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8. What is in umbilicaria pustulata?: A metagenomic approach to reconstruct the holo-genome of a lichen

Author

Tzovaras, B. G., Segers, F. H. I. D., Bicker, A., Dal Grande, F., Otte, J., Anvar, S. Y., Hankeln, T., Schmitt, I., and Ebersberger, I.

Subjects
Genome, Lichens, sequencing error, food and beverages, SPAdes, microbiome, chlorophyta, gene loss, symbiosis, Chlorophyta, Gene loss, Metagenome assembly, Microbiome, Organellar ploidy levels, Sequencing error, Symbiosis, Ascomycota, Phylogeny, Genome, Fungal, Metagenome, Fungal, organellar ploidy levels, ddc:570, metagenome assembly, Research Article
Abstract

Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are poor candidates for experimentation. Obtaining contiguous, high-quality genomes for such symbiotic communities is technically challenging. Here, we present the first assembly of a lichen holo-genome from metagenomic whole-genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis-the fungus Umbilicaria pustulata (33 Mb) and the green alga Trebouxia sp. (53 Mb)-were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative abundance of fungal to algal nuclei of similar to 20:1. Gap-free, circular sequences for all organellar genomes were obtained. The bacterial community is dominated by Acidobacteriaceae and encompasses strains closely related to bacteria isolated from other lichens. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that GC-rich inverted repeats paired with nonrandom sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.

Published
2020

9. From critters to cancers: bridging comparative and clinical research on oxygen sensing, HIF signaling, and adaptations towards hypoxia

Author

Hoogewijs, D., Terwilliger, N.B., Webster, K.A., Powell-Coffman, J.A., Tokishita, S., Yamagata, H., Hankeln, T., Burmester, T., Rytkonen, K.T., Nikinmaa, I., Abele, D., Heise, K., Lucassen, M., Fandrey, J., Maxwell, P.H., Pahlman, S., and Gorr, T.A.

Subjects
Oncology, Experimental -- Conferences, meetings and seminars, Hypoxia -- Conferences, meetings and seminars, Cancer -- Research, Cancer -- Conferences, meetings and seminars, Zoology and wildlife conservation
Abstract

The objective of this symposium at the First International Congress of Respiratory Biology (ICRB) was to enhance communication between comparative biologists and cancer researchers working on [O.sub.2] sensing via the HIF pathway. Representatives from both camps came together on August 13-16, 2006, in Bonn, Germany, to discuss molecular adaptations that occur after cells have been challenged by a reduced (hypoxia) of completely absent (anoxia) supply of oxygen. This brief 'critters-to-cancer' survey discusses current projects and new directions aimed at improving understanding of hypoxic signaling and developing therapeutic interventions.

Published
2007

15. Knockdown of Drosophila hemoglobin suggests a role in 02 homeostasis

Author

Gleixner, E., Ripp, F., Gorr, T., Schuh, R., Wolf, C., Burmester, T., and Hankeln, T.

Subjects
fungi
Abstract

Almost all insects are equipped with a tracheal system, which appears to be sufficient for O-2 supply even in phases of high metabolic activity. Therefore, with the exception of a few species dwelling in hypoxic habitats, specialized respiratory proteins had been considered unnecessary in insects. The recent discovery and apparently universal presence of intracellular hemoglobins in insects has remained functionally unexplained. The fruitfly Drosophila melanogaster harbors three different globin genes (referred to as glob]-3). Glob1 is the most highly expressed globin and essentially occurs in the tracheal system and the fat body. To better understand the functions of insect globins, the levels of glob1 were modulated in Drosophila larvae and adults by RNAi-mediated knockdown and transgenic over-expression. No effects on the development were observed in flies with manipulated glob1 levels. However, the knockdown of glob1 led to a significantly reduced survival rate of adult flies under hypoxia (5% and 1.5% 02). Surprisingly, the glob1 knockdown flies also displayed increased resistance towards the reactive oxygen species forming agent paraquat, which may be explained by a restricted availability of O-2 resulting in decreased formation of harmful O-2(-). In summary, our results suggest an important functional role of glob1 in O-2 homeostasis, possibly by enhancing O-2 supply.

