INSIGHTS | PERSPECTIVES
Argonaute proteins have emerged as the key effectors in virtually all eu- karyotic small RNA–mediated gene silencing pathways (1). Central to all their activities is their association with the small guide RNAs that al-
low them to recognize through sequence
complementarity, and in some cases also
cleave, cellular transcripts.
Curiously, Argonaute-like proteins are
also encoded by many bacteria and archaea
(2) (see the first figure), which apparently
do not have RNA interference (RNAi)–based
silencing systems. Hints about possible
functions came from the Argonaute of the
bacterium Aquifex aeolicus, which showed
a preference for a small DNA rather than
an RNA guide in transcript cleavage assays
(3). Yet subsequent structural work with
eukaryotic Argonautes continued to bolster the RNA guide–RNA target model (4),
and eclipsed research into the putative alternative functions of their odd prokaryotic
This situation has now been rectified by
two recent studies, from Olovnikov et al. (5)
and Swarts et al. (6), that have discovered a
novel Argonaute target in microbes: foreign
DNA. Analyzing the nucleic acids bound to
the Argonautes of the unrelated bacteria
Rhodobacter sphaeroides (5) and Thermus
thermophilus (6), both groups observed a
strong enrichment of short DNA fragments
from plasmids, common extrachromosomal
elements that can easily be transferred be-
tween bacteria. Physiologically, these bacte-
rial Argonautes were shown by both teams
to restrict the acquisition and maintenance
of new plasmids, which suggests that they
may function as a general surveillance sys-
tem to protect their host bacteria from par-
asitic DNA. Indeed, regions of foreign DNA
in the chromosome (such as transposons
and prophage genes) also seem to be se-
lectively targeted. As such, the Argonautes
of R. sphaeroides and T. thermophilus add
to a growing list of mechanisms—ranging
from restriction modification enzymes to
the recently discovered CRISPR/Cas sys-
tems—that collectively help bacteria to fend
off unwanted or invasive DNA. Intriguingly,
because the appearance of these bacterial
Argonautes likely predated their eukary-
otic counterparts, genome defense against
invading DNA may constitute an ancient
function of Argonautes that preceded their
recruitment to RNA-based gene silencing.
Things become more complex when considering the details of the underlying mechanism of the two bacterial Argonautes (see the
second figure). The R. sphaeroides protein
(RsAgo) (5) associates with two classes of
nucleic acids: a class of 15- to 19-nucleotide
RNAs that originate from many cellular transcripts, and a class of 22- to 24-nucleotide
single-stranded DNAs that display complementarity to the small RNAs. Analysis of
these fragments both in R. sphaeroides and
upon expression of RsAgo in the heterologous
host Escherichia coli suggest that the small
RNAs, perhaps originating from degraded
mRNAs, act as guides for RsAgo (they have a
strong bias for U at the first position, like the
guide RNAs of some eukaryotic Argonautes),
and the small DNAs are the remnants of
cleaved targets. How the cleavage occurs is
unclear; RsAgo is inactive as a slicing nuclease because critical residues are mutated (5),
and a suitable in vitro assay to validate the
A bacterial seek-and-destroy
system for foreign DNA
By Jörg Vogel
Bacterial argonaute proteins
defend the cell against exogenous DNA
RNA Biology Group, Institute for Molecular Infection Biology,
University of Würzburg, D-97080 Würzburg, Germany. E-mail:
firstname.lastname@example.org I L L U
Structure of the T. thermophilus Argonaute protein
bound to guide DNA and target DNA, according to (7).
processing can be done routinely. Given that
the study would only report individuals with
resistance to disease, not generalized risks of
disorders across spectrums of disease, both
the regulatory and ethical requirements
would be reduced.
A resilience project (see the figure) approach helps shift thinking on treating disease. Rather than developing therapies that
modify symptoms or the consequences of
inherited diseases, a systematic search for
resilience factors will change the focus in
ways that prevent or modify the course of
diseases. This should initially be easier for
single-gene Mendelian childhood diseases,
but emerging network approaches that define clusters of genes that drive a disease
(such as diabetes, cancer, and Alzheimer’s
disease) could eventually be amenable to
The resilience approach (see the figure)
can well complement emerging eforts to
follow well individuals longitudinally (15)
and to identify and characterize human
“knockouts” (people lacking specific genes)
(16, 17) by more rapidly targeting (in a large
number of individuals and at relatively low
cost) a specific set of genes that harbor what
are thought to be completely penetrant mutations that cause catastrophic disease, to
find people who should have gotten sick,
but did not. Achieving the greatest degree
of success across all of these types of eforts
will require collating and making publicly
accessible the data collected in each study.
The focus on genetic and environmental
factors that ofer protection against disease
as opposed to putting you at risk for disease
may also help engage a public that is more
participatory in sharing their insights and
data to help others. ■
REFERENCES AND NOTES
1. P. D. Stenson et al., Curr. Protoc. Bioinformatics ,
Chapter 1: Unit 1.13 (2012).
2. D. Welter et al., Nucleic Acids Res. 42,D1001(2014).
3. B. W. Ramsey et al., N. Engl. J. Med. 365, 1663 (2011).
4. J. L. Hartman 4th, Proc. Natl. Acad. Sci. U.S.A.104,
5. J. L. Hartman 4th et al., Science291, 1001 (2001).
6. J. L. Hartman 4th, N. P. Tippery, Genome Biol. 5, R49
7. R. J. Louie et al ., Genome Med. 4, 103 (2012).
8. P. R. Gorry et al ., Lancet 359, 1832 (2002).
9. G. Galarneau et al ., Nat. Genet. 42, 1049 (2010).
10. J. Cohen et al ., Nat. Genet. 37, 161 (2005).
11. J. Flannick et al., Nat. Genet. 46, 357 (2014).
12. D. N. Cooper et al ., Hum. Genet. 132, 1077 (2013).
13. P. R. Sosnay et al ., Nat. Genet. 45, 1160 (2013).
14. G. Iyer et al ., Science 338, 221 (2012).
15. L. Hood, N. D. Price, Sci. Transl. Med. 6, 225ed5 (2014).
16. J.Kaiser, Science 344,687(2014).
S. H. F. is a principal investigator of The Resilience Project (www.