YjeH Is a Novel Exporter of l-Methionine and Branched-Chain Amino Acids in Escherichia coli

Enhanced l-serine synthesis in Corynebacterium glutamicum by exporter engineering and Bayesian optimization of the medium composition

l-serine is a versatile, high value-added amino acid, widely used in food, medicine and cosmetics. However, the low titer of l-serine has limited its industrial production. In this study, a cell factory without plasmid for efficient production of l-serine was constructed based on transport engineering. Firstly, the effects of l-serine exporter SerE overexpression and deletion on the cell growth and l-serine titer were investigated in Corynebacterium glutamicum (C. glutamicum) A36, overexpression of s erE using a plasmid led to a 15.1% increase in l-serine titer but also caused a 15.1% decrease in cell growth. Subsequently, to increase the export capacity of SerE, we conducted semi-rational design and bioinformatics analysis, combined with alanine mutation and site-specific saturation mutation. The mutant E277K was obtained and exhibited a 53.2% higher export capacity compared to wild-type SerE, resulting in l-serine titer increased by 39.6%. Structural analysis and molecular dynamics simulations were performed to elucidate the mechanism. The results showed that the mutation shortened the hydrogen bond distance between the exporter and l-serine, enhanced complex stability, and reduced the binding energy. Finally, Bayesian optimization was employed to further improve l-serine titer of the mutant strain C-E277K. Under the optimized conditions, 47.77 g/L l-serine was achieved in a 5-L bioreactor, representing the highest reported titer for C. glutamicum to date. This study provides a basis for the transformation of l-serine export pathway and offers a new strategy for increasing l-serine titer.

Enhancing Ergothioneine Production by Combined Protein and Metabolic Engineering Strategies

Ergothioneine (ERG), a sulfur-containing histidine derivative recognized for its high stability, is of significant value across multiple sectors, including food, cosmetics, and medicine. In comparison to chemical synthesis, the establishment of microbial cell factories for ERG production represents a more efficient, environmentally friendly, and sustainable strategy. In this study, we achieved de novo synthesis of ERG in Escherichia coli by introducing genes from Trichoderma reesei. Protein engineering was subsequently employed to enable the soluble expression of the key genes Tr1 and Tr2, which resulted in a 198.1% increase in ERG production. Furthermore, strain modifications, including the knockout of competing pathways and optimization of key gene copies, were used to enhance ERG production. Following strategic combinations and medium optimization, strain E25 produced 430.9 mg/L ERG in an Erlenmeyer flask and 2331.58 mg/L via fed-batch fermentation in a 5 L bioreactor. This study not only establishes a solid foundation for the efficient and sustainable scale-up production of ERG and its derivatives but also provides valuable insights and references for its industrial production.

Identification and Characterization of a Novel d-Branched-Chain Amino Acids Importer from Lactobacillus fermentum

Various lactic acid bacteria synthesize d-branched-chain amino acids (d-BCAA) during growth, but their physiological function remains largely elusive. The pyridoxal phosphate-dependent enzyme isoleucine 2-epimerase (ILEP) has been identified as the key enzyme responsible for d-BCAA biosynthesis. Comparative genomic analyses revealed that genes encoding ILEP and an uncharacterized amino acid-polyamine-organocation (APC) family transporter are adjacent in several d-BCAA-producing bacteria, suggesting a functional link between these two proteins in d-BCAA metabolism. In this study, we investigated the function of the APC family transporter from Lactobacillus fermentum (LfAAP). Using heterologous expression systems in Escherichia coli and Lactococcus lactis, we demonstrated that LfAAP functions as a non-stereospecific BCAA importer. Mutational analysis revealed that Ala119 and Met331 play critical roles in substrate recognition. Heterologous expression of LfAAP and/or LfILEP in a L. lactis strain, which lacks the ILEP-AAP genes operon, revealed that ILEP functions as both synthetic and catabolic enzyme for d-BCAA. Our findings suggest that the ILEP-AAP system contribute to storage and subsequent utilization of BCAA in a form that is less accessible by other organisms, providing a potential competitive advantage in microbial environments.

