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Dynamic evolution of selenocysteine utilization in bacteria: a balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues
Yan Zhang, Hector Romero, Gustavo Salinas, Vadim N Gladyshev
Genome Biol. 2006; 7(10): R94. Published online 2006 October 20. doi: 10.1186/gb-2006-7-10-r94
PMCID:
PMC1794560
Abstract Full Text PDF–514K Supplementary Material
 Is Cited by the Following 24 Articles in this Archive:
General metabolism of Laribacter hongkongensis: a genome-wide analysis
Shirly O Curreem, Jade L Teng, Herman Tse, Kwok-Yung Yuen, Susanna K Lau, Patrick C Woo
Cell Biosci. 2011; 1: 16. Published online 2011 April 19. doi: 10.1186/2045-3701-1-16
PMCID:
PMC3125206
Abstract Full Text PDF–5.4M
Plasmids with a Chromosome-Like Role in Rhizobia
Cristina Landeta, Araceli Dávalos, Miguel Ángel Cevallos, Otto Geiger, Susana Brom, David Romero
J Bacteriol. 2011 March; 193(6): 1317–1326. Published online 2011 January 7. doi: 10.1128/JB.01184-10
PMCID:
PMC3067620
Abstract Full Text PDF–531K Supplementary Material
In silico identification of the sea squirt selenoproteome
Liang Jiang, Qiong Liu, Jiazuan Ni
BMC Genomics. 2010; 11: 289. Published online 2010 May 10. doi: 10.1186/1471-2164-11-289
PMCID:
PMC2874816
Abstract Full Text PDF–884K Supplementary Material
Structure–Function Relations, Physiological Roles, and Evolution of Mammalian ER-Resident Selenoproteins
Valentina A. Shchedrina, Yan Zhang, Vyacheslav M. Labunskyy, Dolph L. Hatfield, Vadim N. Gladyshev
Antioxid Redox Signal. 2010 April 1; 12(7): 839–849. doi: 10.1089/ars.2009.2865
PMCID:
PMC2864662
Abstract Full Text PDF–318K
Recode-2: new design, new search tools, and many more genes
Michaël Bekaert, Andrew E. Firth, Yan Zhang, Vadim N. Gladyshev, John F. Atkins, Pavel V. Baranov
Nucleic Acids Res. 2010 January; 38(Database issue): D69–D74. Published online 2010 January. doi: 10.1093/nar/gkp788
PMCID:
PMC2808893
Abstract Full Text PDF–1.4M
General Trends in Trace Element Utilization Revealed by Comparative Genomic Analyses of Co, Cu, Mo, Ni, and Se
Yan Zhang, Vadim N. Gladyshev
J Biol Chem. 2010 January 29; 285(5): 3393–3405. Published online 2009 November 2. doi: 10.1074/jbc.M109.071746
PMCID:
PMC2823458
Abstract Full Text Supplementary Material
The Selenoproteome of Clostridium sp. OhILAs: Characterization of Anaerobic Bacterial Selenoprotein Methionine Sulfoxide Reductase A
Hwa-Young Kim, Yan Zhang, Byung Cheon Lee, Jae-Ryong Kim, Vadim N. Gladyshev
Proteins. Author manuscript; available in PMC 2010 March 1.
Published in final edited form as: Proteins. 2009 March; 74(4): 1008–1017. doi: 10.1002/prot.22212
PMCID:
PMC2671064
Abstract Full Text PDF–1.0M Supplementary Material
Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization
Yan Zhang, Dmitry A Rodionov, Mikhail S Gelfand, Vadim N Gladyshev
BMC Genomics. 2009; 10: 78. Published online 2009 February 10. doi: 10.1186/1471-2164-10-78
PMCID:
PMC2667541
Abstract Full Text PDF–558K Supplementary Material
Adaptations to Submarine Hydrothermal Environments Exemplified by the Genome of Nautilia profundicola
Barbara J. Campbell, Julie L. Smith, Thomas E. Hanson, Martin G. Klotz, Lisa Y. Stein, Charles K. Lee, Dongying Wu, Jeffrey M. Robinson, Hoda M. Khouri, Jonathan A. Eisen, S. Craig Cary
PLoS Genet. 2009 February; 5(2): e1000362. Published online 2009 February 6. doi: 10.1371/journal.pgen.1000362
PMCID:
PMC2628731
Abstract Full Text PDF–1.4M Supplementary Material
Evolutionary Patterns in the Sequence and Structure of Transfer RNA: A Window into Early Translation and the Genetic Code
Feng-Jie Sun, Gustavo Caetano-Anollés
PLoS ONE. 2008; 3(7): e2799. Published online 2008 July 30. doi: 10.1371/journal.pone.0002799
PMCID:
PMC2474678
Abstract Full Text PDF–455K Supplementary Material
Amino acid modifications on tRNA
Jing Yuan, Kelly Sheppard, Dieter Söll
Acta Biochim Biophys Sin (Shanghai) Author manuscript; available in PMC 2008 October 6.
Published in final edited form as: Acta Biochim Biophys Sin (Shanghai). 2008 July; 40(7): 539–553.
