High-definition macromolecular composition of yeast RNA-processing complexes.
A remarkably large collection of evolutionarily conserved proteins has been implicated in processing of noncoding RNAs and biogenesis of ribonucleoproteins. To better define the physical and functional relationships among these proteins and their cognate RNAs, we performed 165 highly stringent affinity purifications of known or predicted RNA-related proteins from Saccharomyces cerevisiae. We systematically identified and estimated the relative abundance of stably associated polypeptides and RNA species using a combination of gel densitometry, protein mass spectrometry, and oligonucleotide microarray hybridization. Ninety-two discrete proteins or protein complexes were identified comprising 489 different polypeptides, many associated with one or more specific RNA molecules. Some of the pre-rRNA-processing complexes that were obtained are discrete sub-complexes of those previously described. Among these, we identified the IPI complex required for proper processing of the ITS2 region of the ribosomal RNA primary transcript. This study provides a high-resolution overview of the modular topology of noncoding RNA-processing machinery.
Krogan
Nevan J
NJ
Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada.
Peng
Wen-Tao
WT
Cagney
Gerard
G
Robinson
Mark D
MD
Haw
Robin
R
Zhong
Gouqing
G
Guo
Xinghua
X
Zhang
Xin
X
Canadien
Veronica
V
Richards
Dawn P
DP
Beattie
Bryan K
BK
Lalev
Atanas
A
Zhang
Wen
W
Davierwala
Armaity P
AP
Mnaimneh
Sanie
S
Starostine
Andrei
A
Tikuisis
Aaron P
AP
Grigull
Jorg
J
Datta
Nira
N
Bray
James E
JE
Hughes
Timothy R
TR
Emili
Andrew
A
Greenblatt
Jack F
JF
D000595:Amino Acid Sequence; D015152:Blotting, Northern; D005656:Fungal Proteins / Q000737:chemistry; D013058:Mass Spectrometry; D008954:Models, Biological; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional; D012335:RNA, Ribosomal / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000502:physiology; D017386:Sequence Homology, Amino Acid; D013997:Time Factors
D005656:Fungal Proteins; D012335:RNA, Ribosomal; D012313:RNA