L Aravind

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Biol 7:R60. 2006
  2. pmc MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 3:8. 2008
  3. ncbi request reprint Comparative genomics and structural biology of the molecular innovations of eukaryotes
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Curr Opin Struct Biol 16:409-19. 2006
  4. pmc Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Genomics 5:45. 2004
  5. pmc Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    Nucleic Acids Res 33:3875-96. 2005
  6. ncbi request reprint Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains
    V Anantharaman
    National Center for Biotechnology Information National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
    J Mol Biol 307:1271-92. 2001
  7. pmc The alpha/beta fold uracil DNA glycosylases: a common origin with diverse fates
    L Aravind
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 1:RESEARCH0007. 2000
  8. pmc Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 32:5260-79. 2004
  9. pmc The SWIRM domain: a conserved module found in chromosomal proteins points to novel chromatin-modifying activities
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 3:RESEARCH0039. 2002
  10. pmc A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 5:R30. 2004

Collaborators

Detail Information

Publications110 found, 100 shown here

  1. pmc The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Biol 7:R60. 2006
    ..Hence, the evolutionary assembly of the eukaryotic Ub-signaling apparatus remains unclear...
  2. pmc MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 3:8. 2008
    ....
  3. ncbi request reprint Comparative genomics and structural biology of the molecular innovations of eukaryotes
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Curr Opin Struct Biol 16:409-19. 2006
    ....
  4. pmc Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Genomics 5:45. 2004
    ..The identification of these RNA-binding domains may throw light on the emergence of eukaryote-specific systems of RNA metabolism...
  5. pmc Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    Nucleic Acids Res 33:3875-96. 2005
    ..These observations point to a functional equivalence of the two classes of primases, which seem to have repeatedly displaced each other in various extrachromosomal replicons...
  6. ncbi request reprint Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains
    V Anantharaman
    National Center for Biotechnology Information National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
    J Mol Biol 307:1271-92. 2001
    ..Using the "guilt by association approach", the identification of SMBDs allowed prediction of functions and mode of regulation for a variety of previously uncharacterized proteins...
  7. pmc The alpha/beta fold uracil DNA glycosylases: a common origin with diverse fates
    L Aravind
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 1:RESEARCH0007. 2000
    ..The structural and evolutionary relationships between the rest of the UDGs remain uncertain...
  8. pmc Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 32:5260-79. 2004
    ....
  9. pmc The SWIRM domain: a conserved module found in chromosomal proteins points to novel chromatin-modifying activities
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 3:RESEARCH0039. 2002
    ..These modifications have an important role in the regulation of chromatin structure and are mediated by large multisubunit complexes that contain modular proteins with several conserved catalytic and noncatalytic adaptor domains...
  10. pmc A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 5:R30. 2004
    ..These studies provide a framework for characterization of novel lineages within this fold and prediction of their functional properties...
  11. pmc The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons
    M Madan Babu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 34:6505-20. 2006
    ..We also use the WRKY-GCM1 superfamily as an example to illustrate the importance of transposons in the emergence of new TFs in different lineages...
  12. pmc The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 2:RESEARCH0007. 2001
    ....
  13. ncbi request reprint Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda 20894, USA
    J Mol Biol 360:213-27. 2006
    ..We believe that the results presented here might provide a framework for testing the role of co-regulatory associations in eukaryotic transcriptional control...
  14. pmc Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 11:1365-74. 2001
    ..A hypothesis is proposed that the Ku homolog, together with the associated gene products, comprise a previously unrecognized prokaryotic system for repair of double-strand breaks in DNA...
  15. pmc Quoderat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences
    L M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 2:RESEARCH0051. 2001
    ..Computational predictions are critical for directing the experimental study of protein functions. Therefore it is paradoxical when an apparently erroneous computational prediction seems to be supported by experiment...
  16. ncbi request reprint Classification of the caspase-hemoglobinase fold: detection of new families and implications for the origin of the eukaryotic separins
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Proteins 46:355-67. 2002
    ..The acquisition of the caspase-hemoglobinase-fold domains by eukaryotes might have been critical in the evolution of important eukaryotic processes, such as mitosis and programmed cell death...
  17. pmc Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:5261-79. 2010
    ..The specificity of wybutosine hydroxylase/peroxidase probably relates to the structural similarity of the modified moiety to the ancestral amino acid substrate of this superfamily...
