Lactate dehydrogenase has no control on lactate production but has a strong negative control on formate production in Lactococcus lactis

Efficient Metabolic Pathway Modification in Various Strains of Lactic Acid Bacteria using CRISPR/Cas9 System for elevated synthesis of Antimicrobial Compounds

Lactic acid bacteria (LAB) are known to exhibit various beneficial roles in fermentation, serving as probiotics, and producing a plethora of valuable compounds including compounds with antimicrobial activity including bacteriocin-like inhibitory substance (BLIS) that can be used as biopreservative to improve food safety and quality. However, the yield of BLIS is often limited, which poses a challenge to be commercially competitive with the current preservation practice. Therefore, the present work aimed to establish an optimised two-plasmid CRISPR/Cas9 system to redirect the carbon flux away from lactate towards compounds with antimicrobial activity by disrupting lactate dehydrogenase gene (ldh) on various strains of LAB. The lactic acid-deficient (ldhΔ) strains caused a metabolic shift resulting in increased inhibitory activity against selected foodborne pathogens up to 78% than the wild-type (WT) strain. The most significant effect was depicted by Enterococcus faecalis-ldh∆ which displayed prominent bactericidal effects against all foodborne pathogens as compared to the WT that showed no antimicrobial activity. The present work provided a framework model for economically important LAB and other beneficial bacteria to synthesise and increase the yield of valuable food and industrial compounds. The present work reported for the first time that the metabolism of selected LAB can be manipulated by modifying ldh to attain metabolites with higher antimicrobial activity.

Use of the mCherry fluorescent protein to optimize the expression of class I lanthipeptides in Escherichia coli

BACKGROUND

Lanthipeptides are a rapidly expanding family of ribosomally synthesized and post-translationally modified natural compounds with diverse biological functions. Lanthipeptide structural and biosynthetic genes can readily be identified in genomic datasets, which provides a substantial repository for unique peptides with a wide range of potentially novel bioactivities. To realize this potential efficiently optimized heterologous production systems are required. However, only a few class I lanthipeptides have been successfully expressed using Escherichia coli as heterologous producer. This may be attributed to difficulties experienced in the co-expression of structural genes and multiple processing genes as well as complex optimization experiments.

RESULTS

Here, an optimized modular plasmid system is presented for the complete biosynthesis for each of the class I lanthipeptides nisin and clausin, in E. coli. Genes encoding precursor lanthipeptides were fused to the gene encoding the mCherry red fluorescent protein and co-expressed along with the required synthetases from the respective operons. Antimicrobially active nisin and clausin were proteolytically liberated from the expressed mCherry fusions. The mCherry-NisA expression system combined with in vivo fluorescence monitoring was used to elucidate the effect of culture media composition, promoter arrangement, and culture conditions including choice of growth media and inducer agents on the heterologous expression of the class I lanthipeptides. To evaluate the promiscuity of the clausin biosynthetic enzymes, the optimized clausin expression system was used for the heterologous expression of epidermin.

CONCLUSION

We succeeded in developing novel mCherry-fusion based plug and play heterologous expression systems to produce two different subgroups of class I lanthipeptides. Fully modified Pre-NisA, Pre-ClausA and Pre-EpiA fused to the mCherry fluorescence gene was purified from the Gram-negative host E. coli BL21 (DE3). Our study demonstrates the potential of using in vivo fluorescence as a platform to evaluate the expression of mCherry-fused lanthipeptides in E. coli. This allowed a substantial reduction in optimization time, since expression could be monitored in real-time, without the need for extensive and laborious purification steps or the use of in vitro activity assays. The optimized heterologous expression systems developed in this study may be employed in future studies for the scalable expression of novel NisA derivatives, or novel genome mined derivatives of ClausA and other class I lanthipeptides in E. coli.

Holin-assisted bacterial recombinant protein export

A simple generic method for enhancing extracellular protein yields in engineered bacteria is still lacking. Here, we demonstrated that phage-encoded holin can be used to export proteins to the extracellular medium in both Gram-negative Escherichia coli and -positive Lactococcus lactis. When a putative holin gene LLNZ_RS10380 annotated in the genome of L. lactis NZ9000 (hol380) was recombinantly expressed in E. coli BL21(DE3), the Hol380 oligomerized up to hexamer in the cytoplasmic membrane, yielding membrane pore to allow the passage of cytosolic β-galatosidase (116 kDa), whose extracellular production reached 54.59 U/μL, accounting for 76.37% of the total activity. However, the overexpressed Hol380 could not release cytosolic proteins across the membrane in L. lactis NZ9000, but increased the secretory production of staphylococcal nuclease to 2.55-fold and fimbrial adhesin FaeG to 2.40-fold compared with those guided by signal peptide Usp45 alone. By using a combination of proteomics and transcriptional level analysis, we found that overexpression of the Hol380 raised the accumulation of Ffh and YidC involved in the signal recognition particle pathway in L. lactis, suggesting an alternative road participating in protein secretion. This study proposed a new approach by expressing holin in bacterial cell factories to export target proteins of economic or medical interest. This article is protected by copyright. All rights reserved.

Probiotic Effects and Metabolic Products of Enterococcus faecalis LD33 with Respiration Capacity

Respiration metabolism could improve the long-term survival of lactic acid bacteria (LAB); however, its effect on potential probiotic traits of LAB was not reported. The difference made by Enterococcus faecalis LD33 that was cultured under respiration-permissive and fermentation conditions, such as the biomass, metabolites, antimicrobial activity, tolerance to acid and bile salt, adhesion capabilities, and the ability to inhibit the proliferation of cancer cells were studied. Under a respiration-permissive condition, the final biomass of the culture was about twice as compared to that of fermentation condition. When the metabolites were measured, glucose was exhausted within 8 h. Two-folds of acetic acid, triple of both acetoin and diacetyl, and less than half of lactic acid, were accumulated under the respiratory-permissive condition. No discrimination of growth inhibition on Salmonella enterica serovar Typhimurium ATCC 14028 and Shigella sonnei ATCC 25931 was observed when Enterococcus faecalis LD33 was cultured under both conditions; however, under respiration-permissive condition, the strain presented significant antimicrobial activities to Listeria monocytogenes ATCC19111 and Staphylococcus aureus ATCC6538P. Enterococcus faecalis LD33 displayed relatively strong bile salt tolerance and adherence capability but weaker acid tolerance when undergoing respiration metabolism. There was no significant difference in the anti-cancer effect of the viable bacterial cells on both growth modes; however, the supernatant showed a higher inhibition effect on HT-29 cells than the live bacteria, and there was no significant difference between the supernatant and the 5-Fluorouracil (7 μg/mL). Consequently, the Enterococcus faecalis LD33 undergoing respiration metabolism could bring higher biomass, more flavor metabolites, and better antimicrobial and anti-cancer activities. This study extends our knowledge of respiratory metabolism in LAB and its impact on probiotic traits. E. faecalis LD33 qualifies as a suitable strain against foodborne pathogens, cancer therapy, and eventual application in the food and pharmaceutical industries.

