Genomes and Genes
Experts and Doctors on conserved sequence in Toronto, Ontario, Canada
Locale: Toronto, Ontario, Canada
Topic: conserved sequence
- Pineda Lucena A, Liao J, Wu B, Yee A, Cort J, Kennedy M, et al. NMR structure of the hypothetical protein encoded by the YjbJ gene from Escherichia coli. Proteins. 2002;47:572-4 pubmed
- Martinek N, Zou R, Berg M, Sodek J, Ringuette M. Evolutionary conservation and association of SPARC with the basal lamina in Drosophila. Dev Genes Evol. 2002;212:124-33 pubmed
- Snider J, Gutsche I, Lin M, Baby S, Cox B, Butland G, et al. Formation of a distinctive complex between the inducible bacterial lysine decarboxylase and a novel AAA+ ATPase. J Biol Chem. 2006;281:1532-46 pubmed..Data obtained suggest that the RavA-LdcI interaction may be important for the regulation of RavA activity against its targets. ..
- Irimia M, Maeso I, Roy S, Fraser H. Ancient cis-regulatory constraints and the evolution of genome architecture. Trends Genet. 2013;29:521-8 pubmed publisher..We discuss implications, questions raised, and new research directions arising from these studies, as well as evidence for similar phenomena in other eukaryotic groups. ..
- Pilon M, Peng X, Spence A, Plasterk R, Dosch H. The diabetes autoantigen ICA69 and its Caenorhabditis elegans homologue, ric-19, are conserved regulators of neuroendocrine secretion. Mol Biol Cell. 2000;11:3277-88 pubmed
- Carson A, Cheung J, Scherer S. Duplication and relocation of the functional DPY19L2 gene within low copy repeats. BMC Genomics. 2006;7:45 pubmed..Our results show that the DPY19L family has expanded throughout the vertebrate lineage and has undergone recent primate-specific evolution within LCRs. ..
- Zhang G, Jung B, Ho W, Jugloff D, Cheung H, Gurd J, et al. Isolation and characterization of LCHN: a novel factor induced by transient global ischemia in the adult rat hippocampus. J Neurochem. 2007;101:263-73 pubmed..Taken together, these data suggest that LCHN could play a role in neuritogenesis, as well as in neuronal recovery and/or restructuring in the hippocampus following transient cerebral ischemia. ..
- Ray D, Wu B, White K. A second functional RNA domain in the 5' UTR of the Tomato bushy stunt virus genome: intra- and interdomain interactions mediate viral RNA replication. RNA. 2003;9:1232-45 pubmed..Modifications that reduced accumulation did not appreciably affect DI RNA stability in vivo, indicating that the DSD and SL5 act to facilitate viral RNA replication. ..
- Chan E, Quon G, Chua G, Babak T, Trochesset M, Zirngibl R, et al. Conservation of core gene expression in vertebrate tissues. J Biol. 2009;8:33 pubmed publisher..A major challenge will be to understand the precise mechanisms by which many gene expression patterns remain similar despite extensive cis-regulatory restructuring. ..
- Pike K, Ratcliffe M. Dual requirement for the Ig alpha immunoreceptor tyrosine-based activation motif (ITAM) and a conserved non-Ig alpha ITAM tyrosine in supporting Ig alpha beta-mediated B cell development. J Immunol. 2005;174:2012-20 pubmed..However, coexpression of the cytoplasmic domain of Igbeta partially complemented the Igalpha Y3 mutation, rescuing higher levels of BLNK phosphorylation and, more strikingly, supporting B cell development. ..
- Ganoza M, Kiel M, Aoki H. Evolutionary conservation of reactions in translation. Microbiol Mol Biol Rev. 2002;66:460-85, table of contents pubmed..The possible mechanisms of a new initiation factor and two elongation factors are discussed in this context. ..
- Turner M, Simpson A, McInnes R, Howell P. Human argininosuccinate lyase: a structural basis for intragenic complementation. Proc Natl Acad Sci U S A. 1997;94:9063-8 pubmed..These "native" active sites give rise to the observed partial recovery of enzymatic activity. ..
