Tandem Gene Amplification Research Articles

Heteroresistance to piperacillin/tazobactam in Klebsiella pneumoniae is mediated by increased copy number of multiple β-lactamase genes.

Piperacillin/tazobactam is a β-lactam/β-lactamase inhibitor combination with a broad spectrum of activity that is often used as empirical and/or targeted therapy among hospitalized patients. Heteroresistance (HR) is a form of antibiotic resistance in which a minority population of resistant cells coexists with a majority susceptible population that has been found to be a cause of antibiotic treatment failure in murine models. To determine the prevalence of HR and mechanisms of HR to piperacillin/tazobactam among Klebsiella pneumoniae bloodstream infection (BSI) isolates. From July 2018 to June 2021, K. pneumoniae piperacillin/tazobactam-susceptible BSI isolates were collected from two tertiary hospitals in Atlanta, GA, USA. Only first isolates from each patient per calendar year were included. Population analysis profiling (PAP) and WGS were performed to identify HR and its mechanisms. Among 423 K. pneumoniae BSI isolates collected during the study period, 6% (25/423) were found to be HR with a subpopulation surviving above the breakpoint. WGS of HR isolates grown in the presence of piperacillin/tazobactam at concentrations 8-fold that of the MIC revealed copy number changes of plasmid-located β-lactamase genes blaCTX-M-15, blaSHV33, blaOXA-1 and blaTEM-1 by tandem gene amplification or plasmid copy number increase. Prevalence of HR to piperacillin/tazobactam among bloodstream isolates was substantial. The HR phenotype appears to be caused by tandem amplification of β-lactamase genes found on plasmids or plasmid copy number increase. This raises the possibility of dissemination of HR through horizontal gene transfer and requires further study.

High prevalence of heteroresistance in Staphylococcus aureus is caused by a multitude of mutations in core genes.

Heteroresistance (HR) is an enigmatic phenotype where, in a main population of susceptible cells, small subpopulations of resistant cells exist. This is a cause for concern, as this small subpopulation is difficult to detect by standard antibiotic susceptibility tests, and upon antibiotic exposure the resistant subpopulation may increase in frequency and potentially lead to treatment complications or failure. Here, we determined the prevalence and mechanisms of HR for 40 clinical Staphylococcus aureus isolates, against 6 clinically important antibiotics: daptomycin, gentamicin, linezolid, oxacillin, teicoplanin, and vancomycin. High frequencies of HR were observed for gentamicin (69.2%), oxacillin (27%), daptomycin (25.6%), and teicoplanin (15.4%) while none of the isolates showed HR toward linezolid or vancomycin. Point mutations in various chromosomal core genes, including those involved in membrane and peptidoglycan/teichoic acid biosynthesis and transport, tRNA charging, menaquinone and chorismite biosynthesis and cyclic-di-AMP biosynthesis, were the mechanisms responsible for generating the resistant subpopulations. This finding is in contrast to gram-negative bacteria, where increased copy number of bona fide resistance genes via tandem gene amplification is the most prevalent mechanism. This difference can be explained by the observation that S. aureus has a low content of resistance genes and absence of the repeat sequences that allow tandem gene amplification of these genes as compared to gram-negative species.

Fluorometric Detection of SARS-CoV-2 Single-Nucleotide Variant L452R Using Ligation-Based Isothermal Gene Amplification.

