Journal of Molecular Evolution (2019) 87:93–105 https://doi.org/10.1007/s00239-019-09889-1
ORIGINAL ARTICLE
Conserved Critical Evolutionary Gene Structures in Orthologs
Miguel A. Fuertes1 · José R. Rodrigo2 · Carlos Alonso1
Received: 19 July 2018 / Accepted: 13 February 2019 / Published online: 28 February 2019 © Springer Science+Business Media, LLC, part of Springer Nature 2019
Abstract Unravelling gene structure requires the identification and understanding of the constraints that are often associated with the evolutionary history and functional domains of genes. We speculated in this manuscript with the possibility of the existence in orthologs of an emergent highly conserved gene structure that might explain their coordinated evolution during speciation events and their parental function. Here, we will address the following issues: (1) is there any conserved hypothetical struc- ture along ortholog gene sequences? (2) If any, are such conserved structures maintained and conserved during speciation events? The data presented show evidences supporting this hypothesis. We have found that, (1) most orthologs studied share highly conserved compositional structures not observed previously. (2) While the percent identity of nucleotide sequences of orthologs correlates with the percent identity of composon sequences, the number of emergent compositional structures conserved during speciation does not correlate with the percent identity. (3) A broad range of species conserves the emergent compositional stretches. We will also discuss the concept of critical gene structure.
Keywords Molecular evolution · Triplet-composon · Gene structure · Human–mouse orthologs
Introduction DNA patterns in genes and genomes requires comparing the compositional characteristics that genes show in and among The apparent lack of patterns resulting from the distribu- species. Between others, the methods for the identification of tion of bases in gene sequences has been for a long time DNA patterns have been based on genetic and evolutionary one of the most interesting and intriguing question marks considerations (Sueoka 1962), on linear regression models of molecular biology. In fact, intense research efforts have (Dai et al. 2007), on the analysis of nucleotide (NT) asym- been made to identify whether and how these patterns are metries (Arnold et al. 1988) and on graphical representations distributed along the length of genomic sequences and how of DNA sequences (Gates 1986; Leong and Morgenthaler these patterns can be visualized. Actually, the search for 1995; Nandy 2009; Roy et al. 1988) among others. Thus, an important and significant step forward toward the iden- tification of genomic patterns will be based on the detec- Handling editor: Hideki Innan. tion of genes and signals able to rule the function of genes across species (Notebaart et al. 2005). In addition, it is of Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00239-019-09889-1) contains the outmost relevance identifying the functional information supplementary material, which is available to authorized users. contained in genomes and the way in which the informa- tional content is arranged in chromosomes and in the high * Miguel A. Fuertes order chromatin organization (Gingeras 2009; Takeda 2012). [email protected] This debate exemplifies the relevance of the identification José R. Rodrigo and analysis of DNA patterns and the clarification of their [email protected] functional significance. Thus, the analysis of the structure Carlos Alonso of genes and of the linear organization of nucleotides along [email protected] the DNA sequence constitutes an active and wide field of 1 Centro de Biología Molecular “Severo Ochoa” investigation (Zhu et al. 2009). For example, while mouse (CSIC‑UAM), Universidad Autónoma de Madrid, c/Nicolás and humans have maintained a substantial divergence at Cabrera 1, 28049 Madrid, Spain the DNA level (Yue et al. 2014), their genomic differences 2 Telefónica de España S.A., Gran Vía 28, Madrid, Spain
Vol.:(0123456789)1 3 94 Journal of Molecular Evolution (2019) 87:93–105 remain to be fully characterized. In fact, it has been recently Materials and Methods realized that intron patterns may harbour a variety of ele- ments that regulate transcription (Comeron 2001; Gazave DNA Sequence Acquisition and Pre‑processing et al. 2007), a variety of elements that may harbour the role of non-coded RNAs (Mattick and Gagen 2001) and ele- Human–mouse orthologs were downloaded from Ensembl ments that regulate the splicing control (Majewski and Ott gene database release 86—Oct 2016 © WTSI/EMBL-EBI 2002). Thus, while the function of exon sequences would (Yates et al. 2016). The criteria to collect the orthologs be to encode proteins (Gilbert 1978) the function of intron takes into account that all selected orthologs must