Abstract
The Sm proteins are a conserved protein family with Sm motifs. The family includes Sm and Sm-like proteins, which play important roles in pre-mRNA splicing. Most research on the Sm proteins have been conducted in herbaceous plants, and less in woody plants such as Dimocarpus longan (longan). And the embryo development status significantly affects the quality and yield of longan. In this study, we conducted a genome-wide analysis of longan Sm genes (DlSm) to clarify their roles during somatic embryogenesis (SE) and identified 29 Sm genes. Phylogenetic analysis deduced longan Sm proteins clustered into 17 phylogenetic groups with the homologous Sm proteins of Arabidopsis thaliana. We also analyzed the gene structures, motif compositions, and conserved domains of the longan Sm proteins. The promoter sequences of the DlSm genes contained many light, endosperm development, hormone, and temperature response elements, which suggested their possible functions. In the non-embryogenic callus(NEC) and during early SE in longan, the alternative splicing(AS) events of DlSm genes indicated that these genes may influence SE development by changing gene structures and sequences. The kinetin(KT) hormone, and blue and white light treatments affected the differentiation and growth of longan embryonic callus(EC) probably by affecting the AS events of DlSm genes. Expression profiles showed the possible functional divergence among Sm genes, and different hormones and light qualities affected their expression levels. The expression trends of the DlSm genes determined by RNA sequencing as fragments per kilobase of exon model per million mapped reads (FPKM) and by real-time quantitative PCR(qRT-PCR) during early SE in longan showed that the expression of the DlSm genes was affected by the growth and differentiation of longan SE, and decreased as the somatic embryo differentiation progressed. The results will contributed to understanding the longan Sm gene family and provide a basis for future functional validation studies.
Highlights
Sm family proteins are a family of RNA-binding proteins found in bacteria, archaea, and eukaryotes, including Sm and Sm-like (LSm) proteins[1]
To identify members of the longan Sm gene(DlSm) family, the amino acid sequences of Arabidopsis Sm proteins were listed as probe sequences, and we searched the sequences by using local blast and NCBIBLAST
We found that only one base in the coding sequences of Dlo_022245.1 and Dlo_032946.1(LSm6) was different, the translated amino acid sequences were exactly the same, and the translated start sites were the same, so we regarded them as the same sequence, and used the Dlo_032946.1 for further analysis
Summary
Sm family proteins are a family of RNA-binding proteins found in bacteria, archaea, and eukaryotes, including Sm and Sm-like (LSm) proteins[1]. The Sm core proteins include mainly SmB, SmB0, SmN, SmD1, SmD2, SmD3, SmE, SmF and SmG, which stably bind with U1, U2, U4 and U5 small nuclear RNAs (snRNAs) and other proteins to form particles called small nuclear ribonucleoproteins or snRNPs in the nucleus of cells[6, 7]. These snRNPs can form a larger complex, the spliceosome, which can cleave introns not encoded by the pre-mRNAs, splicing the exons together, and undergoing a series of modifications to become mRNAs[6], and the mRNAs are transported through the nuclear pores into the cytosol and eventually translated into proteins by ribosomes eventually [6].The central component of the spliceosome, U6 snRNA, is very specific, it binds only to the LSm proteins and not to Sm proteins[7, 8]. Larger proteins that have an LSm domain and other protein domains, (e.g., LSm10-16, ataxin-2, and archaeal Sm3) have been found recently[11]
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