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Results for “strain improvement”

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PubMed2026

A CRISPR-Cas9 Toolkit Enabling Tunable Integration and Transient Homologous Recombination Enhancement in Yarrowia lipolytica.

Although the oleaginous yeast Yarrowia lipolytica is a promising microbial cell factory, its application remains constrained by inefficient homology-directed repair (HDR) and a lack of precise genomic integration tools. To address these limitations, we developed a comprehensive genetic toolkit featuring three synergistic advancements. First, we systematically identified 55 neutral integration sites with tunable expression profiles, enabling stable, position-independent gene integration with predictable transcriptional output across a 12.88-fold dynamic range. Second, we established a dual-readout high-throughput screening platform combining colony morphology analysis with hrGFP fluorescence. This approach accurately measures locus-specific homologous recombination (HR) efficiency while eliminating false positives by dominant non-homologous end joining (NHEJ). Third, we engineered a transient HR enhancement system by fusing the Sae2 exonuclease to Cas9 via a flexible (GGGGS)3 linker. This fusion significantly boosts HR efficiency and surpasses the cleavage activity of unmodified Cas9 without introducing permanent genomic modifications or compromising cellular fitness. Finally, HR efficiency for single-gene integration was increased from 46.5% to 77.5% while the dual-locus editing efficiency reached 64.1% when using 500-bp homology arms, and the engineered strains demonstrated improved genetic stability compared to those with constitutive HR enhancement.

Yarrowia↗

PubMed1979

Influence of trace elements and nitrogen sources on versicolorin production by a mutant strain of Aspergillus parasiticus.

A mutant strain of Aspergillus parasiticus blocked in aflatoxin biosynthesis accumulates versicolorin A and versicolorin C. The effect of trace elements on the growth and versicolorin production by this strain was studied in a defined medium. The omission of manganese was slightly stimulatory to versicolorin production; when zinc was omitted from the medium, no detectable versicolorins were produced. Experiments on nitrogen sources in a high-sucrose medium indicated that fourfold to fivefold increases in versicolorin yields could be obtained by substituting 3 ml/l corn steep liquor or 0.1 M NH4NO3 for the 0.023 M (NH4)2SO3 used previously as the nitrogen source in studies on versicolorin production by this strain. These improved yields will facilitate attempts to accumulate enough versicolorin A and versicolorin C for toxicity and carcinogenicity testing. Chromatographic profiles of mycelial extracts of cultures grown in a defined medium with 0.1 M NH4NO3 as the nitrogen source revealed 2 previously unrecognized compounds. The accumulation of these new metabolites in a mutant blocked in aflatoxin production may indicate that they are biosynthetically related to aflatoxin.

Anthraquinones↗

PubMed1976

Partial suppression of the LexA phenotype by mutations (rnm) which restore ultraviolet resistance but not ultraviolet mutability to Escherichia coli B/r uvr A lexA.

In Escherichia coli, lexA mutations eliminate expression of UV-inducible functions, causing pleiotropic effects which include sensitivity to ultraviolet (UV) light and loss of UV mutability. Selection for UV resistance, after 5-bromouracil (BU) treatment of E. coli B/r uvrA lexA-102, has yielded derivatives more resistant than lexA but still refractory to UV mutagenesis. The mutation responsible for the UV-resistant UV-nonmutable phenotype (rnm) is cotransducible with malB to about the same extent as is lexA-102 and is tightly linked to lexA-102 in at least one strain. The rnm mutation may therefore be an intragenic partial suppressor of the LexA phenotype. In addition to increased UV resistance and lack of UV mutability, rnm strains show improved ability to perform postreplication repair and to control postirradiation DNA degration compared to the lexA parent. We ascribe the properties of rnm mutants to their having reacquired control of Exonuclease V activity without having reacquired UV-inducible error-prone postreplication repair. We relate our results to current interpretations of UV mutagenesis and to models of coordinate regulation of UV-inducible functions.

Escherichia coli↗

PubMed2026

Genome-wide epigenomic atlas and multi-omics responses of Eriocheir sinensis to natural extreme heat.

