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Metabolic engineering of propanediol pathways.

Microbial fermentation is an important technology for the conversion of renewable resources to chemicals. In this paper, we describe the application of metabolic engineering for the development of two new fermentation processes: the microbial conversion of sugars to 1,3-propanediol (1,3-PD) and 1,2-propanediol (1,2-PD). A variety of naturally occurring organisms ferment glycerol to 1,3-PD, but no natural organisms ferment sugars directly to 1,3-PD. We first describe the fed-batch fermentation of glycerol to 1,3-PD by Klebsiella pneumoniae. We then present various approaches for the conversion of sugars to 1,3-PD, including mixed-culture fermentation, cofermentation of glycerol and glucose, and metabolic engineering of a "sugars to 1,3-PD" pathway in a single organism. Initial results are reported for the expression of genes from the K. pneumoniae 1,3-PD pathway in Saccharomyces cerevisiae. The best naturally occurring organism for the fermentation of sugars to 1,2-PD is Thermoanaerobacterium thermosaccharolyticum. We describe the fermentation of several different sugars to 1,2-PD by this organism in batch and continuous culture. We report that Escherichia coli strains engineered to express either aldose reductase or glycerol dehydrogenase convert glucose to (R)-1,2-PD. We then analyze the ultimate potential of fermentation processes for the production of propanediols. Linear optimization studies indicate that, under aerobic conditions, propanediol yields that approach the theoretical maximum are possible and CO2 is the primary coproduct. Without the need to produce acetate, final product titers in the range of 100 g/L should be possible; the high titers and low coproduct levels should make product recovery and purification straightforward. The examples given in this paper illustrate the importance of metabolic engineering for fermentation process development in general.

Biotechnology↗

Material characterization of the brainstem from oscillatory shear tests.

Traumatic damage to the brainstem occurs frequently when the brain skull complex experiences injurious loading especially during those traumatic situations that produce diffuse axonal injury (DAI). DAI has been shown to be dependent on load direction and correlated with regional tissue deformation in response to rotational inertial loads. Possible mechanisms for the selective vulnerability of the brainstem are (1) the geometry of the central nervous system is responsible for producing high tissue strains in these regions, (2) regional differences in overall material stiffness result in larger deformations at these sites, and (3) the anisotropic mechanical properties of these regions lead to a sensitivity to the rotational load direction and magnitude. This paper investigates the latter two hypotheses by performing oscillatory shear tests on adult porcine brainstem in three mutually perpendicular directions. The complex shear moduli were calculated over a range of frequencies (20-200 Hz), for three levels of peak engineering strain (2.5%, 5.0%, and 7.5%). The directional data demonstrated that the brainstem exhibits significant transversely isotropic behavior. Both components of the complex modulus in which the axonal fibers are oriented parallel to the plane of shear but transverse to the shear direction were significantly higher than those of the other two, mutually indistinguishable test cases across the range of strains tested. By comparison with similar tests on cerebral tissue, these data demonstrated that the brainstem displays a stiffer biomechanical response. These differences were present for both components of the complex shear modulus and were greater as the magnitude of the applied strain increased. The regional stiffness and anisotropic response of the brainstem coupled with its location as a narrow bridge between CNS regions interact to result in the selective vulnerability of this region in rotational loading.

Animals↗

[Cloning and secretory expression of staphylokinase in Streptomyces lividans].

OBJECTIVE: Construct a recombinant Streptomyces strain by which staphylokinase can be secretory expressed. METHODS: With the total DNA extracted from strains of Staphylococcus aureus isolated in clinic as template DNA, one 730 bp DNA fragment including secretory signal peptide sequence and structure gene of staphylokinase was amplified by PCR. After cloning into plasmid pUC19 and sequencing, this fragment was confirmed to have the same nucleotide sequence as that of staphylokinase gene reported before. Then the fragment was inserted into Streptomyces plasmid pIJ459 following strong promoter. Recombinant plasmid pIJ459SAK was transformed into S. lividans TK54. RESULTS: The 72 hours culture supernatant of the secretory-type genetic engineering strain that harbored pIJ459SAK was analyzed by 15% SDS-PAGE. One specific protein band with molecular weight about 16,000 can be seen after staining the gel with silver nitrate. The fibrinolytic activity of Staphylokinase can be also detected in the 72 hours culture supernatant in the fibrin-plate assay. CONCLUSIONS: Staphylokinase can be successfully secreted into fermentation culture by the recombinant Streptomyces strain.

