Sole Carbon Source Research Articles

Functional impact of a deletion in Mycobacterium bovis BCG Moreau celA1 gene

Several mycobacterial species are known to cause human diseases, such as tuberculosis and leprosy. In addition to these pathogenic species, there are also saprophytic representatives, which occasionally cause opportunistic infections. It is well established that numerous mycobacteria produce biofilms containing cellulose, and their genomes frequently harbor genes involved in cellulose degradation, such as celA1. Notably, the BCG Moreau vaccine strain carries a specific deletion of two-base pairs, resulting in a predicted protein with fewer than 100 amino acids in the catalytic portion at the C-terminal end. We investigated the functional consequences of this polymorphism and observed that recombinant enzyme from the Moreau strain lack catalytic activity. Furthermore, compared to the Pasteur strain, Moreau is unable to utilize carboxymethylcellulose (CMC) as the sole carbon source. These findings suggest an absence of cellulolytic activity in this strain, which may influence the bacterium virulence.

Methylocystis borbori sp.nov., a novel methanotrophic bacterium from the sludge of a freshwater lake and its metabolic properties.

A novel methanotrophic strain 9NT was isolated from the sludge of a freshwater lake. Cells were aerobic, Gram-stain-negative, non-motile pleomorphic rods with intracytoplasmic membrane systems that appropriate type-II methanotrophs and hemispherical and spherical exocellular formations on the perimeter of the cell wall surface. The novel isolate grows only on methane or methanol as the sole carbon and energy source, at 10-37°C (optimum 28-30°C), pH 4.5-9.0 (optimum 7.0-7.5), up to 1% NaCl (optimum 0.3-0.5%). Methanol supported the growth of the strain 9NT in a wide range of concentrations from 0.05 to 5.0% (v/v) with an optimum of 0.5% (v/v). The major fatty acids were C18:1ω8c and C18:1ω7c. Based on 16S rRNA gene sequence phylogenetic analysis, strain 9NT was closely related to representatives of the genus Methylocystis (96.5-98.3%). The genome of strain 9NT was 3.34Mbp in size with 63.5% of G + C content. The average nucleotide identity and digital DNA-DNA hybridization values between strain 9NT and closely related type strains of genus Methylocystis were 78.0-82.4% and 20.9-24.3%, respectively. The careful genome annotation of the novel strain shows it possessed genes for the detoxification of arsenate and cyanides as well as genes potentially involved in plant growth promotion (such as biosynthesis of indoles, cytokinins, polyhydroxybutyrate, siderophore production, and nitrogen fixation). Based on the phylogenetic, phenotypic, chemotaxonomic and genomic data, we propose Methylocystis borbori sp. nov. as novel species of the genus Methylocystis. The type strain is 9NT (= VKM B-3616T = KCTC 92566T).

Enrichment of LDPE-degrading bacterial consortia: Community succession and enhanced degradation efficiency through various pretreatment methods

Low-density polyethylene (LDPE) is a widely used plastic that significantly contributes to environmental pollution, and its biodegradation remains challenging. This study investigates the dynamics of bacterial communities in consortia enriched with LDPE as the sole carbon source. The potential for microbial diversity to adapt to polluted environments underscores its role in bioremediation. Community analysis identified Actinobacteria and Proteobacteria as key contributors to LDPE degradation, with dominant genera including Mycobacterium, Cupriavidus, Gordonia, Ochrobactrum, Nocardia, Agromyces, Amycolatopsis, and Cellulosimicrobium. The biodegradation of untreated and pretreated LDPE films was also examined, revealing that UV pretreatment significantly enhances degradation, with weight losses of 2.22–5.17% after 120 days. In contrast, sunlight and thermal treatments resulted in lower weight losses of 1.67–4.56% and 1.42–3.22%, respectively, while untreated LDPE showed only 1.32–2.80% weight loss. These findings underscore the importance of UV pretreatment in facilitating plastic biodegradation. Furthermore, potential LDPE-degrading Actinobacteria and Proteobacteria were isolated, identified as key players in the communities and co-occurrence networks, suggesting promising candidates for developing sustainable plastic waste management solutions. Moreover, this study is the first to reveal the potential LDPE degradation abilities of several genera, including Mesorhizobium, Agromyces, Amycolatopsis, Olivibacter, Aquamicrobium, Pseudaminobacter, and others.

