Mutant Mut Research Articles

Ultrahigh-throughput screening-assisted in vivo directed evolution for enzyme engineering.

Classical directed evolution is a powerful approach for engineering biomolecules with improved or novel functions. However, it traditionally relies on labour- and time-intensive iterative cycles, due in part to the need for multiple molecular biology steps, including DNA transformation, and limited screening throughput. In this study, we present an ultrahigh throughput in vivo continuous directed evolution system with thermosensitive inducible tunability, which is based on error-prone DNA polymerase expression modulated by engineered thermal-responsive repressor cI857, and genomic MutS mutant with temperature-sensitive defect for fixation of mutations in Escherichia coli. We demonstrated the success of the in vivo evolution platform with β-lactamase as a model, with an approximately 600-fold increase in the targeted mutation rate. Furthermore, the platform was combined with ultrahigh-throughput screening methods and employed to evolve α-amylase and the resveratrol biosynthetic pathway. After iterative rounds of enrichment, a mutant with a 48.3% improvement in α-amylase activity was identified via microfluidic droplet screening. In addition, when coupled with an in vivo biosensor in the resveratrol biosynthetic pathway, a variant with 1.7-fold higher resveratrol production was selected by fluorescence-activated cell sorting. In this study, thermal-responsive targeted mutagenesis coupled with ultrahigh-throughput screening was developed for the rapid evolution of enzymes and biosynthetic pathways.

Impact of transient acquired hypermutability on the inter- and intra-species competitiveness of Pseudomonas aeruginosa.

Once acquired, hypermutation is unrelenting, and in the long-term, leads to impaired fitness due to its cumulative impact on the genome. This raises the question of why hypermutators arise so frequently in microbial ecosystems. In this work, we explore this problem by examining how the transient acquisition of hypermutability affects inter- and intra-species competitiveness, and the response to environmental insults such as antibiotic challenge. We do this by engineering Pseudomonas aeruginosa to allow the expression of an important mismatch repair gene, mutS, to be experimentally controlled over a wide dynamic range. We show that high levels of mutS expression induce genomic stasis (hypomutation), whereas lower levels of induction lead to progressively higher rates of mutation. Whole-genome sequence analyses confirmed that the mutational spectrum of the inducible hypermutator is similar to the distinctive profile associated with mutS mutants obtained from the airways of people with cystic fibrosis (CF). The acquisition of hypermutability conferred a distinct temporal fitness advantage over the wild-type P. aeruginosa progenitor strain, in both the presence and the absence of an antibiotic selection pressure. However, over a similar time-scale, acquisition of hypermutability had little impact on the population dynamics of P. aeruginosa when grown in the presence of a competing species (Staphylococcus aureus). These data indicate that in the short term, acquired hypermutability primarily confers a competitive intra-species fitness advantage.

1736. Xeruborbactam (QPX) Potentiates the Activity of Multiple β-Lactams Against Highly Resistant Pseudomonas aeruginosa to a Greater Degree than Other β-Lactamase Inhibitors

Abstract Background Pseudomonas aeruginosa (PA) is an important pathogen notorious for antibiotic resistance. Xeruborbactam (QPX) is a potent ultra-broad-spectrum boronic acid β-lactam inhibitor (BLI) that, in combination with selected BL antibiotics, has excellent in vitro activity against carbapenem-resistant Enterobacterales (CRE), and Acinetobacter baumanii or PA producing class A/B or D carbapenemases. We evaluated QPX in combination with anti-pseudomonal BLs against clinical PA isolates from tertiary care US hospitals. Methods We tested PA clinical isolates resistant to ≥1 BL (imipenem (IMP), meropenem (MEM), cefepime (FEP), piperacillin-tazobactam (PIP-TAZ), aztreonam (ATM), ceftolozane-tazobactam (TOL-TZP), ceftazidime-avibactam (CZA), IMI-relebactam (IMI-REL), MEM-vaborbactam (MVB)) against QPX (in fixed concentration of 8 µg/mL) combined with anti-pseudomonal BLs. We performed whole-genome sequencing on isolates using the MiSeq platform (Illumina). Results Antibiograms and resistance determinants of 77 isolates tested to date are summarized in Figs 1, 2. 91% of isolates were CR; 43%, 58% and 61% were resistant to CZA, IMI-REL and MVB, respectively. No isolates produced class A/B/D carbapemases. All except 2 isolates carried PDC variants. 92% either had oprD porin single nucleotide polymorphism (SNP) or deletions. mutS mutations (present in 23% of isolates) were associated with resistance to IPM/QPX (p=.04), but not TOL-QPX or PIP-QPX. Addition of QPX significantly reduced MIC50 of IPM (32-fold), PIP (16-fold), FEP and ATM (4-fold) (all p< .0001, Fig 3). Addition of QPX to MEM or TOL reduced MIC50 by 2-fold (p=.02, p< .0001). QPX reduced IMP and PIP MICs more than did REL (32 vs 8-fold, p< .0001) or TZP (16 vs nil, p=.0007), respectively. Addition of QPX reduced BL resistance, especially for TOL, PIP and IMP (Fig 4). We identified factors associated with BL/QPX resistance by logistic regression; for IMP/QPX: IMP resistance (p=.001), SNP in mexB (p=.01); for TOL/QPX: TOL resistance (p=.02); for PIP/QPX (SNP in mexR and mexB (p=.03). Conclusion QPX enhanced the activity of BLs, especially TOL and PIP, against PA with baseline resistance to BL, more so than other BLIs. TOL/QPX and PIP/QPX are less impacted by PA efflux and porin mutations than IMP/QPX. Disclosures Cornelius J. Clancy, MD, receives research funding paid to his institution from Astellas and Merck: Grant/Research Support|serves as an advisory Board member for Astellas, Cidara, and Scynexis, served on the advisory board for Merck, Qpex Biopharma, and Shionogi: Advisor/Consultant|Venatorx and Needham & Associates: Advisor/Consultant.

