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Comparative Study
. 2007 Jun;99(6):1131-41.
doi: 10.1093/aob/mcm044. Epub 2007 Apr 7.

Portrait of the expansin superfamily in Physcomitrella patens: comparisons with angiosperm expansins

Robert E Carey  1 , Daniel J Cosgrove
Affiliations
Comparative Study

Portrait of the expansin superfamily in Physcomitrella patens: comparisons with angiosperm expansins

Robert E Carey et al. Ann Bot. 2007 Jun.

Abstract

Background and aims: Expansins are plant cell wall loosening proteins important in a variety of physiological processes. They comprise a large superfamily of genes consisting of four families (EXPA, EXPB, EXLA and EXLB) whose evolutionary relationships have been well characterized in angiosperms, but not in basal land plants. This work attempts to connect the expansin superfamily in bryophytes with the evolutionary history of this superfamily in angiosperms.

Methods: The expansin superfamily in Physcomitrella patens has been assembled from the Physcomitrella sequencing project data generated by the Joint Genome Institute and compared with angiosperm expansin superfamilies. Phylogenetic, motif, intron and distance analyses have been used for this purpose.

Key results: A gene superfamily is revealed that contains similar numbers of genes as found in arabidopsis, but lacking EXLA or EXLB genes. This similarity in gene numbers exists even though expansin evolution in Physcomitrella diverged from the angiosperm line approx. 400 million years ago. Phylogenetic analyses suggest that there were a minimum of two EXPA genes and one EXPB gene in the last common ancestor of angiosperms and Physcomitrella. Motif analysis seems to suggest that EXPA protein function is similar in bryophytes and angiosperms, but that EXPB function may be altered.

Conclusions: The EXPA genes of Physcomitrella are likely to have maintained the same biochemical function as angiosperm expansins despite their independent evolutionary history. Changes seen at normally conserved residues in the Physcomitrella EXPB family suggest a possible change in function as one mode of evolution in this family.

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Figures

F<sc>ig</sc>. 1.
Fig. 1.
Bayesian likelihood tree for EXPA family. Burnin was set to 60. The tree was rooted manually at groups A, B and C. Clade and groupings are marked with circles (or bars when they are poorly resolved as in the case of clades EXPA-I, EXPA-II and EXPA-III). Physcomitrella patens sequences are unshaded, rice sequences are shaded in black, arabidopsis sequences boxed, and a Populus sequence in grey text. Intron patterns (‘o’ indicates an intronless gene) are given next to each gene's name, and the typical EXPA intron pattern is indicated.
F<sc>ig</sc>. 2.
Fig. 2.
Model of intron evolution for Physcomitrella EXPA family. Black bars represent from left to right, the EXPA family, putative Physcomitrella homologous groupings, and genes within these groupings. Intron losses are indicated below the lines leading to each group.
F<sc>ig</sc>. 3.
Fig. 3.
Bayesian likelihood tree for EXPB family. Burnin was set to 10. The tree was rooted at AtEXPA1. Clade and groupings are marked with circles or bars. Physcomitrella patens sequences are unshaded, rice sequences are shaded in black, and arabidopsis sequences boxed. Intron patterns are given next to each gene's name (‘o’ represents an intronless gene and ‘n’ represents a novel intron), and the typical EXPB intron pattern is indicated.
F<sc>ig</sc>. 4.
Fig. 4.
Average distances of Physcomitrella expansin gene families to their angiosperm counterparts. (A) Between group average distances for the EXPA gene family. Values indicated are the average Poisson-corrected amino acid distance to the arabidopsis EXPA family. Error bars are standard errors based on 500 bootstrap replicates. (B) Between group average distances for the EXPB gene family. Values indicated are the average Poisson-corrected amino acid distance to the arabidopsis EXPA family. Error bars are standard errors based on 500 bootstrap replicates.
F<sc>ig</sc>. 5.
Fig. 5.
Model of intron evolution for Physcomitrella EXPB family. Black bars represent from left to right, the EXPB family, putative Physcomitrella homologous groupings, and genes within these groupings. Intron losses are indicated below the lines and intron gains above the lines leading to each group.
F<sc>ig</sc>. 6.
Fig. 6.
SeqLOGO for the EXPA family. In each pair, the top lines are rice/arabidopsis sequences and the lower lines are Physcomitrella. The height of the letters indicates frequency of the amino acid in that group of sequences. Boxed residues represent those that are normally conserved in all four expansin families.
F<sc>ig</sc>. 7.
Fig. 7.
SeqLOGO for the EXPB family. In each pair, the top lines are rice/arabidopsis sequences and the lower lines are Physcomitrella. The height of the letters indicates frequency of the amino acid in that group of sequences. Boxed residues represent those that are normally conserved in all four expansin families. Black arrows indicate changes in the Physcomitrella EXPB family to normally conserved residues in EXPB genes. Codes indicate the region of the protein in which the change resides. LBS = long binding surface; HC = hydrophobic core; BDC = between domain contacts; SBP = short binding pocket (Yennawar et al., 2006).
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