Hamiltonella defensa, genome evolution of protective
bacterial endosymbiont from pathogenic ancestors
Patrick H. Degnana,1, Yeisoo Yub, Nicholas Sisnerosb, Rod A. Wingb, and Nancy A. Morana
aDepartment of Ecology and Evolutionary Biology,bArizona Genomics Institute, University of Arizona, Tucson, AZ 85721
Edited by Edward F. DeLong, Massachusetts Institute of Technology, Cambridge, MA, and approved April 14, 2009 (received for review January 7, 2009)
Eukaryotes engage in a multitude of beneficial and deleterious
interactions with bacteria. Hamiltonella defensa, an endosymbiont
of aphids and other sap-feeding insects, protects its aphid host
from attack by parasitoid wasps. Thus H. defensa is only condi-
tionally beneficial to hosts, unlike ancient nutritional symbionts,
such as Buchnera, that are obligate. Similar to pathogenic bacteria,
H. defensa is able to invade naive hosts and circumvent host
immune responses. We have sequenced the genome of H. defensa
to identify possible mechanisms that underlie its persistence in
healthy aphids and protection from parasitoids. The 2.1-Mb ge-
nome has undergone significant reduction in size relative to its
closest free-living relatives, which include Yersinia and Serratia
species (4.6–5.4 Mb). Auxotrophic for 8 of the 10 essential amino
by Buchnera. Despite these losses, the H. defensa genome retains
more genes and pathways for a variety of cell structures and
processes than do obligate symbionts, such as Buchnera. Further-
more, putative pathogenicity loci, encoding type-3 secretion sys-
tems, and toxin homologs, which are absent in obligate symbionts,
are abundant in the H. defensa genome, as are regulatory genes
that likely control the timing of their expression. The genome is
also littered with mobile DNA, including phage-derived genes,
plasmids, and insertion-sequence elements, highlighting its dy-
namic nature and the continued role horizontal gene transfer plays
in shaping it.
Acyrthosiphon pisum ? facultative endosymbiont ? mobile DNA ?
to mutualism (1, 2). Genome sequencing of noncultivatable
parasitic bacteria has revealed possible mechanisms responsible
for reproductive manipulations (3–5), whereas genomes of ob-
ligate mutualists of ants, aphids, psyllids, tsetse flies, and sharp-
shooters have documented biosynthetic abilities important to
host nutrition (6–10). Heritable endosymbionts that protect
their hosts from parasites and pathogens are increasingly being
recognized as common. Because they are occasionally trans-
ferred horizontally, sometimes between distantly related species,
these symbionts provide a conduit for the transfer of highly
adaptive and stably inherited traits (resistance and defense)
between host species. So far, no such defensive symbiont has
been studied using genome sequencing.
Hamiltonella defensa, a gamma-proteobacterium, is a mater-
nally transmitted defensive endosymbiont found sporadically in
sap-feeding insects, including aphids, psyllids, and whiteflies
(11–13). In pea aphids (Acyrthosiphon pisum), H. defensa can
block larval development of the solitary endoparasitoid wasps
Aphidius ervi and Aphidius eadyi, rescuing the aphid host (14–
16). The reduction in aphid mortality is variable among H.
defensa strains and is correlated to the presence of a temperate,
lambda-like bacteriophage APSE, which infects H. defensa (17–
20). H. defensa occurs sporadically in A. pisum and is beneficial
only when parasitoids are present (21). Consequently, infection
frequencies increase under strong parasitoid pressure but de-
crease when parasitoids are absent. H. defensa and APSE can
nsects host a wide diversity of noncultivable bacteria, which
have important ecological phenotypes ranging from parasitism
also be transmitted horizontally either intraspecifically [e.g.,
sexually (22)] or interspecifically (12, 17). Moreover, protection
by H. defensa has been shown to be transferable between
distantly related aphid species (19).
Although H. defensa confers protection, it also exhibits many
novel hosts, and a preliminary survey of its genome content
showed that it contains many pathogenicity factors related to
host invasion (18). APSE strains encode toxins, including cyto-
lethal distending toxin and Shiga-like toxin, intimating a role of
horizontal gene transfer (HGT) in modulating the protection
conferred by H. defensa (18, 23).
