Research Article
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Year 2019, Volume: 5 Issue: 2, 101 - 146, 27.12.2019

Abstract

References

  • Büyük İ, Soydam-Aydın S, Aras S. Bitkilerin stres koşullarına verdiği moleküler cevaplar. Türk Hij ve Deney Biyol Derg 2012.
  • Chinnusamy V, Schumaker K, Zhu JK. Molecular genetic perspectives on cross-talk and specificity in abiotic stress signalling in plants. J. Exp. Bot., 2004. https://doi.org/10.1093/jxb/erh005.
  • Galau GA, Wang HY, Hughes DW. Cotton Lea5 and Lea14 encode atypical late embryogenesis-abundant proteins. Plant Physiol 1993. https://doi.org/10.1104/pp.101.2.695.
  • Dure L, Galau G. Developmental Biochemistry of Cottonseed Embryogenesis and Germination: XIII. Regulation of Biosynthesis of Principal Storage Proteins. Plant Physiol 1981. https://doi.org/10.1104/pp.68.1.187.
  • Dure L, Crouch M, Harada J, Ho THD, Mundy J, Quatrano R, et al. Common amino acid sequence domains among the LEA proteins of higher plants. Plant Mol Biol 1989. https://doi.org/10.1007/BF00036962.
  • Du D, Zhang Q, Cheng T, Pan H, Yang W, Sun L. Genome-wide identification and analysis of late embryogenesis abundant (LEA) genes in Prunus mume. Mol Biol Rep 2013. https://doi.org/10.1007/s11033-012-2250-3.
  • Wu C, Hu W, Yan Y, Tie W, Ding Z, Guo J, et al. The late embryogenesis abundant protein family in cassava (manihot esculenta crantz): Genome-wide characterization and expression during abiotic stress. Molecules 2018;23:1–15. https://doi.org/10.3390/molecules23051196.
  • Battaglia M, Olvera-Carrillo Y, Garciarrubio A, Campos F, Covarrubias AA. The enigmatic LEA proteins and other hydrophilins. Plant Physiol 2008. https://doi.org/10.1104/pp.108.120725.
  • Muvunyi BP, Yan Q, Wu F, Min X, Yan ZZ, Kanzana G, et al. Mining late embryogenesis abundant (Lea) family genes in cleistogenes songorica, a xerophyte perennial desert plant. Int J Mol Sci 2018. https://doi.org/10.3390/ijms19113430.
  • Karıncalı M. (Ziziphus Jujuba Mill. Hünnap) Bitkisinin Morfolojik, Anatomik, Ekolojik ve Polen Özelliklerinin Araştırılması. Pamukkale Üniversitesi, 2003.
  • Gün S. Hünnap meyvesinin (Ziziphus jujuba Mill.) soğukta muhafaza performansı üzerine farklı olgunluk safhası ve modifiye atmosfer paketlemenin (MAP) etkisi. Ordu Universitesi, 2017.
  • Akbolat D, Ertekin C, Menges HO, Ekinci K, Erdal I. Physical and nutritional properties of jujube (Zizyphus jujuba Mill.) growing in Turkey. Asian J Chem 2008.
  • Jianping Chen, Xiaoyan Liu, Zhonggui Li, Airong Qi, Ping Yao, Zhongyu Zhou, Tina T. X. Dong and KWKT. A review of dietary Ziziphus jujuba Fruit (Jujube): developing health food supplements for brain protection. Evidence-Based Complement Altern Med 2017:10 pages. https://doi.org/https://doi.org/10.1155/2017/3019568.
  • Liu MJ, Zhao J, Cai Q Le, Liu GC, Wang JR, Zhao ZH, et al. The complex jujube genome provides insights into fruit tree biology. Nat Commun 2014. https://doi.org/10.1038/ncomms6315.
  • Liu Z, Zhang L, Xue C, Fang H, Zhao J, Liu M. Genome-wide identification and analysis of MAPK and MAPKK gene family in Chinese jujube (Ziziphus jujuba Mill.). BMC Genomics 2017. https://doi.org/10.1186/s12864-017-4259-4.
  • Letunic I, Bork P. Interactive Tree Of Life (iTOL): An online tool for phylogenetic tree display and annotation. Bioinformatics 2007. https://doi.org/10.1093/bioinformatics/btl529.
  • Conesa A, Götz S. Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics 2008. https://doi.org/10.1155/2008/619832.
  • Celik Altunoglu Y, Baloglu P, Yer EN, Pekol S, Baloglu MC. Identification and expression analysis of LEA gene family members in cucumber genome. Plant Growth Regul 2016. https://doi.org/10.1007/s10725-016-0160-4.
  • Chen Y, Li C, Zhang B, Yi J, Yang Y, Kong C, et al. The role of the Late Embryogenesis-Abundant (LEA) protein family in development and the abiotic stress response: A comprehensive expression analysis of potato (Solanum Tuberosum). Genes (Basel) 2019. https://doi.org/10.3390/genes10020148.
  • Nagaraju M, Kumar SA, Reddy PS, Kumar A, Rao DM, Kavi Kishor PB. Genome-scale identification, classification, and tissue specific expression analysis of late embryogenesis abundant (LEA) genes under abiotic stress conditions in Sorghum bicolor L. PLoS One 2019. https://doi.org/10.1371/journal.pone.0209980.
