uu.seUppsala University Publications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Dynamics of Microbial Genome Evolution
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
2003 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The success of microbial life on Earth can be attributed not only to environmental factors, but also to the surprising hardiness, adaptability and flexibility of the microbes themselves. They are able to quickly adapt to new niches or circumstances through gene evolution and also by sheer strength of numbers, where statistics favor otherwise rare events.

An integral part of adaptation is the plasticity of the genome; losing and acquiring genes depending on whether they are needed or not. Genomes can also be the birthplace of new gene functions, by duplicating and modifying existing genes. Genes can also be acquired from outside, transcending species boundaries. In this work, the focus is set primarily on duplication, deletion and import (lateral transfer) of genes – three factors contributing to the versatility and success of microbial life throughout the biosphere.

We have developed a compositional method of identifying genes that have been imported into a genome, and the rate of import/deletion turnover has been appreciated in a number of organisms. Furthermore, we propose a model of genome evolution by duplication, where through the principle of gene amplification, novel gene functions are discovered within genes with weak- or secondary protein functions. Subsequently, the novel function is maintained by selection and eventually optimized. Finally, we discuss a possible synergic link between lateral transfer and duplicative processes in gene innovation.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis , 2003. , p. 45
Series
Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1104-232X ; 796
Keywords [en]
Bioinformatics
Keywords [sv]
Bioinformatik
National Category
Bioinformatics and Systems Biology
Research subject
Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-3283ISBN: 91-554-5510-7 (print)OAI: oai:DiVA.org:uu-3283DiVA, id: diva2:162314
Public defence
2003-02-21, Linddahlssalen, EBC, Uppsala, 13:00
Opponent
Available from: 2003-01-29 Created: 2003-01-29Bibliographically approved
List of papers
1. Gradients in nucleotide and codon usage along Escherichia coli genes
Open this publication in new window or tab >>Gradients in nucleotide and codon usage along Escherichia coli genes
2000 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 28, no 18, p. 3517-3523Article in journal (Refereed) Published
Abstract [en]

The usage of codons and nucleotide combinations varies along genes and systematic variation causes gradients in usage. We have studied such gradients of nucleotides and nucleotide combinations and their immediate context in Escherichia coli. To distinguish mutational and selectional effects, the genes were subdivided into three groups with different codon usage bias and the gradients of nucleotide usage were studied in each group. Some combinations that can be associated with a propensity for processivity errors show strong negative gradients that become weaker in genes with low codon bias, consistent with a selection on translational efficiency. One of the strongest gradients is for third position G, which shows a pervasive positive gradient in usage in most contexts of surrounding bases.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-90104 (URN)10.1093/nar/28.18.3517 (DOI)110745 (PubMedID)
Available from: 2003-01-29 Created: 2003-01-29 Last updated: 2017-12-14Bibliographically approved
2. Detection of genes with atypical nucleotide sequence in microbial genomes
Open this publication in new window or tab >>Detection of genes with atypical nucleotide sequence in microbial genomes
2002 (English)In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 54, no 3, p. 365-375Article in journal (Refereed) Published
Abstract [en]

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 to the observed mean dinucleotide frequencies of an entire genome, forming a distance measure for each gene. It is found that genes from different genomes can be separated with a high degree of accuracy, according to these distance values. In particular, we address the problem of recent horizontal gene transfer, and how imported genes may be evaluated by their poor assimilation to the host's context biases. By concentrating on the third- and succeeding first position nucleotides, we eliminate most spurious contributions from codon usage and amino-acid requirements, focusing mainly on mutational effects. Since imported genes are expected to converge only gradually to genomic signatures, it is possible to question whether a gene present in only one of two closely related organisms has been imported into one organism or deleted in the other. Striking correlations between the proposed distance measure and poor homology are observed when Escherichia coli genes are compared to Salmonella typhi, indicating that sets of outlier genes in E. coli may contain a high number of genes that have been imported into E. coli, and not deleted in S. typhi.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-90105 (URN)10.1007/s00239-001-0051-8 (DOI)11847562 (PubMedID)
Available from: 2003-01-29 Created: 2003-01-29 Last updated: 2017-12-14Bibliographically approved
3. Gene Import or Deletion: A Study of the Different Genes in Escherichia coli Strains K12 and O157:H7
Open this publication in new window or tab >>Gene Import or Deletion: A Study of the Different Genes in Escherichia coli Strains K12 and O157:H7
2002 (English)In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 55, no 6, p. 734-744Article in journal (Refereed) Published
Abstract [en]

By comparing two strains of Escherichia coli (K12 and O157:H7) with an outgroup of Salmonella and Klebsiella species and analyzing the sets of genes which are present or absent in either of the three groups, we study the gene history of K12, in particular, since the respective divergences of these bacteria. Furthermore, by using a compositional method based on context bias, we evaluate not only recently imported genes but also deleted genes. In addition, we examine recent gene duplications in the two E. coli strains. It is found that turnover of DNA is high in E. coli and, more importantly, that turnover is highest for genes of low GC content. Although levels of import are high, most of the imported genes seem to be "junk" or have poorly understood functions. Nevertheless, selected genes do persist, and may even define some E. coli strains as pathogenic. Our results support the conclusion that some of the pathogenic islands in O157:H7 are likely to have been imported in recent time.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-90106 (URN)10.1007/s00239-002-2369-2 (DOI)12486532 (PubMedID)
Available from: 2003-01-29 Created: 2003-01-29 Last updated: 2017-12-14Bibliographically approved
4. On the nature of gene innovation: Duplication patterns in microbial genomes.
Open this publication in new window or tab >>On the nature of gene innovation: Duplication patterns in microbial genomes.
In: Mol Biol EvolArticle in journal (Refereed) Submitted
Identifiers
urn:nbn:se:uu:diva-90107 (URN)
Available from: 2003-01-29 Created: 2003-01-29Bibliographically approved
5. Duplication is more common among lateral-transfer genes
Open this publication in new window or tab >>Duplication is more common among lateral-transfer genes
Manuscript (Other academic)
Identifiers
urn:nbn:se:uu:diva-90108 (URN)
Available from: 2003-01-29 Created: 2003-01-29 Last updated: 2010-01-13Bibliographically approved

Open Access in DiVA

fulltext(445 kB)1132 downloads
File information
File name FULLTEXT01.pdfFile size 445 kBChecksum MD5
eff02dc3d39f83ca3cfe4ddd1bda07ceceb8007055542c1f3896c7dc0175987c77f31b9a
Type fulltextMimetype application/pdf
Buy this publication >>

By organisation
Molecular Evolution
Bioinformatics and Systems Biology

Search outside of DiVA

GoogleGoogle Scholar
Total: 1132 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

isbn
urn-nbn

Altmetric score

isbn
urn-nbn
Total: 829 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf