Database searches

Human and mouse Max dimerization protein (Max-like protein X; gene symbol: MLX), Mlx interacting protein (MondoA; gene symbol: MLXIP), Mlx interacting protein-like (ChREBP, MondoB, WSCBR14; gene symbol: MLXIPL), and Drosophila melanogaster Mondo (Mlx interactor; gene symbol: Mio) coding, genomic, and protein sequences were downloaded from the Ensembl genome database (www.ensembl.org). Additional Mlx, Mlxip, and Mlxipl coding sequences and genes were identified from genome sequences maintained in the Ensembl database via similarity searches with the tblastn algorithm [29] using protein sequences encoded by the human genes as queries. Searches were conducted with the genomes that were available in the Ensembl database release 80 in May 2015. Additional blast searches were conducted with diverse Mlx, MondoA, ChREBP protein sequences identified by these searches. All sequences that had E-scores below 0.01 were examined. Sequences identified in the blast searches were used in reciprocal blastx searches of the human and mouse proteomes to ensure that their best matches were Mlx, MondoA, or ChREBP protein sequences. As some genomes did not yield all of the expected intact genes, the NCBI sequence database (www.ncbi.nlm.nih.gov) was also searched for a few sequences (see S1 Table).

Coding exons in the Mlx, Mlxip, and Mlxipl genes were identified from genomic alignments generated with MultiPipMaker [30,31]. Human gene sequences were used as master sequences with the locations of coding sequences and exons obtained from the Ensembl annotations. Repetitive elements in the human (and other) genes were identified using RepeatMasker [32]. Additional MultiPipMaker alignments were generated for genomic sequences if exons could not be identified when the human gene sequences were used as the master sequence. For these genomic alignments other species were used as the master sequence, where these genes contained all the coding exons and if possible were more closely related to the species with the missing exons. If these searches also failed to find the missing exons, then the gene annotations from Ensembl were examined to determine whether any appropriate exon had been predicted by the annotations. Mlx genes that contained all 8 coding exons and Mlxip and Mlxipl genes that had 17 coding exons were used to predict coding sequences for subsequent analyses.

Protein coding sequence alignments and evolutionary analyses

Initial alignment of the human and mouse Mlx, MondoA, and ChREBP protein sequences and the Drosophila melanogaster Mondo protein sequence was generated using Clustal Omega (http://www.ebi.ac.uk/Tools/msa/clustalo/) [33]. Use of other aligners yielded similar alignments. Intron positions were mapped onto the multiple protein sequence alignment based on the annotations of the genes from the Ensembl database. Subsequent DNA alignments of Mlx, Mlxip, and Mlxipl coding sequences were generated at the codon level using MAFFT [34] as implemented on the Guidance web server (http://guidance.tau.ac.il) [35], using default parameters. Translating the DNA coding sequence alignments generated protein sequence alignments.

Phylogenetic trees of Mlx, Mlxip, and Mlxipl sequences were generated using Bayesian methods with MrBayes 3.2.2 [36], maximum likelihood with PhyML 3.0 [37], and neighbor-joining distance approaches with MEGA6.0 [38]. Bayesian trees were generated from the coding sequences using parameters selected by hierarchical likelihood ratio tests with ModelTest version 3.8 [39], as implemented on the FindModel server (www.hiv.lanl.gov/content/sequence/findmodel/findmodel.html). MrBayes was run for 2,000,000 generations with four simultaneous Metropolis-coupled Monte Carlo Markov chains sampled every 100 generations. The average standard deviation of the split frequencies dropped to less than 0.02 for all analyses. The first 25% of the trees were discarded as burn-in with the remaining samples used to generate the consensus trees. Trace files generated by MrBayes were examined by Tracer (tree.bio.ed.ac.uk/software/tracer/) to verify that they had converged. Bootstrapped maximum likelihood trees, 100 replications, were generated with PhyML [37] on the PhyML webserver (www.atgc-montpellier.fr/phyml/) using parameters for the substitution model suggested by ModelTest. Maximum likelihood searches was initiated from trees generated by BIONJ and the best tree was identified after heuristic searches using the nearest neighbor interchange (NNI) algorithm. MEGA6.0 [38] was used to construct bootstrapped (1000 replications) neighbor-joining distance trees, using either Maximum Composite Likelihood distances for the DNA sequences or JTT distances for the protein sequences. Choice of alignment method (MAFFT [34] or Clustal Omega [33]), or the use of full-length or trimmed (based on Guidance scores [35]) alignments had little influence on the key findings of these analyses. Methods that relied on shorter sequences (i.e., trimmed alignments or protein sequences) or simpler models of sequence evolution (i.e., neighbor-joining) tended to yield weaker support for the earlier diverging lineages, but none of our analyses were in significant conflict with the key inferences of our inferred phylogenies.

