Comparative Analysis of Codon Usage Patterns of Helical Interspersed Subtelomeric (PHIST) Proteins

Overview

Journal Front Microbiol

Specialty Microbiology

Date 2023 Dec 29

PMID 38156001

Authors

Baoling Yang

Ziwen Cheng

Like Luo

Kuo Cheng

Shengqi Gan

Yuyi Shi

Che Liu

Dawei Wang

Affiliations

Soon will be listed here.

Abstract

Background: is a protozoan parasite that causes the most severe form of malaria in humans worldwide, which is predominantly found in sub-Saharan Africa, where it is responsible for the majority of malaria-related deaths. helical interspersed subtelomeric (PHIST) proteins are a family of proteins, with a conserved PHIST domain, which are typically located at the subtelomeric regions of the chromosomes and play crucial roles in the interaction between the parasite and its human host, such as cytoadherence, immune evasion, and host cell remodeling. However, the specific utilization of synonymous codons by PHIST proteins in is still unknown.

Methods: Codon usage bias (CUB) refers to the unequal usage of synonymous codons during translation, resulting in over- or underrepresentation of certain nucleotide patterns. This imbalance in CUB can impact various cellular processes, including protein expression levels and genetic variation. To investigate this, the CUB of 88 PHIST protein coding sequences (CDSs) from 5 subgroups were analyzed in this study.

Results: The results showed that both codon base composition and relative synonymous codon usage (RSCU) analysis identified a higher occurrence of AT-ended codons (AGA and UUA) in PHIST proteins of . The average effective number of codons (ENC) for these PHIST proteins was 36.69, indicating a weak codon preference among them, as it was greater than 35. Additionally, the correlation analysis among codon base composition (GC1, GC2, GC3, GCs), codon adaptation index (CAI), codon bias index (CBI), frequency of optimal codons (FOP), ENC, general average hydropathicity (GRAVY), aromaticity (AROMO), length of synonymous codons (L_sym), and length of amino acids (L_aa) revealed the influence of base composition and codon usage indices on codon usage bias, with GC1 having a significant impact in this study. Furthermore, the neutrality plot analysis, PR2-bias plot analysis, and ENC-GC3 plot analysis provided additional evidence that natural selection plays a crucial role in determining codon bias in PHIST proteins.

Conclusion: In conclusion, this study has enhanced our understanding of the characteristics of codon usage and genetic evolution in PHIST proteins, thereby providing data foundation for further research on antimalarial drugs or vaccines.

References

Munjal A, Khandia R, Shende K, Das J . Mycobacterium lepromatosis genome exhibits unusually high CpG dinucleotide content and selection is key force in shaping codon usage. Infect Genet Evol. 2020; 84:104399. DOI: 10.1016/j.meegid.2020.104399. View

Tripathi J, Zhu L, Nayak S, Stoklasa M, Bozdech Z . Stochastic expression of invasion genes in Plasmodium falciparum schizonts. Nat Commun. 2022; 13(1):3004. PMC: 9151791. DOI: 10.1038/s41467-022-30605-z. View

Gorlov I, Pikielny C, Frost H, Her S, Cole M, Strohbehn S . Gene characteristics predicting missense, nonsense and frameshift mutations in tumor samples. BMC Bioinformatics. 2018; 19(1):430. PMC: 6245819. DOI: 10.1186/s12859-018-2455-0. View

Yang C, Zhao Q, Wang Y, Zhao J, Qiao L, Wu B . Comparative Analysis of Genomic and Transcriptome Sequences Reveals Divergent Patterns of Codon Bias in Wheat and Its Ancestor Species. Front Genet. 2021; 12:732432. PMC: 8417831. DOI: 10.3389/fgene.2021.732432. View

Wu C, Xiao K, Wang L, Wang J, Song Q, Stanley D . Identification and expression profiling of serine protease-related genes in Tenebrio molitor. Arch Insect Biochem Physiol. 2022; 111(3):e21963. DOI: 10.1002/arch.21963. View

Lee S, Low L, Andersen J, Yeoh L, Valenzuela Leon P, Drew D . The direct binding of AMA1 to erythrocytes defines a RON2-independent invasion pathway. Proc Natl Acad Sci U S A. 2022; 120(1):e2215003120. PMC: 9910450. DOI: 10.1073/pnas.2215003120. View

