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J Mol Evol (2008) 66:266–275
DOI 10.1007/s00239-008-9082-8
Replacement of the Arginine Biosynthesis Operon
in Xanthomonadales by Lateral Gene Transfer
Wanessa C. Lima Æ Carlos F. M. Menck
Received: 24 March 2007 / Accepted: 25 January 2008 / Published online: 28 February 2008
Ó Springer Science+Business Media, LLC 2008
Abstract The role of lateral gene transfer (LGT) in
prokaryotes has been shown to rapidly change the genome
content, providing new gene tools for environmental
adaptation. Features related to pathogenesis and resistance
to strong selective conditions have been widely shown to
be products of gene transfer between bacteria. The genomes of the c-proteobacteria from the genus Xanthomonas,
composed mainly of phytopathogens, have potential
genomic islands that may represent imprints of such evolutionary processes. In this work, the evolution of genes
involved in the pathway responsible for arginine biosynthesis in Xanthomonadales was investigated, and several
lines of evidence point to the foreign origin of the arg
genes clustered within a potential operon. Their presence
inside a potential genomic island, bordered by a tRNA
gene, the unusual ranking of sequence similarity, and the
atypical phylogenies indicate that the metabolic pathway
for arginine biosynthesis was acquired through LGT in the
Xanthomonadales group. Moreover, although homologues
were also found in Bacteroidetes (Flavobacteria group), for
many of the genes analyzed close homologues are detected
in different life domains (Eukarya and Archaea), indicating
that the source of these arg genes may have been outside
the Bacteria clade. The possibility of replacement of a
complete primary metabolic pathway by LGT events supports the selfish operon hypothesis and may occur only
W. C. Lima C. F. M. Menck
Department of Microbiology, Institute of Biomedical Sciences,
University of São Paulo, São Paulo, SP, Brazil
C. F. M. Menck (&)
Av. Prof. Lineu Prestes 1374, CEP 05508-900 São Paulo,
SP, Brazil
e-mail: [email protected]
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under very special environmental conditions. Such rare
events reveal part of the history of these interesting mosaic
Xanthomonadales genomes, disclosing the importance of
gene transfer modifying primary metabolism pathways and
extending the scenario for bacterial genome evolution.
Keywords Lateral gene transfer Horizontal gene transfer Xanthomonas Xanthomonadales Arginine biosynthesis Selfish operon
Introduction
Lateral gene transfer (LGT) has been considered a major
driver of genome evolution in prokaryotes, since it can
dramatically alter the biochemical repertoire of host
organisms and potentially create structural or functional
novelties, thus allowing for the exploitation of new environments and survival under strong selection regimes
(Ochman et al. 2000). However, the successful mobilization of complex metabolic traits requires the physical
clustering of genes, and as a result, lateral inheritance will
select for gene clusters and operons (Lawrence and Roth
1996). LGT can bring not only entirely new sequence
families into the genome, but also sequences that are
homologous to existing genes, which may lead to the
replacement of autochthonous sequences with the acquired
copies (Ochman 2001). The potential for acquiring and
replacing an existing gene generally decreases with the
phylogenetic distance between the donor and the recipient
lineages, due to sequence checking barriers, such as mismatch repair (Vulic et al. 1999). However, this is still a
matter of debate, as growing evidence suggests that LGT
may occur at vast phylogenetic distances, changing the
metabolic character of bacterial species.
J Mol Evol (2008) 66:266–275
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The extent of potential LGT in two phytopathogenic
bacteria from the genus Xanthomonas, X. axonopodis pv.
citri and X. campestris pv. campestris, was previously
assessed, based on atypical similarity ranking, unusual
nucleotide composition, and atypical phylogenetic reconstruction (Lima et al. 2005, 2008). Several genomic islands
were detected by this approach, including clusters of genes
related to essential metabolic functions. In particular, the
genomic island bearing the genes responsible for arginine
biosynthesis showed striking features; these are investigated further in this work.
