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Chang PK. Creating large chromosomal segment deletions in Aspergillus flavus by a dual CRISPR/Cas9 system: Deletion of gene clusters for production of aflatoxin, cyclopiazonic acid, and ustiloxin B. Fungal Genet Biol 2024; 170:103863. [PMID: 38154756 DOI: 10.1016/j.fgb.2023.103863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 12/30/2023]
Abstract
Aspergillus flavus produces hepatocarcinogenic aflatoxin that adversely impacts human and animal health and international trade. A promising means to manage preharvest aflatoxin contamination of crops is biological control, which employs non-aflatoxigenic A. flavus isolates possessing defective aflatoxin gene clusters to outcompete field toxigenic populations. However, these isolates often produce other toxic metabolites. The CRISPR/Cas9 technology has greatly advanced genome editing and gene functional studies. Its use in deleting large chromosomal segments of filamentous fungi is rarely reported. A system of dual CRISPR/Cas9 combined with a 60-nucleotide donor DNA that allowed removal of A. flavus gene clusters involved in production of harmful specialized metabolites was established. It efficiently deleted a 102-kb segment containing both aflatoxin and cyclopiazonic acid gene clusters from toxigenic A. flavus morphotypes, L-type and S-type. It further deleted the 27-kb ustiloxin B gene cluster of a resulting L-type mutant. Overall efficiencies of deletion ranged from 66.6 % to 85.6 % and efficiencies of deletions repaired by a single copy of donor DNA ranged from 50.5 % to 72.7 %. To determine the capacity of this technique, a pigment-screening setup based on absence of aspergillic acid gene cluster was devised. Chromosomal segments of 201 kb and 301 kb were deleted with efficiencies of 57.7 % to 69.2 %, respectively. This system used natural A. flavus isolates as recipients, eliminated a forced-recycling step to produce recipients for next round deletion, and generated maker-free deletants with sequences predefined by donor DNA. The research provides a method for creating genuine atoxigenic biocontrol strains friendly for field trial release.
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Affiliation(s)
- Perng-Kuang Chang
- Southern Regional Research Center, Agricultural Research Service, U. S. Department of Agriculture, 1100 Allen Toussaint Boulevard, New Orleans, LA 70124, United States.
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Chang PK. A Simple CRISPR/Cas9 System for Efficiently Targeting Genes of Aspergillus Section Flavi Species, Aspergillus nidulans, Aspergillus fumigatus, Aspergillus terreus, and Aspergillus niger. Microbiol Spectr 2023; 11:e0464822. [PMID: 36651760 PMCID: PMC9927283 DOI: 10.1128/spectrum.04648-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/23/2022] [Indexed: 01/19/2023] Open
Abstract
For Aspergillus flavus, a pathogen of considerable economic and health concern, successful gene knockout work for more than a decade has relied nearly exclusively on using nonhomologous end-joining pathway (NHEJ)-deficient recipients via forced double-crossover recombination of homologous sequences. In this study, a simple CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease) genome editing system that gave extremely high (>95%) gene-targeting frequencies in A. flavus was developed. It contained a shortened Aspergillus nidulans AMA1 autonomously replicating sequence that maintained good transformation frequencies and Aspergillus oryzae ptrA as the selection marker for pyrithiamine resistance. Expression of the codon-optimized cas9 gene was driven by the A. nidulans gpdA promoter and trpC terminator. Expression of single guide RNA (sgRNA) cassettes was controlled by the A. flavus U6 promoter and terminator. The high transformation and gene-targeting frequencies of this system made generation of A. flavus gene knockouts with or without phenotypic changes effortless. Additionally, multiple-gene knockouts of A. flavus conidial pigment genes (olgA/copT/wA or olgA/yA/wA) were quickly generated by a sequential approach. Cotransforming sgRNA vectors targeting A. flavus kojA, yA, and wA gave 52%, 40%, and 8% of single-, double-, and triple-gene knockouts, respectively. The system was readily applicable to other section Flavi aspergilli (A. parasiticus, A. oryzae, A. sojae, A. nomius, A. bombycis, and A. pseudotamarii) with comparable transformation and gene-targeting efficiencies. Moreover, it gave satisfactory gene-targeting efficiencies (>90%) in A. nidulans (section Nidulantes), A. fumigatus (section Fumigati), A. terreus (section Terrei), and A. niger (section Nigri). It likely will have a broad application in aspergilli. IMPORTANCE CRISPR/Cas9 genome editing systems have been developed for many aspergilli. Reported gene-targeting efficiencies vary greatly and are dependent on delivery methods, repair mechanisms of induced double-stranded breaks, selection markers, and genetic backgrounds of transformation recipient strains. They are also mostly strain specific or species specific. This developed system is highly efficient and allows knocking out multiple genes in A. flavus efficiently either by sequential transformation or by cotransformation of individual sgRNA vectors if desired. It is readily applicable to section Flavi species and aspergilli in other sections ("section" is a taxonomic rank between genus and species). This cross-Aspergillus section system is for wild-type isolates and does not require homologous donor DNAs to be added, NHEJ-deficient strains to be created, or forced recycling of knockout recipients to be performed for multiple-gene targeting. Hence, it simplifies and expedites the gene-targeting process significantly.
