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Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae
Journal article   Open access   Peer reviewed

Codon usage comparison of novel genes in clinical isolates of Haemophilus influenzae

John Gladitz, Kai Shen, Patricia Antalis, Fen Ze Hu, J Christopher Post and Garth D Ehrlich
Nucleic acids research, v 33(11), pp 3644-3658
2005
DOI: https://doi.org/10.1093/nar/gki670
PMID: 15983137
Featured in Collection :   UN Sustainable Development Goals @ Drexel
url
https://doi.org/10.1093/nar/gki670View
Published, Version of Record (VoR) Open

Abstract

Genes, Bacterial Haemophilus influenzae - metabolism Data Interpretation, Statistical Gene Expression Genome, Bacterial Genomics Humans Haemophilus influenzae - genetics DNA, Bacterial - chemistry Gene Transfer, Horizontal Phylogeny Haemophilus influenzae - isolation & purification Codon Base Sequence
A similarity statistic for codon usage was developed and used to compare novel gene sequences found in clinical isolates of Haemophilus influenzae with a reference set of 80 prokaryotic, eukaryotic and viral genomes. These analyses were performed to obtain an indication as to whether individual genes were Haemophilus-like in nature, or if they probably had more recently entered the H.influenzae gene pool via horizontal gene transfer from other species. The average and SD values were calculated for the similarity statistics from a study of the set of all genes in the H.influenzae Rd reference genome that encoded proteins of 100 amino acids or longer. Approximately 80% of Rd genes gave a statistic indicating that they were most like other Rd genes. Genes displaying codon usage statistics >1 SD above this range were either considered part of the highly expressed group of H.influenzae genes, or were considered of foreign origin. An alternative determinant for identifying genes of foreign origin was when the similarity statistics produced a value that was much closer to a non-H.influenzae reference organism than to any of the Haemophilus species contained in the reference set. Approximately 65% of the novel sequences identified in the H.influenzae clinical isolates displayed codon usages most similar to Haemophilus sp. The remaining novel sequences produced similarity statistics closer to one of the other reference genomes thereby suggesting that these sequences may have entered the H.influenzae gene pool more recently via horizontal transfer.

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Web of Science research areas
Biochemistry & Molecular Biology
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