Arginine biosynthesis is notable for its complexity and
variability at the genetic level and for its connection with
several other pathways, such as pyrimidine and polyamine
biosynthesis, besides diverse degradative pathways.
Moreover, the pattern of arginine synthesis is not unique,
since two completely different enzymes may catalyze the
formation of a key intermediate, ornithine (Fig. 1) (Xu
et al. 2000). The initial steps in the arginine biosynthetic
pathway from glutamate proceed via N-acetylated intermediates. Two alternative ways have evolved to split off
the acetyl group from N-acetylornithine: in the linear
pathway, which is mostly found in the Enterobacteriaceae,
acetylornithine deacetylase (EC 3.5.1.16; encoded by
argE) catalyzes the hydrolysis of N-acetylornithine into the
arginine precursor ornithine and acetate. Other prokaryotes
and the eukaryotic microbes use an energetically more
economic pathway which recycles the acetyl group onto
glutamate, yielding acetylglutamate. This reaction is catalyzed by ornithine acetyltransferase (OAT; EC 2.3.1.35;
encoded by argJ). In these organisms the first step in the
pathway fulfills an anaplerotic role: once N-acetylornithine
Fig. 1 General scheme of the arginine biosynthesis pathway. The
linear pathway proceeds from argA to argH. Left: The reactions
catalyzed by the bifunctional enzyme ArgJ. Right: The different roles
played by the proteins encoded by argE’ and argF’ in Xanthomonadales. In each text box are shown the enzyme name and synonyms,
the EC number, and the coding gene
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is synthesized, the action of N-acetylglutamate synthase
(NAGS; EC 2.3.1.1; encoded by argA) becomes superfluous (Cunin et al. 1986; Glansdorff 1987).
In Xanthomonas, biosynthesis proceeds via the linear
pathway, but with notable modifications (Fig. 1). While in
the canonical biosynthetic pathway, acetylornithine
deacetylase catalyzes the conversion of N-acetylornithine
to ornithine, which is then converted to citrulline by ornithine transcarbamylase (OTCase; encoded by argF), in
Xanthomonas, the argF’-encoded enzyme shows no catalytic activity toward ornithine (Shi et al 2005a). Instead, a
novel N-acetylornithine transcarbamylase (AOTCase) catalyzes the carbamylation of N-acetylornithine rather than
ornithine. In the same way, a novel N-acetylcitrulline
deacetylase (encoded by argE’) is able to catalyze the
deacetylation of N-acetylcitrulline to produce citrulline
(Shi et al 2005b). Consequently, a new pathway has been
proposed for Xanthomonas, inverting the order of transcarbamylation and deacetylation (Morizono et al. 2006).
Moreover, recently the argB found in the Xanthomonas
genus was proposed to encode a fusion protein with both
NAGS and NAG kinase activities (NAGS/K) (Shi et al.
2006; Qu et al. 2007).
Working with the genomic data of Xanthomonadales,
we investigated the evolution of the genes involved in
arginine biosynthesis, which are mostly found as a cluster
forming a potential operon (referred hereafter as arg
operon). Not only do these bacteria show a distinct pathway, as described above, but also most of the genes in the
arg operon have atypical phylogenies, branching close to
homologues from otherwise unrelated organisms. The data
provide strong evidence for a foreign origin of the whole
operon coding for this pathway. This supports an important
role for LGT that may directly affect primary metabolism
through gene replacement from distantly related organisms.
J Mol Evol (2008) 66:266–275
BRENDA enzyme database (Schomburg et al. 2004;
http://www.brenda.uni-koeln.de), and the Genome Properties server (Haft et al. 2005; http://cmr.tigr.org).