  18. pmc Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics
    Dapeng Zhang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 7:18. 2012
    ..Prior analysis revealed a striking diversity of nuclease and deaminase domains among the toxin modules. We systematically investigated polymorphic toxin systems using comparative genomics, sequence and structure analysis...
  19. pmc A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems
    Dapeng Zhang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 39:4532-52. 2011
    ....
  20. ncbi request reprint SWIM, a novel Zn-chelating domain present in bacteria, archaea and eukaryotes
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Trends Biochem Sci 27:384-6. 2002
    ..This domain was designated SWIM after SWI2/SNF2 and MuDR, and is predicted to have DNA-binding and protein-protein interaction functions in different contexts...
  21. ncbi request reprint Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Gene 335:73-88. 2004
    ....
  22. ncbi request reprint Diversification of catalytic activities and ligand interactions in the protein fold shared by the sugar isomerases, eIF2B, DeoR transcription factors, acyl-CoA transferases and methenyltetrahydrofolate synthetase
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Biol 356:823-42. 2006
    ....
  23. pmc Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily
    Raja Mazumder
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:5229-43. 2002
    ..Initially, this domain appears to have been involved in RNA processing and it appears to have been recruited to perform various other functions in later stages of evolution...
  24. pmc Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach
    E V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 11:240-52. 2001
    ....
  25. ncbi request reprint TRAM, a predicted RNA-binding domain, common to tRNA uracil methylation and adenine thiolation enzymes
    V Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    FEMS Microbiol Lett 197:215-21. 2001
    ..In addition, sequence analysis of the MiaB family enzymes showed that they share the predicted catalytic site with biotin and lipoate synthases and probably employ the same mechanism for sulfur insertion into their respective substrate...
  26. ncbi request reprint Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer
    C P Ponting
    National Center for Biotechnology Information National Library of Medicine, National Institutes of Health, Bldg 38A, Bethesda, MD, 20894, USA
    J Mol Biol 289:729-45. 1999
    ..A number of transfers of signalling domains from eukaryotes to bacteria were confidently identified, in contrast to only a single case of apparent transfer from eukaryotes to archaea...
  27. pmc Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics
    K S Makarova
    Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814-4799, USA
    Microbiol Mol Biol Rev 65:44-79. 2001
    ..In combination, these observations suggest that several different biological mechanisms contribute to the multiple DNA repair-dependent phenotypes of this organism...
  28. ncbi request reprint IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
    A A Schaffer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 15:1000-11. 1999
    ..One popular program for constructing a PSSM and comparing it with a database of sequences is Position-Specific Iterated BLAST (PSI-BLAST)...
  29. pmc Eukaryote-specific domains in translation initiation factors: implications for translation regulation and evolution of the translation system
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD 20894, USA
    Genome Res 10:1172-84. 2000
    ....
  30. pmc The RAGNYA fold: a novel fold with multiple topological variants found in functionally diverse nucleic acid, nucleotide and peptide-binding proteins
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 35:5658-71. 2007
    ..3) We also present evidence for a bacterial origin of the GYF domain and propose how this version of the fold might have been utilized in peptide interactions in the context of nucleoprotein complexes...
  31. ncbi request reprint The emergence of catalytic and structural diversity within the beta-clip fold
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Proteins 55:977-91. 2004
    ..We also describe how assembly of this fold from a basic three-stranded unit has been utilized to accommodate a variety of activities in its different versions...
  32. pmc The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 4:R64. 2003
    ..Here we use comparative genomics and sequence profile analysis to predict potential alternative functions of the Alba proteins...
  33. pmc The role of lineage-specific gene family expansion in the evolution of eukaryotes
    Olivier Lespinet
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 12:1048-59. 2002
    ..LSEs seem to be one of the principal means of adaptation and one of the most important sources of organizational and regulatory diversity in crown-group eukaryotes...
  34. ncbi request reprint Adaptations of the helix-grip fold for ligand binding and catalysis in the START domain superfamily
    L M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Proteins 43:134-44. 2001
    ..Thus, the START domain superfamily is a rare case of the adaptation of a protein fold with a conserved ligand-binding mode for both a broad variety of catalytic activities and noncatalytic regulatory functions. Proteins 2001;43:134-144...
  35. ncbi request reprint Apoptotic molecular machinery: vastly increased complexity in vertebrates revealed by genome comparisons
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Science 291:1279-84. 2001
    ..A considerable repertoire of apoptotic protein domains was detected in Actinomycetes and Cyanobacteria, which suggests a major contribution of horizontal gene transfer to the early evolution of apoptosis...
