Natural genetic transformation: prevalence, mechanisms and function

Johnsborg, Ola; Eldholm, Vegard; Håvarstein, Leiv Sigve

doi:10.1016/j.resmic.2007.09.004

Cited by 282 publications

(283 citation statements)

References 142 publications

Supporting

Mentioning

278

Contrasting

Unclassified

Order By: Relevance

“…We believe the most plausible scenario to explain this observation is an interdomain lateral gene transfer (LGT) event in the eukaryote-to-prokaryote direction, because integrin β is present in many eukaryote taxa but only in a single known prokaryotic genome. The lack of introns in the Amastigomonas integrin β (in contrast to the other integrins described herein) may have facilitated its integration into a cyanobacterial genome as would the property of natural competence (i.e., the ability to take up DNA) known in Cyanobacteria (54). Even though eukaryote-to-prokaryote LGT events are not as common as LGTs in the opposite direction, other cases have been described in T. erythraeum (55).…”

Section: Discussionmentioning

confidence: 72%

Ancient origin of the integrin-mediated adhesion and signaling machinery

Sebé-Pedrós

Roger

Lang

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

225

276

View full text Add to dashboard Cite

The evolution of animals (metazoans) from their unicellular ancestors required the emergence of novel mechanisms for cell adhesion and cell-cell communication. One of the most important cell adhesion mechanisms for metazoan development is integrinmediated adhesion and signaling. The integrin adhesion complex mediates critical interactions between cells and the extracellular matrix, modulating several aspects of cell physiology. To date this machinery has been considered strictly metazoan specific. Here we report the results of a comparative genomic analysis of the integrin adhesion machinery, using genomic data from several unicellular relatives of Metazoa and Fungi. Unexpectedly, we found that core components of the integrin adhesion complex are encoded in the genome of the apusozoan protist Amastigomonas sp., and therefore their origins predate the divergence of Opisthokonta, the clade that includes metazoans and fungi. Furthermore, our analyses suggest that key components of this apparatus have been lost independently in fungi and choanoflagellates. Our data highlight the fact that many of the key genes that had formerly been cited as crucial for metazoan origins have a much earlier origin. This underscores the importance of gene cooption in the unicellular-to-multicellular transition that led to the emergence of the Metazoa.cell adhesion | lateral gene transfer | metazoan origins | multicellularity

show abstract

Section: Discussionmentioning

confidence: 72%

Ancient origin of the integrin-mediated adhesion and signaling machinery

Sebé-Pedrós

Roger

Lang

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

225

276

View full text Add to dashboard Cite

show abstract

“…(3) The gut is a closed environment with less input of environmental strains due to the bottleneck imposed by stomach acidity. (4) The capability of S. oralis to undergo natural transformation has contributed to increased genome diversity ( Johnsborg et al 2007). …”

Section: Gel Microdroplets Produce Complete Genomesmentioning

confidence: 99%

Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome

Fitzsimons

Novotny

et al. 2013

Genome Res.

View full text Add to dashboard Cite

The majority of microbial genomic diversity remains unexplored. This is largely due to our inability to culture most microorganisms in isolation, which is a prerequisite for traditional genome sequencing. Single-cell sequencing has allowed researchers to circumvent this limitation. DNA is amplified directly from a single cell using the whole-genome amplification technique of multiple displacement amplification (MDA). However, MDA from a single chromosome copy suffers from amplification bias and a large loss of specificity from even very small amounts of DNA contamination, which makes assembling a genome difficult and completely finishing a genome impossible except in extraordinary circumstances. Gel microdrop cultivation allows culturing of a diverse microbial community and provides hundreds to thousands of genetically identical cells as input for an MDA reaction. We demonstrate the utility of this approach by comparing sequencing results of gel microdroplets and single cells following MDA. Bias is reduced in the MDA reaction and genome sequencing, and assembly is greatly improved when using gel microdroplets. We acquired multiple near-complete genomes for two bacterial species from human oral and stool microbiome samples. A significant amount of genome diversity, including single nucleotide polymorphisms and genome recombination, is discovered. Gel microdroplets offer a powerful and high-throughput technology for assembling whole genomes from complex samples and for probing the pan-genome of naturally occurring populations.

show abstract

“…Natural transformation, as well as other modes of HGT (transduction and conjugation), ensures that adaptive evolution in bacterial species competent for transformation is not limited to the selection of slowly accumulating point mutations and genetic rearrangements (Ochman et al, 2000;Redfield, 2001; Thomas and Nielsen, 2005). Retrospective genome sequence analyses demonstrate that recombination following HGT has an important role in shaping bacterial genomes (Johnsborg et al, 2007;Didelot and Maiden, 2010). Bacteria competent for natural transformation have a potential advantage during niche expansion (Levin and Bergstrom, 2000;Ochman et al, 2000) and may, from one generation to the next, respond to abrupt environmental shifts that require genomic changes inaccessible by point mutations.…”

Section: Introductionmentioning

confidence: 99%

Growth phase-specific evolutionary benefits of natural transformation in Acinetobacter baylyi

et al. 2015

View full text Add to dashboard Cite

Natural transformation in bacteria facilitates the uptake and genomic integration of exogenous DNA. This allows horizontal exchange of adaptive traits not easily achieved by point mutations, and has a major role in the acquisition of adaptive traits exemplified by antibiotic resistance determinants and vaccination escape. Mechanisms of DNA uptake and genomic integration are well described for several naturally transformable bacterial species; however, the selective forces responsible for its evolution and maintenance are still controversial. In this study we evolved transformation-proficient and -deficient Acinetobacter baylyi for 175 days in serial transfer cultures where stress was included. We found that natural transformation-proficient populations adapted better to active growth and early stationary phase. This advantage was offset by the reduced performance in the late stationary/death phase. We demonstrate fitness trade-offs between adaptation to active growth and survival in stationary/death phase caused by antagonistic pleiotropy. The presented data suggest that the widely held assumption that recombination speeds up adaptation by rapid accumulation of multiple adaptive mutations in the same genetic background is not sufficient to fully account for the maintenance of natural transformation in bacteria.

show abstract

Natural genetic transformation: prevalence, mechanisms and function

Cited by 282 publications

References 142 publications

Ancient origin of the integrin-mediated adhesion and signaling machinery

Ancient origin of the integrin-mediated adhesion and signaling machinery

Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome

Growth phase-specific evolutionary benefits of natural transformation in Acinetobacter baylyi

Contact Info

Product

Resources

About