Since the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant was first discovered, several variants showing different infectivity and immune responses have emerged globally. As the conventional method, whole-genome sequencing following polymerase chain reaction (PCR) is currently used for diagnosis of SARS-CoV-2 mutations. However, these conventional PCR-based direct DNA sequencing methods are time-consuming, complicated, and require expensive DNA sequencing modules. Here, we developed a fluorometric method for the accurate detection of a single missense mutation of U to G in the spike (S) gene that changes leucine to arginine (L452R) in SARS-CoV-2 genomic RNA. Our method for the detection of single-nucleotide mutations (SNM) in the viral RNA genome includes RNA sequence-dependent DNA ligation and tandem isothermal gene amplification methods, such as strand displacement amplification (SDA) and rolling circle amplification (RCA) generating G-quadruplex (GQ). In the presence of SNM in the viral RNA, ligation of both ends of the probe DNAs occurs between 5'-phosphorylated hairpin DNA and linear probe DNA that can discriminate a single base mismatch. The ligated DNAs were then extended to generate long-stem hairpin DNAs that are subjected to the first isothermal gene amplification (SDA). SDA produces multitudes of short ssDNA from the long-stem hairpin DNAs, which then serve as primers by annealing to circular padlock DNA for the second isothermal gene amplification (RCA). RCA produces a long stretch of ssDNA containing GQ structures. Thioflavin T (ThT) is then intercalated into GQ and emits green fluorescence, which allows the fluorometric identification of SARS-CoV-2 variants. This fluorometric analysis sensitively distinguished SNM in the L452R variant of SARS-CoV-2 RNA as low as 10 pM within 2 h. Hence, this fluorometric detection method using ligation-assisted tandem isothermal gene amplification can be applied for the diagnosis of SARS-CoV-2 SNM variants with high accuracy and sensitivity, without the need for cumbersome whole-genome DNA sequencing.

Detection of SARS-CoV-2 RNA through tandem isothermal gene amplification without reverse transcription

Diagnosis of SARS-CoV-2 infection through rapid, accurate, and sensitive testing is the most important and fundamental step in coping with the COVID-19 epidemic. We have developed a sensitive fluorometric assay to detect SARS-CoV-2 viral RNA without thermal cycling. This assay system, based on tandem isothermal gene amplification (TIGA), is composed of ternary rolling circle amplification (t-RCA) and subsequent strand displacement amplification (SDA) coupled with G-quadruplex-generating RCA (SDA/GQ-RCA). Without the need to convert viral RNA into cDNA, viral RNA forms a ternary complex composed of hairpin primer (HP) and dumbbell padlock DNA during the t-RCA process. t-RCA generates a long chain of single-stranded DNA (ssDNA) with tandemly repeated hairpin structures that are subjected to SDA. SDA produces multiple short ssDNAs from t-RCA products, which then serve as primers for the second RCA reaction. A long ssDNA harboring repeated copies of the G-quadruplex is produced in the second round of RCA. Emission of enhanced fluorescence by thioflavin T, which intercalates into the G-quadruplex, allows fluorometric detection of amplified viral genes. This fluorometric analysis sensitively detected SARS-CoV-2 RNA as low as 5.9 aM, with a linear range between 0.2 fM and 200 fM within 1 h. Hence, this isothermal gene amplification method without reverse transcription of viral RNA can be applied to diagnose COVID-19 with high sensitivity and accuracy as an alternative to current PCR-based diagnosis.

Tandem gene amplification restores photosystem II accumulation in cytochrome b559 mutants of cyanobacteria.

Summary Cytochrome (Cyt) b 559 is a key component of the photosystem II complex (PSII) that is essential for its proper functioning and assembly. Site‐directed mutants of the model cyanobacterium Synechocystis sp. PCC6803 with mutated heme axial ligands of Cyt b 559 have little PSII and are therefore unable to grow photoautotrophically.Here we describe two types of Synechocystis autotrophic transformants that retained the same mutations in Cyt b 559 but are able to accumulate PSII and grow photoautotrophically. Whole‐genome sequencing revealed that all of these autotrophic transformants carried a variable number of tandem repeats (from 5 to 15) of chromosomal segments containing the psbEFLJ operon.RNA‐seq analysis showed greatly increased transcript levels of the psbEFLJ operon in these autotrophic transformants. Multiple copies of the psbEFLJ operon in these transformants were only maintained during autotrophic growth, while its copy numbers gradually decreased under photoheterotrophic conditions. Two‐dimensional PAGE analysis of membrane proteins revealed a strong deficiency in PSII complexes in the Cyt b 559 mutants that was reversed in the autotrophic transformants.These results illustrate how tandem gene amplification restores PSII accumulation and photoautotrophic growth in Cyt b 559 mutants of cyanobacteria, and may serve as an important adaptive mechanism for cyanobacterial survival.

