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The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like β-grasp domains
Lakshminarayan M Iyer, A Maxwell Burroughs, L Aravind
Genome Biol. 2006; 7(7): R60. Published online 2006 July 19. doi: 10.1186/gb-2006-7-7-r60
PMCID:
PMC1779556
Abstract Full Text PDF–4.2M Supplementary Material
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 Is Cited by the Following 31 Articles in this Archive:
Uncovering Ubiquitin and Ubiquitin-like Signaling Networks
Alfred C. O. Vertegaal
Chem Rev. 2011 December 14; 111(12): 7923–7940. Published online 2011 October 17. doi: 10.1021/cr200187e
PMCID:
PMC3238414
Full Text PDF–4.7M
Uncovering Ubiquitin and Ubiquitin-like Signaling Networks
Alfred C. O. Vertegaal
Chem Rev. 2011 December 14; 111(12): 7923–7940. Published online 2011 October 17. doi: 10.1021/cr200187e
PMCID:
PMC3238414
Full Text PDF–4.7M
The phylogenomic analysis of the anaphase promoting complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes
Laura Eme, Aurélie Trilles, David Moreira, Céline Brochier-Armanet
BMC Evol Biol. 2011; 11: 265. Published online 2011 September 23. doi: 10.1186/1471-2148-11-265
PMCID:
PMC3195147
Abstract Full Text PDF–545K Supplementary Material
Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems
Lakshminarayan M. Iyer, Dapeng Zhang, Igor B. Rogozin, L. Aravind
Nucleic Acids Res. 2011 December; 39(22): 9473–9497. Published online 2011 September 2. doi: 10.1093/nar/gkr691
PMCID:
PMC3239186
Abstract Full Text PDF–18M
E1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea
Hugo V. Miranda, Nikita Nembhard, Dan Su, Nathaniel Hepowit, David J. Krause, Jonathan R. Pritz, Cortlin Phillips, Dieter Söll, Julie A. Maupin-Furlow
Proc Natl Acad Sci U S A. 2011 March 15; 108(11): 4417–4422. Published online 2011 February 28. doi: 10.1073/pnas.1018151108
PMCID:
PMC3060232
Abstract Full Text PDF–860K Supplementary Material
A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems
Dapeng Zhang, Lakshminarayan M. Iyer, L. Aravind
Nucleic Acids Res. 2011 June; 39(11): 4532–4552. Published online 2011 February 8. doi: 10.1093/nar/gkr036
PMCID:
PMC3113570
Abstract Full Text PDF–28M Supplementary Material
Urm1 couples sulfur transfer to ubiquitin-like protein function in oxidative stress
Matthew D. Petroski, Guy S. Salvesen, Dieter A. Wolf
Proc Natl Acad Sci U S A. 2011 February 1; 108(5): 1749–1750. Published online 2011 January 18. doi: 10.1073/pnas.1019043108
PMCID:
PMC3033263
Full Text PDF–537K
Role of the ubiquitin-like protein Urm1 as a noncanonical lysine-directed protein modifier
Annemarthe G. Van der Veen, Kenji Schorpp, Christian Schlieker, Ludovico Buti, Jadyn R. Damon, Eric Spooner, Hidde L. Ploegh, Stefan Jentsch
Proc Natl Acad Sci U S A. 2011 February 1; 108(5): 1763–1770. Published online 2011 January 5. doi: 10.1073/pnas.1014402108
PMCID:
PMC3033243
Abstract Full Text PDF–1.1M Supplementary Material
Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group
Takuro Nunoura, Yoshihiro Takaki, Jungo Kakuta, Shinro Nishi, Junichi Sugahara, Hiromi Kazama, Gab-Joo Chee, Masahira Hattori, Akio Kanai, Haruyuki Atomi, Ken Takai, Hideto Takami
Nucleic Acids Res. 2011 April; 39(8): 3204–3223. Published online 2010 December 15. doi: 10.1093/nar/gkq1228
PMCID:
PMC3082918
Abstract Full Text PDF–3.5M Supplementary Material
SAMPyling Proteins in Archaea
K. Heran Darwin, Kay Hofmann
Trends Biochem Sci. Author manuscript; available in PMC 2011 June 1.