Thiosulfate as the electron acceptor in Sulfur Bioconversion-Associated Process (SBAP) for sewage treatment

The sulfur bioconversion-associated processes (SBAP) for sewage treatment have been extensively reported so far. In this study, biological thiosulfate reduction (BTR)-driven biotechnology for high rate sulfidogenesis and organic removal was explored to further close the gap of our knowledge on the sulfur cycle-based sewage treatment bioprocess. With thiosulfate as the electron acceptor, the sulfidogenic rate in the UASB rector is 105.6 mg S/L/h with the sludge yield of only 0.044 g MLVSS/g COD_substrate. Thus providing sufficient electron donors or chemical sources (i.e. HS^-) for the downstream autotrophic denitrification or for the cost-effective heavy metal precipitation. Thiosulfate disproportionation was not observed in BTR reactor. High-throughput pyrosequencing analysis reveals that Desulfobulbus and Desulfomicrobium are the predominant thiosulfate-reducing genera and the thiosulfate disproportionation-bacteria were at much lower genus level. The specific thiosulfate-reducer i.e. Dethiosulfatibacter which could utilize thiosulfate but not sulfate as the electron acceptor was also identified. Batch testing results indicate that the sulfidogenic activity on thiosulfate was 1.5 times that on sulfate. The optimal pH for BTR activity was between 7.0 and 8.0, a typical pH range of the municipal sewage. Thiosulfate can be efficiently recovered in the sulfide-driven denitritation reactor enriched with abundant sulfide-oxidizing genera (mainly including Thiobacillus and Sulfurimonas). Finally, a conceptual model of the sulfur cycle based on the biotransformation between thiosulfate and sulfide was established, offering new insights into the sustainable SBAP with sludge minimization.

Roles of sulfite and internal recirculation on organic compound removal and the microbial community structure of a sulfur cycle-driven biological wastewater treatment process

A sulfur cycle-driven bioprocess was developed for co-treatment wet flue gas desulfurization wastes with municipal sewage, as a result of sludge minimization. In this process, organics removal (one of the main objectives in sewage treatment) is closely associated with biological sulfate/sulfite reduction (BSR). In the previous studies, both the pros and corns of sulfite (SO₃^2-) in microbial activities were demonstrated. In this study, we are motivated to unveil the detailed role of SO₃^2- in organic compound removal in the sulfur conversion-associated process. In addition, the effect of internal recirculation (IR) of UASB reactor was also explored. The results demonstrated that sulfite does inhibit the organic removal rate via depressing the acetate oxidation to inorganic carbon. And the inhibition is reversible when influent sulfite concentration decreased from 400 to 132 mg S/L, corresponding to the relative sulfate/sulfite-reducing genera increased from 18.66 to 38.62%. And the fermenting-related bacteria significantly decreased when an internal recirculation was employed for the UASB reactor. The results of this study could shed light on the understanding of the roles of sulfite and IR in organic compound removal performance and microbial community structures in BSR, which could be in turn beneficial to optimize the organic removal capacity of the sulfur bionconversion-concerning sewage treatment technology.

Genetics of Lactococci

Lactococcus lactis is the best characterized species among the lactococci, and among the most consumed food-fermenting bacteria worldwide. Thanks to their importance in industrialized food production, lactococci are among the lead bacteria understood for fundamental metabolic pathways that dictate growth and survival properties. Interestingly, lactococci belong to the Streptococcaceae family, which includes food, commensal and virulent species. As basic metabolic pathways (e.g., respiration, metal homeostasis, nucleotide metabolism) are now understood to underlie virulence, processes elucidated in lactococci could be important for understanding pathogen fitness and synergy between bacteria. This chapter highlights major findings in lactococci and related bacteria, and covers five themes: distinguishing features of lactococci, metabolic capacities including the less known respiration metabolism in Streptococcaceae, factors and pathways modulating stress response and fitness, interbacterial dialogue via metabolites, and novel applications in health and biotechnology.

Systems Biology - A Guide for Understanding and Developing Improved Strains of Lactic Acid Bacteria

Lactic Acid Bacteria (LAB) are extensively employed in the production of various fermented foods, due to their safe status, ability to affect texture and flavor and finally due to the beneficial effect they have on shelf-life. More recently, LAB have also gained interest as production hosts for various useful compounds, particularly compounds with sensitive applications, such as food ingredients and therapeutics. As for all industrial microorganisms, it is important to have a good understanding of the physiology and metabolism of LAB in order to fully exploit their potential, and for this purpose, many systems biology approaches are available. Systems metabolic engineering, an approach that combines optimization of metabolic enzymes/pathways at the systems level, synthetic biology as well as in silico model simulation, has been used to build microbial cell factories for production of biofuels, food ingredients and biochemicals. When developing LAB for use in foods, genetic engineering is in general not an accepted approach. An alternative is to screen mutant libraries for candidates with desirable traits using high-throughput screening technologies or to use adaptive laboratory evolution to select for mutants with special properties. In both cases, by using omics data and data-driven technologies to scrutinize these, it is possible to find the underlying cause for the desired attributes of such mutants. This review aims to describe how systems biology tools can be used for obtaining both engineered as well as non-engineered LAB with novel and desired properties.

Maintaining maximal metabolic flux by gene expression control

One of the marvels of biology is the phenotypic plasticity of microorganisms. It allows them to maintain high growth rates across conditions. Studies suggest that cells can express metabolic enzymes at tuned concentrations through adjustment of gene expression. The associated transcription factors are often regulated by intracellular metabolites. Here we study metabolite-mediated regulation of metabolic-gene expression that maximises metabolic fluxes across conditions. We developed an adaptive control theory, qORAC (for ‘Specific Flux (q) Optimization by Robust Adaptive Control’), and illustrate it with several examples of metabolic pathways. The key feature of the theory is that it does not require knowledge of the regulatory network, only of the metabolic part. We derive that maximal metabolic flux can be maintained in the face of varying N environmental parameters only if the number of transcription-factor binding metabolites is at least equal to N. The controlling circuits appear to require simple biochemical kinetics. We conclude that microorganisms likely can achieve maximal rates in metabolic pathways, in the face of environmental changes.

