Modifying plants for biofuel and biomaterial production

Leveraging Walnut Somatic Embryos as a Biomanufacturing Platform for Recombinant Proteins and Metabolites

Biomanufacturing enables novel sources of compounds with constant demand, such as food coloring and preservatives, as well as new compounds with peak demand, such as diagnostics and vaccines. The COVID-19 pandemic has highlighted the need for alternative sources of research materials, thrusting research on diversification of biomanufacturing platforms. Here, we show initial results exploring the walnut somatic embryogenic system expressing the recombinant receptor binding domain (RBD) and ectodomain of the spike protein (Spike) from the SARS-CoV-2 virus. Stably transformed walnut embryo lines were selected and propagated in vitro. Both recombinant proteins were detected at 3-14 µg/g dry weight of tissue culture material. Although higher yields of recombinant protein have been obtained using more conventional biomanufacturing platforms, we also report on the production of the red pigment betanin in somatic embryos, reaching yields of 650 mg/g, even higher than red beet Beta vulgaris. This first iteration shows the potential of biomanufacturing using somatic walnut embryos that can now be further optimized for different applications sourcing specialized proteins and metabolites.

Systematic synthesis and identification of monolignol pathway metabolites

Monolignol serves as the building blocks to constitute lignin, the second abundant polymer on Earth. Despite two decades of diligent efforts, complete identification of all metabolites in the currently proposed monolignol biosynthesis pathway has proven elusive. This limitation also hampers their potential application. One of the primary obstacles is the challenge of assembling a collection of all molecules, because many are commercially unavailable or prohibitively costly. In this study, we established systematic pipelines to synthesize all 24 molecules through the conversions between functional groups on a core structure followed by the application to other core structures. We successfully identified all of them in Populus trichocarpa and Eucalyptus grandis, two representative species respectively from malpighiales and myrtales in angiosperms. Knowledge about monolignol metabolite chemosynthesis and identification will form the foundation for future studies.

Harnessing genetic engineering to drive economic bioproduct production in algae

Our reliance on agriculture for sustenance, healthcare, and resources has been essential since the dawn of civilization. However, traditional agricultural practices are no longer adequate to meet the demands of a burgeoning population amidst climate-driven agricultural challenges. Microalgae emerge as a beacon of hope, offering a sustainable and renewable source of food, animal feed, and energy. Their rapid growth rates, adaptability to non-arable land and non-potable water, and diverse bioproduct range, encompassing biofuels and nutraceuticals, position them as a cornerstone of future resource management. Furthermore, microalgae's ability to capture carbon aligns with environmental conservation goals. While microalgae offers significant benefits, obstacles in cost-effective biomass production persist, which curtails broader application. This review examines microalgae compared to other host platforms, highlighting current innovative approaches aimed at overcoming existing barriers. These approaches include a range of techniques, from gene editing, synthetic promoters, and mutagenesis to selective breeding and metabolic engineering through transcription factors.

Organelle-targeted gene delivery in plants by nanomaterials

Genetic engineering of plants has revolutionized agriculture and has had a significant impact on our everyday life. It has allowed for the production of crops with longer shelf lives, enhanced yields and resistance to pests and disease. The application of nanomaterials in plant genetic engineering has further augmented these programs with higher delivery efficiencies, biocompatibility and the potential for plant regeneration. In particular, subcellular targeting using nanomaterials has recently become possible with the cutting-edge developments within nanomaterials, but remains challenging despite the promise in organellar engineering for the introduction of useful traits and the elucidation of subcellular interactions. This feature article provides an overview of nanomaterial delivery within plants and highlights the application of recent progress in nanomaterials for subcellular organelle-targeted delivery.

Microbiome differences in sugarcane and metabolically engineered oilcane accessions and their implications for bioenergy production

Oilcane is a metabolically engineered sugarcane (Saccharum spp. hybrid) that hyper-accumulates lipids in its vegetable biomass to provide an advanced feedstock for biodiesel production. The potential impact of hyper-accumulation of lipids in vegetable biomass on microbiomes and the consequences of altered microbiomes on plant growth and lipid accumulation have not been explored so far. Here, we explore differences in the microbiome structure of different oilcane accessions and non-modified sugarcane. 16S SSU rRNA and ITS rRNA amplicon sequencing were performed to compare the characteristics of the microbiome structure from different plant compartments (leaf, stem, root, rhizosphere, and bulk soil) of four greenhouse-grown oilcane accessions and non-modified sugarcane. Significant differences were only observed in the bacterial microbiomes. In leaf and stem microbiomes, more than 90% of the entire microbiome of non-modified sugarcane and oilcane was dominated by similar core taxa. Taxa associated with Proteobacteria led to differences in the non-modified sugarcane and oilcane microbiome structure. While differences were observed between multiple accessions, accession 1566 was notable in that it was consistently observed to differ in its microbial membership than other accessions and had the lowest abundance of taxa associated with plant-growth-promoting bacteria. Accession 1566 is also unique among oilcane accessions in that it has the highest constitutive expression of the WRI1 transgene. The WRI1 transcription factor is known to contribute to significant changes in the global gene expression profile, impacting plant fatty acid biosynthesis and photomorphogenesis. This study reveals for the first time that genetically modified oilcanes associate with distinct microbiomes. Our findings suggest potential relationships between core taxa, biomass yield, and TAG in oilcane accessions and support further research on the relationship between plant genotypes and their microbiomes.

