Download Rhizobial plasmids - replication, structure and

Cent. Eur. J. Biol. • 7(4) • 2012 • 571-586
DOI: 10.2478/s11535-012-0058-8
Central European Journal of Biology
Rhizobial plasmids - replication, structure
and biological role
Review Article
Andrzej Mazur*, Piotr Koper
Department of Genetics and Microbiology,
Maria Curie-Skłodowska University,
20-033 Lublin, Poland
Received 19 March 2012; Accepted 10 May 2012
Abstract: Soil bacteria, collectively named rhizobia, can establish mutualistic relationships with legume plants. Rhizobia often have multipartite
genome architecture with a chromosome and several extrachromosomal replicons making these bacteria a perfect candidate for
plasmid biology studies. Rhizobial plasmids are maintained in the cells using a tightly controlled and uniquely organized replication
system. Completion of several rhizobial genome-sequencing projects has changed the view that their genomes are simply composed
of the chromosome and cryptic plasmids. The genetic content of plasmids and the presence of some important (or even essential)
genes contribute to the capability of environmental adaptation and competitiveness with other bacteria. On the other hand, their mosaic
structure results in the plasticity of the genome and demonstrates a complex evolutionary history of plasmids. In this review, a genomic
perspective was employed for discussion of several aspects regarding rhizobial plasmids comprising structure, replication, genetic
content, and biological role. A special emphasis was placed on current post-genomic knowledge concerning plasmids, which has
enriched the view of the entire bacterial genome organization by the discovery of plasmids with a potential chromosome-like role.
Keywords: Rhizobium • Plasmid • Replication • RepABC • Genome organization
© Versita Sp. z o.o.
1. Introduction
A classical view of genome architecture in bacteria
comprises one indispensable chromosome containing
housekeeping genes for the basic metabolic function
and a dispensable plasmid (or plasmids) coding
for some accessory features e.g., dealing with a
challenging environment, or different lifestyles.
Alphaproteobacteria from the order Rhizobiales
contain, among many others, genera of soil bacteria
such as Rhizobium, Bradyrhizobium, Mesorhizobium,
Sinorhizobium
(Ensifer),
Azorhizobium
and
Agrobacterium, which can establish relationships
with plants. Most Agrobacterium species are plantpathogens, whereas members of the remaining
genera are agriculturally important nitrogen-fixing
legume symbionts [1]. The bacterium-plant symbiotic
interaction is a complex process in which specific
plant and bacterial signals are exchanged resulting
in formation of nodules, where rhizobia in the form
of bacteroids fix nitrogen [2-5]. Rhizobiaceae and
especially the fast-growing rhizobia have multipartite
and diverse genome architectures. A genome is
usually composed of a single chromosome and
several plasmids of various sizes ranging from several
kb to over 2 Mb [6-8], making rhizobia a perfect
candidate for plasmid biology studies. Regarding
rhizobial plasmids, at least some topics are of
special interest and deserve detailed discussion.
First, how are multiple replicons maintained and
segregated during the cell cycle? What mechanisms
are employed for stable plasmid propagation? Next,
what is the structure and genetic content of rhizobial
plasmids, and how (if at all) does the plasmid affect
the phenotypic and metabolic properties of bacteria
possessing multipartite genomes? Finally, how has
the current knowledge gained from complete rhizobial
genomes, changed and enriched the view of the
entire bacterial genome organization by the discovery
of plasmids with a chromosome-like role in rhizobia?
* E-mail: [email protected]
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2. Rhizobial plasmid maintenance
systems
One of the most crucial challenges faced by bacteria
during the life cycle is ensuring that their genetic
inheritance is accurately passed onto daughter cells.
An important feature of rhizobial plasmids is their lowcopy number in the cell. Such replicons especially
require an efficient mechanism that ensures their stable
propagation. Plasmid-partitioning systems are well
described for bacterial strains harboring single wellknown plasmids (plasmid R, P1) [9,10]. Namely, they
comprise polymer-based DNA segregation machinery
that consists of three indispensable elements: a
centromere-like DNA sequence called parS and two
proteins: a motor protein, generally an ATPase, and a
centromere-binding protein [11]. The ATPase is able to
polymerize into filaments (ParA) and the second protein
(ParB) binds both to parS and ATPase, acting as an
adaptor between the plasmids and the filaments that
are responsible for the segregation [12]. Despite the
precisely working partition machinery, the remarkable
segregation stability of low copy plasmids is also
Figure 1.
achieved by sophisticated regulation of the expression
of partition genes, in which the centromere-like parS
sequence in conjunction with partition proteins play a
significant role [13].
It was proposed to consider rhizobial plasmids as
members of the repC superfamily, which includes at
least three closely related but different families [14].
First is the repABC family, widespread among the
rhizobial plasmids, comprising all replicons containing a
repABC operon, which was further described in details
(Figure 1). The second is the repC family of replicons
containing ctRNA–repC without associated repA or
repB genes nearby, like the one in pRmeGR4a of
S. meliloti GR4 [15] or pSmeSM11a, found in addition
to the repABC module [16]. Third constitute the repAC
family, like repAC genes of pRL7JI of R. leguminosarum
bv. viciae, in which a replication system consists only of
a repA and a tightly linked repC without repB or ctRNA
genes [17] (Figure 1). Besides the families employing
the RepC protein for plasmid replication there is at
least one exception. Barran et al. [8] demonstrated that
pRme1132f, small (7.2 kb) cryptic plasmid of S. meliloti
is able to replicate via a rolling-circle-replicating (RCR)
Examples of diversity of genetic organization of rhizobial plasmid maintenance systems. White arrows represent individual rep genes.
Small black arrows in opposite direction to the rep genes transcription show the positions of incα region comprising a gene encoding
antisense RNA (ctRNA). Grey boxes represent putative promoters of incα regions. The positions parS-sites were marked as open
circles. Black square boxes indicate the promoter positions, and diamonds the position of tra boxes. The triangles show the location of
single stranded and double strand origin of replication (sso and dso respectively) of a rolling-circle-replicating (RCR) plasmid.
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model. The minimal replicon contained a rep gene,
whose product does not share similarity with RepC
proteins and single- and double-stranded origins of
replication [8] (Figure 1).
The replication system prevailing among rhizobial
plasmids is the one based on the repABC module. An
unusual feature of repABC replicons is that all elements
necessary for active segregation/partition (repAB) and
replication (repC), as well as those responsible for
incompatibility, are located in the same transcriptional unit
[18,19]. So far, the repABC replicons are the only identified
plasmids in which partitioning and replication genes are
expressed as a single transcriptional unit (Figure 1). In
all other plasmids, partitioning and replication genes
are independently expressed from different promoters
[20]. The operons comprise three genes - repA, repB
and repC, always in the same relative order. RepA and
RepB are members of the ParAB family of partitioning
proteins [21], and their similarity extends to the SopAB
and ParAB proteins from Escherichia coli F plasmid
and P1 phage, respectively [22]. The size of particular
RepA proteins and their N-terminal DNA binding domain
suggest that the segregation systems of most rhizobial
repABC replicons are Type Ia and thus are members
of the MinD/ParA superfamily [14,23]. RepA and RepB
proteins in conjunction with parS, a centromere-like
sequence, provide the plasmid segregation machinery,
which is required for efficient maintenance of the lowcopy DNA replicons in a dividing population of rhizobial
cells [18,20,24]. The third protein-encoding gene of
the operon, repC, is essential for plasmid replication
(Figure 1). RepC, an initiator protein, functions by binding
to the origin of replication oriV located within its own
coding sequence, close to or inside of a large A+T region
[18,24,25]. The repC gene is the minimal region sufficient
for replication when inserted into a non-replicating (e.g.
suicide) vector [18,24,25].
Another element that is commonly present in
repABC operons is the incompatibility determinant called
incα (Figure 1). It is located within the non-translated
repB-repC intergenic region and comprises a gene
transcribed from a strand opposite to repABC, encoding
small antisense RNA (ctRNA) [18,26-28]. ctRNA
gene was also found in the minimal region required
for stable replication of the repC family pRmeGR4a
plasmid from S. meliloti GR4 (Figure 1). The secondary
structure forming ctRNA is a trans incompatibility factor,
modulating RepC levels and thereby the plasmid copy
number [28,29]. It was shown that the ctRNA region
introduced in trans exerts incompatibility against the
parental plasmid [15,18,30].
Despite the obvious overall similarity in terms of the
genetic organization, repABC operons are diverse at the
DNA level and with respect to specific structural elements
[14]. The differences may be related to transcriptional
regulatory elements, the presence of peptide-encoding
minigenes within the repABC operon [31] and,
especially, the number and position of centromerelike parS sequences [20,32] (Figure 1). The latter
ones usually consist of one or more copies of a 16-bp
palindromic consensus sequence. Furthermore, they
are essential for plasmid stability. They are incompatible
with their respective parental plasmid when provided
in trans, similar to centromere-like sequences from
many other plasmids [33,34], and they are the binding
sites for RepB proteins [31]. Single-point mutations in
the parS sequence of the S. meliloti pSymA plasmid
eliminated incompatibility and reduced RepB binding
to this sequence [20]. The number of parS sites may
vary significantly among known repABC replicons. For
example, in the pRetCFN42d plasmid of R. etli CFN42,
there is one identified parS-site consensus element
[18,35], pTiR10 from Agrobacterium tumefaciens
contains two of these elements [31], whereas pSymA
from S. meliloti has six of them [20] (Figure 1). Particular
repABC replicons also differ in the position of par-site
consensus sequences. In some cases, the parS locus
is located downstream from repC like in pRetCFN42d
forming the incβ region [18], in others these sequences
are situated within the repA-repB intergenic region like
in pRetCFN42b [36], pRL8JI of R. leguminosarum bv.
viciae [17], and pSymB of S. meliloti [37]; some carry parsites upstream from repA like pSymA forming the incγ
region [20]. The location of parS seems to be irrelevant
for plasmid segregation. Moving parS upstream from
repA only has a small effect on the stability and plasmid
copy number [20,31]. In the case of pTiC58 and pTiR10
of A. tumefaciens, two parS sequences are situated
within a minigene (repD) coding for only 78 aa, mapped
in the repA-repB intergenic region and being a part of the
repABC operon [31] (Figure 1). A considerable diversity
of the number and location of centromere-like parSsites was found in the plasmids of R. leguminosarum
bv. trifolii TA1 strain. Plasmids pRleTA1b and pRleTA1c
contain two nearly canonical parS sites. In both cases,
one of them is located upstream of repA and the other
within repB and in the repB-repC intergenic region,
respectively. In turn, no such elements were detected
in the proximity of repABC in pRleTA1d and pRleTA1a
[30]. However, it is known that only one or at least one
par-site located near or within the repABC operon is
needed for normal operon activity and adequate plasmid
partitioning [20].
