Engineering of Bioenergy Crops: Dominant Genetic Approaches to Improve Polysaccharide Properties and Composition in Biomass

Millet as a promising C4 model crop for sustainable biofuel production

The rapid depletion of conventional fuel resources and rising energy demand has accelerated the search for alternative energy sources. Further, the expanding need to use bioenergy crops for sustainable fuel production has enhanced the competition for agricultural land, raising the "food vs. fuel" competition. Considering this, producing bioenergy crops on marginal land has a great perspective for achieving sustainable bioenergy production and mitigating the negative impacts of climate change. C4 crops are dual-purpose crops with better efficiency to fix atmospheric CO2 and convert solar energy into lignocellulosic biomass. Of these, millets have gained worldwide attention due to their climate resilience and nutraceutical properties. Due to close synteny with contemporary C4 bioenergy crops, millets are being considered a model crop for studying diverse agronomically important traits associated with biomass production. Millets can be cultivated on marginal land with minimum fertilizer inputs and maximum biomass production. In this regard, advanced molecular approaches, including marker-assisted breeding, multi-omics approaches, and gene-editing technologies, can be employed to genetically engineer these crops for enhanced biofuel production efficiency. The current study aims to provide an overview of millets as a sustainable bioenergy source and underlines the significance of millets as a C4 model to elucidate the genes and pathways involved in lignocellulosic biomass production using advanced molecular biology approaches.

A miniaturized feedstocks-to-fuels pipeline for screening the efficiency of deconstruction and microbial conversion of lignocellulosic biomass

Sustainably grown biomass is a promising alternative to produce fuels and chemicals and reduce the dependency on fossil energy sources. However, the efficient conversion of lignocellulosic biomass into biofuels and bioproducts often requires extensive testing of components and reaction conditions used in the pretreatment, saccharification, and bioconversion steps. This restriction can result in a significant and unwieldy number of combinations of biomass types, solvents, microbial strains, and operational parameters that need to be characterized, turning these efforts into a daunting and time-consuming task. Here we developed a high-throughput feedstocks-to-fuels screening platform to address these challenges. The result is a miniaturized semi-automated platform that leverages the capabilities of a solid handling robot, a liquid handling robot, analytical instruments, and a centralized data repository, adapted to operate as an ionic-liquid-based biomass conversion pipeline. The pipeline was tested by using sorghum as feedstock, the biocompatible ionic liquid cholinium phosphate as pretreatment solvent, a "one-pot" process configuration that does not require ionic liquid removal after pretreatment, and an engineered strain of the yeast Rhodosporidium toruloides that produces the jet-fuel precursor bisabolene as a conversion microbe. By the simultaneous processing of 48 samples, we show that this configuration and reaction conditions result in sugar yields (~70%) and bisabolene titers (~1500 mg/L) that are comparable to the efficiencies observed at larger scales but require only a fraction of the time. We expect that this Feedstocks-to-Fuels pipeline will become an effective tool to screen thousands of bioenergy crop and feedstock samples and assist process optimization efforts and the development of predictive deconstruction approaches.

GhMYB52 Like: A Key Factor That Enhances Lint Yield by Negatively Regulating the Lignin Biosynthesis Pathway in Fibers of Upland Cotton (Gossypium hirsutum L.)

In the context of sustainable agriculture and biomaterial development, understanding and enhancing plant secondary cell wall formation are crucial for improving crop fiber quality and biomass conversion efficiency. This is especially critical for economically important crops like upland cotton (Gossypium hirsutum L.), for which fiber quality and its processing properties are essential. Through comprehensive genome-wide screening and analysis of expression patterns, we identified a particularly high expression of an R2R3 MYB transcription factor, GhMYB52 Like, in the development of the secondary cell wall in cotton fiber cells. Utilizing gene-editing technology to generate a loss-of-function mutant to clarify the role of GhMYB52 Like, we revealed that GhMYB52 Like does not directly contribute to cellulose synthesis in cotton fibers but instead represses a subset of lignin biosynthesis genes, establishing it as a lignin biosynthesis inhibitor. Concurrently, a substantial decrease in the lint index, a critical measure of cotton yield, was noted in parallel with an elevation in lignin levels. This study not only deepens our understanding of the molecular mechanisms underlying cotton fiber development but also offers new perspectives for the molecular improvement of other economically important crops and the enhancement of biomass energy utilization.

