Genome-wide identification and characterization caleosin genes in lima-bean (Phaseolus lunatus)
DOI:
https://doi.org/10.36560/18320252068Palavras-chave:
Caleosin, Genomic analysis, Lima-Bean, Protein modeling, Stress toleranceResumo
Phaseolus lunatus, commonly known as lima bean or butter bean, is a leguminous crop with significant agricultural and nutritional value, particularly in tropical regions. Caleosin, a lipid-associated protein, plays a crucial role in seed germination, stress response, and lipid metabolism, presenting potential targets for genetic improvement. This study aimed to identify and characterize caleosin genes (PlCLOs) in P. lunatus using in silico methods. Six genes encoding caleosin proteins were identified, exhibiting molecular weights between 16.58 and 27.28 kDa and subcellular localization predominantly in chloroplasts. Conserved motifs, such as calcium-binding and phosphorylation sites, were identified, alongside structural elements crucial for lipid droplet anchoring. Phylogenetic analysis revealed three evolutionary groups, suggesting functional divergence. Structural modeling confirmed high-quality protein models dominated by α-helices and irregular loops. Functional annotations highlighted roles in stress tolerance, calcium signaling, and lipid metabolism. These findings deepen the understanding of caleosins role in plant biology, providing insights for sustainable agricultural practices and genetic improvement of P. lunatus.
Referências
ADEBO, J. A. A Review on the Potential Food Application of Lima Beans (Phaseolus lunatus L.), an Underutilized Crop. Applied Sciences, [s. l.], v. 13, n. 3, p. 1996, jan. 2023. https://doi.org/10.3390/app13031996. DOI: https://doi.org/10.3390/app13031996
BITOCCHI, E.; RAU, D.; BELLUCCI, E.; RODRIGUEZ, M.; MURGIA, M. L.; GIOIA, T.; SANTO, D.; NANNI, L.; ATTENE, G.; PAPA, R. Beans (Phaseolus ssp.) as a Model for Understanding Crop Evolution. Frontiers in Plant Science, [s. l.], v. 8, 8 maio 2017. DOI 10.3389/fpls.2017.00722. Disponível em: https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2017.00722/full. Acesso em: 22 ago. 2024. DOI: https://doi.org/10.3389/fpls.2017.00722
BROOKS, B. R.; BROOKS III, C. L.; MACKERELL JR., A. D.; NILSSON, L.; PETRELLA, R. J.; ROUX, B.; WON, Y.; ARCHONTIS, G.; BARTELS, C.; BORESCH, S.; CAFLISCH, A.; CAVES, L.; CUI, Q.; DINNER, A. R.; FEIG, M.; FISCHER, S.; GAO, J.; HODOSCEK, M.; IM, W.; KUCZERA, K.; LAZARIDIS, T.; MA, J.; OVCHINNIKOV, V.; PACI, E.; PASTOR, R. W.; POST, C. B.; PU, J. Z.; SCHAEFER, M.; TIDOR, B.; VENABLE, R. M.; WOODCOCK, H. L.; WU, X.; YANG, W.; YORK, D. M.; KARPLUS, M. CHARMM: The biomolecular simulation program. Journal of Computational Chemistry, [s. l.], v. 30, n. 10, p. 1545–1614, 2009. https://doi.org/10.1002/jcc.21287. DOI: https://doi.org/10.1002/jcc.21287
BRUNETTI, S. C.; ARSENEAULT, M. K. M.; GULICK, P. J. The caleosin CLO7 and its role in the heterotrimeric G-protein signalling network. Journal of Plant Physiology, [s. l.], v. 279, p. 153841, dez. 2022. https://doi.org/10.1016/j.jplph.2022.153841. DOI: https://doi.org/10.1016/j.jplph.2022.153841
BRUNETTI, S. C.; ARSENEAULT, M. K. M.; WRIGHT, J. A.; WANG, Z.; EHDAEIVAND, M.-R.; LOWDEN, M. J.; RIVOAL, J.; KHALIL, H. B.; GARG, G.; GULICK, P. J. The stress induced caleosin, RD20/CLO3, acts as a negative regulator of GPA1 in Arabidopsis. Plant Molecular Biology, [s. l.], v. 107, n. 3, p. 159–175, out. 2021. https://doi.org/10.1007/s11103-021-01189-x. DOI: https://doi.org/10.1007/s11103-021-01189-x
