title: RNA-Seq approach for genetic improvement of meat quality in pig and evolutionary insight into the substrate specificity of animal carbonyl reductases.
abstract: Changes in meat quality traits are strongly associated with alterations in postmortem metabolism which depend on genetic variations, especially nonsynonymous single nucleotide variations (nsSNVs) having critical effects on protein structure and function. To selectively identify metabolism-related nsSNVs, next-generation transcriptome sequencing (RNA-Seq) was carried out using RNAs from porcine liver, which contains a diverse range of metabolic enzymes. The multiplex SNV genotyping analysis showed that various metabolism-related genes had different nsSNV alleles. Moreover, many nsSNVs were significantly associated with multiple meat quality traits. Particularly, ch7:g.22112616A>G SNV was identified to create a single amino acid change (Thr/Ala) at the 145th residue of H1.3-like protein, very close to the putative 147th threonine phosphorylation site, suggesting that the nsSNV may affect multiple meat quality traits by affecting the epigenetic regulation of postmortem metabolism-related gene expression. Besides, one nonsynonymous variation, probably generated by gene duplication, led to a stop signal in porcine testicular carbonyl reductase (PTCR), resulting in a C-terminal (E281-A288) deletion. Molecular docking and energy minimization calculations indicated that the binding affinity of wild-type PTCR to 5α-DHT, a C(21)-steroid, was superior to that of C-terminal-deleted PTCR or human carbonyl reductase, which was very consistent with experimental data, reported previously. Furthermore, P284 was identified as an important residue mediating the specific interaction between PTCR and 5α-DHT, and phylogenetic analysis showed that P284 is an evolutionarily conserved residue among animal carbonyl reductases, which suggests that the C-terminal tails of these reductases may have evolved under evolutionary pressure to increase the substrate specificity for C(21)-steroids and facilitate metabolic adaptation. Altogether, our RNA-Seq revealed that selective nsSNVs were associated with meat quality traits that could be useful for successful marker-assisted selection in pigs and also represents a useful resource to enhance understanding of protein folding, substrate specificity, and the evolution of enzymes such as carbonyl reductase.
authors.affiliation: Department of Animal Resources Technology, Gyeongnam National University of Science and Technology, Jinju, Korea.
authors.forename: Won Yong
authors.initials: WY
authors.lastname: Jung
authors.forename: Seul Gi
authors.initials: SG
authors.lastname: Kwon
authors.forename: Minky
authors.initials: M
authors.lastname: Son
authors.forename: Eun Seok
authors.initials: ES
authors.lastname: Cho
authors.forename: Yuno
authors.initials: Y
authors.lastname: Lee
authors.forename: Jae Hwan
authors.initials: JH
authors.lastname: Kim
authors.forename: Byeong-Woo
authors.initials: BW
authors.lastname: Kim
authors.forename: Da Hye
authors.initials: DH
authors.lastname: Park
authors.forename: Jung Hye
authors.initials: JH
authors.lastname: Hwang
authors.forename: Tae Wan
authors.initials: TW
authors.lastname: Kim
authors.forename: Hwa Choon
authors.initials: HC
authors.lastname: Park
authors.forename: Beom Young
authors.initials: BY
authors.lastname: Park
authors.forename: Jong-Soon
authors.initials: JS
authors.lastname: Choi
authors.forename: Kwang Keun
authors.initials: KK
authors.lastname: Cho
authors.forename: Ki Hwa
authors.initials: KH
authors.lastname: Chung
authors.forename: Young Min
authors.initials: YM
authors.lastname: Song
authors.forename: Il Suk
authors.initials: IS
authors.lastname: Kim
authors.forename: Sang Keun
authors.initials: SK
authors.lastname: Jin
authors.forename: Doo Hwan
authors.initials: DH
authors.lastname: Kim
authors.forename: Seung-Won
authors.initials: SW
authors.lastname: Lee
authors.forename: Keun Woo
authors.initials: KW
authors.lastname: Lee
authors.forename: Woo Young
authors.initials: WY
authors.lastname: Bang
authors.forename: Chul Wook
authors.initials: CW
authors.lastname: Kim
mesh_terms: D000429:Alcohol Oxidoreductases / Q000235:genetics / Q000378:metabolism*; D000818:Animals; D001483:Base Sequence; D044127:Epigenesis, Genetic; D019143:Evolution, Molecular; D006801:Humans; D008099:Liver / Q000201:enzymology*; D008297:Male; D008460:Meat / Q000032:analysis* / Q000592:standards; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011180:Postmortem Changes; D040901:Proteomics; D019655:Quantitative Trait, Heritable; D012641:Selection, Genetic; D017423:Sequence Analysis, RNA; D013379:Substrate Specificity; D034421:Sus scrofa / Q000235:genetics*; D013737:Testis / Q000201:enzymology*; D059467:Transcriptome
chemical_list: D000429:Alcohol Oxidoreductases