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Affiliation(s)
- Perng-Kuang Chang
- Southern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, New Orleans, Louisiana, USA
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Habibi A, Afzali D. Aspergillus Section Flavi from Four Agricultural Products and Association of Mycotoxin and Sclerotia Production with Isolation Source. Curr Microbiol 2021; 78:3674-3685. [PMID: 34398304 DOI: 10.1007/s00284-021-02620-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 07/26/2021] [Indexed: 11/25/2022]
Abstract
Many agricultural products are susceptible to contamination by aflatoxin-producing species from Aspergillus section Flavi. The objectives of this study were to determine the occurrence of Aspergillus section Flavi in four agricultural products, such as pistachio, walnut, hazelnut, and dried fruits, collected from market and retail shops in various areas of Kerman County and obtain information on the relationships between isolation source and ability to produce sclerotia and potential for aflatoxin production. Aspergillus species were identified based on morphological characteristics as well as subsequent sequencing of the parts of the β-tubulin and calmodulin genes. From 207 isolated strains, the following species were identified: A. flavus, A. tamarii A. nomius, A. parasiticus, A. arachidicola, A. caelatus, A. pseudotamarii, and A. leporis. To the best of our knowledge, this is the first report of A. pseudotamarii and A. arachidicola with the potential to produce aflatoxins from dried apricots and hazelnuts, respectively. Sclerotial type was significantly different between isolates from different isolation sources. From 192 tested isolates, 38% were aflatoxin producer from which 5% were scored as strong aflatoxin producers and 33% as average aflatoxin producers. A significant difference in the population of aflatoxin-producing strains across the isolation sources was observed which may reflect host adaptation and thereby different vulnerabilities to aflatoxin-producing species among the examined products.
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Affiliation(s)
- Azadeh Habibi
- Department of Biodiversity, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
| | - Daryoush Afzali
- Department of Environment, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
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Khan R, Ghazali FM, Mahyudin NA, Samsudin NIP. Biocontrol of Aflatoxins Using Non-Aflatoxigenic Aspergillus flavus: A Literature Review. J Fungi (Basel) 2021; 7:jof7050381. [PMID: 34066260 PMCID: PMC8151999 DOI: 10.3390/jof7050381] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 02/06/2023] Open
Abstract
Aflatoxins (AFs) are mycotoxins, predominantly produced by Aspergillus flavus, A. parasiticus, A. nomius, and A. pseudotamarii. AFs are carcinogenic compounds causing liver cancer in humans and animals. Physical and biological factors significantly affect AF production during the pre-and post-harvest time. Several methodologies have been developed to control AF contamination, yet; they are usually expensive and unfriendly to the environment. Consequently, interest in using biocontrol agents has increased, as they are convenient, advanced, and friendly to the environment. Using non-aflatoxigenic strains of A. flavus (AF−) as biocontrol agents is the most promising method to control AFs’ contamination in cereal crops. AF− strains cannot produce AFs due to the absence of polyketide synthase genes or genetic mutation. AF− strains competitively exclude the AF+ strains in the field, giving an extra advantage to the stored grains. Several microbiological, molecular, and field-based approaches have been used to select a suitable biocontrol agent. The effectiveness of biocontrol agents in controlling AF contamination could reach up to 99.3%. Optimal inoculum rate and a perfect time of application are critical factors influencing the efficacy of biocontrol agents.