To shed light on the interactions of H. defensa, its insect hosts,
bacteriophage, and invading parasitoids, we have sequenced the
H. defensa genome from a strain previously shown to confer
protection to A. pisum (16). The H. defensa genome combines
mechanisms known from both symbiotic and pathogenic bacte-
Results and Discussion
Both general and specific features of the H. defensa genome
reflect its lifestyle as a host-restricted, mutualist symbiont that
invades host cells. The moderately reduced genome consists of
a 2,110,331-bp circular chromosome and a 59,034-bp conjugative
plasmid with average G ? C contents of 40.1% and 45.3%,
respectively (Table 1, Fig. 1). The chromosome contains a
canonical origin of replication (oriC) situated between mnmG
(gidA) and mioC. Of the 2,100 predicted coding sequences
(CDS), 1,665 (79%) have homologs present in GenBank. Most
remaining unique hypothetical proteins (75%) are ?100 aa
(AA), making their identity as true genes equivocal. In addition,
188 readily identifiable pseudogenes were present; this number
is similar to that in Escherichia coli genomes (24).
Phylogenies based on single loci place H. defensa in the
Enterobacteriaceae, but are otherwise poorly resolved (12, 25).
In analyses of multigene alignments of conserved, single-copy,
core proteins, H. defensa and another aphid endosymbiont,
Regiella insecticola, consistently fell within a clade containing
these nodes are elevated by removing Hamiltonella and Regiella
from analyses, suggesting that the long branches reduce confi-
dence. Regardless, the phylogeny suggests that Hamiltonella and
Regiella form a lineage distinct from the entomopathogenic
nematode symbionts Photorhabdus and Xenorhabdus, and from
the sequenced tsetse symbiont Sodalis glossinidius.
Author contributions: P.H.D., Y.Y., R.A.W., and N.A.M. designed research; P.H.D. and N.S.
performed research; P.H.D. analyzed data; and P.H.D. and N.A.M. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
database (accession nos. CP001277, CP001278).
1To whom correspondence should be addressed. E-mail: email@example.com.
This article contains supporting information online at www.pnas.org/cgi/content/full/
June 2, 2009 ?
vol. 106 ?
no. 22 ?
Complementarity of Host and Symbiont Metabolisms. The metabo-
lism of H. defensa inferred from the genome confirms that it is
host-dependent. It is an aerobic heterotroph that shares its
central metabolic machinery with that of most free-living enteric
bacteria (Fig. 3). Unlike most endosymbionts, Hamiltonella is
also capable of the fermentation of pyruvate to lactate (pykF,
ldhA) and acetyl-CoA to acetate (pta, ackA). Thus, H. defensa
appears able to produce energy even under oxygen-limiting
Biosynthesis of essential amino acids and vitamins is a hall-
mark of nutritional endosymbionts, exemplified by Buchnera.
Based on its gene set, H. defensa synthesizes only 2 essential and
7 nonessential amino acids, but can make most essential vitamins
except thiamine (B1) and pantothenate (B5) (see Fig. 3). Unlike
Buchnera, which lacks most active transport mechanisms, H.
defensa likely acquires missing building blocks via substrate-
The essential amino acids that H. defensa requires are largely
lacking from the insect diet of phloem sap (26). Our data suggest
that both H. defensa and the host insect rely on Buchnera, the
required endosymbionts that synthesize essential amino acids
from this limited carbon and nitrogen source (9, 10). Except for
the glutamate/aspartate transporter (gltP), the H. defensa ge-
genes. This suggests that, unlike S. glossinidius, which very
recently became host-restricted (27, 28), H. defensa has had a
long-term association with insects (Table S1) consistent with
previous evidence (12).
Putative Virulence Mechanisms Involved in Symbiosis. H. defensa’s
abilities to invade novel insect hosts, to persist in them, and to
kill their endoparasites are likely dependent on the presence of
numerous loci commonly involved in pathogenicity (18). Our
results give a complete inventory of these pathogenicity or
symbiosis factors and indicate that some of these loci have been
rearranged or disrupted. For example, H. defensa carries two
Table 1. Comparison of H. defensa genome features to those of relevant Enterobacteriaceae
B. aphidicola APS
H. defensa 5AT
S. glossindius E. coli K12
Y. pestis CO92
Total G ? C (%)
Total predicted CDS
Coding density (%)
Average CDS size (bp)
CDS, coding sequences.
(black), and putative virulence loci (pink); (v) mobile genetic elements IS elements (light green), group II introns (dark green), phage (blue), or plasmid (purple)
islands. Lines connect repeated phage (blue) or plasmid (purple) blocks that are on the same strand (light) or inverted (dark). Asterisk indicates the location of
the APSE prophage and the dashed line in (ii) is the location of the incomplete genome juncture. (B) Schematic of plasmid pHD5AT: outer ring (i) coordinates
in kb; (ii) predicted coding sequences (CDS) of plasmid origin (purple), hypothetical (yellow), pseudogene (gray), IS elements (light green), and group II introns
(dark green); inner ring (iii) G ? C skew of hexamers. (C) Graph of primary functional roles for chromosomal CDS and pseudogenes (stippled).