Single-molecule nanopore sequencing reveals extreme target copy number heterogeneity in arylomycin-resistant mutants

Tandem gene amplification is a frequent and dynamic source of antibiotic resistance in bacteria. Ongoing expansions and contractions of repeat arrays during population growth are expected to manifest as cell-to-cell differences in copy number (CN). As a result, a clonal bacterial culture could comprise subpopulations of cells with different levels of antibiotic sensitivity that result from variable gene dosage. Despite the high potential for misclassification of heterogenous cell populations as either antibiotic-susceptible or fully resistant in clinical settings, and the concomitant risk of inappropriate treatment, CN distribution among cells has defied analysis. Here, we use the MinION single-molecule nanopore sequencer to uncover CN heterogeneity in clonal populations of Escherichia coli and Acinetobacter baumannii grown from single cells isolated while selecting for resistance to an optimized arylomycin, a member of a recently discovered class of Gram-negative antibiotic. We found that gene amplification of the arylomycin target, bacterial type I signal peptidase LepB, is a mechanism of unstable arylomycin resistance and demonstrate in E. coli that amplification instability is independent of RecA. This instability drives the emergence of a nonuniform distribution of lepB CN among cells with a range of 1 to at least 50 copies of lepB identified in a single clonal population. In sum, this remarkable heterogeneity, and the evolutionary plasticity it fuels, illustrates how gene amplification can enable bacterial populations to respond rapidly to novel antibiotics. This study establishes a rationale for further nanopore-sequencing studies of heterogeneous cell populations to uncover CN variability at single-molecule resolution.

Fluorometric Detection of Low-Abundance EGFR Exon 19 Deletion Mutation Using Tandem Gene Amplification.

Epidermal growth factor receptor (EGFR) mutations are not only genetic markers for diagnosis but also biomarkers of clinical-response against tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC). Among the EGFR mutations, the in-frame deletion mutation in EGFR exon 19 kinase domain (EGFR exon 19-del) is the most frequent mutation, accounting for about 45% of EGFR mutations in NSCLCs. Development of sensitive method for detecting the EGFR mutation is highly required to make a better screening for drug-response in the treatment of NSCLC patients. Here, we developed a fluorometric tandem gene amplification assay for sensitive detection of low-abundance EGFR exon 19-del mutant genomic DNA. The method consists of pre-amplification with PCR, thermal cycling of ligation by Taq ligase, and subsequent rolling circle amplification (RCA). PCR-amplified DNA from genomic DNA samples was used as splint DNA to conjugate both ends of linear padlock DNA, generating circular padlock DNA template for RCA. Long stretches of ssDNA harboring multiple copies of G-quadruplex structure was generated in RCA and detected by thioflavin T (ThT) fluorescence, which is specifically intercalated into the G-quadruplex, emitting strong fluorescence. Sensitivity of tandem gene amplification assay for detection of the EGFR exon 19-del from gDNA was as low as 3.6 pg, and mutant gDNA present in the pooled normal plasma was readily detected as low as 1% fraction. Hence, fluorometric detection of low-abundance EGFR exon 19 deletion mutation using tandem gene amplification may be applicable to clinical diagnosis of NSCLC patients with appropriate TKI treatment.

Fluorometric detection of single-nucleotide mutations using tandem gene amplification

