The expanding CRISPR toolbox for natural product discovery and engineering in filamentous fungi

Covering: up to May 2022Fungal genetics has transformed natural product research by enabling the elucidation of cryptic metabolites and biosynthetic steps. The enhanced capability to add, subtract, modulate, and rewrite genes via CRISPR/Cas technologies has opened up avenues for the manipulation of biosynthetic gene clusters across diverse filamentous fungi. This review discusses the innovative and diverse strategies for fungal natural product discovery and engineering made possible by CRISPR/Cas-based tools. We also provide a guide into multiple angles of CRISPR/Cas experiment design, and discuss current gaps in genetic tool development for filamentous fungi and the promising opportunities for natural product research.

Cre/lox-Mediated Chromosomal Integration of Biosynthetic Gene Clusters for Heterologous Expression in Aspergillus nidulans

Building strains of filamentous fungi for stable long-term heterologous expression of large biosynthetic pathways is limited by the low transformation efficiency or genetic stability of current methods. Here, we developed a system for targeted chromosomal integration of large biosynthetic gene clusters in Aspergillus nidulans based on site-specific recombinase-mediated cassette exchange. We built A. nidulans strains harboring a chromosomal landing pad for Cre/lox-mediated recombination and demonstrated efficient targeted integration of a 21 kb DNA fragment in a single step. We further evaluated the integration at two loci by analyzing the expression of a fluorescent reporter and the production of a heterologous polyketide metabolite. We compared chromosomal expression at those landing loci to episomal AMA1-based expression, which also shed light on uncharacterized aspects of episomal expression in filamentous fungi. This is the first demonstration of site-specific recombinase-mediated integration in filamentous fungi, setting the foundations for the further development of this tool.

Heterologous Expression of Fungal Biosynthetic Pathways in Aspergillus nidulans Using Episomal Vectors

Filamentous fungi produce a wide diversity of secondary metabolites, whose biosynthesis is encoded in biosynthetic gene clusters (BGCs). As novel BGCs are often found in fungal species that are genetically intractable or difficult to cultivate, heterologous expression is increasingly being used for compound discovery. In addition, heterologous expression is a useful strategy to elucidate the function of the genes within a BGC and shed light on their enzymatic mechanisms. Here, we describe a method for BGC elucidation using multi-marker AMA1-based pYFAC vectors for episomal expression in the fungal host Aspergillus nidulans. The pYFAC vectors have the advantage of high transformation efficiency and support high compound production. In addition, different pathway intermediates can be easily evaluated by testing different vector combinations. This protocol encompasses different AMA1-based strategies for BGC expression such as cloning of a BGC native sequence, promoter exchange or transcription factor overexpression. We also describe procedures for A. nidulans protoplasting, transformation, and small-scale culture analysis of strains containing AMA1 vectors.

Characterisation and heterologous biosynthesis of burnettiene A, a new polyene-decalin polyketide from Aspergillus burnettii

Chemical exploration of the recently described Australian fungus, Aspergillus burnettii, uncovered a new metabolite, burnettiene A. Here, we characterise the structure of burnettiene A as a polyene-decalin polyketide. Bioinformatic analysis of the genome of A. burnettii identified a putative biosynthetic gene cluster for burnettiene A (bue), consisting of eight genes and sharing similarity to the fusarielin gene cluster. Introduction of the reassembled bue gene cluster into Aspergillus nidulans for heterologous expression resulted in the production of burnettiene A under native promoters. Omission of bueE encoding a cytochrome P450 led to the production of preburnettiene A, confirming that BueE is responsible for catalysing the regiospecific multi-oxidation of terminal methyl groups to carboxylic acids. Similarly, bueF was shown to encode an ester-forming methyltransferase, with its omission resulting in the production of the tricarboxylic acid, preburnettiene B. Introduction of an additional copy of the transcription factor bueR under the regulation of the gpdA promoter significantly improved the heterologous production of the burnettienes. Burnettiene A displayed strong in vitro cytotoxicity against mouse myeloma NS-1 cells (MIC 0.8 μg mL^-1).

