Eliminating a global regulator of carbon catabolite repression enhances the conversion of aromatic lignin monomers to muconate in Pseudomonas putida KT2440

Multi-Omics integration can be used to rescue metabolic information for some of the dark region of the Pseudomonas putida proteome

In every omics experiment, genes or their products are identified for which even state of the art tools are unable to assign a function. In the biotechnology chassis organism Pseudomonas putida, these proteins of unknown function make up 14% of the proteome. This missing information can bias analyses since these proteins can carry out functions which impact the engineering of organisms. As a consequence of predicting protein function across all organisms, function prediction tools generally fail to use all of the types of data available for any specific organism, including protein and transcript expression information. Additionally, the release of Alphafold predictions for all Uniprot proteins provides a novel opportunity for leveraging structural information. We constructed a bespoke machine learning model to predict the function of recalcitrant proteins of unknown function in Pseudomonas putida based on these sources of data, which annotated 1079 terms to 213 proteins. Among the predicted functions supplied by the model, we found evidence for a significant overrepresentation of nitrogen metabolism and macromolecule processing proteins. These findings were corroborated by manual analyses of selected proteins which identified, among others, a functionally unannotated operon that likely encodes a branch of the shikimate pathway.

Engineering Novosphingobium aromaticivorans to produce cis,cis-muconic acid from biomass aromatics

The platform chemical cis,cis-muconic acid (ccMA) provides facile access to a number of monomers used in the synthesis of commercial plastics. It is also a metabolic intermediate in the β-ketoadipic acid pathway of many bacteria and, therefore, a current target for microbial production from abundant renewable resources via metabolic engineering. This study investigates Novosphingobium aromaticivorans DSM12444 as a chassis for the production of ccMA from biomass aromatics. The N. aromaticivorans genome predicts that it encodes a previously uncharacterized protocatechuic acid (PCA) decarboxylase and a catechol 1,2-dioxygenase, which would be necessary for the conversion of aromatic metabolic intermediates to ccMA. This study confirmed the activity of these two enzymes in vitro and compared their activity to ones that have been previously characterized and used in ccMA production. From these results, we generated one strain that is completely derived from native genes and a second that contains genes previously used in microbial engineering synthesis of this compound. Both of these strains exhibited stoichiometric production of ccMA from PCA and produced greater than 100% yield of ccMA from the aromatic monomers that were identified in liquor derived from alkaline pretreated biomass. Our results show that a strain completely derived from native genes and one containing homologs from other hosts are both capable of stoichiometric production of ccMA from biomass aromatics. Overall, this work combines previously unknown aspects of aromatic metabolism in N. aromaticivorans and the genetic tractability of this organism to generate strains that produce ccMA from deconstructed biomass.IMPORTANCEThe production of commodity chemicals from renewable resources is an important goal toward increasing the environmental and economic sustainability of industrial processes. The aromatics in plant biomass are an underutilized and abundant renewable resource for the production of valuable chemicals. However, due to the chemical composition of plant biomass, many deconstruction methods generate a heterogeneous mixture of aromatics, thus making it difficult to extract valuable chemicals using current methods. Therefore, recent efforts have focused on harnessing the pathways of microorganisms to convert a diverse set of aromatics into a single product. Novosphingobium aromaticivorans DSM12444 has the native ability to metabolize a wide range of aromatics and, thus, is a potential chassis for conversion of these abundant compounds to commodity chemicals. This study reports on new features of N. aromaticivorans that can be used to produce the commodity chemical cis,cis-muconic acid from renewable and abundant biomass aromatics.

Improving microbial bioproduction under low-oxygen conditions

Microbial bioconversion provides access to a wide range of sustainably produced chemicals and commodities. However, industrial-scale bioproduction process operations are preferred to be anaerobic due to the cost associated with oxygen transfer. Anaerobic bioconversion generally offers limited substrate utilization profiles, lower product yields, and reduced final product diversity compared with aerobic processes. Bioproduction under conditions of reduced oxygen can overcome the limitations of fully aerobic and anaerobic bioprocesses, but many microbial hosts are not developed for low-oxygen bioproduction. Here, we describe advances in microbial strain engineering involving the use of redox cofactor engineering, genome-scale metabolic modeling, and functional genomics to enable improved bioproduction processes under low oxygen and provide a viable path for scaling these bioproduction systems to industrial scales.

Crossing bacterial boundaries: The carbon catabolite repression system Crc-Hfq of Pseudomonas putida KT2440 as a tool to control translation in E. coli

As a global regulatory mechanism, carbon catabolite repression allows bacteria and eukaryal microbes to preferentially utilize certain substrates from a mixture of carbon sources. The mechanism varies among different species. In Pseudomonas spp., it is mainly mediated by the Crc-Hfq complex which binds to the 5' region of the target mRNAs, thereby inhibiting their translation. This molecular mechanism enables P. putida to rapidly adjust and fine-tune gene expression in changing environments. Hfq is an RNA-binding protein that is ubiquitous and highly conserved in bacterial species. Considering the characteristics of Hfq, and the widespread use and rapid response of Crc-Hfq in P. putida, this complex has the potential to become a general toolbox for post-transcriptional multiplex regulation. In this study, we demonstrate for the first time that transplanting the pseudomonal catabolite repression protein, Crc, into E. coli causes multiplex gene repression. Under the control of Crc, the production of a diester and its precursors was significantly reduced. The effects of Crc introduction on cell growth in both minimal and rich media were evaluated. Two potential factors - off-target effects and Hfq-sequestration - could explain negative effects on cell growth. Simultaneous reduction of off-targeting and increased sequestration of Hfq by the introduction of the small RNA CrcZ, indicated that Hfq sequestration plays a more prominent role in the negative side-effects. This suggests that the negative growth effect can be mitigated by well-controlled expression of Hfq. This study reveals the feasibility of controlling gene expression using heterologous regulation systems.

