Download The FtsH Proteases of Oryza sativa and Arabidopsis thaliana

The FtsH Proteases of Oryza sativa and
Arabidopsis thaliana – Orthologs and Parologs?
Anna Tan-Wilson and Karl Wilson
Binghamton University
Department of Biological Sciences
Arabidopsis thaliana is a
dicot for which a complete
genome sequence is
available. The plant seems
to have an unusually large
number of genes coding for
proteolytic enzymes. These
genes belong to a few multigene families. Among these
is the multi-gene family
representing the FtsH
proteases, typified by the
presence of an ATP-binding
domain and energy requirement coming from ATP
hydrolysis.
Oryza sativa (rice) is a
monocot for which a complete
genome sequence has only
recently been completed. The
presence of such information
allows us to ask the question:
Did the multiple FtsH
proteases of Arabidopsis
thaliana arise before or after
divergence of the monocots
and dicots?
PROCEDURE:
1. Amino acid sequences of FtsH proteases of
Arabidopsis thaliana were retrieved from NCBI.
To prevent taking redundant genes, the Blink
function was used.
2. Amino acid sequences of FtsH proteases of
Oryza sativa, japonica cultivar, were retrieved
from NCB
3. The sequences were compiled in Biology
workbench, and the sequence headings
renamed to make the output more intelligible.
4. The sequences were aligned using ClustalW
(default parameters) and an unrooted
phylogenetic tree was constructed.
RESULTS:
Unrooted tree of FtsH proteases from
Arabidopsis and Oryza.
The phylogenetic tree that was constructed
based on the ClustalW alignment suggests
that:
 The pair of Arabidopsis thaliana FtsH
proteases designated TO2610 and At2g26140
in the tree have fewer differences from the pair
of Oryza sativa FtsH proteases designated
BAB91902 and BAB91903, than from other
Arabidopsis thaliana FtsH proteases.
 There are at least two more clusters of 4
Arabidopsis FtsH proteases each that
diverged more recently.
 Three other rice FtsH proteases diverged
earlier – but this result may be an artifact of
incomplete data since the rice genome
sequencing has just been completed and
some annotations may not yet have made it
into the database.
 Curiously, in attempts to provide distant
sequences so as to generate a rooted tree,
the program did not select those sequences to
be the root. We first selected one from
Nostoc, then from E. coli, then even one from
C. elegans.
Programs that can add interest:
Although the chloroplast FtsH protease is best
studied, there are indications that some of the
Arabidopsis thaliana paralogs are predicted to be
mitochondrial. Identification of organellar
localization of the sequences on the phylogenetic
tree could be very interesting.
The FtsH proteases typically bear an AAA protein
domain. Comparison of the tree arising when
aligning only the AAA domain as compared to the
whole proteins would be interesting.
Papers that can add interest:
Genes Cells. 2002 Aug;7(8):769-80.
Related Articles, Links
The VAR1 locus of Arabidopsis encodes a chloroplastic FtsH and
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Sakamoto W, Tamura T, Hanba-Tomita Y, Murata M; Sodmergen.
J Biol Chem. 2002 Jan 18;277(3):2006-11. Epub 2001 Nov 20.
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Bailey S, Thompson E, Nixon PJ, Horton P, Mullineaux CW, Robinson C, Mann NH.
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