K Stuart

Summary

Affiliation: University of Washington
Country: USA

Publications

  1. ncbi request reprint An RNA ligase essential for RNA editing and survival of the bloodstream form of Trypanosoma brucei
    A Schnaufer
    Seattle Biomedical Research Institute, Seattle, WA 98109, USA
    Science 291:2159-62. 2001
  2. ncbi request reprint Investigating the mechanism and machinery of RNA editing
    K Stuart
    Seattle Biomedical Research Institute, Washington 98109 1651, USA
    Methods 15:3-14. 1998
  3. ncbi request reprint RNA editing: complexity and complications
    Kenneth Stuart
    Seattle Biomedical Research Institute, WA 98109, USA
    Mol Microbiol 45:591-6. 2002
  4. ncbi request reprint Complex management: RNA editing in trypanosomes
    Kenneth D Stuart
    Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
    Trends Biochem Sci 30:97-105. 2005
  5. pmc Composition of the editing complex of Trypanosoma brucei
    K Stuart
    Seattle Biomedical Research Institute, 4 Nickerson Street, Seattle, WA 98109, USA
    Philos Trans R Soc Lond B Biol Sci 357:71-9. 2002
  6. pmc RNA editing in kinetoplastid protozoa
    K Stuart
    Seattle Biomedical Research Institute, Washington 98109 1651, USA
    Microbiol Mol Biol Rev 61:105-20. 1997
  7. ncbi request reprint Kinetoplastid RNA editing: complexes and catalysts
    K Stuart
    Seattle Biomedical Research Institute, 4 Nickerson Street, WA 98109 1651, USA
    Curr Opin Chem Biol 1:340-6. 1997
  8. ncbi request reprint An extensively edited mitochondrial transcript in kinetoplastids encodes a protein homologous to ATPase subunit 6
    G J Bhat
    Seattle Biomedical Research Institute, Washington 98109 1651
    Cell 61:885-94. 1990
  9. pmc Creation of AUG initiation codons by addition of uridines within cytochrome b transcripts of kinetoplastids
    J E Feagin
    Seattle Biomedical Research Institute, WA 98109 1651
    Proc Natl Acad Sci U S A 85:539-43. 1988
  10. ncbi request reprint Genomic organization and gene function in Leishmania
    P J Myler
    Seattle Biomedical Research Institute, 4 Nickerson Street, Seattle, WA 98109 1651, USA
    Biochem Soc Trans 28:527-31. 2000

Collaborators

  • ACHIM C SCHNAUFER
  • P J Myler
  • J E Feagin
  • D J Koslowsky
  • A Ivens
  • L Simpson
  • A W Stadnyk
  • Christine E Clayton
  • S Lawson
  • Frederic Bringaud
  • Neil Hall
  • Masahiro Inoue
  • Maria Schumacher
  • Nancy Lewis Ernst
  • Reza Salavati
  • Aswini K Panigrahi
  • Alena Zíková
  • Jason Carnes
  • Robert P Igo
  • Setareh S Palazzo
  • James Raffaello Trotter
  • Bingbing Wang
  • Brian Panicucci
  • Salvador Zipagan Tarun
  • Alfredo Hernandez
  • Rachel A Dalley
  • Michele Fleck
  • Vinod Kumar Babbarwal
  • S Yan
  • Julius Lukes
  • Eva Vondrusková
  • Annelise Sahin
  • Jeff O'Rear
  • Elodie Ghedin
  • Elizabeth A Worthey
  • Maciej Drozdz
  • S Martinez-Calvillo
  • Aswini Panigrahi
  • Jorge Cruz-Reyes
  • Adam Peltan
  • Emanuela Handman
  • Yuko Ogata
  • Atashi Anupama
  • Nathalie Acestor
  • Wim Hol
  • Catherine Cifuentes-Rojas
  • Rosemary Proff
  • Anastasia Sacharidou
  • Lukas Trantirek
  • Jana Kopecná
  • Alessandro D Uboldi
  • Junpeng Deng
  • Troy Gilliam
  • Salvador Tarun
  • Rob Benne
  • Alodie Steinberg
  • Janny van den Burg
  • Claire M Fraser
  • Norbert Bakalara
  • Lee Murphy
  • Emmanuel Tetaud
  • Jonathan Eisen
  • Esteban Bontempi
  • Guillaume Lemercier
  • Jeremy Peterson
  • Gilles Merlin
  • Mark D Adams
  • Sam Angiuoli
  • Bjorn Andersson
  • Matthew Berriman
  • Nicola Lennard
  • Anna Von Arx
  • Steven Salzberg
  • Owen White
  • Benoit Espiau
  • Najib M A El-Sayed
  • David Wanless
  • I Saira Mian
  • Nicole Carmean
  • Nancy L Ernst
  • Paul A Haynes
  • Thomas E Allen
  • Steven P Gygi
  • David S Weston
  • Stefan Heidmann
  • Barbara A Morach
  • M Fox
  • S M Sunkin
  • G J Bhat
  • B L Smiley