Simultaneous carbon catabolite repression governs sugar and aromatic co-utilization in Pseudomonas putida M2

Pseudomonas putida have emerged as promising biocatalysts for the conversion of sugars and aromatic compounds obtained from lignocellulosic biomass. Understanding the role of carbon catabolite repression (CCR) in these strains is critical to optimize biomass conversion to fuels and chemicals. The CCR functioning in P. putida M2, a strain capable of consuming both hexose and pentose sugars as well as aromatic compounds, was investigated by cultivation experiments, proteomics, and CRISPRi-based gene repression. Strain M2 co-utilized sugars and aromatic compounds simultaneously; however, during cultivation with glucose and aromatic compounds (p-coumarate and ferulate) mixture, intermediates (4-hydroxybenzoate and vanillate) accumulated, and substrate consumption was incomplete. In contrast, xylose-aromatic consumption resulted in transient intermediate accumulation and complete aromatic consumption, while xylose was incompletely consumed. Proteomics analysis revealed that glucose exerted stronger repression than xylose on the aromatic catabolic proteins. Key glucose (Eda) and xylose (XylX) catabolic proteins were also identified at lower abundance during cultivation with aromatic compounds implying simultaneous catabolite repression by sugars and aromatic compounds. Reduction of crc expression via CRISPRi led to faster growth and glucose and p-coumarate uptake in the CRISPRi strains compared to the control, while no difference was observed on xylose+p-coumarate. The increased abundances of Eda and amino acid biosynthesis proteins in the CRISPRi strain further supported these observations. Lastly, small RNAs (sRNAs) sequencing results showed that CrcY and CrcZ homologues levels in M2, previously identified in P. putida strains, were lower under strong CCR (glucose+p-coumarate) condition compared to when repression was absent (p-coumarate or glucose only).IMPORTANCEA newly isolated Pseudomonas putida strain, P. putida M2, can utilize both hexose and pentose sugars as well as aromatic compounds making it a promising host for the valorization of lignocellulosic biomass. Pseudomonads have developed a regulatory strategy, carbon catabolite repression, to control the assimilation of carbon sources in the environment. Carbon catabolite repression may impede the simultaneous and complete metabolism of sugars and aromatic compounds present in lignocellulosic biomass and hinder the development of an efficient industrial biocatalyst. This study provides insight into the cellular physiology and proteome during mixed-substrate utilization in P. putida M2. The phenotypic and proteomics results demonstrated simultaneous catabolite repression in the sugar-aromatic mixtures, while the CRISPRi and sRNA sequencing demonstrated the potential role of the crc gene and small RNAs in carbon catabolite repression.

Lignin conversion to β-ketoadipic acid by Pseudomonas putida via metabolic engineering and bioprocess development

Bioconversion of a heterogeneous mixture of lignin-related aromatic compounds (LRCs) to a single product via microbial biocatalysts is a promising approach to valorize lignin. Here, Pseudomonas putida KT2440 was engineered to convert mixed p-coumaroyl- and coniferyl-type LRCs to β-ketoadipic acid, a precursor for performance-advantaged polymers. Expression of enzymes mediating aromatic O-demethylation, hydroxylation, and ring-opening steps was tuned, and a global regulator was deleted. β-ketoadipate titers of 44.5 and 25 grams per liter and productivities of 1.15 and 0.66 grams per liter per hour were achieved from model LRCs and corn stover-derived LRCs, respectively, the latter representing an overall yield of 0.10 grams per gram corn stover-derived lignin. Technoeconomic analysis of the bioprocess and downstream processing predicted a β-ketoadipate minimum selling price of $2.01 per kilogram, which is cost competitive with fossil carbon-derived adipic acid ($1.10 to 1.80 per kilogram). Overall, this work achieved bioproduction metrics with economic relevance for conversion of lignin-derived streams into a performance-advantaged bioproduct.

Engineering the Metabolic Landscape of Microorganisms for Lignocellulosic Conversion

Bacteria and yeast are being intensively used to produce biofuels and high-added-value products by using plant biomass derivatives as substrates. The number of microorganisms available for industrial processes is increasing thanks to biotechnological improvements to enhance their productivity and yield through microbial metabolic engineering and laboratory evolution. This is allowing the traditional industrial processes for biofuel production, which included multiple steps, to be improved through the consolidation of single-step processes, reducing the time of the global process, and increasing the yield and operational conditions in terms of the desired products. Engineered microorganisms are now capable of using feedstocks that they were unable to process before their modification, opening broader possibilities for establishing new markets in places where biomass is available. This review discusses metabolic engineering approaches that have been used to improve the microbial processing of biomass to convert the plant feedstock into fuels. Metabolically engineered microorganisms (MEMs) such as bacteria, yeasts, and microalgae are described, highlighting their performance and the biotechnological tools that were used to modify them. Finally, some examples of patents related to the MEMs are mentioned in order to contextualize their current industrial use.

Deriving high value products from depolymerized lignin oil, aided by (bio)catalytic funneling strategies

Lignin holds tremendous and versatile possibilities to produce value-added chemicals and high performing polymeric materials. Over the years, different cutting-edge lignin depolymerization methodologies have been developed, mainly focusing on achieving excellent yields of mono-phenolic products, some even approaching the theoretical maximum. However, due to lignin's inherent heterogeneity and recalcitrance, its depolymerization leads to relatively complex product streams, also containing dimers, and higher molecular weight fragments in substantial quantities. The subsequent chemo-catalytic valorization of these higher molecular weight streams, containing difficult-to-break, mainly C-C covalent bonds, is tremendously challenging, and has consequently received much less attention. In this minireview, we present an overview of recent advances on the development of sustainable biorefinery strategies aimed at the production of well-defined chemicals and polymeric materials, the prime focus being on depolymerized lignin oils, containing high molecular weight fractions. The key central unit operation to achieve this is (bio)catalytic funneling, which holds great potential to overcome separation and purification challenges.

Lignin Valorization: Production of High Value-Added Compounds by Engineered Microorganisms

Lignin is the second most abundant polymer in nature, which is also widely generated during biomass fractionation in lignocellulose biorefineries. At present, most of technical lignin is simply burnt for energy supply although it represents the richest natural source of aromatics, and thus it is a promising feedstock for generation of value-added compounds. Lignin is heterogeneous in composition and recalcitrant to degradation, with this substantially hampering its use. Notably, microbes have evolved particular enzymes and specialized metabolic pathways to degrade this polymer and metabolize its various aromatic components. In recent years, novel pathways have been designed allowing to establish engineered microbial cell factories able to efficiently funnel the lignin degradation products into few metabolic intermediates, representing suitable starting points for the synthesis of a variety of valuable molecules. This review focuses on recent success cases (at the laboratory/pilot scale) based on systems metabolic engineering studies aimed at generating value-added and specialty chemicals, with much emphasis on the production of cis,cis-muconic acid, a building block of recognized industrial value for the synthesis of plastic materials. The upgrade of this global waste stream promises a sustainable product portfolio, which will become an industrial reality when economic issues related to process scale up will be tackled.