Cloning, Molecular↗

Expression analysis of the tylosin-biosynthetic gene cluster: pivotal regulatory role of the tylQ product.

Expression analysis by RT-PCR, applied to the entire tyl cluster, revealed that the pattern of transcription is more complex than expected. For example, the five tylG polyketide synthase genes are not necessarily cotranscribed or even coregulated. Among the regulatory genes, tylQ has emerged as a key factor. Although several genes (including the positive regulator, tylS) were possibly expressed constitutively, only tylQ was silent during secondary metabolism. Analysis of engineered strains, in which tylQ was disrupted or overexpressed, showed that the TylQ protein is a transcriptional repressor that blocks tylosin biosynthesis by controlling expression of the activator, tylR. Before tylosin production can be triggered, tylQ must be switched off, or at least downregulated.

Base Sequence↗

Functional expression of a P450 flavonoid hydroxylase for the biosynthesis of plant-specific hydroxylated flavonols in Escherichia coli.

Flavonols are plant polyphenolic compounds that belong to the class of molecules collectively known as flavonoids. Because of their demonstrated health benefits towards a wide array of human pathological conditions, a great interest has emerged for their biosynthesis from well-characterized microbial hosts. We present the functional expression in Escherichia coli of a plant P450 flavonoid 3', 5'-hydroxylase (F3'5'H) as a fusion protein with a P450 reductase. This expression allowed metabolic engineering of E. coli to produce the flavonol kaempferol and the 3', 4' B-ring hydroxylated flavonol quercetin from the p-coumaric acid precursor by simultaneously co-expressing the fusion protein with 4-coumaroyl:CoA-ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3beta-hydroxylase (FHT) and flavonol synthase (FLS). Biosynthesis of the B-ring tri-hydroxylated flavonol myricetin from the engineered strains was accomplished when flavanones rather than phenylpropanoid acids were used as precursor molecules. Cultivation of the recombinant strains in rich medium increased the synthesis of all flavonoids with the exception of myricetin. The present work opens the possibility of the future production of several other hydroxylated flavonoid molecules in E. coli.

Cytochrome P-450 Enzyme System↗

[Anti-plague vaccination: past and future perspectives].

The impact of the three historic plague pandemics will remain engraved forever in the collective memory. During the first half of the XXth century, the development of vaccines inducing protection against bubonic plague, the first production of antibiotics, insecticides and raticides, could have lead some people to think that eradication was possible. But according to the data of epidemiological surveillance, far from disappearing, plague is remaining or so increasing that it is considered, in some places, as a reemerging disease. Yersinia pestis is highly variable, and a multidrug resistant strain has been isolated in 1995 in the Ambalavo district of Madagascar. This high-level of resistance includes the drugs recommended for plague prophylaxis and therapy, and this observation pointed the fact that Yersinia pestis is able to acquire the plasmid carrying the resistance genes, under natural conditions. Consequently, it is not unreasonable to think that clinically ominous events could occur again. Moreover, currently available vaccines do not induce protection against the pneumonic form of plague, and are reactogenic. Lastly, according to some accurate sources, one cannot turn down the assumption of a genetically engineered strain of Yersinia pestis used as a biological weapon by a terrorist organization. So, the surveillance of plague remains a topical activity, as the development of none reactogenic live and/or inactivated new vaccines, inducing protection against the pneumonic form of the disease.

Drug Resistance, Microbial↗

[Cloning and expression of lumbrokinase gene in Pichia pastoris].