The PrfA regulon of Listeria monocytogenes is induced by growth in low-oxygen microaerophilic conditions.

Listeria monocytogenes is a food-borne pathogen that must adapt to several environments both inside and outside the host. One such environment is the microaerophilic conditions encountered in the host intestine proximal to the mucosal surface. The aim of this study was to investigate the expression of the PrfA regulon in response to microaerophilic growth conditions in the presence of either glucose or glycerol as a carbon source using four transcriptional (Phly, PactA, P/prfA and P/plcA) gene fusions. Further, RNAseq analysis was used to identify global changes in gene expression during growth in microaerophilic conditions. Following microaerophilic growth, there was a PrfA-dependent increase in transcription from the Phly, PactA and P/plcA promoters, indicating that microaerophilic growth induces the PrfA regulon regardless of the carbon source with increased expression of the PrfA, LLO and ActA proteins. A sigB mutation had no effect on the induction of the PrfA regulon under microaerophilic conditions when glucose was used as a carbon source. In contrast, when glycerol was the carbon source, a sigB mutation increased expression from the Phly and PactA promoters regardless of the level of oxygen. The RNAseq analysis showed that 273 genes were specifically regulated by microaerophilic conditions either up or down including the PrfA regulon virulence factors. Overall, these data indicated that L. monocytogenes PrfA regulon is highly responsive to the low-oxygen conditions likely to be encountered in the small intestine and that SigB has an input into the regulation of the PrfA regulon when glycerol is the sole carbon source.

A synthetic co-culture for bioproduction of ammonia from methane and air.

Fixed nitrogen fertilizers feed fifty percent of the global population, but most fixed nitrogen production occurs using energy-intensive Haber-Bosch-based chemistry combining nitrogen (N2) from air with gaseous hydrogen (H2) from methane (CH4) at high temperatures and pressures in large-scale facilities sensitive to supply chain disruptions. This work demonstrates the biological transformation of atmospheric nitrogen (N2) into ammonia (NH3) using methane (CH4) as the sole carbon and energy source in a single vessel at ambient pressure and temperature, representing a biological 'room-pressure and room-temperature' route to ammonia (NH3) that could ultimately be developed to support compact, remote, ammonia (NH3) production facilities amenable to distributed biomanufacturing. The synthetic microbial co-culture of engineered methanotroph Methylomicrobium buryatense (now Methylotuvimicrobium buryatense) and diazotroph Azotobacter vinelandii converted three methane (CH4) molecules to L-lactate (C3H6O3) and powered gaseous nitrogen (N2) conversion to ammonia (NH3). The design used division of labor and mutualistic metabolism strategies to address the oxygen sensitivity of nitrogenase and maximize methane oxidation efficiency. Media pH and salinity were central variables supporting co-cultivation. Carbon concentration heavily influenced ammonia production. Smaller scale ammonia (NH3) production near dispersed, abundant, and renewable methane (CH4) sources could reduce disruption risks and capitalize on untapped energy resources.

The fall armyworm converts maize endophytes into its own probiotics to detoxify benzoxazinoids and promote caterpillar growth

