Radhey S Gupta

Summary

Affiliation: McMaster University
Country: Canada

Publications

  1. pmc BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species
    Emma Griffiths
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
    BMC Genomics 7:14. 2006
  2. pmc Molecular Signatures for the PVC Clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of Bacteria Provide Insights into Their Evolutionary Relationships
    Radhey S Gupta
    Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada
    Front Microbiol 3:327. 2012
  3. pmc A phylogenomic and molecular signature based approach for characterization of the phylum Spirochaetes and its major clades: proposal for a taxonomic revision of the phylum
    Radhey S Gupta
    Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada
    Front Microbiol 4:217. 2013
  4. pmc Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution
    Vaibhav Bhandari
    Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada
    Front Cell Infect Microbiol 2:98. 2012
  5. doi request reprint Molecular signatures for the class Coriobacteriia and its different clades; proposal for division of the class Coriobacteriia into the emended order Coriobacteriales, containing the emended family Coriobacteriaceae and Atopobiaceae fam. nov., and Eggerthe
    Radhey S Gupta
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
    Int J Syst Evol Microbiol 63:3379-97. 2013
  6. doi request reprint Molecular signatures for the phylum Aquificae and its different clades: proposal for division of the phylum Aquificae into the emended order Aquificales, containing the families Aquificaceae and Hydrogenothermaceae, and a new order Desulfurobacteriales or
    Radhey S Gupta
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
    Antonie Van Leeuwenhoek 104:349-68. 2013
  7. doi request reprint Origin and spread of photosynthesis based upon conserved sequence features in key bacteriochlorophyll biosynthesis proteins
    Radhey S Gupta
    Department of Biochemistry, McMaster University, Hamilton, ON, Canada
    Mol Biol Evol 29:3397-412. 2012
  8. doi request reprint Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades; proposal for division of the class Chloroflexia class. nov. [corrected] into the suborder Chloroflexineae subord. nov., consisting of the emended family Os
    Radhey S Gupta
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
    Antonie Van Leeuwenhoek 103:99-119. 2013
  9. pmc Phylogenomics and signature proteins for the alpha proteobacteria and its main groups
    Radhey S Gupta
    Department of Biochemistry and Biomedical Science, McMaster University, Hamilton L8N3Z5, Canada
    BMC Microbiol 7:106. 2007
  10. doi request reprint Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I)
    Radhey S Gupta
    Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
    Int J Syst Evol Microbiol 59:285-94. 2009

Collaborators

Detail Information

Publications106 found, 100 shown here

  1. pmc BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species
    Emma Griffiths
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
    BMC Genomics 7:14. 2006
    ..The obligate intracellular nature of chlamydiae has also limited their genetic and biochemical studies. Thus, it is of importance to develop additional means for their identification and characterization...
  2. pmc Molecular Signatures for the PVC Clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of Bacteria Provide Insights into Their Evolutionary Relationships
    Radhey S Gupta
    Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada
    Front Microbiol 3:327. 2012
    ..The molecular markers described here in addition to clarifying the evolutionary relationships among the PVC clade of bacteria also provide novel tools for their identification and for genetic and biochemical studies on these organisms...
  3. pmc A phylogenomic and molecular signature based approach for characterization of the phylum Spirochaetes and its major clades: proposal for a taxonomic revision of the phylum
    Radhey S Gupta
    Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada
    Front Microbiol 4:217. 2013
    ..nov., Brachyspiriales ord. nov., and Leptospiriales ord. nov.). It is further proposed that the genera Borrelia and Cristispira be transferred to a new family Borreliaceae fam. nov. within the order Spirochaetales. ..
  4. pmc Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution
    Vaibhav Bhandari
    Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada
    Front Cell Infect Microbiol 2:98. 2012
    ..The identified CSIs and CSPs also provide novel and highly specific means for identification of different groups of microbes and for taxonomical and biochemical studies...
  5. doi request reprint Molecular signatures for the class Coriobacteriia and its different clades; proposal for division of the class Coriobacteriia into the emended order Coriobacteriales, containing the emended family Coriobacteriaceae and Atopobiaceae fam. nov., and Eggerthe
    Radhey S Gupta
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
    Int J Syst Evol Microbiol 63:3379-97. 2013
    ..and three families (viz. Coriobacteriaceae, Atopobiaceae fam. nov. and Eggerthellaceae fam. nov.). Additionally, descriptions of the class Coriobacteriia, the order Coriobacteriales and the family Coriobacteriaceea are also emended. ..
