Phylogenetic Analysis and Selection Pressures of 5-HT Receptors in Human and Non-human Primates: Receptor of an Ancient Neurotransmitter

Molecular evolution of a collage of cholesterol interaction motifs in transmembrane helix V of the serotonin1A receptor

The human serotonin_1A receptor is a representative member of the superfamily of G protein-coupled receptors (GPCRs) and an important drug target for neurological disorders. Using a combination of biochemical, biophysical and molecular dynamics simulation approaches, we and others have shown that membrane cholesterol modulates the organization, dynamics and function of vertebrate serotonin_1A receptors. Previous studies have shown that the cytoplasmic portion of transmembrane helix V (TM V) and the extramembraneous intracellular loop 3 are critical for G-protein coupling, phosphorylation and desensitization of the receptor. We have recently resolved a collage of putative cholesterol interaction motifs from the amino acid sequence overlapping this region. In this paper, we explore the sequence plasticity of this fragment that may have adapted to altered membrane lipidome, after vertebrates evolved from primordial invertebrates. Since invertebrates have lower levels of membrane cholesterol relative to vertebrates, we compared TM V sequence fragments from invertebrate serotonin₁ receptors with vertebrate orthologs to infer the sequence plasticity in TM V. We report that the average number of cholesterol interaction motifs in TM V for diverse phyla represents an increasing trend that could mirror vertebrate evolution from primordial invertebrates. By statistical modeling, we propose that the collage of cholesterol interaction motifs in TM V of the human serotonin_1A receptor may have evolved from rudimentary collages, reminiscent of primordial invertebrate orthologs. Taken together, we propose that a repertoire of cholesterol-philic nonsynonymous substitutions may have enhanced collage complexity in TM V during vertebrate evolution.

Design of novel dopamine D2 and serotonin 5-HT2A receptors dual antagonists toward schizophrenia: An integrated study with QSAR, molecular docking, virtual screening and molecular dynamics simulations

The extrapyramidal side effects of schizophrenia treatment can be significantly reduced by simultaneously targeting dopamine D₂ and serotonin 5-HT_2A receptors. In this study, three-dimensional quantitative structure-activity relationship (3D-QSAR) models of D₂ receptor (CoMFA-1, q² = 0.767, r² = 0.969; CoMSIA-1, q² = 0.717, r² = 0.978) and 5-HT_2A receptor antagonists (CoMFA-2, q² = 0.703, r² = 0.946; CoMSIA-2, q² = 0.675, r² = 0.916) were successfully constructed using 35 tetrahydropyridopyrimidinone derivatives. Topomer CoMFA and HQSAR models were then constructed to further validate and supplement above models. Results showed that all models had good predictive power and stability. Contour map analysis revealed that the electrostatic and hydrophobic fields played vital roles in the bioactivity of dual antagonists. Molecular docking and molecular dynamic studies also suggested that the hydrogen bonding, electrostatic and hydrophobic interactions played key roles in the formation of stable binding sites. Meanwhile, several key residues like ASP114, TRP100, PHE389 of dopamine D₂ receptor and ASP134, PHE328, TRP324 of serotonin 5-HT_2A receptor were identified. Based on above findings, seven compounds were obtained through bioisostere replacement and ten compounds were designed by contour map analysis, in which the predicted activity of compounds S6 and DS2 were equivalent to that of the template compound 15. 3D-QSAR and ADMET predictions indicated that all newly designed compounds had great biological activity and physicochemical properties. Moreover, based on the best pharmacophore model, four compounds (Z1, Z2, Z3 and Z4) with new backbones were obtained by virtual screening. Overall, this study could provide theoretical guidance for the structural optimization, design and synthesis of novel dopamine D₂ and serotonin 5-HT_2A receptors dual antagonists. Abbreviations3D-QSARThree-dimensional quantitative structure-activity relationship5-HT_2ARSerotonin 5-hydroxytryptamine 5-HT_2A receptor5-HT_2CRSerotonin 5-hydroxytryptamine 5-HT_2C receptor receptorCADDComputer-aided drug designCoMFAComparative molecular field analysisCoMSIAComparative molecular similarity index analysisD₂RDopamine D(2) receptorGPCRG-protein coupled receptorPLSPartial least squares regressionHQSARHologram quantitative structure-activity relationship. Communicated by Ramaswamy H. Sarma.

