scholarly journals Gene families and evolution of trehalose metabolism in plants

2007 ◽  
Vol 34 (6) ◽  
pp. 550 ◽  
Author(s):  
John E. Lunn
Keyword(s):  
Physcomitrella Patens ◽  
Oryza Sativa L ◽  
Populus Trichocarpa ◽  
Gene Families ◽  
Class I ◽  
Trehalose Metabolism ◽  
Genes Encoding ◽  
Catalytically Active ◽  
Large Families ◽  
Selaginella Moellendorffii

The genomes of Arabidopsis thaliana L., rice (Oryza sativa L.) and poplar (Populus trichocarpa Torr. & A.Gray) contain large families of genes encoding trehalose-phosphate synthase (TPS) and trehalose-phosphatase (TPP). The class I subfamily of TPS genes encodes catalytically active TPS enzymes, and is represented by only one or two genes in most species. A. thaliana is atypical in having four class I TPS genes, three of which (AtTPS2–4) encode unusual short isoforms of TPS that appear to be found only in members of the Brassicaceae family. The class II TPS genes encode TPS-like proteins with a C-terminal TPP-like domain, but there is no experimental evidence that they have any enzymatic activity and their function is unknown. Both classes of TPS gene are represented in the genomes of chlorophyte algae (Ostreococcus species) and non-flowering plants [Physcomitrella patens (Hedw.) Bruch & Schimp.(B.S.G.) and Selaginella moellendorffii (Hieron. in Engl. & Prantl.)]. This survey shows that the gene families encoding the enzymes of trehalose metabolism are very ancient, pre-dating the divergence of the streptophyte and chlorophyte lineages. It also provides a frame of reference for future studies to elucidate the function of trehalose metabolism in plants.

Genome-wide analyses of phenylpropanoid-related genes in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa: the Populus lignin toolbox and conservation and diversification of angiosperm gene familiesThis article is one of a selection of papers published in the Special Issue on Poplar Research in Canada.

2007 ◽  
Vol 85 (12) ◽  
pp. 1182-1201 ◽  
Author(s):  
Björn Hamberger ◽  
Margaret Ellis ◽  
Michael Friedmann ◽  
Clarice de Azevedo Souza ◽  
Brad Barbazuk ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Populus Trichocarpa ◽  
Rice Genome ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Comparative Approach ◽  
Expression Data ◽  
Poplar Genome ◽  
Genes Encoding ◽  
Bona Fide

The completion of the Populus trichocarpa (Torr. & A. Gray) (poplar) genome sequence offers an opportunity to study complete genome families in a third fully sequenced angiosperm (after Arabidopsis and rice) and to conduct comparative genomics studies of angiosperm gene family evolution. We focussed on gene families encoding phenylpropanoid and phenylpropanoid-like enzymes, and identified and annotated the full set of genes encoding these and related enzymes in the poplar genome. We used a similar approach to identify an analogous set of genes from the rice genome and generated phylogenetic trees for nine phenylpropanoid gene families from aligned poplar, Arabidopsis, and rice predicted protein sequences. This enabled us to identify the likely full set of bona fide poplar lignin-related phenylpropanoid genes (poplar “lignification toolbox”) apparent within well-defined clades in all phylogenetic trees. Analysis of expression data for poplar genes confirmed and refined annotations of lignin-related genes, which generally showed high expression in wood-forming tissues. Expression data from both poplar and Arabidopsis were used to make inferences regarding biochemical and biological functions of phenylpropanoid-like genes with unknown functions. The comparative approach also provided insights into the evolution of angiosperm phenylpropanoid-like gene families, illustrating lineage-specific clades as well as ancient clades containing genes with apparent conserved function.

scholarly journals The Poplar-Poplar Rust Interaction: Insights from Genomics and Transcriptomics

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Stéphane Hacquard ◽  
Benjamin Petre ◽  
Pascal Frey ◽  
Arnaud Hecker ◽  
Nicolas Rouhier ◽  
...  
Keyword(s):  
Populus Trichocarpa ◽  
Rust Fungus ◽  
Gene Families ◽  
Genetic Determinants ◽  
Plant Host ◽  
Recombinant Protein Purification ◽  
Functional Studies ◽  
Regulated Expression ◽  
Genes Encoding ◽  
Host Tissues