Sensitive and accurate identification of single-nucleotide mutations (SNMs) has become crucial in the field of molecular diagnosis and personalized medicine. Here, we developed a highly sensitive fluorometric assay for detecting multiple SNMs by tandem gene amplification; reverse transcription PCR (RT-PCR) coupled with rolling circle amplification generating G-quadruplex (GQ-RCA). In tandem gene amplification, RT-PCR-amplified DNA from sample RNA was digested with lambda exonuclease, which degraded the strand harboring the phosphorylated 5′-end of amplicon DNA to generate single-stranded DNA (ssDNA). The resulting ssDNA was hybridized with padlock probe DNA, which can discriminate a single base mismatch. Depending on the presence of mismatched bases between the amplicon ssDNA and padlock probe DNA, ligation of both ends of the padlock DNA was evaluated. If ligation occurred, a circular form of padlock DNA was generated, which was eligible for RCA. The RCA process generates long stretches of ssDNA containing tandem repeats of G-quadruplex structures. The amplified ssDNA harboring G-quadruplex was fluorescently visualized and quantified using Thioflavin T fluorophore. Our assay detected mutant RNA containing an SNM as low as 8.3 fg and detected mutant RNA with a concentration as low as 0.53 % in the mixture with wild-type RNA. The fluorometric SNM detection method with tandem gene amplification was successfully applied for multiplex detection of SNMs in clinical samples derived from patients with chronic myeloid leukemia. Our method would be useful in clinical diagnosis for early detection and monitoring of multiple SNMs in cancer patients with proper treatment.

Label-free fluorometric detection of influenza viral RNA by strand displacement coupled with rolling circle amplification.

Since influenza occurs globally every year, it is important to develop a facile and accurate method to detect the influenza virus. This study aimed at developing a sensitive fluorometric assay for detecting influenza viral RNA through tandem gene amplification methods including reverse transcription PCR (RT-PCR), followed by strand displacement amplification (SDA) coupled with rolling circle amplification (RCA). Influenza viral RNA was initially amplified by RT-PCR with a tailed reverse primer containing an additional sequence for SDA. The RT-PCR amplicon was then subjected to SDA, yielding multiple copies of single-stranded DNA (ssDNA) that can be used as a primer for subsequent RCA. Thereafter, a long ssDNA segment harboring tandem repeated G-quadruplexes that were generated through RCA was intercalated by Thioflavin T, yielding a strong fluorescence signal indicating the presence of the target viral RNA. Fluorometric analysis detected influenza viral RNA ranging from 50 pg to 500 pg with a limit of detection of 6.2 pg with a signal-to-background ratio of 10 and identified each influenza virus strain (H1N1, H3N2, and influenza B). Thus, the present method for the label-free fluorometric detection of viral RNA via tandem gene amplifications combining RT-PCR-coupled SDA and G-quadruplex-generating RCA would facilitate the efficient diagnosis of influenza infection.

Glyphosate resistance reduces kochia fitness: Comparison of segregating resistant and susceptible F2 populations

Glyphosate is considered the world’s most important herbicide, but widespread and continual use has resulted in the evolution of resistance. Kochia scoparia (kochia) has evolved resistance via tandem gene amplification of glyphosate’s target, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) and resistant populations have been reported from the Canadian Prairies and the Northern Great Plains. Here, we evaluated the fitness costs of EPSPS amplification in kochia by comparing susceptible and resistant full siblings from segregating F2 populations generated from within six populations. Kochia was expected to be highly diverse because of strong gene flow; however, six of the seven field-collected parents with higher EPSPS copy number were homozygous. Under competitive greenhouse conditions, the EPSPS type of the line’s maternal parent showed persistent effects: delayed emergence, delayed flowering, and reductions in viable seed count and weight overall. High EPSPS copy number individuals had reduced seed count and weight, reduced competitive ability, and reduced final height in mixed stands, but better germination of the F3. However, all characteristics were highly variable and fitness costs were not constant across genetic backgrounds. In the absence of selection from glyphosate, kochia with increased EPSPS copy number will be at a competitive disadvantage in some genetic backgrounds.

