K S Makarova

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park
    Mircea Podar
    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
    Biol Direct 8:9. 2013
  2. pmc Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer
    Yuri I Wolf
    National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 7:46. 2012
  3. 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
  4. pmc A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 1:7. 2006
  5. pmc Francisella RNA polymerase contains a heterodimer of non-identical α subunits
    Damir Mukhamedyarov
    Department of Biochemistry and Molecular Biology and Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
    BMC Mol Biol 12:50. 2011
  6. pmc The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes
    Kira S Makarova
    National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, Maryland 20894, USA
    Biol Direct 7:7. 2012
  7. pmc Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1
    Jimmy H Saw
    Department of Microbiology, University of Hawai i, 2538 The Mall, Honolulu, HI 96822, USA
    Genome Biol 9:R161. 2008
  8. pmc A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans
    Mircea Podar
    Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA
    Genome Biol 9:R158. 2008
  9. 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
  10. pmc The prokaryotic V4R domain is the likely ancestor of a key component of the eukaryotic vesicle transport system
    Mircea Podar
    Biosciences Division and the Bioenergy Science Center, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA
    Biol Direct 3:2. 2008

Detail Information

Publications74

  1. pmc Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park
    Mircea Podar
    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
    Biol Direct 8:9. 2013
    ..A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes...
  2. pmc Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer
    Yuri I Wolf
    National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 7:46. 2012
    ..Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs). Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea...
  3. 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
    ....
  4. pmc A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 1:7. 2006
    ..However, the proximity of CRISPR and cas genes strongly suggests that they have related functions which is hard to reconcile with the repair hypothesis...
  5. pmc Francisella RNA polymerase contains a heterodimer of non-identical α subunits
    Damir Mukhamedyarov
    Department of Biochemistry and Molecular Biology and Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
    BMC Mol Biol 12:50. 2011
    ..Based on an observation that both α1 and α2 are incorporated into Francisella RNAP, Charity et al. (2007) previously suggested that up to four different species of RNAP core enzyme might form in the same Francisella cell...
  6. pmc The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes
    Kira S Makarova
    National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, Maryland 20894, USA
    Biol Direct 7:7. 2012
    ..Here we present the results of in-depth phylogenomic analysis of RecJ homologs in archaea...
  7. pmc Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1
    Jimmy H Saw
    Department of Microbiology, University of Hawai i, 2538 The Mall, Honolulu, HI 96822, USA
    Genome Biol 9:R161. 2008
    ..The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life...
  8. pmc A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans
    Mircea Podar
    Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA
    Genome Biol 9:R158. 2008
    ..Little is known about the mechanisms that enable this relationship...
  9. 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)...
  10. pmc The prokaryotic V4R domain is the likely ancestor of a key component of the eukaryotic vesicle transport system
    Mircea Podar
    Biosciences Division and the Bioenergy Science Center, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA
    Biol Direct 3:2. 2008
    ..This suggests, for the first time, a prokaryotic origin for one of the key eukaryotic trafficking proteins...
  11. pmc A highly conserved family of inactivated archaeal B family DNA polymerases
    Igor B Rogozin
    National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda, MD, 20894, USA
    Biol Direct 3:32. 2008
    ..The inactivated derivative of the archaeal DNA polymerase could form a complex with the active paralog and play a structural role in DNA replication...
  12. pmc Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and "Korarchaeota"
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 2:38. 2007
    ..These findings suggest that all 12 core subunits of eukaryotic RNAPs were already present in the last common ancestor of the extant archaea...
  13. pmc Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia
    Shaobin Hou
    Advance Studies in Genomics, Proteomics and Bioinformatics, College of Natural Sciences, University of Hawaii, Keller Hall 319, Honolulu, Hawaii, 96822, USA
    Biol Direct 3:26. 2008
    ..Similar organisms were independently isolated from geothermal systems in Italy and Russia...
  14. pmc Two new families of the FtsZ-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea
    Kira S Makarova
    National Center for Biotechnology Information, NLM, National Institutes of Health Bethesda, Maryland 20894, USA
    Biol Direct 5:33. 2010
    ....
  15. pmc Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol epsilon and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors
    Tahir H Tahirov
    Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198 7696, USA
    Biol Direct 4:11. 2009
    ..However, the details of the evolutionary relationships between DNA polymerases of archaea and eukaryotes remain unresolved...
  16. pmc Evolutionary primacy of sodium bioenergetics
    Armen Y Mulkidjanian
    School of Physics, University of Osnabruck, D 49069 Osnabruck, Germany
    Biol Direct 3:13. 2008
    ..The prevalent proton-dependent ATPases are generally viewed as the primary form of the enzyme whereas the sodium-translocating ATPases of some prokaryotes are usually construed as an exotic adaptation to survival in extreme environments...
