Ujjwal Kumar

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Evolution of bacterial type III protein secretion systems
    Milton H Saier
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Trends Microbiol 12:113-5. 2004
  2. ncbi request reprint Probiotics and prebiotics in human health
    Milton H Saier
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093, USA
    J Mol Microbiol Biotechnol 10:22-5. 2005
  3. ncbi request reprint The bacterial chromosome
    Milton H Saier
    Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 0116, USA
    Crit Rev Biochem Mol Biol 43:89-134. 2008
  4. doi request reprint Comparative genomics of transport proteins in developmental bacteria: Myxococcus xanthus and Streptomyces coelicolor
    Ilya Getsin
    Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093 0116, USA
    BMC Microbiol 13:279. 2013
  5. pmc Microcompartments and protein machines in prokaryotes
    Milton H Saier
    Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, Calif 92093 0116, USA
    J Mol Microbiol Biotechnol 23:243-69. 2013
  6. pmc Evolutionary relationships of ATP-Binding Cassette (ABC) uptake porters
    Wei Hao Zheng
    Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093 0116, USA
    BMC Microbiol 13:98. 2013
  7. pmc Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control
    Robert S Coyne
    Genomic Medicine, J Craig Venter Institute, Rockville, MD 20850, USA
    Genome Biol 12:R100. 2011
  8. pmc Transposon-mediated adaptive and directed mutations and their potential evolutionary benefits
    Zhongge Zhang
    Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, USA
    J Mol Microbiol Biotechnol 21:59-70. 2011
  9. pmc Evolution of the oligopeptide transporter family
    Kenny M Gomolplitinant
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    J Membr Biol 240:89-110. 2011
  10. pmc Defense against cannibalism: the SdpI family of bacterial immunity/signal transduction proteins
    Tatyana Leonidovna Povolotsky
    Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093 0116, USA
    J Membr Biol 235:145-62. 2010

Research Grants

Collaborators

Detail Information

Publications97

  1. ncbi request reprint Evolution of bacterial type III protein secretion systems
    Milton H Saier
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Trends Microbiol 12:113-5. 2004
  2. ncbi request reprint Probiotics and prebiotics in human health
    Milton H Saier
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093, USA
    J Mol Microbiol Biotechnol 10:22-5. 2005
    ..Can these bacteria be engineered, through human-promoted accelerative evolution, so that they stimulate their own growth and that of other probiotic bacteria so as to crowd pathogens out of the intestine?..
  3. ncbi request reprint The bacterial chromosome
    Milton H Saier
    Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 0116, USA
    Crit Rev Biochem Mol Biol 43:89-134. 2008
    ..Some of the most throughly understood processes that underlie the dynamics of genomic structure and function in prokaryotes are examined...
  4. doi request reprint Comparative genomics of transport proteins in developmental bacteria: Myxococcus xanthus and Streptomyces coelicolor
    Ilya Getsin
    Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093 0116, USA
    BMC Microbiol 13:279. 2013
    ..Although the genomes of Sco and Mxa are the same size (~9 Mbp), Sco has 10% more genes that are on average 10% smaller than those in Mxa...
  5. pmc Microcompartments and protein machines in prokaryotes
    Milton H Saier
    Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, Calif 92093 0116, USA
    J Mol Microbiol Biotechnol 23:243-69. 2013
    ..These two symposia, taken together, provide the interested reader with an objective view of the remarkable complexity of what was once thought of as a simple noncompartmentalized cell. ..
  6. pmc Evolutionary relationships of ATP-Binding Cassette (ABC) uptake porters
    Wei Hao Zheng
    Department of Molecular Biology, University of California at San Diego, La Jolla, CA 92093 0116, USA
    BMC Microbiol 13:98. 2013
    ..In a few cases, high resolution 3-dimensional structures were available, and in these cases, their structures plus primary sequence analyses allowed us to predict evolutionary pathways of origin...
  7. pmc Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control
    Robert S Coyne
    Genomic Medicine, J Craig Venter Institute, Rockville, MD 20850, USA
    Genome Biol 12:R100. 2011
    ..Indeed, it is closely related to the model organism Tetrahymena thermophila. Genomic studies represent a promising strategy to reduce the impact of this disease and to understand the evolutionary transition to parasitism...
  8. pmc Transposon-mediated adaptive and directed mutations and their potential evolutionary benefits
    Zhongge Zhang
    Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, CA, USA
    J Mol Microbiol Biotechnol 21:59-70. 2011
    ..The results establish the principle of transposon-mediated directed mutation, identify a protein responsible for its regulation, and define essential aspects of the mechanism...
