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The polyphenol oxidase gene family in land plants: Lineage-specific duplication and expansion.

Tran LT, Taylor JS, Constabel CP - BMC Genomics (2012)

Bottom Line: We found that many PPOs contained one or two introns often near the 3' terminus.While we found variation in intron numbers and positions, overall PPO gene structure is congruent with the phylogenetic relationships based on primary sequence data.The dynamic nature of this gene family differentiates PPO from other oxidative enzymes, and is consistent with a protein important for a diversity of functions relating to environmental adaptation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Forest Biology and Department of Biology, University of Victoria, Station CSC, Victoria, BC, Canada.

ABSTRACT

Background: Plant polyphenol oxidases (PPOs) are enzymes that typically use molecular oxygen to oxidize ortho-diphenols to ortho-quinones. These commonly cause browning reactions following tissue damage, and may be important in plant defense. Some PPOs function as hydroxylases or in cross-linking reactions, but in most plants their physiological roles are not known. To better understand the importance of PPOs in the plant kingdom, we surveyed PPO gene families in 25 sequenced genomes from chlorophytes, bryophytes, lycophytes, and flowering plants. The PPO genes were then analyzed in silico for gene structure, phylogenetic relationships, and targeting signals.

Results: Many previously uncharacterized PPO genes were uncovered. The moss, Physcomitrella patens, contained 13 PPO genes and Selaginella moellendorffii (spike moss) and Glycine max (soybean) each had 11 genes. Populus trichocarpa (poplar) contained a highly diversified gene family with 11 PPO genes, but several flowering plants had only a single PPO gene. By contrast, no PPO-like sequences were identified in several chlorophyte (green algae) genomes or Arabidopsis (A. lyrata and A. thaliana). We found that many PPOs contained one or two introns often near the 3' terminus. Furthermore, N-terminal amino acid sequence analysis using ChloroP and TargetP 1.1 predicted that several putative PPOs are synthesized via the secretory pathway, a unique finding as most PPOs are predicted to be chloroplast proteins. Phylogenetic reconstruction of these sequences revealed that large PPO gene repertoires in some species are mostly a consequence of independent bursts of gene duplication, while the lineage leading to Arabidopsis must have lost all PPO genes.

Conclusion: Our survey identified PPOs in gene families of varying sizes in all land plants except in the genus Arabidopsis. While we found variation in intron numbers and positions, overall PPO gene structure is congruent with the phylogenetic relationships based on primary sequence data. The dynamic nature of this gene family differentiates PPO from other oxidative enzymes, and is consistent with a protein important for a diversity of functions relating to environmental adaptation.

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Neighbour-joining phylogenetic tree from four major land plant lineages, together with corresponding visual representation of conserved regions, functional motifs, and relative intron positions. A putative tyrosinase sequence from the cyanobacterium A. marina (GenBank accession ACJ76786) was used to root the tree. Bootstrap replicates (1000) were used to determine the level of support at each node (only values > 50% are shown). The conserved first five amino acids for each of the CuA and CuB domains is shown at the end of each branch as HxxxC / HxxxH. Predicted targeting sequences are colored as green (chloroplast transit peptide), black (signal peptide), or grey (unknown). The CuA and CuB domains are colored blue, and C-terminal conserved areas dark grey. Approximate intron positions are shown as vertical bars, mapped onto the predicted protein. Shared colors indicating the same intron positions, and black bars mark unique introns. The introns are named by their location: N, N-terminus; A, CuA domain; L, linker; D, DWL domain; K, KFDV domain; C, C-terminus. Exact intron positions are listed in Additional file4. The PPO sequences are numbered and named based on species names as follows: P. patens, Ppa; S. moellendorffii , Smo; B. distachyon, Bda; O. sativa, Osa; S. italica, Sit; S. bicolor, Sbi; Z. mays, Zma; A. coerulea, Aco; G. max, Gma; M. esculenta, Mes; M. guttatus, Mgu; P. trichocarpa, Ptr; R. communis, Rco; V. vinifera, Vvi. Mexican poppy (Argenome mexicana) AmePPO1 (GenBank accession ACJ76786) was also included in the phylogeny because of our interest in the Eudicot I clade.
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Figure 2: Neighbour-joining phylogenetic tree from four major land plant lineages, together with corresponding visual representation of conserved regions, functional motifs, and relative intron positions. A putative tyrosinase sequence from the cyanobacterium A. marina (GenBank accession ACJ76786) was used to root the tree. Bootstrap replicates (1000) were used to determine the level of support at each node (only values > 50% are shown). The conserved first five amino acids for each of the CuA and CuB domains is shown at the end of each branch as HxxxC / HxxxH. Predicted targeting sequences are colored as green (chloroplast transit peptide), black (signal peptide), or grey (unknown). The CuA and CuB domains are colored blue, and C-terminal conserved areas dark grey. Approximate intron positions are shown as vertical bars, mapped onto the predicted protein. Shared colors indicating the same intron positions, and black bars mark unique introns. The introns are named by their location: N, N-terminus; A, CuA domain; L, linker; D, DWL domain; K, KFDV domain; C, C-terminus. Exact intron positions are listed in Additional file4. The PPO sequences are numbered and named based on species names as follows: P. patens, Ppa; S. moellendorffii , Smo; B. distachyon, Bda; O. sativa, Osa; S. italica, Sit; S. bicolor, Sbi; Z. mays, Zma; A. coerulea, Aco; G. max, Gma; M. esculenta, Mes; M. guttatus, Mgu; P. trichocarpa, Ptr; R. communis, Rco; V. vinifera, Vvi. Mexican poppy (Argenome mexicana) AmePPO1 (GenBank accession ACJ76786) was also included in the phylogeny because of our interest in the Eudicot I clade.