  17. pmc Identification of an ortholog of the eukaryotic RNA polymerase III subunit RPC34 in Crenarchaeota and Thaumarchaeota suggests specialization of RNA polymerases for coding and non-coding RNAs in Archaea
    Fabian Blombach
    Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
    Biol Direct 4:39. 2009
    ..These findings suggest that functional separation of RNA polymerases for protein-coding genes and non-coding RNAs might predate the origin of the Eukaryotes...
  18. pmc Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance
    Marina V Omelchenko
    Department of Pathology, F E Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814 4799, USA
    BMC Evol Biol 5:57. 2005
    ..radiodurans is a mesophile, which is highly radiation- and desiccation-resistant. Here we present an in-depth comparison of the genomes of these two related but differently adapted bacteria...
  19. ncbi request reprint Filling a gap in the central metabolism of archaea: prediction of a novel aconitase by comparative-genomic analysis
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
    FEMS Microbiol Lett 227:17-23. 2003
    ..The prediction of aconitase X completes the TCA cycle for Methanothermobacter thermoautotrophicus and Archaeoglobus fulgidus and suggests that most archaea have a full TCA cycle...
  20. pmc Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements
    Kira S Makarova
    National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, Maryland 20894, USA
    Biol Direct 4:29. 2009
    ..Many prokaryotes also encode homologs of Argonaute-PIWI proteins but their functions remain unknown...
  21. pmc Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes
    Kira S Makarova
    National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, Maryland 20894, USA
    Biol Direct 4:19. 2009
    ....
  22. pmc Evolutionary genomics of lactic acid bacteria
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Bacteriol 189:1199-208. 2007
  23. pmc Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    PLoS ONE 2:e955. 2007
    ....
  24. ncbi request reprint Specific expansion of protein families in the radioresistant bacterium Deinococcus radiodurans
    K S Makarova
    Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
    Genetica 108:25-34. 2000
    ..Such unique proteins are good targets for knock-out and gene expression studies, which are aimed to shed light on the unusual features of this interesting bacterium...
  25. pmc Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 2:33. 2007
    ..One of the practical strategies involves construction of refined COGs for phylogenetically compact subsets of genomes...
  26. 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
    ....
  27. pmc Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics
    K S Makarova
    Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814-4799, USA
    Microbiol Mol Biol Rev 65:44-79. 2001
    ..In combination, these observations suggest that several different biological mechanisms contribute to the multiple DNA repair-dependent phenotypes of this organism...
  28. 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...
  29. pmc Lineage-specific gene expansions in bacterial and archaeal genomes
    I K Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 11:555-65. 2001
    ..The topology of the resulting graph seems to reflect a combined effect of common ancestry, horizontal transfer, and lineage-specific gene loss...
  30. pmc Conservation of the binding site for the arginine repressor in all bacterial lineages
    K S Makarova
    Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
    Genome Biol 2:RESEARCH0013. 2001
    ..Here, we apply the comparative genomic approach to the prediction of the ArgR-binding sites in all completely sequenced bacterial genomes...
  31. pmc Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 33:4626-38. 2005
    ..The results of this study demonstrate a major increase in the level of gene paralogy as a hallmark of the early evolution of eukaryotes...
  32. 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
    ....
  33. pmc The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 4:R19. 2003
    ....
  34. pmc Connected gene neighborhoods in prokaryotic genomes
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:2212-23. 2002
    ..Gene neighborhoods appear to evolve via complex rearrangement, with different combinations of genes from a neighborhood fixed in different lineages...
  35. ncbi request reprint Horizontal gene transfer in prokaryotes: quantification and classification
    E V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Annu Rev Microbiol 55:709-42. 2001
    ....
  36. pmc Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins
    K S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 2:RESEARCH 0033. 2001
    ..Here we analyze all such cases and attempt to reconstruct the evolutionary history of these ribosomal proteins...
  37. ncbi request reprint Gene conversions in genes encoding outer-membrane proteins in H. pylori and C. pneumoniae
    I K Jordan
    National Center for Biotechnology Information, National Institutes of Health, Building 38A Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Trends Genet 17:7-10. 2001
    ..pylori strains and two C. pneumoniae strains, we identify multiple independent conversions among these genes. Such recombination events might provide a selective advantage for these bacterial pathogens...
  38. pmc The deep archaeal roots of eukaryotes
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Mol Biol Evol 25:1619-30. 2008
    ..Thus, the archaeal genes in eukaryotes appear to descend from a distinct, ancient, and otherwise uncharacterized archaeal lineage that acquired some euryarchaeal and crenarchaeal genes via early horizontal gene transfer...