Effects of vitamin B12 supply on cellular processes of the facultative vitamin B12 consumer Vibrio campbellii

Vitamin B12 (cobalamin, herein B12) is a key cofactor for most organisms being involved in essential metabolic processes. In microbial communities, B12 is often scarce, largely because only few prokaryotes can synthesize B12 de novo and are thus considered B12-prototrophs. B12-auxotrophy is mostly manifested by the absence of the B12-independent methionine synthase, MetE. Here, we focus on bacteria that we classified as facultative B12 consumers as they encode both B12-independent and -dependent (MetH) methionine synthases yet largely cannot synthesize B12 de novo. The genus Vibrio belongs to this group, and our work shows that upon B12 supply growth of Vibrio campbellii is accelerated and autoinducer-2 (AI-2) concentrations are enhanced. We speculate that methionine synthesis efficiency, dependent on B12 availability, is linked to AI-2 synthesis. The precursor for AI-2 synthesis is S-adenosyl-L-homocysteine (SAH), which in turn requires methionine as a precursor. In almost all Vibrio species studied, btuF (B12-binding protein), which is required for B12 uptake, and cobD (Adenosylcobinamide-phosphate synthase), which enables remodeling of B12-like compounds, are encoded on the same operon as pfs (or mtnN, Adenosylhomocysteine nucleosidase), the first enzyme in the two-step AI-2 synthesis reaction. Transcriptomic analyses show that virulence factors, such as toxin synthesis, fimbriae formation, and activation of the type-6 secretion system, which have been shown to be regulated by quorum sensing via AI-2, are significantly upregulated in V. campbellii when B12 is available. Our results demonstrate that V. campbellii is a facultative B12 consumer and indicate that B12 availability affects AI-2 levels and thus potentially virulence factor regulation.IMPORTANCEMetabolites play a key role in microbial metabolism and communication. While vitamin B12 is an essential cofactor for important enzymatic reactions, autoinducer-2 mediates interspecies signaling and can regulate the expression of genes that are crucial for virulence and survival. In our study, we hypothesize and present findings how these two important metabolites are linked in Vibrio species. Vibrio campbellii grows without B12 but at an accelerated rate when B12 is present, and we detect higher AI-2 values in cultures with B12 amendment. Transcriptome analyses show how vitamin B12 availability significantly upregulates gene expression of virulence factors such as toxin synthesis, fimbrial formation, and activation of the type-6 secretion system in V. campbellii.

Available Strategies for Improving the Biosynthesis of Methionine: A Review

Methionine is the only nonpolar α-amino acid containing sulfur among the eight essential amino acids and is closely related to the metabolism of sulfur-containing compounds in the human body. Widely used in feed, medicine, food, and other fields, the market demand is increasing annually. However, low productivity and high cost largely limit the industrial production of methionine, and many novel production methods still have their own disadvantages. In this paper, the available methods for synthesizing methionine are reviewed and discussed. The latest strategies for improving methionine production are further introduced, including culture medium optimization, mutation technology, expression of key genes in the metabolic pathway, knockout and recombination, as well as the engineering of membrane transporters, the fermentation-enzymatic coupling route, and innovation of CO2 biotransformation.

Engineering of a Substrate Affinity Reduced S-Adenosyl-methionine Synthetase as a Novel Biosensor for Growth-Coupling Selection of L-Methionine Overproducers

Biosensors are powerful tools for monitoring specific metabolites or controlling metabolic flux towards the products in a single cell, which play important roles in microbial cell factory construction. Despite their potential role in metabolic flux monitoring, the development of biosensors for small molecules is still limited. Reported biosensors often exhibit bottlenecks of poor specificity and a narrow dynamic range. Moreover, fine-tuning the substrate binding affinity of a crucial enzyme can decrease its catalytic activity, which ultimately results in the repression of the corresponding essential metabolite biosynthesis and impairs cell growth. However, increasing intracellular substrate concentration can elevate the availability of the essential metabolite and may lead to restore cellular growth. Herein, a new strategy was proposed for constructing whole-cell biosensors based on enzyme encoded by essential gene that offer inherent specificity and universality. Specifically, S-adenosyl-methionine synthetase (MetK) in E. coli was chosen as the crucial enzyme, and a series of MetK variants were identified that were sensitive to L-methionine concentration. This occurrence enabled the engineered cell to sense L-methionine and exhibit L-methionine dose-dependent cell growth. To improve the biosensor's dynamic range, an S-adenosyl-methionine catabolic enzyme was overexpressed to reduce the intracellular availability of S-adenosyl-methionine. The resulting whole-cell biosensor effectively coupled the intracellular concentration of L-methionine with growth and was successfully applied to select strains with enhanced L-methionine biosynthesis from random mutagenesis libraries. Overall, our study presents a universal strategy for designing and constructing growth-coupled biosensors based on crucial enzyme, which can be applied to select strains overproducing high value-added metabolites in cellular metabolism.