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Affiliation(s)
- Rahim Khan
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang 43400, Malaysia; (R.K.); (N.I.P.S.)
| | - Farinazleen Mohamad Ghazali
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang 43400, Malaysia; (R.K.); (N.I.P.S.)
- Correspondence: ; Tel.: +60-12219-8912
| | - Nor Ainy Mahyudin
- Department of Food Service and Management, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang 43400, Malaysia;
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Nik Iskandar Putra Samsudin
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang 43400, Malaysia; (R.K.); (N.I.P.S.)
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Malaysia
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Abstract
We report here a chromosome-level genome assembly of the aflatoxigenic fungus Aspergillus flavus strain CA14. This strain is the basis for numerous studies in fungal physiology and secondary metabolism. This full-length assembly will aid in subsequent genomics research. We report here a chromosome-level genome assembly of the aflatoxigenic fungus Aspergillus flavus strain CA14. This strain is the basis for numerous studies in fungal physiology and secondary metabolism. This full-length assembly will aid in subsequent genomics research.
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Recent progress of the effect of environmental factors on Aspergillus flavus growth and aflatoxins production on foods. FOOD QUALITY AND SAFETY 2020. [DOI: 10.1093/fqsafe/fyz040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Abstract
The contamination of Aspergillus flavus and subsequent aflatoxins (AFs) has been considered as one of the most serious food safety problems due to their acute and chronic adverse effects on humans and animals. This review collects the available information from recent years on the effect of the major environmental factors such as water activity (aw), temperature, CO2, and pH on the fungal growth, the expression of AFs-related genes, and AFs production by A. flavus on foods. In particular, the relationship between the relative expression of key regulatory (aflR and aflS) and structural genes (aflD, aflO, aflQ, etc.) and AFs production under different environmental conditions are collected and discussed. The information collected in this review can be used to design control strategies of A. flavus and AFs contamination in practical applications, primarily during storage and processing. These data suggest that integrating various post-harvest methods with synergistic functions may be more efficient for the control of A. flavus growth and AFs production, although the individual environmental factors alone have an impact.
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Genome Sequence of an Aspergillus flavus CA14 Strain That Is Widely Used in Gene Function Studies. Microbiol Resour Announc 2019; 8:8/33/e00837-19. [PMID: 31416879 PMCID: PMC6696654 DOI: 10.1128/mra.00837-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Aspergillus flavus produces aflatoxins that adversely impact human health and the economy. We report the genome sequence of A. flavus CA14 that has been widely used in gene function studies. The information will benefit A. flavus functional genomics studies on fungal development, secondary metabolite production, and fungus-host plant interactions. Aspergillus flavus produces aflatoxins that adversely impact human health and the economy. We report the genome sequence of A. flavus CA14 that has been widely used in gene function studies. The information will benefit A. flavus functional genomics studies on fungal development, secondary metabolite production, and fungus-host plant interactions.
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Hua SST, Parfitt DE, Sarreal SBL, Sidhu G. Dual culture of atoxigenic and toxigenic strains of Aspergillus flavus to gain insight into repression of aflatoxin biosynthesis and fungal interaction. Mycotoxin Res 2019; 35:381-389. [PMID: 31161589 DOI: 10.1007/s12550-019-00364-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 03/27/2019] [Accepted: 05/06/2019] [Indexed: 11/24/2022]
Abstract
Application of atoxigenic strains to compete against toxigenic strains of Aspergillus flavus strains has emerged as one of the practical strategies for reducing aflatoxin contamination in corn, peanut, and tree nuts. The actual mechanism that results in aflatoxin reduction is not fully understood. Real-time RT-PCR and relative quantification of gene expression protocol were applied to elucidate the molecular mechanism. Transcriptional analyses of aflatoxin biosynthetic gene cluster in dual culture of toxigenic and atoxigenic A. flavus strains were carried out. Six targeted genes, aflR, aflJ, omtA, ordA, pksA, and vbs, were downregulated to variable levels depending on paired strains of toxigenic and atoxigenic A. flavus. Consistent with the decreased gene expression levels, the aflatoxin concentrations in dual cultures were reduced significantly in comparison with toxigenic cultures. Fluorescent images showed fungal hyphae in dual culture displayed green fluorescent, and contacts of live hyphae were seen. A coconut agar plate assay was used to show that toxigenic A. flavus colony produced blue fluorescence under long UV exposure, suggesting that aflatoxin is exported outside fungal hyphae. Furthermore, the assay was applied to demonstrate the potential role of thigmo-regulation in fungal interaction.
