Biology subjects

Niittyla, T.

Publications and source records attributed to Niittyla, T..

6 recordsLinked to original sources

bioRxiv2024

New insights into the mechanisms of post-rubisco isotope fractionation from combined analysis of intramolecular 13C and deuterium abundances in Pinus nigra tree-ring glucose

Understanding isotope fractionation mechanisms is fundamental for analyses of plant ecophysiology and paleoclimate based on tree-ring isotope data. To gain new insights into isotope fractionation, we analysed intramolecular 13C discrimination in tree-ring glucose ({Delta}i, i = C-1 to C-6) and metabolic deuterium fractionation at H1 and H2 ({varepsilon}met) combinedly. This dual-isotope approach was used for isotope-signal deconvolution. We found evidence for metabolic processes affecting{Delta} 1 and{Delta} 3 which respond to air vapour pressure deficit (VPD), and processes affecting{Delta} 1,{Delta} 2, and{varepsilon} met which respond to precipitation but not VPD. These relationships exhibit change points dividing a period of homeostasis (1961-1980) from a period of metabolic adjustment (1983-1995). Homeostasis may result from sufficient groundwater availability. Additionally, we found{Delta} 5 and{Delta} 6 relationships with radiation and temperature which are temporally stable and consistent with previously proposed isotope fractionation mechanisms. Based on the multitude of climate covariables, intramolecular carbon isotope analysis has a remarkable potential for climate reconstruction. While isotope fractionation beyond leaves is currently considered to be constant, we propose significant parts of the carbon and hydrogen isotope variation in tree-ring glucose originate in stems (precipitation-dependent signals). As basis for follow-up studies, we propose mechanisms introducing{Delta} 1,{Delta} 2,{Delta} 3, and{varepsilon} met variability.

plant biology↗

bioRxiv2021

Fluorescence lifetime imaging as an in situ and label-free readout for the chemical composition of lignin

Important structures and functions within living organisms rely on naturally fluorescent polymeric molecules such as collagen, keratin, elastin, resilin, or lignin. Theoretical physics predict that fluorescence lifetime of these polymers is related to their chemical composition. We verified this prediction for lignin, a major structural element in plant cell walls and one of the most abundant components of wood. Lignin is composed of different types of phenylpropanoid units, and its composition affects its properties, biological functions, and the utilization of wood biomass. We carried out fluorescence lifetime imaging microscopy (FLIM) measurements of wood cell wall lignin in a population of 90 hybrid aspen trees genetically engineered to display differences in cell wall chemistry and structure. We also measured wood cell wall composition by classical analytical methods in the wood cell walls of these trees. Using statistical modelling and machine learning algorithms, we identified parameters of fluorescence lifetime that predict the content of S-type and G-type lignin units, the two main types of units in the lignin of angiosperm plants. Finally, we show how quantitative measurements of lignin chemical composition by FLIM can reveal the dynamics of lignin biosynthesis in two different biological contexts, including in vivo while lignin is being synthesized in the walls of living cells.

plant biology↗

bioRxiv2021

Golgi-localized GALT7 and GALT8 participate in cellulose biosynthesis

Arabinogalactan protein (AGP) glycan biosynthesis in the Golgi apparatus contributes to plant cell wall assembly, but the mechanisms underlying this process are largely unknown. Here, we show that two putative galactosyltransferases -named GALT7 and GALT8 -from the glycosyltransferase family 31 (GT31) of Arabidopsis thaliana participate in cellulose biosynthesis. galt7galt8 mutants show primary cell wall defects manifesting as impaired growth and cell expansion in seedlings and etiolated hypocotyls, along with secondary cell wall defects, apparent as collapsed xylem vessels and reduced xylem wall thickness in the inflorescence stem. These phenotypes were associated with a [~]30% reduction in cellulose content, a [~]50% reduction in secondary cell wall CELLULOSE SYNTHASE (CESA) protein levels and reduced cellulose biosynthesis rate. CESA transcript levels were not significantly altered in galt7galt8 mutants, suggesting that the reduction in CESA levels was caused by a post-transcriptional mechanism. We provide evidence that both GALT7 and GALT8 localise to the Golgi apparatus, while quantitative proteomics experiments revealed reduced levels of the entire FLA subgroup B in the galt7galt8 mutants. This leads us to hypothesize that a defect in FLA subgroup B glycan biosynthesis reduces cellulose biosynthesis rate in galt7galt8 mutants.

plant biology↗

bioRxiv2021

Sucrose synthase activity is not required for cellulose biosynthesis in Arabidopsis

Biosynthesis of plant cell walls requires UDP-glucose as the substrate for cellulose biosynthesis, and as an intermediate for the synthesis of other matrix polysaccharides. The sucrose cleaving enzyme sucrose synthase (SUS) is thought to have a central role in UDP-glucose biosynthesis, and a long held and much debated hypothesis postulates that SUS is required to supply UDP-glucose to cellulose biosynthesis. To investigate the role of SUS in cellulose biosynthesis of Arabidopsis thaliana we characterized mutants in which four, or all six Arabidopsis SUS genes were disrupted. These sus mutants showed no growth phenotypes, vascular tissue cell wall defects or changes in cellulose content. Moreover, the UDP-glucose content of rosette leaves of the sextuple sus mutants was increased by approximately 20% compared to wild type. It can thus be concluded that cellulose biosynthesis is able to employ alternative UDP-glucose biosynthesis pathway(s), and thereby the model of SUS requirement for cellulose biosynthesis in Arabidopsis can be refuted.

plant biology↗

bioRxiv2020

Golgi-localized exo-β1,3-galactosidases involved in AGP modification and root cell expansion in Arabidopsis

Plant arabinogalactan proteins (AGPs) are a diverse group of cell surface- and wall-associated glycoproteins. Functionally important AGP glycans are synthesized in the Golgi apparatus, but the relationships between their glycosylation, processing, and functionality are poorly understood. Here we report the identification and functional characterization of two Golgi-localized exo-{beta}-1,3-galactosidases from the glycosyl hydrolase 43 (GH43) family in Arabidopsis thaliana. GH43 loss of function mutants exhibit root cell expansion defects in sugar-containing growth media. This root phenotype is associated with an increase in the extent of AGP cell wall association, as demonstrated by Yariv phenylglycoside dye quantification and comprehensive microarray polymer profiling of sequentially extracted cell walls. Recombinant GH43 characterization showed that the exo-{beta}-1,3-galactosidase activity of GH43s is hindered by {beta}-1,6 branches on {beta}-1,3-galactans. In line with this steric hindrance, the recombinant GH43s did not release galactose from cell wall extracted glycoproteins or AGP rich gum arabic. These results show that Arabidopsis GH43s are involved in AGP glycan biosynthesis in the Golgi, and suggest their exo-{beta}-1,3-galactosidase activity influences AGP and cell wall matrix interactions, thereby adjusting cell wall extensibility.

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↗