  36. pmc Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Struct Biol 3:1. 2003
    ..No evolutionary relationship between RDRP and other polymerases has been reported so far, hence the origin of this eukaryote-specific polymerase remains a mystery...
  37. doi request reprint Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Mol Biosyst 8:3142-65. 2012
    ..In some eukaryotes, certain components of the ter system appear to be recruited to function in conjunction with the ubiquitin system and calcium-signaling pathways...
  38. ncbi request reprint MEDS and PocR are novel domains with a predicted role in sensing simple hydrocarbon derivatives in prokaryotic signal transduction systems
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 21:2805-11. 2005
    ..Hence it is possible that these sigma factors, involved in aerial mycelium development and stress response in the actinomycetes, might be under the regulation of as yet uncharacterized small molecules...
  39. pmc Application of comparative genomics in the identification and analysis of novel families of membrane-associated receptors in bacteria
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Genomics 4:34. 2003
    ..So far, they are relatively rare in the prokaryotes, and are restricted to the well-characterized sensory rhodopsins of various phototropic prokaryotes...
  40. pmc Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Cell Cycle 8:1698-710. 2009
    ....
  41. pmc A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 380, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:482-96. 2002
    ....
  42. pmc CYSTM, a novel cysteine-rich transmembrane module with a role in stress tolerance across eukaryotes
    Thiago M Venancio
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 26:149-52. 2010
    ..Thus, CYSTM proteins are likely to be part of a novel cellular protective mechanism that is widely active in eukaryotes, including humans...
  43. ncbi request reprint Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Biol 360:204-12. 2006
    ..Thus, an "over-engineered" backup system in the form of distributed architecture is likely to be a major determinant of the "evolvability" of the gene expression in organisms faced with environmental diversity...
  44. pmc Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Biol Direct 6:38. 2011
    ..Comparative analysis of the Cas protein sequences and structures led to the classification of the CRISPR-Cas systems into three Types (I, II and III)...
  45. pmc Pathogenic roles of CD14, galectin-3, and OX40 during experimental cerebral malaria in mice
    Miranda S Oakley
    Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics and Evaluation Research, Food and Drug Administration, Bethesda, MD, USA
    PLoS ONE 4:e6793. 2009
    ..We find that OX40, a marker of both T cell activation and memory, is selectively upregulated in the brain during ECM and its distribution among CD4(+) and CD8(+) T cells accumulated in the brain vasculature is approximately equal...
  46. ncbi request reprint Evolutionary genomics of nucleo-cytoplasmic large DNA viruses
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Virus Res 117:156-84. 2006
    ....
  47. ncbi request reprint Gene duplication with displacement and rearrangement: origin of the bacterial replication protein PriB from the single-stranded DNA-binding protein Ssb
    Vladimir A Ponomarev
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    J Mol Microbiol Biotechnol 5:225-9. 2003
    ....
  48. ncbi request reprint HutC/FarR-like bacterial transcription factors of the GntR family contain a small molecule-binding domain of the chorismate lyase fold
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    FEMS Microbiol Lett 222:17-23. 2003
    ..An ancestral, generic small-molecule-binding domain appears to have given rise to the enzymatic and non-catalytic ligand-binding versions of the same fold under the influence of different selective pressures...
  49. pmc Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 41:7635-55. 2013
    ..These results open opportunities for the investigation of the biology of these systems and their use in biotechnology. ..
  50. ncbi request reprint The ASCH superfamily: novel domains with a fold related to the PUA domain and a potential role in RNA metabolism
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 22:257-63. 2006
    ....
  51. pmc Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
    Biol Direct 7:40. 2012
    ....
  52. pmc Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 39:9473-97. 2011
    ..These observations greatly expand the distribution of possible unidentified mutagenic processes catalyzed by nucleic acid deaminases...
  53. pmc Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 3:45. 2008
    ..Reviewers: This article was reviewed by M. Madan Babu and Andrei Osterman...
  54. pmc Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation
    A Maxwell Burroughs
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Struct Biol 162:205-18. 2008
    ..These features are likely to form a critical mechanical element of the fold required for catalysis. The results presented here could aid in new experiments to understand E2 catalysis...
  55. ncbi request reprint The HIRAN domain and recruitment of chromatin remodeling and repair activities to damaged DNA
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Cell Cycle 5:775-82. 2006
    ....