A collage of cholesterol interaction motifs in the serotonin1A receptor: An evolutionary implication for differential cholesterol interaction

The serotonin_1A receptor is a representative member of the G protein-coupled receptor (GPCR) superfamily and acts as an important drug target. In our previous work, we comprehensively demonstrated that membrane cholesterol is necessary in the organization, dynamics and function of the serotonin_1A receptor. In this context, analysis of high-resolution GPCR crystal structures in general and in silico studies of the serotonin_1A receptor in particular, have suggested the presence of cholesterol interaction sites (hotspots) in various regions of the receptor. In this work, we have identified an evolutionarily conserved collage of four categories of cholesterol interaction motifs associated with transmembrane helix V and the adjacent intracellular loop 3 fragment of the vertebrate serotonin_1A receptor. This collage of motifs represents a total of twenty diverse context-dependent cholesterol interaction configurations. We envision that the gamut of cholesterol interaction sites, characterized by sequence plasticity in cholesterol interaction, could be relevant in receptor-cholesterol interaction in membranes of varying cholesterol content and organization, as found in diverse cell types. We conclude that an evolutionarily conserved mechanism of GPCR-cholesterol interaction allows the serotonin_1A receptor to adapt to diverse membrane cholesterol levels during natural evolution.

A QSAR model of Olanzapine derivatives as potential inhibitors for 5-HT2A Receptor

Schizophrenia is a complex, chronic mental disorder, affecting about 21 million people worldwide. It is characterized by symptoms, including distortions in thinking, perception, emotions, disorganized speech, sense of self and behavior. Recently, a numbers of marketed drugs for Schizophrenia are available against dopamine D2 and serotonin 5-HT2A receptors. Here, we docked Olanzapine derivatives (collected from literature) with 5-HT2A Receptor using the program AutoDock 4.2. The docked protein inhibitor complex structure was optimized using molecular dynamics simulation for 5ps with the CHARMM-22 force field using NAMD (NAnoscale Molecular Dynamics program) incorporated in visual molecular dynamics (VMD 1.9.2) and then evaluating the stability of complex structure by calculating RMSD values. NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. A quantitative structure activity relationship (QSAR) model was built using energy-based descriptors as independent variable and pKi value as dependent variable of eleven known Olanzapine derivatives with 5-HT2A Receptor, yielding correlation coefficient r2 of 0.63861. The predictive performance of QSAR model was assessed using different crossvalidation procedures. Our results suggest that a ligand-receptor binding interaction for 5-HT2A receptor using a QSAR model is promising approach to design more potent 5-HT2A receptor inhibitors prior to their synthesis.

Comprehensive, structurally-informed alignment and phylogeny of vertebrate biogenic amine receptors

Biogenic amine receptors play critical roles in regulating behavior and physiology in both vertebrates and invertebrates, particularly within the central nervous system. Members of the G-protein coupled receptor (GPCR) family, these receptors interact with endogenous bioamine ligands such as dopamine, serotonin, and epinephrine, and are targeted by a wide array of pharmaceuticals. Despite the clear clinical and biological importance of these receptors, their evolutionary history remains poorly characterized. In particular, the relationships among biogenic amine receptors and any specific evolutionary constraints acting within distinct receptor subtypes are largely unknown. To advance and facilitate studies in this receptor family, we have constructed a comprehensive, high-quality sequence alignment of vertebrate biogenic amine receptors. In particular, we have integrated a traditional multiple sequence approach with robust structural domain predictions to ensure that alignment columns accurately capture the highly-conserved GPCR structural domains, and we demonstrate how ignoring structural information produces spurious inferences of homology. Using this alignment, we have constructed a structurally-partitioned maximum-likelihood phylogeny from which we deduce novel biogenic amine receptor relationships and uncover previously unrecognized lineage-specific receptor clades. Moreover, we find that roughly 1% of the 3039 sequences in our final alignment are either misannotated or unclassified, and we propose updated classifications for these receptors. We release our comprehensive alignment and its corresponding phylogeny as a resource for future research into the evolution and diversification of biogenic amine receptors.