Genomic characteristics of H. defensa str. 5AT. (A) H. defensa genome schematic; rings starting from outer to innermost: (i) coordinates in kb; (ii) G ?
www.pnas.org?cgi?doi?10.1073?pnas.0900194106Degnan et al.
type-3 secretion systems (T3SS), which are similar in gene
content and order to T3SS in Salmonella typhimurium LT2
(SPI-1, SPI-2) (18). These protein translocation systems are
normally used by pathogens to invade host cells and evade host
immune responses (29) and are required for the maintenance of
the Sodalis-tsetse fly symbiosis (28, 30). Although both H.
defensa T3SS are complete, neither forms a single genomic
island. Putative secreted effector proteins are scattered through-
out the genome and were probably acquired by multiple HGT
events (Table S2).
The most abundant putative virulence factors are RTX (re-
peats in toxin) toxins: a protein family that includes a variety of
exported proteins including ?-hemolysin and leukotoxin (31).
These proteins have highly variable lengths (800–6,000 AA) and
contain a tandemly repeated nonapeptide sequence that is
involved in binding calcium. The toxin genes (rtxA) tend to occur
in operons containing an activating acyltransferase (rtxC) and an
ABC transporter (rtxBD). H. defensa contains 32 CDS with
similarity to rtxA, 2 copies of rtxB, and only a single copy of rtxD.
These sequences are significantly diverged from known RTX
toxins (20–40% AA identity), and several are possibly paralogs
(60–92% AA identity). The rtxA copies include both intact (n ?
10) and fragmented (n ? 22) CDS. Together, these data suggest
past duplication and diversification of these toxin genes, fol-
lowed by mutation and inactivation of some copies.
Response of H. defensa to Changing Environments. Despite the
constrained biosynthetic capabilities of H. defensa, it has con-
siderably more cell structural, DNA replication, recombination,
and repair genes than do obligate endosymbionts (2). H. defensa
also retains more regulatory genes, including global regulators
(e.g., 4 sigma factors), specific regulators of biosynthetic path-
ways (e.g., for production of biotin, cysteine, fatty acids), 4 pairs
of putative 2-component regulators, and 3 genes involved in
Pathogenic bacteria typically express virulence factors under
strict regulatory controls. In H. defensa, putative regulatory
genes flank both T3SS, one of which is homologous to hilA, the
key regulator for SPI-1 (32). We have also identified homologs
of Hha and SlyA, which activate the expression of hemolysins
Escherichia coli O157:H7
Enterobacter sp. 638
Sodalis glossinidius – I
Regiella insecticola – I
Hamiltonella defensa – I
Yersinia pestis – I
Photorhabdus luminescens – I
Xenorhabdus nematophila – I
Pseudomonas entomophila – I
0.1 amino acid substitutions per site
Escherichia coli K12
iaceae using 88 single-copy orthologous proteins. Bacteria engaged in asso-
ciations with insects are indicated (I). Support values are reported from 100
bootstrap replicates from RaxML, and PhyML analyses values greater than 80
are indicated by asterisks.
Phylogenetic reconstruction of H. defensa and related Enterobacter-
glucose, fructose, glucosamine, mannose
NADH dehydrogenase I
in addition to producing both prymidines and purines. Essential (red) and nonessential (green) amino acids are either synthesized de novo or imported by a
substrate-specific transporter. Most vitamins and cofactors (blue) are synthesized, although pantothenate and thiamin must be imported. Circles indicate genes
in a particular pathway that are present (filled) or absent (open). *Putative ‘‘polar’’ amino acid transporter may transport histidine or threonine.
Metabolic reconstruction of H. defensa indicates that it can complete glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway,
Degnan et al.PNAS ?
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(33, 34), and 2-component regulators and quorum-sensing genes
are also known to influence expression of virulence factors. The
diversity of regulatory genes suggests a mechanism by which H.
defensa copes with changing environments, such as invasion of a
new host species or attack of hosts by parasitoids.
