Misplaced Pages

#858141

23-420: Sankoff is a surname. Notable people with the surname include: David Sankoff (born 1942), mathematician, bioinformatician, computer scientist and linguist Gillian Sankoff , sociolinguist Irene Sankoff , musical theatre creator [REDACTED] Surname list This page lists people with the surname Sankoff . If an internal link intending to refer to

46-506: A joint estimation method for phylogeny and multiple sequence alignment of 5S ribosomal RNA , laying the algorithmic foundations of comparative genomics . In 1975, Sankoff and Václav Chvátal studied the behavior of the longest common subsequence problem on random inputs; the constants of proportionality arising in this study have come to be known as the Chvátal–Sankoff constants . In 1980, Robert Cedergen and David Sankoff created

69-440: A polycistronic precursor . A particularity of eukaryotic nuclear genomes is the occurrence of multiple 5S rRNA gene copies (5S rDNA) clustered in tandem repeats, with copy number varying from species to species. Eukaryotic 5S rRNA is synthesized by RNA polymerase III , whereas other eukaryotic rRNAs are cleaved from a 45S precursor transcribed by RNA polymerase I . In Xenopus oocytes , it has been shown that fingers 4–7 of

92-472: A Y-like structure. Loops C and D are terminal hairpins and loops B and E are internal. According to phylogenetic studies, helices I and III are likely ancestral. Helix III includes two highly conserved adenosines. Helix V, with its hairpin structure, is thought to interact with TFIIIA. Using a variety of molecular techniques, including immuno-electron microscopy , cryo-electron microscopy , intermolecular chemical cross-linking , and X-ray crystallography ,

115-504: A lower global level of 5S rRNA. Translation machineries of mitochondria and plastids (organelles of endosymbiotic bacterial origin), and their bacterial relatives share many features but also display marked differences. Organelle genomes encode SSU and LSU rRNAs without exception, yet the distribution of 5S rRNA genes ( rrn5 ) is most uneven. Rrn5 is easily identified and common in genomes of most plastids. In contrast, mitochondrial rrn5 initially appeared to be restricted to plants and

138-555: A small number of protists. Additional, more divergent organellar 5S rRNAs were only identified with specialized covariance models that incorporate information on the pronounced sequence composition bias and structural variation. This analysis pinpointed additional 5S rRNA genes not only in mitochondrial genomes of most protist lineages, but also in genomes of certain apicoplasts (non-photosynthetic plastids of pathogenic protozoa such as Toxoplasma gondii and Eimeria tenella ). Mitochondrial 5S rRNAs of most stramenopiles comprise

161-462: A specific person led you to this page, you may wish to change that link by adding the person's given name (s) to the link. Retrieved from " https://en.wikipedia.org/w/index.php?title=Sankoff&oldid=908298004 " Category : Surnames Hidden categories: Articles with short description Short description is different from Wikidata All set index articles David Sankoff David Sankoff (born December 31, 1942)

184-526: A ‘stamp collection' of ill-defined problems into a rigorous discipline with important biological applications." Sankoff published his first paper in 1963 while he was an undergraduate student in Mathematics at McGill University . Starting with his doctoral research, he developed mathematical formulations to a number of pivotal concepts in socio- and historical linguistics, including glottochronology , variable rules analysis (with Henrietta Cedergren),

207-760: Is a Canadian mathematician, bioinformatician , computer scientist and linguist. He holds the Canada Research Chair in Mathematical Genomics in the Mathematics and Statistics Department at the University of Ottawa , and is cross-appointed to the Biology Department and the School of Information Technology and Engineering. He was founding editor of the scientific journal Language Variation and Change (Cambridge) and serves on

230-466: Is assembled from four rRNAs and over 80 proteins. Once transcribed, the 3' ends of 5S rRNA can only be trimmed to mature length by functional homologues of RNase T , for example Rex1p in Saccharomyces cerevisiae . The 60S and 40S ribosomal subunits are exported from the nucleus to the cytoplasm where they join to form the mature and translation -competent 80S ribosome. When exactly 5S rRNA

253-497: Is integrated into the ribosome remains controversial, but it is generally accepted that 5S rRNA is incorporated into the 90S particle, which is a precursor to 60S particle, as part of a small ribosome-independent RNP complex formed by 5S rRNA and ribosomal protein L5. Several important proteins which interact with 5S rRNA are listed below. Interaction of 5S rRNA with the La protein prevents

SECTION 10

#1732764861859

276-457: Is not yet clear. In Escherichia coli , 5S rRNA gene deletions reduce the protein synthesis rate and have a more profound detrimental effect on cell fitness than deletions of a comparable number of copies of other ( 16S and 23S ) rRNA genes. Crystallographic studies indicate that 5S rRNA-binding proteins and other proteins of the central protuberance of the LSU plays a role in binding tRNAs. Also,

