Solutions for dissolution--engineering cell walls for deconstruction

Native lignin extraction from soft- and hardwood by green and benign sub/supercritical fluid extraction methodologies

Lignin constitutes an impressive resource of high-value low molecular weight compounds. However, robust methods for isolation of the extractable fraction from lignocellulose are yet to be established. In this study, supercritical fluid extraction (SFE) and CO₂-expanded liquid extraction (CXLE) were employed to extract lignin from softwood and hardwood chips. Ethanol, acetone, and ethyl lactate were investigated as green organic co-solvents in the extractions. Additionally, the effects of temperature, CO₂ percentage and the water content of the co-solvent were investigated using a design of experiment approach employing full factorial designs. Ethyl lactate and acetone provided the highest gravimetric yields. The water content in the extraction mixture had the main impact on the amount of extractable lignin monomers (LMs) and lignin oligomers (LOs) while the type of organic solvent was of minor importance. The most effective extraction was achieved by using a combination of liquid CO₂/acetone/water (10/72/18, v/v/v) at 60 °C, 350 bar, 30 min and 2 mL min^-1 flow rate. The optimized method provided detection of 13 LMs and 6 lignin dimers (LDs) from the hardwood chips. The results demonstrate the potential of supercritical fluids and green solvents in the field of mild and bening lignin extraction from wood.

Sorption of Organic Contaminants by Stable Organic Matter Fraction in Soil

Soil organic matter (SOM) and its heterogeneous nature constitutes the main factor determining the fate and transformation of organic chemicals (OCs). Thus, the aim of thus research was to analyze the influence of the molecular chemodiversity of a stable SOM (S-SOM) on the sorption potential of different groups of OCs (organochloride pesticides—OCPs, and non-chlorinated pesticides—NCPs, polycyclic aromatic hydrocarbons—PAHs). The research was conducted as a batch experiment. For this purpose, a S-SOM was separated from six soils (TOC = 15.0−58.7 gkg−1; TN = 1.4−6.6 gkg−1, pH in KCl = 6.4−7.4 and WRB taxonomy: fluvisols, luviosols, leptosols) by alkaline urea and dimethylsulphoxide with sulfuric acid. Isolated S-SOM fraction was evaluated by UV−VIS, FT-IR and EEM spectroscopy to describe molecular diversity, which allowed the assessment of its potential sorption properties regarding OCs. In order to directly evaluate the sorption affinity of individual OCs to S-SOM, the mixture of the 3 deuterated contaminants: chrysene (PAHs), 4,4′DDT (OCPs) atrazine (NCPs) were applied. The sorption experiment was carried out according to the 106 OECD Guidelines. The OCs concentration was analyzed by gas chromatography triple mass spectrometry (GC-MS/MS). OCs were characterized by different sorption rates to S-SOM fractions according to the overall trend: atrazine (87.5−99.9%) > 4,4′DDT (64−81.6%) > chrysene (35.2−79.8%). Moreover, atrazine exhibited the highest saturation dynamic with fast bounding time amounting to 6 h of contact with S-SOM. Proportionally, the chrysene showed the slowest binding time achieving an average of 55% sorption after 78 h. Therefore, S-SOM isolated from different soils demonstrated varying binding capacity to OCs (CoV = 21%, 27% and 33% for atrazine, DDT and chrysene, respectively). Results indicate that each sample contains S-SOM with different degrees of transformation and sorption properties that affect the OCs availability in soil. Spectroscopic analyses have shown that the main component of S-SOM are biopolymers at various stages of transformation that contain numerous aromatic−aliphatic groups with mostly hydrophilic substituents.

Understanding the Modus Operandi of Class II KNOX Transcription Factors in Secondary Cell Wall Biosynthesis

Lignocellulosic biomass from the secondary cell walls of plants has a veritable potential to provide some of the most appropriate raw materials for producing second-generation biofuels. Therefore, we must first understand how plants synthesize these complex secondary cell walls that consist of cellulose, hemicellulose, and lignin in order to deconstruct them later on into simple sugars to produce bioethanol via fermentation. Knotted-like homeobox (KNOX) genes encode homeodomain-containing transcription factors (TFs) that modulate various important developmental processes in plants. While Class I KNOX TF genes are mainly expressed in the shoot apical meristems of both monocot and eudicot plants and are involved in meristem maintenance and/or formation, Class II KNOXTF genes exhibit diverse expression patterns and their precise functions have mostly remained unknown, until recently. The expression patterns of Class II KNOX TF genes in Arabidopsis, namely KNAT3, KNAT4, KNAT5, and KNAT7, suggest that TFs encoded by at least some of these genes, such as KNAT7 and KNAT3, may play a significant role in secondary cell wall formation. Specifically, the expression of the KNAT7 gene is regulated by upstream TFs, such as SND1 and MYB46, while KNAT7 interacts with other cell wall proteins, such as KNAT3, MYB75, OFPs, and BLHs, to regulate secondary cell wall formation. Moreover, KNAT7 directly regulates the expression of some xylan synthesis genes. In this review, we summarize the current mechanistic understanding of the roles of Class II KNOX TFs in secondary cell wall formation. Recent success with the genetic manipulation of Class II KNOX TFs suggests that this may be one of the biotechnological strategies to improve plant feedstocks for bioethanol production.