Published
2016

17. The Yeast Genome Directory

Author

Goffeau, A., Aert, R., Agostini-Carbone, M. L., Ahmed, A., Aigle, M., Alberghina, L., Albermann, K., Albers, M., Aldea, M., Alexandraki, D., Aljinovic, G., Allen, E., Alt-Mörbe, J., André, B., Andrews, S., Ansorge, W., Antoine, G., Anwar, R., Aparicio, A., Araujo, R., Arino, J., Arnold, F., Arroyo, J., Aviles, E., Backes, U., Baclet, M. C., Badcock, K., Bahr, A., Baladron, V., Ballesta, J. P. G., Bankier, A. T., Banrevi, A., Bargues, M., Baron, L., Barreiros, T., Barrell, B. G., Barthe, C., Barton, A. B., Baur, A., Bécam, A.-M., Becker, A., Becker, I., Beinhauer, J., Benes, V., Benit, P., Berben, G., Bergantino, E., Bergez, P., Berno, A., Bertani, I., Biteau, N., Bjourson, A. J., Blöcker, H., Blugeon, C., Bohn, C., Boles, E., Bolle, P. A., Bolotin-Fukuhara, M., Bordonné, R., Boskovic, J., Bossier, P., Botstein, D., Bou, G., Bowman, S., Boyer, J., Brandt, P., Brandt, T., Brendel, M., Brennan, T., Brinkman, R., Brown, A., Brown, A. J. P., Brown, D., Brückner, M., Bruschi, C. V., Buhler, J. M., Buitrago, M. J., Bussereau, F., Bussey, H., Camasses, A., Carcano, C., Carignani, G., Carpenter, J., Casamayor, A., Casas, C., Castagnoli, L., Cederberg, H., Cerdan, E., Chalwatzis, N., Chanet, R., Chen, E., Chéret, G., Cherry, J. M., Chillingworth, T., Christiansen, C., Chuat, J.-C., Chung, E., Churcher, C., Churcher, C. M., Clark, M. W., Clemente, M. L., Coblenz, A., Coglievina, M., Coissac, E., Colleaux, L., Connor, R., Contreras, R., Cooper, J., Copsey, T., Coster, F., Coster, R., Couch, J., Crouzet, M., Cziepluch, C., Daignan-Fornier, B., Dal Paro, F., Dang, D. V., D’Angelo, M., Davies, C. J., Davis, K., Davis, R. W., De Antoni, A., Dear, S., Dedman, K., Defoor, E., De Haan, M., Delaveau, Th., Del Bino, S., Delgado, M., Delius, H., Delneri, D., Del Rey, F., Demolder, J., Démolis, N., Devlin, K., de Wergifosse, P., Dietrich, F. S., Ding, H., Dion, C., Dipaolo, T., Doignon, F., Doira, C., Domdey, H., Dover, J., Du, Z., Dubois, E., Dujon, B., Duncan, M., Durand, P., Düsterhöft, A., Düsterhus, S., Eki, T., El Bakkoury, M., Eide, L. G., Entian, K.-D., Eraso, P., Erdmann, D., Erfle, H., Escribano, V., Esteban, M., Fabiani, L., Fabre, F., Fairhead, C., Fartmann, B., Favello, A., Faye, G., Feldmann, H., Fernandes, L., Feroli, F., Feuermann, M., Fiedler, T., Fiers, W., Fleig, U. N., Flöth, M., Fobo, G. M., Fortin, N., Foury, F., Francingues-Gaillard, M. C., Franco, L., Fraser, A., Friesen, J.D., Fritz, C., Frontali, L., Fukuhara, H., Fulton, L., Fuller, L. J., Gabel, C., Gaillardin, C., Gaillon, L., Galibert, F., Galisson, F., Galland, P., Gamo, F.