Tianqi WANG Xiaoyuan SHI Ziwen LIU Changfa WANG
Abstract DNA damage binding protein 1 (DDB1) and CUL4-associated factor 7 (DCAF7), also known as WDR68, regulate a series of biological activities such as growth and development of organisms. In this paper, the nucleotide sequence and the secondary structure and tertiary structure of the encoded protein were analyzed by an online bioinformatics program, and the biological function, deletion effects and expression level of the gene in different tissues were reviewed, in order to provide reference for the study of this gene as a genetic marker affecting livestock production performance.
Key words DCAF7; Structural characteristics; Growth and development; Bioinformatics; Livestock
Received: June 13, 2022 Accepted: August 15, 2022
Supported by National Natural Science Foundation of China (31671287); Taishan Leading Industry Talents-Agricultural Science of Shandong Province (LJNY201713); Well-bred Program of Shandong Province (2017LZGC020); Shandong Province Modern Agricultural Technology System Donkey Industrial Innovation Team (SDAIT-27).
Tianqi WANG (1997-), female, P. R. China, master, devoted to research about animal genetics.
*Corresponding author. E-mail: wangcf1967@ 163.com.
The DCAF7 gene belongs to the DCAFs family, and 60 subtypes such as DCAF1, DCAF6, DCAF7, and DCAF16 have been found in the DCAFs family[1]. With the widespread use of the second-generation sequencing technology, researchers can obtain more comprehensive and in-depth genomic, transcriptomic and proteomic data at a lower price, so they have conducted more in-depth research on many genes. In recent years, there have been many studies on the DCAF7 gene, which is closely related to the growth and development of organisms, but reviews of the structure and function of this gene have not yet been reported. In this paper, the structural characteristics and biological functions of the DCAF7 gene were reviewed, in order to provide a reference for the in-depth understanding and study of the structure and function of the DCAF7 gene, and the gene as a genetic marker affecting livestock production performance.
Nucleotide Sequence of DCAF7 Gene and Structure of Encoded Protein
Nucleotide sequence of DCAF7 gene
We searched NCBI for DCAF7 genes of Bos taurus, Przewalskii, Mus musculus, Ovis aries, Equus asinus and Sus scrofa, respectively (Table 1). The comparison found that the DCAF7 genes of the 6 species have 7 exons. The nucleotide sequence diagram of the DCAF7 gene of Przewalskii and the amino acid sequence of the coding region were analyzed, and it was found that although the full length of the gene and the chromosome in which it is located are different in various species, the DCAF7 gene encodes the exact same 342 amino acid sequence[2], and the amino acid sequences of the coding regions of B. taurus, Przewalskii, M. musculus, O. aries, E. asinus and S. scrofa showed 100% similarity. The nucleotide sequences of the coding regions of six species of B. taurus, Przewalskii, M. musculus, O. aries, E. asinus and S. scrofa were aligned pairwise using the DNAMAN software, and the results are shown in Fig. 1. The results of homology analysis showed that the similarity between B. taurus and O. aries was the highest, at 98.03%; the second was between S. scrofa and E. asinus, at 95.34%; and the similarity between M. musculus and Przewalskii was the lowest, at 87.38%. The overall similarity of the nucleotide sequences in the coding regions of these six species was 93.66%, indicating that although the amino acid sequence similarity was 100%, there were certain differences in the nucleotide sequences.
Structure of DCAF7 protein
Secondary and tertiary structures of DCAF7 protein
It is of great significance to clarify the structure of the DCAF7 protein for further exploration of its functions. At present, there is no report on the secondary structure and tertiary structure of the DCAF7 protein. We used the Psipred online program to predict the secondary structure of the DCAF7 protein, and the results (Fig. 2) showed that the secondary structure of the protein was dominated by random coils, consisting of 175 amino acid residues, accounting for 51.2% of the entire secondary structure; α-helixes are composed of 58 amino acid residues, accounting for 16.96%; and the extended chains are composed of 109 amino acid residues, accounting for 31.87%. The functional domain of the protein was predicted using the CDD database in NCBI (https:∥www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi). The results showed that the 19th-295th amino acid region of the protein encoded by the DCAF7 gene is a WD40 super family domain, in which W represents tryptophan and D represents aspartic acid. The tertiary structure of the DCAF7 protein was predicted using the Normol model in the Phyre2 online tool. The three-dimensional model used c3cfvA as a template, and the results showed that the homology was 94% and the confidence was 100%. The tertiary structure of the DCAF7 protein is shown in Fig. 3. The tertiary structure was dominated by random coils and extended chains, which was consistent with the predicted results of the secondary structure, and reflected the structure of the DCAF7 protein to a certain extent.