Lignin for Bioeconomy: The Present and Future Role of Technical Lignin

Lignin, the term commonly used in literature, represents a group of heterogeneous aromatic compounds of plant origin. Protolignin or lignin in the cell wall is entirely different from the commercially available technical lignin due to changes during the delignification process. In this paper, we assess the status of lignin valorization in terms of commercial products. We start with existing knowledge of the lignin/protolignin structure in its native form and move to the technical lignin from various sources. Special attention is given to the patents and lignin-based commercial products. We observed that the technical lignin-based commercial products utilize coarse properties of the technical lignin in marketed formulations. Additionally, the general principles of polymers chemistry and self-assembly are difficult to apply in lignin-based nanotechnology, and lignin-centric investigations must be carried out. The alternate upcoming approach is to develop lignin-centric or lignin first bio-refineries for high-value applications; however, that brings its own technological challenges. The assessment of the gap between lab-scale applications and lignin-based commercial products delineates the challenges lignin nanoparticles-based technologies must meet to be a commercially viable alternative.

A systems biology view of wood formation in Eucalyptus grandis trees submitted to different potassium and water regimes

Wood production in fast-growing Eucalyptus grandis trees is highly dependent on both potassium (K) fertilization and water availability but the molecular processes underlying wood formation in response to the combined effects of these two limiting factors remain unknown. E. grandis trees were submitted to four combinations of K-fertilization and water supply. Weighted gene co-expression network analysis and MixOmics-based co-regulation networks were used to integrate xylem transcriptome, metabolome and complex wood traits. Functional characterization of a candidate gene was performed in transgenic E. grandis hairy roots. This integrated network-based approach enabled us to identify meaningful biological processes and regulators impacted by K-fertilization and/or water limitation. It revealed that modules of co-regulated genes and metabolites strongly correlated to wood complex traits are in the heart of a complex trade-off between biomass production and stress responses. Nested in these modules, potential new cell-wall regulators were identified, as further confirmed by the functional characterization of EgMYB137. These findings provide new insights into the regulatory mechanisms of wood formation under stressful conditions, pointing out both known and new regulators co-opted by K-fertilization and/or water limitation that may potentially promote adaptive wood traits.

The Self-Assembly of Lignin and Its Application in Nanoparticle Synthesis: A Short Review

Lignin serves as a significant contributor to the natural stock of non-fossilized carbon, second only to cellulose in the biosphere. In this review article, we focus on the self-assembly properties of lignin and their contribution to its effective utilization and valorization. Traditionally, investigations on self-assembly properties of lignin have aimed at understanding the lignification process of the cell wall and using it for efficient delignification for commercial purposes. In recent years (mainly the last three years), an increased number of attempts and reports of technical-lignin nanostructure synthesis with controlled particle size and morphology have been published. This has renewed the interests in the self-assembly properties of technical lignins and their possible applications. Based on the sources and processing methods of lignin, there are significant differences between its structure and properties, which is the primary obstacle in the generalized understanding of the lignin structure and the lignification process occurring within cell walls. The reported studies are also specific to source and processing methods. This work has been divided into two parts. In the first part, the aggregation propensity of lignin based on type, source and extraction method, temperature, and pH of solution is discussed. This is followed by a critical overview of non-covalent interactions and their contribution to the self-associative properties of lignin. The role of self-assembly towards the understanding of xylogenesis and nanoparticle synthesis is also discussed. A particular emphasis is placed on the interaction and forces involved that are used to explain the self-association of lignin.

A New Calmodulin-Binding Protein Expresses in the Context of Secondary Cell Wall Biosynthesis and Impacts Biomass Properties in Populus

A greater understanding of biosynthesis, signaling and regulatory pathways involved in determining stem growth and secondary cell wall chemistry is important for enabling pathway engineering and genetic optimization of biomass properties. The present study describes a new functional role of PdIQD10, a Populus gene belonging to the IQ67-Domain1 family of IQD genes, in impacting biomass formation and chemistry. Expression studies showed that PdIQD10 has enhanced expression in developing xylem and tension-stressed tissues in Populus deltoides. Molecular dynamics simulation and yeast two-hybrid interaction experiments suggest interactions with two calmodulin proteins, CaM247 and CaM014, supporting the sequence-predicted functional role of the PdIQD10 as a calmodulin-binding protein. PdIQD10 was found to interact with specific Populus isoforms of the Kinesin Light Chain protein family, shown previously to function as microtubule-guided, cargo binding and delivery proteins in Arabidopsis. Subcellular localization studies showed that PdIQD10 localizes in the nucleus and plasma membrane regions. Promoter-binding assays suggest that a known master transcriptional regulator of secondary cell wall biosynthesis (PdWND1B) may be upstream of an HD-ZIP III gene that is in turn upstream of PdIQD10 gene in the transcriptional network. RNAi-mediated downregulation of PdIQD10 expression resulted in plants with altered biomass properties including higher cellulose, wall glucose content and greater biomass quantity. These results present evidence in support of a new functional role for an IQD gene family member, PdIQD10, in secondary cell wall biosynthesis and biomass formation in Populus.

EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species

Tree species of the genus Eucalyptus are the most valuable and widely planted hardwoods in the world. Given the economic importance of Eucalyptus trees, much effort has been made towards the generation of specimens with superior forestry properties that can deliver high-quality feedstocks, customized to the industrýs needs for both cellulosic (paper) and lignocellulosic biomass production. In line with these efforts, large sets of molecular data have been generated by several scientific groups, providing invaluable information that can be applied in the development of improved specimens. In order to fully explore the potential of available datasets, the development of a public database that provides integrated access to genomic and transcriptomic data from Eucalyptus is needed. EUCANEXT is a database that analyses and integrates publicly available Eucalyptus molecular data, such as the E. grandis genome assembly and predicted genes, ESTs from several species and digital gene expression from 26 RNA-Seq libraries. The database has been implemented in a Fedora Linux machine running MySQL and Apache, while Perl CGI was used for the web interfaces. EUCANEXT provides a user-friendly web interface for easy access and analysis of publicly available molecular data from Eucalyptus species. This integrated database allows for complex searches by gene name, keyword or sequence similarity and is publicly accessible at http://www.lge.ibi.unicamp.br/eucalyptusdb. Through EUCANEXT, users can perform complex analysis to identify genes related traits of interest using RNA-Seq libraries and tools for differential expression analysis. Moreover, all the bioinformatics pipeline here described, including the database schema and PERL scripts, are readily available and can be applied to any genomic and transcriptomic project, regardless of the organism.

Database URL:http://www.lge.ibi.unicamp.br/eucalyptusdb

Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing

As a consequence of their remarkable adaptability, fast growth, and superior wood properties, eucalypt tree plantations have emerged as key renewable feedstocks (over 20 million ha globally) for the production of pulp, paper, bioenergy, and other lignocellulosic products. However, most biomass properties such as growth, wood density, and wood chemistry are complex traits that are hard to improve in long-lived perennials. Systems genetics, a process of harnessing multiple levels of component trait information (e.g., transcript, protein, and metabolite variation) in populations that vary in complex traits, has proven effective for dissecting the genetics and biology of such traits. We have applied a network-based data integration (NBDI) method for a systems-level analysis of genes, processes and pathways underlying biomass and bioenergy-related traits using a segregating Eucalyptus hybrid population. We show that the integrative approach can link biologically meaningful sets of genes to complex traits and at the same time reveal the molecular basis of trait variation. Gene sets identified for related woody biomass traits were found to share regulatory loci, cluster in network neighborhoods, and exhibit enrichment for molecular functions such as xylan metabolism and cell wall development. These findings offer a framework for identifying the molecular underpinnings of complex biomass and bioprocessing-related traits. A more thorough understanding of the molecular basis of plant biomass traits should provide additional opportunities for the establishment of a sustainable bio-based economy.

Natural acetylation impacts carbohydrate recovery during deconstruction of Populus trichocarpa wood

BACKGROUND

Significant variation in the inherent degree of acetylation naturally exists in the xylem cell walls of Populus trichocarpa. During pretreatment, endogenous acetate hydrolyzes to acetic acid that can subsequently catalyze the breakdown of poplar wood, increasing the efficiency of biomass pretreatment.

RESULTS

Poplar genotypes varying in cell wall composition were pretreated in 0.3% H₂SO₄ in non-isothermal batch reactors. Acetic acid released from the wood was positively related to sugar release during pretreatment (R ≥ 0.9), and inversely proportional to the lignin content of the poplar wood (R = 0.6).

CONCLUSION

There is significant variation in wood chemistry among P. trichocarpa genotypes. This study elucidated patterns of cell wall deconstruction and clearly links carbohydrate solubilization to acetate release. Tailoring biomass feedstocks for acetate release could enhance pretreatment efficiencies.

Gene Expression Patterns of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium Are Influenced by Wood Substrate Composition during Degradation

Identification of the specific genes and enzymes involved in the fungal degradation of lignocellulosic biomass derived from feedstocks with various compositions is essential to the development of improved bioenergy processes. In order to elucidate the effect of substrate composition on gene expression in wood-rotting fungi, we employed microarrays based on the annotated genomes of the brown- and white-rot fungi, Rhodonia placenta (formerly Postia placenta) and Phanerochaete chrysosporium, respectively. We monitored the expression of genes involved in the enzymatic deconstruction of the cell walls of three 4-year-old Populus trichocarpa (poplar) trees of genotypes with distinct cell wall chemistries, selected from a population of several hundred trees grown in a common garden. The woody substrates were incubated with wood decay fungi for 10, 20, and 30 days. An analysis of transcript abundance in all pairwise comparisons highlighted 64 and 84 differentially expressed genes (>2-fold, P < 0.05) in P. chrysosporium and P. placenta, respectively. Cross-fungal comparisons also revealed an array of highly differentially expressed genes (>4-fold, P < 0.01) across different substrates and time points. These results clearly demonstrate that gene expression profiles of P. chrysosporium and P. placenta are influenced by wood substrate composition and the duration of incubation. Many of the significantly expressed genes encode "proteins of unknown function," and determining their role in lignocellulose degradation presents opportunities and challenges for future research.

IMPORTANCE

This study describes the variation in expression patterns of two wood-degrading fungi (brown- and white-rot fungi) during colonization and incubation on three different naturally occurring poplar substrates of differing chemical compositions, over time. The results clearly show that the two fungi respond differentially to their substrates and that several known and, more interestingly, currently unknown genes are highly misregulated in response to various substrate compositions. These findings highlight the need to characterize several unknown proteins for catalytic function but also as potential candidate proteins to improve the efficiency of enzymatic cocktails to degrade lignocellulosic substrates in industrial applications, such as in a biochemically based bioenergy platform.

