A number of models that are not mutually exclusive have been proposed to account for
the formation and evolution of operons. Two broad aspects need to be considered,
transfer of genes between organisms, as well as gathering and distributing genes
within a genome. There is strong support for horizontal gene transfer as a driving
force for evolution of gene clusters . More recently, it has been shown that genes acquired by horizontal gene
transfer events appear to evolve more quickly than genes that have arisen by gene
duplication events . Within a genome the “piece-wise” model suggests that complex
operons can evolve through the independent clustering of smaller
“sub-operons” due to selection pressures for the optimization for
equimolarity and co-regulation of gene products . Finally it has been suggested that the final stages of operon building
can be the loss of “ORFan” genes [4, 6].
The data presented here provide examples supporting these models of operon evolution.
The components of the polyol catabolic loci we have identified have been involved in
at least 3 horizontal gene transfers within the proteobacteria (Figure 2). In addition, components such as the transporter
eryEFG have been moved from the R. leguminosarum clade of loci
into the M. ciceri bv. biserrulae polyol locus (see Figure
3A and 3B). The later species based
on its phylogenetic position and category of polyol locus (S. meliloti)
would have been expected to contain the mtpA gene. The presence of possible
paralogs of lalA (Figure 4) and the presence of
tpiB xenologs (Figure 5) are also evidence
for duplication and horizontal transfer events. Since S. fredii also
contains a homolog to tpiA of S. meliloti (data not
shown), to our knowledge, this is the only example of an organism
containing three triose-phosphate isomerases (Figure 2,
A striking example of a horizontal gene transfer and genetic rearrangement is
exemplified by M. ciceri (Figure 1,
Figure 2). It is likely that an exchange between M.
loti and a common ancestor of S. meliloti, S. medicae and S.
fredii NGR234 occurred. M. loti is located in the same clade as
the Brucella and O. anthropi in the species tree (Figure
2). Despite this, M. loti contains many of the
genes corresponding to the adonitol and L-arabitol type loci of other species that
cluster close to the base of the species tree such as Bradyrhizobium spp.
(Figure 2). The presence of these factors in addition to
the chimeric composition of the M. loti locus leads us to hypothesise that
an ancestor of M. loti may have contained both an erythritol locus like
that of the Brucella as well as a polyol type locus like that seen in the
Bradyrhizobia, A. cryptum and V. eiseniae.
The lalA, rbtB, rbtC suboperon appears to be the key component of the polyol
locus in the Bradyrhizobium type loci (Figure 1). Among the 19 loci identified, these three genes can be linked into a
suboperon, embedded within the main locus (eg. R. litoralis) or split among
two transcriptional units (see A. cryptum or V.
eiseniae). As well, the gene module (or suboperon) eryR, tpiB- rpiB is
presumably found in all erythritol utilizing bacteria. The acquisition of this
module along with the lalA, rbtB and rbtC suboperon may have
allowed for the evolution of the more complex S. meliloti type locus (see
The absence of fucA in S. fredii NGR234 and M. loti
appears to be an example of the loss of an “ORFan” gene event having
occurred. The gene is still present in S. meliloti however it has been
shown that it is not necessary for the catabolism of erythritol, adonitol, or
L-arabitol . It is likely that it was lost during the divergence of M. loti
and S. fredii NGR234 from their common ancestors to S. meliloti.
If this is true, it may be reasonable to assume that fucA may eventually
also be lost from the S. meliloti erythritol locus.
In S. meliloti, erythritol uptake has been shown to be carried out by the
proteins encoded by mptABCDE[15, 16], whereas in R. leguminosarum growth using erythritol is
dependent upon the eryEFG. Although both transporters appear to carry out the same function, the
phylogenetic analysis clearly shows that they have distinct ancestors and may be
best classified as analogues rather than orthologues (Figure 3). In addition, it has been shown that MptABCDE is also capable of
transporting adonitol and L-arabitol . We note that these polyols appear to have stereo-chemical identity over
three carbons and that EryA of S. meliloti can also use adonitol and
L-arabitol as substrates . It is unknown whether EryA from R. leguminosarum has the
ability to interact with these substrates.
The three distinct groups of loci we have identified probably correspond to the
metabolic potential of these regions to utilize polyols. The locus of S.
meliloti has been shown to contain the full complement of genes required to
confer growth on using both erythritol and adonitol and L-arabitol as sole carbon
sources [15, 16]. Given that S. fredii NGR234 and M. loti each contain
homologs to all of these genes, except for fucA which is not necessary for
the catabolism of any of the sugars , it follows that these two loci may also be capable of catabolising all
three polyols. It has also been established that the B. abortus and R.
leguminosarum type loci are used for erythritol catabolism, and given the
annotation and degree of relatedness (E value = 0) of proteins belonging
to all species in the clade, it is not expected that these loci would be capable of
breaking down additional polyols [20, 21]. This is supported by the fact that the introduction of the R.
leguminosarum cosmid containing the erythritol locus into S.
meliloti strains unable to utilize erythritol, adonitol, and L-arabitol
were unable to be complemented for growth on adonitol and L-arabitol . It is however necessary to remember that some of identified loci are
only correlated with polyol utilization based on our analysis and that basic
biological function, such as the ability to utilize these polyols has not been
With the advent of newer generations of sequencing technologies a greater number of
bacterial genomes will be sequenced. It is likely that more examples of
rearrangements of catabolic loci through bacterial lineages will be observed. Since
the ability to catabolize erythritol is found in relatively few bacterial species,
operons that encode erythritol and other associated polyols may be ideal models to
observe operon evolution.