Microbial production of sulfur-containing amino acids using metabolically engineered Escherichia coli

L-Cysteine and L-methionine, as the only two sulfur-containing amino acids among the canonical 20 amino acids, possess distinct characteristics and find wide-ranging industrial applications. The use of different organisms for fermentative production of L-cysteine and L-methionine is gaining increasing attention, with Escherichia coli being extensively studied as the preferred strain. This preference is due to its ability to grow rapidly in cost-effective media, its robustness for industrial processes, the well-characterized metabolism, and the availability of molecular tools for genetic engineering. This review focuses on the genetic and molecular mechanisms involved in the production of these sulfur-containing amino acids in E. coli. Additionally, we systematically summarize the metabolic engineering strategies employed to enhance their production, including the identification of new targets, modulation of metabolic fluxes, modification of transport systems, dynamic regulation strategies, and optimization of fermentation conditions. The strategies and design principles discussed in this review hold the potential to facilitate the development of strain and process engineering for direct fermentation of sulfur-containing amino acids.

The live biotherapeutic SYNB1353 decreases plasma methionine via directed degradation in animal models and healthy volunteers

Methionine is an essential proteinogenic amino acid, but its excess can lead to deleterious effects. Inborn errors of methionine metabolism resulting from loss of function in cystathionine β-synthase (CBS) cause classic homocystinuria (HCU), which is managed by a methionine-restricted diet. Synthetic biotics are gastrointestinal tract-targeted live biotherapeutics that can be engineered to replicate the benefits of dietary restriction. In this study, we assess whether SYNB1353, an E. coli Nissle 1917 derivative, impacts circulating methionine and homocysteine levels in animals and healthy volunteers. In both mice and nonhuman primates (NHPs), SYNB1353 blunts the appearance of plasma methionine and plasma homocysteine in response to an oral methionine load. A phase 1 clinical study conducted in healthy volunteers subjected to an oral methionine challenge demonstrates that SYNB1353 is well tolerated and blunts plasma methionine by 26%. Overall, SYNB1353 represents a promising approach for methionine reduction with potential utility for the treatment of HCU.

Systemic intracellular analysis for balancing complex biosynthesis in a transcriptionally deregulated Escherichia coli l-Methionine producer

l-Methionine (l-Met) has gained remarkable interest due to its multifaceted and versatile applications in the fields of nutrition, pharmaceuticals and clinical practice. In this study, the fluxes of the challenging l-Met biosynthesis in the producer strain Escherichia coli (E. coli) DM2853 were fine-tuned to enable improved l-Met production. The potential bottlenecks identified in sulfur assimilation and l-Met synthesis downstream of O-succinyl-l-homoserine (OSHS) were addressed by overexpressing glutaredoxin 1 (grxA), thiosulfate sulfurtransferase (pspE) and O-succinylhomoserine lyase (metB). Although deemed as a straightforward target for improving glucose-to-Met conversion, the yields remained at approximately 12%-13% (g/g). Instead, intracellular l-Met pools increased by up to four-fold with accelerated kinetics. Overexpression of the Met exporter ygaZH may serve as a proper valve for releasing the rising internal Met pressure. Interestingly, the export kinetics revealed maximum saturated export rates already at low growth rates. This scenario is particularly advantageous for large-scale fermentation when product formation is ideally uncoupled from biomass formation to achieve maximum performance within the technical limits of large-scale bioreactors.

Progress advances in the production of bio-sourced methionine and its hydroxyl analogues

The essential sulphur-containing amino acid, methionine, is becoming a mass-commodity product with an annual production that exceeded 1,500,000 tons in 2018. This amino acid is today almost exclusively produced by chemical process from fossil resources. The environmental problems caused by this industrial process, and the expected scarcity of oil resources in the coming years, have recently accelerated the development of bioprocesses for producing methionine from renewable carbon feedstock. After a brief description of the chemical process and the techno-economic context that still justify the production of methionine by petrochemical processes, this review will present the current state of the art of biobased alternatives aiming at a sustainable production of this amino acid and its hydroxyl analogues from renewable carbon feedstock. In particular, this review will focus on three bio-based processes, namely a purely fermentative process based on the metabolic engineering of the natural methionine pathway, a mixed process combining the production of the O-acetyl/O-succinyl homoserine intermediate of this pathway by fermentation followed by an enzyme-based conversion of this intermediate into L-methionine and lately, a hybrid process in which the non-natural chemical synthon, 2,4-dihydroxybutyric acid, obtained by fermentation of sugars is converted by chemo-catalysis into hydroxyl methionine analogues. The industrial potential of these three bioprocesses, as well as the major technical and economic obstacles that remain to be overcome to reach industrial maturity are discussed. This review concludes by bringing up the assets of these bioprocesses to meet the challenge of the "green transition", with the accomplishment of the objective "zero carbon" by 2050 and how they can be part of a model of Bioeconomy enhancing local resources.