- Chi S, Ayed A, Arrowsmith C. Solution structure of a conserved C-terminal domain of p73 with structural homology to the SAM domain. EMBO J. 1999;18:4438-45 pubmed..However, the SAM-like C-terminal domains of p73 and p63 are monomeric and do not interact with one another, suggesting that this domain may interact with additional, as yet uncharacterized proteins in a signaling and/or regulatory role. ..
- Saridakis V, Christendat D, Thygesen A, Arrowsmith C, Edwards A, Pai E. Crystal structure of Methanobacterium thermoautotrophicum conserved protein MTH1020 reveals an NTN-hydrolase fold. Proteins. 2002;48:141-3 pubmed
- Loreto M, Berry D, McGlade C. Functional cooperation between c-Cbl and Src-like adaptor protein 2 in the negative regulation of T-cell receptor signaling. Mol Cell Biol. 2002;22:4241-55 pubmed..These results suggest that the mechanism of action of SLAP-2 and the related protein SLAP is to promote c-Cbl-dependent degradation of the tyrosine kinases SYK and ZAP-70 and down-regulation of CD3 at the cell surface. ..
- Martinek N, Shahab J, Sodek J, Ringuette M. Is SPARC an evolutionarily conserved collagen chaperone?. J Dent Res. 2007;86:296-305 pubmed..Hence, SPARC may also play a role in regulating post-endoplasmic reticulum events that promote collagen fibrillogenesis. ..
- Kwok T, Hui K, Kostelecki W, Ricker N, Selman G, Feng Z, et al. A genetic screen for dihydropyridine (DHP)-resistant worms reveals new residues required for DHP-blockage of mammalian calcium channels. PLoS Genet. 2008;4:e1000067 pubmed publisher..elegans as a screening tool to identify residues important for DHP interaction with mammalian Ca(v)1 channels. ..
- Sun M, Sikora M, Costanzo M, Boone C, Kim P. Network evolution: rewiring and signatures of conservation in signaling. PLoS Comput Biol. 2012;8:e1002411 pubmed publisher..In summary, we uncover several network evolution mechanisms likely to generalize across peptide recognition modules. ..
- Naeeni A, Conte M, Bayfield M. RNA chaperone activity of human La protein is mediated by variant RNA recognition motif. J Biol Chem. 2012;287:5472-82 pubmed publisher..This work delineates the structural elements required for La-mediated RNA chaperone activity and provides a basis for understanding how La can enhance the folding of its various RNA targets...
- Ding H, Schertzer M, Wu X, Gertsenstein M, Selig S, Kammori M, et al. Regulation of murine telomere length by Rtel: an essential gene encoding a helicase-like protein. Cell. 2004;117:873-86 pubmed..spretus chromosomes in F1 cells. We conclude that Rtel is an essential gene that regulates telomere length and prevents genetic instability. ..
- Guo Y, Rowe Magnus D. Overlapping and unique contributions of two conserved polysaccharide loci in governing distinct survival phenotypes in Vibrio vulnificus. Environ Microbiol. 2011;13:2888-990 pubmed publisher..vulnificus to 'fine tune' its biofilm lifestyle to the prevailing environmental conditions and maximally benefit from the characteristics associated with each polysaccharide...
- Tram E, Savas S, Ozcelik H. Missense variants of uncertain significance (VUS) altering the phosphorylation patterns of BRCA1 and BRCA2. PLoS ONE. 2013;8:e62468 pubmed publisher..We propose that rare VUS affecting phosphorylation may be a novel and important mechanism for which BRCA1 and BRCA2 functions are disrupted in breast cancer. ..
- Freund C, Gregory Evans C, Furukawa T, Papaioannou M, Looser J, Ploder L, et al. Cone-rod dystrophy due to mutations in a novel photoreceptor-specific homeobox gene (CRX) essential for maintenance of the photoreceptor. Cell. 1997;91:543-53 pubmed..Mutations in the CRX gene cause adCRD either by haploinsufficiency or by a dominant negative effect and demonstrate that CRX is essential for the maintenance of mammalian photoreceptors. ..
- Phillips M, Fujii J, Khanna V, DeLeon S, Yokobata K, de Jong P, et al. The structural organization of the human skeletal muscle ryanodine receptor (RYR1) gene. Genomics. 1996;34:24-41 pubmed..Knowledge of the structure of the RYR1 gene will provide an invaluable resource for the discovery of mutations in the gene that are causal of human malignant hyperthermia and central core disease. ..
