Rajangam AS et al. (2008), Evolution of a domain conserved in microtubule-...

XB-ART-44327

Adv Appl Bioinform Chem 2008 Jan 01;1:51-69. doi: 10.2147/aabc.s3211.

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Evolution of a domain conserved in microtubule-associated proteins of eukaryotes.

Rajangam AS , Yang H , Teeri TT , Arvestad L .

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The microtubule network, the major organelle of the eukaryotic cytoskeleton, is involved in cell division and differentiation but also with many other cellular functions. In plants, microtubules seem to be involved in the ordered deposition of cellulose microfibrils by a so far unknown mechanism. Microtubule-associated proteins (MAP) typically contain various domains targeting or binding proteins with different functions to microtubules. Here we have investigated a proposed microtubule-targeting domain, TPX2, first identified in the Kinesin-like protein 2 in Xenopus. A TPX2 containing microtubule binding protein, PttMAP20, has been recently identified in poplar tissues undergoing xylogenesis. Furthermore, the herbicide 2,6-dichlorobenzonitrile (DCB), which is a known inhibitor of cellulose synthesis, was shown to bind specifically to PttMAP20. It is thus possible that PttMAP20 may have a role in coupling cellulose biosynthesis and the microtubular networks in poplar secondary cell walls. In order to get more insight into the occurrence, evolution and potential functions of TPX2-containing proteins we have carried out bioinformatic analysis for all genes so far found to encode TPX2 domains with special reference to poplar PttMAP20 and its putative orthologs in other plants.

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Species referenced: Xenopus
Genes referenced: tbx2 tpx2

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References [+] :

Amos, Microtubules and maps. 2005, Pubmed

	Figure 1. Sequence alignment of M20L proteins made with the MAFFT alignment tool. The TPX2 domain is marked with a black bar and the extended TPX2 domain by a dotted line under the sequences. Notes above the TPX2 domain indicate sites where residues are lost relative to the Pfam domain model of TPX2. The identity or similarity to a consensus sequence is indicated in blue and red (respectively), the last codon of an exon in orange, and the exon/intron boundary in frame 2 in yellow.
	Figure 2. (a) A multiple alignment made with DNA sequences of the extended TPX2 domains of the M20L protein sequences. Differences with respect to A. thaliana are noted, and the conserved bases are indicated by dots. The third codon position is printed in grey. (b) Similarity plot graph made with the extended TPX2 domain with reference to relative residue position (both DNA and Protein sequences) using EMBOSS plotcon software using a standard window size of 4.
	Figure 3. Phylogenetic tree made with all the available and newly found eukaryotic proteins containing a TPX2 domain. The Bayesian posterior probability is indicated by numbers to the right of the edge in question. The clades with M20L proteins and KLEEK motif are marked. Genes with reported phenotypes in Arabidopsis are marked in red (Yuen et al 2003). The gene noted as AtTPX2 by (Perrin et al 2007) is annotated in green.
	Figure 4. A phylogenetic tree made with the extended TPX2 domain.
	Figure 5. Genomic organization (to scale) of TPX2 genes in the genomes of (a) Populus trichocarpa, (b) Oryza sativa, and (c) Arabidopsis thaliana.
	Figure 6. Relative expression levels of the TPX2 genes in different tissue types of Arabidopsis thaliana. Data from http://www.arabidopsis.org/. The expression patterns for WDL1 (At3g04630) and WVD2 (At1g3780) are roughly the same, with elevated levels in inflorescence tissue.
	Figure 7. M20L gene structure: the positions (in base pairs from the translation start) of gene CDS are marked, to scale, with dark boxes while the thick lines correspond to introns. The TPX2 regions are marked with dark red lines.
	Figure 8. Possible regulatory elements and promoters of M20L. Upstream regions with predicted TATA boxes are indicated by a green triangle, motif 1 by a red box, motif 2 by a blue box, and EST hit regions by dark pink lines. For A. thaliana, the core promoter given in AGRIS (Palaniswamy et al 2006) is indicated by a red line. The lines are scaled to actual sequence length and positions are given in base pairs from translation start.
	Figure 9. Sequence alignments for the motifs 1 and 2. Blue color indicates identity to the consensus sequence. The left flank of motif 1 shows the extension of this motif in dicots.