Evolutionary dynamics of overlapped genes in Salmonella.

Presence of overlapping genes (OGs) is a common phenomenon in bacterial genomes. Most frequently, overlapping genes share coding regions with as few as one nucleotide to as many as thousands of nucleotides. Overlapping genes are often co-regulated, transcriptionally and translationally. Overlapping genes are also subject to the whims of evolution, as the gene overlap is known to be disrupted in some species/strains and participating genes are sometimes lost in independent lineages. Therefore, a better understanding of evolutionary patterns and rates of the disruption of overlapping genes is an important component of genome structure and evolution of gene function. In this study, we investigate the fate of ancestrally overlapping genes in complete genomes from 15 contemporary strains of Salmonella species. We find that the fates of overlapping genes inside and outside operons are distinctly different. A larger fraction of overlapping genes inside operons conserves their overlap as compared to gene pairs outside of the operons (average 0.89 vs. 0.83 per genome). However, when overlapping genes in the operons separate, one partner is lost more frequently than in those separated genes outside of operons (average 0.02 vs. 0.01 per genome). We also investigate the fate of a pan set of overlapping genes at the present and ancestral nodes over a phylogenetic tree based on genome sequence data, respectively. We propose that co-regulation plays important roles on the fates of genes. Furthermore, a vast majority of disruptions occurred prior to the common ancestor of all 15 Salmonella strains, which enables us to obtain an estimate of disruptions between Salmonella and E. coli.

Introduction

Genome sequencing technologies are now rapidly producing a large number of microbial genomes [1], [2]. Within the last 15 years, the availability of molecular data has increased from a single complete genome (Haemophilus influenza; [3], to thousands of microbial genomes that will soon exceed 3,000 [4]. These genome sequence data are providing opportunities to better understand sequence and genome structure evolution [5], [6], [7], [8], [9]. In particular, comparative genome analyses of closely related species are giving us a unique opportunity to investigate the microevolution of genome structures [10], [11]. One such question pertains to the evolution of overlapping genes (OGs) in bacteria, as many genes have been found to share genomic stretches of their coding regions.

Overlapping genes are a common feature of microbial genomes with more than 30% of the genes showing genomic overlaps [12], [13]. Evolutionary trends of gain and loss of these genes are not yet well understood and their functional importance remains enigmatic [12], [14], [15], [16], [17], [18], [19]. Some consider gene region overlaps to be useful to organisms because shorter genomes are needed to contain all the genes [20], [21], [22]. Others suggest that gene overlaps mitigate detrimental effects of mutation, as selection pressures from multiple genes will remove mutations in the overlapped regions [22], [23].

Irrespective of the evolutionary or selective importance, sequence overlap directly impacts the functional characteristics of the genes involved both at transcriptional and translational levels. When overlapped, gene expression and translation is coupled, which is sometimes considered to be important for coordinated regulation and/or subsequent protein-protein interaction [16], [24], [25], [26], [27].

In bacteria, a large fraction of overlapping genes is found within operons, which are important and well-defined functional units in microbes. Genes in operons are usually co-transcribed and often encode functionally linked proteins [28], [29]. Functional coupling is an efficient way for regulation, especially for complex regulation, because coupling of functionally related genes with one complex promoter would arise more rapidly than two independent complex promoters. In other words, functional coupling results in more economical and efficient mechanisms for functioning [30], [31].

As a genomic tool, overlapping genes are able to display principles of genome evolution, such as indicating phylogenetic relationship among prokaryotes [32], [33]. Interestingly, not all overlapping genes in one species are found to be overlapping in another species. This is true not only for closely related species, but also for strains of a species [13], [34]. This means that new gene couplings can be established and existing ones disrupted by genome-scale mutations [12], [35]. Knowledge of origins of new overlaps and the decay of existing overlaps is useful to gain insights into the evolution of operons and patterns of regulation and gene expression. Therefore, we conducted an analysis of genes that have been historically coupled in the complete genomes of 15 strains of Salmonella and constructed a system for querying gain and loss of any pair of overlapping genes in a lineage on a predetermined phylogenetic tree.

