Detection of Genes with Atypical Nucleotide Sequence in Microbial Genomes

@article{Hooper2001DetectionOG,
  title={Detection of Genes with Atypical Nucleotide Sequence in Microbial Genomes},
  author={Sean D. Hooper and Otto G. Berg},
  journal={Journal of Molecular Evolution},
  year={2001},
  volume={54},
  pages={365-375}
}
Along the gene, nucleotides in various codon positions tend to exert a slight but observable influence on the nucleotide choice at neighboring positions. Such context biases are different in different organisms and can be used as genomic signatures. In this paper, we will focus specifically on the dinucleotide composed of a third codon position nucleotide and its succeeding first position nucleotide. Using the 16 possible dinucleotide combinations, we calculate how well individual genes conform… 
View on Springer
ncbi.nlm.nih.gov
47 Citations
Highly Influential Citations
4
Background Citations
18
Methods Citations
14

47 Citations

Citation Type

Citation Type

Measuring Genome Divergence in Bacteria: A Case Study Using Chlamydian Data
TLDR
No examples of horizontal gene transfer subsequent to species divergence were identified, nor any evidence for an excessive number of tandem gene duplications, which is indicative of a low frequency of vertical gene transfer events.
Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models
TLDR
SIGI-HMM is a sensitive tool for the identification of GIs in microbial genomes that allows to interactively analyze genomes in detail and to generate or to test hypotheses about the origin of acquired genes.
A new computational method for the detection of horizontal gene transfer events
TLDR
This paper introduces and discusses a novel computational method for identifying horizontal transfers that relies on a gene's nucleotide composition and obviates the need for knowledge of codon boundaries and can be easily extended to the case of clusters of horizontally transferred genes.
A Biased Urn Model for Taxonomic Identification
TLDR
Biological relations are found to reflect themselves in the geometry of the parameter space, enabling us to predict the phylum of the organism that a given genomic sequence belongs to, allowing applications in the context of metagenomics.
Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori
TLDR
A new methodology combining aspects of established signature analysis with textual analysis approaches is used to analyze the two available genome sequences of H. pylori, revealing a wide range of genes related to both virulence behaviour and the strain differences that have been relatively recently acquired from other sequence backgrounds.
SIGI: score-based identification of genomic islands
TLDR
The method reliably allows to identify genomic island and the likely origin of alien genes and the taxonomical relation among those species responsible for significant scores was interpreted.
A Benchmark of Parametric Methods for Horizontal Transfers Detection
TLDR
The results of this benchmark concerning 16 representative parametric methods showed a great variety of efficiencies, and it is proposed using two methods in combination, a gene based one for specificity and a windowbased one for sensitivity.
Inferring Horizontal Gene Transfer
TLDR
HGT is a major source of phenotypic innovation and a mechanism of niche adaptation, and as HGT can bring into genomes radically different genotypes from distant lineages, or even new genes bearing new functions, it can be difficult to ascertain all but simple and clear-cut HGT events.
Towards more robust methods of alien gene detection
TLDR
By including additional genomic information in a multiple-threshold framework, a remarkable improvement in the performance of several popular, but algorithmically distinct, methods for alien gene detection is observed.
Identification and characterization of pathogenicity and other genomic islands using base composition analyses.
  • L. Guy
  • Biology
    Future microbiology
  • 2006
TLDR
Future availability of fast, high-throughput, inexpensive genome sequencing emphasizes the need for user-friendly applications able to detect, characterize and analyze putative GIs and PAIs, and in silico methods to detect putative PAIs and GIs within them.
...
...

References

SHOWING 1-10 OF 17 REFERENCES
Codon contexts in enterobacterial and coliphage genes.
  • M. Gouy
  • Biology
    Molecular biology and evolution
  • 1987
TLDR
The extent to which highly expressed protein genes can modulate base usage at two successive codon positions III, given the constraints on codon usage and protein sequence that act on them, was quantified and demonstrates that the above-mentioned favored patterns are not a characteristic of weakly expressed genes but occur in all genes in which codon context can vary appreciably.
Differences in dinucleotide frequencies of human, yeast, and Escherichia coli genes.
TLDR
The most significant finding is that human genomic DNA sequences, including genes and introns together, exhibit the largest deviation of dinucleotide occurrence from the random expectation.
Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA.
TLDR
Genome signature comparisons show that plasmids, both specialized and broad-range, and their hosts have substantially compatible (similar) genome signatures, and the archaea are not a coherent clade.
Amelioration of Bacterial Genomes: Rates of Change and Exchange
TLDR
Estimates of amelioration times indicate that the entire Escherichia coli chromosome contains more than 600 kb of horizontally transferred, protein-coding DNA, which predicts that the E. coli and Salmonella enterica lineages have each gained and lost more than 3 megabases of novel DNA since their divergence.
Computational DNA sequence analysis.
TLDR
New developments in computer and statistical analysis of DNA and protein sequences are reviewed with respect to bacteriophage genomes, to megabase amounts of several eukaryotic sequences, to a diverse collection of bacterial sets, to mitochondrial chromosomes, and to a broad assembly of viral genomes.
Comparisons of eukaryotic genomic sequences.
  • S. Karlin, I. Ladunga
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1994
TLDR
Assessment of general relatedness of genomes as distinguished from phylogenetic reconstructions demonstrates that the relative abundance distances almost always differ more for genomic interspecific sequence comparisons than for genomic intraspecific sequence comparisons, indicating congruence over different genome sequence samples.
Synonymous Nucleotide Divergence and Saturation: Effects of Site-Specific Variations in Codon Bias and Mutation Rates
  • O. Berg
  • Biology
    Journal of Molecular Evolution
  • 1999
TLDR
It is shown that when site-specific variation in mutation rates is introduced, there is no need to invoke assumptions of saturation and a large variability in codon preference and the same rate variation will also bring average mutation rates as estimated from synonymous sequence divergence into numerical agreement with experimental values.
Codon bias in Escherichia coli: the influence of codon context on mutation and selection.
TLDR
The codon bias in Escherichia coli for all two-fold degenerate amino acids was studied as dependent on the context from the six bases in the nearest surrounding codons to identify specific molecular processes, repair or avoidance of frame shift, that lead to the context dependence of the bias.
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.
TLDR
A simple, effective measure of synonymous codon usage bias, the Codon Adaptation Index, is detailed, useful for predicting the level of expression of a gene, for assessing the adaptation of viral genes to their hosts, and for making comparisons ofCodon usage in different organisms.
A DNA structural atlas for Escherichia coli.
TLDR
A computational analysis of DNA structural features in 18 fully sequenced prokaryotic genomes using models for DNA curvature, DNA flexibility, and DNA stability finds that most ribosomal genes (protein-encoding as well as rRNA genes) cluster together, and it is suggested that DNA structure may play a role in the transcription of these highly expressed genes.
...
...