Detail Information

Publications43

  1. ncbi request reprint An RNA ligase essential for RNA editing and survival of the bloodstream form of Trypanosoma brucei
    A Schnaufer
    Seattle Biomedical Research Institute, Seattle, WA 98109, USA
    Science 291:2159-62. 2001
    ..The editing complex, which is present in all kinetoplastid parasites, may thus be a chemotherapeutic target...
  2. ncbi request reprint Investigating the mechanism and machinery of RNA editing
    K Stuart
    Seattle Biomedical Research Institute, Washington 98109 1651, USA
    Methods 15:3-14. 1998
    ..This complex is composed of multiple proteins and contains several catalytic activities. It is in the early stages of characterization. The methods described here are intended to assist in its further analysis...
  3. ncbi request reprint RNA editing: complexity and complications
    Kenneth Stuart
    Seattle Biomedical Research Institute, WA 98109, USA
    Mol Microbiol 45:591-6. 2002
    ..It also contains domains for anchor duplex and upstream RNA binding, which position the sequence to be edited in the catalysis domain...
  4. ncbi request reprint Complex management: RNA editing in trypanosomes
    Kenneth D Stuart
    Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
    Trends Biochem Sci 30:97-105. 2005
    ..The dynamic processes, which might entail interactions among multiprotein complexes and changes in their composition and conformation, remain to be elucidated...
  5. pmc Composition of the editing complex of Trypanosoma brucei
    K Stuart
    Seattle Biomedical Research Institute, 4 Nickerson Street, Seattle, WA 98109, USA
    Philos Trans R Soc Lond B Biol Sci 357:71-9. 2002
    ..This is surprising because mutants devoid of genes encoding RNAs that become edited survive as bloodstream forms but encouraging since editing complex components may be targets for chemotherapy...
  6. pmc RNA editing in kinetoplastid protozoa
    K Stuart
    Seattle Biomedical Research Institute, Washington 98109 1651, USA
    Microbiol Mol Biol Rev 61:105-20. 1997
    ..The origin of editing, its developmental regulation which helps control the switching between terminal respiratory systems during the life cycle of trypanosomes, and other areas for future study are discussed...
  7. ncbi request reprint Kinetoplastid RNA editing: complexes and catalysts
    K Stuart
    Seattle Biomedical Research Institute, 4 Nickerson Street, WA 98109 1651, USA
    Curr Opin Chem Biol 1:340-6. 1997
    ..Recent studies have resolved the general mechanism of editing, and show that editing occurs in association with a macromolecular complex...
  8. ncbi request reprint An extensively edited mitochondrial transcript in kinetoplastids encodes a protein homologous to ATPase subunit 6
    G J Bhat
    Seattle Biomedical Research Institute, Washington 98109 1651
    Cell 61:885-94. 1990
    ..In addition, their hydropathic profiles are quite similar to those of other species. We therefore conclude that MURF4 encodes ATPase subunit 6 genes...
  9. pmc Creation of AUG initiation codons by addition of uridines within cytochrome b transcripts of kinetoplastids
    J E Feagin
    Seattle Biomedical Research Institute, WA 98109 1651
    Proc Natl Acad Sci U S A 85:539-43. 1988
    ..Since some other kinetoplastid mitochondrial genes also lack conventional initiation codons, creation of initiation codons may be an important function of uridine addition...
  10. ncbi request reprint Genomic organization and gene function in Leishmania
    P J Myler
    Seattle Biomedical Research Institute, 4 Nickerson Street, Seattle, WA 98109 1651, USA
    Biochem Soc Trans 28:527-31. 2000
    ..Recombinant ORFF antigen shows promise as a serodiagnostic. We have also developed a tetracycline-regulated promoter system, which allows us to modulate gene expression in Leishmania...
  11. pmc The trypanosome leucine repeat gene in the variant surface glycoprotein expression site encodes a putative metal-binding domain and a region resembling protein-binding domains of yeast, Drosophila, and mammalian proteins
    B L Smiley
    Seattle Biomedical Research Institute, Washington 98109 1651
    Mol Cell Biol 10:6436-44. 1990
    ..The leucine-rich repeat and putative metal-binding domains suggest a possible regulatory role that may involve adenylate cyclase activity or nucleic acid binding...
