Genetic selection system for improving recombinant membrane protein expression in E. coli

A major barrier to the physical characterization and structure determination of membrane proteins is low yield in recombinant expression. To address this problem, we have designed a selection strategy to isolate mutant strains of Escherichia coli that improve the expression of a targeted membrane protein. In this method, the coding sequence of the membrane protein of interest is fused to a C‐terminal selectable marker, so that the production of the selectable marker and survival on selective media is linked to expression of the targeted membrane protein. Thus, mutant strains with improved expression properties can be directly selected. We also introduce a rapid method for curing isolated strains of the plasmids used during the selection process, in which the plasmids are removed by in vivo digestion with the homing endonuclease I‐CreI. We tested this selection system on a rhomboid family protein from Mycobacterium tuberculosis (Rv1337) and were able to isolate mutants, which we call EXP strains, with up to 75‐fold increased expression. The EXP strains also improve the expression of other membrane proteins that were not the target of selection, in one case roughly 90‐fold.     

Isolation of quizalofop-resistant mutants of Nannochloropsis oculata (Eustigmatophyceae) with high eicosapentaenoic acid following N-methyl-N-nitrosourea-induced random mutagenesis

Nannochloropsis oculata was subjected to N-methyl-N-nitrosourea-induced mutagenesis under the selection pressure of quizalofop, a known inhibitor of acetyl-CoA carboxylase (ACCase) activity with the objective of generating genetically tractable mutants with altered fatty acid metabolism. Two mutants, QUIZ1 and QUIZ2, with stable resistance to quizalofop were isolated and partially characterized. The growth properties and morphology of the mutants appeared identical with the parent strain. However thermo-tolerance was observed in the mutants. Enhanced resistance to quizalofop suggested the presence of herbicide resistant isoforms of ACCase. In vitro assays for ACCase activity showed that ACCase in the wild strains was much more sensitive to quizalofop than the mutant strains. Gas chromatographic analysis of fatty acids revealed that the mutant strains were rich in polyunsaturated fatty acids (n– 3PUFAs), as well as total fatty acid contents; this was accompanied by a concomitant increase in triacylglycerol (TAG) followed by linoleic acid (18:2), arachidonic acid (20:4 n– 6) and EPA (20:5 n– 3). These results suggest that an increased substrate pool (malonyl-CoA) (due to increased specific activity of ACCase) in the mutant strains in vivo and in vitro may have led to the increased TAG accumulation. Random mutagenesis was shown to be a good tool to manipulate PUFAs and EPA in Nannochloropsis. The strains developed will be useful in understanding fatty acid metabolism using genetic and biochemical approaches and also for their direct use in mariculture.     

Strain-specific detection of two Aureobasidium pullulans strains, fungal biocontrol agents of fire blight by new, developed multiplex-PCR

Aim:  The aim of this study was to develop a specific and sensitive identification method for two Aureobasidium pullulans biocontrol strains, CF10 and CF40, based on a sequence-characterized amplified region (SCAR) derived from RAPD – and multiplex-RAPD PCR analysis. Methods and Results:  The random amplified polymorphic DNA (RAPD) and multiplex RAPD-PCR techniques were used for a preliminary screening of A. pullulans genetic variability among 200 isolates. This approach allowed the selection of ten fragments present solely in strains CF10 and CF40. The RAPD fragments were cloned, sequenced and used to design two SCAR primers. Two primer pairs obtained from SCH3RAPD fragment of CF 40 and 6RAPD of CF10 were highly specific and sensitive. Conclusions:  In this study, we developed strain-specific multiplex-PCR based on sequence-characterized amplified region (SCAR) markers to simultaneously detect both strains in a single PCR. Significance and Impact of the Study:  This new multiplex-PCR provides a valuable tool for specific and sensitive identification of CF10 and CF40, and could be used in studies on the efficacy and persistence of introduced strains of A. pullulans for fire blight control.     