Cell wall ester modifications and volatile emission signatures of plant response to abiotic stress

Growth suppression and defence signalling are simultaneous strategies that plants invoke to respond to abiotic stress. Here, we show that the drought stress response of poplar trees (Populus trichocarpa) is initiated by a suppression in cell wall derived methanol (MeOH) emissions and activation of acetic acid (AA) fermentation defences. Temperature sensitive emissions dominated by MeOH (AA/MeOH <30%) were observed from physiologically active leaves, branches, detached stems, leaf cell wall isolations and whole ecosystems. In contrast, drought treatment resulted in a suppression of MeOH emissions and strong enhancement in AA emissions together with volatiles acetaldehyde, ethanol, and acetone. These drought-induced changes coincided with a reduction in stomatal conductance, photosynthesis, transpiration, and leaf water potential. The strong enhancement in AA/MeOH emission ratios during drought (400%-3500%) was associated with an increase in acetate content of whole leaf cell walls, which became significantly ¹³ C₂ -labelled following the delivery of ¹³ C₂ -acetate via the transpiration stream. The results are consistent with both enzymatic and nonenzymatic MeOH and AA production at high temperature in hydrated tissues associated with accelerated primary cell wall growth processes, which are downregulated during drought. While the metabolic source(s) require further investigation, the observations are consistent with drought-induced activation of aerobic fermentation driving high rates of foliar AA emissions and enhancements in leaf cell wall O-acetylation. We suggest that atmospheric AA/MeOH emission ratios could be useful as a highly sensitive signal in studies investigating environmental and biological factors influencing growth-defence trade-offs in plants and ecosystems.

Polymer-coated carbon nanotube hybrids with functional peptides for gene delivery into plant mitochondria

The delivery of genetic material into plants has been historically challenging due to the cell wall barrier, which blocks the passage of many biomolecules. Carbon nanotube-based delivery has emerged as a promising solution to this problem and has been shown to effectively deliver DNA and RNA into intact plants. Mitochondria are important targets due to their influence on agronomic traits, but delivery into this organelle has been limited to low efficiencies, restricting their potential in genetic engineering. This work describes the use of a carbon nanotube-polymer hybrid modified with functional peptides to deliver DNA into intact plant mitochondria with almost 30 times higher efficiency than existing methods. Genetic integration of a folate pathway gene in the mitochondria displays enhanced plant growth rates, suggesting its applications in metabolic engineering and the establishment of stable transformation in mitochondrial genomes. Furthermore, the flexibility of the polymer layer will also allow for the conjugation of other peptides and cargo targeting other organelles for broad applications in plant bioengineering.

The delivery of genetic material into plants is challenging due to the cell wall barrier. Here, the authors hybridize polymer-coated carbon nanotubes with functional peptides to deliver plasmid DNA cargo into intact plant mitochondria for transient expression and homologous recombination at high efficiency.

Recent Developments in Lignocellulosic Biofuels, a Renewable Source of Bioenergy

Biofuel consists of non-fossil fuel derived from the organic biomass of renewable resources, including plants, animals, microorganisms, and waste. Energy derived from biofuel is known as bioenergy. The reserve of fossil fuels is now limited and continuing to decrease, while at the same time demand for energy is increasing. In order to overcome this scarcity, it is vital for human beings to transfer their dependency on fossil fuels to alternative types of fuel, including biofuels, which are effective methods of fulfilling present and future demands. The current review therefore focusses on second-generation lignocellulosic biofuels obtained from non-edible plant biomass (i.e., cellulose, lignin, hemi-celluloses, non-food material) in a more sustainable manner. The conversion of lignocellulosic feedstock is an important step during biofuel production. It is, however, important to note that, as a result of various technical restrictions, biofuel production is not presently cost efficient, thus leading to the need for improvement in the methods employed. There remain a number of challenges for the process of biofuel production, including cost effectiveness and the limitations of various technologies employed. This leads to a vital need for ongoing and enhanced research and development, to ensure market level availability of lignocellulosic biofuel.

Energy plants as biofuel source and as accumulators of heavy metals

Fossil fuel depletion and soil and water pollution gave impetus to the development of a novel perspective of sustainable development. In addition to the use of plant biomass for ethanol production, plants can be used to reduce the concentration of heavy metals in soil and water. Due to tolerance to high levels of metals, many plant species, crops, non-crops, medicinal, and pharmaceutical energy plants are well-known metal hyperaccumulators. This paper focuses on studies investigating the potential of Miscanthus sp., Beta vulgaris L., Saccharum sp., Ricinus communis L. Prosopis sp. and Arundo donax L. in heavy metal removal and biofuel production. Phytoremediation employing these plants showed great potential for bioaccumulation of Co, Cr, Cu, Al, Pb, Ni, Fe, Cd, Zn, Hg, Se, etc. This review presents the potential of lignocellulose plants to remove pollutants being a valuable substrate for biofuel production. Also, pretreat-ments, dealing with toxic biomass, and biofuel production are discussed.

Physiological, nutritional, and molecular responses of Brazilian sugarcane cultivars under stress by aluminum

Background

Sugarcane is a crop of global importance and has been expanding to areas with soils containing high levels of exchangeable aluminum (Al), which is a limiting factor for crop development in acidic soils. The study of the sugarcane physiological and nutritional behavior together with patterns of gene expression in response to Al stress may provide a basis for effective strategies to increase crop productivity in acidic soils.

Methods

Sugarcane cultivars were evaluated for physiological parameters (photosynthesis, stomatal conductance, and transpiration), nutrient (N, P, K, Ca, Mg, and S) and Al contents in leaves and roots and gene expression, of the genes MDH, SDH by qPCR, both related to the production of organic acids, and SOD, related to oxidative stress.

Results

Brazilian sugarcane RB867515, RB928064, and RB935744 cultivars exhibited very different responses to induced stress by Al. Exposure to Al caused up-regulation (SOD and MDH) or down-regulation (SDH, MDH, and SOD), depending on the cultivar, Al level, and plant tissue. The RB867515 cultivar was the most Al-tolerant, showing no decline of nutrient content in plant tissue, photosynthesis, transpiration, and stomatal conductance after exposure to Al; it exhibited the highest Al content in the roots, and showed important MDH and SOD gene expression in the roots. RB928064 only showed low expression of SOD in roots and leaves, while RB935744 showed important expression of the SOD gene only in the leaves. Sugarcane cultivars were classified in the following descending Al-tolerance order: RB867515 > RB928064 = RB935744. These results may contribute to the obtention of Al-tolerant cultivars that can play their genetic potential in soils of low fertility and with low demand for agricultural inputs; the selection of potential plants for breeding programs; the elucidation of Al detoxification mechanisms employed by sugarcane cultivars.