BackgroundThe fall armyworm (FAW, Spodoptera frugiperda) threatens maize production worldwide, and benzoxazinoids (Bxs) are known as the main secondary metabolites produced by maize to defend against FAW. However, we do not yet know whether and in what ways certain endophytes in the digestive system of FAW can metabolize Bxs, thus enhancing the fitness of FAW when feeding on maize.ResultsUsing Bxs as the sole carbon and nitrogen source, we isolated Pantoea dispersa from the guts of FAW. P. dispersa can colonize maize roots and leaves as indicated by GFP-labeling and further successfully established itself as an endophyte in the Malpighian tubules and the gut of FAW after FAW feeding activities. Once established, it can be vertically transmitted through FAW eggs, suggesting the potential that FAW can convert maize-derived endophytes into symbiotic bacteria for intergenerational transmission. The prevalence of P. dispersa in FAW guts and maize leaves was also confirmed over large geographic regions, indicating its evolutionary adaptation in fields. Bxs determination in the gut and frass of FAW combined with bioassays performance on maize bx2 mutants revealed that the colonization of P. dispersa can promote FAW growth by metabolizing Bxs rather than other metabolites. Additionally, genome and transcriptome analyses identified plasmid-borne genes, rather than chromosomes of this species, were crucial for Bxs metabolism. This was further validated through in vitro prokaryotic expression assays by expressing two candidate genes form the plasmid.ConclusionsFAW can convert maize endophytes into its own probiotics to detoxify Bxs and thus enhance caterpillar growth. This represents a novel strategy for lepidopteran pests—transforming allies of the host into its own—thereby shedding light on the rapid spread of FAW and enhancing our understanding of ecological and evolutionary mechanisms underlying the pest-microbe–plant interactions.2f6JcKQYnKTEdqap9saLkxVideo

Metagenome-assembled genomes of freshwater Hyphomicrobium sp. G-191 and Methylophilus sp. enriched from Cedar Swamp, Woods Hole, MA.

Hyphomicrobium are facultative denitrifying anaerobes capable of using one-carbon compounds as a sole carbon source. Hyphomicrobium sp. G-191 was enriched from Cedar Swamp, Woods Hole, Massachusetts, using a selective medium for methanol-utilizing bacteria. We present two draft metagenome-assembled genomes (MAGs) of a Hyphomicrobium and a Methylophilus species.

Repeated Fed-Batch Culture Strategy for the Synthesis of Polyhydroxybutyrate (PHB) Biopolymers from Sugar Cane Juice Using Azotobacter vinelandii.

In this research work, a main biopolymer group of polyhydroxyalkanoates (PHAs) in the form of polyhydroxybutyrate (PHB) was synthesised by a pure bacterial strain of Azotobacter vinelandii via repeated fed-batch fermentation. An agricultural crop, sugar cane, was used as the sole carbon source. Firstly, batch fermentation was investigated considering variations in incubation times (24 h, 48 h, and 96 h). The highest dry cell weight (DCW) and PHAs of 5.15 ± 0.04 g/L and 4.00 ± 0.04 g/L were obtained after 48 h of incubation time. The optimum time obtained was further varied to investigate the effect of the sugar concentrations in the medium. It was found that bacteria could grow very well and produced the highest DCW and PHAs (11.17 ± 0.15 g/L and 8.77 ± 0.06 g/L) when the culture medium with a 100 g/L sugar concentration was added. Later, repeated fed-batch fermentation was carried out to improve productivity. The results obtained revealed that PHA production was increased in the next cycle of the process. Furthermore, the final productivity (0.104 g/L·h) was increased 1.65-fold compared to the first cycle (0.063 g/L·h). Moreover, the culture strategy showed remarkable results, with reductions in both fermentation time and preparation cost.

Biodegradation of Crude Oil and Aniline by Heavy Metal-Tolerant Strain Rhodococcus sp. DH-2.

