Bioinformatic and phylogenetic analysis of the CLAVATA3/EMBRYO-SURROUNDING REGION (CLE) and the CLE-LIKE signal peptide genes in the Pinophyta.

Background: There is a rapidly growing awareness that plant peptide signalling molecules are numerous and varied and they are known to play fundamental roles in angiosperm plant growth and development. Two closely related peptide signalling molecule families are the CLAVATA3-EMBRYO-SURROUNDING REGION (CLE) and CLE-LIKE (CLEL) genes, which encode precursors of secreted peptide ligands that have roles in meristem maintenance and root gravitropism. Progress in peptide signalling molecule research in gymnosperms has lagged behind that of angiosperms.

Golgi enrichment and proteomic analysis of developing Pinus radiata xylem by free-flow electrophoresis.

Our understanding of the contribution of Golgi proteins to cell wall and wood formation in any woody plant species is limited. Currently, little Golgi proteomics data exists for wood-forming tissues. In this study, we attempted to address this issue by generating and analyzing Golgi-enriched membrane preparations from developing xylem of compression wood from the conifer Pinus radiata.

Potential transgenic routes to increase tree biomass.

Biomass is a prime target for genetic engineering in forestry because increased biomass yield will benefit most downstream applications such as timber, fiber, pulp, paper, and bioenergy production. Transgenesis can increase biomass by improving resource acquisition and product utilization and by enhancing competitive ability for solar energy, water, and mineral nutrients. Transgenes that affect juvenility, winter dormancy, and flowering have been shown to influence biomass as well.

The Arabidopsis wood model-the case for the inflorescence stem.

Arabidopsis thaliana has successfully served as a model to discover genes and proteins that have roles in a wide range of plant traits, including wood-related traits, such as lignin, cellulose and hemicellulose biosynthesis, secondary growth regulation, and secondary cell wall synthesis. Both the radially thickened hypocotyl and the inflorescence stem (flower stalk) have been studied. In this review, we address lingering doubts regarding the utility of Arabidopsis as a model for wood development by highlighting studies that provide new biochemical and biophysical evidence that extend support for the Arabidopsis inflorescence stem as a model for wood development beyond what is currently thought.

A survey of the natural variation in biomechanical and cell wall properties in inflorescence stems reveals new insights into the utility of Arabidopsis as a wood model.

The natural trait variation in Arabidopsis thaliana (L.) Heynh. accessions is an important resource for understanding many biological processes but it is underexploited for wood-related properties.

Proteomic phenotyping of Novosphingobium nitrogenifigens reveals a robust capacity for simultaneous nitrogen fixation, polyhydroxyalkanoate production, and resistance to reactive oxygen species.

Novosphingobium nitrogenifigens Y88(T) (Y88) is a free-living, diazotrophic Alphaproteobacterium, capable of producing 80% of its biomass as the biopolymer polyhydroxybutyrate (PHB). We explored the potential utility of this species as a polyhydroxybutyrate production strain, correlating the effects of glucose, nitrogen availability, dissolved oxygen concentration, and extracellular pH with polyhydroxybutyrate production and changes in the Y88 proteomic profile. Using two-dimensional differential in-gel electrophoresis and tandem mass spectrometry, we identified 217 unique proteins from six growth conditions.

Draft genome sequence of Novosphingobium nitrogenifigens Y88(T).

Novosphingobium nitrogenifigens was originally isolated from pulp and paper mill wastewater, a low-nitrogen, high-carbon environment. N. nitrogenifigens is the first known nitrogen-fixing, polyhydroxyalkanoate-accumulating sphingomonad, and we report the annotated draft genome sequence of the type strain Y88(T) here.

Proteomic analysis of membrane preparations from developing Pinus radiata compression wood.

For coniferous gymnosperms, few data exist as to the contribution of the membrane-associated proteome to cell wall and wood formation. In this study, we begin to address this knowledge deficiency by examining the proteomic profile of Golgi-enriched membrane preparations derived from developing Pinus radiata compression wood. These membrane preparations were generated by a combination of discontinuous sucrose gradient centrifugation and Triton X-114-based phase separation.

CLE genes in plant development: Gain-of-function analyses, pleiotropy, hypermorphy and neomorphy.

In Arabidopsis, the CLE genes encode a family of at least 32 peptide ligands. Our gain-of-function studies demonstrated that all of the 18 genes we examined caused pleiotropic and often opposing phenotypes, including various combinations of increased root and rosette growth, root stunting, dwarfing, shoot apical meristem (SAM) arrest, asymmetric leaf development, and "shrublike" phenotypes. Many CLE genes caused similar phenotypes that correlated with common amino acid substitutions among subsets of the genes, suggesting key amino acids necessary for certain phenotypes.

Exploring the ultrastructural localization and biosynthesis of beta(1,4)-galactan in Pinus radiata compression wood.

Softwood species such as pines react to gravitropic stimuli by producing compression wood, which unlike normal wood contains significant amounts of beta(1,4)-galactan. Currently, little is known regarding the biosynthesis or physiological function of this polymer or the regulation of its deposition. The subcellular location of beta(1,4)-galactan in developing tracheids was investigated in Pinus radiata D.

Gain-of-function phenotypes of many CLAVATA3/ESR genes, including four new family members, correlate with tandem variations in the conserved CLAVATA3/ESR domain.

Secreted peptide ligands are known to play key roles in the regulation of plant growth, development, and environmental responses. However, phenotypes for surprisingly few such genes have been identified via loss-of-function mutant screens. To begin to understand the processes regulated by the CLAVATA3 (CLV3)/ESR (CLE) ligand gene family, we took a systems approach to gene identification and gain-of-function phenotype screens in transgenic plants.