Genomic profiling and outcomes of BRAF V600E mutated papillary thyroid cancer.

e18086 Background: BRAF (BRAF mut) is the most common mutation in PTC (45% prevalence). It is associated with a higher clinical stage, tumor recurrence, absence of tumor avidity, and treatment failure. Methods: BRAF WT or BRAF mut (n = 538) PTC tumors tested with NextGen Sequencing on DNA (592 genes or WES) and RNA (WTS) by Caris Life Sciences (Phoenix, AZ) were analyzed. PD-L1 expression was tested by IHC (22c3 antibody, ≥1 combined positive score (CPS) being positive). Real world overall survival (rwOS) was obtained from insurance claims data, calculated from treatment start to last contact. Time-on-treatment (TOT) is calculated from start to end of treatment. Kaplan-Meier estimates were used for comparison. Statistical significance was determined using Fisher’s-Exact/Mann Whitney/X2 test with Benjamini-Hochberg correction. Differential gene expression was analyzed using the Limma R package (q < 0.001, logFC > 1.5, -log10 FDR > 20). Gene Set Enrichment Analysis (GSEA) was used with a p < 0.01 cutoff. Results: BRAF mut were found in PTC (69%, 369/538) but not in the follicular subtype (0/117). No gender difference was seen in BRAF mut PTC (F: 53%, 297/538). BRAF mut were more prevalent in metastases compared to primary/local tumors (42% vs. 30%) and BRAF mut was highest in metastatic lymph nodes (55%, 130/235). TERT promoter was the most common mutation in both BRAF mut and WT groups but higher in BRAF mut (64% vs 40%, q < 0.0001), while NRAS (0.2% vs 23%, q < 0001), HRAS (0% vs 8.8%, q < 0001), KRAS (0.4% vs 5.4%, q < 0001), and EIF1AX (0% vs 6.6%, q = 0.0005) mutations were more prevalent in BRAF WT PTC. PD-L1 expression was higher in the BRAF mut patients compared to WT (37% vs 22%, q < 0.01). BRAF mut PTCs were associated with higher immune cell infiltrate including M1 macrophages, and Treg cells, but lower M2 macrophages, NK cells, CD4+ T cells, and myeloid dendritic cells (all q < 0.01). GSEA analysis revealed enrichment in IL6, JAK, and STAT3 signaling, inflammatory response, apoptosis, and interferon gamma response (all NES = 1.5 - 1.8, p < 0.01) gene sets. DCSTAMP was the most differentially expressed gene in BRAF mut tumors relative to WT (logFC = 4.4). When comparing BRAF mut with WT, no significant difference in rwOS was seen (NR vs 50 mo, HR 0.73, P> 0.2). In BRAF mut patients, treatment with multikinase inhibitors (n = 32) was associated with longer rwOS compared to BRAF inhibitor treatment (n = 37) (61 mo vs 27 mo, HR 0.364, P< 0.05). Despite small patient number, data suggests BRAF mut patients may benefit from immunotherapy (n = 4) when compared to BRAF inhibitors (n = 31) (TOT, HR = 0.35, p = 0.07). Conclusions: Our data highlights new genomic signatures that indicate potential new, while also validating current targets for BRAF mut PTC: higher PD-L1 expression, immune infiltrate, and inflammatory gene signature. Clinical trials are needed to assess the best sequencing of therapies used in this group, particularly TKIs vs BRAF inhibitors and the role of immunotherapy.

