PlantProm: A database of plant promoter sequences

Abstract

PlantProm DB, a plant promoter database, is an annotated, non-redundant collection of proximal promoter sequences for RNA
polymerase II with experimentally determined transcription start site(s), TSS, from various plant species. The first release
(2002.01) of PlantProm DB contains 305 entries including 71, 220 and 14 promoters from monocot, dicot and other plants, respectively.
It provides DNA sequence of the promoter regions (−200 : +51) with TSS on the fixed position +201, taxonomic/promoter type
classification of promoters and Nucleotide Frequency Matrices (NFM) for promoter elements: TATA-box, CCAAT-box and TSS-motif
(Inr). Analysis of TSS-motifs revealed that their composition is different in dicots and monocots, as well as for TATA and
TATA-less promoters. The database serves as learning set in developing plant promoter prediction programs. One such program
(TSSP) based on discriminant analysis has been created by Softberry Inc. and the application of a support ftp: vector machine
approach for promoter identification is under development. PlantProm DB is available at http://mendel.cs.rhul.ac.uk/ and http://www.softberry.com/.

Full text

PlantProm: a database of plant promoter sequences
Ilham A. Shahmuradov, Alex J. Gammerman, John M. Hancock, Peter M. Bramley
1
and
Victor V. Solovyev
2,
*
Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK,
1
School of
Biological Sciences, Royal Holloway, University of London, UK and
2
Softberry Inc., 116 Radio Circle, Suite 400, Mount
Kisco, NY 10549, USA
Received August 15, 2002, Revised September 25, 2002, Accepted October 2, 2002
ABSTRACT
PlantProm DB, a plant promoter database, is an
annotated, non-redundant collection of proximal
promoter sequences for RNA polymerase II with
experimentally determined transcription start
site(s), TSS, from various plant species. The first
release (2002.01) of PlantProm DB contains 305
entries including 71, 220 and 14 promoters from
monocot, dicot and other plants, respectively. It
provides DNA sequence of the promoter regions
(200 : þ51) with TSS on the fixed position þ201,
taxonomic/promoter type classification of promo-
ters and Nucleotide Frequency Matrices (NFM) for
promoter elements: TATA-box, CCAAT-box and
TSS-motif (Inr). Analysis of TSS-motifs revealed
that their composition is different in dicots and
monocots, as well as for TATA and TATA-less
promoters. The database serves as learning set in
developing plant promoter prediction programs.
One such program (TSSP) based on discriminant
analysis has been created by Softberry Inc. and the
application of a support vector machine approach
for promoter identification is under development.
PlantProm DB is available at http://mendel.cs.
rhul.ac.uk/ and http://www.softberry.com/.
INTRODUCTION
Draft nuclear genome sequences of Arabidopsis thaliana (1)
and Oryza sativa (2,3), representing dicotyledonous and
monocotyledonous higher plants, respectively, have been
published. In addition, the putative gene contents of these
genomes, predicted mostly by computer methods, are available
(2,3,4; ftp://ftp.ncbi.nih.gov/genbank/genomes/A_thaliana;
http://www.tigr.org/tdb/e2k1/ath1; http://mendel.cs.rhul.ac.uk/
Arabidopsis). However, as both computer programs and
experimental approaches for gene discovery have known
limitations, we are still far from a fine picture of genome
architecture. In particular, for all widely used gene prediction
methods, one of the difficulties is accurate detection of the first
(non-coding or partially coding) exon. The most accurate
approach to solve this problem is to use information on full-
length cDNAs. Unfortunately, no such information is available
for most plant genes. Therefore, as well as being of special
importance in understanding the regulation of gene expression,
identification of plant promoters may serve as an essential
element in gene annotation as well as in developing
computational promoter prediction approaches. Currently,
promoter identification is one of the most challenging
problems in computational biology.
The term ‘promoter’ is used to designate a region in the
genome sequence upstream of a gene transcription start site
(TSS), although sequences downstream of TSS may also affect
transcription initiation. Promoter elements select the transcrip-
tion initiation point, transcription specificity and rate.
Depending on the distance from the TSS, the terms of
‘proximal promoter’ (several hundreds nucleotides around the
TSS) and ‘distal promoter’ (thousands and more nucleotides
upstream of the TSS) are also used. Both proximal and distal
promoters include sets of various elements participating in the
complex process of cell-, issue-, organ-, developmental stage-
and environmental factors-specific regulation of transcription.
Most promoter elements regulating TSS selection are localized
in the proximal promoter.
To date, there are a number of databases with information on
cis-acting elements that control the transcription initiation by
binding corresponding nuclear factors. These include
TRANSFAC (5), TRRD (6), ooTFD (7), COMPEL (8),
PlantCARE (9), PLACE (10) and RegSite (http://softberry.
com). The last three databases are plant-oriented collections of
transcription regulatory elements. The Eukaryotic Promoter
Database (EPD) is only established collection of sequences of
eukaryotic Pol II promoters (11). The latest release (#71)
includes a total of 1402 entries, mainly of promoters from
animals, with only about 200 from plant species.
In the course of development of a new computer method for
predicting Pol II promoters of plant genes, we have collected
Pol II promoter sequences from various plants. These data are
incorporated on a new bioinformatics web server (http://
*To whom correspondence should be addressed. Email: victor@softberry.com
Present address:
John M. Hancock, MRC Mammalian Genetics Unit, Harwell, Oxfordshire, UK
114–117 Nucleic Acids Research, 2003, Vol. 31, No. 1
#
2003 Oxford University Press
DOI: 10.1093/nar/gkg041

