Cytosine deaminase MX cassettes as positive/negative selectable markers in Saccharomyces cerevisiae

Cyanamide-inducible expression of homing nuclease I- SceI for selectable marker removal and promoter characterisation in Saccharomyces cerevisiae

In synthetic biology, microbial chassis including yeast Saccharomyces cerevisiae are iteratively engineered with increasing complexity and scale. Wet-lab genetic engineering tools are developed and optimised to facilitate strain construction but are often incompatible with each other due to shared regulatory elements, such as the galactose-inducible (GAL) promoter in S. cerevisiae. Here, we prototyped the cyanamide-induced I- SceI expression, which triggered double-strand DNA breaks (DSBs) for selectable marker removal. We further combined cyanamide-induced I- SceI-mediated DSB and maltose-induced MazF-mediated negative selection for plasmid-free in situ promoter substitution, which simplified the molecular cloning procedure for promoter characterisation. We then characterised three tetracycline-inducible promoters showing differential strength, a non-leaky β-estradiol-inducible promoter, cyanamide-inducible DDI2 promoter, bidirectional MAL32/MAL31 promoters, and five pairs of bidirectional GAL1/GAL10 promoters. Overall, alternative regulatory controls for genome engineering tools can be developed to facilitate genomic engineering for synthetic biology and metabolic engineering applications.

An Overview on Selection Marker Genes for Transformation of Saccharomyces cerevisiae

For genetic manipulation of yeast, numerous selection marker genes have been employed. These include prototrophic markers, markers conferring drug resistance, autoselection markers, and counterselectable markers. This chapter describes the different classes of selection markers and provides a number of examples for different applications.

Cytosine deamination and base excision repair cause R-loop-induced CAG repeat fragility and instability in Saccharomyces cerevisiae

CAG/CTG repeats are structure-forming repetitive DNA sequences, and expansion beyond a threshold of ∼35 CAG repeats is the cause of several human diseases. Expanded CAG repeats are prone to breakage, and repair of the breaks can cause repeat contractions and expansions. In this study, we found that cotranscriptional R-loops formed at a CAG-70 repeat inserted into a yeast chromosome. R-loops were further elevated upon deletion of yeast RNaseH genes and caused repeat fragility. A significant increase in CAG repeat contractions was also observed, consistent with previous human cell studies. Deletion of yeast cytosine deaminase Fcy1 significantly decreased the rate of CAG repeat fragility and contractions in the rnh1Δrnh201Δ background, indicating that Fcy1-mediated deamination is one cause of breakage and contractions in the presence of R-loops. Furthermore, base excision repair (BER) is responsible for causing CAG repeat contractions downstream of Fcy1, but not fragility. The Rad1/XPF and Rad2/XPG nucleases were also important in protecting against contractions, but through BER rather than nucleotide excision repair. Surprisingly, the MutLγ (Mlh1/Mlh3) endonuclease caused R-loop-dependent CAG fragility, defining an alternative function for this complex. These findings provide evidence that breakage at expanded CAG repeats occurs due to R-loop formation and reveal two mechanisms for CAG repeat instability: one mediated by cytosine deamination of DNA engaged in R-loops and the other by MutLγ cleavage. Since disease-causing CAG repeats occur in transcribed regions, our results suggest that R-loop-mediated fragility is a mechanism that could cause DNA damage and repeat-length changes in human cells.

Introducing MX Cassettes into Saccharomyces cerevisiae

The Saccharomyces cerevisiae genome can be readily and precisely modified with the use of knock out (KO) marker cassettes to delete genes. The most frequently used family of KO cassettes is the MX cassettes. This protocol describes how to use the different types of MX cassettes by selecting for prototrophy, utilization of cytosine or acetamide as a sole nitrogen source, or resistance to one of six different drugs.