  • İbrahime M, Kibar U, Kazan K, Yüksel Özmen C, Mutaf F, Demirel Aşçı S, et al. Genome-wide identification of the LEA protein gene family in grapevine (Vitis vinifera L.). Tree Genet Genomes 2019;15. https://doi.org/10.1007/s11295-019-1364-3.
  • Wang W, Gao T, Chen J, Yang J, Huang H, Yu Y. The late embryogenesis abundant gene family in tea plant (Camellia sinensis): Genome-wide characterization and expression analysis in response to cold and dehydration stress. Plant Physiol Biochem 2019;135:277–86. https://doi.org/10.1016/j.plaphy.2018.12.009.
  • Cao J, Shi F, Liu X, Huang G, Zhou M. Phylogenetic analysis and evolution of aromatic amino acid hydroxylase. FEBS Lett 2010. https://doi.org/10.1016/j.febslet.2010.11.005.
  • Magwanga RO, Lu P, Kirungu JN, Lu H, Wang X, Cai X, et al. Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton. BMC Genet 2018. https://doi.org/10.1186/s12863-017-0596-1.
  • Liu D, Sun J, Zhu D, Lyu G, Zhang C, Liu J, et al. Genome-Wide Identification and Expression Profiles of Late Embryogenesis-Abundant (LEA) Genes during Grain Maturation in Wheat (Triticum aestivum L.). Genes (Basel) 2019. https://doi.org/10.3390/genes10090696.
  • Liang Y, Xiong Z, Zheng J, Xu D, Zhu Z, Xiang J, et al. Genome-wide identification, structural analysis and new insights into late embryogenesis abundant (LEA) gene family formation pattern in Brassica napus. Sci Rep 2016. https://doi.org/10.1038/srep24265.
  • Kamisugi Y, Cuming AC. The evolution of the Abscisic acid-response in land plants: Comparative analysis of Group 1 LEA gene expression in moss and cereals. Plant Mol Biol 2005. https://doi.org/10.1007/s11103-005-0909-z.
  • Battaglia M, Covarrubias AA. Late Embryogenesis Abundant (LEA) proteins in legumes. Front Plant Sci 2013. https://doi.org/10.3389/fpls.2013.00190.
  • Filiz E, Ozyigit II, Tombuloglu H, Koc I. In silico comparative analysis of LEA (Late Embryogenesis Abundant) proteins in Brachypodium distachyon L. Plant Omics 2013.
  • Cao J, Li X. Identification and phylogenetic analysis of late embryogenesis abundant proteins family in tomato (Solanum lycopersicum). Planta 2014. https://doi.org/10.1007/s00425-014-2215-y.
  • Artur MAS, Zhao T, Ligterink W, Schranz E, Hilhorst HWM. Dissecting the genomic diversification of late embryogenesis abundant (LEA) protein gene families in plants. Genome Biol Evol 2019. https://doi.org/10.1093/gbe/evy248.
  • Gao J, Lan T. Functional characterization of the late embryogenesis abundant (LEA) protein gene family from Pinus tabuliformis (Pinaceae) in Escherichia coli. Sci Rep 2016. https://doi.org/10.1038/srep19467.
  • Eldem V, Okay S, Ünver T. Plant micrornas: New players in functional genomics. Turkish J Agric For 2013. https://doi.org/10.3906/tar-1206-50.
  • Yang T, Xue L, An L. Functional diversity of miRNA in plants. Plant Sci 2007. https://doi.org/10.1016/j.plantsci.2006.10.009.
  • Axtell MJ, Bowman JL. Evolution of plant microRNAs and their targets. Trends Plant Sci 2008. https://doi.org/10.1016/j.tplants.2008.03.009.
  • Kavas M, Kızıldoğan AK, Abanoz B. Comparative genome-wide phylogenetic and expression analysis of SBP genes from potato (Solanum tuberosum). Comput Biol Chem 2017. https://doi.org/10.1016/j.compbiolchem.2017.01.001.
  • Büyük İ, Inal B, Ilhan E, Tanriseven M, Aras S, Erayman M. Genome-wide identification of salinity responsive HSP70s in common bean. Mol Biol Rep 2016. https://doi.org/10.1007/s11033-016-4057-0.
  • Goyal K, Tisi L, Basran A, Browne J, Burnell A, Zurdo J, et al. Transition from natively unfolded to folded state induced by desiccation in an anhydrobiotic nematode protein. J Biol Chem 2003. https://doi.org/10.1074/jbc.M212007200.
  • Pukacka S. Possible role of LEA proteins and sHSPs in seed protection: a short review. Biol Lett 2007.
  • Hundertmark M, Hincha DK. LEA (Late Embryogenesis Abundant) proteins and their encoding genes in Arabidopsis thaliana. BMC Genomics 2008. https://doi.org/10.1186/1471-2164-9-118.
  • Chen Y, Cao J. Comparative genomic analysis of the Sm gene family in rice and maize. Gene 2014. https://doi.org/10.1016/j.gene.2014.02.006.
  • Charfeddine S, Saïdi MN, Charfeddine M, Gargouri-Bouzid R. Genome-wide identification and expression profiling of the late embryogenesis abundant genes in potato with emphasis on dehydrins. Mol Biol Rep 2015. https://doi.org/10.1007/s11033-015-3853-2.