belong sequences might be to encode gene regulation information in mouse and human to different tCP-clusters (Online (Costas et al. 2004; Robart et al. 2007; Robart and Zimmerly Resources 1 and 2) (Fuertes et al. 2016b). Consequently, 2005; Rogozin et al. 2005; Wang et al. 2005). In order to the human–mouse orthologs selected will diverge in their maintain an efficient gene function (Amit et al. 2012; Parm- tCP-sequences. In the study we only consider the genes ley et al. 2007) it is critical to retain the structural informa- coding for the longest transcripts (Fuertes et al. 2016c). tion of the coding and non-coding DNA. The fine regulation We identified the genes of the dataset by the gene name of the splicing machinery (Gelfman et al. 2012; Keren et al. and their corresponding protein description. Online 2010; Rogozin et al. 2002) suggests that to maintain the Resource 1 also indicates how many genes are in each structural DNA patterns there might be strong compositional cluster. In parallel, a sample of human–mouse orthologs constraints acting at the DNA and chromatin level (Louie contained in the same tCP-cluster (named sample 2) were et al. 2003; Schwartz et al. 2009). also analysed (see Online Resource 3). In this paper, Recently, based on the composon concept (Fuertes et al. we analysed the coding sequences of all human–mouse 2011), a new method revealing emerging DNA patterns orthologs from samples 1 and 2. not observed previously has been proposed. This outcome results from the application of the tCP-methodology to human–mouse orthologs (Fuertes et al. 2016b). The fre- Calculation Methods quency-usage of sets of DNA triplets having the same gross composition, called triplet-composons (or briefly, tCPs), is To analyse the similarities and dissimilarities of the measurement parameter of the tCP-methodology. It is human–mouse orthologs in relation to the gene length we recognized that the use of this method results to be useful set up an analysis based on the tCP-methodology (Fuertes for categorizing by their tCP-usage the coding and intron et al. 2011, 2016b). We agreed to use this method to sequences from a large number of orthologs in a few num- investigate because it is very difficult to obtain the con- ber of families. By using this method it has been shown served DNA structures here in described by other exist- that exons and introns of human–mouse orthologs do not ing methods. The justification for the tCP-methodology evolve independently (Fuertes et al. 2016a). In addition, the is theoretical and based on the existence of exclusionary analysis of a large number of genes from some of those cat- multiplets characterized by the presence or absence of par- egorizations revealed that the bulk of these orthologs share ticular bases. It was demonstrated that the number of such common functional similarities (Fuertes et al. 2016c) despite groups of exclusionary multiplets (later called “triplet- having dissimilar NT-sequences. For example, while at the composons” or tCPs), resulted to be 14 and the minimum NT-level some of the genes contained in the Rhodopsin length of the multiplet was 3 NTs (a triplet) (Fuertes et al. G-protein coupled receptor superfamily were considered not 2011). The 14 tCPs contain all possible nearest-neighbours to be orthologs, they have a high degree of similarity when that can be formed with four DNA bases, forming in this we look at their tCP-usage (Fuertes et al. 2016b). The main way a close system (see Table 1). The “fully overlapping difference between the data and the analyses presented in reading” guarantees that all triplets of a DNA sequence are this manuscript and those previously reported is that to elab- considered in the study avoiding the lack of information. orate the data previously reported we counted NT-triplets in Finally, we consider that the lost triplets, when reading the DNA sequence in a fully overlapping way analysing the the DNA in non-overlapping way (as is the case of the tCP-usage frequency. The tCP-usage gives information about genetic code), gives relevant evolutionary information. how many and what tCPs are contained in the entire DNA The notation of tCPs and their associated sets of NT-tri- sequence but not about their distribution along the length of plets are in Table 1. To evaluate the distribution of tCPs the sequence. In this paper, however, we counted tCPs focus- along the gene length we estimated the cumulative tCP- sing on their distribution along the length. By the analysis of usage. The cumulative tCP-usage would be then the sum the tCP distribution, the NT-compositional architecture of of all previous tCP events up to the current length. To orthologs emerges. In this context, we will also discuss the facilitate the visualization of the distribution of tCPs along concept of NT- and tCP-homology.
