L Aravind

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi 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. ncbi 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 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. ncbi 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. ncbi 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 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. ncbi 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
  8. ncbi 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
  9. ncbi 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. ncbi 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

Detail Information

Publications107 found, 100 shown here

  1. ncbi 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
    ..Several of these Ub-like proteins and the associated protein families are likely to function together in signaling systems just as in eukaryotes...
  2. ncbi 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 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. ncbi 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. ncbi 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 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. ncbi 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
    ....
  8. ncbi 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...
  9. ncbi 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. ncbi 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. ncbi 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. ncbi 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...
  13. ncbi 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
    ....
  14. ncbi 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...
  15. ncbi 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...
  16. ncbi 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. ncbi 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. ncbi 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. ncbi 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
    ....
  20. ncbi 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...
  21. ncbi 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
    ....
  22. ncbi 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...
  23. ncbi 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
    ..Also, it is considerably faster when run with a large database of PSSMs than is BLAST or PSI-BLAST when run against the complete non-redundant protein database...
  24. ncbi 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 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
    ....
  26. ncbi 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...
  27. ncbi 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...
  28. ncbi 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...
  29. ncbi 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...
  30. ncbi 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 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...
  32. ncbi 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...
  33. ncbi 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 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...
  35. ncbi 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
    ....
  36. ncbi 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...
  37. ncbi 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
    ....
  38. ncbi 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...
  39. ncbi 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)...
  40. ncbi 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...
  41. ncbi 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. ncbi 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
    ....
  43. ncbi 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
    ....
  44. ncbi 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. CONTACT: ...
  45. ncbi 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online...
  46. ncbi 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...
  47. ncbi 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...
  48. ncbi 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
    ....
  49. ncbi 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...
  50. ncbi 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...
  51. ncbi 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...
  52. ncbi 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...
  53. ncbi 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
    ....
  54. ncbi 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...
  55. ncbi 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...
  56. ncbi 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 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...
  58. ncbi 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...
  59. ncbi 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
    ....
  60. ncbi 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...
  61. ncbi 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...
  62. ncbi 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...
  63. ncbi 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
    ....
  64. ncbi 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...
  65. ncbi 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...
  66. ncbi 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...
  67. ncbi 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
  68. ncbi 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)...
  69. ncbi 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
    ....
  70. ncbi 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...
  71. ncbi 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...
  72. ncbi 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
    ....
  73. ncbi 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...
  74. ncbi 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...
  75. ncbi 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...
  76. ncbi 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...
  77. ncbi 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...
  78. ncbi 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...
  79. ncbi 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...
  80. ncbi 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
    ....
  81. ncbi 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
  82. ncbi 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 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...
  84. ncbi 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...
  85. ncbi 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...
  86. ncbi 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...
  87. ncbi 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. ncbi 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...
  89. ncbi 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...
  90. ncbi 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...
  91. ncbi 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/...
  92. ncbi 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...
  93. ncbi 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...
  94. ncbi A bipolar DNA helicase gene, herA, clusters with rad50, mre11 and nurA genes in thermophilic archaea
    F Constantinesco
    , UMR CNRS no8621, , , 91405 Orsay Cedex, France
    Nucleic Acids Res 32:1439-47. 2004
    ....
  95. ncbi Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome
    Rati Verma
    Department of Biology and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
    Science 298:611-5. 2002
    ..Our findings reveal an unexpected coupling between substrate deubiquitination and degradation and suggest a unifying rationale for the presence of the lid in eukaryotic proteasomes...
  96. ncbi 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...
  97. ncbi Human and mouse homologs of Escherichia coli DinB (DNA polymerase IV), members of the UmuC/DinB superfamily
    V L Gerlach
    Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75235 9072, USA
    Proc Natl Acad Sci U S A 96:11922-7. 1999
    ..In a phylogenetic tree, the mouse and human DinB1 proteins specifically group with E. coli DinB, suggesting a mitochondrial origin for these genes. The human DINB1 gene is localized to chromosome 5q13 and is widely expressed...
  98. ncbi 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...
  99. ncbi 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
    ..The phyletic patterns and phylogenetic relationships suggest the possibility that the metazoan receptors emerged through an early lateral transfer from a prokaryotic source, before the divergence of extant metazoan lineages...
  100. ncbi YjeQ, an essential, conserved, uncharacterized protein from Escherichia coli, is an unusual GTPase with circularly permuted G-motifs and marked burst kinetics
    Denis M Daigle
    Antimicrobial Research Centre, Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
    Biochemistry 41:11109-17. 2002
    ..8 h(-)(1)). In summary, E. coli YjeQ is an unusual, circularly permuted P-loop-containing GTPase, which catalyzes GTP hydrolysis at a rate 45 000 times greater than that of turnover...
  101. ncbi Cloning the human and mouse MMS19 genes and functional complementation of a yeast mms19 deletion mutant
    L Queimado
    Laboratory of Molecular Pathology, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390 9072, USA
    Nucleic Acids Res 29:1884-91. 2001
    ..Both the mouse and human genes are ubiquitously expressed as multiple transcripts, some of which appear to derive from alternative splicing. The ratio of different transcripts varies in several different tissue types...