Materials and Methods

Genome data

We downloaded 15 Salmonella, 1 Shigella, and 2 E. coli genomes from the NCBI database (ftp://ftp.ncbi.nih.gov/genomes/Bacteria; September 2008; Table 1). Overlapping genes were identified from genome structure annotations using in-house PERL scripts. There were a total of 14,295 gene pairs in 18 genomes, excluding 12 genes that had ambiguous start positions. In order to minimize the effect of artificial error during the identification of overlapping genes, we also removed the genes that were annotated with different start or stop sites from their homologous genes in either of two well-annotated model organisms Salmonella Typhimurium LT2 (STym) or Salmonella Typhi CT18 (STyiCT18) [36], [37]. Of these, 86% genes were translated in the same direction [→→] from the RNA transcript, and the rest showed opposite directions (10.7% facing each other [→←] and 3. 3% facing away from other [←→]).

Table 1

Completely sequenced genomes analyzed in this study.

Species	Brief name of species	Accession No.	Genome length (bp)	No. of cds	No. of overlapping genes within E. coli operons (pair)	No. of overlapping genes outside of E. coli operons (pair)
S. typhimurium LT2	STym*	NC_003197	4857432	4423	661	114
S. Typhi Ty2	STyiTy2*	NC_004631	4791961	4318	649	96
S. Typhi str. CT18	STyiCT18*	NC_003198	4809037	4395	682	97
S. Schwarzengrund str. CVM19633	SSch	NC_011094	4709075	4500	625	158
S. Paratyphi C strain RKS4594	SPtyC	NC_012125	4833080	4578	566	125
S. Paratyphi B str. SPB7	SPtyB	NC_010102	4858887	5592	802	373
S. Paratyphi A str. ATCC 9150	SPtyAATCC*	NC_006511	4585229	4093	578	106
S. Paratyphi A str. AKU_12601	SPtyAAKU	NC_011147	4581797	4078	555	102
S. Newport str. SL254	SNew	NC_011080	4827641	4612	676	154
S. Heidelberg str. SL476	SHei	NC_011083	4888768	4650	659	150
S. Gallinarum str. 287/91	SGal	NC_011274	4658697	3965	538	94
S. Enteritidis str. P125109	SEnt	NC_011294	4685848	4206	594	104
S. Dublin str. CT_02021853	SDub	NC_011205	4842908	4514	662	154
S. Choleraesuis str. SC-B67	SCho*	NC_006905	4755700	4413	614	142
S. Agona str. SL483	SAgo	NC_011149	4798660	4562	613	170
E. coli str. K-12 substr MG1655	EColK12*	NC_000913	4639675	4295	556	153
E. coli O157_H7 str. Sakai	EColO157*	NC_002695	5498450	5230	877	163
S. flexneri 2a str. 2457T	SFle*	NC_004741	4599354	4061	623	110

Genomes with pre-identified orthlogous clusters in ATGC [10].

For each gene in Salmonella, we identified a putative ortholog in the E. coli genome by using reciprocal BLAST (threshold E < 10−4 and > 40% similarity). E. coli K-12 genome was used as a reference genome because its genome annotation is the most accurate and almost all of its operons have been examined experimentally [38], [39], [40].

As a first approximation, we assumed that pairs of overlapping genes in E. coli represent the ancestral state for their orthologs in the Salmonella genomes. Based on this assumption, all Salmonella genes with orthologs in E. coli overlapping genes were categorized into four different configurations. Genes were called coupled (C) if the E. coli overlapping genes were also overlapping in the given Salmonella genome. They were called separated (S) if the E. coli overlapping genes were no longer overlapping in the Salmonella genomes. If only one of the two E. coli genes was found in Salmonella, then we call it widowed (W). If neither E. coli gene had a homolog in the given Salmonella species, then we refer to the pair as being dead (D).

For analyses involving E. coli operons, we retrieved E. coli K-12 from RegulonDB (version 6.4), which stores comprehensive and highly confident information of operons in E. coli [40]. For overlapping genes in other genomes, we used the operons determined in the Database of prOkaryotic OpeRons (DOOR; http://csbl1.bmb.uga.edu/OperonDB) [41].

