| SIRT family is a NAD+ dependent class III deacetylase family, which is involved in the modification of histone or non-histone proteins. In addition to having deacetylase, some members of the SIRT family also have ADP-ribosylase and other activities, which play an important role in the regulation of energy metabolism and oxidative stress resistance. The SIRT family exists widely in prokaryotes and eukaryotes and is mainly divided into five classes. SIRT1–SIRT3 is class Ⅰ, SIRT4 is class Ⅱ, SIRT5 is class Ⅲ, SIRT6 and SIRT7 are class Ⅳ, and class U exists only in the SIRT family from archaea to bacteria. The number and distribution of SIRT genes vary among different organisms. All members of the SIRT family have been shown to be expressed in mammalian ovaries and are widely involved in the regulation of ovarian development, including meiosis regulation, energy metabolism, mitochondrial quality control, maintenance of redox homeostasis, and hormone secretion. In this study, bioinformatics methods were used to systematically analyze the chromosome distribution, gene structure, amino acid sequence, protein motifs and conserved domains, physical and chemical properties, subcellular localization, secondary and tertiary structures, phylogenetic relationships, and protein interaction networks of zebrafish SIRT family genes and to explore their expression changes at different developmental stages of follicles. The results showed that eight SIRT genes were distributed on eight chromosomes of Zebrafish, the sequence length was different [the longest was SIRT6 (140,265 bp) and the shortest was SIRT4 (7,101bp)], and the coding regions ranged from 3 to 14. The amino acid sequence similarity of zebrafish SIRT protein was low, and the 10 most conserved motifs were predicted. The adjacent homologous genes in the same branch had nearly the same motif composition, with the number of motifs varying among branches. Among the 10 motifs, motif 2, motif 3, and motif 5 were found in all zebrafish SIRT amino acid sequences, indicating that these protein motifs are highly conserved during development. Conserved domain analysis showed that all SIRT1-7 proteins contained the Sir2 domain. Analysis of physical and chemical properties of proteins showed that SIRT1 had the highest molecular weight, encoding 710 amino acids, whereas SIRT5 had the lowest molecular weight, encoding 305 amino acids. The isoelectric points ranged from 4.88 to 9.60, and all of them were hydrophilic proteins. Except SIRT3, the rest were unstable proteins. Subcellular localization prediction showed that SIRT1, SIRT4, SIRT5, and SIRT7 were located in the cytoplasm/nucleus, SIRT3.2 in the cytoplasm, SIRT6 in the nucleus, SIRT2 in the cytoskeleton, and SIRT3 in mitochondria. Secondary structure analysis showed that the SIRT family proteins had similar secondary structure, and α-helix and random curling were the main components of the protein secondary structure. The tertiary structure prediction showed that the SIRT protein family had zinc finger and Rossmann fold structures. Phylogenetic analysis showed that the fish SIRT family could be divided into three branches. The first branch consisted of three subbranches, in which SIRT1 and SIRT2 were isolated and SIRT3 and SIRT3.2 were clustered into one branch. The second largest branch consisted of SIRT4 and SIRT5, which were clustered separately into one branch. The third branch consisted of SIRT6 and SIRT7, each of which is a separate branch. The eight SIRT proteins of Zebrafish had low homology and were distributed far in the evolutionary tree. Compared with other species, zebrafish SIRT1 is closely related to rainbow trout SIRT1, whereas other family members are closely related to goldfish and electric eel SIRT. Furthermore, four family members (SIRT1, SIRT2, SIRT3.2, and SIRT4) showed collinearity between blue killifish and zebrafish, while the other family members except SIRT6 showed collinearity between goldfish and zebrafish. In addition, zebrafish SIRT4 and SIRT5 showed collinearity with two genes of goldfish. PPI prediction showed that SIRT proteins interact with ESR1, FOXOs, SOD, HSPs, etc. Real-time fluorescence quantitative PCR analysis showed that SIRT1 and SIRT2 were mainly expressed at the midvitellogenic (MV) stage during follicular development. SIRT3 and SIRT4 were mainly expressed at the full-grown immature (FG) stage. SIRT3.2, SIRT5, SIRT6, and SIRT7 were mainly expressed at the germinal vesicle breakdown (GVBD) stage. In summary, this study used bioinformatics methods for the first time to analyze chromosome localization, gene structure, amino acid sequences, physical and chemical properties, subcellular localization prediction, phylogenetic characteristics, PPI network prediction, and follicle expression at different developmental stages of zebrafish SIRT gene family. The results showed that the gene structure and amino acid sequences of eight members of the Zebrafish SIRT family were different, but all had a Sir2 conserved domain and similar protein structure. Phylogenetic analysis suggested that there may be replication or fusion events among SIRT gene family members in different species. SIRT is expressed in zebrafish follicles at different developmental stages with different expression patterns, suggesting that the SIRT plays an important role in the regulation of follicle development, providing a reference for further functional studies as well as the study of the complex molecular regulatory network of fish follicle development. |