  6. doi request reprint Molecular signatures for the phylum Aquificae and its different clades: proposal for division of the phylum Aquificae into the emended order Aquificales, containing the families Aquificaceae and Hydrogenothermaceae, and a new order Desulfurobacteriales or
    Radhey S Gupta
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
    Antonie Van Leeuwenhoek 104:349-68. 2013
    ..nov. The emended descriptions of the phylum Aquificae and its three families incorporating information for different molecular signatures are also provided. ..
  7. doi request reprint Origin and spread of photosynthesis based upon conserved sequence features in key bacteriochlorophyll biosynthesis proteins
    Radhey S Gupta
    Department of Biochemistry, McMaster University, Hamilton, ON, Canada
    Mol Biol Evol 29:3397-412. 2012
    ..Some implications of these observations regarding the origin and spread of photosynthesis are discussed...
  8. doi request reprint Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades; proposal for division of the class Chloroflexia class. nov. [corrected] into the suborder Chloroflexineae subord. nov., consisting of the emended family Os
    Radhey S Gupta
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
    Antonie Van Leeuwenhoek 103:99-119. 2013
    ....
  9. pmc Phylogenomics and signature proteins for the alpha proteobacteria and its main groups
    Radhey S Gupta
    Department of Biochemistry and Biomedical Science, McMaster University, Hamilton L8N3Z5, Canada
    BMC Microbiol 7:106. 2007
    ..Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales), very few or no distinctive molecular or biochemical characteristics are known...
  10. doi request reprint Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I)
    Radhey S Gupta
    Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
    Int J Syst Evol Microbiol 59:285-94. 2009
    ..These species form a well-defined clade in the phylogenetic trees and this indel provides a potential molecular marker for this clostridial cluster...
  11. pmc Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species
    Radhey S Gupta
    Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, ON, Canada
    BMC Evol Biol 7:71. 2007
    ..In contrast, all Chlorobi are anoxygenic obligate photoautotrophs. Very few (or no) biochemical or molecular characteristics are known that are distinctive characteristics of these bacteria, or are commonly shared by them...
  12. ncbi request reprint Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades
    Radhey S Gupta
    Department of Biochemistry, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
    Int J Syst Evol Microbiol 59:2510-26. 2009
    ..The species-distribution patterns of these synapomorphies also indicate that the plant/plastid homologues are not derived from the clade A or C cyanobacteria...
  13. pmc Signature proteins for the major clades of Cyanobacteria
    Radhey S Gupta
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
    BMC Evol Biol 10:24. 2010
    ..The phylogeny and taxonomy of cyanobacteria is currently poorly understood due to paucity of reliable markers for identification and circumscription of its major clades...
  14. ncbi request reprint Application of the character compatibility approach to generalized molecular sequence data: branching order of the proteobacterial subdivisions
    Radhey S Gupta
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada L8N 3Z5
    J Mol Evol 64:90-100. 2007
    ..Based on molecular sequences, it should be possible to obtain very large datasets of compatible characters that should prove very helpful in clarifying difficult to resolve phylogenetic relationships...
  15. ncbi request reprint Chlamydiae-specific proteins and indels: novel tools for studies
    Radhey S Gupta
    Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton L8N 3Z5, Ontario, Canada
    Trends Microbiol 14:527-35. 2006
    ..These novel signatures have possible applications for advancing our understanding of the chlamydiae...
  16. ncbi request reprint Molecular signatures for the main phyla of photosynthetic bacteria and their subgroups
    Radhey S Gupta
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
    Photosynth Res 104:357-72. 2010
    ..The cellular functions of these conserved indels, or most of the signature proteins are presently unknown, but they provide valuable means for discovering novel properties that are unique to different groups of photosynthetic bacteria...
  17. pmc Molecular signatures (unique proteins and conserved indels) that are specific for the epsilon proteobacteria (Campylobacterales)
    Radhey S Gupta
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, L8N 3Z5, Canada
    BMC Genomics 7:167. 2006
    ..The epsilon proteobacteria, which include many important human pathogens, are presently recognized solely on the basis of their branching in rRNA trees. No unique molecular or biochemical characteristics specific for this group are known...
  18. doi request reprint Molecular signatures for the Crenarchaeota and the Thaumarchaeota
    Radhey S Gupta
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
    Antonie Van Leeuwenhoek 99:133-57. 2011
    ..Functional studies on these signature proteins could lead to discovery of novel biochemical properties that are unique to these groups of archaea...
  19. doi request reprint Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups
    Radhey S Gupta
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
    Antonie Van Leeuwenhoek 100:1-34. 2011
    ..Additionally, these CSIs also provide valuable tools for genetic and biochemical studies that could lead to discovery of novel properties that are unique to these bacteria...
