plants Article Exploration of Autophagy Families in Legumes and Dissection of the ATG18 Family with a Special Focus on Phaseolus vulgaris Elsa-Herminia Quezada Rodríguez 1 , Homero Gómez-Velasco 2 , Manoj-Kumar Arthikala 1 , Miguel Lara 3 , Antonio Hernández-López 1 and Kalpana Nanjareddy 1, *   Citation: Rodríguez, E.-H.Q.; Gómez-Velasco, H.; Arthikala, M.-K.; Lara, M.; Hernández-López, A.; Nanjareddy, K. Exploration of Autophagy Families in Legumes and Dissection of the ATG18 Family with a Special Focus on Phaseolus vulgaris. Plants 2021, 10, 2619. https:// doi.org/10.3390/plants10122619 Academic Editors: Olga V. Voitsekhovskaja and Cecilia Gotor Received: 7 September 2021 Accepted: 3 November 2021 Published: 29 November 2021 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). 1 Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (UNAM), León C.P. 37684, Mexico; qrelsa@gmail.com (E.-H.Q.R.); manoj@enes.unam.mx (M.-K.A.); ahernandez@enes.unam.mx (A.H.-L.) 2 Instituto de Química, Universidad Nacional Autónoma de México (UNAM), Cuidad Universitaria, Cuidad de Mexico C.P. 04510, Mexico; antropofagomer@hotmail.com 3 Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca C.P. 62271, Mexico; mflara@ibt.unam.mx * Correspondence: kalpana@enes.unam.mx; Tel.: +52-477-1940800 (ext. 43462) Abstract: Macroautophagy/autophagy is a fundamental catabolic pathway that maintains cellular homeostasis in eukaryotic cells by forming double-membrane-bound vesicles named autophago- somes. The autophagy family genes remain largely unexplored except in some model organisms. Legumes are a large family of economically important crops, and knowledge of their important cellu- lar processes is essential. Here, to first address the knowledge gaps, we identified 17 ATG families in Phaseolus vulgaris, Medicago truncatula and Glycine max based on Arabidopsis sequences and elucidated their phylogenetic relationships. Second, we dissected ATG18 in subfamilies from early plant lineages, chlorophytes to higher plants, legumes, which included a total of 27 photosynthetic organisms. Third, we focused on the ATG18 family in P. vulgaris to understand the protein structure and developed a 3D model for PvATG18b. Our results identified ATG homologs in the chosen legumes and differential expression data revealed the nitrate-responsive nature of ATG genes. A multidimensional scaling analysis of 280 protein sequences from 27 photosynthetic organisms classified ATG18 homologs into three subfamilies that were not based on the BCAS3 domain alone. The domain structure, protein motifs (FRRG) and the stable folding conformation structure of PvATG18b revealing the possible lipid-binding sites and transmembrane helices led us to propose PvATG18b as the functional homolog of AtATG18b. The findings of this study contribute to an in-depth understanding of the autophagy process in legumes and improve our knowledge of ATG18 subfamilies. Keywords: homologs; phylogeny; ATG18; FRRG motif; principal component; 3D model; expres- sion profile 1. Introduction Autophagy is a degradation process essential in the maintenance of homeostasis in eukaryotic cells and is related to a wide variety of physiological and pathophysio- logical roles, such as host defense, development, infection, and tumorigenesis [1,2]. Au- tophagy/macroautophagy is a process in which cytosolic components are sequestered within double-membrane vesicles called autophagosomes, which fuse with lysosomes or vacuoles for degradation/recycling [3]. This process is mediated by evolutionarily conserved genes known as autophagy genes (ATGs) [4], which were originally discovered in and isolated from Saccharomyces cerevisiae [5–8]. Three major intracellular autophagy pathways, namely, macroautophagy, microautophagy and chaperone-mediated autophagy (CMA), have been elucidated, and these differ in the mode of cargo delivery to the lyso- some or vacuole [9,10]. Macroautophagy can be nonselective or selective: Nonselective autophagy is a cellular response to nutrient deprivation that involves the random uptake of Plants 2021, 10, 2619. https://doi.org/10.3390/plants10122619 https://www.mdpi.com/journal/plants