Selenocysteine-containing proteins in mammals

Gladyshev, Vadim N.; Hatfield, Dolph L.

doi:10.1007/bf02255899

Cited by 160 publications

(49 citation statements)

References 86 publications

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“…Sec appears to be present in only 25 mammalian proteins and is mostly limited to enzyme active sites (Burk, 2002, Gladyshev and Hatfield, 1999, Kasaikina et al, 2012). In contrast, GenBank protein files indicate that the human genome encodes about 214,000 Cys unique residues and, excluding about 19,800 first Met in sequences, about 172,000 Met residues (Jones, 2008).…”

Section: The Cysteine Proteome Co-evolved With Structural and Functiomentioning

confidence: 99%

Thiol/disulfide redox states in signaling and sensing

Jones

2013

Critical Reviews in Biochemistry and Molecular Biology

207

135

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Rapid advances in redox systems biology are creating new opportunities to understand complexities of human disease and contributions of environmental exposures. New understanding of thiol-disulfide systems have occurred during the past decade as a consequence of the discoveries that thiol and disulfide systems are maintained in kinetically controlled steady-states displaced from thermodynamic equilibrium, that a widely distributed family of NADPH oxidases produces oxidants that function in cell signaling, and that a family of peroxiredoxins utilize thioredoxin as a reductant to complement the well-studied glutathione antioxidant system for peroxide elimination and redox regulation. This review focuses on thiol/disulfide redox state in biologic systems and the knowledge base available to support development of integrated redox systems biology models to better understand the function and dysfunction of thiol-disulfide redox systems. In particular, central principles have emerged concerning redox compartmentalization and utility of thiol/disulfide redox measures as indicators of physiologic function. Advances in redox proteomics show that, in addition to functioning in protein active sites and cell signaling, cysteine residues also serve as redox sensors to integrate biologic functions. These advances provide a framework for translation of redox systems biology concepts to practical use in understanding and treating human disease. Biological responses to cadmium, a widespread environmental agent, are used to illustrate the utility of these advances to the understanding of complex pleiotropic toxicities.

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Section: The Cysteine Proteome Co-evolved With Structural and Functiomentioning

confidence: 99%

Thiol/disulfide redox states in signaling and sensing

Jones

2013

Critical Reviews in Biochemistry and Molecular Biology

207

135

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“…The number of internal UGA transcripts noted for each of our identified targets ranged from 1 to 20 for mouse transcripts and 1 to 36 for rat transcripts. While the transcripts that contain more than 1 UGA codon could be RefSeq annotation errors, we note that transcripts for selenoproteins can include 1 to 10 internal UGA codons [12, 43], with Sepp1 corresponding to the latter in both our mouse and rat datasets (Tables I and II). …”

Section: Resultsmentioning

confidence: 98%

“…The regulation of gene expression by specific patterns of codon usage has been established for both prokaryotic and eukaryotic systems [7–12]. In bacterial systems where transcription is coupled to translation, the expression of tryptophan metabolic enzymes from the Trp operon is linked to the translation of the UGG-UGG dicodon, where UGG codes for tryptophan, in a short leader peptide.…”

Section: Introductionmentioning

confidence: 99%

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Gene- and genome-based analysis of significant codon patterns in yeast, rat and mice genomes with the CUT Codon UTilization tool

Doyle

Leonardi

Endres

et al. 2016

Methods

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The translation of mRNA in all forms of life uses a three-nucleotide codon and aminoacyl-tRNAs to synthesize a protein. There are 64 possible codons in the genetic code, with codons for the ~20 amino acids and 3 stop codons having 1- to 6-fold degeneracy. Recent studies have shown that families of stress response transcripts, termed modification tunable transcripts (MoTTs), use distinct codon biases that match specifically modified tRNAs to regulate their translation during a stress. Similarly, translational reprogramming of the UGA stop codon to generate selenoproteins or to perform programmed translational read-through (PTR) that results in a longer protein, requires distinct codon bias (i.e., more than one stop codon) and, in the case of selenoproteins, a specifically modified tRNA. In an effort to identify transcripts that have codon usage patterns that could be subject to translational control mechanisms, we have used existing genome and transcript data to develop the gene-specific Codon UTilization (CUT) tool and database, which details all 1-, 2-, 3-, 4- and 5-codon combinations for all genes or transcripts in yeast (Saccharomyces cerevisiae), mice (Mus musculus) and rats (Rattus norvegicus). Here, we describe the use of the CUT tool and database to characterize significant codon usage patterns in specific genes and groups of genes. In yeast, we demonstrate how the CUT database can be used to identify genes that have runs of specific codons (e.g., AGA, GAA, AAG) linked to translational regulation by tRNA methyltransferase 9 (Trm9). We further demonstrate how groups of genes can be analyzed to find significant dicodon patterns, with the 80 Gcn4-regulated transcripts significantly (P < 0.00001) over-represented with the AGA-GAA dicodon. We have also used the CUT database to identify mouse and rat transcripts with internal UGA codons, with the surprising finding of 45 and 120 such transcripts, respectively, which is much larger than expected. The UGA data suggest that there could be many more translationally reprogrammed transcripts than currently reported. CUT thus represents a multi-species codon-counting database that can be used with mRNA-, translation- and proteomics-based results to better understand and model translational control mechanisms.

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“…This does not imply that Cys is more important than Sec or Met. Sec is present in only 25 human proteins, but these include central redox enzymes, Trx reductases, and GSH peroxidases (21). The Met proteome is similar to the Cys proteome but is less studied.…”

Section: Definition Of Redox Proteomicsmentioning

confidence: 99%

The Redox Proteome

Jones

2013

Journal of Biological Chemistry

231

194

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The redox proteome consists of reversible and irreversible covalent modifications that link redox metabolism to biologic structure and function. These modifications, especially of Cys, function at the molecular level in protein folding and maturation, catalytic activity, signaling, and macromolecular interactions and at the macroscopic level in control of secretion and cell shape. Interaction of the redox proteome with redox-active chemicals is central to macromolecular structure, regulation, and signaling during the life cycle and has a central role in the tolerance and adaptability to diet and environmental challenges.

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Selenocysteine-containing proteins in mammals

Cited by 160 publications

References 86 publications

Thiol/disulfide redox states in signaling and sensing

Thiol/disulfide redox states in signaling and sensing

Gene- and genome-based analysis of significant codon patterns in yeast, rat and mice genomes with the CUT Codon UTilization tool

The Redox Proteome

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