Phylogenetic inference

We used the outgroup genome Yersinia pestis CO92 (YPes) to root the tree of 15 Salmonella strains, E. coli K-12 (EColK12), E. coli O157:H7 (EColO157), and Shigella flexneri (SFle), which was derived from a set of reliable orthologous clusters across genomes. To construct these clusters we first obtained a set of orthologs from 8 genomes (see Table 1) from ATGC database, which identifies orthologs between closely-related microbial genomes [10]. Then, we conducted reciprocal BLAST searches in our genomes missing from the ATGC database. We only included genes that share a high degree of amino acid similarity (E < 10−10 and > 80% similarity) to take a conservative approach. All “hypothetical”, “unknown”, and “putative” genes were excluded in order to generate clusters of genes with known functions only.

Because phylogenetic analysis can be misled by genes with extremely different GC contents within and among species, we excluded all genes whose GC content showed outlier tendencies as compared to the other orthologs using the Grubb’s test [42]. We also constructed gene-by-gene multiple sequence alignment using MUSCLE in MEGA5 [43], and then computed synonymous divergence using yn00 model in PAML4 [44]. All genes containing gene pairs with synonymous divergence > 1.5 substitutions per site were excluded, because high sequence divergence among strains or species can mislead phylogenetic inference. Short proteins (<150 amino acids) were also removed.

Even after all these exclusions, the final dataset contained 474 genes and 214,491 codons. These genes were concatenated head-to-tail and the fourfold-degenerate sites across all genomes were extracted in MEGA5 (66,202 sites) for phylogenetic analysis; we focus on fourfold-degenerate sites because Salmonella genomes are extremely similar to each other at the protein sequence level. We used Neighbor-Joining, Maximum Likelihood, and Bayesian methods for phylogenetic analysis [43]; [45], [46] with a GTR+G+I model for nucleotide substitution from the report of modelTest [47].

Ancestral states reconstruction

We determined pan-Overlaps, which are pairs of genes overlapping in at least one of the 18 genomes (15 Salmonella, 2 E. coli and 1 Shigella). Using the phylogeny, we constructed a system for querying ancestral states of pan-Overlaps across genomes. Sequence alignments were constructed by using the four possible configurations (C, S, W, and D) of overlapping genes in pan-Overlaps as the state symbols. We then inferred ancestral states using parsimony with a user defined matrix (mymatrix) in PAUP 4.0 [48]. The mymatrix was defined as

The transforming possibility between C and S is higher than that among C and W and D because it is rare that widowed and dead overlapping genes become overlapped again as compared with the separated genes to be overlapped during evolution.

Formation and degradation rates of overlapping genes

To estimate the rate of formation and degradation of overlapping genes, it is necessary to know the number of overlapping genes in Salmonella that were newly generated or degraded after diverging from E. coli. To obtain the number of newly generated overlapping genes (n) in Salmonella, we first determined the number of overlapping genes (n) contained in each Salmonella genome and then calculated the number of pairs of genes (n) that are not only overlapping in E. coli but also overlapping in Salmonella. The number of newly generated Salmonella overlapping genes was thus determined as .

For the number of newly degraded E. coli overlapping genes in Salmonella, we first calculated the number of pairs of genes that are overlapping in E. coli but have been separated (n) or widowed (n) in Salmonella. Since the information on dead overlapping genes have been totally lost in Salmonella, we used the number of E. coli overlapping genes (n) that do not have any homologous genes in Salmonella as a proxy for the number of dead overlapping genes in Salmonella. The number of degenerated E. coli overlapping genes in Salmonella was thus defined as .

The rates (r and r) of formation and degradation of overlapping genes in each Salmonella genome i were then calculated with the formulas and (i  =  1 … 15). The divergence time t between E. coli and Salmonella was estimated to be 100 MY [49]. The rates of formation and degradation of overlapping genes (r and r) were then estimated by the average r and r of the 15 studied Salmonella genomes.