Microbial production of L-methionine and its precursors using systems metabolic engineering

L-methionine is an essential amino acid with versatile applications in food, feed, cosmetics and pharmaceuticals. At present, the production of L-methionine mainly relies on chemical synthesis, which conflicts with the concern over serious environmental problems and sustainable development goals. In recent years, microbial production of natural products has been amply rewarded with the emergence and rapid development of system metabolic engineering. However, efficient L-methionine production by microbial fermentation remains a great challenge due to its complicated biosynthetic pathway and strict regulatory mechanism. Additionally, the engineered production of L-methionine precursors, L-homoserine, O-succinyl-L-homoserine (OSH) and O-acetyl-L-homoserine (OAH), has also received widespread attention because they can be catalyzed to L-methionine via a high-efficiently enzymatic reaction in vitro, which is also a promising alternative to chemical route. This review provides a comprehensive overview on the recent advances in the microbial production of L-methionine and its precursors, highlighting the challenges and potential solutions for developing L-methionine microbial cell factories from the perspective of systems metabolic engineering, aiming to offer guidance for future engineering.

Conversion of methionine biosynthesis in Escherichia coli from trans- to direct-sulfurylation enhances extracellular methionine levels

Methionine is an essential amino acid in mammals and a precursor for vital metabolites required for the survival of all organisms. Consequently, its inclusion is required in diverse applications, such as food, feed, and pharmaceuticals. Although amino acids and other metabolites are commonly produced through microbial fermentation, high-yield biosynthesis of L-methionine remains a significant challenge due to the strict cellular regulation of the biosynthesis pathway. As a result, methionine is produced primarily synthetically, resulting in a racemic mixture of D,L-methionine. This study explores methionine bio-production in E. coli by replacing its native trans-sulfurylation pathway with the more common direct-sulfurylation pathway used by other bacteria. To this end, we generated a methionine auxotroph E. coli strain (MG1655) by simultaneously deleting metA and metB genes and complementing them with metX and metY from different bacteria. Complementation of the genetically modified E. coli with metX/metY from Cyclobacterium marinum or Deinococcus geothermalis, together with the deletion of the global repressor metJ and overexpression of the transporter yjeH, resulted in a substantial increase of up to 126 and 160-fold methionine relative to the wild-type strain, respectively, and accumulation of up to 700 mg/L using minimal MOPS medium and 2 ml culture. Our findings provide a method to study methionine biosynthesis and a chassis for enhancing L-methionine production by fermentation.

Multivariate modular metabolic engineering for enhanced L-methionine biosynthesis in Escherichia coli

BACKGROUND

L-Methionine is the only bulk amino acid that has not been industrially produced by the fermentation method. Due to highly complex and strictly regulated biosynthesis, the development of microbial strains for high-level L-methionine production has remained challenging in recent years.

RESULTS

By strengthening the L-methionine terminal synthetic module via site-directed mutation of L-homoserine O-succinyltransferase (MetA) and overexpression of metA^fbr, metC, and yjeH, L-methionine production was increased to 1.93 g/L in shake flask fermentation. Deletion of the pykA and pykF genes further improved L-methionine production to 2.51 g/L in shake flask fermentation. Computer simulation and auxotrophic experiments verified that during the synthesis of L-methionine, equimolar amounts of L-isoleucine were accumulated via the elimination reaction of cystathionine γ-synthetase MetB due to the insufficient supply of L-cysteine. To increase the supply of L-cysteine, the L-cysteine synthetic module was strengthened by overexpression of cysE^fbr, serA^fbr, and cysDN, which further increased the production of L-methionine by 52.9% and significantly reduced the accumulation of the byproduct L-isoleucine by 29.1%. After optimizing the addition of ammonium thiosulfate, the final metabolically engineered strain MET17 produced 21.28 g/L L-methionine in 64 h with glucose as the carbon source in a 5 L fermenter, representing the highest L-methionine titer reported to date.

CONCLUSIONS

In this study, a high-efficiency strain for L-methionine production was derived from wild-type Escherichia coli W3110 by rational metabolic engineering strategies, providing an efficient platform for the industrial production of L-methionine.

Thorough research and modification of one-carbon units cycle for improving L-methionine production in Escherichia coli

Methionine is the only one of the essential amino acids that contain sulfur, widely used as a feed additive in agriculture. In this study, the availability of 5-methyl-tetrahydrofolate was confirmed as the main limitation in the complex multibranched biosynthetic pathway of L-methionine. The cycle of one-carbon units was thoroughly investigated and modified to supply 5-methyl-tetrahydrofolate for L-methionine production, such as enhancing the supply of precursor, expediting the conversion rate of the cycle, introducing exogenous serine hydroxymethyltransferase and increasing pool size of one-carbon units carrier. The final strain MYA/pAmFA-4 was able to produce 20.89 g/L L-methionine by fed-batch fermentation, which was the highest titer reported in the literatures. This study is instructive for other metabolites biosynthesized needing one-carbon units or having a complex multibranched biosynthetic pathway.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03625-9.