Selection of spontaneous mutants ofYarrowia lipolytica by inositol-less death

Summary A procedure was developed for the selection of spontaneous mutants of the yeastYarrowia lipolytica. An inositol-requiring mutant of a wild-typeY. lipolytica, YB 3-122, was derived by mutagenesis and screening. The mutant had a reversion frequency of less than 6×10^–9. A mutant selection procedure based on inositolless death was then developed using this mutant strain. The selection procedure killed growingY. lipolytica cells and enriched for mutants yielding cultures that consisted of 60–98% spontaneous mutants after two rounds of inositol-less death. The procedure enriched for four classes of mutants, strains that were auxotrophic, metabolite analog sensitive, temperature sensitive, or unable to grow on citric acid as the sole carbon source. Since strain YB 3-122 is now available to yeast researchers, inositol-less death will be useful for the routine isolation of spontaneous mutants ofY. lipolytica.     

Mutagen sensitivity of Drosophila melanogaster. I. Isolation and preliminary characterization of a methyl methanesulphonate-sensitive strain

Sensitivity to the monofunctional alkylating agent methyl methanesulfonate (MMS) has been tested as a selection technique to isolate mutant strains which can provide insights into the genetic control of DNA replication, DNA repair and recombination in the complex eucaryote, Drosophila melanogaster. The successful isolation of an X-linked MMS-sensitive strain, mut^s, has suggested that mutagen sensitivity is a feasible methodology for the selection of mutant strains of Drosophila which will be useful in the genetic and biochemical analysis of these cellular functions. Preliminary characterization of this mutant strain indicates that: (A) it is extremely sensitive to killing by MMS; (B) it is more mutable by MMS than the parent wildtype strain; and (C) it appears to possess mutator gene activity.     

Mutant selection and phenotypic and genetic characterization of ethanol-tolerant strains of <Emphasis Type="Italic">Clostridium thermocellum</Emphasis>

Clostridium thermocellum is a model microorganism for converting cellulosic biomass into fuels and chemicals via consolidated bioprocessing. One of the challenges for industrial application of this organism is its low ethanol tolerance, typically 1–2% (w/v) in wild-type strains. In this study, we report the development and characterization of mutant C. thermocellum strains that can grow in the presence of high ethanol concentrations. Starting from a single colony, wild-type C. thermocellum ATCC 27405 was sub-cultured and adapted for growth in up to 50 g/L ethanol using either cellobiose or crystalline cellulose as the growth substrate. Both the adapted strains retained their ability to grow on either substrate and displayed a higher growth rate and biomass yield than the wild-type strain in the absence of ethanol. With added ethanol in the media, the mutant strains displayed an inverse correlation between ethanol concentration and growth rate or biomass yield. Genome sequencing revealed six common mutations in the two ethanol-tolerant strains including an alcohol dehydrogenase gene and genes involved in arginine/pyrimidine biosynthetic pathway. The potential role of these mutations in ethanol tolerance phenotype is discussed.     

RAPD molecular differentiation of the cultivated strains of the jelly mushrooms, <Emphasis Type="Italic">Auricularia auricula</Emphasis> and <Emphasis Type="Italic">A. polytricha</Emphasis>

Auricularia mushrooms are the fourth most important cultivated mushrooms in the world, with a unique jelly taste and horizontal-septated basidium which are significantly different from other cultivated mushrooms. Differentiation of commercial cultivated strains is difficult to conduct, due to the lack of useful distinguishable characters. In this study, we used the RAPD technique to differentiate 11 commercial strains of A. auricula and five commercial strains of A. polytricha and one white-fruitbody mutant strain, and to characterize their genetic diversity. Results showed that all the strains tested could be differentiated by pooled RAPD data, and even one individual primer (S10) could also discriminate all tested strains. RAPD analysis could differentiate strains having identical rDNA RFLP and supports the classification of the white-fruitbody mutant to the species of A. polytricha. Genetic similarity analysis and grouping derived from RAPD markers reveals a high level of genetic diversity of commercial strains of Auricularia auricula and A. polytricha. Therefore, the RAPD technique can provide a powerful tool to discriminate the commercialAuricularia strains and offer the molecular information useful for breeding systems.     

