The superfamily of G-protein-coupled receptors (GPCRs) is very diverse in structure and function and its members are among the most pursued targets for drug development. We identified more than 800 human GPCR sequences and simultaneously analyzed 342 unique functional nonolfactory human GPCR sequences with phylogenetic analyses. Our results show, with high bootstrap support, five main families, named glutamate, rhodopsin, adhesion, frizzled/taste2, and secretin, forming the GRAFS classification system. The rhodopsin family is the largest and forms four main groups with 13 subbranches. Positions of the GPCRs in chromosomal paralogons regions indicate the importance of tetraploidizations or local gene duplication events for their creation. We also searched for "fingerprint" motifs using Hidden Markov Models delineating the putative inter-relationship of the GRAFS families. We show several common structural features indicating that the human GPCRs in the GRAFS families share a common ancestor. This study represents the first overall map of the GPCRs in a single mammalian genome. Our novel approach of analyzing such large and diverse sequence sets may be useful for studies on GPCRs in other genomes and divergent protein families.

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Following the identification of the C-C chemokines RANTES, MIP-1alpha and MIP-1beta as major human immunodeficiency virus (HIV)-suppressive factors produced by CD8+ T cells, several chemokine receptors were found to serve as membrane co-receptors for primate immunodeficiency lentiretroviruses. The two most widely used co-receptors thus far recognized, CCR5 and CXCR4, are expressed by both activated T lymphocytes and mononuclear phagocytes. CCR5, a specific RANTES, MIP-1alpha and MIP-1 receptor, is used preferentially by non-MT2-tropic HIV-1 and HIV-2 strains and by simian immunodeficiency virus (SIV), whereas CXCR4, a receptor for the C-X-C chemokine SDF-1, is used by MT2-tropic HIV-1 and HIV-2, but not by SIV. Other receptors with a more restricted cellular distribution, such as CCR2b, CCR3 and STRL33, can also function as co-receptors for selected viral isolates. The third variable region (V3) of the gp120 envelope glycoprotein of HIV-1 has been fingered as a critical determinant of the co-receptor choice. Here, we document a consistent pattern of evolution of viral co-receptor usage and sensitivity to chemokine-mediated suppression in a longitudinal follow-up of children with progressive HIV-1 infection. Viral isolates obtained during the asymptomatic stages generally used only CCR5 as a co-receptor and were inhibited by RANTES, MIP-1alpha and MIP-1beta, but not by SDF-1. By contrast, the majority of the isolates derived after the progression of the disease were resistant to C-C chemokines, having acquired the ability to use CXCR4 and, in some cases, CCR3, while gradually losing CCR5 usage. Surprisingly, most of these isolates were also insensitive to SDF-1, even when used in combination with RANTES. An early acquisition of CXCR4 usage predicted a poor prognosis. In children who progressed to AIDS without a shift to CXCR4 usage, all the sequential isolates were CCR5-dependent but showed a reduced sensitivity to C-C chemokines. Discrete changes in the V3 domain of gp120 were associated with the loss of sensitivity to C-C chemokines and the shift in co-receptor usage. These results suggest an adaptive evolution of HIV-1 in vivo, leading to escape from the control of the antiviral C-C chemokines.

The superfamily of G-protein-coupled receptors (GPCRs) is one of the largest and most studied families of proteins. We created Hidden Markov Models derived from sorted groups of GPCRs from our previous detailed phylogenetic classification of human GPCRs and added several other models derived from receptors not found in mammals. We used these models to search entire Genscan data sets from 13 species whose genomes are nearly completely sequenced. We found more than 5000 unique GPCRs that were divided into 15 main groups, and the largest one, the Rhodopsin family, was subdivided into 13 subclasses. The results show that the main families in the human genome, Glutamate, Rhodopsin, Adhesion, Frizzled, and Secretin, arose before the split of nematodes from the chordate lineage. Moreover, several of the subgroups of the Rhodopsin family arose before the split of the linage leading to vertebrates. We also searched expressed sequence tag (EST) databases and identified more than 20,000 sequences that match GPCRs. Although the GPCRs represent typically 1 to 2% of the Genscan predictions, the ESTs that match GPCRs are typically only 0.01 to 0.001%, indicating that GPCRs in most of the groups are expressed at low levels. We also provide searchable data sets that may be used for annotation and further detailed analysis of the GPCR family. This study provides an extensive overview of the expansion of the gene repertoire for families and subgroups of GPCRs.A tremendous amount of primary sequence information has been made available from the recent sequencing projects, providing a near-to-full coverage of the entire genome from a diversity of animal species. The fully sequenced genomes include the mammals mouse and human, two species from the bony fish line (pufferfish Takifugu rubripes and zebrafish Danio rerio), two protochordates from the tunicate linage (Ciona intestinalis and Ciona savignyi) together with two nematodes (Caenorhabditis elegans and Caenorhabditis briggsae), and the insects fruit fly (Drosophila melanogaster) and mosquito (Anopheles gambiae). Moreover, the plants thale cress (Arabidopsis thaliana) and rice (Oryza sativa) are sequenced, as well as several unicellular species of yeast from the fungi linage such as the bakers' yeast (Schizosaccharomyces pombe) and budding yeast (Saccharomyces cerevisiae).

