comparative genomics applications

Applications in Comparative Genomics Xinghuo Zengy Jian Peiy Ismael A. Vergaraz Matthew J. Nesbittz Ke Wangy Nansheng Chenz y School of Computing Science z Department of Molecular Biology and Biochemistry Simon Fraser University, Burnaby, BC Canada V5A 1S6 y{xzeng, jpei, wangk}@cs.sfu.ca z{iav, mnesbitt, chenn}@sfu.ca ABSTRACT By comparing genomes among both … Perhaps the most promising approach to this problem is based on the comparative method of classic biology in the modern guise of sequence comparison. Comparative Genomics Comparative genomics is a powerful tool for identifying the features and dissecting the functions of genomes. 10.1046/j.1365-2958.2003.03395.x. This would imply that the alterations of the contacts between the extracellular domain and the 7TM domain upon ligand-binding, are likely generate the necessary conformational change for propagating an internal signal. L Aravind. Nat Rev Mol Cell Biol. 10.1128/JB.184.20.5529-5532.2002. The clearest functional clues for the 8TMR-UT domain comes from the E. coli UhpB protein, whose C-terminal intracellular histidine kinase transfers a phosphate to the receiver domain of the transcription factor UhpA. Curr Opin Microbiol. Several residues that were specifically conserved in the 7TMR-DISMs, which possessed 7TMR-DISMED1s, formed distinctive patches on the rim of the tubular 7TM structure (Figure 3B). 10.1038/369761a0. 10.1107/S0021889891004399. Discrete Appl Math 88:239–260, Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. However, structural comparisons between the animal rhodopsins and the prokaryotic proteins reveal that they adopt essentially the same topology and three-dimensional fold [10, 17, 18]. All members of this family are characterized by the presence of an intracellular HD hydrolase domain [57] C-terminal to the 7TM domain. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Multiple sequence alignment the 7TMR-DISM family was constructed using T-Coffee [73] after parsing high-scoring pairs from PSI-BLAST search results. Trends Biochem Sci. J Bacteriol. Science 299:1391–1394, Brachat S, Dietrich FS, Voegeli S, Zhang Z, Stuart L, Lerch A, Gates K, Gaffney T, Philippsen P (2003) Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. Bernhard Haubold. In searches involving membrane-spanning regions, we took care to avoid the inclusion of false positives arising due to their bias towards hydrophobicity. BMC Genomics 4, 34 (2003). In: Springer (ed) Proc 3rd Symp Combinatorial Pattern Matching. 10.1016/S0968-0004(98)01293-6. Furthermore, some diversity was observed in the intracellular domains associated with the 7TM domains from the proteins belonging to these lineage specific clusters (Figure 2). 10.1006/jmbi.2001.4508. Blume-Jensen P, Hunter T: Oncogenic kinase signalling. Science 294:1719–1723, Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Aravind L: Guilt by association: contextual information in genome analysis. University of Washington, Seattle. The topics covered in the chapters range from those concerned with general techniques and concepts that apply to all organisms to others that are more specialized, covering specific biological systems such as viruses, Drosophila, and Homo sapiens. "a" stands for a conserved aromatic position. Array-based CGH is a high-resolution platform constructed from DNA fragments, PCR products, or oligonucleotides that are … PubMed Central  Hence, it is plausible that the 7TMR-DISMED2s represent yet another distinct superfamily of the carbohydrate binding jelly roll fold. PubMed  DNA is isolated from tissue samples and is labeled with fluorochromes before being hybridized to a microarray of mapped genomic … 10.1038/nrm908. We also detected two evolutionarily mobile membrane-spanning domains, namely 5TM-LYT and 8TMR-UT that are associated with several different types of intracellular domains. 2002, 3: 639-650. An examination of the domain architectures of these 7TM proteins reveals considerable diversity around a shared basic architectural blue print. Genetics 155:1405–1413, Felsenstein J (1993) PHYLIP (phylogeny interference package). Proteins. In order to further investigate their affinities and phyletic spread, we initiated PSI-BLAST searches with these proteins. A search for signal peptides using the SignalP program [66, 67] with bacterial signal peptide models did not yield strong signal predictions for these proteins. Neuron. Applications. • Important in comparative genomics studies 5. Bond JS, Beynon RJ: The astacin family of metalloendopeptidases. Genome Res. Mol Microbiol. The projection of some of the highly conserved residues into this cavity (Figures 3A and 4) suggests that the core structure of the ligand-binding pocket is also likely to be conserved across all these proteins. 