Comparative analysis of codon usage patterns of Plasmodium helical interspersed subtelomeric (PHIST) proteins DOI Creative Commons

Baoling Yang,

Ziwen Cheng,

Like Luo

и другие.

Frontiers in Microbiology, Год журнала: 2023, Номер 14

Опубликована: Дек. 14, 2023

Background Plasmodium falciparum is a protozoan parasite that causes the most severe form of malaria in humans worldwide, which predominantly found sub-Saharan Africa, where it responsible for majority malaria-related deaths. helical interspersed subtelomeric (PHIST) proteins are family proteins, with conserved PHIST domain, typically located at regions chromosomes and play crucial roles interaction between its human host, such as cytoadherence, immune evasion, host cell remodeling. However, specific utilization synonymous codons by still unknown. Methods Codon usage bias (CUB) refers to unequal during translation, resulting over- or underrepresentation certain nucleotide patterns. This imbalance CUB can impact various cellular processes, including protein expression levels genetic variation. To investigate this, 88 coding sequences (CDSs) from 5 subgroups were analyzed this study. Results The results showed both codon base composition relative (RSCU) analysis identified higher occurrence AT-ended (AGA UUA) . average effective number (ENC) these was 36.69, indicating weak preference among them, greater than 35. Additionally, correlation (GC1, GC2, GC3, GCs), adaptation index (CAI), (CBI), frequency optimal (FOP), ENC, general hydropathicity (GRAVY), aromaticity (AROMO), length (L_sym), amino acids (L_aa) revealed influence indices on bias, GC1 having significant Furthermore, neutrality plot analysis, PR2-bias ENC-GC3 provided additional evidence natural selection plays role determining proteins. Conclusion In conclusion, study has enhanced our understanding characteristics evolution thereby providing data foundation further research antimalarial drugs vaccines.

Язык: Английский

Codon Usage Bias in the Photolyase Gene of Amsacta moorei Entomopoxvirus DOI
Yeşim Aktürk Dizman

Biology Bulletin, Год журнала: 2024, Номер 51(S1), С. S52 - S65

Опубликована: Дек. 1, 2024

Язык: Английский

Процитировано

0
Analysis of codon usage bias of thioredoxin in apicomplexan protozoa DOI Creative Commons
Dawei Wang,

Baoling Yang

Parasites & Vectors, Год журнала: 2023, Номер 16(1)

Опубликована: Ноя. 21, 2023

Apicomplexan protozoa are a diverse group of obligate intracellular parasites causing many diseases that affect humans and animals, such as malaria, toxoplasmosis, cryptosporidiosis. possess unique thioredoxins (Trxs) have been shown to regulate various cellular processes including metabolic redox regulation, parasite survival, host immune evasion. However, it is still unknown how synonymous codons used by apicomplexan Trxs. Codon usage bias (CUB) the unequal during translation which leads over- or underrepresentation certain nucleotide patterns. This imbalance in CUB can impact variety protein expression levels genetic variation. study analyzed 32 Trx coding sequences (CDS) from 11 protozoa. The results showed both codon base composition relative (RSCU) analysis revealed AT-ended were more frequently Cryptosporidium spp. Plasmodium spp., while Eimeria Babesia Hammondia hammondi, Neospora caninum, Toxoplasma gondii tended end G/C. average effective number (ENC) value these 46.59, > 35, indicating weak preference among Furthermore, correlation (GC1, GC2, GC3, GCs), adaptation index (CAI), (CBI), frequency optimal (FOP), ENC, general hydropathicity (GRAVY), aromaticity (AROMO), length (L_sym), amino acids (L_aa) indicated influence indices on CUB. Additionally, neutrality plot analysis, PR2-bias ENC-GC3 further demonstrated natural selection plays an important role Trxs bias. In conclusion, this increased understanding characteristics evolution Trxs, expanded new ideas for vaccine drug research.