BackgroundMembrane proteins form key nodes in mediating the cell's interaction with the surroundings, which is one of the main reasons why the majority of drug targets are membrane proteins.ResultsHere we mined the human proteome and identified the membrane proteome subset using three prediction tools for alpha-helices: Phobius, TMHMM, and SOSUI. This dataset was reduced to a non-redundant set by aligning it to the human genome and then clustered with our own interactive implementation of the ISODATA algorithm. The genes were classified and each protein group was manually curated, virtually evaluating each sequence of the clusters, applying systematic comparisons with a range of databases and other resources. We identified 6,718 human membrane proteins and classified the majority of them into 234 families of which 151 belong to the three major functional groups: receptors (63 groups, 1,352 members), transporters (89 groups, 817 members) or enzymes (7 groups, 533 members). Also, 74 miscellaneous groups with 697 members were determined. Interestingly, we find that 41% of the membrane proteins are singlets with no apparent affiliation or identity to any human protein family. Our results identify major differences between the human membrane proteome and the ones in unicellular organisms and we also show a strong bias towards certain membrane topologies for different functional classes: 77% of all transporters have more than six helices while 60% of proteins with an enzymatic function and 88% receptors, that are not GPCRs, have only one single membrane spanning α-helix. Further, we have identified and characterized new gene families and novel members of existing families.ConclusionHere we present the most detailed roadmap of gene numbers and families to our knowledge, which is an important step towards an overall classification of the entire human proteome. We estimate that 27% of the total human proteome are alpha-helical transmembrane proteins and provide an extended classification together with in-depth investigations of the membrane proteome's functional, structural, and evolutionary features.

lem. There are about one billion adults that are overweight with a body mass index (BMI) over 25, and 300 million are obese with a BMI over 30 (http://www.who.int). Today there are more people overweight than underweight. It causes costly health problems, reduces life expectancy, and is associated with stigma and discrimination, which has a major effect on the quality of life. Obesity and overweight substantially increase the risk of morbidity from hypertension, dyslipidemia, type 2 diabetes, and coronary heart disease. Obesity is also important for the development of obstructive sleep apnea and respiratory problems, gallbladder disease, osteoarthritis, and nonalcoholic fatty liver disease as well as endometrial, breast, prostate, and colon cancers.There are several genes associated with obesity on the human obesity map (1) such as the melanocortin 4 receptor (MC4R), leptin and the leptin receptor. However, the contribution of each specific gene to obesity is low, being highest for the MC4R gene ranging from 1-6% (2). The overall inheritability of BMI is estimated to be about 50 -60%. Recently, three reports have shown a strong association of a singlenucleotide polymorphism (SNP) in a gene called FTO with both childhood and adult obesity. Frayling and colleagues (3) performed a genome-wide association study for about 490,000 autosomal SNPs in a type 2 diabetes population in the United Kingdom. They found that SNP rs9939609 in the FTO gene was strongly associated with type 2 diabetes, but this allele was also strongly associated with an increased BMI. The association between this FTO SNP and type 2 diabetes was abolished by adjustment for the BMI, suggesting that it was due to the increased BMI. The association of this variant with the BMI was replicated in 13 cohorts with over 38,000 individuals. Interestingly, 16% of the adults who were homozygous for this SNP weighed about 3 kg more and had 1.67-fold increased odds of obesity. This association was observed from age 7 yr upward, and it reflects a specific increase in fat mass (3). Independently, Dina et al. (4) found another SNP, rs1121980, in the first intron of the FTO gene, that was strongly associated with severe (BMI Ͼ 40) adult obesity with odds ratio of 1.55 in a population of French individuals of European ancestry). Further genotyping showed a similarly strong association of several SNPs in a cohort of about 900 severely obese adults and 2700 nonobese French controls. Three of the four most significantly associated SNPs (rs17817449, rs3751812, and rs1421085) are puta-

Understanding differences in the repertoire of orthologous gene pairs is vital for interpretation of pharmacological and physiological experiments if conclusions are conveyed between species. Here we present a comprehensive dataset for G protein-coupled receptors (GPCRs) in both human and mouse with a phylogenetic road map. We performed systematic searches applying several search tools such as BLAST, BLAT, and Hidden Markov models and searches in literature data. We aimed to gather a full-length version of each human or mouse GPCR in only one copy referring to a single chromosomal position. Moreover, we performed detailed phylogenetic analysis of the transmembrane regions of the receptors to establish accurate orthologous pairs. The results show the identity of 495 mouse and 400 human functional nonolfactory GPCRs. Overall, 329 of the receptors are found in one-to-one orthologous pairs, while 119 mouse and 31 human receptors originate from species-specific expansions or deletions. The average percentage similarity of the orthologue pairs is 85%, while it varies between the main GRAFS families from an average of 59 to 94%. The orthologous pairs for the lipid-binding GPCRs had the lowest levels of conservation, while the biogenic amines had highest levels of conservation. Moreover, we searched for expressed sequence tags (ESTs) and identified more than 17,000 ESTs matching GPCRs in mouse and human, providing information about their expression patterns. On the whole, this is the most comprehensive study of the gene repertoire that codes for human and mouse GPCRs. The datasets are available for downloading.

We report seven new members of the superfamily of human G protein-coupled receptors (GPCRs) found by searches in the human genome databases, termed GPR100, GPR119, GPR120, GPR135, GPR136, GPR141, and GPR142. We also report 16 orthologues of these receptors in mouse, rat, fugu (pu¡er¢sh) and zebra¢sh. Phylogenetic analysis shows that these are additional members of the family of rhodopsintype GPCRs. GPR100 shows similarity with the orphan receptor SALPR. Remarkably, the other receptors do not have any close relative among other known human rhodopsin-like GPCRs. Most of these orphan receptors are highly conserved through several vertebrate species and are present in single copies. Analysis of expressed sequence tag (EST) sequences indicated individual expression patterns, such as for GPR135, which was found in a wide variety of tissues including eye, brain, cervix, stomach and testis. Several ESTs for GPR141 were found in marrow and cancer cells, while the other receptors seem to have more restricted expression patterns.