  20. ncbi request reprint The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins
    R S Gupta
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    Int Microbiol 4:187-202. 2001
    ....
  21. ncbi request reprint Critical issues in bacterial phylogeny
    Radhey S Gupta
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
    Theor Popul Biol 61:423-34. 2002
    ..The approach described here thus provides a reliable and internally consistent means for understanding various critical and long outstanding issues in bacterial phylogeny...
  22. pmc Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes
    Radhey S Gupta
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
    Antonie Van Leeuwenhoek 100:171-82. 2011
    ..This argues against the origin of monoderm prokaryotes from diderm bacteria by loss of outer membrane...
  23. ncbi request reprint The phylogeny and signature sequences characteristics of Fibrobacteres, Chlorobi, and Bacteroidetes
    Radhey S Gupta
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    Crit Rev Microbiol 30:123-43. 2004
    ..Signature sequences in a number of other proteins provide evidence that the FCB group of bacteria diverged at a similar time as the Chlamydiae group, and that the Spirochetes and Aquificales groups are its closest relatives...
  24. pmc Molecular characterization of Chinese hamster cells mutants affected in adenosine kinase and showing novel genetic and biochemical characteristics
    Xianying A Cui
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, L8N 3Z5, Canada
    BMC Biochem 12:22. 2011
    ..Two isoforms of the enzyme adenosine kinase (AdK), which differ at their N-terminal ends, are found in mammalian cells. However, there is no information available regarding the unique functional aspects or regulation of these isoforms...
  25. ncbi request reprint Protein signatures distinctive of alpha proteobacteria and its subgroups and a model for alpha-proteobacterial evolution
    Radhey S Gupta
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
    Crit Rev Microbiol 31:101-35. 2005
    ..The shared presence of many of these signatures in the mitochondrial (eukaryotic) homologs also provides evidence of the alpha-proteobacterial ancestry of mitochondria...
  26. doi request reprint Conserved inserts in the Hsp60 (GroEL) and Hsp70 (DnaK) proteins are essential for cellular growth
    Bhag Singh
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, L8N 3Z5, Canada
    Mol Genet Genomics 281:361-73. 2009
    ..We postulate that these conserved inserts that are localized in loop regions on protein surfaces, are involved in some ancillary functions that are essential for the groups of bacteria where they are found...
  27. ncbi request reprint Protein signatures distinctive of chlamydial species: horizontal transfers of cell wall biosynthesis genes glmU from archaea to chlamydiae and murA between chlamydiae and Streptomyces
    Emma Griffiths
    Department of Biochemistry, McMaster University, Hamilton, Ontario, CanadaL8N 3Z5
    Microbiology 148:2541-9. 2002
    ..These signatures are also potentially useful for screening of the chlamydiae species...
  28. ncbi request reprint Lateral transfers of serine hydroxymethyltransferase (glyA) and UDP-N-acetylglucosamine enolpyruvyl transferase (murA) genes from free-living Actinobacteria to the parasitic chlamydiae
    Emma Griffiths
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, L8N 3Z5, Canada
    J Mol Evol 63:283-96. 2006
    ....
  29. pmc Signature proteins that are distinctive of alpha proteobacteria
    Pinay Kainth
    Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, L8N 3Z5, Canada
    BMC Genomics 6:94. 2005
    ..The genomes of three alpha-proteobacteria, Rickettsia prowazekii (RP), Caulobacter crescentus (CC) and Bartonella quintana (BQ), were analyzed in order to search for proteins that are unique to this group...
  30. ncbi request reprint Inhibition of adenosine kinase by phosphonate and bisphosphonate derivatives
    Jae Park
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
    Mol Cell Biochem 283:11-21. 2006
    ..This information should prove helpful in the design and synthesis of more potent inhibitors of AK...
  31. ncbi request reprint Mycobacterial adenosine kinase is not a typical adenosine kinase
    Jae Park
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
    FEBS Lett 583:2231-6. 2009
    ..coli RK) and it was not stimulated by phosphate or inhibited by several AK inhibitors. These results raise questions over MTub protein's true function and whether it functions as AK in cells...
  32. ncbi request reprint Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae
    Emma Griffiths
    Department of Biochemistry and Biomedical Sciences, 1200 Main Street West, Hamilton, L8N 3Z5, Canada
    Microbiology 153:2648-54. 2007
    ..These results suggest that Verrucomicrobia may be the closest free-living relatives of the parasitic chlamydiae...
  33. doi request reprint Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria
    Beile Gao
    Department of Biochemistry, McMaster University, Hamilton, ON L8N 3Z5, Canada
    Int J Syst Evol Microbiol 59:234-47. 2009
    ....