To attain high growth rates, microorganisms need to sustain high activities of metabolic reactions. Since the catalysing enzymes are in finite supply, cells need to carefully tune their concentrations. When conditions change, cells need to adjust those concentrations. How cells maintain high metabolism rates across conditions by way of gene regulatory mechanisms and whether they can maximise metabolic activity is far from clear. Here we present a general theory that solves this metabolic control problem, which we have called qORAC for specific flux (q) Optimisation by Robust Adaptive Control. It considers that external changes are sensed by internal “sensor” metabolites that bind to transcription factors in order to regulate enzyme-synthesis rates. We show that such a combined system of metabolism and its gene network can self-optimise its metabolic activity across conditions. We present the mathematical conditions for the required adaptive control for robust system-steering to optimal states across conditions. We provide explicit examples of such self-optimising coupled metabolism and gene network systems. We prove that a cell can be robust to changes in K parameters, e.g. external conditions, if at least K internal metabolite concentrations act transcription-factor binding sensors. We find that the optimal relation of the enzyme synthesis rates of self-optimising systems and the concentration of the sensor metabolites can generally be implemented by basic biochemistry. Our results indicate how cells are able to maintain maximal reaction rates, even in changing conditions.

Getting value from the waste: recombinant production of a sweet protein by Lactococcus lactis grown on cheese whey

Background

Recent biotechnological advancements have allowed for the adoption of Lactococcus lactis, a typical component of starter cultures used in food industry, as the host for the production of food-grade recombinant targets. Among several advantages, L. lactis has the important feature of growing on lactose, the main carbohydrate in milk and a majoritarian component of dairy wastes, such as cheese whey.

Results

We have used recombinant L. lactis NZ9000 carrying the nisin inducible pNZ8148 vector to produce MNEI, a small sweet protein derived from monellin, with potential for food industry applications as a high intensity sweetener. We have been able to sustain this production using a medium based on the cheese whey from the production of ricotta cheese, with minimal pre-treatment of the waste. As a proof of concept, we have also tested these conditions for the production of MMP-9, a protein that had been previously successfully obtained from L. lactis cultures in standard growth conditions.

Conclusions

Other than presenting a new system for the recombinant production of MNEI, more compliant with its potential applications in food industry, our results introduce a strategy to valorize dairy effluents through the synthesis of high added value recombinant proteins. Interestingly, the possibility of using this whey-derived medium relied greatly on the choice of the appropriate codon usage for the target gene. In fact, when a gene optimized for L. lactis was used, the production of MNEI proceeded with good yields. On the other hand, when an E. coli optimized gene was employed, protein synthesis was greatly reduced, to the point of being completely abated in the cheese whey-based medium. The production of MMP-9 was comparable to what observed in the reference conditions.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-0974-z) contains supplementary material, which is available to authorized users.

Next generation microbiological risk assessment meta-omics: The next need for integration

The development of a multi-omics approach has provided a new approach to the investigation of microbial communities allowing an integration of data, which can be used to better understand the behaviour of and interactions between community members. Metagenomics, metatranscriptomics, metaproteomics and metabolomics have the potential of producing a large amount of data in a very short time, however an important challenge is how to exploit and interpret these data to assist risk managers in food safety and quality decisions. This can be achieved by integrating multi-omics data in microbiological risk assessment. In this paper we identify limitations and challenges of the multi-omics approach, underlining promising potentials, but also identifying gaps, which should be addressed for its full exploitation. A view on how this new way of investigation will impact the traditional microbiology schemes in the food industry is also presented.

A review on Lactococcus lactis: from food to factory

Lactococcus lactis has progressed a long way since its discovery and initial use in dairy product fermentation, to its present biotechnological applications in genetic engineering for the production of various recombinant proteins and metabolites that transcends the heterologous species barrier. Key desirable features of this gram-positive lactic acid non-colonizing gut bacteria include its generally recognized as safe (GRAS) status, probiotic properties, the absence of inclusion bodies and endotoxins, surface display and extracellular secretion technology, and a diverse selection of cloning and inducible expression vectors. This have made L. lactis a desirable and promising host on par with other well established model bacterial or yeast systems such as Escherichia coli, Saccharomyces [corrected] cerevisiae and Bacillus subtilis. In this article, we review recent technological advancements, challenges, future prospects and current diversified examples on the use of L. lactis as a microbial cell factory. Additionally, we will also highlight latest medical-based applications involving whole-cell L. lactis as a live delivery vector for the administration of therapeutics against both communicable and non-communicable diseases.

Characterization of a New Cell Envelope Proteinase PrtP from Lactobacillus rhamnosus CGMCC11055

Cell envelope proteinases (CEPs) play essential roles in lactic acid bacteria growth in milk and health-promoting properties of fermented dairy products. The genome of Lactobacillus rhamnosus CGMCC11055 possesses two putative CEP genes prtP and prtR2, and the PrtP displays the distinctive domain organization from PrtR2 reported. The PrtP was purified and biochemically characterized. The results showed that the optimal activity occurred at 44 °C, pH 6.5. p-Amidinophenylmethylsulfonyl fluoride obviously inhibited enzymatic activity, suggesting PrtP was a member of serine proteinases. Under the optimal conditions, β-casein was a favorite substrate over αS1- and κ-casein, and 35 oligopeptides were identified in the β-casein hydrolysate, including the phosphoserine peptide and bioactive isoleucine-proline-proline. By analysis of the amino acid sequences of those oligopeptides, proline was the preferred residue at the breakdown site. Therefore, we speculated that PrtP was a new type of CEPs from Lb. rhamnosus.