Polyketides produced by the entomopathogenic fungus Metarhizium anisopliae induce Candida albicans growth

Metarhizium anisopliae is an important entomopathogenic species and model for arthropod-fungus interaction studies. This fungus harbors a diverse arsenal of unexplored secondary metabolite biosynthetic gene clusters, which are suggested to perform diverse roles during host interaction and soil subsistence as a saprophytic species. Here we explored an unusual carnitine acyltransferase domain-containing highly reducing polyketide synthase found in the genome of M. anisopliae. Employing heterologous expression in Aspergillus nidulans, two new polyketides were obtained, named BAA and BAB, as well as one known polyketide [(2Z,4E,6E)-octa-2,4,6-trienedioic acid]. Intra-hemocoel injection of the most abundant compound (BAA) in the model-arthropod Galleria mellonella larvae did not induce mortality or noticeable alterations, suggesting that this compound may not harbor insecticidal activity. Also, the potential role of such molecules in polymicrobial interactions was evaluated. Determination of minimum inhibitory concentration assays using distinct fungal species revealed that BAA and BAB did not alter Cryptococcus neoformans growth, while BAA exhibited weak antifungal activity against Saccharomyces cerevisiae. Unexpectedly, these compounds increased Candida albicans growth compared to control conditions. Furthermore, BAA can mitigate the fungicidal effects of fluconazole over C. albicans. Although the exact role of these compounds on the M. anisopliae life cycle is elusive, the described results add up to the complexity of secondary metabolites produced by Metarhizium spp. Moreover, up to our knowledge, these are the first polyketides isolated from filamentous fungi that can boost the growth of another fungal species.

Nicotine evoked efferent transmitter release onto immature cochlear inner hair cells

Olivocochlear neurons make temporary cholinergic synapses on inner hair cells of the rodent cochlea in the first 2 to 3 wk after birth. Repetitive stimulation of these efferent neurons causes facilitation of evoked release and increased spontaneous release that continues for seconds to minutes. Presynaptic nicotinic acetylcholine receptors (nAChRs) are known to modulate neurotransmitter release from brain neurons. The present study explores the hypothesis that presynaptic nAChRs help to increase spontaneous release from efferent terminals on cochlear hair cells. Direct application of nicotine (which does not activate the hair cells' α9α10-containing nAChRs) produces sustained efferent transmitter release, implicating presynaptic nAChRs in this response. The effect of nicotine was reduced by application of ryanodine that reduces release of calcium from intraterminal stores.NEW & NOTEWORTHY Sensory organs exhibit spontaneous activity before the onset of response to external stimuli. Such activity in the cochlea is subject to modulation by cholinergic efferent neurons that directly inhibit sensory hair cells (inner hair cells). Those efferent neurons are themselves subject to various modulatory mechanisms. One such mechanism is positive feedback by released acetylcholine onto presynaptic nicotinic acetylcholine receptors causing further release of acetylcholine.

CRISPR-Mediated Activation of Biosynthetic Gene Clusters for Bioactive Molecule Discovery in Filamentous Fungi

Accessing the full biosynthetic potential encoded in the genomes of fungi is limited by the low expression of most biosynthetic gene clusters (BGCs) under common laboratory culture conditions. CRISPR-mediated transcriptional activation (CRISPRa) of fungal BGCs could accelerate genomics-driven bioactive secondary metabolite discovery. In this work, we established the first CRISPRa system for filamentous fungi. First, we constructed a CRISPR/dLbCas12a-VPR-based system and demonstrated the activation of a fluorescent reporter in Aspergillus nidulans. Then, we targeted the native nonribosomal peptide synthetase-like (NRPS-like) gene micA in both chromosomal and episomal contexts, achieving increased production of the compound microperfuranone. Finally, multigene CRISPRa led to the discovery of the mic cluster product as dehydromicroperfuranone. Additionally, we demonstrated the utility of the variant dLbCas12aD156R-VPR for CRISPRa at room temperature culture conditions. Different aspects that influence the efficiency of CRISPRa in fungi were investigated, providing a framework for the further development of fungal artificial transcription factors based on CRISPR/Cas.

