Genome-Wide Identification, Phylogenetic and Expression Analyses of the Ubiquitin-Conjugating Enzyme Gene Family in Maize

Abstract

BackgroundUbiquitination is a post-translation modification where ubiquitin is attached to a substrate. Ubiquitin-conjugating enzymes (E2s) play a major role in the ubiquitin transfer pathway, as well as a variety of functions in plant biological processes. To date, no genome-wide characterization of this gene family has been conducted in maize (Zea mays).Methodology/Principal FindingsIn the present study, a total of 75 putative ZmUBC genes have been identified and located in the maize genome. Phylogenetic analysis revealed that ZmUBC proteins could be divided into 15 subfamilies, which include 13 ubiquitin-conjugating enzymes (ZmE2s) and two independent ubiquitin-conjugating enzyme variant (UEV) groups. The predicted ZmUBC genes were distributed across 10 chromosomes at different densities. In addition, analysis of exon-intron junctions and sequence motifs in each candidate gene has revealed high levels of conservation within and between phylogenetic groups. Tissue expression analysis indicated that most ZmUBC genes were expressed in at least one of the tissues, indicating that these are involved in various physiological and developmental processes in maize. Moreover, expression profile analyses of ZmUBC genes under different stress treatments (4°C, 20% PEG6000, and 200 mM NaCl) and various expression patterns indicated that these may play crucial roles in the response of plants to stress.ConclusionsGenome-wide identification, chromosome organization, gene structure, evolutionary and expression analyses of ZmUBC genes have facilitated in the characterization of this gene family, as well as determined its potential involvement in growth, development, and stress responses. This study provides valuable information for better understanding the classification and putative functions of the UBC-encoding genes of maize.

The Ubiquitin Conjugating Enzyme: An Important Ubiquitin Transfer Platform in Ubiquitin-Proteasome System

“…E2 enzymes belong to the polygenic family, and the number of members varies from a dozen to dozens in different species. 20 E2 enzymes have been found in Caenorhabditis elegans [77], 40 in A. thaliana [68], 14 in Saccharomyces cerevisiae [78], 37 in human [67], 48 in rice [79], 75 in maize [80], 72 in banana [81], 43 in Vitis vinifera [82], 34 in Carica papaya [83], 59 in tomato [84], 40 in Dimocarpus longan Lour. [85], and 57 in potato [86].…”

“…UBC32 mutants are extremely sensitive to paraquat treatment compared with overexpression plants, suggesting that UBC32 is an essential ERAD component and plays an important part in the response to oxidative stress and salt stress [114]. Although changes in expression of UBC genes in A. thaliana and rice are not induced by cold stress treatment [103], some reports have found that the UBCs gene in other species have responses to cold and heat stresses [80,82]. UBC24 (pho2) is regulated by microRNA399 (miR399) to control inorganic phosphate (Pi) homeostasis and Pi translocation and remobilization [115][116][117][118].…”

Evolution and Expression Divergence of E2 Gene Family under Multiple Abiotic and Phytohormones Stresses inBrassica rapa

“…The B. rapa sequences were downloaded from the database ( http://brassicadb.org/brad/ ), while for other species rice [ 9 ] ( http://rice.plantbiology.msu.edu/ ), tomato [ 8 ] ( https://solgenomics.net/organism/Solanum_lycopersicum/ genome ), Maize [ 10 ] ( https://www.maizegdb.org/ ), Vitis vinifera [ 7 ], and Carica papaya [ 11 ] sequences were downloaded based on the reported studies. From Pfam database ( https://pfam.sanger.ac.uk/ ) the E2 UBC domains (PF00179) were first downloaded and Hidden Markov Model (HMM) search was carried out in Brassica genome with default parameters.…”

“…Some of the recent studies highlighted that involvement of E2 genes family exited as multifunctional and playing key parts in various physiological activities. In several crops, such as in grapes 43 [ 7 ], tomato 59 [ 8 ], rice 39 [ 9 ], maize 75 [ 10 ], Carica papaya 34 [ 11 ], and Arabidopsis 41 [ 12 ], genes were identified, respectively, as during the process of evolution the number of genes of E2 increases with the complex nature and the development of organism [ 13 ]. For example, fewer genes ≤ 20 in algae were found in ancestral eukaryotes compared to certain plants and animals > 40 [ 14 ].…”

New ubiquitin-dependent mechanisms regulating the Aurora B–protein phosphatase 1 balance in Saccharomyces cerevisiae

“…There is a clear hierarchy in the abundance and conservation of these enzyme classes. One or a few highly conserved E1 enzymes activate ∼10 to ∼70 E2s, depending on the species (Jue et al, 2015). E3s number in the hundreds (Finley et al, 2012).…”