Metabolic profiling: a new tool in the study of wood formation

Cellular and Metabolite Changes in the Secondary Phloem of Chinese Fir (Cuninghamia lanceolata (Lamb.) Hook.) during Dormancy Release

Wood in the cold temperate zone is the product of the alternation of the growing season and the dormant period of trees, but our knowledge of the process of dormancy release in trees remains limited. Chinese fir (Cuninghamia lanceolata (Lamb.) Hook.) was used to investigate cellular and metabolite changes in the secondary phloem tissue during dormancy release. The sampling dates were 2 March, 28 March, and 13 April. The microsections of wood-forming tissue were prepared using the paraffin embedding technique to observe the formation of cambium cells; metabolites in secondary phloem cells were extracted using a methanol/chloroform organic solvent system. The results showed that the secondary phloem consists of phloem fibers, sieve cells and phloem parenchyma. The cells were regularly arranged in continuous tangential bands and were in the order of Phloem fiber-Sieve cell-Phloem parenchyma-Sieve cell-Phloem parenchyma-Sieve cell-Phloem parenchyma-Sieve cell-Sieve cell-Phloem parenchyma-. The Chinese fir cambium was in dormancy on 2 March and 28 March, while on 13 April, it was already in the active stage and two layers of xylem cells with several layers of phloem cells were newly formed. The width of the cambium zone increased from 18.7 ± 5.7 μm to 76.5 ± 3.0 μm and the average radial diameter of sieve cells expanded from 15.4 ± 7.5 μm to 21.5 ± 7.4 μm after dormancy release. The cambium zone width and the average radial diameter of sieve cells before and after dormancy release were significantly different (p < 0.01). The phloem parenchyma cells without resin were squeezed and deformed by the sieve cells, and the width of the phloem during the active period was 197.0 ± 8.5 μm, which was larger than that during the dormant period. Ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS)-based metabolomics was employed to analyze the secondary phloem of Chinese fir on 28 March and 13 April. Thirty-nine differential metabolites during dormancy release were detected. The results showed that the composition of Chinese fir metabolites was different before and after dormancy release. The relative increase in pyruvic acid and ascorbic acid contents proved that the rate of energy metabolism in Chinese fir increased substantially after dormancy release. Changes in cell development and the composition of metabolites revealed that the dormancy release of Chinese fir was at early April and the formation period of phloem tissue is earlier than xylem tissue.

Assessing the between-background stability of metabolic effects arising from lignin-related transgenic modifications, in two Populus hybrids using non-targeted metabolomics

The advances in 'high-throughput' biology have significantly expanded our fundamental understanding of complex biological processes inherent to tree growth and development. Relative to the significant achievements attained with whole genome re-sequencing and transcriptomics efforts, the development and power of post-transcriptional tools such as proteomics and metabolomics continue to lag behind in tree biology. However, the inclusion of these powerful functional genomics platforms should substantially enable systems biology assessments of tree development, physiology and response(s) to biotic and abiotic stresses. Herein, we employ a non-targeted metabolomics platform to elucidate the metabolic plasticity of xylem lignification in distinct hybrid poplar genetic backgrounds, as well as in transgenic trees in these backgrounds expressing two common constructs: the first construct (C4H::F5H) augments monolignol content (syringyl:guaiacyl (S:G) ratio), while the second construct (C3'H-RNAi) reduces cell wall lignification. The results clearly show that genotype-specific metabolism exists, and provide an appropriate foundation for properly comparing the influence of background on the relationships between metabolic and specific phenotypic traits. Moreover, it was apparent that transgene-induced phenotypic gradients in cell wall chemical wood can be associated with global metabolism of secondary xylem biosynthesis, however in a genotype-specific manner. This result implies that the same may be true for phenotypic gradients arising through natural genetic variation, intensive breeding or environmental factors. It is also apparent that while distinct, at a global level the wood-forming metabolisms of different poplar hybrids can, to some extent, respond similarly to the influences of genetic manipulation of lignin-related genes. This further implies that with the correct approach, it may be possible to associate the emergence of specific wood traits from different genetic backgrounds-be they transgene-induced or otherwise-with stable metabolic signatures.

A chemometric-assisted method based on gas chromatography-mass spectrometry for metabolic profiling analysis

An automatic and efficient data analysis method for comprehensive metabolic profiling analysis is urgently required. In this study, a new chemometric-assisted method for metabolic profiling analysis (CAMMPA) was developed to discover potentially valuable metabolites automatically and efficiently. The proposed method mainly consists of three stages. First, automatic chromatographic peak detection is performed based on the total ion chromatograms of samples to extract chromatographic peaks that can be accurately quantified. Second, a novel peak-shift alignment technique based on peak detection results is implemented to resolve time-shift problems across samples. Consequently, aligned results, including aligned chromatograms, and peak area tables, among others, can be successfully obtained. Third, statistical analysis using results from unsupervised and supervised classification results, together with ANOVA and partial least square-discriminate analysis, is performed to extract potential metabolites. To demonstrate the proposed technique, a complex GC-MS metabolic profiling dataset was measured to identify potential metabolites in tobacco plants of different growth stages as well as different plant tissues after maturation. Results indicated that the efficiency of the routine metabolic profiling analysis procedure can be significantly improved and potential metabolites can be accurately identified with the aid of CAMMPA.