Complementarity of medium-throughput in situ RNA hybridization and tissue-specific transcriptomics: case study of Arabidopsis seed development kinetics

The rationale of this study is to compare and integrate two heterologous datasets intended to unravel the spatiotemporal specificities of gene expression in a rapidly growing and complex organ. We implemented medium-throughput RNA in situ hybridization (ISH) for 39 genes mainly corresponding to cell wall proteins for which we have particular interest, selected (i) on their sequence identity (24 class III peroxidase multigenic family members and 15 additional genes used as positive controls) and (ii) on their expression levels in a publicly available Arabidopsis thaliana seed tissue-specific transcriptomics study. The specificity of the hybridization signals was carefully studied, and ISH results obtained for the 39 selected genes were systematically compared with tissue-specific transcriptomics for 5 seed developmental stages. Integration of results illustrates the complementarity of both datasets. The tissue-specific transcriptomics provides high-throughput possibilities whereas ISH provides high spatial resolution. Moreover, depending on the tissues and the developmental stages considered, one or the other technique appears more sensitive than the other. For each tissue/developmental stage, we finally determined tissue-specific transcriptomic threshold values compatible with the spatiotemporally-specific detection limits of ISH for lists of hundreds to tens-of-thousands of genes.

Identification of Transcription Factors ZmMYB111 and ZmMYB148 Involved in Phenylpropanoid Metabolism

Maize is the leading crop worldwide in terms of both planting area and total yields, but environmental stresses cause significant losses in productivity. Phenylpropanoid compounds play an important role in plant stress resistance; however, the mechanism of their synthesis is not fully understood, especially in regard to the expression and regulation of key genes. Phenylalanine ammonia-lyase (PAL) is the first key enzyme involved in phenylpropanoid metabolism, and it has a significant effect on the synthesis of important phenylpropanoid compounds. According to the results of sequence alignments and functional prediction, we selected two conserved R2R3-MYB transcription factors as candidate genes for the regulation of phenylpropanoid metabolism. The two candidate R2R3-MYB genes, which we named ZmMYB111 and ZmMYB148, were cloned, and then their structural characteristics and phylogenetic placement were predicted and analyzed. In addition, a series of evaluations were performed, including expression profiles, subcellular localization, transcription activation, protein-DNA interaction, and transient expression in maize endosperm. Our results indicated that both ZmMYB111 and ZmMYB148 are indeed R2R3-MYB transcription factors and that they may play a regulatory role in PAL gene expression.

Efficient Eucalypt Cell Wall Deconstruction and Conversion for Sustainable Lignocellulosic Biofuels

In order to meet the world's growing energy demand and reduce the impact of greenhouse gas emissions resulting from fossil fuel combustion, renewable plant-based feedstocks for biofuel production must be considered. The first-generation biofuels, derived from starches of edible feedstocks, such as corn, create competition between food and fuel resources, both for the crop itself and the land on which it is grown. As such, biofuel synthesized from non-edible plant biomass (lignocellulose) generated on marginal agricultural land will help to alleviate this competition. Eucalypts, the broadly defined taxa encompassing over 900 species of Eucalyptus, Corymbia, and Angophora are the most widely planted hardwood tree in the world, harvested mainly for timber, pulp and paper, and biomaterial products. More recently, due to their exceptional growth rate and amenability to grow under a wide range of environmental conditions, eucalypts are a leading option for the development of a sustainable lignocellulosic biofuels. However, efficient conversion of woody biomass into fermentable monomeric sugars is largely dependent on pretreatment of the cell wall, whose formation and complexity lend itself toward natural recalcitrance against its efficient deconstruction. A greater understanding of this complexity within the context of various pretreatments will allow the design of new and effective deconstruction processes for bioenergy production. In this review, we present the various pretreatment options for eucalypts, including research into understanding structure and formation of the eucalypt cell wall.

Supramolecular Interactions in Secondary Plant Cell Walls: Effect of Lignin Chemical Composition Revealed with the Molecular Theory of Solvation

Plant biomass recalcitrance, a major obstacle to achieving sustainable production of second generation biofuels, arises mainly from the amorphous cell-wall matrix containing lignin and hemicellulose assembled into a complex supramolecular network that coats the cellulose fibrils. We employed the statistical-mechanical, 3D reference interaction site model with the Kovalenko-Hirata closure approximation (or 3D-RISM-KH molecular theory of solvation) to reveal the supramolecular interactions in this network and provide molecular-level insight into the effective lignin-lignin and lignin-hemicellulose thermodynamic interactions. We found that such interactions are hydrophobic and entropy-driven, and arise from the expelling of water from the mutual interaction surfaces. The molecular origin of these interactions is carbohydrate-π and π-π stacking forces, whose strengths are dependent on the lignin chemical composition. Methoxy substituents in the phenyl groups of lignin promote substantial entropic stabilization of the ligno-hemicellulosic matrix. Our results provide a detailed molecular view of the fundamental interactions within the secondary plant cell walls that lead to recalcitrance.

Modifying plants for biofuel and biomaterial production

The productivity of plants as biofuel or biomaterial crops is established by both the yield of plant biomass per unit area of land and the efficiency of conversion of the biomass to biofuel. Higher yielding biofuel crops with increased conversion efficiencies allow production on a smaller land footprint minimizing competition with agriculture for food production and biodiversity conservation. Plants have traditionally been domesticated for food, fibre and feed applications. However, utilization for biofuels may require the breeding of novel phenotypes, or new species entirely. Genomics approaches support genetic selection strategies to deliver significant genetic improvement of plants as sources of biomass for biofuel manufacture. Genetic modification of plants provides a further range of options for improving the composition of biomass and for plant modifications to assist the fabrication of biofuels. The relative carbohydrate and lignin content influences the deconstruction of plant cell walls to biofuels. Key options for facilitating the deconstruction leading to higher monomeric sugar release from plants include increasing cellulose content, reducing cellulose crystallinity, and/or altering the amount or composition of noncellulosic polysaccharides or lignin. Modification of chemical linkages within and between these biomass components may improve the ease of deconstruction. Expression of enzymes in the plant may provide a cost-effective option for biochemical conversion to biofuel.