Loss of COMT activity reduces lateral root formation and alters the response to water limitation in sorghum brown midrib (bmr) 12 mutant

Lignin is a key target for modifying lignocellulosic biomass for efficient biofuel production. Brown midrib 12 (bmr12) encodes the sorghum caffeic acid O-methyltransferase (COMT) and is one of the key enzymes in monolignol biosynthesis. Loss of function mutations in COMT reduces syringyl (S) lignin subunits and improves biofuel conversion rate. Although lignin plays an important role in maintaining cell wall integrity of xylem vessels, physiological and molecular consequences due to loss of COMT on root growth and adaptation to water deficit remain unexplored. We addressed this gap by evaluating the root morphology, anatomy and transcriptome of bmr12 mutant. The mutant had reduced lateral root density (LRD) and altered root anatomy and response to water limitation. The wild-type exhibits similar phenotypes under water stress, suggesting that bmr12 may be in a water deficit responsive state even in well-watered conditions. bmr12 had increased transcript abundance of genes involved in (a)biotic stress response, gibberellic acid (GA) biosynthesis and signaling. We show that bmr12 is more sensitive to exogenous GA application and present evidence for the role of GA in regulating reduced LRD in bmr12. These findings elucidate the phenotypic and molecular consequences of COMT deficiency under optimal and water stress environments in grasses.

Biomass potential of novel interspecific and intergeneric hybrids of Saccharum grown in sub-tropical climates

Sugarcane-derived biomass is a promising source of renewable energy to meet the growing demands for biofuel. Currently, modern sugarcane cultivars are unable to provide enough biomass due to their narrow genetic base and susceptibility to abiotic and biotic stresses. We have evaluated total of 23 hybrids derived from diverse genetic backgrounds of different Saccharum spp. and allied genera, one inbred and compared with commercial checks. Intergeneric hybrids (IGHs) KGS 99-100 and GU 04-432, produced significantly higher biomass (43.37 t ha⁻¹ and 35.24 t ha⁻¹, respectively) than commercial sugarcane have genes derived from Erianthus arundinaceus. Interspecific hybrids (ISHs) GU 07-3704 and 99-489, also produced significantly higher amounts of biomass (37.24 t ha⁻¹ and 33.25 t ha⁻¹, respectively) than commercial checks have genes from S. officinarum and S. spontaneum backgrounds. ISHs recorded significantly higher biomass yield, number of stalks and total dry matter percentage whereas, IGH group recorded significantly higher fibre percent. Furthermore, the clones resistant to red rot and sugarcane borers were identified. The estimated energy value for seven hybrid clones was found to be very high. Cluster analysis of genetic traits revealed two major clusters in traits improving biomass. Our study has revealed that the genetic diversity present in these hybrids could be used for improving biomass production and tolerance to abiotic and biotic stresses in cultivated sugarcanes.

CRISPR base editing and prime editing: DSB and template-free editing systems for bacteria and plants

CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated) has been extensively exploited as a genetic tool for genome editing. The RNA guided Cas nucleases generate DNA double-strand break (DSB), triggering cellular repair systems mainly Non-homologous end-joining (NHEJ, imprecise repair) or Homology-directed repair (HDR, precise repair). However, DSB typically leads to unexpected DNA changes and lethality in some organisms. The establishment of bacteria and plants into major bio-production platforms require efficient and precise editing tools. Hence, in this review, we focus on the non-DSB and template-free genome editing, i.e., base editing (BE) and prime editing (PE) in bacteria and plants. We first highlight the development of base and prime editors and summarize their studies in bacteria and plants. We then discuss current and future applications of BE/PE in synthetic biology, crop improvement, evolutionary engineering, and metabolic engineering. Lastly, we critically consider the challenges and prospects of BE/PE in PAM specificity, editing efficiency, off-targeting, sequence specification, and editing window.

Genomic index selection provides a pragmatic framework for setting and refining multi-objective breeding targets in Miscanthus

BACKGROUND

Miscanthus has potential as a biomass crop but the development of varieties that are consistently superior to the natural hybrid M. × giganteus has been challenging, presumably because of strong G × E interactions and poor knowledge of the complex genetic architectures of traits underlying biomass productivity and climatic adaptation. While linkage and association mapping studies are starting to generate long lists of candidate regions and even individual genes, it seems unlikely that this information can be translated into effective marker-assisted selection for the needs of breeding programmes. Genomic selection has emerged as a viable alternative, and prediction accuracies are moderate across a range of phenological and morphometric traits in Miscanthus, though relatively low for biomass yield per se.

METHODS

We have previously proposed a combination of index selection and genomic prediction as a way of overcoming the limitations imposed by the inherent complexity of biomass yield. Here we extend this approach and illustrate its potential to achieve multiple breeding targets simultaneously, in the absence of a priori knowledge about their relative economic importance, while also monitoring correlated selection responses for non-target traits. We evaluate two hypothetical scenarios of increasing biomass yield by 20 % within a single round of selection. In the first scenario, this is achieved in combination with delaying flowering by 44 d (roughly 20 %), whereas, in the second, increased yield is targeted jointly with reduced lignin (-5 %) and increased cellulose (+5 %) content, relative to current average levels in the breeding population.

KEY RESULTS

In both scenarios, the objectives were achieved efficiently (selection intensities corresponding to keeping the best 20 and 4 % of genotypes, respectively). However, the outcomes were strikingly different in terms of correlated responses, and the relative economic values (i.e. value per unit of change in each trait compared with that for biomass yield) of secondary traits included in selection indices varied considerably.

