Codon Bias of the Gene and Transcription Factor EHF in Multiple Species

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2024 Oct 16

PMID 39409024

Authors

Zhiyong Zhang

Wenxi Li

Ziyang Wang

Shuya Ma

Fangyuan Zheng

Hongyu Liu

Xiaodong Zhang

Yueyun Ding

Zongjun Yin

Xianrui Zheng

Affiliations

Soon will be listed here.

Abstract

Milk production is an essential economic trait in cattle, and understanding the genetic regulation of this trait can enhance breeding strategies. The discoidin domain receptor 1 () gene has been identified as a key candidate gene that influences milk production, and ETS homologous factor (EHF) is recognized as a critical transcription factor that regulates expression. Codon usage bias, which affects gene expression and protein function, has not been fully explored in cattle. This study aims to examine the codon usage bias of and EHF transcription factors to understand their roles in dairy production traits. Data from 24 species revealed that both and EHF predominantly used G/C-ending codons, with the GC3 content averaging 75.49% for and 61.72% for EHF. Synonymous codon usage analysis identified high-frequency codons for both and EHF, with 17 codons common to both genes. Correlation analysis indicated a negative relationship between the effective number of codons and codon adaptation index for both and EHF. Phylogenetic and clustering analyses revealed similar codon usage patterns among closely related species. These findings suggest that EHF plays a crucial role in regulating expression, offering new insights into genetically regulating milk production in cattle.

References

Liu Y . A code within the genetic code: codon usage regulates co-translational protein folding. Cell Commun Signal. 2020; 18(1):145. PMC: 7488015. DOI: 10.1186/s12964-020-00642-6. View

Ikemura T . Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol. 1981; 146(1):1-21. DOI: 10.1016/0022-2836(81)90363-6. View

Barker K, Martindale J, Mitchell P, Kamalati T, Page M, Phippard D . Expression patterns of the novel receptor-like tyrosine kinase, DDR, in human breast tumours. Oncogene. 1995; 10(3):569-75. View

Chakraborty S, Uddin A, Choudhury M . Factors affecting the codon usage bias of SRY gene across mammals. Gene. 2017; 630:13-20. DOI: 10.1016/j.gene.2017.08.003. View

Wang H, Liu S, Zhang B, Wei W . Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts. PLoS One. 2016; 11(11):e0166260. PMC: 5125587. DOI: 10.1371/journal.pone.0166260. View

Lee S, Weon S, Lee S, Kang C . Relative codon adaptation index, a sensitive measure of codon usage bias. Evol Bioinform Online. 2010; 6:47-55. PMC: 2880845. DOI: 10.4137/ebo.s4608. View

Quax T, Claassens N, Soll D, van der Oost J . Codon Bias as a Means to Fine-Tune Gene Expression. Mol Cell. 2015; 59(2):149-61. PMC: 4794256. DOI: 10.1016/j.molcel.2015.05.035. View

Romero H, Zavala A, Musto H . Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces. Nucleic Acids Res. 2000; 28(10):2084-90. PMC: 105376. DOI: 10.1093/nar/28.10.2084. View

Brenne K, Nymoen D, Hetland T, Trope C, Davidson B . Expression of the Ets transcription factor EHF in serous ovarian carcinoma effusions is a marker of poor survival. Hum Pathol. 2011; 43(4):496-505. DOI: 10.1016/j.humpath.2011.05.023. View

10.

Xie G, Xia M, Miao Y, Luo M, Zhang Q, Guo A . FFLtool: a web server for transcription factor and miRNA feed forward loop analysis in human. Bioinformatics. 2019; 36(8):2605-2607. DOI: 10.1093/bioinformatics/btz929. View

11.

Saul A, Battistutta D . Codon usage in Plasmodium falciparum. Mol Biochem Parasitol. 1988; 27(1):35-42. DOI: 10.1016/0166-6851(88)90022-9. View

12.

Pedersen A, Wiuf C, Christiansen F . A codon-based model designed to describe lentiviral evolution. Mol Biol Evol. 1998; 15(8):1069-81. DOI: 10.1093/oxfordjournals.molbev.a026006. View

13.

Weidemuller P, Kholmatov M, Petsalaki E, Zaugg J . Transcription factors: Bridge between cell signaling and gene regulation. Proteomics. 2021; 21(23-24):e2000034. DOI: 10.1002/pmic.202000034. View

14.

Batard Y, Hehn A, Nedelkina S, Schalk M, Pallett K, Schaller H . Increasing expression of P450 and P450-reductase proteins from monocots in heterologous systems. Arch Biochem Biophys. 2000; 379(1):161-9. DOI: 10.1006/abbi.2000.1867. View

15.

Dhindsa R, Copeland B, Mustoe A, Goldstein D . Natural Selection Shapes Codon Usage in the Human Genome. Am J Hum Genet. 2020; 107(1):83-95. PMC: 7332603. DOI: 10.1016/j.ajhg.2020.05.011. View

16.

Toscani A, Aguilera P, Coluccio Leskow F . Discoidin domain receptor 1 regulates ErbB2/ErbB3 signaling in mammary epithelial cells. FEBS Lett. 2022; 596(21):2795-2807. DOI: 10.1002/1873-3468.14522. View

17.

Novoa E, Pavon-Eternod M, Pan T, Ribas de Pouplana L . A role for tRNA modifications in genome structure and codon usage. Cell. 2012; 149(1):202-13. DOI: 10.1016/j.cell.2012.01.050. View

18.

Baeza M, Sepulveda D, Cifuentes V, Alcaino J . Codon usage bias in yeasts and its correlation with gene expression, growth temperature, and protein structure. Front Microbiol. 2024; 15:1414422. PMC: 11260810. DOI: 10.3389/fmicb.2024.1414422. View

19.

Radrizzani S, Kudla G, Izsvak Z, Hurst L . Selection on synonymous sites: the unwanted transcript hypothesis. Nat Rev Genet. 2024; 25(6):431-448. DOI: 10.1038/s41576-023-00686-7. View

20.

Biswas S, Banerjee S, Baker G, Kuo C, Chowdhury I . The Mammary Gland: Basic Structure and Molecular Signaling during Development. Int J Mol Sci. 2022; 23(7). PMC: 8998991. DOI: 10.3390/ijms23073883. View