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Genome-wide investigation and expression analysis suggest diverse roles of auxin-responsive GH3 genes during development and response to different stimuli in tomato (Solanum lycopersicum)

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Abstract

In plants, auxin-mediated responses are regulated by diverse proteins. One such class of proteins, i.e. GH3, is involved in the conjugation of IAA to amino acids and provides a negative feedback loop to control auxin homoeostasis. In order to have a better understanding of the mechanism of the auxin action, 15 genes encoding GH3 members were identified using existing EST databases of tomato. Their orthologs were identified from tobacco, potato, N. benthemiana, pepper, and petunia. Phylogenetic analysis of AtGH3, SlGH3, and their Solanaceae orthologs provided insights into various orthologous relationships among these proteins. These genes were found to be responsive to a variety of signals including, phytohormones and environmental stresses. Analysis of AuxRE elements in their promoters showed variability in the sequence as well as number of this element. Up-regulation of only 11 SlGH3 genes, in response to exogenous auxin, suggested possible relationship between the diversity in the sequence and number of AuxRE element with the auxin inducibility. Expression analysis of SlGH3 genes in different vegetative and reproductive tissues/stages suggested limited or no role for most of the SlGH3 genes at the initiation of fruit ripening. However, up-regulation of SlGH3-1 and -2 at the onset of fruit ripening indicates that these genes could have a role in fruit ripening. The present study characterizes GH3 gene family of tomato and its evolutionary relationship with members of this family from other Solanaceae species and Arabidopsis. It could help in the identification of GH3 genes and revelation of their function during vegetative/reproductive development stages from other Solanaceae members.

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Acknowledgments

This work was financially supported by grants received from the Department of Biotechnology, Government of India. RK and PA acknowledge CSIR and UGC, respectively, for the fellowship granted during their tenure as research fellows. Authors also acknowledge the Solanaceae Genomics Network as Tomato BAC Sequence and WGS (Sl2.40) Databases were used to retrieve putative promoter sequences.

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Authors and Affiliations

  1. Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India

    Rahul Kumar, Priyanka Agarwal, Akhilesh K. Tyagi & Arun K. Sharma

  2. National Institute of Plant Genome Research, New Delhi, 110067, India

    Akhilesh K. Tyagi

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  1. Rahul Kumar
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  2. Priyanka Agarwal
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  3. Akhilesh K. Tyagi
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  4. Arun K. Sharma
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Correspondence to Arun K. Sharma.

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Communicated by S. Hohmann.

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Supplementary file S1: List of SlGH3 primers used for QPCR analysis.

Supplementary file S2: Protein sequences encoded by SlGH3 genes in tomato.

Supplementary file S3: Percentage identities among the SlGH3 proteins.

Supplementary file S4: Cis-element study of promoter architecture (2 kb upstream sequence from the start codon) of SlGH3 genes.

Supplementary file S5: Identification of SlGH3 orthologous genes from six Solanaceae species.

Supplementary file S6: Protein sequences encoded by SlGH3 orthologous genes from other Solanaceae members.

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Kumar, R., Agarwal, P., Tyagi, A.K. et al. Genome-wide investigation and expression analysis suggest diverse roles of auxin-responsive GH3 genes during development and response to different stimuli in tomato (Solanum lycopersicum). Mol Genet Genomics 287, 221–235 (2012). https://doi.org/10.1007/s00438-011-0672-6

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