Isolation of <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis> Specific Phages with Broad Activity Spectra

The aim of the study was to screen various kinds of samples for Pseudomonas aeruginosa specific phages and to isolate and partially characterize those with broad activity spectra. The Pseudomonas specific phages were isolated using an enrichment procedure with single strains or the cocktail of P. aeruginosa strains as hosts. Using the described procedure, phages were successfully isolated only from water samples, while in soil and feces no Pseudomonas specific phages were detected. The lytic spectra of isolated phages were determined by spot method on lawns of 33 P. aeruginosa strains and five species belonging to family Enterobacteriaceae. The results showed that among isolated phages, 001A, δ, and I possessed the broad activity spectra, as were able to plaque on more than 50% of tested P. aeruginosa strains, while none of the phages were able to lyse the other tested species. Significant differences in phage activity spectra were not observed when P. aeruginosa cocktail was applied for sample enrichment. The most of the phages examined by electron microscopy belonged to family Siphoviridae, while the broad activity spectra isolates, except for 001A, possessed morphological characteristics of family Podoviridae. Digested DNA of the phages δ and I showed similar patterns, indicating the prevalence and success of this phage type in the environment.     

Stability of entomopathogenic bacteria, <Emphasis Type="Italic">Xenorhabdus nematophila</Emphasis> and <Emphasis Type="Italic">Photorhabdus luminescens</Emphasis>, during in vitro culture

The entomopathogenic nematode–bacteria complexes Heterorhabditis bacteriophora/Photorhabdus luminescens and Steinernema carpocapsae/Xenorhabdus nematophila are mass produced for use as biological insecticides. Stability of the bacterial partner in culture is essential for maintaining traits important for both biological control and production. Two geographically distinct strains of each bacterial species were isolated from their nematode partners and serially subcultured on in vitro media to assess trait stability. Subculturing resulted in a shift to secondary cell production in one P. luminescens strain and both X. nematophila strains within ten in vitro culture cycles. However, when cell phenotypic variation was controlled in X. nematophila strains by regular selection for primary variants, no trait change was detected in the primary variant after prolonged subculture. When P. luminescens cell phenotypic variation was controlled by selection for primary variants, changes in the primary variant of both strains were noted including reductions in cell and inclusion body size and inclusion body prevalence. Bacterial ability to cause lethal infections following injection into the hemocoel of Tenebrio molitor larvae declined by more than half in primary variants of one P. luminescens strain. Conversely, yield was enhanced, with the subcultured P. luminescens strains showing 53.5 and 75.8% increases in primary cell density. Field adapted traits of primary variant P. luminescens strains tend to deteriorate during in vitro culture as tradeoffs for gains in yield. In vitro producers of the P. luminescens/H. bacteriophora complex must weigh the need for superior bacterial yield against the need to preserve traits important for biological control.     

Relationship between virulence and enzymatic profiles in the cuticle of <Emphasis Type="Italic">Tenebrio molitor</Emphasis> by 2-deoxy-<Emphasis Type="SmallCaps">d</Emphasis>-glucose-resistant mutants of <Emphasis Type="Italic">Beauveria bassiana</Emphasis> (Bals.) Vuill

The secretion of hydrolases by Beauveria bassiana is a main factor in the degradation of cuticle, while in filamentous fungi the resistance to 2-deoxy-d-glucose (2DG) is related to enzymatic deregulation. A series of 2DG-resistant B. bassiana strains were classified according to the phenotypes of germination (G) and radial growth rate (U_r), in addition to their virulence parameters on Tenebrio molitor. This analysis allowed distinction between mutants with greater (881.2) and lesser (884.5) G and U_r values, relative to the wild-type strain (88), which correlated with virulence parameters including maximal mortality (M) and time to reach 50% mortality (LT₅₀). Subsequently, using the cuticle of T. molitor as the substrate for these strains, an enzymatic analysis (total proteases, Pr1, chitinases and β-N-acetylglucosaminidase) showed that the contrasting virulence traits were associated with different deregulation patterns: higher specific activities (up to 100%) for the more virulent mutant 881.2 and lower enzymatic levels for mutant 884.5, specifically chitinases (33% reduction), relative to the wild-type strain (88) for both mutants. The differences in cuticle-degrading enzymes were consistent with the appearance of hyphal bodies within infected insects. This is the first study describing the altered enzymatic profiles in 2DG-resistant mutants of B. bassiana with practical implications in the selection of improved strains for biological control.     

