Evolution of Brain-Expressed Biogenic Amine Receptors into Olfactory Trace Amine-Associated Receptors

The family of trace amine-associated receptors (TAARs) is distantly related to G protein-coupled biogenic aminergic receptors. TAARs are found in the brain as well as in the olfactory epithelium where they detect biogenic amines. However, the functional relationship of receptors from distinct TAAR subfamilies and in different species is still uncertain. Here, we perform a thorough phylogenetic analysis of 702 TAAR-like (TARL) and TAAR sequences from 48 species. We show that a clade of Tarl genes has greatly expanded in lampreys, whereas the other Tarl clade consists of only one or two orthologs in jawed vertebrates and is lost in amniotes. We also identify two small clades of Taar genes in sharks related to the remaining Taar genes in bony vertebrates, which are divided into four major clades. We further identify ligands for 61 orphan TARLs and TAARs from sea lamprey, shark, ray-finned fishes, and mammals, as well as novel ligands for two 5-hydroxytryptamine receptor 4 orthologs, a serotonin receptor subtype closely related to TAARs. Our results reveal a pattern of functional convergence and segregation: TARLs from sea lamprey and bony vertebrate olfactory TAARs underwent independent expansions to function as chemosensory receptors, whereas TARLs from jawed vertebrates retain ancestral response profiles and may have similar functions to TAAR1 in the brain. Overall, our data provide a comprehensive understanding of the evolution and ligand recognition profiles of TAARs and TARLs.     

Inverse Agonistic Action of 3-Iodothyronamine at the Human Trace Amine-Associated Receptor 5

ObjectiveApplication of 3-iodothyronamine (3-T₁AM) results in decreased body temperature and body weight in rodents. The trace amine-associated receptor (TAAR) 1, a family A G protein-coupled receptor, is a target of 3-T₁AM. However, 3-T₁AM effects still persist in mTaar1 knockout mice, which suggest so far unknown further receptor targets that are of physiological relevance. TAAR5 is a highly conserved TAAR subtype among mammals and we here tested TAAR5 as a potential 3-T₁AM target. First, we investigated mouse Taar5 (mTaar5) expression in several brain regions of the mouse in comparison to mTaar1. Secondly, to unravel the full spectrum of signaling capacities, we examined the distinct G_s-, G_i/o-, G_12/13-, G_q/11- and MAP kinase-mediated signaling pathways of mouse and human TAAR5 under ligand-independent conditions and after application of 3-T₁AM. We found overlapping localization of mTaar1 and mTaar5 in the amygdala and ventromedial hypothalamus of the mouse brain. Second, the murine and human TAAR5 (hTAAR5) display significant basal activity in the G_q/11 pathway but show differences in the basal activity in G_s and MAP kinase signaling. In contrast to mTaar5, 3-T₁AM application at hTAAR5 resulted in significant reduction in basal IP₃ formation and MAP kinase signaling. In conclusion, our data suggest that the human TAAR5 is a target for 3-T₁AM, exhibiting inhibitory effects on IP₃ formation and MAP kinase signaling pathways, but does not mediate G_s signaling effects as observed for TAAR1. This study also indicates differences between TAAR5 orthologs with respect to their signaling profile. In consequence, 3-T₁AM-mediated effects may differ between rodents and humans.     

Biogenic Trace Amine-Associated Receptors (TAARS) are encoded in avian genomes: evidence and possible implications

Recent studies of mammals and fish indicate that most trace amine-associated receptors (TAARs) may be involved in the detection of volatile biogenic compounds. It has therefore been suggested that this new class of "olfactory" receptors could be highly relevant for social communication and individual recognition. To determine if TAAR orthologues are encoded in avian genomes, we initiated BLAST searches of the Gallus gallus genome and public avian expressed sequence tags databases and performed associated phylogenetic analyses of the TAAR homologues identified. Our results suggest that a minimum of 3 TAAR paralogues are encoded in the G. gallus genome and that these are putative orthologues of the human/mouse genes TAAR1, TAAR2, and TAAR5. It is noteworthy that TAAR5 is activated by compounds that have been found in avian feces. We tentatively suggest that avian TAARs may compensate for the lack of an avian equivalent of the mammalian vomeronasal system and therefore may be important mediators of socially important avian chemical cues.     

