Biology subjects

Tuominen, H.

Publications and source records attributed to Tuominen, H..

3 recordsLinked to original sources

bioRxiv2018

Cell death in cells overlying lateral root primordia contributes to organ growth in Arabidopsis

Unlike animal development, plant organ growth is widely accepted to be determined by cell division without any contribution of cell elimination. We investigated this paradigm during Arabidopsis lateral root formation when growth of the new primordia (LRP) from pericycle-derived stem cells deep inside the root is reportedly facilitated by remodeling of the walls of overlying cells without apparent cell death. However, we observed the induction of marker genes for cell types undergoing developmental cell death in several cells overlying the growing LRP. Transmission electron microscopy, time-lapse confocal and light sheet microscopy techniques were used to establish that cell death occurred at least in a subset of endodermal LRP-overlying cells during organ emergence. Significantly, organ emergence was retarded in mutants lacking a positive cell death regulator, and restored by inducing cell death in cells overlying LRP. Hence, we conclude that in the case of LRP, cell elimination contributes to organ growth.

plant biology↗

bioRxiv2017

A Collection Of Genetically Engineered Populus Trees Reveals Wood Biomass Traits That Predict Glucose Yield From Enzymatic Hydrolysis

Wood represents a promising source of lignocellulosic biomass for the production of bio-based renewables, especially biofuels. However, woody feedstocks must be improved to become competitive against petroleum. We created a collection of Populus trees consisting of 40 genetically engineered lines to modify and to better understand wood biomass properties. A total of 65 traits were measured in these trees and in the corresponding wild-type clone, including growth parameters, wood anatomical and structural properties, cell wall composition and analytical saccharification. The relationships between saccharification of glucose and biomass traits were investigated using multivariate data analysis methods and mathematical modeling. To circumvent potential trade-offs between biomass production and saccharification potential, we also estimated the \"total-wood glucose yield\" (TWG) expected after pretreatment and 72h of enzymatic hydrolysis from whole trees. A mathematical model estimated TWG from a subset of 22 wood biomass traits with good predictivity (Q2 = 0.8), while saccharification of glucose could be predicted from seven biomass traits (Q2 = 0.49). Among the seven diagnostic traits for saccharification, four also affected biomass production, such as the ratio of S- to G-lignin which was beneficial for saccharification but detrimental for growth. The contents of various matrix polysaccharides appeared important for predicting both saccharification and TWG, including low abundance monosaccharides. In particular, fucose and mannose contents negatively correlated with TWG, apparently by negatively associating with biomass production. Both biomass production and saccharification, and hence TWG, negatively correlated with arabinose and rhamnose contents, suggesting that these low abundance monosaccharides represent markers/targets for improving feedstocks.

plant biology↗

bioRxiv2016

High-spatial-resolution transcriptome profiling reveals uncharacterized regulatory complexity underlying cambial growth and wood formation in Populus tremula

Trees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose. There is significant scope for yield and quality improvement in these largely undomesticated species, and efforts to engineer new, elite varieties will benefit from an improved understanding of the transcriptional network underlying cambial growth and wood formation. We generated high-spatial-resolution RNA Sequencing data spanning the secondary phloem, vascular cambium and wood forming tissues. The transcriptome comprised 28,294 expressed, previously annotated genes, 78 novel protein-coding genes and 567 long intergenic non-coding RNAs. Most paralogs originating from the Salicaceae whole genome duplication were found to have diverged expression, with the notable exception of those with high expression during secondary cell wall deposition. Co-expression network analysis revealed that the regulation of the transcriptome underlying cambial growth and wood formation comprises numerous modules forming a continuum of active processes across the tissues. The high spatial resolution enabled identification of novel roles for characterised genes involved in xylan and cellulose biosynthesis, regulators of xylem vessel and fiber differentiation and lignification. The associated web resource (AspWood, http://aspwood.popgenie.org) integrates the data within a set of interactive tools for exploring the expression profiles and co-expression network.

plant biology↗