Local metabolic response of Escherichia coli to the module genetic perturbations in l-methionine biosynthetic pathway

l-Methionine biosynthesis is through multilevel regulated and multibranched biosynthetic pathway (MRMBP). Because of the complex regulatory mechanism and the imbalanced metabolic flux between branched pathways, microbial production of l-methionine has not been commercialized. In this study, local metabolic response in MRMBP of l-methionine was investigated and various crucial genes in branched pathways were determined. In l-serine pathway, the crucial gene was serABC. In O-succinyl homoserine (OSH) pathway, which was the C4 backbone of l-methionine, metB and metL controlled the metabolic flux jointly. In l-cysteine pathway, the crucial gene cysE^fbr could disturb the flux distribution of local network in l-methionine biosynthesis. However, no crucial gene for l-methionine production in 5-methyl tetrahydrofolate (CH₃-THF) pathway was found. The relation between these pathways was also researched. l-Serine pathway, as the upstream pathway of l-cysteine and CH₃-THF, played a crucial role in l-methionine biosynthesis. l-Cysteine pathway showed the strongest controlling force of the metabolic flux, and OSH pathway was second to l-cysteine pathway. In contrast, CH₃-THF pathway was the weakest, which was probably the mainly limited steps at present and had great potential in further research. In addition, constructed W3110 IJAHFEBC/pA∗HAmL was able to produce 2.62 g/L l-methionine in flask. This study is instructive for l-methionine biosynthesis and provides a new research method of biosynthesizing other metabolic products in MRMBPs.

The Escherichia coli Amino Acid Uptake Protein CycA: Regulation of Its Synthesis and Practical Application in l-Isoleucine Production

Amino acid transport systems perform important physiological functions; their role should certainly be considered in microbial production of amino acids. Typically, in the context of metabolic engineering, efforts are focused on the search for and application of specific amino acid efflux pumps. However, in addition, importers can also be used to improve the industrial process as a whole. In this study, the protein CycA, which is known for uptake of nonpolar amino acids, was characterized from the viewpoint of regulating its expression and range of substrates. We prepared a cycA-overexpressing strain and found that it exhibited high sensitivity to branched-chain amino acids and their structural analogues, with relatively increased consumption of these amino acids, suggesting that they are imported by CycA. The expression of cycA was found to be dependent on the extracellular concentrations of substrate amino acids. The role of some transcription factors in cycA expression, including of Lrp and Crp, was studied using a reporter gene construct. Evidence for the direct binding of Crp to the cycA regulatory region was obtained using a gel-retardation assay. The enhanced import of named amino acids due to cycA overexpression in the l-isoleucine-producing strain resulted in a significant reduction in the generation of undesirable impurities. This work demonstrates the importance of uptake systems with respect to their application in metabolic engineering.

Importance of transmembrane helix 4 of l-alanine exporter AlaE in oligomer formation and substrate export activity in Escherichia coli

AlaE is the smallest amino acid exporter identified in Escherichia coli. It exports l-alanine using the proton motive force and plays a pivotal role in maintaining intracellular l-alanine homeostasis by acting as a safety valve. However, our understanding of the molecular mechanisms of substrate export by AlaE is still limited because structural information is lacking. Due to its small size (149 amino acid residues), it has been speculated that AlaE functions by forming an oligomer. In this study, we performed chemical cross-linking and pull-down assays and showed that AlaE indeed generates homo-oligomers as a functional unit. Previous random mutagenesis experiments identified three loss-of-function AlaE point mutations in the predicted transmembrane helix 4 (TM4) region, two of which are present in the GxxxG motif. When alanine-scanning mutagenesis was applied to the TM4 region, the AlaE derivatives that had amino acid substitutions around the GxxxG motif showed low l-alanine export activities, indicating that the GxxxG motif in TM4 plays an important role in substrate export. However, these AlaE variants with low activity could still form oligomers. We therefore concluded that AlaE forms homo-oligomers and that the GxxxG motif in the TM4 region plays an essential role in AlaE activity but is not involved in AlaE oligomer formation.

Functional Characterization of Transporters for L-Aspartate in Bacillus licheniformis

Amino acid efflux and influx transport systems play vital roles in industrial microorganisms’ cell growth and metabolism. However, although biochemically characterized, most of them remain unknown at the molecular level in Bacillus licheniformis. In this study, three proteins, namely, YdgF, YvbW, and YveA, were predicted to be involved in the active transport of L-aspartate (L-Asp). This was verified by manipulating their encoding genes. When growing in the minimal medium with L-Asp as the only carbon and nitrogen source, the growth of strains lacking proteins YdgF, YvbW, and YveA was significantly inhibited compared with the wild-type strains, while supplementing the expression of the corresponding proteins in the single-gene knockout strains could alleviate the inhibition. Upon overexpression, the recombinant proteins mediated the accumulation of L-aspartate to varying degrees. Compared with the wild-type strains, the single knockout strains of the three protein genes exhibited reduced absorption of L-aspartate. In addition, this study focused on the effects of these three proteins on the absorption of β-alanine, L-glutamate, D-serine, D-alanine, and glycine.