Customized valorization of waste streams by Pseudomonas putida: State-of-the-art, challenges, and future trends

Preventing catastrophic climate events warrants prompt action to delay global warming, which threatens health and food security. In this context, waste management using engineered microbes has emerged as a long-term eco-friendly solution for addressing the global climate crisis and transitioning to clean energy. Notably, Pseudomonas putida can valorize industry-derived synthetic wastes including plastics, oils, food, and agricultural waste into products of interest, and it has been extensively explored for establishing a fully circular bioeconomy through the conversion of waste into bio-based products, including platform chemicals (e.g., cis,cis-muconic and adipic acid) and biopolymers (e.g., medium-chain length polyhydroxyalkanoate). However, the efficiency of waste pretreatment technologies, capability of microbial cell factories, and practicability of synthetic biology tools remain low, posing a challenge to the industrial application of P. putida. The present review discusses the state-of-the-art, challenges, and future prospects for divergent biosynthesis of versatile products from waste-derived feedstocks using P. putida.

Engineering Microorganisms to Produce Bio-Based Monomers: Progress and Challenges

Bioplastics are polymers made from sustainable bio-based feedstocks. While the potential of producing bio-based monomers in microbes has been investigated for decades, their economic feasibility is still unsatisfactory compared with petroleum-derived methods. To improve the overall synthetic efficiency of microbial cell factories, three main strategies were summarized in this review: firstly, implementing approaches to improve the microbial utilization ability of cheap and abundant substrates; secondly, developing methods at enzymes, pathway, and cellular levels to enhance microbial production performance; thirdly, building technologies to enhance microbial pH, osmotic, and metabolites stress tolerance. Moreover, the challenges of, and some perspectives on, exploiting microorganisms as efficient cell factories for producing bio-based monomers are also discussed.

Microbial lignin valorization through depolymerization to aromatics conversion

Lignin is the most abundant source of renewable aromatic biopolymers and its valorization presents significant value for biorefinery sustainability, which promotes the utilization of renewable resources. However, it is challenging to fully convert the structurally complex, heterogeneous, and recalcitrant lignin into high-value products. The in-depth research on the lignin degradation mechanism, microbial metabolic pathways, and rational design of new systems using synthetic biology have significantly accelerated the development of lignin valorization. This review summarizes the key enzymes involved in lignin depolymerization, the mechanisms of microbial lignin conversion, and the lignin valorization application with integrated systems and synthetic biology. Current challenges and future strategies to further study lignin biodegradation and the trends of lignin valorization are also discussed.

Metabolic engineering of Pseudomonas taiwanensis VLB120 for rhamnolipid biosynthesis from biomass-derived aromatics

Lignin is a ubiquitously available and sustainable feedstock that is underused as its depolymerization yields a range of aromatic monomers that are challenging substrates for microbes. In this study, we investigated the growth of Pseudomonas taiwanensis VLB120 on biomass-derived aromatics, namely, 4-coumarate, ferulate, 4-hydroxybenzoate, and vanillate. The wild type strain was not able to grow on 4-coumarate and ferulate. After integration of catabolic genes for breakdown of 4-coumarate and ferulate, the metabolically engineered strain was able to grow on these aromatics. Further, the specific growth rate of the strain was enhanced up to 3-fold using adaptive laboratory evolution, resulting in increased tolerance towards 4-coumarate and ferulate. Whole-genome sequencing highlighted several different mutations mainly in two genes. The first gene was actP, coding for a cation/acetate symporter, and the other gene was paaA coding for a phenyl acetyl-CoA oxygenase. The evolved strain was further engineered for rhamnolipid production. Among the biomass-derived aromatics investigated, 4-coumarate and ferulate were promising substrates for product synthesis. With 4-coumarate as the sole carbon source, a yield of 0.27 (Cmol_rhl/Cmol_4-coumarate) was achieved, corresponding to 28% of the theoretical yield. Ferulate enabled a yield of about 0.22 (Cmol_rhl/Cmol_ferulate), representing 42% of the theoretical yield. Overall, this study demonstrates the use of biomass-derived aromatics as novel carbon sources for rhamnolipid biosynthesis.

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Enabling 4-coumarate and ferulate degradation in Pseudomonas taiwanensis VLB120.

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The growth rate and tolerance was enhanced towards non-native substrates.

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Genetic mutations in actP and paaA contributed to the enhanced tolerance.

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Production of mono-rhamnolipids was established using all the chosen aromatics.

Recent advances and challenges in the bioconversion of acetate to value-added chemicals

Acetate is a major byproduct of the bioconversion of the greenhouse gas carbon dioxide, pretreatment of lignocellulose biomass, and microbial fermentation. The utilization and valorization of acetate have been emphasized in transforming waste to clean energy and value-added platform chemicals, contributing to the development of a closed carbon loop toward a low-carbon circular bio-economy. Acetate has been used to produce several platform chemicals, including succinate, 3-hydroxypropionate, and itaconic acid, highlighting the potential of acetate to synthesize many biochemicals and biofuels. On the other hand, the yields and titers have not reached the theoretical maximum. Recently, recombinant strain development and pathway regulation have been suggested to overcome this limitation. This review provides insights into the important constraints limiting the yields and titers of the biochemical and metabolic pathways of bacteria capable of metabolizing acetate for acetate bioconversion. The current developments in recombinant strain engineering are also discussed.

Recent Advancements and Challenges in Lignin Valorization: Green Routes towards Sustainable Bioproducts

The aromatic hetero-polymer lignin is industrially processed in the paper/pulp and lignocellulose biorefinery, acting as a major energy source. It has been proven to be a natural resource for useful bioproducts; however, its depolymerization and conversion into high-value-added chemicals is the major challenge due to the complicated structure and heterogeneity. Conversely, the various pre-treatments techniques and valorization strategies offers a potential solution for developing a biomass-based biorefinery. Thus, the current review focus on the new isolation techniques for lignin, various pre-treatment approaches and biocatalytic methods for the synthesis of sustainable value-added products. Meanwhile, the challenges and prospective for the green synthesis of various biomolecules via utilizing the complicated hetero-polymer lignin are also discussed.

Microbial production of 2-pyrone-4,6-dicarboxylic acid from lignin derivatives in an engineered Pseudomonas putida and its application for the synthesis of bio-based polyester

Lignin valorization depends on microbial upcycling of various aromatic compounds in the form of a complex mixture, including p-coumaric acid and ferulic acid. In this study, an engineered Pseudomonas putida strain utilizing lignin-derived monomeric compounds via biological funneling was developed to produce 2-pyrone-4,6-dicarboxylic acid (PDC), which has been considered a promising building block for bioplastics. The biosynthetic pathway for PDC production was established by introducing the heterologous ligABC genes under the promoter P_tac in a strain lacking pcaGH genes to accumulate a precursor of PDC, i.e., protocatechuic acid. Based on the culture optimization, fed-batch fermentation of the final strain resulted in 22.7 g/L PDC with a molar yield of 1.0 mol/mol and productivity of 0.21 g/L/h. Subsequent purification of PDC at high purity was successfully implemented, which was consequently applied for the novel polyester.