Patterns of genetic variation and the role of selection in HTR1A and HTR1B in macaques (Macaca)

Background

Research has increasingly highlighted the role of serotonin in behavior. However, few researchers have examined serotonin in an evolutionary context, although such research could provide insight into the evolution of important behaviors. The genus Macaca represents a useful model to address this, as this genus shows a wide range of behavioral variation. In addition, many genetic features of the macaque serotonin system are similar to those of humans, and as common models in biomedical research, knowledge of the genetic variation and evolution of serotonin functioning in macaques are particularly relevant for studies of human evolution. Here, we examine the role of selection in the macaque serotonin system by comparing patterns of genetic variation for two genes that code for two types of serotonin receptors – HTR1A and HTR1B – across five species of macaques.

Results

The pattern of variation is significantly different for HTR1A compared to HTR1B. Specifically, there is an increase in between-species variation compared to within-species variation for HTR1A. Phylogenetic analyses indicate that portions of HTR1A show an elevated level of nonsynonymous substitutions. Together these analyses are indicative of positive selection acting on HTR1A, but not HTR1B. Furthermore, the haplotype network for HTR1A is inconsistent with the species tree, potentially due to both deep coalescence and selection.

Conclusions

The results of this study indicate distinct evolutionary histories for HTR1A and HTR1B, with HTR1A showing evidence of selection and a high level of divergence among species, a factor which may have an impact on biomedical research that uses these species as models. The wide genetic variation of HTR1A may also explain some of the species differences in behavior, although further studies on the phenotypic effect of the sequenced polymorphisms are needed to confirm this.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-014-0116-5) contains supplementary material, which is available to authorized users.

Nonhuman primate models of depression: effects of early experience and stress

Depression causes significant morbidity in the human population. The Diathesis-Stress/Two-Hit model of depression hypothesizes that stress interacts with underlying (probably genetic) predispositions to produce a central nervous system that is primed to express psychopathology when confronted with stressful experiences later in life. Nonhuman primate (NHP) studies have been extensively utilized to test this model. NHPs are especially useful for studying effects of early experience, because many aspects of NHP infancy are similar to humans, whereas development occurs at an accelerated rate and therefore allows for more rapid assessment of experimental variables. In addition, the ability to manipulate putative risk factors, including introducing experimental stress during development, allows inference of causality not possible with human studies. This manuscript reviews experimental paradigms that have been utilized to model early adverse experience in NHPs, including peer-rearing, maternal separation, and variable foraging. It also provides examples of how this model has been used to investigate the effects of early experience on later neurobiology, physiology, and behavior associated with depression. We conclude that the NHP offers an excellent model to research mechanisms contributing to the Diathesis-Stress/Two-Hit model of depression.

The pectin lyases in Arabidopsis thaliana: evolution, selection and expression profiles

Pectin lyases are a group of enzymes that are thought to contribute to many biological processes, such as the degradation of pectin. However, until this study, no comprehensive study incorporating phylogeny, chromosomal location, gene duplication, gene organization, functional divergence, adaptive evolution, expression profiling and functional networks has been reported for Arabidopsis. Sixty-seven pectin lyase genes have been identified, and most of them possess signal sequences targeting the secretory pathway. Phylogenetic analyses identified five gene groups with considerable conservation among groups. Pectin lyase genes were non-randomly distributed across chromosomes and clustering was evident. Functional divergence and adaptive evolution analyses suggested that purifying selection was the main force driving pectin lyase evolution, although some critical sites responsible for functional divergence might be the consequence of positive selection. A stigma- and receptacle-specific expression promoter was identified, and it had increased expression in response to wounding. Two hundred and eighty-eight interactions were identified by functional network analyses, and most of these were involved in cellular metabolism, cellular transport and localization, and stimulus responses. This investigation contributes to an improved understanding of the complexity of the Arabidopsis pectin lyase gene family.

