Because VirE2 was shown to be important
(2004) Definition of a bac- Pre-exisƟng
for protecting T-strands in the plant [4],
Li et al. investigated the integrity of T-DNA
integrated into the Arabidopsis genome fol-
lowing transformation by VirE3 proficient or
virE3[25_TD$IF] mutant Agrobacterium strains. Inte-
grated T-DNA molecules delivered from the
virE3 mutant Agrobacterium strain had
more extensive deletions at their 30 ends,
implying that a lack of VirE3 protein resulted
in less protection of T-strands by VirE2.
Taken together, these results suggest
that VirE3 protein, localized in the plant
plasma membrane, serves as an anchor
for secreted VirE2 protein that, in turn,
can bind incoming VirD2/T-strands.
Thus, VirE3 may serve as a nucleation
site to bring together the single-strand
DNA binding protein VirE2 with the
incoming single-strand T-DNA (Figure 1).
As the authors point out, it is not clear
how VirD2/T-DNA/VirE2 complexes,
once formed on the plant plasma mem-
brane, are released into the cytoplasm. Li
et al. [7] suggest that the plant AP-2
complex may interact with VirE2, releas-
ing VirE2 (and by implication, VirD2/T-
strand/VirE2 complexes) into clathrin
coated vesicles via endocytosis. The
AP-2 complex may thus compete with
VirE3 for VirE2 interaction, releasing T-
complexes into the cell for their journey
to the nucleus.
1
Department of Biological Sciences, Purdue University,
West Lafayette, IN, USA
*Correspondence: gelvin@purdue.edu (S.B. Gelvin).
https://doi.org/10.1016/j.tim.2018.10.003
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Figure 1. A Scheme for Classifying Different
Types of Pollutant. Humans drive the spread of
pollutants, which are either pre-existing or have
novel/anthropogenic origins. These pollutants can
Forum be further divided into finite pollutants, whose con-
centrations do not increase in the environment; and
Pollutants That replicative pollutants, which have the potential to
Replicate: Xenogenetic
exponentially increase in abundance. Replicative pol-
lutants can persist indefinitely, invade new locations
DNAs
far from the original point of release, and can evolve in
unpredictable ways. The different classes of pollu-
tants illustrated here can interact, since the classes
M.R. Gillings ,1,* M. Westoby,1 of finite pollutants can drive the dispersal and increase
and T.M. Ghaly1 the abundance of replicative pollutants.
fundamental properties (Figure 1). We
Pollution is the dissemination of include two novel kinds of pollutant, distin-
material that has harmful effects. guished by their ability to replicate: invasive
Mobile DNA elements and antibi- species; and the mobile DNA elements that
otic-resistance genes are being are selected and disseminated as a con-
disseminated into the environ- sequence of human activities.
ment via human activity, and are
increasingly being viewed as seri- Conventional pollutants are naturally
ous pollutants. These pollutants occurring materials whose distribution
differ from conventional contami- or abundance has been changed by
human activity. Crude oil, nitrates, phos-
nants in important ways: they can
phates, and greenhouse gases fall into
replicate, and they can evolve.
this category. Xenobiotic pollutants are
synthetic chemical compounds and
Pollutants in the Environment radioisotopes that originate solely via
Pollution adversely influences ecosystem human agency (Figure 1). The environ-
function, affecting seven of the nine plane- mental residence of both conventional
tary boundaries that are tipping points for and xenobiotic pollutants is determined
human welfare [1]. Understanding pollut- by their half-lives.
ant dynamics and interactions is a key step
towards management. We have con- New Classes of Pollutant
structed a scheme for classifying different There is an emerging type of pollutant that
pollutant types, based on their is analogous to xenobiotic compounds.
Trends in Microbiology, December 2018, Vol. 26, No. 12 975
 Box 1. Xenogenetic DNA
Xenogenetic DNA describes DNA molecules with a recent origin, and whose assembly and dissemination has been driven by human activity. The term was conceived
as an analogue of the term ‘xenobiotic’, these being chemical compounds synthesized by humans, and that were not present on the planet prior to human industrial
activity. Likewise, xenogenetic DNA elements are mosaic gene assemblies that were not present in biological systems prior to the Industrial Revolution. Human use of
antimicrobial compounds and heavy metals after this time provided the selective forces to sequentially assemble resistance determinants into complex, mosaic DNA
molecules containing multiple resistance genes. These same selective forces also favoured xenogenetic DNAs that could recruit mobile DNA elements such as
plasmids, transposons, and integrons. These complex assemblies of genes from different taxa would never have been assembled but for human activity.
Xenogenetic elements exhibit similar environmental profiles to xenobiotic pollutants: they are increasing in structural complexity and diversity; they are disseminated
by human activity; they are recalcitrant pollutants of environmental compartments; and their concentration in these compartments is increasing. The definition of
xenogenetic DNAs also extends to genetically modified organisms and synthetic genomes, although these are not necessarily pollutants.