Expanding the Biological Role of Lipo-Chitooligosaccharides and Chitooligosaccharides in Laccaria bicolor Growth and Development

The role of lipo-chitooligosaccharides (LCOs) as signaling molecules that mediate the establishment of symbiotic relationships between fungi and plants is being redefined. New evidence suggests that the production of these molecular signals may be more of a common trait in fungi than what was previously thought. LCOs affect different aspects of growth and development in fungi. For the ectomycorrhizal forming fungi, Laccaria bicolor, the production and effects of LCOs have always been studied with a symbiotic plant partner; however, there is still no scientific evidence describing the effects that these molecules have on this organism. Here, we explored the physiological, molecular, and metabolomic changes in L. bicolor when grown in the presence of exogenous sulfated and non-sulfated LCOs, as well as the chitooligomers, chitotetraose (CO4), and chitooctaose (CO8). Physiological data from 21 days post-induction showed reduced fungal growth in response to CO and LCO treatments compared to solvent controls. The underlying molecular changes were interrogated by proteomics, which revealed substantial alterations to biological processes related to growth and development. Moreover, metabolite data showed that LCOs and COs caused a downregulation of organic acids, sugars, and fatty acids. At the same time, exposure to LCOs resulted in the overproduction of lactic acid in L. bicolor. Altogether, these results suggest that these signals might be fungistatic compounds and contribute to current research efforts investigating the emerging impacts of these molecules on fungal growth and development.

Bioconversion of lignin-derived aromatics into the building block pyridine 2,4-dicarboxylic acid by engineering recombinant Pseudomonas putida strains

2,4 pyridine dicarboxylic acid (2,4 PDCA) is an analogue of terephthalate, and hence a target chemical in the field of bio-based plastics. Here, Pseudomonas putida KT2440 strains were engineered to efficiently drive the metabolism of lignin-derived monoaromatics towards 2,4 PDCA in a resting cells-based bioprocess that alleviates growth-coupled limitations and allows biocatalysts recycling. Native β-ketoadipate pathway was blocked by replacing protocatechuate 3,4-dioxygenase by the exogenous LigAB extradiol dioxygenase. Overexpression of pcaK encoding a transporter increased 8-fold 2,4 PDCA productivity from protocatechuate, reaching the highest value reported so far (0.58 g L^-1h^-1). Overexpression of the 4-hydroxybenzoate monooxygenase (pobA) speed up drastically the production of 2,4 PDCA from 4-hydroxybenzoate (0.056 g L^-1h^-1) or p-coumarate (0.012 g L^-1h^-1) achieving values 15-fold higher than those reported with Rhodococcus jostii biocatalysts. 2,4 PDCA was also bioproduced by using soda lignin as feedstock, paving the way for future polymeric lignin valorization approaches.

Debottlenecking 4-hydroxybenzoate hydroxylation in Pseudomonas putida KT2440 improves muconate productivity from p-coumarate

The transformation of 4-hydroxybenzoate (4-HBA) to protocatechuate (PCA) is catalyzed by flavoprotein oxygenases known as para-hydroxybenzoate-3-hydroxylases (PHBHs). In Pseudomonas putida KT2440 (P. putida) strains engineered to convert lignin-related aromatic compounds to muconic acid (MA), PHBH activity is rate-limiting, as indicated by the accumulation of 4-HBA, which ultimately limits MA productivity. Here, we hypothesized that replacement of PobA, the native P. putida PHBH, with PraI, a PHBH from Paenibacillus sp. JJ-1b with a broader nicotinamide cofactor preference, could alleviate this bottleneck. Biochemical assays confirmed the strict preference of NADPH for PobA, while PraI can utilize either NADH or NADPH. Kinetic assays demonstrated that both PobA and PraI can utilize NADPH with comparable catalytic efficiency and that PraI also efficiently utilizes NADH at roughly half the catalytic efficiency. The X-ray crystal structure of PraI was solved and revealed absolute conservation of the active site architecture to other PHBH structures despite their differing cofactor preferences. To understand the effect in vivo, we compared three P. putida strains engineered to produce MA from p-coumarate (pCA), showing that expression of praI leads to lower 4-HBA accumulation and decreased NADP⁺/NADPH ratios relative to strains harboring pobA, indicative of a relieved 4-HBA bottleneck due to increased NADPH availability. In bioreactor cultivations, a strain exclusively expressing praI achieved a titer of 40 g/L MA at 100% molar yield and a productivity of 0.5 g/L/h. Overall, this study demonstrates the benefit of sampling readily available natural enzyme diversity for debottlenecking metabolic flux in an engineered strain for microbial conversion of lignin-derived compounds to value-added products.

Microbial valorization of lignin: Prospects and challenges

Lignin is the world's second most prevalent biomaterial, but its effective value-added product valorization methods are still being developed. The most common preparation processes for converting lignin to platform chemicals and biofuels are fragmentation and depolymerization. Due to its structural diversity, fragmentation generally produces a variety of products, necessitating tedious separation and purifying methods to isolate the desired products. Bacterial-based techniques are commonly utilized for lignin fragmentation due to their high metabolitic activity. Recent advancements in lignin valorization utilizing bacteria, such as lignin decomposing microbes and major pathways involved that can breakdown lignin into various valuable products namely lipids, furfural, vanillin, polyhydroxybutyrate, poly lactic acid blends were discussed in this review. This review also covers the genetic and fermentation methodologies to enhance lignin decomposition, challenges and future trends of microbe based lignin valorization.

Guiding stars to the field of dreams: Metabolically engineered pathways and microbial platforms for a sustainable lignin-based industry

Lignin is an important structural component of terrestrial plants and is readily generated during biomass fractionation in lignocellulose processing facilities. Due to lacking alternatives the majority of technical lignins is industrially simply burned into heat and energy. However, regarding its vast abundance and a chemically interesting richness in aromatics, lignin is presently regarded as the most under-utilized and promising feedstock for value-added applications. Notably, microbes have evolved powerful enzymes and pathways that break down lignin and metabolize its various aromatic components. This natural pathway atlas meanwhile serves as a guiding star for metabolic engineers to breed designed cell factories and efficiently upgrade this global waste stream. The metabolism of aromatic compounds, in combination with success stories from systems metabolic engineering, as reviewed here, promises a sustainable product portfolio from lignin, comprising bulk and specialty chemicals, biomaterials, and fuels.