  56. pmc Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment
    Raja Jothi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Bioinformatics 8:173. 2007
    ..Here, proteins with similar profiles are inferred to be functionally related under the assumption that proteins involved in the same metabolic pathway or cellular system are likely to have been co-inherited during evolution...
  57. ncbi request reprint Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes
    A Maxwell Burroughs
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Biol 361:1003-34. 2006
    ..The newly identified relationships and functional predictions provided here are likely to aid the future exploration of the numerous poorly understood members of this large superfamily of enzymes...
  58. pmc Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 33:3994-4006. 2005
    ....
  59. ncbi request reprint Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Proteins 48:1-14. 2002
    ..Thus, substantial evolutionary diversification of protein domains occurred well before the modern version of the protein-dependent translation machinery was established, i.e., still in the RNA world...
  60. pmc Natural history of the E1-like superfamily: implication for adenylation, sulfur transfer, and ubiquitin conjugation
    A Maxwell Burroughs
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Proteins 75:895-910. 2009
    ..In light of this, we present evidence that in eukaryotes other E1-like enzymes such as Urm1 were independently recruited for Ubl conjugation, probably functioning without conventional E2-like enzymes...
  61. ncbi request reprint Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex
    Ben J Mans
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20892, USA
    Cell Cycle 3:1612-37. 2004
    ..A primitive NPC with approximately 20 proteins and a Src1p-Man1-like membrane protein with a DNA-tethering HEH domain are inferred to have been integral perinuclear components in the las common ancestor of modern eukaryotes...
  62. ncbi request reprint Estimating the prevalence and regulatory potential of the telomere looping effect in yeast transcription regulation
    M Madan Babu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Cell Cycle 5:2354-63. 2006
    ..Based on these observations, we also propose that genome-wide chromatin immunoprecipitation data might be useful to systematically uncover long-range chromatin looping effects in gene expression...
  63. ncbi request reprint The WWE domain: a common interaction module in protein ubiquitination and ADP ribosylation
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Trends Biochem Sci 26:273-5. 2001
    ..It was named the WWE domain after its most conserved residues and is predicted to mediate specific protein-protein interactions in ubiquitin and ADP-ribose conjugation systems...
  64. ncbi request reprint Differential action of natural selection on the N and C-terminal domains of 2'-5' oligoadenylate synthetases and the potential nuclease function of the C-terminal domain
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Biol 326:1449-61. 2003
    ....
  65. pmc Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Mol Biosyst 5:1636-60. 2009
    ..We present an evolutionary scenario for the multiple convergent origins of peptide ligases in various folds and clarify the bacterial origin of eukaryotic peptide-tagging enzymes of the TTL family...
  66. ncbi request reprint The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies
    V Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Proteins 56:795-807. 2004
    ..Thus, the SHS2 domain is an example of a simple module that has been adapted to perform an entire spectrum of functions ranging from protein-protein interactions to small-molecule recognition and catalysis...
  67. ncbi request reprint Fold prediction and evolutionary analysis of the POZ domain: structural and evolutionary relationship with the potassium channel tetramerization domain
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA
    J Mol Biol 285:1353-61. 1999
    ..Phylogenetic analysis of the POZ domains suggests that the common ancestor of the crown group eukaryotes already possessed this domain; POZ domains have undergone independent expansion in plants and in different animal lineages...
  68. pmc HPC2 and ubinuclein define a novel family of histone chaperones conserved throughout eukaryotes
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Mol Biosyst 5:269-75. 2009
    ..Hence, we propose that Hpc2p homologs are probably involved in recruitment of the ancient conserved histone-loading Hir-Asf1 complex to different lineage-specific chromatin reorganization processes...
  69. ncbi request reprint A novel superfamily of predicted cysteine proteases from eukaryotes, viruses and Chlamydia pneumoniae
    K S Makarova
    Dept of Pathology, F E Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814 4799, USA
    Trends Biochem Sci 25:50-2. 2000
  70. pmc The PRC-barrel: a widespread, conserved domain shared by photosynthetic reaction center subunits and proteins of RNA metabolism
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 3:RESEARCH0061. 2002
    ..It contains a distinct cytoplasmic beta-barrel domain whose fold has no close structural relationship to any other well known beta-barrel domain...
  71. pmc Differences in evolutionary pressure acting within highly conserved ortholog groups
    Teresa M Przytycka
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 8:208. 2008
    ..g. Proteobacteria or Firmicutes)...
