Page 6 - Molecular Plant Breeding

Molecular Plant Breeding 2011, Vol.2, No.15, 101-108
http://mpb.sophiapublisher.com
102
the RuBisCo small subunit (rbcS) is synthesized in
cytoplasm 80S ribosome because the gene exists in
cell nucleus genome, and then transfers to chloroplast
as precursor protein to assemble with large subunit
after processed (Ellis, 1987; Roy H, 1989). To date,
the rbcL gene has been cloned from a great many
plants, such as Oryza sativa subsp. Japonica
(Hiratsuka et al., 1989), Zea mays (Maier et al., 1995),
Nicotiana tabacum (Shinozaki et al., 1986), Arabidopsis
thaliana (Sato et al., 1999), Citrus sinensis (Bausher
et al., 2006), Phalaenopsis aphrodite susp. Formosana
(Chang et al., 2006), Astragalus mongholicus (Guo et
al., 2010), Marchantia polymorpha (Ohyama et al.,
1986; 1988), Picea abies (Relle et al., 1995).
In this study, the rbcL nucleotide sequences and
deduced amino acid (AA) sequences from various
higher plants were analyzed by the tools of
bioinformatics, expecting to provide some theoretical
reference for further studies on plant RuBisCo. The
plants include Zea mays, Arabidopsis thaliana, Pisum
sativum, Citrus sinensis, Phalaenopsis aphrodite susp.
formosana, and so on, emphasizing Oryza sativa
subsp. japonica . And the following aspects were
involved in the analysis: the compositions and the
physical and chemical characteristics, signal peptide,
transmembrane topological structure, hydrophobicity
or hydrophilicity, secondary structure, sequence
comparison, and molecular systemic evolution.
1 Results
1.1 The compositions and the physical and chemical
characteristics analysis of rbcL nucleotide sequences
and deduced amino acid sequences from plants
The compositions and the physical and chemical
characteristics of rbcL nucleotide sequences and
deduced AA sequences were discribed by ORF Finder,
DNAstar, ProtParam and pI/Mw. The analyzed rbcLs
data were derived from Oryza sativa subsp. japonica,
Zea mays, Arabidopsis thaliana , Pisum sativum,
Citrus sinensis, Phalaenopsis aphrodite subsp.
formosana. All the initiation codons of the rbcLs
genes are ATG, and the termination codons are TAG or
TAA. The lengths of ORFs are about 1434 bps, and
the encoding proteins are approximately 477 AA
residues. The molecular weight and theoretical
isoelectric point of the polypeptides are similar among
different plants. The proportions of acidic AA,
alkaline AA, total electric AA, polar AA and
hydrophobic AA in the total AA residues of the rbcLs
show tiny differences. On the whole, the most
abundant AA residues are Gly, Ala, Leu, Glu and Val.
The rbcLs of Pisum sativum and Citrus sinensis
belong to stable protein, while that of the other three
plants are unstable protein, but the instability indexes
of all rbcLs are close to 40% (Table 1).
1.2 The signal peptide analysis of plant rbcLs
The rbcL AA sequence signal peptide of Oryza sativa
subsp. japonica was predicted by SignalP Server v. 3.0
online program (Nielsen et al., 1997; Bendtsen et al.,
2004). The analysis was performed using Neural
Networks Model (NN) method. The top values of
original shearing site (C score), signal peptide (S
score), and synthesized shearing site (Y score) are
0.059, 0.133, and 0.021, which locate at the 24 th, 4th,
and 8th AA residues, respectively (Figure 1). All the
scores are far less than the critical threshold. Moreover,
the probability of presence of signal peptide in the
analysis of polypeptide applying Hidden Markov
Models (HMM) method is zero. Therefore, it indicates
that no signal peptide shearing site exists in the rbcL
polypeptide. The similar results were observed in the
prediction of rbcL AA sequences of Zea mays,
Triticum aestivum, Arabidopsis thaliana, Citrus
sinensis . Accordingly, it was inferred that the rbcLs
polypeptide synthesized in higher plants chloroplast
don't require to be protein transmembrane transfered.
1.3 The transmembrane topological structure analysis
of plant rbcLs
The rbcL AA sequence transmembrane topological
structure of Oryza sativa subsp. japonica was
explored applying TMHMM Server v. 2.0 program
(Ikeda et al., 2002). The total rbcL polypeptide locates
outside the membrane (Figure 2), namely, it is absent
of transmembrane topological structure in the rbcL AA
sequence of Oryza sativa subsp. japonica. The same
results can be gained from the analysis of rbcL AA
sequences of Zea mays, Lolium perenne, Oncidium
Gower Ramsey , Calycanthus floridus var. glaucus,
Phalaenopsis aphrodite subsp. formosana , and so on.