Antagonism, non-native interactions and non-two-state folding in S6 revealed by double-mutant cycle analysis

When folding to the native state N in the presence of salt, the apparent two-state folder S6 transiently forms a transient off-pathway state C with substantial secondary and tertiary structure. Fifteen double mutant cycles were analysed to compare side-chain interaction energies DeltaDeltaG(int) in C, N and TS (the transition state between N and the denatured state). The kinetic signatures of these destabilizing mutants suggest folding scenarios involving unfolding intermediates and even alternative unfolding pathways. However, restricting the kinetic data to linear parts of the chevron plot allows reliable extrapolation to zero molar denaturant of rate constants of folding, unfolding and misfolding. Side-chain interactions appear to contribute to the stability of C, but in a substantially non-native environment, as shown by changes in the sign of DeltaDeltaG(int) between C and N. Remarkably, there appear to be significant (0.7-2 kcal/mol) antagonistic interactions between the two residues Leu30 and Leu75 in N and TS, which may be linked to subtle structural changes seen in the crystal structures of the mutants. A small number of overlapping residues are involved in these kinds of antagonistic interactions in N, TS and C, suggesting that repulsive interactions are coded into the protein topology whether the protein folds or misfolds. Destabilizing double mutants indicate that apparent two-state folders can be induced to behave in more complex ways provided that the native state is suitably destabilized.     

DNA transformations of Candida tropicalis with replicating and integrative vectors.

The alkane-assimilating yeast Candida tropicalis was used as a host for DNA transformations. A stable ade2 mutant (Ha900) obtained by UV-mutagenesis was used as a recipient for different vectors carrying selectable markers. A first vector, pMK16, that was developed for the transformation of C. albicans and carries an ADE2 gene marker and a Candida autonomously replicating sequence (CARS) element promoting autonomous replication, was compatible for transforming Ha900. Two transformant types were observed: (i) pink transformants which easily lose pMK16 under non-selective growth conditions; (ii) white transformants, in which the same plasmid exhibited a higher mitotic stability. In both cases pMK16 could be rescued from these cells in Escherichia coli. A second vector, pADE2, containing the isolated C. tropicalis ADE2, gene, was used to transform Ha900. This vector integrated in the yeast genome at homologous sites of the ade2 locus. Different integration types were observed at one or both ade2 alleles in single or in tandem repeats.     

Performance of Lactobacillus helveticus Spontaneous Phage-resistant Mutants in Hard Cheese Production

From the strain Lactobacillus helveticus ATCC 15807, a total of 66 clones were isolated using the lytic phages hv and ATCC 15807-B1. Phenotypic parameters related to their phage resistance capacity (efficiency of plaquing, phage resistance stability, lysogeny and adsorption rates) were determined. The morphological, biochemical (sugar fermentation patterns) and technological (acidifying power, proteolytic activity and slime production) characteristics of the isolates were also studied. Phage resistance stability was a variable property among the isolates but a high level of resistance was exhibited as quantified by the efficiency of plaquing. Furthermore, a total absence of acquired lysogeny was demonstrated. The phage-resistant variants were completely or partially unable to bind phages and did not show differences with Lb. helveticus ATCC 15807 in their biochemical characteristics. However, the technological properties (acidifying powers and proteolytic activities) were heterogeneously distributed among the mutants. The variant RB1-28 (isolated under selective pressure of the phage ATCC 15807-B1) was evaluated for the technological performance in Sardo cheese production in comparison with Lb. helveticus ATCC 15807. There were no significant differences between the two types of cheeses, taking in consideration physicochemical parameters (proteolysis level, dry matter, total and soluble proteins, moisture), microbiological counts or sensory analysis. These phage-resistant variants could be employed in starter strain rotation programs for cheesemaking.     

