The FtsH Proteases of Oryza sativa and Arabidopsis thaliana – Orthologs and Parologs?
Anna Tan-Wilson and Karl Wilson
BinghamtonUniversity
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 multi-gene 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:
- Amino acid sequences of FtsH proteases of Arabidopsis thaliana were retrieved from NCBI. To prevent taking redundant genes, the Blink function was used.
- Amino acid sequences of FtsH proteases of Oryza sativa, japonica cultivar, were retrieved from NCB
- The sequences were compiled in Biology workbench, and the sequence headings renamed to make the output more intelligible.
- 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 is responsible for leaf variegation in the mutant alleles.
Sakamoto W, Tamura T, Hanba-Tomita Y, Murata M; Sodmergen.
A critical role for the Var2 FtsH homologue of Arabidopsis thaliana in the photosystem II repair cycle in vivo.
Bailey S, Thompson E, Nixon PJ, Horton P, Mullineaux CW, Robinson C, Mann NH.
Auxiliary functions in photosynthesis: the role of the FtsH protease.
Bailey S, Silva P, Nixon P, Mullineaux C, Robinson C, Mann N.
The thylakoid FtsH protease plays a role in the light-induced turnover of the photosystem II D1 protein.
Lindahl M, Spetea C, Hundal T, Oppenheim AB, Adam Z, Andersson B.