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Fasulye bitkisinde phospholipase D gen ailesinin tuz ve kuraklık stresi altında genom çaplı karakterizasyonu

Year 2022, Issue: 34, 585 - 593, 31.03.2022
https://doi.org/10.31590/ejosat.1083532

Abstract

Fosfolipaz, bitkilerde fosfolipidlerin metabolizmasından ve sentezinden sorumlu bir enzim sınıfıdır. Bitkilerdeki en önemli fosfolipaz türü, fosfolipitleri hidrolize edebilen PLD (Phospholipase D)’dir. PLD birçok bitki türünde biyotik ve abiyotik stres koşulları altında çalışılmıştır. Ancak yapılan literatür taramalarında P. vulgaris genomunda herhangi bir genom çaplı karakterizasyon yapılmadığı görülmüştür. Yapılan analizler sonucunda P. vulgaris, G.max ve A. thaliana türlerine ait sırasıyla 17, 27 ve 12 adet aday PLD geni tespit edilmiştir. Yapılan bu çalışmada tanımlanan 17 PvPLD geni fasulyenin 2, 5, 7, 8, 9 ve 10 numaralı kromozomları üzerinde dağıldığı tespit edilmiştir. Belirlenen kromozomlar üzerinde en düşük bir, en yüksek 5 PvPLD geni olduğu bulunmuştur. PvPLD genlerine ait teorik izoelektrik noktaları (pI) 5,3-8,21 değerleri arasında değişmekte olduğu ve on yedi PvPLD geninin 14’ü asidik özellik ve 3 tanesi de bazik özellik göstermektedir. Moleküler ağırlıklar analiz edildiğinde ortaya çıkan en düşük ağırlık (17,5 kDa) PvPLD-15’te iken en yüksek (127,8 kDa) ağırlık PvPLD-12’de olduğu belirlenmiştir. PvPLD genlerinin muhtemel 5 farklı domaine ayrıldığı görülmüştür. Yapılan filogenetik analizler sonucunda P. vulgaris, G.max ve A. thaliana türlerine ait karşılaştırmada PLD gen ailesi üyelerinin 6 farklı gruba ayrıldığı tespit edildi. PvPLD genleri arasında yapılan tandem ve segmental duplikasyon analizleri sonucunda 5 adet segmental ve 3 adet tandem duplikasyon belirlenmiştir. Tuz ve kuraklık altındaki ifade seviyeleri incelendiğinde 4 farklı PvPLD geninde kontrole göre belirgin farklılıklar görülmüştür. Bu çalışmada yapılan in siliko analizler fasulyede PLD genlerinin işlevi hakkında önemli bilgiler sunulmakta ve yapılması planlanan çalışmalar için temel niteliği taşımaktadır.