Aniline and crude oil are common environmental pollutants that present a significant risk to both the ecological and human health environments. The implementation of efficacious bioremediation strategies is imperative for the elimination of these contaminants. In this study, a bacterial strain designated DH-2 was isolated from soil contaminated with aniline. The strain was identified as belonging to the genus Rhodococcus. The optimal conditions for the growth and aniline degradation by strain DH-2 were determined to be pH 8.0 and 35 °C, respectively. Under these conditions, the degradation rate of aniline at a concentration of 1000 mg/L exceeded 90% within 36 h. Even in the presence of 4% NaCl, the degradation rate remained above 60%. HPLC-MS analysis revealed that the aniline degradation pathway of strain DH-2 follows the catechol pathway. Additionally, strain DH-2 is capable of utilizing crude oil as the sole carbon source, achieving a degradation rate of 91.0% for 2% crude oil concentration within 4 days. In soil modeling experiments, strain DH-2 was observed to degrade aniline and crude oil under triple stress conditions, including 1000 mg/L aniline, 2% crude oil, and 20 mg/L Fe(II) or Pb(II). Complete degradation of aniline and crude oil was achieved after 3 days and 12 days, respectively. The addition of Fe(II) or Pb(II) ions was found to enhance the degradation ability of DH-2. These results demonstrate that strain DH-2 is an extremely effective biodegradable strain, with potential applications in the remediation of environments contaminated with aniline and crude oil, even in the presence of heavy metals.

Bacterial Degradation of Ibuprofen: Insights into Metabolites, Enzymes, and Environmental Fate Biodegradation of Ibuprofen by Achromobacter Species

In recent years, pharmaceuticals have emerged as pollutants due to their incomplete degradation in sewage treatment plants and their ability to cause physiological problems in humans even at low doses. Understanding the environmental fate of pharmaceutical pollutants and the mechanisms involved in their degradation is crucial for developing strategies to mitigate their impact on ecosystems and human health. In this study, the degradation of pharmaceutical compound ibuprofen was achieved by employing two bacterial strains, Achromobacter spanius strain S11 and Achromobacter piechaudii S18, previously isolated from contaminated water. These strains were capable of degrading ibuprofen as their sole carbon source. The study aimed to identify intermediate metabolites, determine the enzymes involved, and detect specific genes related to ibuprofen degradation. Different concentrations of ibuprofen, temperatures, and pH levels were tested. Both A. spanius S11 and A. piechaudii S18 successfully degraded ibuprofen. A. spanius S11 showed a degradation efficiency of 91.18% after only 72 h and reached 95.7% after 144 h, while A. piechaudii S18 exhibited degradation efficiencies of 72.39% and 73.01% after three and seven days, respectively. The LC-MS technique was used to identify biodegradation metabolites produced by A. spanius S11. The results indicated that the first step was hydroxylation followed by oxidation via the combination of monooxygenases that catalyze the C-H hydroxylation and dehydrogenases. Furthermore, the detection of intermediate metabolites of trihydroxyibuprofen suggested that the biodegradation of ibuprofen by A. spanius S11 can occur through multiple mechanisms. The highest enzyme activities were recorded for catechol 1,2-dioxygenase, 4.230 ± 0.026 U/mg, followed by laccase, 2.001 ± 0.215 U/mg. This study demonstrates the potential of Achromobacter strains, particularly A. spanius (S11), in degrading ibuprofen. These findings provide insights into the ibuprofen degradation process, intermediate metabolites, and relevant genes.

Development of a starch-fermenting Zymomonas mobilis strain for bioethanol production

BackgroundBiorefinery using microorganisms to produce biofuels and value-added biochemicals derived from renewable biomass offers a promising alternative to meet our sustainable energy and environmental goals. The ethanologenic strain Zymomonas mobilis is considered as an excellent chassis for constructing microbial cell factories for diverse biochemicals due to its outstanding industrial characteristics in ethanol production, high specific productivity, and Generally Recognized as Safe (GRAS) status. Nonetheless, the restricted substrate range constrains its application.ResultsThe truncated ice nucleation protein InaK from Pseudomonas syringae was used as an autotransporter passenger, and α-amylase was fused to the C- terminal of InaK to equip the ethanol-producing bacterium with the capability to ferment renewable biomass. Western blot and flow cytometry analysis confirmed that the amylase was situated on the outer membrane. Whole-cell activity assays demonstrated that the amylase maintained its activity on the cell surface. The recombinant Z. mobilis facilitated the hydrolysis of starch into oligosaccharides and enabled the streamlining of simultaneous saccharification and fermentation (SSF) processes. In a 5% starch medium under SSF, recombinant strains containing Peno reached a maximum titer of 13.61 ± 0.12 g/L within 48 h. This represents an increase of 111.0% compared to the control strain's titer of titer of 6.45 ± 0.25 g/L.ConclusionsBy fusing the truncated ice nucleation protein InaK with α-amylase, we achieved efficient expression and surface display of the enzyme on Z. mobilis. This fusion protein exhibited remarkable enzymatic activity. Its presence enabled a cost-effective bioproduction process using starch as the sole carbon source, and it significantly reduced the required cycle time for SSF. This study not only provides an excellent Z. mobilis chassis for sustainable bioproduction from starch but also highlights the potential of Z. mobilis to function as an effective cellular factory for producing high-value products from renewable biomass.