An important point concerning low-copy number
plasmids is the control of initiation of their replication,
involving various mechanisms like antisense RNAs,
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transcriptional repressors, iterons, and DNA methylation
[38]. Rhizobial repABC replicons possess a complex
regulatory network that ensures an appropriate amount
of the replication initiator protein and of partitioning
proteins to provide a stable replication and segregation
of plasmids into the daughter cells. Because repABC
operons of rhizobial plasmids usually have a single
promoter located upstream of repA, common regulation
of repAB and repC occurs. The elements involved
in this regulation act at the transcriptional and posttranscriptional levels. RepA, by itself or with RepB,
has been implicated in transcriptional repression of the
repABC operon [19,39]. Based on detailed analyses of
pRetCFN42d and pTiR10, RepA was recognized as the
major cis-acting negative regulator of the transcription
of the repABC operon [19,39]. RepA, stimulated by
RepB binds to the operator region (consisting of an
imperfect palindrome sequence), located upstream
of repA gene (Figure 1). Deletion of the operator
region causes constitutive expression of the repABC
operon [19]. Centromere-like sequences also play a
crucial role in the transcriptional regulation. In the Ti
plasmid of A. tumefaciens, RepA protein enhances the
binding of RepB (just as RepB increases the affinity
of RepA for binding sites at the repABC promoter) at
parS sites located within the minigene repD (Figure 1).
That interaction is required for plasmid stability and
for maximal repression of repABC transcription. It was
shown that constructs containing the operator region,
the parS locus and the repA and repB genes, repress
their own transcription more strongly than similar
constructs lacking the parS locus. A mechanism has
been proposed in which repABC operon expression
is repressed through loops interlinking a RepA-RepB
complex with the operator and parS sequence. Such
complexes might occur within one plasmid as well as
between two copies of the plasmid [31].
Another level of repABC operon regulation concerns
the post-transcriptional stage of its expression and
occurs via small regulatory RNA. The secondary
structure forming ctRNA is a negative posttranscriptional
regulator of repC, which modulates RepC levels and
thereby the plasmid copy number [15,28,29]. The
interaction of the ctRNA with the target RNA induces
a refolding of the sequence placed downstream of the
anchoring site, resulting in formation of two stem-loop
structures in the unpaired region of the target RNA. One
of them, namely the S-element, behaves as an intrinsic
transcriptional terminator. Recently, the nucleotides of
the ctRNA left arm, crucial for the interaction with the
target mRNA, have been mapped in pRetCFN42d [26].
At least in some cases, repABC expression and
therefore the copy number is further regulated by
TraR - LuxR type quorum-sensing transcription factors
[40,41]; thus, plasmids with the repABC operon linked to
the traI-trb operon may modulate their copy number in
response to bacterial population density. The repABCtraI-trb region of A. tumefaciens pTiR10 contains four
promoters (P1-P4) located upstream of repA as well as
tra boxes situated immediately upstream from P1 and
P3 promoters (Figure 1). In the presence of particular
acyl homoserine lactones (AHL), dimers of TraR
can bind to tra boxes at target promoters, enabling
transcription of genes situated downstream [42].
Addition of AHLs causes a significant increase in the
plasmid copy-number, probably due to the increased
RepC concentration [40].
Analyses of RepABC proteins were also proven to be
valuable for assessment of the phylogenetic relatedness
among the rhizobial plasmids [43,44]. Despite the wide
distribution and importance of plasmids for rhizobia, their
evolutionary history has been incompletely explored,
mainly because of the lack of extensive similarity
between plasmids, with the exception of replication
and transfer function [45]. Recently, complete genomic
sequences of R. leguminosarum bv. viciae 3841 [17],
R. etli CFN42 [36] and R. leguminosarum bv. trifolii
WSM2304 and WSM1325 [46,47], containing multiple
(4-6) plasmids have been obtained. In the context of the
functional and especially evolutionary studies of plasmid
and replication systems, such genomes are of great
interest because each of them has several plasmids,
all belonging to the repABC family. Additionally, some of
these plasmids (i.e. pRetCFN42f, pRetCFN42a, pRL7JI)
carry more than one (complete or partial) repABC
regions. Firstly, the maintenance of multiple plasmids in
the cell indicates the presence of several incompatibility
groups within the repABC plasmid family [19,30,48].
Secondly, phylogenetic analyses of rep regions showed
that repABC plasmids coexisting in the same strain
most probably arose through separate events of lateral
gene transfer, further forcing the appearance of different
new incompatibility groups and allowing co-residence
of plasmids equipped with the same type of replication/
partition machinery in one bacterial cell [30,48,49]. In
regards to the evolution of the repABC operon itself, it
was hypothesized that it presumably originated through
integration of the ctRNA-repC cassette between the
repAB genes and the par-site located immediately
downstream of the repB, separating the repAB genes
from the parS. Afterwards acquisition of some mutations
eliminated the weak promoter of the repC gene [15].
Moreover it was demonstrated that repABC structure
was affected by horizontal gene transfer, resulting in its
dynamic state and different evolutionary history of each
member of the operon [49].
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3. Rhizobial plasmids structure, gene
content and impact on bacterial
cell biology
In recent years, the multipartite genomes have been
sequenced in several symbiotic rhizobial species
including: S. meliloti 1021 [50-52], S. medicae
WSM419 [53], Mesorhizobium loti MAFF303099 [54],
R. leguminosarum: bv. viciae 3841 [17], and trifolii
WSM2304 and WSM1325 [46,47], R. etli CFN42 [36],
R. etli CIAT652 [55] and Sinorhizobium fredii NGR234
(previously Rhizobium sp. NGR234) [56-58], as well
as in phytopathogenic Agrobacterium, namely A.
tumefaciens C58 [59,60], A. radiobacter K84 and A. vitis
S2 [61]. These achievements provided a comprehensive
picture of the distribution of genes and sequences
among multiple replicons in a single cell. They constitute
a virtual gold mine of new available information from
which valuable understanding of the megaplasmid
biology can be extracted.
The model bacterium S. meliloti’s (Sme) 1021
genome is distributed among three replicons: a
chromosome of 3.65 Mb where most housekeeping
and essential genes are found, and two megaplasmids:
pSymA, 1.4 Mb, and pSymB, 1.7 Mb [37,50-52], however
many wild type strains of this species harbor accessory
plasmids ranging in size from 133-150 kb [62]. pSymA
is absolutely necessary for symbiosis, bearing the
nodule formation (nod) and most nitrogen fixation, as
well as some catabolic genes and transporters, but
no essential genes [50-52]. The plasmid can be cured
without affecting growth on complex and minimal media;
however, the strain becomes defective in utilization of
certain carbon sources [63]. Nevertheless, the bacterial
benefit of harboring pSymA seems not to be limited only
to symbiotic properties. It was suggested that pSymA
plays a role in the regulation of the expression of genes
from the other replicons including chromosome and
pSymB [64]. On the other hand, the pSymB cannot
be entirely eliminated from the cell, despite that up to
1.4 Mb of pSymB (pSmeSU47b of Sme strain SU47
- ancestor of Sme 1021), may be deleted, indicating
that the majority of the plasmid is not essential for cell
viability [65]. Plasmid pSymB encodes the biosynthesis
of different surface polysaccharides (12% of the genes),
dicarboxylate transport/utilization, a large number of
solutes transport (20% of the genes), thiamine and
asparagine biosynthesis, amino acids, alcohols, and
aromatic compounds utilization, and a few essential
genes (for example a gene for arg-tRNA.) It also carries
minCDE genes with putative function in cell division,
however they can be deleted without affecting cell
survival [37,52,66,67]. A large segment of this replicon
is required for dulcitol, arabinose, melibiose, raffinose,
P-hydroxybutyrate, acetoacetate, protocatechuate and
quinate utilization [65,68]. Thus, it appears that pSymB
allows the bacteria to take up and metabolize many
different compounds from the environment and plays
an important role in the survival of the bacterium in the
soil under diverse nutritional conditions and adaptation
to both saprophytic and endosymbiotic lifestyles.
Despite the lack of genes directly involved in nodulation
and nitrogen fixation, mutations in some pSymB
genes completely abolish symbiotic nitrogen fixation
[37]. Dinucleotide compositional and codon usage of
pSymB resembles the chromosome and is different
in comparison to pSymA [69,70]. The comparative
analyses of genomic features and a single-nucleotide
polymorphism pattern on different replicons of
Sinorhizobium spp. genomes clearly demonstrated that
DNA recombination among closely related bacteria was
a major event in the diversification of these genomes,
especially in pSymA, resulting in its mosaic structure
[71-73].
The genome of S. medicae WSM419 contains a
chromosome and three plasmids pSmed01 - pSmed03
[53]. The strain is of great agricultural importance because
of its saprophytic competence in the acidic, infertile soils
and its high effectiveness in nitrogen fixation with a
broad range of annual medics of Mediterranean origin.
It was shown that enhanced viability of cells exposed
to lethal acid conditions depended on the pSmed02
located, acid-activated lpiA gene transcription, which
was dispensable for normal cell growth [74].