灵长目动物TRIM5基因的进化及其抗逆转录病毒的种属差异性

灵长目动物TRIM5基因能编码TRIM5α蛋白,它在逆转录病毒侵染宿主细胞的早期阶段抑制病毒复制。同时科学家也在灵长目动物中发现了TRIM5基因的另外一种融合蛋白基因型——TRIMCyp,由于发生的剪接机制不同,新、旧大陆猴分别形成了不同的融合蛋白,从而导致它们抗病毒活性的广泛差异。TRIM5基因在灵长目动物进化过程中产生了很多突变位点,这些突变位点也使灵长目动物抗逆转录病毒的活性存在种属差异。本文简述了TRIM5基因及编码蛋白的结构,从自然选择的角度阐述了灵长目动物TRIM5基因的进化,揭示了由TRIM5基因多样性所造成的抗病毒种属差异,从而为研究灵长目动物的进化以及人猴共患疾病模式生物的构建提供一定的指导。     

Functional Diversity and Evolution of Bitter Taste Receptors in Egg-Laying Mammals

Egg-laying mammals (monotremes) are a sister clade of therians (placental mammals and marsupials) and a key clade to understand mammalian evolution. They are classified into platypus and echidna, which exhibit distinct ecological features such as habitats and diet. Chemosensory genes, which encode sensory receptors for taste and smell, are believed to adapt to the individual habitats and diet of each mammal. In this study, we focused on the molecular evolution of bitter taste receptors (TAS2Rs) in monotremes. The sense of bitter taste is important to detect potentially harmful substances. We comprehensively surveyed agonists of all TAS2Rs in platypus (Ornithorhynchus anatinus) and short-beaked echidna (Tachyglossus aculeatus) and compared their functions with orthologous TAS2Rs of marsupial and placental mammals (i.e., therians). As results, the agonist screening revealed that the deorphanized monotreme receptors were functionally diversified. Platypus TAS2Rs had broader receptive ranges of agonists than those of echidna TAS2Rs. While platypus consumes a variety of aquatic invertebrates, echidna mainly consumes subterranean social insects (ants and termites) as well as other invertebrates. This result indicates that receptive ranges of TAS2Rs could be associated with feeding habits in monotremes. Furthermore, some orthologous receptors in monotremes and therians responded to β-glucosides, which are feeding deterrents in plants and insects. These results suggest that the ability to detect β-glucosides and other substances might be shared and ancestral among mammals.     

Structural and Functional Characteristics of Insulin Receptors in Rat Neuroblastoma Cells

Insulin receptors were detected in a variety of rat neuroblastoma and glioma cell lines. The binding of 125I-insulin to B103 neuroblastoma cells had characteristics typical of insulin receptors in other tissues, including high affinity for insulin, low affinity for insulin-like growth factor I (IGF-I), and curvilinear Scatchard plots. Using photoaffinity labeling procedures and sodium dodecyl sulfate (SDS) gel electrophoresis to analyze the subunit structure of insulin receptors in B103 cells, the predominantly labeled protein had an apparent molecular weight of 125K and the mobility of this protein was shifted after removal of sialic acid residues. On the basis of size and susceptibility to neuraminidase, the insulin binding subunit in neuroblastoma cells was identical to the alpha-subunit of insulin receptors in adipocytes and different from the 115K subunit found in brain. The presence of an "adipocyte" form of the insulin receptor in clonal cells derived from brain is probably a consequence of transformation and results from more extensive oligosaccharide processing of the 115K receptor expressed in normal brain cells. The fully glycosylated receptors in neuroblastoma cells were capable of exerting functions typical of insulin receptors in adipocytes such as internalization of insulin and stimulation of glucose transport.     