Combinatorial pathway balancing provides biosynthetic access to 2-fluoro-cis,cis-muconate in engineered Pseudomonas putida

The wealth of bio-based building blocks produced by engineered microorganisms seldom include halogen atoms. Muconate is a platform chemical with a number of industrial applications that could be broadened by introducing fluorine atoms to tune its physicochemical properties. The soil bacterium Pseudomonas putida naturally assimilates benzoate via the ortho-cleavage pathway with cis,cis-muconate as intermediate. Here, we harnessed the native enzymatic machinery (encoded within the ben and cat gene clusters) to provide catalytic access to 2-fluoro-cis,cis-muconate (2-FMA) from fluorinated benzoates. The reactions in this pathway are highly imbalanced, leading to accumulation of toxic intermediates and limited substrate conversion. By disentangling regulatory patterns of ben and cat in response to fluorinated effectors, metabolic activities were adjusted to favor 2-FMA biosynthesis. After implementing this combinatorial approach, engineered P. putida converted 3-fluorobenzoate to 2-FMA at the maximum theoretical yield. Hence, this study illustrates how synthetic biology can expand the diversity of nature's biochemical catalysis.

Microbial assimilation of lignin-derived aromatic compounds and conversion to value-added products

Lignin is an abundant and sustainable source of aromatic compounds that can be converted to value-added products. However, lignin is underutilized, since depolymerization produces a complex mixture of aromatic compounds that is difficult to convert to a single product. Microbial conversion of mixed aromatic substrates provides a potential solution to this conversion challenge. Recent advances have expanded the range of lignin-derived aromatic substrates that can be assimilated and demonstrated efficient conversion via central metabolism to new potential products. The development of additional non-model microbial hosts and genetic tools for these hosts have accelerated engineering efforts. However, yields with real depolymerized lignin are still low, and additional work will be required to achieve viable conversion processes.

Channelling carbon flux through the meta-cleavage route for improved poly(3-hydroxyalkanoate) production from benzoate and lignin-based aromatics in Pseudomonas putida H

Lignin-based aromatics are attractive raw materials to derive medium-chain length poly(3-hydroxyalkanoates) (mcl-PHAs), biodegradable polymers of commercial value. So far, this conversion has exclusively used the ortho-cleavage route of Pseudomonas putida KT2440, which results in the secretion of toxic intermediates and limited performance. Pseudomonas putida H exhibits the ortho- and the meta-cleavage pathways where the latter appears promising because it stoichiometrically yields higher levels of acetyl-CoA. Here, we created a double-mutant H-ΔcatAΔA2 that utilizes the meta route exclusively and synthesized 30% more PHA on benzoate than the parental strain but suffered from catechol accumulation. The single deletion of the catA2 gene in the H strain provoked a slight attenuation on the enzymatic capacity of the ortho route (25%) and activation of the meta route by nearly 8-fold, producing twice as much mcl-PHAs compared to the wild type. Inline, the mutant H-ΔcatA2 showed a 2-fold increase in the intracellular malonyl-CoA abundance - the main precursor for mcl-PHAs synthesis. As inferred from flux simulation and enzyme activity assays, the superior performance of H-ΔcatA2 benefited from reduced flux through the TCA cycle and malic enzyme and diminished by-product formation. In a benzoate-based fed-batch, P. putida H-ΔcatA2 achieved a PHA titre of 6.1 g l-1 and a volumetric productivity of 1.8 g l-1 day-1 . Using Kraft lignin hydrolysate as feedstock, the engineered strain formed 1.4 g l- 1 PHA. The balancing of carbon flux between the parallel catechol-degrading routes emerges as an important strategy to prevent intermediate accumulation and elevate mcl-PHA production in P. putida H and, as shown here, sets the next level to derive this sustainable biopolymer from lignin hydrolysates and aromatics.

Current Progress in Production of Building-Block Organic Acids by Consolidated Bioprocessing of Lignocellulose

Several organic acids have been indicated among the top value chemicals from biomass. Lignocellulose is among the most attractive feedstocks for biorefining processes owing to its high abundance and low cost. However, its highly complex nature and recalcitrance to biodegradation hinder development of cost-competitive fermentation processes. Here, current progress in development of single-pot fermentation (i.e., consolidated bioprocessing, CBP) of lignocellulosic biomass to high value organic acids will be examined, based on the potential of this approach to dramatically reduce process costs. Different strategies for CBP development will be considered such as: (i) design of microbial consortia consisting of (hemi)cellulolytic and valuable-compound producing strains; (ii) engineering of microorganisms that combine biomass-degrading and high-value compound-producing properties in a single strain. The present review will mainly focus on production of organic acids with application as building block chemicals (e.g., adipic, cis,cis-muconic, fumaric, itaconic, lactic, malic, and succinic acid) since polymer synthesis constitutes the largest sector in the chemical industry. Current research advances will be illustrated together with challenges and perspectives for future investigations. In addition, attention will be dedicated to development of acid tolerant microorganisms, an essential feature for improving titer and productivity of fermentative production of acids.

Comparative analysis of alfalfa (Medicago sativa L.) seedling transcriptomes reveals genotype-specific drought tolerance mechanisms

Drought is one of the main abiotic factors that affect alfalfa yield. The identification of genes that control this complex trait can provide important insights for alfalfa breeding. However, little is known about how alfalfa responds and adapts to drought stress, particularly in cultivars of differing drought tolerance. In this study, the drought-tolerant cultivar Dryland 'DT' and the drought-sensitive cultivar WL343HQ 'DS' were used to characterize leaf and root physiological responses and transcriptional changes in response to water deficit. Under drought stress, Dryland roots (DTR) showed more differentially expressed genes than WL343HQ roots (DSR), whereas WL343HQ leaves (DSL) showed more differentially expressed genes than Dryland leaves (DTL). Many of these genes were involved in stress-related pathways, carbohydrate metabolism, and lignin and wax biosynthesis, which may have improved the drought tolerance of alfalfa. We also observed that several genes related to ABA metabolism, root elongation, peroxidase activity, cell membrane stability, ubiquitination, and genetic processing responded to drought stress in alfalfa. We highlighted several candidate genes, including sucrose synthase, xylan 1,4-beta-xylosidase, primary-amine oxidase, and alcohol-forming fatty acyl-CoA reductase, for future studies on drought stress resistance in alfalfa and other plant species. In summary, our results reveal the unique drought adaptation and resistance characteristics of two alfalfa genotypes. These findings, which may be valuable for drought resistance breeding, warrant further gene functional analysis to augment currently available information and to clarify the drought stress regulatory mechanisms of alfalfa and other plants.