www.mendel.cs.rhul.ac.uk) developed by the Department of
Computer Science at Royal Holloway, University of London,
in collaboration with Softberry Inc. (USA). It is designed to
present information about plant genomes, genes and new
approaches to their analysis. This article describes the criteria
used for the promoter data collecting procedure, specific
features of plant promoter sequences and Plant Promoter
Database (PlantProm DB).
Description of PlantProm DB
Criteria for selecting promoter sequences. For collecting
plant gene promoters the following rules were followed.
(i) There is experimental evidence of the TSS position(s) of
the gene, published in the literature. For genes with
multiple TSSs the nearest to the CDS start position is
taken, if no additional information on the predominance
of one of them is available (positions of other TSSs are
given in the name line of the sequence written in the
FASTA format).
(ii) The length of known promoter sequence upstream of
chosen TSS is 200 bp or more; all stored promoter
sequences are the same length, 251 bp, where the position
201 corresponds to the TSS, i.e. collected sequences
occupy the region (200 : þ51), with the TSS in the
position þ1, and, thus, present proximal promoters
mentioned above.
(iii) An entry corresponds to the gene mapped on the genomic
sequences.
(iv) Various alleles of a gene are presented in the database by a
single entry.
(v) Genes with more than one non-allelic copy in the genome
as well as paralogous genes are taken as different entries.
Information content of the database
The annotated, non-redundant PlantProm DBL (release
2002.01) has 305 entries including 71, 220 and 14 promoters
for RNA polymerase II from monocot, dicot and other plants,
respectively. It provides the following information on plant
promoters with experimentally known transcription start
site(s):
(i) DNA sequence of the promoter region (200 : þ51);
(ii) Nucleotide Frequency Matrices (NFM) for canonical
promoter elements (TATA-box, CCAAT-box and TSS-
motif or Initiator element, Inr);
(iii) Taxonomic and promoter type classification of promoters.
To compute nucleotide frequency matrices for various
promoter elements, a pairwise comparison of a region
[50 : þ1) of 305 plant promoters has been performed and
one of the couple of promoters showing more than 90%
homology has been excluded from the initial collection. As a
result, 4 promoters were excluded and are denoted by
‘Excluded’ in the name line of these promoters sequences.
In simple implementation of Expectation Maximization
(EM) algorithm (12), we considered the sequence of motif
X ¼ (x
1
,x
2
, ..., x
l
), where l is the motif length. If P
i
(x
j
) is the
empiric frequency of the nucleotide x
j
in position i (computed
on previous iteration), then the weight of this motif is
computed as
W ðX Þ¼
log
Q
P
i
ðx
j
Þ
0:25
Using the EM procedure for 10 iterations, the initial
collection of 305 (301 unrelated) promoters was divided into
the 2 classes: 175 (171 unrelated) TATA promoters and 130
TATA-less promoters. In calculations of TATA matrices, the
Table 1. Nucleotide frequencies matrix for TATA box from 171 unrelated plant promoters
a
<2 <112345678>1 >2
A 0.28 0.16 0.03 0.95 0.00 1.00 0.62 0.97 0.38 0.73 0.13 0.30
C 0.27 0.63 0.01 0.00 0.04 0.00 0.00 0.00 0.01 0.08 0.42 0.42
G 0.17 0.05 0.00 0.00 0.00 0.00 0.00 0.02 0.00 0.10 0.28 0.16
T 0.28 0.16 0.96 0.05 0.96 0.00 0.38 0.01 0.61 0.09 0.18 0.11
c T A T A A/T A T/A A
a
The mean distance between TATA box and TSS is 26 bp.
Table 2. Nucleotide frequencies matrix for CCAAT box from 131 unrelated plant promoters
a
<4 <3 <2 <112345>1 >2 >3 >4
A 0.31 0.34 0.27 0.30 0.31 0.00 1.00 1.00 0.00 0.28 0.32 0.29 0.40
C 0.19 0.17 0.16 0.18 0.34 1.00 0.00 0.00 0.00 0.20 0.20 0.25 0.17
G 0.20 0.20 0.27 0.21 0.15 0.00 0.00 0.00 0.00 0.20 0.18 0.15 0.15
T 0.30 0.29 0.30 0.31 0.20 0.00 0.00 0.00 1.00 0.32 0.30 0.31 0.28
n CAAT
a
The mean distance between CCAAT box and TSS is 75 bp.
Nucleic Acids Research, 2003, Vol. 31, No. 1 115