Язык: Английский

Процитировано

1
Analysis of Codon Usage Bias of Thioredoxin in Apicomplexan Protozoa DOI Creative Commons
Dawei Wang,

Baoling Yang

Research Square (Research Square), Год журнала: 2023, Номер unknown

Опубликована: Июнь 29, 2023

Abstract Background Apicomplexan protozoa are a diverse group of obligate intracellular parasites causing many diseases that affect humans and animals such as malaria, toxoplasmosis, cryptosporidiosis. possess unique thioredoxins (Trxs) have been shown to regulate various cellular processes including metabolic redox regulation, parasite survival, host immune evasion. However, it is still unknown how synonymous codons used by apicomplexan Trxs. Methods Codon Usage Bias (CUB) the unequal usage during translation which leads over or underrepresentation certain nucleotide patterns. This imbalance in CUB can impact variety protein expression levels genetic variation. study analyzed 32 Trx coding sequences (CDS) from 11 protozoa. Results The results showed both codon base composition relative (RSCU) analysis revealed AT-ended were more frequently Cryptosporidium spp . Plasmodium ., while Eimeria spp. , Babesia Hammondia hammondi Neospora caninum Toxoplasma gondii tended end G/C. average effective number (ENC) value these 46.59, > 35, indicating weak preference among Furthermore, correlation (GC1, GC2, GC3, GCs), adaptation index (CAI), bias (CBI), frequency optimal (FOP), ENC, general hydropathicity (GRAVY), aromaticity (AROMO), length (L_sym) amino acids (L_aa) indicated influence indices on CUB. Additionally, neutrality plot analysis, PR2-bias ENC-GC3 further demonstrated natural selection plays an important role Trxs bias. Conclusions In conclusion, this increased understanding characteristics evolution Trxs, expanded new ideas for function research.

Язык: Английский

Процитировано

0
Evolution is All You Need in Promoter Design and Optimization DOI Creative Commons

Ruohan Ren,

Hongyu Yu,

Jiahao Teng

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Ноя. 18, 2023

Abstract Predicting the strength of promoters and guiding their directed evolution is a crucial task in synthetic biology. This approach significantly reduces experimental costs conventional promoter engineering. Previous studies employing machine learning or deep methods have shown some success this task, but outcomes were not satisfactory enough, primarily due to neglect evolutionary information. In paper, we introduce Chaos-Attention net for Promoter Evolution (CAPE) address limitations existing methods. We comprehensively extract information within using chaos game representation process overall with DenseNet Transformer. Our model achieves state-of-the-art results on two kinds distinct tasks. The incorporation enhances model’s accuracy, transfer further extending its adaptability. Furthermore, confirm CAPE’s efficacy simulating silico promoters, marking significant advancement predictive modeling prokaryotic strength. paper also presents user-friendly website practical implementation promoters.

Язык: Английский

Процитировано

0
Comparative analysis of codon usage patterns of Plasmodium helical interspersed subtelomeric (PHIST) proteins DOI Creative Commons

Baoling Yang,

Ziwen Cheng,

Like Luo

и другие.

Frontiers in Microbiology, Год журнала: 2023, Номер 14

Опубликована: Дек. 14, 2023

Background Plasmodium falciparum is a protozoan parasite that causes the most severe form of malaria in humans worldwide, which predominantly found sub-Saharan Africa, where it responsible for majority malaria-related deaths. helical interspersed subtelomeric (PHIST) proteins are family proteins, with conserved PHIST domain, typically located at regions chromosomes and play crucial roles interaction between its human host, such as cytoadherence, immune evasion, host cell remodeling. However, specific utilization synonymous codons by still unknown. Methods Codon usage bias (CUB) refers to unequal during translation, resulting over- or underrepresentation certain nucleotide patterns. This imbalance CUB can impact various cellular processes, including protein expression levels genetic variation. To investigate this, 88 coding sequences (CDSs) from 5 subgroups were analyzed this study. Results The results showed both codon base composition relative (RSCU) analysis identified higher occurrence AT-ended (AGA UUA) . average effective number (ENC) these was 36.69, indicating weak preference among them, greater than 35. Additionally, correlation (GC1, GC2, GC3, GCs), adaptation index (CAI), (CBI), frequency optimal (FOP), ENC, general hydropathicity (GRAVY), aromaticity (AROMO), length (L_sym), amino acids (L_aa) revealed influence indices on bias, GC1 having significant Furthermore, neutrality plot analysis, PR2-bias ENC-GC3 provided additional evidence natural selection plays role determining proteins. Conclusion In conclusion, study has enhanced our understanding characteristics evolution thereby providing data foundation further research antimalarial drugs vaccines.

Язык: Английский

Процитировано

0