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. 2012 Mar;235(3):453-71. doi: 10.1007/s00425-011-1518-5. Epub 2011 Sep 25.


Physical clustering of genes has been shown in plants; however, little is known about gene clusters that have different functions, particularly those expressed in the tomato fruit. 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 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. Characteristic C and D, and C' and D', boxes are conserved in SlsnoR12.1 and SlU24a while the upstream flanking region of SlsnoR12.1 carries TATA box 1, homol-E and homol-D box-like cis sequences, TM6 promoter, and an uncharacterized tomato EST. Molecular phylogenetic analysis revealed that this particular arrangement of shsps is conserved in tomato genome but is distinct from other species. The intronless genomic sequence is decorated with cis elements previously shown to be responsive to cues from plant hormones, dehydration, cold, heat, and MYC/MYB and WRKY71 transcription factors. Chromosomal mapping localized the tomato genomic sequence on the short arm of chromosome 6 in the introgression line (IL) 6-3. Quantitative polymerase chain reaction analysis of gene cluster members revealed differential expression during ripening of tomato fruit, and relatively different abundances in other plant parts.

MeSH terms

  • Amino Acid Sequence
  • Chromosomes, Plant / genetics*
  • Fruit / genetics
  • Gene Expression Regulation, Plant
  • Heat-Shock Proteins, Small / chemistry
  • Heat-Shock Proteins, Small / classification
  • Heat-Shock Proteins, Small / genetics*
  • Lycopersicon esculentum / genetics*
  • Molecular Sequence Data
  • Phylogeny
  • Plant Proteins / chemistry
  • Plant Proteins / classification
  • Plant Proteins / genetics*
  • Polymerase Chain Reaction
  • RNA, Small Nucleolar / chemistry
  • RNA, Small Nucleolar / classification
  • RNA, Small Nucleolar / genetics*
  • Sequence Homology, Amino Acid


  • Heat-Shock Proteins, Small
  • Plant Proteins
  • RNA, Small Nucleolar