Unraveling the Diverse Roles of Neglected Genes Containing Domains of Unknown Function (DUFs): Progress and Perspective

Lv, Peiyun; Wan, Jinlu; Chunting, Zhang; Hina, Aiman; Golpour, Amin; Begum, Naheeda; Zhao, Tuanjie

doi:10.3390/ijms24044187

Cited by 13 publications

(7 citation statements)

References 118 publications

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“…Among 126 F2 populations, no recombination was found in the corresponding locus of CmoCh14G005820 gene, so this gene was predicted to be a candidate gene conferring white-flower phenotype in pumpkin. and plant response to abiotic stress (Gu & Cheng, 2014;Lv et al, 2023;Qin et al, 2013;Zhou et al, 2020). Gene annotation showed that CmoCh14G005820 encoded a CmoDUF1997 protein in pumpkin, but the relationship between this protein and flower-colour formation was not characterised.…”

Section: Discussionmentioning

confidence: 99%

“…They contain at least one highly conserved DUF domain in their protein structure. Studies have shown that DUF genes play an important role in regulating the wall development of plant cells, plant growth and development, flower and fruit development, plant defence response to pests and diseases and plant response to abiotic stress (Gu & Cheng, 2014; Lv et al, 2023; Qin et al, 2013; Zhou et al, 2020). Gene annotation showed that CmoCh14G005820 encoded a CmoDUF1997 protein in pumpkin, but the relationship between this protein and flower‐colour formation was not characterised.…”

Section: Discussionmentioning

confidence: 99%

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Genetic analysis and characterisation of Cmowf, a gene controlling the white petal colour phenotype in pumpkin (Cucurbita moschata D)

Min,

Li,

Sun

et al. 2023

Plant Breeding

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Flower colour, as an important morphological marker, plays an essential role in improving the identification efficiency of the purity seed in hybrid production. However, the molecular mechanism of white‐flower trait has not been reported in pumpkin (Cucurbita moschata D.). In this study, we obtained a white‐flower mutant (wf) through the ethyl methane sulfonate (EMS) mutagenesis of inbred line N87 (yellow flower). F2 populations were then constructed by crossing wf mutant and N87 plant to fine map the genes controlling white‐flower trait in pumpkin. Phenotypic identification revealed that carotenoid content significantly decreased in the petals of wf mutants compared with N87 plants. Genetic analysis indicated that the white flower mutant trait was controlled by a single recessive gene, Cmowf. Using bulked segregant analysis and KASP phenotyping, Cmowf was mapped to a 762 kb region on chromosome 14 containing three annotated genes. Among them, a nonsynonymous single‐nucleotide polymorphisms mutation was identified only in CmoCh14G005820 gene, which encoded a DUF1997 family protein. Compared with CmoDUF1997 amino acid sequences between the wf mutants and N87 plants, the critical amino acid mutations (early termination of amino acids) occurred in wf mutants, so CmoCh14G005820 was predicted as a potential candidate for controlling the white‐flower trait. RNA‐sequencing analysis revealed that the expression of CmoCh14G005820 and most genes involved in carotenoid biosynthesis was significantly downregulated in wf mutants, whereas the expression of several genes responsible for carotenoid degradation was upregulated in wf mutants. This finding suggested that carotenoid metabolism may participate in the formation of flower colour in pumpkin. Overall, our results provided a theoretical basis for understanding the genetic mechanisms underlying white‐flower formation in pumpkin.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Genetic analysis and characterisation of Cmowf, a gene controlling the white petal colour phenotype in pumpkin (Cucurbita moschata D)

Min,

Li,

Sun

et al. 2023

Plant Breeding

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“…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 ]. The following protein domains have undergone functional characterization in Arabidopsis thaliana : DUF6 [ 25 ], DUF26 [ 26 ], DUF246 [ 27 ], DUF538 [ 28 ], DUF579 [ 29 ], DUF617 [ 30 ], DUF642 [ 31 ], DUF647 [ 32 ], DUF724 [ 33 ], DUF784 [ 34 ], DUF1117 [ 35 ], DUF1218 [ 36 ], DUF4005 [ 37 ] and DUF4228 [ 38 ].…”

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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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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“…The domains of unknown function (DUF) family refers to a series of protein families whose functions have not yet been annotated [ 6 ]. Currently, the Pfam database (V35.0) contains 4795 DUF families, accounting for 24% of all Pfam families [ 7 ]. Studies showed that different DUF proteins have a variety of functions.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification, Characterization and Expression Analysis of the TaDUF724 Gene Family in Wheat (Triticum aestivum)

Yuan,

Yin,

Han

et al. 2023

IJMS

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Unknown functional domain (DUF) proteins constitute a large number of functionally uncharacterized protein families in eukaryotes. DUF724s play crucial roles in plants. However, the insight understanding of wheat TaDUF724s is currently lacking. To explore the possible function of TaDUF724s in wheat growth and development and stress response, the family members were systematically identified and characterized. In total, 14 TaDUF724s were detected from a wheat reference genome; they are unevenly distributed across the 11 chromosomes, and, according to chromosome location, they were named TaDUF724-1 to TaDUF724-14. Evolution analysis revealed that TaDUF724s were under negative selection, and fragment replication was the main reason for family expansion. All TaDUF724s are unstable proteins; most TaDUF724s are acidic and hydrophilic. They were predicted to be located in the nucleus and chloroplast. The promoter regions of TaDUF724s were enriched with the cis-elements functionally associated with growth and development, as well as being hormone-responsive. Expression profiling showed that TaDUF724-9 was highly expressed in seedings, roots, leaves, stems, spikes and grains, and strongly expressed throughout the whole growth period. The 12 TaDUF724 were post-transcription regulated by 12 wheat MicroRNA (miRNA) through cleavage and translation. RT-qPCR showed that six TaDUF724s were regulated by biological and abiotic stresses. Conclusively, TaDUF724s were systematically analyzed using bioinformatics methods, which laid a theoretical foundation for clarifying the function of TaDUF724s in wheat.

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Unraveling the Diverse Roles of Neglected Genes Containing Domains of Unknown Function (DUFs): Progress and Perspective

Cited by 13 publications

References 118 publications

Genetic analysis and characterisation of Cmowf, a gene controlling the white petal colour phenotype in pumpkin (Cucurbita moschata D)

Genetic analysis and characterisation of Cmowf, a gene controlling the white petal colour phenotype in pumpkin (Cucurbita moschata D)

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

Genome-Wide Identification, Characterization and Expression Analysis of the TaDUF724 Gene Family in Wheat (Triticum aestivum)

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