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PMID: 7813418 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't

Complete DNA sequence of yeast chromosome II.

The EMBO journal ·Vol. 13 ·No. 24 ·1994-12-15 ·Pages 5795-809

Feldmann H, Aigle M, Aljinovic G, André B, Baclet MC, Barthe C, Baur A, Bécam AM, Biteau N, Boles E, Brandt T, Brendel M, Brückner M, Bussereau F, Christiansen C, Contreras R, Crouzet M, Cziepluch C, Démolis N, Delaveau T, Doignon F, Domdey H, Düsterhus S, Dubois E, Dujon B, El Bakkoury M, Entian KD, Feurmann M, Fiers W, Fobo GM, Fritz C, Gassenhuber H, Glandsdorff N, Goffeau A, Grivell LA, de Haan M, Hein C, Herbert CJ, Hollenberg CP, Holmstrøm K, Jacq C, Jacquet M, Jauniaux JC, Jonniaux JL, Kallesøe T, Kiesau P, Kirchrath L, Kötter P, Korol S, Liebl S, Logghe M, Lohan AJ, Louis EJ, Li ZY, Maat MJ, Mallet L, Mannhaupt G, Messenguy F, Miosga T, Molemans F, Müller S, Nasr F, Obermaier B, Perea J, Piérard A, Piravandi E, Pohl FM, Pohl TM, Potier S, Proft M, Purnelle B, Ramezani Rad M, Rieger M, Rose M, Schaaff-Gerstenschläger I, Scherens B, Schwarzlose C, Skala J, Slonimski PP, Smits PH, Souciet JL, Steensma HY, Stucka R, Urrestarazu A, van der Aart QJ, van Dyck L, Vassarotti A, Vetter I, Vierendeels F, Vissers S, Wagner G, de Wergifosse P, Wolfe KH, Zagulski M, Zimmermann FK, Mewes HW, Kleine K

Abstract

In the framework of the EU genome-sequencing programmes, the complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome II (807 188 bp) has been determined. At present, this is the largest eukaryotic chromosome entirely sequenced. A total of 410 open reading frames (ORFs) were identified, covering 72% of the sequence. Similarity searches revealed that 124 ORFs (30%) correspond to genes of known function, 51 ORFs (12.5%) appear to be homologues of genes whose functions are known, 52 others (12.5%) have homologues the functions of which are not well defined and another 33 of the novel putative genes (8%) exhibit a degree of similarity which is insufficient to confidently assign function. Of the genes on chromosome II, 37-45% are thus of unpredicted function. Among the novel putative genes, we found several that are related to genes that perform differentiated functions in multicellular organisms of are involved in malignancy. In addition to a compact arrangement of potential protein coding sequences, the analysis of this chromosome confirmed general chromosome patterns but also revealed particular novel features of chromosomal organization. Alternating regional variations in average base composition correlate with variations in local gene density along chromosome II, as observed in chromosomes XI and III. We propose that functional ARS elements are preferably located in the AT-rich regions that have a spacing of approximately 110 kb. Similarly, the 13 tRNA genes and the three Ty elements of chromosome II are found in AT-rich regions. In chromosome II, the distribution of coding sequences between the two strands is biased, with a ratio of 1.3:1. An interesting aspect regarding the evolution of the eukaryotic genome is the finding that chromosome II has a high degree of internal genetic redundancy, amounting to 16% of the coding capacity.

MeSH Terms
Base Composition Base Sequence Chromosome Mapping/methods Chromosomes, Fungal/genetics Cloning, Molecular Cosmids/genetics DNA, Fungal/genetics Genes, Fungal/genetics Molecular Sequence Data Open Reading Frames Quality Control Repetitive Sequences, Nucleic Acid Reproducibility of Results Saccharomyces cerevisiae/genetics Sequence Analysis, DNA Sequence Homology, Amino Acid Telomere/genetics
Chemicals
DNA, Fungal
Authors & Affiliations
97 authors, click to expand affiliations / ORCID
Feldmann H
Institut für Physiologische Chemie, Physikalische Biochemie und Zellbiologie, Universität München, Germany.