Conservation of proteins sequences was assessed using two measures. Conservation within a protein alignment was measured using Jenson-Shannon (JS) divergence scores (http://compbio.cs.princeton.edu/conservation/) [40], using a window size of 3 and the BLOSUM62 matrix as background. In addition, pairwise protein sequence differences (p-distance) distances were measured for the entire protein, or protein domains, using MEGA6.0 [38]. Consensus sequences of domains within the protein sequences were generated using Weblogo (http://weblogo.berkeley.edu/logo.cgi) [41].

Structure of the gene for the ancestor of Mlxip and Mlxipl

To better understand the evolution of genes, full-length gene sequences are desirable, however, identification of a full-length gene structure can be difficult, even with complete genome sequences, as gene prediction programs can misannotate genes [42,43]. Most available genomes are not complete and contain unsequenced gaps, as well as occasional sequencing errors, that increase the likelihood of obtaining incomplete gene predictions. Identification of ancestral gene structures should help identify gene structures in extant genomes. Previous studies have shown that Mlxip and Mlxipl genes are most closely related, being the products of a gene duplication early on the vertebrate lineage, with Mlx being their most closely related paralog [24]. Annotated human MLXIP (ENSG00000009950) and MLXIPL (ENSG00000175727) genes are both composed of 17 exons that contain coding sequence. However, Mlxip and Mlxipl genes annotated in the genomes of many vertebrate species present in the Ensembl database display a variable number of exons, raising the possibility of incorrect or incomplete annotation. To determine the structure of the ancestor of the MLXIP and MLXIPL genes, we compared the structures of well-characterized Mlxip and Mlxipl genes from human (MLXIP: ENSG00000175727 and MLXIPL: ENSG00000009950) and mouse (Mlxip: ENSMUSG00000038342 and Mlxipl: ENSMUSG00000005373), the Drosophila melagastor ortholog Mio (FBgn0032940), and their closest paralog, Mlx genes from human (ENSG00000108788) and mouse (ENSMUSG00000017801). The locations and phases (i.e., position within a codon interrupted by an intron [44]) of introns were mapped to an alignment of the protein sequences predicted by these genes (Fig 1). As expected, intron positions and phases were perfectly conserved between the mouse and human orthologs of the Mlxip, Mlxipl, and Mlx genes (Fig 1). Introns that are in similar positions in an amino acid alignment and have identical phase likely have a shared origin [44]. All Mlxip, Mlxipl, Mio, and Mlx genes shared a single intron, at codon 728 in the human MLXIPL gene sequence, consistent with a very ancient origin for these diverse genes (see [24]). At least 10 introns were shared between the Mlxip, Mlxipl, and Mio genes, with all 16 introns in the Mlxip and Mlxipl genes being located in similar positions in the amino acid alignment and having identical intron phase (Fig 1). These results strongly suggest that the ancestor of the Mlxip and Mlxipl genes was composed of 17 coding exons, separated by 16 introns, although this does not exclude the possibility of lineage specific changes in gene structure that may have occurred to some genes on specific lineages. This conclusion was also obtained for protein sequence alignments generated by other methods (which only yielded slightly differing protein sequence alignments).

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Fig 1. Introns in Mlxip and Mlxipl genes are at homologous locations.

Alignment of human and mouse ChREBP, MondoA, and Mlx (encoded by MLXIPL, MLXIP, and MLX, respectively) protein sequences and Drosophila melanogaster Mondo (encoded by Mio) protein sequence with locations of introns, and phases indicated. Protein sequences were aligned with Clustal Omega. Locations of introns are indicated by ^ with the number referring to the phase of the codon interrupted by the intron. Introns at near identical locations, and of the same phase are boxed, with solid boxes indicated very similar locations, while dotted boxes are similar.

https://doi.org/10.1371/journal.pone.0149682.g001

Mlxip, Mlxipl, and Mlx genes in vertebrates

As the ancestor of the Mlxip and Mlxipl genes was composed of 17 coding exons, we searched vertebrate genomes in the Ensembl database (www.ensembl.org) for sequences that could predict Mlxip and Mlxipl genes and contain 17 coding exons (see S1 Table and S1 and S2 Figs). Genomic sequences that predict protein sequences similar to MondoA and ChREBP identified Mlxip genes in all but one vertebrate species (alpaca), and Mlxipl genes in all but three species (tarsier, alpaca, and lamprey) (S1 Table). Similar searches for Mlx, the closest related paralog to Mlxip and Mlxipl, found this gene in all examined species (S1 Table and S3 Fig). These results are consistent with the previous conclusion that Mlxip and Mlxipl genes originated via genome duplication early in vertebrate evolution and that the Mlx gene diverged much earlier [24].