CONCLUSIONS

Although these calculations rely on multiple assumptions, they highlight the need to evaluate breeding objectives and explicitly consider correlated responses in silico, prior to committing extensive resources. The proposed approach is broadly applicable for this purpose and can readily incorporate high-throughput phenotyping data as part of integrated breeding platforms.

The Impact of cDNA Normalization on Long-Read Sequencing of a Complex Transcriptome

Normalization of cDNA is widely used to improve the coverage of rare transcripts in analysis of transcriptomes employing next-generation sequencing. Recently, long-read technology has been emerging as a powerful tool for sequencing and construction of transcriptomes, especially for complex genomes containing highly similar transcripts and transcript-spliced isoforms. Here, we analyzed the transcriptome of sugarcane, a highly polyploidy plant genome, by PacBio isoform sequencing (Iso-Seq) of two different cDNA library preparations, with and without a normalization step. The results demonstrated that, while the two libraries included many of the same transcripts, many longer transcripts were removed, and many new generally shorter transcripts were detected by normalization. For the same input cDNA and data yield, the normalized library recovered more total transcript isoforms and number of predicted gene families and orthologous groups, resulting in a higher representation for the sugarcane transcriptome, compared to the non-normalized library. The non-normalized library, on the other hand, included a wider transcript length range with more longer transcripts above ∼1.25 kb and more transcript isoforms per gene family and gene ontology terms per transcript. A large proportion of the unique transcripts comprising ∼52% of the normalized library were expressed at a lower level than the unique transcripts from the non-normalized library, across three tissue types tested including leaf, stalk, and root. About 83% of the total 5,348 predicted long noncoding transcripts was derived from the normalized library, of which ∼80% was derived from the lowly expressed fraction. Functional annotation of the unique transcripts suggested that each library enriched different functional transcript fractions. This demonstrated the complementation of the two approaches in obtaining a complete transcriptome of a complex genome at the sequencing depth used in this study.

Integration of sugarcane production technologies for enhanced cane and sugar productivity targeting to increase farmers' income: strategies and prospects

The idea of doubling the farmers' income in next 5 years has been slated by the Government of India. The specific target of increasing sugarcane farmers' income could be achieved by developing cost-effective technologies, transferring them from laboratory to land, educating the farmers and creating a linkage between all stakeholders. Consistent efforts shall be required to harness all possible sources for increasing farmer's income in and outside the agriculture sector with respect to improvement in sugarcane and sugar productivity, enhancement in resource use efficiency and adopting various other ways and means including intercropping, management of pests and diseases, use of biotechnological tools and minimizing post-harvest deterioration. The advances in sugarcane biotechnology could become remarkable in the coming years, both in terms of improving productivity as well as increasing the value and utility of this crop substantially. In future, genetically modified sugarcane varieties with increased resistance to different biotic and abiotic stresses would serve more towards sugarcane crop improvement. Any possibility of enhancement in the income of sugarcane farmers shall also be dependent upon the profitability and sustainability of the sugar industry. Integration of sugarcane production technologies for improvement in farm productivity, diversified sugarcane production system, reduced cost of cultivation along with increased processing plant efficiency and diversification to produce value added products shall ensure smooth and higher payment to the farmers. Development of low-cost technologies to convert "waste to resource" on a smaller scale shall also help the farmers to increase their income further. This paper focuses on possible measures to be taken up in each aspects of sugarcane cultivation including biotechnological approaches to achieve the goal of enhancing the income of sugarcane farmers substantially, particularly in the sub-tropical region of India.

Removal of non-structural components from poplar whole-tree chips to enhance hydrolysis and fermentation performance

BACKGROUND

Whole-tree chips will be a likely feedstock for future biorefineries because of their low cost. Non-structural components (NSC), however, represent a significant part of whole-tree chips. The NSC can account for more than 10% of whole-tree poplar mass when the trees are grown in short rotation cycles. The influence of NSC, however, on the production of fuels and chemicals is not well known. In this study, we assessed the impact of NSC removal from poplar whole-tree chips on pretreatment and enzymatic hydrolysis yields, overall sugar recovery, and fermentation yield. In addition, we evaluated the economics of preprocessing as a new unit operation in the biorefinery.

RESULTS

Poplar whole-tree chips were preprocessed by neutral or acidic washing before steam pretreatment, enzymatic hydrolysis, and fermentation. Preprocessing of poplar reduced ash and extractives content as much as 70 and 50%, respectively. The overall sugar yield after pretreatment and hydrolysis was 18-22% higher when the biomass had been preprocessed, which was explained by higher sugar yields in liquid fraction and more efficient enzymatic hydrolysis of the solid fraction. The liquid fraction ethanol fermentation yield was 36-50% higher for the preprocessed biomass.

CONCLUSIONS

It appears that preprocessing reduced the buffering capacity of the biomass due to ash removal, and thereby improved the enzymatic hydrolysis. Removal of extractives during preprocessing improved the fermentation yield. The economic modeling shows that a preprocessing unit could have significant economic benefits in a biorefinery, where poplar whole-tree chips are used as bioconversion feedstock.

The Challenge of Analyzing the Sugarcane Genome

Reference genome sequences have become key platforms for genetics and breeding of the major crop species. Sugarcane is probably the largest crop produced in the world (in weight of crop harvested) but lacks a reference genome sequence. Sugarcane has one of the most complex genomes in crop plants due to the extreme level of polyploidy. The genome of modern sugarcane hybrids includes sub-genomes from two progenitors Saccharum officinarum and S. spontaneum with some chromosomes resulting from recombination between these sub-genomes. Advancing DNA sequencing technologies and strategies for genome assembly are making the sugarcane genome more tractable. Advances in long read sequencing have allowed the generation of a more complete set of sugarcane gene transcripts. This is supporting transcript profiling in genetic research. The progenitor genomes are being sequenced. A monoploid coverage of the hybrid genome has been obtained by sequencing BAC clones that cover the gene space of the closely related sorghum genome. The complete polyploid genome is now being sequenced and assembled. The emerging genome will allow comparison of related genomes and increase understanding of the functioning of this polyploidy system. Sugarcane breeding for traditional sugar and new energy and biomaterial uses will be enhanced by the availability of these genomic resources.