  9. pmc Evolution of the oligopeptide transporter family
    Kenny M Gomolplitinant
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    J Membr Biol 240:89-110. 2011
    ..These observations provide guides for future structural and functional analyses of OPT family members...
  10. pmc Defense against cannibalism: the SdpI family of bacterial immunity/signal transduction proteins
    Tatyana Leonidovna Povolotsky
    Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093 0116, USA
    J Membr Biol 235:145-62. 2010
    ..Our analyses allow us to propose structure-function relationships that may be applicable to most family members...
  11. pmc Bioinformatic characterization of p-type ATPases encoded within the fully sequenced genomes of 26 eukaryotes
    Mark D Thever
    Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, 92093 0116, CA, USA
    J Membr Biol 229:115-30. 2009
    ..tcdb.org , Saier et al. in Nucleic Acids Res 34:181-186, 2006; Nucleic Acids Res 37:274-278, 2009)...
  12. pmc State-dependent block of Na+ channels by articaine via the local anesthetic receptor
    Ging Kuo Wang
    Department of Anesthesia, Harvard Medical School and Brigham and Women s Hospital, Boston, MA 02115, USA
    J Membr Biol 229:1-9. 2009
    ..7 and rNav1.8 Na+ channels, with IC(50) values of 8.8 +/- 0.1 and 22.0 +/- 0.5 microM, respectively (n = 5), indicating that the high-affinity open-channel block by articaine is indeed preserved in neuronal Na+ channel isoforms...
  13. 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...
  14. pmc The Transporter Classification Database: recent advances
    Milton H Saier
    Division of Biological Sciences and Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Nucleic Acids Res 37:D274-8. 2009
    ..The availability of these tools has resulted in recognition of distant phylogenetic relationships and tremendous expansion of the information available to TCDB users...
  15. ncbi request reprint Evolution of the bacterial phosphotransferase system: from carriers and enzymes to group translocators
    M H Saier
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Biochem Soc Trans 33:220-4. 2005
    ..The work described provides detailed insight into the process of catalytic protein evolution...
  16. ncbi request reprint Protein secretion and membrane insertion systems in gram-negative bacteria
    Milton H Saier
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    J Membr Biol 214:75-90. 2006
    ..Comparisons between these systems suggest specific biogenic, mechanistic and evolutionary similarities as well as major differences...
  17. ncbi request reprint Tracing pathways of transport protein evolution
    Milton H Saier
    Division of Biological Sciences, University of California at San Diego, La Jolla 92093 0116, USA
    Mol Microbiol 48:1145-56. 2003
    ..The results summarized in this microreview establish the independent origins of many transporter families and allow postulation of the specific pathways taken for their appearance...
  18. pmc Animal Ca2+ release-activated Ca2+ (CRAC) channels appear to be homologous to and derived from the ubiquitous cation diffusion facilitators
    Madeleine G Matias
    Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 0116, USA
    BMC Res Notes 3:158. 2010
    ..We here report results that define the evolutionary relationship of the CRAC channel proteins of animals, and the ubiquitous Cation Diffusion Facilitator (CDF) carrier proteins...
  19. pmc TCDB: the Transporter Classification Database for membrane transport protein analyses and information
    Milton H Saier
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Nucleic Acids Res 34:D181-6. 2006
    ..TCDB not only provides curated information and a tool for classifying newly identified membrane proteins, but also serves as a genome transporter-annotation tool...
  20. ncbi request reprint Evolutionary origins of multidrug and drug-specific efflux pumps in bacteria
    M H Saier
    Department of Biology, University of California at San Diego, La Jolla 92093 0116, USA
    FASEB J 12:265-74. 1998
    ..A speculative model is presented that may explain the apparent capability of these multidrug transport systems to mediate drug transport from the cytoplasm or directly from the phospholipid bilayer...
  21. ncbi request reprint Molecular phylogeny as a basis for the classification of transport proteins from bacteria, archaea and eukarya
    M H Saier
    Department of Biology, University of California at San Diego, La Jolla 92093 0116, USA
    Adv Microb Physiol 40:81-136. 1998
    ..The classification system, which will be continuously updated, is available on our World Wide Web site (http:/(/)www-biology.ucsd.edu/ approximately msaier/transport/titlepage.html)...