These we call xenogenetic DNAs (Box 1).
These DNA elements most often present
as novel rearrangements of existing genes,
assembled from many different taxa. They
are commonly composed of resistance
genes and the diverse mobile DNA ele-
ments that aid their dissemination. Their
novelty lies in the assembly of diverse resis-
tance genes, insertion elements, and
transposons into tightly linked regions of
DNA that are often themselves mobile, by
virtue of location on plasmids or other con-
jugative elements. Xenogenetics are
increasingly being treated as pollutants
[2]. These DNAs arise through human
attempts to control bacterial growth, cou-
pled with the capacity of bacteria to accu-
mulate genes for resistance to such
attempts. Sequential exposure to different
selective agents, such as heavy metals,
disinfectants, and antibiotics, drives
sequential acquisition of similarly diverse
resistance determinants. This leads to de
novo assembly of mobile DNA molecules
that contain a mosaic of DNA modules,
each with diverse phylogenetic origins [3].
These DNAs are xenogenetic because
they would never have been assembled
but for the sustained selection pressures
imposed by humans [4]. While multiresist-
ance elements are the clearest example
of xenogenetics, agricultural, medical,
and industrial practices all offer opportu-
nities for de novo assembly of new gene
combinations in mobile DNAs. Artificial
constructs used during genetic modifica-
tion of plants and microorganisms are
also a form of xenogenetic DNA, although
not necessarily a pollutant. The ultimate
xenogenetic DNAs are entire synthetic Waste streams that disseminate bacteria
genomes [5]. carrying xenogenetic DNAs often also con-
tain antibiotics, disinfectants, and heavy
For pollutants like xenogenetic DNAs, metals. This provides selection pressure
local abundance is determined by the for xenogenetics to be retained, and to
rates of release, transport, and replica- spread into new cell lineages. Conse-
tion. Invasive species have similar char- quently, both interactions between different
acteristics (Figure 1) in that their xenogenetic DNAs, and the selection
distribution and abundance has been imposed by conventional pollutants, serve
vastly expanded by humans. Invasives to increase the diversity, distribution, and
can also be considered as pollutants, abundance of these elements. This amal-
since they have significant environmental gam of interactive selection and recombi-
effects. Both translocated species and natorial mechanisms did not occur in natural
xenogenetic elements can increase in systems before the advent of the Anthro-
abundance long after even an initially pocene [4,9].
small pollution event (Figure 1). However,
xenogenetic elements in particular repre- These examples demonstrate the ongo-
sent a new kind of biological entity, with a ing potential for unanticipated synergies
recent origin and unusual properties. between different types of pollution.
Some interactions are well known, such
Emergent Properties and as nitrogen and phosphorus pollution
Interactions promoting the spread of invasive weeds.
Xenogenetic DNAs carry multiple genes More recent examples include the mega-
that confer diverse traits, physically linked rafting of exotic species on marine plas-
to different families of mobile elements. tics and fiberglass [10].
Interactions between these genetic mod-
ules allow xenogenetic DNAs to generate Survival and dissemination of xenoge-
their own diversity via combinatorial netic elements is promoted by each of
assembly and transposition [6,7], and the other three pollutant types illustrated
thus they continue to evolve. Because in Figure 1. Heavy metals, antibiotics
xenogenetic DNAs confer multiple adap- (both natural and synthetic), and other
tive traits, exposure to any one selective xenobiotic compounds can promote the
agent coselects for all the component selection and replication of xenogenetic
genes via hitch-hiking, and promotes elements. Humans, agricultural animals
the survival of any mobile DNAs associ- and other non-native species disseminate
ated with the element [8]. Competition mobile DNAs around the globe (as can
between xenogenetic DNAs then gener- native species), and act as microcosms
ates second-order rounds of selection for for the selection and fixation of xenoge-
increases in stability, horizontal transmis- netic elements. These interactions help
sion rate, and host range. to explain the global scale and high levels

976 Trends in Microbiology, December 2018, Vol. 26, No. 12

of pollution with antibiotic-resistance potentially leading to a decline in the Whatever direction we take, these pollu-
genes [11]. abundance of cells that carry them. tants do not respect geopolitical bound-
aries. Like other environmental crises,
Concluding Remarks: Managing Before becoming invasive, exotic spe- they need global action.
Pollutants That Replicate cies are often present at very low levels. 1
Department of Biological Sciences, Macquarie University,
In the case of replicating and evolving Local adaptation or some specific trigger Sydney NSW 2109, Australia
pollutants, we might apply ecological may be needed for invasiveness. Xeno-
and evolutionary principles to their con- genetic DNAs form de novo, and there- *Correspondence:
michael.gillings@mq.edu.au (M.R. Gillings).
trol. In particular, there is a strong poten- fore originate as single DNA molecules.
https://doi.org/10.1016/j.tim.2018.08.003
tial for applying strategies developed for There may be thousands of such mole-
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