Applications and opportunities of click chemistry in plant science

The Nobel Prize in Chemistry for 2022 was awarded to the pioneers of Lego-like 'click chemistry': combinatorial chemistry with remarkable modularity and diversity. It has been applied to a wide variety of biological systems, from microorganisms to plants and animals, including humans. Although click chemistry is a powerful chemical biology tool, comparatively few studies have examined its potential in plant science. Here, we review click chemistry reactions and their applications in plant systems, highlighting the activity-based probes and metabolic labeling strategies combined with bioorthogonal click chemistry to visualize plant biological processes. These applications offer new opportunities to explore and understand the underlying molecular mechanisms regulating plant composition, growth, metabolism, defense, and immune responses.

Harnessing Plant Sugar Metabolism for Glycoengineering

Plants possess an innate ability to generate vast amounts of sugar and produce a range of sugar-derived compounds that can be utilized for applications in industry, health, and agriculture. Nucleotide sugars lie at the unique intersection of primary and specialized metabolism, enabling the biosynthesis of numerous molecules ranging from small glycosides to complex polysaccharides. Plants are tolerant to perturbations to their balance of nucleotide sugars, allowing for the overproduction of endogenous nucleotide sugars to push flux towards a particular product without necessitating the re-engineering of upstream pathways. Pathways to produce even non-native nucleotide sugars may be introduced to synthesize entirely novel products. Heterologously expressed glycosyltransferases capable of unique sugar chemistries can further widen the synthetic repertoire of a plant, and transporters can increase the amount of nucleotide sugars available to glycosyltransferases. In this opinion piece, we examine recent successes and potential future uses of engineered nucleotide sugar biosynthetic, transport, and utilization pathways to improve the production of target compounds. Additionally, we highlight current efforts to engineer glycosyltransferases. Ultimately, the robust nature of plant sugar biochemistry renders plants a powerful chassis for the production of target glycoconjugates and glycans.

Emerging trends and advances in valorization of lignocellulosic biomass to biofuels

Sustainable technologies pave the way to address future energy demand by converting lignocellulosic biomass into fuels, carbon-neutral materials, and chemicals which might replace fossil fuels. Thermochemical and biochemical technologies are conventional methods that convert biomass into value-added products. To enhance biofuel production, the existing technologies should be upgraded using advanced processes. In this regard, the present review explores the advanced technologies of thermochemical processes such as plasma technology, hydrothermal treatment, microwave-based processing, microbial-catalyzed electrochemical systems, etc. Advanced biochemical technologies such as synthetic metabolic engineering and genomic engineering have led to the development of an effective strategy to produce biofuels. The microwave-plasma-based technique increases the biofuel conversion efficiency by 97% and the genetic engineering strains increase the sugar production by 40%, inferring that the advanced technologies enhances the efficiency. So understanding these processes leads to low-carbon technologies which can solve the global issues on energy security, the greenhouse gases emission, and global warming.

It's time to go glyco in cell wall bioengineering

Tailoring the structure of cellulose, hemicellulose or pectin in plant cell walls can modulate growth, disease resistance, biomass yield and other important agronomic traits. Recent advances in the biosynthesis of microfibrils and matrix polysaccharides force us to re-examine old assumptions about the assembly and functions of cell wall components. The engineering of living or hybrid materials in microorganisms could be adapted to plant biopolymers or to inspire the development of new plant-based composites. High-throughput cellular factories and synthetic biology toolkits could unveil the biological roles and biotechnological potential of the large, unexplored space of carbohydrate-active enzymes. Increasing automation and enhanced carbohydrate detection methods are unlocking new routes to design plant glycans for a sustainable bioeconomy.

Organic waste recycling for carbon smart circular bioeconomy and sustainable development: A review

The development of sustainable and low carbon impact processes for a suitable management of waste and by-products coming from different factors of the industrial value chain like agricultural, forestry and food processing industries. Implementing this will helps to avoid the negative environmental impact and global warming. The application of the circular bioeconomy (CB) and the circular economic models have been shown to be a great opportunity for facing the waste and by-products issues by bringing sustainable processing systems which allow to the value chains be more responsible and resilient. In addition, biorefinery approach coupled to CB context could offer different solution and insights to conquer the current challenges related to decrease the fossil fuel dependency as well as increase efficiency of resource recovery and processing cost of the industrial residues. It is worth to remark the important role that the biotechnological processes such as fermentative, digestive and enzymatic conversions play for an effective waste management and carbon neutrality.