The most relevant genomic sequences for this study
were as follows: Xanthomonas axonopodis pv. citri 306
(XAC; GenBank accession no. AE008923), Xanthomonas
campestris pv. campestris ATCC33913 (XCC; GenBank
accession no. AE008922), Xanthomonas campestris 8004
(XC_; GenBank accession no. CP000050), Xanthomonas
campestris pv. vesicatoria str. 85–10 (XCV; GenBank
accession no. AM039952), Xanthomonas oryzae
KACC10331 (XOO; GenBank accession no. AE013598),
Xanthomonas oryzae pv. oryzicola BLS256 (XOM; GenBank accession no. NZ_AAQN00000000), Xanthomonas
campestris pv. armoraciae 756C (XCA; no GenBank
accession number associated; sequenced by TIGR institute), Xylella fastidiosa 9a5c (XF; GenBank accession no.
AE003849), and Xylella fastidiosa Temecula1 (PD; GenBank accession no. AE009442).
Phylogenetic Analyses
Materials and Methods
Protein sequences were aligned with the CLUSTALX
program (Thompson et al. 1997), and regions of the
alignments that were ambiguous, were hypervariable, or
contained gaps were excluded from subsequent analysis
(GENEDOC program [Nicholas et al. 1997]). Distancebase phylogenetic trees were generated using a neighborjoining algorithm (Neighbor-Joining program from the
PHYLIP package [Felsenstein 1989]). Bootstrap assessment of tree topology (1000 replicates) was performed with
the SEQBOOT program (PHYLIP). Maximum likelihood
trees were made using TREE-PUZZLE (Schmidt et al.
2002), and parameters used were 100,000 puzzling quartets, gamma-distributed rates over eight categories and the
c-parameter estimated from the data set, and an automatically selected model of substitution. Trees were visualized
using the TREEVIEW program (Page 1996).
Identification of the Arginine Biosynthetic Genomic
Island in Xanthomonadales
Results
The pipeline for detection of laterally transferred islands in
Xanthomonas genomes was previously described (Lima
et al. 2005). Sequence similarity searches were performed
using the BLASTP program as implemented in the NCBI
server (http://www.ncbi.nlm.nih.gov/), Expasy Proteomics
Server (Gasteiger et al. 2003; http://us.expasy.org/), and
CMR-TIGR (Peterson et al. 2001; http://cmr.tigr.org/). The
database used for these searches was completely set up from
fully sequenced genomes by December 2006. Metabolic
pathways were analyzed through the KEGG web service
(Kanehisa et al. 2006; http://www.genome.jp/kegg/), the
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Identification of the Genomic Island Coding for
Arginine Biosynthesis in Xanthomonadales
In previous studies, potential laterally transferred genomic
islands were identified in the genome of both Xanthomonas
axonopodis pv. citri (XAC) and Xanthomonas campestris
pv. campestris (XCC) (Lima et al. 2005). Several of these
islands contained gene clusters related to primary metabolism, including biosynthesis of cysteine, NAD
metabolism, the TCA cycle, and energetic metabolism.
One of the most interesting islands contained the genes
J Mol Evol (2008) 66:266–275
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responsible for arginine metabolism, and this potential arg
operon was further investigated in this work.
The presence of such an arg operon was also found in
seven other Xanthomonadales genomes, with minor modifications (Fig. 2). In the Xanthomonas genus, the island
comprises almost 15 kbp and contains 13 to 15 genes,
depending on the genome considered, 8 of which may be
related to the arginine metabolism pathway, and the region is
flanked by a Pro-tRNA in all organisms. All genes coding for
the eight steps of the arginine pathway, from glutamate to
arginine, are present within the island (Table 1), except for
the argD gene, which is found elsewhere in the genome.
Although NAGS and NAGK represent a fusion gene (argB),
one putative acetyltransferase GNAT-family gene (designated gnat) was detected, and it might perform an analogue
glutamate synthase function. Two other genes, proA and
proB, are not directly related to arginine metabolism but
share glutamate as the initial substrate. These genes are close
to each other, being transcribed in the same direction, thus
suggesting that they form an operon.
