The U-box family genes in Medicago truncatula: Key elements in response to salt, cold, and drought stresses

Song, Jianbo; Mo, Xiaowei; Yang, Haiqi; Yue, Luming; Song, Jun; Mo, Beixin

doi:10.1371/journal.pone.0182402

Cited by 41 publications

(38 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The presence of the various regulatory elements in the promoter region of the genes is vital evidence to support the participation of the U-box E3 gene family in the various tomato signaling mechanisms. The previous reports of the promoter analysis in the Medicago truncatula provide similar patterns of the elements that suggest a common association of the U-box E3 gene family in stress and hormonal regulatory pathways of plants 72 .…”

Section: Gene Expression Patterns In Duplicated Genes the Gene Expresupporting

confidence: 68%

“…The gene expression profile under abiotic stress and hormone treatment conditions show a variety of the expression of the U-box E3 genes in tomato. The U-box E3 ubiquitin ligases were reported to be involved in plant abiotic stress and hormone signaling 29,30,72 . The Cluster 4 and 5 genes expression were significantly altered under hormone and abiotic conditions in tomato.…”

Section: Gene Expression Patterns In Duplicated Genes the Gene Exprementioning

confidence: 99%

See 1 more Smart Citation

Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato

Sharma

Taganna²

2020

Sci Rep

View full text Add to dashboard Cite

E3 ubiquitin ligases are a central modifier of plant signaling pathways that act through targeting proteins to the degradation pathway. U-box E3 ubiquitin ligases are a distinct class of E3 ligases that utilize intramolecular interactions for its scaffold stabilization. U-box E3 ubiquitin ligases are prevalent in plants in comparison to animals. However, the evolutionary aspects, genetic organizations, and functional fate of the U-box E3 gene family in plant development, especially in tomato is not well understood. In the present study, we have performed in-silico genome-wide analysis of the U-box E3 ubiquitin ligase gene family in Solanum lycopersicum. We have identified 62 U-box genes with U-box/ Ub Fusion Degradation 2 (UFD2) domain. The chromosomal localization, phylogenetic analysis, gene structure, motifs, gene duplication, syntenic regions, promoter, physicochemical properties, and ontology were investigated. The U-box gene family showed significant conservation of the U-box domain throughout the gene family. Duplicated genes discerned noticeable functional transitions among duplicated genes. The gene expression profiles of U-box E3 family members show involvement in abiotic and biotic stress signaling as well as hormonal pathways. We found remarkable participation of the U-box gene family in the vegetative and reproductive tissue development. It is predicted to be actively regulating flowering time and endosperm formation. Our study provides a comprehensive picture of distribution, structural features, promoter elements, evolutionary relationship, and gene expression of the U-box gene family in the tomato. We predict the crucial participation of the U-box gene family in tomato plant development and stress responses. Ubiquitin mediated proteasomal degradation is one of the major mechanisms for post-translational regulation of gene expression and protein quality control in eukaryotes 1,2. The Ubiquitin Proteasome System (UPS) degrades the aberrant or truncated, active, and short-lived proteins from various cellular pathways and thereby controls the protein loads of the cell 3-5. The major characteristic feature of the ubiquitination is the addition of the ubiquitin protein molecule (M r : 8.5 kDa) on the lysine residues of the acceptor protein 4-7. The ubiquitination is mediated by a three-step enzymatic process. Ubiquitin forms a thioester bond in an ATP-dependent reaction at cysteine residue with ubiquitin-activating enzyme E1. It is followed by the transfer of the ubiquitin to ubiquitin-conjugating enzyme E2, at conserved cysteine residue on the active site. Then, the ubiquitin ligase enzyme E3 mediates the transfer of ubiquitin to the target protein. An isopeptide bond is formed between the carboxyl terminus of ubiquitin and the ε-amino group of a lysine residue on the target protein. The process utilizes the 26S proteasome (made up of 19S regulatory particles and 20S core proteases) for the degradation of the ubiquitinated proteins 3-5,8. The E3 ubiquitin ligases are the largest family among all three ...