Published in final edited form as: Trends Biochem Sci. 2010 June; 35(6): 348–351. Published online 2010 May 23. doi: 10.1016/j.tibs.2010.03.003
PMCID:
PMC2892244
Abstract Full Text PDF–624K
Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase
Lakshminarayan M. Iyer, Saraswathi Abhiman, Robson F. de Souza, L. Aravind
Nucleic Acids Res. 2010 September; 38(16): 5261–5279. Published online 2010 April 27. doi: 10.1093/nar/gkq265
PMCID:
PMC2938197
Abstract Full Text PDF–18M
Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution
Thomas Cavalier-Smith
Biol Direct. 2010; 5: 7. Published online 2010 February 4. doi: 10.1186/1745-6150-5-7
PMCID:
PMC2837639
Abstract Full Text PDF–2.3M
Ubiquitin-like Small Archaeal Modifier Proteins (SAMPs) in Haloferax volcanii
Matthew A. Humbard, Hugo V. Miranda, Jae-Min Lim, David J. Krause, Jonathan R. Pritz, Guangyin Zhou, Sixue Chen, Lance Wells, Julie A. Maupin-Furlow
Nature. Author manuscript; available in PMC 2010 July 7.
Published in final edited form as: Nature. 2010 January 7; 463(7277): 54–60. doi: 10.1038/nature08659
PMCID:
PMC2872088
Abstract Full Text PDF–1.3M Supplementary Material
Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins
Lakshminarayan M. Iyer, Saraswathi Abhiman, A. Maxwell Burroughs, L. Aravind
Mol Biosyst. Author manuscript; available in PMC 2012 January 29.
Published in final edited form as: Mol Biosyst. 2009 December; 5(12): 1636–1660. Published online 2009 October 13. doi: 10.1039/b917682a
PMCID:
PMC3268129
Abstract Full Text PDF–5.5M Supplementary Material
Natural history of the E1-like superfamily: implication for adenylation, sulfur transfer and ubiquitin conjugation
A. Maxwell Burroughs, Lakshminarayan M. Iyer, L. Aravind
Proteins. Author manuscript; available in PMC 2010 June 1.
Published in final edited form as: Proteins. 2009 June; 75(4): 895–910. doi: 10.1002/prot.22298
PMCID:
PMC2732565
Abstract Full Text PDF–4.3M Supplementary Material
Ubiquitin, infinitely seductive. Symposium on The Many Faces of Ubiquitin
Michael Rape
EMBO Rep. 2009 June; 10(6): 558–562. Published online 2009 May 22. doi: 10.1038/embor.2009.104
PMCID:
PMC2711821
Full Text PDF–307K
What Was the Set of Ubiquitin and Ubiquitin-Like Conjugating Enzymes in the Eukaryote Common Ancestor?
Caroline Michelle, Patrick Vourc’h, Laurence Mignon, Christian R. Andres
J Mol Evol. 2009 June; 68(6): 616–628. Published online 2009 May 19. doi: 10.1007/s00239-009-9225-6
PMCID:
PMC2691932
Abstract Full Text PDF–456K Supplementary Material
Reconstructing the ubiquitin network - cross-talk with other systems and identification of novel functions
Thiago M Venancio, S Balaji, Lakshminarayan M Iyer, L Aravind
Genome Biol. 2009; 10(3): R33. Published online 2009 March 30. doi: 10.1186/gb-2009-10-3-r33
PMCID:
PMC2691004
Abstract Full Text PDF–1.8M Supplementary Material
Origin and Function of Ubiquitin-like Protein Conjugation
Mark Hochstrasser
Nature. Author manuscript; available in PMC 2010 March 26.