The other five genes present inside this island are not
clearly correlated among themselves (Table 1). The aehX
Fig. 2 Graphical representation of the arginine biosynthesis genomic
island in Xanthomonadales. Genes are represented by arrows
according to their transcription direction; the arrow length is not
proportional to the gene length. Gene names are shown above the
arrows. In dark gray, genes related to the arginine pathway; the black
arrow indicates a Pro-tRNA; within the arrows, the corresponding
gene number (as defined during the initial sequencing project). XAC,
Xanthomonas axonopodis pv. citri 306; XCC, Xanthomonas campestris pv. campestris ATCC33913; XC_, Xanthomonas campestris
8004; XOO, Xanthomonas oryzae KACC10331; XOM, Xanthomonas
oryzae pv. oryzicola BLS256; XCA, Xanthomonas campestris pv.
armoraciae 756C; XCV, Xanthomonas campestris pv. vesicatoria str.
85–10; XF, Xylella fastidiosa 9a5c; PD, Xylella fastidiosa Temecula1
Table 1 Genes within the arg genomic island, in X. axonopodis pv. citri (XAC) and X. campestris pv. campestris (XCC)
XAC
XCC
Gene name
Gene function
TIGR-associated role
2340
2236
cynX
MFS transporter
Transport and binding
2341
2237
aehX
a-Amino acid ester hydrolase
Cellular processes
2342
2238
proA
c-Glutamyl phosphate reductase
Amino acid biosynthesis
2343
2239
proB
Glutamate 5-kinase
Amino acid biosynthesis
2344
2240
–
Hypothetical protein
Hypothetical
–
2241
–
Hypothetical protein
Hypothetical
2345
2242
argH
Argininosuccinate lyase
Amino acid biosynthesis
2346
2243
argC
Glutamyl-phosphate reductase
Amino acid biosynthesis
2347
2244
Gnat1
Acetyltransferase GNAT family
Amino acid biosynthesis
2348
2349
2245
2246
argB
argE
Acetylglutamate kinase
N-Acetylcitrulline deacetylase
Amino acid biosynthesis
Amino acid biosynthesis
2350
–
Gnat2
Acetyltransferase GNAT family
Amino acid biosynthesis
2351
2247
argG
Argininosuccinate synthase
Amino acid biosynthesis
–
2248
ohr
Organic hydroperoxide resistance protein
Cellular processes
2352
2249
argF
N-Acetylornithine transcarbamylase
Amino acid biosynthesis
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J Mol Evol (2008) 66:266–275
gene encodes for an a-amino acid ester hydrolase,
responsible for the hydrolysis and synthesis of esters and
acids with an a-amino group, and is economically
important for b-lactam antibiotics synthesis in a more
efficient way (Barends et al. 2003). The ohr gene encodes
for an organic hydroperoxide resistance protein, involved
in the detoxification of organic hydroperoxides generated
by the host plant during microbial infection. This gene
may play an important role in the oxidative stress
response in host-pathogen interactions (Mongkolsuk et al.
1998). The cynX gene belongs to a family of MFS
transporters, specifically involved in the active transport
of cyanate and detoxification of environmental cyanate
(Sung and Fuchs 1988).
The gene order of the genomic island is conserved
among all Xanthomonas genomes (Fig. 2). Few differences
involve the hypothetical genes flanking the proA and proB
genes, the ohr gene, and a second copy of the putative
acetyltransferase GNAT-family gene (gnat2). In Xylella,
however, only genes related to arginine metabolism plus
proAB genes are present.
Analysis of nucleotide composition revealed no atypical
features. The average GC content of XAC and XCC genomes is 65%, and the average GC content on the arg island
is 65% for XAC and 66% for XCC. Other parameters, such
as dinucleotide frequency and codon usage, are also similar
to the genome average. The same is observed for the other
genomes (data not shown). The similarity of nucleotide
composition of this island with the host genome is in fact
expected, as it was probably acquired by an ancestral
xanthomonad, and with time, it may have evolved and
ameliorated (Lawrence and Ochman 1997).