BACKGROUND: Global climate warming has led to increasingly frequent and prolonged extreme summer heat events, posing severe environmental challenges to aquaculture systems. Extreme summer heat can disrupt the performance of pond-cultured ectotherms. The Chinese mitten crab (Eriocheir sinensis) is an economically important freshwater crustacean, but coordinated molecular differences following contrasting natural summers remain incompletely characterized. RESULTS: We performed a comprehensive multi-omics analysis integrating meteorological monitoring, mRNA/lncRNA transcriptomics, small-RNA profiling of miRNAs, DNA methylomics, and LC-MS metabolomics in E. sinensis populations collected from Yancheng, China, between 2020 and 2024. Across the ten farms, survival was significantly lower in 2024, whereas yield and the proportion of large individuals showed nonsignificant downward trends. Gene-set analyses showed negative enrichment of cellular heat-response, protein-folding, oxidative-phosphorylation, and mitochondrial ATP-production terms in the 2024 cohort at the time of sampling. The integrated transcript annotation contained 72,240 lncRNAs and 63,833 mRNAs, and CpG was the predominant methylation context. Differential methylation analysis identified 73 regions and 185 cytosines, with hypomethylated events predominating within the significant subset. Metabolomic profiles differed between annual cohorts and mapped to carbohydrate, lipid, and amino-acid pathways. Cross-omics integration prioritized eight candidate genes-ADCY9, UNC79, UBN1, IFT52, ACO2, LOC126986070, LOC127001126, and LOC126997895-and qPCR reproduced the reported directions of expression for selected RNAs. CONCLUSION: This study provides the first integrative multi-omics framework for understanding chronic heat adaptation in E. sinensis. By linking transcriptomic, epigenomic, and metabolic remodeling, we elucidate the molecular mechanisms underlying energy imbalance, epigenetic reprogramming, and immune dysregulation during prolonged thermal stress. These findings offer valuable insights and genomic resources for breeding heat-tolerant crab strains and improving aquaculture resilience under ongoing climate change.

DNA methylation↗

PubMed1977

Enhancement of isoleucine hydroxamate-mediated growth inhibition and improvement of isoleucine-producing strains of Serratia marcescens.

Growth inhibition by isoleucine hydroxamate in Serratia marcescens was significantly enhanced by adding valine plus leucine and by using glycerol as the carbon source. Isoleucine hydroxamate-resistant mutants were isolated under conditions in which growth inhibition was enhanced. One of the mutants, strain GIHVLr2179, lacked both feedback inhibition and repression of threonine deaminase. An alpha-aminobutyric acid-resistant mutant derived from strain GIHVLr2179, strain GIHVLAr2795, produced 12 mg of isoleucine per ml in the medium containing glucose and urea as carbon and nitrogen sources (a twofold increase over prior reports). This strain had increased activities of threonine deaminase, acetohydroxy acid synthase, aspartokinase, and homoserine dehydrogenase.

Acetolactate Synthase↗

PubMed1979

Rapid diagnosis of influenza A infection by direct immunofluorescence of nasopharyngeal aspirates in adults.

The efficacy for direct immunofluorescence of a commercial conjugate for influenza A virus prepared against whole A/Udorn (H3NS) virus was studied. The conjugate was specific for influenza A virus, but its sensitivity varied depending upon the strain of influenza A tested. Nasopharyngeal aspirates collected from 25 patients during an outbreak of influenza were examined for viral antigen with the conjugates and inoculated onto monkey kidney (MK) cells for virus isolation. Fifteen patients had isolates for influenza A/USSR/90/77 (H1N1); nasopharyngeal secretions were fluorescent antibody positive in 12. Fluorescent antibody was copositive with culture in 11/15 patients (73.3%) and conegative in 9/10 (90%). The one fluorescent antibody-positive, culture-negative patient had negative serology for influenza A and the fluorescent antibody result was considered to be a false positive. At a 1:10 dilution, the conjugate stained nasopharyngeal and MK cells infected with A/USSR (H1N1) 2 to 3+, whereas cells infected with H3N2 virus stained 4+. A conjugate made specifically against the ribonucleoprotein antigen, which is universal to all influenza A strains, may improve the sensitivity of the direct immunofluorescent test.

Adult↗

PubMed2025

Physiological and metabolic responses of Zymomonas mobilis to lignocellulosic hydrolysate.