M. loti (Mlo) strain MAFF303099 is composed of a
single large (7 Mb) chromosome and two small plasmids:
pMLa and pMLb [54]. In contrast to Sme, virtually all
symbiotic genes of Mlo are localized to a ~0.6 Mb
“symbiosis island” on the chromosome, emphasizing
the accessory nature of the genes and their ability to
be acquired via horizontal gene transfer [75,76]. In Mlo
strain R7A, the symbiosis island is transmissible and
its transfer seems to be regulated via quorum sensing
mechanism [76,77]. The plasmids of Mlo do not carry
genes directly involved in symbiosis despite a copy
of noeC gene on pMLa. Moreover, genes of conjugal
transfer, transport system, signal transduction, and
phosphate uptake were found on the plasmids. Mlo
genome appears to be a highly dynamic entity and this is
particularly reflected by the presence of many insertion
sequence (IS) elements and transposases within the
region encoding symbiotic functions [54].
The S. fredii NGR234 (Sfr) genome is partitioned into
three replicons. The 3.93-Mbp chromosome encodes
most functions required for cellular growth. Few
essential metabolic functions and exopolysaccharide
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synthesis are encoded on the 2.43-Mbp megaplasmid
(pNGR234b), and none are present on the second
0.54-Mbp symbiotic plasmid (pNGR234a) [78]. The
complete sequence of pNGR234a showed the presence
of a large amount of reiterated sequences, mainly IS [56],
possibly participating in intragenomic rearrangements
[79,80]. Among many striking features like the ability
to nodulate above hundred of legumes, the genome
encodes more different secretion systems than any
other known rhizobia - many of them are located in
the pNGR234b. Moreover, some genes related to the
biosynthesis of amino acids and cofactors (thi) are
located on this plasmid. In spite of this, there is no firm
indication that pNGR234b is essential for the survival of
the strain [81].
R. etli (Rhe), R. leguminosarum bvs. viciae (Rlv)
and trifoli (Rlt) are closely related species differing
in their host-specificity but displaying very similar
genome organization: a single circular chromosome
and several large plasmids. Each of them carries the
majority of nod-nif-fix genes on the plasmid, named
pSym [17,36,46,47,82], but the pSyms of Rhe, Rlv and
Rlt belong to different incompatibility groups and have
quite different genes content other than those related
to symbiotic performance [14,30,83]. In contrast to
Sme, several major cluster of genes engaged in the
biosynthesis of various surface polysaccharides are
chromosomal. Polysaccharide biosynthesis regions
show a high degree of synteny and sequence identity
between R. leguminosarum and R. etli [84]. Frequently,
no specific function is assigned to the numerous, nonsymbiotic plasmids, but there are also some exceptions.
Most essential Rlv 3841 genes (encoding
transcriptional machinery, ribosomal biosynthesis,
chaperones and cell division) are chromosomal.
Nevertheless, some genes for the biosynthesis of
thiamin, cobalamin, and NAD are located on the
pRL11JI plasmid. Other essential plasmid genes include
major heat-shock chaperone genes cpn10/cpn60
(groES/groEL) on pRL12JI, and ribosomal protein
S21 on pRL10JI (pSym); however, these genes have
chromosomal paralogs so the different copies may be
simply functionally redundant [17,85]. pRL12JI similarly
to the pRetCFN42f of Rhe carries some genes for
flagella biosynthesis and oxidative stress protection [83].
Elimination of pRL12JI from Rlv 1061 strain (derivative
of the same parental strain as the sequenced Rlv 3841),
resulted in an auxotrophic phenotype, which might
severely compromise fitness in nature [86]. Moreover,
in Rlv plasmids, the genes related to intermediary
metabolism, coding for regulation functions, transport
and binding proteins as well as those for cell envelope
structure are fairly abundant [17]. Furthermore, the
plasmid pRL8JI can be considered pea rhizosphere
specific, enabling adaptation of bacteria to their host
in terms of adjusting of the microsymbiont metabolism
to the rhizosphere resources of a particular plant [87].
One of the Rlv plasmids, named pRL7JI, is absolutely
different from the rest of the genome, with more than
80% of its genes being apparently foreign, of unknown
function, or coding for transposases or related proteins.
The plasmid has accumulated multiple mobile elements.
The six plasmids of Rhe CFN42 share many
orthologs with pSymA and pSymB of Sme and the
linear chromosome of A. tumefaciens. Several cluster
of ortholog (COG) categories are overrepresented in
the Rhe plasmid, namely carbohydrate transport and
metabolism, amino acid transport and metabolism,
and transcription (35% of transcriptional regulator
genes are located in the plasmid). The genes related
to nucleotide transport and metabolism, translation,
ribosomal structure, cell wall structure, and biogenesis
and posttranslational modification are absent from the
plasmid. Surprisingly, genes associated with defense
mechanisms are mostly chromosomal [36]. In contrast
to the chromosome, plasmids lack synteny, but the gene
composition of plasmids pRetCNF42b, pRetCNF42c,
pRetCNF42e and pRetCNF42f, and orthologs content
might suggest their membership in the ancestral
genome [36]. Plasmid pRetCNF42a and pRetCNF42d
(pSym), the poorest conserved replicons of Rhe, contain
genes coding for type III and IV transport systems and
ISs. IS elements located on either side of the 125 kb
symbiotic region of the mosaic pRetCNF42d plasmid
and putative integrase gene raises the possibility that
this region itself may be mobile [88]. In general, rather
no essential genes were located on the plasmids.
However deletion analysis of pRetCNF42e led to the
identification of two genes, encoding a hypothetical
protein with a probable winged helix-turn-helix motif
and a probable two-component sensor histidine kinase/
response regulator hybrid protein, respectively, which
are essential for growth in rich medium [89]. Moreover,
pRetCNF42f of Rhe carries panC and panB genes,
which are indispensable for pantothenate synthesis
and required for growth in minimal medium [90].
Putative nitric oxide removal genes are also located
on this plasmid [83]. Nearly 11% of the genes of the
pRetCNF42e are involved in primary metabolism, both
in biosynthetic functions (cobalamin, cardiolipin, NAD,
thiamine) and degradation (asparagine and melibiose)
[36]. Previously, it was suggested that functional
interactions among sequences scattered throughout the
different plasmids of Rhe were required for a successful
completion of both symbiotic and saprophytic lifestyles
[91,92]. The analyses of functional relationships among
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the replicons performed after completion of Rhe genomic
sequence seem to confirm this data. The chromosome
and pRetCNF42b, pRetCNF42c, pRetCNF42e and
pRetCNF42f have a high connectivity value (a predicted
number of interactions per gene), in comparison
to pRetCNF42a and pRetCNF42d. Furthermore
pRetCNF42b,
pRetCNF42c,
pRetCNF42e
and
pRetCNF42f are more interconnected with each other
and to the chromosome than with either pRetCNF42a or
pRetCNF42d, supporting the recent external acquisition
of these two plasmids [36].
Many Rhizobium field isolates appear to carry
several nonsymbiotic plasmids variable in size that
may confer some benefits with regard to overall fitness.
One such plasmid 144 kb pSmeSM11a from Sme has
been sequenced [16]. The genes encoding for proteins
involved in DNA replication, recombination, and repair
as well as those for various metabolic enzymes and
transport systems were found. Furthermore, the
acdS gene (1-amino-cyclopropane-1-carboxylic adcid
deaminase) whose product was postulated to indirectly
promote plant growth during symbiosis by decreasing
ethylene levels was found [93]. The pSmeSM11a-like
plasmid prevailed in indigenous Sme strains isolated
from the field experiments, indirectly confirming the
beneficial traits encoded on such an element [62].
Among Rlt isolates from root nodules of clover plants
growing at the same site, substantial divergence of their
genome organization, especially as regards the plasmid
DNA content, was demonstrated [94]. The strains
harbored from 3 to 6 plasmids (mostly equipped with
repABC type replication system), whose size ranged
approximately from 150 kb to 1380 kb. Most of Rlt
strains had a large (>1 Mb), extrachromosomal replicon.
The genes located on individual plasmids differed in
their adaptation to the host genome, indicating that
the putative evolutionary acquisition of these plasmids
occurred at different times [94]. Furthermore, it was found
that the Rlt nodule strains belonging to defined genetic
groups and varying in the plasmid profile differ also in
metabolic capabilities and symbiotic effectiveness with
clover [95]. It was also demonstrated that Rlt mutants
in plasmid-located rhamnose utilization genes were
significantly impaired in nodulation competitiveness
[96,97]. The rhamnose catabolic genes were inducible
by clover root extracts, suggesting their important role
for early stages of the interaction of Rlt with the host
plant. Similar genes were plasmid-encoded in virtually
all R. leguminosarum strains from all three biovars from
a variety of different geographic origin [96].
Many examples indicate that rhizobial plasmids
contain functionally important genes, which may
contribute to adaptiveness and competitiveness of this
group of bacteria in the rhizosphere. Rhizobia occupy
highly complex and heterogeneous soil habitats, and
their large and multipartite genomes in which the
plasmid component encodes many potentially useful
metabolic traits might be advantageous by enhancing
the adaptive potential [17,89]. In pRL1JI, a pSym
plasmids of R. leguminosarum 248 strain, genes
encoding bacteriocins were identified [98]. Nodulation
competition experiments showed that the presence
of bacteriocin activity in this strain may influence
its competitiveness [99]. Besides aforementioned
rhamonse utilization there are also other examples of
plasmid encoded potentially advantageous catabolic
genes. Rlt plasmids carry genes necessary for utilization
of adonitol, arabinose, catechol, inositol, lactose,
malate and glycerol, which may contribute significantly
to the saprophytic competence of rhizobia in soil
[100-102]. Rlv mutants in glp and ery operons located
on pRlvVF39c and pRlvVF39f of Rlv VF39 unable to
use glycerol and erythritol respectively, were deficient
in competitiveness for nodulation of peas suggesting
that these catabolism genes confer advantages to the
bacterium in the rhizosphere or in the infection threads
[103,104]. The plasmid-cured derivatives of Rhe CFN42
were unable to use glycerol, dulcitol and trigonelline as
a carbon source. Their growth on cellobiose, galactose,
xylitol, and succinate was also diminished [92].
