Genomic Identification, Evolution and Sequence Analysis of the Heat-Shock Protein Gene Family in Buffalo

Abstract

Heat-shock proteins (HSP) are conserved chaperones crucial for protein degradation, maturation, and refolding. These adenosine triphosphate dependent chaperones were classified based on their molecular mass that ranges between 10–100 kDA, including; HSP10, HSP40, HSP70, HSP90, HSPB1, HSPD, and HSPH1 family. HSPs are essential for cellular responses and imperative for protein homeostasis and survival under stress conditions. This study performed a computational analysis of the HSP protein family to better understand these proteins at the molecular level. Physiochemical properties, multiple sequence alignment, and phylogenetic analysis were performed for 64 HSP genes in the Bubalus bubalis genome. Four genes were identified as belonging to the HSP90 family, 10 to HSP70, 39 to HSP40, 8 to HSPB, one for each HSPD, HSPH1, and HSP10, respectively. The aliphatic index was higher for HSP90 and HSP70 as compared to the HSP40 family, indicating their greater thermostability. Grand Average of hydropathicity Index values indicated the hydrophilic nature of HSP90, HSP70, and HSP40. Multiple sequence alignment indicated the presence of highly conserved consensus sequences that are plausibly significant for the preservation of structural integrity of proteins. In addition, this study has expanded our current knowledge concerning the genetic diversity and phylogenetic relatedness of HSPs of buffalo with other mammalian species. The phylogenetic tree revealed that buffalo is more closely related to Capra hircus and distantly associated with Danio rerio. Our findings provide an understanding of HSPs in buffalo at the molecular level for the first time. This study highlights functionally important HSPs and indicates the need for further investigations to better understand the role and mechanism of HSPs.

Evidence-Based Tracking of MDR E. coli from Bovine Endometritis and Its Elimination by Effective Novel Therapeutics

“…Pattern motifs in the current study were found similar to those reported on different species in literature by using MEME [ 27 , 40 , 41 ]. The present study revealed that the 23S rRNA nucleotides sequence of the local E. coli isolate showed 98% similarity to the nucleotide sequence of the reference E. coli strain (accession number CP067311.1).…”

“…The present study revealed that the 23S rRNA nucleotides sequence of the local E. coli isolate showed 98% similarity to the nucleotide sequence of the reference E. coli strain (accession number CP067311.1). Gene sequencing has been proven to be a reliable conformational genetic marker as it is present in all bacteria, and its function has not changed over time [ 41 , 42 , 43 ]. Sanger sequencing of the variable gene (23S rRNA) was used for bacterial identification [ 42 , 44 ].…”

Comparative Genomics, Evolutionary and Gene Regulatory Regions Analysis of Casein Gene Family in Bubalus bubalis

“…Buffalo is a luxurious genetic resource with multiple utilities (as a dairy, draft, and meat animal) and economic significance in the tropical and subtropical regions of the globe ( Rehman et al, 2019 , 2020 ; Luo et al, 2020 ). The domesticated buffalo is grouped into river buffalo with karyotype 2n = 50 primarily present in southwestern Asia, India, south Mediterranean Europe, and Egypt and swamp buffalo with 2n = 48 distributed across Southeast Asia, southern and southeast China, where the swamp buffalo is used as draft power in the rice paddy fields while the river buffalo is mainly reared for milk production ( Moioli et al, 2001 ; Fan et al, 2020 ; Luo et al, 2020 ).…”

Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges

“…Molecular mass-based classification characterizes HSPs into HSPB1 , HSPD , HSPH1 , HSP40 , HSP10 , HSP70 , and HSP90 gene families. A total of 64 HSP genes were reported in buffaloes, of which 39 genes belong to the HSP40 family; 4 to HSP90 ; 8 to HSPB ; 10 to HSP70 ; and 1 each to HSPH1 , HSP10 , and HSPD [ 59 ]. In thermal stress conditions, the expression of HSPs distinctively increases to enhance the thermotolerance ability and serve as the first line of defense against heat shock to protect cells and tissues [ 60 , 61 ].…”

“…Moreover, the SNPs in the genic, untranslated, and promoter regions of HSPs have shown significant association with higher milk production, heat tolerance, stress resilience, and disease vulnerability in livestock [ 21 , 68 , 69 , 70 ]. Furthermore, a recent whole-genome sequence-based study reported evidence of positive selection related to thermotolerance in buffaloes [ 21 , 59 ]. Luo et al [ 21 ] reported HSP gene family expansion in both buffalo subspecies (river and swamp), which are stress-inducible molecular chaperones and responsible for environmental adaptation in buffaloes.…”