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At least 1,171 records · Page 65Linked to original sources
PubMed2004

Enhanced production of acetoin and butanediol in recombinant Enterobacter aerogenes carrying Vitreoscilla hemoglobin gene.

Microbial production of butanediol and acetoin has received increasing interest because of their diverse potential practical uses. Although both products are fermentative in nature, their optimal production requires a low level of oxygen. In this study, the use of a recombinant oxygen uptake system on production of these metabolites was investigated. Enterobacter aerogenes was transformed with a pUC8-based plasmid carrying the gene (vgb) encoding Vitreoscilla (bacterial)hemoglobin (VHb). The presence of vgb and production of VHb by this strain resulted in an increase in viability from 72 to 96 h in culture, but no overall increase in cell mass. Accumulation of the fermentation products acetoin and butanediol were enhanced (up to 83%) by the presence of vgb/VHb. This vgb/VHb related effect appears to be due to an increase of flux through the acetoin/butanediol pathway, but not at the expense of acid production.

Acetoin↗
PubMed1990

Protein secretion systems in microbial and mammalian cells.

Secretion is an attractive production mode for proteins that require posttranslational modifications carried out in the secretory pathway. For example, amino acid chains fold properly, disulfide bonds form correctly, and glycosylation occurs accurately as the protein is secreted. In addition, recovery of secreted proteins is simplified by the fact that cells need not be broken and the product may be a major species present in a minimal synthetic culture medium. The current state of the art permits the production and secretion of proteins by heterologous cells. While future efforts will be required to improve the efficiency of secretion, current methods yield commercially interesting levels of secretion from E. coli, B. subtilis, S. cerevisiae, Aspergilli, and many mammalian cell types. Each of these systems offers certain advantages, and the choice of system depends on the specific protein to be secreted. High-value human therapeutic products such as plasminogen activators are reasonable candidates for secretion from mammalian cell lines, while industrial proteins such as calf prochymosin require a more economical host, such as baker's yeast or Aspergillus. The wide variety of posttranslational modifications observed in nature may prevent any single secretion system from dominating the field for many years to come.

Animals↗
PubMed2000

On-line monitoring of growth of Escherichia coli in batch cultures by bioluminescence.

Bioluminescence was used to monitor growth of Escherichia coli in batch cultures on-line. Light emission of a strain engineered for constitutive bioluminescence was monitored with a simple set-up consisting of a photodiode, a photodetector amplifier and a recorder. Bioluminescence and colony forming units (CFU) of the cultures increased and decreased proportionally and were correlated during every growth phase at temperatures between 28 degrees C and 40 degrees C. Up to the late log (deceleration) phase, both light emission and CFU increased rapidly. Beyond the stationary phase these characteristics decreased very slowly at lower temperatures, while at higher ones they declined more rapidly. Towards the end of the cultivation, light emission of the cultures dropped to undetectable levels, even though CFU were recovered. This was particularly marked at lower temperatures where non-luminescent cultures retained very high CFU. This indicates that the actual metabolism of cells in a culture can be at a very low level or completely shut down, yet cells retain their capability to be culturable. The on-line technology described here has a number of potential uses in the laboratory and industry.

Bacteriological Techniques↗
PubMed1999

Microbial conversion of indene to indandiol: a key intermediate in the synthesis of CRIXIVAN.

Indene is oxidized to mixtures of cis- and trans-indandiols and related metabolites by Pseudomonas putida and Rhodococcus sp. isolates. Indene metabolism is consistent with monooxygenase and dioxygenase activity. P. putida resolves enantiomeric mixtures of cis-1,2-indandiol by further selective oxidation of the 1R, 2S-enantiomer yielding high enantiomeric purity of cis-(1S, 2R)-indandiol, a potential intermediate in the synthesis of indinavir sulfate (CRIXIVAN), a protease inhibitor used in the treatment of AIDS. Molecular cloning of P. putida toluene dioxygenase in Escherichia coli confirmed the requirement for the dihydrodiol dehydrogenase in resolving racemic mixtures of cis-indandiol. Rhodococcus sp. isolates convert indene to cis-(1S, 2R)-indandiol at high initial enantiomeric excess and one isolate also produces trans-(1R, 2R)-indandiol, suggesting the presence of monooxygenase activity. Scale up and optimization of the bioconversions to these key synthons for chiral synthesis of potential intermediates for commercial manufacture of indinavir sulfate are described.

Drug Design↗
PubMed1997

Attenuated replication of human immunodeficiency virus type 1 with a didanosine-selected reverse transcriptase mutation.