Zymomonas mobilis is a promising biocatalyst for the sustainable conversion of lignocellulosic sugars into biofuels and bioproducts, yet its response to lignocellulosic hydrolysates remains poorly understood. Here, we investigate the physiological response of Z. mobilis to ammonia fiber expansion (AFEX)-pretreated switchgrass hydrolysate using a systems-level approach integrating LC-MS/MS-based lipidomics and shotgun proteomics. Growth on hydrolysate induced substantial shifts in fatty acid and membrane phospholipid composition, alongside broad proteomic remodeling. Notably, Z. mobilis exhibited a stress response characterized by the upregulation of heat shock proteins and efflux transporters and the downregulation of cell motility proteins. Unexpectedly, hydrolysate exposure also led to a robust upregulation of the Entner-Doudoroff pathway, the ethanol fermentation pathway, and other central carbon metabolism enzymes, indicating a substantial cellular investment potentially driven by additional nutrient availability in hydrolysate. These findings provide new insights into the metabolic adaptations of Z. mobilis to lignocellulosic hydrolysates, informing strategies to enhance its biofuel production capabilities.IMPORTANCEBiomass pretreatment processes release fermentable sugars from lignocellulosic biomass, but they also generate inhibitors that can impact microbial metabolism. This study provides a systems-level evaluation of how Zymomonas mobilis responds to hydrolysate stress, revealing distinct physiological and lipid membrane remodeling responses. While some stress responses overlap with those induced by ethanol and isobutanol toxicity, both valuable biofuels, hydrolysate exposure elicits unique metabolic shifts. These findings offer valuable insights for engineering Z. mobilis strains with improved tolerance and performance for efficient bioconversion of lignocellulosic hydrolysates into biofuels and bioproducts.

Zymomonas↗

PubMed1976

Research and development of unconventional systems for immunization.

The problems raised by the ever expanding world population justify the work of USAID (U.S. Agency for International Development). Continual efforts must be made to develop and efficiently operate methods of control of the microbial and parasitic infections which menace our sources of protein. This programme includes immunization, technical methods in bacterial and viral genetics to obtain attenuated strains, and improvements in production, preservation and distribution of preparations. An example of an unconventional but promising system of application is the pilot study recently begun in the Missouri-Mississippi River region.

Animals↗

PubMed1976

Replication of the deoxyribonucleic acid of multiple-drug-resistance factor in Escherichia coli.

1. It was shown that a system previously described for labelling R-factor DNA during transfer to an irradiated recipient strain of Escherichia coli did not allow high selectivity in the incorporation of thymine into R-factor DNA. 2. Lack of selectivity was shown to be due to cross-feeding from recipient to donor strain. 3. An improved system using a nalidixic acid-resistant recipient strain is described in which incorporation of thymine into the DNA of donor cells is minimized by addition of nalidixic acid after completion of transfer of the plasmid during conjugation.

Conjugation, Genetic↗

PubMedDate not supplied

Drug sensitivity of M. leprae isolated from leprosy patients administered DDS for long period of time.

Drug sensitivity was tested using liquid medium on three stains isolated from the subcutaneous nodules of L-type patients who have long been administered DDS alone. The results revealed that the first strain was resistant to DDS up to the concentration of 1.0 microgram/ml suggesting as if it were DDS dependent or enhanced strain, whereas the second strain was completely sensitive to DDS even at the lowest concentration of 0.01 microgram/ml suggesting possible inactivation of this drug in the host patient. The third strain was completely resistant to 0.1 microgram/ml, but sensitive to 1.0 microgram/ml of DDS, suggesting that the therapeutic effect can not be expected any more, when the strain becomes resistant to 0.1 microgram/ml of DDS. All of the three strains were sensitive to REP at the concentration of 0.01 microgram/ml, and the host patients of the former two strains showed rapid improvement of the clinical symptomes after REP administration. That the second strain was sensitive to INH at the concentratin of 0.01 microgram/ml suggested the availability of the combined use of INH in the chemotherapy of leprosy.

Dapsone↗

PubMed1977

Effects of pre- and post-trial caffeine administrations on simultaneous visual discrimination in three inbred strains of mice.