  39. 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
  40. ncbi request reprint Evolution of eukaryotic gene repertoire and gene structure: discovering the unexpected dynamics of genome evolution
    I B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Cold Spring Harb Symp Quant Biol 68:293-301. 2003
  41. pmc Congruent evolution of different classes of non-coding DNA in prokaryotic genomes
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:4264-71. 2002
    ..In contrast, the gene set is optimized for the particular environmental niche of the given microbe, which results in the lack of correlation between the gene number and the characteristics of non-coding regions...
  42. ncbi request reprint Accumulation of Mn(II) in Deinococcus radiodurans facilitates gamma-radiation resistance
    M J Daly
    Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
    Science 306:1025-8. 2004
    ..In contrast, Shewanella oneidensis and Pseudomonas putida have high iron but low intracellular manganese concentrations and are very sensitive. We propose that Mn(II) accumulation facilitates recovery from radiation injury...
  43. 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...
  44. ncbi request reprint The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    Bioinformatics 22:2581-4. 2006
    ..Thus, the HicAB module is predicted to be a novel TAS whose mechanism involves RNA-binding and, possibly, cleavage...
  45. pmc Comparative genomics of Archaea: how much have we learned in six years, and what's next?
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 4:115. 2003
    ..The majority of archaeal genes have not been experimentally characterized, but novel functional pathways have been predicted...
  46. ncbi request reprint Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 22:1297-301. 2006
    ....
  47. pmc Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ
    Marina V Omelchenko
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 4:R55. 2003
    ....
  48. pmc A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 5:R7. 2004
    ....
  49. ncbi request reprint Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes
    Igor B Rogozin
    NCBI NLM NIH, 8600 Rockville Pike, Bldg 38A, Bethesda, MD 20894, USA
    Brief Bioinform 5:131-49. 2004
    ..In this review, we discuss various computational approaches for identification of conserved gene strings and construction of local alignments of gene orders in prokaryotic genomes...
  50. ncbi request reprint How radiation kills cells: survival of Deinococcus radiodurans and Shewanella oneidensis under oxidative stress
    Debabrota Ghosal
    Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
    FEMS Microbiol Rev 29:361-75. 2005
    ....
  51. pmc Abundance of type I toxin-antitoxin systems in bacteria: searches for new candidates and discovery of novel families
    Elizabeth M Fozo
    Eunice Kennedy Shriver National Institute of Child Health and Human Development and National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:3743-59. 2010
    ..Our results suggest that type I toxin-antitoxin modules are much more widely distributed among bacteria than previously appreciated...
  52. pmc Evolution of diverse cell division and vesicle formation systems in Archaea
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Nat Rev Microbiol 8:731-41. 2010
    ..By contrast, eukaryotes seem to have inherited all three ancestral systems...
  53. ncbi request reprint Potential genomic determinants of hyperthermophily
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Trends Genet 19:172-6. 2003
    ....
  54. 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
    ....
  55. ncbi request reprint The Zn-peptidase superfamily: functional convergence after evolutionary divergence
    K S Makarova
    National Center for Biotechnology Information National Library of Medicine, National Institutes of Health, Bethesda, MA 20894, USA
    J Mol Biol 292:11-7. 1999
    ..This is a result of functional convergence that apparently occurred after the divergence of the two families...
  56. pmc ATGL has a key role in lipid droplet/adiposome degradation in mammalian cells
    Elena Smirnova
    Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
    EMBO Rep 7:106-13. 2006
    ..Depletion of ATGL by RNA interference leads to a significant increase in the size of LDs. These results show that ATGL has an important role in LD/adiposome turnover in mammalian cells...
  57. ncbi request reprint Evolutionary and functional genomics of the Archaea
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Curr Opin Microbiol 8:586-94. 2005
    ....
  58. ncbi request reprint Recurrent intragenomic recombination leading to sequence homogenization during the evolution of the lipoyl-binding domain
    Marina V Omelchenko
    Department of Pathology, F E Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814 4799, USA
    FEMS Microbiol Lett 209:255-60. 2002
    ..This appears to be the first case of sequence homogenization at the level of an individual domain in prokaryotes...
  59. pmc Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome
    Alexis Dufresne
    Station Biologique, Unité Mixte de Recherche 7127, Centre National de la Recherche Scientifique et Université Paris 6, BP74, 29682 Roscoff Cedex, France
    Proc Natl Acad Sci U S A 100:10020-5. 2003
    ..Because of its remarkable compactness, the genome of P. marinus SS120 might approximate the minimal gene complement of a photosynthetic organism...
  60. pmc A korarchaeal genome reveals insights into the evolution of the Archaea
    James G Elkins
    Lehrstuhl fur Mikrobiologie und Archaeenzentrum, Universitat Regensburg, D 93053 Regensburg, Germany
    Proc Natl Acad Sci U S A 105:8102-7. 2008
    ..In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form...