Bridging the gap between feedstock growers and users: the study of a coppice poplar-based biorefinery

BACKGROUND

In the biofuel industry, land productivity is important to feedstock growers and conversion process product yield is important to the biorefinery. The crop productivity, however, may not positively correlate with bioconversion yield. Therefore, it is important to evaluate sugar yield and biomass productivity. In this study, 2-year-old poplar trees harvested in the first coppice cycle, including one low-productivity hybrid and one high-productivity hybrid, were collected from two poplar tree farms. Through steam pretreatment and enzymatic hydrolysis, the bioconversion yields of low- and high-productivity poplar hybrids were compared for both sites.

RESULTS

The low-productivity hybrids had 9-19% higher sugar yields than the high-productivity hybrids, although they have the similar chemical composition. Economic calculations show the impact on the plantation and biorefinery of using the two feedstocks. Growing a high-productivity hybrid means the land owner would use 11-26% less land (which could be used for other crops) or collect $2.53-$3.46 MM/year extra revenue from the surplus feedstock. On the other side, the biorefinery would receive 5-10% additional revenue using the low-productivity hybrid.

CONCLUSION

We propose a business model based on the integration of the plantation and the biorefinery. In this model, different feedstocks are assessed using a metric of product tonnage per unit land per year. Use of this new economic metric bridges the gap between feedstock growers and users to maximize the overall production efficiency.

Increased drought tolerance in plants engineered for low lignin and low xylan content

BACKGROUND

We previously developed several strategies to engineer plants to produce cost-efficient biofuels from plant biomass. Engineered Arabidopsis plants with low xylan and lignin content showed normal growth and improved saccharification efficiency under standard growth conditions. However, it remains to be determined whether these engineered plants perform well under drought stress, which is the primary source of abiotic stress in the field.

RESULTS

Upon exposing engineered Arabidopsis plants to severe drought, we observed better survival rates in those with a low degree of xylan acetylation, low lignin, and low xylan content compared to those in wild-type plants. Increased pectic galactan content had no effect on drought tolerance. The drought-tolerant plants exhibited low water loss from leaves, and drought-responsive genes (RD29A, RD29B, DREB2A) were generally up-regulated under drought stress, which did not occur in the well-watered state. When compared with the wild type, plants with low lignin due to expression of QsuB, a 3-dehydroshikimate dehydratase, showed a stronger response to abscisic acid (ABA) in assays for seed germination and stomatal closure. The low-lignin plants also accumulated more ABA in response to drought than the wild-type plants. On the contrary, the drought tolerance in the engineered plants with low xylan content and low xylan acetylation was not associated with differences in ABA content or response compared to the wild type. Surprisingly, we found a significant increase in galactose levels and sugar released from the low xylan-engineered plants under drought stress.

CONCLUSIONS

This study shows that plants engineered to accumulate less lignin or xylan are more tolerant to drought and activate drought responses faster than control plants. This is an important finding because it demonstrates that modification of secondary cell walls does not necessarily render the plants less robust in the environment, and it shows that substantial changes in biomass composition can be achieved without compromising plant resilience.

A pepper mottle virus-based vector enables systemic expression of endoglucanase D in non-transgenic plants

Plant-virus-based expression vectors have been used as an alternative to the creation of transgenic plants. Using a virus-based vector, we investigated the feasibility of producing the endoglucanase D (EngD) from Clostridium cellulovorans in Nicotiana benthamiana. This protein has endoglucanase, xylanase, and exoglucanase activities and may be of value for cellulose digestion in the generation of biofuels from plant biomass. The EngD gene was cloned between the nuclear inclusion b (NIb)- and coat protein (CP)-encoding sequences of pSP6PepMoV-Vb1. In vitro transcripts derived from the clone (pSP6PepMoV-Vb1/EngD) were infectious in N. benthamiana but caused milder symptoms than wild-type PepMoV-Vb1. RT-PCR amplification of total RNA from non-inoculated upper leaves infected with PepMoV-Vb1/EngD produced the target band for the CP, partial NIb and EngD-CP regions of PepMoV-V1/EngD, in addition to nonspecific bands. Western blot analysis showed the CP target bands of PepMoV-Vb1/EngD as well as non-target bands. EngD enzymatic activity in infected plants was detected using a glucose assay. The plant leaves showed increased senescence compared with healthy and PepMoV-Vb1-infected plants. Our study suggests the feasibility of using a viral vector for systemic infection of plants for expression of heterologous engD for the purpose of digesting a cellulose substrate in plant cells for biomass production.

Genetic engineering of grass cell wall polysaccharides for biorefining

Grasses represent an abundant and widespread source of lignocellulosic biomass, which has yet to fulfil its potential as a feedstock for biorefining into renewable and sustainable biofuels and commodity chemicals. The inherent recalcitrance of lignocellulosic materials to deconstruction is the most crucial limitation for the commercial viability and economic feasibility of biomass biorefining. Over the last decade, the targeted genetic engineering of grasses has become more proficient, enabling rational approaches to modify lignocellulose with the aim of making it more amenable to bioconversion. In this review, we provide an overview of transgenic strategies and targets to tailor grass cell wall polysaccharides for biorefining applications. The bioengineering efforts and opportunities summarized here rely primarily on (A) reprogramming gene regulatory networks responsible for the biosynthesis of lignocellulose, (B) remodelling the chemical structure and substitution patterns of cell wall polysaccharides and (C) expressing lignocellulose degrading and/or modifying enzymes in planta. It is anticipated that outputs from the rational engineering of grass cell wall polysaccharides by such strategies could help in realizing an economically sustainable, grass-derived lignocellulose processing industry.

