, Alain Krol, Vadim N. Gladyshev, Roderic Guigo

Vadim Gladyshev Publications

While the genome sequence and gene content are available for an increasing number of organisms, eukaryotic selenoproteins remain poorly characterized. The dual role of the UGA codon confounds the identification of novel selenoprotein genes. Here, we describe a comparative genomics approach that relies on the genome-wide prediction of genes with in-frame TGA codons, and the subsequent comparison of predictions from different genomes, wherein conservation in regions flanking the TGA codon suggests selenocysteine coding function. Application of this method to human and fugu genomes identified a novel selenoprotein family, named SelU, in the puffer fish. The selenocysteinecontaining form also occurred in ...


Reconsidering The Evolution Of Eukaryotic Selenoproteins: A Novel Nonmammalian Family With Scattered Phylogenetic Distribution, Sergi Castellano, Sergey V. Novoselov, Gregory V. Kryukov, Alain Lescure, Enrique Blanco, Alain Krol, Vadim N. Gladyshev, Roderic Guigo Jan 2004

Reconsidering The Evolution Of Eukaryotic Selenoproteins: A Novel Nonmammalian Family With Scattered Phylogenetic Distribution, Sergi Castellano, Sergey V. Novoselov, Gregory V. Kryukov, Alain Lescure, Enrique Blanco, Alain Krol, Vadim N. Gladyshev, Roderic Guigo

Vadim Gladyshev Publications

While the genome sequence and gene content are available for an increasing number of organisms, eukaryotic selenoproteins remain poorly characterized. The dual role of the UGA codon confounds the identification of novel selenoprotein genes. Here, we describe a comparative genomics approach that relies on the genome-wide prediction of genes with in-frame TGA codons, and the subsequent comparison of predictions from different genomes, wherein conservation in regions flanking the TGA codon suggests selenocysteine coding function. Application of this method to human and fugu genomes identified a novel selenoprotein family, named SelU, in the puffer fish. The selenocysteinecontaining form also occurred in ...


Identification Of Trace Element-Containing Proteins In Genomic Databases, Vadim N. Gladyshev, Gregory V. Kryukov, Dmitri E. Fomenko, Dolph L. Hatfield Jan 2004

Identification Of Trace Element-Containing Proteins In Genomic Databases, Vadim N. Gladyshev, Gregory V. Kryukov, Dmitri E. Fomenko, Dolph L. Hatfield

Vadim Gladyshev Publications

Development of bioinformatics tools provided researchers with the ability to identify full sets of trace element–containing proteins in organisms for which complete genomic sequences are available. Recently, independent bioinformatics methods were used to identify all, or almost all, genes encoding selenocysteine-containing proteins in human, mouse, and Drosophila genomes, characterizing entire selenoproteomes in these organisms. It also should be possible to search for entire sets of other trace element–associated proteins, such as metal-containing proteins, although methods for their identification are still in development.