Lister 427 VSG summary

 

MITat1

Preferred name1

Lab of origin2

Local Names3

Copies4

BES5

GenBank Number

Comments6

1.1

Lister 427-1

Cross

060

?

 

X56761

Genbank sequence by Carrington Lab

1.2

Lister 427-2

Cross

221

1

1

X56762

Genbank sequence by Carrington Lab

1.3

Lister 427-3

Cross

224 (Luisa 17.9)

2

6 & 7

AY935575

Genbank sequence by Cross Lab

1.4

Lister 427-4

Cross

117

>5

 

V01387

Genbank sequence by Cross Lab

1.5

Lister 427-5

Cross

118

2

 

X56763

Genbank sequence by Carrington Lab

1.6

Lister 427-6

Cross

121

4–5

3

X56764

Genbank sequence by Carrington Lab

1.7

Lister 427-7

Cross

055

?

 

AJ937311

Genbank sequence by Carrington Lab

1.8

Lister 427-8

Borst/Cross

1.8 (Dreesen OD1)

?

12 & 14??

AY935574

Genbank sequence by Cross Lab

1.9

Lister 427-9

Borst/Cross

Luisa 17. 23 (Borst VO2)

2

2

AY935573

Genbank sequence by Cross Lab

1.10

Lister 427-10

Cross

VSG K (Navarro)

?

 

no sequence

 

1.11

Lister 427-11

Cross

bR2 (Davies)

2–3

15

AY935571

Genbank sequence by Cross Lab

1.12

Lister 427-12

Cross

Oliver 501c2 (Navarro B)

?

 

AY935577

Genbank sequence by Cross Lab

1.13

Lister 427-13

Cross

Luisa 17.13

2

17

AY935576

Genbank sequence by Cross Lab

1.14

Lister 427-14

Rudenko

TAR64

 

8

FM162575

Sanger sequencing

1.15

Lister 427-15

Rudenko

TAR134

 

10

FM162576

Sanger sequencing

1.16

Lister 427-16

Rudenko

TAR122

 

11

FM162577

Sanger sequencing

1.17

Lister 427-17

Cross

Luisa 17.7 (Rudenko JS1)

1

13

DQ826504

Genbank sequence by Cross Lab

1.18

Lister 427-18

Cross/Hajduk

Luisa 17.22 (Hajduk 800)

?

5

DQ826505

DQ667685

Genbank sequence by Cross Lab (top) Hajduk sequence (bottom)

1.19

Lister 427-19

Rudenko

TAR10

 

14

FM162580

Sanger sequencing

1.20

Lister 427-20

 

 

 

 

 

To be assigned

1.21

Lister 427-21

Cross

Luisa 17.21 (Horn T3)

2/3

4

AY935572

Genbank sequence by Cross Lab

 

1.22

Lister 427-22

Borst/Clayton

222

?

 

AJ007019

Genbank sequence by Clayton Lab

1.23

Lister 427-23

Papavasiliou

28

1

MC

FJ798214

Papavasiliou Lab

1.24

Lister 427-24

Papavasiliou

31

1

MC

FJ798212

Papavasiliou Lab

1.25

Lister 427-25

Papavasiliou

42

1

MC

FJ798213

Papavasiliou Lab

1.26

Lister 427-26

 

 

 

 

 

To be assigned

1.27

Lister 427-27

 

 

 

 

 

To be assigned

1.28

Lister 427-28

 

 

 

 

 

To be assigned

1.29

Lister 427-29

 

 

 

 

 

To be assigned

1.30

Lister 427-30

Gull

S8

1

MC

AF294806

Genbank sequence by Gull Lab. Absent from our cells.

1.31

Lister 427-31

Gull

G4

?

MC

AF294807

Genbank sequence by Gull Lab. Multi-copy (most on MCs)

 

 

Rudenko

NA1

?

 

 

identified in 2005 Mol Micro paper

 

 

 

 

 

 

 

 

                                                   

                                               

Comments omitted from edited GenBank files of our newly submitted sequences

New entries from our lab, unless otherwise annotated, were amplified by RT-PCR using primers corresponding  to the 5« spliced leader and the VSG 3« UTR conserved 14-mer (for protocol see our web site), both of which  are excluded from the sequence shown, which starts at the first nt following  the spliced leader and ends before the first nt of the conserved 3« UTR sequence.