Improvements of the productivity and saccharification efficiency of the cellulolytic \u03b2-glucosidase D2-BGL in Pichia pastoris via directed evolution

Backgroundβ-Glucosidases are essential for cellulose hydrolysis by catalyzing the final cellulolytic degradation of cello-oligomers and cellobiose to glucose. D2-BGL is a fungal glycoside hydrolase family 3 (GH3) β-glucosidase isolated from Chaetomella raphigera with high substrate affinity, and is an efficient β-glucosidase supplement to Trichoderma reesei cellulase mixtures for the saccharification of lignocellulosic biomass.ResultsWe have carried out error-prone PCR to further increase catalytic efficiency of wild-type (WT) D2-BGL. Three mutants, each with substitution of two amino acids on D2-BGL, exhibited increased activity in a preliminary mutant screening in Saccharomyces cerevisiae. Effects of single amino acid replacements on catalysis efficiency and enzyme production have been investigated by subsequent expression in Pichia pastoris. Substitution F256M resulted in enhancing the tolerance to substrate inhibition and specific activity, and substitution D224G resulted in increasing the production of recombinant enzyme. The best D2-BGL mutant generated, Mut M, was constructed by combining beneficial mutations D224G, F256M and Y260D. Expression of Mut M in Pichia pastoris resulted in 2.7-fold higher production of recombinant protein, higher Vmax and greater substrate inhibition tolerance towards cellobiose relative to wild-type enzyme. Surprisingly, Mut M overexpression induced the ER unfolded protein response to a level lower than that with WT D2 overexpression in P. pastoris. When combined with the T. reesei cellulase preparation Celluclast 1.5L, Mut M hydrolyzed acid-pretreated sugarcane bagasse more efficiently than WT D2.ConclusionsD2-BGL mutant Mut M was generated successfully by following directed evolution approach. Mut M carries three mutations that are not reported in other directed evolution studies of GH3 β-glucosidases, and this mutant exhibited greater tolerance to substrate inhibition and higher Vmax than wild-type enzyme. Besides the enhanced specific activity, Mut M also exhibited a higher protein titer than WT D2 when it was overexpressed in P. pastoris. Our study demonstrates that both catalytic efficiency and productivity of a cellulolytic enzyme can be enhanced via protein engineering.

Strategic aromatic residues in the catalytic cleft of the xyloglucanase MtXgh74 modifying thermostability, mode of enzyme action, and viscosity reduction ability.

The thermostable endo-processive xyloglucanase MtXgh74 from Myceliophthora thermophila was used to study the influence of aromatic amino acids in the catalytic cleft on the mode of action and the ability of enzyme to reduce xyloglucan viscosity. The enzyme derivative Mut I with mutations W64A/W67A in the "negative" subsites of the catalytic cleft resulted in a 5.5-fold increase of the Km value. Mut I produced oligosaccharides of various lengths in addition to xyloglucan building blocks. The W320A/W321A substitutions in the "positive" subsites of the mutated enzyme Mut II catalytic cleft increased the Km value 54-fold and resulted in an endo-dissociative mode of action. The ability of Mut II to reduce the viscosity of xyloglucan at 50 °C was much better than that of other MtXgh74 variants. Besides, Mut II efficiently reduced viscosity of a natural substrate, the pulp of xyloglucan-containing tamarind seed flour. The Km, Vmax, and kcat values and viscosity reduction ability of the enzyme derivative Mut III (W320A/W321A/G446Y) returned to levels close to that of MtXgh74. The pattern of xyloglucan hydrolysis by Mut III was typical for endo-processive xyloglucanases. The thermostability of Mut I and Mut II at 60 °C decreased significantly compared to the wild type, whereas the thermostability of Mut III at 60 °C restored almost to the MtXgh74-wt value. All mutants lost the ability to cleave the backbone of xyloglucan building blocks which was a characteristic of MtXgh74. Instead they acquired a low branch removing activity. Molecular dynamics simulations revealed the role of mutated amino acids in the complex action mechanism of GH74 enzymes. KEY POINTS: • Endo-processive mode of action of the xyloglucanase MtXgh74 was altered by rational design. • The endo-dissociative mutant Mut II (W320A/W321A) efficiently reduced XyG viscosity. • The substitutions W320A/W321A/G446Y in Mut III recovered the endo-processive mode. • Mut II can be used to reduce the viscosity of biomass slurries containing tamarind seed flour.