CAO, Y.; ZHAN, Y.; LIU, J.; TANG, T.; LI, J.; ZHAO, R.; ZHANG, Q.; HU, S.; CAO, W.; GAO, Y. Identification and Analysis of Expression Patterns of the Caleosin Genes in Hickory (Carya cathayensis Sarg.). Forests, [s. l.], v. 15, n. 4, p. 609, abr. 2024. https://doi.org/10.3390/f15040609. DOI: https://doi.org/10.3390/f15040609
CHAPMAN, K. D.; DYER, J. M.; MULLEN, R. T. Biogenesis and functions of lipid droplets in plants: Thematic Review Series: Lipid Droplet Synthesis and Metabolism: from Yeast to Man. Journal of Lipid Research, [s. l.], v. 53, n. 2, p. 215–226, fev. 2012. https://doi.org/10.1194/jlr.R021436. DOI: https://doi.org/10.1194/jlr.R021436
CULVER, K. D.; SADECKI, P. W.; JACKSON, J. K.; BROWN, Z. A.; HNILICA, M. E.; WU, J.; SHAW, L. N.; WOMMACK, A. J.; HICKS, L. M. Identification and Characterization of CC-AMP1-like and CC-AMP2-like Peptides in Capsicum spp. Journal of Proteome Research, [s. l.], v. 23, n. 8, p. 2948–2960, 2 ago. 2024. https://doi.org/10.1021/acs.jproteome.3c00597. DOI: https://doi.org/10.1021/acs.jproteome.3c00597
FENG, P.; HAI-XIA, Y. U.; KUN, Z.; YING-YING, L. I. U.; GUI-YU, T. a. N. Review on the Regulation of Caleosin on Plant Lipid Droplet. Biotechnology Bulletin, [s. l.], v. 40, n. 4, p. 33, 26 abr. 2024. https://doi.org/10.13560/j.cnki.biotech.bull.1985.2023-1051.
GARCIA, T.; DUITAMA, J.; ZULLO, S. S.; GIL, J.; ARIANI, A.; DOHLE, S.; PALKOVIC, A.; SKEEN, P.; BERMUDEZ-SANTANA, C. I.; DEBOUCK, D. G.; MARTÍNEZ-CASTILLO, J.; GEPTS, P.; CHACÓN-SÁNCHEZ, M. I. Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean. Nature Communications, [s. l.], v. 12, n. 1, p. 702, 29 jan. 2021. https://doi.org/10.1038/s41467-021-20921-1. DOI: https://doi.org/10.1038/s41467-021-20921-1
HANANO, A.; BLÉE, E.; MURPHY, D. J. Caleosin/peroxygenases: multifunctional proteins in plants. Annals of Botany, [s. l.], v. 131, n. 3, p. 387–409, 16 fev. 2023. https://doi.org/10.1093/aob/mcad001. DOI: https://doi.org/10.1093/aob/mcad001
HEREDIA-PECH, M.; CHÁVEZ-PESQUEIRA, M.; ORTIZ-GARCÍA, M. M.; ANDUEZA-NOH, R. H.; CHACÓN-SÁNCHEZ, M. I.; MARTÍNEZ-CASTILLO, J. Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (Phaseolus lunatus L.) in its Mesoamerican diversity area. PeerJ, [s. l.], v. 10, p. e13690, 2022. https://doi.org/10.7717/peerj.13690. DOI: https://doi.org/10.7717/peerj.13690
JIANG, P.-L.; TZEN, J. T. C. Caleosin serves as the major structural protein as efficient as oleosin on the surface of seed oil bodies. Plant Signaling & Behavior, [s. l.], v. 5, n. 4, p. 447–449, abr. 2010. https://doi.org/10.4161/psb.5.4.10874. DOI: https://doi.org/10.4161/psb.5.4.10874
KIM, Y. Y.; JUNG, K. W.; YOO, K. S.; JEUNG, J. U.; SHIN, J. S. A stress-responsive caleosin-like protein, AtCLO4, acts as a negative regulator of ABA responses in Arabidopsis. Plant & Cell Physiology, [s. l.], v. 52, n. 5, p. 874–884, maio 2011. https://doi.org/10.1093/pcp/pcr039. DOI: https://doi.org/10.1093/pcp/pcr039
KUMAR, S.; STECHER, G.; TAMURA, K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Molecular Biology and Evolution, [s. l.], v. 33, n. 7, p. 1870–1874, 1 jul. 2016. https://doi.org/10.1093/molbev/msw054. DOI: https://doi.org/10.1093/molbev/msw054
LASKOWSKI, R. A.; JABŁOŃSKA, J.; PRAVDA, L.; VAŘEKOVÁ, R. S.; THORNTON, J. M. PDBsum: Structural summaries of PDB entries. Protein Science, [s. l.], v. 27, n. 1, p. 129–134, 2018. https://doi.org/10.1002/pro.3289. DOI: https://doi.org/10.1002/pro.3289
