TrypsNetDB

References

The following list includes the set of references that were used to extract protein-interaction data.

1. 3' adenylation determines mRNA abundance and monitors completion of RNA editing in T. brucei mitochondria.
   Etheridge RD, Aphasizheva I, Gershon PD, Aphasizhev R.
   EMBO J , 2008
2. A core MRB1 complex component is indispensable for RNA editing in insect and human infective stages of Trypanosoma brucei.
   Ammerman ML, Tomasello DL, Faktorová D, Kafková L, Hashimi H, Lukeš J, Read LK.
   PLoS One , 2013
3. A divergent transcription factor TFIIB in trypanosomes is required for RNA polymerase II-dependent spliced leader RNA transcription and cell viability.
   Palenchar JB, Liu W, Palenchar PM, Bellofatto V.
   Eukaryot Cell , 2006
4. A kinetoplastid BRCA2 interacts with DNA replication protein CDC45.
   Oyola SO, Bringaud F, Melville SE.
   Int J Parasitol , 2009
5. A minimal anaphase promoting complex/cyclosome (APC/C) in Trypanosoma brucei.
   Bessat M, Knudsen G, Burlingame AL, Wang CC
   PloS one , 2013
6. A multiple aminoacyl-tRNA synthetase complex that enhances tRNA-aminoacylation in African trypanosomes.
   Cestari I, Kalidas S, Monnerat S, Anupama A, Phillips MA, Stuart K
   Molecular and cellular biology , 2014
7. A novel association between two trypanosome-specific factors and the conserved L5-5S rRNA complex.
   Ciganda M, Prohaska K, Hellman K, Williams N.
   PLoS One , 2012
8. A Novel Basal Body Protein That Is a Polo-like Kinase Substrate Is Required for Basal Body Segregation and Flagellum Adhesion in Trypanosoma brucei.
   Hu H, Zhou Q, Li Z.
   J Biol Chem , 2015
9. A novel member of the RNase D exoribonuclease family functions in mitochondrial guide RNA metabolism in Trypanosoma brucei.
   Zimmer SL, McEvoy SM, Li J, Qu J, Read LK.
   J Biol Chem , 2011
10. A novel Rho-like protein TbRHP is involved in spindle formation and mitosis in trypanosomes.
    Abbasi K, DuBois KN, Leung KF, Dacks JB, Field MC.
    PLoS One , 2011
11. A novel role of centrin in flagellar motility: stabilizing an inner-arm dynein motor in the flagellar axoneme.
    Li Z.
    Microb Cell , 2014
12. A Protein Complex Map of Trypanosoma brucei
    Gazestani VH, Nikpour N, Mehta V, Najafabadi HS, Moshiri H, Jardim A, Salavati R
    PLoS Negl Trop Dis. , 2016
13. A protein-protein interaction map of trypanosome ~20S editosomes.
    Schnaufer A, Wu M, Park YJ, Nakai T, Deng J, Proff R, Hol WG, Stuart KD
    The Journal of biological chemistry , 2010
14. A role for Caf1 in mRNA deadenylation and decay in trypanosomes and human cells.
    Schwede A, Ellis L, Luther J, Carrington M, Stoecklin G, Clayton C
    Nucleic acids research , 2008
15. A TFIIH-associated mediator head is a basal factor of small nuclear spliced leader RNA gene transcription in early-diverged trypanosomes.
    Lee JH, Cai G, Panigrahi AK, Dunham-Ems S, Nguyen TN, Radolf JD, Asturias FJ, Günzl A
    Molecular and cellular biology , 2010
16. A trypanosomal pentatricopeptide repeat protein stabilizes the mitochondrial mRNAs of cytochrome oxidase subunits 1 and 2.
    Pusnik M, Schneider A
    Eukaryotic cell , 2012
17. Active RNA polymerase I of Trypanosoma brucei harbors a novel subunit essential for transcription.
    Nguyen TN, Schimanski B, Günzl A.
