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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)

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Abstract

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.

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Abbreviations

shsp:

Small heat shock protein

nt:

Nucleotide

Q-PCR:

Quantitative polymerase chain reaction

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Acknowledgments

We thank Prof. Marvin Edelman for his constructive comments and edits on the manuscript. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.

Author information

Author notes

  1. Ravinder K. Goyal

    Present address: Agriculture and Agri-Food Canada-Lethbridge Research Centre, P.O. 3000, 5403-1st Ave. South, Lethbridge, AB, T1J 4B1, Canada

  2. Sang Ho Chung

    Present address: Department of Microbiology, Mokwon University, Doan-dong 800, Seo-ku, Taejon, 302-729, Republic of Korea

Authors and Affiliations

  1. U.S. Department of Agriculture, The Henry A. Wallace Beltsville Agricultural Research Center, Agriculture Research Service, Beltsville, MD, 20705-2350, USA

    Ravinder K. Goyal, Vinod Kumar, Vijaya Shukla, Sang Ho Chung & Autar K. Mattoo

  2. University of Maryland Biotechnology Institute, College Park, MD, 20742, USA

    Vijaya Shukla

  3. Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India

    Rohini Mattoo

  4. USDA-ARS, Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA

    Yongsheng Liu & James J. Giovannoni

Authors
  1. Ravinder K. Goyal
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  2. Vinod Kumar
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  3. Vijaya Shukla
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  4. Rohini Mattoo
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  5. Yongsheng Liu
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  6. Sang Ho Chung
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  7. James J. Giovannoni
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  8. Autar K. Mattoo
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Corresponding author

Correspondence to Autar K. Mattoo.

Additional information

R. K. Goyal, V. Kumar and V. Shukla contributed equally to this article.

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Goyal, R.K., Kumar, V., Shukla, V. et al. 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, 453–471 (2012). https://doi.org/10.1007/s00425-011-1518-5

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  • DOI: https://doi.org/10.1007/s00425-011-1518-5

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