Mutation of stcD gene located in pSymB of Sme 1021
prevents growth on stachydrine as a sole carbon and
nitrogen source, increases salt sensitivity, and impairs
competitive colonization on alfalfa roots [105].
In the discussion of rhizobial plasmids gene content
and impact on bacterial cell biology, the conjugative
properties of plasmid should be noticed. The conjugative
plasmids being a part of bacterial mobilome play central
role in rhizobial adaptation and evolution [106,107].
There are many evidences for plasmid conjugal transfer
among rhizobial strains [108,109], and completion of
several rhizobial genome projects identified numerous
genes and sequences potentially involved in conjugal
transfer (see: Ding and Hynes [110] for review).
Taking into consideration transfer abilities of rhizobial
plasmids, they can be included both to the group of selftransmissible i.e. equipped with components for DNA
transfer and replication, and mating pair formation, as
well as mobilizable - able to transfer only in the presence
of self-transmissible plasmid providing mating pair
formation function in trans [110]. In addition, examples
of plasmids mobilizable by means of cointegration with
another self-transmissible plasmid have been reported
[41,111]. At least two different types of rhizobial plasmids
have been described with respect to the mechanisms
of their conjugal transfer regulation. They comprise
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quorum-sensing regulated plasmids, which transfer
only when cell density is high, and the conjugative
systems repressed by rctA gene [41,112-114]. Moreover
the existence of a third type of conjugative plasmids
differing in terms of regulation and sequence, including
numerous replicons from Rlv has been postulated [110].
Presence of additional replicons also results in
a substantial plasticity and dynamics of the rhizobial
genomes [6,79,92,115], which is further influenced by
plasmid conjugal transfer among rhizobial strains and
horizontal gene transfer [110]. Plasmids contribute
to enlargement of the genome and evolutionary
diversification of rhizobia, which is considered to
be a result of the instability of complex genomes,
lateral acquisition of some regions, gene duplications
or losses, and recombination [116,117]. The most
frequently occurring genome rearrangement events
involve homologous recombination between reiterated
DNA sequences. Thus, possible involvement of
extrachromosomal DNA in these rearrangements is very
plausible.
4. The impact of postgenomic
knowledge to rhizobial plasmid
role and multipartite genome
organization
As more rhizobial genome-sequencing projects were
completed, it became clear that multipartite genomes
are abundant among them. More general questions can
be asked here: what mechanisms led to the emergence
of multipartite genomes in rhizobia and what are the
advantages of having a divided genome? Two potential
hypotheses are taken into account. In the first, called
plasmid hypothesis, a megaplasmid could have been
horizontally acquired. In the second, known as schism
hypothesis, a large ancestor chromosome could have
split into two replicons [118]. It has been proposed
that rhizobial genomes have evolved via expansion:
lateral transfer and gene duplication, as means of
dealing with challenging soil lifestyle [119,120]. The
complexity and heterogeneity of a soil environment
forced the bacteria to enlarge genetic and adaptive
potential and the plasmids were capacious reservoirs
of additional genetic information. That makes plasmid
hypothesis of multipartited rhizobial genomes plausible.
The presence of plasmid gene traits in Bradyrhizobium
and Mesorhizobium chromosomes may suggest the
integration of one or more acquired plasmids into
chromosome [61]. One of the potential advantages
of genome division into multiple smaller replicons
may be reduction of the time necessary for the entire
genome replication, faster generation time and thereby
a competitive advantage [121]. Anyway, the known
complexity of the rhizobial plasmid content and the
presence of some important (or even essential) genes
on them, clearly show that nowadays the rhizobial
genome architecture should not be considered simply
as composed of a chromosome and dispensible
plasmids (one of which is called pSym as it carries a
majority of genes for symbiotic interaction with plants
and the others are cryptic). Analyses of the multipartite
genome Rlv allowed Young et al. [17] to suggest that
rhizobial genome should be considered as composed
of two main components: a stable “core,” which exhibits
a higher G+C content, that is mainly (but not solely)
chromosomal, displays a conserved gene content and
order (synteny), and is shared by related organism.
The phylogeny of the core component is consistent
[17,83,84,122]. On the contrary, the “accessory”
component of the genome has a lower content of G+C,
different nucleotide composition from the core, and
comprises mainly plasmids. Plasmids are prototypically
accessory elements composed of genes from different
evolutionary origin; they lack synteny even in closely
related species, except for genes involved in plasmid
replication and symbiotic properties [17,55,83]. The
accessory component is significant to the cell, however,
very variable, and has an apparently mosaic structure. In
some species, such as R. leguminosarum, the accessory
component may comprise up to 35-45% of the total
genome [6,94]. However, accessory genes could also be
found in the chromosome as chromosomal islands. The
chromosomes of Rlv, Rhe and Rlt possess many distinct
gene islands with typical accessory characteristics
(like different G+C content). For example, a majority of
polysaccharide biosynthesis genes are chromosomal
and there is no distinguishable pExo plasmid such as
the one described previously for Sme carrying exo/exs
clusters [17,36,37,84]. It is likely that they form part of
the accessory genome residing, probably temporarily,
in the chromosome [17]. Concomitantly, a considerable
number of core genes are dispersed between plasmids.
They are often maintained in the syntenic blocks and
have a high level of nucleotide sequence identity
among the homologous segments [55]. In Sfr GR64,
a chimeric transmissible plasmid with segments from
two Rhe plasmids and Sfr chromosome was detected
[123]. The structural complexity and DNA sequence
reiteration located in rhizobial extrachromosomal
replicons could be one of the reasons of the tendency
for genomic rearrangements. As previously shown
for pNGR234a and the Rhe genome, repeated DNA
sequences can promote homologous recombination
and thus lead to genomic rearrangements [36,124]. For
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Rhe, more than 200 reiterated DNA families could be
found, indicating that intra-genomic rearrangements
might indeed be frequently occurring events [90,125],
resulting in structural complexity of rhizobial replicons
[36,88,126]. In turn, the rearrangements in complex
rhizobial genomes might enhance the adaptive potential
of the bacterium, allowing the reassortment of essential,
nonessential, and redundant functions to contend
with challenging environments [36]. The accessory
genome is more flexible than the chromosomes, as
it is defined by more frequent gene gains and losses,
even in the same species, and evolves more rapidly.
It was proposed for pRetCFN42d (pSym) of Rhe that
horizontal transfer and recombination of homologous
DNA segments among closely related organisms, rather
than nucleotide substitutions, is the major source of
its genetic diversification [116]. Latest comparisons
of genomic sequences of Rhe seem to confirm the
significant role of horizontal gene transfer, particularly
via pSym in the diversity of Rhe lineages [127]. Plasmid
evolution is further affected by frequent movement
of extrachromosomal replicons among the strains. In
fact, some of these elements may be transferred to
other bacterial cells by itself or in the presence of other
mobilizing plasmids [73,92,110,111]. Cervantes et al.
[123] showed that Sfr plasmids might originate through
the transfer of a symbiotic-conjugative-plasmid from the
Rhe to a Sfr strain and at least two further recombination
events among the Rhe plasmids and the Sfr genome.
Recently, some (not only rhizobial) extrachromosomal
replicons that have distinct properties from both
chromosome and plasmids were reported and named
“chromids” [128]. In silico analyses showed that chromids
have a nucleotide composition and codon usage close to
that of a chromosome, presumably because of spending
a long time in the same cellular environment [69]. They
are characterized by the presence of some genes
essential for growth under all conditions (however there
are no genes that are universally chromid-encoded), and
by contrast, plasmid replication and partition systems
[128]. However, very few of these genes have been
functionally characterized, so their real contribution to
bacterial metabolism is still an open question. Moreover,
some of the putative chromids are easy to cure
[86,129]. The chromids are normally larger than the
remaining plasmid but smaller than the chromosome,
but one should keep in mind that some replicons labeled
chromids are obviously fusions of two replicons e.g.
largest plasmid of Rlt WSM2304 [47]. Recent studies of
Rlt isolates from root nodules of clover plants showed
that three clearly distinguishable genome compartments
could be observed: the chromosome, chromid-like and
‘other plasmids’ including pSym. Most Rlt strains had
a large (>1 Mb) chromid-like replicon. Conservation of
gene location especially those of chromid-like replicons,
was reported. The ‘other plasmids’ genes were less
adapted to the host genome than the chromosome and
chromid-like genes [94]. The properties of chromids,
which may be sometimes inconclusive, raise the question
about the robustness of this concept at all. Taking into
consideration the dynamic nature of large and complex
rhizobial genomes with continuously evolving replicons
it cannot be excluded that the chromid concept will
fail in some cases. Nevertheless, the genes located
on chromids are potentially as stable as those on the
chromosomes and such replicons are usually difficult
to eliminate from the cells [89]. Thus, chromids already
carrying several important, beneficial or essential
genes may facilitate broadening the bacterial metabolic
potential through acquisition of foreign adaptive genes
by horizontal transfer and stabilizing the new set of
advantageous genes in the genome without an actual
chromosome enlargement. It was proposed that the
chromid should be called the “lifestyle-determining
replicon” [130].