    Mol Cell Biol. , 2007
18. Alba-domain proteins of Trypanosoma brucei are cytoplasmic RNA-binding proteins that interact with the translation machinery.
    Mani J, Güttinger A, Schimanski B, Heller M, Acosta-Serrano A, Pescher P, Späth G, Roditi I.
    PLoS One , 2011
19. Alterations in DRBD3 ribonucleoprotein complexes in response to stress in Trypanosoma brucei.
    Fernández-Moya SM, García-Pérez A, Kramer S, Carrington M, Estévez AM.
    PLoS One , 2012
20. An orphan kinesin in trypanosomes cooperates with a kinetoplastid-specific kinesin to maintain cell morphology by regulating subpellicular microtubules.
    Hu H, Hu L, Yu Z, Chasse AE, Chu F, Li Z.
    J Cell Sci , 2012
21. Analysis of spliceosomal proteins in Trypanosomatids reveals novel functions in mRNA processing.
    Tkacz ID, Gupta SK, Volkov V, Romano M, Haham T, Tulinski P, Lebenthal I, Michaeli S
    The Journal of biological chemistry , 2010
22. Architecture of the trypanosome RNA editing accessory complex, MRB1.
    Ammerman ML, Downey KM, Hashimi H, Fisk JC, Tomasello DL, Faktorová D, Kafková L, King T, Lukes J, Read LK
    Nucleic acids research , 2012
23. Arginine methylation of DRBD18 differentially impacts its opposing effects on the trypanosome transcriptome.
    Lott K, Mukhopadhyay S, Li J, Wang J, Yao J, Sun Y, Qu J, Read LK.
    Nucleic Acids Res , 2015
24. Association of two novel proteins, TbMP52 and TbMP48, with the Trypanosoma brucei RNA editing complex.
    Panigrahi AK, Gygi SP, Ernst NL, Igo RP Jr, Palazzo SS, Schnaufer A, Weston DS, Carmean N, Salavati R, Aebersold R, Stuart KD.
    Mol Cell Biol , 2001
25. Biochemical analysis of PIFTC3, the Trypanosoma brucei orthologue of nematode DYF-13, reveals interactions with established and putative intraflagellar transport components.
    Franklin JB, Ullu E
    Molecular microbiology , 2011
26. Biochemical characterization of Trypanosoma brucei RNA polymerase II.
    Das A, Li H, Liu T, Bellofatto V
    Molecular and biochemical parasitology , 2006
27. Characterization of a multisubunit transcription factor complex essential for spliced-leader RNA gene transcription in Trypanosoma brucei.
    Schimanski B, Nguyen TN, Günzl A
    Molecular and cellular biology , 2005
28. Characterization of a novel class I transcription factor A (CITFA) subunit that is indispensable for transcription by the multifunctional RNA polymerase I of Trypanosoma brucei.
    Nguyen TN, Nguyen BN, Lee JH, Panigrahi AK, Günzl A
    Eukaryotic cell , 2013
29. Characterization of a TFIIH homologue from Trypanosoma brucei.
    Lecordier L, Devaux S, Uzureau P, Dierick JF, Walgraffe D, Poelvoorde P, Pays E, Vanhamme L.
    Mol Microbiol , 2007
30. Characterization of subunits of the RNA polymerase I complex in Trypanosoma brucei.
    Walgraffe D, Devaux S, Lecordier L, Dierick JF, Dieu M, Van den Abbeele J, Pays E, Vanhamme L.
    Mol Biochem Parasitol. , 2005
31. Depletion of trypanosome CTR9 leads to gene expression defects.
    Ouna BA, Nyambega B, Manful T, Helbig C, Males M, Fadda A, Clayton C
    PloS one , 2012
32. Discovery of unconventional kinetochores in kinetoplastids.
    Akiyoshi B, Gull K.
    Cell , 2014
33. Disruption of the zinc finger motifs in the Leishmania tarentolae LC-4 (=TbMP63) L-complex editing protein affects the stability of the L-complex.
    Kang X, Falick AM, Nelson RE, Gao G, Rogers K, Aphasizhev R, Simpson L.