  22. ncbi request reprint Phylogenetic characterization of novel transport protein families revealed by genome analyses
    M H Saier
    Department of Biology, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Biochim Biophys Acta 1422:1-56. 1999
    ..We tabulate the currently sequenced members of the 26 families analyzed, describe the properties of these families, and present partial multiple alignments, signature sequences and phylogenetic trees for them all...
  23. ncbi request reprint Novel phosphotransferase genes revealed by bacterial genome sequencing: a gene cluster encoding a putative N-acetylgalactosamine metabolic pathway in Escherichia coli
    J Reizer
    Department of Biology, University of California at San Diego, La Jolla 92093 0116, USA
    Microbiology 142:231-50. 1996
    ..A pathway for the metabolism of N-acetylgalactosamine biochemically similar to that for the metabolism of N-acetylglucosamine is proposed...
  24. ncbi request reprint Multiple mechanisms controlling carbon metabolism in bacteria
    M H Saier
    Department of Biology, University of California at San Diego, La Jolla, California
    Biotechnol Bioeng 58:170-4. 1998
    ..The mechanistic features of the best of such characterized processes are briefly reviewed, and references are provided that will allow the reader to delve more deeply into these subjects...
  25. ncbi request reprint Eukaryotic transmembrane solute transport systems
    M H Saier
    Department of Biology, University of California at San Diego, La Jolla 92093 0116, USA
    Int Rev Cytol 190:61-136. 1999
    ....
  26. ncbi request reprint Genome archeology leading to the characterization and classification of transport proteins
    M H Saier
    Department of Biology University of California at San Diego La Jolla, CA 92093 0116, USA
    Curr Opin Microbiol 2:555-61. 1999
    ....
  27. ncbi request reprint Paralogous genes encoding transport proteins in microbial genomes
    M H Saier
    Department of Biology, University of California at San Diego, La Jolla 92093 0116, USA
    Res Microbiol 150:689-99. 1999
    ..In this short review, we present and discuss the paralogues in some of these families and interpret the most prominent results, particularly those relevant to the largest permease superfamilies...
  28. ncbi request reprint Catabolite repression and inducer control in Gram-positive bacteria
    M H Saier
    Department of Biology, University of California at San Diego, La Jolla 92093 0116, USA
    Microbiology 142:217-30. 1996
    ..It seems clear that these two transmission mechanisms evolved independently. They provide a prime example of functional convergence...
  29. ncbi request reprint Families of transmembrane sugar transport proteins
    M H Saier
    Department of Biology, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Mol Microbiol 35:699-710. 2000
    ..This review provides a comprehensive guide to the diversity of carriers that mediate the transport of sugar-containing molecules across cell and organellar membranes...
  30. pmc A functional-phylogenetic classification system for transmembrane solute transporters
    M H Saier
    Department of Biology, University of California at San Diego, La Jolla, California 92093 0116, USA
    Microbiol Mol Biol Rev 64:354-411. 2000
    ..The tabulations should facilitate familial and functional assignments of newly sequenced transport proteins that will result from future genome sequencing projects...
  31. ncbi request reprint Whole genome analyses of transporters in spirochetes: Borrelia burgdorferi and Treponema pallidum
    M H Saier
    Department of Biology, University of California at San Diego, La Jolla 92093 0116, USA
    J Mol Microbiol Biotechnol 2:393-9. 2000
    ..The largest Spirochete secondary carrier families consist of efflux systems. While both Bbu and Tpa exhibit an unusual degree of transporter diversity, major differences in specificity exist between these two organisms...
  32. ncbi request reprint Transport capabilities encoded within the Bacillus subtilis genome
    Milton H Saier
    Department of Biology University of California at San Diego La Jolla, 92093 0116, USA
    J Mol Microbiol Biotechnol 4:37-67. 2002
    ..The recognized transporters fall into 58 families including 4 channel types, 42 secondary carrier types, 3 primary carrier types, 4 PTS-types and 5 unknown types...
  33. ncbi request reprint Phylogeny of multidrug transporters
    M H Saier
    Department of Biology, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Semin Cell Dev Biol 12:205-13. 2001
    ..In this review article, these families of drug transporters are discussed and evaluated from phylogenetic standpoints...
