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Genome-Wide Characterization of the ADK Gene Family and Analysis of Expression Patterns Under Abiotic Stress in Beans

Year 2025, Volume: 4 Issue: 2, 77 - 88, 13.12.2025
https://doi.org/10.5281/zenodo.17786514

Abstract

In plants, Adenylate Kinase (ADK) genes are essential genetic components that regulate critical processes such as growth, development and response to abiotic and biotic stress factors. In this study, genome-wide identification, bioinformatic analyses and expression profiles of ADK genes in Phaseolus vulgaris leaf tissue under drought and salt stress were investigated. As a result of the study, 7 Phvul-ADK proteins were identified and it was determined that the amino acid lengths of these proteins ranged from 239 to 597 and molecular weights ranged from 26,609.86 to 66,903.70 Da. In addition, it was determined that the number of exons of the genes varied between 3 and 19. Phylogenetic analysis based on ADK proteins from Phaseolus vulgaris, Arabidopsis thaliana, Hordeum vulgare, Oryza sativa and Volvox carteri species revealed that the genes were divided into three different groups. In addition, Phvul-ADK-2 and Phvul-ADK-5 genes were found to show segmental duplication in the bean genome. This study is the first comprehensive genome-wide analysis of the Adenylate Kinase family in bean and highlights the important roles of the ADK gene family in plant development and stress responses. It is evaluated that the findings obtained will provide important contributions to bean breeding studies and stress tolerance research.