  34. pmc Genomic organization and linkage via a bidirectional promoter of the AP-3 (adaptor protein-3) mu3A and AK (adenosine kinase) genes: deletion mutants of AK in Chinese hamster cells extend into the AP-3 mu3A gene
    Bhag Singh
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
    Biochem J 378:519-28. 2004
    ..Detailed phylogenetic analysis of the micro family of proteins presented here also provides insight into how different AP complexes are related and may have evolved...
  35. ncbi request reprint Phosphorylated derivatives that activate or inhibit mammalian adenosine kinase provide insights into the role of pentavalent ions in AK catalysis
    Jae Park
    Department of Biochemistry, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
    Protein J 23:167-77. 2004
    ..The insight provided by these studies concerning the structural features of activators and inhibitors should also prove helpful in the design of more potent inhibitors of AK...
  36. ncbi request reprint Identification and biochemical studies on novel non-nucleoside inhibitors of the enzyme adenosine kinase
    Jae Park
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
    Protein J 26:203-12. 2007
    ....
  37. ncbi request reprint Identification of signature proteins that are distinctive of the Deinococcus-Thermus phylum
    Emma Griffiths
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    Int Microbiol 10:201-8. 2007
    ....
  38. doi request reprint Phylogenomics and molecular signatures for the order Neisseriales: proposal for division of the order Neisseriales into the emended family Neisseriaceae and Chromobacteriaceae fam. nov
    Mobolaji Adeolu
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
    Antonie Van Leeuwenhoek 104:1-24. 2013
    ....
  39. pmc Structural and phylogenetic analysis of a conserved actinobacteria-specific protein (ASP1; SCO1997) from Streptomyces coelicolor
    Beile Gao
    Department of Biochemistry and Biomedical Science, McMaster University, Hamilton L8N3Z5, Canada
    BMC Struct Biol 9:40. 2009
    ..Recent comparative genomic analysis of 19 actinobacterial species determined that only 5 genes of unknown function uniquely define this large phylum 1. The cellular functions of these actinobacteria-specific proteins (ASP) are not known...
  40. ncbi request reprint Subcellular localization of fumarase in mammalian cells and tissues
    Timothy Bowes
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada, L8N 3Z5
    Histochem Cell Biol 127:335-46. 2007
    ....
  41. ncbi request reprint Conserved indels in essential proteins that are distinctive characteristics of Chlamydiales and provide novel means for their identification
    Emma Griffiths
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
    Microbiology 151:2647-57. 2005
    ..These results provide evidence that the divergence between the traditional Chlamydiaceae species and the other chlamydiae families occurred very early in the evolution of this group of bacteria...
  42. doi request reprint Molecular signatures (conserved indels) in protein sequences that are specific for the order Pasteurellales and distinguish two of its main clades
    Hafiz Sohail Naushad
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
    Antonie Van Leeuwenhoek 101:105-24. 2012
    ..These CSIs provide novel means for the identification and circumscription of these groups of Pasteurellales in molecular terms...
  43. pmc Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis
    Beile Gao
    Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Canada
    BMC Genomics 8:86. 2007
    ..The evolutionary relationships among different groups within the Euryarchaeota branch are also not clearly understood...
  44. ncbi request reprint Signature sequences in diverse proteins provide evidence for the late divergence of the Order Aquificales
    Emma Griffiths
    Department of Biochemistry, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
    Int Microbiol 7:41-52. 2004
    ....
  45. ncbi request reprint Molecular signatures in protein sequences that are characteristics of the phylum Aquificae
    Emma Griffiths
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
    Int J Syst Evol Microbiol 56:99-107. 2006
    ....
  46. pmc Structure and protein-protein interaction studies on Chlamydia trachomatis protein CT670 (YscO Homolog)
    Emily Lorenzini
    Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Canada
    J Bacteriol 192:2746-56. 2010
    ..These results suggest that CT670 and CT671 are putative homologs of the YcoO and YscP proteins, respectively, and that they likely form a chaperone-effector pair...
  47. ncbi request reprint Adenosine-AMP exchange activity is an integral part of the mammalian adenosine kinase
    R S Gupta
    Department of Biochemistry, McMaster University Hamilton, Ontario, Canada
    Biochem Mol Biol Int 39:493-502. 1996
    ..Some implications of these observations regarding the catalytic mechanism of AK are discussed...