Table 2 Percentage identity of
proteins from the arg genomic
island to their first-match
organism
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Arginine Biosynthesis Genes Display an Atypical
Similarity Profile
Similarity searches performed for each gene belonging to
the arg genomic island revealed an atypical pattern of
similarity ranking, i.e., to organisms phylogenetically distant from the Xanthomonadales group (Table 2).
Xanthomonadales belong to the c-proteobacteria group,
although phylogenetic reconstructions with several proteins
and methodologies place them as a deep branch of the b-/cproteobacteria group, along with Pseudomonadales (Martins-Pinheiro et al. 2004; Comas et al. 2006).
Of all the genes within the island, only three (argE and
the two acetyltransferases) presented typical best-match
species in a similarity search (i.e., species belonging to bor c-proteobacteria). The other five arg genes and proB
showed atypical best-match organisms, mainly Eukarya
and Bacteroidetes species. This is strong evidence of the
potentially foreign origin of such genes, reinforced by the
high levels of sequence similarity between the Xanthomonas genes and the sequences found as best match
(between 50% and 70% identity) (Table 2). As a matter
of comparison, sequence identity between Xanthomonas
and E. coli genes, a closely related c-proteobacteria,
ranges from 25% to 45% for genes of the arginine
pathway (Table 2).
Phylogenetic Analysis of the arg Genes Reveals an
Atypical Branching Pattern
To further explore the results obtained through similarity
searches, phylogenetic reconstructions were carried out
XAC
XCC
Gene
name
First-match organism
Taxonomic
group
% identity to
1st-match
organism
% identity
to E. coli
homologue
2340
2236
cynX
Nocardia farcinica
Actinobacteria
63
2341
2237
aehX
Zymomonas mobilis
a-Proteobacteria
74
2342
2238
proA
Geobacter metalli-reducens
d-Proteobacteria
70
44
2343
2239
proB
Salinibacter ruber
Bacteroidetes
45
44
2344
2240
–
Nocardia farcinica
Actinobacteria
63
–
2241
–
Bacillus halodurans
Firmicutes
62
2345
2346
2242
2243
argH
argC
Flavobacteria bacterium
Aspergillus fumigatus
Bacteroidetes
Eukarya
57
66
2347
2244
Gnat1
Ralstonia solanacearum
b-Proteobacteria
66
2348
2245
argB
Aspergillus fumigatus
Eukarya
62
27
2349
2246
argE
Marinobacter aquaeolei
c-Proteobacteria
40
26
2350
–
Gnat2
Burkholderia ambifaria
b-Proteobacteria
67
2351
2247
argG
Salinibacter ruber
Bacteroidetes
56
–
2248
ohr
Agrobacterium tumefaciens
a-Proteobacteria
72
2352
2249
argF
Salinibacter ruber
Bacteroidetes
55
32
29
26
31
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271
Table 3 Phylogenetic position of Xanthomonas genes and support assessment
XAC
XCC
Gene name
Nearest neighbor
NJ bootstrap (%)
ML puzzlings (%)
2340
2236
cynX
Actinobacteria
100
97
2341
2237
aehX
a-Proteobacteria
100
98
2342
2238
proA
d-Proteobacteria
93
85
\50
\50
68
66
2343
2239
proB
c-Proteobacteria
2344
2240
–
Actinobacteria
–
2241
–
Actinobacteria and Firmicutes
2345
2242
argH
Bacteroidetes and Eukarya
2346
2243
argC
Eukarya
2347
2244
Gnat1
Actinobacteria and a-proteobacteria
100
99
\50
\50
100
87
80
74
2348
2245
argB
Eukarya
100
84
2349
2350
2246
–
argE
Gnat2
a- and b-proteobacteria
b-/c-Proteobacteria and Eukarya
100
89
56
90
2351
2247
argG
Bacteroidetes and Archaea
–
2248
ohr
Proteobacteria and Actinobacteria
2352
2249
argF
Bacteroidetes and Eukarya
90
60
100
99
90
76
Note: NJ, neighbor joining; ML, maximum likelihood
for each gene belonging to the arg genomic island, using
both minimum distance and maximum likelihood methodologies (Table 3). As expected, the phylogenies were
congruent with the BLAST results, and they are supported
by high bootstrap and quartet puzzling values. In only
three cases was the nearest neighbor in the tree different
from the best-match organism: the proB, argE, and gnat1
genes.