-J., Gancedo, C., Garcia-Cantalejo, J. M., García-Gonzalez, M. I., Garcia-Ramirez, J. J., García-Saéz, M., Gassenhuber, H., Gatius, M., Gattung, S., Geisel, C., Gent, M. E., Gentles, S., Ghazvini, M., Gigot, D., Gilliquet, V., Glansdorff, N., Gómez-Peris, A., Gonzaléz, A., Goulding, S. E., Granotier, C., Greco, T., Grenson, M., Grisanti, P., Grivell, L. A., Grothues, D., Gueldener, U., Guerreiro, P., Guzman, E., Haasemann, M., Habbig, B., Hagiwara, H., Hall, J., Hallsworth, K., Hamlin, N., Hand, N. J., Hanemann, V., Hani, J., Hankeln, T., Hansen, M., Harris, D., Harris, D. E., Hartzell, G., Hatat, D., Hattenhorst, U., Hawkins, J., Hebling, U., Hegemann, J., Hein, C., Hennemann, A., Hennessy, K., Herbert, C. J., Hernandez, K., Hernando, Y., Herrero, E., Heumann, K., Heuss- Neitzel, D., Hewitt, N., Hiesel, R., Hilbert, H., Hilger, F., Hillier, L., Ho, C., Hoenicka, J., Hofmann, B., Hoheisel, J., Hohmann, S., Hollenberg, C. P., Holmstrøm, K., Horaitis, O., Horsnell, T. S., Huang, M.-E., Hughes, B., Hunicke-Smith, S., Hunt, S., Hunt, S. E., Huse, K., Hyman, R. W., Iborra, F., Indge, K. J., Iraqui Houssaini, I., Isono, K., Jacq, C., Jacquet, M., Jacquier, A., Jagels, K., Jäger, W., James, C. M., Jauniaux, J. C., Jia, Y., Jier, M., Jimenez, A., Johnson, D., Johnston, L., Johnston, M., Jones, M., Jonniaux, J.-L., Kaback, D. B., Kallesøe, T., Kalman, S., Kalogeropoulos, A., Karpfinger-Hartl, L., Kashkari, D., Katsoulou, C., Kayser, A., Kelly, A., Keng, T., Keuchel, H., Kiesau, P., Kirchrath, L., Kirsten, J., Kleine, K., Kleinhans, U., Klima, R., Komp, C., Kordes, E., Korol, S., Kötter, P., Krämer, C., Kramer, B., Kreisl, P., Kucaba, T., Kuester, H., Kurdi, O., Laamanen, P., Lafuente, M. J., Landt, O., Lanfranchi, G., Langston, Y., Lashkari, D., Latreille, P., Lauquin, G., Le, T., Legrain, P., Legros, Y., Lepingle, A., Lesveque, H., Leuther, H., Lew, H., Lewis, C., Li, Z. Y., Liebl, S., Lin, A., Lin, D., Logghe, M., Lohan, A. J. E., Louis, E. J., Lucchini, G., Lutzenkirchen, K., Lyck, R., Lye, G., Maarse, A. C., Maat, M. J., Macri, C., Madania, A., Maftahi, M., Maia e Silva, A., Maillier, E., Mallet, L., Mannhaupt, G., Manus, V., Marathe, R., Marck, C., Marconi, A., Mardis, E., Martegani, E., Martin, R., Mathieu, A., Maurer, C. T. C., Mazón, M. J., Mazzoni, C., McConnell, D., McDonald, S., McKee, R. A., McReynolds, A. D. K., Melchioretto, P., Menezes, S., Messenguy, F., Mewes, H. W., Michaux, G., Miller, N., Minenkova, O., Miosga, T., Mirtipati, S., Möller-Rieker, S., Möstl, D., Molemans, F., Monnet, A., Monnier, A-L., Montague, M. A., Moro, M., Mosedale, D., Möstl, D., Moule, S., Mouser, L., Murakami, Y., Müller-Auer, S., Mulligan, J., Murphy, L., Muzi Falconi, M., Naitou, M., Nakahara, K., Namath, A., Nasr, F., Navas, L., Nawrocki, A., Nelson, J., Nentwich, U., Netter, P., Neu, R., Newlon, C. S., Nhan, M., Nicaud, J.