  48. ncbi request reprint Phylogenetic analysis of mycoplasmas based on Hsp70 sequences: cloning of the dnaK (hsp70) gene region of Mycoplasma capricolum
    M Falah
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    Int J Syst Bacteriol 47:38-45. 1997
    ..The phylogenetic trees based on Hsp70 sequences show a polyphyletic branching of archaebacteria with the gram-postive species, which is statistically strongly favored...
  49. ncbi request reprint The use of signature sequences in different proteins to determine the relative branching order of bacterial divisions: evidence that Fibrobacter diverged at a similar time to Chlamydia and the Cytophaga-Flavobacterium-Bacteroides division
    E Griffiths
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    Microbiology 147:2611-22. 2001
    ..succinogenes homologues. These results provide evidence that F. succinogenes does not belong to the proteobacterial division and thus should be placed in a similar position as the Chlamydia and CFB groups of species...
  50. doi request reprint Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria
    Hafiz Sohail Naushad
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
    Int J Syst Evol Microbiol 64:366-83. 2014
    ....
  51. doi request reprint Molecular signatures for the phylum Synergistetes and some of its subclades
    Vaibhav Bhandari
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
    Antonie Van Leeuwenhoek 102:517-40. 2012
    ....
  52. ncbi request reprint Identification and characterization of human ribokinase and comparison of its properties with E. coli ribokinase and human adenosine kinase
    Jae Park
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
    FEBS Lett 581:3211-6. 2007
    ..A number of activators and inhibitors of human AK, produced very similar effects on the human and E. coli RKs, indicating that the catalytic mechanism of RK is very similar to that of the AKs...
  53. pmc Distinctive protein signatures provide molecular markers and evidence for the monophyletic nature of the deinococcus-thermus phylum
    Emma Griffiths
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
    J Bacteriol 186:3097-107. 2004
    ..The identified signatures provide strong evidence for the monophyletic nature of the Deinococcus-Thermus phylum. These molecular markers should prove very useful in the identification of new species related to this group...
  54. doi request reprint Novel mitochondrial extensions provide evidence for a link between microtubule-directed movement and mitochondrial fission
    Timothy Bowes
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada L8N3Z5
    Biochem Biophys Res Commun 376:40-5. 2008
    ..Our observations strongly suggest the existence of a link between microtubule-based mitochondrial trafficking and mitochondrial fission...
  55. ncbi request reprint Molecular signatures in protein sequences that are characteristic of cyanobacteria and plastid homologues
    Radhey S Gupta
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
    Int J Syst Evol Microbiol 53:1833-42. 2003
    ....
  56. ncbi request reprint Signature proteins that are distinctive characteristics of Actinobacteria and their subgroups
    Beile Gao
    Department of Biochemistry and Biomedical Science, McMaster University, L8N3Z5, Hamilton, Canada
    Antonie Van Leeuwenhoek 90:69-91. 2006
    ..The identified proteins also provide potential targets for development of drugs that are specific for actinobacteria...
  57. ncbi request reprint Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes
    R S Gupta
    Department of Biochemistry, McMaster University, Hamilton, Canada
    J Mol Evol 37:573-82. 1993
    ..To explain the phylogenies based on HSP70 and other gene sequences, a model for the origin of eukaryotic cells involving fusion between archaebacteria and gram-negative eubacteria is proposed...
  58. ncbi request reprint Conserved indels in protein sequences that are characteristic of the phylum Actinobacteria
    Beile Gao
    Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Canada
    Int J Syst Evol Microbiol 55:2401-12. 2005
    ..Functional studies on them should prove helpful in understanding novel biochemical and physiological characteristics of this group of bacteria...
  59. doi request reprint Molecular signatures for Bacillus species: demarcation of the Bacillus subtilis and Bacillus cereus clades in molecular terms and proposal to limit the placement of new species into the genus Bacillus
    Vaibhav Bhandari
    Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario, Canada
    Int J Syst Evol Microbiol 63:2712-26. 2013
    ..The identified CSIs, in addition to their usefulness for taxonomic and diagnostic purposes, also provide novel probes for genetic and biochemical studies of these bacteria. ..
  60. ncbi request reprint Unusual cellular disposition of the mitochondrial molecular chaperones Hsp60, Hsp70 and Hsp10
    Radhey S Gupta
    Department of Biochemistry, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
    Novartis Found Symp 291:59-68; discussion 69-73, 137-40. 2008
    ..My paper will review some work in this area and discuss the significance of these results...
  61. ncbi request reprint Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): implications regarding the origin of photosynthesis
    R S Gupta
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
    Mol Microbiol 32:893-906. 1999
    ..Some implications of these results concerning the origin of photosynthesis and the earliest prokaryotic fossils are discussed...
