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The cinnamyl alcohol dehydrogenase gene family in Populus: phylogeny, organization, and expression.

Barakat A, Bagniewska-Zadworna A, Choi A, Plakkat U, DiLoreto DS, Yellanki P, Carlson JE - BMC Plant Biol. (2009)

Bottom Line: CAD genes associated with xylem development (PoptrCAD 4 and PoptrCAD 10) belong to Class I and Class II.The duplication of several CAD genes seems to be associated with a genome duplication event that happened in the ancestor of Salicaceae.Phylogenetic analyses associated with expression profiling and results from previous studies suggest that CAD genes involved in wood development belong to Class I and Class II.

View Article: PubMed Central - HTML - PubMed

Affiliation: The School of Forest Resources, The Huck Institutes of the Life Sciences, Pennsylvania State University, 324 Forest Resources Building, University Park, PA 16802, USA. aub14@psu.edu

ABSTRACT

Background: Lignin is a phenolic heteropolymer in secondary cell walls that plays a major role in the development of plants and their defense against pathogens. The biosynthesis of monolignols, which represent the main component of lignin involves many enzymes. The cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis as it catalyzes the final step in the synthesis of monolignols. The CAD gene family has been studied in Arabidopsis thaliana, Oryza sativa and partially in Populus. This is the first comprehensive study on the CAD gene family in woody plants including genome organization, gene structure, phylogeny across land plant lineages, and expression profiling in Populus.

Results: The phylogenetic analyses showed that CAD genes fall into three main classes (clades), one of which is represented by CAD sequences from gymnosperms and angiosperms. The other two clades are represented by sequences only from angiosperms. All Populus CAD genes, except PoptrCAD 4 are distributed in Class II and Class III. CAD genes associated with xylem development (PoptrCAD 4 and PoptrCAD 10) belong to Class I and Class II. Most of the CAD genes are physically distributed on duplicated blocks and are still in conserved locations on the homeologous duplicated blocks. Promoter analysis of CAD genes revealed several motifs involved in gene expression modulation under various biological and physiological processes. The CAD genes showed different expression patterns in poplar with only two genes preferentially expressed in xylem tissues during lignin biosynthesis.

Conclusion: The phylogeny of CAD genes suggests that the radiation of this gene family may have occurred in the early ancestry of angiosperms. Gene distribution on the chromosomes of Populus showed that both large scale and tandem duplications contributed significantly to the CAD gene family expansion. The duplication of several CAD genes seems to be associated with a genome duplication event that happened in the ancestor of Salicaceae. Phylogenetic analyses associated with expression profiling and results from previous studies suggest that CAD genes involved in wood development belong to Class I and Class II. The other CAD genes from Class II and Class III may function in plant tissues under biotic stresses. The conservation of most duplicated CAD genes, the differential distribution of motifs in their promoter regions, and the divergence of their expression profiles in various tissues of Populus plants indicate that genes in the CAD family have evolved tissue-specialized expression profiles and may have divergent functions.

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Quantitative expression of Populus CAD genes. The name of each gene is indicated at the top of each histogram. Tissues studied are shown at the bottom of the diagrams. Means designated by the same letter do not differ significantly according to Tukey's HSD test; P < 0.05).
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Figure 5: Quantitative expression of Populus CAD genes. The name of each gene is indicated at the top of each histogram. Tissues studied are shown at the bottom of the diagrams. Means designated by the same letter do not differ significantly according to Tukey's HSD test; P < 0.05).

Mentions: Of the 15 CAD genes found in Populus, we analyzed the expression of 13 (see Additional file 1) in several different tissues that were selected based on the previous histochemical studies (Fig. 4). Expression analysis using quantitative real-time RT-PCR (Fig. 5) showed that all CAD genes are expressed in leaves, petioles, bark and xylem, but at different levels among the tissues. PoptrCAD7, for example, is expressed in leaves and petioles, but presents a very low expression in the bark and xylem. The expression patterns vary widely between genes, which were sorted into four groups based on the expression profiles observed in different tissues (Fig. 3). Group 1 (PoptrCAD4; PoptrCAD10) is represented by genes strongly expressed in xylem (lignin associated) – 100 times more highly expressed in xylem than the other CAD genes. Statistical analysis using the Ward linkage method showed that group 1 is significantly different in expression from the other three groups. One-way ANOVA analysis showed that the expression of PoptrCAD4 and PoptrCAD10 (group 1) in the xylem was statistically different from each other (p < 0.005) with PoptrCAD10 more expressed. Group 2 (PoptrCAD13, PoptrCAD7, PoptrCAD12) genes are expressed in all tissues but are most highly expressed in leaves. The group 3 (PoptrCAD9) gene is preferentially expressed in leaves and xylem. Genes from group 4 (PoptrCAD2, PoptrCAD3, PoptrCAD5, PoptrCAD6, PoptrCAD11, PoptrCAD14, PoptrCAD15) did not show any significant expression differences between tissues. As indicated in Fig. 3, group 1 genes are distributed in Class I and Class II, group 2 and group 4 genes are distributed in Class II and Class III, while gene from group 3 belong to Class II.