- Khorchid A, Inouye M, Ikura M. Structural characterization of Escherichia coli sensor histidine kinase EnvZ: the periplasmic C-terminal core domain is critical for homodimerization. Biochem J. 2005;385:255-64 pubmed
- Bashirullah A, Cooperstock R, Lipshitz H. Spatial and temporal control of RNA stability. Proc Natl Acad Sci U S A. 2001;98:7025-8 pubmed..Similar mechanisms are likely to act later in development to restrict certain classes of transcripts to particular cell types within somatic cell lineages. Functions of transcript degradation and protection are discussed. ..
- Marles J, Dahesh S, Haynes J, Andrews B, Davidson A. Protein-protein interaction affinity plays a crucial role in controlling the Sho1p-mediated signal transduction pathway in yeast. Mol Cell. 2004;14:813-23 pubmed..Our experiments also indicate that a second binding surface on the Sho1p SH3 domain is required for its proper in vivo function. ..
- Nagar B, Jones R, Diefenbach R, Isenman D, Rini J. X-ray crystal structure of C3d: a C3 fragment and ligand for complement receptor 2. Science. 1998;280:1277-81 pubmed..The structure supports a model whereby the transition of native C3 to its functionally active state involves the disruption of a complementary domain interface and provides insight into the basis for the interaction between C3d and CR2. ..
- Archambault J, Jansma D, Kawasoe J, Arndt K, Greenblatt J, Friesen J. Stimulation of transcription by mutations affecting conserved regions of RNA polymerase II. J Bacteriol. 1998;180:2590-8 pubmed
- Yakunin A, Proudfoot M, Kuznetsova E, Savchenko A, Brown G, Arrowsmith C, et al. The HD domain of the Escherichia coli tRNA nucleotidyltransferase has 2',3'-cyclic phosphodiesterase, 2'-nucleotidase, and phosphatase activities. J Biol Chem. 2004;279:36819-27 pubmed..The data suggest that the phosphohydrolase activities of the HD domain of the E. coli tRNA nucleotidyltransferase are involved in the repair of the 3'-CCA end of tRNA. ..
- Ku S, Cornell K, Howell P. Structure of Arabidopsis thaliana 5-methylthioribose kinase reveals a more occluded active site than its bacterial homolog. BMC Struct Biol. 2007;7:70 pubmed..Features of the MTR binding site offer an opportunity for a simple organic salt of an MTR analog to specifically inhibit MTR kinase. ..
- Xu J, Attisano L. Mutations in the tumor suppressors Smad2 and Smad4 inactivate transforming growth factor beta signaling by targeting Smads to the ubiquitin-proteasome pathway. Proc Natl Acad Sci U S A. 2000;97:4820-5 pubmed..These studies thus reveal a mechanism for tumorigenesis whereby genetic defects in Smads induce their degradation through the ubiquitin-mediated pathway. ..
- Taylor M, Gokgoz N, Andrulis I, Mainprize T, Drake J, Rutka J. Familial posterior fossa brain tumors of infancy secondary to germline mutation of the hSNF5 gene. Am J Hum Genet. 2000;66:1403-6 pubmed..These findings suggest that germline mutations in hSNF5 are associated with a novel autosomal dominant syndrome with incomplete penetrance that predisposes to malignant posterior fossa brain tumors in infancy. ..
- Booth V, Koth C, Edwards A, Arrowsmith C. Structure of a conserved domain common to the transcription factors TFIIS, elongin A, and CRSP70. J Biol Chem. 2000;275:31266-8 pubmed
- Babak T, Blencowe B, Hughes T. Considerations in the identification of functional RNA structural elements in genomic alignments. BMC Bioinformatics. 2007;8:33 pubmed
- Coppolino M, Leung Hagesteijn C, Dedhar S, Wilkins J. Inducible interaction of integrin alpha 2 beta 1 with calreticulin. Dependence on the activation state of the integrin. J Biol Chem. 1995;270:23132-8 pubmed..The data presented here also demonstrate, for the first time, an inducible interaction of an integrin with an intracellular protein that occurs via the alpha subunit of the integrin. ..