Introduced and registered switchgrass varieties (Panicum virgatum L.) as a source material for breeding for biomass productivity

Purpose. On the basis of multi-year research on the complex of economically valuable characteristics, the best switchgrass varieties (Panicum virgatum L.) ‘Patfinder’, ‘Carthage’, ‘Blackwell’, ‘Morozko’, ‘Liadovske’ and ‘Zoriane’ were singled out as a source material for breeding for productivity. Methods. The research was conducted during 2017–2021 on the basis of the Poltava State Agrarian University. The soils of the experimental site of the “Energy Crops” collection are typical chernozems with a humus content of 3.4%. Plots were planted with randomized placement of options in four-fold repetition according to the methods of experimental work in agronomy. Also, approved scientific-practical and methodical recommendations for growing energy crops were applied. To confirm the significant difference between the studied varieties, dispersion analysis using Excel and Statistica programs was used. Results. Switchgrass varieties were grouped according to the duration of the growing season into: early- (up to 160 days), medium- (161–171 days) and late ripening (more than 170 days). The complex resistance of switchgrass varieties to drought, frost and plant lodging: ‘Cave-in-Rock’, ‘Zoriane’, ‘Morozko’ and ‘Liadovske’ was revealed. It was determined that economically valuable characteristics depend to a greater extent on varietal characteristics than on growing conditions. The yield of ground vegetative mass based on dry residue for the studied varie­ties varied from 12.1 to 15.6 t/ha. Сonclusions. The varieties ‘Cave-in-Rock’, ‘Zoriane’, ‘Morozko’, ‘Liadovske’ were the most adaptable to growing conditions. The switchgrass varieties ‘Kanlow’ and ‘Cave-in-rock’ provided the highest plant stand and switchgrass variety ‘Dacotah’ provided the lowest plant stand. Varieties ‘Pathfinder’, ‘Blackwell’, ‘Shelter’, ‘Carthage’ and ‘Zoriane’ were singled out according to the number of stems and productivity. The latter, together with the Ukrainian variety ‘Zoriane’, are recommended to be used as starting material for crop selection based on biomass productivity.

Recent advances in metabolic engineering of microorganisms for advancing lignocellulose-derived biofuels

Combating climate change and ensuring energy supply to a rapidly growing global population has highlighted the need to replace petroleum fuels with clean, and sustainable renewable fuels. Biofuels offer a solution to safeguard energy security with reduced ecological footprint and process economics. Over the past years, lignocellulosic biomass has become the most preferred raw material for the production of biofuels, such as fuel, alcohol, biodiesel, and biohydrogen. However, the cost-effective conversion of lignocellulose into biofuels remains an unsolved challenge at the industrial scale. Recently, intensive efforts have been made in lignocellulose feedstock and microbial engineering to address this problem. By improving the biological pathways leading to the polysaccharide, lignin, and lipid biosynthesis, limited success has been achieved, and still needs to improve sustainable biofuel production. Impressive success is being achieved by the retouring metabolic pathways of different microbial hosts. Several robust phenotypes, mostly from bacteria and yeast domains, have been successfully constructed with improved substrate spectrum, product yield and sturdiness against hydrolysate toxins. Cyanobacteria is also being explored for metabolic advancement in recent years, however, it also remained underdeveloped to generate commercialized biofuels. The bacterium Escherichia coli and yeast Saccharomyces cerevisiae strains are also being engineered to have cell surfaces displaying hydrolytic enzymes, which holds much promise for near-term scale-up and biorefinery use. Looking forward, future advances to achieve economically feasible production of lignocellulosic-based biofuels with special focus on designing more efficient metabolic pathways coupled with screening, and engineering of novel enzymes.