Molecular Identification and Characterization of LEA Proteins in Jujube Genome

Year 2019, Volume: 5 Issue: 2, 101 - 146, 27.12.2019

Abstract

LEA
proteins, which are involved in the normal growth and development processes of
plants, also play a protective role against abiotic stresses such as salt
stress and drought. Although the LEA gene
family has been identified in many plants to date, no comprehensive study of
the characterization of LEA-encoding genes in the jujube (Ziziphus jujuba Mill.) genome have been performed. As being the
best-known member of Rhamnaceae family, jujube (Ziziphus jujuba Mill.) is grown in Turkey as well as shows
distribution especially in subtropical and tropical regions of the world.
Jujube, containing high amounts of vitamin C and sugar; has economical and
biological importance with anticancer and anti-inflammatory effects. In this
study, it was aimed to define and characterize LEA genes in jujube genome in detail by using bioinformatics tools.
The results of the study will provide comprehensive data about the LEA
gene family and will present
preliminary information for the functional research of jujube LEA proteins.

References

  • Büyük İ, Soydam-Aydın S, Aras S. Bitkilerin stres koşullarına verdiği moleküler cevaplar. Türk Hij ve Deney Biyol Derg 2012.
  • Chinnusamy V, Schumaker K, Zhu JK. Molecular genetic perspectives on cross-talk and specificity in abiotic stress signalling in plants. J. Exp. Bot., 2004. https://doi.org/10.1093/jxb/erh005.
  • Galau GA, Wang HY, Hughes DW. Cotton Lea5 and Lea14 encode atypical late embryogenesis-abundant proteins. Plant Physiol 1993. https://doi.org/10.1104/pp.101.2.695.
  • Dure L, Galau G. Developmental Biochemistry of Cottonseed Embryogenesis and Germination: XIII. Regulation of Biosynthesis of Principal Storage Proteins. Plant Physiol 1981. https://doi.org/10.1104/pp.68.1.187.
  • Dure L, Crouch M, Harada J, Ho THD, Mundy J, Quatrano R, et al. Common amino acid sequence domains among the LEA proteins of higher plants. Plant Mol Biol 1989. https://doi.org/10.1007/BF00036962.
  • Du D, Zhang Q, Cheng T, Pan H, Yang W, Sun L. Genome-wide identification and analysis of late embryogenesis abundant (LEA) genes in Prunus mume. Mol Biol Rep 2013. https://doi.org/10.1007/s11033-012-2250-3.
  • Wu C, Hu W, Yan Y, Tie W, Ding Z, Guo J, et al. The late embryogenesis abundant protein family in cassava (manihot esculenta crantz): Genome-wide characterization and expression during abiotic stress. Molecules 2018;23:1–15. https://doi.org/10.3390/molecules23051196.
  • Battaglia M, Olvera-Carrillo Y, Garciarrubio A, Campos F, Covarrubias AA. The enigmatic LEA proteins and other hydrophilins. Plant Physiol 2008. https://doi.org/10.1104/pp.108.120725.
  • Muvunyi BP, Yan Q, Wu F, Min X, Yan ZZ, Kanzana G, et al. Mining late embryogenesis abundant (Lea) family genes in cleistogenes songorica, a xerophyte perennial desert plant. Int J Mol Sci 2018. https://doi.org/10.3390/ijms19113430.
  • Karıncalı M. (Ziziphus Jujuba Mill. Hünnap) Bitkisinin Morfolojik, Anatomik, Ekolojik ve Polen Özelliklerinin Araştırılması. Pamukkale Üniversitesi, 2003.
  • Gün S. Hünnap meyvesinin (Ziziphus jujuba Mill.) soğukta muhafaza performansı üzerine farklı olgunluk safhası ve modifiye atmosfer paketlemenin (MAP) etkisi. Ordu Universitesi, 2017.