  34. ncbi request reprint Bioinformatic analyses of the bacterial L-ascorbate phosphotransferase system permease family
    Rikki Hvorup
    Division of Biological Sciences, University of California at San Diego, La Jolla, Calif, USA
    J Mol Microbiol Biotechnol 6:191-205. 2003
    ..These results suggest that the Sga and Gat families of PTS permeases comprise a small superfamily in which the transmembrane IIC domains evolved independently of all other known PTS permeases...
  35. ncbi request reprint The YedZ family: possible heme binding proteins that can be fused to transporters and electron carriers
    Torsten von Rozycki
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    J Mol Microbiol Biotechnol 8:129-40. 2004
    ..We propose that YedZ homologues function as heme-binding proteins that can facilitate or regulate oxidoreduction, transmembrane electron flow and transport...
  36. ncbi request reprint The ubiquitous ThrE family of putative transmembrane amino acid efflux transporters
    Ming Ren Yen
    Department of Biology, University of California at San Diego, La Jolla 92093 0116, USA
    Res Microbiol 153:19-25. 2002
    ..The significance of these observations is discussed...
  37. doi request reprint The phagosomal nutrient transporter (Pht) family
    Derek E Chen
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Microbiology 154:42-53. 2008
    ..This work serves to characterize two novel families within the MFS and provides compelling evidence for horizontal transfer of some of the family members...
  38. pmc The ascorbate transporter of Escherichia coli
    Zhongge Zhang
    Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 0116, USA
    J Bacteriol 185:2243-50. 2003
    ..We conclude that SgaT represents a novel prototypical enzyme IIC that functions with SgaA and SgaB to allow phosphoryl transfer from HPr(his-P) to L-ascorbate via the phosphoryl transfer pathway: [pathway: see text]...
  39. ncbi request reprint Phylogeny as a guide to structure and function of membrane transport proteins
    Abraham B Chang
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Mol Membr Biol 21:171-81. 2004
    ..In some cases, available structural and functional data are evaluated in order to substantiate our claim that molecular phylogeny provides a reliable guide to protein structure and function...
  40. pmc Protein-translocating trimeric autotransporters of gram-negative bacteria
    David S H Kim
    Department of Biological Sciences, University of California at San Diego, 9500 Gilman Dr, La Jolla, CA 92093 0116, USA
    J Bacteriol 188:5655-67. 2006
  41. ncbi request reprint The tripartite tricarboxylate transporter (TTT) family
    Brit Winnen
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Res Microbiol 154:457-65. 2003
    ....
  42. ncbi request reprint An automated program to screen databases for members of protein families
    Xiaofeng Zhou
    Division of Biology, University of California at San Diego, La Jolla, California 92093 0116, USA
    J Mol Microbiol Biotechnol 5:7-10. 2003
    ..ST is convenient for easily obtaining nonredundant members of transporter families starting from several homologous query sequences. The program can be applied to any protein family...
  43. doi request reprint Membrane porters of ATP-binding cassette transport systems are polyphyletic
    Bin Wang
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    J Membr Biol 231:1-10. 2009
    ..Currently available high-resolution structural data for ABC porters are fully consistent with our findings. These results provide guides for future structural and mechanistic studies of these important transport systems...
  44. ncbi request reprint The copper transporter (Ctr) family of Cu+ uptake systems
    Quentin C Dumay
    Division of Biological Sciences, University of California at San Diego, La Jolla 92093 0116, USA
    J Mol Microbiol Biotechnol 11:10-9. 2006
    ..We propose that this motif comprises the transmembrane Cu(+)-binding site in oligomeric channels that take up Cu(+) by a passive, membrane potential-dependent mechanism...
  45. ncbi request reprint Topological analysis of integral membrane constituents of prokaryotic ABC efflux systems
    Mirium Khwaja
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Res Microbiol 156:270-7. 2005
    ..These studies define the evolutionary pathway taken for the appearance of a subset of ABC transmembrane transport proteins and provide clues regarding their mechanistic and functional characteristics...
  46. ncbi request reprint Bioinformatic analyses of bacterial HPr kinase/phosphorylase homologues
    Aaron Stonestrom
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Res Microbiol 156:443-51. 2005
    ..HprK homologues were identified in Gram-negative bacteria that appear to lack PTS permeases, suggesting modes of action and substrates that differ from those characterized in Gram-positive bacteria...
  47. ncbi request reprint Biofilm-defective mutants of Bacillus subtilis
    Claudia Chagneau
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    J Mol Microbiol Biotechnol 8:177-88. 2004
    ..Possible mechanistic implications and potential roles of biofilm formation in other developmental processes are discussed...