Studies of the Rhe genome allowed identification,
among the set of its plasmids, of the one (pRetCNF42e)
with a potential chromosome-role (secondary
chromosome) [89]. This data add a new perspective
to the discussion of rhizobial plasmid dispensability or
indispensability. The secondary chromosomes can be
identified both by unique localization of some essential
loci, like rRNA or tRNA in the case of A. tumefaciens
and A. vitis replicons with rRNA operons as well as
genes for prototrophic growth [59,61], and by the
inability of total elimination from the cell, which was the
case for Rhe pRetCNF42e [89,91]. Deletion analyses
of pRetCNF42e revealed the presence of genes, which
are essential for growth in rich medium. The equivalents
of pRetCNF42e are also found in other Rhizobium
species, namely pRL11JI in Rlv 3841 [17], pRLG202 in
Rlt WSM2304 [47], pRLG132502 in Rlt WSM1325 [46],
and pRleTA1b in Rlt TA1 [30]. At least the latter one,
similarly to pRetCNF42e, cannot be entirely eliminated
from the cell by incompatibility purposes leading instead
to its cointegration with other extrachromosomal
replicons residing in the bacterium [30]. From one point
of view such behavior seems to be consistent with the
expectation that the loss of these replicons may be
lethal even in rich medium, and may contribute to their
secondary chromosome role in bacteria. On the other
hand, it was shown previously that using combined
selection of sensitivity to sucrose and exposition to
supra-optimal temperatures derivatives of Rlv strain
1062, 3855, VF39SM [86,129], W11-9, W8-7 [100]
cured of individual plasmid (irrespectively of their size)
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can be obtained. Moreover a plasmid-less derivative of
Rlt W14-2 was obtained [131], indicating that ability of
plasmid curing may be strain specific.
With regards to the evolution of secondary
chromosomes, at least one of the potential forces can be
taken into consideration, i.e. the intragenomic displacement
of genes across replicons also including their replication
systems [49,61,94]. Comparison of genome sequences
of three Agrobacterium biovars showed that most gene
movements have occurred from the ancestral chromosome
to the plasmid replicons with only rare retrotransfers
mediating second-chromosome formation [61]. Thus, a
plasmid became a secondary chromosome presumably
by acquisition of the core genes with simultaneous or
subsequent loss of original copies. This event occurs
rarely, but its effect seems to be evolutionarily stable [128].
Due to difficulties encountered in exact localization
of the “rhizobial core genome,” a pan-genomic concept
was employed for R. etli strains [55]. A pangenome
“determines the core genome, which consists of genes
shared by all the strains studied and probably encoding
functions related to the basic biology and phenotypes of
the species” [132]. The basis of the pangenomic structure
of bacterial genomes emerged from an observation that
each newly sequenced genome enriched the pool of
species-specific genes with new ones [132,133]. Thus
sequencing of genomes of numerous strains makes
it possible to detect, besides the core genomes, the
dispensable genomes composed of both chromosomal
and plasmid genes present only in some of the strains,
which contribute to species diversity and allow adaptation
to new ecological niches and a specific environment
[134]. The complete genome sequence of Rhe CIAT652
and the partial genomic sequences of six additional Rhe
strains of different geographical origins were compared to
each other and to Rhe CFN42 [36,55]. The strains were
variable with respect to the number and size of plasmids.
DNA sequences common to all strains constituted the
greater part of these genomes and they were localized in
both the chromosome and large plasmids. Nevertheless,
a large amount of DNA was unique to individual Rhe
strains. The unique sequences encoding accessory
functions were distributed throughout the chromosome
as individual genes or chromosomal islands and in
plasmids. Surprisingly, the symbiotic plasmids previously
described as a major source of genome diversity of Rhe
lineages [127], showed high levels of nucleotide identity
(about 98 to 99%). These results support the concept
of the pangenomic structure at the multireplicon level of
Rhe with a core genome composed of both chromosomal
and plasmid sequences, including a highly conserved
symbiotic plasmid present in divergent Rhe isolates [55].
Presumably, the postulated core character of the
pSym plasmid could underlie the investigation of a
core “symbiome” - the essential genes required by
all rhizobia for nodulation and nitrogen fixation [135].
However, the comparative genomic studies of 14
rhizobial strains raised some doubts about the feasibility
of such a universal definition. One of the potential
reasons could be the aforementioned complex structure
of rhizobial genomes comprising differences in the set
of symbiotic regions as well as their distribution between
chromosomes and plasmids in various species [135].
5. Conclusions
Rhizobial plasmids have widely evolved a repABCbased replication system, which is unusual in terms
of its organization and the presence of elements
necessary for segregation/partition, replication, and
incompatibility in the same transcriptional unit. The tight
control of replication genes provides plasmid stability
and ensures inheritance of biologically important
genetic material. It is believed that plasmids constitute
a pool of accessory genetic information important to
the cell, enabling adaptation of bacteria to the host
and soil environment. In general, plasmids contribute
to plasticity, enlargement of genome and evolutionary
diversification of rhizobia. As a consequence of
genome rearrangements or lateral transfer, some
rhizobial plasmids evolved into chromids or even
secondary chromosomes presumably by acquisition of
some core genes and became indispensible for normal
growth under all conditions. From that perspective, the
definition of the rhizobial genome comprising strictly
core (chromosomal) and accessory (plasmid) elements
became blurred. Division of the rhizobial genome into
three compartments, i.e. the chromosome, chromids
or chromosome-like replicons and other plasmid
including pSym, also seems not to be fully adequate
given the proposed pangenomic structure of some
rhizobial genomes with the core genome composed of
both chromosomal and plasmid sequences including
a highly conserved symbiotic plasmid. These data
clearly underscore the importance of undertaking
subsequent sequencing projects in resolving the issue
concerning rhizobial genome organization. At least one
conclusion seems to be fully legitimate: for bacteria
possessing multipartite genomes and persisting in
various environments, the cooperation among all the
replicons might be necessary to provide the basic
cellular function and presumably competitiveness with
other microorganisms and in various environments.
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References
[1]
[2]
[3]
[4]
[5]
[6]
[7]
[8]
[9]
[10]
[11]
[12]
[13]
[14]
[15]
Perret X., Staehelin C., Broughton W.J., Molecular
basis of symbiotic promiscuity, Microbiol. Mol. Biol.
Rev., 2000, 64, 180-201
Den Herder G., Parniske M., The unbearable
naivety of legumes in symbiosis, Curr. Opin. Plant.
Biol., 2009,12, 491-9
Gibson K.E., Kobayashi H., Walker G.C., Molecular
determinants of a symbiotic chronic infection,
Annu. Rev. Genet., 2008, 42, 413-41
Jones K.M., Kobayashi H., Davies B.W., Taga
M.E., Walker G.C., How rhizobial symbionts invade
plants: the Sinorhizobium-Medicago model, Nat.
Rev. Microbiol., 2007, 5, 619-633
Masson-Boivin C., Giraud E., Perret X., Batut
J., Establishing nitrogen-fixing symbiosis with
legumes: how many rhizobium recipes?, Trends
Microbiol., 2009, 17, 458-466
Palacios R, Newton W.E., Genomes and genomics
of nitrogen-fixing organisms, (Ed.), Palacios
R., Newton W.E., Springer, Dordrecht, The
Netherlands, 2005
Watson R.J., Heys R., Replication regions of
Sinorhizobium meliloti plasmids, Plasmid, 2006,
55, 87-98
Barran L.R., Ritchot N., Bromfield E.S.P.,
Sinorhizobium meliloti plasmid pRm1132f replicates
by a rolling-circle mechanism, J. Bacteriol., 2001,
183, 2704–2708
Thomas C.M., Paradigm of plasmid organization,
Mol. Microbiol., 2000, 37, 485-491
Campbell S.C., Mullins R.D., In vivo visualization
of type II plasmid segregation: bacterial actin
filaments pushing plasmids, J. Cell Biol., 2007,
179, 1059-1066
Schumacher M.A., Structural biology of plasmid
partition: uncovering the molecular mechanisms of
DNA segregation, Biochem. J., 2008, 412, 1-18
Gerdes K., Howard M., Szardenings F., Pushing
and pulling in prokaryotic DNA segregation, Cell,
2010, 141, 927-942
Hao J.J., Yarmolinsky M., Effects of the P1 plasmid
centromere on expression of P1 partition genes, J.
Bacteriol., 2002, 184, 4857-67
Cevallos M.A., Cervantes-Rivera R., GutiérrezRíos R.M., The repABC plasmid family, Plasmid,
2008, 60, 19-37
Izquierdo J., Venkova-Canova T., Ramírez-Romero
M.A., Téllez-Sosa J., Hernández-Lucas I., Sanjuan
J., et al., An antisense RNA plays a central role in
the replication control of a repC plasmid, Plasmid,
2005, 54, 259-277
[16] Stiens M., Schneiker S., Keller M., Kuhn S.,
Pühler A., Schlüter A., Sequence analysis of the
144-kilobase accessory plasmid pSmeSM11a,
isolated from a dominant Sinorhizobium meliloti
strain identified during a long-term field release
experiment, Appl. Environ. Microbiol., 2006, 72,
3662-3672
[17] Young J.P., Crossman L.C., Johnston A.W.,
Thomson N.R., Ghazoui Z.F., Hull K.H., et al.,
Rhizobium leguminosarum has recognizable core
and accessory components, Genome Biol., 2006,
7, R34
[18] Ramirez-Romero M.A., Soberon N., PerezOsequera A., Tellez-Sosa J., Cevallos M.A.,
Structural elements required for replication and
incompatibility of the Rhizobium etli symbiotic
plasmid, J. Bacteriol., 2000, 182, 3117-3124
[19] Ramírez-Romero M.A., Téllez-Sosa J., Barrios
H., Pérez-Oseguera A., Rosas V., Cevallos M.A.,
RepA negatively autoregulates the transcription of
the repABC operon of the Rhizobium etli symbiotic
plasmid basic replicon, Mol. Microbiol., 2001, 42,
195-204
[20] MacLellan S.R., Zaheer R., Sartor A.L., MacLean
A.M., Finan T.M., Identification of a megaplasmid
centromere reveals genetic structural diversity
within the repABC family of basic replicons, Mol.