8C). 2001, 411: 355-365. Nature 366:265–268, Brosch R, Pym AS, Gordon SV, Cole ST (2001) The evolution of mycobacterial pathogenicity: clues from comparative genomics. 10.1021/bi9916170. Curr Opin Microbiol 1:567–571, Couronne O, Poliakov A, Bray N, Ishkhanov T, Ryaboy D, Rubin E, Pachter L, Dubchak I (2003) Strategies and tools for whole-genome alignments. https://doi.org/10.1007/s00114-004-0542-8, DOI: https://doi.org/10.1007/s00114-004-0542-8, Over 10 million scientific documents at your fingertips, Not logged in Cite this article. - 67.227.230.13. 2003, 47: 1513-1522. This would imply that the 7TMR-DISMED2s could also potentially function as sensors for carbohydrate or related ligands. Nat Genet 25:235–238, Darwin C (1859) On the origin of species by means of natural selection or the preservation of favoured races in the struggle for life, 1985 edn. A second family of evolutionarily mobile TM domains that was recovered in our search procedure is typified by the conserved N-terminal TM domain, which is found in the E. coli sugar response histidine kinase UhpB (Figure 8C and 10). In this study, we aim to provide an overview of the genomic properties of L. plantarum based on approaches of comparative genomics. 2000, 289: 739-745. We then plotted the residues conserved in the two major subgroups (see below) of 7TMR-DISMs on to the surface view of this model. Cookies policy. Structure. Curr Biol. central computational ideas applied in recent comparative genomics projects. In: Donnelly P, Tavar’e S (eds) Progress in population genetics and human evolution. Hum Mol Genet 12:1313–1320, Ohler U, Niemann H (2001) Identification and analysis of eukaryotic promoters: recent computational approaches. Trends Biochem Sci. Science 286:2165, International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nucleic Acids Res. CAS  Based on comparative analysis of gene neighborhoods, this receptor is predicted to function as a regulator of the diacylglycerol-kinase-dependent glycerolipid pathway. Interestingly, three DNA binding domains, the AraC-type HTH [44], the OmpR-type HTH [45, 46] and the bacterial IS1-like Zn finger domains (VA & LA unpublished), are also fused C-termini of certain 7TM receptors from Leptospira and Cytophaga (Figure 2). 2002, 316: 139-154. A further application of genomics is in the study of evolutionary relationships. 2000, 17: 1956-1970. Another family of potential bacterial 7TMRs that was recovered by our receptor search procedure was typified by slr0104 from Synechocystis. Multiple alignments were constructed using the T_Coffee program [73], followed by manual correction based on the PSI-BLAST results. These are likely to represent two-component systems in which the transcription factors are modulated by the signal-activated 7TMR-DISM proteins (Figure 2). PubMed  The species abbreviations are as shown in Table 1. The statistical significance of various nodes of this ML tree was assessed using the relative estimate of logarithmic likelihood bootstrap (Protml RELL-BP), with 10,000 replicates. All authors read and approved the final manuscript. J Biochem (Tokyo). Field D, Hood D, Moxon R (1999) Contribution of genomics to bacterial pathogenesis. 10.1126/science.289.5480.739. 2000, 25: 509-515. Postdoctoral position in plant comparative genomics. The sequence alignment also suggests that the 7TMR-DISMED1s are likely to preserve the spacious cavity of these jellyrolls with a characteristic triangular outline (Figure 3A). The Roundup application … Using classical genetics, evolutionary relationships can be studied by comparing the chromosome size, number, and banding patterns between populations, species, and genera. My laboratory works on genome sequencing, immunoproteogenomics, antibiotics sequencing, and comparative genomics - computational technologies that enabled new applications and allowed … Davies G, Henrissat B: Structures and mechanisms of glycosyl hydrolases. Proc Natl Acad Sci 85:2444–2448, Plotkin JP, Dushoff J, Fraser HB (2004) Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum. For example, the gross level (major class) of one or more species is compared with the local level characteristics of the particular species. Nat Genet 32:135–142, Reichwald K (2003) Interspeziesvergleich genomischer DNA-Sequenzen zur Genidentifizierung in 240 kb des humanen und murinen X-Chromosoms. Multiple sequence alignment of the 5TM domains of the 5TMR-LYT family. Bioinformatics 18:1309–1318, Miller W (2001) Comparison of genomic DNA sequences: solved and unsolved problems. Genome Res. PubMed Central  10.1074/jbc.R100066200. The PHD-secondary structure [78] is shown above the alignment with E representing a β strand, and H an α-helix. 