The Leu-74 to Val (Leu74Val) mutation in human immunodeficiency virus type 1 reverse transcriptase (RT) develops as a consequence of didanosine (ddI) therapy and is associated with a decreased susceptibility to ddI. In this report, we provide evidence that the ddI-associated Leu74Val mutation confers a replication disadvantage to the virus. In a series of experiments, we have shown that (i) a cloned virus with an engineered Leu74Val mutation in RT was attenuated for replication; (ii) a Val-to-Leu revertant of Leu74Val in the pNL4-3 background replicated with an efficiency similar to that of the wild-type virus; (iii) when two isolates from the same patient were compared, a clinical isolate containing mutations Leu74Val and Thr215Tyr was attenuated for replication compared to one in which the Thr215Tyr mutation alone was present; and (iv) the viruses with the Leu74Val mutation showed an 11% loss of fitness in a single passage compared to the wild-type and a mutant virus containing a Lys70Arg mutation. The loss of fitness for viruses grown in drug-free medium could result in an inability to detect a Leu74Val mutant in clinical isolates obtained post-ddI therapy. The decreased replication ability of the Leu74Val mutant virus selected by ddI therapy provides a strong rationale for the lower viral RNA levels observed with ddI therapy compared to zidovudine therapy in clinical trials.

Amino Acid Substitution↗
PubMed2001

Thermozymes and their applications: a review of recent literature and patents.

Enzymes from thermophilic microorganisms, thermozymes, have unique characteristics such as temperature, chemical, and pH stability. They can be used in several industrial processes, in which they replace mesophilic enzymes or chemicals. Thermozymes are often used when the enzymatic process is compatible with existing (high-temperature) process conditions. The main advantages of performing processes at higher temperatures are reduced risk of microbial contamination, lower viscosity, improved transfer rates, and improved solubility of substrates. However, cofactors, substrates, or products might be unstable or other side reactions may occur. Recent developments show that thermophiles are a good source of novel catalysts that are of great industrial interest. Thermostable polymer-degrading enzymes such as amylases, pullulanases, xylanases, proteases, and cellulases are expected to play an important role in food, chemical, pharmaceutical, paper, pulp, and waste-treatment industries. Considerable research efforts have been made to better understand the stability of thermozymes. There are no major conformational differences with mesophilic enzymes, and a small number of extra salt bridges, hydrophobic interactions, or hydrogen bounds seem to confer the extra degree of stabilization. Currently, overexpression of thermozymes in standard Escherichia coli allows the production of much larger quantities of enzymes, which are easy to purify by heat treatment. With wider availability and lower cost, thermophilic enzymes will see more application in industry.

Archaea↗
PubMed2006

Application of microbial risk assessment on a residentially-operated bio-toilet.

The Sustainable Sanitation System is a new wastewater treatment system that incorporates a non-flushing toilet (Bio-toilet) that converts excreta into a reusable resource (as fertilizer or humus for organic agriculture) and reduces the pollution load to environments of the rivers, the lakes, and the sea. However, the risk of exposure to pathogens should be considered, because excrement is stored in the Bio-toilet. The aim of the present work is to analyze the health risk of dealing with the matrix (excreta and urine mixed with sawdust) of the Bio-toilet. Therefore, the fate of pathogenic viruses was investigated using coliphages as a virus index, and the modeling of the die-off rate in matrix was introduced. Then the microbial risk assessment was applied to a Bio-toilet that was actually used in a residential house; the infection risks of rotavirus and enterovirus as reference pathogens were calculated. According to the lab-scale experiment using coliphages for investing the die-off rate of viruses in the Bio-toilet, Qbeta had a higher die-off, which was greatly influenced by the water content and temperature. On the other hand, T4 showed a lower rate and was independent of water content. Therefore, these two phages' data were used as critical examples, such as viruses having high or low possibilities of remaining in the Bio-toilet during the risk assessment analysis. As the result of the risk assessment, the storage time required for an acceptable infectious risk level has wide variations in both rotavirus and enterovirus cases depending on the phage that was used. These were 0-260 days' and 0-160 days' difference, respectively.

Bacteriophage T4↗
PubMed2006

Microbial transformation of benzene to cis-3,5-cyclohexadien-1,2-diols by recombinant bacteria harboring toluene dioxygenase gene tod.