Evolutionary perspective on the origin of Haitian cholera outbreak strain

Cholera epidemic has not been reported in Haiti for at least 100 years, although cholera has been present in Latin America since 1991. Surprisingly, the recent cholera epidemic in Haiti (October 2010) recorded more than 250,000 cases and 4000 deaths in the first 6 months and became one of the most explosive and deadly cholera outbreak in recent history. In the present study, we conducted genomic analyses of pathogenicity islands of three Haitian Vibrio cholerae strains and compared them with nine different V. cholerae O1 El Tor genomes. Although CIRS101 is evolutionarily most similar to the Haitian strains, our study also provides some important differences in the genetic organization of pathogenicity islands of Haitian strains with CIRS101. Evolutionary analysis suggests that unusual functional constraints have been imposed on the Haitian strains and we hypothesize that amino acid substitution is more deleterious in Haitian strains than in nonHaitian strains.

Dynamics of arginase gene evolution in metazoans

In the present study, a comprehensive analysis of the arginase gene family in metazoans was performed. A total of 126 arginase genes have been identified in 44 species. Phylogenetic analyses indicate that arginase genes consist of four groups. Conservative and divergent gene structures are found among the groups. The syntenies also exist in distantly related genomes among multiple species. Adaptive evolution shows that, while purifying selection may have been the main force driving the evolution of the arginases, some of critical sites responsible for the functional divergence may have been under positive selection. Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the arginase gene family and of the function and evolution of this family in metazoans.

Gene re-annotation in genome of the extremophile Pyrobaculum aerophilum by using bioinformatics methods

In this paper, we re-annotated the genome of Pyrobaculum aerophilum str. IM2, particularly for hypothetical ORFs. The annotation process includes three parts. Firstly and most importantly, 23 new genes, which were missed in the original annotation, are found by combining similarity search and the ab initio gene finding approaches. Among these new genes, five have significant similarities with function-known genes and the rest have significant similarities with hypothetical ORFs contained in other genomes. Secondly, the coding potentials of the 1645 hypothetical ORFs are re-predicted by using 33 Z curve variables combined with Fisher linear discrimination method. With the accuracy being 99.68%, 25 originally annotated hypothetical ORFs are recognized as non-coding by our method. Thirdly, 80 hypothetical ORFs are assigned with potential functions by using similarity search with BLAST program. Re-annotation of the genome will benefit related researches on this hyperthermophilic crenarchaeon. Also, the re-annotation procedure could be taken as a reference for other archaeal genomes. Details of the revised annotation are freely available at http://cobi.uestc.edu.cn/resource/paero/

From lipid transport to oxygenation of aromatic compounds: evolution within the Bet v1-like superfamily

In absence of significant sequence similarity, remote homology between proteins can be confused with analogy and in such a case, shared ancestry can be inferred in light of certain unique and common features. In the present study, to understand the evolutionary origin of catalytic domain of large subunit of ring-hydroxylating oxygenases (RHOs), belonging to the Bet v1-like superfamily, structure-based phylogenies have been derived from structural alignment of representative proteins of the superfamily. A careful inspection of the structural relatedness of RHOs with the rest of the families showed closest similarity between RHO catalytic domain and PA1206-like protein. In addition, phylogenetic relationship of the Rieske domain of the large subunit of RHOs with functionally and structurally similar proteins has also been elucidated so as to postulate the most possible events leading to the genesis of the large subunit of RHOs.