An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2,3-butanediol production

Biomedical research and biotechnological production are greatly benefiting from the results provided by the development of dynamic models of microbial metabolism. Although several kinetic models of Lactococcus lactis (a Lactic Acid Bacterium (LAB) commonly used in the dairy industry) have been developed so far, most of them are simplified and focus only on specific metabolic pathways. Therefore, the application of mathematical models in the design of an engineering strategy for the production of industrially important products by L. lactis has been very limited. In this work, we extend the existing kinetic model of L. lactis central metabolism to include industrially relevant production pathways such as mannitol and 2,3-butanediol. In this way, we expect to study the dynamics of metabolite production and make predictive simulations in L. lactis. We used a system of ordinary differential equations (ODEs) with approximate Michaelis-Menten-like kinetics for each reaction, where the parameters were estimated from multivariate time-series metabolite concentrations obtained by our team through in vivo Nuclear Magnetic Resonance (NMR). The results show that the model captures observed transient dynamics when validated under a wide range of experimental conditions. Furthermore, we analyzed the model using global perturbations, which corroborate experimental evidence about metabolic responses upon enzymatic changes. These include that mannitol production is very sensitive to lactate dehydrogenase (LDH) in the wild type (W.T.) strain, and to mannitol phosphoenolpyruvate: a phosphotransferase system (PTS(Mtl)) in a LDH mutant strain. LDH reduction has also a positive control on 2,3-butanediol levels. Furthermore, it was found that overproduction of mannitol-1-phosphate dehydrogenase (MPD) in a LDH/PTS(Mtl) deficient strain can increase the mannitol levels. The results show that this model has prediction capability over new experimental conditions and offers promising possibilities to elucidate the effect of alterations in the main metabolism of L. lactis, with application in strain optimization.

A novel approach to realize SANI process in freshwater sewage treatment--Use of wet flue gas desulfurization waste streams as sulfur source

SANI (Sulfate reduction, Autotrophic denitrification and Nitrification Integrated) process has been approved to be a sludge-minimized sewage treatment process in warm and coastal cities with seawater supply. In order to apply this sulfur-based process in inland cold areas, wet flue gas desulfurization (FGD) can be simplified and integrated with SANI process, to provide sulfite as electron carrier for sulfur cycle in sewage treatment. In this study, a lab-scale system of the proposed novel process was developed and run for over 200 days while temperature varied between 30 and 5 °C, fed with synthetic FGD wastewaters and sewage. The sulfite-reducing upflow anaerobic sludge bed (SrUASB) reactor, as the major bioreactor of the system, removed 86.9% of organics while the whole system removed 94% of organics even when water temperature decreased to around 10 °C. The bactericidal effect of sulfite was not observed in the SrUASB reactor, while thiosulfate was found accumulated under psychrophilic conditions. The sludge yield of the SrUASB reactor was determined to be 0.095 kg VSS/kg COD, higher than of sulfate reduction process but still much lower than of conventional activated sludge processes. The dominant microbes in the SrUASB reactor were determined as Lactococcus spp. rather than sulfate-reducing bacteria, but sulfite reduction still contributed 85.5% to the organic carbon mineralization in this reactor. Ammonia and nitrate were effectively removed in the aerobic and anoxic filters, respectively. This study confirms the proposed process was promising to achieve sludge-minimized sewage treatment integrating with flue gas desulfurization in inland and cold areas.

Engineering strategies aimed at control of acidification rate of lactic acid bacteria

The ability of lactic acid bacteria to produce lactic acid from various sugars plays an important role in food fermentations. Lactic acid is derived from pyruvate, the end product of glycolysis and thus a fast lactic acid production rate requires a high glycolytic flux. In addition to lactic acid, alternative end products--ethanol, acetic acid and formic acid--are formed by many species. The central role of glycolysis in lactic acid bacteria has provoked numerous studies aiming at identifying potential bottleneck(s) since knowledge about flux control could be important not only for optimizing food fermentation processes, but also for novel applications of lactic acid bacteria, such as cell factories for the production of green fuels and chemicals. With respect to the control and regulation of the fermentation mode, some progress has been made, but the question of which component(s) control the main glycolytic flux remains unanswered.

Metabolic engineering of lactic acid bacteria for the production of industrially important compounds

Lactic acid bacteria (LAB) are receiving increased attention for use as cell factories for the production of metabolites with wide use by the food and pharmaceutical industries. The availability of efficient tools for genetic modification of LAB during the past decade permitted the application of metabolic engineering strategies at the levels of both the primary and the more complex secondary metabolism. The recent developments in the area with a focus on the production of industrially important metabolites will be discussed in this review.

Fine tuning of the lactate and diacetyl production through promoter engineering in Lactococcus lactis

Lactococcus lactis is a well-studied bacterium widely used in dairy fermentation and capable of producing metabolites with organoleptic and nutritional characteristics. For fine tuning of the distribution of glycolytic flux at the pyruvate branch from lactate to diacetyl and balancing the production of the two metabolites under aerobic conditions, a constitutive promoter library was constructed by randomizing the promoter sequence of the H₂O-forming NADH oxidase gene in L. lactis. The library consisted of 30 promoters covering a wide range of activities from 7,000 to 380,000 relative fluorescence units using a green fluorescent protein as reporter. Eleven typical promoters of the library were selected for the constitutive expression of the H₂O-forming NADH oxidase gene in L. lactis, and the NADH oxidase activity increased from 9.43 to 58.17-fold of the wild-type strain in small steps of activity change under aerobic conditions. Meanwhile, the lactate yield decreased from 21.15±0.08 mM to 9.94±0.07 mM, and the corresponding diacetyl production increased from 1.07±0.03 mM to 4.16±0.06 mM with the intracellular NADH/NAD⁺ ratios varying from 0.711±0.005 to 0.383±0.003. The results indicated that the reduced pyruvate to lactate flux was rerouted to the diacetyl with an almost linear flux variation via altered NADH/NAD⁺ ratios. Therefore, we provided a novel strategy to precisely control the pyruvate distribution for fine tuning of the lactate and diacetyl production through promoter engineering in L. lactis. Interestingly, the increased H₂O-forming NADH oxidase activity led to 76.95% lower H₂O₂ concentration in the recombinant strain than that of the wild-type strain after 24 h of aerated cultivation. The viable cells were significantly elevated by four orders of magnitude within 28 days of storage at 4°C, suggesting that the increased enzyme activity could eliminate H₂O₂ accumulation and prolong cell survival.

