Basic HTML Version
I
dentification Novel phaC1 Gene Native Pseudomonas putida KT2442 Key Gene for PHA Biosynthesis
20
termination method as described (Tomris et al., 2007)
with a 310 Genetic Analyzer (Perkin Elmer). The
resulting nucleotide sequence was analyzed with
genetic information processing software Bioedit. The
bioinformatics of the amplified sequences were
extracted by using NCBI BLAST program (Wiese et
al., 2011).
3.5 Bioinformatic Method for Phylogenetic Tree
A set of homologous DNA sequences made to build a
tree. The sequence from the PCR-amplified phaC1
gene and feed it into the blastn web interfaces at the
NCBI by pasting it into the main search box. The
following sequence were applied in blastn:
Pseudomonas_putida
_KT2442
aagagcttggtccgcttgtgctggagaacagctggcagactttcatcatcca
ttgggggcaccccgacaactaccacgccaatggggcctgaccacctatgt
cgaggccctcaacgaggccatcgaggtcatcctgtagatcaccggcagcc
acgacctgaacctggtcggcgcctgctccggcg
A list of hits were obtained for which the seventeen
sequences were selected to built a phylogenetic tree
for (partially
phaC1
genes:)
Pseudomonas_putida
_KT2442,
Pseudomonas_aeruginosa
_LESB58,
Pseudomonas_aeruginosa
_PAO1,
Pseudomonas_aeruginosa
_phaC1,
Pseudomonas_aeruginosa
_B136-33,
Pseudomonas_aeruginosa
_DK2,
Pseudomonas_aeruginosa
_M18,
Pseudomonas_aeruginosa
_UCBPP-PA14,
Pseudomonas_aeruginosa
_strain_GS1,
Pseudomonas_aeruginosa
_NCGM2.S1,
Pseudomonas_denitrificans
_ATCC_13867,
Pseudomonas_aeruginosa
_strain_DM2,
Pseudomonas_aeruginosa
_strain_DM1,
Pseudomonas_aeruginosa
_PA7,
Pseudomonas_aeruginosa
_PhaC2,
Pseudomonas_aeruginosa
_PhaC1,
Pseudomonas_aeruginosa
_strain_P5
Acknowledgements
This work partially received financial support from
National Institute of Genetic Engineering and
Biotechnology, NIGEB.
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