To identify intact genes, exons of the Mlxip (S2 Table), Mlxipl (S3 Table), and Mlx (S4 Table) genes were identified through tblastn [29] searches with the protein sequences encoded by the human MLXIP, MLXIPL, and MLX genes, as well as genomic alignments generated by MultiPipMaker [30,31] with the human gene sequences used as master sequences. A total of 21, 16, and 44 intact coding genes were identified for Mlxip, Mlxipl, and Mlx, respectively (S2, S3 and S4 Tables). The higher number of identified intact Mlx genes likely reflects the smaller number of exons (8 exons) in this gene compared to the Mlxip and Mlxipl genes (17 exons). In 10 mammalian species (human, chimpanzee, Vervet-African green monkey (Vervet-AGM), bushbaby, mouse, rat, guinea pig, pig, dog, and opossum) both Mlxip and Mlxipl were found to be intact (S2 and S3 Tables), and these sequences were used in the comparative analyses described below. Searches with protein sequences predicted from other intact or incomplete Mlxip, Mlxipl, and Mlx genes did not find any additional exons (results not shown).

Evolution of Mlxip genes

While Mlxip genes could be found in all but one genome examined (not found in the alpaca), intact 17 coding exon genes were only identified in mammals (16 species) and fish (5 species), (S1 and S2 Tables and S1 and S4 Figs). The Mlxip gene was found in a single copy in all species with the gene, except the marmoset, which had two copies (S1 and S2 Tables). Of the two gene copies in the marmoset, one contained multiple substitutions (resulting in frameshifts or inframe stop codons in 6 exons) incompatible with function indicating that it was a pseudogene (S1 and S2 Tables). None of the Mlxip genes found in any other vertebrate species presented strong evidence of being a pseudogene (i.e., possessing multiple mutations that disrupt the open reading frame), although a few mutations that introduce stop codons or frameshifts were found in some genes (e.g., tree shrew and kangaroo rat, see S2 Table), however all of these were in incomplete genes and often found in genomes with low coverage and thus may simply be sequencing errors. Only a single copy Mlxip gene was found in each of the fish genomes examined, despite these species experiencing a genome duplication [45]. Phylogenetic analysis of the 21 intact Mlxip coding sequences by maximum likelihood, Bayesian, and neighbor-joining methods yielded a phylogeny consistent with the accepted species phylogeny (S5 Fig), with no strong evidence for lineage-specific changes in rates of evolution, suggesting no major changes in the function (and thus selective constraints) of these proteins in the examined species.

Evolution of Mlxipl genes

Like Mlxip, Mlxipl genes were found in almost all vertebrates (not found in only alpaca, tarsier and lamprey), with intact 17 coding exon genes found in mammals (14 species), birds (1 species), and a reptile (1 species), but not in amphibians or fish (S1 and S3 Tables and S2 and S6 Figs). The full-length chicken and rat coding sequences were obtained with sequences from the NCBI database, as the genomic sequence found in the Ensembl database was incomplete (see S3 Table). No evidence for a duplicate Mlxipl gene was found in any species. Again, mutations that introduce stop codons or frameshifts were found in some incomplete Mlxipl genes (e.g., tree shrew and kangaroo rat, see S2 Table), however these were found in genomes with low coverage and may simply be sequencing errors. The opossum Mlxipl gene possessed a frameshift mutation in an otherwise intact coding sequence (see S3 Table), but this mutation was in a portion of the genomic sequence that was of low quality (only three poor quality shotgun sequence reads overlapped this region), thus we considered this to be a sequencing error. Like Mlxip, only a single copy of the Mlxipl gene was found in fish genomes. Phylogenetic analysis of the 16 intact Mlxipl coding sequences by both maximum likelihood and Bayesian methods yielded a phylogeny consistent with the accepted species phylogeny (S7 Fig) with no strong evidence for lineage-specific variations in rates of evolution, thus also suggesting that among the examined ChREBP protein sequences no change in function (or selective constraint) had occurred.