  48. pmc Bioinformatic analyses of transmembrane transport: novel software for deducing protein phylogeny, topology, and evolution
    Ming Ren Yen
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    J Mol Microbiol Biotechnol 17:163-76. 2009
    ..Applications of these tools to specific transporter families are presented. Many of the computational approaches described should be applicable to virtually all classes of proteins and RNA molecules...
  49. pmc Gap junctional proteins of animals: the innexin/pannexin superfamily
    Ming Ren Yen
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Prog Biophys Mol Biol 94:5-14. 2007
    ..These bioinformatic analyses should serve as useful guides for future studies of structure, function and evolutionary aspects of this important superfamily...
  50. ncbi request reprint Topological predictions for integral membrane permeases of the phosphoenolpyruvate:sugar phosphotransferase system
    Thai X Nguyen
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093, USA
    J Mol Microbiol Biotechnol 11:345-60. 2006
    ..Based on our analyses we offer a topological model that resembles, but differs in detail from the two previously proposed models...
  51. ncbi request reprint Dependency of sugar transport and phosphorylation by the phosphoenolpyruvate-dependent phosphotransferase system on membranous phosphatidylethanolamine in Escherichia coli: studies with a pssA mutant lacking phosphatidylserine synthase
    Mohammad Aboulwafa
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Arch Microbiol 181:26-34. 2004
    ..Alteration of the phospholipid composition of the membrane thus allows functional dissection of transport from the phosphorylation activities of PTS enzyme complexes...
  52. pmc Identification of the L-aspartate transporter in Bacillus subtilis
    Graciela Lorca
    Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 0116, USA
    J Bacteriol 185:3218-22. 2003
    ..This 14 TMS protein is the primary aspartate uptake system in B. subtilis and serves as the prototype for a new family within the APC superfamily...
  53. ncbi request reprint Phylogeny of phosphoryl transfer proteins of the phosphoenolpyruvate-dependent sugar-transporting phosphotransferase system
    Kuang Yu Hu
    Division of Biology, University of California at San Diego, La Jolla 92093 0116, USA
    Res Microbiol 153:405-15. 2002
    ..Our findings define the evolutionary histories of these important bacterial proteins and provide guides for functional assignment of PTS-related proteins encoded by genes revealed by genome sequencing...
  54. ncbi request reprint Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella
    Christopher R Peabody
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Microbiology 149:3051-72. 2003
    ..The archaeal TM proteins are twice as large as the bacterial TM proteins, suggesting an oligomeric structure for the latter...
  55. ncbi request reprint The ion transporter superfamily
    Shraddha Prakash
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Biochim Biophys Acta 1618:79-92. 2003
    ..Some but not all of the families include functionally dissimilar paralogues that arose by early extragenic duplication events...
  56. ncbi request reprint Domain analysis of transcriptional regulators bearing PTS regulatory domains
    David B Greenberg
    Division of Biology, University of California at San Diego, La Jolla 92093 0116, USA
    Res Microbiol 153:519-26. 2002
    ..The results allow us to propose an evolutionary pathway for the appearance of these transcription factors and to suggest functional significance for these domains and specific residues within them...
  57. ncbi request reprint Sequence and phylogenetic analyses of the twin-arginine targeting (Tat) protein export system
    Ming Ren Yen
    Department of Biology, University of California at San Diego, La Jolla 92093 0116, USA
    Arch Microbiol 177:441-50. 2002
    ..In contrast to the TatA family, the TatC family shows phylogenetic clustering in strict accordance with organismal type. These results are discussed in terms of their probable structural, functional and evolutionary significance...
  58. ncbi request reprint Sequence similarity between multidrug resistance efflux pumps of the ABC and RND superfamilies
    Se H Kim
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Microbiology 150:2493-5. 2004
  59. ncbi request reprint A web-based Tree View (TV) program for the visualization of phylogenetic trees
    Yufeng Zhai
    Department of Biology, University of California at San Diego, La Jolla 92093 0116, USA
    J Mol Microbiol Biotechnol 4:69-70. 2002
    ..This program has a user-friendly interface and can be easily implemented into other programs for convenient protein sequence analysis. It is available at our web site: http://www.biology.ucsd.edu-yzhai/biotools.html...