Cell wall-related proteins of unknown function: missing links in plant cell wall development

Lignocellulosic biomass is an important feedstock for the pulp and paper industry as well as emerging biofuel and biomaterial industries. However, the recalcitrance of the secondary cell wall to chemical or enzymatic degradation remains a major hurdle for efficient extraction of economically important biopolymers such as cellulose. It has been estimated that approximately 10-15% of about 27,000 protein-coding genes in the Arabidopsis genome are dedicated to cell wall development; however, only about 130 Arabidopsis genes thus far have experimental evidence validating cell wall function. While many genes have been implicated through co-expression analysis with known genes, a large number are broadly classified as proteins of unknown function (PUFs). Recently the functionality of some of these unknown proteins in cell wall development has been revealed using reverse genetic approaches. Given the large number of cell wall-related PUFs, how do we approach and subsequently prioritize the investigation of such unknown genes that may be essential to or influence plant cell wall development and structure? Here, we address the aforementioned question in two parts; we first identify the different kinds of PUFs based on known and predicted features such as protein domains. Knowledge of inherent features of PUFs may allow for functional inference and a concomitant link to biological context. Secondly, we discuss omics-based technologies and approaches that are helping identify and prioritize cell wall-related PUFs by functional association. In this way, hypothesis-driven experiments can be designed for functional elucidation of many proteins that remain missing links in our understanding of plant cell wall biosynthesis.

Molecular characterization of ferulate 5-hydroxylase gene from kenaf (Hibiscus cannabinus L.)

The purpose of this study is to clone and characterize the expression pattern of a F5H gene encoding ferulate 5-hydroxylase in the phenylpropanoid pathway from kenaf (Hibiscus cannabinus L.). Kenaf is a fast-growing dicotyledonous plant valued for its biomass. F5H, a cytochrome P450-dependent monooxygenase (CYP84), is a key enzyme for syringyl lignin biosynthesis. The full length of the F5H ortholog was cloned and characterized. The full-length F5H ortholog consists of a 1,557-bp open reading frame (ORF) encoding 518 amino acids (GenBank Accession number JX524278). The deduced amino acid sequence showed that kenaf F5H had the highest similarity (78%) with that of Populus trichocarpa. Transcriptional analysis of F5H ortholog was conducted using quantitative real-time PCR during the developmental stages of various tissues and in response to various abiotic stresses. The highest transcript level of the F5H ortholog was observed in immature flower tissues and in early stage (6 week-old) of stem tissues, with a certain level of expression in all tissues tested. The highest transcript level of F5H ortholog was observed at the late time points after treatments with NaCl (48 h), wounding (24 h), cold (24 h), abscisic acid (24 h), and methyl jasmonate (24 h).

Characterization and determination of lignin in different types of Iraqi phoenix date palm pruning woods

This study aimed to find analytical data base for Iraqi phoenix date palm pruning woods, which produced by pruning process at the season of date palm production. Lignin has been extracted and purified for five types of Iraqi date palm using Klason lignin method. The weight of the extracted lignin ranged from 0.410 g to 0.720 g, and the lignin % ranged from 17.6 to 36. The other ingredients (waxes, oils, resin, and proteins of wood gums) % ranged from 20 to 29.5. FT-IR characterization showed that the (-OH) phenolic group appear in Ashrasi lignin structure only and disappear in other lignin samples, and the (4-O-5 inter monomeric lignin linkage) showed strong to moderate intensity peaks for all studied samples except the Austa omran sample has a weak intensity peaks. Also (DODO inter monomeric lignin linkage) showed strong intensity peaks for all studied samples except the Barban sample showed moderate intensity peaks. UV-vis characterization showed that the lowest absorption maximum (266 nm) corresponds to Barban lignin sample, while the highest absorption maximum (271 nm) corresponds to Sultani lignin sample.

Induced somatic sector analysis of cellulose synthase (CesA) promoter regions in woody stem tissues

The increasing focus on plantation forestry as a renewable source of cellulosic biomass has emphasized the need for tools to study the unique biology of woody genera such as Eucalyptus, Populus and Pinus. The domestication of these woody crops is hampered by long generation times, and breeders are now looking to molecular approaches such as marker-assisted breeding and genetic modification to accelerate tree improvement. Much of what is known about genes involved in the growth and development of plants has come from studies of herbaceous models such as Arabidopsis and rice. However, transferring this information to woody plants often proves difficult, especially for genes expressed in woody stems. Here we report the use of induced somatic sector analysis (ISSA) for characterization of promoter expression patterns directly in the stems of Populus and Eucalyptus trees. As a case study, we used previously characterized primary and secondary cell wall-related cellulose synthase (CesA) promoters cloned from Eucalyptus grandis. We show that ISSA can be used to elucidate the phloem and xylem expression patterns of the CesA genes in Eucalyptus and Populus stems and also show that the staining patterns differ in Eucalyptus and Populus stems. These findings show that ISSA is an efficient approach to investigate promoter function in the developmental context of woody plant tissues and raise questions about the suitability of heterologous promoters for genetic manipulation in plant species.

