Comprehensive genome-wide analysis of the chicken heat shock protein family: identification, genomic organization, and expression profiles in indigenous chicken with highly pathogenic avian influenza infection

Authors: TRUONG, ANH DUC - National Institute Of Veterinary Research; TRAN, HA THI THANK - National Institute Of Veterinary Research; CHU, NHU THI - National Institute Of Veterinary Research; NGUYEN, HUYEN THI - National Institute Of Veterinary Research; PHAN, LANH - National Institute Of Veterinary Research; PHAN, HOAI THI - National Institute Of Veterinary Research; VU, THI HAO - National Institute Of Veterinary Research; SONG, KI-DUK - Jeonbuk National University; Lillehoj, Hyun; HONG, YEONG HO - Chung-Ang University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/14/2023
Publication Date: 12/20/2023
Citation: Truong, A., Tran, H., Chu, N., Nguyen, H., Phan, L., Phan, H., Vu, T., Song, K., Lillehoj, H.S., Hong, Y. 2023. Comprehensive genome-wide analysis of the chicken heat shock protein family: identification, genomic organization, and expression profiles in indigenous chicken with highly pathogenic avian influenza infection. BMC Genomics. vol.24/793. https://doi.org/10.1186/s12864-023-09908-y.
DOI: https://doi.org/10.1186/s12864-023-09908-y

Interpretive Summary: Heat shock proteins (HSPs) are stress proteins with diverse biological functions and play important roles in host immune response and protection against stress. However, there is very limited information about chicken HSPs. To better understand the role of HSPs in infectious diseases in poultry, ARS scientists and collaborators at the National Institute of Veterinary Research in Vietnam investigated changes in the expression of HSP70 family proteins in response to highly pathogenic avian influenza virus (HPAIV) infection. Based on genomic analysis, a total of 76 genes in chickens and chicken HSPs were associated with protection against a variety of cellular stressors. In-depth analysis chicken HSP genes indicated conservation of the structural architecture of HSP genes in humans, mice, plants, and fish. The results indicated that the main functions of chicken HSPs were associated with the regulation of apoptosis, heat stress response, adaptation to environmental conditions, and immune response to infection. These findings suggested that HSP genes play an important role at different growth stages of chicken early embryo. This is the first study to analyze the expression of HSP family genes in response to HPAIV infection in chickens, and the results suggest that HSP genes have essential functions in the development of the chicken embryo. These findings will contribute to our understanding on the biological evolution of HSPs in chicken, and further sheds light on intercontinental chicken adaptation mechanisms.

Technical Abstract: Background: Heat shock proteins (HSPs) function as molecular chaperones with critical roles in chicken embryogenesis, immune response to infectious diseases, and response to various environmental stresses. However, little is known on HSP genes in chicken. In this study, to understand the roles of chicken HSPs, we performed genome-wide identification, expression, and functional analyses of the HSP family genes in chicken. Results: A total of 76 HSP genes were identified in the chicken genome, which were further classified into eight distinct groups (I-VIII) based on phylogenetic tree analysis. The gene-structure analysis revealed that the members of each clade had the same or similar exon-intron structures. Chromosome mapping suggested that HSP genes were widely dispersed across the chicken genome, except in chromosomes 16, 18, 22, 25, 26, and 28–32, which lacked chicken HSP genes. On the other hand, the interactions among chicken HSPs were limited, indicating that the remaining functions of HSPs could be investigated in chicken. Moreover, KEGG pathway analysis showed that the HSP gene family was involved in the regulation of heat stress, apoptotic, intracellular signaling, and immune response pathways. Finally, RNA sequencing data revealed that, of the 76 chicken HSP genes, 46 were differentially expressed at 21 different growth stages in chicken embryos, and 72 were differentially expressed on post-infection day 3 in two indigenous Ri chicken lines infected with highly pathogenic avian influenza. Conclusions:This study provides significant insights into the potential functions of HSPs in chicken, including the regulation of apoptosis, heat stress, chaperone activity, intracellular signaling, and immune response to infectious diseases.