- Saltzman A, Pan Q, Blencowe B. Regulation of alternative splicing by the core spliceosomal machinery. Genes Dev. 2011;25:373-84 pubmed publisher..Our results thus demonstrate a role for the core spliceosomal machinery in controlling an exon network that appears to modulate the levels of many RNA processing factors. ..
- Stogios P, Prive G. The BACK domain in BTB-kelch proteins. Trends Biochem Sci. 2004;29:634-7 pubmed
- Peng W, Krogan N, Richards D, Greenblatt J, Hughes T. ESF1 is required for 18S rRNA synthesis in Saccharomyces cerevisiae. Nucleic Acids Res. 2004;32:1993-9 pubmed..These data indicate that Esf1p plays a direct role in early pre-rRNA processing. ..
- Klingensmith J, Yang Y, Axelrod J, Beier D, Perrimon N, Sussman D. Conservation of dishevelled structure and function between flies and mice: isolation and characterization of Dvl2. Mech Dev. 1996;58:15-26 pubmed..Thus, Dvl2 encodes a mammalian homolog of dsh which can transduce the Wingless signal. ..
- Larijani M, Yu C, Golub R, Lam Q, Wu G. The role of components of recombination signal sequences in immunoglobulin gene segment usage: a V81x model. Nucleic Acids Res. 1999;27:2304-9 pubmed..Furthermore, the contribution of the heptamer and nonamer to differential VHusage in our assay is correlated inversely with their conservation throughout the VHlocus. ..
- Saltzman A, Kim Y, Pan Q, Fagnani M, Maquat L, Blencowe B. Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay. Mol Cell Biol. 2008;28:4320-30 pubmed publisher..The results further implicate general spliceosomal components in AS regulation. ..
- Yang C, Ornatsky O, McDermott J, Cruz T, Prody C. Interaction of myocyte enhancer factor 2 (MEF2) with a mitogen-activated protein kinase, ERK5/BMK1. Nucleic Acids Res. 1998;26:4771-7 pubmed..Furthermore, when cotransfected with ERK5/BMK1, the transactivation capacity of MEF2 was enhanced. These results suggest that the functions of MEF2 could be regulated through ERK5/BMK1. ..
- Bayfield M, Yang R, Maraia R. Conserved and divergent features of the structure and function of La and La-related proteins (LARPs). Biochim Biophys Acta. 2010;1799:365-78 pubmed publisher..In this review, we summarize recent progress that has led to greater understanding of the structure and function of La proteins and their roles in tRNA processing and RNP assembly dynamics, as well as progress on the different LARPs. ..
- Pardossi Piquard R, Yang S, Kanemoto S, Gu Y, Chen F, BÃ¶hm C, et al. APH1 polar transmembrane residues regulate the assembly and activity of presenilin complexes. J Biol Chem. 2009;284:16298-307 pubmed publisher..These results suggest that the conserved transmembrane histidine residues contribute to APH1 function and can affect presenilin catalytic activity. ..
- Nakhamchik A, Wilde C, Chong H, Rowe Magnus D. Evidence for the horizontal transfer of an unusual capsular polysaccharide biosynthesis locus in marine bacteria. Infect Immun. 2010;78:5214-22 pubmed publisher..Furthermore, several of the encoded proteins appeared to be of Gram-positive and archaebacterial origin. These data indicate that the horizontal transfer of intact and partial CPS loci drives CPS diversity in marine bacteria. ..
- Whitney J, Hay I, Li C, Eckford P, Robinson H, Amaya M, et al. Structural basis for alginate secretion across the bacterial outer membrane. Proc Natl Acad Sci U S A. 2011;108:13083-8 pubmed publisher..Taken together, these studies support a mechanism for exopolysaccharide export across the outer membrane that is distinct from the Wza-mediated translocation observed in canonical capsular polysaccharide export systems. ..
- Li J, Musso G, Zhang Z. Preferential regulation of duplicated genes by microRNAs in mammals. Genome Biol. 2008;9:R132 pubmed publisher..We further present an evolutionary model in which microRNAs not only adjust imbalanced dosage effects created by gene duplication, but also help maintain long-term buffering of the phenotypic consequences of gene deletion or ablation. ..