Alternative promoters, and adjacent first exons, have been described for mammalian Mlxipl genes in a few mammalian species, which generate two different ChREBP isoforms [20,22]. The alpha isoform (ChREBP-α) corresponds the full-length sequence, while the beta isoform (ChREBP-β) is generated using an alternative promoter with alternative splicing that skips exon 1 producing a transcript that allows translation to initiate at a downstream ATG codon in exon 4 [22]. Examination of our predicted ChREBP protein sequences, including partial sequences, shows that the ChREBP-β specific downstream ATG codon in exon 4 is perfectly conserved in mammals, birds, reptiles, and amphibians, but not in bony (e.g., zebrafish and spotted gar) or lobe-finned (i.e., coelacanth) fish where instead this codon codes for isoleucine. No conserved inframe ATG was found in fish, either upstream or downstream of the ChREBP-β isoform ATG codon, which could have suggested a different N-terminus for the β isoform, indicating that the ChREBP-β isoform is tetrapod specific and evolved in the common ancestor of tetrapods after the divergence of this lineage from the lobe-finned fish lineage. Unfortunately, due to the failure to identify intact 17 exon Mlxipl genes in fish, we cannot determine whether changes in the evolutionary constraints (potentially due to a change in protein function) occurred with the origin of the ChREBP-β isoform, although one might expect this to have occurred.

Evolution of Mlx genes

In contrast to Mlxip and Mlxipl, Mlx genes were found in the genomes of all species examined (S1 and S4 Tables and S3 and S8 Figs). A larger number of intact Mlx genes were identified, which may not be unexpected as the gene contains only 8 coding exons. Again, a few mutations (in alpaca and hedgehog, see S4 Table) were identified that disrupt coding potential, but are possibly sequencing errors as they are found in lower quality genomes. Phylogenetic analysis of the 44 intact Mlx coding sequences by both maximum likelihood and Bayesian methods yielded a phylogeny consistent with the accepted species phylogeny (S9 Fig). In contrast to Mlxip and Mlxipl, a duplicated Mlx gene was found in a fish genome, however, the phylogenetic analysis (S9 Fig) indicates that this is a very recent duplication and not a product of the fish-specific genome duplication. Thus, despite an opportunity for sub-functionalization after the fish-specific duplication, the retention of a single Mlx gene suggests that there is strong selection to maintain coordinated interaction between Mlx and both ChREBP and MondoA. Since Mlx interacts with a large number of other basic-helix-loop-helix proteins [19,24], it is not surprising that no evidence for changes in selective constraints acting on this gene was seen in the phylogenetic analysis (S9 Fig).

Differences in the rates of evolution of Mlxip and Mlxipl coding sequences

Both MondoA and ChREBP interact with Mlx to form transcription factors that regulate distinct sets of genes [15,19,25]. As such, it would be expected that the selective forces acting on these two genes should differ. To identify sequences within the MondoA and ChREBP proteins that may evolve in different patterns, we examined the evolution of the Mlxip and Mlxipl genes that encoded full-length coding sequences. To prevent lineage-specific effects, we only examined genes from species that had intact coding sequences for both Mlxip and Mlxipl genes, thus evolved in parallel in the same genomic environments and the differences in evolutionary patterns detected should reflect the consequences of selection for gene-specific functions. Within mammals, a total of 10 species were found to contain intact copies of the Mlxip and Mlxipl genes (S2 and S3 Tables). These sequences were used to compare and contrast the evolution of Mlxip and Mlxipl as they represent the diversity of mammals and their lineages contain equal amounts of evolutionary time and, as they have coexisted in the same genome on all lineages, should have experienced identical evolutionary pressures at the genome level. An alignment of the protein sequences is shown in S10 and S11 Figs, where intron positions are identical within genes and at very similar location in the alignment between genes (similar alignments were generated using other multiple sequence aligners). The phylogeny (Fig 2) of these genes is consistent with phylogenies of the species (with very similar phylogenies generated by other methods), with the gene-specific phylogenies consistent with those from large numbers of genes (S2 and S3 Figs).

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Fig 2. Phylogeny of Mlxip and Mlxipl coding sequences.

Phylogeny inferred by the Bayesian method, implemented in MrBayes version 3.2.2, is shown, using the coding sequence alignment from S2 Fig based on the alignment presented in S12 Fig. The phylogeny is rooted between the sequences for Mlxip (shown in the upper portion) and Mlxipl (lower portion). Branch lengths are proportional to the number of inferred nucleotide substitutions. Numbers at the node represent posterior probabilities after 2,000,000 generations. Similar phylogenies were generated when Maximum likelihood or neighbor-joining methods were used.