Statistical Tests

Statistical analysis was performed in Graphpad Prism 5.0. A contingency test measured the numbers of E. coli coupled overlapping genes inside operons and outside operons that are present or absent as coupled overlapping genes inside operons and outside operons in Salmonella.

Results

E. coli overlapping genes in Salmonella

There are 709 pairs of overlapping genes identified in E. coli K-12. At first, we calculated the number of pairs of homologous E. coli genes in each of the 15 Salmonella genomes. Around one-third (30–35%) pairs have been lost (dead) in each of the Salmonella genomes. The remaining E. coli overlapping genes (65–70%) have either maintained the overlapping status (coupled) or became non-overlapping (separated or widowed) during the evolution. Of these, most E. coli overlapping genes are still coupled in Salmonella (from 82.1% to 90.9%), and the remaining E. coli overlapping genes have been broken up (8.25–16.8% separated and 1.04–2.12% widowed). The significantly larger fraction of coupled overlapping genes in Salmonella indicates that overlapping genes are highly maintained during evolution.

Operons are well defined functional units in microbial genomes. In E. coli, a large part of overlapping genes (78.4%) were found within operons, and only 21.6% were outside of operons. Operons may affect the probability of overlapping genes to remain coupled in other genomes during evolution. In order to see whether there is any correlation between overlapping genes and their functional location (inside or outside of operons), we compared the four possible configurations (C, S, W, and D) of the E. coli overlapping genes inside and outside of operons in the 15 Salmonella genomes, respectively. The total number of the homologous counterparts of the E. coli overlapping genes in each Salmonella genome was defined as the number of all pairs of coupled, separated and widowed overlapping genes in the genome. We were unable to count the number of dead pairs because the information of these E. coli overlapping genes has been completely lost in Salmonella.

Coupled (C). Fractions of the coupled overlapping genes inside and outside operons were calculated against the total number of orthologs in E. coli overlapping genes inside and outside operons. As expected, the fraction of coupled overlapping genes inside operons is consistently larger than that outside of operons (Fig. 1A). The contingency test to each Salmonella strain showed that the numbers of coupled overlapping genes inside and outside operons in 12 Salmonella genomes have significant difference from the numbers of coupled overlapping genes inside and outside of operons in E. coli. Three genomes STyM, SPtyAATCC, and SPtyAAKU didn’t show significant difference. The significant difference was also observed between the numbers of E. coli coupled overlapping genes inside and outside operons and the average numbers that are present and absent as coupled overlapping genes inside and outside of operons in Salmonella genomes (p-value  =  0.015). These results indicate that overlapping genes inside operons are more likely to remain overlapped because of stronger functional constraints. It was proposed that the formation and decay of overlapping genes were kept at an equivalent frequency in genomes during evolution [12], [15]. We found that overlapping genes outside of operons have lower fraction than that inside operons, suggesting that the formation and decay rates of overlapping genes are not consistent within the genome. The difference between the two groups indicates that stronger purifying selection is acting on the coupled overlapping genes inside operons, as compared with those outside of operons. Some studies have shown that overlapping genes could be used as a phylogenetic marker for the prokaryotic phylogenetic inference [13], [32], [33], [50]. The feature that overlapping genes are more conserved within operons could be used to develop a phylogenetic marker based on overlapping genes.

Figure 1

Fate of the E. coli overlapping genes in the studied Salmonella strains.

Percentage of the coupled overlapping genes in E. coli that maintain the overlap (A), became separated (B) or became widowed (C) in Salmonella genomes.

Separated (S). Fractions of the separated overlapping genes against the total number of orthologous counterparts of the E. coli overlapping genes were examined in the two groups, inside operons and outside operons, respectively. It was shown that the fraction of separated overlapping genes inside operons is consistently lower than that outside of operons (Fig. 1B). As pointed out previously, operons are important for efficient regulation and optimal expression of genes [51], [52]. On one hand, disruption of the operons could destroy the co-regulation among the complex of proteins and consequentially the transcription efficiency might drastically decrease in those units that lost the promoter [53]. As observed in the coupled overlapping genes, purifying selection is strongly acting on the genes within operons and thus the fraction of separated overlapping gene pairs is much smaller than that outside of operons. On the other hand, although an operon and the individual genes with regulatory structures can be rearranged [52], [53], several lines of evidence suggest that the rearrangement is a conservative process [54]. For example, the rearrangement is constrained by biological pathways [55]. Therefore, due to the strong purifying selection on the genes within operons, decay of overlapping genes is highly restrained within operons in contrast to that outside of operons.