Published in final edited form as: Nature. 2009 March 26; 458(7237): 422. doi: 10.1038/nature07958
PMCID:
PMC2819001
Abstract Full Text PDF–1.7M
Urm1 at the crossroad of modifications. ‘Protein Modifications: Beyond the Usual Suspects' Review Series
Patrick G A Pedrioli, Sebastian Leidel, Kay Hofmann
EMBO Rep. 2008 December; 9(12): 1196–1202. doi: 10.1038/embor.2008.209
PMCID:
PMC2603462
Abstract Full Text PDF–433K
Common thiolation mechanism in the biosynthesis of tRNA thiouridine and sulphur-containing cofactors
Naoki Shigi, Yuriko Sakaguchi, Shin-ichi Asai, Tsutomu Suzuki, Kimitsuna Watanabe
EMBO J. 2008 December 17; 27(24): 3267–3278. Published online 2008 November 27. doi: 10.1038/emboj.2008.246
PMCID:
PMC2609741
Abstract Full Text PDF–1.5M Supplementary Material
A functional proteomics approach links the ubiquitin-related modifier Urm1 to a tRNA modification pathway
Christian D. Schlieker, Annemarthe G. Van der Veen, Jadyn R. Damon, Eric Spooner, Hidde L. Ploegh
Proc Natl Acad Sci U S A. 2008 November 25; 105(47): 18255–18260. Published online 2008 November 18. doi: 10.1073/pnas.0808756105
PMCID:
PMC2584574
Abstract Full Text PDF–637K Supplementary Material
Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination
Lakshminarayan M Iyer, AM Burroughs, L Aravind
Biol Direct. 2008; 3: 45. Published online 2008 November 3. doi: 10.1186/1745-6150-3-45
PMCID:
PMC2588565
Abstract Full Text PDF–1.8M Supplementary Material
A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism
Elizabeth E Regulski, Ryan H Moy, Zasha Weinberg, Jeffrey E Barrick, Zizhen Yao, Walter L Ruzzo, Ronald R Breaker
Mol Microbiol. 2008 May; 68(4): 918–932. doi: 10.1111/j.1365-2958.2008.06208.x
PMCID:
PMC2408646
Abstract Full Text PDF–596K Supplementary Material
Rethinking Proteasome Evolution: Two Novel Bacterial Proteasomes
Ruben E. Valas, Philip E. Bourne
J Mol Evol. 2008 May; 66(5): 494–504. Published online 2008 April 4. doi: 10.1007/s00239-008-9075-7
PMCID:
PMC3235984
Abstract Full Text PDF–494K
Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation
A. Maxwell Burroughs, Marcie Jaffee, Lakshminarayan M. Iyer, L. Aravind
J Struct Biol. Author manuscript; available in PMC 2009 June 25.
Published in final edited form as: J Struct Biol. 2008 May; 162(2): 205–218. Published online 2008 January 1. doi: 10.1016/j.jsb.2007.12.006
PMCID:
PMC2701696
Abstract Full Text PDF–4.2M Supplementary Material
Small but versatile: the extraordinary functional and structural diversity of the β-grasp fold
A Maxwell Burroughs, S Balaji, Lakshminarayan M Iyer, L Aravind
Biol Direct. 2007; 2: 18. Published online 2007 July 2. doi: 10.1186/1745-6150-2-18
PMCID:
PMC1949818
Abstract Full Text PDF–3.2M Supplementary Material
Sequence and structure evolved separately in a ribosomal ubiquitin variant
André Catic, Zhen-Yu J Sun, Daniel M Ratner, Shahram Misaghi, Eric Spooner, John Samuelson, Gerhard Wagner, Hidde L Ploegh
EMBO J. 2007 July 25; 26(14): 3474–3483. Published online 2007 June 28. doi: 10.1038/sj.emboj.7601772
PMCID:
PMC1933403
Abstract Full Text PDF–531K Supplementary Material
ElaD, a Deubiquitinating Protease Expressed by E. coli
André Catic, Shahram Misaghi, Gregory A. Korbel, Hidde L. Ploegh
PLoS ONE. 2007; 2(4): e381. Published online 2007 April 18. doi: 10.1371/journal.pone.0000381
PMCID:
PMC1847702
Abstract Full Text PDF–746K
Exploitation of Eukaryotic Ubiquitin Signaling Pathways by Effectors Translocated by Bacterial Type III and Type IV Secretion Systems
Aurélie Angot, Annette Vergunst, Stéphane Genin, Nemo Peeters
PLoS Pathog. 2007 January; 3(1): e3. Published online 2007 January 26. doi: 10.1371/journal.ppat.0030003
PMCID:
PMC1781473
Abstract Full Text PDF–391K
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