J Kim

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Autophagy, cytoplasm-to-vacuole targeting pathway, and pexophagy in yeast and mammalian cells
    J Kim
    Section of Microbiology, University of California, Davis, California 95616, USA
    Annu Rev Biochem 69:303-42. 2000
  2. pmc Cvt19 is a receptor for the cytoplasm-to-vacuole targeting pathway
    S V Scott
    Section of Microbiology, University of California, 95616, Davis, CA, USA
    Mol Cell 7:1131-41. 2001
  3. pmc Apg7p/Cvt2p is required for the cytoplasm-to-vacuole targeting, macroautophagy, and peroxisome degradation pathways
    J Kim
    Section of Microbiology, University of California, Davis, California 95616, USA
    Mol Biol Cell 10:1337-51. 1999
  4. pmc Effective inhibition of herpes simplex virus 1 gene expression and growth by engineered RNase P ribozyme
    P Trang
    Program in Infectious Diseases and Immunity, Program in Comparative Biochemistry, School of Public Health, 140 Warren Hall, University of California, Berkeley, CA 94720, USA
    Nucleic Acids Res 29:5071-8. 2001
  5. ncbi request reprint A ribozyme derived from the catalytic subunit of RNase P from Escherichia coli is highly effective in inhibiting replication of herpes simplex virus 1
    P Trang
    Program in Infectious Diseases and Immunity, Program in Comparative Biochemistry School of Public Health, University of California, 140 Warren Hall, Berkeley, CA 94720, USA
    J Mol Biol 301:817-26. 2000
  6. pmc Disruption of the yeast ATH1 gene confers better survival after dehydration, freezing, and ethanol shock: potential commercial applications
    J Kim
    Section of Microbiology, University of California, Davis 95616, USA
    Appl Environ Microbiol 62:1563-9. 1996
  7. pmc Degradation of lipid vesicles in the yeast vacuole requires function of Cvt17, a putative lipase
    S A Teter
    University of Michigan, Department of Biology, Ann Arbor, Michigan 48109, USA
    J Biol Chem 276:2083-7. 2001
  8. pmc Apg2 is a novel protein required for the cytoplasm to vacuole targeting, autophagy, and pexophagy pathways
    C W Wang
    University of Michigan, Department of Biology, Ann Arbor, Michigan 48109, USA
    J Biol Chem 276:30442-51. 2001
  9. pmc Membrane recruitment of Aut7p in the autophagy and cytoplasm to vacuole targeting pathways requires Aut1p, Aut2p, and the autophagy conjugation complex
    J Kim
    Department of Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    J Cell Biol 152:51-64. 2001
  10. pmc Cvt9/Gsa9 functions in sequestering selective cytosolic cargo destined for the vacuole
    J Kim
    Department of Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    J Cell Biol 153:381-96. 2001

Collaborators

  • D J Klionsky
  • F Liu
  • J Guan
  • J Lee
  • Y Ohsumi
  • P Trang
  • S V Scott
  • J L Campbell
  • S A Rifkin
  • S W Jang
  • M Y Lee
  • S O Jung
  • J Seo
  • S A Teter
  • C W Wang
  • J Y Sung
  • Y G Ko
  • W P Huang
  • S C Choi
  • T Noda
  • I S So
  • J Kim-Ha
  • J Y Oh
  • D H Gutmann
  • J Koipally
  • U J Yun
  • S Kim
  • R Dorer
  • B K Choudhury
  • P R Rhode
  • Y H Shin
  • W A Dunn
  • M Kim
  • P E Stromhaug
  • H Abeliovich
  • H Park
  • M U Hutchins
  • T Kim
  • K P Eggerton
  • J H Park
  • A M Fischer
  • W Seol
  • Y S Ahn
  • K C Chung
  • A F Kilani
  • E J Choi
  • Y S Kang
  • S R Paik
  • S Elsasser
  • H S Park
  • Y Song
  • M Baba
  • J K Han
  • A Kilani
  • C Tokunaga
  • A Cashen
  • K Georgopoulos
  • A Renold
  • M Henkemeyer
  • Y J Kim
  • J Liu
  • S Y Kim
  • W J Park
  • P N Adler
  • Y Zhang
  • A Loehr
  • E Bae
  • L H Hartwell
  • S S Li
  • C Boone
  • H F Kung
  • T Kimbrough
  • D M Goo

Detail Information

Publications41

  1. ncbi request reprint Autophagy, cytoplasm-to-vacuole targeting pathway, and pexophagy in yeast and mammalian cells
    J Kim
    Section of Microbiology, University of California, Davis, California 95616, USA
    Annu Rev Biochem 69:303-42. 2000
    ....