Molecular Evolution of Prolactin in Primates

Pituitary prolactin, like growth hormone (GH) and several other protein hormones, shows an episodic pattern of molecular evolution in which sustained bursts of rapid change contrast with long periods of slow evolution. A period of rapid change occurred in the evolution of prolactin in primates, leading to marked sequence differences between human prolactin and that of nonprimate mammals. We have defined this burst more precisely by sequencing the coding regions of prolactin genes for a prosimian, the slow loris (Nycticebus pygmaeus), and a New World monkey, the marmoset (Callithrix jacchus). Slow loris prolactin is very similar in sequence to pig prolactin, so the episode of rapid change occurred during primate evolution, after the separation of lines leading to prosimians and higher primates. Marmoset prolactin is similar in sequence to human prolactin, so the accelerated evolution occurred before divergence of New World monkeys and Old World monkeys/apes. The burst of change was confined largely to coding sequence (nonsynonymous sites) for mature prolactin and is not marked in other components of the gene sequence. This and the observations that (1) there was no apparent loss of function during the episode of rapid evolution, (2) the rate of evolution slowed toward the basal rate after this burst, and (3) the distribution of substitutions in the prolactin molecule is very uneven support the idea that this episode of rapid change was due to positive adaptive selection. In the slow loris and marmoset there is no evidence for duplication of the prolactin gene, and evidence from another New World monkey (Cebus albifrons) and from the chimpanzee and human genome sequences, suggests that this is the general position in primates, contrasting with the situation for GH genes. The chimpanzee prolactin sequence differs from that of human at two residues and comparison of human and chimpanzee prolactin gene sequences suggests that noncoding regions associated with regulating expression may be evolving differently from other noncoding regions.     

Functional Reconstitution of α-Amino-3-Hydroxy-5-Methylisoxazole-4-Propionate (AMPA) Receptors from Rat Brain

Glutamate receptors belonging to the subclass specifically activated by alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) were solubilized from rat forebrain membranes with Triton X-100 and partially purified through a series of three chromatographic steps. Specific [3H]AMPA binding increased 30-60-fold during the isolation procedure. A protein band recognized by antibodies against specific amino acid sequences of the glutamate receptor-A subunit was enriched with each purification step; the molecular mass of this band (105 kDa) corresponded to that of cloned AMPA receptor subunits. Photoaffinity labeling of forebrain membranes with 6-cyano-7-[3H]nitroquinoxaline-2,3-dione, a specific antagonist of the AMPA receptor, labeled a single band that comigrated with the immunolabeled protein. On reconstitution of the partially purified material into bilayer patches, single-channel current fluctuations were elicited by 300 nM AMPA and blocked by 1 microM 6,7-dinitroquinoxaline-2,3-dione.     

Brain Evolution: Mammals,Primates, Chimpanzees,and Humans

Though many modern techniques are available for studying brains, they are difficult to use in evolutionary contexts that require examination of large numbers of specimens and species, and all major parts of the brain. Thus, evolutionary studies of many species and of whole brains still tend to be based upon simpler data such as sizes of brains and brain components. Such investigations, carried out over many decades, have usually employed univariate and bivariate analyses, though a few investigators used early multivariate methods. In mammals, these studies generally show the primacy of the relationship between brain and brain-part sizes with overall body size. More recent multivariate applications have confirmed this (Finlay, B. L., and Darlington, R. B. (1995). Science 268: 1578–1584) and some have also separated the highest level phylogenetic groups: strepsirrhines and haplorrhines (Barton, R. A., and Harvey, P. H. (2000). Nature 405: 1055–1058). Both findings were, in fact, evident in earlier multivariate studies (Holloway, R. L. (1979). In Hahn, M. E., Jensen C., and Dudek, B. C. (eds.), Development and Evolution of Brain Size: Behavioral Implications, Academic Press, New York, pp. 59–88; Sacher, G. A. (1970). In Noback, C. R., and Montagna, W. (eds.), The Primate Brain: Advances in Primatology. Vol. 1, Appleton-Century-Crofts, Educational Division, Meredith Corporation, New York, pp. 245–287). However, new studies employing proportional data aimed at conveying input/output relationships between brain components show further groupings of species that share convergences in lifestyles (de Winter, W., and Oxnard, C. E. (2001). Nature 409: 710–714). The convergences are brought about by combinations of brain variables that seem to be associated with brain functions implied by the specific lifestyles. Our most recent results demonstrate that chimpanzees and humans are especially different from one another, and the difference is not due to size alone. Part of this difference is merely a continuation, from chimpanzees towards humans, of a trend already present across all other primates that relates mainly to neocortical increase. But several other large and independent differences are not in the direction of the overall primate trend, but are differences of humans from all other mammals examined including all nonhuman primates. The combinations of brain variables associated with the latter differences are not related simply to enhancement of the neocortex, but seem to reflect other internal relationships. The overall separation of humans and chimpanzees is so large that it goes far beyond the conventional 98.6% commonality in their DNAs. It fits better with more recent molecular, developmental and evolutionary studies implying a considerably greater difference between chimpanzees and humans than usually recognized.     