Aigle M
Aljinovic G
André B
Baclet M C
Barthe C
Baur A
Bécam A M
Biteau N
Boles E
Brandt T
Brendel M
Brückner M
Bussereau F
Christiansen C
Contreras R
Crouzet M
Cziepluch C
Démolis N
Delaveau T
Doignon F
Domdey H
Düsterhus S
Dubois E
Dujon B
El Bakkoury M
Entian K D
Feurmann M
Fiers W
Fobo G M
Fritz C
Gassenhuber H
Glandsdorff N
Goffeau A
Grivell L A
de Haan M
Hein C
Herbert C J
Hollenberg C P
Holmstrøm K
Jacq C
Jacquet M
Jauniaux J C
Jonniaux J L
Kallesøe T
Kiesau P
Kirchrath L
Kötter P
Korol S
Liebl S
Logghe M
Lohan A J
Louis E J
Li Z Y
Maat M J
Mallet L
Mannhaupt G
Messenguy F
Miosga T
Molemans F
Müller S
Nasr F
Obermaier B
Perea J
Piérard A
Piravandi E
Pohl F M
Pohl T M
Potier S
Proft M
Purnelle B
Ramezani Rad M
Rieger M
Rose M
Schaaff-Gerstenschläger I
Scherens B
Schwarzlose C
Skala J
Slonimski P P
Smits P H
Souciet J L
Steensma H Y
Stucka R
Urrestarazu A
van der Aart Q J
van Dyck L
Vassarotti A
Vetter I
Vierendeels F
Vissers S
Wagner G
de Wergifosse P
Wolfe K H
Zagulski M
Zimmermann F K
Mewes H W
Kleine K
References (69)
69 references, click to expand
  1. Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III.
    Mol Cell Biol. 1990 Aug;10(8):3917-25 PMID: 2196439
  2. Nested chromosomal fragmentation in yeast using the meganuclease I-Sce I: a new method for physical mapping of eukaryotic genomes.
    Nucleic Acids Res. 1992 Nov 11;20(21):5625-31 PMID: 1333585
  3. The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.
    Nucleic Acids Res. 1987 Feb 11;15(3):1281-95 PMID: 3547335
  4. Yeast chromosome replication and segregation.
    Microbiol Rev. 1988 Dec;52(4):568-601 PMID: 3070325
  5. The sequence of an 8 kb segment on the left arm of chromosome II from Saccharomyces cerevisiae identifies five new open reading frames of unknown functions, two tRNA genes and two transposable elements.
    Yeast. 1992 Sep;8(9):777-85 PMID: 1332308
  6. Sequencing and functional analysis of a 32,560 bp segment on the left arm of yeast chromosome II. Identification of 26 open reading frames, including the KIP1 and SEC17 genes.
    Yeast. 1993 Dec;9(12):1355-71 PMID: 8154187
  7. CODONS: a microcomputer program for codon usage analysis.
    J Hered. 1992 May-Jun;83(3):239-40 PMID: 1624775
  8. Improved tools for biological sequence comparison.
    Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444-8 PMID: 3162770
  9. A question of time: replication origins of eukaryotic chromosomes.
    Cell. 1992 Oct 30;71(3):363-6 PMID: 1423601
  10. The complete sequence of a 19,482 bp segment located on the right arm of chromosome II from Saccharomyces cerevisiae.
    Yeast. 1993 Feb;9(2):189-99 PMID: 8465606
  11. Sequencing the yeast genome: the European effort.
    Trends Biotechnol. 1992 Jan-Feb;10(1-2):15-8 PMID: 1367925
  12. The chromosome end in yeast: its mosaic nature and influence on recombinational dynamics.
    Genetics. 1994 Mar;136(3):789-802 PMID: 8005434
  13. A 12.8 kb segment, on the right arm of chromosome II from Saccharomyces cerevisiae including part of the DUR1,2 gene, contains five putative new genes.