Clinical Outcome, Molecular and Gene Expression Analysis of 20 MLL-Rearranged AML from a Single Institution

BackgroundRearrangements of the mixed lineage leukemia (MLL) gene at 11q23 (due to translocation, partial tandem duplication or gene amplification) are frequent in AML. Translocations give rise to fusion genes with AF9, AF6, MLLT10 and ENL, among others; partial tandem duplications or self-fusion fuses the 5' region of an MLL into the other MLL gene; and MLL amplification results in several copies of the wild-type gene.In this work we report the molecular analysis, gene expression profiling and clinical outcome for a cohort of MLL- rearrangedAML.Patients and MethodsHerein we include 20 MLL-rearrangement harboring patients, diagnosed in our institution of AML.MLL gene fusion was detected by cytogenetics; FISH with LSI MLL dual color, Break Apart probe, and chromosome painting probes; 10 cases could be verified by reverse transcription PCR (RT-PCR) and sequencing. Gene expression was analyzed in ten cases by real-time PCR in a reaction with specific primers and SybrGreen. Relative quantification was performed by 2-DDCt method.Survival analysis was carried-out by Kaplan-Meyer method. Overall survival was considered as the time from diagnostics to exitus.ResultsIn a time course from March 2004 to June 2015, the systematic screening for genetic rearrangements in AML patients at diagnosis, revealed 20 patients harboring a rearranged MLL. Fourteen of these were translocations, and in nine of them we could demonstrate the genetic fusion at the mRNA sequence level. There were three amplifications of the MLL gene in double minute (dmin), homogeneously stained region (hsr) and in several marker chromosomes.MLL rearrangement harboring patients had a median overall survival of 284±119 (N=18) days and only 25% of them survive at 1.7 years.Gene expression profiling of AML relevant genes (HOXA5, FLT3, EVI1, MEIS1 and RUNX1) showed a general upregulation of HOXA5, and a heterogenic regulation of FLT3. EVI1 and MEIS1 expression, undetectable in health control's peripheral blood, were upregulated only in some cases, interestingly the only two survivors in the series had undetectable EVI1 expression (Fig 1A). RUNX1 had a downregulation in MLL amplification cases, especially patient with 15-20 MLL copies in HSR in hyperdiploid cells that showed 7.4*107±2.5*107 fold downregulation (p<0.01), almost undetectable by real-time PCR (Fig 1B). Also was significatively (p<0.05) downregulated in two of the four MLL-ENL harboring patients and the only included MLL-AF6 harboring patient.ConclusionsIn this work we show that MLL-rearranged AML have a poor outcome, and most of them should not be included in intermediate-risk karyotype. Accordingly, the classification of MLL cases by the genetic partner or gene expression profile may provide a more precise prognostics. In this sense, overexpression of EVI1 has been previously associated to a worst outcome, but there are other genes that could be useful in prognostics such as MEIS1. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Tandem amplification of a chromosomal segment harboring 5-enolpyruvylshikimate-3-phosphate synthase locus confers glyphosate resistance in Kochia scoparia.

Recent rapid evolution and spread of resistance to the most extensively used herbicide, glyphosate, is a major threat to global crop production. Genetic mechanisms by which weeds evolve resistance to herbicides largely determine the level of resistance and the rate of evolution of resistance. In a previous study, we determined that glyphosate resistance in Kochia scoparia is due to the amplification of the 5-Enolpyruvylshikimate-3-Phosphate Synthase (EPSPS) gene, the enzyme target of glyphosate. Here, we investigated the genomic organization of the amplified EPSPS copies using fluorescence in situ hybridization (FISH) and extended DNA fiber (Fiber FISH) on K. scoparia chromosomes. In both glyphosate-resistant K. scoparia populations tested (GR1 and GR2), FISH results displayed a single and prominent hybridization site of the EPSPS gene localized on the distal end of one pair of homologous metaphase chromosomes compared with a faint hybridization site in glyphosate-susceptible samples (GS1 and GS2). Fiber FISH displayed 10 copies of the EPSPS gene (approximately 5 kb) arranged in tandem configuration approximately 40 to 70 kb apart, with one copy in an inverted orientation in GR2. In agreement with FISH results, segregation of EPSPS copies followed single-locus inheritance in GR1 population. This is the first report of tandem target gene amplification conferring field-evolved herbicide resistance in weed populations.