In Planta Cell Wall Engineering: From Mutants to Artificial Cell Walls

To mitigate the effects of global warming and to preserve the limited fossil fuel resources, an increased exploitation of plant-based materials and fuels is required, which would be one of the most important innovations related to sustainable development. Cell walls account for the majority of plant dry biomass and so is the target of such innovations. In this review, we discuss recent advances in in planta cell wall engineering through genetic manipulations, with a focus on wild-type-based and mutant-based approaches. The long history of using a wild-type-based approach has resulted in the development of many strategies for manipulating lignin, hemicellulose and pectin to decrease cell wall recalcitrance. In addition to enzyme-encoding genes, many transcription factor genes important for changing relevant cell wall characteristics have been identified. Although mutant-based cell wall engineering is relatively new, it has become feasible due to the rapid development of genome-editing technologies and systems biology-related research; we will soon enter an age of designed artificial wood production via complex genetic manipulations of many industrially important trees and crops.

Enzyme Production Potential of Penicillium oxalicum M1816 and Its Application in Ferulic Acid Production

The present study focused on isolating an efficient enzyme production microorganism for ferulic acid (FA) production from wheat bran. A wild-type cellulase-, xylanase-, and feruloyl esterase-producing strain was isolated and identified as Penicillium oxalicum M1816. The genome was sequenced and assembled into 30.5 Mb containing 8301 predicted protein-coding genes. In total, 553 genes were associated with carbohydrate metabolism. Genomic CAZymes analysis indicated that P. oxalicum M1816, comprising 39 cellulolytic enzymes and 111 hemicellulases (including 5 feruloyl esterase genes), may play a vital role in wheat bran degradation and FA production. The crude enzyme of strain M1816 could release 1.85 ± 0.08 mg·g-1 FA from de-starched wheat bran (DSWB) at 12 h, which was significantly higher than other commercial enzymes. Meanwhile, when the strain M1816 was cultured in medium supplemented with DSWB, up to 92.89% of the total alkali-extractable FA was released. The process parameters of solid-state fermentation were optimized to enhance enzyme production. The optimized wheat bran Qu of P. oxalicum M1816 was applied to huangjiu fermentation, and the FA content was increased 12.4-fold compared to the control group. These results suggest that P. oxalicum M1816 is a good candidate for the development of fermented foods bio-fortified with FA.

Targeted genome editing of plants and plant cells for biomanufacturing

Plants have provided humans with useful products since antiquity, but in the last 30 years they have also been developed as production platforms for small molecules and recombinant proteins. This initially niche area has blossomed with the growth of the global bioeconomy, and now includes chemical building blocks, polymers and renewable energy. All these applications can be described as "plant molecular farming" (PMF). Despite its potential to increase the sustainability of biologics manufacturing, PMF has yet to be embraced broadly by industry. This reflects a combination of regulatory uncertainty, limited information on process cost structures, and the absence of trained staff and suitable manufacturing capacity. However, the limited adaptation of plants and plant cells to the requirements of industry-scale manufacturing is an equally important hurdle. For example, the targeted genetic manipulation of yeast has been common practice since the 1980s, whereas reliable site-directed mutagenesis in most plants has only become available with the advent of CRISPR/Cas9 and similar genome editing technologies since around 2010. Here we summarize the applications of new genetic engineering technologies to improve plants as biomanufacturing platforms. We start by identifying current bottlenecks in manufacturing, then illustrate the progress that has already been made and discuss the potential for improvement at the molecular, cellular and organism levels. We discuss the effects of metabolic optimization, adaptation of the endomembrane system, modified glycosylation profiles, programmable growth and senescence, protease inactivation, and the expression of enzymes that promote biodegradation. We outline strategies to achieve these modifications by targeted gene modification, considering case-by-case examples of individual improvements and the combined modifications needed to generate a new general-purpose "chassis" for PMF.

Emerging technologies for biofuel production: A critical review on recent progress, challenges and perspectives

Due to increasing anthropogenic activities, especially industry and transport, the fossil fuel demand and consumption have increased proportionally, causing serious environmental issues. This attracted researchers and scientists to develop new alternative energy sources. Therefore, this review covers the biofuel production potential and challenges related to various feedstocks and advances in process technologies. It has been concluded that the biofuels such as biodiesel, ethanol, bio-oil, syngas, Fischer-Tropsch H_2, and methane produced from crop plant residues, micro- and macroalgae and other biomass wastes using thermo-bio-chemical processes are an eco-friendly route for an energy source. Biofuels production and their uses in industries and transportation considerably minimize fossil fuel dependence. Literature analysis showed that biofuels generated from energy crops and microalgae could be the most efficient and attractive process. Recent progress in the field of biofuels using genetic engineering has larger perspectives in commercial-scale production. However, its large-scale production is still challenging; hence, to resolve this problem, it is essential to convert biomass in biofuels by developing novel technology to increase biofuel production to fulfil the current and future energy demand.