-M., Niedenthal, R. K., Nombela, C., Noone, D., Norgren, R., Nußbaumer, B., Obermaier, B., Odell, C., Öfner, P., Oh, C., Oliver, K., Oliver, S. G., Ouellette, B. F., Ozawa, M., Paces, V., Pallier, C., Pandolfo, D., Panzeri, L., Paoluzi, S., Parle-Mcdermott, A. G., Pascolo, S., Patricio, N., Pauley, A., Paulin, L., Pearson, B. M., Pearson, D., Peluso, D., Perea, J., Pérez-Alonso, M., Pérez-Ortin, J. E., Perrin, A., Petel, F. X., Pettersson, B., Pfeiffer, F., Philippsen, P., Piérard, A., Piravandi, E., Planta, R. J., Plevani, P., Poch, O., Poetsch, B., Pohl, F. M., Pohl, T. M., Pöhlmann, R., Poirey, R., Portetelle, D., Portillo, F., Potier, S., Proft, M., Prydz, H., Pujol, A., Purnelle, B., Puzos, V., Rajandream, M. A., Ramezani Rad, M., Rasmussen, S. W., Raynal, A., Rechmann, S., Remacha, M., Revuelta, J. L., Rice, P., Richard, G-F., Richterich, P., Rieger, M., Rifken, L., Riles, L., Rinaldi, T., Rinke, M., Roberts, A. B., Roberts, D., Rodriguez, F., Rodriguez-Belmonte, E., Rodriguez-Pousada, C., Rodriguez-Torres, A. M., Rose, M., Rossau, R., Rowley, N., Rupp, T., Ruzzi, M., Saeger, W., Saiz, J. E., Saliola, M., Salom, D., Saluz, H. P., Sánchez-Perez, M., Santos, M. A., Sanz, E., Sanz, J. E., Saren, A.-M., Sartorello, F., Sasanuma, M., Sasanuma, S-I., Scarcez, T., Schaaf-Gerstenschläger, I., Schäfer, B., Schäfer, M., Scharfe, M., Scherens, B., Schroff, N., Sen-Gupta, M., Shibata, T., Schmidheini, T., Schmidt, E. R., Schneider, C., Scholler, P., Schramm, S., Schreer, A., Schröder, M., Schwager, C., Schwarz, S., Schwarzlose, C., Schweitzer, B., Schweizer, M., Sdicu, A-M., Sehl, P., Sensen, C., Sgouros, J. G., Shogren, T., Shore, L., Shu, Y., Skala, J., Skelton, J., Slonimski, P. P., Smit, P. H. M., Smith, V., Soares, H., Soeda, E., Soler-Mira, A., Sor, F., Soriano, N., Souciet, J. L., Soustelle, C., Spiegelberg, R., Stateva, L. I., Steensma, H. Y., Stegemann, J., Steiner, S., Stellyes, L., Sterky, F., Storms, R. K., St. Peter, H., Stucka, R., Taich, A., Talla, E., Tarassov, I., Tashiro, H., Taylor, P., Teodoru, C., Tettelin, H., Thierry, A., Thireos, G., Tobiasch, E., Tovan, D., Trevaskis, E., Tsuchiya, Y., Tzermia, M., Uhlen, M., Underwood, A., Unseld, M., Urbanus, J. H. M., Urrestarazu, A., Ushinsky, S., Valens, M., Valle, G., Van Broekhoven, A., Vandenbol, M., Van Der Aart, Q. J. M., Van Der Linden, C. G., Van Dyck, L., Vanoni, M., Van Vliet-Reedijk, J. C., Vassarotti, A., Vaudin, M., Vaughan, K., Verhasselt, P., Vetter, I., Vierendeels, F., Vignati, D., Vilela, C., Vissers, S., Vleck, C., Vo, D. T., Vo, D. H., Voet, M., Volckaert, G., Von Wettstein, D., Voss, H., Vreken, P., Wagner, G., Walsh, S. V., Wambutt, R., Wang, H., Wang, Y., Warmington, J. R., Waterston, R., Watson, M. D., Weber, N., Wedler, E., Wedler, H., Wei, Y., Whitehead, S., Wicksteed, B. L., Wiemann, S., Wilcox, L., Wilson, C., Wilson, R., Winant, A., Winnett, E., Winsor, B., Wipfli, P., Wölfl, S., Wohldman, P., Wolf, K., Wolfe, K. H., Wright, L. F., Wurst, H., Xu, G., Yamasaki, M., Yelton, M. A., Yokohama, K., Yoshikawa, A., Yuping, S., Zaccaria, P., Zagulski, M., Zimmermann, F. K., Zimmermann, J., Zimmermann, M., Zhong, W-W., Zollner, A., and Zumstein, E.