Lumbrokinase gene F238 was amplified by RT-PCR from the total RNA of earthworm (Eisenia fetida). The gene including signal peptide sequence was inserted into pUCm-T vector to construct pUCm-T-F238. The product was sequenced. The GenBank accession number was DQ202401. Lumbrokinase F238 comprised 738bp and included an open reading frame that encoded a polypeptide of 245 amino acid residues, containing a signal peptide of 7 amino acid residues and a mature peptide of 238 amino acid residues. Both nucleotide and amino acid sequences homologies were 99% after the sequence was compared with Lumbricus rubellus F-III-2. There were two base pair mutations, which subsequently caused two amino acid mutations. The characteristics and structure of F238 was analysed and predicted with biology softwares and databases. The pl of F238 was 4.61. It had eleven Cysteines, which formed three disulfide bonds. Its secondary structure mainly consisted of beta-sheet. Lumbrokinase F238 had serine active center. It was a protease in trypsin family of serine protease superfamily. Lumbrokinase gene F238-m without signal peptide sequence was obtained by PCR using pUCm-T-F238 as template. The expression vector pPIC9-F238-m was constructed by inserting gene F238-m into yeast expression and secretion plasmid pPIC9. Plasmid pPIC9-F238-m was linearized with BgIII and then transformed into Pichia pastoris strain GS115 cell by electroporation method. Phenotypes of transformants were screened in MM and MD plates to ensure the integration of lumbrokinase gene F238-m into yeast chromosome DNA. Methanol was added to a final concentration of 0.5% for the expression of recombination protein every 24h to maintain induction. The result of SDS-PAGE showed that the molecular weight of the expression product was about 28 kDa, in correspondence with the theoretical molecular weight. After the induction of expression, the fibrinolytic activity of the supernatant was measured using artificial fibrin plates. Then the engineering strain of high activity was obtained, and the fibrinolytic activity was up to 100 U/mL.

Animals↗

The production of strains highly expressing human interleukin-2 cDNA.

The plasmid pTLIL-2, which only directed a low-level expression of human interleukin 2(IL-2) cDNA in E. coli, was reconstructed: a series of deletions were made in 3' non-coding region of human IL-2 cDNA, and 7 recombinant plasmids with different deletions were selected, on the other hand, a Tac promoter sequence from pDR540 was inserted to upstream of IL-2 cDNA in pTLIL-2 so that pTLIL-2DT, which contains double Tac promoters, was constructed. And then, E. coli JM103 was transformed with the above 8 recombinant plasmids respectively. The expression efficiency of IL-2 cDNA in E. coli transformed with different plasmids was evaluated by means of SDS-PAGE and measuring 3H-TdR incorporation of IL-2-dependent activated T lymphocytes in the presence of bacterial extracts. Three engineering strains with high efficiency of IL-2 expression were selected, and all of these strains could produce recombinant IL-2(rIL-2) 4 times more than E. coil JM103/pTLIL-2.

DNA Transposable Elements↗

Engineered Bacillus thuringiensis GO33A with broad insecticidal activity against lepidopteran and coleopteran pests.

A recombinant plasmid pSTK-3A containing cry3Aa7 gene encoding a coleopteran-specific insecticidal protein was constructed and introduced into wild Bacillus thuringiensis subsp. aizawai G03, which contained cry1Aa, cry1Ac, cry1Ca, and cry2Ab genes and was highly toxic to lepidopteran insect pests. The genetically engineered strain were named G033A. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot analysis demonstrated that the cry3Aa7 gene was expressed normally and produced a 67 kDa protein in G033A, and the flat rectangular crystals of Cry3Aa7 toxin protein was observed under scanning electron microscope. The recombinant plasmid was maintained in bacteria cultured for 180 generations in culture media containing no antibiotics. Synthesis of the Cry3Aa7 toxin conferred high and broad toxicity to the recombinant strain G033A against coleopteran order, elm leaf beetle (Pyrrhalta aenescens) (LC(50) 0.35 mg/ml), for which the parental strain G03 was not toxic. Both the parental strain G03 and recombinant strain G033A showed strong insecticidal activity to lepidopteran pests, beet armyworm (Spodoptera exigua), diamondback moth (Plutella xylostella), and cotton bollworm (Helicoverpa amigera), respectively. The lethal concentration 50% (LC(50)) of G033A against S. exigua, P. xylostella, and H. amigera was 4.26, 0.86, and 1.76 microg/ml, respectively.

