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Nucleic Acids Research Pages 295-296  

SV40 large tumor antigen (T antigen): database of mutants
Introduction
Database Information
Database Availability
Acknowledgements
References

SV40 large tumor antigen (T antigen): database of mutants

SV40 large tumor antigen (T antigen): database of mutants

Clifford G. Robinson, James M. Pipas*

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA

Received October 23, 1997; Accepted October 24, 1997

ABSTRACT

The SV40 T antigen database (http://www.pitt.edu/~pipaslab/ ) lists viruses and plasmids expressing mutant forms of large T antigen. Each entry contains information regarding the mutant designation, mutant type, virus strain, nucleotide change, amino acid change and pertinent references. The database is now available as an internet searchable index.

INTRODUCTION

The large tumor antigen (T antigen) encoded by simian virus 40 (SV40) is truly a marvelous molecule. This 708 amino acid protein is essential for numerous steps in viral productive infection including viral DNA replication, transcription control and virion assembly. In addition, T antigen is capable of inducing tumors in animals, and thus, is a viral oncogene. Because SV40 contains such a simple genome (5243 bp) encoding just six or seven gene products, it has been utilized extensively as a model system. During the course of these studies many laboratories have generated SV40 mutants that encode for altered T antigens.

DATABASE INFORMATION

We have created a database listing many of the published SV40 mutants. Entries within the database represent mutations constructed in vitro and several isolated from cell culture systems. The parental wild-type SV40 strain and nucleotide sequence changes are listed where possible. Entries exist for mutations that result in either premature chain termination, deletion, substitution, duplication, insertion or gene fusion.

The database was originally created using FileMaker Pro 2.0 for the Macintosh, and contains entries for 498 mutants (1). The bulk of the information comes from published mutations that have been sequenced. In situations where the mutations are not published, an indication is made in the references field. The database is now available as a searchable index on the World Wide Web, complete with interactive submission form for new entries.

The FileMaker Pro database itself is composed of six data entry fields as follows.


Figure 1 Screenshot of the search engine front end.


Field One (mutant designation). This field contains the name given to a particular T antigen mutant by the laboratory which created it. (dl 2456, Ad2+ND2 56K, etc.)

Field Two (mutant type). This field contains the type of mutation (substitution, deletion, truncation, insertion, deletion/trunctation, C-terminal fragment).

Field Three (parental virus strain). This field contains the parental SV40 viral strain for each T antigen mutant (e.g. 776, VA45-54, 777, SV-S, WT830, Baylor, NR).

Field Four (nucleotide change). This field contains information on how the T antigen coding sequence has been affected by each mutation. The limits of each nucleotide change(s) are shown using the numbering system of Tooze (2). Several abbreviations are used; dl = deletion, ins = insertion, bp = base pair, and > = nucleotide change from the nucleotide indicated before the symbol to the nucleotide indicated after the symbol.

Field Five (amino acids affected). This field contains information on the effect of the indicated nucleotide change on the resulting encoded T antigen. The single letter amino acid code has been used in this field. Several abbreviations are used; dl = amino acid residues missing from the mutant large T antigen, ins = insertion, aa = amino acid residue, > = amino acid change from the residue indicated before the symbol to the residue indicated after the symbol, STOP = termination codon.

Field Six (reference). This field contains the number of the reference from which the information for a particular T antigen mutant was derived. For more information on a particular database entry, the indicated reference should be consulted.

DATABASE AVAILABILITY

The database is now available as a World Wide Web searchable index. The search engine front-end can be accessed at http://www.pitt.edu/~pipaslab/ . The database is also available as a Macintosh FileMaker Pro 3.0 document or hard copy printout from the authors.

Searching of the database is accomplished through a web based front-end (Fig. 1) linked to the FileMaker Pro database. The page is hosted on an Apple Macintosh computer running Star Nine's WebSTAR 2.1 and Blue World's Lasso ACGI script. Each one of the fields (see Database Information for field definitions) can be searched independently of the others, or together with another field to narrow down the results. The database can also be browsed without any search terms.


Figure 2 Screenshot of a sample search return using the browsing option.


Figure 3 Screenshot of a detail page for mutant 5005.

Output is generated on the fly by the Lasso ACGI script and sent to the web browser formatted according to the Sort and Return selections made from the search page. The mutant designation, mutant type and amino acid aberration are listed first (Fig. 2), and additional information (e.g., virus strain, nucleotide change and references) can be retrieved by clicking on the mutant designation (Fig. 3). Full documentation for basic and advanced searching is available on the web page.

Also available on the web page is an interactive submission form for new entries to the database. Use of Netscape 3.0.1 or greater is highly recommended since the form relies heavily on JavaScript. For users who do not have a JavaScript capable browser, an alternate submission form is available as well.

Researchers who make use of the web based T Antigen Mutant Database in their publications should cite this article.

ACKNOWLEDGEMENTS

This work was supported by NIH grant CA40586 and a grant from the Pittsburgh Supercomputer Center (MCB040031P) to J.M.P.

REFERENCES

1. Kierstead,T.D. and Pipas,J.M. (1996) Nucleic Acids Res., 24, 125-126. MEDLINE Abstract

2. Tooze,J. (1981) In Tooze,J. (ed.) DNA Tumor Viruses: Molecular Biology of Tumor Viruses. Second edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

*To whom correspondence should be addressed. Tel: +1 412 624 4691; Fax: +1 412 624 4759; Email: pipas+{at}pitt.edu

This page is run by Oxford University Press, Great Clarendon Street, Oxford OX2 6DP, as part of the OUP Journals Comments and feedback: www-admin{at}oup.co.uk
Last modification: 17 Dec 1997
Copyright© Oxford University Press, 1998.

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