Home LiteratureArticle Details
PMID: 12907728 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

The sequence and analysis of Trypanosoma brucei chromosome II.

Nucleic acids research ·Vol. 31 ·No. 16 ·2003-08-15 ·Pages 4856-63

El-Sayed NM, Ghedin E, Song J, MacLeod A, Bringaud F, Larkin C, Wanless D, Peterson J, Hou L, Taylor S, Tweedie A, Biteau N, Khalak HG, Lin X, Mason T, Hannick L, Caler E, Blandin G, Bartholomeu D, Simpson AJ, Kaul S, Zhao H, Pai G, Van Aken S, Utterback T, Haas B, Koo HL, Umayam L, Suh B, Gerrard C, Leech V, Qi R, Zhou S, Schwartz D, Feldblyum T, Salzberg S, Tait A, Turner CM, Ullu E, White O, Melville S, Adams MD, Fraser CM, Donelson JE

Abstract

We report here the sequence of chromosome II from Trypanosoma brucei, the causative agent of African sleeping sickness. The 1.2-Mb pairs encode about 470 predicted genes organised in 17 directional clusters on either strand, the largest cluster of which has 92 genes lined up over a 284-kb region. An analysis of the GC skew reveals strand compositional asymmetries that coincide with the distribution of protein-coding genes, suggesting these asymmetries may be the result of transcription-coupled repair on coding versus non-coding strand. A 5-cM genetic map of the chromosome reveals recombinational 'hot' and 'cold' regions, the latter of which is predicted to include the putative centromere. One end of the chromosome consists of a 250-kb region almost exclusively composed of RHS (pseudo)genes that belong to a newly characterised multigene family containing a hot spot of insertion for retroelements. Interspersed with the RHS genes are a few copies of truncated RNA polymerase pseudogenes as well as expression site associated (pseudo)genes (ESAGs) 3 and 4, and 76 bp repeats. These features are reminiscent of a vestigial variant surface glycoprotein (VSG) gene expression site. The other end of the chromosome contains a 30-kb array of VSG genes, the majority of which are pseudogenes, suggesting that this region may be a site for modular de novo construction of VSG gene diversity during transposition/gene conversion events.