  12. ncbi request reprint Tetracycline regulated gene expression in Leishmania donovani
    S Yan
    Seattle Biomedical Research Institute, 4 Nickerson Street, Seattle, WA 98109-1651, USA
    Mol Biochem Parasitol 112:61-9. 2001
    ..There was no linear relationship between the level of TETR expression and the regulation, and changing of positions of operator did not increase regulation...
  13. ncbi request reprint The two ATPase 6 mRNAs of Leishmania tarentolae differ at their 3' ends
    G J Bhat
    Seattle Biomedical Research Institute, WA 98109 1651
    Mol Biochem Parasitol 48:139-49. 1991
    ..Although variation in the length of the 3' untranslated region cannot be excluded, the size difference is probably to be due to variation in the length of the poly(A) tail...
  14. ncbi request reprint Identification and characterization of trypanosome RNA-editing complex components
    Kenneth Stuart
    Seattle Biomedical Research Institute, and Department of Pathobiology, University of Washington, Seattle, USA
    Methods Mol Biol 265:273-91. 2004
    ..This chapter describes the methods used to purify the RNA-editing complex, to identify the proteins by mass spectrometry, and to demonstrate the functions for some of the proteins...
  15. pmc KREPA6 is an RNA-binding protein essential for editosome integrity and survival of Trypanosoma brucei
    Salvador Zipagan Tarun
    Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
    RNA 14:347-58. 2008
    ..It functions in RNA binding perhaps primarily through the gRNA 3' oligo(U) tail. The significance of these findings to key steps in editing is discussed...
  16. pmc TbMP44 is essential for RNA editing and structural integrity of the editosome in Trypanosoma brucei
    Bingbing Wang
    Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
    Eukaryot Cell 2:578-87. 2003
    ..These data indicate that TbMP44 is a component of the editosome that is essential for editing and critical for the structural integrity of the editosome...
  17. pmc KREPA4, an RNA binding protein essential for editosome integrity and survival of Trypanosoma brucei
    Reza Salavati
    Seattle Biomedical Research Institute, Washington 98109 5219, USA
    RNA 12:819-31. 2006
    ..These data suggest that KREPA4 is an RNA binding protein that may be specific for the gRNA Utail and also is important for 20S editosome stability...
  18. pmc An essential role of KREPB4 in RNA editing and structural integrity of the editosome in Trypanosoma brucei
    Vinod Kumar Babbarwal
    Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
    RNA 13:737-44. 2007
    ..These data suggest that KREPB4 is important for the structural integrity of approximately 20S editosomes, editing endonuclease activity, and the viability of PF T. brucei cells...
  19. ncbi request reprint Endoribonuclease activities of Trypanosoma brucei mitochondria
    Reza Salavati
    Seattle Biomedical Research Institute and Department of Pathobiology, University of Washington, 4 Nickerson Street, Seattle, WA 98109, USA
    Mol Biochem Parasitol 120:23-31. 2002
    ....
  20. pmc RNA sequence and base pairing effects on insertion editing in Trypanosoma brucei
    Robert P Igo
    Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
    Mol Cell Biol 22:1567-76. 2002
    ..Thus, several aspects of mRNA-gRNA interaction, as well as gRNA base pairing with added U's, optimize editing efficiency, although they are not required for insertion editing...
  21. ncbi request reprint Genomic organization and functional characterization of the Leishmania major Friedlin ribosomal RNA gene locus
    S Martinez-Calvillo
    Seattle Biomedical Research Institute, 4 Nickerson Street, Seattle, WA 98109 1651, USA
    Mol Biochem Parasitol 116:147-57. 2001
    ..Nuclear run-on analyses demonstrated that only the rRNA-coding strand is transcribed, downstream of this RNA polymerase I (pol I) promoter. These experiments also suggested that transcription terminates upstream of the IGSRE...
  22. pmc RNA editing in Trypanosoma brucei requires three different editosomes
    Jason Carnes
    Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, USA
    Mol Cell Biol 28:122-30. 2008
    ..This unexpected finding reveals an additional level of complexity in the RNA editing process and suggests a mechanism for how the selection of sites for editing in vivo is controlled...
