Gene expression regulatory networks in Trypanosoma brucei: insights into the role of the mRNA-binding proteome

被引:81
作者
Lueong, Smiths [1 ]
Merce, Clementine [2 ,4 ]
Fischer, Bernd [3 ]
Hoheisel, Jorg D. [1 ]
Erben, Esteban D. [2 ]
机构
[1] Deutsch Krebsforschungszentrum DKFZ, Funct Genome Anal, Neuenheimer Feld 580, D-69120 Heidelberg, Germany
[2] Univ Heidelberg ZMBH, Zentrum Mol Biol, DKFZ ZMBH Alliance, Neuenheimer Feld 282, Heidelberg 69120, Germany
[3] Deutsch Krebsforschungszentrum DKFZ, Computat Genome Biol, Neuenheimer Feld 580, Heidelberg 69120, Germany
[4] Deutsch Krebsforschungszentrum DKFZ, Mol Genome Anal, Neuenheimer Feld 460, D-69120 Heidelberg, Germany
关键词
BLOOD-STREAM; RECOMBINATIONAL CLONING; CCCH PROTEIN; IDENTIFICATION; COMPLEX; YEAST; DIFFERENTIATION; REVEALS; DEADENYLATION; CYTOKINESIS;
D O I
10.1111/mmi.13328
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Control of gene expression at the post-transcriptional level is essential in all organisms, and RNA-binding proteins play critical roles from mRNA synthesis to decay. To fully understand this process, it is necessary to identify the complete set of RNA-binding proteins and the functional consequences of the protein-mRNA interactions. Here, we provide an overview of the proteins that bind to mRNAs and their functions in the pathogenic bloodstream form of Trypanosoma brucei. We describe the production of a small collection of open-reading frames encoding proteins potentially involved in mRNA metabolism. With this ORFeome collection, we used tethering to screen for proteins that play a role in post-transcriptional control. A yeast two-hybrid screen showed that several of the discovered repressors interact with components of the CAF1/NOT1 deadenylation complex. To identify the RNA-binding proteins, we obtained the mRNA-bound proteome. We identified 155 high-confidence candidates, including many not previously annotated as RNA-binding proteins. Twenty seven of these proteins affected reporter expression in the tethering screen. Our study provides novel insights into the potential trypanosome mRNPs composition, architecture and function.
引用
收藏
页码:457 / 471
页数:15
相关论文
共 84 条
[1]   Single-locus targeting constructs for reliable regulated RNAi and transgene expression in Trypanosoma brucei [J].
Alsford, Sam ;
Horn, David .
MOLECULAR AND BIOCHEMICAL PARASITOLOGY, 2008, 161 (01) :76-79
[2]   High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome [J].
Alsford, Sam ;
Turner, Daniel J. ;
Obado, Samson O. ;
Sanchez-Flores, Alejandro ;
Glover, Lucy ;
Berriman, Matthew ;
Hertz-Fowler, Christiane ;
Horn, David .
GENOME RESEARCH, 2011, 21 (06) :915-924
[3]   The mRNAs associated to a zinc finger protein from Trypanosoma cruzi shift during stress conditions [J].
Alves, Lysangela Ronalte ;
Oliveira, Camila ;
Moerking, Patricia Alves ;
Kessler, Rafael Luis ;
Martins, Sharon Toledo ;
Alves Romagnoli, Bruno Accioly ;
Marchini, Fabricio Kerrynton ;
Goldenberg, Samuel .
RNA BIOLOGY, 2014, 11 (07) :921-933
[4]   Trypanosoma brucei PUF9 Regulates mRNAs for Proteins Involved in Replicative Processes over the Cell Cycle [J].
Archer, Stuart K. ;
Luu, Van-Duc ;
de Queiroz, Rafael A. ;
Brems, Stefanie ;
Clayton, Christine .
PLOS PATHOGENS, 2009, 5 (08)
[5]   The MEME Suite [J].
Bailey, Timothy L. ;
Johnson, James ;
Grant, Charles E. ;
Noble, William S. .
NUCLEIC ACIDS RESEARCH, 2015, 43 (W1) :W39-W49
[6]   The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts [J].
Baltz, Alexander G. ;
Munschauer, Mathias ;
Schwanhaeusser, Bjoern ;
Vasile, Alexandra ;
Murakawa, Yasuhiro ;
Schueler, Markus ;
Youngs, Noah ;
Penfold-Brown, Duncan ;
Drew, Kevin ;
Milek, Miha ;
Wyler, Emanuel ;
Bonneau, Richard ;
Selbach, Matthias ;
Dieterich, Christoph ;
Landthaler, Markus .
MOLECULAR CELL, 2012, 46 (05) :674-690
[7]   The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs [J].
Beckmann, Benedikt M. ;
Horos, Rastislav ;
Fischer, Bernd ;
Castello, Alfredo ;
Eichelbaum, Katrin ;
Alleaume, Anne-Marie ;
Schwarzl, Thomas ;
Curk, Tomaz ;
Foehr, Sophia ;
Huber, Wolfgang ;
Krijgsveld, Jeroen ;
Hentze, Matthias W. .
NATURE COMMUNICATIONS, 2015, 6
[8]   The F-box protein CFB2 is required for cytokinesis of bloodstream-form Trypanosoma brucei [J].
Benz, Corinna ;
Clayton, Christine E. .
MOLECULAR AND BIOCHEMICAL PARASITOLOGY, 2007, 156 (02) :217-224
[9]   The Trypanosoma brucei zinc finger protein ZC3H18 is involved in differentiation [J].
Benz, Corinna ;
Mulindwa, Julius ;
Ouna, Benard ;
Clayton, Christine .
MOLECULAR AND BIOCHEMICAL PARASITOLOGY, 2011, 177 (02) :148-151
[10]   Vectors for inducible expression of toxic gene products in bloodstream and procyclic Trypanosoma brucei [J].
Biebinger, S ;
Wirtz, LE ;
Lorenz, P ;
Clayton, C .
MOLECULAR AND BIOCHEMICAL PARASITOLOGY, 1997, 85 (01) :99-112