Microalgae-bacterial consortiums for enhanced degradation of nonylphenol: Biodegradability and kinetic analysis

The widespread use of non-ionic surfactant nonylphenol (NP) has led to significant water pollution, posing a threat to both ecological stability and human health. However, the efficient biodegradation method and system of NP-biodegradation remain complex scientific challenges. In this study, we isolated and characterized three Pseudomonas sp. strains SW-1 (Scenedesmus quadricauda-associated), ZL-2 (Ankistrodesmus acicularis-associated), XQ-3 (Chlorella vulgaris-associated), and one NP-degrading Cupriavidus sp. strain EB-4, which exhibited the ability to utilize NP as the sole carbon source. Furthermore, four consortiums of microalgae-bacterial, S. quadricauda and SW-1 (S-SW), A. acicularis and ZL-2 (A-ZL), C. vulgaris and XQ-3 (C-XQ), S. quadricauda and EB-4 (S-EB), were constructed to investigate their biodegradability and kinetic characteristics of NP degradation from water. The consortiums showed higher degradation efficiency compared to individual microalgae or bacteria. The C-XQ consortium exhibited the highest degradation rate, removing over 94% of NP within just seven days. The first-order model with the following order of degradation rate by consortiums was C-XQ (0.3960 d−1) > S-SW (0.3506 d−1) > A-ZL (0.1968 d−1) > S-EB (0.1776 d−1). Compared with the results of our previous study, the interaction between microalgae and bacteria is not a simple additive relationship. Our findings highlight the potential of an algal-bacterial consortium for the remediation of NP-contaminated environments.

Long-chain fatty acids as sole carbon source in polyhydroxyalkanoates production by Cupriavidus necator H16.

Polyhydroxyalkanoates (PHA) are promising eco-friendly alternatives to petrochemical plastics. This study investigated the impact of the main fatty acids present in waste and fresh oils -palmitic, stearic, oleic, and linoleic acid-on PHA production using Cupriavidus necator H16, focusing on production yield, polymer composition, thermal properties, and microbial viability. Experiments were conducted with low (5 g/L) and high (15 g/L) carbon content for 168 h. Oleic acid was the most effective carbon source, yielding higher PHA production rates, especially noticeable at higher concentrations. The monomer composition and thermal properties of PHAs varied with the type and concentration of fatty acid used. Stearic acid produced PHAs with more 3-hydroxyvalerate and medium-chain length monomers. Microbial viability was consistent across all conditions, except for linoleic acid, which had a detrimental effect. These findings provide key insights into optimizing fatty acid selection to enhance PHA production and tailor polymer properties for industrial applications.