    J Biol Chem , 2004
34. DRBD1 is the Trypanosoma brucei homologue of the spliceosome-associated protein 49.
    Manful T, Cristodero M, Clayton C
    Molecular and biochemical parasitology , 2009
35. Editosome accessory factors KREPB9 and KREPB10 in Trypanosoma brucei.
    Lerch M, Carnes J, Acestor N, Guo X, Schnaufer A, Stuart K
    Eukaryotic cell , 2012
36. eIF4F-like complexes formed by cap-binding homolog TbEIF4E5 with TbEIF4G1 or TbEIF4G2 are implicated in post-transcriptional regulation in Trypanosoma brucei.
    Freire ER, Vashisht AA, Malvezzi AM, Zuberek J, Langousis G, Saada EA, Nascimento Jde F, Stepinski J, Darzynkiewicz E, Hill K, De Melo Neto OP, Wohlschlegel JA, Sturm NR, Campbell DA.
    RNA , 2014
37. Endonuclease associations with three distinct editosomes in Trypanosoma brucei.
    Carnes J, Soares CZ, Wickham C, Stuart K.
    J Biol Chem , 2011
38. Essential role of a trypanosome U4-specific Sm core protein in small nuclear ribonucleoprotein assembly and splicing.
    Jaé N, Wang P, Gu T, Hühn M, Palfi Z, Urlaub H, Bindereif A.
    Eukaryot Cell , 2010
39. Evidence for a degradosome-like complex in the mitochondria of Trypanosoma brucei.
    Mattiacio JL, Read LK.
    FEBS Lett , 2009
40. Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor.
    DeGrasse JA, DuBois KN, Devos D, Siegel TN, Sali A, Field MC, Rout MP, Chait BT
    Molecular & cellular proteomics : MCP , 2009
41. Evolutionarily divergent type II protein arginine methyltransferase in Trypanosoma brucei.
    Pasternack DA, Sayegh J, Clarke S, Read LK.
    Eukaryot Cell , 2007
42. Functional characterization and protein-protein interactions of trypanosome splicing factors U2AF35, U2AF65 and SF1.
    Vazquez MP, Mualem D, Bercovich N, Stern MZ, Nyambega B, Barda O, Nasiga D, Gupta SK, Michaeli S, Levin MJ.
    Mol Biochem Parasitol , 2009
43. Functional characterization of the 11 non-ATPase subunit proteins in the trypanosome 19 S proteasomal regulatory complex.
    Li Z, Wang CC
    The Journal of biological chemistry , 2003
44. Functional characterization of the trypanosome translational repressor SCD6.
    Cristodero M, Schimanski B, Heller M, Roditi I.
    Biochem J , 2014
45. Functional characterization of two paralogs that are novel RNA binding proteins influencing mitochondrial transcripts of Trypanosoma brucei.
    Kafková L, Ammerman ML, Faktorová D, Fisk JC, Zimmer SL, Sobotka R, Read LK, Lukes J, Hashimi H
    RNA (New York, N.Y.) , 2012
46. Gene expression regulatory networks in Trypanosoma brucei: insights into the role of the mRNA-binding proteome.
    Lueong S, Merce C, Fischer B, Hoheisel JD, Erben ED.
    Mol Microbiol. , 2016
47. Guide RNA biogenesis involves a novel RNase III family endoribonuclease in Trypanosoma brucei.
    Madina BR, Kuppan G, Vashisht AA, Liang YH, Downey KM, Wohlschlegel JA, Ji X, Sze SH, Sacchettini JC, Read LK, Cruz-Reyes J
    RNA (New York, N.Y.) , 2011
48. Guide RNA-binding complex from mitochondria of trypanosomatids.
    Weng J, Aphasizheva I, Etheridge RD, Huang L, Wang X, Falick AM, Aphasizhev R
    Molecular cell , 2008
49. Identification and characterization of nuclear non-canonical poly(A) polymerases from Trypanosoma brucei.
    Etheridge RD, Clemens DM, Gershon PD, Aphasizhev R.