Investigating Anti-mutagenic Activities of Lantana camara L. (Verbenaceae) Applying Salmonella typhimurium and the Ames Test

Introduction: Genetic mutations have a significant role in causing cancers, and plants are effective on cancer recovery by producing metabolites. In this regard, the present study aimed to evaluate the Lantana camera anti-mutation effects applying Salmonella typhimurium in the Ames test. Methods: To this end, the plant was prepared from the Iran National Botanical Garden in 2018 (Tehran, Iran), and the methanolic extracts of its leaves and flowers were obtained by the percolation method. Then, anti-mutagenic activities were studied by the Ames method and the assessment of the rate of reverse mutations in mutant Salmonella typhimurium. Mutant strains cannot grow on minimal mineral media thus only those bacteria that have acquired a wild genotype after reverse mutation in the presence of the mutagen are able to grow on this medium. The plant extract, along with a mutagen substance was used to evaluate its anti-mutagenic effects by counting grown colonies and calculating the mean mutation inhibitory index according to the "Ong" formula. Finally, anti-mutagenic activities were retested by adding the sterile extract of the mouse liver (S9), and the data were analyzed by SPSS statistical software, version 22.Results: In general, the results showed that the mean number of grown colonies decreased significantly despite the plant material in comparison with the standard. According to the "Ong" formula, the percentage of inhibition was [1-T/M]×100. Based on the results, T grew a number of colonies on each petri dish despite the mutagen and extract, and M grew a number of colonies in positive control plates. Eventually, mutation inhibition percentages in leaf extracts were significantly higher than those of flower extracts, which were 75.59 ± 0.73 (+S9) and 84.79 ± 0.17 (-S9), as well as 49.57 ± 0.55 (+S9) and 62.32 ± 0.23 (-S9), respectively (P < 0.05). Conclusion: In general, the leaves and flowers of L. camara demonstrated anti-mutagenic activities with higher activities in the leaves compared to flowers.

Genes and Proteomes Associated With Increased Mutation Frequency and Multidrug Resistance of Naturally Occurring Mismatch Repair-Deficient Salmonella Hypermutators.

The emergence of antibiotic-resistant Salmonella through mutations led to mismatch repair (MMR) deficiency that represents a potential hazard to public health. Here, four representative MMR-deficient Salmonella hypermutator strains and Salmonella Typhimurium LT2 were used to comprehensively reveal the influence of MMR deficiency on antibiotic resistance among Salmonella. Our results indicated that the mutation frequency ranged from 3.39 × 10–4 to 5.46 × 10–2 in the hypermutator. Mutation sites in MutS, MutL, MutT, and UvrD of the four hypermutators were all located in the essential and core functional regions. Mutation frequency of the hypermutator was most highly correlated with the extent of mutation in MutS. Mutations in MMR genes (mutS, mutT, mutL, and uvrD) were correlated with increased mutation in antibiotic resistance genes, and the extent of antibiotic resistance was significantly correlated with the number of mutation sites in MutL and in ParC. The number of mutation sites in MMR genes and antibiotic resistance genes exhibited a significant positive correlation with the number of antibiotics resisted and with expression levels of mutS, mutT, and mutL. Compared to Salmonella Typhimurium LT2, a total of 137 differentially expressed and 110 specifically expressed proteins were identified in the four hypermutators. Functional enrichment analysis indicated that the proteins significantly overexpressed in the hypermutators primarily associated with translation and stress response. Interaction network analysis revealed that the ribosome pathway might be a critical factor for high mutation frequency and multidrug resistance in MMR-deficient Salmonella hypermutators. These results help elucidate the mutational dynamics that lead to hypermutation, antibiotic resistance, and activation of stress response pathways in Salmonella.

Inactivation of Genes Encoding MutL and MutS Proteins Influences Adhesion and Biofilm Formation by Neisseria gonorrhoeae.

Neisseria gonorrhoeae is an etiological agent of gonorrhea, which remains a global health problem. This bacterium possesses MutL and MutS DNA repair proteins encoded by mutL and mutS genes, whose inactivation causes a mutator phenotype. We have demonstrated the differential gene expression in N. gonorrhoeae mutL and mutS mutants using DNA microarrays. A subset of differentially expressed genes encodes proteins that can influence adhesion and biofilm formation. Compared to the wild-type strain, N. gonorrhoeae mutL and mutS mutants formed denser biofilms with increased biofilm-associated biomass on the abiotic surface. The N. gonorrhoeae mutS::km, but not the mutL mutant, was also more adherent and invasive to human epithelial cells. Further, during infection of epithelial cells with N. gonorrhoeae mutS::km, the expression of some bacterial genes encoding proteins that can influence gonococcal adhesion was changed compared with their expression in cells infected with the wild-type gonococcus, as well as of human genes’ encoding receptors utilized by N. gonorrhoeae (CD46, CEACAM 1, HSPG 2). Thus, deficiency in the mutS gene resulting in increased mutation frequency in singular organisms can be beneficial in populations because these mutants can be a source of features linked to microbial fitness.

Point mutations in topoisomerase I alter the mutation spectrum in E. coli and impact the emergence of drug resistance genotypes.