References

  • Bailey, T. L., Williams, N., Misleh, C., & Li, W. W. (2006). MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic acids research, 34(suppl_2), W369-W373.
  • Bargmann, B. O., & Munnik, T. (2006). The role of phospholipase D in plant stress responses. Current opinion in plant biology, 9(5), 515-522.
  • Bargmann, B. O., Laxalt, A. M., Riet, B. T., Van Schooten, B., Merquiol, E., Testerink, C., ... & Munnik, T. (2009). Multiple PLDs required for high salinity and water deficit tolerance in plants. Plant and Cell Physiology, 50(1), 78-89.
  • Büyük, İ., İlhan, E., Şener, D., Özsoy, A. U., & Aras, S. (2019). Genome-wide identification of CAMTA gene family members in Phaseolus vulgaris L. and their expression profiling during salt stress. Molecular biology reports, 46(3), 2721-2732.
  • Chen, C., Chen, H., Zhang, Y., Thomas, H. R., Frank, M. H., He, Y., & Xia, R. (2020). TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular plant, 13(8), 1194-1202.
  • Delgado-Salinas, A., Turley, T., Richman, A., & Lavin, M. (1999). Phylogenetic analysis of the cultivated and wild species of Phaseolus (Fabaceae). Systematic Botany, 438-460.
  • Eliáš, M., Potocký, M., Cvrčková, F., & Žárský, V. (2002). Molecular diversity of phospholipase D in angiosperms. BMC genomics, 3(1), 1-15.
  • Hanahan, D. J., & Chaikoff, I. L. (1947). A new phospholipide-splitting enzyme specific for the ester linkage between the nitrogenous base and the phosphoric acid grouping. Journal of Biological Chemistry, 169(3), 699-705.
  • Horton, P., Park, K.-J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C. J., & Nakai, K. (2007). WoLF PSORT: protein localization predictor. Nucleic acids research, 35(suppl_2), W585-W587.
  • Hu, B., Jin, J., Guo, A.-Y., Zhang, H., Luo, J., & Gao, G. (2015). GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics (Oxford, England), 31(8), 1296-1297. https://doi.org/10.1093/bioinformatics/btu817
  • İlhan, E. (2018). Eucalyptus grandis YABBY Transkripsiyon Faktörlerinin Genom Bazında Analizi. Türkiye Tarımsal Araştırmalar Dergisi, 5(2), 158-166.
  • Juretic, N., Hoen, D. R., Huynh, M. L., Harrison, P. M., & Bureau, T. E. (2005). The evolutionary fate of MULE-mediated duplic ations of host gene fragments in rice. Genome research, 15(9), 1292-1297.
  • Kasapoglu, A. G., İlhan, E., Kızılkaya, D., Pour, A. H., & Haliloğlu, K. (2020). Sorgum [Sorghum bicolor (L.) Moench] Genomunda BES1 Transkripsiyon Faktör Ailesinin Genom Çaplı Analizi. Türkiye Tarımsal Araştırmalar Dergisi, 7(1), 85-95.
  • Lescot, M., Déhais, P., Thijs, G., Marchal, K., Moreau, Y., Van de Peer, Y., ... & Rombauts, S. (2002). PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic acids research, 30(1), 325-327.
  • Letunic, I., & Bork, P. (2011). Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic acids research, 39(suppl_2), W475-W478.
  • Li, G., Lin, F., & Xue, H. W. (2007). Genome-wide analysis of the phospholipase D family in Oryza sativa and functional characterization of PLDβ1 in seed germination. Cell research, 17(10), 881-894.
  • Li, L., Zhang, C., Zhang, M., Yang, C., Bao, Y., Wang, D., ... & Chen, Y. (2021). Genome-wide analysis and expression profiling of the Phospholipase D gene family in Solanum tuberosum. Biology, 10(8), 741.
  • Liu, Q., Zhang, C., Yang, Y., & Hu, X. (2010). Genome-wide and molecular evolution analyses of the phospholipase D gene family in Poplar and Grape. BMC plant biology, 10(1), 1-15.
  • Mane, S. P., Vasquez-Robinet, C., Sioson, A. A., Heath, L. S., & Grene, R. (2007). Early PLDα-mediated events in response to progressive drought stress in Arabidopsis: a transcriptome analysis. Journal of experimental botany, 58(2), 241-252.
  • Mehan, M. R., Freimer, N. B., & Ophoff, R. A. (2004). A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture. Human genomics, 1(5), 1-10.
  • Nichols, N. N., Sutivisedsak, N., Dien, B. S., Biswas, A., Lesch, W. C., & Cotta, M. A. (2011). Conversion of starch from dry common beans (Phaseolus vulgaris L.) to ethanol. Industrial Crops and Products, 33(3), 644-647.
  • Qin, C., & Wang, X. (2002). The Arabidopsis phospholipase D family. Characterization of a calcium-independent and phosphatidylcholine-selective PLDζ1 with distinct regulatory domains. Plant physiology, 128(3), 1057-1068.
  • Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., & Lopez, R. (2005). InterProScan: protein domains identifier. Nucleic acids research, 33(suppl_2), W116-W120.
  • Roshan, N. M., Ashouri, M., & Sadeghi, S. M. (2021). Identification, evolution, expression analysis of phospholipase D (PLD) gene family in tea (Camellia sinensis). Physiology and Molecular Biology of Plants, 27(6), 1219-1232.
  • Roshan, N. M., Ashouri, M., & Sadeghi, S. M. (2021). Identification, evolution, expression analysis of phospholipase D (PLD) gene family in tea (Camellia sinensis). Physiology and Molecular Biology of Plants, 27(6), 1219-1232.
  • Sadat, M., Ullah, M., Hossain, M., Ahmed, B., & Bashar, K. K. (2022). Genome-wide in silico identification of phospholipase D (PLD) gene family from Corchorus capsularis and Corchorus olitorius: reveals their responses to plant stress. Journal of Genetic Engineering and Biotechnology, 20(1), 1-12.
  • Sagar, S., Biswas, D. K., Chandrasekar, R., & Singh, A. (2021). Genome-wide identification, structure analysis and expression profiling of phospholipases D under hormone and abiotic stress treatment in chickpea (Cicer arietinum). International Journal of Biological Macromolecules, 169, 264-273.
  • Simontacchi, M., Galatro, A., Ramos-Artuso, F., & Santa-María, G. E. (2015). Plant survival in a changing environment: the role of nitric oxide in plant responses to abiotic stress. Frontiers in plant science, 6, 977.
  • Suyama, M., Torrents, D., & Bork, P. (2006). PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic acids research, 34(suppl_2), W609-W612.
  • Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular biology and evolution, 28(10), 2731-2739.
  • Tang, K., Dong, C. J., & Liu, J. Y. (2016). Genome-wide comparative analysis of the phospholipase D gene families among allotetraploid cotton and its diploid progenitors. PloS one, 11(5), e0156281.
  • Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., & Higgins, D. G. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic acids research, 25(24), 4876-4882.
  • Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D. R., . . . Pachter, L. (2012). Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature protocols, 7(3), 562-578.
  • Voorrips, R. E. (2002). MapChart: software for the graphical presentation of linkage maps and QTLs. Journal of heredity, 93(1), 77-78.
  • Wan, S., Li, M., Ma, F., Yuan, J., Liu, Z., Zheng, W., & Zhan, J. (2019, June). Genome-wide identification of phospholipase D (PLD) gene family and their responses to low-temperature stress in peach. In AIP Conference Proceedings (Vol. 2110, No. 1, p. 020011). AIP Publishing LLC.
  • Wang, X. (2002). Phospholipase D in hormonal and stress signaling. Current opinion in plant biology, 5(5), 408-414.
  • Wang, X. (2005). Regulatory functions of phospholipase D and phosphatidic acid in plant growth, development, and stress responses. Plant physiology, 139(2), 566-573.
  • Welti, R., Li, W., Li, M., Sang, Y., Biesiada, H., Zhou, H. E., ... & Wang, X. (2002). Profiling membrane lipids in plant stress responses: role of phospholipase Dα in freezing-induced lipid changes in Arabidopsis. Journal of Biological Chemistry, 277(35), 31994-32002.
  • Yang, Z. (2007). PAML 4: phylogenetic analysis by maximum likelihood. Molecular biology and evolution, 24(8), 1586-1591.
  • Zhao, J., Zhou, D., Zhang, Q., & Zhang, W. (2012). Genomic analysis of phospholipase D family and characterization of GmPLDαs in soybean (Glycine max). Journal of plant research, 125(4), 569-578.