Weed Management Practices to Improve Establishment of Selected Lignocellulosic Crops

Lignocellulosic biomass is one of the dominant renewable energy resources suited for the production of sustainable biofuels and other energy purposes. This study was focused on weed management strategies that can improve the establishment of six lignocellulosic crops. The studied crops included: giant miscanthus, switchgrass, giant reed, cardoon, sweet sorghum, and kenaf. Delayed planting, increased planting densities, and mulching techniques can suppress weeds in giant miscanthus. Weed competition is detrimental for switchgrass establishment. Seedbed preparation and cultivar selection can determine its ability to compete with weeds. Giant reed is unlikely to get outcompeted by weeds, and any weed control operation is required only for the first growing season. Competitive cultivars and increased seeding rates maximize the competitiveness of cardoon against weeds. Several cultural practices can be used for non-chemical weed management in sweet sorghum and kenaf. For all crops, pre-emergence herbicides can be applied. The available safe post-emergence herbicides are limited. Mechanical weed control during crucial growth stages can provide solutions for sweet sorghum, kenaf, and perennial grasses. Further research is required to develop effective weed management strategies, with emphasis on cultural practices, that can improve the establishment of these prominent lignocellulosic crops.

Recent advances in the valorization of plant biomass

Plant biomass is a highly abundant renewable resource that can be converted into several types of high-value-added products, including chemicals, biofuels and advanced materials. In the last few decades, an increasing number of biomass species and processing techniques have been developed to enhance the application of plant biomass followed by the industrial application of some of the products, during which varied technologies have been successfully developed. In this review, we summarize the different sources of plant biomass, the evolving technologies for treating it, and the various products derived from plant biomass. Moreover, the challenges inherent in the valorization of plant biomass used in high-value-added products are also discussed. Overall, with the increased use of plant biomass, the development of treatment technologies, and the solution of the challenges raised during plant biomass valorization, the value-added products derived from plant biomass will become greater in number and more valuable.

Current and future advances in fluorescence-based visualization of plant cell wall components and cell wall biosynthetic machineries

Plant cell wall-derived biomass serves as a renewable source of energy and materials with increasing importance. The cell walls are biomacromolecular assemblies defined by a fine arrangement of different classes of polysaccharides, proteoglycans, and aromatic polymers and are one of the most complex structures in Nature. One of the most challenging tasks of cell biology and biomass biotechnology research is to image the structure and organization of this complex matrix, as well as to visualize the compartmentalized, multiplayer biosynthetic machineries that build the elaborate cell wall architecture. Better knowledge of the plant cells, cell walls, and whole tissue is essential for bioengineering efforts and for designing efficient strategies of industrial deconstruction of the cell wall-derived biomass and its saccharification. Cell wall-directed molecular probes and analysis by light microscopy, which is capable of imaging with a high level of specificity, little sample processing, and often in real time, are important tools to understand cell wall assemblies. This review provides a comprehensive overview about the possibilities for fluorescence label-based imaging techniques and a variety of probing methods, discussing both well-established and emerging tools. Examples of applications of these tools are provided. We also list and discuss the advantages and limitations of the methods. Specifically, we elaborate on what are the most important considerations when applying a particular technique for plants, the potential for future development, and how the plant cell wall field might be inspired by advances in the biomedical and general cell biology fields.