Chassalevris T, Chaintoutis S, Apostolidi E, Giadinis N, Vlemmas I, Brellou G . A highly sensitive semi-nested real-time PCR utilizing oligospermine-conjugated degenerate primers for the detection of diverse strains of small ruminant lentiviruses. Mol Cell Probes. 2020; 51:101528. DOI: 10.1016/j.mcp.2020.101528. View

Shen X, Song S, Li C, Zhang J . Synonymous mutations in representative yeast genes are mostly strongly non-neutral. Nature. 2022; 606(7915):725-731. PMC: 9650438. DOI: 10.1038/s41586-022-04823-w. View

Benisty H, Hernandez-Alias X, Weber M, Anglada-Girotto M, Mantica F, Radusky L . Genes enriched in A/T-ending codons are co-regulated and conserved across mammals. Cell Syst. 2023; 14(4):312-323.e3. DOI: 10.1016/j.cels.2023.02.002. View

10.

Jiang Y, Neti S, Sitarik I, Pradhan P, To P, Xia Y . How synonymous mutations alter enzyme structure and function over long timescales. Nat Chem. 2022; 15(3):308-318. PMC: 11267483. DOI: 10.1038/s41557-022-01091-z. View

11.

Wiser M . Knobs, Adhesion, and Severe Falciparum Malaria. Trop Med Infect Dis. 2023; 8(7). PMC: 10385726. DOI: 10.3390/tropicalmed8070353. View

12.

Liu X, Li Y, Ji K, Zhu J, Ling P, Zhou T . Genome-wide codon usage pattern analysis reveals the correlation between codon usage bias and gene expression in Cuscuta australis. Genomics. 2020; 112(4):2695-2702. DOI: 10.1016/j.ygeno.2020.03.002. View

13.

Parvathy S, Udayasuriyan V, Bhadana V . Codon usage bias. Mol Biol Rep. 2021; 49(1):539-565. PMC: 8613526. DOI: 10.1007/s11033-021-06749-4. View

14.

Chen F, Yang J . Distinct codon usage bias evolutionary patterns between weakly and strongly virulent respiratory viruses. iScience. 2022; 25(1):103682. PMC: 8704784. DOI: 10.1016/j.isci.2021.103682. View

15.

Pulido-Quevedo F, Arevalo-Pinzon G, Castaneda-Ramirez J, Barreto-Santamaria A, Patarroyo M, Patarroyo M . Plasmodium falciparum rhoptry neck protein 4 has conserved regions mediating interactions with receptors on human erythrocytes and hepatocyte membrane. Int J Med Microbiol. 2023; 313(3):151579. DOI: 10.1016/j.ijmm.2023.151579. View

16.

Kumar V, Behl A, Sharma R, Sharma A, Hora R . Plasmodium helical interspersed subtelomeric family-an enigmatic piece of the Plasmodium biology puzzle. Parasitol Res. 2019; 118(10):2753-2766. DOI: 10.1007/s00436-019-06420-9. View

17.

Chakraborty S, Yengkhom S, Uddin A . Analysis of codon usage bias of chloroplast genes in Oryza species : Codon usage of chloroplast genes in Oryza species. Planta. 2020; 252(4):67. DOI: 10.1007/s00425-020-03470-7. View

18.

Patil S, Indrabalan U, Suresh K, Shome B . Analysis of codon usage bias of classical swine fever virus. Vet World. 2021; 14(6):1450-1458. PMC: 8304411. DOI: 10.14202/vetworld.2021.1450-1458. View

19.

Beelagi M, Kumar S, Indrabalan U, Patil S, Prasad A, Suresh K . Synonymous codon usage pattern among the S, M, and L segments in Crimean-congo hemorrhagic fever virus. Bioinformation. 2021; 17(4):479-491. PMC: 8450151. DOI: 10.6026/97320630017479. View

20.

Shakya B, Kilili G, Wang L, Nakayasu E, LaCount D . Identification of Exported Proteins That Bind to the Erythrocyte Cytoskeleton. Microorganisms. 2022; 10(7). PMC: 9320996. DOI: 10.3390/microorganisms10071438. View