Serum anti-Müllerian hormone levels are negatively related to Follicular Output RaTe (FORT) in normo-cycling women undergoing controlled ovarian hyperstimulation

BACKGROUND

Since in rodents anti-Müllerian hormone (AMH) has been shown to inhibit antral follicle responsiveness to FSH, we aimed at verifying whether a relationship exists between serum AMH levels and antral follicle responsiveness to exogenous FSH in normo-cycling women.

METHODS

Serum AMH, estradiol (E(2)) and FSH levels were prospectively measured on cycle day 3 in patients undergoing controlled ovarian hyperstimulation (COH) with a time-release GnRH agonist and standardized FSH doses. In 162 patients, follicles were counted after pituitary suppression and before FSH administration (baseline; small antral follicles; 3-8 mm), and on the day of hCG (dhCG; pre-ovulatory follicles; 16-22 mm). Antral follicle responsiveness to FSH was estimated by the Follicular Output RaTe (FORT), determined by the ratio pre-ovulatory follicle count on dhCG × 100/small antral follicle count at baseline.

RESULTS

Serum AMH levels were positively correlated with the number of small antral follicles at baseline (r = 0.59; P < 0.0001) and pre-ovulatory follicles on dhCG (r = 0.17; P < 0.04). Overall, FORT was 47.5 ± 1.4% and failed to be influenced by the woman's age, BMI or basal E(2) and FSH level. Conversely, multiple regression analysis showed that FORT was negatively correlated with AMH levels (r = -0.30; P < 0.001), irrespective of duration of COH and total FSH dose.

CONCLUSIONS

The percentage of follicles that effectively respond to FSH by reaching pre-ovulatory maturation is negatively and independently related to serum AMH levels. Although the mechanisms underlying this finding remain unclear, it is in keeping with the hypothesis that AMH inhibits follicle sensitivity to FSH.

Results of cochlear implantation in two children with mutations in the OTOF gene

OBJECTIVE

The purpose of the study is to present the results of cochlear implantation in case of deafness involving mutations in the OTOF gene. This form of deafness is characterized by the presence of transient evoked otoacoustic emissions (TEOAE). In cases of profound deafness with preserved TEOAE, two main etiologies should be considered: either an auditory neuropathy (a retrocochlear lesion) or an endocochlear lesion. It is essential to differentiate these two entities with regards to therapy and screening.

PATIENTS

We report two children who presented with profound prelingual deafness, confirmed by the absence of detectable responses to auditory evoked potentials (AEP), associated with the presence of bilateral TEOAE. Genetic testing revealed mutations in OTOF, confirming DFNB9 deafness. Both patients have been successfully implanted (with a follow-up of 18 and 36 months, respectively).

MAIN OUTCOME MEASURES

Clinical (oral production, closed and open-set words and sentences list, meaningful auditory integration scale), audiometric evaluation (TEOAE, AEP) before and after implantation, and neural response telemetry (NRT).

RESULTS

Both patients present a good quality of clinical responses and electrophysiological tests after implantation, indicating satisfactory functioning of the auditory nerve. This confirms the endocochlear origin of DFNB9 and suggests that these mutations in OTOF lead to functional alteration of inner hair cells.

CONCLUSION

In the absence of a context of neurological syndrome, the combination of absent AEP and positive TEOAE should lead to a genetic screening for mutations in OTOF, in order to undertake the appropriate management.

Auditory Neuropathy or Endocochlear Hearing Loss?

AIMS

The purpose of the study was to define boundaries between endocochlear hearing loss and auditory neuropathy in children with congenital profound hearing loss and positive otoacoustic emissions.

PATIENT

A child presented with bilateral profound hearing loss, which was confirmed by the absence of evoked auditory potentials at 110 dB and with conserved otoacoustic emissions. The lack of any relevant medical history, a normal neurologic pediatric examination, and the improvement obtained with powerful hearing aids suggested an endocochlear cause. Genetic testing identified mutations in OTOF, responsible for the DFNB9 recessive form of hearing loss.