Widowed (W). Fractions of the widowed overlapping genes inside and outside of operons were carefully calculated against the total number of orthologous counterparts of E. coli overlapping genes in each Salmonella genome, respectively. Surprisingly, the fraction of the widowed overlapping genes inside operons is much larger than that outside of operons except for two outliers STyiCT18 and SCho (Fig. 1C). There were no widowed overlapping genes located outside of E. coli operons in STym, SNew, SHei, SSch, SDub, SEnt, and SPtyC. Although decay of overlapping genes is highly restrained inside operons as discussed above, it seems that in those cases in which the overlap decays one of the genes is likely to be lost. The second gene inside the operon is located further away from the promoter compared to the first one, and tends to be lost because it is not being transcribed [53]. Alternatively, if either one in the overlapping gene pairs in E. coli became a pseudogene [56], the overlapping gene pair was widowed in Salmonella. Therefore, the separated E. coli overlapping genes were widowed in Salmonella. In contrast, genes outside of operons were proposed with no functional coupling. The decay of overlap thus has a smaller impact on the transcription of the second gene outside of the operons than the one inside operons. In other words, both genes are still being transcribed when the overlapping genes are separated and located outside of the operons. The result is also supported by the significantly larger distance between two separated overlapping genes inside operons compared to that of genes outside operons (at the level of 0.05, p-value  =  0.02). However, this pattern does not hold for two of the genomes, STyiCT18 and SCho. One possible reason is that genes might still be co-regulated without being in the same operons. Alternatively, the disruption of overlap does not necessary destroy the structure of operons.

Dead (D). Any pair of overlapping genes can be lost in three possible ways: (I) A pair of overlapping genes was entirely deleted from the genome by an evolutionary event. In our case, E. coli overlapping genes become dead overlapping genes in Salmonella in one evolutionary event. (II) E. coli overlapping genes were separated in Salmonella by point mutations, and subsequently lost in tandem or became pseudogene(s). (III) Either one of the two individual genes in the overlap was lost, followed by loss of the other one during evolution.

Even though the information of the E. coli overlapping genes was totally lost in Salmonella when the overlapping genes are dead, it is interesting to know which overlapping genes tend to get lost during evolution. There are 22 and 10 pairs of E. coli overlapping genes inside and outside of operons, respectively, that have been lost in all the Salmonella genomes. Not surprisingly, most genes that tend to be lost are related to phage genes or insertion elements in E. coli. However, there is an obvious difference between the dead genes inside and outside of operons. For example, except for two pairs with unknown functions, genes in the remaining 8 pairs outside of operons were all classified into the functional group ‘Replication, recombination and repair’ based on COG, but the genes inside operons have various functions. Most genes inside operons have clear biological functions (e.g., glcDEFGBA is related to Glyoxylate and dicarboxylate metabolism, alsBACE is D-allose transporter subunits, and rpiR is DNA-binding transcriptional repressor) or are involved in important pathways (e.g., atoDAEB is a highly inducible system for acetoacetate and butyrate degradation [57], and gspCDEFGHIJKLMO is involved in cryptic general secretory pathway [58] in E. coli). Although operons are under strong purifying selection [29], [30], known operons in E. coli that have been either particularly or entirely lost in other species indicates that genome rearrangements within operons are not rare in bacterial genomes.