Five arg genes (argB, argC, argF, argG, and argH)
branched with Eukarya or Archaea species with high
support (except for argH, with \50%) (Table 3). To
illustrate the most prominent examples, Figs. 3–5 present
the phylogenetic trees for the argB, argC, and argG
genes. The argB and argC genes have as ‘‘nearest
neighbor’’ several species of Fungi, and this group is
supported by high bootstrap values (100%) (Figs. 3 and
4). It is important to note that the phylogenetic reconstruction of the argB gene was carried out only with the
domain encoding NAGK activity. Phylogenetic trees
generated with the NAGS domain (corresponding to
argA) place the Xanthomonadales along with fungi and
mammalian orthologues (data not shown). On the other
hand, the argG gene branches with Bacteroidetes and
Archaea species (90% bootstrap support) (Fig. 5). It is
interesting to note that genes coding for the arginine
pathway are widespread throughout all domains, appearing in Eukarya, Archaea, and Bacteria, and in several
bacterial groups (such as proteobacteria, high-GC gram
positives, and cyanobacteria). In spite of this, the Xanthomonas genes present a clearly atypical branching
pattern, which significant evidence for lateral acquisition
of the operon.
Discussion
The evolution of metabolic pathways is a subject of much
current interest, and the current availability of several
completely sequenced genomes makes this question easier
to address. In this work, we provide evidence of the
acquisition of a primary metabolic pathway through LGT
in the Xanthomonadales group, with the data pointing to a
foreign origin for the arginine biosynthesis operon. It is
well known that the acquisition of genes from other species
is by far the most rapid evolutionary process, frequently
occurring without loss of existing functions, and is central
to the evolution of bacteria, increasing fitness in certain
environmental niches. However, how does it occur for
genes related to central functions, such as amino acid
metabolic pathways?
It has been argued that core genes are unlikely to be
successfully transferred, since recipient taxa would already
bear functional orthologues which would have experienced
long-term coevolution with the rest of the cellular
machinery. In contrast, it is proposed that those under weak
or transient selection (such as nonessential catabolic processes, new operons, or those providing new niche adaptive
changes) are likely to be successfully transferred and
retained (Lawrence 1999a). However, we found that LGT
is not limited to genes associated with niche adaptation,
virulence, or pathogenicity, but rather it also occurs with
genes related to primary metabolism (Lima et al. 2008).
Omelchenko et al. (2003), on analyzing 41 complete
genomes, found several instances of ‘‘neighborhood genes’’
that probably originated via LGT, with different evolutionary scenarios, involving either the transfer of whole
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Fig. 3 Distance tree of argB gene computed by the neighbor-joining method. Numbers within the tree correspond to bootstrap assessment (based
on 1000 replicates). Values \50% are not shown
operons or a patchy inheritance (generating operon mosaicism). Among their findings, the displacement of
tryptophan and arginine biosynthesis genes (argB and
argG) is related. In another, more recent work, Qu et al.
(2007) also observed the relationship among Xanthomonadales fusion ArgB protein and mammalian homologues.
These results are in agreement with those presented here,
and indicate that LGT of entire operons is the most likely
explanation for most of the findings of colocalized alien
genes in a genome, which is generally consistent with the
selfish operon model. This model proposes that a gene
cluster was initially beneficial to the genes themselves, not
to their host organism; since individual genes cannot confer
a selectable function alone, the clustering is essential for
successful lateral transfer. In this way, the selfish operon
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allows phenotypic information to be transferred among
genomes, because all genes conferring a selectable function
may be introduced simultaneously (Lawrence 1999b).