Identifying the molecular mechanisms that give rise to genetic variation is essential for the understanding of evolutionary processes. Previously, we have used adaptive laboratory evolution to enable biomass synthesis from CO2 in Escherichia coli. Genetic analysis of adapted clones from two independently evolving populations revealed distinct enrichment for insertion and deletion mutational events. Here, we follow these observations to show that mutations in the gene encoding for DNA topoisomerase I (topA) give rise to mutator phenotypes with characteristic mutational spectra. Using genetic assays and mutation accumulation lines, we find that point mutations in topA increase the rate of sequence deletion and duplication events. Interestingly, we observe that a single residue substitution (R168C) results in a high rate of head-to-tail (tandem) short sequence duplications, which are independent of existing sequence repeats. Finally, we show that the unique mutation spectrum of topA mutants enhances the emergence of antibiotic resistance in comparison to mismatch-repair (mutS) mutators, and leads to new resistance genotypes. Our findings highlight a potential link between the catalytic activity of topoisomerases and the fundamental question regarding the emergence of de novo tandem repeats, which are known modulators of bacterial evolution.

A Deep-sequencing-assisted, Spontaneous Suppressor Screen in the Fission Yeast Schizosaccharomyces pombe.

A genetic screen for mutant alleles that suppress phenotypic defects caused by a mutation is a powerful approach to identify genes that belong to closely related biochemical pathways. Previous methods such as the Synthetic Genetic Array (SGA) analysis, and random mutagenesis techniques using ultraviolet (UV) or chemicals like ethyl methanesulfonate (EMS) or N-ethyl-N- nitrosourea (ENU), have been widely used but are often costly and laborious. Also, these mutagen-based screening methods are frequently associated with severe side effects on the organism, inducing multiple mutations that add to the complexity of isolating the suppressors. Here, we present a simple and effective protocol to identify suppressor mutations in mutants which confer a growth defect in Schizosaccharomyces pombe. The fitness of cells with a growth deficiency in standard rich liquid media or synthetic liquid media can be monitored for recovery using an automated 96-well plate reader over an extended period. Once a cell acquires a suppressor mutation in the culture, its descendants outcompete those of the parental cells. The recovered cells that have a competitive growth advantage over the parental cells can then be isolated and backcrossed with the parental cells. The suppressor mutations are then identified using whole-genome sequencing. Using this approach, we have successfully isolated multiple suppressors that alleviate the severe growth defects caused by loss of Elf1, an AAA+ family ATPase that is important in nuclear mRNA transport and maintenance of genomic stability. There are currently over 400 genes in S. pombe with mutants conferring a growth defect. As many of these genes are uncharacterized, we propose that our method will hasten the identification of novel functional interactions with this user-friendly, high-throughput approach.

Newborn Screening for Methylmalonic Acidemia in a Chinese Population: Molecular Genetic Confirmation and Genotype Phenotype Correlations

Background: Methylmalonic acidemia (MMA) incidence was evaluated based on newborn screening in Xuzhou from November 2015 to December 2017, and the clinical, biochemical and molecular characteristics of patients with MMA harboring MMACHC and MUT mutations were summarized.Methods: During the study, 236,368 newborns were screened for MMA by tandem mass spectrometry (MS/MS) in the Maternity and Child Health Care Hospital of Xuzhou. C3, C3/C2 and methionine, and tHcy if necessary, were measured during the first screening. Blood samples from the infants and/or their family members were used for DNA analysis. The entire coding regions of the MMACHC and MUT genes associated with MMA were sequenced by DNA MassARRAY and next-generation sequencing (NGS).Results: Eleven patients with MMACHC mutations and three with MUT mutations were identified among the 236,368 screened newborns; the estimated total incidence of MMA was 1:16,883. Among the MMA patients, two died of infection-triggered metabolic crisis approximately 3 months after birth. All the patients identified had two mutant alleles except for one individual with early-onset disease. The most common MMACHC mutation was c.609G > A. The laboratory levels of C3 and C3/C2 were elevated in MMA individuals compared to other infants. Importantly, we demonstrate that accelerated C2 degradation is related to air temperature and humidity.Conclusion: Our study reports the clinical characteristics of MMA and diagnosis through MS/MS and NGS. There was a higher incidence of MMA with homocysteinemia than of isolated MMA in Xuzhou. Insight from this study may help explain the high false-positive rate of MMA in summer.

Hypermutation-induced in vivo oxidative stress resistance enhances Vibrio cholerae host adaptation.