BALB/cJ, DBA/2J, and C57BL/6J mice were injected with caffeine and tested, in the five choice Yerkes-Thompson Bryant-Bovt Nitti apparatus for patterns discrimination, in two sets of experiments. In the first the patterns were opposite oriented oblique bars, in the second U-shaped figures, one opened toward the right, the other toward the left. As concerns the saline injected animals in both sets of experiments, the BALB mice showed the highest learning abilities; in the second set the C57 strain, whose performance had not been different from that of the DBA mice in the first set, performed at the lowest level. Pre- and post-trial caffeine (5 mg/kg) administrations were followed by performance impairment in the BALB strain, while performance improvements were evident in the drugged animals belonging to the other two strains.

Animals↗

PubMed1975

Genes affecting the productivity of alpha-amylase in Bacillus subtilis Marburg.

Genetic control of alpha-amylase (alpha-1,4-glucan glucanohydrolase, EC 3.2.1.1.) production by Bacillus subtilis 168 was studied from the standpoint that alpha-amylase production by bacteria is dependent on a long-lived messenger ribonucleic acid and obeys the following equation: E = kappa integral of X-DT where x = cell mass at time t, E = alpha amylase produced, t = culture time, and kappa = productivity constant. So a productivity constand (kappa) is obtained from the slope of the straight line plot of alpha-amylase formed versus the total mass of cells accumulated over that time during the culture process. The following results were obtained. (i) Two sequential mutants, derived from the 168(kappa = 20) strain and having improved alpha-amylase productivity (168 leads to 196), were analyzed for their serine and metal protease production. Strain 128 (kappa = 40) produced half the amount of both proteases, but strain 196 (kappa = 60 similar to 80) produced 20 times that in the original strain. (ii) Amy+ transformants, using the 196 strain as the other three had higher productivity (kappa = 37 similar to 46). These transformants (J71, J47, groups. Seventy-one of 74 Amy+ transformants had a kappa value of 21.0 plus or minus 2.1 and the other three had higher productivity (kappa = 37 similar to 46). These transformants (J71,J47, and J10) produced levels of serine and metal proteases 20 times higher than the other transformants. (iii) Strains 196, J71, J47, and J10 were found to be nonmotile and resistant to phage PBS1, whereas other strains, including strains 168, 128, 3 revertants of strain J71 and 2 revertants of strain 196, were all motile and sensitive to the phage. (iv) Strains 196 and J71 were nonflagellated under electron microscopic observation but strain 168, 128 and a revertant of J71 were flagellated. From the above experimental results, the existence of a quality controlling gene (amyB) was deduced, which is loosely linked to the structural gene and controls productivities of alpha-amylase and proteases, and flagellation. The probable existence of another regulatory gene, amyC, is also discussed.

Amylases↗

PubMed2026

Deciphering the genetic background of an industrial 2-ketogluconic acid-producing strain Pseudomonas plecoglossicida JUIM01 using whole-genome sequencing.

2-Ketogluconic acid (2KGA) is an important precursor for the food antioxidant erythorbic acid, currently produced via microbial fermentation using Pseudomonas species. To facilitate the genetic improvement of production strains, the complete genome of an industrial 2KGA producer P. plecoglossicida JUIM01 was sequenced and analyzed. The genome consists of a 5.13-Mb circular chromosome with a GC content of 63.58%, encoding 4,517 predicted proteins. Comprehensive functional annotation identified a putative global regulatory network comprising 75 core regulators, which were classified into six functionally cooperative modules, potentially governing the strain's metabolism and environmental adaptability. We further delineated the genetic determinants hypothetically linked to efficient 2KGA synthesis, including glucose metabolism, fatty acid metabolism, and the oxidative phosphorylation system. These outputs could provide the genomic resource for elucidating high productivity and robustness, and rationally engineering the high-performance chassis cells toward robust 2KGA production.

P. plecoglossicida↗

PubMed1978

Increased production of the antibiotic aurodox (X-5108) by aurodox-resistant mutants.

Conventional strain and media improvement techniques were of limited success in increasing yields of the antibiotic aurodox (X-5108) above 0.5 g/liter. Higher yields were obtained by reversion of a zero producer followed by the selection of mutants resistant to aurodox. Resistant strains of Streptomyces goldiniensis ATCC 21386 able to grow on 2 g/liter of aurodox produced greater than 2.5 g/liter of antibiotic. The rate of yield increase leveled off as the strains became resistant to greater than 2 g/liter of aurodox. These strains, in contrast to those sensitive to aurodox, gave a positive response to conventional mutagenic methods for further yield increases.