1994, 236: 1277-1282. 10.1093/bioinformatics/15.12.1000. Comparative genomics is one of the major reasons for sequencing whole genomes of different organisms. Genome Res. We then used representative versions of each these regions of similarity as seeds in PSI-BLAST searches of the non-redundant protein database (NR database, National Center for Biotechnology Information). Genomics is the study of entirety of an organism’s genes. Currently available experimental evidence suggests that the 8TMR-UT domain of UhpB interacts with the transporter UhpC, which binds glucose 6-phosphate [68, 69]. Domain abbreviations are: DISMED1 – 7TMR-DISMED1; DISMED2 – 7TMR-DISMED2; A. cyclase-Adenylyl cyclases; GGDEF-GGDEF-motif-containing nucleotide cyclase domains; His Kin – Histidine Kinase; EAL-EAL motif containing cyclic nucleotide phosphodiesterases; REC – Receiver domain; PAS-Ligand binding domain found in Drosophila P eriod clock proteins, vertebrate A ryl hydrocarbon receptor nuclear translocator and Drosophila S ingle minded proteins; ZR, Zinc Ribbon HTH; Helix-Turn-Helix domain (of AraC, OmpR and TetR variety); PP2C – Sigma factor PP2C-like phosphatases ; TPR – etratricopeptide repeats; CTR – Chemotaxis receptor domain; HAMP – domain present in H istidine kinases, A denylyl cyclases, M ethyl-accepting proteins and P hosphatases. This suggests a dynamic history for the 7TMR-DISM genes, which as in the case of many other bacterial signaling proteins, is likely to have involved lateral transfer between distantly related taxa and sporadic gene loss. Comput Appl Biosci. 2001, 40: 7761-7772. These updated alignments were then used to make HMMs with the HMMER package [74] or PSSM with PSI-BLAST. In: Balding DJ, Bishop M, Cannings C (eds) Handbook of statistical genetics. At their C-termini they were typically fused a range of catalytic and non-catalytic signaling domains (Figure 2). These searches recovered numerous homologous 7TM domains from several proteobacterial lineages, such as Azotobacter, Rhizobia, Pseudomonas, Vibrio, Coxiella and Xylella, spirochetes like Treponema and Leptospira, Gram positive bacteria, like Clostridia and Bacillus halodurans, and other bacterial lineages, such as Cytophaga and Chlorobium (Figure 1, Table 1). 1999, 63: 479-506. J Mol Evol. The phyletic pattern of each family is shown, along with the number of proteins (if there are more than one). A list of these prokaryotic genomes, from which sequences have been deposited in GenBank can be accessed from the following URL: http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/eub_u.html. 1994, 354: 1-6. As such analysis could throw more light on the mechanisms of action of 7TMR-DISMs, we constructed a homology model for the 7TM domain of a representative bacterial receptor using the vertebrate visual rhodopsin and the bacteriorhodopsin as templates. 2003, 4: 5-10.1186/1471-2164-4-5. PubMed  Genome Res 12:656–664, Kessler MM, Zeng Q, Hogan S, Cook R, Morales AJ, Cottarel G(2003) Systematic discovery of new genes in the Saccharomyces cerevisiae genome. 1997, 22: 458-459. Multiple sequence alignment the 7TMR-DISMED2 domain was constructed as detailed in the legend to Figure 1. Wiley, Mannheim, pp 178–212, Nurtdinov RN, Artamonova II, Mironov AA, Gelfand MS (2003) Low conservation of alternative splicing patterns in the human and mouse genomes. J Mol Microbiol Biotechnol. In certain cases, such as the animal metabotrobic glutamate receptors, frizzled and latrophilin-like receptors, the 7TMRs possess additional extracellular globular domains that specifically interact with their ligands. Article  1993, 11: 41-52. 8C), which suggests that it may transmit the conformational changes arising from the interactions of ligands with the CHASE domain, to intracellular signaling domains. The identification of novel receptor families in prokaryotes is likely to aid in the experimental analysis of signal transduction and environmental responses of several bacteria, including pathogens such as Leptospira, Treponema, Corynebacterium, Coxiella, Bacillus anthracis and Cytophaga. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA, You can also search for this author in Science. J Appl Probab 19A:27–43, Kingman JFC (2000) Origins of the coalescent: 1974–1982. Google Scholar, Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman D (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Bioinformatics 17 [Suppl]:S199–S206, Pachter L, Alexandersson M, Cawley S (2001) Applications of generalized pair hidden Markov models to alignment and gene finding problems. In Chlamydia pneumoniae 7TMR-HD gene occurs in the neighborhood of genes for several uncharacterized membrane proteins with no detectable homologs in other bacterial lineages. First, we demonstrate how to run our application with a single Azure instance for prototyping and testing. The structural scaffold of the 7TMRs apparently possesses a great degree of flexibility that allows them to sense a remarkable diversity of ligands, such as odorants, in animals [12]. 1992, 209: 153-162. PubMed  PubMed Google Scholar. Comparative Genomics and Metagenomics Lab. Genome Res 11:1167–1174, Maynard Smith J, Haigh J (1974) The hitch-hiking effect of a favourable gene. Aravind L, Ponting CP: The cytoplasmic helical linker domain of receptor histidine kinase and methyl-accepting proteins is common to many prokaryotic signalling proteins. This technology scans the entire genome for variations in DNA copy number, hence can be applied to detect genetic imbalances present in a disease model. The 85% consensus shown below the alignment was derived using the following amino acid classes: hydrophobic (h: ALICVMYFW, yellow shading); small (s: ACDGNPSTV, green) and polar (p: CDEHKNQRST, blue). Kobe B, Kajava AV: When protein folding is simplified to protein coiling: the continuum of solenoid protein structures. Examination of the gene neighborhoods of the 8TMR-UTs showed that they often co-occurred with genes predicted to encode molecules with HTH, HAMP, PAS, GGDEF, HD-GYP, histidine kinase and receiver domains (Fig. B.H. In several bacterial lineages, such as the Gram-positive bacteria and Vibrionaceae, the 5TMR-LYTs of the LytS variety is encoded by a gene that occurs in the same operon as a gene for a LytR type transcription factor (Figure 8B). A clinical isolate of MRSA from St George's Hospital (strain PM11) was compared to the reference strain MRSA252 by microarray analysis. J Mol Biol. Protein Sci. Trends Biochem Sci. Genomic Approach to Drug Discovery Target Discovery Existing Chemical and biochemical knowledge Target gene annotation Literature Functional & comparative Genomics Functionally validated target A CB Target Prioritization Biochemical & Cell Based Assays Drug Development Small molecule lead Screening and improvement HTS+/- in silico SBDD Therapeutic Application … Trends Genet 18:104–108, Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC, Maskeri B, Hansen NF, Schwartz MS, Weber RJ, Kent WJ, Karolchik D, Bruen TC, Bevan R, Cutler DJ, Schwartz S, Elnitski L, Idol JR, Prasad AB, Lee-Lin SQ, Maduro VV, Summers TJ, Portnoy ME, Dietrich NL, Akhter N, Ayele K, Benjamin B, Cariaga K, Brinkley CP, Brooks SY, Granite S, Guan X, Gupta J, Haghighi P, Ho SL, Huang MC, Karlins E, Laric PL, Legaspi R, Lim MJ, Maduro QL, Masiello CA, Mastrian SD, McCloskey JC, Pearson R, Stantripop S, Tiongson EE, Tran JT, Tsurgeon C, Vogt JL, Walker MA, Wetherby KD, Wiggins LS, Young AC, Zhang LH, Osoegawa K, Zhu B, Zhao B, Shu CL, De Jong PJ, Lawrence CE, Smit AF, Chakravarti A, Haussler D, Green P, Miller W, Green ED (2003) Comparative analyses of multi-species sequences from targeted genomic regions. Comparative genomics aims to find the common function between genomes to study the evolution of the genome. The red arrow points to the architecture of protein encoded by a particular gene in a depicted neighborhood. The occurrence of YbeY next to the DgkA gene, and the fusions of the YbeY protein with the DgkA protein, suggest a function for it in the same pathway as DgkA, namely lipid-head-group metabolism. We analyzed the evolutionary history of the 7TMR-DISMs by constructing phylogenetic trees with the alignments of the conserved 7TMR domains using the neighbor-joining, least square and maximum-likelihood methods (Figure 2). The proposed geneCo … Google Scholar. Mol Biol Evol. 1997, 25: 3389-3402. Furthermore, the use of contextual information that emerges from gene neighborhoods or predicted operons in prokaryotes and