Use of genomic history to improve phylogeny and understanding of births and deaths in a gene family

Sampedro, Javier; Lee, Yi; Carey, Robert E.; dePamphilis, Claude W.; Cosgrove, Daniel J.

doi:10.1111/j.1365-313x.2005.02540.x

Cited by 83 publications

(119 citation statements)

References 41 publications

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“…EXPB1 is a member of the group-1 grass pollen allergens, which comprise a subset of the larger EXPB family. The EXPB family is notably larger in grasses than in other groups of land plants, and part of this expansion involved the unique evolution and radiation of the pollen allergen class of EXPBs, which are encoded by multiple genes (49). For instance, we classified 5 of the 19 EXPB genes in the rice genome as group-1 allergens (49).…”

Section: Expansins As Cysteine Proteases?mentioning

confidence: 99%

Crystal structure and activities of EXPB1 (Zea m 1), a β-expansin and group-1 pollen allergen from maize

Yennawar¹,

Li²,

Dudzinski

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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230

247

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Expansins are small extracellular proteins that promote turgordriven extension of plant cell walls. EXPB1 (also called Zea m 1) is a member of the ␤-expansin subfamily known in the allergen literature as group-1 grass pollen allergens. EXPB1 induces extension and stress relaxation of grass cell walls. To help elucidate expansin's mechanism of wall loosening, we determined the structure of EXPB1 by x-ray crystallography to 2.75-Å resolution. EXPB1 consists of two domains closely packed and aligned so as to form a long, shallow groove with potential to bind a glycan backbone of Ϸ10 sugar residues. The structure of EXPB1 domain 1 resembles that of family-45 glycoside hydrolase (GH45), with conservation of most of the residues in the catalytic site. However, EXPB1 lacks a second aspartate that serves as the catalytic base required for hydrolytic activity in GH45 enzymes. Domain 2 of EXPB1 is an Ig-like ␤-sandwich, with aromatic and polar residues that form a potential surface for polysaccharide binding in line with the glycan binding cleft of domain 1. EXPB1 binds to maize cell walls, most strongly to xylans, causing swelling of the cell wall. Tests for hydrolytic activity by EXPB1 with various wall polysaccharides proved negative. Moreover, GH45 enzymes and a GH45-related protein called ''swollenin'' lacked wall extension activity comparable to that of expansins. We propose a model of expansin action in which EXPB1 facilitates the local movement and stress relaxation of arabinoxylancellulose networks within the wall by noncovalent rearrangement of its target.plant cell wall

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Section: Expansins As Cysteine Proteases?mentioning

confidence: 99%

Crystal structure and activities of EXPB1 (Zea m 1), a β-expansin and group-1 pollen allergen from maize

Yennawar¹,

Li²,

Dudzinski

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

230

247

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“…However, the current widespread usage of the term synteny, which we adopt, now implies conserved collinearity and genomic context. Synteny data are widely used to establish the occurrence of ancient polyploidy events, to identify chromosomal rearrangements, to examine the expansion and contraction of gene families, and to establish gene orthology (Sampedro et al, 2005;Tang et al, 2008a;Dewey, 2011;. Synteny likely reflects important relationships between the genomic context of genes both in terms of function and regulation and thus is often used as a "proxy for the conservation or constraint of gene function" (Dewey, 2011;Lv et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Phylogenomic Synteny Network Analysis of MADS-Box Transcription Factor Genes Reveals Lineage-Specific Transpositions, Ancient Tandem Duplications, and Deep Positional Conservation

et al. 2017

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Conserved genomic context provides critical information for comparative evolutionary analysis. With the increase in numbers of sequenced plant genomes, synteny analysis can provide new insights into gene family evolution. Here, we exploit a network analysis approach to organize and interpret massive pairwise syntenic relationships. Specifically, we analyzed synteny networks of the MADS-box transcription factor gene family using 51 completed plant genomes. In combination with phylogenetic profiling, several novel evolutionary patterns were inferred and visualized from synteny network clusters. We found lineage-specific clusters that derive from transposition events for the regulators of floral development (APETALA3 and PI) and flowering time (FLC) in the Brassicales and for the regulators of root development (AGL17) in Poales. We also identified two large gene clusters that jointly encompass many key phenotypic regulatory Type II MADS-box gene clades (SEP1, SQUA, TM8, SEP3, FLC, AGL6, and TM3). Gene clustering and gene trees support the idea that these genes are derived from an ancient tandem gene duplication that likely predates the radiation of the seed plants and then expanded by subsequent polyploidy events. We also identified angiosperm-wide conservation of synteny of several other less studied clades. Combined, these findings provide new hypotheses for the genomic origins, biological conservation, and divergence of MADS-box gene family members.

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“…1C). A previous analysis of the 25 EXPA gene sequences allowed their classification into a number of clades (Sampedro et al, 2005) that are color coded in Figure 1D. The order of the expansin genes was arranged according to their clade classification and similarity in expression pattern.…”

Section: Expansin Gene Expression During Leaf Developmentmentioning

confidence: 99%

Inducible Repression of Multiple Expansin Genes Leads to Growth Suppression during Leaf Development

et al. 2012

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Expansins are cell wall proteins implicated in the control of plant growth via loosening of the extracellular matrix. They are encoded by a large gene family, and data linked to loss of single gene function to support a role of expansins in leaf growth remain limited. Here, we provide a quantitative growth analysis of transgenics containing an inducible artificial microRNA construct designed to down-regulate the expression of a number of expansin genes that an expression analysis indicated are expressed during the development of Arabidopsis (Arabidopsis thaliana) leaf 6. The results support the hypothesis that expansins are required for leaf growth and show that decreased expansin gene expression leads to a more marked repression of growth during the later stage of leaf development. In addition, a histological analysis of leaves in which expansin gene expression was suppressed indicates that, despite smaller leaves, mean cell size was increased. These data provide functional evidence for a role of expansins in leaf growth, indicate the importance of tissue/organ developmental context for the outcome of altered expansin gene expression, and highlight the separation of the outcome of expansin gene expression at the cellular and organ levels.

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Use of genomic history to improve phylogeny and understanding of births and deaths in a gene family

Cited by 83 publications

References 41 publications

Crystal structure and activities of EXPB1 (Zea m 1), a β-expansin and group-1 pollen allergen from maize

Crystal structure and activities of EXPB1 (Zea m 1), a β-expansin and group-1 pollen allergen from maize

Phylogenomic Synteny Network Analysis of MADS-Box Transcription Factor Genes Reveals Lineage-Specific Transpositions, Ancient Tandem Duplications, and Deep Positional Conservation

Inducible Repression of Multiple Expansin Genes Leads to Growth Suppression during Leaf Development

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