Metabolic regulation in the yeast Hansenula polymorpha. Growth of dihydroxyacetone kinase/glycerol kinase-negative mutants on mixtures of methanol and xylose in continuous cultures

The physiological responses of Hansenula polymorpha wild-type and mutant strains 17B (dihydroxyacetone kinase-negative) and 17BG51 (dihydroxyacetone kinase- and glycerol kinase-negative) to growth on mixtures of xylose and methanol in chemostats were investigated. Increasing methanol concentrations (0–110 mM ) in the feed of the wild-type culture resulted in increasing cell densities and a gradual switch towards methanol metabolism. At the lower methanol feed concentrations the mutant cultures used methanol and xylose to completion and changes in enzyme patterns comparable to the wild type were observed. This was not reflected in significant changes in cell densities. Instead, formaldehyde assimilation resulted in dihydroxyacetone (DHA) production, which was proportional to the amount of methanol added. At intermediate methanol concentration the cultures showed a strong variation in DHA levels and cell densities. Further increased in the methanol feed concentrations resulted in a drop in DHA accumulation rates, repression of alcohol oxidase synthesis and accumulation of residual methanol. The phenomena were studied in more detail in transition experiments and with gradients of methanol. The results indicate that xylulose-5-phosphate (Xu5P) generated in xylose metabolism served as acceptor molecule for formaldehyde assimilation by the peroxisomal enzyme DHA synthase. Accumulation of DHA in the mutant cultures, however, further diminished the availability of carbon for growth. The data suggest that with increasing methanol concentrations Xu5P eventually became growth rate limiting. This resulted in an unstable situation but wash-out of the culture did not occur to a significant extent. Instead, DHA accumulation ceased and cell densities, and enzymes specifically involved in xylose metabolism increase, indicating that the organism resumed its xylose metabolism. The molecular mechanisms controlling the partitioning of Xu5P over xylose (pentose phosphate pathway) and methanol (peroxisome) metabolism under these conditions remain to be elucidated.     

A Survey of Industrial Strains of Saccharomyces cerevisiae Reveals Numerous Altered Patterns of Maltose and Sucrose Utilisation

A model fermentation system was used to define the abilities of 25 Saccharomyces cerevisiae strains, representing the brewing, baking, winemaking and distilling industries, to utilise maltose and sucrose in the presence of glucose and fructose. Three categories of sucrose and maltose utilisers were observed; repressible, constitutive and non‐utilisers. In terms of fermentation kinetics, neither high rates of sucrose hydrolysis nor the early onset of maltose utilisation were correlated with reduced fermentation duration in the experimental system used. Instead better positive correlations were found between this parameter and biomass formation (R² = 0.62) and rates of maltose or monosaccharide removal (R² = 0.87 and 0.82, respectively). Additionally, invertase activity of brewing strains was seen to occur in two forms: cell‐associated and non‐cell‐associated. This survey exposed a number of novel phenotypes that could be harnessed as a means of producing strains with rapid and efficient utilisation of fermentable carbohydrates.     

Assembly of amine oxidase and D-amino acid oxidase in the cytosol of peroxisome-deficient mutants of the yeast Hansenula polymorpha during growth of cells on glucose in the presence of primary amines or D-alanine as the sole nitrogen source

We have studied growth of two peroxisome-deficient mutant strains of Hansenula polymorpha on glucose in the presence of different organic nitrogen sources (methylamine, ethylamine and D -alanine), the metabolism of which is mediated by peroxisome-borne oxidases in wild-type (WT) cells. Both strains grew well on each of these substrates with growth rates comparable to WT cells. Growth on both methylamine and ethylamine was associated with enhanced levels of catalase and amine oxidase in the cells; in D -alanine-grown cells D -amino acid oxidase activity and increased. In WT cells of H-polymorpha the activities of these enzymes were confined to the peroxisomal matrix; however, in both peroxisome-deficient strains their activities were localized in the cytosol. Electron microscopy indicated that, dependent on the stage of growth, the enzymes may form large protein aggregates. The molecular masses of both amine oxidase and D -amino acid oxidase in the mutant strains were identical to their respective counterparts in WT cells, indicating that both proteins were correctly assembled and active in the cytosol.     