Identifying transcription factors that reduce wood recalcitrance and improve enzymatic degradation of xylem cell wall in Populus

Developing an efficient deconstruction step of woody biomass for biorefinery has been drawing considerable attention since its xylem cell walls display highly recalcitrance nature. Here, we explored transcriptional factors (TFs) that reduce wood recalcitrance and improve saccharification efficiency in Populus species. First, 33 TF genes up-regulated during poplar wood formation were selected as potential regulators of xylem cell wall structure. The transgenic hybrid aspens (Populus tremula × Populus tremuloides) overexpressing each selected TF gene were screened for in vitro enzymatic saccharification. Of these, four transgenic seedlings overexpressing previously uncharacterized TF genes increased total glucan hydrolysis on average compared to control. The best performing lines overexpressing Pt × tERF123 and Pt × tZHD14 were further grown to form mature xylem in the greenhouse. Notably, the xylem cell walls exhibited significantly increased total xylan hydrolysis as well as initial hydrolysis rates of glucan. The increased saccharification of Pt × tERF123-overexpressing lines could reflect the improved balance of cell wall components, i.e., high cellulose and low xylan and lignin content, which could be caused by upregulation of cellulose synthase genes upon the expression of Pt × tERF123. Overall, we successfully identified Pt × tERF123 and Pt × tZHD14 as effective targets for reducing cell wall recalcitrance and improving the enzymatic degradation of woody plant biomass.

Silencing Folylpolyglutamate Synthetase1 (FPGS1) in Switchgrass (Panicum virgatum L.) Improves Lignocellulosic Biofuel Production

Switchgrass (Panicum virgatum L.) is a lignocellulosic perennial grass with great potential in bioenergy field. Lignocellulosic bioenergy crops are mostly resistant to cell wall deconstruction, and therefore yield suboptimal levels of biofuel. The one-carbon pathway (also known as C1 metabolism) is critical for polymer methylation, including that of lignin and hemicelluloses in cell walls. Folylpolyglutamate synthetase (FPGS) catalyzes a biochemical reaction that leads to the formation of folylpolyglutamate, an important cofactor for many enzymes in the C1 pathway. In this study, the putatively novel switchgrass PvFPGS1 gene was identified and its functional role in cell wall composition and biofuel production was examined by RNAi knockdown analysis. The PvFPGS1-downregulated plants were analyzed in the field over three growing seasons. Transgenic plants with the highest reduction in PvFPGS1 expression grew slower and produced lower end-of-season biomass. Transgenic plants with low-to-moderate reduction in PvFPGS1 transcript levels produced equivalent biomass as controls. There were no significant differences observed for lignin content and syringyl/guaiacyl lignin monomer ratio in the low-to-moderately reduced PvFPGS1 transgenic lines compared with the controls. Similarly, sugar release efficiency was also not significantly different in these transgenic lines compared with the control lines. However, transgenic plants produced up to 18% more ethanol while maintaining congruent growth and biomass as non-transgenic controls. Severity of rust disease among transgenic and control lines were not different during the time course of the field experiments. Altogether, the unchanged lignin content and composition in the low-to-moderate PvFPGS1-downregulated lines may suggest that partial downregulation of PvFPGS1 expression did not impact lignin biosynthesis in switchgrass. In conclusion, the manipulation of PvFPGS1 expression in bioenergy crops may be useful to increase biofuel potential with no growth penalty or increased susceptibility to rust in feedstock.

Engineering microbial pathways for production of bio-based chemicals from lignocellulosic sugars: current status and perspectives

Lignocellulose is the most abundant biomass on earth with an annual production of about 2 × 10¹¹ tons. It is an inedible renewable carbonaceous resource that is very rich in pentose and hexose sugars. The ability of microorganisms to use lignocellulosic sugars can be exploited for the production of biofuels and chemicals, and their concurrent biotechnological processes could advantageously replace petrochemicals' processes in a medium to long term, sustaining the emerging of a new economy based on bio-based products from renewable carbon sources. One of the major issues to reach this objective is to rewire the microbial metabolism to optimally configure conversion of these lignocellulosic-derived sugars into bio-based products in a sustainable and competitive manner. Systems' metabolic engineering encompassing synthetic biology and evolutionary engineering appears to be the most promising scientific and technological approaches to meet this challenge. In this review, we examine the most recent advances and strategies to redesign natural and to implement non-natural pathways in microbial metabolic framework for the assimilation and conversion of pentose and hexose sugars derived from lignocellulosic material into industrial relevant chemical compounds leading to maximal yield, titer and productivity. These include glycolic, glutaric, mesaconic and 3,4-dihydroxybutyric acid as organic acids, monoethylene glycol, 1,4-butanediol and 1,2,4-butanetriol, as alcohols. We also discuss the big challenges that still remain to enable microbial processes to become industrially attractive and economically profitable.