Epstein-Barr Virus Protocols

394 Pages·2010·2.271 MB·English

by  Joanna B. Wilson, Gerhard H. W. May

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EBV: B95-8 Strain Map 3
1
Epstein-Barr Virus
The B95-8 Strain Map
Paul J. Farrell
1. Introduction
This chapter summarizes the genes and mRNAs that have been mapped on to the
B95-8 EBV genome. The complete sequence of this strain of Epstein-Barr Virus (EBV)
was established (1,2) and data from many publications has been integrated into the
map, which is an update of that published previously (3). The B95-8 strain grows well
in laboratory culture and transforms human B lymphocytes efficiently, but B95-8 EBV
has about 11.8 kb deleted relative to other strains of EBV. The sequence of that region
has been determined in the Raji strain of EBV and a map has been published (4).
Detailed literature citations for most of the features have been published (3). The map
should be used in conjunction with the B95-8 EBV DNA sequence, which can be
accessed in the European Molecular Biology Laboratory (EMBL; embl:ebv.seq) or
Genbank databases. The feature tables shown in those database files have not yet been
revised so the information shown in this map is considerably more up to date.
2. Repeat Sequences
There are several regions of the genome that contain tandem repeat sequences.
Some of these are large repeat units (for example, the major internal repeat is 3072 bp
and the terminal repeat is 538 bp) but some are much simpler repeats. In most virus
preparations, there will be a distribution of copy number of these repeats, so it is impor-
tant to appreciate that the viral map and coordinates are just one reference example of
genome structure. Generally the repeat numbers in the B95-8 map are thought to be
typical, although it now appears that the 11.5 copies of the major internal repeat
inserted into the B95-8 sequence may be an over-estimate, about 8.5 being more usual
in B95-8 EBV (5).
The restriction maps for EcoRI and BamHI are shown beneath the scale bar in kb.
The restriction fragments are labeled according to size, A being the largest fragment
From:Methods in Molecular Biology, Vol. 174:Epstein-Barr Virus Protocols
Edited by: J. B. Wilson and G. H. W. May © Humana Press Inc., Totowa, NJ
3
4 Farrell
Table 1
EBV Gene Nomenclature
EBNA-3A EBNA-3
EBNA-3B EBNA-4
EBNA-3C EBNA-6
EBNA-LP EBNA-5
LMP-2A TP-1
LMP-2B TP-2
BZLF1 ZEBRA, EB1, Zta
BRLF1 Rta, R
BARF transcripts BART, CST
EBNA, Epstein-Barr virus nuclear antigen; LMP,
latent membrane protein; TP, terminal protein; BART,
Bam A rightward transcripts; CST, complementary
strand transcripts.
and lower case letters being used for additional fragments when there are more
than26.
3. Open Reading Frames
The major open reading frames, presumed to correspond to the protein coding parts
of genes are shown as boxes, pointed at one end to indicate the direction of translation.
Coordinates shown below are generally from the presumed initiator methionine to the
last translated amino acid. When there is no obvious initiator methionine or the RNA
structure is uncertain, the coordinates of the reading frame are shown from the begin-
ning of the open reading frame to the last translated amino acid; these reading frames
are marked “orf” after the coordinates. Initiator methionine residues have generally
not been confirmed by mutagenesis so it is important to appreciate that the map is an
interpretation in this respect.
4. Nomenclature
Open reading frames of EBV are named systematically according to the BamHI
restriction fragment in which their transcription commences, designated L or R accord-
ing to the direction and then marked F followed by a number. So BALF4 is the fourth
leftward reading frame commencing in the BamHI A restriction fragment. Many of the
genes are also known by more common and useful names, which may describe their
function. Abbreviations used here are EBNA, Epstein-Barr virus nuclear antigen,
LMP, latent membrane protein, EBER, Epstein-Barr virus encoded RNA. There is
unfortunately some variation in nomenclature for EBV genes in the published litera-
ture. A guide to equivalents is shown in Table 1; terms on the same horizontal line
refer to the same gene that shown on the left, being the standard used in this map.
5. Gene Expression
The open reading frames are shaded according to their expression class. These
classes are defined operationally in EBV. Latent cycle genes are expressed constitu-
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