Biodiversity of wild strains of <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> as tool to complement and optimize wine quality

The principal agent in winemaking is the yeast Saccharomyces cerevisiae, which is characterized by a significant strain biodiversity. Here we report the characterization of 80 wild S. cerevisiae strains, isolated from grapes of different varieties in southern Italy, for genetic and technological variability. By PCR amplification with M13 primer a significant polymorphism was recorded and 12 different biotypes were identified among the strains. The specific strain-pattern could be used to follow the dynamics of different biotypes during the fermentation process. The analysis of experimental wines obtained by inoculated fermentations with the 80 strains showed significant differences among the wines. The level of each compound was a function of the strain performing the fermentative process. The main variables for the strain differentiation were the production of acetaldehyde and acetic acid, which ranged from 53 to 282 mg/l and from 0.20 to 1.88 g/l, respectively. Selected strains were tested in fermentation with two different grape musts, yielding experimental wines differing in the levels of secondary compounds and polyphenol content, in function of the interaction “grape must composition/yeast strain”. This finding has an applicative value for the potentiality of utilizing the resource of strain variability as a tool to individuate suitable starter cultures, which are able to complement and optimize grape quality.     

lac‐1 and lag‐1 with ras‐1 affect aging and the biological clock in Neurospora crassa

Using an automated cell counting technique developed previously (Case et al., Ecology and Evolution 2014; 4: 3494), we explore the lifespan effects of lac‐1, a ceramide synthase gene paralogous to lag‐1 in Neurospora crassa in conjunction with the band bd (ras‐1) gene. We find that the replicative lifespan of a lac‐1^KO bd double mutants is short, about one race tube cycle, and this double mutant lacks a strong ~21‐hr clock cycle as shown by race tube and fluorometer analysis of fluorescent strains including lac‐1^KO. This short replicative lifespan phenotype is contrasted with a very long estimated chronological lifespan for lac‐1^KO bd double mutants from 247 to 462 days based on our regression analyses on log viability, and for the single mutant lac‐1^KO, 161 days. Both of these estimated lifespans are much higher than that of previously studied WT and bd single mutant strains. In a lac‐1 rescue and induction experiment, the expression of lac‐1⁺ as driven by a quinic acid‐dependent promoter actually decreases the median chronological lifespan of cells down to only 7 days, much lower than the 34‐day median lifespan found in control bd conidia also grown on quinic acid media, which we interpret as an effect of balancing selection acting on ceramide levels based on previous findings from the literature. Prior work has shown phytoceramides can act as a signal for apoptosis in stressed N. crassa cells. To test this hypothesis of balancing selection on phytoceramide levels, we examine the viability of WT, lag‐1^KO bd, and lac‐1^KO bd strains following the dual stresses of heat and glycolysis inhibition, along with phytoceramide treatments of different dosages. We find that the phytoceramide dosage–response curve is altered in the lag‐1^KO bd mutant, but not in the lac‐1^KO bd mutant. We conclude that phytoceramide production is responsible for the previously reported longevity effects in the lag‐1^KO bd mutant, but a different ceramide may be responsible for the longevity effect observed in the lac‐1^KO bd mutant.     