MeSH Terms
Animals Antigens, Protozoan/genetics Chromosome Mapping Chromosomes/genetics DNA, Protozoan/chemistry,genetics Gene Duplication Genes, Protozoan/genetics Molecular Sequence Data Pseudogenes/genetics Recombination, Genetic Sequence Analysis, DNA Trypanosoma brucei brucei/genetics
Chemicals
Antigens, Protozoan DNA, Protozoan
Authors & Affiliations
44 authors, click to expand affiliations / ORCID
El-Sayed Najib M A
The Institute for Genomic Research, Rockville, MD 20850, USA. [email protected]
Ghedin Elodie
Song Jinming
MacLeod Annette
Bringaud Frederic
Larkin Christopher
Wanless David
Peterson Jeremy
Hou Lihua
Taylor Sonya
Tweedie Alison
Biteau Nicolas
Khalak Hanif G
Lin Xiaoying
Mason Tanya
Hannick Linda
Caler Elisabet
Blandin Gaëlle
Bartholomeu Daniella
Simpson Anjana J
Kaul Samir
Zhao Hong
Pai Grace
Van Aken Susan
Utterback Teresa
Haas Brian
Koo Hean L
Umayam Lowell
Suh Bernard
Gerrard Caroline
Leech Vanessa
Qi Rong
Zhou Shiguo
Schwartz David
Feldblyum Tamara
Salzberg Steven
Tait Andrew
Turner C Michael R
Ullu Elisabetta
White Owen
Melville Sara
Adams Mark D
Fraser Claire M
Donelson John E
References (46)
46 references, click to expand
  1. Inactivation of transcription by UV irradiation of T. brucei provides evidence for a multicistronic transcription unit including a VSG gene.
    Cell. 1987 Oct 23;51(2):273-81 PMID: 3664637
  2. Genetic and physical maps of Saccharomyces cerevisiae, Edition 11.
    Yeast. 1992 Oct;8(10):817-902 PMID: 1413997
  3. Asymmetries generated by transcription-coupled repair in enterobacterial genes.
    Science. 1996 Apr 5;272(5258):107-9 PMID: 8600517
  4. Asymmetric substitution patterns in the two DNA strands of bacteria.
    Mol Biol Evol. 1996 May;13(5):660-5 PMID: 8676740
  5. A new strategy for genome sequencing.
    Nature. 1996 May 30;381(6581):364-6 PMID: 8632789
  6. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
    Protein Eng. 1997 Jan;10(1):1-6 PMID: 9051728
  7. Molecular evidence for an ancient duplication of the entire yeast genome.
    Nature. 1997 Jun 12;387(6634):708-13 PMID: 9192896
  8. Strand compositional asymmetry in bacterial and large viral genomes.
    Proc Natl Acad Sci U S A. 1998 Mar 31;95(7):3720-5 PMID: 9520433
  9. Correlation between transcription and C to T mutations in the non-transcribed DNA strand.
    Biol Chem. 1998 Apr-May;379(4-5):549-51 PMID: 9628351
  10. The molecular karyotype of the megabase chromosomes of Trypanosoma brucei and the assignment of chromosome markers.
    Mol Biochem Parasitol. 1998 Aug 1;94(2):155-73 PMID: 9747967
  11. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes.
    J Mol Evol. 1998 Dec;47(6):691-6 PMID: 9847411
  12. Tandem repeats finder: a program to analyze DNA sequences.
    Nucleic Acids Res. 1999 Jan 15;27(2):573-80 PMID: 9862982
  13. Leishmania major Friedlin chromosome 1 has an unusual distribution of protein-coding genes.
    Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2902-6 PMID: 10077609
  14. The fall and rise of sleeping sickness.
    Lancet. 1999 Apr 3;353(9159):1113-4 PMID: 10209970
  15. Genetic exchange in the trypanosomatidae.
    Adv Parasitol. 1999;43:1-46 PMID: 10214689
  16. Multiple causes of size variation in the diploid megabase chromosomes of African tyrpanosomes.
    Chromosome Res. 1999;7(3):191-203 PMID: 10421379
  17. Predominance of duplicative VSG gene conversion in antigenic variation in African trypanosomes.
    Mol Cell Biol. 1999 Sep;19(9):5839-46 PMID: 10454531
  18. Improved microbial gene identification with GLIMMER.
    Nucleic Acids Res. 1999 Dec 1;27(23):4636-41 PMID: 10556321
  19. Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms.
    Gene. 1999 Sep 30;238(1):65-77 PMID: 10570985
  20. Genome organization in dicots: genome duplication in Arabidopsis and synteny between soybean and Arabidopsis.
    Proc Natl Acad Sci U S A. 2000 Apr 11;97(8):4168-73 PMID: 10759555
  21. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
    Nat Genet. 2000 May;25(1):25-9 PMID: 10802651
  22. The unusual gene organization of Leishmania major chromosome 1 may reflect novel transcription processes.
    Nucleic Acids Res. 2000 Jul 15;28(14):2800-3 PMID: 10908338
  23. Minisatellite marker analysis of Trypanosoma brucei: reconciliation of clonal, panmictic, and epidemic population genetic structures.