Toluene dioxygenase (TDO) catalyzes asymmetric cis-dihydroxylation of aromatic compounds. To achieve high efficient biotransformation of benzene to benzene cis-diols, Pseudomonas putida KT2442, Pseudomonas stutzeri 1317, and Aeromonas hydrophila 4AK4 were used as hosts to express TDO gene tod. Plasmid pSPM01, a derivative of broad-host plasmid pBBR1MCS-2 harboring tod from plasmid pKST11, was constructed and introduced into the above three strains. Their abilities to catalyze the biotransformation of benzene to benzene cis-diols, namely, cis-3,5-cyclohexadien-1,2-diols abbreviated as DHCD, were examined. In shake-flask cultivation under optimized culture media and growth condition, benzene cis-diols production by recombinant P. putida KT2442 (pSPM01), P. stutzeri 1317 (pSPM01), and A. hydrophila 4AK4 (pSPM01) were 2.68, 2.13, and 1.17 g/l, respectively. In comparison, Escherichia coli JM109 (pSPM01) and E. coli JM109 (pKST11) produced 0.45 and 0.53 g/l of DHCD, respectively. When biotransformation was run in a 6-l fermenter, DHCD production in P. putida KT2442 (pSPM01) was approximately 60 g/l; this is the highest DHCD production yield reported so far.

Aeromonas hydrophila↗
PubMed2005

Efficient production of a soluble fusion protein containing human beta-defensin-2 in E. coli cell-free system.

Human beta-defensin-2 (hBD2), a small cationic peptide, exhibits a broad range of antimicrobial activity and does not cause microbial resistance. In order to produce hBD2 efficiently, an Escherichia coli cell-free biosynthesis system has been developed as an alternative method. A specific plasmid pIVEX2.4c-trxA-shBD2 was constructed for the cell-free expression of fusion protein (hBD2 linked with His-Tag and Trx-Tag). This allowed enhancement of protein stability and facilitated downstream purification process. Significant amount of target fusion protein was synthesized in the batch-mode bioreactor by optimizing the reaction conditions. About five-fold improvement of productivity (ca. 2.0 mg/ml soluble fusion protein) could be achieved by using a continuous exchange cell-free (CECF) system compared to batch system. One-step affinity chromatographic process was developed to recover high purity fusion protein (95.2%) with overall recovery ratio of about 50%. The fusion protein was cleaved by cyanogens bromide (CNBr), and the mature hBD2 had demonstrated strong inhibition on the growth of E. coli D31 at low concentration.

Bioreactors↗
PubMed1997

Microbial and animal limitations to fiber digestion and utilization.

The ruminal microbial populations attack, degrade and ferment structural carbohydrates in forage cell walls and thereby provide volatile fatty acids and protein to the host animal. Microbial colonization of fiber is quite rapid; however, the rate and extent to which fiber is degraded is determined to a considerable degree by factors such as microbial accessibility to substrate, physical and chemical nature of the forage and kinetics of ruminal digestion. The physical and chemical nature of forages can present a barrier to their complete digestion in the rumen, especially the association of lignin with polysaccharide constituents. Adhesin proteins allow bacteria with cell-bound enzymes to come into intimate contact with their substrates, ensuring that the degradation products are preferentially available. Research on various fibrolytic enzymes and cellulose binding domains may allow for the transfer of novel genetic material to bacteria for enhancing the hydrolysis of plant cell walls. Fungi may also play an important synergistic role in the ruminal digestion of forages by physically disrupting the lignified stem tissue. This allows the ruminal microbes greater access to the plant stem and the digestible portions of the plant. New developments in fiber utilization by ruminants are currently under investigation and include genetic manipulation of ruminal bacteria, chemical and biological treatments of forages, and manipulation of dietary inputs and feeding management.

Animal Feed↗
PubMed2001

Engineering photocycle dynamics. Crystal structures and kinetics of three photoactive yellow protein hinge-bending mutants.

Crystallographic and spectroscopic analyses of three hinge-bending mutants of the photoactive yellow protein are described. Previous studies have identified Gly(47) and Gly(51) as possible hinge points in the structure of the protein, allowing backbone segments around the chromophore to undergo large concerted motions. We have designed, crystallized, and solved the structures of three mutants: G47S, G51S, and G47S/G51S. The protein dynamics of these mutants are significantly affected. Transitions in the photocycle, measured with laser induced transient absorption spectroscopy, show rates up to 6-fold different from the wild type protein and show an additive effect in the double mutant. Compared with the native structure, no significant conformational differences were observed in the structures of the mutant proteins. We conclude that the structural and dynamic integrity of the region around these mutations is of crucial importance to the photocycle and suggest that the hinge-bending properties of Gly(51) may also play a role in PAS domain proteins where it is one of the few conserved residues.

Amino Acid Sequence↗
PubMed2002

Role of Vibrio cholerae O139 surface polysaccharides in intestinal colonization.