    Yeast. 1993 Jul;9(7):797-806 PMID: 8368014
  14. Sequence analysis of a 31 kb DNA fragment from the right arm of Saccharomyces cerevisiae chromosome II.
    Yeast. 1994 Jul;10(7):959-64 PMID: 7985423
  15. At least three distinct proteins are necessary for the reconstitution of a specific multiprotein complex at a eukaryotic chromosomal origin of replication.
    Proc Natl Acad Sci U S A. 1992 Dec 1;89(23):11156-60 PMID: 1454793
  16. Chromosomal ARS and CEN elements bind specifically to the yeast nuclear scaffold.
    Cell. 1988 Sep 23;54(7):967-78 PMID: 2843296
  17. An 11.4 kb DNA segment on the left arm of yeast chromosome II carries the carboxypeptidase Y sorting gene PEP1, as well as ACH1, FUS3 and a putative ARS.
    Yeast. 1992 Sep;8(9):769-76 PMID: 1441754
  18. Sequence and function analysis of a 2.73 kb fragment of Saccharomyces cerevisiae chromosome II.
    Yeast. 1993 Nov;9(11):1273-7 PMID: 8109177
  19. The effect on chromosome stability of deleting replication origins.
    Mol Cell Biol. 1993 Jan;13(1):391-8 PMID: 8417338
  20. How many yeast genes code for membrane-spanning proteins?
    Yeast. 1993 Jul;9(7):691-702 PMID: 8368003
  21. Sequence of a 12.7 kb segment of yeast chromosome II identifies a PDR-like gene and several new open reading frames.
    Yeast. 1992 Sep;8(9):761-8 PMID: 1441753
  22. Corrected sequence for the right telomere of Saccharomyces cerevisiae chromosome III.
    Yeast. 1994 Feb;10(2):271-4 PMID: 8203168
  23. PIM1 encodes a mitochondrial ATP-dependent protease that is required for mitochondrial function in the yeast Saccharomyces cerevisiae.
    J Biol Chem. 1994 Jan 7;269(1):238-42 PMID: 8276800
  24. YBR1012 an essential gene from S. cerevisiae: construction of an RNA antisense conditional allele and isolation of a multicopy suppressor.
    C R Acad Sci III. 1994 Jul;317(7):607-13 PMID: 7882146
  25. Hotspots for unselected Ty1 transposition events on yeast chromosome III are near tRNA genes and LTR sequences.
    Cell. 1993 Jun 4;73(5):1007-18 PMID: 8388781
  26. A yeast chromosomal origin of DNA replication defined by multiple functional elements.
    Science. 1992 Feb 14;255(5046):817-23 PMID: 1536007
  27. The complete sequence of a 33 kb fragment on the right arm of chromosome II from Saccharomyces cerevisiae reveals 16 open reading frames, including ten new open reading frames, five previously identified genes and a homologue of the SCO1 gene.
    Yeast. 1994 Apr;10 Suppl A:S75-80 PMID: 8091864
  28. Approaching the function of new genes by detection of their potential upstream activation sequences in Saccharomyces cerevisiae: application to chromosome III.
    Curr Genet. 1994 May;25(5):396-406 PMID: 8082184
  29. Genetic and physical maps of Saccharomyces cerevisiae, Edition 11.
    Yeast. 1992 Oct;8(10):817-902 PMID: 1413997
  30. The complete sequence of the 8.2 kb segment left of MAT on chromosome III reveals five ORFs, including a gene for a yeast ribokinase.
    Yeast. 1990 Nov-Dec;6(6):521-34 PMID: 1964349
  31. Analysis of a 70 kb region on the right arm of yeast chromosome II.
    Yeast. 1994 Oct;10(10):1363-81 PMID: 7900426
  32. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex.