Spectral deconvolution for gas chromatography mass spectrometry-based metabolomics: current status and future perspectives

Mass spectrometry coupled to gas chromatography (GC-MS) has been widely applied in the field of metabolomics. Success of this application has benefited greatly from computational workflows that process the complex raw mass spectrometry data and extract the qualitative and quantitative information of metabolites. Among the computational algorithms within a workflow, deconvolution is critical since it reconstructs a pure mass spectrum for each component that the mass spectrometer observes. Based on the pure spectrum, the corresponding component can be eventually identified and quantified. Deconvolution is challenging due to the existence of co-elution. In this review, we focus on progress that has been made in the development of deconvolution algorithms and provide thoughts on future developments that will expand the application of GC-MS in metabolomics.

Predicting the regenerative capacity of conifer somatic embryogenic cultures by metabolomics

Somatic embryogenesis in gymnosperms is an effective approach to clonally propagating germplasm. However, embryogenic cultures frequently lose regenerative capacity. The interactions between metabolic composition, physiological state, genotype and embryogenic capacity in Pinus taeda (loblolly pine) somatic embryogenic cultures were explored using metabolomics. A stepwise modelling procedure, using the Bayesian information criterion, generated a 47 metabolite predictive model that could explain culture productivity. The model performed extremely well in cross-validation, achieving a correlation coefficient of 0.98 between actual and predicted mature embryo production. The metabolic composition and structure of the model implied that variation in culture regenerative capacity was closely linked to the physiological transition of cultures from the proliferation phase to the maturation phase of development. The propensity of cultures to advance into this transition appears to relate to nutrient uptake and allocation in vivo, and to be associated with the tolerance and response of cultures to stress, during the proliferation phase.

Nutriomic analysis of fresh and processed fruit products. 1. During in vitro digestions

Nutriomic analysis is a postgenomic-based study of nutritious components (nutriome). There is a need for an in vitro digestion and absorption model to unravel interactive factors varying nutriome release from various food materials that cannot be directly studied in humans. Effects of processing and in vitro digestion steps on carotenoid, sugar, and organic acid release from tomato, papaya, and mango products were comprehensively studied for the first time in this research. In vivo chewing experiments using 24 healthy adult volunteers was carried out prior to chewing simulation. Microscopy showed that cutting and blending alone were unlikely to mimic chewing at swallowing point. Using general linear model (GLM) ANOVA and principal component analysis (PCA), effects of interaction between digestion steps and processing types on the nutriome release were significant (p < 0.05) when 90% particles of 0.5 (dried) and 1.5 cm (fresh) were digested in vitro. Generally, dried and fresh fruits released lower levels of nutriome components than juices. PCA indicated nutriome release from tomato products was affected by the factors studied more than those from papaya and mango products. Fruit type is the main determinant factor relative to processing and digestion steps because it determines the extent of matrix that breaks down and consequent nutriome diffusion rates. It is predicted that pectin plays a role in determining the rate of nutriome release and absorption, which requires further investigation.

Metabolite profiling of Douglas-fir (Pseudotsuga menziesii) field trials reveals strong environmental and weak genetic variation

The primary objective of this study was to assess metabolomics for its capacity to discern biological variation among 10 full-sib families of a Douglas-fir tree breeding population, replicated on two sites. The differential accumulation of small metabolites in developing xylem was examined through metabolite profiles (139 metabolites common to 181 individual trees) generated by gas chromatography mass spectrometry and a series of statistical analyses that incorporated family, site, and tree growth and quantitative phenotypic wood traits (wood density, microfibril angle, wood chemistry and fiber morphology). Multivariate discriminant, canonical discriminant and factor analyses and broad-sense heritabilities revealed that metabolic and phenotypic traits alike were strongly related to site, while similar associations relating to genetic (family) structure were weak in comparison. Canonical correlation analysis subsequently identified correlations between specific phenotypic traits (i.e. tree growth, fibre morphology and wood chemistry) and metabolic traits (i.e. carbohydrate and lignin biosynthetic metabolites), demonstrating a coherent relationship between genetics, metabolism, environmental and phenotypic expression in wood-forming tissue. The association between cambial metabolites and tree phenotype, as revealed by metabolite profiling, demonstrates the value of metabolomics for systems biology approaches to understanding tree growth and secondary cell wall biosynthesis in plants.

The potential of metabolite profiling as a selection tool for genotype discrimination in Populus

Differences between wild-type Populus tremulaxalba and two transgenic lines with modified lignin monomer composition, were interrogated using metabolic profiling. Analysis of metabolite abundance data by GC-MS, coupled with principal components analysis (PCA), successfully differentiated between lines that had distinct phenotypes, whether samples were taken from the cambial zone or non-lignifying suspension tissue cultures. Interestingly, the GC-MS analysis detected relatively few phenolic metabolites in cambial extracts, although a single metabolite associated with the differentiation between lines was directly related to the phenylpropanoid pathway or other down-stream aspects of lignin biosynthesis. In fact, carbohydrates, which have only an indirect relationship with the modified lignin monomer composition, featured strongly in the line-differentiating aspects of the statistical analysis. Traditional HPLC analysis was employed to verify the GC-MS data. These findings demonstrate that metabolic traits can be dissected reliably and accurately by metabolomic analyses, enabling the discrimination of individual genotypes of the same tree species that exhibit marked differences in industrially relevant wood traits. Furthermore, this validates the potential of using metabolite profiling techniques for marker generation in the context of plant/tree breeding for industrial applications.

Biotechnology and the domestication of forest trees

Wood is one of the major renewable materials. To compensate for the ever-increasing demand for wood and to reduce pressure on native forests, more wood of higher quality will need to be produced on less land by planting highly productive trees. Biotechnology has shown great promise for forest tree improvement and over the past 10 years this field has flourished. Not only has the potential of transgenic trees with optimized yield and quality traits been demonstrated in field trials, but progress in genetical genomics and association genetics promise quantum leaps forward for tree improvement.