References

  • AbuQamar, S., Luo, H., Laluk, K., Mickelbart, M. V., & Mengiste, T. (2009). Crosstalk between biotic and abiotic stress responses in tomato is mediated by the AIM1 transcription factor. The Plant Journal, 58(2), 347-360.
  • Arteaga, S., Yabor, L., Díez, M. J., Prohens, J., Boscaiu, M., & Vicente, O. (2020). The use of proline in screening for tolerance to drought and salinity in common bean (Phaseolus vulgaris L.) genotypes. Agronomy, 10(6), 817.
  • Bartels, D., & Sunkar, R. (2005). Drought and salt tolerance in plants.Critical reviews in plant sciences,24(1), 23-58.
  • Bray, E. A. (2000). Responses to abiotic stresses. Biochemistry and molecular biology of plants, 1158-1203.
  • Beebe, S. E., Rao, I. M., Devi, M. J., & Polania, J. (2014). Common beans, biodiversity, and multiple stresses: challenges of drought resistance in tropical soils. Crop and Pasture Science, 65(7), 667-675.
  • Beier, S., Himmelbach, A., Colmsee, C., Zhang, X. Q., Barrero, R. A., Zhang, Q., ... & Mascher, M. (2017). Construction of a map-based reference genome sequence for barley, Hordeum vulgare L. Scientific data, 4(1), 1-24.
  • Buttanri, A., Kasapoğlu, A. G., Öner, B. M., Aygören, A. S., Muslu, S., İlhan, E., ... & Aydin, M. (2024). Predicting the role of β-GAL genes in bean under abiotic stress and genome-wide characterization of β-GAL gene family members. Protoplasma, 1-19.
  • Carrari, F., Coll-Garcia, D., Schauer, N., Lytovchenko, A., Palacios-Rojas, N., Balbo, I., ... & Fernie, A. R. (2005). Deficiency of a plastidial adenylate kinase in Arabidopsis results in elevated photosynthetic amino acid biosynthesis and enhanced growth. Plant Physiology, 137(1), 70-82.
  • Chang, H.Y.; Fu, C.Y. Adenylate Kinase. Encycl. Food Microbiol. 2014, 1, 16–24.
  • Chen, C., Wu, Y., Li, J., Wang, X., Zeng, Z., Xu, J., ... & Xia, R. (2023). TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining. Molecular plant, 16(11), 1733-1742.
  • Chen, Z., Fu, H., Liu, D., Chang, P. F. L., Narasimhan, M., Ferl, R., ... & Bressan, R. A. (1994). A NaCl‐regulated plant gene encoding a brain protein homolog that activates ADP ribosyltransferase and inhibits protein kinase C. The Plant Journal, 6(5), 729-740.
  • Dzeja, P., & Terzic, A. (2009). Adenylate kinase and AMP signaling networks: metabolic monitoring, signal communication and body energy sensing. International journal of molecular sciences, 10(4), 1729-1772.
  • Dzheia, P. P., Kal'venas, A. A., Toleĭkis, A. I., & Prashkiavichius, A. K. (1986). The role of adenylate kinase in the regulation of the rate and effectiveness of energy transfer from mitochondria to hexokinase in vitro. Biokhimiia (Moscow, Russia), 51(6), 974-979.
  • Feki, K., Tounsi, S., Jemli, S., Boubakri, H., Saidi, M. N., Mrabet, M., ... & Mhadhbi, H. (2024). Genome-wide identification of PR10 family members and expression profile analysis of PvPR10 in common bean (Phaseolus vulgaris L.) in response to hormones and several abiotic stress conditions. Plant Growth Regulation, 102(2), 279-295.
  • Gong, P., Zhang, J., Li, H., Yang, C., Zhang, C., Zhang, X., ... & Ye, Z. (2010). Transcriptional profiles of drought-responsive genes in modulating transcription signal transduction, and biochemical pathways in tomato. Journal of experimental botany, 61(13), 3563-3575.
  • Hampp, R., Goller, M., & Ziegler, H. (1982). Adenylate levels, energy charge, and phosphorylation potential during dark-light and light-dark transition in chloroplasts, mitochondria, and cytosol of mesophyll protoplasts from Avena sativa L. Plant Physiology, 69(2), 448-455.
  • Hiz MC, Canher B, Niron H, Turet M (2014) Transcriptome analysis of salt tolerant common bean (Phaseolus vulgaris L.) under saline conditions. PloS one 9(3):e92598
  • Holland PW, Garcia-Fernàndez J, Williams NA, Sidow A (1994) Gene duplications and the origins of vertebrate development. Development 1994(Supplement):125–133
  • Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35:585–587
  • Huang, P., Lin, Z., Zhang, Y., Gao, Y., Tan, S., Wang, S., ... & Ma, X. (2024). Genome-Wide Identification and Expression Analysis of ADK Gene Family Members in Cotton under Abiotic Stress. International Journal of Molecular Sciences, 25(14), 7821.
  • Kawai, M., Kidou, S. I., Kato, A., & Uchimiya, H. (1992). Molecular characterization of cDNA encoding for adenylate kinase of rice (Oryza sativa L.). The Plant Journal, 2(6), 845-854.
  • Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. (2015). The Phyre2 web portal for protein modeling, prediction and analysis. Nature protocols, 10(6), 845-858.