allowed variation of a distance between the right boundary of
the TATA-core box and the TSS was 18: 7 40 bp and only
TATAWAWA-core was used for calculating the weight. As an
initial TATA-box matrix, the TATA-matrix computed for 134
plant promoters from EPD (http://www.epd.isb-sib.ch/) was
used. The computed TATA-matrix (Table 1) is in a good
agreement with the TATA-matrix from EPD.
For computation of the CCAAT-box matrix, we considered
the possible distance between the right boundary of CCAAT-
core and the TSS within 50: 7 100 bp. The CCAAT-core was
used for weight calculation and, in accordance with the
available data (13), CCAAT boxes were identified on both
DNA strands. The CAAT matrix is presented in Table 2.
The TSS-motif matrix of 5 bp in length has been computed,
where the 3rd nucleotide was the annotated (anTSS). No strong
consensus was revealed. When the EM approach was used to
analyze all possible pentanucleotides with an assumed TSS
(asTSS) location in the range (anTSS 7 2 : anTSS þ 2), it was
observed that the composition of asTSS-motifs is different in
dicot and monocot plants (Tables 3 and 4), as well as for TATA
and TATA-less promoters (Tables 5 and 6). This finding seems
to be a novel feature of plant promoters.
PlantProm DB, release 2002.01, is available at the web sites
http://mendel.cs.rhul.ac.uk and http://www.softberry.com. The
database will be regularly updated by collection and analysis of
new experimental data on plant promoters as it becomes
available in the literature. PlantProm DB serves as a learning
set in developing plant promoter prediction programs. One
such program (TSSP), based on discriminant analysis of
sequence features and plant regulatory motifs (RegSiteDB),
has been developed by Softberry Inc. (http://www.softberry.
com/berry.phtml?topic=promoter). The application of a sup-
port vector machine approach for promoter identification is
under development.
ACKNOWLEDGEMENTS
PlantProm DB is funded by grant 111/BIO14428 ‘Pattern
Recognition Techniques for Gene Identification in Plant
Genomic Sequences’, from the UK Biotechnology and
Biological Sciences Research Council (BBSRC) and is
designed and maintained at Royal Holloway, University of
London in collaboration with Softberry Inc. (USA).
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a
4 3 2 1 þ1 þ2 þ3 þ4
A 0.341 0.249 0.286 0.005 0.604 0.475 0.226 0.272
C 0.184 0.286 0.041 0.507 0.332 0.028 0.359 0.240
G 0.101 0.124 0.041 0.161 0.065 0.101 0.129 0.198
T 0.373 0.341 0.631 0.327 0.000 0.396 0.286 0.290
W n T/a C/t A/c w
a
In 75 cases, the high scoring TSS coincided with the annotated TSS.
Table 4. Nucleotide frequencies matrix for a TSS-motif from 70 unrelated
monocot plants’ promoters
a
4 3 2 1 þ1 þ2 þ3 þ4
A 0.114 0.214 0.557 0.157 0.186 0.000 0.871 0.143
C 0.443 0.286 0.114 0.386 0.314 0.786 0.114 0.371
G 0.186 0.200 0.143 0.257 0.200 0.143 0.014 0.171
T 0.257 0.300 0.186 0.200 0.300 0.071 0.000 0.314
aNnCA
a
In 17 cases, the high scoring TSS coincided with the annotated TSS.
Table 5. Nucleotide frequencies matrix for a TSS-motif from 171 unrelated
TATA promoters of plants
a
4 3 2 1 þ1 þ2 þ3 þ4
A 0.322 0.263 0.099 0.035 0.865 0.246 0.345 0.368
C 0.251 0.222 0.234 0.719 0.023 0.292 0.421 0.257
G 0.117 0.152 0.111 0.105 0.023 0.105 0.082 0.146
T 0.310 0.363 0.556 0.140 0.088 0.357 0.152 0.228
T/c C A n M
a
In 64 cases, the high scoring TSS coincided with the annotated TSS.
Table 6. Nucleotide frequencies matrix for a TSS-motif from 130 unrelated
TATA-less promoters of plants
a
4 3 2 1 þ1 þ2 þ3 þ4
A 0.385 0.215 0.262 0.023 0.554 0.438 0.331 0.231
C 0.231 0.246 0.231 0.315 0.323 0.292 0.015 0.262
G 0.146 0.200 0.000 0.269 0.123 0.054 0.208 0.215
T 0.238 0.338 0.508 0.392 0.000 0.215 0.446 0.292
T/a/c Y A/c a/c/t t/a/g
a
In 46 cases, the high scoring TSS coincided with the annotated TSS.
116 Nucleic Acids Research, 2003, Vol. 31, No. 1

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Nucleic Acids Research, 2003, Vol. 31, No. 1 117