  • Akbolat D, Ertekin C, Menges HO, Ekinci K, Erdal I. Physical and nutritional properties of jujube (Zizyphus jujuba Mill.) growing in Turkey. Asian J Chem 2008.
  • Jianping Chen, Xiaoyan Liu, Zhonggui Li, Airong Qi, Ping Yao, Zhongyu Zhou, Tina T. X. Dong and KWKT. A review of dietary Ziziphus jujuba Fruit (Jujube): developing health food supplements for brain protection. Evidence-Based Complement Altern Med 2017:10 pages. https://doi.org/https://doi.org/10.1155/2017/3019568.
  • Liu MJ, Zhao J, Cai Q Le, Liu GC, Wang JR, Zhao ZH, et al. The complex jujube genome provides insights into fruit tree biology. Nat Commun 2014. https://doi.org/10.1038/ncomms6315.
  • Liu Z, Zhang L, Xue C, Fang H, Zhao J, Liu M. Genome-wide identification and analysis of MAPK and MAPKK gene family in Chinese jujube (Ziziphus jujuba Mill.). BMC Genomics 2017. https://doi.org/10.1186/s12864-017-4259-4.
  • Letunic I, Bork P. Interactive Tree Of Life (iTOL): An online tool for phylogenetic tree display and annotation. Bioinformatics 2007. https://doi.org/10.1093/bioinformatics/btl529.
  • Conesa A, Götz S. Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics 2008. https://doi.org/10.1155/2008/619832.
  • Celik Altunoglu Y, Baloglu P, Yer EN, Pekol S, Baloglu MC. Identification and expression analysis of LEA gene family members in cucumber genome. Plant Growth Regul 2016. https://doi.org/10.1007/s10725-016-0160-4.
  • Chen Y, Li C, Zhang B, Yi J, Yang Y, Kong C, et al. The role of the Late Embryogenesis-Abundant (LEA) protein family in development and the abiotic stress response: A comprehensive expression analysis of potato (Solanum Tuberosum). Genes (Basel) 2019. https://doi.org/10.3390/genes10020148.
  • Nagaraju M, Kumar SA, Reddy PS, Kumar A, Rao DM, Kavi Kishor PB. Genome-scale identification, classification, and tissue specific expression analysis of late embryogenesis abundant (LEA) genes under abiotic stress conditions in Sorghum bicolor L. PLoS One 2019. https://doi.org/10.1371/journal.pone.0209980.
  • İbrahime M, Kibar U, Kazan K, Yüksel Özmen C, Mutaf F, Demirel Aşçı S, et al. Genome-wide identification of the LEA protein gene family in grapevine (Vitis vinifera L.). Tree Genet Genomes 2019;15. https://doi.org/10.1007/s11295-019-1364-3.
  • Wang W, Gao T, Chen J, Yang J, Huang H, Yu Y. The late embryogenesis abundant gene family in tea plant (Camellia sinensis): Genome-wide characterization and expression analysis in response to cold and dehydration stress. Plant Physiol Biochem 2019;135:277–86. https://doi.org/10.1016/j.plaphy.2018.12.009.
  • Cao J, Shi F, Liu X, Huang G, Zhou M. Phylogenetic analysis and evolution of aromatic amino acid hydroxylase. FEBS Lett 2010. https://doi.org/10.1016/j.febslet.2010.11.005.
  • Magwanga RO, Lu P, Kirungu JN, Lu H, Wang X, Cai X, et al. Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton. BMC Genet 2018. https://doi.org/10.1186/s12863-017-0596-1.
  • Liu D, Sun J, Zhu D, Lyu G, Zhang C, Liu J, et al. Genome-Wide Identification and Expression Profiles of Late Embryogenesis-Abundant (LEA) Genes during Grain Maturation in Wheat (Triticum aestivum L.). Genes (Basel) 2019. https://doi.org/10.3390/genes10090696.