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Affiliation(s)
- Sui Sheng T Hua
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA.
| | - Dan E Parfitt
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Siov Bouy L Sarreal
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Gaganjot Sidhu
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
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Identification of a copper-transporting ATPase involved in biosynthesis of A. flavus conidial pigment. Appl Microbiol Biotechnol 2019; 103:4889-4897. [DOI: 10.1007/s00253-019-09820-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/28/2019] [Accepted: 03/31/2019] [Indexed: 01/18/2023]
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10
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Pennerman KK, Gonzalez J, Chenoweth LR, Bennett JW, Yin G, Hua SST. Biocontrol strain Aspergillus flavus WRRL 1519 has differences in chromosomal organization and an increased number of transposon-like elements compared to other strains. Mol Genet Genomics 2018; 293:1507-1522. [DOI: 10.1007/s00438-018-1474-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/10/2018] [Indexed: 12/14/2022]
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Yin G, Hua SST, Pennerman KK, Yu J, Bu L, Sayre RT, Bennett JW. Genome sequence and comparative analyses of atoxigenic Aspergillus flavus WRRL 1519. Mycologia 2018; 110:482-493. [PMID: 29969379 DOI: 10.1080/00275514.2018.1468201] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aflatoxins are toxic secondary metabolites produced by Aspergillus flavus and a few other closely related species of Aspergillus. These highly toxigenic and carcinogenic mycotoxins contaminate global food and feed supplies, posing widespread health risks to humans and domestic animals. Field application of nonaflatoxigenic strains of A. flavus to compete against aflatoxigenic strains has emerged as one of the best management practices for reducing aflatoxins contamination, yielding successful commercial products for corn, cotton seed, and peanuts. In this study, we sequenced the genome and transcriptome of atoxigenic (does not produce aflatoxin or cyclopiazonic acid) A. flavus strain WRRL 1519 isolated from a tree nut orchard to define the genetic characteristics of the strain in relation to aflatoxigenic and other nonaflatoxigenic A. flavus strains. WRRL 1519 strain was similar to other strains in size (38.0 Mb), GC content (47.2%), number of predicted secondary metabolite gene clusters (46), and number of putative proteins (12 121). About 87.4% of the predicted proteome had high shared identity with protein sequences derived from other A. flavus genomes. However, the atoxigenic A. flavus strain WRRL 1519 had deletions, or low shared identity, for many genes in the clusters required for aflatoxins and cyclopiazonic acid (CPA) synthesis. Over half of the aflatoxin synthesis gene cluster was missing, and none of the components of the CPA gene cluster were identified with high sequence similarity. Importantly, the strain appeared to maintain functional sequences of several genes thought to be required for high infectivity. Since the ability to grow on target crop is an important attribute for a successful biocontrol agent, these results indicate that the nonaflatoxigenic A. flavus strain WRRL 1519 would be a good candidate as a biocontrol agent for reducing aflatoxin and CPA accumulation in high-value nut crops.