Factors affecting DCAF7 protein folding
The correct folding of the DCAF7 protein is affected by WD-repeat proteins and the T-complex protein 1-ring complex/chaperonin containing T-complex protein 1 (TRiC/CCT).
DCAF7 protein is an evolutionarily conserved protein with only one WD-repeat protein, which is highly conserved in both animals and plants[3]. WD-repeat proteins play key roles in many basic biological functions, including signal transduction, transcriptional regulation, and apoptosis[4]. WD-repeat proteins are generally composed of 4 to 10 tandem repeats of WD40[5]. WD40 is also called WD motif, and each WD motif consists of 40 to 60 amino acid residues, including a four-strand anti-parallel β-sheet, which coordinates the combination of multiple protein complexes, and these conserved residues form a strong hydrogen bond network that stabilizes the repeated folding of WD motifs[6]. The DCAF7 protein contains five WD40s[1], and the protein sequence homology in vertebrates is 100%[7]. These five WD40s play a major role in the correct folding of the DCAF7 protein. The results of Miyata et al.[1] on the positions of WD40s in the DCAF7 protein showed that the first WD40 is located between the 65th and 101st positions of the amino acid sequence of the coding region, consisting of 37 amino acid residues, and on the second exon of the nucleotide sequence of the coding region; the second WD40 is located between the 115th and 150th positions of the amino acid sequence of the coding region, consisting of 36 amino acid residues, and on the third exon of the nucleotide sequence of the coding region; the third WD40 is located between positions 170 and 206 of the amino acid sequence of the coding region, consisting of 37 amino acid residues, and on the fourth exon of the nucleotide sequence of the coding region; the fourth WD40 is located between positions 218 and 252 in the amino acid sequence of the coding region, consists of 35 amino acid residues, and on the fifth exon of the nucleotide sequence of the coding region; and the fifth WD40 is located between positions 262 and 292 of the amino acid sequence of the coding region, consisting of 31 amino acid residues, and on the sixth exon of the nucleotide sequence of the coding region (Fig. 2).
The TRiC/CCT is essential for the proper folding and functional maintenance of the DCAF7 protein. It belongs to the chaperone protein family, and is a class of conserved 800 ku large bicyclic complexes surrounding a central cavity, which present in the cytoplasm of all eukaryotic cells[8]. The TRiC/CCT assists in the folding of 10% of cell membrane proteins, including many key structural and regulatory proteins[8-9]. After the TRiC/CCT binds to the DCAF7 protein, it can regulate its structure and affect its binding to dual-specificity regulated kinase 1A (DYRK1A)[1]. DYRK1A is a kinase associated with Down syndrome. After knocking out the TRiC/CCT in cells, the structure of the DCAF7 protein is abnormal, and the activity of DCAFT protein binding to DYRK1A is reduced, and the nuclear accumulation of the DCAF7 protein is also inhibited. Cell aggregates form when the DCAF7 protein is overexpressed in TRiC/CCT-deficient cells[1].