Aurodox↗

PubMed2026

Paradigm shift for cry gene expression in Bacillus thuringiensis.

In most Bacillus thuringiensis strains, the cry genes are transcribed by RNA polymerases containing sporulation-sigma factors E or K, leading to the formation of an insecticidal crystal within the mother cell along spore development. The kurstaki HD1 strain, a parent of commercial strains, also releases the insecticidal proteins Cry1I and Vip3A in the extracellular medium. vip3A expression is activated by the transcriptional regulator VipR at the onset of the stationary phase. Here, we expanded the VipR regulon in strain HD1 by identifying the VipR-binding box upstream from the cry2Aa, cry2Ab, and cry1Ia genes, and conducting transcription assays. Unexpectedly, a VipR box was located in the promoter of a putative N-acetylmuramoyl-l-alanine amidase (ami) gene upstream from cry1Ac in strain kurstaki HD73, closely related to the HD1 but devoid of vipR. Introduction of vipR in this strain led to the expression of the ami-cry1Ac operon, resulting in an early and increased production of Cry1Ac. We demonstrated that Cry1Ac was also produced in a VipR-dependent manner in an HD73 ∆spo0A mutant. Similarly, an HD1 ∆spo0A strain produces all the insecticidal proteins encoded in its genome, including cry2Ab, previously considered unexpressed. A genomic analysis also revealed the presence of putative VipR-binding sequences in lepidopteran-active strains, upstream from cry genes such as cry1E, cry1F, cry9D, and cry9E. Overall, our results break the dogma on the regulation of cry1A and cry2A genes and provide evidence of sporulation-independent Cry toxin production in biopesticidal Bt strains.IMPORTANCEBacillus thuringiensis is a remarkably efficient entomopathogen due to its ability to produce various insecticidal proteins, such as Cry or Vip. This property has made it a highly effective biopesticide used worldwide. Our work modifies the paradigm of cry1 and cry2 genes being regulated solely by sporulation-specific sigma factors and thus exclusively expressed during this process. Indeed, we demonstrated that the VipR regulator controls the transcription of vip3Aa, cry2Aa, cry2Ab, cry1Ia, and the ami-cry1A operons encoded by a strain closely related to that of commercial biopesticides and specifically turns on their expression from the onset of the stationary phase, leading to the production of insecticidal crystals independently of sporulation. By providing new knowledge on the regulation of insecticidal protein genes, these findings bring new insight for the genetic improvement of Bt strains used as commercial biopesticides.

Bacillus thuringiensis↗

PubMed1978

Ribostamycin production by a mutant of butirosin producing bacteria.

By the use of our improved colony selection technique, xylostasin and ribostamycin producing mutants were isolated from nitrosoguanidine treated Bacillus circulans B15M, a producer of butirosins A and B. Among these structurally related aminoglycosides, ribostamycin is the well-known product of a Steptomyces and has not been isolated as a bacterial metabolite. A selected mutant of strain 306, which produces xylostasin and ribostamycin, was futher mutagenized in expectation of getting an improved strain having the ability to accumulate a large amount of ribostamycin in the culture broth. One mutant, strain 451, derived from strain 306, produced ribostamycin free of xylostasin.

Anti-Bacterial Agents↗

PubMed1976

Homothallism in wine yeasts.

In an attempt to improve by hybridisation strains of pure-culture wine yeasts it could be shown, that of the seven strains used five are homothallic. Evidence is presented suggesting that the remainder are also homothallic.

Crosses, Genetic↗

PubMed1978

Improved production of citric acid by a diploid strain of Aspergillus niger.

Aspergillus niger strain CGU 87 was treated with UV radiation and some auxotrophic mutants were obtained. These mutants were less productive than CGU 87, which produced an average of 7.4% citric acid. All possible crosses in pair wise combinations were carried out between these auxotrophs, and three heterokaryons were synthesised. Finally, one heterozygous diploid was isolated from each of them. These heterokaryons and diploids showed improved productivity when compared with their component parents, but except in one diploid D5, all others produced less citric acid than CGU 87. The yield of D5 exceeded that of CGU 87 by 1.2 times and it produced 9% citric acid. This is a significant improvement and the increased productivity seems to be the result of successful adaptation of D5 to its fermentation environment.

Aspergillus niger↗