Animals↗

Heterologous expression of nonribosomal peptide synthetases in B. subtilis: construction of a bi-functional B subtilis/E coli shuttle vector system.

A major obstacle in investigating the biosynthesis of pharmacologically important peptide antibiotics is the heterologous expression of the giant biosynthetic genes. Recently, the genetically engineered strain Bacillus subtilis KE30 has been reported as an excellent surrogate host for the heterologous expression of an entire nonribosomal peptide synthetase (NRPS) gene cluster. In this study, we expand the applicability of this strain, by the development of four Escherichia coli/B. subtilis shuttle expression vectors. Comparative overproduction of hybrid NRPS proteins derived from both organisms revealed a significant beneficial effect of overproducing proteins in B. subtilis KE30 as underlined by the production of stable nondegradative proteins, as well as the formation of active phosphopantetheinylated holo-proteins.

Anti-Bacterial Agents↗

Purification, characterization and analysis of rolipram inhibition of a human type-IVA cyclic AMP-specific phosphodiesterase expressed in yeast.

Analyses were done on a human type-IV cyclic AMP (cAMP) phosphodiesterase (hPDE-IVA-h6.1) expressed in an engineered strain of Saccharomyces cerevisiae. This strain (YMS6) expressed soluble PDE activity, together with an insoluble activity which was not released by re-homogenization, treatment with high-ionic-strength solutions or with the detergent Triton X-100. Pellet and soluble PDE activities were typical of type-IV PDE. They were cAMP-specific, insensitive to the addition of either cGMP (1 microM) or Ca2+/calmodulin, and inhibited by rolipram. Thermostability studies showed both activities to decay as single exponentials, indicating the presence of homogeneous PDE protein species in each fraction. Pellet PDE activity was more thermostable than the soluble enzyme. Mg2+ and Mn2+ dose-dependently increased PDE activity and reversed the inactivating effect of EDTA.h6.1 was engineered to express a C-terminal five-histidine motif (h6.1his5). This allowed purification of the PDE to apparent homogeneity in a simple two-step process involving a rolipram affinity column and a Ni2(+)-chelate column. A single monomeric protein of subunit molecular mass approximately 73 kDa and native molecular mass approximately 74 kDa resulted after a approximately 53000-fold purification. This exhibited a Km for cAMP of 8 microM, a true Vmax. of 0.8 mumol of cAMP hydrolysed/min per mg of PDE protein, a kcat. of 3702 s-1, and a value of the specificity constant kcat/Km of 4.6 x 10(8) M-1.s-1, the last implying a diffusion controlled reaction. Rolipram (Ki 0.4 soluble; 0.7 microM pellet) and 3-isobutyl-1-methylxanthine (Ki 15 soluble; 19 microM pellet) served as simple competitive inhibitors for both soluble and pellet forms of h6.1, respectively.

1-Methyl-3-isobutylxanthine↗

Phosphatidylserine decarboxylase from Saccharomyces cerevisiae. Isolation of mutants, cloning of the gene, and creation of a null allele.

Phosphatidylserine decarboxylase plays a pivotal role in the synthesis of phospholipid by the mitochondria. The substrate phosphatidylserine is synthesized extramitochondrially and must be translocated to the mitochondria prior to decarboxylation. To understand the properties of the decarboxylase and exploit its unique topology to address basic questions of interorganelle cooperation in membrane assembly, we have begun to examine this enzyme in Saccharomyces cerevisiae. Strains of the yeast defective in enzyme activity were isolated by modified brute force using 1-acyl-2[N-(6-[7-nitrobenz-2- oxa-1,3-diazo-4-yl)]aminocaproyl] (NBD)-phosphatidyl[1'-14C]serine as substrate for permeabilized cells. Mutant strains with less than 5% wild type activity exhibited no defective growth phenotype. The gene for the phosphatidylserine decarboxylase (PSD) was cloned using an oligonucleotide probe degenerate for the sequence VGAT(I)/(N)VGSI, which is the longest stretch of sequence identity between the Escherichia coli sequence (I at position 5) and the putative CHO cell sequence (N at position 5). The gene encodes a 500 amino acid protein with 28-43% identity to the bacterial and mammalian sequences. The yeast PSD gene maps to the long arm of chromosome 14 between the kex 2 and RAS 2 loci. Null mutations created by disrupting the PSD gene with TRP1 demonstrate that the gene is not essential for cell growth even when the engineered strains are deprived of choline and ethanolamine. Analysis of lipid synthesis and enzyme activity in null mutants indicates that there are two PSD genes.