    Mol Biochem Parasitol , 2009
50. Identification and stage-specific association with the translational apparatus of TbZFP3, a CCCH protein that promotes trypanosome life-cycle development.
    Paterou A, Walrad P, Craddy P, Fenn K, Matthews K.
    J Biol Chem , 2006
51. Identification of a novel chromosomal passenger complex and its unique localization during cytokinesis in Trypanosoma brucei.
    Li Z, Lee JH, Chu F, Burlingame AL, Günzl A, Wang CC
    PloS one , 2008
52. Identification of a novel lipin homologue from the parasitic protozoan Trypanosoma brucei.
    Pelletier M, Frainier AS, Munini DN, Wiemer JM, Karpie AR, Sattora JJ.
    BMC Microbiol , 2013
53. Identification of candidate mitochondrial RNA editing ligases from Trypanosoma brucei.
    McManus MT, Shimamura M, Grams J, Hajduk SL.
    RNA , 2001
54. Identification of novel components of Trypanosoma brucei editosomes.
    Panigrahi AK, Schnaufer A, Ernst NL, Wang B, Carmean N, Salavati R, Stuart K
    RNA (New York, N.Y.) , 2003
55. Identification of ORC1/CDC6-interacting factors in Trypanosoma brucei reveals critical features of origin recognition complex architecture.
    Tiengwe C, Marcello L, Farr H, Gadelha C, Burchmore R, Barry JD, Bell SD, McCulloch R
    PloS one , 2012
56. Identification of the ISWI Chromatin Remodeling Complex of the Early Branching Eukaryote Trypanosoma brucei.
    Stanne TM, Narayanan MS, Ridewood S, Ling A, Witmer K, Kushwaha M, Wiesler S, Wickstead B, Wood J, Rudenko G.
    J Biol Chem , 2015
57. Identification, characterization and essentiality of the unusual peroxin 13 from Trypanosoma brucei.
    Verplaetse E, Rigden DJ, Michels PA
    Biochimica et biophysica acta , 2009
58. In vivo monitoring of norepinephrine and its metabolites in skeletal muscle.
    Tokunaga N, Yamazaki T, Akiyama T, Sano S, Mori H
    Neurochemistry international , 2003
59. Integrity of the core mitochondrial RNA-binding complex 1 is vital for trypanosome RNA editing.
    Huang Z, Faktorová D, Krížová A, Kafková L, Read LK, Lukeš J, Hashimi H.
    RNA , 2015
60. Isolation and compositional analysis of trypanosomatid editosomes.
    Panigrahi AK, Schnaufer A, Stuart KD.
    Methods Enzymol , 2007
61. Isolation of Trypanosoma brucei CYC2 and CYC3 cyclin genes by rescue of a yeast G(1) cyclin mutant. Functional characterization of CYC2.
    Van Hellemond JJ, Neuville P, Schwarz RT, Matthews KR, Mottram JC.
    J Biol Chem , 2000
62. Kinetoplastid RNA-editing-associated protein 1 (REAP-1): a novel editing complex protein with repetitive domains.
    Madison-Antenucci S, Sabatini RS, Pollard VW, Hajduk SL.
    EMBO J , 1998
63. Knockdown of APC/C-associated genes and its effect on viability and cell cycle of protozoan parasite of Trypanosoma brucei.
    Bessat M
    Parasitology research , 2014
64. MCM-BP is required for repression of life-cycle specific genes transcribed by RNA polymerase I in the mammalian infectious form of Trypanosoma brucei.
    Kim HS, Park SH, Günzl A, Cross GA
    PloS one , 2013
65. Mitochondrial complexes in Trypanosoma brucei: a novel complex and a unique oxidoreductase complex.
    Panigrahi AK, Zíková A, Dalley RA, Acestor N, Ogata Y, Anupama A, Myler PJ, Stuart KD
    Molecular & cellular proteomics : MCP , 2008
66. Mitochondrial membrane complex that contains proteins necessary for tRNA import in Trypanosoma brucei.
    Seidman D, Johnson D, Gerbasi V, Golden D, Orlando R, Hajduk S
    The Journal of biological chemistry , 2012
67. MRB3010 is a core component of the MRB1 complex that facilitates an early step of the kinetoplastid RNA editing process.