Transcriptomics-guided rational engineering in Bacillus licheniformis for enhancing poly-γ-glutamic acid biosynthesis using untreated molasses

The utilization of non-food raw materials for microbial synthesis of poly-γ-glutamic acid (γ-PGA) presents a promising alternative to conventional food-based biosynthesis. However, the complex carbon source and composition of molasses, a prevalent non-food raw material, may impose constraints on its conversion and utilization by microorganisms. This study aimed to enhance the capacity of Bacillus licheniformis to convert untreated molasses into γ-PGA through transcriptomic analysis to guide metabolic modifications. Initial results from the transcriptomic analysis indicated that the strain utilizing molasses exhibited decreased expression of genes associated with substrate utilization (Module 1) and by-product synthesis (Module 2), while upregulating genes related to precursor synthesis (Module 3). Furthermore, we performed a knockout of the acetolactate synthase (AlsS) to reduce the synthesis of metabolic by-products and a knockout of the global regulator (CcpA) to alleviate carbon catabolite repression (CCR) and then promote substrate utilization. Ultimately, following the tandem overexpression of precursor supplying key genes, the titer of γ-PGA reached 48.26 g/L with a productivity of 1.15 g/L/h, using untreated molasses as the sole carbon source, which was 3.12-fold of the starting strain. These findings offer significant insights into the cost-effective synthesis of γ-PGA by bioconversion of untreated molasses during fermentation.

Utilization of High-Salinity Crude Glycerol Byproduct from Biodiesel Production for Biosynthesis of γ-Aminobutyric Acid in Engineered Halomonas elongata

As the development of renewable energy has become imperative, biodiesel fuel (BDF) has been used as renewable biofuel with the advantage of having lower levels of greenhouse gas emissions. However, the transesterification reaction that produces BDF generates a high-salinity crude glycerol (CG) byproduct, which is difficult to recycle. Halomonas elongata is a moderately halophilic bacterium being used as a cell factory due to its ability to assimilate varieties of substrates for growth in high-salinity conditions. Previously, we engineered a recombinant H. elongata GOP-Gad to biosynthesize and accumulate γ-aminobutyric acid (GABA) as a high-value product. Here, we tested the ability of H. elongata GOP-Gad to use CG as a substrate for cell growth and GABA production. The CG byproduct was obtained from a BDF facility in Unzen City, Nagasaki, Japan, where geothermal energy catalyzed BDF production from waste cooking oil and biomethanol. Prior to use as the sole carbon (C) source in culture media, the CG byproduct was partially purified to remove soap substances and other impurities. Finally, we showed that H. elongata GOP-Gad could grow and accumulate GABA up to 28 μmol/g cell fresh weight in a minimal M63 medium containing 7% w/v NaCl with 4% w/v glycerol from the partially purified CG as a C source and 15 mM (NH4)2SO4 as a nitrogen (N) source. This result demonstrates a new circulatory bioprocess of C and N, in which H. elongata GOP-Gad can use partially purified CG and (NH4)2SO4 as the sole C and N sources for growth and GABA production.

Metabolic engineering of Escherichia coli for the utilization of methylsuccinate, the product of methane activation via fumarate addition

Methylsuccinate is a branched-chain, 5-carbon (C5) dicarboxylate that can be generated from the O2-independent activation of methane via fumarate addition. However, no established metabolic pathway enables growth and product synthesis from methylsuccinate. Here, we report a synthetic pathway that converts methylsuccinate into two precursor metabolites: pyruvate and acetyl-CoA. The pathway was constructed through rational design and validated both in vitro and in vivo using E. coli as the host. Subsequently, growth on methylsuccinate as the sole carbon source was achieved using two parallel strategies: adaptive laboratory evolution and enzyme mining. Through the latter approach, we identified a heterologous electron transfer pathway mediated by previously uncharacterized enzymes and integrated into E. coli enabling the conversion of methylsuccinyl-CoA to mesaconyl-C4-CoA. The engineered strain demonstrated efficient growth on various C5 dicarboxylates including methylsuccinate, mesaconate, and itaconate, with a specific growth rate of 0.11 h−1 on methylsuccinate. This study represents an important step toward achieving synthetic methanotrophy, as the engineered strain can serve as a platform for screening potential methane activation enzymes and ultimately as a production chassis for the bioconversion of methane into various value-added products.