Microevolution of Cryptococcus neoformans Driven by Massive Tandem Gene Amplification

The subtelomeric regions of organisms ranging from protists to fungi undergo a much higher rate of rearrangement than is observed in the rest of the genome. While characterizing these ~40-kb regions of the human fungal pathogen Cryptococcus neoformans, we have identified a recent gene amplification event near the right telomere of chromosome 3 that involves a gene encoding an arsenite efflux transporter (ARR3). The 3,177-bp amplicon exists in a tandem array of 2-15 copies and is present exclusively in strains with the C. neoformans var. grubii subclade VNI A5 MLST profile. Strains bearing the amplification display dramatically enhanced resistance to arsenite that correlates with the copy number of the repeat; the origin of increased resistance was verified as transport-related by functional complementation of an arsenite transporter mutant of Saccharomyces cerevisiae. Subsequent experimental evolution in the presence of increasing concentrations of arsenite yielded highly resistant strains with the ARR3 amplicon further amplified to over 50 copies, accounting for up to ~1% of the whole genome and making the copy number of this repeat as high as that seen for the ribosomal DNA. The example described here therefore represents a rare evolutionary intermediate-an array that is currently in a state of dynamic flux, in dramatic contrast to relatively common, static relics of past tandem duplications that are unable to further amplify due to nucleotide divergence. Beyond identifying and engineering fungal isolates that are highly resistant to arsenite and describing the first reported instance of microevolution via massive gene amplification in C. neoformans, these results suggest that adaptation through gene amplification may be an important mechanism that C. neoformans employs in response to environmental stresses, perhaps including those encountered during infection. More importantly, the ARR3 array will serve as an ideal model for further molecular genetic analyses of how tandem gene duplications arise and expand.

Association of IS5 with divergent tandem blaCMY-2 genes in clinical isolates of Escherichia coli

To characterize a unique tandem bla(CMY-2) gene arrangement found in two non-identical clinical strains of Escherichia coli. Both plasmid and chromosomal DNA were evaluated using PFGE, restriction digest analysis, plasmid profiling and Southern hybridization. bla(CMY-2) gene expression and gene copy number were evaluated by real-time PCR. Susceptibilities to selected β-lactam antibiotics were determined by agar dilution. A tandem arrangement for bla(CMY-2) was identified in both isolates and was the only arrangement for bla(CMY-2) observed. These isolates had distinct PFGE and plasmid profiles. Each strain exhibited 2-fold higher bla(CMY-2) mRNA expression and up to 8-fold lower β-lactam susceptibility compared with a strain with a single copy of bla(CMY-2). This is the first report of IS5 being associated with tandem bla(CMY-2). IS5 has previously been associated with antibiotic resistance through tandem gene amplification. The unique tandem arrangement provides a mechanism for increased bla(CMY-2) expression.

An M13 vector library for cloning DNA with four nucleotide 3′ overhangs

A flexible M13 vector library incorporating the BstXI site has been developed. DNA cut by any currently commercially available restriction endonuclease that generates a 4-nucleotide (nt) 3′ overhang can be ligated into a specific clone of the library. The BstXI enzyme recognizes a 6-bp bipartite palindromic sequence. The central nucleotides are not specified, and form a 4-base, 3′ overhang when cut by BstXI. 5′ CCANNNNN NTGG GGTN NNNNNACC 5′ Since the 4-base overhang formed is not part of the BstXI recognition sequence, it is possible to generate a library of 256 different clones by introducing the BstXI site. 151 of the possible 256-member library have been isolated, including all 13 M13BF clones in which the overhang formed by BstXI digestion is complementary to those formed by currently available restriction endonucleases. Of these 13 vectors, BstXI digestion of six clones results in nonpalindromic cohesive ends and should facilitate in vitro tandem gene amplification. The BstXI site is adjacent to the four codons corresponding to the factor Xa recognition sequence. Hence the vector library could facilitate the expression of a fusion protein that could be proteolytically cleaved by factor Xa.