  • Liang Y, Xiong Z, Zheng J, Xu D, Zhu Z, Xiang J, et al. Genome-wide identification, structural analysis and new insights into late embryogenesis abundant (LEA) gene family formation pattern in Brassica napus. Sci Rep 2016. https://doi.org/10.1038/srep24265.
  • Kamisugi Y, Cuming AC. The evolution of the Abscisic acid-response in land plants: Comparative analysis of Group 1 LEA gene expression in moss and cereals. Plant Mol Biol 2005. https://doi.org/10.1007/s11103-005-0909-z.
  • Battaglia M, Covarrubias AA. Late Embryogenesis Abundant (LEA) proteins in legumes. Front Plant Sci 2013. https://doi.org/10.3389/fpls.2013.00190.
  • Filiz E, Ozyigit II, Tombuloglu H, Koc I. In silico comparative analysis of LEA (Late Embryogenesis Abundant) proteins in Brachypodium distachyon L. Plant Omics 2013.
  • Cao J, Li X. Identification and phylogenetic analysis of late embryogenesis abundant proteins family in tomato (Solanum lycopersicum). Planta 2014. https://doi.org/10.1007/s00425-014-2215-y.
  • Artur MAS, Zhao T, Ligterink W, Schranz E, Hilhorst HWM. Dissecting the genomic diversification of late embryogenesis abundant (LEA) protein gene families in plants. Genome Biol Evol 2019. https://doi.org/10.1093/gbe/evy248.
  • Gao J, Lan T. Functional characterization of the late embryogenesis abundant (LEA) protein gene family from Pinus tabuliformis (Pinaceae) in Escherichia coli. Sci Rep 2016. https://doi.org/10.1038/srep19467.
  • Eldem V, Okay S, Ünver T. Plant micrornas: New players in functional genomics. Turkish J Agric For 2013. https://doi.org/10.3906/tar-1206-50.
  • Yang T, Xue L, An L. Functional diversity of miRNA in plants. Plant Sci 2007. https://doi.org/10.1016/j.plantsci.2006.10.009.
  • Axtell MJ, Bowman JL. Evolution of plant microRNAs and their targets. Trends Plant Sci 2008. https://doi.org/10.1016/j.tplants.2008.03.009.
  • Kavas M, Kızıldoğan AK, Abanoz B. Comparative genome-wide phylogenetic and expression analysis of SBP genes from potato (Solanum tuberosum). Comput Biol Chem 2017. https://doi.org/10.1016/j.compbiolchem.2017.01.001.
  • Büyük İ, Inal B, Ilhan E, Tanriseven M, Aras S, Erayman M. Genome-wide identification of salinity responsive HSP70s in common bean. Mol Biol Rep 2016. https://doi.org/10.1007/s11033-016-4057-0.
  • Goyal K, Tisi L, Basran A, Browne J, Burnell A, Zurdo J, et al. Transition from natively unfolded to folded state induced by desiccation in an anhydrobiotic nematode protein. J Biol Chem 2003. https://doi.org/10.1074/jbc.M212007200.
  • Pukacka S. Possible role of LEA proteins and sHSPs in seed protection: a short review. Biol Lett 2007.
  • Hundertmark M, Hincha DK. LEA (Late Embryogenesis Abundant) proteins and their encoding genes in Arabidopsis thaliana. BMC Genomics 2008. https://doi.org/10.1186/1471-2164-9-118.
  • Chen Y, Cao J. Comparative genomic analysis of the Sm gene family in rice and maize. Gene 2014. https://doi.org/10.1016/j.gene.2014.02.006.
  • Charfeddine S, Saïdi MN, Charfeddine M, Gargouri-Bouzid R. Genome-wide identification and expression profiling of the late embryogenesis abundant genes in potato with emphasis on dehydrins. Mol Biol Rep 2015. https://doi.org/10.1007/s11033-015-3853-2.
There are 42 citations in total.