Isolation and characterization of mutants corresponding to the MENA,MENB, MENC and MENE enzymatic steps of 5′‐monohydroxyphylloquinone biosynthesis in Chlamydomonas reinhardtii

Phylloquinone (PhQ), or vitamin K₁, is an essential electron carrier (A₁) in photosystem I (PSI). In the green alga Chlamydomonas reinhardtii, which is a model organism for the study of photosynthesis, a detailed characterization of the pathway is missing with only one mutant deficient for MEND having been analyzed. We took advantage of the fact that a double reduction of plastoquinone occurs in anoxia in the A₁ site in the mend mutant, interrupting photosynthetic electron transfer, to isolate four new phylloquinone‐deficient mutants impaired in MENA, MENB, MENC (PHYLLO) and MENE. Compared with the wild type and complemented strains for MENB and MENE, the four men mutants grow slowly in low light and are sensitive to high light. When grown in low light they show a reduced photosynthetic electron transfer due to a specific decrease of PSI. Upon exposure to high light for a few hours, PSI becomes almost completely inactive, which leads in turn to lack of phototrophic growth. Loss of PhQ also fully prevents reactivation of photosynthesis after dark anoxia acclimation. In silico analyses allowed us to propose a PhQ biosynthesis pathway in Chlamydomonas that involves 11 enzymatic steps from chorismate located in the chloroplast and in the peroxisome.     

Glyphosate Resistance as a Versatile Selection Marker for <Emphasis Type="Italic">Arabidopsis</Emphasis> Transformation

Molecular genetic studies on the model plant Arabidopsis thaliana often involve multiple rounds of Agrobacterium-mediated transformation. Such procedures require multiple marker genes that would allow for efficient selection of transgenic plants in each cycle of transformation. Here, we report on a selection marker cassette based on a codon-modified glyphosate N-acetyltransferase (GAT) gene whose expression is driven by a powerful EL2Ω promoter. After introduction of the GAT expression cassette into A. thaliana via Agrobacterium-mediated transformation, glyphosate-resistant primary transformants are efficiently selected by glyphosate, either added to the culture medium or by spraying a glyphosate solution onto seedlings grown in soil. Robust glyphosate-resistant phenotypes are always associated with the presence of the GAT cassette. In addition, RT-PCR analysis of T₂ transformants has demonstrated that resistance to glyphosate is associated with higher levels of GAT expression. Resistance conferred by GAT is specific to glyphosate and not to other commonly used selection chemical compounds. These results demonstrate the versatility of the GAT cassette suitable for both large-scale, soil-based selection system of transgenic plants as well as their characterization in vitro.     

Methods designed for the identification and characterization of<Emphasis Type="Italic">in vitro</Emphasis> and<Emphasis Type="Italic">in vivo</Emphasis> chromatin assembly mutants in<Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>

Assembly of DNA into chromatin allows for the formation of a barrier that protects naked DNA from protein and chemical agents geared to degrade or metabolize DNA. Chromatin assembly occurs whenever a length of DNA becomes exposed to the cellular elements, whether during DNA synthesis or repair. This report describes tools to study chromatin assembly in the model systemSaccharomyces cerevisiae. Modifications to anin vitro chromatin assembly assay are described that allowed a brute force screen of temperature sensitive (ts) yeast strains in order to identify chromatin assembly defective extracts. This screen yielded mutations in genes encoding two ubiquitin protein ligases (E3s):RSP5, and a subunit of the Anaphase Promoting Complex (APC),APC5. Additional modifications are described that allow for a rapid analysis and anin vivo characterization of yeast chromatin assembly mutants, as well as any other mutant of interest. Our analysis suggests that thein vitro andin vivo chromatin assembly assays are responsive to different cellular signals, including cell cycle cues that involve different molecular networks. Published: July 3, 2003     

Biological synthesis of quercetin 3-<Emphasis Type="Italic">O</Emphasis>-<Emphasis Type="Italic">N</Emphasis>-acetylglucosamine conjugate using engineered <Emphasis Type="Italic">Escherichia coli</Emphasis> expressing <Emphasis Type="Italic">UGT78D2</Emphasis>