Microbial methionine transporters and biotechnological applications

Methionine (Met) is an essential amino acid with commercial value in animal feed, human nutrition, and as a chemical precursor. Microbial production of Met has seen intensive investigation towards a more sustainable alternative to the chemical synthesis that currently meets the global Met demand. Indeed, efficient Met biosynthesis has been achieved in genetically modified bacteria that harbor engineered enzymes and streamlined metabolic pathways. Very recently, the export of Met as the final step during its fermentative production has been studied and optimized, primarily through identification and expression of microbial Met efflux transporters. In this mini-review, we summarize the current knowledge on four families of Met export and import transporters that have been harnessed for the production of Met and other valuable biomolecules. These families are discussed with respect to their function, gene regulation, and biotechnological applications. We cover methods for identification and characterization of Met transporters as the basis for the further engineering of these proteins and for exploration of other solute carrier families. The available arsenal of Met transporters from different species and protein families provides blueprints not only for fermentative production but also synthetic biology systems, such as molecular sensors and cell-cell communication systems. KEY POINTS: • Sustainable production of methionine (Met) using microbes is actively explored. • Met transporters of four families increase production yield and specificity. • Further applications include other biosynthetic pathways and synthetic biology.

Characterizing and ranking computed metabolic engineering strategies

MOTIVATION

The computer-aided design of metabolic intervention strategies has become a key component of an integrated metabolic engineering approach and a broad range of methods and algorithms has been developed for this task. Many of these algorithms enforce coupling of growth with product synthesis and may return thousands of possible intervention strategies from which the most suitable strategy must then be selected.

RESULTS

This work focuses on how to evaluate and rank, in a meaningful way, a given pool of computed metabolic engineering strategies for growth-coupled product synthesis. Apart from straightforward criteria, such as a preferably small number of necessary interventions, a reasonable growth rate and a high product yield, we present several new criteria useful to pick the most suitable intervention strategy. Among others, we investigate the robustness of the intervention strategies by searching for metabolites that may disrupt growth coupling when accumulated or secreted and by checking whether the interventions interrupt pathways at their origin (preferable) or at downstream steps. We also assess thermodynamic properties of the pathway(s) favored by the intervention strategy. Furthermore, strategies that have a significant overlap with alternative solutions are ranked higher because they provide flexibility in implementation. We also introduce the notion of equivalence classes for grouping intervention strategies with identical solution spaces. Our ranking procedure involves in total ten criteria and we demonstrate its applicability by assessing knockout-based intervention strategies computed in a genome-scale model of E.coli for the growth-coupled synthesis of l-methionine and of the heterologous product 1,4-butanediol.

AVAILABILITY AND IMPLEMENTATION

The MATLAB scripts that were used to characterize and rank the example intervention strategies are available at http://www2.mpi-magdeburg.mpg.de/projects/cna/etcdownloads.html.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

High-yield production of L-serine through a novel identified exporter combined with synthetic pathway in Corynebacterium glutamicum

Background

l-Serine has wide and increasing applications in industries with fast-growing market demand. Although strategies for achieving and improving l-serine production in Corynebacterium glutamicum (C. glutamicum) have focused on inhibiting its degradation and enhancing its biosynthetic pathway, l-serine yield has remained relatively low. Exporters play an essential role in the fermentative production of amino acids. To achieve higher l-serine yield, l-serine export from the cell should be improved. In C. glutamicum, ThrE, which can export l-threonine and l-serine, is the only identified l-serine exporter so far.

Results

In this study, a novel l-serine exporter NCgl0580 was identified and characterized in C. glutamicum ΔSSAAI (SSAAI), and named as SerE (encoded by serE). Deletion of serE in SSAAI led to a 56.5% decrease in l-serine titer, whereas overexpression of serE compensated for the lack of serE with respect to l-serine titer. A fusion protein with SerE and enhanced green fluorescent protein (EGFP) was constructed to confirm that SerE localized at the plasma membrane. The function of SerE was studied by peptide feeding approaches, and the results showed that SerE is a novel exporter for l-serine and l-threonine in C. glutamicum. Subsequently, the interaction of a known l-serine exporter ThrE and SerE was studied, and the results suggested that SerE is more important than ThrE in l-serine export in SSAAI. In addition, probe plasmid and electrophoretic mobility shift assays (EMSA) revealed NCgl0581 as the transcriptional regulator of SerE. Comparative transcriptomics between SSAAI and the NCgl0581 deletion strain showed that NCgl0581 is a positive regulator of NCgl0580. Finally, by overexpressing the novel exporter SerE, combined with l-serine synthetic pathway key enzyme serAΔ197, serC, and serB, the resulting strain presented an l-serine titer of 43.9 g/L with a yield of 0.44 g/g sucrose, which is the highest l-serine titer and yield reported so far in C. glutamicum.