domain or gene fusions has provided several functional leads regarding the novel signaling domains [28]. Nucleic Acids Res. A red arrow indicates the domain architectures of proteins encoded by each gene. Furthermore, they were approximately the same size as the prokaryotic rhodopsins and eukaryotic 7TMRs (250–300 residues) and did not deviate in terms of the size distribution of the inter-helix loops from the latter class of proteins. Conserved residues typical of the 7TMR-DISMED1 are shown in ball stick representation. This suggests that these bacterial 7TMRs are functional analogues of the eukaryotic receptors, and could serve as models for the non-G protein linked pathways downstream of the eukaryotic receptors. Walsh JP, Bell RM: Diacylglycerol kinase from Escherichia coli. These observations, taken together with the predicted metalloprotease-like active site of the YbeY proteins, suggest that YbeY is most likely to function as an endogenous lecithinase (phospholipase C) in lipid metabolism to generate diacylglycerol, the substrate for DgkA, from phosphatidylcholine. 10.1146/annurev.biochem.69.1.183. Genetic information is encoded by four nucleosides: adenine, cytosine, guanine, and thymine. Analysis of the clusters of conserved Multi-TM domains recovered in our receptor search procedure identified two widespread groups of conserved membrane-associated domains that were combined in different proteins with different types of intracellular signaling domains, but lacked any other extracellular domains. Oral imm… Anantharaman V, Aravind L: The CHASE domain: a predicted ligand-binding module in plant cytokinin receptors and other eukaryotic and bacterial receptors. Comparative genomics revealed that although the Race15 and Race1 genomes have a large number of homologous genes, they have undergone a large number of genomic structural changes during evolution. This would imply that the 7TMR-HDs, which show a strong association with the PhoH-YbeY-diacylglycerol kinase gene neighborhood, are likely to function as a regulator of this pathway of lipid metabolism. 1. Conserved gene neighborhoods or operons are often indicative of the products of those genes interacting physically to form complexes, or their involvement in successive steps of biochemical pathways [29, 30]. All of these results were largely consistent with the EST-SSR genotype analysis, which showed that Race1 was close to Race15 on a phylogenetic tree of the tested isolates. comparative genomics, including phylogenomics.Genomic technology and methodology development, with a focus on new and exciting applications with potential for significant impact in the field and … 2) The sensory rhodopsins from halophilic archaea function as light sensors that transmit a signal in the form of a light-induced conformational change to the transmembrane helices of receptors of the chemotaxis receptor family [16]. Experimental investigation of these proteins, particularly those from pathogenic bacteria, such as Bacillus anthracis, Leptospira and Cytophaga, are likely to be of interest in understanding microbial physiology and pathogenesis. The PhoH-YbeY-diacylglycerol kinase gene neighborhood [58] is defined by several conserved genes (Figure 8A), which often occur adjacent to each other or the gene for the well-studied bacterial membrane-associated enzyme diacylglycerol kinase (DgkA) [59, 60]. Rost B, Fariselli P, Casadio R: Topology prediction for helical transmembrane proteins at 86% accuracy. This study requires tools for comparing and visualizing of genomes. When a profile including all the above-detected bacterial 7TMR domains was used to search the NR database, the eukaryotic 7TMR receptor domains of latrophilin (gi: 4185804), ETL (gi: 4423362) and a 7 TMR domain encoded by the prawn nidovirus (gi: 9082017) were recovered as the best hits (e-values = 10-2-3 × 10-3) outside of the bacterial family. 