Mentions: A neighbour-joining phylogenetic reconstruction was generated from a multiple sequence alignment of the copper-binding domains and the PPO1_DWL domain of PPO protein sequences from 14 of the 25 plant genomes we had surveyed (Additional file3). The genomes were chosen to be representative and to cover a broad range of plant lineages. The analysis separated PPOs into a number of distinct clades (Figure2). While the nodes at the base of the larger clades were not well supported (low scores in the bootstrap reanalyses), nodes at the base of many smaller clades were robust (bootstrap values > 70%). In Physcomitrella, Selaginella, and in the eudicots, PPO diversification is largely a consequence of species-specific gene duplication and divergence. Thus, 12 of the 13 Physcomitrella sequences occur in one group, and eight of the eleven Selaginella sequences form one clade, with the remaining three genes forming a second clade. Among the eudicots, 10 of the 11 Glycine PPOs form a monophyletic group, seven of the 10 Populus PPOs form a monophyletic group, and all but one of the nine Mimulus PPOs occur in a single clade. While these data show that PPO gene diversification has occurred independently in different eudicots, we note that these species also have one or two PPOs on separate branches, sometimes in well-supported clades with other eudicot genes. This indicates that the common ancestor of the eudicot lineage had several PPO genes.


The polyphenol oxidase gene family in land plants: Lineage-specific duplication and expansion.

Tran LT, Taylor JS, Constabel CP - BMC Genomics (2012)

Neighbour-joining phylogenetic tree from four major land plant lineages, together with corresponding visual representation of conserved regions, functional motifs, and relative intron positions. A putative tyrosinase sequence from the cyanobacterium A. marina (GenBank accession ACJ76786) was used to root the tree. Bootstrap replicates (1000) were used to determine the level of support at each node (only values > 50% are shown). The conserved first five amino acids for each of the CuA and CuB domains is shown at the end of each branch as HxxxC / HxxxH. Predicted targeting sequences are colored as green (chloroplast transit peptide), black (signal peptide), or grey (unknown). The CuA and CuB domains are colored blue, and C-terminal conserved areas dark grey. Approximate intron positions are shown as vertical bars, mapped onto the predicted protein. Shared colors indicating the same intron positions, and black bars mark unique introns. The introns are named by their location: N, N-terminus; A, CuA domain; L, linker; D, DWL domain; K, KFDV domain; C, C-terminus. Exact intron positions are listed in Additional file4. The PPO sequences are numbered and named based on species names as follows: P. patens, Ppa; S. moellendorffii , Smo; B. distachyon, Bda; O. sativa, Osa; S. italica, Sit; S. bicolor, Sbi; Z. mays, Zma; A. coerulea, Aco; G. max, Gma; M. esculenta, Mes; M. guttatus, Mgu; P. trichocarpa, Ptr; R. communis, Rco; V. vinifera, Vvi. Mexican poppy (Argenome mexicana) AmePPO1 (GenBank accession ACJ76786) was also included in the phylogeny because of our interest in the Eudicot I clade.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472199&req=5