  60. ncbi request reprint Evolutionary appearance of H+-translocating pyrophosphatases
    Ka M Au
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Microbiology 152:1243-7. 2006
  61. ncbi request reprint A transporter of Escherichia coli specific for L- and D-methionine is the prototype for a new family within the ABC superfamily
    Zhongge Zhang
    Division of Biological Sciences, University of California at San Diego, CA 92093 0116, La Jolla, USA
    Arch Microbiol 180:88-100. 2003
    ....
  62. ncbi request reprint Molecular modeling of the bacterial outer membrane receptor energizer, ExbBD/TonB, based on homology with the flagellar motor, MotAB
    Yu Feng Zhai
    Division of Biological Sciences 0116, University of California at San Diego, 9500 Gilam Drive, La Jolla, CA 92093 0116, USA
    Biochim Biophys Acta 1614:201-10. 2003
    ....
  63. ncbi request reprint The IUBMB-endorsed transporter classification system
    Wolfgang Busch
    Division of Biological Sciences, University of California, San Diego, La Jolla, USA
    Methods Mol Biol 227:21-36. 2003
  64. ncbi request reprint In vitro interconversion of the soluble and membrane- integrated forms of the Escherichia coli glucose enzyme II of the phosphoenolpyruvate-dependent sugar-transporting phosphotransferase system
    Mohammad Aboulwafa
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    J Mol Microbiol Biotechnol 12:263-8. 2007
    ..Conversion of SII to MII is promoted by: (1) high protein concentration, (2) adherence to and elution from an Ni(2+) column, (3) neutral pH, and (4) incorporation into phospholipid liposomes...
  65. doi request reprint Characterization of the E. coli glucose permease fused to the maltose-binding protein
    Mohammad Aboulwafa
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    J Basic Microbiol 48:3-9. 2008
    ..The results show that the monomeric II Glc-MBP exhibits no substrate inhibition although the oligomeric form does. Purification promotes subunit association, an increase in catalytic activity, and restoration of substrate inhibition...
  66. ncbi request reprint Reversing transmembrane electron flow: the DsbD and DsbB protein families
    Richard A Kimball
    Division of Biology, University of California at San Diego, La Jolla, Calif 92093 0116, USA
    J Mol Microbiol Biotechnol 5:133-49. 2003
    ....
  67. ncbi request reprint Web-based programs for the display and analysis of transmembrane alpha-helices in aligned protein sequences
    Xiaofeng Zhou
    Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 0116, USA
    J Mol Microbiol Biotechnol 5:1-6. 2003
    ..They also facilitate the estimation of protein topology and the determination of evolutionary pathways...
  68. doi request reprint Comprehensive analyses of transport proteins encoded within the genome of "Aromatoleum aromaticum" strain EbN1
    Dorjee G Tamang
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    J Membr Biol 229:53-90. 2009
    ..We predict that these findings will have important implications for our ecophysiological understanding of bioremediation...
  69. ncbi request reprint The transporter classification (TC) system, 2002
    Wolfgang Busch
    Division of Biology, University of California at San Diego, La Jolla 92093 0116, USA
    Crit Rev Biochem Mol Biol 37:287-337. 2002
    ..The results argue against appreciable horizontal transfer of genes encoding transporters between the three domains of life over the last 2 billion years...
  70. pmc The autoinducer-2 exporter superfamily
    Rachael E Rettner
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    J Mol Microbiol Biotechnol 18:195-205. 2010
    ..The results presented provide guides for future functional studies on members of this superfamily of bacterial transporters...
  71. pmc The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes
    Yufeng Zhai
    Department of Biology, University of California at San Diego, La Jolla, California 92093 0116, USA
    Protein Sci 11:2196-207. 2002
    ..This program should be useful for predicting the occurrence of outer membrane proteins in bacteria with completely sequenced genomes...
  72. ncbi request reprint Protein-translocating outer membrane porins of Gram-negative bacteria
    Ming Ren Yen
    Division of Biology 0116, 9500 Gilman Drive, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Biochim Biophys Acta 1562:6-31. 2002
    ..The resultant in silico analyses are correlated with available experimental evidence to formulate models relevant to the structures and evolutionary origins of these proteins...
  73. pmc Transport capabilities of eleven gram-positive bacteria: comparative genomic analyses
    Graciela L Lorca
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Biochim Biophys Acta 1768:1342-66. 2007
    ..The analyses lead to important physiological predictions regarding the preferred signalling and metabolic activities of these industrially important bacteria...