RESULTS

In recent years, cases of children with hearing loss associated with positive otoacoustic emissions have been labeled as "auditory neuropathy." Classically, this form of hearing loss is refractory to the use of hearing aids and cochlear implants. Mutations in OTOF lead to inner hair cells dysfunction, whereas the outer hair cells are initially functionally preserved. As this form of endocochlear hearing loss can be detected at a molecular level, genetic testing can be proposed for cases of nonsyndromic auditory neuropathy, as those children could benefit from cochlear implantation.

CONCLUSION

It is advisable to reserve the term "auditory neuropathy" for patients who present hearing loss and conserved otoacoustic emissions in the context of a neurologic syndrome or for children with suggestive perinatal history. In other cases, genetic testing for mutations in OTOF should be carried out.

[Comparative study of the acceptability of a new estradiol Tx 11323 (A) gel and a transdermal matrix system]

OBJECTIVE

to compare the acceptability of a new estradiol gel TX 11323 (A) and a transdermal matrix system.

METHOD

this randomised open crossed study was conducted on 80 healthy menopausal female volunteers treated successively with 1.5 mg of estradiol per day in gel form (Estreva Gel, Theramex, Monaco) and by a transdermal matrix twice-weekly system delivering 50 micrograms/24 h of estradiol (Oesclim 50, Fournier, Dijon-France). The treatment was applied for 25 days with an interval of 6 days between the 2 administration cycles. Acceptability was evaluated and compared by a self-questionnaire given on D1 and D25 of each therapeutic cycle.

RESULTS

the 2 treatments, after 25 days of use, were judged convenient, easy and fast to use by more than 90% of subjects. There was, nevertheless, a significant difference in favour of the gel in respect of the estimation of the "visual aspect" of the treatment, reported skin problems, problems with application technique, as well as discomfort during intimacy found in 11% of cases using the transdermal system. It is noted that 80% of the women consider the gel treatment more feminine (p < 0.001) and that 61.3% prefer this treatment compared to 32.5% preferring the transdermal system studied (p = 0.005).

CONCLUSION

this study shows a better acceptability of the estradiol gel TX 11323 (A) compared to that of the transdermal matrix system studied.

Comparison of antimicrobial properties of monoterpenes and their carbonylated products

Some monoterpenes and their carbonylated products were evaluated for their antibacterial and antifungal properties. The carbonylation of tested monoterpenes was shown to increase the bacteriostatic and fungistatic activities specifically by the contact method. Concerning the killing effects, only (1R,2S,5R)-isopulegol, its carbonylated products, and (R)-carvone showed significant bactericidal activities, particularly against Enterococcus faecium and Escherichia coli above a concentration of 10 microliters/ml. A fungicidal efficiency of (1R,2S,5R)-isopulegol and (R)-carvone against Aspergillus niger was also noted. It seems that the presence of an oxygenated function in the framework increases the antimicrobial properties. However, monoterpenes were more active using a micro-atmosphere method.

[Comparative evaluation of the acceptability of a new estradiol gel TX11323(A) and a reference gel]

This randomized, crossed, single-blind study compared the acceptability and drying time of the new estradiol gel TX11323(A) (Estréva Gel, Laboratoire Théramex) to that of a reference gel (CEstrodose, Laboratories Besins-Iscovesco), in two phases. In phase 1, 48 healthy menopausal female volunteers applied 1.5 mg estradiol of each form of estradiol gel on the outer side of the arm for 8 days, with a free period of 7 days between the two treatments. Acceptability, evaluated by self-questionnaire and drying time for the two treatments were noted at day 1 and day 8. The second phase applied only to 16 subjects who followed the same therapeutic protocol, except that this time application was made on the antero-external side of the thighs. Only the subjectively and objectively quantified drying-time was taken into account. A significant difference was found in favor of TX11323(A) gel in terms of the following items: consistency, ease of application and penetration, quantity of gel to apply, sensation of lasting stickness. We note that 68.8% subjects prefer TX11323(A) gel and 27.1% prefer the reference gel (p = 0.001). The timed drying-time for TX11323(A) gel is significantly reduced, 40 to 50% on average depending on the phase, compared to that of the reference gel. The subjective evaluation of the subjects confirms this shorter drying time.