https://doi.org/10.1371/journal.pone.0149682.g002

To identify portions of the MondoA and ChREBP protein sequences that are evolving in different patterns we compared the conservation of the sequences across the lengths of these proteins. Jenson-Shannon Divergence (JS) scores, which measure conservation over a window of sites [40], were used to assess the conservation of the sequences across the entire protein sequence (S5 Table), with the results displayed in Fig 3. As expected, the previously identified functional domains typically show higher JS scores, especially the Mondo Conserved Regions (MCR1-6) and the basic-helix-loop-helix leucine-zipper (bHLH-Zip) and dimerization and cytoplasmic localization (DCD) domains (Fig 3). Despite equal amounts of evolutionary time being represented by the MondoA and ChREBP sequences, some differences in the JS divergence scores can be seen across the protein length (Fig 3). To quantify differences in the conservation in the domains of the MondoA and ChREBP proteins we averaged the JS Divergence Scores for each domain (Table 1).

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Fig 3. Variability in MondoA and ChREBP protein sequences.

JS Divergence scores across the alignment of MondoA and ChREBP protein sequences. Plots of JS Scores for MondoA, ChREBP and combined MondoA and ChREBP protein sequences are shown. JS Scores for each position are presented in S5 Table. A schematic organization of the domains in MondoA and ChREBP is shown below the plot. Alignment of sequences and locations of domains are shown in S7 Fig.

https://doi.org/10.1371/journal.pone.0149682.g003

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Table 1. Comparison of the average JS Divergence scores for domains in MondoA and ChREBP protein sequences.

https://doi.org/10.1371/journal.pone.0149682.t001

When the divergence of the different domains in the MondoA and ChREBP protein sequences are compared, the LID, GRACE, Proline-rich, and bHLH-Zip domains the ChREBP sequences show lower levels of sequence conservation, while the MondoA proteins show lower conservation levels only for the DCD domain (Table 1). A similar pattern is observed if pairwise observed sequence difference is examined, where the majority of the pairwise differences for ChREBP sequence are greater than those for MondoA sequences for the LID, GRACE, Proline-rich, and bHLH-Zip domains, but lower for the DCD domain (S6 Table). To examine more closely the effects of the differing levels of constraints we focused on the consensus sequences for the Mondo Conserved Regions (MCR1-6), bHLH-Zip, and DCD domains, portions of the sequences that have functional roles [15,20,26–28]. Consensus sequences for the domains in ChREBP and MondoA from the 10 mammals were calculated using WebLogo [41] and shown in Fig 4.

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Fig 4. Consensus sequences for MCR1-6, bHLH-Zip and DCD domains in mammalian MondoA and ChREBP protein sequences.

Consensus sequences from 10 mammalian ChREBP and MondoA protein sequences of Mondo Conserved Regions (MCR1-6), basic helix-loop helix leucine-zipper (bHLH-Zip) and the dimerization and cytoplasmic localization (DCD) domains are displayed by WebLogos. Numbers below residues indicate position in alignments of the 10 mammalian ChREBP or MondoA sequences. Heights of letters indicate abundance of that residue in the 10 sequences. Color of residues indicate chemical properties, with green being polar amino acids (G, S, T, Y, C, Q, and N), blue are basic (K, R, and H), red are acidic (D and E) and black are hydrophobic (A, V, L, I, P, W, F, and M).

https://doi.org/10.1371/journal.pone.0149682.g004

As shown in Fig 4, the majority of differences between the consensus sequences in ChREBP and MondoA involve replacements of residues with those of similar chemical properties (e.g., position 2 of MCR1 and position 4 of MCR2), however some more radical substitutions were detected (e.g., positions 16 and 17 of MCR3, position 20 of MCR4, and position 9 of MCR5). Variations in the length of MCR5 and MCR6 were detected between ChREBP and MondoA, with MCR5 being one residue longer in ChREBP and MCR6 being one longer in MondoA (Fig 4). MCR1 and MCR2 displayed very similar sequences, with the only differences being those that retain chemical properties, suggesting that they function similarly. Greater levels of variation are seen in the consensus sequences for the remaining MCRs (MCR3-6), with the ChREBP sequences generally showing lower levels of conservation (also seen in Table 1), suggests that differences in function and constraints exist between these sequences, potentially due to interacting with a smaller number of proteins. These patterns suggest that stronger selection acted on the MondoA sequence than on ChREBP, implying that MondoA is more crucial for survival. Differences in the consensus sequences for the bHLH-Zip and DCD domains likely yield differences in binding site preferences and the regulation of downstream genes. Intriguingly, the bHLH-Zip shows less constraint in ChREBP, while the DCD domain is more variable in MondoA (Table 1). Thus it appears that changes in their downstream target genes and pathways have been acquired by mutations occurring in parallel in these two different domains of the proteins.