299-467: The linguistic marketplace and code switching . After completing his Ph.D. in Mathematics, Sankoff began his academic career at the University of Montreal in 1969. In 1971, Sankoff became interested in molecular sequence comparison and devised the first quadratic-time variant of the Needleman–Wunsch algorithm for pairwise sequence alignment . In 1973, Sankoff and Robert Cedergren developed

322-588: The 5S rRNA forming a pre-ribosomal ribonucleoprotein particle (RNP) that is found in both cytosol and the nucleus. L5 deficiency prevents transport of 5S rRNA to the nucleus and results in decreased ribosomal assembly. In prokaryotes the 5S rRNA binds to the L5, L18 and L25 ribosomal proteins, whereas in eukaryotes 5S rRNA is only known to bind the L5 ribosomal protein . In T. brucei , the causative agent of sleeping sickness , 5S rRNA interacts with two closely related RNA-binding proteins, P34 and P37, whose loss results in

345-450: The RNA from degradation by exonucleases in the cell. La protein is found in the nucleus in all eukaryotic organisms and associates with several types of RNAs transcribed by RNA pol III. La protein interacts with these RNAs (including the 5S rRNA) through their 3' oligo-uridine tract, aiding stability and folding of the RNA. In eukaryotic cells, ribosomal protein L5 associates and stabilizes

368-547: The editorial boards of a number of bioinformatics, computational biology and linguistics journals. Sankoff is best known for his pioneering contributions in computational linguistics and computational genomics . He is considered to be one of the founders of bioinformatics . In particular, he had a key role in introducing dynamic programming for sequence alignment and other problems in computational biology . In Pavel Pevzner 's words, " Michael Waterman and David Sankoff are responsible for transforming bioinformatics from

391-416: The first research group in bioinformatics at the University of Montreal . Sankoff's work in bioinformatics addresses RNA secondary structure , genome rearrangements , sequence alignment , genome evolution and phylogenetics . 5S ribosomal RNA In prokaryotes, the 5S rRNA gene is typically located in the rRNA operons downstream of the small and the large subunit rRNA, and co-transcribed into

414-427: The gene. The central protuberance , otherwise occupied by 5S rRNA and its associated proteins (see Figure 2 ), was remodeled in various ways. In the fungal mitochondrial ribosomes, 5S rRNA is replaced by LSU rRNA expansion sequences. In kinetoplastids (euglenozoans), the central protuberance is made entirely of evolutionarily novel mitochondrial ribosomal proteins. Lastly, animal mitochondrial ribosomes have coopted

437-447: The largest diversity of secondary structures. The permuted mitochondrial 5S rRNAs in brown algae represent the most unconventional case, where the closing helix I, which otherwise brings together the molecule's 5′ and 3′ ends, is replaced by a (closed) hairpin resulting in an open three-way junction. Current evidence indicates that mitochondrial DNA of only a few groups, notably animals , fungi , alveolates and euglenozoans lacks

460-470: The location of the 5S rRNA within the large ribosomal subunit has been determined to great precision. In bacteria and archaea , the large ribosomal subunit (LSU) itself is composed of two RNA moieties, the 5S rRNA and another larger RNA known as 23S rRNA , along with numerous associated proteins. In eukaryotes, the LSU contains 5S, 5.8S , and 28S rRNAs and even more proteins. The structure of LSU in 3-dimensions shows one relatively smooth surface and

483-436: The nine- zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Binding between 5S rRNA and TFIIIA serves to both repress further transcription of the 5S RNA gene and stabilize the 5S RNA transcript until it is required for ribosome assembly. The secondary structure of 5S rRNA consists of five helices (denoted I–V in roman numerals ), four loops (B-E), and one hinge (A), which form together

SECTION 20

#1732764861859

506-652: The opposite surface having three projections, notably the L1 protuberance, the central protuberance (CP), and the L7/L12 stalk. The L1 protuberance and L7/L12 stalk are arranged laterally surrounding CP. The 5S rRNA is located in the CP and participates in formation and structure of this projection. The other major constituents of the central protuberance include the 23S rRNA (or alternatively 28S in eukaryotes) and several proteins including L5, L18, L25, and L27. The exact function of 5S rRNA

529-417: The topographical and physical proximity between 5S rRNA and 23S rRNA, which forms the peptidyl transferase and GTPase-associating center, suggests that 5S rRNA acts as a mediator between the two functional centers of the ribosome by forming, together with 5S rRNA-binding proteins and other components of the central protuberance, intersubunit bridges and tRNA-binding sites. In eukaryotes, the cytosolic ribosome

#858141