Bacterial pathogens are highly adaptable organisms, a quality that enables them to overcome changing hostile environments. For example, Vibrio cholerae, the causative agent of cholera, is able to colonize host small intestines and combat host-produced reactive oxygen species (ROS) during infection. To dissect the molecular mechanisms utilized by V. cholerae to overcome ROS in vivo, we performed a whole-genome transposon sequencing analysis (Tn-seq) by comparing gene requirements for colonization using adult mice with and without the treatment of the antioxidant, N-acetyl cysteine. We found that mutants of the methyl-directed mismatch repair (MMR) system, such as MutS, displayed significant colonization advantages in untreated, ROS-rich mice, but not in NAC-treated mice. Further analyses suggest that the accumulation of both catalase-overproducing mutants and rugose colony variants in NAC- mice was the leading cause of mutS mutant enrichment caused by oxidative stress during infection. We also found that rugose variants could revert back to smooth colonies upon aerobic, in vitro culture. Additionally, the mutation rate of wildtype colonized in NAC- mice was significantly higher than that in NAC+ mice. Taken together, these findings support a paradigm in which V. cholerae employs a temporal adaptive strategy to battle ROS during infection, resulting in enriched phenotypes. Moreover, ΔmutS passage and complementation can be used to model hypermuation in diverse pathogens to identify novel stress resistance mechanisms.

Agronomic evaluation and molecular characterisation of the acetolactate synthase gene in imazapyr tolerant sugarcane (Saccharum hybrid) genotypes.

Mutagenesis had no effect on number of stalks/plot, stalk height, fibre and sucrose content of mutants. Imazapyr tolerance is likely due to a S622N mutation in the acetolactate synthase gene. The herbicidal compound imazapyr is effective against weeds such as Cynodon and Rottboellia species that constrain sugarcane production. This study aimed to compare agronomic characteristics of three imazapyr tolerant mutants (Mut 1, Mut 6 and Mut 7) with the non-mutated N12 control after 18 months of growth, and to sequence the acetolactate synthase (ALS) gene to identify any point mutations conferring imazapyr tolerance. There were no significant differences in the number of stalks/plot, stalk height, fibre and sucrose contents of the mutants compared with the N12 control. However, Mut 1 genotype was more susceptible to the Lepidopteran stalk borer, Eldana saccharina when compared with the non-mutated N12 (11.14 ± 1.37 and 3.89 ± 0.52% internodes bored, respectively), making Mut 1 less desirable for commercial cultivation. Molecular characterisation of the ALS gene revealed non-synonymous mutations in Mut 6. An A to G change at nucleotide position 1857 resulted in a N513D mutation, while a G to A change at nucleotide position 2184 imposed a S622N mutation. Molecular dynamics simulations revealed that the S622N mutation renders an asparagine side chain clash with imazapyr, hence this mutation is effective in conferring imazapyr tolerance.

Heterogeneous phenotypes, genotypes, treatment and prevention of 1 003 patients with methylmalonic acidemia in the mainland of China

Objective: To analyz the current situation of the diagnosis, treatment and prevention of methylmalonic acidemia, the phenotypes, biochemical features and genotypes of the patients in the mainland of China, were investigated. Methods: Tottally 1 003 patients of methylmalonic acidemia from 26 provinces and municipalities of the mainland of China were enrolled. The clinical data, biochemical features and gene mutations were studied. Blood aminoacids and acylcarnitines, urine organic acids, and plasma total homocysteine were determined for the biochemical diagnosis. Gene analyses were performed for the genetic study of 661 patients. The patients were treated with individual intervention and long-term follow up. Prenatal diagnoses were carried out for 165 fetuses of the families. Results: Among 1 003 patients (580 boys and 423 girls), 296 cases (29.5%) had isolated methylmalonic acidemia; 707 cases (70.5%) had combined homocysteinemia; 59 patients (5.9%) were detected by newborn screening; 944 patients (94.1%) had the onset at the ages from several minutes after birth to 25 years and diagnosed at 3 days to 25 years of age. The main clinical presentations were psychomotor retardation and metabolic crisis. Multi-organ damage, including hematological abnormalities, pulmonary hypertension, kidney damage, were found. MMACHC, MUT, MMAA, MMAB, HCFC1, SUCLG1, SUCLA2 mutations were found in 631 patients (96.6%) out of 661 patients who accepted gene analysis. MMACHC mutations were detected in 460 patients (94.7%) out of 486 cases of methylmalonic acidemia combined with homocysteinemia. MUT mutations were found in 158 (90.3%) out of 169 cases of isolated methylmalonic acidemia. The development of 59 patients detected by newborn screening were normal; 918 cases (97.2%) were diagnosed after onset accepted the treatment. Forty-five of them completely recovered with normal development. Twenty-six patients (2.7%) died; 873 (92.5%) patients had mild to severe psychomotor retardation. Methylmalonic acidemia were found in 35 out of 165 fetuses by metabolites assay of amniotic fluid and amniocytes gene analysis. Conclusion: Combined methylmalonic acidemia and homocysteinemia is the common type of methylmalonic acidemia in the mainland of China. CblC defect due to MMACHC mutations is the most common type of methylmalonic acidemia combined with homocysteinemia. MUT gene mutations are frequent in the patients with isolated methylmalonic acidemia. Newborn screening is key for the early diagnosis and the better outcome. Combined diagnosis of biochemical assays and gene analysis are reliable for the prenatal diagnosis of methylmalonic acidemia.

