L Aravind

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 8:15. 2013
  2. 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
  3. pmc Novel autoproteolytic and DNA-damage sensing components in the bacterial SOS response and oxidized methylcytosine-induced eukaryotic DNA demethylation systems
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 8:20. 2013
  4. pmc Two novel PIWI families: roles in inter-genomic conflicts in bacteria and Mediator-dependent modulation of transcription in eukaryotes
    A Maxwell Burroughs
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 8:13. 2013
  5. pmc Gene flow and biological conflict systems in the origin and evolution of eukaryotes
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD, USA
    Front Cell Infect Microbiol 2:89. 2012
  6. pmc ALOG domains: provenance of plant homeotic and developmental regulators from the DNA-binding domain of a novel class of DIRS1-type retroposons
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 7:39. 2012
  7. 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
  8. pmc Female Anopheles gambiae antennae: increased transcript accumulation of the mosquito-specific odorant-binding-protein OBP2
    Seth A Hoffman
    Sanaria Inc, 9800 Medical Center Dr, Rockville, MD 20850, USA
    Parasit Vectors 5:27. 2012
  9. doi request reprint Identification of novel components of NAD-utilizing metabolic pathways and prediction of their biochemical functions
    Robson Francisco de Souza
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Mol Biosyst 8:1661-77. 2012
  10. pmc The HARE-HTH and associated domains: novel modules in the coordination of epigenetic DNA and protein modifications
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Cell Cycle 11:119-31. 2012