  74. ncbi request reprint Functional characterization of the heterooligomeric EbrAB multidrug efflux transporter of Bacillus subtilis
    Zhongge Zhang
    Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 0116, USA
    Biochemistry 46:5218-25. 2007
    ..Our studies support a model in which functional residues in EbrAB are relegated to at least two sets that participate in distinct steps of the active drug transport process...
  75. pmc Characterization of soluble enzyme II complexes of the Escherichia coli phosphotransferase system
    Mohammad Aboulwafa
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    J Bacteriol 186:8453-62. 2004
    ..coli. Thus, both phosphoenolpyruvate-dependent phosphotransferase system enzymes exist in soluble and membrane-integrated forms that exhibit dissimilar physical and kinetic properties...
  76. ncbi request reprint Carbonic anhydrases fused to anion transporters of the SulP family: evidence for a novel type of bicarbonate transporter
    Jeremy Felce
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    J Mol Microbiol Biotechnol 8:169-76. 2004
    ..Phylogenetic analyses reveal the relationships of these proteins and protein domains to each other and show that in some cases, but not in others, the hydrophilic domains/proteins have coevolved with the transporters...
  77. ncbi request reprint The multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) exporter superfamily
    Rikki N Hvorup
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Eur J Biochem 270:799-813. 2003
    ..The results serve to define a large superfamily of transporters that we predict function to export substrates using a monovalent cation antiport mechanism...
  78. ncbi request reprint The IUBMB-endorsed transporter classification system
    Wolfgang Busch
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Mol Biotechnol 27:253-62. 2004
    ..Such advances are discussed...
  79. pmc Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli
    Zhongge Zhang
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    J Bacteriol 187:980-90. 2005
    ..Relevant published data were evaluated, putative Crp and Fur binding sites were identified, and representative results were confirmed by real-time PCR. Molecular explanations for some, but not all, of these effects are provided...
  80. ncbi request reprint The iron/lead transporter superfamily of Fe/Pb2+ uptake systems
    Aurore J Debut
    Division of Biological Sciences, University of California at San Diego, La Jolla 92093 0116, USA
    J Mol Microbiol Biotechnol 11:1-9. 2006
    ..The results serve to characterize and provide evolutionary insight into a novel superfamily of heavy metal uptake transporters...
  81. ncbi request reprint The cecropin superfamily of toxic peptides
    Dorjee G Tamang
    Division of Biological Sciences, University of California at San Diego, La Jolla 92093 0116, USA
    J Mol Microbiol Biotechnol 11:94-103. 2006
    ..This study serves to characterize a large superfamily of toxic peptides that perform host defense functions in a range of animal kingdoms...
  82. ncbi request reprint The urea transporter (UT) family: bioinformatic analyses leading to structural, functional, and evolutionary predictions
    Ranjeet Minocha
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Receptors Channels 9:345-52. 2003
    ..The results suggest that vertebrates acquired UT genetic information from bacteria only once and that all current orthologues and paralogues in the animal kingdom arose from this one primordial system...
  83. ncbi request reprint Extra domains in secondary transport carriers and channel proteins
    Ravi D Barabote
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Biochim Biophys Acta 1758:1557-79. 2006
    ..These studies provide useful information about the evolution of extra domains in channels and secondary carriers and provide novel clues concerning function...
  84. ncbi request reprint Mechanism of CcpA-mediated glucose repression of the resABCDE operon of Bacillus subtilis
    Soo Keun Choi
    Division of Biological Sciences, University of California at San Diego, La Jolla, Calif, USA
    J Mol Microbiol Biotechnol 11:104-10. 2006
    ..Both CRE sites proved to be essential for full CcpA-mediated glucose repression of res operon expression. We propose that both looping and road block mechanisms are involved in res operon control by CcpA...
  85. ncbi request reprint The principal chloroquine resistance protein of Plasmodium falciparum is a member of the drug/metabolite transporter superfamily
    Can V Tran
    Division of Biological Science, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Microbiology 150:1-3. 2004
  86. pmc Combinatorial transcriptional control of the lactose operon of Escherichia coli
    Thomas Kuhlman
    Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093 0374, USA
    Proc Natl Acad Sci U S A 104:6043-8. 2007
    ..Specifically, our analysis indicates that the sensitivity of the inducer response results from LacR-mediated DNA looping, which is significantly enhanced by CRP...