Repetitious Genomics. The genome of H. defensa is riddled with
mobile DNA. Insertion sequences (IS), group II introns, inte-
grated prophage, and plasmids comprise 21% of the genome
(444,936 bp) (see Fig. 1). Estimates of genetic diversity for the
most prevalent, intact IS elements are very low (? ? 0.000–
0.040), suggesting recent transpositional activity or gene con-
version (see Table S3). The single active group II intron also
appears to have undergone recent retrotransposition (see Fig. 1,
and Table S3). The lack of site specificity has resulted in
retrotransposition within and between genes, as well as into
previously retrotransposed group II introns. PCR screens of H.
defensa strains from different hosts showed that ISHde1,
ISHde2, and ISHde3 were widespread, whereas ISHde4 and the
group II intron were in fewer than half of tested strains (see
Table S3). Proliferation of repeats is expected in intracellular
bacteria, as they tend to have small effective population sizes
(Ne) because of recurrent transmission bottlenecks, increasing
the level of genetic drift (35).
Genome evolution and virulence in H. defensa, as in many
free-living bacteria, has been influenced by interactions with
bacteriophage (23). Apart from the APSE prophage, H. defensa
contains 22 phage-like gene blocks (153,384 bp), several of which
have undergone partial duplication (see Fig. 1 and Table S4).
The prophage islands were readily identified because of both
gene content (e.g., phage integrases) and elevated G ? C%
(mean 46.5%). Except for APSE, the prophage appear to be
inactive, as all of the islands are fragmentary and most contain
inactivated or truncated genes. Mobile elements were probably
involved in the inactivation, rearrangement, and duplication of
the gene blocks, most of which (16 of 22) are flanked on one or
more sides by either an IS element or group II intron.
H. defensa bears a conjugative IncFII plasmid pHD5AT. The
type IV secretion system (T4SS) and pilus it encodes are similar
to the tra and pil loci from the Serratia entomophila plasmid
pADAP. These loci underlie the mobilization and dissemination
of pADAP, which carries genes responsible for the cessation of
has no genes implicated in virulence or resistance.
fraction of pseudogenes or truncated proteins, and flanking IS
elements or group II introns. Two of the islands are the result of
chromosomal integration and decay of pHD5AT, as indicated by
missing or inactivated genes (Fig. S1 and SI Methods). Two other
plasmid islands are inactivated T4SS, yet are phylogenetically
distinct from the tra locus on pHD5AT (see Table S4). The
precise assignation of fragments to plasmids or integration events
are difficult because of recombination.
H. defensa Proteome. To explore the expression of H. defensa
genes and proteins, we performed a proteomics experiment on
a sample of purified H. defensa cells, using the genome sequence
for peptide and protein identification. Implementing conserva-
tive identity cutoffs, we identified 89 expressed proteins (Fig. 4
and Table S5). Several phage APSE proteins and one T3SS
protein (SseC) were recovered. Among the most highly ex-
pressed proteins were those involved bacterial responses to stress
and membrane components. Indeed, the most abundant protein,
protein in other obligate and facultative endosymbionts (37).
Other recovered H. defensa proteins include ones involved in
core processes (e.g., transcription, translation) and conserved or
hypothetical proteins encoded in the genome but having un-
The reduced size and compositional bias in the genome of H.
defensa reflects a long-term, stable association with its insect
hosts. In this respect, the H. defensa genome is similar to
Wolbachia genomes, which are small, have highly reduced bio-
synthetic capabilities, and encode an abundance of mobile
genetic elements (3, 5). Whereas Wolbachia is known mostly as
a reproductive parasite and antagonist of its hosts, H. defensa
protects hosts from parasites. Genes for toxins, effector proteins,
and 2 T3SS are likely to be critical elements underlying this
mutualistic role. The presence of numerous homologs of known
virulence factors, which have homologs in other insect symbionts
and in mammalian and plant pathogens, reiterates how con-
served genetic mechanisms involved in bacterial-eukaryotic
cellular interactions can result in vastly different outcomes.
Some of the virulence-gene homologs (e.g., rtxA) are not intact,
suggesting a changing role for the toxins in this symbiosis. These
shifting gene sets likely reflect the inherent dynamism of antag-
onistic interactions, which impose ongoing selection for counter-
adaptations in parasites, hosts, and symbionts. Gene losses and
inactivations in H. defensa are tempered by gene gains via HGT,
evidenced by the abundance of plasmid and phage islands.
to contribute to parasitoid protection, the H. defensa genome
reveals a history of association with other phage and plasmids
that likely played an earlier role in resorting ecologically impor-
tant genes among H. defensa strains and possibly other bacteria.
DNA Isolation and Construction of Libraries. We used 2 complementary se-
quencing strategies to complete the H. defensa genome: (i) subcloning and
Sanger sequencing a large insert BAC library and (ii) pyrosequencing (Fig. S2).
