The Expansion of Sirtuin Gene Family in Gilthead Sea Bream (Sparus aurata)-Phylogenetic, Syntenic, and Functional Insights across the Vertebrate/Fish Lineage

Abstract

The Sirtuin (SIRT1-7) family comprises seven evolutionary-conserved enzymes that couple cellular NAD availability with health, nutrition and welfare status in vertebrates. This study re-annotated the sirt3/5 branch in the gilthead sea bream, revealing three paralogues of sirt3 (sirt3.1a/sirt3.1b/sirt3.2) and two of sirt5 (sirt5a/sirt5b) in this Perciform fish. The phylogeny and synteny analyses unveiled that the Sirt3.1/Sirt3.2 dichotomy was retained in teleosts and aquatic-living Sarcopterygian after early vertebrate 2R whole genome duplication (WGD). Additionally, only certain percomorphaceae and gilthead sea bream showed a conserved tandem-duplicated synteny block involving the mammalian-clustered sirt3.1 gene (psmd13-sirt3.1a/b-drd4-cdhr5-ctsd). Conversely, the expansion of the Sirt5 branch was shaped by the teleost-specific 3R WGD. As extensively reviewed in the literature, human-orthologues (sirt3.1/sirt5a) showed a high, conserved expression in skeletal muscle that increased as development advanced. However, recent sirt3.2 and sirt5b suffered an overall muscle transcriptional silencing across life, as well as an enhanced expression on immune-relevant tissues and gills. These findings fill gaps in the ontogeny and differentiation of Sirt genes in the environmentally adaptable gilthead sea bream, becoming a good starting point to advance towards a full understanding of its neo-functionalization. The mechanisms originating from these new paralogs also open new perspectives in the study of cellular energy sensing processes in vertebrates.

Keywords: adaptive plasticity; gene duplication; gilthead sea bream; neo-functionalization; phylogeny; sirtuin; synteny.

Figure 1

(A) Graphical representation of all gilthead sea bream Sirt proteins. The catalytic core domain (in green) and the surrounding N- and C-terminal regions (in grey) are represented. The mitochondrial target peptides of mitochondrial Sirts (framed in red) are indicated in yellow. Numbers correspond to amino acid residues. Accession numbers of genes are listed below: sirt3.1a (OR394775; XP_030270596.1), sirt3.1b (OR394776), and sirt3.2 (AHX56275); human SIRT5 (Gene ID: 23408); GSB sirt5a (AHX56277); and sirt5b (OR394777). (B) Percentages of amino acid sequence identity and similarity (in parentheses) among gilthead sea bream Sirt family members.

Figure 2

Schematic representation of the exon–intron structure of the SIRT3 (A) and SIRT5 (B) paralogs of gilthead sea bream and human. White and black boxes represent the noncoding and coding exons, respectively. Introns are shown as connecting lines. Scale bars are 100 bp. Numbers indicate the total length of the sequences from ATG to the stop codon including and excluding (in brackets) introns.

Figure 3

Phylogenetic tree of vertebrate SIRT3, generated by maximum likelihood algorithm in Mega software version 11. The sequences included in the analysis correspond to full protein sequences from 23 vertebrate species. The accession numbers from GenBank, OrthoDB, and IATS-CSIC gilthead seabream genome are included in brackets. Numbers in branches indicate the bootstrap confidence in the resulting phylogenetic tree measured by auto-bootstrapping mode.

Figure 4

Gene synteny of sirt3.1a/b (A) and sirt3.2 (B) in different vertebrate species. The synteny was analyzed with Genomicus v100.01 using the gene orders of gilthead seabream as reference. Orthologs of sirts in other species are shown in matching colors. A line between two genes is equivalent to a break in the continuity of the alignment. A red discontinuous square corresponds to the conserved syntenic block in different species.

Figure 5

Phylogenetic tree of vertebrate SIRT5, generated by maximum likelihood algorithm in Mega 11 software. The sequences included in the analysis correspond to full protein sequences from 23 vertebrate species. The accession numbers from GenBank, OrthoDB, and IATS-CSIC gilthead seabream genome are included in brackets. Numbers in branches indicate the bootstrap confidence in the resulting phylogenetic tree measured by auto-bootstrapping mode.

Figure 6

Gene synteny of Sirt5a (A) and Sirt5b (B) copies in different vertebrate species. The synteny was analyzed with Genomicus v100.01 using the gene orders of gilthead seabream as reference. Orthologs of sirts in other species are shown in matching colors. A line between two genes is equivalent to a break in the continuity of the alignment. The red discontinuous square corresponds to the conserved syntenic blocks in different species.

Figure 7

Hierarchical heatmap of the gene expression pattern of sirts in 11 tissues with different metabolic capabilities (A). Ratio between sirt3.1 and sirt3.2 (B) or sirt5a and sirt5b (C) gene duplications in 11 tissues of gilthead sea bream.