Published
1997
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19. Evolution of the globin superfamily and its function

Author

Vinogradov, S N, Hoogewijs, D, Vanfleteren, J, Dewilde, S, Moens, L, Hankeln, T, University of Zurich, and Nagai, M

Subjects
10076 Center for Integrative Human Physiology, 570 Life sciences, biology, 610 Medicine & health, 10052 Institute of Physiology
Published
2011

20. Old proteins - new locations: myoglobin, haemoglobin, neuroglobin and cytoglobin in solid tumours and cancer cells

Author

Gorr, T A, Wichmann, D, Pilarsky, C, Theurillat, J P, Fabrizius, A, Laufs, T, Bauer, T, Koslowski, M, Horn, S, Burmester, T, Hankeln, T, Kristiansen, G, University of Zurich, and Gorr, T A

Subjects
10049 Institute of Pathology and Molecular Pathology, 570 Life sciences, biology, 610 Medicine & health, 1314 Physiology, 10081 Institute of Veterinary Physiology
Published
2011
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21. The globin gene family of the cephalochordate amphioxus : implications for chordate globin evolution

Author

Ebner, B., Panopoulou, G., Vinogradov, S., Kiger, L., Marden, M., Burmester, T., and Hankeln, T.

Subjects
animal structures, hemic and lymphatic diseases
Abstract

BACKGROUND: The lancelet amphioxus (Cephalochordata) is a close relative of vertebrates and thus may enhance our understanding of vertebrate gene and genome evolution. In this context, the globins are one of the best studied models for gene family evolution. Previous biochemical studies have demonstrated the presence of an intracellular globin in notochord tissue and myotome of amphioxus, but the corresponding gene has not yet been identified. Genomic resources of Branchiostoma floridae now facilitate the identification, experimental confirmation and molecular evolutionary analysis of its globin gene repertoire. RESULTS: We show that B. floridae harbors at least fifteen paralogous globin genes, all of which reveal evidence of gene expression. The protein sequences of twelve globins display the conserved characteristics of a functional globin fold. In phylogenetic analyses, the amphioxus globin BflGb4 forms a common clade with vertebrate neuroglobins, indicating the presence of this nerve globin in cephalochordates. Orthology is corroborated by conserved syntenic linkage of BflGb4 and flanking genes. The kinetics of ligand binding of recombinantly expressed BflGb4 reveals that this globin is hexacoordinated with a high oxygen association rate, thus strongly resembling vertebrate neuroglobin. In addition, possible amphioxus orthologs of the vertebrate globin X lineage and of the myoglobin/cytoglobin/hemoglobin lineage can be identified, including one gene as a candidate for being expressed in notochord tissue. Genomic analyses identify conserved synteny between amphioxus globin-containing regions and the vertebrate beta-globin locus, possibly arguing against a late transpositional origin of the beta-globin cluster in vertebrates. Some amphioxus globin gene structures exhibit minisatellite-like tandem duplications of intron-exon boundaries ("mirages"), which may serve to explain the creation of novel intron positions within the globin genes. CONCLUSIONS: The identification of putative orthologs of vertebrate globin variants in the B. floridae genome underlines the importance of cephalochordates for elucidating vertebrate genome evolution. The present study facilitates detailed functional studies of the amphioxus globins in order to trace conserved properties and specific adaptations of respiratory proteins at the base of chordate evolution.

Published
2010

29. Androglobin: a chimeric globin in metazoans that is preferentially expressed in mammalian testes

Author

Hoogewijs, D, Ebner, B, Germani, F, Hoffmann, F G, Fabrizius, A, Moens, L, Burmester, T, Dewilde, S, Storz, J F, Vinogradov, S N, Hankeln, T, Hoogewijs, D, Ebner, B, Germani, F, Hoffmann, F G, Fabrizius, A, Moens, L, Burmester, T, Dewilde, S, Storz, J F, Vinogradov, S N, and Hankeln, T

Abstract

Comparative genomic studies have led to the recent identification of several novel globin types in the Metazoa. They have revealed a surprising evolutionary diversity of functions beyond the familiar O2 supply roles of hemoglobin and myoglobin. Here we report the discovery of a hitherto unrecognized family of proteins with a unique modular architecture, possessing an N-terminal calpain-like domain, an internal, circular permuted globin domain, and an IQ calmodulin-binding motif. Putative orthologs are present in the genomes of many metazoan taxa, including vertebrates. The calpain-like region is homologous to the catalytic domain II of the large subunit of human calpain-7. The globin domain satisfies the criteria of a myoglobin-like fold but is rearranged and split into two parts. The recombinantly expressed human globin domain exhibits an absorption spectrum characteristic of hexacoordination of the heme iron atom. Molecular evolutionary analyses indicate that this chimeric globin family is phylogenetically ancient and originated in the common ancestor to animals and choanoflagellates. In humans and mice, the gene is predominantly expressed in testis tissue, and we propose the name ‘‘androglobin’’ (Adgb). Expression is associated with postmeiotic stages of spermatogenesis and is insensitive to experimental hypoxia. Evidence exists for increased gene expression in fertile compared with infertile males.

