HDACs MADS-domain Protein Interaction: a Case Study of HDA15 and XAL1 in

Overview

Journal Plant Signal Behav

Specialty Biology

Date 2024 May 21

PMID 38771929

Authors

Andrea Sanjuan-Badillo

Leon P Martinez-Castilla

Ricardo Garcia-Sandoval

Patricia Ballester

Cristina Ferrandiz

Maria de la Paz Sanchez

Berenice Garcia-Ponce

Adriana Garay-Arroyo

Elena R Alvarez-Buylla

Affiliations

Soon will be listed here.

Abstract

Cellular behavior, cell differentiation and ontogenetic development in eukaryotes result from complex interactions between epigenetic and classic molecular genetic mechanisms, with many of these interactions still to be elucidated. Histone deacetylase enzymes (HDACs) promote the interaction of histones with DNA by compacting the nucleosome, thus causing transcriptional repression. MADS-domain transcription factors are highly conserved in eukaryotes and participate in controlling diverse developmental processes in animals and plants, as well as regulating stress responses in plants. In this work, we focused on finding out putative interactions of HDACs and MADS-domain proteins using an evolutionary perspective combined with bioinformatics analyses and testing the more promising predicted interactions through classic molecular biology tools. Through bioinformatic analyses, we found similarities between HDACs proteins from different organisms, which allowed us to predict a putative protein-protein interaction between the deacetylase HDA15 and the MADS-domain protein XAANTAL1 (XAL1). The results of two-hybrid and Bimolecular Fluorescence Complementation analysis demonstrated and HDA15-XAL1 interaction in the nucleus. Likely, this interaction might regulate developmental processes in plants as is the case for this type of interaction in animals.

References

Wang Z, Qin G, Zhao T . HDAC4: mechanism of regulation and biological functions. Epigenomics. 2014; 6(1):139-50. PMC: 4380265. DOI: 10.2217/epi.13.73. View

Bouckaert R, Vaughan T, Barido-Sottani J, Duchene S, Fourment M, Gavryushkina A . BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 2019; 15(4):e1006650. PMC: 6472827. DOI: 10.1371/journal.pcbi.1006650. View

Gu X, Wang Y, He Y . Photoperiodic regulation of flowering time through periodic histone deacetylation of the florigen gene FT. PLoS Biol. 2013; 11(9):e1001649. PMC: 3760768. DOI: 10.1371/journal.pbio.1001649. View

Silva P . Assessing the reliability of sequence similarities detected through hydrophobic cluster analysis. Proteins. 2007; 70(4):1588-94. DOI: 10.1002/prot.21803. View

Tapia-Lopez R, Garcia-Ponce B, Dubrovsky J, Garay-Arroyo A, Perez-Ruiz R, Kim S . An AGAMOUS-related MADS-box gene, XAL1 (AGL12), regulates root meristem cell proliferation and flowering transition in Arabidopsis. Plant Physiol. 2008; 146(3):1182-92. PMC: 2259045. DOI: 10.1104/pp.107.108647. View

Dong C, Yang X, Zhang C, Liu Y, Zhou R, Cheng Q . Myocyte enhancer factor 2C and its directly-interacting proteins: A review. Prog Biophys Mol Biol. 2017; 126:22-30. DOI: 10.1016/j.pbiomolbio.2017.02.002. View

Tsuchiya Y, Yamamori Y, Tomii K . Protein-protein interaction prediction methods: from docking-based to AI-based approaches. Biophys Rev. 2022; 14(6):1341-1348. PMC: 9759050. DOI: 10.1007/s12551-022-01032-7. View

Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L . Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Adv Bioinformatics. 2009; 2008:420747. PMC: 2777001. DOI: 10.1155/2008/420747. View

Felsenstein J . CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP. Evolution. 2017; 39(4):783-791. DOI: 10.1111/j.1558-5646.1985.tb00420.x. View

10.

Hill K, Wang H, Perry S . A transcriptional repression motif in the MADS factor AGL15 is involved in recruitment of histone deacetylase complex components. Plant J. 2007; 53(1):172-85. DOI: 10.1111/j.1365-313X.2007.03336.x. View

11.

Alinsug M, Chen F, Luo M, Tai R, Jiang L, Wu K . Subcellular localization of class II HDAs in Arabidopsis thaliana: nucleocytoplasmic shuttling of HDA15 is driven by light. PLoS One. 2012; 7(2):e30846. PMC: 3281883. DOI: 10.1371/journal.pone.0030846. View

12.

Zhao L, Lu J, Zhang J, Wu P, Yang S, Wu K . Identification and characterization of histone deacetylases in tomato (Solanum lycopersicum). Front Plant Sci. 2015; 5:760. PMC: 4285013. DOI: 10.3389/fpls.2014.00760. View

13.

Castelan-Munoz N, Herrera J, Cajero-Sanchez W, Arrizubieta M, Trejo C, Garcia-Ponce B . MADS-Box Genes Are Key Components of Genetic Regulatory Networks Involved in Abiotic Stress and Plastic Developmental Responses in Plants. Front Plant Sci. 2019; 10:853. PMC: 6636334. DOI: 10.3389/fpls.2019.00853. View

14.

Huelsenbeck J, Larget B, Alfaro M . Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Mol Biol Evol. 2004; 21(6):1123-33. DOI: 10.1093/molbev/msh123. View

15.

Rodriguez-Bolanos M, Martinez T, Juarez S, Quiroz S, Dominguez A, Garay-Arroyo A . Reveals an Additional Level of Flowering Regulation in the Shoot Apical Meristem in Response to Light and Increased Temperature in Arabidopsis. Int J Mol Sci. 2023; 24(16). PMC: 10454237. DOI: 10.3390/ijms241612773. View

16.

Lee J, Oh M, Park H, Lee I . SOC1 translocated to the nucleus by interaction with AGL24 directly regulates leafy. Plant J. 2008; 55(5):832-43. DOI: 10.1111/j.1365-313X.2008.03552.x. View

17.

Seto E, Yoshida M . Erasers of histone acetylation: the histone deacetylase enzymes. Cold Spring Harb Perspect Biol. 2014; 6(4):a018713. PMC: 3970420. DOI: 10.1101/cshperspect.a018713. View

18.

Katoh K, Standley D . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4):772-80. PMC: 3603318. DOI: 10.1093/molbev/mst010. View

19.

Yan Y, Tao H, He J, Huang S . The HDOCK server for integrated protein-protein docking. Nat Protoc. 2020; 15(5):1829-1852. DOI: 10.1038/s41596-020-0312-x. View

20.

Pacheco-Escobedo M, Ivanov V, Ransom-Rodriguez I, Arriaga-Mejia G, Avila H, Baklanov I . Longitudinal zonation pattern in Arabidopsis root tip defined by a multiple structural change algorithm. Ann Bot. 2016; 118(4):763-776. PMC: 5055628. DOI: 10.1093/aob/mcw101. View