Conclusions

This study provides a novel target for l-serine and l-threonine export engineering as well as a new global transcriptional regulator NCgl0581 in C. glutamicum.

Regulation of homoserine O-succinyltransferase for efficient production of L-methionine in engineered Escherichia coli

l-Methionine biosynthesis in Eschericha coli consists of multiple unit modules with various enzymes involved and the imbalance between different modules always restricted its productivity. In this study, the key enzymes participating in the pathway were investigated for their effect on l-methionine production and the pivotal enzyme homoserine O-succinyltransferase (MetA) was designed to be regulated. The surface amino acid residues of MetA were effectively modified through site-saturation mutagenesis and single mutants L63F, A28V, P298L and double mutant L63F/A28V were obtained with improved l-methionine productivity. The structure analysis revealed that the involved residues were on the surface loop regions, which was proposed to be conducive to the refolding of MetA and thus reduce the inhibition effect caused by l-methionine. After expression of the selected single mutant L63F in engineered E. coli ΔIJA-HFEBC strain with l-methionine efflux pump and mutated 3-phosphoglycerate dehydrogenase, the l-methionine production was significantly improved, with a final yield of 3528 mg/L. The results demonstrated the efficiency of MetA regulation for enhanced production of l-methionine and meanwhile provided important guidance for further engineering of MetA with increased l-methionine productivity.

Cystine import is a valuable but risky process whose hazards Escherichia coli minimizes by inducing a cysteine exporter

The structure of free cysteine makes it vulnerable to oxidation by molecular oxygen; consequently, organisms that live in oxic habitats have acquired the ability to import cystine as a sulfur source. We show that cystine imported into Escherichia coli can transfer disulfide bonds to cytoplasmic proteins. To minimize this problem, the imported cystine is rapidly reduced. However, this conversion of cystine to cysteine precludes product inhibition of the importer, so cystine import continues into cells that are already sated with cysteine. The burgeoning cysteine pool is itself hazardous, as cysteine promotes the formation of reactive oxygen species, triggers sulfide production and competitively inhibits a key enzyme in the isoleucine biosynthetic pathway. The Lrp transcription factor senses the excess cysteine and induces AlaE, an export protein that pumps cysteine back out of the cell until transcriptional controls succeed in lowering the amount of the importer. While it lasts, the overall phenomenon roughly doubles the NADPH demand of the cell. It comprises another example of the incompatibility of the reduced cytoplasms of microbes with the oxic world in which they dwell. It also reveals one natural source of cytoplasmic disulfide stress and sheds light on a role for broad-spectrum amino acid exporters.

L-Alanine Exporter, AlaE, of Escherichia coli Functions as a Safety Valve to Enhance Survival under Feast Conditions

The intracellular level of amino acids is determined by the balance between their anabolic and catabolic pathways. L-alanine is anabolized by three L-alanine synthesizing enzymes and catabolized by two racemases and D-amino acid dehydrogenase (DadA). In addition, its level is regulated by L-alanine movement across the inner membrane. We identified the novel gene alaE, encoding an L-alanine exporter. To elucidate the physiological function of L-Alanine exporter, AlaE, we determined the susceptibility of alaE-, dadA-, and alaE/dadA-deficient mutants, derived from the wild-type strain MG1655, to L-alanyl-L-alanine (Ala-Ala), which shows toxicity to the L-alanine-nonmetabolizing variant lacking alaE. The dadA-deficient mutant has a similar minimum inhibitory concentration (MIC) (>1.25 mg/mL) to that observed in MG1655. However, alaE- and alaE/dadA-deficient mutants had MICs of 0.04 and 0.0025 mg/mL, respectively. The results suggested that the efficacy of AlaE to relieve stress caused by toxic intracellular accumulation of L-alanine was higher than that of DadA. Consistent with this, the intracellular level of alanine in the alaE-mutant was much higher than that in MG1655 and the dadA-mutant. We, therefore, conclude that AlaE functions as a ‘safety-valve’ to prevent the toxic level accumulation of intracellular L-alanine under a peptide-rich environment, such as within the animal intestine.