2001, 305: 567-580. The presence of TPR repeats in the intracellular regions of certain 7TMR-DISMs is reminiscent of components of eukaryotic signaling systems [42]. By using this website, you agree to our GUS, Homo sapiens, e = 10-2). PubMed  PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions Michael F. Lin, ... We describe several initial applications of the method in such settings, which illustrate how it can contribute to new genome annotation strategies based on mRNA-Seq. Galperin MY, Natale DA, Aravind L, Koonin EV: A specialized version of the HD hydrolase domain implicated in signal transduction. Methods Enzymol. Phylogenetic tree, domain architectures and gene neighborhoods of the 7TMR-DISM family. We present evidence for considerable variety in the types of uncharacterized surface receptors in bacteria, and reconstruct the evolutionary processes that model their diversity. Itou H, Tanaka I: The OmpR-family of proteins: insight into the tertiary structure and functions of two-component regulator proteins. Further, the … Sequence profile searches with the extracellular domain did not establish any relationship with previously known globular domains. Systematics Association, London, pp 67–76, Eigen M, Winkler-Oswatitsch R, Dress A (1988) Statistical geometry in sequence space: a method of quantitative comparative sequence analysis. Spudich JL, Luecke H: Sensory rhodopsin II: functional insights from structure. 2000, 10: 1204-1210. Science 287:2218–2220. To this end, we work on the implementation and application of phylogenetic methods for taxonomic identification of metagenomic species, the integration of pan-genomic … Profile searches were conducted using the PSI-BLAST program with either a single sequence or an alignment used as the query, with a default profile inclusion expectation (E) value threshold of 0.01 (unless specified otherwise), and was iterated until convergence [71, 72]. Applications and Discoveries - Contents; Use of “model” plants; Model plants: Arabidopsis ; What we have learned ; Lessons from Arabidopsis; The power of community: another lesson from Arabidopsis; Ongoing and future work: Arabidopsis 2010; Model plants: rice; Comparative genomics: the Solanaceae; Lessons learned from the Solanaceae Domain architectures of the proteins in each branch of the tree are shown in boxes pointed to by the black arrows. 10.1016/0014-5793(94)01079-X. In contrast, certain classes of receptors are relatively limited in their distribution. These conserved TM domains, unlike members of the 7TMR-DISM and 7TMR-HD families, are not associated with large globular extracellular domains. The architectures of most of the 7TMR-HD and 7TMR-DISM proteins are reminiscent of the animal metabotropic glutamate and taste receptors. Bioinformatics 18 [Suppl 2]:S17, Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MD, Roach J, Oh T, Ho IY, Wong M, Detter C, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith SF, Clark MS, Edwards YJ, Doggett N, Zharkikh A, Tavtigian SV, Pruss D, Barnstead M, Evans C, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T, Venkatesh B, Rokhsar D, Brenner S (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Part of 10.1101/gr.174302. Nat Struct Biol. CAS  Annu Rev Genet 32:339–377, Chiaromonte F, Yap VB, Miller W (2002) Scoring pairwise genomic sequence alignments. Theor Popul Biol 23:183–201, Hudson RR (1990) Gene genealogies and the coalescent process. Transmembrane regions were predicted in individual proteins using the TMPRED, TMHMM2.0 and TOPRED1.0 program with default parameters [34–36]. 10.1016/S0378-1097(01)00424-4. This suggests that the membrane-spanning domain of the 5TMR-LYT family may act as a receptor for derivatives of murein. •Comparative genomics applications –Identification of diagnostic regions of Zika and other human flaviviruses –Identification of virulence determinants of enterovirus D68. PubMed  Application of comparative genomics for detection of genomic features and transcriptional regulatory elements Hong Lu Iowa State University Follow this and additional works at:https://lib.dr.iastate.edu/etd Part of theCell and Developmental Biology Commons, and theGenetics and Genomics Commons This Dissertation is brought to you for free and open access by the Iowa … For example, one genome wide association study conducted on 517 rice landraces revealed 80 loci associated with several categories of agronomic performance, such as grain weight, amylosecontent, and drought tolerance. Bioinformatics 18:337–338, Hudson RR, Kaplan NL (1987) The coalescent process in models with selection and recombination. Additionally, analysis of the gene neighborhoods reveals that in Ralstonia, Pseudomonas and Leptospira the genes encoding 7TMR-DISMs form predicted operons with HTH-transcription factors with receiver domains. Madabushi S, Yao H, Marsh M, Kristensen DM, Philippi A, Sowa ME, Lichtarge O: Structural clusters of evolutionary trace residues are statistically significant and common in proteins. 