Intact H. defensa cells were purified from whole insects to minimize contam-
ination with aphid and Buchnera DNA, as described previously (18). A BAC
library was constructed, fingerprinted, and minimal tiling paths were chosen
(as in ref. 38). Individual BACs were then subcloned, sequenced bi-
directionally with ABI3730xl sequencers, and assembled using Phred, Phrap,
and Consed (39–41). Overlapping and validated BACs were then merged.
Bacterial genomes contain nonclonable fragments, so we performed py-
rosequencing as an unbiased sequencing method. High molecular weight
DNA was isolated directly from the purified H. defensa cells using the Pure-
gene Tissue Core Kit B (Qiagen). We generated a standard and paired-end
single-stranded template DNA (sstDNA) library using the GS DNA Library
analysis. (A) The 89 identified proteins are divided by principle functional roles.
Numbers in parentheses indicate the number of expressed (open, ?1.0) and
highly expressed (stippled, ?1.0) proteins in each category based on exponen-
expressed proteins, the number of peptides recovered for each protein, and
emPAI values. Colors correspond to the assigned functional roles in (A).
Functional distribution of H. defensa proteins recovered from MudPit
www.pnas.org?cgi?doi?10.1073?pnas.0900194106Degnan et al.
and sequenced on a GS-FLX (454 Life Sciences). The 454 reads were assembled
with Newbler (v1.1.03.24) using default parameters.
Final Assembly and Genome Closure. Putative H. defensa contigs generated
from the 454 reads and distinct from the finished BACs were sorted and
oriented using linking information from the paired ends. PCR primers were
designed at the contig ends, and products were amplified and sequenced
using standard protocols described elsewhere (23). The 454 reads for each
scaffold were then reassembled with Newbler, and Sanger reads were incor-
porated in Consed using Phrap.
Genome Annotation. Genes were predicted for the finished H. defensa ge-
nome using Glimmer v3.02 (protein-coding genes), tRNAscan-SE (tRNAs) and
annotated using consensus of BlastP similarity searches to NR, all microbial
Pfam?ls database (42). CDS without hits having expectation values less than
10?10(BlastP) and 10?4(Pfam) were annotated as hypothetical, and CDS with
conflicting results were assigned as putative. Predicted start codons were
if present. Intergenic regions were rescreened with BlastX for possible CDS
missed by Glimmer. CDS with truncations ?40% length or fragmented CDS
were designated pseudogenes in the final annotation. Boundaries of multi-
copy repeats (e.g., insertion sequences, group II introns) were identified by
consensus alignments. Gene functions were inferred from those of identified
homologs, and the integration of genes into metabolic pathways was deter-
mined using EcoCyc (43).
determine the relationship of H. defensa with other gamma-proteobacteria.
Briefly, we identified 88 of 203 single copy orthologs (SICO) in H. defensa and
29 other genomes (Table S6) (44). Protein sequences of each ortholog were
removed. Individual protein alignments were then concatenated into 4 align-
ments (Table S7). Alignments without H. defensa and R. insecticola sequences
were also generated to assess impact of of long-branch attraction or other
artifacts. Each dataset was analyzed with RaXML and PhyML (46, 47), and
unique topologies were compared using the SH-test in TREE-PUZZLE 5.2 (48).
The topology with the lowest log likelihood and that disagreed with the
fewest datasets is presented. Support values were estimated from 100 non-
parametric bootstrap replicates.
Protein Expression. Briefly, H. defensa cells were isolated as above and imme-
diately frozen at –80 °C. The cell pellet was thawed, homogenized, and
centrifuged, and proteins were precipitated. The resulting pellet was dis-
and subjected to alkylation and in-gel tryptic digestion. The tryptic peptides
were extracted from each gel section, concentrated, and injected into an
LC-MS/MS system. Resultant tandem mass spectra were processed and ana-
lyzed with Mascot 2.2 (Matrix Science), using a database of H. defensa, B.
aphidicola, and A. pisum protein sequences. The results were filtered using a
the false-discovery rate for H. defensa peptides was 0.2%.
ACKNOWLEDGMENTS. The authors thank K. Hammond, B. Nankivell, K.
Sunitsch and J. Currie, T.R. Mueller, K. Collura, R. He, and J.L. Goicoechea of the
Arizona Genomics Institute. We also thank J. Ewbank and H. Goodrich-Blair for
access to unpublished genome data and Q. Lin at the University of Albany
Proteomics Facility for running the protein sample. This research was supported
by National Science Foundation Grant 0313737 (to N.A.M.). P.H.D. received
funding from National Science Foundation Integrative Graduate Education and
Research Traineeship Fellowship in Evolutionary and Functional Genomics, the
Center for Insect Science at the University of Arizona, and National Science
Foundation Doctoral Dissertation Improvement Grant Award 0709992.
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