Popping Out MX Cassettes from Saccharomyces cerevisiae

MX cassettes are frequently used to generate knockout (KO) mutations in Saccharomyces cerevisiae. The recycling or "popping out" of an MX cassette flanked by direct repeats allows the same cassette to be reused in a strain to generate additional KO mutations. Popping out MX cassettes also eliminates MX homology in a strain, which facilitates the subsequent generation of additional KO mutations with other MX cassettes. MX cassettes can be recycled or "popped out" of the genome by spontaneous recombination between large, cassette-borne MX3 or PR direct repeats and by Cre-mediated, site-specific recombination between small, cassette-borne loxP direct repeats. Both of these techniques leave a mutation with a cassette-encoded "scar." For the URA3MX, LYS5MX, FCA1/FCY1MX, and amdSYM cassettes, there are counterselections. Counterselections are extremely useful as they allow for positive selection for plasmid shuffling, transplacement of mutant alleles into the genome, and recycling or popping out cassettes flanked by cassette-encoded direct repeats to yield mutations with a cassette-encoded scar. Finally, after amplifying with the appropriately designed primers, integrated counterselectable MX cassettes can be popped out to generate seamless or "scar-free" deletion mutations, as well as indel and point mutations.

MX Cassettes for Knocking Out Genes in Yeast

Precise modifications of the Saccharomyces cerevisiae genome use marker cassettes, most often in the form of "knockout" (KO) marker cassettes, to delete genes. Many different KO marker cassettes exist, some of which require strains with specific genotypes, such as auxotrophic mutations, and others that have no strain genotype requirements, such as selections for drug resistance and one of two selections for nitrogen source utilization. This introduction focuses on the most frequently used family of KO cassettes-the MX cassettes. In particular, we focus on and describe the different types of MX cassettes and selections; specifically, selections for prototrophy; selections for utilization of cytosine or acetamide as sole nitrogen sources; and selections for resistance to six different drugs. The use of cassettes to place genes under regulated control is briefly discussed. Also discussed are strain genotype requirements (where applicable); media requirements; how to "recycle" or "pop out" cassettes; and counterselections against specific KO cassettes.

The blue-light receptor CmWC-1 mediates fruit body development and secondary metabolism in Cordyceps militaris

Light is an essential factor for pigment formation and fruit body development in Cordyceps militaris, a well-known edible and medicinal fungus. Cmwc-1, a homolog of the blue-light receptor gene white collar-1 (wc-1) in Neurospora crassa, was cloned from the C. militaris genome in our previous study. Here, Cmwc-1 gene inactivation results in thicker aerial hyphae, disordered fruit body development, a significant reduction in conidial formation, and carotenoid and cordycepin production. These characteristics were restored when the ΔCmwc-1 strains were hybridized with wild-type strains of the opposite mating type. A genome-wide expression analysis revealed that there were 1042 light-responsive genes in the wild-type strain and only 458 in the ΔCmwc-1 strain. Among five putative photoreceptors identified, Vivid, cryptochrome-1, and cyclobutane pyrimidine dimer photolyase are strongly induced by light in a Cmwc-1-dependent manner, while phytochrome and cryptochrome-2 were not induced. The transcription factors involved in the fungal light reaction were mainly of the Zn2Cys6 type. CmWC-1 regulates adenylosuccinate synthase, an important enzyme for adenosine de novo synthesis, which could explain the reduction in cordycepin production. Some G protein-coupled receptors that control fungal fruit body formation and the sexual cycle were regulated by CmWC-1, and the cAMP pathway involved in light signal transduction in N. crassa was not critical for the photoreaction in the fungus here. A transcriptional analysis indicated that steroid biosynthesis was more active in the ΔCmwc-1 strain, suggesting that CmWC-1 might switch the vegetative growth state to primordia differentiation by suppressing the expression of related genes.