Evolution of the mandibular symphysis in Notharctinae (Adapidae,Primates)

The Eocene Notharctinae provide a record of increasing fusion of the mandibular symphysis. The two sympatric genera,Notharctus andSmilodectes, differed through time in two respects.Notharctus increased in body size and evolved a partially fused mandibular symphysis.Smilodectes changed little in body size and retained an unfused symphysis. Similarities in molar morphology between these two genera and extant leaf-eating mammals suggest thatNotharctus andSmilodectes were specialized for folivory, a dietary regime correlated with partial symphyseal fusion in many extant mammals. It is concluded that the presence and the extant of symphyseal fusion is a function of body size, diet, and jaw mechanics, complicated by lineagespecific factors that vary among higher mammalian taxa.     

Structural and Functional Properties of Platelet-Derived Growth Factor and Stem Cell Factor Receptors

The receptors for platelet-derived growth factor (PDGF) and stem cell factor (SCF) are members of the type III class of PTK receptors, which are characterized by five Ig-like domains extracellularly and a split kinase domain intracellularly. The receptors are activated by ligand-induced dimerization, leading to autophosphorylation on specific tyrosine residues. Thereby the kinase activities of the receptors are activated and docking sites for downstream SH2 domain signal transduction molecules are created; activation of these pathways promotes cell growth, survival, and migration. These receptors mediate important signals during the embryonal development, and control tissue homeostasis in the adult. Their overactivity is seen in malignancies and other diseases involving excessive cell proliferation, such as atherosclerosis and fibrotic diseases. In cancer, mutations of PDGF and SCF receptors—including gene fusions, point mutations, and amplifications—drive subpopulations of certain malignancies, such as gastrointestinal stromal tumors, chronic myelomonocytic leukemia, hypereosinophilic syndrome, glioblastoma, acute myeloid leukemia, mastocytosis, and melanoma.The type III tyrosine kinase receptor family consists of platelet-derived growth factor (PDGF) receptor α and β, stem cell factor (SCF) receptor (Kit), colony-stimulating factor-1 (CSF-1) receptor, and Flt-3 (Blume-Jensen and Hunter 2001). Members of this receptor family are characterized by five Ig-like domains in their extracellular part, a single transmembrane domain, and an intracellular part consisting of a rather well-conserved juxtamembrane domain, a tyrosine kinase domain with a characteristic inserted sequence without homology with kinases, and a less well-conserved carboxy-terminal tail. The ligands for these receptors are all dimeric molecules, and on binding they induce receptor dimerization. Although the overall mechanisms for the activation of the type III tyrosine kinase receptors and the signaling pathways they induce are similar, the receptors are expressed on different cell types and thus have different functions in vivo.Here we will describe the structural and functional properties of the PDGF receptors and Kit.     

Relationships between Structural Dynamics and Functional Kinetics in Oligomeric Membrane Receptors

Recent efforts to broaden understanding of the molecular mechanisms of membrane receptors in signal transduction make use of rate-equilibrium free-energy relationships (REFERs), previously applied to chemical reactions, enzyme kinetics, and protein folding. For oligomeric membrane receptors, we distinguish between a), the Leffler parameter α_L, to characterize the global transition state for the interconversion between conformations; and b), the Fersht parameter, ϕ_F, to assign the degree of progression of individual residue positions at the transition state. For both α_L and ϕ_F, insights are achieved by using harmonic energy profiles to reflect the dynamic nature of proteins, as illustrated with single-channel results reported for normal and mutant nicotinic receptors. We also describe new applications of α_L based on published results. For large-conductance calcium-activated potassium channels, data are satisfactorily fit with an α_L value of 0.65, in accord with REFERs. In contrast, results reported for the flip conformational state of glycine and nicotinic receptors are in disaccord with REFERs, since they yield α_L values outside the usual limits of 0–1. Concerning published ϕ_F values underlying the conformational wave hypothesis for nicotinic receptors, we note that interpretations may be complicated by variations in the width of harmonic energy profiles.     