  23. pmc An essential RNase III insertion editing endonuclease in Trypanosoma brucei
    Jason Carnes
    Seattle Biomedical Research Institute, Seattle, WA 98109, USA
    Proc Natl Acad Sci U S A 102:16614-9. 2005
    ..These data indicate that KREPB3 is an RNA editing endonuclease that is specific for insertion sites and is accordingly renamed KREN2 (kinetoplastid RNA editing endonuclease 2)...
  24. pmc Differential functions of two editosome exoUases in Trypanosoma brucei
    Nancy Lewis Ernst
    Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
    RNA 15:947-57. 2009
    ..Furthermore, although KREX2 appears dispensable for cell growth, the increased inhibition of editing and parasite viability upon knockdown of both KREX1 and KREX2 together suggests that both proteins have roles in editing...
  25. ncbi request reprint A deletion site editing endonuclease in Trypanosoma brucei
    James Raffaello Trotter
    Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
    Mol Cell 20:403-12. 2005
    ..These data indicate that KREPB1 is an endoribonuclease that is specific for RNA editing deletion sites...
  26. ncbi request reprint In vitro assays for kinetoplastid U insertion-deletion editing and associated activities
    Kenneth Stuart
    Seattle Biomedical Research Institute, and Department of Pathobiology, University of Washington, Seattle, USA
    Methods Mol Biol 265:251-72. 2004
    ..Studies using these assays have shown that the characteristics of each activity contribute to editing site selection, U addition and removal, and RNA ligation resulting in accurately edited mRNAs...
  27. ncbi request reprint Kinetoplastid RNA editing ligases: complex association, characterization, and substrate requirements
    Setareh S Palazzo
    Seattle Biomedical Research Institute, 4 Nickerson St, Seattle, WA 98109, USA
    Mol Biochem Parasitol 127:161-7. 2003
    ..The substrate specificity and catalytic characteristics indicate that RNA ligase activity contributes to the accuracy of RNA editing...
  28. pmc Role of uridylate-specific exoribonuclease activity in Trypanosoma brucei RNA editing
    Robert P Igo
    Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
    Eukaryot Cell 1:112-8. 2002
    ..ExoUase is stereospecific and cannot remove (Rp)alpha-thio-U. The specificity of the exoUase activity thus contributes to the precision of RNA editing...
  29. pmc Identification of novel components of Trypanosoma brucei editosomes
    Aswini K Panigrahi
    Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
    RNA 9:484-92. 2003
    ..Five of the proteins are interrelated, as are two others, and one is related to four previously identified editosome proteins. The implications of these findings are discussed...
  30. ncbi request reprint TbMP57 is a 3' terminal uridylyl transferase (TUTase) of the Trypanosoma brucei editosome
    Nancy Lewis Ernst
    Seattle Biomedical Research Institute, Seattle, WA 98109, USA
    Mol Cell 11:1525-36. 2003
    ..Recombinant TbMP57 specifically interacts with the editosome protein TbMP81, and this interaction enhances the TUTase activity. These results suggest that TbMP57 catalyzes U addition to pre-mRNA during editing...
  31. ncbi request reprint Mass spectrometric analysis of the editosome and other multiprotein complexes in Trypanosoma brucei
    Aswini K Panigrahi
    Department of Pathobiology, University of Washington, and Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
    J Am Soc Mass Spectrom 14:728-35. 2003
    ..Analyses of mitochondrial fractions identified several non-editosome proteins and multi-protein complexes. These studies contribute to the functional annotation of T. brucei genome...
  32. pmc Comparative analysis of editosome proteins in trypanosomatids
    Elizabeth A Worthey
    Seattle Biomedical Research Institute, Seattle, WA 98109, USA
    Nucleic Acids Res 31:6392-408. 2003
    ..These domains are generally conserved within other protein families, but some are found in novel combinations in the editosome proteins...
  33. pmc A hammerhead ribozyme substrate and reporter for in vitro kinetoplastid RNA editing
    Bingbing Wang
    Department of Pathobiology, University of Washington, Seattle, 98195, USA
    RNA 8:548-54. 2002
    ..Hammerhead ribozymes are thus sensitive tools to assay in vitro RNA editing...
  34. ncbi request reprint Separate insertion and deletion subcomplexes of the Trypanosoma brucei RNA editing complex