Syringyl-rich lignin renders poplars more resistant to degradation by wood decay fungi

In order to elucidate the effects of lignin composition on the resistance of wood to degradation by decay fungi, wood specimens from two transgenic poplar lines expressing an Arabidopsis gene encoding ferulate 5-hydroxylase (F5H) driven by the cinnimate-4-hydroxylase promoter (C4H::F5H) that increased syringyl/guaiacyl (S/G) monolignol ratios relative to those in the untransformed control wood were incubated with six different wood decay fungi. Alterations in wood weight and chemical composition were monitored over the incubation period. The results showed that transgenic poplar lines extremely rich in syringyl lignin exhibited a drastically improved resistance to degradation by all decay fungi evaluated. Lignin monomer composition and its distribution among cell types and within different cell layers were the sole wood chemistry parameters determining wood durability. Since transgenic poplars with exceedingly high syringyl contents were recalcitrant to degradation, where wood durability is a critical factor, these genotypes may offer improved performance.

Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control and genetic correlations

The increasing ecological and economical importance of Populus species and hybrids has stimulated research into the investigation of the natural variation of the species and the estimation of the extent of genetic control over its wood quality traits for traditional forestry activities as well as the emerging bioenergy sector. A realized kinship matrix based on informative, high-density, biallelic single nucleotide polymorphism (SNP) genetic markers was constructed to estimate trait variance components, heritabilities, and genetic and phenotypic correlations. Seventeen traits related to wood chemistry and ultrastructure were examined in 334 9-yr-old Populus trichocarpa grown in a common-garden plot representing populations spanning the latitudinal range 44° to 58.6°. In these individuals, 9342 SNPs that conformed to Hardy-Weinberg expectations were employed to assess the genomic pair-wise kinship to estimate narrow-sense heritabilities and genetic correlations among traits. The range-wide phenotypic variation in all traits was substantial and several trait heritabilities were > 0.6. In total, 61 significant genetic and phenotypic correlations and a network of highly interrelated traits were identified. The high trait variation, the evidence for moderate to high heritabilities and the identification of advantageous trait combinations of industrially important characteristics should aid in providing the foundation for the enhancement of poplar tree breeding strategies for modern industrial use.

Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research

Glycoside hydrolases (GH) catalyze the hydrolysis of glycosidic bonds in cell wall polymers and can have major effects on cell wall architecture. Taking advantage of the massive datasets available in public databases, we have constructed a rice phylogenomic database of GHs (http://ricephylogenomics.ucdavis.edu/cellwalls/gh/). This database integrates multiple data types including the structural features, orthologous relationships, mutant availability, and gene expression patterns for each GH family in a phylogenomic context. The rice genome encodes 437 GH genes classified into 34 families. Based on pairwise comparison with eight dicot and four monocot genomes, we identified 138 GH genes that are highly diverged between monocots and dicots, 57 of which have diverged further in rice as compared with four monocot genomes scanned in this study. Chromosomal localization and expression analysis suggest a role for both whole-genome and localized gene duplications in expansion and diversification of GH families in rice. We examined the meta-profiles of expression patterns of GH genes in twenty different anatomical tissues of rice. Transcripts of 51 genes exhibit tissue or developmental stage-preferential expression, whereas, seventeen other genes preferentially accumulate in actively growing tissues. When queried in RiceNet, a probabilistic functional gene network that facilitates functional gene predictions, nine out of seventeen genes form a regulatory network with the well-characterized genes involved in biosynthesis of cell wall polymers including cellulose synthase and cellulose synthase-like genes of rice. Two-thirds of the GH genes in rice are up regulated in response to biotic and abiotic stress treatments indicating a role in stress adaptation. Our analyses identify potential GH targets for cell wall modification.

Isolation and structural characterization of lignin from cotton stalk treated in an ammonia hydrothermal system

To investigate the potential for the utilization of cotton stalk, ammonia hydrothermal treatment was applied to fractionate the samples into aqueous ammonia-soluble and ammonia-insoluble portions. The ammonia-soluble portion was purified to yield lignin fractions. The lignin fractions obtained were characterized by wet chemistry (carbohydrate analysis) and spectroscopy methods (FT-IR, ¹³C and ¹H-¹³C HSQC NMR spectroscopy) as well as gel permeation chromatography (GPC). The results showed that the cotton stalk lignin fractions were almost absent of neutral sugars (0.43%–1.29%) and had relatively low average molecular weights (1255–1746 g/mol). The lignin fractions belonged to typical G-S lignin, which was composed predominately of G-type units (59%) and noticeable amounts of S-type units (40%) together with a small amount of H-type units (~1%). Furthermore, the ammonia-extractable lignin fractions were mainly composed of β-O-4′ inter-unit linkages (75.6%), and small quantities of β-β′ (12.2%), together with lower amounts of β-5′ carbon-carbon linkages (7.4%) and p-hydroxycinnamyl alcohol end groups.

Epigallocatechin gallate incorporation into lignin enhances the alkaline delignification and enzymatic saccharification of cell walls

BACKGROUND

Lignin is an integral component of the plant cell wall matrix but impedes the conversion of biomass into biofuels. The plasticity of lignin biosynthesis should permit the inclusion of new compatible phenolic monomers such as flavonoids into cell wall lignins that are consequently less recalcitrant to biomass processing. In the present study, epigallocatechin gallate (EGCG) was evaluated as a potential lignin bioengineering target for rendering biomass more amenable to processing for biofuel production.