  72. ncbi request reprint The bacterial replicative helicase DnaB evolved from a RecA duplication
    D D Leipe
    National Center for Biotechnology Information NCBI, National Library of Medicine, National Institutes of Health, Bethesda Maryland 20894 USA
    Genome Res 10:5-16. 2000
    ....
  73. ncbi request reprint Novel predicted peptidases with a potential role in the ubiquitin signaling pathway
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Cell Cycle 3:1440-50. 2004
    ..More specifically, genetic evidence implicates the WLM family in de-SUMOylation. If validated experimentally, the WLM family proteins will represent the first case of a Zincin-like metalloprotease involvement in Ub-signaling...
  74. ncbi request reprint Evolutionary dynamics of prokaryotic transcriptional regulatory networks
    M Madan Babu
    National Center for Biotechnology Information, National Institutes of Health, MD 20894, USA
    J Mol Biol 358:614-33. 2006
    ..The methods for biological network analysis introduced here can be applied generally to study other networks, and these predictions can be used to guide specific experiments...
  75. ncbi request reprint The CHASE domain: a predicted ligand-binding module in plant cytokinin receptors and other eukaryotic and bacterial receptors
    V Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Trends Biochem Sci 26:579-82. 2001
    ..The domain is predicted to bind diverse low molecular weight ligands, such as the cytokinin-like adenine derivatives or peptides, and mediate signal transduction through the respective receptors...
  76. pmc The GOLD domain, a novel protein module involved in Golgi function and secretion
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 3:research0023. 2002
    ..The p24 proteins form hetero-oligomeric complexes and are believed to function as receptors for specific secretory cargo...
  77. pmc BEN: a novel domain in chromatin factors and DNA viral proteins
    Saraswathi Abhiman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 24:458-61. 2008
    ..The presence of BEN domains in a poxviral early virosomal protein and in polydnaviral proteins also suggests a possible role for them in organization of viral DNA during replication or transcription...
  78. pmc Molecular cloning, expression, and structural prediction of deoxyhypusine hydroxylase: a HEAT-repeat-containing metalloenzyme
    Jong Hwan Park
    Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 103:51-6. 2006
    ..However, metal coordination sites composed of four strictly conserved histidine-glutamate sequences were identified, suggesting that DOHH enzymes have convergently evolved an iron-dependent hydroxylation mechanism...
  79. ncbi request reprint Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Int J Parasitol 38:1-31. 2008
    ..This evolutionary synthesis offers a robust scaffold for future investigation of transcription and chromatin structure in parasitic protists...
  80. pmc OST-HTH: a novel predicted RNA-binding domain
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 5:13. 2010
    ..Using sequence profile searches we identify a novel domain in these proteins that is widely conserved across eukaryotes and bacteria...
  81. ncbi request reprint Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events
    Y I Wolf
    National Center for Biotechnology Information NCBI, National Library of Medicine, National Institutes of Health NIH, Bethesda Maryland 20894, USA
    Genome Res 9:689-710. 1999
    ....
  82. ncbi request reprint Trends in protein evolution inferred from sequence and structure analysis
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Curr Opin Struct Biol 12:392-9. 2002
    ....
  83. ncbi request reprint The NYN domains: novel predicted RNAses with a PIN domain-like fold
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    RNA Biol 3:18-27. 2006
    ..Given the localization of Nedd4-BP1 to punctuate nuclear bodies, it is likely that they are parts of nuclear RNA-processing complexes that are dependent on monoubiquitination for their assembly...
  84. ncbi request reprint SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Microbiol Biotechnol 4:71-5. 2002
  85. ncbi request reprint Classification and evolution of P-loop GTPases and related ATPases
    Detlef D Leipe
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Biol 317:41-72. 2002
    ..In addition to the classification of previously known families of GTPases and related ATPases, we introduce several previously undetected families and describe new functional predictions...
  86. ncbi request reprint MOSC domains: ancient, predicted sulfur-carrier domains, present in diverse metal-sulfur cluster biosynthesis proteins including Molybdenum cofactor sulfurases
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    FEMS Microbiol Lett 207:55-61. 2002
    ..The identification of this domain may clarify the mechanism of biogenesis of various metallo-enzymes including Molybdenum cofactor-containing enzymes that are compromised in human type II xanthinuria...
  87. ncbi request reprint Evolution and classification of P-loop kinases and related proteins
    Detlef D Leipe
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Biol 333:781-815. 2003
    ..The results could serve as a framework for systematic experimental characterization of new biochemical and biological functions of kinases...
