Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis

Panda, Arup; Tuller, Tamir

doi:10.1038/s41522-023-00372-w

Cited by 5 publications

(1 citation statement)

References 79 publications

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“…Bioinformatics tools analyze the codon usage patterns of both the source organism and the host organism [ 167 , 170 ]. Researchers can then modify the gene sequence to replace rarely used codons with preferred codons of the host organism, a process known as codon optimization [ 171 – 173 ].…”

Section: Importance Of Bioinformatics For Rmp Analysismentioning

confidence: 99%

Recombinant multiepitope proteins expressed in Escherichia coli cells and their potential for immunodiagnosis

Gonçalves,

Ribeiro,

Resende

et al. 2024

Microb Cell Fact

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Recombinant multiepitope proteins (RMPs) are a promising alternative for application in diagnostic tests and, given their wide application in the most diverse diseases, this review article aims to survey the use of these antigens for diagnosis, as well as discuss the main points surrounding these antigens. RMPs usually consisting of linear, immunodominant, and phylogenetically conserved epitopes, has been applied in the experimental diagnosis of various human and animal diseases, such as leishmaniasis, brucellosis, cysticercosis, Chagas disease, hepatitis, leptospirosis, leprosy, filariasis, schistosomiasis, dengue, and COVID-19. The synthetic genes for these epitopes are joined to code a single RMP, either with spacers or fused, with different biochemical properties. The epitopes’ high density within the RMPs contributes to a high degree of sensitivity and specificity. The RMPs can also sidestep the need for multiple peptide synthesis or multiple recombinant proteins, reducing costs and enhancing the standardization conditions for immunoassays. Methods such as bioinformatics and circular dichroism have been widely applied in the development of new RMPs, helping to guide their construction and better understand their structure. Several RMPs have been expressed, mainly using the Escherichia coli expression system, highlighting the importance of these cells in the biotechnological field. In fact, technological advances in this area, offering a wide range of different strains to be used, make these cells the most widely used expression platform. RMPs have been experimentally used to diagnose a broad range of illnesses in the laboratory, suggesting they could also be useful for accurate diagnoses commercially. On this point, the RMP method offers a tempting substitute for the production of promising antigens used to assemble commercial diagnostic kits.

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Section: Importance Of Bioinformatics For Rmp Analysismentioning

confidence: 99%

Recombinant multiepitope proteins expressed in Escherichia coli cells and their potential for immunodiagnosis

Gonçalves,

Ribeiro,

Resende

et al. 2024

Microb Cell Fact

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Metagenomics for microbial degradation and detoxification of heavy metals

Rekadwad,

Warghane

2024

Microbiome-Assisted Bioremediation

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Prediction of new likely emergent amino acid point mutations from USA, UK, Italy, France, Brazil, and India SARS-CoV-2 variants: a possible source for more reliable cocktail coronavirus vaccine

Alhaji Saganuwan

2024

RPS Pharmacy and Pharmacology Reports

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Objectives The interaction between genome components of the vaccines, host cells and SARS-CoV-2 variants can cause mutation of amino acids at high random frequency. Hence the present study is aimed at using the codon bases –amino acids components of some available strains with a view to determing new likely emergent strains of SARS-CoV-2. Methods Some genome sizes and lengths of SARS-CoV-2 variants were either searched from literatures calculated. Point mutation of a single amino acid was deduced from 2/3 of sets of codon bases responsible for expression of amino acids. One base pair of 0.0047nm Codon Base Table was used to deduce the likely missense amino acids at probability of one-twentieth. Keyfindings New generated codon bases gave rise to new emergent strains of varying number of amino acid pairs. Amino acids have reappeared and disappeared in some strains. Nine strains altogether have shown stop codon bases and the remaining strains have tendency to form stop codons. Adenine has highest frequency of the stop codon bases whereas cytosine is not among stop codon. A total of 906 new variants were deduced from 54 coronavirus strains which initially lacked stop codons. The newly predicted strains may become less pathogenic and serve as immunogen via glycosylation. Strains with higher number of codon bases undergo mutation faster than that may end up in stop codons. Conclusion Hence the likely emergent strains could be less virulent, less pathogenic and many from glycans that could serve as source for manufacturing of more reliable coronavirus vaccines.

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Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis

Cited by 5 publications

References 79 publications

Recombinant multiepitope proteins expressed in Escherichia coli cells and their potential for immunodiagnosis

Recombinant multiepitope proteins expressed in Escherichia coli cells and their potential for immunodiagnosis

Metagenomics for microbial degradation and detoxification of heavy metals

Prediction of new likely emergent amino acid point mutations from USA, UK, Italy, France, Brazil, and India SARS-CoV-2 variants: a possible source for more reliable cocktail coronavirus vaccine

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