  62. ncbi request reprint The sequences of heat shock protein 40 (DnaJ) homologs provide evidence for a close evolutionary relationship between the Deinococcus-thermus group and cyanobacteria
    K Bustard
    Department of Biochemistry, McMaster University, 1200 Main Street West, Hamilton, ON L8N 3Z5, Canada
    J Mol Evol 45:193-205. 1997
    ..However, in phylogenetic trees based on Hsp40 sequences, the two archaebacterial homologs showed a polyphyletic branching within Gram-positive bacteria, similar to that seen with Hsp70 sequences...
  63. ncbi request reprint The natural evolutionary relationships among prokaryotes
    R S Gupta
    Department of Biochemistry, McMaster University Hamilton, Ontario, Canada
    Crit Rev Microbiol 26:111-31. 2000
    ....
  64. ncbi request reprint The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes
    R S Gupta
    Department of Biochemistry, McMaster University, L8N 3Z5, Hamilton, Ont, Canada
    FEMS Microbiol Rev 24:367-402. 2000
    ..These signatures generally support the origin of mitochondria from an alpha-proteobacterium and provide evidence that the nuclear cytosolic homologs of many genes are also derived from proteobacteria...
  65. pmc Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes
    R S Gupta
    Department of Biochemistry, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
    Microbiol Mol Biol Rev 62:1435-91. 1998
    ..In this model, the ancestral eukaryotic cell is a chimera that resulted from a unique fusion event between the two separate groups of prokaryotes followed by integration of their genomes...
  66. ncbi request reprint What are archaebacteria: life's third domain or monoderm prokaryotes related to gram-positive bacteria? A new proposal for the classification of prokaryotic organisms
    R S Gupta
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    Mol Microbiol 29:695-707. 1998
    ..These observations provide evidence for an alternate view of the evolutionary relationship among living organisms that is different from the currently popular three-domain proposal...
  67. pmc Cloning of the hsp70 (dnaK) genes from Rhizobium meliloti and Pseudomonas cepacia: phylogenetic analyses of mitochondrial origin based on a highly conserved protein sequence
    M Falah
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    J Bacteriol 176:7748-53. 1994
    ..The analysis presented here also suggests a monophyletic origin of the mitochondrial homologs...
  68. ncbi request reprint The influence of inorganic phosphate on the activity of adenosine kinase
    M Maj
    Department of Biochemistry, McMaster University, Hamilton, Ont, Canada
    Biochim Biophys Acta 1476:33-42. 2000
    ..The effect that phosphate exerts on AK may be either to protect the enzyme from inactivation at high adenosine and H(+) concentrations or to stabilize substrate binding at the active site...
  69. ncbi request reprint Life's third domain (Archaea): an established fact or an endangered paradigm?
    R S Gupta
    Department of Biochemistry, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
    Theor Popul Biol 54:91-104. 1998
    ..A new classifica- tion of organisms consistent with phenotype and macromolecular sequence data is proposed...
  70. pmc Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria
    Beile Gao
    Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, Canada
    Microbiol Mol Biol Rev 76:66-112. 2012
    ..Genetic and biochemical studies on these Actinobacteria-specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups of Actinobacteria...
  71. doi request reprint Subcellular localization of adenosine kinase in mammalian cells: The long isoform of AdK is localized in the nucleus
    Xianying Amy Cui
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ont, Canada
    Biochem Biophys Res Commun 388:46-50. 2009
    ..AdK in nucleus is likely required for sustaining methylation reactions...
  72. pmc Cloning of the HSP70 gene from Halobacterium marismortui: relatedness of archaebacterial HSP70 to its eubacterial homologs and a model for the evolution of the HSP70 gene
    R S Gupta
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    J Bacteriol 174:4594-605. 1992
    ..mazei) and the gram-positive group of bacteria constitutes the ancestral form of the protein and that all other HSP70s (viz., other eubacteria as well as eukaryotes) containing the insert have evolved from this ancient protein...
  73. ncbi request reprint Cloning and characterization of cDNA for adenosine kinase from mammalian (Chinese hamster, mouse, human and rat) species. High frequency mutants of Chinese hamster ovary cells involve structural alterations in the gene
    B Singh
    Department of Biochemistry, McMaster University, Hamilton, Canada
    Eur J Biochem 241:564-71. 1996
    ..The sequence similarity data support the possibility that adenosine kinase shares a common evolutionary ancestor with these protein sequences...
  74. ncbi request reprint The effect of inorganic phosphate on the activity of bacterial ribokinase
    M C Maj
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    J Protein Chem 20:139-44. 2001
    ..The similar effect of PVI on distantly related enzymes suggests that a common mechanism for activity is shared among PfkB family members...
