Genomic evidence of adaptive evolution in the reptilian SOCS gene family.

Tian Xia,Xiufeng Yang,Honghai Zhang,Guolei Sun,Lei Zhang

doi:10.7717/peerj.11677

Abstract

The suppressor of the cytokine signaling (SOCS) family of proteins play an essential role in inhibiting cytokine receptor signaling by regulating immune signal pathways. Although SOCS gene functions have been examined extensively, no comprehensive study has been performed on this gene family’s molecular evolution in reptiles. In this study, we identified eight canonical SOCS genes using recently-published reptilian genomes. We used phylogenetic analysis to determine that the SOCS genes had highly conserved evolutionary dynamics that we classified into two types. We identified positive SOCS4 selection signals in whole reptile lineages and SOCS2 selection signals in the crocodilian lineage. Selective pressure analyses using the branch model and Z-test revealed that these genes were under different negative selection pressures compared to reptile lineages. We also concluded that the nature of selection pressure varies across different reptile lineages on SOCS3, and the crocodilian lineage has experienced rapid evolution. Our results may provide a theoretical foundation for further analyses of reptilian SOCS genes’ functional and molecular mechanisms, as well as their roles in reptile growth and development.

Highlights

Cytokines are multifunctional proteins and essential intercellular regulators that are involved in innate and adaptive inflammatory organism defense, cell development, and repair processes via different signaling mechanisms (Oppenheim, 2001)
The reptilian genomes were obtained from National Center for Biotechnology Information (NCBI) and included Testudines (Apalone spinifera, Malaclemys terrapin, Cuora mccordi, Chelonoidis abingdonii, Gopherus agassizii, Platysternon megacephalum, Malaclemys terrapin, Cuora mccordi, Chelonoidis abingdonii, Gopherus agassizii, Platysternon megacephalum), Serpentes (Crotalus viridis, Vipera berus, Crotalus horridus, Protobothrops flavoviridis, Pantherophis guttatus, Ophiophagus hannah, Crotalus pyrrhus, Hydrophis cyanocinctus, Hydrophis hardwickii, Thermophis baileyi), Sauria (Lacerta viridis, Lacerta bilineata, Paroedura picta, Podarcis muralis, Sphenodon punctatus), and Crocodilia (Alligator mississippiensis, Gavialis gangeticus)
A total of 260 suppressor of the cytokine signaling (SOCS) sequences were identified in reptiles, and this detailed phylogenetic analysis offers a great basis for further functional studies

Summary

Introduction

Cytokines are multifunctional proteins and essential intercellular regulators that are involved in innate and adaptive inflammatory organism defense, cell development, and repair processes via different signaling mechanisms (Oppenheim, 2001). Suppressors of cytokine signaling (SOCS) are some of the most crucial feedback inhibitors in the prevention of excessive cytokine signaling and maintenance of homeostasis and normal cellular functions (Hong-Jian et al, 2008). The SOCS proteins function as negative feedback inhibitors, controlling particular cytokine signals in order to regulate cellular responses and maintain a stable environment (Linossi, Calleja & Nicholson, 2018). During the phosphorylation of signal transducer and activator of transcription (STAT) proteins, SOCS proteins helps regulate various cytokines by combining the kinase inhibitory region (KIR) and members of the Janus kinase (JAK) family (Tannahill et al, 2005). The SOCS gene family was initially identified in mammals and was comprised of eight members, including SOCS1–7 and the cytokine-inducible SH2-containing protein (CISH) (Linossi & Nicholson, 2015).

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