Plant Molecular Biology 38: 1137–1146, 1998.
© 1998 Kluwer Academic Publishers. Printed in the Netherlands.
Characterization of tomato PHYB1 and identiﬁcation of molecular defects
in four mutant alleles
Galina I. Lazarova
, Tamayo Kubota
, Shannon Frances
, Martin J. G.
, Jörg Brandstädter
, Minami Matsui
, Richard E. Kendrick
and Lee H. Pratt
Laboratory for Photoperception and Signal Transduction, Frontier Research Program, The Institute of Physical
and Chemical Research (RIKEN), Hirosawa 2-1, Wako-shi, Saitama 351-01, Japan;
Department of Botany,
University of Georgia, Athens, GA 30602, USA (∗ authors for correspondence); Present addresses:
of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada;
Department of Biochem-
istry, McMaster University, Hamilton, Ontario, Canada;
QIAGEN GmbH, Max-Volmer-Strasse 4, 40724 Hilden,
Plant Biology Institute, Biological Research Centre of the Hungarian Academy of Sciences, P.O. Box
521, 6701 Szeged, Hungary
Received 22 December 1997; accepted in revised form 30 June 1998
Key words: photomorphogenic mutants, phytochrome, pre-mRNA splicing, alternative splicing, tomato
The structure of the gene encoding the apoprotein of phytochrome B1 (PHYB1) in tomato has been determined
from genomic and cDNA sequences. In contrast to PHYA, PHYB1 lacks an intron upstream of the ﬁrst ATG.
A single transcription start site was found by 5
RACE at –116. Tomato PHYB1 spans 7 kb starting from the
ﬁrst ATG. The coding region is organized into four exons as for other angiosperm PHY. The deduced apoprotein
consists of 1131 amino acids, with a molecular mass of 125.4 kDa. Tomato phytochrome B1 shares 78% and
74% identity with Arabidopsis phytochromes B and D, respectively. Along with the normally spliced full-length
transcripts, sequences of reverse transcriptase-PCR clones revealed ﬁve types of alternative transcripts. Each type
of alternative transcript was missing a considerable part of the coding region, including the chromophore-binding
The four putative PHYB1 mutants in tomato, which are temporarily red-light insensitive (tri), were each
conﬁrmed to have a mutation in PHYB1. Each mutation arose from a different, single-base substitution. Allele
is presumably a null because the mutation introduces a stop at codon 92. In tri
, val-238 is replaced by Phe.
The importance of this valine residue is evidenced by the fact that the tri
phenotype is as strong as that of tri
encode proteins truncated at their C-termini. The former lacks either 170 or 438 amino acids,
depending upon which of two types of splicing occurs during transcript maturation, while the latter lacks 225.
Phytochromes (phy) are photoreceptors that mon-
itor a wide range of light parameters and relay
this information to one or more signal transduc-
tion chains, thereby modulating many developmental
The nucleotide sequence reported will appear in the GenBank,
EMBO and DDBJ Nucleotide Sequence Databases under the acces-
sion numbers AJ002281 (PHYB1)and AJ002282 through AJ002287
and physiological processes in plants [7, 17]. Phy
are also chromoproteins whose apoproteins in an-
giosperms are encoded by a multigene family. Five
phy-apoprotein (PHY)-encoding genes (PHY)have
been identiﬁed in both Arabidopsis (PHYA, PHYB,
PHYC, PHYD, PHYE) and tomato (PHYA, PHYB1,
PHYB2, PHYE, PHYF).
Data on the structure of various PHY are accu-
mulating rapidly, thus allowing the analysis of the