  75. pmc Primary structure of a human mitochondrial protein homologous to the bacterial and plant chaperonins and to the 65-kilodalton mycobacterial antigen
    S Jindal
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    Mol Cell Biol 9:2279-83. 1989
    ..The observed high degree of homology between human P1 and mycobacterial antigen also suggests the possible involvement of this protein in certain autoimmune diseases...
  76. doi request reprint Adenosine kinase and ribokinase--the RK family of proteins
    J Park
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada L8N 3Z5
    Cell Mol Life Sci 65:2875-96. 2008
    ..The cellular metabolism and transport of ribose and adenosine are also briefly discussed, as well as the beneficial effects of ribose and adenosine in physiology and how these effects can be harnessed for pharmacological purposes...
  77. ncbi request reprint Cloning and characterization of multiple groEL chaperonin-encoding genes in Rhizobium meliloti
    E Rusanganwa
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    Gene 126:67-75. 1993
    ..The presence of multiple GroEL homologues in R. meliloti suggests a possible role of the GroEL or HSP60 chaperonins in the nodulation (symbiosis) and nitrogen fixation processes...
  78. ncbi request reprint Immunoelectron microscopic localization of the 60-kDa heat shock chaperonin protein (Hsp60) in mammalian cells
    B J Soltys
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    Exp Cell Res 222:16-27. 1996
    ..These findings raise interesting questions concerning the possible role of Hsp60 at extramitochondrial sites...
  79. ncbi request reprint A novel ubiquitous protein 'chaperonin' supports the endosymbiotic origin of mitochondrion and plant chloroplast
    R S Gupta
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    Biochem Biophys Res Commun 163:780-7. 1989
    ..The sequence data for this protein thus support the contention that the endosymbiont that gave rise to mitochondrion was a member of purple bacteria, while plant chloroplast originated from a member of the cyanobacterial lineage...
  80. pmc Phylogenomics and molecular signatures for species from the plant pathogen-containing order xanthomonadales
    Hafiz Sohail Naushad
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
    PLoS ONE 8:e55216. 2013
    ....
  81. ncbi request reprint Comparative proteome analysis of Acidaminococcus intestini supports a relationship between outer membrane biogenesis in Negativicutes and Proteobacteria
    Chantal Campbell
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
    Arch Microbiol 196:307-10. 2014
    ..In addition, we have identified key proteins involved in outer membrane biogenesis in A. intestini. This work highlights the need for further studies to define the relationships and evolutionary history of the Negativicutes. ..
  82. ncbi request reprint Mitochondrial import of human and yeast fumarase in live mammalian cells: retrograde translocation of the yeast enzyme is mainly caused by its poor targeting sequence
    Bhag Singh
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada L8N 3Z5
    Biochem Biophys Res Commun 346:911-8. 2006
    ....
  83. ncbi request reprint Pentavalent ions dependency is a conserved property of adenosine kinase from diverse sources: identification of a novel motif implicated in phosphate and magnesium ion binding and substrate inhibition
    Mary C Maj
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada, L8N 3Z5
    Biochemistry 41:4059-69. 2002
    ..These observations support the view that N239 and E242 play an important role in the binding of PO4 and Mg2+ ions required for the catalytic activity of adenosine kinase...
  84. ncbi request reprint Cloning of HSP60 (GroEL) operon from Clostridium perfringens using a polymerase chain reaction based approach
    E Rusanganwa
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    Biochim Biophys Acta 1130:90-4. 1992
    ..The approach described here, employing this set of degenerate oligonucleotide primers, could be used to clone HSP60 gene/cDNA from any species...
  85. ncbi request reprint Nucleotide sequence of mouse HSP60 (chaperonin, GroEL homolog) cDNA
    T J Venner
    Department of Biochemistry, McMaster University, Hamilton, Canada
    Biochim Biophys Acta 1087:336-8. 1990
    ..The deduced amino acid sequence of mouse hsp60 protein differs from the corresponding proteins from Chinese hamster and human cells in 7 and 13 residues, respectively, most of which are conservative replacements...
  86. ncbi request reprint Phylogenetic analysis of 70 kD heat shock protein sequences suggests a chimeric origin for the eukaryotic cell nucleus
    R S Gupta
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    Curr Biol 4:1104-14. 1994
    ....
  87. ncbi request reprint Mitochondrial-matrix proteins at unexpected locations: are they exported?
    B J Soltys
    Dept of Biochemistry, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
    Trends Biochem Sci 24:174-7. 1999
    ..We suggest that mitochondria, as organelles of bacterial origin, possess specific mechanisms for export of proteins to other compartments...
