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Yang B, Cheng Z, Luo L, Cheng K, Gan S, Shi Y, Liu C, Wang D. Comparative analysis of codon usage patterns of Plasmodium helical interspersed subtelomeric (PHIST) proteins. Front Microbiol 2023; 14:1320060. [PMID: 38156001 PMCID: PMC10752978 DOI: 10.3389/fmicb.2023.1320060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/28/2023] [Indexed: 12/30/2023] Open
Abstract
Background Plasmodium falciparum 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. Plasmodium 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 Plasmodium falciparum 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 Plasmodium falciparum 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 Plasmodium falciparum. 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.
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Affiliation(s)
- Baoling Yang
- College of Basic Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Ziwen Cheng
- College of Basic Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Like Luo
- College of Basic Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Kuo Cheng
- College of Basic Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Shengqi Gan
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Yuyi Shi
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Che Liu
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Dawei Wang
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou, Liaoning Province, China
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Wang D, Yang B. Analysis of codon usage bias of thioredoxin in apicomplexan protozoa. Parasit Vectors 2023; 16:431. [PMID: 37990340 PMCID: PMC10664530 DOI: 10.1186/s13071-023-06002-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/06/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Apicomplexan protozoa are a diverse group of obligate intracellular parasites causing many diseases that affect humans and animals, such as malaria, toxoplasmosis, and cryptosporidiosis. Apicomplexan protozoa possess unique thioredoxins (Trxs) that have been shown to regulate various cellular processes including metabolic redox regulation, parasite survival, and host immune evasion. However, it is still unknown how synonymous codons are used by apicomplexan protozoa Trxs. METHODS Codon usage bias (CUB) is the unequal usage of synonymous codons during translation which leads to the over- or underrepresentation of certain nucleotide patterns. This imbalance in CUB can impact a variety of cellular processes including protein expression levels and genetic variation. This study analyzed the CUB of 32 Trx coding sequences (CDS) from 11 apicomplexan protozoa. RESULTS The results showed that both codon base composition and relative synonymous codon usage (RSCU) analysis revealed that AT-ended codons were more frequently used in Cryptosporidium spp. and Plasmodium spp., while the Eimeria spp., Babesia spp., Hammondia hammondi, Neospora caninum, and Toxoplasma gondii tended to end in G/C. The average effective number of codon (ENC) value of these apicomplexan protozoa is 46.59, which is > 35, indicating a weak codon preference among apicomplexan protozoa Trxs. Furthermore, 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) indicated the influence of base composition and codon usage indices on CUB. Additionally, the neutrality plot analysis, PR2-bias plot analysis, and ENC-GC3 plot analysis further demonstrated that natural selection plays an important role in apicomplexan protozoa Trxs codon bias. CONCLUSIONS In conclusion, this study increased the understanding of codon usage characteristics and genetic evolution of apicomplexan protozoa Trxs, which expanded new ideas for vaccine and drug research.
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Affiliation(s)
- Dawei Wang
- Jinzhou Medical University, Jinzhou, 121000, Liaoning Province, China
| | - Baoling Yang
- Jinzhou Medical University, Jinzhou, 121000, Liaoning Province, China.
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Lamolle G, Iriarte A, Simón D, Musto H. Amino acid usage and protein expression levels in the flatworm Schistosoma mansoni. Mol Biochem Parasitol 2023; 255:111581. [PMID: 37478919 DOI: 10.1016/j.molbiopara.2023.111581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023]
Abstract
Schistosoma mansoni is a parasitic flatworm that causes a human disease called schistosomiasis, or bilharzia. At the genomic level, S. mansoni is AT-rich, but has some compositional heterogeneity. Indeed, some regions of its genome are GC-rich, mainly in the regions located near the extreme ends of the chromosomes. Recently, we showed that, despite the strong bias towards A/T ending codons, highly expressed genes tend to use GC-rich codons. Here, we address the following question: are highly expressed sequences biased in their amino acid frequencies? Our analyses show that these sequences in S. mansoni, as in species ranging from bacteria to human, are strongly biased in nucleotide composition. Highly expressed genes tend to use GC-rich codons (in the first and second codon positions), which code the energetically cheapest amino acids. Therefore, we conclude that amino acid usage, at least in highly expressed genes, is strongly shaped by natural selection to avoid energetically expensive residues. Whether this is an adaptation to the parasitic way of life of S. mansoni, is unclear since the same pattern occurs in free-living species.
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Affiliation(s)
- Guillermo Lamolle
- Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Andrés Iriarte
- Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay; Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Avenida A. Navarro 3051, 11600 Montevideo, Uruguay
| | - Diego Simón
- Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay; Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Universidad de la República, Mataojo 2055, 11400 Montevideo, Uruguay; Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
| | - Héctor Musto
- Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
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Wu P, Xiao W, Luo Y, Xiong Z, Chen X, He J, Sha A, Gui M, Li Q. Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes. Front Microbiol 2023; 14:1170790. [PMID: 37213503 PMCID: PMC10192751 DOI: 10.3389/fmicb.2023.1170790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/12/2023] [Indexed: 05/23/2023] Open
Abstract
Introduction Codon usage bias is a prevalent phenomenon observed across various species and genes. However, the specific attributes of codon usage in the mitochondrial genome of Ganoderma species remain unknown. Methods In this study, we investigated the codon bias of 12 mitochondrial core protein-coding genes (PCGs) in 9 Ganoderma species, including 13 Ganoderma strains. Results The codons of all Ganoderma strains showed a preference for ending in A/T. Additionally, correlations between codon base composition and the codon adaptation index (CAI), codon bias index (CBI) and frequency of optimal codons (FOP) were identified, demonstrating the impact of base composition on codon bias. Various base bias indicators were found to vary between or within Ganoderma strains, including GC3s, the CAI, the CBI, and the FOP. The results also revealed that the mitochondrial core PCGs of Ganoderma have an average effective number of codons (ENC) lower than 35, indicating strong bias toward certain codons. Evidence from neutrality plot and PR2-bias plot analysis indicates that natural selection is a major factor affecting codon bias in Ganoderma. Additionally, 11 to 22 optimal codons (ΔRSCU>0.08 and RSCU>1) were identified in 13 Ganoderma strains, with GCA, AUC, and UUC being the most widely used optimal codons in Ganoderma. By analyzing the combined mitochondrial sequences and relative synonymous codon usage (RSCU) values, the genetic relationships between or within Ganoderma strains were determined, indicating variations between them. Nevertheless, RSCU-based analysis illustrated the intra- and interspecies relationships of certain Ganoderma species. Discussion This study deepens our insight into the synonymous codon usage characteristics, genetics, and evolution of this important fungal group.
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Affiliation(s)
- Peng Wu
- Yunnan Plateau Characteristic Agricultural Industry Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Wenqi Xiao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Yingyong Luo
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Zhuang Xiong
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Xiaodie Chen
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Jing He
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Ajia Sha
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Mingying Gui
- Yunnan Plateau Characteristic Agricultural Industry Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China
- *Correspondence: Mingying Gui,
| | - Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
- Qiang Li,
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