Metabolic engineering of E. coli for the production of O-succinyl-l-homoserine with high yield

O-succinyl-l-homoserine (OSH) is a promising platform chemical for the production of C4 chemicals with huge market potential which can be produced by fermentation from glucose. To construct a strain capable of producing OSH with high yield, the metJ (encodes transcriptional repressor) and metI (encodes a subunit of dl-methionine transporter) were deleted in Escherichia coli W3110 to obtain a strain E. coli ∆JI. Then, overexpression of metL (encodes bifunctional aspartate kinase/homoserine dehydrogenase II) and inactivation of metB (encodes cystathionine γ-synthase) were implemented in one step, and the OSH titer of the resulting strain E. coli ∆JIB^* TrcmetL was dramatically increased to 7.30 g/L. The feedback regulation was further relieved by progressively overexpressing metA^fbr (encodes homoserine O-succinyltransferase), yjeH (encodes l-methionine exporter), and thrA^fbr (encodes bifunctional aspartate kinase/homoserine dehydrogenase I) to increase the metabolic flux from aspartate to OSH. The 100% rationally designed strain E. coli ∆JIB^* TrcmetL/pTrc-metA^fbr -Trc-thrA^fbr -yjeH produced 9.31 g/L OSH from 20 g/L glucose (0.466 g/g glucose) in batch fermentation, which represents the highest OSH yield from glucose reported to date. The culture profiles of the newly constructed strains were recorded to investigate their productive properties. The effects of l-methionine addition on the fermentation process of the optimal strain were also studied. Our results demonstrate that tuning the expression level of metL, inactivation of metB, and attenuation of feedback resistance of the crucial enzymes in the biosynthetic pathway are the key factors that impact the OSH production in E. coli.

Robust identification of metabolic control for microbial l-methionine production following an easy-to-use puristic approach

The identification of promising metabolic engineering targets is a key issue in metabolic control analysis (MCA). Conventional approaches make intensive use of model-based studies, such as exploiting post-pulse metabolic dynamics after proper perturbation of the microbial system. Here, we present an easy-to-use, purely data-driven approach, defining pool efflux capacities (PEC) for identifying reactions that exert the highest flux control in linear pathways. Comparisons with linlog-based MCA and data-driven substrate elasticities (DDSE) showed that similar key control steps were identified using PEC. Using the example of l-methionine production with recombinant Escherichia coli, PEC consistently and robustly identified main flux controls using perturbation data after a non-labeled ¹²C-l-serine stimulus. Furthermore, the application of full-labeled ¹³C-l-serine stimuli yielded additional insights into stimulus propagation to l-methionine. PEC analysis performed on the ¹³C data set revealed the same targets as the ¹²C data set. Notably, the typical drawback of metabolome analysis, namely, the omnipresent leakage of metabolites, was excluded using the ¹³C PEC approach.

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12

EcoCyc (EcoCyc.org) is a freely accessible, comprehensive database that collects and summarizes experimental data for Escherichia coli K-12, the best-studied bacterial model organism. New experimental discoveries about gene products, their function and regulation, new metabolic pathways, enzymes and cofactors are regularly added to EcoCyc. New SmartTable tools allow users to browse collections of related EcoCyc content. SmartTables can also serve as repositories for user- or curator-generated lists. EcoCyc now supports running and modifying E. coli metabolic models directly on the EcoCyc website.

Metabolic engineering of Escherichia coli W3110 for the production of L-methionine

In this study, we constructed an L-methionine-producing recombinant strain from wild-type Escherichia coli W3110 by metabolic engineering. To enhance the carbon flux to methionine and derepression met regulon, thrBC, lysA, and metJ were deleted in turn. Methionine biosynthesis obstacles were overcome by overexpression of metA ^Fbr (Fbr, Feedback resistance), metB, and malY under control of promoter pN25. Recombinant strain growth and methionine production were further improved by attenuation of metK gene expression through replacing native promoter by metK84p. Blocking the threonine pathway by deletion of thrBC or thrC was compared. Deletion of thrC showed faster growth rate and higher methionine production. Finally, metE, metF, and metH were overexpressed to enhance methylation efficiency. Compared with the original strain E. coli W3110, the finally obtained Me05 (pETMA^Fbr-B-Y/pKKmetH) improved methionine production from 0 to 0.65 and 5.62 g/L in a flask and a 15-L fermenter, respectively.

Sulfate reduction in microorganisms-recent advances and biotechnological applications

Sulfur, the least common of the five macroelements, plays an important role in biochemistry due to its ability to be easily reduced or oxidized, leading to a great amount of research concerning sulfur bioconversion. Interestingly, new studies concerning microbial sulfate reduction pathways in the last half decade have become increasingly sparse, indicating that most of the pathways involved have been discovered and studied. Despite this, systems biology approaches to model these pathways are often missing or not used. As the products of microbial sulfate reduction play important roles in the environment, biotechnology, and industry, modeling sulfur bioconversion remains an untapped research space for future work.