A bacterial gene codA encoding cytosine deaminase is an effective conditional negative selectable marker in Glycine max

KEY MESSAGE

Research describes the practical application of the codA negative selection marker in Soybean. Conditions are given for codA selection at both the shooting and rooting stages of regeneration. Conditional negative selection is a powerful technique whereby the absence of a gene product allows survival in otherwise lethal conditions. In plants, the Escherichia coli gene codA has been employed as a negative selection marker. Our research demonstrates that codA can be used as a negative selection marker in soybean, Glycine max. Like most plants, soybean does not contain cytosine deaminase activity and we show here that wild-type seedlings are not affected by inclusion of 5-FC in growth media. In contrast, transgenic G. max plants expressing codA and grown in the presence of more than 200 μg/mL 5-FC exhibit reductions in hypocotyl and taproot lengths, and severe suppression of lateral root development. We also demonstrate a novel negative selection-rooting assay in which codA-expressing aerial tissues or shoot cuttings are inhibited for root formation in media containing 5-FC. Taken together these techniques allow screening during either the regeneration or rooting phase of tissue culture.

An overview on selection marker genes for transformation of Saccharomyces cerevisiae

For genetic manipulation of yeast, numerous selection marker genes have been employed. These include prototrophic markers, markers conferring drug resistance, autoselection markers, and counterselectable markers. This chapter describes the different classes of selection markers and provides a number of examples for different applications.

Precise manipulation of the Clostridium difficile chromosome reveals a lack of association between the tcdC genotype and toxin production

Clostridium difficile causes a potentially fatal diarrheal disease through the production of its principal virulence factors, toxin A and toxin B. The tcdC gene is thought to encode a negative regulator of toxin production. Therefore, increased toxin production, and hence increased virulence, is often inferred in strains with an aberrant tcdC genotype. This report describes the first allele exchange system for precise genetic manipulation of C. difficile, using the codA gene of Escherichia coli as a heterologous counterselection marker. It was used to systematically restore the Δ117 frameshift mutation and the 18-nucleotide deletion that occur naturally in the tcdC gene of C. difficile R20291 (PCR ribotype 027). In addition, the naturally intact tcdC gene of C. difficile 630 (PCR ribotype 012) was deleted and then subsequently restored with a silent nucleotide substitution, or "watermark," so the resulting strain was distinguishable from the wild type. Intriguingly, there was no association between the tcdC genotype and toxin production in either C. difficile R20291 or C. difficile 630. Therefore, an aberrant tcdC genotype does not provide a broadly applicable rationale for the perceived notion that PCR ribotype 027 strains are "high-level" toxin producers. This may well explain why several studies have reported that an aberrant tcdC gene does not predict increased toxin production or, indeed, increased virulence.

Selection systems based on dominant-negative transcription factors for precise genetic engineering

Diverse tools are available for performing genetic modifications of microorganisms. However, new methods still need to be developed for performing precise genomic engineering without introducing any undesirable side-alteration. Indeed for functional analyses of genomic elements, as well as for some industrial applications, only the desired mutation should be introduced at the locus considered. This article describes a new approach fulfilling these requirements, based on the use of selection systems consisting in truncated genes encoding dominant-negative transcription factors. We have demonstrated dominant-negative effects mediated by truncated Gal4p and Arg81p proteins in Saccharomyces cerevisiae, interfering with galactose and arginine metabolic pathways, respectively. These genes can be used as positive and negative markers, since they provoke both growth inhibition on substrates and resistance to specific drugs. These selection markers have been successfully used for precisely deleting HO and URA3 in wild yeasts. This genetic engineering approach could be extended to other microorganisms.

A general life-death selection strategy for dissecting protein functions

Clonal selection strategies are central tools in molecular biology. We developed a general strategy to dissect protein functions through positive and negative clonal selection for protein-protein interactions, based on a protein-fragment complementation assay using Saccharomyces cerevisiae cytosine deaminase as a reporter. We applied this method to mutational or chemical disruption of protein-protein interactions in yeast and to dissection of the functions of an allosterically activated transcription factor, Swi6.

Cytosine deaminase as a negative selection marker for gene disruption and replacement in the genus Streptomyces and other actinobacteria

We developed a novel negative selection system for actinobacteria based on cytosine deaminase (CodA). We constructed vectors that include a synthetic gene encoding the CodA protein from Escherichia coli optimized for expression in Streptomyces species. Gene disruption and the introduction of an unmarked in-frame deletion were successfully achieved with these vectors.