RESULTS

In vitro peroxidase-catalyzed polymerization experiments revealed that both gallate and pyrogallyl (B-ring) moieties in EGCG underwent radical cross-coupling with monolignols mainly by β-O-4-type cross-coupling, producing benzodioxane units following rearomatization reactions. Biomimetic lignification of maize cell walls with a 3:1 molar ratio of monolignols and EGCG permitted extensive alkaline delignification of cell walls (72 to 92%) that far exceeded that for lignified controls (44 to 62%). Alkali-insoluble residues from EGCG-lignified walls yielded up to 34% more glucose and total sugars following enzymatic saccharification than lignified controls.

CONCLUSIONS

It was found that EGCG readily copolymerized with monolignols to become integrally cross-coupled into cell wall lignins, where it greatly enhanced alkaline delignification and subsequent enzymatic saccharification. Improved delignification may be attributed to internal trapping of quinone-methide intermediates to prevent benzyl ether cross-linking of lignin to structural polysaccharides during lignification, and to the cleavage of ester intra-unit linkages within EGCG during pretreatment. Overall, our results suggest that apoplastic deposition of EGCG for incorporation into lignin would be a promising plant genetic engineering target for improving the delignification and saccharification of biomass crops.

Analysis of soluble lignin in sugarcane by ultrahigh performance liquid chromatography-tandem mass spectrometry with a do-it-yourself oligomer database

Lignin is a polymer found in the cell wall of plants and is one of the main obstacles to the implementation of second-generation ethanol production because it confers the recalcitrance of the lignocellulosic material. The recalcitrance of biomass is affected by the amount of lignin, by its monomer composition, and the way the monomers are arranged in the plant cell wall. Analysis of lignin structure demands mass spectrometry analysis, and identification of oligomers is usually based on libraries produced by laborious protocols. A robust method to build a do-it-yourself lignin oligomer library was tested. This library can be built using commercially available enzymes, standards, and reagents and is relatively easy to accomplish. An ultrahigh performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method for the separation and characterization of monomers and oligomers was developed and was equally applicable to the synthetic lignin and to soluble lignin extracted from a sample of sugar cane.

Whole plant cell wall characterization using solution-state 2D NMR

Recent advances in nuclear magnetic resonance (NMR) technology have made it possible to rapidly screen plant material and discern whole cell wall information without the need to deconstruct and fractionate the plant cell wall. This approach can be used to improve our understanding of the biology of cell wall structure and biosynthesis, and as a tool to select plant material for the most appropriate industrial applications. This is particularly true in an era when renewable materials are vital to the emerging bio-based economies. This protocol describes procedures for (i) the preparation and extraction of a biological plant tissue, (ii) solubilization strategies for plant material of varying composition and (iii) 2D NMR acquisition (for typically 15 min-5 h) and integration methods used to elucidate lignin subunit composition and lignin interunit linkage distribution, as well as cell wall polysaccharide profiling. Furthermore, we present data that demonstrate the utility of this new NMR whole cell wall characterization procedure with a variety of degradative methods traditionally used for cell wall compositional analysis.

Designed for deconstruction--poplar trees altered in cell wall lignification improve the efficacy of bioethanol production

• There is a pressing global need to reduce the increasing societal reliance on petroleum and to develop a bio-based economy. At the forefront is the need to establish a sustainable, renewable, alternative energy sector. This includes liquid transportation fuel derived from lignocellulosic plant materials. However, one of the current limiting factors restricting the effective and efficient conversion of lignocellulosic residues is the recalcitrance of the substrate to enzymatic conversion. • In an attempt to assess the impact of cell wall lignin on recalcitrance, we subjected poplar trees engineered with altered lignin content and composition to two potential industrial pretreatment regimes, and evaluated the overall efficacy of the bioconversion to ethanol process. • It was apparent that total lignin content has a greater impact than monomer ratio (syringyl : guaiacyl) on both pretreatments. More importantly, low lignin plants showed as much as a 15% improvement in the efficiency of conversion, with near complete hydrolysis of the cellulosic polymer. • Using genomic tools to breed or select for modifications in key cell wall chemical and/or ultrastructural traits can have a profound effect on bioenergy processing. These techniques may therefore offer means to overcome the current obstacles that underpin the recalcitrance of lignocellulosic substrates to bioconversion.

Cellulose factories: advancing bioenergy production from forest trees

Fast-growing, short-rotation forest trees, such as Populus and Eucalyptus, produce large amounts of cellulose-rich biomass that could be utilized for bioenergy and biopolymer production. Major obstacles need to be overcome before the deployment of these genera as energy crops, including the effective removal of lignin and the subsequent liberation of carbohydrate constituents from wood cell walls. However, significant opportunities exist to both select for and engineer the structure and interaction of cell wall biopolymers, which could afford a means to improve processing and product development. The molecular underpinnings and regulation of cell wall carbohydrate biosynthesis are rapidly being elucidated, and are providing tools to strategically develop and guide the targeted modification required to adapt forest trees for the emerging bioeconomy. Much insight has already been gained from the perturbation of individual genes and pathways, but it is not known to what extent the natural variation in the sequence and expression of these same genes underlies the inherent variation in wood properties of field-grown trees. The integration of data from next-generation genomic technologies applied in natural and experimental populations will enable a systems genetics approach to study cell wall carbohydrate production in trees, and should advance the development of future woody bioenergy and biopolymer crops.