    Nature. 1992 May 14;357(6374):128-34 PMID: 1579162
  33. Basic local alignment search tool.
    J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712
  34. The isochore organization of the human genome and its evolutionary history--a review.
    Gene. 1993 Dec 15;135(1-2):57-66 PMID: 8276279
  35. Regional base composition variation along yeast chromosome III: evolution of chromosome primary structure.
    Nucleic Acids Res. 1993 Jan 25;21(2):179-83 PMID: 8441625
  36. A comprehensive set of sequence analysis programs for the VAX.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387-95 PMID: 6546423
  37. TKL2, a second transketolase gene of Saccharomyces cerevisiae. Cloning, sequence and deletion analysis of the gene.
    Eur J Biochem. 1993 Oct 1;217(1):487-92 PMID: 7916691
  38. The sequence of an 8.8 kb segment on the left arm of chromosome II from Saccharomyces cerevisiae reveals four new open reading frames including homologs of animal DNA polymerase alpha-primases and bacterial GTP cyclohydrolase II.
    Yeast. 1994 Apr;10 Suppl A:S13-24 PMID: 8091857
  39. Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes.
    Science. 1992 Aug 7;257(5071):771-8 PMID: 1379743
  40. The complete sequence of a 6794 bp segment located on the right arm of chromosome II of Saccharomyces cerevisiae. Finding of a putative dUTPase in a yeast.
    Yeast. 1993 Oct;9(10):1131-7 PMID: 8256522
  41. A putative P-type Cu(2+)-transporting ATPase gene on chromosome II of Saccharomyces cerevisiae.
    Yeast. 1994 Sep;10(9):1217-25 PMID: 7754711
  42. RIM2, MSI1 and PGI1 are located within an 8 kb segment of Saccharomyces cerevisiae chromosome II, which also contains the putative ribosomal gene L21 and a new putative essential gene with a leucine zipper motif.
    Yeast. 1993 Jun;9(6):645-59 PMID: 8346681
  43. The project of sequencing the entire Bacillus subtilis genome.
    Res Microbiol. 1991 Sep-Oct;142(7-8):905-12 PMID: 1784829
  44. Telomere maintenance and gene repression: a common end?
    Curr Opin Cell Biol. 1994 Jun;6(3):373-9 PMID: 7917328
  45. Yeast. Genes in search of functions.
    Nature. 1994 May 12;369(6476):101-2 PMID: 8177314
  46. Cycloheximide-resistant temperature-sensitive lethal mutations of Saccharomyces cerevisiae.
    Genetics. 1988 Jun;119(2):303-15 PMID: 3294103
  47. Discovering simple DNA sequences by the algorithmic significance method.
    Comput Appl Biosci. 1993 Aug;9(4):407-11 PMID: 8402207
  48. Sequence around the centromere of Saccharomyces cerevisiae chromosome II: similarity of CEN2 to CEN4.
    Yeast. 1994 Apr;10 Suppl A:S41-6 PMID: 8091860
  49. The sequence of 12.5 kb from the right arm of chromosome II predicts a new N-terminal sequence for the IRA1 protein and reveals two new genes, one of which is a DEAD-box helicase.
    Yeast. 1994 Sep;10(9):1227-34 PMID: 7754712
  50. Sequence of a 4.8 kb fragment of Saccharomyces cerevisiae chromosome II including three essential open reading frames.
    Yeast. 1993 Mar;9(3):289-93 PMID: 8488729
  51. Specific interaction between a Saccharomyces cerevisiae protein and a DNA element associated with certain autonomously replicating sequences.
    Proc Natl Acad Sci U S A. 1988 Feb;85(3):743-6 PMID: 3277180
  52. Sequence and function analysis of a 4.3 kb fragment of Saccharomyces cerevisiae chromosome II including three open reading frames.