Saccharomyces boulardii inhibits secretagogue-mediated adenosine 3',5'-cyclic monophosphate induction in intestinal cells

BACKGROUND/AIMS

The yeast Saccharomyces boulardii inhibits the secretion induced by cholera toxin (CT) in rat jejunum. The present study was aimed at unraveling the mechanism by which S. boulardii protects intestinal cells against CT.

METHODS

CT-induced adenosine 3',5'-cyclic monophosphate (cAMP) levels were measured by radioimmunoassay in intestinal epithelial cells IEC-6 or HT29-D4 cells exposed to whole yeast or to culture medium conditioned by S. boulardii (Sb-conditioned medium).

RESULTS

Sb-conditioned medium significantly reduced CT-induced cAMP levels in IEC-6 cells. This effect was eliminated by heat treatment, trypsin hydrolysis, and trichloroacetic acid precipitation of Sb-conditioned medium. When conditioned medium was fractionated on polyacrylamide gel under nondenaturing conditions, neutralizing activity was shown to be associated with a 120-kilodalton protein. The neutralizing activity was not attributable to proteolytic activity against CT. Sb-conditioned medium reduced the amount of cAMP induced by CT as well as Escherichia coli thermolabile toxin or forskolin in HT29-D4 cells. The modulation of secretagogue-induced cAMP by Sb-conditioned medium did not occur in the presence of pertussis toxin.

CONCLUSIONS

These results suggest that the neutralization of CT by S. boulardii is mediated by a specific yeast protein and involves a receptor that is negatively coupled to adenylate cyclase.

Prediction of the halothane (Hal) genotypes by means of linked marker loci (Phi, Po2, Pgd) in Quebec Landrace pigs

Quebec Landrace pigs (n = 896) were halothane tested and blood samples were taken for the determination of Phi, Po2 and Pgd phenotypes. The incidence of the halothane positive pigs was 5.3%. The frequencies of the favorable alleles PhiA, Po2S and PdgA were respectively 29.2%, 39.6% and 64.4%. The highest linkage disequilibrium was found between Hal-Phi (0.0606) followed by Hal-Pgd (0.0428) and Hal-Po2 (-0.0308). Alleles PhiB, PgdB and Po2F were associated respectively with 97%, 81% and 74% of Haln haplotypes. It was concluded that a selection in order to increase the favorable marker loci PhiA and PgdA would reduce the Haln frequency in Quebec Landrace pigs.

Erythrocyte osmotic fragility, serum creatine kinase and its isoenzymes related to body weight in porcine malignant hyperthermia

Erythrocyte osmotic fragility, serum creatine kinase (CK) and its isoenzymes (CK-MM, CK-MB and CK-BB) were determined in pigs susceptible (SMH) and resistant (RMH) to malignant hyperthermia at three different body weights (Group 1, 10 to 25 kg; Group 2, 26 to 55 kg; Group 3, 56 to 95 kg). The halothane challenge test was used for determining susceptibility to malignant hyperthermia (MH). Significantly (P less than 0.05) greater erythrocyte haemolysis at saline concentrations of 80 to 100 mM NaCl occurred only between SMH and RMH pigs for body weight group 2. The determination of blood enzyme activities revealed also a significant (P less than 0.001) increase for total CK, CK-MM and CK-BB in SMH and RMH pigs of body weight Group 2. Furthermore in SMH pigs, total CK, CK-MM and CK-MB activities were significantly (P less than 0.05) greater in the animals of body weight Group 2. It was concluded that, in SMH pigs, weighing between 26 and 55 kg, there is a relationship between erythrocyte osmotic fragility, plasma CK, CK isoenzyme activities and muscle development.