Accelerating the domestication of forest trees in a changing world

In light of impending water and arable land shortages, population growth and climate change, it is more important than ever to examine how forest tree domestication can be accelerated to sustainably meet future demands for wood, biomass, paper, fuel and biomaterials. Because of long breeding cycles, tree domestication cannot be rapidly achieved through traditional genetic improvement methods alone. Integrating modern genetic and genomic techniques with conventional breeding will expedite tree domestication. Breeders will only embrace these technologies if they are cost-effective and readily accessible, and forest landowners will only adopt end-products that meet with regulatory approval and public acceptance. All parties involved must work together to achieve these objectives for the benefit of society.

Supramolecular self-assembled chaos: polyphenolic lignin's barrier to cost-effective lignocellulosic biofuels

Phenylpropanoid metabolism yields a mixture of monolignols that undergo chaotic, non-enzymatic reactions such as free radical polymerization and spontaneous self-assembly in order to form the polyphenolic lignin which is a barrier to cost-effective lignocellulosic biofuels. Post-synthesis lignin integration into the plant cell wall is unclear, including how the hydrophobic lignin incorporates into the wall in an initially hydrophilic milieu. Self-assembly, self-organization and aggregation give rise to a complex, 3D network of lignin that displays randomly branched topology and fractal properties. Attempts at isolating lignin, analogous to archaeology, are instantly destructive and non-representative of in planta. Lack of plant ligninases or enzymes that hydrolyze specific bonds in lignin-carbohydrate complexes (LCCs) also frustrate a better grasp of lignin. Supramolecular self-assembly, nano-mechanical properties of lignin-lignin, lignin-polysaccharide interactions and association-dissociation kinetics affect biomass deconstruction and thereby cost-effective biofuels production.

Supramolecular self-assembled chaos: polyphenolic lignin's barrier to cost-effective lignocellulosic biofuels

Phenylpropanoid metabolism yields a mixture of monolignols that undergo chaotic, non-enzymatic reactions such as free radical polymerization and spontaneous self-assembly in order to form the polyphenolic lignin which is a barrier to cost-effective lignocellulosic biofuels. Post-synthesis lignin integration into the plant cell wall is unclear, including how the hydrophobic lignin incorporates into the wall in an initially hydrophilic milieu. Self-assembly, self-organization and aggregation give rise to a complex, 3D network of lignin that displays randomly branched topology and fractal properties. Attempts at isolating lignin, analogous to archaeology, are instantly destructive and non-representative of in planta. Lack of plant ligninases or enzymes that hydrolyze specific bonds in lignin-carbohydrate complexes (LCCs) also frustrate a better grasp of lignin. Supramolecular self-assembly, nano-mechanical properties of lignin-lignin, lignin-polysaccharide interactions and association-dissociation kinetics affect biomass deconstruction and thereby cost-effective biofuels production.

Automated saccharification assay for determination of digestibility in plant materials

BACKGROUND

Cell wall resistance represents the main barrier for the production of second generation biofuels. The deconstruction of lignocellulose can provide sugars for the production of fuels or other industrial products through fermentation. Understanding the biochemical basis of the recalcitrance of cell walls to digestion will allow development of more effective and cost efficient ways to produce sugars from biomass. One approach is to identify plant genes that play a role in biomass recalcitrance, using association genetics. Such an approach requires a robust and reliable high throughput (HT) assay for biomass digestibility, which can be used to screen the large numbers of samples involved in such studies.

RESULTS

We developed a HT saccharification assay based on a robotic platform that can carry out in a 96-well plate format the enzymatic digestion and quantification of the released sugars. The handling of the biomass powder for weighing and formatting into 96 wells is performed by a robotic station, where the plant material is ground, delivered to the desired well in the plates and weighed with a precision of 0.1 mg. Once the plates are loaded, an automated liquid handling platform delivers an optional mild pretreatment (< 100°C) followed by enzymatic hydrolysis of the biomass. Aliquots from the hydrolysis are then analyzed for the release of reducing sugar equivalents. The same platform can be used for the comparative evaluation of different enzymes and enzyme cocktails. The sensitivity and reliability of the platform was evaluated by measuring the saccharification of stems from lignin modified tobacco plants, and the results of automated and manual analyses compared.

CONCLUSIONS

The automated assay systems are sensitive, robust and reliable. The system can reliably detect differences in the saccharification of plant tissues, and is able to process large number of samples with a minimum amount of human intervention. The automated system uncovered significant increases in the digestibility of certain lignin modified lines in a manner compatible with known effects of lignin modification on cell wall properties. We conclude that this automated assay platform is of sufficient sensitivity and reliability to undertake the screening of the large populations of plants necessary for mutant identification and genetic association studies.

Potential of Arabidopsis systems biology to advance the biofuel field

Plant biomass is a renewable and potentially sustainable resource for the production of liquid biofuels and a multitude of bio-based materials. To tailor plants for biofuel production, a powerful gene discovery program targeted to cell wall recalcitrance genes is needed. In parallel, a system is required that reveals the pleiotropic effects of gene modifications and that delivers the fundamental knowledge necessary for successful gene stacking. In our opinion, these objectives can be pioneered through a systems biology approach in Arabidopsis. We develop our ideas with a focus on the lignin biosynthetic pathway, because lignin is among the most important factors determining cell wall recalcitrance.