Multi-omic profiling of a novel Myrothecium species reveals its potential mechanism of lignin degradation

Lignin utilization is one of the key challenges in the valorziation of lignocellulose. Filamentous fungi are promising candidates for lignin degradation and mineralization. However, novel lignin-degrading species are underexplored and the mechanism of lignin degradation is not fully understood. Here we isolated and characterized a novel species, Myrothecium wuxin, capable of utilizing lignosulfonate as the sole carbon source. To understand the mechanism of lignin degradation, genomic, transcriptomic and metabolic analyses were performed. The genome was sequenced, and assembled to a size of 48.55 Mb, with a contig N50 size of 5.67Mb. A total of 14,221 protein-coding genes were predicted, including a high number of potential ligninolytic enzymes. Transcriptomic analysis revealed a pronounced effect of lignosulfonate on gene expression profiles. More than twenty intermediate aromatic metabolites were identified during lignosulfonate utilization. Through genomic annotation, the genes potentially involved in lignin degradation were identified, and more than nine metabolic pathways of lignin-derived aromatic intermediates were predicted, including the homogentisate pathway, benzoic acid pathway, as well as the tree-branched β-ketoadipate pathway. The genomic information will provide a valuable resource for lignin degradation, while the elucidated catabolic pathways and associated enzymes provide exciting biotechnological opportunities for lignin valorization and production of valuable chemicals.

Production of L-lactic acid from methanol by engineered yeast Pichia pastoris

Lactic acid (LA) serves as a widely used platform compound and has received significant attention as a raw material for synthesis of biodegradable polylactic acid. Currently, LA is mainly produced through microbial fermentation, but its high costs undermine its competitive advantage against other materials, necessitating the development of novel production routes. Methanol bioconversion represents an emerging low-carbon circular economy, where LA could become an outstanding representative product. This study successfully established an efficient methanol-based LA synthesis route in Pichia pastoris. Through systematic metabolic engineering strategies, including screening lactate dehydrogenase, modification of cofactor preference, blocking LA consumption pathway, and mitochondrial LA synthesis compartmentalization, 4.2 g/L L-LA was produced in fed-batch fermentation by using methanol as the sole carbon source. Through multi-dimensional and spatial engineering of enzyme, a cell factory was developed for efficient synthesis of L-LA, highlights the significant potential of the low-carbon synthesis route for L-LA via methanol bioconversion.

Draft genome of hydrocarbon-degrader Burkholderia cepacia BCTT, isolated from soil chronically polluted with crude oil in Trinidad.

Burkholderia cepacia BCTT, isolated from chronically polluted soil in Trinidad, shows a capacity to survive in crude oil as a sole carbon source. Here, we report its high-quality draft genome sequence and highlight those pathways and genes involved in xenobiotic degradation. These data give a clearer insight into this organism's biotechnological potential.

Lignin valorization to bioplastics with an aromatic hub metabolite-based autoregulation system

Exploring microorganisms with downstream synthetic advantages in lignin valorization is an effective strategy to increase target product diversity and yield. This study ingeniously engineers the non-lignin-degrading bacterium Ralstonia eutropha H16 (also known as Cupriavidus necator H16) to convert lignin, a typically underutilized by-product of biorefinery, into valuable bioplastic polyhydroxybutyrate (PHB). The aromatic metabolism capacities of R. eutropha H16 for different lignin-derived aromatics (LDAs) are systematically characterized and complemented by integrating robust functional modules including O-demethylation, aromatic aldehyde metabolism and the mitigation of by-product inhibition. A pivotal discovery is the regulatory element PcaQ, which is highly responsive to the aromatic hub metabolite protocatechuic acid during lignin degradation. Based on the computer-aided design of PcaQ, we develop a hub metabolite-based autoregulation (HMA) system. This system can control the functional genes expression in response to heterologous LDAs and enhance metabolism efficiency. Multi-module genome integration and directed evolution further fortify the strain’s stability and lignin conversion capacities, leading to PHB production titer of 2.38 g/L using heterologous LDAs as sole carbon source. This work not only marks a leap in bioplastic production from lignin components but also provides a strategy to redesign the non-LDAs-degrading microbes for efficient lignin valorization.