Identification of key transcription factors and their functional role involved in Salmonella typhimurium infection in chicken using integrated transcriptome analysis and bioinformatics approach

Syed Mudasir Ahmad; Sahar Saleem Bhat; Shaista Shafi; Mashooq Ahmad Dar; Afnan Saleem; Zulfqarul Haq; Nida Farooq; Junaid Nazir; Basharat Bhat

doi:10.1186/s12864-023-09315-3

Identification of key transcription factors and their functional role involved in Salmonella typhimurium infection in chicken using integrated transcriptome analysis and bioinformatics approach

BMC Genomics. 2023 Apr 25;24(1):214. doi: 10.1186/s12864-023-09315-3.

Authors

Affiliations

¹ Division of Animal Biotechnology, FVSc & AH, Shuhama, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, 190006, India. mudasirbio@skuastkashmir.ac.in.
² Division of Animal Biotechnology, FVSc & AH, Shuhama, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, 190006, India.
³ Department of Clinical Biochemistry, University of Kashmir, Srinagar, India.
⁴ Division of Livestock Production and Management, FVSc & AH, Shuhama, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, 190006, India.
⁵ Division of Animal Biotechnology, FVSc & AH, Shuhama, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, 190006, India. basharatbhat09@gmail.com.

^# Contributed equally.

Abstract

Salmonella enterica serovar typhimurium is the cause of significant morbidity and mortality worldwide that causes economic losses to poultry and is able to cause infection in humans. Indigenous chicken breeds are a potential source of animal protein and have the added advantage of being disease resistant. An indigenous chicken, Kashmir favorella and commercial broiler were selected for understanding the mechanism of disease resistance. Following infection in Kashmir favorella, three differentially expressed genes Nuclear Factor Kappa B (NF-κB1), Forkhead Box Protein O3 (FOXO3) and Paired box 5 (Pax5) were identified. FOXO3, a transcriptional activator, is the potential marker of host resistance in Salmonella infection. NF-κB1 is an inducible transcription factor which lays the foundation for studying gene network of the innate immune response of Salmonella infection in chicken. Pax5 is essential for differentiation of pre-B cells into mature B cell. The real time PCR analysis showed that in response to Salmonella Typhimurium infection a remarkable increase of NF-κB1 (P˂0.01)_, FOXO3 (P˂0.01) gene expression in liver and Pax5 (P˂0.01) gene expression in spleen of Kashmir favorella was observed. The protein-protein interaction (PPI) and protein-TF interaction network by STRINGDB analysis suggests that FOXO3 is a hub gene in the network and is closely related to Salmonella infection along with NF-κB1. All the three differentially expressed genes (NF-κB1, FOXO3 and PaX5) showed their influence on 12 interacting proteins and 16 TFs, where cyclic adenosine monophosphate Response Element Binding protein (CREBBP), erythroblast transformation-specific (ETSI), Tumour-protein 53(TP53I), IKKBK, lymphoid enhancer-binding factor-1 (LEF1), and interferon regulatory factor-4 (IRF4) play role in immune responses. This study shall pave the way for newer strategies for treatment and prevention of Salmonella infection and may help in increasing the innate disease resistance.

Keywords: Bioinformatics; Chicken; RNA seq; Salmonella typhimurium; Transcription factors.

MeSH terms

Animals
Chickens* / genetics
Disease Resistance
Gene Expression Profiling
Humans
Salmonella Infections, Animal* / genetics
Salmonella typhimurium / genetics
Transcription Factors / genetics

Substances

Transcription Factors

Grants and funding

EMR/2017/000580./Science and Engineering Research Board, Department of Science and Technology