- Colwill K, Pawson T, Andrews B, Prasad J, Manley J, Bell J, et al. The Clk/Sty protein kinase phosphorylates SR splicing factors and regulates their intranuclear distribution. EMBO J. 1996;15:265-75 pubmed..Overexpression of the active Clk/Sty kinase caused a redistribution of SR proteins within the nucleus. These results suggest that Clk/Sty kinase directly regulates the activity and compartmentalization of SR splicing factors. ..
- Wang D, Claus C, Vaccarelli G, Braunstein M, Schmitt T, Zuniga Pflucker J, et al. The basic helix-loop-helix transcription factor HEBAlt is expressed in pro-T cells and enhances the generation of T cell precursors. J Immunol. 2006;177:109-19 pubmed..Therefore, HEBAlt and HEBCan are functionally distinct transcription factors, and HEBAlt is specifically required for the efficient generation of early T cell precursors. ..
- Xin X, Gfeller D, Cheng J, Tonikian R, Sun L, Guo A, et al. SH3 interactome conserves general function over specific form. Mol Syst Biol. 2013;9:652 pubmed publisher..Nevertheless, orthologous SH3 domain-mediated interactions are highly rewired. Our results suggest a model of network evolution where general function of the SH3 domain network is conserved over its specific form. ..
- Alexson T, Hitoshi S, Coles B, Bernstein A, van der Kooy D. Notch signaling is required to maintain all neural stem cell populations--irrespective of spatial or temporal niche. Dev Neurosci. 2006;28:34-48 pubmed..Regardless, these findings demonstrate that PS1, and presumably Notch signaling, is required to maintain all NSCs. ..
- DeVries M, Cao H, Wang J, Xu L, Kelvin A, Ran L, et al. Genomic organization and evolution of the CX3CR1/CCR8 chemokine receptor locus. J Biol Chem. 2003;278:11985-94 pubmed
- Moran M, Koch C, Sadowski I, Pawson T. Mutational analysis of a phosphotransfer motif essential for v-fps tyrosine kinase activity. Oncogene. 1988;3:665-72 pubmed
- Scorilas A, Chiang P, Katsaros D, Yousef G, Diamandis E. Molecular characterization of a new gene, CEAL1, encoding for a carcinoembryonic antigen-like protein with a highly conserved domain of eukaryotic translation initiation factors. Gene. 2003;310:79-89 pubmed..The CEAL1 gene was found to be down-regulated by dexamethasone in BT-474 breast cancer cell lines. Our data suggest that this gene is overexpressed in a subset of ovarian cancers which are clinically more aggressive. ..
- McCracken S, Longman D, Johnstone I, Caceres J, Blencowe B. An evolutionarily conserved role for SRm160 in 3'-end processing that functions independently of exon junction complex formation. J Biol Chem. 2003;278:44153-60 pubmed..Our combined results provide evidence for an evolutionarily conserved interaction between SRm160 and the 3'-end cleavage machinery that functions independently of EJC formation. ..
- Haudry A, Platts A, Vello E, Hoen D, Leclercq M, Williamson R, et al. An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet. 2013;45:891-8 pubmed publisher..Overall, these CNSs highlight both similarities and several key differences between the regulatory DNA of plants and other species. ..
- van der Geer P, Wiley S, Lai V, Olivier J, Gish G, Stephens R, et al. A conserved amino-terminal Shc domain binds to phosphotyrosine motifs in activated receptors and phosphopeptides. Curr Biol. 1995;5:404-12 pubmed..In this way, Shc may function as an adaptor protein to bring two tyrosine-phosphorylated proteins together. ..
- Sampaleanu L, Bonanno J, Ayers M, Koo J, Tammam S, Burley S, et al. Periplasmic domains of Pseudomonas aeruginosa PilN and PilO form a stable heterodimeric complex. J Mol Biol. 2009;394:143-59 pubmed publisher..Our results suggest that PilN/O heterodimers form the foundation of the inner-membrane PilM/N/O/P complex, which is critical for the assembly of a functional T4P complex...
