Genome-wide polysomal analysis of a yeast strain with mutated ribosomal protein S9.
BACKGROUND
The yeast ribosomal protein S9 (S9) is located at the entrance tunnel of the mRNA into the ribosome. It is known to play a role in accurate decoding and its bacterial homolog (S4) has recently been shown to be involved in opening RNA duplexes. Here we examined the effects of changing the C terminus of S9, which is rich in acidic amino acids and extends out of the ribosome surface.


RESULTS
We performed a genome-wide analysis to reveal effects at the transcription and translation levels of all yeast genes. While negligible relative changes were observed in steady-state mRNA levels, a significant number of mRNAs appeared to have altered ribosomal density. Notably, 40% of the genes having reliable signals changed their ribosomal association by more than one ribosome. Yet, no general correlations with physical or functional features of the mRNA were observed. Ribosome Density Mapping (RDM) along four of the mRNAs with increased association revealed an increase in ribosomal density towards the end of the coding region for at least two of them. Read-through analysis did not reveal any increase in read-through of a premature stop codon by the mutant strain.


CONCLUSIONS
The ribosomal protein rpS9 appears to be involved in the translation of many mRNAs, since altering its C terminus led to a significant change in ribosomal association of many mRNAs. We did not find strong correlations between these changes and several physical features of the mRNA, yet future studies with advanced tools may allow such correlations to be determined. Importantly, our results indicate an accumulation of ribosomes towards the end of the coding regions of some mRNAs. This suggests an involvement of S9 in ribosomal dissociation during translation termination.
Pnueli
Lilach
L
Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel. lilach@tx.technion.ac.il
Arava
Yoav
Y
D015966:Gene Expression Regulation, Fungal; D023281:Genomics / Q000379:methods; D009154:Mutation; D014176:Protein Biosynthesis / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D000091243:Ribosomal Protein S9; D012269:Ribosomal Proteins / Q000235:genetics / Q000502:physiology*; D014158:Transcription, Genetic / Q000235:genetics; D015003:Yeasts
D012333:RNA, Messenger; D000091243:Ribosomal Protein S9; D012269:Ribosomal Proteins
Mol Cell Proteomics. 2004 May;3(5):478-89
14766929
Nucleic Acids Res. 1987 Feb 11;15(3):1281-95
3547335
Mol Cell. 2002 Jan;9(1):31-44
11804584
Eukaryot Cell. 2004 Dec;3(6):1619-26
15590835
Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3889-94
12660367
Genetics. 1992 Oct;132(2):375-86
1427034
Mol Cell. 2005 Jun 10;18(6):675-86
15949442
J Mol Recognit. 2001 Jul-Aug;14(4):199-214
11500966
RNA. 2005 Aug;11(8):1317-28
16043510
Mol Cell Biol. 2006 Feb;26(3):1014-27
16428454
Cell. 2001 Jul 27;106(2):233-41
11511350
J Mol Biol. 1998 Sep 11;282(1):13-24
9733638
Mol Cell Biol. 2001 Feb;21(3):916-27
11154278
J Mol Biol. 1986 Mar 20;188(2):207-14
3522920
Nature. 2004 Sep 2;431(7004):99-104
15343339
Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5860-5
11972065
Proteins. 2005 Nov 1;61(2):258-71
16121397
Methods Mol Biol. 2003;224:79-87
12710667
Genome Biol. 2003;5(1):R2
14709174
J Biol Chem. 1982 Mar 25;257(6):3026-31
7037777
Science. 2001 May 4;292(5518):883-96
11283358
Proc Int Conf Intell Syst Mol Biol. 1994;2:28-36
7584402
Mol Cell. 2004 Jan 16;13(1):113-24
14731399
Mol Cell Biol. 1995 Feb;15(2):883-91
7823954
Genetics. 1979 Sep;93(1):67-79
17248970
Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17846-51
17101987
Nat Struct Biol. 2003 Dec;10(12):1039-47
14608375
Cell. 2001 Nov 2;107(3):373-86
11701127
EMBO Rep. 2003 Apr;4(4):387-93
12671682
Cell. 2005 Jan 14;120(1):49-58
15652481
Mol Cell. 2005 May 13;18(4):403-12
15893724
Nucleic Acids Res. 1997 Dec 15;25(24):4872-5
9396790
Nucleic Acids Res. 2005;33(8):2421-32
15860778
Mol Microbiol. 2006 Mar;59(6):1651-63
16553873
J Mol Biol. 1981 Apr 15;147(3):373-9
6273576
J Mol Biol. 1981 Apr 15;147(3):391-7
7031259
Genes Dev. 2005 Dec 15;19(24):3004-16
16357218
J Mol Biol. 1981 Apr 15;147(3):381-90
7031258
Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
12824337