Published
2012

30. Endogenous myoglobin in breast cancer is hypoxia-inducible by alternative transcription and functions to impair mitochondrial activity: a role in tumor suppression?

Author

Kristiansen, G, Hu, J, Wichmann, D, Stiehl, D P, Rose, M, Gerhardt, J, Bohnert, A, Ten Haaf, A, Moch, H, Raleigh, J, Varia, M A, Subarsky, P, Scandurra, F M, Gnaiger, E, Gleixner, E, Bicker, A, Gassmann, M, Hankeln, T, Dahl, E, Gorr, T A, Kristiansen, G, Hu, J, Wichmann, D, Stiehl, D P, Rose, M, Gerhardt, J, Bohnert, A, Ten Haaf, A, Moch, H, Raleigh, J, Varia, M A, Subarsky, P, Scandurra, F M, Gnaiger, E, Gleixner, E, Bicker, A, Gassmann, M, Hankeln, T, Dahl, E, and Gorr, T A

Abstract

Recently, immunohistochemical analysis of myoglobin (MB) in human breast cancer specimens has revealed a surprisingly widespread expression of MB in this non-muscle context. The positive correlation with hypoxia-inducible factor 2 and carbonic anhydrase IX suggested that oxygen regulates myoglobin expression in breast carcinomas. Here we report that MB mRNA and protein levels are robustly induced by prolonged hypoxia in breast cancer cell lines, in part via HIF-1/-2 dependent transactivation. The hypoxia-induced MB mRNA originated from a novel, alternative transcription start site 6 kb upstream of the ATG codon. MB regulation in normal and tumor tissue may thus be fundamentally different. Functionally, the knockdown of MB in MDA-MB468 breast cancer cells resulted in an unexpected increase of O2 uptake and elevated activities of mitochondrial enzymes during hypoxia. Silencing of MB transcription attenuated proliferation rates and motility capacities of hypoxic and, surprisingly, also fully oxygenated breast cancer cells. Endogenous MB in cancer cells is apparently involved in controlling oxidative cell energy metabolism, contrary to the mouse heart, where the targeted disruption of the Mb gene did not effect myocardial energetics and O2 consumption. This control function of MB seemingly impacts mitochondria and influences cell proliferation and motility, but it does so in ways not directly related to the facilitated diffusion or storage of O2. Hypothetically, myoglobins mitochondria-impairing role in hypoxic cancer cells is part of a novel tumor-suppressive function.

Published
2011

32. The nucleotide sequence of Saccharomyces cerevisiae chromosome IV

Author

Jacq, C., Altmorbe, J., Andre, B., Arnold, W., Bahr, A., Ballesta, Jpg, Bargues, M., Baron, L., Becker, A., Biteau, N., Blocker, H., Blugeon, C., Boskovic, J., Brandt, P., Bruckner, M., Buitrago, Mj, Coster, F., Delaveau, T., Delrey, F., Dujon, B., Eide, Lg, Garciacantalejo, Jm, Goffeau, A., Gomezperis, A., Granotier, C., Hanemann, V., Hankeln, T., Hoheisel, Jd, Jager, W., Jimenez, A., Jonniaux, Jl, Kramer, C., Kuster, H., Laamanen, P., Legros, Y., Louis, E., Mollerrieker, S., Monnet, A., Moro, M., Mullerauer, S., Nussbaumer, B., Paricio, N., Paulin, L., Perea, J., Perezalonso, M., Perezortin, Je, Pohl, Tm, Prydz, H., Purnelle, B., Rasmussen, Sw, Remacha, M., Jose Luis Revuelta, Rieger, M., Salom, D., Saluz, Hp, Saiz, Je, Saren, Am, Schafer, M., Scharfe, M., Schmidt, Er, Schneider, C., Scholler, P., Schwarz, S., Solermira, A., Urrestarazu, La, Verhasselt, P., Vissers, S., Voet, M., Volckaert, G., Wagner, G., Wambutt, R., Wedler, E., Wedler, H., Wolfl, S., Harris, DE, Bowman, S., Brown, D., Churcher, Cm, Connor, R., Dedman, K., Gentles, S., Hamlin, N., Hunt, S., Jones, L., Mcdonald, S., Murphy, L., Niblett, D., Odell, C., Oliver, K., Rajandream, Ma, Richards, C., Shore, L., Walsh, Sv, Barrell, Bg, Dietrich, Fs, Mulligan, J., Allen, E., Araujo, R., Aviles, E., Berno, O., Carpenter, J., Chen, E., Cherry, Jm, Chung, E., Duncan, M., Hunickesmith, S., Hyman, R., Komp, C., Lashkari, D., Lew, H., Lin, D., Mosedale, D., Nakahara, K., Namath, A., Oefner, P., Oh, C., Petel, Fx, Roberts, D., Schramm, S., Schroeder, M., Shogren, T., Shroff, N., Winant, A., Yelton, M., Botstein, D., Davis, Rw, Johnston, M., Hillier, L., Riles, L., Albermann, K., Hani, J., Heumann, K., Kleine, K., Mewes, Hw, Zollner, A., and Zaccaria, P.

