Understanding Genome Evolution with the Help of Plasmid Gene Pools

The Science

Understanding how genomes of organisms change over time underlies much of biology and its practical applications. Plasmids are DNA molecules that can replicate independently of chromosomal DNA in a cell. This enables organisms to “collect” and move genes to other organisms through lateral gene transfer (like “genomic email”) and contributes to prokaryotic genome evolution. To understand the depth and breadth of the prokaryote plasmid gene pool, scientists have isolated, sequenced, and compared plasmids from two wastewater sludge communities. The authors studied the “mobilome,” a name for the mobile elements in a community genome, by specifically targeting, separating, and purifying closed circular supercoiled DNAs (CCSD) originating from the plasmids. They found that the plasmids isolated from the sludge wastewater microbial communities turned out to contain primarily uncharacterized coding sequences. Besides lending credence to the idea that plasmids are crucial to genome innovation, evolution, and community structure and functioning, this study generated a large library of new genes involved in wastewater sludge degradation and processing that could enable new approaches to microbial wastewater cleanup. The study was enabled by the DOE Joint Genome Institute.

The Impact

Researchers describe for the first time in great depth plasmid replicons from two complex communities, recover a number of fully closed replicons and show substantial difference in plasmid gene content as a result of selective conditions at the community level. This study shows the technical possibilities to conduct specific plasmid metagenome analysis without culturing bias, and to study system level differences in the mobilome of microbial communities.

Summary

Plasmids have long been recognized as an important driver of DNA exchange and genetic innovation in prokaryotes. The success of plasmids has been attributed to their independent replication from the host’s chromosome and their frequent self-transfer.

Functionally, the two metagenomes strongly differed in several ways, including a greater abundance of genes for carbohydrate metabolism in the industrial and of general defense factors in the household activated sludge plasmid metagenome. This suggests that plasmids not only contribute to the adaptation of single individual prokaryotic species, but of the prokaryotic community as a whole under local selective conditions.

BER Program Manager

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]

References

Sentchilo, V., A. P. Mayer, L. Guy, R. Miyazaki, S. G. Tringe, K. Barry, S. Malfatti, A. Goessmann, M. Robinson-Rechavi, and J. R. van der Meer. 2013. “Community-Wide Plasmid Gene Mobilization and Selection,” The ISME Journal, DOI: 10.1038/ismej.2013.13.