    Ammerman ML, Hashimi H, Novotná L, Cicová Z, McEvoy SM, Lukes J, Read LK
    RNA (New York, N.Y.) , 2011
68. Multifunctional class I transcription in Trypanosoma brucei depends on a novel protein complex.
    Brandenburg J, Schimanski B, Nogoceke E, Nguyen TN, Padovan JC, Chait BT, Cross GA, Günzl A
    The EMBO journal , 2007
69. Mutational analysis of Trypanosoma brucei editosome proteins KREPB4 and KREPB5 reveals domains critical for function.
    Carnes J, Schnaufer A, McDermott SM, Domingo G, Proff R, Steinberg AG, Kurtz I, Stuart K
    RNA (New York, N.Y.) , 2012
70. Pentatricopeptide repeat proteins stimulate mRNA adenylation/uridylation to activate mitochondrial translation in trypanosomes.
    Aphasizheva I, Maslov D, Wang X, Huang L, Aphasizhev R
    Molecular cell , 2011
71. Proteins associated with SF3a60 in T. brucei
    Nyambega B, Helbig C, Masiga DK, Clayton C, Levin MJ
    PLoS One , 2014
72. Proteomic analysis of clathrin interactions in trypanosomes reveals dynamic evolution of endocytosis
    Adung'a VO, Gadelha C, Field MC
    Traffic. , 2013
73. Purification of an eight subunit RNA polymerase I complex in Trypanosoma brucei.
    Nguyen TN, Schimanski B, Zahn A, Klumpp B, Günzl A.
    Mol Biochem Parasitol. , 2006
74. REH2 RNA helicase in kinetoplastid mitochondria: ribonucleoprotein complexes and essential motifs for unwinding and guide RNA (gRNA) binding.
    Hernandez A, Madina BR, Ro K, Wohlschlegel JA, Willard B, Kinter MT, Cruz-Reyes J
    The Journal of biological chemistry , 2010
75. RNA polymerase II-dependent transcription in trypanosomes is associated with a SNAP complex-like transcription factor.
    Das A, Bellofatto V
    Proceedings of the National Academy of Sciences of the United States o, 2003
76. Separate insertion and deletion subcomplexes of the Trypanosoma brucei RNA editing complex.
    Schnaufer A, Ernst NL, Palazzo SS, O'Rear J, Salavati R, Stuart K
    Molecular cell , 2003
77. Sm core variation in spliceosomal small nuclear ribonucleoproteins from Trypanosoma brucei.
    Wang P, Palfi Z, Preusser C, Lücke S, Lane WS, Kambach C, Bindereif A
    The EMBO journal , 2006
78. Special Sm core complex functions in assembly of the U2 small nuclear ribonucleoprotein of Trypanosoma brucei.
    Preusser C, Palfi Z, Bindereif A
    Eukaryotic cell , 2009
79. Spliceosomal proteomics in Trypanosoma brucei reveal new RNA splicing factors.
    Luz Ambrósio D, Lee JH, Panigrahi AK, Nguyen TN, Cicarelli RM, Günzl A
    Eukaryotic cell , 2009
80. TbG63, a golgin involved in Golgi architecture in Trypanosoma brucei.
    Ramirez IB, de Graffenried CL, Ebersberger I, Yelinek J, He CY, Price A, Warren G.
    J Cell Sci. , 2008
81. TbPRMT6 is a type I protein arginine methyltransferase that contributes to cytokinesis in Trypanosoma brucei
    Fisk JC, Zurita-Lopez C, Sayegh J, Tomasello DL, Clarke SG, Read LK
    Eukaryot Cell , 2010
82. TbRGG1, an essential protein involved in kinetoplastid RNA metabolism that is associated with a novel multiprotein complex.