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Fig. 1 Distribution of the tCP
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◂Fig. 2 Panel comparing the fourteen tCP-profiles with the length Since these correlations were near the cut-off but lower, of the human–mouse ortholog CYP1A2. Red and blue lines corre- they were discarded from the analysis. Low correlation spond to distributions of tCPs along the trend line of the mouse and r the human cumulative tCP-usages, respectively. The insets display in levels ranging from 0.403 < < 0.644 were also observed the upper right corner the name of the ortholog, the mouse (7) and for ,
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Fig. 3 Percent identity and gaps calculated per human–mouse sequences of samples 1 and 2. (C) Correlation observed in the per- ortholog in samples 1 and 2 (Online Resources 2 and 3). (A) The cent of gaps between NT- and tCP-sequences of samples 1 and 2. percent identity in alignments of NT- (upper black line) and tCP- Insets of (B, C) illustrate differences on the percent identity and gaps sequences (upper blue line) and the percent of gaps in alignments between NT- (filled black square) and tCP-sequences (filled grey of NT- (lower black line) and tCP-sequences (lower blue line). (B) square), respectively. (Color figure online) Correlation observed in the percent identity between NT- and tCP-
Distribution of Conserved tCPs Along Human– are per ortholog in both samples. We noticed that 90% of Mouse Orthologs orthologs from sample 1 and 74% from sample 2 share less than 6 out of the 14 tCPs. Thus, a notable fraction of the Since the NT- and tCP-sequences are highly correlated, we orthologs analysed share less than half of all tCPs, inde- further will analyse the type and amount of tCPs shared by pendently on the percent identity of both the NT- and tCP- the orthologs of samples 1 and 2. When representing the ortholog sequences. Only 10% of sample 1 and 26% of sam- number of orthologs sharing the same tCP (Fig. 4A), we ple 2 share more than six tCPs. We also observed that 10% observed that the sequences maintain, in most cases, the of orthologs from sample 1 and 6% of sample 2 does not tCP
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Fig. 4 (A) Distribution of orthologs relative to the type of tCP con- sequences per ortholog relative to the number of conserved tCPs. In served (in %). (B) Distribution of orthologs relative to the number of all cases, we represent together the sample 1 (black) and 2 (white) for tCPs conserved. (C) Graph representing the percent identity of NT- comparison identity between the NT-sequences the higher the number The alignment of the NT-sequences of SAMD12 revealed of conserved tCPs. There are also cases in which high per- 89% identity between human and mouse. However, human cent identity between NT-sequences is associated with low SAMD12 and its mouse-ortholog share only 4 out of 14 number of conserved tCPs. The result illustrates a basic tCPs (< T>,
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Fig. 5 NT-sequence alignment of the human–mouse ortholog SAMD12. The grey shaded areas of both sequences repre- sent the conserved NT-triplets (see Table 1) contained in the conserved tCPs
to fluctuations about the mean. Some of these changes, Critical Emerging Evolutionary Gene Structures probably, could correspond to tCPs non-correlated at all or even negative-correlated. The limited number of changes It has been accepted that the critical processes leading to the in the conserved sequence can be a consequence of strong evolution of gene structure are the generation of mutations evolutionary constrains acting over the conserved tCP and the filtering of these mutations by natural selection. The stretches. The calculations demonstrated that the number existence of conserved emerging gene structures, as those of NT-mismatches for the conserved tCPs
1 3 Journal of Molecular Evolution (2019) 87:93–105 101 from other species. In addition to Homo sapiens (humans) entirely conserved stretches, the tCP
Fig. 6 Evolutionary relationships of taxa and conserved gene struc- those of the evolutionary distances used to infer the phylogenetic tree. tures. (A) The histogram shows the percent of complete structures The evolutionary distances were computed using the Maximum Com- (open square) and the partial conserved structures (filled black posite Likelihood method (Tamura et al. 2004) and are in the units square) in each species. (B) The evolutionary history of SAMD12 of the number of base substitutions per site. The analysis involved 12 was inferred using the UPGMA method (Sneath and Sokal 1973). NT-sequences. All positions containing gaps and missing data were The optimal tree with their corresponding branch lengths is shown. eliminated. There was a total of 434 positions in the final dataset. The tree is drawn to scale, with branch lengths in the same units as Evolutionary analysis was conducted in MEGA7 (Kumar et al. 2016)