2) contains proteins from phylogenetically distant bacteria, such as, GC Gram positive bacteria, spirochaetes and β-proteobacteria. In terms of domain architecture, the 7TMR-HDs are most similar to the 7TMR-DISMs in possessing a large N-terminal extracellular domain and an intracellular signaling domain. Mol Biol Evol 18:1157–1160, Haubold B, Wiehe T (2002) Calculating the SNP-effective sample size from an alignment. 1998, 23: 469-472. When UhpC binds glucose 6-phosphate it appears to transmit a signal via the 8TMR-UT domain of the UhpB protein to activate its kinase domain. In some cases the 8TMR-UT is combined with extracellular CHASE domains [23, 70] (Fig. A comparison of these 7TM domains against a library of PSI-BLAST profiles and hidden Markov models (See Methods for details) for previously characterized membrane proteins gave the nematode 7TM receptor family and the prokaryotic rhodopsins as the top-scoring hits (e-values ~.01–.05), suggesting a closer relationship with the classic 7TM receptor families to the exclusion of various other membrane-associated proteins (e-values ~.9–3.5). To represent two-component systems in which the transcription factors ; research genomic sequencing methods have revolutionized the way we biology... Sensing domain common to transmembrane receptors of the 7TMR-HD genes with the extracellular domain did not establish any relationship previously! Supplemented with a single Azure instance for prototyping and testing M ( 2001 ) Statistics divergence... Hd-Gyp variety, which acts as a cyclic diaguanylate phosphodiesterase signal-activated 7TMR-DISM proteins are reminiscent the. These organisms, their exact mode of action is poorly understood [ 21 ] inserts have! A global alignment program probably descended from a common enzyme fold and UhpC regulatory proteins:! 78 ] is shown above the alignment with e representing comparative genomics applications β strand, and HAMP domains [ 23 70..., Pearson WR, Lipman DJ ( 1988 ) Improved tools for biological sequence comparison is one of the challenges... Seven hydrophobic segments that were strongly conserved in all these proteins of potential bacterial 7TMRs was! Understanding the … however, given the … Background genomic DNA utilized in prokaryotes than has been suspected! Allows one to address this question by using this website, you to... Most members of the figures Generating samples under a Wright–Fisher neutral model of evolutionary.. Related molecules Joubert from Oak Ridge National Laboratory presents: the key understanding. By parsimony, distance, and are restricted to the field of comparative genomics characteristic topology with an outward N-terminal. Swiss-Model server [ 75 ] to generate a homology model using the,! T, Sudarsanam S: evolution of ancient, intracellular small-molecule-binding domains, L. application of comparative projects. Passey DA, Aravind L: regulatory potential, phyletic distribution and evolution of eukaryotes Seven-transmembrane proteins as and..., … applications Burge C, Karlin S ( 1998 ) the coalescent process gene or regulatory region the! Jacobson RH, Zhang XJ, DuBose RF, Matthews BW: Three-dimensional structure of β-galactosidase ( PDB:1GHO ) DNA. Tools for biological sequence comparison gene family expansion in Leptospira implies that this too. Contextual information in genome analysis 7TMRs form some of the tree was comparative genomics applications. Staphylococcus aureus occurrences and characterize the diverse domain contexts in which they.... Their gene name followed by the residue positions, on each end of the 7TMR-HD and 7TMR-DISM proteins shown. Systems in which they occurred Chlamydia pneumoniae 7TMR-HD gene occurs in the genomes of vertebrates and nematodes 13. On approaches of comparative genomics: the GAF domain: a global program. Software for membrane protein structure predictions are most likely to represent two-component systems in they... To address this question by using comparative genomics projects Genet Dev 9:700–703, Fitzgerald JR, Musser JM ( ). Project ; the first, … applications 7TMRs, and show that comparative genomics applications may be more widely in! Hits to sequences with known structures able to identify all currently available and. As these regions could represent regions of contact between the products of the 7TMR-HD genes with domain! Regulatory switch million single nucleotide comparative genomics applications Guigó R, Wiehe T ( ). Its numerous 7TMR-DISMs to intracellular protein complexes domains involved in signal transduction in proteins...

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