  61. pmc Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation
    Yongqing Liu
    Environmental Sciences and Life Sciences Divisions, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Proc Natl Acad Sci U S A 100:4191-6. 2003
    ..Components of this network include a predicted distinct ATP-dependent DNA ligase and metabolic pathway switching that could prevent additional genomic damage elicited by metabolism-induced free radicals...
  62. pmc The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens
    Alexei I Slesarev
    Fidelity Systems, Gaithersburg, MD 20879, USA
    Proc Natl Acad Sci U S A 99:4644-9. 2002
    ..Also, M. kandleri appears to have fewer genes acquired via lateral transfer than other archaea. These features might reflect the extreme habitat of this organism...
  63. pmc Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae
    Eugene Kolker
    BIATECH, 19310 North Creek Parkway, Suite 115, Bothell, WA 98011, USA
    Nucleic Acids Res 32:2353-61. 2004
    ....
  64. pmc Identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism
    Thijs J G Ettema
    Laboratory of Microbiology, Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
    J Bacteriol 186:7754-62. 2004
    ..The newly identified atPEPC, with its distinct properties, constitutes yet another example of the versatility of the enzymes of the central carbon metabolic pathways in the archaeal domain...
  65. pmc Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy
    Shaobin Hou
    Department of Microbiology, University of Hawaii, Snyder Hall 111, 2538 The Mall, Honolulu, HI 96822, USA
    Proc Natl Acad Sci U S A 101:18036-41. 2004
    ..In summary, the I. loihiensis genome reveals an integrated mechanism of metabolic adaptation to the constantly changing deep-sea hydrothermal ecosystem...
  66. pmc Role of hypermutability in the evolution of the genus Oenococcus
    Angela M Marcobal
    Department of Viticulture and Enology, University of California, One Shields Ave, Davis, CA 95616, USA
    J Bacteriol 190:564-70. 2008
    ..The hypermutable status of the genus Oenococcus explains the observed high level of allelic polymorphism among known O. oeni isolates and likely contributed to the unique adaptation of this genus to acidic and alcoholic environments...
  67. ncbi request reprint Dimeric dUTPases, HisE, and MazG belong to a new superfamily of all-alpha NTP pyrophosphohydrolases with potential "house-cleaning" functions
    Olga V Moroz
    York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK
    J Mol Biol 347:243-55. 2005
    ..We outline probable tertiary and quaternary structures of the all-alpha NTP pyrophosphatase superfamily members...
  68. ncbi request reprint Small CRISPR RNAs guide antiviral defense in prokaryotes
    Stan J J Brouns
    Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, Netherlands
    Science 321:960-4. 2008
    ..Our results demonstrate that the formation of mature guide RNAs by the CRISPR RNA endonuclease subunit of Cascade is a mechanistic requirement for antiviral defense...
  69. pmc The cyanobacterial genome core and the origin of photosynthesis
    Armen Y Mulkidjanian
    School of Physics, University of Osnabruck, D 49069 Osnabruck, Germany
    Proc Natl Acad Sci U S A 103:13126-31. 2006
    ..From procyanobacteria, photosynthesis spread to other phyla by way of lateral gene transfer...
  70. pmc A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats
    Natalia Beloglazova
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
    J Biol Chem 283:20361-71. 2008
    ..Thus, CAS2 proteins are sequence-specific endoribonucleases, and we propose that their role in the CRISPR-mediated anti-phage defense might involve degradation of phage or cellular mRNAs...
  71. ncbi request reprint Inventing the dynamo machine: the evolution of the F-type and V-type ATPases
    Armen Y Mulkidjanian
    School of Physics, University of Osnabruck, Osnabrück D 49069, Germany
    Nat Rev Microbiol 5:892-9. 2007
    ..We suggest that in these ancestral translocases, the position of the central stalk was occupied by the translocated polymer...
  72. pmc Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20
    Eugene Kolker
    BIATECH, Bothell, Washington 98011, USA
    J Bacteriol 185:4593-602. 2003
    ..The direct proteomics approach to studying protein expression in vivo reported here is a powerful method that is applicable to proteome analysis of any (micro)organism...
  73. ncbi request reprint In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium
    Anu Raghunathan
    Department of Bioengineering, University of California at San Diego, La Jolla, California, USA
    OMICS 8:25-41. 2004
    ..This study demonstrates the significance of an integrated approach to the characterization of H. influenzae metabolism...
  74. pmc Myosin XI-K Is required for rapid trafficking of Golgi stacks, peroxisomes, and mitochondria in leaf cells of Nicotiana benthamiana
    Dror Avisar
    Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
    Plant Physiol 146:1098-108. 2008
    ....