Weighted relative entropy for alignment-free sequence comparison based on Markov model

In this paper, we introduce a probabilistic measure for computing the similarity between two biological sequences without alignment. The computation of the similarity measure is based on the Kullback-Leibler divergence of two constructed Markov models. We firstly validate the method on clustering nine chromosomes from three species. Secondly, we give the result of similarity search based on our new method. We lastly apply the measure to the construction of phylogenetic tree of 48 HEV genome sequences. Our results indicate that the weighted relative entropy is an efficient and powerful alignment-free measure for the analysis of sequences in the genomic scale.

Genome-wide identification and evolutionary analysis of Arabidopsis sm genes family

Sm proteins are members of a family of small proteins that are widespread in biosphere and found associated with RNA metabolism. To date, to our knowledge, only Arabidopsis SAD1 gene has been studied functionally in plant. In this study, 42 Sm genes are identified through comprehensive analysis in Arabidopsis. And a complete overview of this gene family is presented, including the gene structures, phylogeny, chromosome locations, selection pressure and expression. The results reveal that gene duplication contributes to the expansion of the Sm gene family in Arabidopsis genome, diverse expression patterns suggest their functional differentiation and divergence analysis indicates purifying selection as a key role in evolution. Our comparative genomics analysis of Sm genes will provide the first step towards the future experimental research on determining the functions of these genes.

An efficient binomial model-based measure for sequence comparison and its application

Sequence comparison is one of the major tasks in bioinformatics, which could serve as evidence of structural and functional conservation, as well as of evolutionary relations. There are several similarity/dissimilarity measures for sequence comparison, but challenges remains. This paper presented a binomial model-based measure to analyze biological sequences. With help of a random indicator, the occurrence of a word at any position of sequence can be regarded as a random Bernoulli variable, and the distribution of a sum of the word occurrence is well known to be a binomial one. By using a recursive formula, we computed the binomial probability of the word count and proposed a binomial model-based measure based on the relative entropy. The proposed measure was tested by extensive experiments including classification of HEV genotypes and phylogenetic analysis, and further compared with alignment-based and alignment-free measures. The results demonstrate that the proposed measure based on binomial model is more efficient.

Lipid-binding surfaces of membrane proteins: evidence from evolutionary and structural analysis

Membrane proteins function in the diverse environment of the lipid bilayer. Experimental evidence suggests that some lipid molecules bind tightly to specific sites on the membrane protein surface. These lipid molecules often act as co-factors and play important functional roles. In this study, we have assessed the evolutionary selection pressure experienced at lipid-binding sites in a set of α-helical and β-barrel membrane proteins using posterior probability analysis of the ratio of synonymous vs. nonsynonymous substitutions (ω-ratio). We have also carried out a geometric analysis of the membrane protein structures to identify residues in close contact with co-crystallized lipids. We found that residues forming cholesterol-binding sites in both β(2)-adrenergic receptor and Na(+)-K(+)-ATPase exhibit strong conservation, which can be characterized by an expanded cholesterol consensus motif for GPCRs. Our results suggest the functional importance of aromatic stacking interactions and interhelical hydrogen bonds in facilitating protein-cholesterol interactions, which is now reflected in the expanded motif. We also find that residues forming the cardiolipin-binding site in formate dehydrogenase-N γ-subunit and the phosphatidylglycerol binding site in KcsA are under strong purifying selection pressure. Although the lipopolysaccharide (LPS)-binding site in ferric hydroxamate uptake receptor (FhuA) is only weakly conserved, we show using a statistical mechanical model that LPS binds to the least stable FhuA β-strand and protects it from the bulk lipid. Our results suggest that specific lipid binding may be a general mechanism employed by β-barrel membrane proteins to stabilize weakly stable regions. Overall, we find that the residues forming specific lipid binding sites on the surfaces of membrane proteins often experience strong purifying selection pressure.