The cinnamyl alcohol dehydrogenase gene family in Populus: phylogeny, organization, and expression.

Barakat A, Bagniewska-Zadworna A, Choi A, Plakkat U, DiLoreto DS, Yellanki P, Carlson JE - BMC Plant Biol. (2009)

Quantitative expression of Populus CAD genes. The name of each gene is indicated at the top of each histogram. Tissues studied are shown at the bottom of the diagrams. Means designated by the same letter do not differ significantly according to Tukey's HSD test; P < 0.05).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2662859&req=5

Figure 5: Quantitative expression of Populus CAD genes. The name of each gene is indicated at the top of each histogram. Tissues studied are shown at the bottom of the diagrams. Means designated by the same letter do not differ significantly according to Tukey's HSD test; P < 0.05).
Mentions: Of the 15 CAD genes found in Populus, we analyzed the expression of 13 (see Additional file 1) in several different tissues that were selected based on the previous histochemical studies (Fig. 4). Expression analysis using quantitative real-time RT-PCR (Fig. 5) showed that all CAD genes are expressed in leaves, petioles, bark and xylem, but at different levels among the tissues. PoptrCAD7, for example, is expressed in leaves and petioles, but presents a very low expression in the bark and xylem. The expression patterns vary widely between genes, which were sorted into four groups based on the expression profiles observed in different tissues (Fig. 3). Group 1 (PoptrCAD4; PoptrCAD10) is represented by genes strongly expressed in xylem (lignin associated) – 100 times more highly expressed in xylem than the other CAD genes. Statistical analysis using the Ward linkage method showed that group 1 is significantly different in expression from the other three groups. One-way ANOVA analysis showed that the expression of PoptrCAD4 and PoptrCAD10 (group 1) in the xylem was statistically different from each other (p < 0.005) with PoptrCAD10 more expressed. Group 2 (PoptrCAD13, PoptrCAD7, PoptrCAD12) genes are expressed in all tissues but are most highly expressed in leaves. The group 3 (PoptrCAD9) gene is preferentially expressed in leaves and xylem. Genes from group 4 (PoptrCAD2, PoptrCAD3, PoptrCAD5, PoptrCAD6, PoptrCAD11, PoptrCAD14, PoptrCAD15) did not show any significant expression differences between tissues. As indicated in Fig. 3, group 1 genes are distributed in Class I and Class II, group 2 and group 4 genes are distributed in Class II and Class III, while gene from group 3 belong to Class II.

Bottom Line: CAD genes associated with xylem development (PoptrCAD 4 and PoptrCAD 10) belong to Class I and Class II.The duplication of several CAD genes seems to be associated with a genome duplication event that happened in the ancestor of Salicaceae.Phylogenetic analyses associated with expression profiling and results from previous studies suggest that CAD genes involved in wood development belong to Class I and Class II.

View Article: PubMed Central - HTML - PubMed

Affiliation: The School of Forest Resources, The Huck Institutes of the Life Sciences, Pennsylvania State University, 324 Forest Resources Building, University Park, PA 16802, USA. aub14@psu.edu

ABSTRACT

Background: Lignin is a phenolic heteropolymer in secondary cell walls that plays a major role in the development of plants and their defense against pathogens. The biosynthesis of monolignols, which represent the main component of lignin involves many enzymes. The cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis as it catalyzes the final step in the synthesis of monolignols. The CAD gene family has been studied in Arabidopsis thaliana, Oryza sativa and partially in Populus. This is the first comprehensive study on the CAD gene family in woody plants including genome organization, gene structure, phylogeny across land plant lineages, and expression profiling in Populus.

Results: The phylogenetic analyses showed that CAD genes fall into three main classes (clades), one of which is represented by CAD sequences from gymnosperms and angiosperms. The other two clades are represented by sequences only from angiosperms. All Populus CAD genes, except PoptrCAD 4 are distributed in Class II and Class III. CAD genes associated with xylem development (PoptrCAD 4 and PoptrCAD 10) belong to Class I and Class II. Most of the CAD genes are physically distributed on duplicated blocks and are still in conserved locations on the homeologous duplicated blocks. Promoter analysis of CAD genes revealed several motifs involved in gene expression modulation under various biological and physiological processes. The CAD genes showed different expression patterns in poplar with only two genes preferentially expressed in xylem tissues during lignin biosynthesis.

Conclusion: The phylogeny of CAD genes suggests that the radiation of this gene family may have occurred in the early ancestry of angiosperms. Gene distribution on the chromosomes of Populus showed that both large scale and tandem duplications contributed significantly to the CAD gene family expansion. The duplication of several CAD genes seems to be associated with a genome duplication event that happened in the ancestor of Salicaceae. Phylogenetic analyses associated with expression profiling and results from previous studies suggest that CAD genes involved in wood development belong to Class I and Class II. The other CAD genes from Class II and Class III may function in plant tissues under biotic stresses. The conservation of most duplicated CAD genes, the differential distribution of motifs in their promoter regions, and the divergence of their expression profiles in various tissues of Populus plants indicate that genes in the CAD family have evolved tissue-specialized expression profiles and may have divergent functions.

Show MeSH
Related in: MedlinePlus