Biotechnological Strategies to Improve Plant Biomass Quality for Bioethanol Production

The transition from an economy dependent on nonrenewable energy sources to one with higher diversity of renewables will not be a simple process. It requires an important research effort to adapt to the dynamics of the changing energy market, sort costly processes, and avoid overlapping with social interest markets such as food and livestock production. In this review, we analyze the desirable traits of raw plant materials for the bioethanol industry and the molecular biotechnology strategies employed to improve them, in either plants already under use (as maize) or proposed species (large grass families). The fundamentals of these applications can be found in the mechanisms by which plants have evolved different pathways to manage carbon resources for reproduction or survival in unexpected conditions. Here, we review the means by which this information can be used to manipulate these mechanisms for commercial uses, including saccharification improvement of starch and cellulose, decrease in cell wall recalcitrance through lignin modification, and increase in plant biomass.

Utilizing Anaerobic Fungi for Two-stage Sugar Extraction and Biofuel Production from Lignocellulosic Biomass

Lignocellulosic biomass is a vast and underutilized resource for the production of sugars and biofuels. However, the structural complexity of lignocellulosic biomass and the need for multiple pretreatment and enzymatic steps for sugar release renders this process economically challenging. Here, we report a novel approach for direct, single container, exogenous enzyme-free conversion of lignocellulosic biomass to sugars and biofuels using the anaerobic fungal isolate strain C1A. This approach utilizes simple physiological manipulations for timely inhibition and uncoupling of saccharolytic and fermentative capabilities of strain C1A, leading to the accumulation of sugar monomers (glucose and xylose) in the culture medium. The produced sugars, in addition to fungal hyphal lysate, are subsequently converted by Escherichia coli strain K011 to ethanol. Using this approach, we successfully recovered 17.0% (w/w) of alkali-pretreated corn stover (20.0% of its glucan and xylan content) as sugar monomers in the culture media. More importantly, 14.1% of pretreated corn stover (17.1% of glucan and xylan content) was recovered as ethanol at a final concentration of 28.16 mM after the addition of the ethanologenic strain K011. The high ethanol yield obtained is due to its accumulation as a minor fermentation end product by strain C1A during its initial growth phase, the complete conversion of sugars to ethanol by strain K011, and the possible conversion of unspecified substrates in the hyphal lysate of strain C1A to ethanol by strain K011. This study presents a novel, versatile, and exogenous enzyme-free strategy that utilizes a relatively unexplored group of organisms (anaerobic fungi) for direct biofuel production from lignocellulosic biomass.

Xylogenesis in zinnia (Zinnia elegans) cell cultures: unravelling the regulatory steps in a complex developmental programmed cell death event

MAIN CONCLUSION

Physiological and molecular studies support the view that xylogenesis can largely be determined as a specific form of vacuolar programmed cell death (PCD). The studies in xylogenic zinnia cell culture have led to many breakthroughs in xylogenesis research and provided a background for investigations in other experimental models in vitro and in planta . This review discusses the most essential earlier and recent findings on the regulation of xylem elements differentiation and PCD in zinnia and other xylogenic systems. Xylogenesis (the formation of water conducting vascular tissue) is a paradigm of plant developmental PCD. The xylem vessels are composed of fused tracheary elements (TEs)-dead, hollow cells with patterned lignified secondary cell walls. They result from the differentiation of the procambium and cambium cells and undergo cell death to become functional post-mortem. The TE differentiation proceeds through a well-coordinated sequence of events in which differentiation and the programmed cellular demise are intimately connected. For years a classical experimental model for studies on xylogenesis was the xylogenic zinnia (Zinnia elegans) cell culture derived from leaf mesophyll cells that, upon induction by cytokinin and auxin, transdifferentiate into TEs. This cell system has been proven very efficient for investigations on the regulatory components of xylem differentiation which has led to many discoveries on the mechanisms of xylogenesis. The knowledge gained from this system has potentiated studies in other xylogenic cultures in vitro and in planta. The present review summarises the previous and latest findings on the hormonal and biochemical signalling, metabolic pathways and molecular and gene determinants underlying the regulation of xylem vessels differentiation in zinnia cell culture. Highlighted are breakthroughs achieved through the use of xylogenic systems from other species and newly introduced tools and analytical approaches to study the processes. The mutual dependence between PCD signalling and the differentiation cascade in the program of TE development is discussed.

The TcEG1 beetle (Tribolium castaneum) cellulase produced in transgenic switchgrass is active at alkaline pH and auto-hydrolyzes biomass for increased cellobiose release

BACKGROUND

Genetically engineered biofuel crops, such as switchgrass (Panicum virgatum L.), that produce their own cell wall-digesting cellulase enzymes would reduce costs of cellulosic biofuel production. To date, non-bioenergy plant models have been used in nearly all studies assessing the synthesis and activity of plant-produced fungal and bacterial cellulases. One potential source for cellulolytic enzyme genes is herbivorous insects adapted to digest plant cell walls. Here we examine the potential of transgenic switchgrass-produced TcEG1 cellulase from Tribolium castaneum (red flour beetle). This enzyme, when overproduced in Escherichia coli and Saccharomyces cerevisiae, efficiently digests cellulose at optima of 50 °C and pH 12.0.

RESULTS

TcEG1 that was produced in green transgenic switchgrass tissue had a range of endoglucanase activity of 0.16-0.05 units (µM glucose release/min/mg) at 50 °C and pH 12.0. TcEG1 activity from air-dried leaves was unchanged from that from green tissue, but when tissue was dried in a desiccant oven (46 °C), specific enzyme activity decreased by 60%. When transgenic biomass was "dropped-in" into an alkaline buffer (pH 12.0) and allowed to incubate at 50 °C, cellobiose release was increased up to 77% over non-transgenic biomass. Saccharification was increased in one transgenic event by 28%, which had a concurrent decrease in lignin content of 9%. Histological analysis revealed an increase in cell wall thickness with no change to cell area or perimeter. Transgenic plants produced more, albeit narrower, tillers with equivalent dry biomass as the control.