Microbiol., 2006, 59, 1559-1575
[21] Bignel C., Thomas C.M., The bacterial ParA-ParB
partitioning proteins, J. Biotechnol., 2001, 91, 1-34
[22] Williams D.R., Thomas C.M., Active partitioning of
bacterial plasmids, J. Gen. Microbiol., 1992, 138,
1-16
[23] Gerdes K., Møller-Jensen J., Bugge-Jensen R.,
Plasmid and chromosome partitioning: surprises
from phylogeny, Mol. Microbiol., 2000, 37, 455-66
[24] Bartosik D., Baj J., Włodarczyk M., Molecular and
functional analysis of pTAV320. a repABC-type
replicon of the Paracoccus versutus composite
plasmid pTAV1, Microbiol., 1998, 144, 3149-3157
[25] Cervantes-Rivera R., Pedraza-López F., PérezSegura G., Cevallos M.A., The replication origin of
a repABC plasmid, BMC Microbiol., 2011, 11, 158
[26] Cervantes-Rivera R., Romero-López C., BerzalHerranz A., Cevallos M.A., Analysis of the
mechanism of action of the antisense RNA that
controls the replication of the repABC plasmid
p42d, J. Bacteriol., 2010, 192, 3268-78
[27] MacLellan S.R., Smallbone L.A., Sibley C.D.,
Finan T.M., The expression of a novel antisense
gene mediates incompatibility within the large
581
Unauthenticated
Download Date | 6/19/17 6:30 AM
Rhizobial plasmids - replication, structure
and biological role
[28]
[29]
[30]
[31]
[32]
[33]
[34]
[35]
[36]
[37]
[38]
[39]
repABC family of alpha-proteobacterial plasmids,
Mol. Microbiol., 2005, 55, 611-623
Venkova-Canova T., Soberón N.E., RamírezRomero M.A., Cevallos M.A., Two discrete elements
are required for the replication of a repABC plasmid:
an antisense RNA and a stem-loop structure, Mol.
Microbiol., 2004, 54, 1431-1444
Chai Y., Winans S.C., A small antisense RNA
downregulates expression of an essential
replicase protein of an Agrobacterium tumefaciens
Ti plasmid, Mol Microbiol., 2005, 56, 1574-1585
Mazur A., Majewska B., Stasiak G., Wielbo J.,
Skorupska A., repABC-based replication systems of
Rhizobium leguminosarum bv. trifolii TA1 plasmids:
incompatibility and evolutionary analyses, Plasmid,
2011, 66, 53-66
Chai Y., Winans S.C., RepB protein of an
Agrobacterim tumefaciens Ti plasmid binds to two
adjacent sites between repA and repB for plasmid
partitioning and autorepression, Mol. Microbiol.,
2005, 58, 1114-1129
Livny J., Yamaichi Y., Waldor M.K., Distribution
of centromere-like parS sites in bacteria: insights
from comparative genomics, J. Bacteriol., 2007,
189, 8693-8703
Novick, R.P., Plasmid incompatibility, Microbiol
Rev., 1987, 51, 381–395
Austin S., Nordström K., Partition-mediated
incompatibility of bacterial plasmids, Cell, 1990,
60, 351-354
Soberón N., Venkova-Canova T., Ramírez-Romero
M.A., Téllez-Sosa J., Cevallos M.A., Incompatibility
and the partitioning site of the repABC basic
replicon of the symbiotic plasmid from Rhizobium
etli, Plasmid, 2004, 51, 203-216
Gonzalez V., Santamaria R.I., Bustos S.,
Hernandez-Gonzales I., Medrano-Soto A., MorenoHagelsieb G., et al., The partitioned Rhizobium etli
genome: genetic and metabolic redundancy in
seven interacting replicons, Proc. Natl. Acad. Sci.
USA, 2006, 103, 3834-3839
Finan T.M., Weidner S., Wong K., Buhrmester
J., Chain P., Vorhölter F.J., et al., The complete
sequence of the 1,683-kb pSymB megaplasmid
from the N2-fixing endosymbiont Sinorhizobium
meliloti, Proc. Natl. Acad. Sci. USA, 2001, 98.
9889-9894
Park K., Chattoraj D.K., DnaA boxes in the P1
plasmid origin: the effect of their position on the
directionality of replication and plasmid copy
number, J. Mol. Biol., 2001, 310, 69-81
Pappas K.M., Winans S.C., The RepA and RepB
autorepressors and TraR play opposing roles in
[40]
[41]
[42]
[43]
[44]
[45]
[46]
[47]
[48]
[49]
[50]
the regulation of a Ti plasmid repABC operon, Mol.
Microbiol., 2003, 49, 441-455
Pappas K.M., Winans S.C., A LuxR-type regulator
from Agrobacterium tumefaciens elevates Ti
plasmid copy number by activating transcription of
plasmid replication genes, Mol. Microbiol., 2003,
28, 1059-1073
Tun-Garrido C., Bustos P., González V., Brom S.,
Conjugative transfer of p42a from rhizobium etli
CFN42, which is required for mobilization of the
symbiotic plasmid, is regulated by quorum sensing,
J Bacteriol., 2003, 185,1681-1692
White C.E., Winans S.C., The quorum-sensing
transcription factor TraR decodes its DNA binding
site by direct contacts with DNA bases and by
detection of DNA flexibility, Mol. Microbiol., 2007,
64, 245-56
Turner S.L., Rigottier-Gois L., Power R.S., Amarger
N., Young J.P., Diversity of repC plasmid-replication
sequences
in
Rhizobium
leguminosarum,
Microbiology, 1996, 142, 1705-1713
Palmer K.M., Turner S.L., Young J.P., Sequence
diversity of the plasmid replication gene repC in the
Rhizobiaceae, Plasmid, 2000, 44, 209-219
Fondi M., Bacci G., Brilli M., Papaleo M.C.,
Mengoni A., Vaneechoutte M., et al., Exploring
the evolutionary dynamics of plasmids: the
Acinetobacter pan-plasmidome, BMC Evol. Biol.,
2010, 24, 10-59
Reeve W., O’Hara G., Chain P., Ardley J., Brau L.,
Nandesena K., et al., Complete genome sequence of
Rhizobium leguminosarum bv. trifolii strain WSM1325,
an effective microsybiont of annual Mediterranean
clovers, Stand. Genomic Sci., 2010, 2, 347-356
Reeve W., O’Hara G., Chain P., Ardley J., Brau
L., Nandesena K., et al., Complete genome
sequence of Rhizobium leguminosarum bv. trifolii
strain WSM2304, an effective microsymbiont of
the South America clover Trifolium polymorphum,
Stand. Genomic. Sci., 2010, 2, 66-76
Cevallos M.A., Porta H., Izquierdo J., Tun-Garrido
C., García-de-los-Santos A., Dávila G., et al.,
Rhizobium etli CFN42 contains at least three
plasmids of the repABC family: a structural and
evolutionary analysis, Plasmid, 2002, 48, 104-116
Castillo-Ramírez S., Vázquez-Castellanos J.F.,
González V., Cevallos M.A., Horizontal gene
transfer and diverse functional constrains within
a common replication-partitioning system in
Alphaproteobacteria: the repABC operon, BMC
Genomics, 2009, 18, 536
Barnett M.J., Fisher R.F., Jones T., Komp C., Abola
A.P., Barloy-Hubler F., et al., Nucleotide sequence
582
Unauthenticated
Download Date | 6/19/17 6:30 AM
A. Mazur, P. Koper
[51]
[52]
[53]
[54]
[55]
[56]
[57]
[58]
[59]
[60]
[61]
and predicted functions of the entire Sinorhizobium
meliloti pSymA megaplasmid, Proc. Natl. Acad.
Sci. USA, 2001, 98, 9883-9888
Capela D., Barloy-Hubler F., Gouzy J., Bothe
G., Ampe F., Batut J., et al., Analysis of the
chromosome sequence of the legume symbiont
Sinorhizobium meliloti strain 1021, Proc. Natl.
Acad. Sci. USA, 2001, 98, 9877-9882
Galibert F., Finan T.M., Long S.R., Puhler A., Abola
P., Ampe F., et al., The composite genome of the
legume symbiont Sinorhizobium meliloti, Science,
2001, 293, 668-672
Reeve W., Chain P., O’Hara G., Ardley J.,
Nandesena K., Bräu L., et al., Complete genome
sequence of the Medicago microsymbiont Ensifer
(Sinorhizobium) medicae strain WSM419, Stand.
Genomic Sci., 2010, 2, 77-86
Kaneko T., Nakamura Y., Sato S., Asamizu E.,
Kato T., Sasamoto S., et al., Complete genome
structure of the nitrogen-fixing symbiotic bacterium
Mesorhizobium loti, DNA Res., 2000, 7, 331–338
González V., Acosta J.L., Santamaría R.I., Bustos
P., Fernández J.L., Hernández-González I.L., et
al., Conserved symbiotic plasmid DNA sequences
in the multireplicon pangenomic structure of
Rhizobium etli, Appl. Environ. Microbiol., 2010, 76.
1604-1614
Freiberg C., Fellay R., Bairoch A., Broughton
W.J., Rosenthal A., Perret X., Molecular basis
of symbiosis between Rhizobium and legumes,
Nature, 1997, 387, 394-401
Streit W.R., Schmitz R.A., Perret X., Staehelin C.,
Deakin W.J., Raasch C., Liesegang H., Broughton
W.J., An evolutionary hot spot: the pNGR234b
replicon of Rhizobium sp. strain NGR234, J.