Tandem gene amplification in vitro for rapid and efficient expression in animal cells

Plasmid vectors pHSG293 and pHSG747, suitable for in vitro gene amplification for subsequent animal-cell expression, were developed. A cosmid vector pHSG293 confers Km resistance to Escherichia coli host cells and G418 resistance to animal cells and contains a single BstXI recognition/cleavage site, CCA CGGGG/C TGG , near the cos site (the recognition site is underlined). The cassette vector plasmid pHSG747 contains a multiple cloning site (MCS) between the simian virus 40 early promoter and the poly(A) signal sequence flanked by the same BstXI sites and confers Cm resistance to E. coli host cells. After inserting a coding fragment for human protein C or its derivative in the appropriate orientation in the MCS of pHSG747, the BstXI expression unit fragment was purified, mixed with BstXI-digested pHSG293 DNA at a molecular ratio of 20 to 40:1 and ligated. This allowed for tandem gene amplification due to asymmetric cohesive ends. Ligation products were packaged in λ phage particles, amplified in E. coli cells as large cosmid molecules, and then introduced into CHO cells. G418 R transformants were found to produce and secrete recombinant protein molecules at a high level. The plasmid vectors developed in this work will provide a rapid screening system useful for protein engineering in animal cells.

A New Class of TOL Plasmid Deletion Mutants in Pseudomonas putida MT15 and Their Reversion by Tandem Gene Amplification

Pseudomonas putida MT15 contains a large plasmid, pWW15, of about 250 kbp, which encodes the genes for toluene and xylene catabolism. Growth on benzoate selects strongly against the wild-type and results in the segregation of three phenotypically distinguishable mutant types. (1) B1 mutants, which have lost the complete plasmid. (2) B3 mutants, in which the plasmid has undergone a large deletion of about 90 kbp which appears to affect the regulation of the catabolic enzymes; these mutants retain the ability to grow on m-xylene and toluene (Mxy+ Tln+) but no longer grow on the metabolite of m-xylene, m-toluate (Mtol–). (3) A novel class not previously described, the B5 mutants, which still grow well on toluene but grow very poorly on m-xylene and do not grow on m-toluate (Mxy– Tln+ Mtol–). The B5 mutants appear to share the regulatory lesion of the B3 mutants but in addition do not express the xylF and xylG gene products, 2-hydroxymuconic semialdehyde hydrolase and 2-hydroxymuconic semialdehyde dehydrogenase. The plasmids in the B5 mutants have also undergone a deletion of about 90 kbp similar to, but distinguishable from, that in the B3 mutants. Both B3 and B5 mutants can revert to growth on m-toluate. The revertants all show elevated constitutive levels of catechol 2,3-oxygenase, 2-hydroxymuconic semialdehyde dehydrogenase and 2-hydroxymuconic semialdehyde hydrolase which are not further induced by m-toluate. The reversion is accompanied by the tandem amplification of a region of 23–28 kbp on either side of the original deletion. As a result of Southern hybridizations, it was shown that the amplified region contains the structural genes of some of the enzymes which metabolize m-toluate but not the enzymes which convert m-xylene to m-toluate.

Tandem gene amplification mediates copper resistance in yeast.

Resistance to copper's toxicity in yeast is controlled by the CUP1r locus. This gene was cloned by transforming sensitive recipients (cup1(8)) with a collection of hybrid DNA molecules, consisting of random yeast DNA fragments inserted into the vector YRp7. Four resistant transformants were studied in detail. Autonomously replicating or integrated by homologous recombination into chromosomal sites, the corresponding plasmids and several subclones confer resistance on sensitive recipients carrying the natural variant allele, cup1(8). Tetrad analysis and genetic mapping established that integration occurs typically at the cup1(8) site located 28 centimorgans distal to thr1, a chromosome VIII marker. Restriction endonuclease cleavage and electrophoretic mobility studies revealed that the CUP1r locus consists of a tandem array of repetitive units. Each unit is 1.95 kilobases in length and contains single sites for Kpn I and Xba I and two Sau3A sites. The sensitive allele represents one repeat and the resistant allele embraces 15 tandemly arrayed repeat units. Progressive selections in higher copper concentrations establish strains with markedly enhanced resistance. Resistance, we propose, is mediated by a gene amplification mechanism based on unequal sister chromatid exchange.