Pan-Overlaps in Salmonella

A set of pan-Overlaps was determined based on all of the overlapping genes identified in the 15 Salmonella, two E. coli and one Shigella. In total, there were 3062 pairs of overlapping genes in the pan-Overlaps containing two groups, 2301 pairs inside operons and 761 pairs outside of operons (See Table S1, the first sheet contains all pan-Overlaps inside operons and the second sheet contains all pan-Overlaps outside operons). As have been defined previously, each pair of overlapping genes in the pan-Overlaps has one of four possible configurations (C, S, W, and D). We compared the distribution of the configurations over the 15 Salmonella groups (Fig. 2). Percentage of the coupled overlapping genes (C) in pan-Overlaps inside operons is much higher than that outside of operons (average 28% and 19%, respectively), suggesting that gene pairs inside operons have greater propensity of overlap as compared with that outside of operons. However, interestingly, although dead overlapping genes (D) both inside and outside of operons have high percentages (average 32% and 20%, respectively), D inside operons shows the largest percentage among the four configurations, indicating that although overlapping genes are highly maintained within operons, these genes may be subject to the whims of evolution. Paired comparison analysis also shows the significant difference among the four configurations (two tailed t-test at p-value < 0.05). For the gene pairs outside of operons, W shows the highest percentage among the configuration (average 52%), which is more than two times higher than that for the genes inside operons (average 21%). The significantly larger percentage of W genes compared to S genes (two tailed t-test at p-value < 0.0001) implies that genes tend to die (particularly one partner gets lost more frequently than the other one) when the overlaps are broken. The difference between the W and the D configuration outside of operons (two tailed t-test at p-value < 0.0001) shows that genes outside of operons were widowed more frequently but less frequently lost as compared to those inside operons. We also observed that there is no significant difference between the C configuration and the D configuration outside of operons, which indicates that coupled overlapping genes outside of operons might not be maintained during the evolution. Separated overlapping genes (S) both inside and outside of operons have the smallest percentages among the four configurations (19% and 9%, respectively), indicating that pairs of overlapping genes tend to be lost or widowed rather than kept presenting a new (separated) configuration. In summary, the overlapping genes are highly maintained inside operons as compared with those outside of operons, however, when the overlaps are disrupted, genes inside operons tend to be lost rather than kept as separated genes.

Figure 2

Fate of the genes in pan-Overlaps in Salmonella strains.

(A) Average of the percentages of the genes inside operons. (B) Average of the percentages of the genes outside of operons.

Phylogeny

The finding of a strong, reliable phylogenetic tree allows the inference of states dynamics of overlapping genes along the history of the species. To determine the ancestral states of the overlapping genes in pan-Overlaps, we firstly determined a phylogenetic tree of the 19 studied genomes (including the outgroup YPes). The phylogenies were obtained using NJ, ML and Bayesian methods based on the four-fold degenerate sites of a concatenated data set of the 474 genes (see 1 for the ML tree, Fig. S2 for the NJ tree, and Fig. S3 for the Bayesian tree). The topologies of the ML, NJ, and Bayesian trees are highly similar except for two taxa (SCho and SPtyC) that show controversial positions with low bootstrap value in the ML tree but high bootstrap values in the NJ and Bayesian trees (Fig. S2, S3). In the ML and Bayesian trees, the group SCho and SPtyC were located close to the tip node (SEnt, SGal, and SDub), a position similar to that found recently in a phylogeny based on 2,898 single-copy genes [59]. Differently, the group SCho and SPtyC was closer to the group (SAgo and SSch) with the taxa STym being more recent in the NJ tree; this position is comparable to that inferred using presence-absence predictions for genes that exhibit inconsistent distributions within Salmonella [60]. For this reason, and because the ML and Bayesians trees are in good agreement, despite the poor support of several nodes in the ML phylogeny, we decided to use the ML tree in the following analysis (Fig. S1, Fig. 3).

Figure 3

The ML phylogeny inferred from the four-fold degenerate sites of 474 genes.

The internal nodes are labeled 19–35, with node 35 being the divergent point between E. coli and Salmonella and node 32 being the root node of the ingroup Salmonella.

Ancestral states of pan-Overlaps

To understand the evolutionary history of overlapping genes, it is necessary to know not only the present character states, but also their ancestral states [61], [62]. Reconstructing ancestral states of overlapping genes from present data can provide a unifying framework for understanding the origins and evolution of overlapping genes. Using the ML tree built based on the four-fold degenerate sites, we reconstructed the possible evolutionary states (C, S, W, and D) for each pair of overlapping genes in pan-Overlaps over the studied strains [48] (Fig. 3).

