RESEARCH ARTICLE SUMMARY
◥PLASMID EVOLUTION
Unexpected conservation and global transmission
of agrobacterial virulence plasmids
Alexandra J. Weisberg, Edward W. Davis II, Javier Tabima, Michael S. Belcher, Marilyn Miller,
Chih-Horng Kuo, Joyce E. Loper, Niklaus J. Grünwald, Melodie L. Putnam, Jeff H. Chang*
INTRODUCTION:Plasmids are autonomously
replicating, nonessential DNA molecules that
accelerate the evolution of many important
bacterial-driven processes. For example, plas-
mids spread antibiotic resistance genes, which
are a pressing problem for human and animal
health. Plasmids can also encode complex traits
that allow bacteria to interact intimately with
eukaryotes. Acquisition of an oncogenic tumor-
inducing (Ti) or root-inducing (Ri) plasmid
by saprophytic soil agrobacteria changes them
into pathogens capable of genetically trans-
forming and causing disease in a broad range
of plant species.
Plasmids are also biotechnology tools that
can advance our understanding of life. They
can be used to generate organisms with un-
usual traits and innovative applications. The
potential for using oncogenic plasmids to
accelerate research was recognized early in
their discovery. Along with strains of agro-
bacteria, disarmed plasmids are mainstays
as tools in plant biology and plant genetic
engineering.
RATIONALE:Inferring evolutionary relation-
ships is foundational for classifying plas-
mids, accurately assessing the influence of
plasmids on disease outbreaks, developing
appropriate strategies for mitigating disease,
and expediting efforts to leverage plasmid
diversity for biotechnology. However, such
research is complicated because plasmids
consist of diverse structural variants and are
extraordinarily dynamic, modular molecules
thatcanbereshuffledandbroadlytransmitted
horizontally.
We focused on oncogenic plasmids of agro-
bacteria because of their important roles in
causing disease and as biotechnology tools.
Two genomic datasets were developed. One
consisted of diverse, broadly sampled his-
torical strains and was intended to serve as
the basis for an evolutionary framework. The
other consisted of contemporaneous strains
hierarchically sampled from managed plant
production sites, for the purpose of cali-
brating epidemiology methods. The datasets
were combined to identify epidemiological
patterns.RESULTS:We combined analyses of chromo-
somal ancestry and plasmids to uncover their
contributions and accurately model the global
spread of disease. Phylogenetic, genomic, and
time tree analyses of thousands of strains from
the Rhizobiales order yielded a robust phylo-
genetic history of agrobacteria. We developed
a strategy that uses phylogenetic and network
approaches as well as different scales of ge-
netic information to infer the evolution of
diverse oncogenic plasmids. By combining
results, we uncovered global epidemiological
patterns supporting movement of pathogens
clonally and plasmids horizontally in space
and time.This study has three major findings: (i)
Lineages of agrobacteria emerged indepen-
dently and at different times from within a
genus-level group that also circumscribes
multiple lineages of rhizobia. (ii) Agrobac-
terial Ti and Ri plasmids are descended from
onlysixandthreeline-
ages (types), respectively.
Few evolutionary events
are sufficient to explain
the relationships observed
among types. Each type
is subject to different
pressuresandshowsdifferentdegreesof
within-group variation, but their evolution
is nonetheless guided by similar principles.
The extent of modularity is high, and genes
and functional modules are frequently re-
shuffled via recombination within conserved
loci. Yet plasmid diversification is nonethe-
less constrained by the spatial structure of
loci that interact genetically. (iii) Transmis-
sion of oncogenic plasmids, especially within
agricultural settings, promotes the massive
spread of disease.CONCLUSION:Our strategy for inferring the
evolution and transmission of virulence plas-
mids has potential applications in plant and
human or animal health and food safety, as
well as for understanding the ecology and
evolution of other plasmid-mediated pro-
cesses such as mutualistic symbioses. In ad-
dition, this strategy can be applied to study
other mobile and modular elements, such as
integrative conjugative elements and path-
ogenicity or symbiosis islands. We have shown
that plasmids once viewed as too diverse to be
classified have distinct lineages, and that ac-
curate modeling of the spread of disease can
be accomplished by robustly defining their
evolutionary relationships.
▪RESEARCH
Weisberget al.,Science 368 , 1080 (2020) 5 June 2020 1of1
The list of author affiliations is available in the full article online.
*Corresponding author. Email: [email protected]
Cite this article as A. J. Weisberget al.,Science 368 , eaba5256
(2020). DOI: 10.1126/science.aba5256Combined genomic analyses
of chromosomal and plasmid
identities to model disease
spread.Genomic data from
hundreds of strains of
agrobacteria were parsed
and analyzed to infer
the evolutionary histories
of chromosomes and
oncogenic Ti and Ri plasmids.
The data were overlaid to
uncover the roles of bacteria
and plasmids in the global
spread of disease.
ON OUR WEBSITE◥Read the full article
at https://dx.doi.
org/10.1126/
science.aba5256
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