    Hashimi H, Zíková A, Panigrahi AK, Stuart KD, Lukes J
    RNA (New York, N.Y.) , 2008
83. The CAF1-NOT complex of trypanosomes.
    Erben E, Chakraborty C, Clayton C.
    Front Genet. , 2014
84. The Cdc45·Mcm2-7·GINS protein complex in trypanosomes regulates DNA replication and interacts with two Orc1-like proteins in the origin recognition complex.
    Dang HQ, Li Z
    The Journal of biological chemistry , 2011
85. The F(0)F(1)-ATP synthase complex contains novel subunits and is essential for procyclic Trypanosoma brucei.
    Zíková A, Schnaufer A, Dalley RA, Panigrahi AK, Stuart KD
    PLoS pathogens , 2009
86. The importance of the 45 S ribosomal small subunit-related complex for mitochondrial translation in Trypanosoma brucei.
    Ridlon L, Škodová I, Pan S, Lukeš J, Maslov DA
    The Journal of biological chemistry , 2014
87. The nuclear mRNA export receptor Mex67-Mtr2 of Trypanosoma brucei contains a unique and essential zinc finger motif.
    Dostalova A, Käser S, Cristodero M, Schimanski B
    Molecular microbiology , 2013
88. The RACK1 signal anchor protein from Trypanosoma brucei associates with eukaryotic elongation factor 1A: a role for translational control in cytokinesis.
    Regmi S, Rothberg KG, Hubbard JG, Ruben L.
    Mol Microbiol. , 2008
89. The roles of intersubunit interactions in exosome stability.
    Estévez AM, Lehner B, Sanderson CM, Ruppert T, Clayton C
    The Journal of biological chemistry , 2003
90. The spliceosomal PRP19 complex of trypanosomes.
    Ambrósio DL, Badjatia N, Günzl A
    Molecular microbiology , 2015
91. Transcriptionally active TFIIH of the early-diverged eukaryote Trypanosoma brucei harbors two novel core subunits but not a cyclin-activating kinase complex.
    Lee JH, Jung HS, Günzl A
    Nucleic acids research , 2009
92. Trypanosoma brucei mitochondrial respiratome: composition and organization in procyclic form.
    Acestor N, Zíková A, Dalley RA, Anupama A, Panigrahi AK, Stuart KD
    Molecular & cellular proteomics : MCP , 2012
93. Trypanosoma brucei mitochondrial ribosomes: affinity purification and component identification by mass spectrometry.
    Zíková A, Panigrahi AK, Dalley RA, Acestor N, Anupama A, Ogata Y, Myler PJ, Stuart K
    Molecular & cellular proteomics : MCP , 2008
94. Trypanosoma brucei spliced leader RNA maturation by the cap 1 2'-O-ribose methyltransferase and SLA1 H/ACA snoRNA pseudouridine synthase complex.
    Zamudio JR, Mittra B, Chattopadhyay A, Wohlschlegel JA, Sturm NR, Campbell DA
    Molecular and cellular biology , 2009
95. Trypanosoma brucei translation initiation factor homolog EIF4E6 forms a tripartite cytosolic complex with EIF4G5 and a capping enzyme homolog.
    Freire ER, Malvezzi AM, Vashisht AA, Zuberek J, Saada EA, Langousis G, Nascimento JD, Moura D, Darzynkiewicz E, Hill K, de Melo Neto OP, Wohlschlegel JA, Sturm NR, Campbell DA
    Eukaryotic cell , 2015
96. Trypanosome CNOT10 is essential for the integrity of the NOT deadenylase complex and for degradation of many mRNAs.
    Färber V, Erben E, Sharma S, Stoecklin G, Clayton C.
    Nucleic Acids Res. , 2013
97. Trypanosome MKT1 and the RNA-binding protein ZC3H11: interactions and potential roles in post-transcriptional regulatory networks.
    Singh A, Minia I, Droll D, Fadda A, Clayton C, Erben E.
    Nucleic Acids Res. , 2014