By Philip Lee Williams
University of
Georgia

Plasmids, small independently replicating DNA segments found
mostly in bacteria and archaebacteria, are molecular trucks,
buses and taxicabs. Different plasmids can spread resistance
against antibiotics, turn a benign bacterium into a virulent
pathogen or degrade environmental contaminants.

By transferring genes among them, plasmids enable the ongoing
evolution of these tiny and ever-present microbes.

Now, the National Science Foundation has awarded a grant of
$1.1 million to a team of researchers from the University of
Georgia to study how plasmids work in the natural bacterial
world, especially on hosts important in agricultural, clinical
or ecological processes.

“This is the first major grant awarded by any federal agency
specifically for genomic studies of these ubiquitous mobile
genetic elements,” said UGA microbiologist and team leader Anne
Summers.

Others on the UGA team from the department of microbiology
include Tim Hoover, Jan Mrazek, Joy Peterson, Barny Whitman and
Juergen Wiegel. Also on the team from the Franklin College of
Arts and Sciences are Mary Ann Moran, department of marine
sciences, and Michael W. Adams, department of biochemistry and
molecular biology. Other colleagues include Margie Lee from the
department of population medicine in the College of Veterinary
Medicine, and Timothy Denny, the department of plant pathology
in the College of Agricultural and Environmental Sciences.

Only the end products of plasmids’ work can be observed by
using the sequenced chromosomes of bacteria, all of which have
been found, surprisingly, to contain a large proportion of
genes not native to the bacterium. Still, the plasmids
themselves had often been lost from sequenced bacterial strains
that had long been propagated in laboratories in conditions
unlike their natural habitats.

The new project will study plasmids isolated directly from
freshly obtained and carefully preserved bacteria and
archaebacteria. This is the first project to examine natural
isolates in a wide range of such otherwise well-studied
prokaryotes, the domain of organisms lacking a cell nuclear
membrane.

Many prokaryotes are known to transfer some of their genes to
other such simple microbes, and a few even transfer DNA into
specific plants. Transferred genes may be scattered throughout
the chromosomes of their new hosts, but many prokaryotic
cellular chromosomes have patches or “islands” of such foreign
DNA that have traces of well-known mobile genetic elements,
including plasmids. Unfortunately, little of the genetic
information from these elements has been studied, and the new
project will remedy that.

The Summers lab recently overcame a major bottleneck in
determining the DNA sequence of plasmids by devising a fast,
cheap and easy method of purifying high-quality DNA from
individual large plasmids.

“Large plasmids are the 18-wheelers of horizontal gene transfer
but presently comprise less than 20 percent of all sequenced
plasmids because traditional methods of preparing them require
expensive instruments and toxic reagents,” said Summers.

Using this new plasmid preparation method, Summers and her
students found that large plasmids are 10-fold more prevalent
than previously documented in standard reference collections of
the important pathogens Salmonella and E. coli.

The researchers will use the new method to screen plasmid
profiles from 20-25 wild isolates each provided by UGA
colleagues who work on marine bacteria, heat-loving and extreme-
heat-loving bacteria, and plant and animal pathogens, among
other things.

“UGA is unique in the U.S., perhaps in the world, in having
expertise in such a wide range of diverse prokaryotes as well
as in plasmid biology,” said Summers.

Since this is the first such study that will examine these
plasmids in freshly isolated prokaryotes, it could change the
perceptions of these cellular components among those who study
them. There’s another important aspect of the grant, too,
Summers notes.

“The project includes graduate and undergraduate components
designed to give aspiring scientists an appreciation for the
significance of horizontal gene transfer,” she said. “They will
gain hands-on experience with both bench and computer analyses
of these phenomena.”

Undergraduates from outside UGA will also join in all stages of
the process during eight-week research projects available each
summer during the three-year period of the award.