  2. pmc Cvt19 is a receptor for the cytoplasm-to-vacuole targeting pathway
    S V Scott
    Section of Microbiology, University of California, 95616, Davis, CA, USA
    Mol Cell 7:1131-41. 2001
    ..These results suggest that Cvt19 is a receptor protein for prAPI that allows for the selective transport of this protein by both the Cvt and Apg pathways...
  3. pmc Apg7p/Cvt2p is required for the cytoplasm-to-vacuole targeting, macroautophagy, and peroxisome degradation pathways
    J Kim
    Section of Microbiology, University of California, Davis, California 95616, USA
    Mol Biol Cell 10:1337-51. 1999
    ....
  4. pmc Effective inhibition of herpes simplex virus 1 gene expression and growth by engineered RNase P ribozyme
    P Trang
    Program in Infectious Diseases and Immunity, Program in Comparative Biochemistry, School of Public Health, 140 Warren Hall, University of California, Berkeley, CA 94720, USA
    Nucleic Acids Res 29:5071-8. 2001
    ....
  5. ncbi request reprint A ribozyme derived from the catalytic subunit of RNase P from Escherichia coli is highly effective in inhibiting replication of herpes simplex virus 1
    P Trang
    Program in Infectious Diseases and Immunity, Program in Comparative Biochemistry School of Public Health, University of California, 140 Warren Hall, Berkeley, CA 94720, USA
    J Mol Biol 301:817-26. 2000
    ..Thus, M1GS ribozyme is highly effective in inhibiting HSV-1 growth and can be used as a general gene-targeting agent for anti-HSV applications...
  6. pmc Disruption of the yeast ATH1 gene confers better survival after dehydration, freezing, and ethanol shock: potential commercial applications
    J Kim
    Section of Microbiology, University of California, Davis 95616, USA
    Appl Environ Microbiol 62:1563-9. 1996
    ..The improved resistance to stress conditions exhibited by the delta ath1 strain may make this strain useful in commercial applications, including baking and brewing...
  7. pmc Degradation of lipid vesicles in the yeast vacuole requires function of Cvt17, a putative lipase
    S A Teter
    University of Michigan, Department of Biology, Ann Arbor, Michigan 48109, USA
    J Biol Chem 276:2083-7. 2001
    ..The active-site serine of this motif is required for subvacuolar vesicle lysis. This is the first characterization of a putative lipase implicated in vacuolar function in yeast...
  8. pmc Apg2 is a novel protein required for the cytoplasm to vacuole targeting, autophagy, and pexophagy pathways
    C W Wang
    University of Michigan, Department of Biology, Ann Arbor, Michigan 48109, USA
    J Biol Chem 276:30442-51. 2001
    ..Apg2 localizes to the previously identified perivacuolar compartment that contains Apg9, the only characterized integral membrane protein that is required for autophagosome/Cvt vesicle formation...
  9. pmc Membrane recruitment of Aut7p in the autophagy and cytoplasm to vacuole targeting pathways requires Aut1p, Aut2p, and the autophagy conjugation complex
    J Kim
    Department of Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    J Cell Biol 152:51-64. 2001
    ..These findings define a series of steps that results in the modification of Aut7p and its subsequent binding to the sequestering transport vesicles of the autophagy and cytoplasm to vacuole targeting pathways...
  10. pmc Cvt9/Gsa9 functions in sequestering selective cytosolic cargo destined for the vacuole
    J Kim
    Department of Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    J Cell Biol 153:381-96. 2001
    ..These biochemical and morphological results demonstrate that Cvt9 and the P. pastoris homologue Gsa9 may function at the step of selective cargo sequestration...