  88. ncbi request reprint Cloning of HSP70 (dnaK) gene from Clostridium perfringens using a general polymerase chain reaction based approach
    K A Galley
    Department of Biochemistry, McMaster University, Hamilton, Canada
    Biochim Biophys Acta 1130:203-8. 1992
    ..The HSP70s from C. perfringens as well as other Gram-positive groups of bacteria contain a large deletion of 25 amino acids, near the N-terminal end, which is not seen in HSP70 from other sources...
  89. ncbi request reprint Gene structure for adenosine kinase in Chinese hamster and human: high-frequency mutants of CHO cells involve deletions of several introns and exons
    B Singh
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    DNA Cell Biol 20:53-65. 2001
    ..The endpoints of these deletions lie in the large introns within the AK gene...
  90. ncbi request reprint Structure-activity studies on mammalian adenosine kinase
    M C Maj
    Department of Biochemistry, McMaster University, Hamilton, Ontario, L8N 3Z5, Canada
    Biochem Biophys Res Commun 275:386-93. 2000
    ....
  91. doi request reprint Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotoga
    Vaibhav Bhandari
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8N 3Z5, Canada
    Antonie Van Leeuwenhoek 105:143-68. 2014
    ..EMP, Thermotoga sp. A7A and Thermotoga sp. RQ2 while the other Thermotoga species (viz. Tt. lettingae, Tt. thermarum, Tt. elfii, Tt. subterranean and Tt. hypogea) be transferred to a new genus, Pseudothermotoga gen. nov. ..
  92. ncbi request reprint Induction of mitochondrial fusion by cysteine-alkylators ethacrynic acid and N-ethylmaleimide
    Timothy J Bowes
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    J Cell Physiol 202:796-804. 2005
    ..In live BSC-1 cells, EA induced fusion of mitochondria occurred very rapidly (<20 min), which suggests that it is inducing fusion by modifying certain critical cysteine residue(s) in proteins involved in the process...
  93. ncbi request reprint Localization of mitochondrial DNA encoded cytochrome c oxidase subunits I and II in rat pancreatic zymogen granules and pituitary growth hormone granules
    Skanda K Sadacharan
    Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada, L8N 3Z5
    Histochem Cell Biol 124:409-21. 2005
    ....
  94. ncbi request reprint Mitochondrial import of the human chaperonin (HSP60) protein
    B Singh
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    Biochem Biophys Res Commun 169:391-6. 1990
    ..ornithine carbamoyltransferase and uncoupling protein) much less binding of pre P1 to mitochondria was observed. The significance of this latter observation at present is unclear...
  95. ncbi request reprint Immunogold localization of mitochondrial aspartate aminotransferase in mitochondria and on the cell surface in normal rat tissues
    J D Cechetto
    Department of Biochemistry, McMaster University, Hamilton, Canada
    Histol Histopathol 17:353-64. 2002
    ..These results have implications for the role of mitochondria in apoptosis and different diseases...
  96. ncbi request reprint Nucleotide sequences and novel structural features of human and Chinese hamster hsp60 (chaperonin) gene families
    T J Venner
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    DNA Cell Biol 9:545-52. 1990
    ..The sequence data, however, suggest that most of these genes, except one (per haploid genome), are likely to be nonfunctional pseudogenes...
  97. pmc Investigation of the relationship between altered intracellular pH and multidrug resistance in mammalian cells
    D Boscoboinik
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    Br J Cancer 61:568-72. 1990
    ..Therefore, except for the effect of cyclosporin A on the CHRC5 line, the effects of other agents on reversal of multidrug resistance and intracellular pH did not correlate with each other...
  98. pmc Nucleotide sequence of rat hsp60 (chaperonin, GroEL homolog) cDNA
    T J Venner
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    Nucleic Acids Res 18:5309. 1990
  99. ncbi request reprint Cell surface localization of the 60 kDa heat shock chaperonin protein (hsp60) in mammalian cells
    B J Soltys
    Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada
    Cell Biol Int 21:315-20. 1997
    ..The finding of hsp60 on the cell surface of mammalian cells may signify chaperone involvement in surface functions...
  100. ncbi request reprint Induction of Hsp60 by Photofrin-mediated photodynamic therapy
    J G Hanlon
    Hamilton Regional Cancer Centre, 699 Concession Street, ON, L8V 5C2, Hamilton, Canada
    J Photochem Photobiol B 64:55-61. 2001
    ..These results indicate that the presence of PII and the subsequent oxidative stress of PDT can induce Hsp60 and implicated it as a common factor that may contribute to the resistance observed in the induced resistant cells...