mRNA sequence features that contribute to translational regulation in Arabidopsis.
DNA microarrays were used to evaluate the regulation of the proportion of individual mRNA species in polysomal complexes in leaves of Arabidopsis thaliana under control growth conditions and following a mild dehydration stress (DS). The analysis determined that the percentage of an individual gene transcript in polysomes (ribosome loading) ranged from over 95 to <5%. DS caused a decrease in ribosome loading from 82 to 72%, with maintained polysome association for over 60% of the mRNAs with an increased abundance. To identify sequence features responsible for translational regulation, ribosome loading values and features of full-length mRNA sequences were compared. mRNAs with extreme length or high GU content in the 5'-untranslated regions (5'-UTRs) were generally poorly translated. Under DS, mRNAs with both a high GC content in the 5'-UTR and long open reading frame showed a significant impairment in ribosome loading. Evaluation of initiation A+1UG codon context revealed distinctions in the frequency of adenine in nucleotides -10 to -1 (especially at -4 and -3) in mRNAs with different ribosome loading values. Notably, the mRNA features that contribute to translational regulation could not fully explain the variation in ribosome loading, indicating that additional factors contribute to translational regulation in Arabidopsis.
Kawaguchi
Riki
R
Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California Riverside, CA 92521, USA.
Bailey-Serres
Julia
J
D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D003062:Codon; D018387:Codon, Initiator; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames; D011132:Polyribosomes / Q000378:metabolism; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000737:chemistry*; D018749:RNA, Plant / Q000737:chemistry; D038621:Regulatory Sequences, Ribonucleic Acid; D012270:Ribosomes / Q000378:metabolism
D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D003062:Codon; D018387:Codon, Initiator; D012333:RNA, Messenger; D018749:RNA, Plant; D038621:Regulatory Sequences, Ribonucleic Acid
Nucleic Acids Res. 2001 May 15;29(10):2135-44
11353083
Proc Natl Acad Sci U S A. 2002 Aug 20;99(17):11513-8
12167669
Trends Genet. 2001 Dec;17(12):685-7
11718907
Mol Cell Proteomics. 2004 May;3(5):478-89
14766929
Gene Expr. 1991 May;1(2):111-5
1820208
Proc Natl Acad Sci U S A. 1999 Oct 12;96(21):12150-5
10518591
Plant J. 2004 Jun;38(5):823-39
15144383
Plant Mol Biol. 2002 Dec;50(6):949-70
12516864
Brain Res Mol Brain Res. 2001 Jul 13;91(1-2):81-95
11457495
Curr Opin Cell Biol. 2001 Jun;13(3):326-31
11343903
Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3889-94
12660367
Proc Natl Acad Sci U S A. 1999 Nov 9;96(23):13118-23
10557283
Ann Bot. 2002 Feb;89(2):183-9
12099349
Gene. 2002 Oct 16;299(1-2):1-34
12459250
Plant Mol Biol. 1997 Dec;35(6):993-1001
9426620
Plant Physiol. 1992 Feb;98(2):516-24
16668670
Curr Opin Plant Biol. 2002 Oct;5(5):460-5
12183186
Plant Sci. 2000 May 15;154(1):89-98
10725562
Nucleic Acids Res. 2000 Aug 1;28(15):2943-53
10908358
Trends Plant Sci. 1999 Apr;4(4):142-148
10322548
Biochem J. 2002 Sep 15;366(Pt 3):767-75
12059785
Gene. 2002 Jun 26;293(1-2):123-31
12137950
Genome Res. 2003 Jun;13(6B):1273-89
12819125
Mol Cell Biol. 2001 Feb;21(3):916-27
11154278
Trends Biochem Sci. 2003 Feb;28(2):91-8
12575997
Mol Cell Biol. 1989 Nov;9(11):5134-42
2601712
Gene. 1997 Oct 24;200(1-2):149-56
9373149
Int J Biochem Cell Biol. 1996 Mar;28(3):247-57
8920634
Mol Cell Biol. 1996 Jan;16(1):146-56
8524291
Arch Biochem Biophys. 1995 Oct 1;322(2):475-85
7574724
Genome Biol. 2002;3(6):RESEARCH0029
12093376
Bioinformatics. 2001 Oct;17(10):890-900
11673233
Proc Natl Acad Sci U S A. 1999 Sep 14;96(19):10632-6
10485877
Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8354-9
12821781
Nature. 2002 Aug 15;418(6899):793-7
12181571
Cell. 1980 Nov;22(1 Pt 1):7-8
7000367
Mol Cell Biol. 2001 Mar;21(6):1899-907
11238926
Trends Biochem Sci. 2001 Apr;26(4):225-9
11295554
J Mol Biol. 1990 Oct 5;215(3):403-10
2231712
Genes Dev. 2000 Jun 15;14(12):1415-29
10859161
Biochimie. 1994;76(9):815-21
7880897
Science. 1989 Apr 7;244(4900):48-52
2468181
Science. 2002 Apr 5;296(5565):141-5
11910074
Cell. 2002 Feb 22;108(4):501-12
11909521
Plant J. 2002 Oct;32(1):129-37
12366806
Proc Int Conf Intell Syst Mol Biol. 1995;3:21-9
7584439
Nucleic Acids Res. 1987 Aug 25;15(16):6643-53
3628002
Nucleic Acids Res. 2003 Jul 1;31(13):3446-9
12824343
Nat Genet. 2000 May;25(1):58-62
10802657
Nat Struct Biol. 2003 Dec;10(12):1039-47
14608375
Genome Res. 1999 Dec;9(12):1288-93
10613851
Plant Mol Biol. 1992 Feb;18(4):815-8
1373083
Plant Mol Biol. 1996 Oct;32(1-2):89-106
8980476
J Biol Chem. 2003 Oct 31;278(44):43034-40
12939267
Cell. 2001 Aug 24;106(4):477-87
11525733
Bioessays. 2003 Dec;25(12):1201-11
14635255
Int J Mol Med. 2000 Feb;5(2):111-23
10639588
Mol Cell Proteomics. 2003 Mar;2(3):191-204
12684541
J Biol Chem. 2002 Jun 21;277(25):22175-84
11943782
Mol Cell Biol. 2000 Apr;20(7):2297-307
10713153
Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
12824337
Nat Struct Biol. 2002 Nov;9(11):790-1
12402032
Mol Microbiol. 2003 Aug;49(4):859-67
12890013
Biochim Biophys Acta. 2003 Jul 9;1628(1):50-5
12850272