Alleles↗

Efficient expression of vip184DeltaP gene under the control of promoters plus Shine-Dalgarno (SD) sequences of cry genes from Bacillus thuringiensis.

AIMS: To compare vip184DeltaP gene expression time course and Vip184 protein yield under the control of promoters and Shine-Dalgarno (SD) sequences of vip184, cry3A and cry1A gene from Bacillus thuringiensis respectively. METHODS AND RESULTS: Derived from the shuttle vector pHT3101, recombinant plasmids pHPT3, pHTP3A(Delta)P and pHTP1A(Delta)P were constructed with the native vip184 gene and the vip184(Delta)P gene, either under the control of promoters and SD sequences of cry3A or cry1A genes. When the above plasmids were transformed into an acrystalliferous B. thuringiensis strain Cry(-)B, their expression time course were consistent with those of vip184, cry3A and cry1A gene respectively. The maximum yields of Vip184 protein were increased when under the control of promoters plus SD sequences of cry3A and cry1A gene. CONCLUSIONS: The results showed that both cry3A and cry1A promoter/SD sequence combinations were able to enhance synthesis of Vip184 and change its expression time course. SIGNIFICANCE AND IMPACT OF THE STUDY: Both cry3A and cry1A promoter/SD systems offer a method for improving the expression efficacy of the vip184 gene in B. thuringiensis and it is possible to co-express the vip184 gene and cry genes and accumulate Vip184 in the form of inclusion bodies by these systems in order to construct novel useful B. thuringiensis engineered strains.

Animals↗

An efficient endogenous type I-E CRISPR-Cas genome-editing platform for producing transglutaminase in Streptomyces mobaraensis.

Streptomyces mobaraensis is an industrially important actinomycete capable of producing transglutaminase (TGase), a valuable crosslinking enzyme that is widely used in the food, pharmaceutical, and textile industries. However, its genetic manipulation remains challenging owing to the lack of efficient genome-editing tools. Here, we characterized an endogenous type I-E CRISPR-Cas system in S. mobaraensis IPIO2 through bioinformatics analysis and plasmid interference assays, identifying the protospacer adjacent motif as 5'-AAC-3'. We engineered an artificial editing plasmid, pCRISPR, by inserting a mini-CRISPR array (repeat-spacer-repeat) and homologous recombination repair templates into the replicative plasmid pJTU1278. This system exhibited high editing efficiencies, achieving 70% for single-gene deletions and 75-80% for large DNA fragment deletions ranging from 10 to 40 kb. Based on this system, deletion of four genes consistently downregulated during TGase production, identified through comparative proteomics, enhanced TGase production by 8.5-18.5%. Furthermore, deleting the pseudouridimycin and piericidin A1 biosynthetic gene clusters using this system significantly improved the safety profile of TGase production, resulting in a 17% increase in TGase yield. This study established a robust and efficient endogenous CRISPR-Cas-based genome-editing platform in S. mobaraensis, providing a powerful tool for strain engineering and industrial optimization of TGase production.

Comparative proteomics↗

Development of bespoke bioluminescent reporters with the potential for in situ deployment within a phenolic-remediating wastewater treatment system.