  • Khan, N., You, F. M., Datla, R., Ravichandran, S., Jia, B., & Cloutier, S. (2020). Genome-wide identification of ATP binding cassette (ABC) transporter and heavy metal associated (HMA) gene families in flax (Linum usitatissimum L.). BMC genomics, 21, 1-14.
  • Lange, P. R., Geserick, C., Tischendorf, G., & Zrenner, R. (2008). Functions of chloroplastic adenylate kinases in Arabidopsis. Plant physiology, 146(2), 492.
  • Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R ... Huala E (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40(D1):D1202-D1210
  • Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, 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 Res 30:325–327
  • Letunic I, Bork P (2011) Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39(suppl_2):W475-W478
  • Li, J., Zhang, Z., Vang, S., Yu, J., Wong, G. K. S., & Wang, J. (2009). Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage. Journal of molecular evolution, 68, 414-423.
  • Li, X., Lyu, C., Song, J., Lu, Y., Zeng, F., Lu, L., & Li, L. (2023). Identification and Expression Analysis of Adenylate Kinase Gene Family in Potato. Horticulturae, 9(9), 1025.
  • Lone, A. A., Khan, M. N., Gul, A., Dar, Z. A., Iqbal, A. M., Lone, B. A., ... & Nisar, F. (2021). Common beans and abiotic stress challenges. Curr. J. Appl. Sci. Technol, 40, 41-53.
  • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628
  • Ouyang, S., Zhu, W., Hamilton, J., Lin, H., Campbell, M., Childs, K., ... & Buell, C. R. (2007). The TIGR rice genome annotation resource: improvements and new features. Nucleic acids research, 35(suppl_1), D883-D887.
  • Peterson, T. A., Nieman, R. H., & Clark, R. A. (1987). Nucleotide metabolism in salt-stressed Zea mays L. Root tips: I. Adenine and uridine nucleotides. Plant Physiology, 85(4), 984-989.
  • Pettersen, E. F. (2004). TDG, Conrad C Huang, Gregory S Couch, Daniel M Greenblatt, Elaine C Meng, Thomas E Ferrin. UCSF Chimera--a visualization system for exploratory research and analysis. Journal of computational chemistry, 25, 13.
  • Prochnik, S. E., Umen, J., Nedelcu, A. M., Hallmann, A., Miller, S. M., Nishii, I., ... & Rokhsar, D. S. (2010). Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science, 329(5988), 223-226.
  • 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.
  • Ramegowda, V., & Senthil-Kumar, M. (2015). The interactive effects of simultaneous biotic and abiotic stresses on plants: mechanistic understanding from drought and pathogen combination. Journal of plant physiology, 176, 47-54.
  • Raveneau, M. P., Benamar, A., & Macherel, D. (2017). Water content, adenylate kinase, and mitochondria drive adenylate balance in dehydrating and imbibing seeds. Journal of Experimental Botany, 68(13), 3501-3512.
  • Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J ... Jackson SA (2014) A reference genome for common bean and genome-wide analysis of dual domestications. Nature Genetics 46(7):707–713
  • Stitt, M., Lilley, R. M., & Heldt, H. W. (1982). Adenine nucleotide levels in the cytosol, chloroplasts, and mitochondria of wheat leaf protoplasts. Plant physiology, 70(4), 971-977.
  • Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P, Jensen LJ, von Mering C (2021) The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res 49(D1):D605–D612
  • 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. Mol Biol Evol 28:2731–2739
  • Xu, G., Guo, C., Shan, H., & Kong, H. (2012). Divergence of duplicate genes in exon–intron structure. Proceedings of the national academy of sciences, 109(4), 1187-1192.
  • Yang, L., Cao, H., Zhang, X., Gui, L., Chen, Q., Qian, G., ... & Li, Z. (2021). Genome-wide identification and expression analysis of tomato ADK gene family during development and stress. International Journal of Molecular Sciences, 22(14), 7708.
  • Zhou, S., Wei, S., Boone, B., & Levy, S. (2007). Microarray analysis of genes affected by salt stress in tomato. African Journal of Environmental Science and Technology, 1(2), 14-26.
There are 45 citations in total.

Details

Primary Language English
Subjects Plant Cell and Molecular Biology
Journal Section Research Article
Authors

Azize Buttanrı 0009-0005-7398-0083

Ayşe Gül Kasapoğlu 0000-0002-6447-4921

Cemile Güneş 0009-0004-8874-3948

Submission Date September 24, 2025
Acceptance Date November 3, 2025
Early Pub Date December 11, 2025
Publication Date December 13, 2025
Published in Issue Year 2025 Volume: 4 Issue: 2

Cite

APA Buttanrı, A., Kasapoğlu, A. G., & Güneş, C. (2025). Genome-Wide Characterization of the ADK Gene Family and Analysis of Expression Patterns Under Abiotic Stress in Beans. Eurasian Journal of Molecular and Biochemical Sciences, 4(2), 77-88. https://doi.org/10.5281/zenodo.17786514