Bacterial genes jump to host

Bacteria living within insects, nematodes and other eukaryotes transfer genes into their hosts more often than previously thought, according to a study published online this week in Science.

"This could be a rapid mechanism by which organisms acquire new genes and evolve new features," said John Werren of the University of Rochester in New York, who was a senior coauthor on the study.

The findings may also affect how researchers sequence genomes of eukaryotes, the authors suggest. Bacterial sequences are routinely discarded in such studies in the belief that the data reflect contamination. In fact, coauthor Julie Dunning Hotopp of the J. Craig Venter Institute in Rockville, Md., told The Scientist, "any bacterial sequences they discover may not be the result of contamination, but rather the result of gene transfers."

Geneticists have long debated the extent to which bacterial genes jump to eukaryotes. "Early on in the Human Genome Project, there were suggestions that more than 200 genes in humans were of bacterial origin, but those were later largely discredited, so there's quite a bit of skepticism regarding lateral gene transfer from bacteria to eukaryotes," said Fred Dietrich of Duke University in Durham, N.C., who did not participate in the study.

Werren and his colleagues investigated the question in the bacterium Wolbachia pipientis, a maternally inherited microbe that infects the eggs and sperm of nematodes and at least 20 percent of all insect species. Recent studies have found Wolbachia genes in the genomes of a bean beetle and two nematode species, but those results were also met with skepticism, Dunning Hotopp said.

The researchers compared the bacterium's published genome to the genomes of different species of fruit flies disinfected of Wolbachia. They identified nearly the entire Wolbachia genome on the second chromosome of a Hawaiian fruit fly strain. The bacterium's genes were also seen in Indian, Malaysian and Indonesian strains, although they were absent in US, Mexican and Australian strains. Investigation of 26 other genomes pinpointed Wolbachia inserts in three other insect species and four other nematode species. Potential gene transfers were also detected computationally in three different insect genomes.

"These findings show good evidence of transfer from Wolbachia to its host species," Dietrich told The Scientist.

Whether these genes are functional "remains an open question," noted Werren. "But we've found these kinds of gene transfers are so common, it seems inevitable that some will prove functional."

In the present study, reverse transcription PCR analyses revealed that 2 percent of the Wolbachia genes, or 28 of 1,206 genes studied, were transcribed in disinfected fruit flies, suggesting they do play a role in the host organism. Future studies could analyze whether the genes are differentially transcribed in different organs, or get translated into proteins, Dunning Hotopp said.

Growing strains of flies with or without incorporated Wolbachia genes under stressful conditions such as starvation or heat could also tease out the bacterial genes' function, Werren said, by determining if those genes benefit host survival.

Wolbachia may not be the only bacterium to engage in such extensive lateral gene transfer. "There are a lot of heritable endosymbiotic bacteria in invertebrates that could be good candidates for this process," Nancy Moran at the University of Arizona in Tucson, who was not involved in the study, told The Scientist. One example, she said, may be Carsonella, which has just 180 genes and an 160-kilobase genome, the smallest known in the bacterial world. "It seems to have too few genes to support proper function, so maybe it's transferred genes to its insect hosts."

While this mechanism has been confirmed in invertebrates, it's unclear whether it occurs in vertebrates, said Dunning Hotopp. Heritable lateral gene transfer is unlikely, she noted, because bacteria are not usually found in or near vertebrate germ cells. The process could happen between bacteria and vertebrate somatic cells, she said, but since those genes would not get inherited by offspring, it would be "incredibly difficult to detect or study" even if it is widespread, she said.

Charles Q. Choi
mail@the-scientist.com

Links within this article:

J.C. Dunning Hotopp et al., "Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes," Science, published online August 30, 2007.
http://www.sciencemag.org

John Werren
http://www.rochester.edu/College/BIO/labs/WerrenLab/index.html

Julie Dunning Hotopp
http://www.tigr.org/~jdunning/cv.html

International Human Genome Sequencing Consortium, "Initial sequencing and analysis of the human genome," Nature, February 15, 2001.
http://www.the-scientist.com/pubmed/11237011

S.L. Salzberg et al., "Microbial Genes in the Human Genome: Lateral Transfer or Gene Loss?" Science, June 8, 2001.
http://www.the-scientist.com/pubmed/11358996

S. Bunk, "Lateral thinking," The Scientist, July 9, 2001.
http://www.the-scientist.com/article/display/12497

Fred Dietrich
http://www.genome.duke.edu/people/faculty/dietrichM

D. Secko, "A sleek genome, except for all the junk," The Scientist, April 12, 2004.
http://www.the-scientist.com/article/print/14594

T. Tom, "Bacterial offender in parasitic infection," The Scientist, March 13, 2002.
http://www.the-scientist.com/article/display/20268

N. Kondo et al., "Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect," PNAS, October 29, 2002.
http://www.the-scientist.com/pubmed/12386340

K. Fenn et al., "Phylogenetic Relationships of the Wolbachia of Nematodes and Arthropods," PLoS Pathogens, October 13, 2006.
http://www.the-scientist.com/pubmed/17040125

F.D. Bushman, "Evolutionary teamwork," The Scientist, May 10, 2004.
http://www.the-scientist.com/2004/5/10/33/1/

Nancy Moran
http://eebweb.arizona.edu/faculty/moran

A. Nakabachi et al., "The 160-kilobase genome of the bacterial endosymbiont Carsonella,"
http://www.the-scientist.com/pubmed/17038615