A suite of ecologically relevant, site-specific bioreporters was constructed by transposon mutagenesis of microorganisms isolated from a polluted phenolic-remediating wastewater treatment system. Four Pseudomonad species were engineered to carry a stable chromosomal copy of the lux operon (luxCDABE) derived from Photorhabdus luminescens. These recombinant reporter microorganisms were tested for bioluminescence response to relevant phenol concentrations in the laboratory and to phenolic-containing effluents generated by an industrial wastewater treatment plant. The reporters displayed proportional responses of bioluminescence decay with increasing phenol concentrations up to 800 mg l(-1) of phenol. When deployed against samples from the treatment system, they showed superior operational range and sensing capabilities to that observed for industry standard microorganisms such as Vibrio fischeri. Specifically, the engineered strains accurately predicted toxicity shifts in all the treatment compartments under study (with phenolic concentrations ranging from approximately 10 to 600 mg l(-1)) with a low coefficient of variation of replicate determinations (between 1.16% and 8.32%). This work highlights the utility of genetic modification of native microorganisms from sites of interest to provide robust and ecologically relevant organism-based reagents for toxicity monitoring with the potential for in situ deployment.

Biodegradation, Environmental↗

Volunteer studies of deletion mutants of Vibrio cholerae O1 prepared by recombinant techniques.

Vibrio cholerae O1 A-B- vaccine strain JBK 70 and A-B+ CVD 101 prepared by recombinant DNA techniques from pathogenic EI Tor Inaba N16961 and classical Ogawa 395, respectively, were fed to 38 volunteers in single doses of 10(4) to 10(10). Although severe diarrhea did not occur in any vaccine, more than one-half developed mild diarrhea. These attenuated strains colonized well and elicited prominent vibriocidal and antitoxic (CVD 101) antibody responses. Recipients of a single dose of JBK 70 were significantly protected when challenged with 10(6) wild-type N16961. Diarrhea occurred in 7 of 8 controls but in only 1 of 10 vaccines (P less than 0.003, 89% vaccine efficacy), demonstrating the potency of immune mechanisms that do not involve cholera antitoxin. Further derivatives were prepared to explore the pathogenesis of the residual diarrhea, considering that either intestinal colonization by the vaccine itself or accessory toxins might be responsible. CVD 102, an auxotrophic mutant of CVD 101, did not cause diarrhea but colonized poorly and elicited feeble immune responses. Derivatives of JBK 70 and CVD 101 (CVD 104 and 105) deleted of genes encoding the EI Tor hemolysin still caused mild diarrhea. Genetically engineered strains can be colonizing, highly immunogenic, and protective single-dose oral vaccines, but they must be further attenuated before they can be considered for use as public health tools.

ABO Blood-Group System↗

Upcycling Vegetable Waste Into Functional Food Ingredients via Synergistic Microbial Engineering and Artificial Intelligence.

The escalating generation of global vegetable waste represents a critical loss of bioactive resources, necessitating a paradigm shift from passive disposal to active nutrient upcycling. However, the industrial conversion of this heterogeneous biomass into standardized functional food ingredients is currently impeded by significant techno-economic barriers, primarily structural recalcitrance, compositional inconsistency, and the presence of toxic fermentation inhibitors. This review provides a comprehensive analysis of the synergistic application of microbial engineering and artificial intelligence (AI) to resolve these bioprocessing bottlenecks within a food-to-food closed-loop framework (as shown in the graphical abstract). We evaluate recent advances in engineering food-grade microbial chassis (e.g., Saccharomyces cerevisiae and Escherichia coli) to enhance lignocellulose degradation and stress tolerance. Concurrently, we examine the integration of AI across the entire value chain, covering deep learning-based rational enzyme design, genome-scale metabolic modeling, and intelligent process control for precision fermentation. Current evidence demonstrates that the hardware-software coupling of engineered strains and AI algorithms significantly enhances conversion efficiency and process robustness. Key findings highlight that AI-driven Design-Build-Test-Learn cycles facilitate the de novo creation of enzymes with superior kinetics and strains with adaptive stress response capabilities against toxins. Moreover, dynamic digital twin models effectively mitigate the impact of substrate variability, ensuring the batch-to-batch consistency required for food applications. We conclude that this data-driven synergistic paradigm is pivotal for establishing a resilient circular bioeconomy, enabling the reliable bioconversion of waste into high-value single-cell proteins, natural flavor additives, and sustainable packaging materials.

Artificial Intelligence↗