Since the first occurrence of O139 Vibrio cholerae as a cause of cholera epidemics, this serogroup has been investigated intensively, and it has been found that its pathogenicity is comparable to that of O1 El Tor strains. O139 isolates express a thin capsule, composed of a polymer of repeating units structurally identical to the lipopolysaccharide (LPS) O side chain. In this study, we investigated the role of LPS O side chain and capsular polysaccharide (CPS) in intestinal colonization by with genetically engineered mutants. We constructed CPS-negative, CPS/LPS O side chain-negative, and CPS-positive/LPS O side chain-negative mutants. Furthermore, we constructed two mutants with defects in LPS core oligosaccharide (OS) assembly. Loss of LPS O side chain or CPS resulted in a approximately 30-fold reduction in colonization of the infant mouse small intestine, indicating that the presence of both LPS O side chain and CPS is important during the colonization process. The strain lacking both CPS and LPS O side chain and a CPS-positive, LPS O side chain-negative core OS mutant were both essentially unable to colonize. To characterize the role of surface polysaccharides in survival in the host intestine, resistance to several antimicrobial substances was investigated in vitro. These investigations revealed that the presence of CPS protects the cell against attack of the complement system and that an intact core OS is necessary for survival in the presence of bile.

Animals↗
PubMedDate not supplied

Peptidyl linkers for protein heterodimerization catalyzed by microbial transglutaminase.

Specific peptidyl linkers that result in the heterodimerization of functional proteins, which is catalyzed by microbial transglutaminase from Streptomyces mobaraensis (MTG), were generated based on a ribonuclease S-peptide using site-directed mutagenesis. The peptidyl linkers designated as Lys-tag and Gln-tag were designed to possess sole reactive Lys or Gln residue that was amenable for selective Lys-Gln cross-linkage of different proteins. Green fluorescent protein variants, ECFP and EYFP, were employed as model proteins, and those Lys- and Gln-tags were fused to the N-termini of ECFP and EYFP, respectively. As a result, we succeeded in solely obtaining the ECFP-EYFP heterodimer without forming multiply cross-linked byproducts. It was found that the reactivity of peptidyl linkers varied according to the type of amino acid to be replaced. Peptidyl linkers with a basic amino acid (Arg) exhibited the highest reactivity in the cross-linking reaction, suggesting the cationic residue substrate preference of MTG. Kinetic analysis utilizing fluorescent resonance energy transfer (FRET), that is only observed upon the heterodimeric ECFP-EYFP conjugation, revealed that the amino acid replacement contributed to the acceleration of cross-linking reactions by increasing catalytic turnover (k(cat)), rather than substrate binding affinity (K(m)). Finally, using a ribonuclease S-protein, the manipulation of enzymatic protein cross-linking based on specific S-peptide:S-protein interactions was explored. Since newly designed Lys- and Gln-tags retained binding affinities to the S-protein, the heterodimerization was perfectly restrained by wrapping them with the S-protein. The results suggest the possibility of limited protein conjugation by tuning steric hindrance against the MTG. Tailoring enzymatic posttranslational modifications with either engineering peptidyl substrates or by taking specific peptide-protein interactions into consideration may facilitate the development of a new sequential protein conjugation method for the preparation of multifunctional protein.

Catalysis↗
PubMed2006

Understanding and manipulating glycopeptide pathways: the example of the dalbavancin precursor A40926.

Glycopeptide antibiotics represent an important class of microbial compounds produced by several genera of actinomycetes. The emergence of resistance to glycopeptides among enterococci and staphylococci has prompted the search for second-generation drugs of this class and semi-synthetic derivatives are currently under clinical trials. Dalbavancin is obtained by chemical modification of the natural glycopeptide A40926, produced by a Nonomuraea sp. Recently, there has been considerable progress in the elucidation of biosynthesis of glycopeptide antibiotics; several gene clusters have been characterized, thus providing an understanding of the biosynthesis of these chemically complex molecules. Furthermore, such investigations have yielded the first glycopeptide derivatives produced by genetic or enzymatic intervention. We have isolated and characterized the dbv clusters, involved in the formation of the glycopeptides A40926. The development of a gene-transfer system for Nonomuraea sp. has allowed the manipulation of the A40926 pathway. New derivatives were obtained by inactivating selected dbv genes. In addition, our data suggest differences in the biosynthetic routes for heptapeptide formation between the vancomycin and the teicoplanin families of glycopeptides.

Actinomycetales↗
PubMed1997

A low molecular weight artificial RNA of unique size with multiple probe target regions.