Clonal expansion of environmentally-adapted Escherichia coli contributes to propagation of antibiotic resistance genes in beef cattle feedlots

Livestock wastewater lagoons represent important environmental reservoirs of antibiotic resistance genes (ARGs), although factors contributing to their proliferation within these reservoirs remain poorly understood. Here, we characterized Escherichia coli from feedlot cattle feces and associated wastewater lagoons using CRISPR1 subtyping, and demonstrated that while generic E. coli were genetically diverse, populations were dominated by several ‘feedlot-adapted’ CRISPR types (CTs) that were widely distributed throughout the feedlot. Moreover, E. coli bearing beta-lactamase genes, which confer reduced susceptibility to third-generation cephalosporin's, predominantly belonged to these feedlot-adapted CTs. Remarkably, the genomic region containing the CRISPR1 allele was more frequently subject to genetic exchange among wastewater isolates compared to fecal isolates, implicating this region in environmental adaptation. This allele is proximal to the mutS-rpoS-nlpD region, which is involved in regulating recombination barriers and adaptive stress responses. There were no loss-of-function mutS or rpoS mutations or beneficial accessory genes present within the mutS-rpoS-nlpD region that would account for increased environmental fitness among feedlot-adapted isolates. However, comparative sequence analysis revealed that protein sequences within this region were conserved among most feedlot-adapted CTs, but not transient fecal CTs, and did not reflect phylogenetic relatedness, implying that adaptation to wastewater environments may be associated with genetic variation related to stress resistance. Collectively, our findings suggest adaptation of E. coli to feedlot environments may contribute to propagation of ARGs in wastewater lagoons.

Investigating the Link Between Mutations in MutS DNA Repair Protein and Lynch Cancer Syndrome

The Mismatch Repair (MMR) pathway is responsible for correcting errors in DNA and is thus essential for maintaining genome stability in all living organisms. Several studies have shown that mutations causing defects in MMR protein structure and function lead to hypermutation. The increased level of mutations results in serious consequences for human health, highlighted by Lynch Syndrome (LS), a hereditary predisposition to colorectal and other cancers (1). The first protein in the MMR pathway, MutS, recognizes mispaired bases or short insertion‐deletion loops (IDLs) and utilizes its ATPase activity to initiate DNA repair (2). A long‐term study in the Hingorani laboratory examines cancer‐linked single amino acid mutants of the human MutS protein (using Thermus aquaticus MutS as a model system) in order to understand how the changes affect protein structure and function, and alter MMR. This work involves kinetic analysis of MutS activities, and related dynamic conformational changes in the protein as it utilizes ATP to work on DNA. The results will enable construction of a complete mechanism of action for each mutant protein, and help us determine whether the mutants are compromised in their ability to target mismatches, and/or bind and hydrolyze ATP, and/or undergo necessary conformational changes, and therefore understand why they disrupt DNA mismatch repair and give rise to Lynch Syndrome. My project focuses on fluorescence‐based stopped flow kinetic experiments to monitor the conformational changes of wild type MutS and several LS‐linked mutants as they bind +T insertion‐containing DNA and catalyze ATP hydrolysis. In addition to generating new information on each mutant, the findings will advance the proof‐of‐principle concept that detailed analysis of the structure, dynamics, and catalytic activities of individual MutS mutants is both feasible and can reveal critical information for understanding the molecular basis of Lynch Syndrome.Support or Funding InformationNational Institutes of Health R15 GM114743; The Beckman Scholars Program, Arnold and Mabel Beckman FoundationThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Heterogeneous Antimicrobial Susceptibility Characteristics in Pseudomonas aeruginosa Isolates from Cystic Fibrosis Patients.