Figure 2: Neighbour-joining phylogenetic tree from four major land plant lineages, together with corresponding visual representation of conserved regions, functional motifs, and relative intron positions. A putative tyrosinase sequence from the cyanobacterium A. marina (GenBank accession ACJ76786) was used to root the tree. Bootstrap replicates (1000) were used to determine the level of support at each node (only values > 50% are shown). The conserved first five amino acids for each of the CuA and CuB domains is shown at the end of each branch as HxxxC / HxxxH. Predicted targeting sequences are colored as green (chloroplast transit peptide), black (signal peptide), or grey (unknown). The CuA and CuB domains are colored blue, and C-terminal conserved areas dark grey. Approximate intron positions are shown as vertical bars, mapped onto the predicted protein. Shared colors indicating the same intron positions, and black bars mark unique introns. The introns are named by their location: N, N-terminus; A, CuA domain; L, linker; D, DWL domain; K, KFDV domain; C, C-terminus. Exact intron positions are listed in Additional file4. The PPO sequences are numbered and named based on species names as follows: P. patens, Ppa; S. moellendorffii , Smo; B. distachyon, Bda; O. sativa, Osa; S. italica, Sit; S. bicolor, Sbi; Z. mays, Zma; A. coerulea, Aco; G. max, Gma; M. esculenta, Mes; M. guttatus, Mgu; P. trichocarpa, Ptr; R. communis, Rco; V. vinifera, Vvi. Mexican poppy (Argenome mexicana) AmePPO1 (GenBank accession ACJ76786) was also included in the phylogeny because of our interest in the Eudicot I clade.
Mentions: A neighbour-joining phylogenetic reconstruction was generated from a multiple sequence alignment of the copper-binding domains and the PPO1_DWL domain of PPO protein sequences from 14 of the 25 plant genomes we had surveyed (Additional file3). The genomes were chosen to be representative and to cover a broad range of plant lineages. The analysis separated PPOs into a number of distinct clades (Figure2). While the nodes at the base of the larger clades were not well supported (low scores in the bootstrap reanalyses), nodes at the base of many smaller clades were robust (bootstrap values > 70%). In Physcomitrella, Selaginella, and in the eudicots, PPO diversification is largely a consequence of species-specific gene duplication and divergence. Thus, 12 of the 13 Physcomitrella sequences occur in one group, and eight of the eleven Selaginella sequences form one clade, with the remaining three genes forming a second clade. Among the eudicots, 10 of the 11 Glycine PPOs form a monophyletic group, seven of the 10 Populus PPOs form a monophyletic group, and all but one of the nine Mimulus PPOs occur in a single clade. While these data show that PPO gene diversification has occurred independently in different eudicots, we note that these species also have one or two PPOs on separate branches, sometimes in well-supported clades with other eudicot genes. This indicates that the common ancestor of the eudicot lineage had several PPO genes.

Bottom Line: We found that many PPOs contained one or two introns often near the 3' terminus.While we found variation in intron numbers and positions, overall PPO gene structure is congruent with the phylogenetic relationships based on primary sequence data.The dynamic nature of this gene family differentiates PPO from other oxidative enzymes, and is consistent with a protein important for a diversity of functions relating to environmental adaptation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Forest Biology and Department of Biology, University of Victoria, Station CSC, Victoria, BC, Canada.

ABSTRACT

Background: Plant polyphenol oxidases (PPOs) are enzymes that typically use molecular oxygen to oxidize ortho-diphenols to ortho-quinones. These commonly cause browning reactions following tissue damage, and may be important in plant defense. Some PPOs function as hydroxylases or in cross-linking reactions, but in most plants their physiological roles are not known. To better understand the importance of PPOs in the plant kingdom, we surveyed PPO gene families in 25 sequenced genomes from chlorophytes, bryophytes, lycophytes, and flowering plants. The PPO genes were then analyzed in silico for gene structure, phylogenetic relationships, and targeting signals.

Results: Many previously uncharacterized PPO genes were uncovered. The moss, Physcomitrella patens, contained 13 PPO genes and Selaginella moellendorffii (spike moss) and Glycine max (soybean) each had 11 genes. Populus trichocarpa (poplar) contained a highly diversified gene family with 11 PPO genes, but several flowering plants had only a single PPO gene. By contrast, no PPO-like sequences were identified in several chlorophyte (green algae) genomes or Arabidopsis (A. lyrata and A. thaliana). We found that many PPOs contained one or two introns often near the 3' terminus. Furthermore, N-terminal amino acid sequence analysis using ChloroP and TargetP 1.1 predicted that several putative PPOs are synthesized via the secretory pathway, a unique finding as most PPOs are predicted to be chloroplast proteins. Phylogenetic reconstruction of these sequences revealed that large PPO gene repertoires in some species are mostly a consequence of independent bursts of gene duplication, while the lineage leading to Arabidopsis must have lost all PPO genes.

Conclusion: Our survey identified PPOs in gene families of varying sizes in all land plants except in the genus Arabidopsis. While we found variation in intron numbers and positions, overall PPO gene structure is congruent with the phylogenetic relationships based on primary sequence data. The dynamic nature of this gene family differentiates PPO from other oxidative enzymes, and is consistent with a protein important for a diversity of functions relating to environmental adaptation.

Show MeSH
Related in: MedlinePlus