show abstract

Section: Gene Expression Patterns In Duplicated Genes the Gene Expresupporting

confidence: 68%

Section: Gene Expression Patterns In Duplicated Genes the Gene Exprementioning

confidence: 99%

Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato

Sharma

Taganna²

2020

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Based on the completion of M . truncatula genome sequencing 28 , many gene families were identified and characterized at the whole-genome level, including CCCH 29 , LBD 30 , WRKY 31 , AP2/ERF 32 , Dof 33 , GH3 34 , CAMTA 35 , LEA 36 , MAPKKK 37 , U-box 38 , MYB 39 , 40 and GRAS 41 , 42 . In this study, PP2C genes in M .…”

Section: Discussionmentioning

confidence: 99%

Genome-wide Identification of PP2C Genes and Their Expression Profiling in Response to Drought and Cold Stresses in Medicago truncatula

Yang

Liu

Niu

et al. 2018

Sci Rep

View full text Add to dashboard Cite

Type 2 C protein phosphatases (PP2Cs) represent the major group of protein phosphatases in plants and play important roles in various plant processes. In this study, 94 MtPP2C genes were identified from Medicago truncatula and further phylogenetically classified into 13 subfamilies, as supported by exon-intron organization and conserved motif composition. Collinearity analysis indicated that segmental duplication events played a crucial role in the expansion of MtPP2C gene families in M. truncatula. Furthermore, the expression profiles of MtPP2Cs under different abiotic treatments were analyzed using qRT-PCR. Results showed that these MtPP2Cs genes displayed different expression patterns in response to drought, cold and ABA stress conditions and some of the key stress responsive MtPP2Cs genes have been identified. Our study presents a comprehensive overview of the PP2C gene family in M. truncatula, which will be useful for further functional characterization of MtPP2Cs in plant drought and cold stress responses.

show abstract

“…jgi.doe.gov/Mtrun catul a), and drafted to the chromosomes of M. truncatula using the GenomePixelizer software (http:// www.atgc.org/Genom ePixe lizer ) (Kozik et al 2002). The segmental gene duplication event was marked based on the previously described criteria: the sequence alignment length covered more than 80% of the longer gene, and the identity of the aligned regions was over 70% (Jia et al 2017;Song et al 2017). The tandem duplicated genes were defined as two or more homologous genes located on one single chromosome with a distance of 100 kb without any intervening gene (Kayum et al 2017).…”

Section: Chromosomal Distribution and Gene Duplicationmentioning

confidence: 99%

In silico identification and expression analysis of superoxide dismutase (SOD) gene family in Medicago truncatula

et al. 2018

Self Cite

View full text Add to dashboard Cite

Superoxide dismutase (SOD) proteins are crucial antioxidant enzymes that play critical roles in plant growth, development, and response to various abiotic stresses. The gene family has been characterized in various plant species, but not in yet. Here, a total of 7 genes were first identified from the whole genome of, including 1 , 2, and 4 /, which are unevenly distributed in five out of the eight chromosomes. Phylogenetic analysis showed that SOD proteins from and other plant species could be classified into two main categories (Cu/ZnSODs and Fe-MnSODs), which could be further divided into eight subgroups, and members within the same subgroup tended to share the same subcellular localization. In addition, genes together with and within the same subgroup also displayed similar motif compositions and exon-intron structures. Most genes were ubiquitously expressed in various tissues, particularly in leaves, seeds and root nodules at different developmental stages. Moreover, microarray analysis and high-throughput sequencing showed that most genes were differentially expressed under salt, drought, and cold treatments, indicating their pivotal roles in stress response of . These findings provide useful information for the functional characterization of family genes for growth, development, and stress response of .

show abstract

The U-box family genes in Medicago truncatula: Key elements in response to salt, cold, and drought stresses

Cited by 41 publications

References 43 publications

Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato

Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato

Genome-wide Identification of PP2C Genes and Their Expression Profiling in Response to Drought and Cold Stresses in Medicago truncatula

In silico identification and expression analysis of superoxide dismutase (SOD) gene family in Medicago truncatula

Contact Info

Product

Resources

About