We compared the distributions of ancestral states of the genes in pan-Overlaps inside operons with that outside of operons. It shows the distribution of ancestral states of pan-Overlaps represents a similar pattern to that of the overlapping genes at the present nodes, but has much more significant variance among the four configurations (Fig. 4). Four configurations C, S, W, and D both inside (Fig. 4A) and outside operons (Fig. 4B) show significant variance at two tailed t-test p-value < 0.05). Interestingly, dominance of the four configurations (C, S, W, and D) represents the same order at all of the internal in-group nodes (19–32; Fig. 3) both inside (D > C > W > S) and outside of operons (W > D > C > S). However, Grubbs' test shows that there is no deviation among all of the internal nodes at p-value  =  0.05 level. No significant changes among the internodes means there is no significant propensity of loss of overlapping genes among the internodes. Our study indicates that there is no significant relationship between the formation and decay of overlapping genes and the evolutionary distance among the strains.

Figure 4

Fate of the gene pairs in pan-Overlaps over the internal nodes of the phylogeny of the studied genomes.

(see Fig. 3 for node numbering). (A) Average of the percentages of the gene pairs inside operons over the internal nodes of the phylogeny. (B) Average of the percentages of the gene pairs outside of operons over the internal nodes of the phylogeny.

Rates of formation and degradation of overlapping genes

It is obvious that the degeneration and formation of overlapping genes are common events in bacterial genomes. Some researchers have proposed that the degenerate rate might equal the formation rate since there is a very good correlation between the number of ORFs and the number of overlapping genes observed [12]. However, in our study, we found that the overlapping genes inside operons show different evolutionary histories than those outside of operons, suggesting that the evolutionary rate of overlapping genes within the genomes are different. Using the known divergence time between E. coli and Salmonella, we estimated the rates of formation of overlapping genes as 4.5×10−9 and 1.6×10−9 per pair per year, inside and outside of operons, respectively. The rates of degeneration of overlapping genes are 4.1×10−9 and 2.6×10−9 per pair per year, inside and outside of operons, respectively.

Formation of operons might be driven by the horizontal gene transfer [63], [64], or by co-function [30]. It is probable that many overlapping genes were generated during the formation of operons. As we expected, the degeneration rate of overlapping genes inside operons is much lower than that outside of operons, indicating overlapping genes are highly maintained inside operons due to stronger selection compared with the overlapping genes outside of operons.

Discussion

Possible influence of dynamic evolution in E. coli

In this analysis, we used E. coli K-12 as the reference to the Salmonella. The discussion about the detected patterns of four configurations (C, S, W, and D) of the E. coli overlapping genes inside and outside of operons in Salmonella genomes is based on the assumption that no dynamic evolution in E. coli after the divergence of Salmonella from E. coli. However, the scenario could be influenced by the dynamic evolution of overlapping genes in E. coli because overlapping genes in E. coli can also have evolutionary dynamics similar to the detection in Salmonella in this study. For example, we found that the relative fractions of dead overlapping genes are higher inside operons than outside of operons. If we considered the dynamic evolution in E. coli as in Salmonella, which also has a higher rate of formation of overlapping genes inside operons than outside operons, then it would explain that the relative higher fraction of dead overlapping genes inside operons than outside operons in Salmonella. This conclusion would be different from the original explanation that higher fraction of dead overlapping genes inside operons than outside operons is due to the strong purifying selection in operons. Newly formed operons in E. coli could also influence the original explanation to the scenario of dead overlapping genes in Salmonella. On one hand, because such newly formed operons in E. coli will not be found in Salmonella, they will be considered as dead in Salmonella. On the other hand, it is possible that genes appearing as newly formed ones in Salmonella could be originally present in common ancestor of E. coli and Salmonella, but were afterwards subject to decay in E. coli. In this study, we simplified the complex process of evolution. The dynamic evolution in Salmonella is addressed based on a basic model that E. coli overlapping genes is a static frame of reference, however, the scenarios we discussed here could be influenced due to the evolution of overlapping genes in E. coli in parallel to Salmonella.