Clinical isolates of Pseudomonas aeruginosa from patients with cystic fibrosis (CF) are known to differ from those associated with non-CF hosts by colony morphology, drug susceptibility patterns, and genomic hypermutability. Pseudomonas aeruginosa isolates from CF patients have long been recognized for their overall reduced rate of antimicrobial susceptibility, but their intraclonal MIC heterogeneity has long been overlooked. Using two distinct cohorts of clinical strains (n = 224 from 56 CF patients, n = 130 from 68 non-CF patients) isolated in 2013, we demonstrated profound Etest MIC heterogeneity in CF P.aeruginosa isolates in comparison to non-CF P.aeruginosa isolates. On the basis of whole-genome sequencing of 19 CF P.aeruginosa isolates from 9 patients with heterogeneous MICs, the core genome phylogenetic tree confirmed the within-patient CF P.aeruginosa clonal lineage along with considerable coding sequence variability. No extrachromosomal DNA elements or previously characterized antibiotic resistance mutations could account for the wide divergence in antimicrobial MICs between P.aeruginosa coisolates, though many heterogeneous mutations in efflux and porin genes and their regulators were present. A unique OprD sequence was conserved among the majority of isolates of CF P.aeruginosa analyzed, suggesting a pseudomonal response to selective pressure that is common to the isolates. Genomic sequence data also suggested that CF pseudomonal hypermutability was not entirely due to mutations in mutL, mutS, and uvr. We conclude that the net effect of hundreds of adaptive mutations, both shared between clonally related isolate pairs and unshared, accounts for their highly heterogeneous MIC variances. We hypothesize that this heterogeneity is indicative of the pseudomonal syntrophic-like lifestyle under conditions of being "locked" inside a host focal airway environment for prolonged periods. IMPORTANCE Patients with cystic fibrosis endure "chronic focal infections" with a variety of microorganisms. One microorganism, Pseudomonas aeruginosa, adapts to the host and develops resistance to a wide range of antimicrobials. Interestingly, as the infection progresses, multiple isogenic strains of P.aeruginosa emerge and coexist within the airways of these patients. Despite a common parental origin, the multiple strains of P.aeruginosa develop vastly different susceptibility patterns to actively used antimicrobial agents-a phenomenon we define as "heterogeneous MICs." By sequencing pairs of P.aeruginosa isolates displaying heterogeneous MICs, we observed widespread isogenic gene lesions in drug transporters, DNA mismatch repair machinery, and many other structural or cellular functions. Coupled with the heterogeneous MICs, these genetic lesions demonstrated a symbiotic response to host selection and suggested evolution of a multicellular syntrophic bacterial lifestyle. Current laboratory standard interpretive criteria do not address the emergence of heterogeneous growth and susceptibilities in vitro with treatment implications.

Engineering a thermostable highly active glucose 6-phosphate dehydrogenase and its application to hydrogen production in vitro.

Glucose 6-phosphate dehydrogenase (G6PDH) is one of the most important dehydrogenases responsible for generating reduced NADPH for anabolism and is also the rate-limiting enzyme in the Entner-Doudoroff pathway. For in vitro biocatalysis, G6PDH must possess both high activity and good thermostability due to requirements of efficient use and low expense of biocatalyst. Here, we used directed evolution to improve thermostability of the highly active G6PDH from Zymomonas mobilis. Four generations of random mutagenesis and Petri-dish-based double-layer screening evolved the thermolabile wild-type enzyme to the thermostable mutant Mut 4-1, which showed a more than 124-fold increase in half-life time (t1/2) at 60°C, a 3.4°C increase in melting temperature (T m ), and a 5°C increase in optimal temperature (Topt), without compromising the specific activity. In addition, the thermostable mutant was conducted to generate hydrogen from maltodextrin via in vitro synthetic biosystems (ivSB), gaining a more than 8-fold improvement of productivity rate with 76% of theoretical yield at 60°C. Thus, the engineered G6PDH has been shown to effectively regenerate NADPH at high temperatures and will be applicable for NAD(P)H regeneration in numerous in vitro biocatalysis applications.

Eight novel MUT loss-of-function missense mutations in Chinese patients with isolated methylmalonic academia.

Isolated methylmalonic acidemia is a rare autosomal recessive metabolic disorder mostly caused by mutations in the methylmalonyl coenzyme A mutase (MCM) gene (MUT). This study aimed to verify whether missense mutations in MUT in Chinese patients affect the stability and enzymatic activity of MCM. Eight Chinese patients were identified with novel mutations. Plasmids carrying the wild-type and mutated MUT cDNA were constructed and transfected into HEK293T cells for functional analyses. The expression and activity of MCM were determined by western blot and ultra-performance liquid chromatography, respectively. All patients had high levels of blood propionylcarnitine and urinary methylmalonyl acid. By the end of the study, two patients were lost to follow-up, three died, and three survived with mental retardation. Compared to the wild-type protein, the expression levels of all missense mutations of in vitro MCM protein were decreased (P<0.05) except those for I597R, and the MCM activity of the mutations was reduced in a permissive assay. The missense mutations L140P, A141T, G161V, W309G, I505T, Q514K, I597R and G723D affected the stability and enzymatic activity of MCM, indicating that they had a disease-causing capacity.