Rice sHsp genes: genomic organization and expression profiling under stress and development.
BACKGROUND
Heat shock proteins (Hsps) constitute an important component in the heat shock response of all living systems. Among the various plant Hsps (i.e. Hsp100, Hsp90, Hsp70 and Hsp20), Hsp20 or small Hsps (sHsps) are expressed in maximal amounts under high temperature stress. The characteristic feature of the sHsps is the presence of alpha-crystallin domain (ACD) at the C-terminus. sHsps cooperate with Hsp100/Hsp70 and co-chaperones in ATP-dependent manner in preventing aggregation of cellular proteins and in their subsequent refolding. Database search was performed to investigate the sHsp gene family across rice genome sequence followed by comprehensive expression analysis of these genes.


RESULTS
We identified 40 alpha-crystallin domain containing genes in rice. Phylogenetic analysis showed that 23 out of these 40 genes constitute sHsps. The additional 17 genes containing ACD clustered with Acd proteins of Arabidopsis. Detailed scrutiny of 23 sHsp sequences enabled us to categorize these proteins in a revised scheme of classification constituting of 16 cytoplasmic/nuclear, 2 ER, 3 mitochondrial, 1 plastid and 1 peroxisomal genes. In the new classification proposed herein nucleo-cytoplasmic class of sHsps with 9 subfamilies is more complex in rice than in Arabidopsis. Strikingly, 17 of 23 rice sHsp genes were noted to be intronless. Expression analysis based on microarray and RT-PCR showed that 19 sHsp genes were upregulated by high temperature stress. Besides heat stress, expression of sHsp genes was up or downregulated by other abiotic and biotic stresses. In addition to stress regulation, various sHsp genes were differentially upregulated at different developmental stages of the rice plant. Majority of sHsp genes were expressed in seed.


CONCLUSIONS
We identified twenty three sHsp genes and seventeen Acd genes in rice. Three nucleocytoplasmic sHsp genes were found only in monocots. Analysis of expression profiling of sHsp genes revealed that these genes are differentially expressed under stress and at different stages in the life cycle of rice plant.
Sarkar
Neelam K
NK
Department of Plant Molecular Biology, University of Delhi South Campus, N Delhi 110021, India. neelamksarkar@gmail.com
Kim
Yeon-Ki
YK
Grover
Anil
A
D018744:DNA, Plant / Q000235:genetics; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D006360:Heat-Shock Proteins / Q000235:genetics / Q000378:metabolism*; D006358:Hot Temperature; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012639:Seeds / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D017422:Sequence Analysis, DNA; D013312:Stress, Physiological
D018744:DNA, Plant; D006360:Heat-Shock Proteins; D010940:Plant Proteins
FEBS Lett. 2004 Jan 16;557(1-3):265-8
14741379
Plant Physiol. 1998 Jan;116(1):439-444
9449851
J Exp Bot. 2007;58(7):1627-35
17431025
Nat Genet. 2002 Aug;31(4):415-8
12134150
Plant Physiol. 1998 Jun;117(2):651-8
9625718
Plant Physiol. 2000 Jan;122(1):189-98
10631262
Plant Mol Biol. 2003 Mar;51(5):677-86
12678556
Plant Physiol. 1999 Nov;121(3):723-30
10557220
Cell Stress Chaperones. 2008 Summer;13(2):183-97
18369739
J Biol Chem. 2005 Jun 24;280(25):23869-75
15845535
Cell Stress Chaperones. 2001 Jul;6(3):225-37
11599564
Trends Genet. 2008 Aug;24(8):375-8
18586348
Mol Plant Microbe Interact. 2007 Nov;20(11):1376-83
17977149
Proc Natl Acad Sci U S A. 1997 Sep 30;94(20):10967-72
9380743
Plant Mol Biol. 2003 Mar;51(4):543-53
12650620
Plant Physiol. 2007 May;144(1):218-31
17369434
FEBS J. 2005 Oct;272(20):5230-43
16218954
Proc Natl Acad Sci U S A. 2004 Jul 6;101(27):9971-5
15226500
Plant Physiol. 1992 Aug;99(4):1279-84
16669033
Plant Mol Biol. 2001 Mar;45(4):489-500
11352467
Proc Int Conf Intell Syst Mol Biol. 1994;2:28-36
7584402
Nucleic Acids Res. 2002 Feb 15;30(4):e15
11842121
Mol Plant. 2008 Sep;1(5):851-7
19825587
Trends Genet. 2006 Oct;22(10):528-32
16934358
Gene. 2007 Nov 15;403(1-2):60-9
17888590
Mol Biol Evol. 2008 Jan;25(1):111-9
17974547
Plant Physiol. 2006 May;141(1):47-60
16531488
Plant Mol Biol. 1995 Oct;29(2):293-301
7579180
J Biol Chem. 2005 Jun 24;280(25):23861-8
15843375
Plant Mol Biol. 2004 Nov;56(5):795-809
15803416
Biochim Biophys Acta. 2002 Aug 19;1577(1):1-9
12151089
Plant J. 1998 Feb;13(4):437-46
9680992
J Exp Bot. 2008;59(8):2267-76
18453530
Plant Physiol. 1996 Oct;112(2):747-57
8883386
J Biosci. 2007 Apr;32(3):611-9
17536180
Plant Cell Rep. 2008 Feb;27(2):329-34
17968552
EMBO J. 1982;1(11):1473-7
6327271
J Plant Physiol. 2007 Apr;164(4):505-13
16687190
Gene. 2000 Mar 21;245(2):283-90
10717479
Funct Integr Genomics. 2008 Feb;8(1):69-78
17578610
Cell Stress Chaperones. 2008 Summer;13(2):127-42
18759000
Plant Cell Physiol. 2008 Oct;49(10):1451-64
18835840
Nature. 2005 Aug 11;436(7052):793-800
16100779