1 3 102 Journal of Molecular Evolution (2019) 87:93–105 mutations would have a larger biological impact than would About the Correlations Between tCP mutations in CDS (King and Wilson 1975). The methodol- and NT‑Sequences ogy herein used to reveal emergent compositional structures use the concept of triplet-composon or tCP that provides In addition to the fact that there is a correlation between useful evolutionary information in and out CDS (Fuertes the NT-composition of a DNA sequence and its tCP-usage et al. 2011, 2016a, b). Although the tCP-code is close to (Fuertes et al. 2016b) the data presented in this paper show the genetic code in many aspects, it is very different in oth- that there are correlations between percent of tCP- and NT- ers. We think, however, the tCP-code is a code in a strict identities and gaps (Fig. 3 and Online Resources 2 and 3). sense (Table 1) because an input generates an output. Actu- Gaps are due to insertions and deletions (INDELs) into the ally, there are properties shared by both codes: (i) to decode sequences compared (Bhangale et al. 2005; Weber et al. genomic information both codes operate reading NT-triplets 2002). We noticed in addition that the identities obtained and (ii) both codes are degenerated. However, the genetic from alignments of ortholog NT-sequences were always code and the tCP-code differ in some basic aspects: (i) in the higher that those observed in alignments of their corre- genetic code the DNA is read in a non-overlapping way in sponding tCP-sequences (Fig. 3B). This is because a single the correct reading frame (CDS), while the tCP-code is read substitution in a NT-sequence implies 1–3 changes in the in fully overlapping way, and consequently, in any reading corresponding tCP-sequence because of the fully overlap- frame. (ii) The genetic code translates NT-sequences (CDS) ping reading during translation of NT- to tCP-sequences. into protein sequences while the tCP-code translates NT- Moreover, when INDELs are present the number of differ- sequences into tCP-sequences. Alignments of tCP-sequences ences between NT- and tCP-sequences increases faster in are the basis to obtain useful evolutionary information from tCP-sequences than in NT-sequences (Fig. 3C). A notable ortholog genes since they clearly manifest, between others, decrease in the number of INDELs in NT-sequences indi- the existence of highly conserved stretches. NT- and tCP- cates that the percent identity observed would be higher in sequences are connected by compositional parameters as the NT-sequence alignments that in tCP-sequence alignments. tCP-usage and the NT-composition (Fuertes et al. 2016b). In In agreement with our data, simulations carried out on this paper, we demonstrated that there are local conserved human–mouse orthologs indicate (with an error of 2%) that structures inside CDS (see Fig. 3). We show that orthologs INDEL rates are up to twice higher than it would be deduced share common compositional structures not observed previ- from the NT-sequence alignments (Lunter 2007). In human, ously which are interspersed along the length of CDS. To small INDELs are found often in exons. Some lines of evi- do that, we have use a modified version of the original tCP- dence point to such variations as a major determinant of the method consisting in the identification of the position of human biological diversity (Mills et al. 2011). each tCP along the gene length. The data presented indicate that evolution may take advantage of such inner structures About the New Conserved tCP‑Structure suggesting in some cases shared biology and in other cases revealing differences that could shed light on what makes We know that an accepted strategy for finding functional species different. sequences is the search for conserved nucleotide stretches We conclude by indicating the strengths of analysing through species (Hardison et al. 1997; Kellis et al. 2003; tCP-sequences instead of nucleotide sequences: (i) the Woolfe et al. 2005). The accumulation of sequenced “fully overlapping reading” guarantee that all triplets of a genomes and the increase and the improvement of tools DNA sequence are taken into account, avoiding the lack of that permit whole genomes to be aligned (Blanchette et al. relevant contextual evolutionary information. (ii) The inde- 2004; Bray and Pachter 2004) lead us to search for con- pendence on the reading frame allows to study not only CDS served sequences and to use the data obtained to create new but also introns, intergenic sequences, etc., that could be of hypotheses and experiments (Frazer et al. 2001; Woolfe et al. interest in mutational analysis, helping to research on gene 2005). We think that the main outcome of this paper high- structure and function, species identification and in the study lights when we align and compare ortholog tCP-sequences. of genetic diseases. (iii) The simplicity of the method allows The outcome deals with the existence of highly conserved an easy access to both the numerical and the visual data in compositional structures of conserved tCPs. The number of a fast way. (iv) The control of the correlation coefficient conserved compositional structures will depend on the tun- allows tuning the level of constriction of the study. (v) The ing of the cut-off. As indicated in Material and Methods the concept of “composon” as a group of triplets with the same tuning was fixed to r ≥ 0.85. Decoding the tCP-sequences gross composition (see Table 1) brings a new perspective to into NTs (using Table 1) allowed us to find the correspond- the study of compositional aspects not considered previously ing conserved NT-stretches. This conserved stretches would revealing innovative properties of DNA sequences as those be suitable for functional studies, elucidate new genetic reported in this paper. structures or assist in mutational studies, among others.