Detail Information

Publications141 found, 100 shown here

  1. pmc Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 8:15. 2013
    ..Typically, toxins evolve rapidly hampering the identification of these proteins by sequence analysis. Here we analyze an unexpectedly widespread superfamily of toxin domains most of which possess RNase activity...
  2. 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
    ....
  3. pmc Novel autoproteolytic and DNA-damage sensing components in the bacterial SOS response and oxidized methylcytosine-induced eukaryotic DNA demethylation systems
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 8:20. 2013
    ..Hence, its autoproteolytic activity might help it act as a switch that recruits DNA repair enzymes to remove these oxidized methylcytosine species as part of the DNA demethylation pathway downstream of the TET enzymes...
  4. pmc Two novel PIWI families: roles in inter-genomic conflicts in bacteria and Mediator-dependent modulation of transcription in eukaryotes
    A Maxwell Burroughs
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 8:13. 2013
    ..It binds a guide strand which helps it target complementary nucleic strands...
  5. pmc Gene flow and biological conflict systems in the origin and evolution of eukaryotes
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD, USA
    Front Cell Infect Microbiol 2:89. 2012
    ....
  6. pmc ALOG domains: provenance of plant homeotic and developmental regulators from the DNA-binding domain of a novel class of DIRS1-type retroposons
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 7:39. 2012
    ..Hence, they add to the growing evidence for derivation of DNA-binding domains of eukaryotic specific TFs from mobile and selfish elements...
  7. 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...
  8. pmc Female Anopheles gambiae antennae: increased transcript accumulation of the mosquito-specific odorant-binding-protein OBP2
    Seth A Hoffman
    Sanaria Inc, 9800 Medical Center Dr, Rockville, MD 20850, USA
    Parasit Vectors 5:27. 2012
    ..Understanding olfactory function could lead to development of control strategies based on repelling parasite-carrying mosquitoes or attracting them into a fatal trap...
  9. doi request reprint Identification of novel components of NAD-utilizing metabolic pathways and prediction of their biochemical functions
    Robson Francisco de Souza
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Mol Biosyst 8:1661-77. 2012
    ..We use the data derived from this analysis to understand the origin and early evolutionary trajectories of key NAD-utilizing enzymes and present targets for future biochemical investigations...
  10. pmc The HARE-HTH and associated domains: novel modules in the coordination of epigenetic DNA and protein modifications
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Cell Cycle 11:119-31. 2012
    ....
  11. pmc Reconstructing prokaryotic transcriptional regulatory networks: lessons from actinobacteria
    Thiago M Venancio
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Biol 8:29. 2009
    ..Recent studies, including one in BMC Systems Biology, address this problem in the relatively underexplored actinobacteria clade, which includes major pathogenic and economically relevant taxa...
  12. 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...
  13. pmc Reconstructing the ubiquitin network: cross-talk with other systems and identification of novel functions
    Thiago M Venancio
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    Genome Biol 10:R33. 2009
    ..While several studies have concentrated on structure-function relationships and evolution of individual components of the Ub-system, a study of the system as a whole is largely lacking...
  14. 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...
  15. 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...
  16. 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...
  17. 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)...
  18. pmc A new family of polymerases related to superfamily A DNA polymerases and T7-like DNA-dependent RNA polymerases
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 3:39. 2008
    ..They also provide evidence that enigmatic DNA viruses, such as Sputnik, might have emerged from mobile elements coding these polymerases...
  19. pmc The Anabaena sensory rhodopsin transducer defines a novel superfamily of prokaryotic small-molecule binding domains
    Robson F de Souza
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 4:25; discussion 25. 2009
    ..The analysis of this superfamily also provides new data to investigate the evolution of carbohydrate binding modes in beta-sandwich domains with very different topologies...
  20. 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...
  21. pmc Presence of a classical RRM-fold palm domain in Thg1-type 3'- 5'nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 5:43. 2010
    ....
  22. pmc Novel eukaryotic enzymes modifying cell-surface biopolymers
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 5:1. 2010
    ..Using comparative genomics and sequence profile analysis we identify several novel enzymes that could be potentially involved in the modification of cell-surface glycans or glycoproteins...
  23. 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...
  24. pmc Ancient conserved domains shared by animal soluble guanylyl cyclases and bacterial signaling proteins
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Genomics 4:5. 2003
    ..Soluble guanylyl cyclases (SGCs) are dimeric enzymes that transduce signals downstream of nitric oxide (NO) in animals. They sense NO by means of a heme moiety that is bound to their N-terminal extensions...
  25. 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)...
  26. 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...
  27. 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...
  28. ncbi request reprint The many faces of the helix-turn-helix domain: transcription regulation and beyond
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 5N50, Bethesda, MD 20894, USA
    FEMS Microbiol Rev 29:231-62. 2005
    ..This differential relationship of their basal and specific transcriptional machinery poses an apparent conundrum regarding the origins of their transcription apparatus...
  29. 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...
  30. 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...
  31. ncbi request reprint Plasmodium biology: genomic gleanings
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Cell 115:771-85. 2003
    ..Plasmodium possesses many cell surface molecules with "animal-like" adhesion modules. Potential genetic footprints of the ancestral eukaryotic algal precursor of the apicoplast are also detectable in its genome...
  32. ncbi request reprint Intraproteomic networks: new forays into predicting interaction partners
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, 20894, USA
    Genome Res 12:1156-8. 2002
  33. 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...
  34. ncbi request reprint Provenance of SET-domain histone methyltransferases through duplication of a simple structural unit
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Cell Cycle 2:369-76. 2003
    ..Thus, the SET domain provides a model for the innovation of a complex enzymatic fold through the duplications of a structurally simple non-enzymatic unit...
  35. ncbi request reprint Evolutionary connections between bacterial and eukaryotic signaling systems: a genomic perspective
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Curr Opin Microbiol 6:490-7. 2003
    ....
  36. 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...
  37. pmc Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 3:RESEARCH0012. 2002
    ....
  38. 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...
  39. pmc Apprehending multicellularity: regulatory networks, genomics, and evolution
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Birth Defects Res C Embryo Today 87:143-64. 2009
    ....
  40. 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
    ....
  41. pmc Predicted class-I aminoacyl tRNA synthetase-like proteins in non-ribosomal peptide synthesis
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 5:48. 2010
    ..The least studied of these systems are those utilizing tRNAs or aminoacyl-tRNA synthetases (AAtRS) in non-ribosomal peptide ligation...
  42. pmc SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 28:3417-32. 2000
    ..This analysis resulted in the prediction of numerous previously unnoticed nucleases, some of which are likely to be new restriction enzymes...
  43. 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
    ....
  44. ncbi request reprint Origin of multicellular eukaryotes - insights from proteome comparisons
    L Aravind
    Department of Biology, Texas A and M University, College Station, 77843, USA
    Curr Opin Genet Dev 9:688-94. 1999
    ..Similar comparisons with the available sequence data from the plant Arabidopsis thaliana produce consistent results. These observations have provided useful insights regarding the origin of multicellular organisms...
  45. 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...
  46. pmc DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 27:1609-18. 1999
    ....
  47. 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...
  48. pmc Domain architectures of the Scm3p protein provide insights into centromere function and evolution
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
    Cell Cycle 6:2511-5. 2007
    ..Hence, the C-terminal DNA binding motifs found in large Scm3p proteins may, along with CenH3, serve as a key epigenetic signal by recognizing and accommodating the lineage-specific diversity of centromere DNA in course of evolution...
  49. 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...
  50. ncbi request reprint THUMP--a predicted RNA-binding domain shared by 4-thiouridine, pseudouridine synthases and RNA methylases
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Trends Biochem Sci 26:215-7. 2001
    ..We predict that this domain is an RNA-binding domain that adopts an alpha/beta fold similar to that found in the C-terminal domain of translation initiation factor 3 and ribosomal protein S8...
  51. 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...
  52. 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...
  53. 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...
  54. 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...
  55. 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
    ....
  56. 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...
  57. 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...
  58. 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...
  59. 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...
  60. 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...
  61. 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
    ....
  62. 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...
  63. 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...
  64. 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...
  65. 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
    ....
  66. 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)...
  67. 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...
  68. 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
    ....
  69. 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...
  70. 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
    ....
  71. 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
    ....
  72. 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...
  73. ncbi request reprint Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1
    Gregory A Cope
    Department of Biology, California Institute of Technology Caltech, Pasadena, CA 91125, USA
    Science 298:608-11. 2002
    ..We propose that JAMM isopeptidases play important roles in a variety of physiological pathways...
  74. 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...
  75. 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...
  76. 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
  77. 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...
  78. 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...
  79. 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
    ....
  80. 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...
  81. 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...
  82. 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...
  83. 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...
  84. 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...
  85. 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...
  86. pmc Molecular correlates of experimental cerebral malaria detectable in whole blood
    Miranda S Oakley
    Division of Bacterial, Parasitic, and Allergenic Products Center for Biologics Evaluation and Research, Food and Drug Administration, Rockville, Maryland, USA
    Infect Immun 79:1244-53. 2011
    ..A subset of these mediators of ECM warrant validation in P. falciparum-infected young African children as diagnostic markers of CM...
  87. 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...
  88. 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
    ....
  89. 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
    ....
  90. 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...
  91. 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...
  92. 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...
  93. 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
    ....
  94. 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...
  95. 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...
  96. 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...
  97. 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
    ....
  98. 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...
  99. 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
    ....
  100. 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...
  101. 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...