Identification of auxotrophic mutants of the yeast Kluyveromyces marxianus by non‐homologous end joining‐mediated integrative transformation with genes from Saccharomyces cerevisiae

The isolation and application of auxotrophic mutants for gene manipulations, such as genetic transformation, mating selection and tetrad analysis, form the basis of yeast genetics. For the development of these genetic methods in the thermotolerant fermentative yeast Kluyveromyces marxianus, we isolated a series of auxotrophic mutants with defects in amino acid or nucleic acid metabolism. To identify the mutated genes, linear DNA fragments of nutrient biosynthetic pathway genes were amplified from Saccharomyces cerevisiae chromosomal DNA and used to directly transform the K. marxianus auxotrophic mutants by random integration into chromosomes through non‐homologous end joining (NHEJ). The appearance of transformant colonies indicated that the specific S. cerevisiae gene complemented the K. marxianus mutant. Using this interspecific complementation approach with linear PCR‐amplified DNA, we identified auxotrophic mutations of ADE2, ADE5,7, ADE6, HIS2, HIS3, HIS4, HIS5, HIS6, HIS7, LYS1, LYS2, LYS4, LYS9, LEU1, LEU2, MET2, MET6, MET17, TRP3, TRP4 and TRP5 without the labour‐intensive requirement of plasmid construction. Mating, sporulation and tetrad analysis techniques for K. marxianus were also established. With the identified auxotrophic mutant strains and S. cerevisiae genes as selective markers, NHEJ‐mediated integrative transformation with PCR‐amplified DNA is an attractive system for facilitating genetic analyses in the yeast K. marxianus. Copyright © 2013 John Wiley & Sons, Ltd.     

Selection and analysis of bacteriophage‐insensitive mutants of Streptococcus thermophilus isolated in Ukraine

Bacteriophage‐insensitive Streptococcus thermophilus mutants (BIMs) were obtained by treating the phage‐sensitive industrial strains with virulent phages. Five BIMs acquired resistance to S. thermophilus phages of two (cos and pac) main groups selected at Ukrainian dairy processing enterprises. In addition, the valuable biotechnological properties of BIMs were characterised. During fermentation, they formed fermented milk curds with a homogeneous, dense consistency, with pleasant taste and flavour. The BIMs were identified as S. thermophilus by phenotypic and species‐specific PCR methods. The BIMs could be used as starters to stabilise the fermentation process under phage infection conditions.     

CMuJava:一个面向Java程序并发变异体生成系统

并发程序由多个共享存储空间并发执行的流程组成.由于流程之间执行次序的不确定性,使得并发软件系统的测试比较困难.变异测试是一种基于故障的软件测试技术,广泛用于评估测试用例集的充分性和测试技术的有效性.将变异测试应用于并发程序的一个关键问题是,如何高效地生成大量的模拟并发故障的变异体集合.给出了一种并发程序的变异测试框架,...     

Study of Seed Ageing in lpa1-1 Maize Mutant and Two Possible Approaches to Restore Seed Germination

Phytic acid (PA) is a strong anti-nutritional factor with a key antioxidant role in countering reactive oxygen species. Despite the potential benefits of low phytic acid (lpa) mutants, the reduction of PA causes pleiotropic effects, e.g., reduced seed germination and viability loss related to seed ageing. The current study evaluated a historical series of naturally aged seeds and showed that lpa1-1 seeds aged faster as compared to wildtype. To mimic natural ageing, the present study set up accelerated ageing treatments at different temperatures. It was found that incubating the seeds at 57 °C for 24 h, the wildtype germinated at 82.4% and lpa1-1 at 40%. The current study also hypothesized two possible solutions to overcome these problems: (1) Classical breeding was used to constitute synthetic populations carrying the lpa1-1 mutation, with genes pushing anthocyanin accumulation in the embryo (R-navajo allele). The outcome showed that the presence of R-navajo in the lpa1-1 genotype was not able to improve the germinability (−20%), but this approach could be useful to improve the germinability in non-mutant genotypes (+17%). (2) In addition, hydropriming was tested on lpa1-1 and wildtype seeds, and germination was improved by 20% in lpa1-1, suggesting a positive role of seed priming in restoring germination. Moreover, the data highlighted metabolic differences in the metabolome before and after hydropriming treatment, suggesting that the differences in germination could also be mediated by differences in the metabolic composition induced by the mutation.