Genome-wide characterization of the phospholipase D gene family under salt and drought stress in the bean plant.

Year 2022, Issue: 34, 585 - 593, 31.03.2022
https://doi.org/10.31590/ejosat.1083532

Abstract

Phospholipase is a group of enzymes in plants that are involved in the metabolism and production of phospholipids. Phospholipase D (PLD) is the most significant form of phospholipase in plants, as it can hydrolyze phospholipids. Many plant species have been studied for PLD under biotic and abiotic stress conditions. However, no genome-wide characterisation of the P. vulgaris genome was found in the literature reviews. The research found 17, 27, and 12 potential PLD genes in the P. vulgaris, G.max, and A. thaliana species, respectively. The 17 PvPLD genes identified in this study are distributed on chromosomes 2, 5, 7, 8, 9, and 10 of beans. On the determined chromosomes, one lowest and five highest PvPLD genes were discovered. PvPLD genes have theoretical isoelectric points (pI) ranging from 5.3 to 8.21, with 14 of the seventeen PvPLD genes having acidic values and three having basic values. The lowest molecular weight (17.5 kDa) was identified in PvPLD-15, while the highest (127.8 kDa) was recorded in PvPLD-12. PvPLD genes were found to be grouped into five potential domains. In the study of P. vulgaris, G.max, and A. thaliana species, phylogenetic analysis revealed that the PLD gene family members were separated into six distinct groups. Five segmental and three tandem duplications were discovered as a result of tandem and segmental duplication analyses between PvPLD genes. Significant changes in expression levels under salt and drought were found in four separate PvPLD genes when compared to the control. The in-silico analyses used in this study provide crucial information regarding the function of PLD genes in beans, which will be useful in future research.