Artificial RNAs (aRNAs) containing novel sequence segments embedded in a deletion mutant of Vibrio proteolyticus 5S rRNA have previously been shown to be expressed from a plasmid borne growth rate regulated promoter in E. coli. These aRNAs accumulate to high levels and their detection is a promising tool for studies in molecular microbial ecology and in environmental monitoring. Herein a new construct is described which illustrates the versatility of detection that is possible with aRNAs. This 3xPen aRNA construct carries a 72 nucleotide insert with three copies of a unique 17 base probe target sequence. This aRNA is 160 nucleotides in length and again accumulates to high levels in the E. coli cytoplasm without incorporating into ribosomes. The 3xPen aRNA illustrates two improvements in detection. First, by appropriate selection of insert size, we obtained an aRNA which provides a unique and hence, easily quantifiable peak, on a high resolution gel profile of low molecular weight RNAs. Second, the existence of multiple probe targets results in a nearly commensurate increase in signal when detection is by hybridization. These aRNAs are naturally amplified and carry sequence segments that are not found in known rRNA sequences. It thus may be possible to detect them directly. An experimental step involving RT-PCR or PCR amplification of the gene could therefore be avoided.

Base Sequence↗
PubMed2006

Micro-colony array based high throughput platform for enzyme library screening.

Enzymes are becoming increasingly important tools for synthesizing and modifying fine and bulk chemicals. The availability of biocatalysts which fulfil the requirements of industrial processes is often limited. Recruiting suited enzymes from natural (e.g. metagenomes) and artificial (e.g. directed evolution) biodiversity is based on screening libraries of microbial clones expressing enzyme variants. However, exploring the complex diversity of such libraries needs efficient screening methods. Overcoming the "screening bottleneck" requires rapid high throughput technology allowing the analysis of a large diversity of different enzymes and applying different screening conditions. Facing these facts an efficient and cost effective method for high throughput screening of large enzyme libraries at the colony level was developed. Therefore, ordered high density micro-colony arrays were combined with optical sensor technology and automated image analysis. The system generally allows the simultaneous monitoring of enzyme activities reflected by up to 7000 micro-colonies spotted on a filter in the size of a micro-titer plate. A developed replica option also allows the analysis of clones under varying external conditions. The method was verified by a model screening using esterases and was proved to provide reliable enzyme activity measurements within single micro-colonies allowing the discrimination of activity differences in the range of 10-20%.

Calibration↗
PubMed2004

Programmed population control by cell-cell communication and regulated killing.

De novo engineering of gene circuits inside cells is extremely difficult, and efforts to realize predictable and robust performance must deal with noise in gene expression and variation in phenotypes between cells. Here we demonstrate that by coupling gene expression to cell survival and death using cell-cell communication, we can programme the dynamics of a population despite variability in the behaviour of individual cells. Specifically, we have built and characterized a 'population control' circuit that autonomously regulates the density of an Escherichia coli population. The cell density is broadcasted and detected by elements from a bacterial quorum-sensing system, which in turn regulate the death rate. As predicted by a simple mathematical model, the circuit can set a stable steady state in terms of cell density and gene expression that is easily tunable by varying the stability of the cell-cell communication signal. This circuit incorporates a mechanism for programmed death in response to changes in the environment, and allows us to probe the design principles of its more complex natural counterparts.

Cell Division↗
PubMed1999

Rapid evaluation of biocidal activity using a transposon-encoded catechol 2,3-dioxygenase from Pseudomonas putida.

Pseudomonas putida (UWC1), containing a genetically-engineered plasmid (pQM899), that encodes for the production of catechol 2,3-dioxygenase (C230), was used as a potential means of rapidly estimating bactericidal activity of chlorhexidine diacetate (CHA), phenol, cetylpyridinium chloride (CPC) and phenylmercuric nitrate (PMN). Enzyme C230 converts catechol to 2-hydroxymuconic semialdehyde (2-HMS), which is yellow in colour, via a meta cleavage pathway. Ideal conditions for production and measurement spectrophotometrically of 2-HMS were determined. However, the correlation between this method and viable plate counts was not sufficiently accurate to enable 2-HMS production to provide a sufficiently sensitive determination of biocidal activity. An alternative method, synchronous scanning fluorimetry, in which the decrease in catechol concentration was measured under standardized conditions, provided a good dose-response histogram for all the biocides tested. Although, in comparison with plate counts, there was an underestimation of the bactericidal effects of phenol an PMN, the results of this study suggest that this method has potential in determining the bactericidal efficacy of agents such as CHA and CPC.

Catechol 2,3-Dioxygenase↗