    Achim Schnaufer
    Seattle Biomedical Research Institute, 4 Nickerson Street, Suite 200, Seattle, WA 98109, USA
    Mol Cell 12:307-19. 2003
    ..This study provides insight into the molecular architecture of the editosome and supports the existence of separate subcomplexes for deletion and insertion editing...
  35. pmc Trypanosoma brucei mitochondrial ribosomes: affinity purification and component identification by mass spectrometry
    Alena Zíková
    Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
    Mol Cell Proteomics 7:1286-96. 2008
    ..Nevertheless most of the identified proteins have no homology outside Kinetoplastida implying very low conservation and/or a divergent function in kinetoplastid mitochondria...
  36. pmc Structural and functional association of Trypanosoma brucei MIX protein with cytochrome c oxidase complex
    Alena Zíková
    Seattle Biomedical Research Institute, 307 Westlake Ave North, Suite 500, Seattle, WA 98109 5219, USA
    Eukaryot Cell 7:1994-2003. 2008
    ..The specific function of MIX is unknown, but it appears to be important for the function of complex IV and for mitochondrial segregation and cell division in T. brucei...
  37. pmc Determinants for association and guide RNA-directed endonuclease cleavage by purified RNA editing complexes from Trypanosoma brucei
    Alfredo Hernandez
    Department of Biochemistry and Biophysics, Texas A and M University, 2128 TAMU, College Station, TX 77843, USA
    J Mol Biol 381:35-48. 2008
    ..A model is proposed whereby one or more RNase III-type endonucleases mediate the initial binding and scrutiny of potential ligands and subsequent catalytic selectivity triggers either insertion or deletion editing enzymes...
  38. pmc Structure and function of the native and recombinant mitochondrial MRP1/MRP2 complex from Trypanosoma brucei
    Alena Zíková
    Institute of Parasitology, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
    Int J Parasitol 38:901-12. 2008
    ..A mechanism of catalysed annealing of gRNA/pre-mRNA by the MRP1/MRP2 complex is proposed...
  39. pmc TbMP81 is required for RNA editing in Trypanosoma brucei
    Maciej Drozdz
    Zentrum fur Molekulare Biologie, Heidelberg, Germany
    EMBO J 21:1791-9. 2002
    ..These results indicate that TbMP81 is required for RNA editing and suggest that the editing complex is functionally partitioned...
  40. ncbi request reprint The 14-3-3 proteins of Trypanosoma brucei function in motility, cytokinesis, and cell cycle
    Masahiro Inoue
    Department of Parasitology, Kurume University School of Medicine, 67 Asahi Machi, Kurume, Fukuoka 830 0011, Japan
    J Biol Chem 280:14085-96. 2005
    ..These findings indicate that the 14-3-3 proteins play important roles in cell motility, cytokinesis, and the cell cycle...
  41. ncbi request reprint RNA interference analyses suggest a transcript-specific regulatory role for mitochondrial RNA-binding proteins MRP1 and MRP2 in RNA editing and other RNA processing in Trypanosoma brucei
    Eva Vondrusková
    Institute of Parasitology, Czech Academy of Sciences, and Faculty of Biology, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
    J Biol Chem 280:2429-38. 2005
    ..These data indicate that MRP1 and MRP2 are not essential for RNA editing per se but, rather, play a regulatory role in the editing of specific transcripts and other RNA processing activities...
  42. ncbi request reprint Trypanosomatid flagellum biogenesis: ARL-3A is involved in several species
    Annelise Sahin
    Laboratoire de Genomique Fonctionnelle des Trypanosomatides, UMR CNRS 5162, Universite Bordeaux 2, 146 rue Leo Saignat, 33000 Bordeaux, France
    Exp Parasitol 108:126-33. 2004
    ..Potential significance for the protein function is discussed as well as future strategies for stopping the transmission of several neglected parasitic diseases...
  43. ncbi request reprint Gene synteny and evolution of genome architecture in trypanosomatids
    Elodie Ghedin
    Parasity Genomics, The Institute for Genomics Research, 9712 Medical Center Dr Rockville, MD 20850, USA
    Mol Biochem Parasitol 134:183-91. 2004
    ..major by examining the regions near breakage points of the synteny. This is the first such element found in L. major suggesting that retroelements were found in the common ancestor of all three species...