Interaction between DCAF7 protein and kinase
The DCAF7 protein itself has no catalytic activity and needs to interact with other kinases to function[10]. The DCAF7 protein can interact with a variety of kinases, including homeodomain-interacting protein kinase-2 (HIPK2) and two important members of the dual substrate-specific tyrosine phosphorylation-regulated kinase gene family, DYRK1A and DYRK1B[11]. The DCAF7 protein acts as a scaffold protein in the process of signal transduction[12]. The DCAF7 protein first forms a complex with DYRK1B, which can shuttle between the cytoplasm and nucleus for signal transduction[13]. The research results of Skurat et al.[14] also proved the above point of view. There are many reports about the interaction between the DCAF7 protein and DYRK1A, and among all the proteins that bind to DYRK1A, the DCAF7 protein has the highest enrichment[12]. It is the major chaperone of DYRK1A, and the DCAF7-DYRK1A complex promotes the normal development of multiple organs and inhibits the growth/transformation of inappropriate cells by regulating the balance between proliferation and differentiation in a multicellular environment[1]. In addition, DYRK1A can specifically bind to the DCAF7 protein in cells to induce the nuclear translocation of the DCAF7 protein[11]. Yousefelahiyeh et al.[15] used mouse C2C12 cells to study the relationship between the DCAF7 protein and DYRK1A and found that overexpression of the DCAF7 protein could increase the expression level of DYRK1A, while overexpression of DYRK1A had no effect on the expression level of the DCAF7 protein. Glenewinkel et al.[10] determined that the DCAF7 protein is the linker of adenovirus E1A protein binding to DYRK1A and HIPK2 by immunoprecipitation and glutathione S transferase (GST) fusion protein sedimentation technology. In addition, E1A protein is hyperphosphorylated in cells overexpressing DYRK1A or HIPK2. RING finger protein 169 (RNF169) is a RING-domain ubiquitin ligase involved in DNA double-strand break repair. It is another newly discovered protein that can bind to DYRK1A[16], and can bind to the N-terminus of DYRK1A independently of the DCAF7 protein[12]. Anathapadmanabhan et al.[12] showed that the interaction between the DCAF7 protein and RNF169 was also disrupted after the application of CRISPR-Cas9 gene editing technology to disrupt the expression of DYRK1A gene in human osteosarcoma cells, confirming that DYRK1A is required for the interaction between the DCAF7 protein and RNF169.
Agricultural Biotechnology2022
DCAF7 Gene with Growth and Development
DCAF7 gene with craniofacial development
The DCAF7 gene plays a certain role in the growth and development of the craniofacial region. The DCAF7 protein is a highly conserved scaffold protein required for craniofacial development[3]. Leslie et al.[17] used genome-wide association analysis (GWAS) to study new cleft lip loci in 6 480 volunteers (including 1 319 patients with cleft lip) and found that the 17q23 region of the human genome was significantly associated with cleft lip traits, while the DCAF7 gene is in the region. The results of Nissen et al.[18] showed that the highly conserved DCAF7-DYRK1A protein complex can promote zebrafish craniofacial development, but the mechanism needs further study.
DCAF7 gene with muscle development
The DCAF7 gene affects muscle development by affecting myogenin expression and activating the transcription of key myogenic genes. The DCAF7 protein can form a complex with DYRK1B and is widely present in cells, and DYRK1B plays the role of a "molecular switch" for differentiation during muscle development[19]. DYRK1B can enhance the expression of various muscle-specific functional proteins such as troponin and myosin heavy chain, and silencing the DYRK1B gene can block the expression of myosin[20]. The DCAF7 gene can activate the transcription of key myogenic genes, and the DCAF7-DYRK1A complex exists stably and binds to RNA polymerase II (Pol II), indicating that the DCAF7-DYRK1A complex can co-migrate with Pol II and phosphorylate along the myogenic locus[21]. Therefore, the DCAF7 protein can regulate the signal output of DYRK1A on Pol II, stimulate myogenic transcription, and then regulate the bodys myogenesis. The CG14614 gene is homologous to the vertebrate DCAF7 gene. The results of Morriss et al.[22] showed that the CG14614 gene was affected by the mutation of the Drosophila wing vein pattern, and through tissue-specific knockout, it was proved that Drosophila requires the separation of the wing veins to form normal jumping muscles, which further proved that the DCAF7 gene affects muscle formation.
DCAF7 gene with adipogenesis
The DCAF7 gene has a certain regulatory effect on adipogenesis. Condon et al.[23] applied the CRISPR-Cas9 gene screening method based on the flow cytometry fluorescence sorting technology and found many genes affecting mTORC1 activity, including the DCAF7 gene, in the rapamycin complex 1 (mTORC1) pathway. mTORC1 is the core of cells regulating growth metabolism and maintaining homeostasis in response to external stimuli[24], and has the effect of promoting adipocyte generation. Growing cells require sufficient lipids for the formation and expansion of new cell membranes, and mTORC1 promotes fat synthesis through the sterol response element binding protein transcription factor[25]. The DCAF7 gene regulates adipogenesis by affecting the activity of mTORC1, thereby promoting growth and development ZNF703 is a cofactor for the nuclear complex consisting of 3 genes including the DCAF7 gene. The results of Sircoulomb et al.[26] showed that ZNF703 is involved in the regulation of E2F1 transcription factors. After knocking out the E2F1 transcription factor, the expression of peroxisome proliferator-activated receptor γ was down-regulated, which affected the metabolism of adipose-derived stem cells, thereby inhibiting the generation of adipocytes[27], indicating that the DCAF7 gene can affect the survival of adipocytes by regulating the E2F1 transcription factor.