Tunable promoters in synthetic and systems biology

Synthetic and systems biologists need standardized, modular and orthogonal tools yielding predictable functions in vivo. In systems biology such tools are needed to quantitatively analyze the behavior of biological systems while the efficient engineering of artificial gene networks is central in synthetic biology. A number of tools exist to manipulate the steps in between gene sequence and functional protein in living cells, but out of these the most straight-forward approach is to alter the gene expression level by manipulating the promoter sequence. Some of the promoter tuning tools available for accomplishing such altered gene expression levels are discussed here along with examples of their use, and ideas for new tools are described. The road ahead looks very promising for synthetic and systems biologists as tools to achieve just about anything in terms of tuning and timing multiple gene expression levels using libraries of synthetic promoters now exist.

Genetic modification and bioprocess optimization for S-Adenosyl-L-methionine biosynthesis

S-Adenosyl-L-methionine is an important bioactive sulfur-containing amino acid. Large scale preparation of the amino acid is of great significance. S-Adenosyl-L-methionine can be synthesized from L-methionine and adenosine triphosphate in a reaction catalyzed by methionine adenosyltransferase. In order to enhance S-adenosyl-L-methionine biosynthesis by industrial microbial strains, various strategies have been employed to optimize the process. Genetic manipulation has largely focused on enhancement of expression and activity of methionine adenosyltransferase. This has included its overexpression in Pichia pastoris, Saccharomyces cerevisiae and Escherichia coli, molecular evolution, and fine-tuning of expression by promoter engineering. Furthermore, knocking in of Vitreoscilla hemoglobin and knocking out of cystathionine-β-synthase have also been effective strategies. Besides genetic modification, novel bioprocess strategies have also been conducted to improve S-adenosyl-L-methionine synthesis and inhibit its conversion. This has involved the optimization of feeding modes of methanol, glycerol and L-methionine substrates. Taken together considerable improvements have been achieved in S-adenosyl-L-methionine accumulation at both flask and fermenter scales. This review provides a contemporary account of these developments and identifies potential methods for further improvements in the efficiency of S-adenosyl-L-methionine biosynthesis.

GAP promoter library for fine-tuning of gene expression in Pichia pastoris

A library of engineered promoters of various strengths is a useful genetic tool that enables the fine-tuning and precise control of gene expression across a continuum of broad expression levels. The methylotrophic yeast Pichia pastoris is a well-established expression host with a large academic and industrial user base. To facilitate manipulation of gene expression spanning a wide dynamic range in P. pastoris, we created a functional promoter library through mutagenesis of the constitutive GAP promoter. Using yeast-enhanced green fluorescent protein (yEGFP) as the reporter, 33 mutants were chosen to form the functional promoter library. The 33 mutants spanned an activity range between ∼0.6% and 19.6-fold of the wild-type promoter activity with an almost linear fluorescence intensity distribution. After an extensive characterization of the library, the broader applicability of the results obtained with the yEGFP reporter was confirmed using two additional reporters (β-galactosidase and methionine adenosyltransferase [MAT]) at the transcription and enzyme activity levels. Furthermore, the utility of the promoter library was tested by investigating the influence of heterologous MAT gene expression levels on cell growth and S-adenosylmethionine (SAM) production. The extensive characterization of the promoter strength enabled identification of the optimal MAT activity (around 1.05 U/mg of protein) to obtain maximal volumetric SAM production. The promoter library permits precise control of gene expression and quantitative assessment that correlates gene expression level with physiologic parameters. Thus, it is a useful toolbox for both basic and applied research in P. pastoris.

Characterization of three lactic acid bacteria and their isogenic ldh deletion mutants shows optimization for YATP (cell mass produced per mole of ATP) at their physiological pHs

Several lactic acid bacteria use homolactic acid fermentation for generation of ATP. Here we studied the role of the lactate dehydrogenase enzyme on the general physiology of the three homolactic acid bacteria Lactococcus lactis, Enterococcus faecalis, and Streptococcus pyogenes. Of note, deletion of the ldh genes hardly affected the growth rate in chemically defined medium under microaerophilic conditions. However, the growth rate was affected in rich medium. Furthermore, deletion of ldh affected the ability for utilization of various substrates as a carbon source. A switch to mixed acid fermentation was observed during glucose-limited continuous growth and was dependent on the growth rate for S. pyogenes and on the pH for E. faecalis. In S. pyogenes and L. lactis, a change in pH resulted in a clear change in Y(ATP) (cell mass produced per mole of ATP). The pH that showed the highest Y(ATP) corresponded to the pH of the natural habitat of the organisms.

Functional analysis of the role of CggR (central glycolytic gene regulator) in Lactobacillus plantarum by transcriptome analysis

The level of the central glycolytic gene regulator (CggR) was engineered in Lactobacillus plantarum NC8 and WCFS1 by overexpression and in‐frame mutation of the cggR gene in order to evaluate its regulatory role on the glycolytic gap operon and the glycolytic flux. The repressor role of CggR on the gap operon was indicated through identification of a putative CggR operator and transcriptome analysis, which coincided with decreased growth rate and glycolytic flux when cggR was overexpressed in NC8 and WCFS1. The mutation of cggR did not affect regulation of the gap operon, indicating a more prominent regulatory role of CggR on the gap operon under other conditions than tested (e.g. fermentation of other sugars than glucose or ribose) and when the level of the putative effector molecule FBP is reduced. Interestingly, the mutation of cggR had several effects in NC8, i.e. increased growth rate and glycolytic flux and regulation of genes with functions associated with glycerol and pyruvate metabolism; however, no effects were observed in WCFS1. The affected genes in NC8 are presumably regulated by CcpA, since putative CRE sites were identified in their upstream regions. The interconnection with CggR and CcpA‐mediated control on growth and metabolism needs to be further elucidated.

Multiple control of the acetate pathway in Lactococcus lactis under aeration by catabolite repression and metabolites

To explore the factors controlling metabolite formation under aeration in Lactococcus lactis, metabolic patterns, enzymatic activities, and transcriptional profiles of genes involved in the aerobic pathway for acetate anabolism were compared between a parental L. lactis strain and its NADH-oxidase-overproducer derivative. Deregulated catabolite repression mutans in the ccpA or pstH genes, encoding CcpA or its co-activator HPr, respectively, were compared with a parental strain, as well. Although the NADH-oxidase activity was derepressed in ccpA, but not in the pstH background, a mixed fermentation was displayed by either mutant, with a higher acetate production in the pstH variant. Moreover, transcription of genes encoding phosphotransacetylase and acetate kinase were derepressed, and the corresponding enzymatic activities increased, in both catabolite repression mutants. These results and the dependence on carbon source for acetate production in the NADH-oxidase-overproducer support the conclusion that catabolite repression, rather than NADH oxidation, plays a critical role to control acetate production. Furthermore, fructose 1,6-bisphosphate influenced the in vitro phosphotransacetylase and acetate kinase activities, while the former was sensitive to diacetyl. Our study strongly supports the model that, under aerobic conditions, the homolactic fermentation in L. lactis MG1363 is maintained by CcpA-mediated repression of mixed acid fermentation.