Rapid Evolution by Positive Darwinian Selection in T-Cell Antigen CD4 in Primates

CD4, an integral membrane glycoprotein, plays a critical role in the immune response and in the life cycle of simian and human immunodeficiency virus (SIV and HIV). Pairwise comparisons of orthologous human and mouse genes show that CD4 is evolving much faster than the majority of mammalian genes. The acceleration is too great to be attributed to a simple relaxation of the action of purifying selection alone. Here we show that the selective pressure acting on CD4 is highly variable between regions in the protein and identify codon sites under strong positive selection. We reconstruct the coding sequences for ancestral primate CD4s and model tertiary structures of all ancestral and extant sequences. Structural mapping of positively selected sites shows they distribute on the surface of the D1 domain of CD4, where the exogenous SIV gp120 protein binds. Moreover, structural models of the ancestral sequences show substantially larger variation in the interfacial electrostatic charge on CD4 and in the surface complementary between CD4 and gp120 in CD4 lineages from primates with natural SIV infections than those without. Thus, positive selection on CD4 among primates may reflect forces driven by SIV infection and could provide a link between changes in sequence and structure of CD4 during evolution and the interaction with the immunodeficiency virus.     

电压门控钠通道结构与功能的适应性进化

电压门控钠通道是细胞兴奋性的重要分子基础,在进化演变中远早于神经元。伴随从细菌到脊椎动物的适应性演变,电压门控钠通道逐渐呈现出复杂的结构、功能和亚型多样性,且与诸多人类疾病密切相关。明确电压门控钠通道时空演变的适应性进化,解析电压门控钠通道的功能和结构多样性与人类重大疾病发生机制的相关性,有助于推进电压门控钠通道靶向临床诊疗新策略和新药的发现。     

根瘤感受样基因的进化: 结构歧异与功能分化

豆科植物百脉根(Lotus japonicus)的根瘤感受基因Nin与根瘤的早期发育有关。Nin的同源基因(Nin-like基因)功能上涉及氮代谢过程。从完成测序的豆科和非豆科植物基因组中获取Nin-like基因并进行系统发育分析。在此基础上, 追踪基因和蛋白质结构的歧异式样, 尝试建立结构歧异和功能分化的联系。通过比较, 新的Nin-like基因被鉴别。系统发育分析不仅重现了以前分辨的直系同源群(分支I、II和III), 且识别了它们之间的姐妹群关系。Nin-like基因的结构呈现多样性, 支持系统发育分析的结果。水稻OsNLP5基因缺乏内含子, 可能起源于基因返座事件。NIN-like蛋白结构域组织和功能位点在不同分支中存在差异, 提示它们的功能发生了分化。根瘤固氮植物NIN-like蛋白的GAF结构域中存在一个显著变异区, 三级建模分析显示这个变异区对应于百脉根非固氮NIN-like蛋白的一段保守构象, 这一变异可能使豆科植物具有根瘤固氮能力。研究结果为阐明Nin-like基因的功能提供了新的研究思路。     

An Indel in Transmembrane Helix 2 Helps to Trace the Molecular Evolution of Class A G-Protein-Coupled Receptors

Class A G-protein-coupled receptors (GPCRs) constitute a large family of transmembrane receptors. Helical distortions play a major role in the overall fold of these receptors. Most are related to conserved proline residues. However, in transmembrane helix 2, the proline pattern is not conserved, and when present, proline may be located at position 2.58, 2.59, or 2.60. Sequence analysis, three-dimensional data mining, and molecular modeling were undertaken to investigate the origin of this unusual pattern. Taken together, the data strongly support the assumption that an indel led to two structural motifs for helix 2: a bulged structure in P2.59 and P2.60 receptors and a “typical” proline kink in P2.58 receptors. The proline pattern of helix 2 can be used as an evolutionary marker and helps to trace the molecular evolution of class A GPCRs. Two indel events yielding functional receptors occurred independently. One indel arose very early in GPCR evolution, in a bilaterian ancestor, before the protostome-deuterostome divergence. This indel led to the split between the P2.58 somatostatin/opioid receptors and other peptide receptors with the P2.59 pattern. A second indel also occurred in insect opsins and corresponds to a deletion. Subfamilies with proline at position 2.59 or no proline expanded earlier, whereas P2.60 receptors remained marginal throughout evolution. P2.58 receptors underwent rapid expansion in vertebrates with the development of the chemokine and purinergic receptor subfamilies from somatostatin/opioid-related ancestors. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.