LETUNIC, I.; BORK, P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Research, [s. l.], v. 44, n. W1, p. W242–W245, 8 jul. 2016. https://doi.org/10.1093/nar/gkw290. DOI: https://doi.org/10.1093/nar/gkw290
LIU, X.; YANG, Z.; WANG, Y.; SHEN, Y.; JIA, Q.; ZHAO, C.; ZHANG, M. Multiple caleosins have overlapping functions in oil accumulation and embryo development. Journal of Experimental Botany, [s. l.], v. 73, n. 12, p. 3946–3962, 24 jun. 2022. https://doi.org/10.1093/jxb/erac153. DOI: https://doi.org/10.1093/jxb/erac153
LU, Y.; CHI, M.; LI, L.; LI, H.; NOMAN, M.; YANG, Y.; JI, K.; LAN, X.; QIANG, W.; DU, L.; LI, H.; YANG, J. Genome-Wide Identification, Expression Profiling, and Functional Validation of Oleosin Gene Family in Carthamus tinctorius L. Frontiers in Plant Science, [s. l.], v. 9, p. 1393, 2018. https://doi.org/10.3389/fpls.2018.01393. DOI: https://doi.org/10.3389/fpls.2018.01393
MIKLASZEWSKA, M.; ZIENKIEWICZ, K.; KLUGIER-BOROWSKA, E.; RYGIELSKI, M.; FEUSSNER, I.; ZIENKIEWICZ, A. CALEOSIN 1 interaction with AUTOPHAGY-RELATED PROTEIN 8 facilitates lipid droplet microautophagy in seedlings. Plant Physiology, [s. l.], v. 193, n. 4, p. 2361–2380, 1 dez. 2023. https://doi.org/10.1093/plphys/kiad471. DOI: https://doi.org/10.1093/plphys/kiad471
PALUPI, H. T.; ESTIASIH, T.; YUNIANTA; SUTRISNO, A. Characterization of nutritional and functional properties of Lima bean flour (Phaseolus Lunatus L.). IOP Conference Series: Earth and Environmental Science, [s. l.], v. 924, n. 1, p. 012033, nov. 2021. https://doi.org/10.1088/1755-1315/924/1/012033. DOI: https://doi.org/10.1088/1755-1315/924/1/012033
RAHMAN, F.; HASSAN, M.; ROSLI, R.; ALMOUSALLY, I.; HANANO, A.; MURPHY, D. J. Evolutionary and genomic analysis of the caleosin/peroxygenase (CLO/PXG) gene/protein families in the Viridiplantae. PLOS ONE, [s. l.], v. 13, n. 5, p. e0196669, 17 maio 2018. https://doi.org/10.1371/journal.pone.0196669. DOI: https://doi.org/10.1371/journal.pone.0196669
SAADAT, F. A computational study on the structure–function relationships of plant caleosins. Scientific Reports, [s. l.], v. 13, n. 1, p. 72, 2 jan. 2023. https://doi.org/10.1038/s41598-022-26936-y. DOI: https://doi.org/10.1038/s41598-022-26936-y
SHEN, M.; SALI, A. Statistical potential for assessment and prediction of protein structures. Protein Science, [s. l.], v. 15, n. 11, p. 2507–2524, 2006. https://doi.org/10.1110/ps.062416606. DOI: https://doi.org/10.1110/ps.062416606
SHEN, Y.; LIU, M.; WANG, L.; LI, Z.; TAYLOR, D. C.; LI, Z.; ZHANG, M. Identification, duplication, evolution and expression analyses of caleosins in Brassica plants and Arabidopsis subspecies. Molecular genetics and genomics: MGG, [s. l.], v. 291, n. 2, p. 971–988, abr. 2016. https://doi.org/10.1007/s00438-015-1156-x. DOI: https://doi.org/10.1007/s00438-015-1156-x
SHEN, Y.; XIE, J.; LIU, R.-D.; NI, X.-F.; WANG, X.-H.; LI, Z.-X.; ZHANG, M. Genomic analysis and expression investigation of caleosin gene family in Arabidopsis. Biochemical and Biophysical Research Communications, [s. l.], v. 448, n. 4, p. 365–371, 13 jun. 2014. https://doi.org/10.1016/j.bbrc.2014.04.115. DOI: https://doi.org/10.1016/j.bbrc.2014.04.115
SIEVERS, F.; HIGGINS, D. G. Clustal Omega, Accurate Alignment of Very Large Numbers of Sequences. In: RUSSELL, D. J. (org.). Multiple Sequence Alignment Methods. Totowa, NJ: Humana Press, 2014. p. 105–116. DOI 10.1007/978-1-62703-646-7_6. Disponível em: https://doi.org/10.1007/978-1-62703-646-7_6. Acesso em: 25 jun. 2024. DOI: https://doi.org/10.1007/978-1-62703-646-7_6