Metabolic control analysis: a tool for designing strategies to manipulate metabolic pathways

The traditional experimental approaches used for changing the flux or the concentration of a particular metabolite of a metabolic pathway have been mostly based on the inhibition or over-expression of the presumed rate-limiting step. However, the attempts to manipulate a metabolic pathway by following such approach have proved to be unsuccessful. Metabolic Control Analysis (MCA) establishes how to determine, quantitatively, the degree of control that a given enzyme exerts on flux and on the concentration of metabolites, thus substituting the intuitive, qualitative concept of rate limiting step. Moreover, MCA helps to understand (i) the underlying mechanisms by which a given enzyme exerts high or low control and (ii) why the control of the pathway is shared by several pathway enzymes and transporters. By applying MCA it is possible to identify the steps that should be modified to achieve a successful alteration of flux or metabolite concentration in pathways of biotechnological (e.g., large scale metabolite production) or clinical relevance (e.g., drug therapy). The different MCA experimental approaches developed for the determination of the flux-control distribution in several pathways are described. Full understanding of the pathway properties when is working under a variety of conditions can help to attain a successful manipulation of flux and metabolite concentration.

The metabolic pH response in Lactococcus lactis: an integrative experimental and modelling approach

Lactococcus lactis is characterised by its ability to convert sugar almost exclusively into lactic acid. This organic acid lowers extracellular pH, thus inhibiting growth of competing bacteria. Although L. lactis is able to survive at low pH, glycolysis is strongly affected at pH values below 5, showing reduced rate of glucose consumption. Therefore, in order to deepen our knowledge on central metabolism of L. lactis in natural or industrial environments, an existing full scale kinetic model of glucose metabolism was extended to simulate the impact of lowering extracellular pH in non-growing cells of L. lactis MG1363. Validation of the model was performed using (13)C NMR, (31)P NMR, and nicotinamide adenine dinucleotide hydride auto-fluorescence data of living cells metabolizing glucose at different pH values. The changes in the rate of glycolysis as well as in the dynamics of intracellular metabolites (NADH, nucleotide triphosphates and fructose-1,6-bisphosphate) observed during glucose pulse experiments were reproduced by model simulations. The model allowed investigation of key enzymes at sub-optimum extracellular pH, simulating their response to changing conditions in the complex network, as opposed to in vitro enzyme studies. The model predicts that a major cause of the decrease in the glycolytic rate, upon lowering the extracellular pH, is the lower pool of phosphoenolpyruvate available to fuel glucose uptake via the phosphoenolpyruvate-dependent transport system.

Co-factor engineering in lactobacilli: effects of uncoupled ATPase activity on metabolic fluxes in Lactobacillus (L.) plantarum and L. sakei

The hydrolytic F(1)-part of the F(1)F(0)-ATPase was over-expressed in Lactobacillus (L.) plantarum NC8 and L. sakei Lb790x during fermentation of glucose or ribose, in order to study how changes in the intracellular levels of ATP and ADP affect the metabolic fluxes. The uncoupled ATPase activity resulted in a decrease in intracellular energy level (ATP/ADP ratio), biomass yield and growth rate. Interestingly, the glycolytic and ribolytic flux increased in L. plantarum with uncoupled ATPase activity compared to the reference strain by up to 20% and 50%, respectively. The ATP demand was estimated to have approximately 80% control on both the glycolytic and ribolytic flux in L. plantarum under these conditions. In contrast, the glycolytic and ribolytic flux decreased in L. sakei with uncoupled ATPase activity.

The las enzymes control pyruvate metabolism in Lactococcus lactis during growth on maltose

The fermentation pattern of Lactococcus lactis with altered activities of the las enzymes was examined on maltose. The wild type converted 65% of the maltose to mixed acids. An increase in phosphofructokinase or lactate dehydrogenase expression shifted the fermentation towards homolactic fermentation, and with a high level of expression of the las operon the fermentation was homolactic.

Modelling strategies for the industrial exploitation of lactic acid bacteria

Lactic acid bacteria (LAB) have a long tradition of use in the food industry, and the number and diversity of their applications has increased considerably over the years. Traditionally, process optimization for these applications involved both strain selection and trial and error. More recently, metabolic engineering has emerged as a discipline that focuses on the rational improvement of industrially useful strains. In the post-genomic era, metabolic engineering increasingly benefits from systems biology, an approach that combines mathematical modelling techniques with functional-genomics data to build models for biological interpretation and--ultimately--prediction. In this review, the industrial applications of LAB are mapped onto available global, genome-scale metabolic modelling techniques to evaluate the extent to which functional genomics and systems biology can live up to their industrial promise.

Control analysis as a tool to understand the formation of the las operon in Lactococcus lactis

In Lactococcus lactis the enzymes phosphofructokinase (PFK), pyruvate kinase (PK) and lactate dehydrogenase (LDH) are uniquely encoded in the las operon. We used metabolic control analysis to study the role of this organization. Earlier studies have shown that, at wild-type levels, LDH has no control over glycolysis and growth rate, but high negative control over formate production (C(Jformate)LDH=-1.3). We found that PFK and PK exert no control over glycolysis and growth rate at wild-type enzyme levels but both enzymes exert strong positive control on the glycolytic flux at reduced activities. PK exerts high positive control over formate (C(Jformate)PK=0.9-1.1) and acetate production (C(Jacetate)PK=0.8-1.0), whereas PFK exerts no control over these fluxes at increased expression. Decreased expression of the entire las operon resulted in a strong decrease in the growth rate and glycolytic flux; at 53% expression of the las operon glycolytic flux was reduced to 44% and the flux control coefficient increased towards 3. Increased las expression resulted in a slight decrease in the glycolytic flux. At wild-type levels, control was close to zero on both glycolysis and the pyruvate branches. The sum of control coefficients for the three enzymes individually was comparable with the control coefficient found for the entire operon; the strong positive control exerted by PK almost cancels out the negative control exerted by LDH on formate production. Our analysis suggests that coregulation of PFK and PK provides a very efficient way to regulate glycolysis, and coregulating PK and LDH allows cells to maintain homolactic fermentation during glycolysis regulation.