Bacteriol., 2004, 186, 535-542
Viprey V., Rosenthal A., Broughton W.J., Perret
X., Genetic snapshots of the Rhizobium species
NGR234 genome, Genome Biol., 2000, 1, 0014.1–
0014.17
Goodner B., Hinkle G., Gattung S., Miller N.,
Blanchard M., Qurollo B., et al., Genome sequence
of the plant pathogen and biotechnology agent
Agrobacterium tumefaciens C58, Science, 2001,
294, 2323-2328
Wood D.W., Setubal J.C., Kaul R., Monks D.E.,
Kitajima J.P., Okura V.K., et al., The genome
of the natural genetic engineer Agrobacterium
tumefaciens C58, Science, 2001, 294, 2317-2323
Slater S.C., Goldman B.S., Goodner B., Setubal
J.C., Farrand S.K., Nester E.W., et al., Genome
sequences of tree Agrobacterium biovars help
elucidate the evolution of multichromosome
[62]
[63]
[64]
[65]
[66]
[67]
[68]
[69]
[70]
[71]
[72]
genomes in bacteria, J.Bacteriol., 2009, 191, 25012511
Kuhn S., Stiens M., Pühler A., Schlüter A.,
Prevalence of pSmeSM11a-like plasmids in
indigenous Sinorhizobium meliloti strains isolated
in the course of a field release experiment with
genetically modified S. meliloti strains, FEMS
Microbiol. Ecol., 2008, 63, 118-131
Oresnik I.J., Liu S.L., Yost C.K., Hynes M.F.,
Megaplasmid pRme2011a of Sinorhizobium
meliloti is not required for viability, J. Bacteriol.,
2000, 182, 3582-3586
Chen H., Higgins J., Oresnik I.J., Hynes M.F.,
Natera S., Djordjevic M.A., et al., Proteome
analysis demonstrates complex replicon and
luteolin interactions in pSyma-cured derivatives of
Sinorhizobium meliloti strain 2011, Electrophoresis,
2000, 21, 3833-3842
Charles T.C., Finan T.M., Analysis of a 1600-kilobase
Rhizobium meliloti megaplasmid using defined
deletions generated in vivo, Genetics, 1991, 127,
5-20
Cheng J., Sibley C.D., Zaheer R., Finan T.M.,
A Sinorhizobium meliloti minE mutant has an
altered morphology and exhibits defects in legume
symbiosis, Microbiology, 2007, 153, 2375-2387
Finan T.M., Kunkel B., De Vos G.F., Signer E.R.,
Second symbiotic megaplasmid in Rhizobium
meliloti carrying exopolysaccharide and thiamine
synthesis genes. J. Bacteriol., 167, 66-72
Poysti N.J., Loewen E.D., Wang Z., Oresnik I.J.,
Sinorhizobium meliloti pSymB carries genes
necessary for arabinose transport and catabolism.
Microbiology, 2007, 153, 727-736
Wong K., Finan T.M., Golding G.B., Dinucleotide
compositional analysis of Sinorhizobium meliloti
using the genome signature: distinguishing
chromosomes and plasmids, Funct. Integr.
Genomics, 2002, 2, 274-281
Peixoto L., Zavala A., Romero H., Musto H., The
strength of translational selection for codon usage
varies in the three replicons of Sinorhizobium
meliloti, Gene, 2003, 320, 109-116
Giuntini E., Mengoni A., De Filippo C., Cavalieri
D., Aubin-Horth N., Landry C.R., et al., Largescale genetic variation of the symbiosis-required
megaplasmid pSymA revealed by comparative
genomic analysis of Sinorhizobium meliloti natural
strains, BMC Genomics, 2005, 6, 158
Guo X., Flores M., Morales L., García D., Bustos
P., González V., et al., DNA diversification in two
Sinorhizobium species, J. Bacteriol., 2007, 189,
6474-6476
583
Unauthenticated
Download Date | 6/19/17 6:30 AM
Rhizobial plasmids - replication, structure
and biological role
[73] Bailly X., Olivieri I., Brunel B., Cleyet-Marel J.C.,
Béna G., Horizontal gene transfer and homologous
recombination drive the evolution of the nitrogenfixing symbionts of Medicago species, J. Bacteriol.,
2007, 189, 5223-5236
[74] Reeve W.G., Bräu L., Castelli J., Garau G.,
Sohlenkamp C., Geiger O., et al., The Sinorhizobium
medicae WSM419 lpiA gene is transcriptionally
activated by FsrR and required to enhance survival
in lethal acid conditions, Microbiology, 2006, 152,
3049-3059
[75] Sullivan J.T., Ronson C.W., Evolution of rhizobia
by acquisition of a 500-kb symbiosis island that
integrates into a phe-tRNA gene, Proc. Natl. Acad.
Sci. USA, 1998, 95, 5145-5149
[76] Sullivan J.T., Trzebiatowski J.R., Cruickshank
R.W., Gouzy J., Brown S.D., Elliot R.M., et al.,
Comparative sequence analysis of the symbiosis
island of Mesorhizobium loti strain R7A, J.
Bacteriol., 2002, 184, 3086-3095
[77] Ramsay J.P., Sullivan J.T., Jambari N., Ortori
C.A., Heeb S., Williams P., et al., A LuxRI-family
regulatory system controls excision and transfer
of the Mesorhizobium loti strain R7A symbiosis
island by activating expression of two conserved
hypothetical genes, Mol. Microbiol., 73, 1141–
1155
[78] Flores M., Mavingui P., Girard L., Perret X.,
Broughton W.J., Martínez-Romero E., et al., Three
replicons of Rhizobium sp. Strain NGR234 harbor
symbiotic gene sequences, J. Bacteriol., 1998,
180, 6052-6053
[79] Mavingui P., Flores M., Guo X., Dávila G., Perret
X., Broughton W.J., et al., Dynamics of genome
architecture in Rhizobium sp. strain NGR234, J.
Bacteriol., 2002, 184, 171-176
[80] Flores M., Mavingui P., Perret X., Broughton W.J.,
Romero D., Hernández G., et al., Prediction,
identification, and artificial selection of DNA
rearrangements in Rhizobium: toward a natural
genomic design, Proc. Natl. Acad. Sci. USA, 2000,
97, 9138-9143
[81] Schmeisser C., Liesegang H., Krysciak D., Bakkou
N., Le Quéré A., Wollherr A., et al., Rhizobium sp.
strain NGR234 possesses a remarkable number of
secretion systems, Appl. Environ. Microbiol., 2009,
75, 4035-4045
[82] Król J.E., Mazur A., Marczak M., Skorupska
A., Application of physical and genetic map of
Rhizobium leguminosarum bv. trifolii TA1 to
comparison of three closely related rhizobial
genomes, Mol. Genet. Genomics, 2008, 279, 107121
[83] Crossman L.C., Castillo-Ramírez S., McAnnula
C., Lozano L., Vernikos G.S., Acosta J.L., et al.,
A common genomic framework for a diverse
assembly of plasmids in the symbiotic nitrogen
fixing bacteria, PLoS One, 2008, 3, 2567
[84] Król J.E., Mazur A., Marczak M., Skorupska
A., Syntenic arrangements of the surface
polysaccharide biosynthesis genes in Rhizobium
leguminosarum, Genomics, 2007, 89, 237-247
[85] Rodríguez-Quiñones F., Maguire M., Wallington
E.J., Gould P.S., Yerko V., Downie J.A., et al.,
Two of the three groEL homologues in Rhizobium
leguminosarum are dispensable for normal growth,
Arch. Microbiol., 2005, 183, 253–265
[86] Hynes M.F., Quandt J., O’Connell M.P., Pühler
A., Direct selection for curing and deletion of
Rhizobium plasmids using transposons carrying
the Bacillus subtilis sacB gene, Gene, 1989, 78,
111–120
[87] Ramachandran V.K., East A.K., Karunakaran
R., Downie J.A., Poole P.S., Adaptation of
Rhizobium leguminosarum to pea, alfalfa
and sugar beet rhizospheres investigated by
comparative transcriptomics, Genome Biol.,
2011, 12, R106
[88] González V., Bustos P., Ramírez-Romero M.A.,
Medrano-Soto A., Salgado H., HernándezGonzález I., et al., The mosaic structure of the
symbiotic plasmid of Rhizobium etli CFN42 and its
relation to other symbiotic genome compartments,
Genome Biol., 2003, 4, R36
[89] Landeta C., Davalos A., Cevallos M.A., Geiger O.,
Brom S., Romero D., Plasmids with a chromosomelike role in Rhizobium, J. Bacteriol., 2011, 193,
1317-1326
[90] Villaseñor T., Brom S., Dávalos A., Lozano L.,
Romero D., Los Santos A.G., Housekeeping
genes essential for pantothenate biosynthesis are
plasmid-encoded in Rhizobium etli and Rhizobium
leguminosarum, BMC Microbiol., 2011, 11, 66
[91] Brom S., García de los Santos A., Stepkowsky T.,
Flores M., Dávila G., Romero D., et al., Different
plasmids of Rhizobium leguminosarum bv. phaseoli
are required for optimal symbiotic performance, J.
Bacteriol., 1992, 174, 5183-5189
[92] Brom S., García-de los Santos A., Cervantes L.,
Palacios R., Romero D., In Rhizobium etli symbiotic
plasmid transfer, nodulation competitivity and
cellular growth require interaction among different
replicons, Plasmid, 2000, 44, 34-43
[93] Glick B.R., Modulation of plant ethylene levels
by the bacterial enzyme ACC deaminase, FEMS
Microbiol. Lett., 2005, 251, 1-7
584
Unauthenticated
Download Date | 6/19/17 6:30 AM
A. Mazur, P. Koper
[94]
[95]
[96]
[97]
[98]
[99]
[100]
[101]
[102]
[103]
[104]
Mazur A., Stasiak G., Wielbo J., Kubik-Komar A.,
Marek-Kozaczuk M., Skorupska A., Intragenomic
diversity of Rhizobium leguminosarum bv. trifolii
clover nodule isolates, BMC Microbiol., 2011, 11,
123
Wielbo J., Marek-Kozaczuk M., Mazur A., KubikKomar A., Skorupska A., Genetic and metabolic
divergence within a Rhizobium leguminosarum
bv. trifolii population recovered from clover
nodules, Appl. Environ. Microbiol., 2010, 76,
4593-4600
Oresnik I.J., Pacarynuk L.A., O’Brien S.A.P., Yost
C.K., Hynes M.F., Plasmid-encoded catabolic
genes in Rhizobium leguminosarum bv. trifolii:
evidence for a plant-inducible rhamnose locus
involved in competition for nodulation Mol. PlantMicrobe Interact., 1998, 11, 1175-1185
Richardson J.S., Hynes M.F., Oresnik I.J., A
genetic locus necessary for rhamnose uptake
and catabolism in Rhizobium leguminosarum bv.
trifolii, J. Bacteriol., 2004, 186, 8433-8442
Hirsch P.R., Van Montagu M., Johnston A.W.B.,
Brewin N.J., Schell J., Physical identification of
bacteriocinogenic, nodulation and other plasmids
in strains of Rhizobium leguminosarum, J. Gen.