Poplars are extensively cultivated worldwide, and their susceptibility to the leaf rust fungusMelampsora larici-populinaleads to considerable damages in plantations. Despite a good knowledge of the poplar rust life cycle, and particularly the epidemics on poplar, the perennial status of the plant host and the obligate biotrophic lifestyle of the rust fungus are bottlenecks for molecular investigations. Following the completion of bothM. larici-populinaandPopulus trichocarpagenome sequences, gene families involved in poplar resistance or in rust fungus virulence were investigated, allowing the identification of key genetic determinants likely controlling the outcome of the interaction. Specific expansions of resistance and defense-related genes in poplar indicate probable innovations in perennial species in relation with host-pathogen interactions. The genome ofM. Larici-populinacontains a strikingly high number of genes encoding small secreted proteins (SSPs) representing hundreds of candidate effectors. Transcriptome analyses of interacting partners in compatible and incompatible interactions revealed conserved set of genes involved in poplar defense reactions as well as timely regulated expression of SSP transcripts during host tissues colonisation. Ongoing functional studies of selected candidate effectors will be achieved mainly on the basis of recombinant protein purification and subsequent characterisation.

scholarly journals The COPII components Sec23 and Sec24 form isoform specific subcomplexes with Sec23D/E and Sec24C/D essential for tip growth

2020 ◽  
Author(s):  
Mingqin Chang ◽  
Shu-Zon Wu ◽  
Jacquelyn E. O’Sullivan ◽  
Magdalena Bezanilla
Keyword(s):  
Plasma Membrane ◽  
Tip Growth ◽  
Physcomitrella Patens ◽  
Gene Families ◽  
Vesicle Traffic ◽  
Genes Encoding ◽  
Er Exit Sites

AbstractCOPII, a coat of proteins that form vesicles on the ER, mediates vesicle traffic from the ER to the Golgi. In contrast to metazoans that have few genes encoding each COPII component, plants have expanded these gene families leading to the hypothesis that plant COPII has functionally diversified. Here, we analyzed the gene families encoding for the Sec23/24 heterodimer in the moss Physcomitrium (Physcomitrella) patens. In P. patens, Sec23 and Sec24 gene families are each comprised of seven genes. We discovered that Sec23D is functionally redundant with Sec23E and together they are essential for protonemal development. Sec23D is critical for secretion to the Golgi and the plasma membrane in tip growing protonemata. Sec23D preferentially associates with Sec24C/D, also essential for protonemata. In contrast, the remaining five Sec23 genes are dispensable for tip growth, but are redundant with Sec23D/E for gametophore formation. While Sec23A/B/C/F/G do not quantitatively affect Golgi secretion in protonemata, they do contribute to secretion to the plasma membrane. Furthermore, the three highly expressed Sec23 genes in protonemata, Sec23B/D/G form morphologically distinct ER exit sites. These data suggest that Sec23D/E form unique ER exit sites contributing to secretion that is essential for tip growing protonemata.

scholarly journals A peroxisomal β-oxidative pathway contributes to the formation of C6–C1 aromatic volatiles in poplar

2021 ◽  
Author(s):  
Nathalie D Lackus ◽  
Axel Schmidt ◽  
Jonathan Gershenzon ◽  
Tobias G Köllner
Keyword(s):  
Cinnamic Acid ◽  
Aromatic Compounds ◽  
Populus Trichocarpa ◽  
Alternative Pathway ◽  
Gene Families ◽  
Defense Responses ◽  
In Planta ◽  
Black Cottonwood ◽  
Oxidative Pathway

AbstractBenzenoids (C6–C1 aromatic compounds) play important roles in plant defense and are often produced upon herbivory. Black cottonwood (Populus trichocarpa) produces a variety of volatile and nonvolatile benzenoids involved in various defense responses. However, their biosynthesis in poplar is mainly unresolved. We showed feeding of the poplar leaf beetle (Chrysomela populi) on P. trichocarpa leaves led to increased emission of the benzenoid volatiles benzaldehyde, benzylalcohol, and benzyl benzoate. The accumulation of salicinoids, a group of nonvolatile phenolic defense glycosides composed in part of benzenoid units, was hardly affected by beetle herbivory. In planta labeling experiments revealed that volatile and nonvolatile poplar benzenoids are produced from cinnamic acid (C6–C3). The biosynthesis of C6–C1 aromatic compounds from cinnamic acid has been described in petunia (Petunia hybrida) flowers where the pathway includes a peroxisomal-localized chain shortening sequence, involving cinnamate-CoA ligase (CNL), cinnamoyl-CoA hydratase/dehydrogenase (CHD), and 3-ketoacyl-CoA thiolase (KAT). Sequence and phylogenetic analysis enabled the identification of small CNL, CHD, and KAT gene families in P. trichocarpa. Heterologous expression of the candidate genes in Escherichia coli and characterization of purified proteins in vitro revealed enzymatic activities similar to those described in petunia flowers. RNA interference-mediated knockdown of the CNL subfamily in gray poplar (Populus x canescens) resulted in decreased emission of C6–C1 aromatic volatiles upon herbivory, while constitutively accumulating salicinoids were not affected. This indicates the peroxisomal β-oxidative pathway participates in the formation of volatile benzenoids. The chain shortening steps for salicinoids, however, likely employ an alternative pathway.