References

  • Bailey, T. L., Williams, N., Misleh, C., & Li, W. W. (2006). MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic acids research, 34(suppl_2), W369-W373.
  • Bargmann, B. O., & Munnik, T. (2006). The role of phospholipase D in plant stress responses. Current opinion in plant biology, 9(5), 515-522.
  • Bargmann, B. O., Laxalt, A. M., Riet, B. T., Van Schooten, B., Merquiol, E., Testerink, C., ... & Munnik, T. (2009). Multiple PLDs required for high salinity and water deficit tolerance in plants. Plant and Cell Physiology, 50(1), 78-89.
  • Büyük, İ., İlhan, E., Şener, D., Özsoy, A. U., & Aras, S. (2019). Genome-wide identification of CAMTA gene family members in Phaseolus vulgaris L. and their expression profiling during salt stress. Molecular biology reports, 46(3), 2721-2732.
  • Chen, C., Chen, H., Zhang, Y., Thomas, H. R., Frank, M. H., He, Y., & Xia, R. (2020). TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular plant, 13(8), 1194-1202.
  • Delgado-Salinas, A., Turley, T., Richman, A., & Lavin, M. (1999). Phylogenetic analysis of the cultivated and wild species of Phaseolus (Fabaceae). Systematic Botany, 438-460.
  • Eliáš, M., Potocký, M., Cvrčková, F., & Žárský, V. (2002). Molecular diversity of phospholipase D in angiosperms. BMC genomics, 3(1), 1-15.
  • Hanahan, D. J., & Chaikoff, I. L. (1947). A new phospholipide-splitting enzyme specific for the ester linkage between the nitrogenous base and the phosphoric acid grouping. Journal of Biological Chemistry, 169(3), 699-705.
  • Horton, P., Park, K.-J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C. J., & Nakai, K. (2007). WoLF PSORT: protein localization predictor. Nucleic acids research, 35(suppl_2), W585-W587.
  • Hu, B., Jin, J., Guo, A.-Y., Zhang, H., Luo, J., & Gao, G. (2015). GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics (Oxford, England), 31(8), 1296-1297. https://doi.org/10.1093/bioinformatics/btu817
  • İlhan, E. (2018). Eucalyptus grandis YABBY Transkripsiyon Faktörlerinin Genom Bazında Analizi. Türkiye Tarımsal Araştırmalar Dergisi, 5(2), 158-166.
  • Juretic, N., Hoen, D. R., Huynh, M. L., Harrison, P. M., & Bureau, T. E. (2005). The evolutionary fate of MULE-mediated duplic ations of host gene fragments in rice. Genome research, 15(9), 1292-1297.
  • Kasapoglu, A. G., İlhan, E., Kızılkaya, D., Pour, A. H., & Haliloğlu, K. (2020). Sorgum [Sorghum bicolor (L.) Moench] Genomunda BES1 Transkripsiyon Faktör Ailesinin Genom Çaplı Analizi. Türkiye Tarımsal Araştırmalar Dergisi, 7(1), 85-95.
  • Lescot, M., Déhais, P., Thijs, G., Marchal, K., Moreau, Y., Van de Peer, Y., ... & Rombauts, S. (2002). PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic acids research, 30(1), 325-327.
  • Letunic, I., & Bork, P. (2011). Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic acids research, 39(suppl_2), W475-W478.
  • Li, G., Lin, F., & Xue, H. W. (2007). Genome-wide analysis of the phospholipase D family in Oryza sativa and functional characterization of PLDβ1 in seed germination. Cell research, 17(10), 881-894.
  • Li, L., Zhang, C., Zhang, M., Yang, C., Bao, Y., Wang, D., ... & Chen, Y. (2021). Genome-wide analysis and expression profiling of the Phospholipase D gene family in Solanum tuberosum. Biology, 10(8), 741.
  • Liu, Q., Zhang, C., Yang, Y., & Hu, X. (2010). Genome-wide and molecular evolution analyses of the phospholipase D gene family in Poplar and Grape. BMC plant biology, 10(1), 1-15.
  • Mane, S. P., Vasquez-Robinet, C., Sioson, A. A., Heath, L. S., & Grene, R. (2007). Early PLDα-mediated events in response to progressive drought stress in Arabidopsis: a transcriptome analysis. Journal of experimental botany, 58(2), 241-252.
  • Mehan, M. R., Freimer, N. B., & Ophoff, R. A. (2004). A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture. Human genomics, 1(5), 1-10.
  • Nichols, N. N., Sutivisedsak, N., Dien, B. S., Biswas, A., Lesch, W. C., & Cotta, M. A. (2011). Conversion of starch from dry common beans (Phaseolus vulgaris L.) to ethanol. Industrial Crops and Products, 33(3), 644-647.
  • Qin, C., & Wang, X. (2002). The Arabidopsis phospholipase D family. Characterization of a calcium-independent and phosphatidylcholine-selective PLDζ1 with distinct regulatory domains. Plant physiology, 128(3), 1057-1068.
  • Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., & Lopez, R. (2005). InterProScan: protein domains identifier. Nucleic acids research, 33(suppl_2), W116-W120.
  • Roshan, N. M., Ashouri, M., & Sadeghi, S. M. (2021). Identification, evolution, expression analysis of phospholipase D (PLD) gene family in tea (Camellia sinensis). Physiology and Molecular Biology of Plants, 27(6), 1219-1232.
  • Roshan, N. M., Ashouri, M., & Sadeghi, S. M. (2021). Identification, evolution, expression analysis of phospholipase D (PLD) gene family in tea (Camellia sinensis). Physiology and Molecular Biology of Plants, 27(6), 1219-1232.
  • Sadat, M., Ullah, M., Hossain, M., Ahmed, B., & Bashar, K. K. (2022). Genome-wide in silico identification of phospholipase D (PLD) gene family from Corchorus capsularis and Corchorus olitorius: reveals their responses to plant stress. Journal of Genetic Engineering and Biotechnology, 20(1), 1-12.
  • Sagar, S., Biswas, D. K., Chandrasekar, R., & Singh, A. (2021). Genome-wide identification, structure analysis and expression profiling of phospholipases D under hormone and abiotic stress treatment in chickpea (Cicer arietinum). International Journal of Biological Macromolecules, 169, 264-273.
  • Simontacchi, M., Galatro, A., Ramos-Artuso, F., & Santa-María, G. E. (2015). Plant survival in a changing environment: the role of nitric oxide in plant responses to abiotic stress. Frontiers in plant science, 6, 977.
  • Suyama, M., Torrents, D., & Bork, P. (2006). PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic acids research, 34(suppl_2), W609-W612.
  • Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular biology and evolution, 28(10), 2731-2739.
  • Tang, K., Dong, C. J., & Liu, J. Y. (2016). Genome-wide comparative analysis of the phospholipase D gene families among allotetraploid cotton and its diploid progenitors. PloS one, 11(5), e0156281.
  • Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., & Higgins, D. G. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic acids research, 25(24), 4876-4882.
  • Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D. R., . . . Pachter, L. (2012). Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature protocols, 7(3), 562-578.
  • Voorrips, R. E. (2002). MapChart: software for the graphical presentation of linkage maps and QTLs. Journal of heredity, 93(1), 77-78.
  • Wan, S., Li, M., Ma, F., Yuan, J., Liu, Z., Zheng, W., & Zhan, J. (2019, June). Genome-wide identification of phospholipase D (PLD) gene family and their responses to low-temperature stress in peach. In AIP Conference Proceedings (Vol. 2110, No. 1, p. 020011). AIP Publishing LLC.
  • Wang, X. (2002). Phospholipase D in hormonal and stress signaling. Current opinion in plant biology, 5(5), 408-414.
  • Wang, X. (2005). Regulatory functions of phospholipase D and phosphatidic acid in plant growth, development, and stress responses. Plant physiology, 139(2), 566-573.
  • Welti, R., Li, W., Li, M., Sang, Y., Biesiada, H., Zhou, H. E., ... & Wang, X. (2002). Profiling membrane lipids in plant stress responses: role of phospholipase Dα in freezing-induced lipid changes in Arabidopsis. Journal of Biological Chemistry, 277(35), 31994-32002.
  • Yang, Z. (2007). PAML 4: phylogenetic analysis by maximum likelihood. Molecular biology and evolution, 24(8), 1586-1591.
  • Zhao, J., Zhou, D., Zhang, Q., & Zhang, W. (2012). Genomic analysis of phospholipase D family and characterization of GmPLDαs in soybean (Glycine max). Journal of plant research, 125(4), 569-578.
There are 40 citations in total.

Details

Primary Language Turkish
Subjects Engineering
Journal Section Articles
Authors

Murat Isıyel 0000-0003-4157-2729

Burak Muhammed Öner 0000-0003-2785-2089

Esra Yaprak 0000-0002-8753-494X

Sümeyra Uçar 0000-0002-7629-0206

Ayşe Gül Kasapoğlu 0000-0002-6447-4921

Ahmed Sidar Aygören 0000-0002-6264-9935

Selman Muslu 0000-0003-4777-0726

Recep Aydınyurt 0000-0002-8404-7900

Emre İlhan 0000-0002-8404-7900

Murat Aydın 0000-0003-1091-0609

Early Pub Date January 30, 2022
Publication Date March 31, 2022
Published in Issue Year 2022 Issue: 34

Cite

APA Isıyel, M., Öner, B. M., Yaprak, E., Uçar, S., et al. (2022). Fasulye bitkisinde phospholipase D gen ailesinin tuz ve kuraklık stresi altında genom çaplı karakterizasyonu. Avrupa Bilim Ve Teknoloji Dergisi(34), 585-593. https://doi.org/10.31590/ejosat.1083532