    Proc Natl Acad Sci U S A. 2000 Nov 21;97(24):13442-7 PMID: 11078512
  24. The InterPro database, an integrated documentation resource for protein families, domains and functional sites.
    Nucleic Acids Res. 2001 Jan 1;29(1):37-40 PMID: 11125043
  25. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.
    J Mol Biol. 2001 Jan 19;305(3):567-80 PMID: 11152613
  26. Characterisation of the growth and differentiation in vivo and in vitro-of bloodstream-form Trypanosoma brucei strain TREU 927.
    Mol Biochem Parasitol. 2001 Feb;112(2):163-71 PMID: 11223123
  27. Control of VSG gene expression sites.
    Mol Biochem Parasitol. 2001 Apr 25;114(1):17-27 PMID: 11356510
  28. Antigenic variation in trypanosomes: enhanced phenotypic variation in a eukaryotic parasite.
    Adv Parasitol. 2001;49:1-70 PMID: 11461029
  29. The Pfam protein families database.
    Nucleic Acids Res. 2002 Jan 1;30(1):276-80 PMID: 11752314
  30. The architecture of variant surface glycoprotein gene expression sites in Trypanosoma brucei.
    Mol Biochem Parasitol. 2002 Jul;122(2):131-40 PMID: 12106867
  31. Life without transcriptional control? From fly to man and back again.
    EMBO J. 2002 Apr 15;21(8):1881-8 PMID: 11953307
  32. Genetic analysis of phenotype in Trypanosoma brucei: a classical approach to potentially complex traits.
    Philos Trans R Soc Lond B Biol Sci. 2002 Jan 29;357(1417):89-99 PMID: 11839186
  33. RNA editing: complexity and complications.
    Mol Microbiol. 2002 Aug;45(3):591-6 PMID: 12139607
  34. A new, expressed multigene family containing a hot spot for insertion of retroelements is associated with polymorphic subtelomeric regions of Trypanosoma brucei.
    Eukaryot Cell. 2002 Feb;1(1):137-51 PMID: 12455980
  35. The temporal distribution of gene duplication events in a set of highly conserved human gene families.
    Mol Biol Evol. 2003 Jan;20(1):154-61 PMID: 12519918
  36. Yeast genome duplication was followed by asynchronous differentiation of duplicated genes.
    Nature. 2003 Feb 20;421(6925):848-52 PMID: 12594514
  37. The DNA sequence of chromosome I of an African trypanosome: gene content, chromosome organisation, recombination and polymorphism.
    Nucleic Acids Res. 2003 Aug 15;31(16):4864-73 PMID: 12907729
  38. An analysis of cosmid clones of nuclear DNA from Trypanosoma brucei shows that the genes for variant surface glycoproteins are clustered in the genome.
    Nucleic Acids Res. 1982 Oct 11;10(19):5905-23 PMID: 6292859
  39. Transcripts coding for variant surface glycoproteins of Trypanosoma brucei have a short, identical exon at their 5' end.
    Gene. 1982 Dec;20(2):281-9 PMID: 7166234
  40. Gene conversion as a mechanism for antigenic variation in trypanosomes.
    Cell. 1983 Sep;34(2):371-81 PMID: 6616615
  41. Modifications of a Trypanosoma b. brucei antigen gene repertoire by different DNA recombinational mechanisms.
    Cell. 1983 Dec;35(3 Pt 2):721-31 PMID: 6197182
  42. Expression of whole and hybrid genes in Trypanosoma equiperdum antigenic variation.
    EMBO J. 1986 May;5(5):1057-63 PMID: 3013613
  43. The use of incomplete genes for the construction of a Trypanosoma equiperdum variant surface glycoprotein gene.
    EMBO J. 1986 May;5(5):1065-70 PMID: 3013614
  44. The 35-nucleotide spliced leader sequence is common to all trypanosome messenger RNA's.
    Science. 1986 Aug 1;233(4763):569-71 PMID: 3523758
  45. Antigenic diversity by the recombination of pseudogenes.
    Genes Dev. 1989 Aug;3(8):1247-54 PMID: 2792762
  46. Evidence that the mechanism of gene exchange in Trypanosoma brucei involves meiosis and syngamy.
    Parasitology. 1990 Dec;101 Pt 3:377-86 PMID: 1982633
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkg673
Email
[email protected]
Published
2003-08-15
Pages
4856-63
Language
English
Region
England
NLM ID
0411011
PMCID
PMC169936
Subset
IM
Grants
Wellcome Trust · United Kingdom
NIAID NIH HHS · R01 AI043062 · United States
NIAID NIH HHS · U01 AI043062 · United States
NIAID NIH HHS · U01 AI43062 · United States
Databases
GENBANK
AC007862, AC007864, AC007865, AC007866, AC008031, AC008368, AC009463, AC012647, AC073246, AC079606, AE017150
External Links
PubMed source DOI: 10.1093/nar/gkg673 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2