  87. ncbi request reprint Active transport in communication, protection and nutrition
    Milton H Saier
    J Mol Microbiol Biotechnol 12:161-4. 2007
  88. ncbi request reprint The bioinformatic study of transmembrane molecular transport
    Milton H Saier
    J Mol Microbiol Biotechnol 11:289-90. 2006
  89. ncbi request reprint The bestrophin family of anion channels: identification of prokaryotic homologues
    Andrew R Hagen
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA, 92093 0116, USA
    Mol Membr Biol 22:291-302. 2005
    ..This suggests that eukaryotic paralogues arose exclusively by recent gene duplication events although both early and late gene duplication events occurred in prokaryotes...
  90. ncbi request reprint Sequence analyses of cyanobacterial bicarbonate transporters and their homologues
    Torsten von Rozycki
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    J Mol Microbiol Biotechnol 7:102-8. 2004
    ..The tree topology suggests that SbtA family members display multiple transport functions...
  91. pmc Comparative genomic analyses of the bacterial phosphotransferase system
    Ravi D Barabote
    Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 0116, USA
    Microbiol Mol Biol Rev 69:608-34. 2005
    ..Our studies provide insight into the development of complex multicomponent enzyme systems and lead to predictions regarding the types of protein-protein interactions that promote efficient PTS-mediated phosphoryl transfer...
  92. pmc Comprehensive analysis of transport proteins encoded within the genome of Bdellovibrio bacteriovorus
    Ravi D Barabote
    Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Genomics 90:424-46. 2007
    ..Our analyses provide a comprehensive, detailed appreciation of the transport capabilities of B. bacteriovorus. They should serve as a guide for functional experimental analyses...
  93. pmc In silico and transcriptional analysis of carbohydrate uptake systems of Streptomyces coelicolor A3(2)
    Ralph Bertram
    Lehrstuhl fur Mikrobiologie, Friedrich Alexander Universitat Erlangen Nurnberg, 91058 Erlangen, Germany
    J Bacteriol 186:1362-73. 2004
    ..Together with the previously surveyed permeases of the phosphotransferase system that accounts for the uptake of fructose and N-acetylglucosamine, the genome of S. coelicolor encodes at least 53 potential carbohydrate uptake systems...
  94. ncbi request reprint Sequence similarity between the channel-forming domains of voltage-gated ion channel proteins and the C-terminal domains of secondary carriers of the major facilitator superfamily
    Rikki N Hvorup
    Microbiology 148:3760-2. 2002
  95. ncbi request reprint Biochemical characterization of phosphoryl transfer involving HPr of the phosphoenolpyruvate-dependent phosphotransferase system in Treponema denticola, an organism that lacks PTS permeases
    Claudio F Gonzalez
    Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093 0116, USA
    Biochemistry 44:598-608. 2005
    ..This paper provides the first biochemical description of PTS phosphoryl-transfer chains in an organism that lacks PTS permeases...
  96. ncbi request reprint Engineering transport protein function: theoretical and technical considerations using the sugar-transporting phosphotransferase system of Escherichia coli as a model system
    Xavier Soberon
    Instituto de Biotecnologia UNAM, Cuernavaca, Mexico
    J Mol Microbiol Biotechnol 11:302-7. 2006
    ....
  97. pmc Two families of mechanosensitive channel proteins
    Christopher D Pivetti
    Division of Biology, University of California San Diego, La Jolla, California 92093 0116, USA
    Microbiol Mol Biol Rev 67:66-85, table of contents. 2003
    ..The presence of a conserved residue pattern for the putative channel-forming TMSs in the MscL and MscS family proteins suggests a common structural organization, gating mechanism, and evolutionary origin...

Research Grants17

  1. The Transporter Classification Database (TCDB)
    Milton Saier; Fiscal Year: 2007
    ..6) Develop approaches that will allow integration of the different lines of functional information revealed in specific aims #4 and 5. ..
  2. ATP-DEPENDENT PROTEIN KINASES IN GRAM-POSITIVE BACTERIA
    Milton Saier; Fiscal Year: 2004
    ..abstract_text> ..
  3. ATP DEPENDENT PROTEIN KINASES IN GRAM POSITIVE BACTERIA
    Milton Saier; Fiscal Year: 2000
    ..The knowledge gained should be applicable to the control of pathogenic bacteria. The protein kinase-mediated regulatory processes under study are expected to be relevant to analogous processes in eukaryotic organisms. ..
  4. The Transporter Classification Database (TCDB)
    Milton Saier; Fiscal Year: 2009
    ..6) Develop approaches that will allow integration of the different lines of functional information revealed in specific aims #4 and 5. ..