Sequence analysis of Pisum sativum post-floral specific gene
In 1997, a Pisum sativum post-floral-specific gene (PPF-1) was identified (Zhu et al) from a cDNA
library of short-day (SD) grown G2 pea tissue. The amino acid sequence encoded by PPF-1 shares
similarity with the Bacillus subtilis gene SP3J, which is required for maintaining vegetative growth.
BLAST search hits with the query sequence of PPF-1 protein contains several bacterial inner membrane
proteins which demonstrate hydrophobic regions in sequences. This suggests that PPF-1 protein may
also have transmembrane helices and locate in the membrane of chloroplast of pea leaves.
We use PPF-1 as a sample to learn how to use bioinformatics tools to analyze both nucleotide
and protein sequence to obtain some information of this gene.
- Find the PPF-1 related papers published by Zhu Yuxian.
- Find the mRNA sequence of PPF-1 from GenBank
- Find the protein sequence of PPF-1 from Swiss-Prot.
- Obtain the coding sequence of PPF-1 with EMBOSS Plotorf, Showorf and Getorf.
- Obtain the coding sequence of PPF-1 with EMBOSS Coderet.
- Make analysis of the primary structure of PPF-1 with WebLab protein sequence analysis tools
and ExPASy primary structure analysis tool
- Predict the membrane helices of PPF-1 with different programs from WebLab and ExPASy tools and compare
- Draw a helical wheel for the four helices of PPF-1 amino acid sequence with different tools in WebLab
- Search PPF-1 homologous sequences from Arabidopsis.
- Search PPF-1 homologous sequences from other plants.
- Search PPF-1 homologous sequences from bacteria.
- Zhu Y, Zhang Y, Luo J, Davies PJ, Ho DT. PPF-1, a post-floral-specific gene
expressed in short-day-grown G2 pea, may be important for its never-senescing
phenotype. Gene. 1998 Feb 16;208(1):1-6.
- Wang DY, Li Q, Cui KM, Zhu YX. PPF1 may suppress plant senescence via
activating TFL1 in transgenic Arabidopsis plants. J Integr Plant Biol. 2008
- Li J, Wang DY, Li Q, Xu YJ, Cui KM, Zhu YX. PPF1 inhibits programmed cell
death in apical meristems of both G2 pea and transgenic Arabidopsis plants
possibly by delaying cytosolic Ca2+ elevation. Cell Calcium. 2004
- Ravaud S, Stjepanovic G, Wild K, Sinning I. The crystal structure of the
periplasmic domain of the Escherichia coli membrane protein insertase YidC
contains a substrate binding cleft. J Biol Chem. 2008 Apr 4;283(14):9350-8.
- Oliver DC, Paetzel M. Crystal structure of the major periplasmic domain of the
bacterial membrane protein assembly facilitator YidC. J Biol Chem. 2008 Feb