DCAF7 gene with skeletal development
At present, there are few studies on the effect of the DCAF7 gene on the skeletal development of livestock, and only studies on zebrafish and Xenopus laevis have been reported. In zebrafish, the DCAF7 gene is required for the formation of the ventral cartilage and the dorsal palatoquadrate cartilage. Alvarado et al.[28] proved that the DCAF7 gene is important for craniofacial skeletal development during zebrafish embryonic development by immunofluorescence. The cartilage of wild-type zebrafish treated with dimethyl sulfoxide (DMSO) at 32 ℃ was markedly developed, while most of the mutant ventral cartilage and the dorsal palatoquadrate cartilage disappeared completely. Bonano et al.[29] showed that DCAF7 gene may be involved in the formation of X. laevis jaws. The differentiation of chondrocytes requires the regulation of sox9 transcription factor. Nissen et al.[18] detected the expression of zebrafish sox9a gene and determined that the DCAF7 gene was required for chondrocyte differentiation.
DCAF7 gene with down syndrome
The interaction between the DCAF7 gene and DYRK1A and huntingtin-associated protein 1 (Hap1) may be one of the causes of Down syndrome, and clarifying the mechanism of action is essential to improve the health rate of newborns. DYRK1A and Hap1 have regulatory effects on Down syndrome. In the cytoplasm, DYRK1A competes with Hap1 for binding to DCAF7 protein, and inhibition of Hap1 can promote the interaction between DCAF7 protein and DYRK1A, and increase the level of the DYRK1A protein. The association of Hap1 with the DCAF7 protein was reduced in the hypothalamus of Down syndrome mice overexpressing DYRK1A[30]. In addition, overexpression of DYRK1A can lead to postnatal growth retardation in mice[30], suggesting that breaking the relative balance between Hap1 and DYRK1A may be one of the causes of Down syndrome.
Deletion of the DCAF7 Gene and Its Effects
Deletion of the DCAF7 gene affects neuronal differentiation, nucleotide repair, and the hematopoietic system. Knockout of the DCAF7 gene in mouse embryonic stem cells led to neuronal differentiation defects, but did not affect neuronal self-renewal; and transcriptome analysis of neural progenitor cells lacking the DCAF7 gene showed that many genes affecting neuronal differentiation were down-regulated[31]. DNA excision repair cross-complementing 1-Xeroderma pigmentosum group F (ERCC1-XPF) heterodimer is a structure-specific endonuclease, which plays a role in a variety of DNA repair pathways. The DCAF7 gene can regulate the expression of ERCC1-XPF, which has a certain effect on nucleotide repair activity. The results of Jiang et al.[32] showed that the deletion of the DCAF7 gene led to inefficient repair of UV-induced DNA damage, and ERCC1-XPF could be restored by ectopic overexpression. Kirsammer et al.[7] showed that targeted deletion of the DCAF7 gene led to hematopoietic diseases, and the DCAF7 gene was essential for maintaining a healthy bone marrow environment and regulating blood cell lineage selection.
Expression of the DCAF7 Gene
Although the relative expression level of the DCAF7 gene in various tissues and organs is of great significance to further verifying the function of this gene, there are few reports about the expression level of the DCAF7 gene in livestock at home and abroad. Wang et al.[33] performed RNA-Seq on 16 tissues including donkey heart, liver, spleen, lung, and kidney, and determined the relative expression of the DCAF7 gene in each tissue (Fig. 4). The expression level was the highest in the testis, the lowest in the liver and cartilage, followed by the muscle. The expression of the DCAF7 gene in other livestock still requires extensive study.
Conclusions and Prospect
At present, the research on the DCAF7 gene and its molecular mechanism of protein is relatively mature. The results of studies in humans and zebrafish show that it plays an important role in biological growth and development such as craniofacial development, muscle formation, fat synthesis, and skeletal development, and can be used as a marker for studying the development of organisms. However, there are very few studies on the gene and the encoded protein structure and its expression in various tissues and organs of the body, and few studies have been conducted on its effects on the growth traits of livestock. Whether the gene can regulate the growth and development of livestock and affect the production of livestock traits still needs further study.
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