- Boocock G, Marit M, Rommens J. Phylogeny, sequence conservation, and functional complementation of the SBDS protein family. Genomics. 2006;87:758-71 pubmed..These findings link Shwachman-Diamond syndrome to other bone marrow failure syndromes with defects in nucleolus-associated processes, including Diamond-Blackfan anemia, cartilage-hair hypoplasia, and dyskeratosis congenita. ..
- Schwartz C, Sampson H, Hlousek D, Percival Smith A, Copeland J, Simmonds A, et al. FTZ-Factor1 and Fushi tarazu interact via conserved nuclear receptor and coactivator motifs. EMBO J. 2001;20:510-9 pubmed..These unexpected findings have important implications for the conserved homologs of the two proteins. ..
- Beloglazova N, Brown G, Zimmerman M, Proudfoot M, Makarova K, Kudritska M, et al. A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats. J Biol Chem. 2008;283:20361-71 pubmed publisher..Thus, CAS2 proteins are sequence-specific endoribonucleases, and we propose that their role in the CRISPR-mediated anti-phage defense might involve degradation of phage or cellular mRNAs...
- Proudfoot M, Sanders S, Singer A, Zhang R, Brown G, Binkowski A, et al. Biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a Zn ribbon-like domain. J Mol Biol. 2008;375:301-15 pubmed..We suggest that, in vivo, some Zn ribbon domains might also bind iron and therefore possess an electron carrier activity, adding another physiological role to this large family of important proteins. ..
- Butland G, Peregrín Alvarez J, Li J, Yang W, Yang X, Canadien V, et al. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature. 2005;433:531-7 pubmed..This study provides insight into the function of previously uncharacterized bacterial proteins and the overall topology of a microbial interaction network, the core components of which are broadly conserved across Prokaryota. ..
- Brierley M, Fish E. Functional relevance of the conserved DNA-binding domain of STAT2. J Biol Chem. 2005;280:13029-36 pubmed..Taken together, these data suggest a role for the conserved DNA-binding domain of STAT2 specific to the activity of ISGF3-independent STAT2-containing complexes. ..
- Nakada S, Chen G, Gingras A, Durocher D. PP4 is a gamma H2AX phosphatase required for recovery from the DNA damage checkpoint. EMBO Rep. 2008;9:1019-26 pubmed publisher..Taken together, these results indicate that PP4 is an evolutionarily conserved gammaH2AX phosphatase. ..
- Commisso C, Boulianne G. The NHR1 domain of Neuralized binds Delta and mediates Delta trafficking and Notch signaling. Mol Biol Cell. 2007;18:1-13 pubmed..Altogether, our data demonstrate that NHR domains can function in facilitating protein-protein interactions and in the case of Neuralized, mediate binding to its ubiquitination target, Delta. ..
- Su M, Lee D, Ganss B, Sodek J. Stereochemical analysis of the functional significance of the conserved inverted CCAAT and TATA elements in the rat bone sialoprotein gene promoter. J Biol Chem. 2006;281:9882-90 pubmed..Thus, the precise location and orientation of the CCAAT element is necessary for optimizing basal transcription of the bone sialoprotein gene. ..
- Fung A, Ou J, Bueler S, Brown G. A conserved domain of Schizosaccharomyces pombe dfp1(+) is uniquely required for chromosome stability following alkylation damage during S phase. Mol Cell Biol. 2002;22:4477-90 pubmed
- Chan E, McQuibban G. The mitochondrial rhomboid protease: its rise from obscurity to the pinnacle of disease-relevant genes. Biochim Biophys Acta. 2013;1828:2916-25 pubmed publisher..In this review, we will summarize the current knowledge and disease relevance of the mitochondrial-localized rhomboid protease. This article is part of a Special Issue entitled: Intramembrane Proteases. ..
- Snow B, Krumins A, Brothers G, Lee S, Wall M, Chung S, et al. A G protein gamma subunit-like domain shared between RGS11 and other RGS proteins specifies binding to Gbeta5 subunits. Proc Natl Acad Sci U S A. 1998;95:13307-12 pubmed..RGS proteins that contain GGL domains appear to act as GAPs for Galpha proteins and form complexes with specific Gbeta subunits, adding to the combinatorial complexity of G protein-mediated signaling pathways. ..