Function of overlaps

It is useful to understand the configuration and evolutionary status of interesting pairs of overlapping genes across a lineage of species because the overlap status of pairs of genes can be used as a phylogenetic trait to infer functions [16], [19]. For example, the couple bcsC-bcsZ is linked to cellulose production in those strains and species in which the overlap is maintained. bcsC and bcsZ are overlapping in the genome STym with the downstream region of bcsC overlapping by 19 bp with the upstream region of bcsZ, while they are separated in E. coli and S. Typhi. The two genes are located in the operon bcsABZC, which is a characteristic cellulose biosynthesis operon [65], [66]. As it is known, cellulose production confers bacterial cell-cell interactions, adhesion to abiotic surfaces for biofilm formation and chlorine resistance to the organism [67]. Regulation of cellulose biosynthesis varies widely among species and even within a species. Studies have shed light on cellulose biosynthesis in several bacterial genomes, such as STym and SEnt [66]. E. coli and S. Typhi do not produce cellulose suggesting that this could be caused by the separation of the bcsC and bcsZ genes leading to a preterminated out-of-frame product. Therefore, based on the evolutionary status of bcsC and bcsZ in the phylogentic tree (Fig. 5A), we would predict that strains STym, SDub, SGal, SCho, SNew, SPtyB, and SPtyA produce cellulose and SPtyC, SHei, SPtyAAKU, SSch, SAgo, STyiTy2, and STyiCT18 have no cellulose because the bcsC-bcsZ have been separated or widowed. Cellulose expression has variable patterns in Salmonella and E. coli, but the linkage with the overlap status would be very important information because it provides a bioinformatic approach to test the presence or absence of a functioning pathway.

Figure 5

Phylogenetic map of the overlapping gene pairs.

(A) Phylogenetic map of the overlapping gene pair (bcsC, bcsZ). (B) Phylogenetic map of the overlapping gene pair (ompR, envZ).

Another example is the couple ompR-envZ, which is linked to virulence of the pathogens. In E. coli, the upstream gene ompR coding for a positive transcription regulator OmpR has 4 bp overlapping with envZ coding for an inner membrane protein EnvZ. It is known that the ompR-envZ two-component regulatory system is essential for the response to environment signals and contributes to virulence in a number of enteric bacterial pathogens [68], [69]. Phosphorylation of OmpR by osmosensor EnvZ modulates synthesis and normal functioning of the proteins OmpC and OmpF located on the external side of the membrane. It has been shown that the translation efficiency of envZ could decrease ten times or more when the translation of ompR is terminated away from the normal stop codon [70]. Although the ompR-envZ locus is highly conserved within the E. coli and Salmonella genomes, the two genes show variable configurations across the Salmonella genomes (Fig. 5B). Overlap of the two genes is maintained in the Salmonella Typhi genomes (STyiTy2 and STyiCT18), STym, SPtyB and SCho, while they have been separated (S) in the remaining Salmonella genomes. The separated status suggests that genes coding for outer membrane porin proteins OmpF and OmpC would not be normally expressed due to the low translation efficiency of envZ that modulates expression of ompF and ompC. Translational interrelation of the synthesized products of overlapping genes is of practical importance. The phylogenetic analysis of the evolutionary status of overlapping genes would provide researchers with a new tool to study the roles of ompR-envZ in the regulation of genes, especially in the virulence secretion system.

The ML tree inferred from the four-fold degenerate sites of 474 genes with 100 bootstrap replicates.

(TIF)

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The NJ tree inferred from the four-fold degenerate sites of 474 genes with 100 bootstrap replicates.

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The Bayesian tree inferred from the four-fold degenerate sites of 474 genes with 100 bootstrap replicates.

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The overall set of pan-Overlaps in and . The first sheet in the Table S1 contains all pan-Overlaps inside operons and the second sheet in the Table S1 contains all pan-Overlaps outside operons.

(XLSX)

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