Subjects
Multidisciplinary, Base Sequence, Molecular Sequence Data, Saccharomyces cerevisiae, Chromosomes, Fungal, DNA, Fungal
Abstract

The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome IV has been determined. Apart from chromosome XII, which contains the 1-2 Mb rDNA cluster, chromosome IV is the longest S. cerevisiae chromosome. It was split into three parts, which were sequenced by a consortium from the European Community, the Sanger Centre, and groups from St Louis and Stanford in the United States. The sequence of 1,531,974 base pairs contains 796 predicted or known genes, 318 (39.9%) of which have been previously identified. Of the 478 new genes, 225 (28.3%) are homologous to previously identified genes and 253 (32%) have unknown functions or correspond to spurious open reading frames (ORFs). On average there is one gene approximately every two kilobases. Superimposed on alternating regional variations in G+C composition, there is a large central domain with a lower G+C content that contains all the yeast transposon (Ty) elements and most of the tRNA genes. Chromosome IV shares with chromosomes II, V, XII, XIII and XV some long clustered duplications which partly explain its origin.

Published
1997

46. A variable intron distribution in globin genes of Chironomus: evidence for recent intron gain

Author

Hankeln, T, Friedl, H, Ebersberger, I, Martin, J, Schmidt, ER, Hankeln, T, Friedl, H, Ebersberger, I, Martin, J, and Schmidt, ER

Abstract

The intron positions found in globin genes of plants, protozoa and invertebrates have been interpreted as evidence for a three-intron-four-exon structure of the ancestral globin gene. In particular, the so-called 'central' introns, which are not found in vertebrate globin genes but are present in a variety of invertebrate and plant species, have been used as an argument for an ancestral gene structure featuring three introns. We have analyzed the presence or absence of central introns in the Gb genes 2beta, 9 and 7A of various European and Australasian species of the insect Chironomus. We find unrelated central introns at different positions in some of the species investigated, while other species completely lack introns in these genes. This variable distribution of introns is parsimoniously explained by independent intron additions. Such a gain of introns may occur convergently at identical positions in unrelated taxa. Insertion by gene conversion may be a viable mechanism to explain intron gain.

Published
1997

50. A P16(ink4a)-insensitive Cdk4 Mutant Targeted By Cytolytic T-lymphocytes in a Human-melanoma

Author

UCL - FSA/MECA - Département de mécanique, Wolfel, T., Hauer, M., Schneider, Jenny, Serrano, M., Wolfel, C., Klehmannhieb, E., De Plaen, Etienne, Hankeln, T., Zumbuschenfelde, KHM., Beach, D., UCL - FSA/MECA - Département de mécanique, Wolfel, T., Hauer, M., Schneider, Jenny, Serrano, M., Wolfel, C., Klehmannhieb, E., De Plaen, Etienne, Hankeln, T., Zumbuschenfelde, KHM., and Beach, D.

Abstract

A mutated cyclin-dependent kinase 4 (CDK4) was identified as a tumor-specific antigen recognized by HL4-A2.1-restricted autologous cytolytic T lymphocytes (CTLs) in a human melanoma. The mutated CDK4 allele was present in autologous cultured melanoma cells and metastasis tissue, but not in the patient's lymphocytes. The mutation, an arginine-to-cysteine exchange at residue 24, was part of the CDK4 peptide recognized by CTLs and prevented binding of the CDK4 inhibitor p16(INK4a), but not of p21 or of p27(KIP1). The same mutation was found in one additional melanoma among 28 melanomas analyzed. These results suggest that mutation of CDK4 can create a tumor-specific antigen and can disrupt the cell-cycle regulation exerted by the tumor suppressor p16(INK4a).

Published
1995

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