Domain of unknown function (DUF) proteins in plants: function and perspective

Luo, Chengke; Akhtar, Maryam; Min, Weifang; Bai, Xiaorong; Ma, Tianli; Liu, Caixia

doi:10.1007/s00709-023-01917-8

Cited by 2 publications

(2 citation statements)

References 108 publications

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“…Domains of unknown function (DUFs), deposited in the protein family database (Pfam), represent conserved amino acid sequences within protein domains whose functions remain uncharacterized [ 22 , 23 ]. Proteins sharing the same DUF are classified into distinct DUF families [ 22 ]. The DUF protein family plays a pivotal role in the regulation of plant growth and development, mediating responses to both biotic and abiotic stresses, as well as fulfilling various regulatory functions throughout the life cycle of plants [ 24 ].…”

Section: Introductionmentioning

confidence: 99%

“…In the evolution of Brassicaceae, gene duplication is the main way to produce new genes [18][19][20], such as L-type LecRKs (Lectin Receptor Kinase) and LLPs (L-type lectin domain proteins), which makes an important contribution to their adaptation to the environment [18,21]. Domains of unknown function (DUFs), deposited in the protein family database (Pfam), represent conserved amino acid sequences within protein domains whose functions remain uncharacterized [22,23]. Proteins sharing the same DUF are classified into distinct DUF families [22].…”

Section: Introductionmentioning

confidence: 99%

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Lineage-specific gene duplication and expansion of DUF1216 gene family in Brassicaceae

Zhang,

Xiong,

Wang

et al. 2024

PLoS ONE

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Proteins containing domain of unknown function (DUF) are prevalent in eukaryotic genome. The DUF1216 proteins possess a conserved DUF1216 domain resembling to the mediator protein of Arabidopsis RNA polymerase II transcriptional subunit-like protein. The DUF1216 family are specifically existed in Brassicaceae, however, no comprehensive evolutionary analysis of DUF1216 genes have been performed. We performed a first comprehensive genome-wide analysis of DUF1216 proteins in Brassicaceae. Totally 284 DUF1216 genes were identified in 27 Brassicaceae species and classified into four subfamilies on the basis of phylogenetic analysis. The analysis of gene structure and conserved motifs revealed that DUF1216 genes within the same subfamily exhibited similar intron/exon patterns and motif composition. The majority members of DUF1216 genes contain a signal peptide in the N-terminal, and the ninth position of the signal peptide in most DUF1216 is cysteine. Synteny analysis revealed that segmental duplication is a major mechanism for expanding of DUF1216 genes in Brassica oleracea, Brassica juncea, Brassica napus, Lepidium meyneii, and Brassica carinata, while in Arabidopsis thaliana and Capsella rubella, tandem duplication plays a major role in the expansion of the DUF1216 gene family. The analysis of Ka/Ks (non-synonymous substitution rate/synonymous substitution rate) ratios for DUF1216 paralogous indicated that most of gene pairs underwent purifying selection. DUF1216 genes displayed a specifically high expression in reproductive tissues in most Brassicaceae species, while its expression in Brassica juncea was specifically high in root. Our studies offered new insights into the phylogenetic relationships, gene structures and expressional patterns of DUF1216 members in Brassicaceae, which provides a foundation for future functional analysis.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Lineage-specific gene duplication and expansion of DUF1216 gene family in Brassicaceae

Zhang,

Xiong,

Wang

et al. 2024

PLoS ONE

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Overexpression of OsDUF6 increases salt stress tolerance in rice

Ma,

Zhang,

2024

BMC Plant Biol

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Background Soil salinity is one of the primary environmental stresses faced in rice production. When plants are exposed to salt stress, a series of cellular balances will be disrupted. Dufulin is an immune-induced antiviral agent used in plants. The DUF gene family influences plant response to abiotic stress, and the functional role of OsDUF6(ABA98726.1) in rice response to salt stress is being investigated here. Results Based on the transcriptome analysis of Dufulin treatment in inducing salt tolerance in rice, we selected the OsDUF6 protein located on the cell membrane and studied its molecular function by overexpressing OsDUF6. Salt-induced decreases in root, stem, and leaf length and increased leaf yellowing rate and Na+ concentration in the wild-type plant were mitigated in the overexpressed lines. OsDUF6 overexpression increased the enzymatic antioxidant activities of superoxide dismutase, peroxidase, catalase, and phenylalanine ammonia-lyase. OsDUF6 also played a positive role in Na+ transport as reflected by the increased growth of a salt-sensitive yeast mutant complemented with OsDUF6 in the presence of salt stress. In addition, Reverse transcription quantitative PCR analysis confirmed that the overexpression of OsDUF6 significantly changed the expression level of other genes related to growth and stress tolerance. Conclusions Combined with previously published data, our results supported the observation that OsDUF6 is an important functional factor in Dufulin-induced promotion of salt stress tolerance in rice.

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Domain of unknown function (DUF) proteins in plants: function and perspective

Cited by 2 publications

References 108 publications

Lineage-specific gene duplication and expansion of DUF1216 gene family in Brassicaceae

Lineage-specific gene duplication and expansion of DUF1216 gene family in Brassicaceae

Overexpression of OsDUF6 increases salt stress tolerance in rice

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