SILVA ALVES, M. C.; CABRAL DA SILVA, R. C.; QUARESMA, S. Characterization of α-hairpinin in the genome of lima bean (Phaseolus lunatus). International Journal of Molecular Biology Open Access, [s. l.], v. 7, n. 1, p. 112–116, 28 ago. 2024. https://doi.org/10.15406/ijmboa.2024.07.00179. DOI: https://doi.org/10.15406/ijmboa.2024.07.00179
SONG, W.; QIN, Y.; ZHU, Y.; YIN, G.; WU, N.; LI, Y.; HU, Y. Delineation of plant caleosin residues critical for functional divergence, positive selection and coevolution. BMC Evolutionary Biology, [s. l.], v. 14, n. 1, p. 124, 9 jun. 2014. https://doi.org/10.1186/1471-2148-14-124. DOI: https://doi.org/10.1186/1471-2148-14-124
STUDER, G.; REMPFER, C.; WATERHOUSE, A. M.; GUMIENNY, R.; HAAS, J.; SCHWEDE, T. QMEANDisCo—distance constraints applied on model quality estimation. Bioinformatics, [s. l.], v. 36, n. 6, p. 1765–1771, 15 mar. 2020. https://doi.org/10.1093/bioinformatics/btz828. DOI: https://doi.org/10.1093/bioinformatics/btz828
VARADI, M.; ANYANGO, S.; DESHPANDE, M.; NAIR, S.; NATASSIA, C.; YORDANOVA, G.; YUAN, D.; STROE, O.; WOOD, G.; LAYDON, A.; ŽÍDEK, A.; GREEN, T.; TUNYASUVUNAKOOL, K.; PETERSEN, S.; JUMPER, J.; CLANCY, E.; GREEN, R.; VORA, A.; LUTFI, M.; FIGURNOV, M.; COWIE, A.; HOBBS, N.; KOHLI, P.; KLEYWEGT, G.; BIRNEY, E.; HASSABIS, D.; VELANKAR, S. AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Research, [s. l.], v. 50, n. D1, p. D439–D444, 7 jan. 2022. https://doi.org/10.1093/nar/gkab1061. DOI: https://doi.org/10.1093/nar/gkab1061
WANG, J.; CHITSAZ, F.; DERBYSHIRE, M. K.; GONZALES, N. R.; GWADZ, M.; LU, S.; MARCHLER, G. H.; SONG, J. S.; THANKI, N.; YAMASHITA, R. A.; YANG, M.; ZHANG, D.; ZHENG, C.; LANCZYCKI, C. J.; MARCHLER-BAUER, A. The conserved domain database in 2023. Nucleic Acids Research, [s. l.], v. 51, n. D1, p. D384–D388, 6 jan. 2023. https://doi.org/10.1093/nar/gkac1096. DOI: https://doi.org/10.1093/nar/gkac1096
WASĄG, P.; SUWIŃSKA, A.; RICHERT, A.; LENARTOWSKA, M.; LENARTOWSKI, R. Plant-specific calreticulin is localized in the nuclei of highly specialized cells in the pistil—new observations for an old hypothesis. Protoplasma, [s. l.], v. 261, n. 6, p. 1171–1184, 1 nov. 2024. https://doi.org/10.1007/s00709-024-01961-y. DOI: https://doi.org/10.1007/s00709-024-01961-y
WEBB, B.; SALI, A. Comparative Protein Structure Modeling Using MODELLER. Current Protocols in Bioinformatics, [s. l.], v. 47, n. 1, p. 5.6.1-5.6.32, 2014. https://doi.org/10.1002/0471250953.bi0506s47. DOI: https://doi.org/10.1002/0471250953.bi0506s47
WIEDERSTEIN, M.; SIPPL, M. J. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, [s. l.], v. 35, n. Web Server issue, p. W407-410, jul. 2007. https://doi.org/10.1093/nar/gkm290. DOI: https://doi.org/10.1093/nar/gkm290
WISSER, R. J.; OPPENHEIM, S. J.; ERNEST, E. G.; MHORA, T. T.; DUMAS, M. D.; GREGORY, N. F.; EVANS, T. A.; DONOFRIO, N. M. Genome assembly of a Mesoamerican derived variety of lima bean: a foundational cultivar in the Mid-Atlantic USA. G3 Genes|Genomes|Genetics, [s. l.], v. 11, n. 11, p. jkab207, 1 nov. 2021. https://doi.org/10.1093/g3journal/jkab207. DOI: https://doi.org/10.1093/g3journal/jkab207
ZHU, Y.; WANG, Y.; WEI, Z.; ZHANG, X.; JIAO, B.; TIAN, Y.; YAN, F.; LI, J.; LIU, Y.; YANG, X.; ZHANG, J.; WANG, X.; MU, Z.; WANG, Q. Analysis of oil synthesis pathway in Cyperus esculentus tubers and identification of oleosin and caleosin genes. Journal of Plant Physiology, [s. l.], v. 284, p. 153961, 1 maio 2023. https://doi.org/10.1016/j.jplph.2023.153961. DOI: https://doi.org/10.1016/j.jplph.2023.153961
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