Challenges and opportunities in biological funneling of heterogeneous and toxic substrates beyond lignin

Significant developments in the understanding and manipulation of microbial metabolism have enabled the use of engineered biological systems toward a more sustainable energy and materials economy. While developments in metabolic engineering have primarily focused on the conversion of carbohydrates, substantial opportunities exist for using these same principles to extract value from more heterogeneous and toxic waste streams, such as those derived from lignin, biomass pyrolysis, or industrial waste. Funneling heterogeneous substrates from these streams toward valuable products, termed biological funneling, presents new challenges in balancing multiple catabolic pathways competing for shared cellular resources and engineering against perturbation from toxic substrates. Solutions to many of these challenges have been explored within the field of lignin valorization. This perspective aims to extend beyond lignin to highlight the challenges and discuss opportunities for use of biological systems to upgrade previously inaccessible waste streams.

Engineering Pseudomonas putida for efficient aromatic conversion to bioproduct using high throughput screening in a bioreactor

Pseudomonas putida KT2440 is an emerging biomanufacturing host amenable for use with renewable carbon streams including aromatics such as para-coumarate. We used a pooled transposon library disrupting nearly all (4,778) non-essential genes to characterize this microbe under common stirred-tank bioreactor parameters with quantitative fitness assays. Assessing differential fitness values by monitoring changes in mutant strain abundance identified 33 gene mutants with improved fitness across multiple stirred-tank bioreactor formats. Twenty-one deletion strains from this subset were reconstructed, including GacA, a regulator, TtgB, an ABC transporter, and PP_0063, a lipid A acyltransferase. Thirteen deletion strains with roles in varying cellular functions were evaluated for conversion of para-coumarate, to a heterologous bioproduct, indigoidine. Several mutants, such as the ΔgacA strain improved fitness in a bioreactor by 35 fold and showed an 8-fold improvement in indigoidine production (4.5 g/L, 0.29 g/g, 23% of maximum theoretical yield) from para-coumarate as the carbon source.

Anaerobic Microbial Metabolism of Dichloroacetate

Dichloroacetate (DCA) commonly occurs in the environment due to natural production and anthropogenic releases, but its fate under anoxic conditions is uncertain. Mixed culture RM comprising "Candidatus Dichloromethanomonas elyunquensis" strain RM utilizes DCA as an energy source, and the transient formation of formate, H2, and carbon monoxide (CO) was observed during growth. Only about half of the DCA was recovered as acetate, suggesting a fermentative catabolic route rather than a reductive dechlorination pathway. Sequencing of 16S rRNA gene amplicons and 16S rRNA gene-targeted quantitative real-time PCR (qPCR) implicated "Candidatus Dichloromethanomonas elyunquensis" strain RM in DCA degradation. An (S)-2-haloacid dehalogenase (HAD) encoded on the genome of strain RM was heterologously expressed, and the purified HAD demonstrated the cofactor-independent stoichiometric conversion of DCA to glyoxylate at a rate of 90 ± 4.6 nkat mg-1 protein. Differential protein expression analysis identified enzymes catalyzing the conversion of DCA to acetyl coenzyme A (acetyl-CoA) via glyoxylate as well as enzymes of the Wood-Ljungdahl pathway. Glyoxylate carboligase, which catalyzes the condensation of two molecules of glyoxylate to form tartronate semialdehyde, was highly abundant in DCA-grown cells. The physiological, biochemical, and proteogenomic data demonstrate the involvement of an HAD and the Wood-Ljungdahl pathway in the anaerobic fermentation of DCA, which has implications for DCA turnover in natural and engineered environments, as well as the metabolism of the cancer drug DCA by gut microbiota.IMPORTANCE Dichloroacetate (DCA) is ubiquitous in the environment due to natural formation via biological and abiotic chlorination processes and the turnover of chlorinated organic materials (e.g., humic substances). Additional sources include DCA usage as a chemical feedstock and cancer drug and its unintentional formation during drinking water disinfection by chlorination. Despite the ubiquitous presence of DCA, its fate under anoxic conditions has remained obscure. We discovered an anaerobic bacterium capable of metabolizing DCA, identified the enzyme responsible for DCA dehalogenation, and elucidated a novel DCA fermentation pathway. The findings have implications for the turnover of DCA and the carbon and electron flow in electron acceptor-depleted environments and the human gastrointestinal tract.

Engineering a Cytochrome P450 for Demethylation of Lignin-Derived Aromatic Aldehydes

Biological funneling of lignin-derived aromatic compounds is a promising approach for valorizing its catalytic depolymerization products. Industrial processes for aromatic bioconversion will require efficient enzymes for key reactions, including demethylation of O-methoxy-aryl groups, an essential and often rate-limiting step. The recently characterized GcoAB cytochrome P450 system comprises a coupled monoxygenase (GcoA) and reductase (GcoB) that catalyzes oxidative demethylation of the O-methoxy-aryl group in guaiacol. Here, we evaluate a series of engineered GcoA variants for their ability to demethylate o-and p-vanillin, which are abundant lignin depolymerization products. Two rationally designed, single amino acid substitutions, F169S and T296S, are required to convert GcoA into an efficient catalyst toward the o- and p-isomers of vanillin, respectively. Gain-of-function in each case is explained in light of an extensive series of enzyme-ligand structures, kinetic data, and molecular dynamics simulations. Using strains of Pseudomonas putida KT2440 already optimized for p-vanillin production from ferulate, we demonstrate demethylation by the T296S variant in vivo. This work expands the known aromatic O-demethylation capacity of cytochrome P450 enzymes toward important lignin-derived aromatic monomers.

Metabolism of syringyl lignin-derived compounds in Pseudomonas putida enables convergent production of 2-pyrone-4,6-dicarboxylic acid

Valorization of lignin, an abundant component of plant cell walls, is critical to enabling the lignocellulosic bioeconomy. Biological funneling using microbial biocatalysts has emerged as an attractive approach to convert complex mixtures of lignin depolymerization products to value-added compounds. Ideally, biocatalysts would convert aromatic compounds derived from the three canonical types of lignin: syringyl (S), guaiacyl (G), and p-hydroxyphenyl (H). Pseudomonas putida KT2440 (hereafter KT2440) has been developed as a biocatalyst owing in part to its native catabolic capabilities but is not known to catabolize S-type lignin-derived compounds. Here, we demonstrate that syringate, a common S-type lignin-derived compound, is utilized by KT2440 only in the presence of another energy source or when vanAB was overexpressed, as syringate was found to be O-demethylated to gallate by VanAB, a two-component monooxygenase, and further catabolized via extradiol cleavage. Unexpectedly, the specificity (k_cat/K_M) of VanAB for syringate was within 25% that for vanillate and O-demethylation of both substrates was well-coupled to O₂ consumption. However, the native KT2440 gallate-cleaving dioxygenase, GalA, was potently inactivated by 3-O-methylgallate. To engineer a biocatalyst to simultaneously convert S-, G-, and H-type monomers, we therefore employed VanAB from Pseudomonas sp. HR199, which has lower activity for 3MGA, and LigAB, an extradiol dioxygenase able to cleave protocatechuate and 3-O-methylgallate. This strain converted 93% of a mixture of lignin monomers to 2-pyrone-4,6-dicarboxylate, a promising bio-based chemical. Overall, this study elucidates a native pathway in KT2440 for catabolizing S-type lignin-derived compounds and demonstrates the potential of this robust chassis for lignin valorization.