  11. pmc Identification of Cdc6 protein domains involved in interaction with Mcm2 protein and Cdc4 protein in budding yeast cells
    S W Jang
    Graduate School of Biotechnology, Department of Genetic Engineering, Kyung Hee University, Yongin, Kyonggi Do, 449 701, Korea
    Biochem J 354:655-61. 2001
    ....
  12. pmc Repression by Ikaros and Aiolos is mediated through histone deacetylase complexes
    J Koipally
    Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
    EMBO J 18:3090-100. 1999
    ....
  13. pmc Localization and signaling of G(beta) subunit Ste4p are controlled by a-factor receptor and the a-specific protein Asg7p
    J Kim
    Department of Cell Biology and Anatomy, Mount Sinai School of Medicine, New York, New York 10029, USA
    Mol Cell Biol 20:8826-35. 2000
    ..These results demonstrate that Asg7p mediates a regulatory process that blocks signaling from a G protein beta subunit and causes its relocalization within the cell...
  14. ncbi request reprint Cloning of androgen-inducible gene 1 (AIG1) from human dermal papilla cells
    J Seo
    Department of Immunology, Kyungpook National University School of Medicine, Daegu, Korea
    Mol Cells 11:35-40. 2001
    ..The level of expression was higher in males than females. In this study, we cloned and initially characterized AIG1. Further study will be needed to understand the functions of AIG1 in the androgen-regulated hair cycle...
  15. ncbi request reprint Induction of neuronal cell death by Rab5A-dependent endocytosis of alpha-synuclein
    J Y Sung
    Department of Pharmacology and Brain Research Institute, The Department of Microbiology, and the Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul 120-752, Korea
    J Biol Chem 276:27441-8. 2001
    ..This was further supported by the fact that the expression of GTPase-deficient Rab5A resulted in a significant decrease of its cytotoxicity as a result of incomplete endocytosis of alpha-synuclein...
  16. ncbi request reprint The VACTERL association: lessons from the Sonic hedgehog pathway
    J Kim
    Program in Developmental Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
    Clin Genet 59:306-15. 2001
    ..We propose that VACTERL could be caused by defective Shh signaling during human embryogenesis and suggest that the Gli mutant mice can serve as useful models for studying the pathogenesis of VACTERL...
  17. ncbi request reprint A rapid screen for putative mislocalization mutations by using a GAL4-hybrid protein
    M Y Lee
    Department of Microbiology, College of Natural Sciences, Chungnam National University, Taejeon, Korea
    Mol Cells 11:275-80. 2001
    ....
  18. ncbi request reprint Apoptosis signal-regulating kinase 1 controls the proapoptotic function of death-associated protein (Daxx) in the cytoplasm
    Y G Ko
    National Creative Research Initiatives Center for ARS Network, College of Pharmacy, Seoul National University, Seoul 151 742, Korea
    J Biol Chem 276:39103-6. 2001
    ..Taken together, we could conclude that ASK1 controls the dual function of Daxx as a transcriptional repressor in the nucleus and as a proapoptotic signal mediator in the cytoplasm...
  19. ncbi request reprint Imprinting and evolution of two Kruppel-type zinc-finger genes, ZIM3 and ZNF264, located in the PEG3/USP29 imprinted domain
    J Kim
    Genomics Division, Biology and Biotechnology Research Program, L 441, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94551, USA
    Genomics 77:91-8. 2001
    ..The reciprocal imprinting of two neighboring mouse genes, Zim3 and Zfp264, is consistent with a pattern observed frequently in other imprinted domains, and suggests that the imprinting of these two genes might be coregulated...
  20. ncbi request reprint Yeast ribosomal protein S3 has an endonuclease activity on AP DNA
    S O Jung
    Laboratory of Biochemistry, Graduate School of Biotechnology and BioInstitute, Korea University, Seoul
    Mol Cells 12:84-90. 2001
    ..From these results, both the mammalian rpS3 and Rps3p appear to be involved in DNA damage processing, but in different modes...
  21. ncbi request reprint Is Ffh required for export of secretory proteins?
    J Kim
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3044, USA
    FEBS Lett 505:245-8. 2001
    ..We show that depletion of SRP, but not trigger factor, affects all the mutants examined. These results suggest secretory proteins with a variety of signal sequences, as well as membrane proteins, require SRP for export...