The parasitic lifestyle of Xanthomonas might contribute
to the explanation of how resident copies could be replaced
by xenologous ones. The probable scenario invokes loss of
the resident pathway and its replacement by laterally
introduced genes. Due to the parasitic lifestyle of all
Xanthomonadales species, we might guess that the ancestor
of the group displayed a similar behavior. Thus, loss of the
original genes responsible for arginine production could
occur if the lack of this amino acid was fulfilled by the
host. Finally, the restriction of this amino acid could lead to
selection of bacteria that have acquired the arg operon
from a eukaryotic donor, or eventually from Bacteroidetes
J Mol Evol (2008) 66:266–275
273
Fig. 4 Distance tree of the argC gene computed by the neighbor-joining method. Numbers within the tree correspond to bootstrap assessment
(based on 1000 replicates). Values \50% are not shown
species, as we cannot discriminate which of the bacteria
received this operon first. One possibility for restriction of
arginine in the medium could occur as a result of an
eventual free-living lifestyle of the bacterium (as also
occurs in Xanthomonas). Selection as a result of adaptation
to a restrictive environment favors the uptake of genes
suitable to the host organism, thus making LGT a powerful
driving force.
Although common features of genomic islands, such as
nucleotide composition bias and the presence of integrases
flanking the island, are not found, the presence of a tRNA
and discordance among the phylogenetic trees and similarity searches of arg genes corroborate the foreign origin
of the entire island. The absence of any significant difference in nucleotide parameters (such as GC content, codon
usage, and dinucleotide frequency) may be explained in
either of two ways: the incoming operon could have had a
nucleotide compositional pattern similar to the average
recipient genome pattern or perhaps enough time has
elapsed since acquisition of the operon in such a way that
mutational pressure has ameliorated the within genes.
Neither explanation contradicts the hypothesis of a foreign
origin for the operon.
The aberrant branching pattern shown for arg genes
branching with Archaea, Eukarya, and the distantly related
Bacteroidetes may be most parsimoniously explained as a
result of LGT events, though we cannot exclude the possibility of hidden paralogies (caused by independent gene
duplications and losses in different groups). However, a
common trend in all ‘‘paralogy scenarios’’ involves multiple copies of the orthologous and paralogous genes,
spread among the different taxonomical groups within the
phylogeny, with random gaps reflecting differential losses.
And this is not the case in all the phylogenies analyzed
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J Mol Evol (2008) 66:266–275
Fig. 5 Distance tree of the argG gene computed by the neighbor-joining method. Numbers within the tree correspond to the bootstrap
assessment (based on 1000 replicates). Values \50% are not shown
here. Just one copy of each gene is present, and the high
bootstrap values support the sister-grouping seen. Moreover, although the arginine pathway is universally
conserved among prokaryotes, Xanthomonadales genes are
grouping with distantly related organisms, indicating the
replacement of native by foreign copies.
In conclusion, this work presents data indicating the
possibility of gene replacement in primary metabolism by
LGT events. Although several features often associated
with laterally acquired DNA are lacking, the presence of a
tRNA integration site, the phylogenetic discordance, and
the genome context information all support the foreign
origin of the arg island in Xanthomonadales. Although this
type of gene substitution is rare in nature, it may play an
important role in the evolution of certain organisms. The
sequencing and analysis of more genomes, especially
bacterial ones, may facilitate the scrutiny of such events,
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thus providing more data for studies of genome evolution
in general and of arginine metabolism in particular.
Acknowledgments This work was supported by FAPESP (São
Paulo, SP, Brazil) and CNPq (Brası́lia, DF, Brazil). W.C.L. has a
fellowship from FAPESP, and C.F.M.M. is a Fellow of the John
Simon Guggenheim Memorial Foundation (New York).
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