Synthetic Biology towards Engineering Microbial Lignin Biotransformation

Lignin is the second most abundant biopolymer on earth and is a major source of aromatic compounds; however, it is vastly underutilized owing to its heterogeneous and recalcitrant nature. Microorganisms have evolved efficient mechanisms that overcome these challenges to depolymerize lignin and funnel complex mixtures of lignin-derived monomers to central metabolites. This review summarizes recent synthetic biology efforts to enhance lignin depolymerization and aromatic catabolism in bacterial and fungal hosts for the production of both natural and novel bioproducts. We also highlight difficulties in engineering complex phenotypes and discuss the outlook for the future of lignin biological valorization.

Pathway discovery and engineering for cleavage of a β-1 lignin-derived biaryl compound

Lignin biosynthesis typically results in a polymer with several inter-monomer bond linkages, and the heterogeneity of linkages presents a challenge for depolymerization processes. While several enzyme classes have been shown to cleave common dimer linkages in lignin, the pathway of bacterial β-1 spirodienone linkage cleavage has not been elucidated. Here, we identified a pathway for cleavage of 1,2-diguaiacylpropane-1,3-diol (DGPD), a β-1 linked biaryl representative of a ring-opened spirodienone linkage, in Novosphingobium aromaticivorans DSM12444. In vitro assays using cell lysates demonstrated that RS14230 (LsdE) converts DGPD to a lignostilbene intermediate, which the carotenoid oxygenase, LsdA, then converts to vanillin. A Pseudomonas putida KT2440 strain engineered with lsdEA expression catabolizes erythro-DGPD, but not threo-DGPD. We further engineered P. putida to convert DGPD to a product, cis,cis-muconic acid. Overall, this work demonstrates the potential to identify new enzymatic reactions in N. aromaticivorans and expands the biological funnel of P. putida for microbial lignin valorization.

Protocatechuic acid production from lignin-associated phenolics

Biobased chemicals are gaining popularity and market in attempts to mitigate the deteriorating environmental and sustainability issues. Components of renewable agricultural and forest biomass residues are projected to serve as abundant precursors to synthesis of expanding range of products. Agroindustrial wastes comprises of several phenolic compounds associated with lignin via ether linkages such as ferulic acid, p-coumaric, syringic acid and vanillin. These aromatic chemicals have myriad industrial applications. In this study, p-coumaric acid and ferulic acid were found to be two major components in corn bran derived lignin hydrolysate. Engineered Pseudomonas putida KT2440 was constructed and found to convert p-coumaric acid and vanillic acid to protocatechuic acid in >90% and >50% yields, respectively. Engineering the strain included deletion of the gene encoding protocatechuate 3,4-dioxygenase, and overexpression of vanillate-O-demethylase gene from Acinetobacter sp. ADP1.

Characterization of aromatic acid/proton symporters in Pseudomonas putida KT2440 toward efficient microbial conversion of lignin-related aromatics

Pseudomonas putida KT2440 (hereafter KT2440) is a well-studied platform bacterium for the production of industrially valuable chemicals from heterogeneous mixtures of aromatic compounds obtained from lignin depolymerization. KT2440 can grow on lignin-related monomers, such as ferulate (FA), 4-coumarate (4CA), vanillate (VA), 4-hydroxybenzoate (4HBA), and protocatechuate (PCA). Genes associated with their catabolism are known, but knowledge about the uptake systems remains limited. In this work, we studied the KT2440 transporters of lignin-related monomers and their substrate selectivity. Based on the inhibition by protonophores, we focused on five genes encoding aromatic acid/H⁺ symporter family transporters categorized into major facilitator superfamily that uses the proton motive force. The mutants of PP_1376 (pcaK) and PP_3349 (hcnK) exhibited significantly reduced growth on PCA/4HBA and FA/4CA, respectively, while no change was observed on VA for any of the five gene mutants. At pH 9.0, the conversion of these compounds by hcnK mutant (FA/4CA) and vanK mutant (VA) was dramatically reduced, revealing that these transporters are crucial for the uptake of the anionic substrates at high pH. Uptake assays using ¹⁴C-labeled substrates in Escherichia coli and biosensor-based assays confirmed that PcaK, HcnK, and VanK have ability to take up PCA, FA/4CA, and VA/PCA, respectively. Additionally, analyses of the predicted protein structures suggest that the size and hydropathic properties of the substrate-binding sites of these transporters determine their substrate preferences. Overall, this study reveals that at physiological pH, PcaK and HcnK have a major role in the uptake of PCA/4HBA and FA/4CA, respectively, and VanK is a VA/PCA transporter. This information can contribute to the engineering of strains for the efficient conversion of lignin-related monomers to value-added chemicals.

Lignin valorization by bacterial genus Pseudomonas: State-of-the-art review and prospects

The most prominent aromatic feedstock on Earth is lignin, however, lignin valorization is still an underrated subject. The principal preparatory strategies for lignin valorization are fragmentation and depolymerization which help in the production of fuels and chemicals. Owing to lignin's structural heterogeneity, these strategies result in product generation which requires tedious separation and purification to extract target products. The bacterial genus Pseudomonas has been dominant for its lignin valorization potency, owing to a robust enzymatic machinery that is used to funnel variable lignin derivatives into certain target products such as polyhydroxyalkanotes (PHAs) and cis, cis-muconic acid (MA). In this review, the potential of genus Pseudomonas in lignin valorization is critically reviewed along with the advanced genetic techniques and tools to ease the use of lignin/lignin-model compounds for the synthesis of bioproducts. This review also highlights the research gaps in lignin biovalorization and discuss the challenges and possibilities for future research.