PMCID:
PMC2561244
Abstract Full Text PDF–1.1M
Trends in Selenium Utilization in Marine Microbial World Revealed through the Analysis of the Global Ocean Sampling (GOS) Project
Yan Zhang, Vadim N. Gladyshev
PLoS Genet. 2008 June; 4(6): e1000095. Published online 2008 June 13. doi: 10.1371/journal.pgen.1000095
PMCID:
PMC2398784
Abstract Full Text PDF–2.1M Supplementary Material
In silico identification of genes involved in selenium metabolism: evidence for a third selenium utilization trait
Yan Zhang, Anton A Turanov, Dolph L Hatfield, Vadim N Gladyshev
BMC Genomics. 2008; 9: 251. Published online 2008 May 29. doi: 10.1186/1471-2164-9-251
PMCID:
PMC2432076
Abstract Full Text PDF–655K Supplementary Material
Molybdoproteomes and evolution of molybdenum utilization
Yan Zhang, Vadim N. Gladyshev
J Mol Biol. Author manuscript; available in PMC 2009 June 13.
Published in final edited form as: J Mol Biol. 2008 June 13; 379(4): 881–899. Published online 2008 April 3. doi: 10.1016/j.jmb.2008.03.051
PMCID:
PMC2670968
Abstract Full Text PDF–1.2M Supplementary Material
From one amino acid to another: tRNA-dependent amino acid biosynthesis
Kelly Sheppard, Jing Yuan, Michael J. Hohn, Brian Jester, Kevin M. Devine, Dieter Söll
Nucleic Acids Res. 2008 April; 36(6): 1813–1825. Published online 2008 April. doi: 10.1093/nar/gkn015
PMCID:
PMC2330236
Abstract Full Text PDF–3.3M
Reduced reliance on the trace element selenium during evolution of mammals
Alexey V Lobanov, Dolph L Hatfield, Vadim N Gladyshev
Genome Biol. 2008; 9(3): R62. Published online 2008 March 31. doi: 10.1186/gb-2008-9-3-r62
PMCID:
PMC2397514
Abstract Full Text PDF–1.8M Supplementary Material
Comparative Genomic Analyses of Copper Transporters and Cuproproteomes Reveal Evolutionary Dynamics of Copper Utilization and Its Link to Oxygen
Perry G. Ridge, Yan Zhang, Vadim N. Gladyshev
PLoS ONE. 2008; 3(1): e1378. Published online 2008 January 2. doi: 10.1371/journal.pone.0001378
PMCID:
PMC2147054
Abstract Full Text PDF–838K Supplementary Material
Factors and Selenocysteine Insertion Sequence Requirements for the Synthesis of Selenoproteins from a Gram-Positive Anaerobe in Escherichia coli
Torsten Gursinsky, Daniel Gröbe, Angelika Schierhorn, Jana Jäger, Jan R. Andreesen, Brigitte Söhling
Appl Environ Microbiol. 2008 March; 74(5): 1385–1393. Published online 2007 December 28. doi: 10.1128/AEM.02238-07
PMCID:
PMC2258645
Abstract Full Text PDF–561K
Identification of a Chlorobenzene Reductive Dehalogenase in Dehalococcoides sp. Strain CBDB1
Lorenz Adrian, Jan Rahnenführer, Johan Gobom, Tina Hölscher
Appl Environ Microbiol. 2007 December; 73(23): 7717–7724. Published online 2007 October 12. doi: 10.1128/AEM.01649-07
PMCID:
PMC2168065
Abstract Full Text PDF–253K
Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life
Alexey V Lobanov, Dmitri E Fomenko, Yan Zhang, Aniruddha Sengupta, Dolph L Hatfield, Vadim N Gladyshev
Genome Biol. 2007; 8(9): R198. Published online 2007 September 19. doi: 10.1186/gb-2007-8-9-r198
PMCID:
PMC2375036
Abstract Full Text PDF–587K Supplementary Material
High content of proteins containing 21st and 22nd amino acids, selenocysteine and pyrrolysine, in a symbiotic deltaproteobacterium of gutless worm Olavius algarvensis
Yan Zhang, Vadim N. Gladyshev
Nucleic Acids Res. 2007 August; 35(15): 4952–4963. Published online 2007 July 11. doi: 10.1093/nar/gkm514
PMCID:
PMC1976440
Abstract Full Text PDF–11M
A recoding element that stimulates decoding of UGA codons by Sec tRNA[Ser]Sec
Michael T. Howard, Mark W. Moyle, Gaurav Aggarwal, Bradley A. Carlson, Christine B. Anderson
RNA. 2007 June; 13(6): 912–920. doi: 10.1261/rna.473907
PMCID:
PMC1869034
Abstract Full Text PDF–451K
Pyrrolysine is not hardwired for cotranslational insertion at UAG codons
Alexandre Ambrogelly, Sarath Gundllapalli, Stephanie Herring, Carla Polycarpo, Carina Frauer, Dieter Söll
Proc Natl Acad Sci U S A. 2007 February 27; 104(9): 3141–3146. Published online 2007 February 20. doi: 10.1073/pnas.0611634104
PMCID:
PMC1805618
Abstract Full Text PDF–562K
RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea
Jing Yuan, Sotiria Palioura, Juan Carlos Salazar, Dan Su, Patrick O'Donoghue, Michael J. Hohn, Alexander Machado Cardoso, William B. Whitman, Dieter Söll
Proc Natl Acad Sci U S A. 2006 December 12; 103(50): 18923–18927. Published online 2006 December 1. doi: 10.1073/pnas.0609703104
PMCID:
PMC1748153
Abstract Full Text PDF–1.1M
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