Effect of a single-gene knockout on the metabolic regulation in Escherichia coli for D-lactate production under microaerobic condition

The effects of several single-gene knockout mutants (pykF, ppc, pflA, pta, and adhE mutants) on the metabolic flux distribution in Escherichia coli were investigated under microaerobic condition. The intracellular metabolite concentrations and enzyme activities were measured, and the metabolic flux distribution was computed to study the metabolic regulation in the cell. The pflA, pta and ppc mutants produced large amount of lactate when using glucose as a carbon source under microaerobic condition. Comparing the flux distribution and the enzyme activities in the mutants, it was shown that the lactate production was promoted by the inactivation of pyruvate formate lyase and the resulting overexpression of lactate dehydrogenase. The flux through Pta-Ack pathways and the ethanol production were limited by the available acetyl coenzyme A. It was shown that the glycolysis was activated in pykF mutant in microaerobic culture. The glycolytic flux was related with Pyk activity except for pykF mutant. The cell growth rate was shown to be affected by the flux through phosphoenolpyruvate carboxylase. The quantitative regulation analysis was made based on the deviation indexes.

Natural-abundance isotope ratio mass spectrometry as a means of evaluating carbon redistribution during glucose-citrate cofermentation by Lactococcus lactis

The cometabolism of citrate and glucose by growing Lactococcus lactis ssp. lactis bv. diacetylactis was studied using a natural-abundance stable isotope technique. By a judicious choice of substrates differing slightly in their 13C/12C ratios, the simultaneous metabolism of citrate and glucose to a range of compounds was analysed. These end-products include lactate, acetate, formate, diacetyl and acetoin. All these products have pyruvate as a common intermediate. With the objective of estimating the degree to which glucose and citrate metabolism through pyruvate may be differentially regulated, the delta13C values of the products accumulated over a wide range of concentrations of citrate and glucose were compared. It was found that, whereas the relative accumulation of different products responds to both the substrate concentration and the ratio between the substrates, the delta13C values of the products primarily reflect the availability of the two substrates over the entire range examined. It can be concluded that in actively growing L. lactis the maintenance of pyruvate homeostasis takes precedence over the redox status of the cells as a regulatory factor.

Effect of pyruvate kinase overproduction on glucose metabolism of Lactococcus lactis

Lactococcus lactis strain NZ9000(pNZpyk), which overproduces pyruvate kinase (PK), was constructed. The pNZpyk plasmid carries the P(nisA)-pyk transcriptional fusion, and the overexpression of its pyk gene was accomplished by using the nisin-inducible expression system of the NZ9000 strain. In vivo (13)C- and (31)P-NMR spectroscopy was used to evaluate the effect of this modification on the metabolism of glucose in non-growing cells. A detailed description of the kinetics of glucose, end products, glycolytic intermediates, NAD(+) and NADH was obtained. A 15-fold increase in the level of PK did not increase the overall glycolytic flux, which, on the contrary, was slightly reduced. Significant differences were observed in (i) the level of 3-phosphoglycerate (3-PGA) and phosphoenolpyruvate (PEP), metabolites associated with starvation; (ii) the rate of fructose 1,6-bisphosphate (FBP) depletion upon glucose exhaustion; and (iii) the NAD(+)/NADH ratio during glucose catabolism. In the mutant, the rate of FBP consumption after glucose depletion was notably accelerated under anaerobic conditions, whereas 3-PGA and PEP decreased to undetectable levels. Furthermore, the level of NAD(+) decreased steadily during the utilization of glucose, probably due to the unanticipated reduction in the lactate dehydrogenase activity in comparison with the control strain, NZ9000(pNZ8020). The results show that PK is an important bottleneck to carbon flux only when glucose becomes limiting; in the overproducer this constriction was no longer present, as evidenced by the faster FBP consumption and lack of accumulation of 3-PGA and PEP in anaerobic as well as aerobic conditions. Despite these clear changes, the PK-overproducing strain showed typical homolactic metabolism under anaerobic conditions, as did the strain harbouring the vector plasmid without the pyk insert. However, under an oxygen atmosphere, there was increased channelling of carbon to the production of acetate and acetoin, to the detriment of lactate production.

IS981-mediated adaptive evolution recovers lactate production by ldhB transcription activation in a lactate dehydrogenase-deficient strain of Lactococcus lactis

Lactococcus lactis NZ9010 in which the las operon-encoded ldh gene was replaced with an erythromycin resistance gene cassette displayed a stable phenotype when grown under aerobic conditions, and its main end products of fermentation under these conditions were acetate and acetoin. However, under anaerobic conditions, the growth of these cells was strongly retarded while the main end products of fermentation were acetate and ethanol. Upon prolonged subculturing of this strain under anaerobic conditions, both the growth rate and the ability to produce lactate were recovered after a variable number of generations. This recovery was shown to be due to the transcriptional activation of a silent ldhB gene coding for an Ldh protein (LdhB) with kinetic parameters different from those of the native las operon-encoded Ldh protein. Nevertheless, cells producing LdhB produced mainly lactate as the end product of fermentation. The mechanism underlying the ldhB gene activation was primarily studied in a single-colony isolate of the recovered culture, designated L. lactis NZ9015. Integration of IS981 in the upstream region of ldhB was responsible for transcription activation of the ldhB gene by generating an IS981-derived -35 promoter region at the correct spacing with a natively present -10 region. Subsequently, analysis of 10 independently isolated lactate-producing derivatives of L. lactis NZ9010 confirmed that the ldhB gene is transcribed in all of them. Moreover, characterization of the upstream region of the ldhB gene in these derivatives indicated that site-specific and directional IS981 insertion represents the predominant mechanism of the observed recovery of the ability to produce lactate.