Pseudomonas spp. as cell factories (MCFs) for value-added products: from rational design to industrial applications

In recent years, there has been increasing interest in microbial biotechnology for the production of value-added compounds from renewable resources. Pseudomonas species have been proposed as a suitable workhorse for high-value secondary metabolite production because of their unique characteristics for fast growth on sustainable carbon sources, a clear inherited background, versatile intrinsic metabolism with diverse enzymatic capacities, and their robustness in an extreme environment. It has also been demonstrated that metabolically engineered Pseudomonas strains can produce several industrially valuable aromatic chemicals and natural products such as phenazines, polyhydroxyalkanoates, rhamnolipids, and insecticidal proteins from renewable feedstocks with remarkably high yields suitable for commercial application. In this review, we summarize cell factory construction in Pseudomonas for the biosynthesis of native and non-native bioactive compounds in P. putida, P. chlororaphis, P. aeruginosa, as well as pharmaceutical proteins production by P. fluorescens. Additionally, some novel strategies together with metabolic engineering strategies in order to improve the biosynthetic abilities of Pseudomonas as an ideal chassis are discussed. Finally, we proposed emerging opportunities, challenges, and essential strategies to enable the successful development of Pseudomonas as versatile microbial cell factories for the bioproduction of diverse bioactive compounds.

Response of Pseudomonas putida to Complex, Aromatic-Rich Fractions from Biomass

There is strong interest in the valorization of lignin to produce valuable products; however, its structural complexity has been a conversion bottleneck. Chemical pretreatment liberates lignin-derived soluble fractions that may be upgraded by bioconversion. Cholinium ionic liquid pretreatment of sorghum produced soluble, aromatic-rich fractions that were converted by Pseudomonas putida (P. putida), a promising host for aromatic bioconversion. Growth studies and mutational analysis demonstrated that P. putida growth on these fractions was dependent on aromatic monomers but unknown factors also contributed. Proteomic and metabolomic analyses indicated that these unknown factors were amino acids and residual ionic liquid; the oligomeric aromatic fraction derived from lignin was not converted. A cholinium catabolic pathway was identified, and the deletion of the pathway stopped the ability of P. putida to grow on cholinium ionic liquid. This work demonstrates that aromatic-rich fractions obtained through pretreatment contain multiple substrates; conversion strategies should account for this complexity.

Industrial biotechnology of Pseudomonas putida: advances and prospects

Pseudomonas putida is a Gram-negative, rod-shaped bacterium that can be encountered in diverse ecological habitats. This ubiquity is traced to its remarkably versatile metabolism, adapted to withstand physicochemical stress, and the capacity to thrive in harsh environments. Owing to these characteristics, there is a growing interest in this microbe for industrial use, and the corresponding research has made rapid progress in recent years. Hereby, strong drivers are the exploitation of cheap renewable feedstocks and waste streams to produce value-added chemicals and the steady progress in genetic strain engineering and systems biology understanding of this bacterium. Here, we summarize the recent advances and prospects in genetic engineering, systems and synthetic biology, and applications of P. putida as a cell factory. KEY POINTS: • Pseudomonas putida advances to a global industrial cell factory. • Novel tools enable system-wide understanding and streamlined genomic engineering. • Applications of P. putida range from bioeconomy chemicals to biosynthetic drugs.

Adaptive laboratory evolution of Pseudomonas putida KT2440 improves p-coumaric and ferulic acid catabolism and tolerance

Pseudomonas putida KT2440 is a promising bacterial chassis for the conversion of lignin-derived aromatic compound mixtures to biofuels and bioproducts. Despite the inherent robustness of this strain, further improvements to aromatic catabolism and toxicity tolerance of P. putida will be required to achieve industrial relevance. Here, tolerance adaptive laboratory evolution (TALE) was employed with increasing concentrations of the hydroxycinnamic acids p-coumaric acid (pCA) and ferulic acid (FA) individually and in combination (pCA ​+ ​FA). The TALE experiments led to evolved P. putida strains with increased tolerance to the targeted acids as compared to wild type. Specifically, a 37 ​h decrease in lag phase in 20 ​g/L pCA and a 2.4-fold increase in growth rate in 30 ​g/L FA was observed. Whole genome sequencing of intermediate and endpoint evolved P. putida populations revealed several expected and non-intuitive genetic targets underlying these aromatic catabolic and toxicity tolerance enhancements. PP_3350 and ttgB were among the most frequently mutated genes, and the beneficial contributions of these mutations were verified via gene knockouts. Deletion of PP_3350, encoding a hypothetical protein, recapitulated improved toxicity tolerance to high concentrations of pCA, but not an improved growth rate in high concentrations of FA. Deletion of ttgB, part of the TtgABC efflux pump, severely inhibited growth in pCA ​+ ​FA TALE-derived strains but did not affect growth in pCA ​+ ​FA in a wild type background, suggesting epistatic interactions. Genes involved in flagellar movement and transcriptional regulation were often mutated in the TALE experiments on multiple substrates, reinforcing ideas of a minimal and deregulated cell as optimal for domesticated growth. Overall, this work demonstrates increased tolerance towards and growth rate at the expense of hydroxycinnamic acids and presents new targets for improving P. putida for microbial lignin valorization.

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Pseudomonas putida was evolved in increasing hydroxycinnamic acid concentrations.

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The lag phase in high p-coumaric acid concentration was reduced.

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The growth rate and tolerance to high ferulic acid concentration was increased.

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PP_3350 and ttgB contribute to the observed phenotypes.

Recent Advances in Microbial Production of cis,cis-Muconic Acid

cis,cis-Muconic acid (MA) is a valuable C6 dicarboxylic acid platform chemical that is used as a starting material for the production of various valuable polymers and drugs, including adipic acid and terephthalic acid. As an alternative to traditional chemical processes, bio-based MA production has progressed to the establishment of de novo MA pathways in several microorganisms, such as Escherichia coli, Corynebacterium glutamicum, Pseudomonas putida, and Saccharomyces cerevisiae. Redesign of the metabolic pathway, intermediate flux control, and culture process optimization were all pursued to maximize the microbial MA production yield. Recently, MA production from biomass, such as the aromatic polymer lignin, has also attracted attention from researchers focusing on microbes that are tolerant to aromatic compounds. This paper summarizes recent microbial MA production strategies that involve engineering the metabolic pathway genes as well as the heterologous expression of some foreign genes involved in MA biosynthesis. Microbial MA production will continue to play a vital role in the field of bio-refineries and a feasible way to complement various petrochemical-based chemical processes.

Harnessing the Power of Enzymes for Tailoring and Valorizing Lignin

Lignin, a structural component of lignocellulosic plants, is an alternative raw material with enormous potential to replace diminishing fossil-based resources for the sustainable production of many chemicals and materials. Unfortunately, lignin's heterogeneity, low reactivity, and strong intra- and intermolecular hydrogen interactions and modifications introduced during the pulping process present significant technical challenges. However, the increasing ability to tailor lignin biosynthesis pathways by targeting enzymes and the continued discovery of more robust biocatalysts are enabling the synthesis of novel valuable products. This review summarizes how enzymes involved in lignin biosynthesis pathways and microbial enzymes are being harnessed to produce chemicals and materials and to upgrade lignin properties for the synthesis of a variety of value-added lignin industrial products.