CONCLUSIONS

This work describes the first study in which an insect cellulase has been produced in transgenic plants; in this case, the dedicated bioenergy crop switchgrass. Switchgrass overexpressing the TcEG1 gene appeared to be morphologically similar to its non-transgenic control and produced equivalent dry biomass. Therefore, we propose TcEG1 transgenics could be bred with other transgenic germplasm (e.g., low-lignin lines) to yield new switchgrass with synergistically reduced recalcitrance to biofuel production. In addition, transgenes for other cell wall degrading enzymes may be stacked with TcEG1 in switchgrass to yield complementary cell wall digestion features and complete auto-hydrolysis.

Evaluation of Relationships between Growth Rate, Tree Size, Lignocellulose Composition, and Enzymatic Saccharification in Interspecific Corymbia Hybrids and Parental Taxa

In order for a lignocellulosic bioenergy feedstock to be considered sustainable, it must possess a high rate of growth to supply biomass for conversion. Despite the desirability of a fast growth rate for industrial application, it is unclear what effect growth rate has on biomass composition or saccharification. We characterized Klason lignin, glucan, and xylan content with response to growth in Corymbia interspecific F1 hybrid families (HF) and parental species Corymbia torelliana and C. citriodora subspecies variegata and measured the effects on enzymatic hydrolysis from hydrothermally pretreated biomass. Analysis of biomass composition within Corymbia populations found similar amounts of Klason lignin content (19.7-21.3%) among parental and hybrid populations, whereas glucan content was clearly distinguished within C. citriodora subspecies variegata (52%) and HF148 (60%) as compared to other populations (28-38%). Multiple linear regression indicates that biomass composition is significantly impacted by tree size measured at the same age, with Klason lignin content increasing with diameter breast height (DBH) (+0.12% per cm DBH increase), and glucan and xylan typically decreasing per DBH cm increase (-0.7 and -0.3%, respectively). Polysaccharide content within C. citriodora subspecies variegata and HF-148 were not significantly affected by tree size. High-throughput enzymatic saccharification of hydrothermally pretreated biomass found significant differences among Corymbia populations for total glucose production from biomass, with parental Corymbia torelliana and hybrids HF-148 and HF-51 generating the highest amounts of glucose (~180 mg/g biomass, respectively), with HF-51 undergoing the most efficient glucan-to-glucose conversion (74%). Based on growth rate, biomass composition, and further optimization of enzymatic saccharification yield, high production Corymbia hybrid trees are potentially suitable for fast-rotation bioenergy or biomaterial production.

Plant Fibre: Molecular Structure and Biomechanical Properties, of a Complex Living Material, Influencing Its Deconstruction towards a Biobased Composite

Plant cell walls form an organic complex composite material that fulfils various functions. The hierarchical structure of this material is generated from the integration of its elementary components. This review provides an overview of wood as a composite material followed by its deconstruction into fibres that can then be incorporated into biobased composites. Firstly, the fibres are defined, and their various origins are discussed. Then, the organisation of cell walls and their components are described. The emphasis is on the molecular interactions of the cellulose microfibrils, lignin and hemicelluloses in planta. Hemicelluloses of diverse species and cell walls are described. Details of their organisation in the primary cell wall are provided, as understanding of the role of hemicellulose has recently evolved and is likely to affect our perception and future study of their secondary cell wall homologs. The importance of the presence of water on wood mechanical properties is also discussed. These sections provide the basis for understanding the molecular arrangements and interactions of the components and how they influence changes in fibre properties once isolated. A range of pulping processes can be used to individualise wood fibres, but these can cause damage to the fibres. Therefore, issues relating to fibre production are discussed along with the dispersion of wood fibres during extrusion. The final section explores various ways to improve fibres obtained from wood.

Transgenic Plant-Produced Hydrolytic Enzymes and the Potential of Insect Gut-Derived Hydrolases for Biofuels

Various perennial C4 grass species have tremendous potential for use as lignocellulosic biofuel feedstocks. Currently available grasses require costly pre-treatment and exogenous hydrolytic enzyme application to break down complex cell wall polymers into sugars that can then be fermented into ethanol. It has long been hypothesized that engineered feedstock production of cell wall degrading (CWD) enzymes would be an efficient production platform for of exogenous hydrolytic enzymes. Most research has focused on plant overexpression of CWD enzyme-coding genes from free-living bacteria and fungi that naturally break down plant cell walls. Recently, it has been found that insect digestive tracts harbor novel sources of lignocellulolytic biocatalysts that might be exploited for biofuel production. These CWD enzyme genes can be located in the insect genomes or in symbiotic microbes. When CWD genes are transformed into plants, negative pleiotropic effects are possible such as unintended cell wall digestion. The use of codon optimization along with organelle and tissue specific targeting improves CWD enzyme yields. The literature teaches several important lessons on strategic deployment of CWD genes in transgenic plants, which is the focus of this review.

From first generation biofuels to advanced solar biofuels

Roadmaps towards sustainable bioeconomy, including the production of biofuels, in many EU countries mostly rely on biomass use. However, although biomass is renewable, the efficiency of biomass production is too low to be able to fully replace the fossil fuels. The use of land for fuel production also introduces ethical problems in increasing the food price. Harvesting solar energy by the photosynthetic machinery of plants and autotrophic microorganisms is the basis for all biomass production. This paper describes current challenges and possibilities to sustainably increase the biomass production and highlights future technologies to further enhance biofuel production directly from sunlight. The biggest scientific breakthroughs are expected to rely on a new technology called "synthetic biology", which makes engineering of biological systems possible. It will enable direct conversion of solar energy to a fuel from inexhaustible raw materials: sun light, water and CO2. In the future, such solar biofuels are expected to be produced in engineered photosynthetic microorganisms or in completely synthetic living factories.

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.