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tCP structures partially conserved can also be detected (Fig. 2 and Online Resource 5) despite the high percent in certain stretches of the ortholog CYP1A2 (Fig. 2) as it identity of NT-sequences (see Online Resource 2). In fact, occurs, in particular, with tCPs < TCG > and < GT > between 90% of orthologs from sample 1 and 74% of sample 2 share 100 and 900 bp and 0–700 bp, respectively. The conserva- less than 6 tCPs (Fig. 4B). We have to underline here that tion of these short fragments does not significantly increase negative-correlated tCP-profiles are more common than we the correlation of the tCP-profile when the entire sequences might think and occur when high values of one variable were aligned. We think, however, that the method proposed tend to be associated with low values of the other. The fact here is suitable for evolutionary analysis of these partial of having negative-correlated profiles gives as a result that coincidences endowing it with a great analytical power by some coincidences in the sequence alignments may mainly either tuning the cut-off or considering only such fragments be due to fluctuations about the mean or at random fits in in the study. We are conscious that the analysis of partially many NTs of the aligned sequences. The fluctuation and conserved structures could have a great potential to extract random fits observed would affect the global computation evolutionary information from the alignment. In summary, of the percent identity between both ortholog NT-sequences. and in order to reinforce the concept of tCP, as an informa- A notable difference between NT-homology and tCP- tive evolutionary parameter, we stress the point that the tCP- homology has to do with the fact that in the NT-ortholog sequence analysis of orthologs reveals the existence of com- sequences, generated by the conserved tCP-ortholog mon inner compositional structures, not described before as sequences, there is some NT-mismatches (see Fig. 5) due far as we know. to the redundancy of the tCP-code (Table 1). These mis- It might be intuitive that in general, a high correlation matches at NT-level do not affect the integrity of the con- must exist between the number of conserved tCPs and served tCP-structure because those changes correspond the percent identity. However, this is not always the case to NT-triplets that are included in some of the conserved (Fig. 3C). The low correlation observed between the percent tCPs (see Table 1). Consequently, the conserved stretch of identity and the number of conserved tCPs in some orthologs a tCP-sequence might not be conserved in the associated from samples 1 and 2 (r = 0.153 and r = 0.251, respectively) NT-sequence. These mismatches at NT-level may imply, in shows that in some cases high sequence identities and a low some cases, alterations in non-synonymous codons having number of conserved tCPs can coexist as the neutral theory an important role in the fitness of the organism because they of evolution predicts. This result is interesting because it are conserved at tCP-level during speciation. allows identifying a fact that have been discussed (Morrison 2009, 2015) having to do with the observed percent identity Critical Gene Structures and Evolution between alignments of gene sequences and their connection with homology (Pearson 2013). Thus, our data could fuel the How relevant is in orthologs the high percent identity of debate that, frequently, high identities in orthologs overlook NT-sequences of non-conserved fragments as those detected inner gene structures biologically relevant. by the tCP-method? In CYP1A2 and SAMD12, the high per- cent identity might be due to the sum of several factors: (i) Differences Between tCP and NT‑Sequence to highly conserved tCP-profiles (r ≥ 0.85) as expected; (ii) Homologies to tCP-profiles with correlations lower but near the cut-off; (iii) to non-correlated tCP-profiles far from the cut-off and The concept of homology (Pearson 2013) is central to the finally, (iv) to negative-correlated tCP-profiles. For exam- analyses of gene sequences. In our dataset, orthology (a type ple, in CYP1A2 the tCPs < C> (r = 0.737) and < TCG> of homology) is established as the selection criterion. All (r = 0.722) have correlations lower but near the cut-off. The genes selected in this study are orthologs. In no case, we same occurs in SAMD12 with < A> (r = 0.720),
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In summary, the high sequence homology detected in Fuertes MA, Rodrigo JR, Alonso C (2016a) Do intron and coding the structure of orthologs interspersed all along the gene sequences of some human–mouse orthologs evolve as a single unit? J Mol Evol 82:247–250. https://doi.org/10.1007/s0023 sequence are frequently masked by a variety of NT coinci- 9-016-9746-8 dences attributable to local fits, to low correlated tCPs or Fuertes MA, Rodrigo JR, Alonso C (2016b) A method for the anno- even to fluctuations about the mean in the case of negative- tation of functional similarities of coding DNA sequences: the correlated tCPs (data not shown). The highly conserved case of a populated cluster of transmembrane proteins. 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