The Life-cycle of Operons Page: 4 of 36
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We found that predicted new operons are highly enriched for ORFan genes (Figure 2A) and often
combine an ORFan with a native gene (Figure 2B). The prevalence of ORFans in new operons is
somewhat surprising given that ORFans are less likely than native or HGT genes to be in operons
(Price et al. 2005b). The most parsimonious evolutionary scenario for constructing a native-ORFan
pair is a single insertion event that transfers the ORFan into the genome and places it adjacent
to the native gene. To test this hypothesis, we compared the evolutionary age of the new operon
to that of the ORFan. The age was determined from the most distant relative that contained the
new operon or ORFan (see Methods). Consistent with the insertion scenario, we found that the
estimated evolutionary age of the native-ORFan operon pair often matches the age of the ORFan
(Figure 2B). We considered that native-ORFan pairs might be a mechanism for ensuring that the
ORFan gene is expressed. Consistent with this view, we found that the native gene is more often
the upstream gene in the pair (Figure 2B; P = 0.03, binomial test), so that the ORFan gene can be
transcribed from a native promoter without perturbing the expression of a native gene.
There are also ORFan-ORFan pairs. The age of these pairs often matches the age of both genes in
the pair (Figure 2B), suggesting that the entire operon was imported in a single event. Thus, many
of the "new" ORFan-ORFan pairs may actually have been horizontally transfered from an unknown
source, such as phage. Because phages have compacted operon-rich genomes, it is surprising that
more ORFans are not in such pairs, and that ORFans are less likely to be in operons than other
genes (Price et al. 2005b). Perhaps the phage operon benefits the phage, whereas only one gene in
the operon would benefit the host.
Because new operons are, by definition, not conserved across many genomes, these operon predic-
tions may be less reliable. However, new operon pairs of each of the three major types discussed
above tend to have strongly correlated expression patterns (Figure 2C). Therefore, most of these
predicted new operon pairs are likely to be operons.
Although ORFans tend to be poorly annotated, a few annotated ORFans are in characterized
operons. The ORFan holD, a regulatory subunit of DNA polymerase III, is co-transcribed with the
native gene riml, a ribosomal protein S18 acetyltransferase. The ORFan chromosomal partitioning
genes mukFEB are co-transcribed with a native methyltransferase (smtA). And flhE is co-transcribed
with native genes flhAB. The native genes flhA and flhB are required for flagellar export, but the
ORFan flhE is not (Minamino et al. 1994; Minamino and Macnab 1999). flhE appears to be
annotated as a flagellar gene purely because of its location. Because many new operons encode
functionally unrelated genes (Price et al. 2005b), we argue that this annotation is likely to be
erroneous. Overall, the genes in these ORFan-native operons do not seem to be functionally related.
If new operons containing ORFans often form by insertion, how do new operon pairs containing only
native genes form? Although we cannot examine the ancestor of E. coli that formed the new operon,
we can examine the gene order in close relatives that lack the operon. Specifically, we examined
new operon pairs that were shared by E. coli K12, Salmonella species, and other Enterobacteria,
but had non-adjacent orthologs in Vibrio species, which are more distantly related. We considered
looking at newer operon pairs, but few of the newer operon pairs consist of two native genes (data4
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Price, Morgan N.; Arkin, Adam P. & Alm, Eric J. The Life-cycle of Operons, article, November 18, 2005; Berkeley, California. (https://digital.library.unt.edu/ark:/67531/metadc875143/m1/4/: accessed April 24, 2024), University of North Texas Libraries, UNT Digital Library, https://digital.library.unt.edu; crediting UNT Libraries Government Documents Department.