scholarly journals Arabidopsis Genes Essential for Seedling Viability: Isolation of Insertional Mutants and Molecular Cloning

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1765-1778
Author(s):  
Gregory J Budziszewski ◽  
Sharon Potter Lewis ◽  
Lyn Wegrich Glover ◽  
Jennifer Reineke ◽  
Gary Jones ◽  
...  
Keyword(s):  
Large Scale ◽  
Protein Translocation ◽  
Gene Families ◽  
Mutant Phenotype ◽  
Lethal Mutant ◽  
A Genome ◽  
Genes Encoding ◽  
High Level ◽  
Mutant Lines ◽  
Genome Scale

Abstract We have undertaken a large-scale genetic screen to identify genes with a seedling-lethal mutant phenotype. From screening ~38,000 insertional mutant lines, we identified >500 seedling-lethal mutants, completed cosegregation analysis of the insertion and the lethal phenotype for >200 mutants, molecularly characterized 54 mutants, and provided a detailed description for 22 of them. Most of the seedling-lethal mutants seem to affect chloroplast function because they display altered pigmentation and affect genes encoding proteins predicted to have chloroplast localization. Although a high level of functional redundancy in Arabidopsis might be expected because 65% of genes are members of gene families, we found that 41% of the essential genes found in this study are members of Arabidopsis gene families. In addition, we isolated several interesting classes of mutants and genes. We found three mutants in the recently discovered nonmevalonate isoprenoid biosynthetic pathway and mutants disrupting genes similar to Tic40 and tatC, which are likely to be involved in chloroplast protein translocation. Finally, we directly compared T-DNA and Ac/Ds transposon mutagenesis methods in Arabidopsis on a genome scale. In each population, we found only about one-third of the insertion mutations cosegregated with a mutant phenotype.

scholarly journals Molecular cloning of RBCS genes in Selaginella and the evolution of the rbcS gene family

2015 ◽  
Vol 67 (2) ◽  
pp. 373-383
Author(s):  
Bo Wang ◽  
Su Yingjuan ◽  
Ting Wang
Keyword(s):  
Gene Family ◽  
Physcomitrella Patens ◽  
Higher Plants ◽  
Genome Wide ◽  
A Genome ◽  
Rbcs Gene ◽  
Rbcs Genes ◽  
Selaginella Moellendorffii ◽  
Insight Into ◽  
Major Domain

Rubisco small subunits (RBCS) are encoded by a nuclear rbcS multigene family in higher plants and green algae. However, owing to the lack of rbcS sequences in lycophytes, the characteristics of rbcS genes in lycophytes is unclear. Recently, the complete genome sequence of the lycophyte Selaginella moellendorffii provided the first insight into the rbcS gene family in lycophytes. To understand further the characteristics of rbcS genes in other Selaginella, the full length of rbcS genes (rbcS1 and rbcS2) from two other Selaginella species were isolated. Both rbcS1 and rbcS2 genes shared more than 97% identity among three Selaginella species. RBCS proteins from Selaginella contained the Pfam RBCS domain F00101, which was a major domain of other plant RBCS proteins. To explore the evolution of the rbcS gene family across Selaginella and other plants, we identified and performed comparative analysis of the rbcS gene family among 16 model plants based on a genome-wide analysis. The results showed that (i) two rbcS genes were obtained in Selaginella, which is the second fewest number of rbcS genes among the 16 representative plants; (ii) an expansion of rbcS genes occurred in the moss Physcomitrella patens; (iii) only RBCS proteins from angiosperms contained the Pfam PF12338 domains, and (iv) a pattern of concerted evolution existed in the rbcS gene family. Our study provides new insights into the evolution of the rbcS gene family in Selaginella and other plants.

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