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United States Department of Agriculture

Agricultural Research Service

Title: Features of a unique intronless cluster of class I small heat shock protein genes in tandem with box C/D snoRNA genes on chromosome 6 in tomato (Solanum lycopersicum)

item Goyal, Ravinder
item Kumar, Vinod
item Shukla, Vijaya
item Mattoo, Rohini
item Yongsheng, Liu
item Chung, Sang
item Giovannoni, James
item Mattoo, Autar

Submitted to: Planta
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/5/2011
Publication Date: 3/1/2012
Citation: Goyal, R.K., Kumar, V., Shukla, V., Mattoo, R., Yongsheng, L., Chung, S.H., Giovannoni, J.J., Mattoo, A.K. 2012. Features of a unique intronless cluster of class I small heat shock protein genes in tandem with box C/D snoRNA genes on chromosome 6 in tomato (Solanum lycopersicum). Planta. 235(3):453-471.

Interpretive Summary: Elucidation of how genes are organized on a chromosome of a plant helps in determining their function as well as phylogenetic relationships and evolution of species. More importantly, the physical clustering of functionally related genes is advantageous for a plant in quickly responding to developmental or external cues. We are using tomato as a model to understand molecular regulation of the fruit-ripening program. There is little information about gene order or gene clusters in tomato, particularly on the ones involved in the regulation of fruit quality. A set of genes implicated in fruit ripening belongs to class I small heat shock proteins. Using one of the small heat shock protein genes as a marker, we succeeded in identifying an 8.3-kilobase genomic fragment harboring this gene from a tomato genomic library. Upon sequencing and sequence analysis, a unique cluster of three class I small heat shock protein genes in tandem with a set of snoRNA genes was revealed. Relevant to the physiology of tomato it was found that the 8.3-kilobase fragment is decorated with important elements that are known to respond to plant hormones and such extreme environments as heat, cold and dehydration. In collaboration with ther colleagues at the USDA-ARS’s Boyce Thompson Institute, Ithaca, this fragment was localized to the short arm of chromosome 6. The particular organization of the kinds of genes identified suggests this gene fragment to be an important site of networks that regulate not only tomato growth but also its responses to abiotic and biotic stresses. This study should be of interest to geneticists, molecular biologists, horticulturists, evolutionary biologists and breeders.

Technical Abstract: A class I 17.6 small heat shock protein (Sl17.6 shsp) gene was cloned and used as a probe to screen a tomato (Solanum lycopersicum) genomic library. An 8.3-kb genomic fragment was isolated and its DNA sequence determined. Analysis of the genomic fragment identified intronless open reading frames of three class I shsp genes (Sl17.6, Sl20.0 and Sl20.1), the Sl17.6 gene being flanked by Sl20.1 and Sl20.0, with complete 5’ and 3’ UTRs. Upstream of the Sl20.0 shsp, and within the shsp gene cluster, resides a box C/D snoRNA cluster made of SlsnoR12.1 and SlU24a separated by a uridine-rich spacer box. Characteristic external (C and D) and internal (C’ and D’) boxes are conserved in SlsnoR12.1 and SlU24a while the upstream flanking region of SlsnoR12.1 carries TATA box1, and homol E and D box-like cis sequences previously described in the genome fragment are: TM6 promoter and an uncharacterized tomato EST harboring a putative polygalacturonase gene. The shsps cluster harbors the consensus heat shock element sequence, 5’-nGAAnnTTCnn-3’, at the upstream UTR as well as in the coding region. This intronless tomato genomic sequence is decorated with cis elements responsive to hormones such as abscisic acid (ABRE), auxin (auxRR), ethylene (ERE), gibberellins, and methyl jasmonate; to dehydration (DRE) and cold (CBF); and to MYC/MYB and WRKY 71 transcription factors. Northern analysis revealed a higher expression of the three class I shsps and SlsnoR12 and SlU24 during early stages of ripening, precipitously declining at later stages. Chromosomal mapping localized the tomato 8.3 kb genomic sequence between TG279 and TG581 on the short arm of chromosome 6 in the introgression line (IL) 6-3. The structural organization together with characteristic cis elements suggest this gene sequence to be an important site of networks that may play regulatory roles in not only plant growth and development but also in responses of tomato to abiotic and biotic stresses.

Last Modified: 06/26/2017
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