    Yeast. 1993 Aug;9(8):915-21 PMID: 8212898
  53. Analysis of yeast chromosomal regions carrying members of the glutamate tRNA gene family: various transposable elements are associated with them.
    Nucleic Acids Res. 1988 Nov 25;16(22):10623-34 PMID: 2849751
  54. Nucleotide sequence of the first cosmid from the Mycobacterium leprae genome project: structure and function of the Rif-Str regions.
    Mol Microbiol. 1993 Jan;7(2):207-14 PMID: 8446028
  55. The complete DNA sequence of yeast chromosome III.
    Nature. 1992 May 7;357(6373):38-46 PMID: 1574125
  56. Nucleotide sequence analysis of an 11.7 kb fragment of yeast chromosome II including BEM1, a new gene of the WD-40 repeat family and a new member of the KRE2/MNT1 family.
    Yeast. 1994 Jun;10(6):819-31 PMID: 7975899
  57. An alternative pathway for yeast telomere maintenance rescues est1- senescence.
    Cell. 1993 Apr 23;73(2):347-60 PMID: 8477448
  58. The membrane proteins encoded by yeast chromosome III genes.
    FEBS Lett. 1993 Jun 28;325(1-2):112-7 PMID: 8513882
  59. PDR3, a new yeast regulatory gene, is homologous to PDR1 and controls the multidrug resistance phenomenon.
    Mol Gen Genet. 1994 Sep 1;244(5):501-11 PMID: 8078477
  60. Arabidopsis thaliana and Plant Molecular Genetics.
    Science. 1985 Sep 20;229(4719):1214-8 PMID: 17770799
  61. The two genes encoding yeast ribosomal protein S8 reside on different chromosomes, and are closely linked to the hsp70 stress protein genes SSA3 and SSA4.
    Yeast. 1994 Aug;10(8):1093-1100 PMID: 7992509
  62. Compilation of tRNA sequences and sequences of tRNA genes.
    Nucleic Acids Res. 1993 Jul 1;21(13):3011-5 PMID: 7687348
  63. Mapping of the Saccharomyces cerevisiae CDC3, CDC25, and CDC42 genes to chromosome XII by chromosome blotting and tetrad analysis.
    Yeast. 1987 Dec;3(4):243-53 PMID: 3332976
  64. An analysis of the sequence of part of the right arm of chromosome II of S. cerevisiae reveals new genes encoding an amino-acid permease and a carboxypeptidase.
    Curr Genet. 1994 Jul;26(1):1-7 PMID: 7954890
  65. The telomere-associated MAL3 locus of Saccharomyces is a tandem array of repeated genes.
    Yeast. 1992 Aug;8(8):655-65 PMID: 1441745
  66. Complete DNA sequence of yeast chromosome XI.
    Nature. 1994 Jun 2;369(6479):371-8 PMID: 8196765
  67. The detection and classification of membrane-spanning proteins.
    Biochim Biophys Acta. 1985 May 28;815(3):468-76 PMID: 3838905
  68. 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans.
    Nature. 1994 Mar 3;368(6466):32-8 PMID: 7906398
  69. Transformation of intact yeast cells treated with alkali cations.
    J Bacteriol. 1983 Jan;153(1):163-8 PMID: 6336730
Article Info
Journal
The EMBO journal
Abbr.
EMBO J
ISSN
0261-4189
Published
1994-12-15
Pages
5795-809
Language
English
Region
England
NLM ID
8208664
PMCID
PMC395553
Subset
IM
Databases
GENBANK
Z35762, Z35763, Z35764, Z35765, Z35766, Z35767, Z35768, Z35769, Z35770, Z35771, Z35773, Z35774, Z35775, Z35776, Z35777, Z35778, Z35779, Z35780, Z35781, Z35782, Z35783, Z35784, Z35785, Z35786, Z35787, Z35788, Z35789, Z35790, Z35791, Z35792
External Links
PubMed source PMC Full Text View journal details
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