Biotransformation of flavonoids using Escherichia coli harboring nucleotide sugar-dependent uridine diphosphate-dependent glycosyltransferases (UGTs) commonly results in the production of a glucose conjugate because most UGTs are specific for UDP-glucose. The Arabidopsis enzyme AtUGT78D2 prefers UDP-glucose as a sugar donor and quercetin as a sugar acceptor. However, in vitro, AtUGT78D2 could use UDP-N-acetylglucosamine as a sugar donor, and whole cell biotransformation of quercetin using E. coli harboring AtUGT78D2 produced quercetin 3-O-N-acetylglucosamine. In order to increase the production of quercetin 3-O-N-acetylglucosamine via biotransformation, two E. coli mutant strains deleted in phosphoglucomutase (pgm) or glucose-1-phosphate uridylyltransferase (galU) were created. The galU mutant produced up to threefold more quercetin 3-O-N-acetylglucosamine than wild type, resulting in the production of 380-mg/l quercetin 3-O-N-acetylglucosamine and a negligible amount of quercetin 3-O-glucoside. These results show that construction of bacterial strains for the synthesis of unnatural flavonoid glycosides is possible through rational selection of the nucleotide sugar-dependent glycosyltransferase and engineering of the nucleotide sugar metabolic pathway in the host strain.     

Isolation and Characterization of the Thylakoid Membranes from the NaCl-Resistant (NaClr) Mutant Strain of the Cyanobacterium Anabaena variabilis

NaCl-induced changes in the thylakoid membrane of wild-type Anabaena variabilis and its NaCl^r mutant strain have been studied. Biochemical characterization of the thylakoid membrane was done by taking its absorption and fluorescence spectra at different wavelength. The thylakoid membranes of both strains were isolated by mechanical disruption of the freeze-dried and lysozyme-treated cells, followed by differential and density gradient centrifugation. The light absorption spectra of the thylakoid membrane showed three and two peaks in NaCl^r mutant strain and its wild-type counterpart respectively at wavelengths of 400–850 nm. These peaks revealed that the thylakoid membrane contains a large amount of carotenoid and chlorophyll a. Fluorescence emission spectra of thylakoid membrane of NaCl^r mutant and its wild-type strain at excitation wavelength of 335 nm showed two different peaks, one at 340 nm and the other at 663 nm respectively. The light absorption and fluorescence spectra of the thylakoid membrane also revealed that the membrane contained carotenoid pigment, chlorophyll (Chl) a, and a pigment with an emission peak at 335 nm. The HPLC analysis of the pigments of the thylakoid membrane indicates that the NaCl^r mutant strain under NaCl stress contained an additional peak for the carotenoid pigment, which was lacking in its wild-type counterpart. The major peak in thylakoid membrane was that of echinenone and β-carotene. Whereas the polypeptide composition of thylakoid membrane differed in the wild-type and its NaCl^r mutant strain, no difference in the cell wall protein pattern was observed in both strains. The thylakoid membrane of NaCl^r mutant strain contained two additional protein bands that were absent in its wild-type counterpart. The thylakoid membrane of the wild-type and its NaCl^r mutant strain also showed morphological variations under NaCl stress. Received: 14 April 2000 / Accepted: 23 May 2000     

Thailand habitats as sources of pullulan-producing strains of <Emphasis Type="Italic">Aureobasidium pullulans</Emphasis>

Summary A variety of habitats were sampled for the presence of Aureobasidium black yeasts with the attempt to find pullulan-producing strains. Habitats included leaves of mango (Mangifera indica Linn.), tamarind (Tamarindus indica Linn.), asoka (Saraca indica Linn.) and latex-painted and bathroom cement-wall surfaces. Parameters for the identification of the isolates included morphology, nutritional parameters, exopolysaccharide (EPS) production, and rDNA internal transcribed spacer (ITS) sequencing. All isolates of black yeasts were polymorphic with blastospores, hyphae, and chlamydospores. ITS analyses showed strong correlation with the GenBankA. pullulanssequences, with alignment using BLAST yielding greater than 95% similarity. All five isolates tested produced pullulan as deduced from infrared spectra and sensitivity to pullulanase. None produced aubasidan as evidenced from their IR spectra. The current studies support the notion that the hot, humid environments facilitate the development of A. pullulansand its tropical variants in diverse phylloplane and walls habitats, and merit support for further isolation and characterization of these black yeasts as a source of unique pullulan-producing strains.