Glyceraldehyde-3-phosphate dehydrogenase has no control over glycolytic flux in Lactococcus lactis MG1363

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has previously been suggested to have almost absolute control over the glycolytic flux in Lactococcus lactis (B. Poolman, B. Bosman, J. Kiers, and W. N. Konings, J. Bacteriol. 169:5887-5890, 1987). Those studies were based on inhibitor titrations with iodoacetate, which specifically inhibits GAPDH, and the data suggested that it should be possible to increase the glycolytic flux by overproducing GAPDH activity. To test this hypothesis, we constructed a series of mutants with GAPDH activities from 14 to 210% of that of the reference strain MG1363. We found that the glycolytic flux was unchanged in the mutants overproducing GAPDH. Also, a decrease in the GAPDH activity had very little effect on the growth rate and the glycolytic flux until 25% activity was reached. Below this activity level, the glycolytic flux decreased proportionally with decreasing GAPDH activity. These data show that GAPDH activity has no control over the glycolytic flux (flux control coefficient = 0.0) at the wild-type enzyme level and that the enzyme is present in excess capacity by a factor of 3 to 4. The early experiments by Poolman and coworkers were performed with cells resuspended in buffer, i.e., nongrowing cells, and we therefore analyzed the control by GAPDH under similar conditions. We found that the glycolytic flux in resting cells was even more insensitive to changes in the GAPDH activity; in this case GAPDH was also present in a large excess and had no control over the glycolytic flux.

Increasing acidification of nonreplicating Lactococcus lactis deltathyA mutants by incorporating ATPase activity

Lactococcus lactis MBP71 deltathyA (thymidylate synthase) cannot synthesize dTTP de novo, and DNA replication is dependent on thymidine in the growth medium. In the nonreplicating state acidification by MBP71 was completely insensitive to bacteriophages (M. B. Pedersen, P. R. Jensen, T. Janzen, and D. Nilsson, Appl. Environ. Microbiol. 68:3010-3023, 2002). For nonreplicating MBP71 the biomass increased 3.3-fold over the first 3.5 h, and then the increase stopped. The rate of acidification increased 2.3-fold and then started to decrease. Shortly after inoculation the lactic acid flux was 60% of that of exponentially growing MBP71. However, when nonspecific ATPase activity was incorporated into MBP71, the lactic acid flux was restored to 100% but not above that point, indicating that control over the flux switched from ATP demand to ATP supply (i.e., to sugar transport and glycolysis). As determined by growing nonreplicating cells with high ATPase activity on various sugar sources, it appeared that glycolysis exerted the majority of the control. ATPase activity also stimulated the rate of acidification by nonreplicating MBP71 growing in milk, and pH 5.2 was reached 40% faster than it was without ATPase activity. We concluded that ATPase activity is a functional means of increasing acidification by nonreplicating L. lactis.

Expression of genes encoding F(1)-ATPase results in uncoupling of glycolysis from biomass production in Lactococcus lactis

We studied how the introduction of an additional ATP-consuming reaction affects the metabolic fluxes in Lactococcus lactis. Genes encoding the hydrolytic part of the F(1) domain of the membrane-bound (F(1)F(0)) H(+)-ATPase were expressed from a range of synthetic constitutive promoters. Expression of the genes encoding F(1)-ATPase was found to decrease the intracellular energy level and resulted in a decrease in the growth rate. The yield of biomass also decreased, which showed that the incorporated F(1)-ATPase activity caused glycolysis to be uncoupled from biomass production. The increase in ATPase activity did not shift metabolism from homolactic to mixed-acid fermentation, which indicated that a low energy state is not the signal for such a change. The effect of uncoupled ATPase activity on the glycolytic flux depended on the growth conditions. The uncoupling stimulated the glycolytic flux threefold in nongrowing cells resuspended in buffer, but in steadily growing cells no increase in flux was observed. The latter result shows that glycolysis occurs close to its maximal capacity and indicates that control of the glycolytic flux under these conditions resides in the glycolytic reactions or in sugar transport.

Is the glycolytic flux in Lactococcus lactis primarily controlled by the redox charge? Kinetics of NAD(+) and NADH pools determined in vivo by 13C NMR

The involvement of nicotinamide adenine nucleotides (NAD(+), NADH) in the regulation of glycolysis in Lactococcus lactis was investigated by using (13)C and (31)P NMR to monitor in vivo the kinetics of the pools of NAD(+), NADH, ATP, inorganic phosphate (P(i)), glycolytic intermediates, and end products derived from a pulse of glucose. Nicotinic acid specifically labeled on carbon 5 was synthesized and used in the growth medium as a precursor of pyridine nucleotides to allow for in vivo detection of (13)C-labeled NAD(+) and NADH. The capacity of L. lactis MG1363 to regenerate NAD(+) was manipulated either by turning on NADH oxidase activity or by knocking out the gene encoding lactate dehydrogenase (LDH). An LDH(-) deficient strain was constructed by double crossover. Upon supply of glucose, NAD(+) was constant and maximal (approximately 5 mm) in the parent strain (MG1363) but decreased abruptly in the LDH(-) strain both under aerobic and anaerobic conditions. NADH in MG1363 was always below the detection limit as long as glucose was available. The rate of glucose consumption under anaerobic conditions was 7-fold lower in the LDH(-) strain and NADH reached high levels (2.5 mm), reflecting severe limitation in regenerating NAD(+). However, under aerobic conditions the glycolytic flux was nearly as high as in MG1363 despite the accumulation of NADH up to 1.5 mm. Glyceraldehyde-3-phosphate dehydrogenase was able to support a high flux even in the presence of NADH concentrations much higher than those of the parent strain. We interpret the data as showing that the glycolytic flux in wild type L. lactis is not primarily controlled at the level of glyceraldehyde-3-phosphate dehydrogenase by NADH. The ATP/ADP/P(i) content could play an important role.

Modulation of gene expression made easy

A new approach for modulating gene expression, based on randomization of promoter (spacer) sequences, was developed. The method was applied to chromosomal genes in Lactococcus lactis and shown to generate libraries of clones with broad ranges of expression levels of target genes. In one example, overexpression was achieved by introducing an additional gene copy into a phage attachment site on the chromosome. This resulted in a series of strains with phosphofructokinase activities from 1.4 to 11 times the wild-type activity level. In this example, the pfk gene was cloned upstream of a gusA gene encoding beta-glucuronidase, resulting in an operon structure in which both genes are transcribed from a common promoter. We show that there is a linear correlation between the expressions of the two genes, which facilitates screening for mutants with suitable enzyme activities. In a second example, we show that the method can be applied to modulating the expression of native genes on the chromosome. We constructed a series of strains in which the expression of the las operon, containing the genes pfk, pyk, and ldh, was modulated by integrating a truncated copy of the pfk gene. Importantly, the modulation affected the activities of all three enzymes to the same extent, and enzyme activities ranging from 0.5 to 3.5 times the wild-type level were obtained.