Potential for Genetic Improvement of Sugarcane as a Source of Biomass for Biofuels

Sugarcane (Saccharum spp. hybrids) has great potential as a major feedstock for biofuel production worldwide. It is considered among the best options for producing biofuels today due to an exceptional biomass production capacity, high carbohydrate (sugar + fiber) content, and a favorable energy input/output ratio. To maximize the conversion of sugarcane biomass into biofuels, it is imperative to generate improved sugarcane varieties with better biomass degradability. However, unlike many diploid plants, where genetic tools are well developed, biotechnological improvement is hindered in sugarcane by our current limited understanding of the large and complex genome. Therefore, understanding the genetics of the key biofuel traits in sugarcane and optimization of sugarcane biomass composition will advance efficient conversion of sugarcane biomass into fermentable sugars for biofuel production. The large existing phenotypic variation in Saccharum germplasm and the availability of the current genomics technologies will allow biofuel traits to be characterized, the genetic basis of critical differences in biomass composition to be determined, and targets for improvement of sugarcane for biofuels to be established. Emerging options for genetic improvement of sugarcane for the use as a bioenergy crop are reviewed. This will better define the targets for potential genetic manipulation of sugarcane biomass composition for biofuels.

High-throughput Screening of Recalcitrance Variations in Lignocellulosic Biomass: Total Lignin, Lignin Monomers, and Enzymatic Sugar Release

The conversion of lignocellulosic biomass to fuels, chemicals, and other commodities has been explored as one possible pathway toward reductions in the use of non-renewable energy sources. In order to identify which plants, out of a diverse pool, have the desired chemical traits for downstream applications, attributes, such as cellulose and lignin content, or monomeric sugar release following an enzymatic saccharification, must be compared. The experimental and data analysis protocols of the standard methods of analysis can be time-consuming, thereby limiting the number of samples that can be measured. High-throughput (HTP) methods alleviate the shortcomings of the standard methods, and permit the rapid screening of available samples to isolate those possessing the desired traits. This study illustrates the HTP sugar release and pyrolysis-molecular beam mass spectrometry pipelines employed at the National Renewable Energy Lab. These pipelines have enabled the efficient assessment of thousands of plants while decreasing experimental time and costs through reductions in labor and consumables.

Engineering of plant cell walls for enhanced biofuel production

The biomass of plants consists predominately of cell walls, a sophisticated composite material composed of various polymer networks including numerous polysaccharides and the polyphenol lignin. In order to utilize this renewable, highly abundant resource for the production of commodity chemicals such as biofuels, major hurdles have to be surpassed to reach economical viability. Recently, major advances in the basic understanding of the synthesis of the various wall polymers and its regulation has enabled strategies to alter the qualitative composition of wall materials. Such emerging strategies include a reduction/alteration of the lignin network to enhance polysaccharide accessibility, reduction of polymer derived processing inhibitors, and increases in polysaccharides with a high hexose/pentose ratio.

Evaluating lignocellulosic biomass, its derivatives, and downstream products with Raman spectroscopy

The creation of fuels, chemicals, and materials from plants can aid in replacing products fabricated from non-renewable energy sources. Before using biomass in downstream applications, it must be characterized to assess chemical traits, such as cellulose, lignin, or lignin monomer content, or the sugars released following an acid or enzymatic hydrolysis. The measurement of these traits allows researchers to gage the recalcitrance of the plants and develop efficient deconstruction strategies to maximize yields. Standard methods for assessing biomass phenotypes often have experimental protocols that limit their use for screening sizeable numbers of plant species. Raman spectroscopy, a non-destructive, non-invasive vibrational spectroscopy technique, is capable of providing qualitative, structural information and quantitative measurements. Applications of Raman spectroscopy have aided in alleviating the constraints of standard methods by coupling spectral data with multivariate analysis to construct models capable of predicting analytes. Hydrolysis and fermentation products, such as glucose and ethanol, can be quantified off-, at-, or on-line. Raman imaging has enabled researchers to develop a visual understanding of reactions, such as different pretreatment strategies, in real-time, while also providing integral chemical information. This review provides an overview of what Raman spectroscopy is, and how it has been applied to the analysis of whole lignocellulosic biomass, its derivatives, and downstream process monitoring.

Multifunctional cellulase catalysis targeted by fusion to different carbohydrate-binding modules

BACKGROUND

Carbohydrate binding modules (CBMs) bind polysaccharides and help target glycoside hydrolases catalytic domains to their appropriate carbohydrate substrates. To better understand how CBMs can improve cellulolytic enzyme reactivity, representatives from each of the 18 families of CBM found in Ruminoclostridium thermocellum were fused to the multifunctional GH5 catalytic domain of CelE (Cthe_0797, CelEcc), which can hydrolyze numerous types of polysaccharides including cellulose, mannan, and xylan. Since CelE is a cellulosomal enzyme, none of these fusions to a CBM previously existed.

RESULTS

CelEcc_CBM fusions were assayed for their ability to hydrolyze cellulose, lichenan, xylan, and mannan. Several CelEcc_CBM fusions showed enhanced hydrolytic activity with different substrates relative to the fusion to CBM3a from the cellulosome scaffoldin, which has high affinity for binding to crystalline cellulose. Additional binding studies and quantitative catalysis studies using nanostructure-initiator mass spectrometry (NIMS) were carried out with the CBM3a, CBM6, CBM30, and CBM44 fusion enzymes. In general, and consistent with observations of others, enhanced enzyme reactivity was correlated with moderate binding affinity of the CBM. Numerical analysis of reaction time courses showed that CelEcc_CBM44, a combination of a multifunctional enzyme domain with a CBM having broad binding specificity, gave the fastest rates for hydrolysis of both the hexose and pentose fractions of ionic-liquid pretreated switchgrass.

CONCLUSION

We have shown that fusions of different CBMs to a single multifunctional GH5 catalytic domain can increase its rate of reaction with different pure polysaccharides and with pretreated biomass. This fusion approach, incorporating domains with broad specificity for binding and catalysis, provides a new avenue to improve reactivity of simple combinations of enzymes within the complexity of plant biomass.