  88. pmc New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 4:R81. 2003
    ..The RelE toxin cleaves ribosome-associated transcripts, whereas another post-segregational cell killing toxin, ParE, functions as a gyrase inhibitor...
  89. ncbi request reprint STAND, a class of P-loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phyletic patterns, and evolution by horizontal gene transfer
    Detlef D Leipe
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Biol 343:1-28. 2004
    ..Transfer of genes for STAND NTPases from bacteria to eukaryotes on several occasions might have played a significant role in the evolution of eukaryotic signaling systems...
  90. pmc Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 4:R11. 2003
    ..Currently characterized members are known to hydrolyze D-gamma-glutamyl-meso-diaminopimelate or N-acetylmuramate-L-alanine linkages...
  91. pmc Comparative genomics and evolution of proteins involved in RNA metabolism
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Building 389, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:1427-64. 2002
    ..In addition to the reconstruction of the evolutionary history of RNA metabolism, this analysis produced numerous functional predictions, e.g. of previously undetected enzymes of RNA modification...
  92. ncbi request reprint Peptide-N-glycanases and DNA repair proteins, Xp-C/Rad4, are, respectively, active and inactivated enzymes sharing a common transglutaminase fold
    V Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Hum Mol Genet 10:1627-30. 2001
    ..The RAD4/Xp-C proteins, along with other inactive transglutaminase-fold proteins, represent a case of functional re-assignment of an ancient domain following the loss of the ancestral enzymatic activity...
  93. pmc A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins
    M Madan Babu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Bacteriol 188:2761-73. 2006
    ..The website, along with additional information on the biosynthetic pathway, statistics on predicted lipoproteins, and related figures, is available at http://www.mrc-lmb.cam.ac.uk/genomes/dolop/...
  94. pmc An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin
    Mitsuoki Kawano
    Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Microbiol 64:738-54. 2007
    ..We suggest that SymE promotion of RNA cleavage may be important for the recycling of RNAs damaged under SOS-inducing conditions...
  95. ncbi request reprint Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Curr Opin Chem Biol 7:12-20. 2003
    ..The biochemical plasticity of a fold seems to hinge on the presence of a generic, symmetrical substrate-binding pocket as opposed to highly specialized binding sites...
  96. ncbi request reprint DOMON: an ancient extracellular domain in dopamine beta-monooxygenase and other proteins
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD 20894, USA
    Trends Biochem Sci 26:524-6. 2001
    ..This domain was predicted to adopt an all-beta fold with seven or eight strands and might function as a module mediating a range of extracellular adhesive interactions...
  97. pmc Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels
    Asba Tasneem
    Beckman Institute, University of Illinois at Urbana Champaign, 405 N Mathews Avenue, Urbana, IL 61801, USA
    Genome Biol 6:R4. 2005
    ..They play a central role in fast synaptic signaling in animal nervous systems and so far have not been found outside of the Metazoa...
  98. pmc Phosphoesterase domains associated with DNA polymerases of diverse origins
    L Aravind
    Department of Biology, Texas A and M University, College Station, TX 77843, USA
    Nucleic Acids Res 26:3746-52. 1998
    ..In these cases, the pyrophosphate may be hydrolyzed by a stand-alone phosphatase, and candidates for such a role were identified among bacterial PHP superfamily members...
  99. pmc Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces
    Oded Beja
    Monterey Bay Aquarium Research Institute, Moss Landing, California 95039, USA
    Appl Environ Microbiol 68:335-45. 2002
    ..Our results also demonstrate that genomic approaches can provide high-resolution information relevant to microbial population genetics, ecology, and evolution, even for microbes that have not yet been cultivated...
  100. pmc A bipolar DNA helicase gene, herA, clusters with rad50, mre11 and nurA genes in thermophilic archaea
    F Constantinesco
    Institut de Genetique et Microbiologie, UMR CNRS no8621, Batiment 409, Universite Paris Sud, 91405 Orsay Cedex, France
    Nucleic Acids Res 32:1439-47. 2004
    ....
  101. ncbi request reprint Complete genome sequence of the apicomplexan, Cryptosporidium parvum
    Mitchell S Abrahamsen
    Department of Veterinary and Biomedical Science, College of Veterinary Medicine, University of Minnesota, St Paul, MN 55108, USA
    Science 304:441-5. 2004
    ..Elucidation of the core metabolism, including enzymes with high similarities to bacterial and plant counterparts, opens new avenues for drug development...