MITat 1.3: Originally identified as clone 224, isolated in 1978 by E.N.  Miller and M.J. Turner (unpublished) as a relapse from clone 221 (MITat 1.2).  VSG purified and characterized by G.A.M. Cross (1979, unpublished).

MITat 1.8: Short 3' end sequence previously reported  (Accession X00625). Michels, P.A.M., van der Ploeg, L.H.T., Liu, A.Y.C. and  Borst, P. (1984) The inactivation and reactivation of an expression-linked  gene copy for a variant surface glycoprotein in Trypanosoma brucei. EMBO J.,  3, 1345-1351.

MITat 1.9: VSG MITat 1.9 sequence previously unpublished  and referred to as VSG VO2, but its expression and chromosomal location have  been described in several papers, the most relevant of which are the two  following.~~Rudenko, G., Chaves, I., Dirks-Mulder, A. and Borst, P. (1998)  Selection for activation of a new variant surface glycoprotein gene  expression site in Trypanosoma brucei can result in deletion of the old one.  Mol. Biochem. Parasitol., 95, 97-109.~~Berriman, M., Hall, N., Sheader, K.,  Bringaud, F., Tiwari, B., Isobe, T., Bowman, S., Corton, C., Clark, L.,  Cross, G.A.M., Hoek, M., Zanders, T., Berberof, M., Borst, P. and Rudenko, G.  (2002) The architecture of variant surface glycoprotein gene expression sites  in Trypanosoma brucei. Mol. Biochem. Parasitol., 122, 131-140.

MITat 1.11: Originally identified as VSG bR2  (Liu, A.Y.,  Michels, P.A., Bernards, A. and Borst, P. (1985) Trypanosome variant surface  glycoprotein genes expressed early in infection. J. Mol. Biol., 175,  383-386).~~Further characterized by Davies, K.P., Carruthers, V.B. and Cross,  G.A.M. (1997) Manipulation of the VSG co-transposed region increases  expression-site switching in Trypanosoma brucei. Mol. Biochem. Parasitol.,  86, 163-177.~~Horn, D. and Cross, G.A.M. (1997) Analysis of Trypanosoma  brucei vsg expression site switching in vitro. Mol. Biochem. Parasitol., 84,  189-201.~~Partly sequenced previously (Davies, K. and Cross, G.A.M.  unpublished).

MITat 1.12: Corresponds to vsgB (Navarro and Cross,  unpublished partial sequence) in Navarro, M. and Cross, G.A.M. (1996) DNA  rearrangements associated with multiple consecutive directed antigenic  switches in Trypanosoma brucei. Mol. Cell. Biol., 16, 3615-3625.

MITat 1.21: Previous partial sequence D. Horn and G.A.M. Cross, unpublished.

 

Footnotes:

1     Although only the original 8 MITat numbers strictly fit the definition for this ÔatÕ-based nomenclature, in being characterized at the Molteno Institute, ÔghostÕ MITat numbers have been assigned to all Lister 427 VSGs. I would much prefer to adopt a strain-designated number. The ancient ÔatÕ system was never satisfactory and is currently totally inappropriate and inadequate as it tags the variant types to particular labs, and it is based on polyvalent phenotyping reagents (antibodies) that do not necessarily resolve genotypes. It is not linked to the genotype! An alternative system would refer to the expressed genotype: Lister 427-13.2, for example, for the variant 13 family gene 2. The gene number only has to be used if it is really necessary to distinguish a particular member of the family and the number can be omitted from the prototype.

2     The lab in which this variant was first characterized plus, if different, the lab from which the complete gene sequence was determined.

3     LabÕs ÔpetÕ name, usually corresponding to or based upon a clone number.

4     The number of copies is likely to vary depending on propagation history among different labs.

5     ES numbers in red indicate Intermediate Chromosome

6     Unless a TAR clone is mentioned, the GenBank sequences are for cDNA. TAR clones are cloned expression sites sequenced by the Sanger Institute.