  22. ncbi request reprint Geometry of gene expression dynamics
    S A Rifkin
    Department of Ecology and Evolutionary Biology, PO Box 208106, Yale University, New Haven, CT 06520, USA
    Bioinformatics 18:1176-83. 2002
    ..Genome wide gene expression has a dynamic structure, especially in studies of development and temporal response. Both visualization and analyses of such data require an explicit attention to the temporal structure...
  23. ncbi request reprint Exon sharing of a novel human zinc-finger gene, ZIM2, and paternally expressed gene 3 (PEG3)
    J Kim
    Human Genome Center, Biology and Biotechnology Research Program, L 452, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94551, USA
    Genomics 64:114-8. 2000
    ....
  24. pmc The Drosophila melanogaster suppressor of Hairy-wing zinc finger protein has minimal effects on gene expression in Saccharomyces cerevisiae
    J Kim
    Program in Molecular Biology, Sloan Kettering Institute for Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
    Genetics 135:343-55. 1993
    ..These observations indicate that the observed effects of SUHW on gene expression in Drosophila require specific interactions with other factors that are absent or unrecognizable in yeast...
  25. ncbi request reprint ROK1, a high-copy-number plasmid suppressor of kem1, encodes a putative ATP-dependent RNA helicase in Saccharomyces cerevisiae
    Y Song
    Department of Microbiology, College of Natural Sciences, Chungnam National University, Daejeon, South Korea
    Gene 166:151-4. 1995
    ..The ROK1 aa sequence contains highly conserved domains found in the DEAD protein family of ATP-dependent RNA helicases. ROK1 is essential for viability and is closely linked to KEM1 on chromosome VII...
  26. ncbi request reprint Isolation and characterization of Saccharomyces cerevisiae SAB2, a suppressor gene for temperature-sensitive phenotype of ARS-binding factor 1 mutant
    Y H Shin
    Department and Institute of Genetic Engineering, Kyung Hee University, Suwon, Korea
    Biochem Mol Biol Int 40:915-21. 1996
    ..Binding of ABF1 to two of the sites tested in this study was detected. Our results indicate that ABF1 may be involved in the transcriptional control of the yeast tryptophan permease gene...
  27. pmc Genetic analysis of default mating behavior in Saccharomyces cerevisiae
    R Dorer
    Fred Hutchinson Cancer Research Center, Seattle, Washington 98104, USA
    Genetics 146:39-55. 1997
    ..We suggest that default mating places a more stringent requirement on some aspects of cell fusion than does chemotropic mating...
  28. pmc The human homolog of a mouse-imprinted gene, Peg3, maps to a zinc finger gene-rich region of human chromosome 19q13.4
    J Kim
    Biology Division, Oak Ridge National Laboratory, Tennessee 37831 8077, USA
    Genome Res 7:532-40. 1997
    ..4 and mouse chromosome 7...
  29. ncbi request reprint Cloning and developmental expression of Xenopus cDNAs encoding the Enhancer of split groucho and related proteins
    B K Choudhury
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Gene 195:41-8. 1997
    ..8 kb and 2.2 kb, respectively, were ubiquitously expressed in the developing embryos. The overall structural relationships of ESG and AES proteins among human, mouse, rat, Xenopus and Drosophila were analysed...
  30. ncbi request reprint Molecular cloning and characterization of the Saccharomyces cerevisiae SAB1 gene that suppresses a temperature-sensitive phenotype of the ARS-binding factor 1 mutant
    I S So
    Department and Institute of Genetic Engineering, Kyung Hee University, Suwon, Korea
    Mol Cells 7:532-6. 1997
    ..Our results suggest that ABF1 might be important for the transcription of the yeast TRP1 gene in addition to having important roles in the stimulation of replication at the ARS1 locus...
  31. pmc Protein-protein interactions among the Aux/IAA proteins
    J Kim
    Plant Gene Expression Center, 800 Buchanan Street, Albany, CA 94710, USA
    Proc Natl Acad Sci U S A 94:11786-91. 1997
    ..These interactions provide a molecular basis for the developmental and tissue-specific manner of auxin action...