Details

Primary Language English
Subjects Engineering
Journal Section Research Articles
Authors

Kevser Betül Ceylan This is me

Yusuf Ceylan This is me

Buket Ustaoğlu This is me

Mehmet Cengiz Baloğlu This is me

Yasemin Çelik Altunoğlu 0000-0003-2940-7464

Publication Date December 27, 2019
Submission Date November 3, 2019
Published in Issue Year 2019 Volume: 5 Issue: 2

Cite

APA Ceylan, K. B., Ceylan, Y., Ustaoğlu, B., Baloğlu, M. C., et al. (2019). Molecular Identification and Characterization of LEA Proteins in Jujube Genome. Kastamonu University Journal of Engineering and Sciences, 5(2), 101-146.
AMA Ceylan KB, Ceylan Y, Ustaoğlu B, Baloğlu MC, Çelik Altunoğlu Y. Molecular Identification and Characterization of LEA Proteins in Jujube Genome. KUJES. December 2019;5(2):101-146.
Chicago Ceylan, Kevser Betül, Yusuf Ceylan, Buket Ustaoğlu, Mehmet Cengiz Baloğlu, and Yasemin Çelik Altunoğlu. “Molecular Identification and Characterization of LEA Proteins in Jujube Genome”. Kastamonu University Journal of Engineering and Sciences 5, no. 2 (December 2019): 101-46.
EndNote Ceylan KB, Ceylan Y, Ustaoğlu B, Baloğlu MC, Çelik Altunoğlu Y (December 1, 2019) Molecular Identification and Characterization of LEA Proteins in Jujube Genome. Kastamonu University Journal of Engineering and Sciences 5 2 101–146.
IEEE K. B. Ceylan, Y. Ceylan, B. Ustaoğlu, M. C. Baloğlu, and Y. Çelik Altunoğlu, “Molecular Identification and Characterization of LEA Proteins in Jujube Genome”, KUJES, vol. 5, no. 2, pp. 101–146, 2019.
ISNAD Ceylan, Kevser Betül et al. “Molecular Identification and Characterization of LEA Proteins in Jujube Genome”. Kastamonu University Journal of Engineering and Sciences 5/2 (December 2019), 101-146.
JAMA Ceylan KB, Ceylan Y, Ustaoğlu B, Baloğlu MC, Çelik Altunoğlu Y. Molecular Identification and Characterization of LEA Proteins in Jujube Genome. KUJES. 2019;5:101–146.
MLA Ceylan, Kevser Betül et al. “Molecular Identification and Characterization of LEA Proteins in Jujube Genome”. Kastamonu University Journal of Engineering and Sciences, vol. 5, no. 2, 2019, pp. 101-46.
Vancouver Ceylan KB, Ceylan Y, Ustaoğlu B, Baloğlu MC, Çelik Altunoğlu Y. Molecular Identification and Characterization of LEA Proteins in Jujube Genome. KUJES. 2019;5(2):101-46.

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