Microbiol., 1980, 120, 403-412
Oresnik I.J., Twelker S., Hynes M.F., Cloning and
characterization of a Rhizobium leguminosarum
gene encoding a bacteriocin with similarities to
RTX toxins. Appl. Environ. Microbiol., 1999, 65,
2833-2840
Baldani J.I., Weaver R. W., Hynes M.F.,
Eardly B.D., Utilization of carbon substrates,
electrophoretic enzyme patterns, and symbiotic
performance of plasmid-cured clover rhizobia,
Appl. Environ. Microbiol., 1992, 58, 2308–2314
Moënne-Loccoz Y., Weaver R.W., Plasmids
influence growth of rhizobia in the rhizosphere
of clover, Soil Biol. Biochem., 1995, 27, 1001–
1004
Moënne-Loccoz Y., Weaver R.W., Involvement of
plasmids in saprophytic performance and sodium
chloride tolerance of clover rhizobia W14-2 in
vitro, App. Soil Ecol., 1996, 3, 137–148
Ding H., Yip C.B., Geddes B.A., Oresnik I.J.,
Hynes M.F., Glycerol utilization by Rhizobium
leguminosarum requires an ABC transporter and
affects competition for nodulation, Microbiology,
2012, 158, 1369-1378
Yost C.K., Rath A.M., Noel T.C., Hynes M.F.,
Characterization of genes involved in erythritol
catabolism in Rhizobium leguminosarum bv.
viciae, Microbiology, 2006, 152, 2061-2074
[105] Phillips D.A., Sande E.S., Vriezen J.A.C., de
Bruijn F.J., Le Rudulier D., Joseph C.M., A
new genetic locus in sinorhizobium meliloti is
involved in stachydrine utilization, Appl. Environ.
Microbiol., 1998, 64, 3954-3960
[106] Pistorio M., Giusti M.A., Del Papa M.F., Draghi
W.O., Lozano M.J., Tejerizo G.T., Lagares A.,
Conjugal properties of the Sinorhizobium meliloti
plasmid mobilome, FEMS Microbiol. Ecol., 2008,
65, 372-382
[107] Toussaint A., Chandler M., Prokaryote genome
fluidity: toward a system approach of the
mobilome, Methods Mol. Biol., 2012, 804, 57-80
[108] Djordjevic M.A., Zurkowski W., Shine J., Rolfe B.G.,
Sym plasmid transfer to various symbiotic mutants
of Rhizobium trifolii, R. leguminosarum, and R.
meliloti, J. Bacteriol., 1983, 156, 1035-1045
[109] Brom S., Girard L., García-de los Santos A.,
Sanjuan-Pinilla J.M., Olivares J., Sanjuan J.,
Conservation of plasmid-encoded traits among
bean-nodulating Rhizobium species, Appl.
Environ. Microbiol., 2002, 68, 2555-2561
[110] Ding H., Hynes M.F., Plasmid transfer systems
in the rhizobia, Can. J. Microbiol., 2009, 55, 917927
[111] Brom S., Girard L., Tun-Garrido C., García-de los
Santos A., Bustos P., González V., et al., Transfer
of the symbiotic plasmid of Rhizobium etli CFN42
requires cointegration with p42a, which may
be mediated by site-specific recombination, J.
Bacteriol., 2004, 186, 7538-7548
[112] Piper K.R., Farrand S.K., Quorum sensing but
not autoinduction of Ti plasmid conjugal transfer
requires control by the opine regulon and the
antiactivator TraM, J. Bacteriol., 2000, 182, 10801088
[113] McAnulla C., Edwards A., Sanchez-Contreras
M., Sawers R.G., Downie J.A., Quorum-sensingregulated transcriptional initiation of plasmid
transfer and replication genes in Rhizobium
leguminosarum biovar viciae, Microbiology,
2007, 153, 2074-2082
[114] Pérez-Mendoza D., Sepúlveda E., Pando
V., Muñoz S., Nogales J., Olivares J., et al.,
Identification of the rctA gene, which is required
for repression of conjugative transfer of rhizobial
symbiotic megaplasmids, J. Bacteriol., 2005,
187, 7341-7350
[115] MacLean A.M., Finan T.M., Sadowsky M.J.,
Genomes of the symbiotic nitrogen-fixing bacteria
of legumes, Plant Physiol., 2007, 144, 615-622
[116] Flores M., Morales L., Avila A., González V.,
Bustos P., García D., et al., Diversification of DNA
585
Unauthenticated
Download Date | 6/19/17 6:30 AM
Rhizobial plasmids - replication, structure
and biological role
[117]
[118]
[119]
[120]
[121]
[122]
[123]
[124]
[125]
sequences in the symbiotic genome of Rhizobium
etli, J. Bacteriol., 2005, 187, 7185-7192
Bentley S.D., Parkhill J., Comparative genomic
structure of prokaryotes, Annu. Rev. Genet.,
2004, 38, 771-792
Egan E.S., Fogel M.A., Waldor M.K., Divided
genomes: negotiating the cell cycle in prokaryotes
with multiple chromosomes, Mol. Microbiol.,
2005, 56, 1129–1138
Batut J., Andersson S.G., O’Callaghan D., The
evolution of chronic infection strategies in the
alpha-proteobacteria, Nat. Rev. Microbiol., 2004,
2, 933-945
Boussau B., Karlberg E.O., Frank A.C., Legault
B.A., Andersson S.G., Computational inference
of scenarios for alpha-proteobacterial genome
evolution, Proc. Natl. Acad. Sci. USA, 2004, 101,
9722-9727
Guo X., Flores M., Mavingui P., Fuentes S.I.,
Hernández G., Dávila G., et al., Natural genomic
design in Sinorhizobium meliloti: novel genomic
architectures, Genome Res., 2003, 13, 1810-1817
Guerrero G., Peralta H., Aguilar A., Díaz
R., Villalobos M.A., Medrano-Soto A., et
al., Evolutionary, structural and functional
relationships revealed by comparative analysis of
syntenic genes in Rhizobiales, BMC Evol. Biol.,
2005, 17, 5-55
Cervantes L., Bustos P., Girard L., Santamaría R.I.,
Dávila G., Vinuesa P., et al., The conjugative plasmid
of a bean-nodulating Sinorhizobium fredii strain
is assembled from sequences of two Rhizobium
plasmids and the chromosome of a Sinorhizobium
strain, BMC Microbiol., 2011, 11, 149
Flores M., González V., Pardo M.A., Leija A.,
Martínez E., Romero D., et al., Genomic instability
in Rhizobium phaseoli, J. Bacteriol., 1988, 170,
1191-1196
Flores M., González V., Brom S., Martínez E.,
Piñero D., Romero D., et al., Reiterated DNA
sequences in Rhizobium and Agrobacterium spp,
J. Bacteriol., 1987, 169, 5782-5788
[126] Girard M., Flores M., Brom S., Romero D.,
Palacios R., Dávila G., Structural complexity of the
symbiotic plasmid of Rhizobium leguminosarum
bv. phaseoli, J Bacteriol., 1991, 173, 2411–2419
[127] Acosta J.L., Eguiarte L.E., Santamaría R.I.,
Bustos P., Vinuesa P., Martínez-Romero E., et al.,
Genomic lineages of Rhizobium etli revealed by
the extent of nucleotide polymorphisms and low
recombination, BMC Evol. Biol., 2011, 11, 305
[128] Harrison P.W., Lower R.P., Kim N.K., Young
J.P., Introducing the bacterial ‘chromid’: not a
chromosome, not a plasmid, Trends Microbiol.,
2010, 18, 141-148
[129] Hynes M.F., McGregor N.F., Two plasmids other
than the nodulation plasmid are necessary for
formation of nitrogen-fixing nodules by Rhizobium
leguminosarum, Mol. Microbiol., 1990, 4, 567-574
[130] Chain P.S., Denef V.J., Konstantinidis K.T., Vergez
L.M., Agulló L., Reyes V.L., et al., Burkholderia
xenovorans LB400 harbors a multi-replicon,
9.73-Mbp genome shaped for versatility, Proc.
Natl. Acad. Sci. USA, 2006, 103, 15280-15287
[131] Moënne-Loccoz Y., Baldani J.I., Weaver R.W.,
Sequential heat-curing of Tn5-Mob-sac labelled
plasmids from Rhizobium to obtain derivatives
with various combinations of plasmids and no
plasmid, Lett. Appl. Microbiol., 1995, 20, 175–
179
[132] Tettelin H., Riley D., Cattuto C., Medini D.,
Comparative genomics: the bacterial pangenome, Curr. Opin. Microbiol., 2008, 11, 472477
[133] Medini D., Donati C., Tettelin H., Masignani V.,
Rappuoli R., The microbial pan-genome, Curr.
Opin. Genet., 2005, 15, 589-594
[134] Bentley S., Sequencing the species pan-genome,
Nat. Rev. Microbiol., 2009, 7, 258-259
[135] Black M., Moolhuijzen P., Chapman B., Barrero
R., Howieson J., Hungria M., et al., The genetics
of symbiotic nitrogen fixation: comparative
genomics of 14 rhizobia strains by resolution of
protein clusters, Genes, 2012, 3, 138-166
586
Unauthenticated
Download Date | 6/19/17 6:30 AM