  32. pmc A nucleolar protein that affects mating efficiency in Saccharomyces cerevisiae by altering the morphological response to pheromone
    J Kim
    Department of Cell Biology and Anatomy, Mount Sinai School of Medicine, New York, New York 10029, USA
    Genetics 149:795-805. 1998
    ....
  33. pmc Receptor inhibition of pheromone signaling is mediated by the Ste4p Gbeta subunit
    J Kim
    Department of Cell Biology and Anatomy, Mount Sinai School of Medicine, New York, New York 10029, USA
    Mol Cell Biol 19:441-9. 1999
    ..The results presented here are consistent with a model in which an a-specific gene product other than Ste2p detects the presence of the a-factor receptor and blocks signaling by inhibiting the function of Ste4p...
  34. pmc Requirement of RBP9, a Drosophila Hu homolog, for regulation of cystocyte differentiation and oocyte determination during oogenesis
    J Kim-Ha
    Center for Molecular Medicine, Samsung Biomedical Research Institute, Sungkyunkwan University College of Medicine, Kangnam Ku, Seoul 135 230, Korea
    Mol Cell Biol 19:2505-14. 1999
    ..Therefore, the concentrated localization of RBP9 protein in the oocyte of the early egg chambers may be required for proper oocyte determination or positioning...
  35. ncbi request reprint Zim1, a maternally expressed mouse Kruppel-type zinc-finger gene located in proximal chromosome 7
    J Kim
    Human Genome Center, Biology and Biotechnology Research Program, L 452, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94551, USA
    Hum Mol Genet 8:847-54. 1999
    ..5/Mmu7 ( H19 / Igf2 ) and suggests that the two genes may be co-regulated. These and other data suggest the presence of an unexplored, conserved imprinted domain in human chromosome 19q13.4 and proximal Mmu7...
  36. pmc ATP hydrolysis activity of the DEAD box protein Rok1p is required for in vivo ROK1 function
    J Y Oh
    Department of Microbiology, College of Natural Sciences, Chungnam National University, Taejeon 305 764, Korea
    Nucleic Acids Res 27:2753-9. 1999
    ..The lack of RNA dependency and some of the mutational phenotypes of ROK1 differentiate this gene from other members of the family...
  37. ncbi request reprint Haploinsufficiency for the neurofibromatosis 1 (NF1) tumor suppressor results in increased astrocyte proliferation
    D H Gutmann
    Department of Neurology, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Oncogene 18:4450-9. 1999
    ..These findings suggest that reduced NF1 expression results in a cell context-dependent increase in astrocyte proliferation that may be sufficient for the development of astrocytic growth abnormalities in patients with NF1...
  38. ncbi request reprint The inturned protein of Drosophila melanogaster is a cytoplasmic protein located at the cell periphery in wing cells
    U J Yun
    Department of Life Science, Kwangju Institute of Science and Technology K JIST, Kwangju, Korea
    Dev Genet 25:297-305. 1999
    ..The In protein is notably insoluble in buffers containing high salt and nonionic detergents. This lack of solubility is significantly reduced in fz and mwh mutants, implying that it may be related to the mechanism of in function...
  39. pmc Apg9p/Cvt7p is an integral membrane protein required for transport vesicle formation in the Cvt and autophagy pathways
    T Noda
    Department of Cell Biology, National Institute for Basic Biology, Okazaki 444 8585, Japan
    J Cell Biol 148:465-80. 2000
    ..From these results, we propose that Apg9p/Cvt7p may serve as a marker for a specialized compartment essential for these vesicle-mediated alternative targeting pathways...
  40. ncbi request reprint Identification and developmental expression of par-6 gene in Xenopus laevis
    S C Choi
    Department of Life Science, Pohang University of Science and Technology, San 31 Hyoja Dong, Pohang, Kyungbuk, South Korea
    Mech Dev 91:347-50. 2000
    ..Therefore, this analysis suggests that Xpar-6 has a regionalized pattern of expression during Xenopus early embryogenesis...
  41. pmc kem mutations affect nuclear fusion in Saccharomyces cerevisiae
    J Kim
    Massachusetts Institute of Technology, Cambridge
    Genetics 126:799-812. 1990
    ..The KEM 1 gene, which is expressed as a 5.5-kb mRNA transcript, contains a 4.6-kb open reading frame encoding a 175-kD protein...