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Genome-wide identification, characterization and expression profiling of LIM family genes in Solanum lycopersicum L.
Plant Physiol Biochem. 2016 Nov; 108:177-190.PP

Abstract

LIM domain proteins, some of which have been shown to be actin binding proteins, are involved in various developmental activities and cellular processes in plants. To date, the molecular defense-related functions of LIM family genes have not been investigated in any solanaceous vegetable crop species. In this study, we identified 15 LIM family genes in tomato (Solanum lycopersicum L.) through genome-wide analysis and performed expression profiling in different organs of tomato, including fruits at six different developmental stages. We also performed expression profiling of selected tomato LIM genes in plants under ABA, drought, cold, NaCl and heat stress treatment. The encoded proteins of the 15 tomato LIM genes were classified into two main groups, i.e., proteins similar to cysteine-rich proteins and plant-specific DAR proteins, based on differences in functional domains and variability in their C-terminal regions. The DAR proteins contain a so far poorly characterized zinc-finger-like motif that we propose to call DAR-ZF. Six of the 15 LIM genes were expressed only in flowers, indicating that they play flower-specific roles in plants. The other nine genes were expressed in all organs and at various stages of fruit development. SlβLIM1b was expressed relatively highly at the later stage of fruit development, but three other genes, SlWLIM2a, SlDAR2 and SlDAR4, were expressed at the early stage of fruit development. Seven genes were induced by ABA, five by cold, seven by drought, eight by NaCl and seven by heat treatment respectively, indicating their possible roles in abiotic stress tolerance. Our results will be useful for functional analysis of LIM genes during fruit development in tomato plants under different abiotic stresses.

Authors+Show Affiliations

Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea. Electronic address: kkr@pstu.ac.bd.Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea. Electronic address: gpb21bau@bau.edu.bd.Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea. Electronic address: jipark@sunchon.ac.kr.Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali, Bangladesh. Electronic address: nasargpb@yahoo.com.Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, Republic of Korea. Electronic address: ckkim@knu.ac.kr.Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, Republic of Korea. Electronic address: kblim@knu.ac.kr.Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea; Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea. Electronic address: salt@sunchon.ac.kr.Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea; Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea. Electronic address: djlee@sunchon.ac.kr.Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea. Electronic address: nis@sunchon.ac.kr.Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea; Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 540-950, Republic of Korea. Electronic address: queen@sunchon.ac.kr.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

27439220

Citation

Khatun, Khadiza, et al. "Genome-wide Identification, Characterization and Expression Profiling of LIM Family Genes in Solanum Lycopersicum L." Plant Physiology and Biochemistry : PPB, vol. 108, 2016, pp. 177-190.
Khatun K, Robin AHK, Park JI, et al. Genome-wide identification, characterization and expression profiling of LIM family genes in Solanum lycopersicum L. Plant Physiol Biochem. 2016;108:177-190.
Khatun, K., Robin, A. H. K., Park, J. I., Ahmed, N. U., Kim, C. K., Lim, K. B., Kim, M. B., Lee, D. J., Nou, I. S., & Chung, M. Y. (2016). Genome-wide identification, characterization and expression profiling of LIM family genes in Solanum lycopersicum L. Plant Physiology and Biochemistry : PPB, 108, 177-190. https://doi.org/10.1016/j.plaphy.2016.07.006
Khatun K, et al. Genome-wide Identification, Characterization and Expression Profiling of LIM Family Genes in Solanum Lycopersicum L. Plant Physiol Biochem. 2016;108:177-190. PubMed PMID: 27439220.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide identification, characterization and expression profiling of LIM family genes in Solanum lycopersicum L. AU - Khatun,Khadiza, AU - Robin,Arif Hasan Khan, AU - Park,Jong-In, AU - Ahmed,Nasar Uddin, AU - Kim,Chang Kil, AU - Lim,Ki-Byung, AU - Kim,Min-Bae, AU - Lee,Do-Jin, AU - Nou,Ill Sup, AU - Chung,Mi-Young, Y1 - 2016/07/13/ PY - 2016/01/21/received PY - 2016/07/08/revised PY - 2016/07/08/accepted PY - 2016/10/21/pubmed PY - 2017/3/31/medline PY - 2016/7/21/entrez KW - Abiotic stress KW - Expression profiling KW - Fruit development KW - LIM genes KW - Solanum lycopersicum SP - 177 EP - 190 JF - Plant physiology and biochemistry : PPB JO - Plant Physiol Biochem VL - 108 N2 - LIM domain proteins, some of which have been shown to be actin binding proteins, are involved in various developmental activities and cellular processes in plants. To date, the molecular defense-related functions of LIM family genes have not been investigated in any solanaceous vegetable crop species. In this study, we identified 15 LIM family genes in tomato (Solanum lycopersicum L.) through genome-wide analysis and performed expression profiling in different organs of tomato, including fruits at six different developmental stages. We also performed expression profiling of selected tomato LIM genes in plants under ABA, drought, cold, NaCl and heat stress treatment. The encoded proteins of the 15 tomato LIM genes were classified into two main groups, i.e., proteins similar to cysteine-rich proteins and plant-specific DAR proteins, based on differences in functional domains and variability in their C-terminal regions. The DAR proteins contain a so far poorly characterized zinc-finger-like motif that we propose to call DAR-ZF. Six of the 15 LIM genes were expressed only in flowers, indicating that they play flower-specific roles in plants. The other nine genes were expressed in all organs and at various stages of fruit development. SlβLIM1b was expressed relatively highly at the later stage of fruit development, but three other genes, SlWLIM2a, SlDAR2 and SlDAR4, were expressed at the early stage of fruit development. Seven genes were induced by ABA, five by cold, seven by drought, eight by NaCl and seven by heat treatment respectively, indicating their possible roles in abiotic stress tolerance. Our results will be useful for functional analysis of LIM genes during fruit development in tomato plants under different abiotic stresses. SN - 1873-2690 UR - https://www.unboundmedicine.com/medline/citation/27439220/Genome_wide_identification_characterization_and_expression_profiling_of_LIM_family_genes_in_Solanum_lycopersicum_L_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0981-9428(16)30273-X DB - PRIME DP - Unbound Medicine ER -