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Affiliation(s)
- Guohua Yin
- a Department of Plant Biology, Rutgers , The State University of New Jersey , New Brunswick , New Jersey 08901.,b New Mexico Consortium and Pebble Labs , Los Alamos , New Mexico 87544
| | - Sui Sheng T Hua
- c Foodborne Toxin Detection and Prevention Research, Western Regional Research Center, Agricultural Research Service , US Department of Agriculture , Albany , California 94710
| | - Kayla K Pennerman
- a Department of Plant Biology, Rutgers , The State University of New Jersey , New Brunswick , New Jersey 08901
| | - Jiujiang Yu
- d Food Quality Laboratory, Agricultural Research Service , US Department of Agriculture, Beltsville Agricultural Research Center , Beltsville , Maryland 20705
| | - Lijing Bu
- e Center for Evolutionary & Theoretical Immunology, Department of Biology , University of New Mexico , Albuquerque , New Mexico 87131
| | - Richard T Sayre
- b New Mexico Consortium and Pebble Labs , Los Alamos , New Mexico 87544
| | - Joan W Bennett
- a Department of Plant Biology, Rutgers , The State University of New Jersey , New Brunswick , New Jersey 08901
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Development of a droplet digital PCR assay for population analysis of aflatoxigenic and atoxigenic Aspergillus flavus mixtures in soil. Mycotoxin Res 2018; 34:187-194. [PMID: 29582253 DOI: 10.1007/s12550-018-0313-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 03/08/2018] [Accepted: 03/13/2018] [Indexed: 10/17/2022]
Abstract
Aflatoxin B1 is a potent hepatotoxin and carcinogen that poses a serious safety hazard to both humans and animals. Aspergillus flavus is the most common aflatoxin-producing species on corn, cotton, peanuts, and tree nuts. Application of atoxigenic strains to compete against aflatoxigenic strains of A. flavus has emerged as one of the most practical strategies for ameliorating aflatoxin contamination in food. Genes directly involved in aflatoxin biosynthesis are clustered on an 82-kb region of the genome. Three atoxigenic strains (CA12, M34, and AF123) were each paired with each of four aflatoxigenic strains (CA28, CA42, CA90, and M52), inoculated into soil and incubated at 28 °C for 2 weeks and 1 month. TaqMan probes, omtA-FAM, and norA-HEX were designed for developing a droplet digital PCR (ddPCR) assay to analyze the soil population of mixtures of A. flavus strains. DNA was extracted from each soil sample and used for ddPCR assays. The data indicated that competition between atoxigenic and aflatoxigenic was strain dependent. Variation in competitive ability among different strains of A. flavus influenced the population reduction of the aflatoxigenic strain by the atoxigenic strain. Higher ratios of atoxigenic to aflatoxigenic strains increased soil population of atoxigenic strains. This is the first study to demonstrate the utility of ddPCR to quantify mixtures of both atoxigenic and aflatoxigenic A. flavus strains in soil and allows for rapid and accurate determination of population sizes of atoxigenic and aflatoxigenic strains. This method eliminates the need for isolation and identification of individual fungal isolates from experimental soil samples.
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Moore GG, Mack BM, Beltz SB, Puel O. Genome sequence of an aflatoxigenic pathogen of Argentinian peanut, Aspergillus arachidicola. BMC Genomics 2018; 19:189. [PMID: 29523080 PMCID: PMC5845213 DOI: 10.1186/s12864-018-4576-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 03/02/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Aspergillus arachidicola is an aflatoxigenic fungal species, first isolated from the leaves of a wild peanut species native to Argentina. It has since been reported in maize, Brazil nut and human sputum samples. This aflatoxigenic species is capable of secreting both B and G aflatoxins, similar to A. parasiticus and A. nomius. It has other characteristics that may result in its misidentification as one of several other section Flavi species. This study offers a preliminary analysis of the A. arachidicola genome. RESULTS In this study we sequenced the genome of the A. arachidicola type strain (CBS 117610) and found its genome size to be 38.9 Mb, and its number of predicted genes to be 12,091, which are values comparable to those in other sequenced Aspergilli. A comparison of 57 known Aspergillus secondary metabolite gene clusters, among closely-related aflatoxigenic species, revealed nearly half were predicted to exist in the type strain of A. arachidicola. Of its predicted genes, 691 were identified as unique to the species and 60% were assigned Gene Ontology terms using BLAST2GO. Phylogenomic inference shows CBS 117610 sharing a most recent common ancestor with A. parasiticus. Finally, BLAST query of A. flavus mating-type idiomorph sequences to this strain revealed the presence of a single mating-type (MAT1-1) idiomorph. CONCLUSIONS Based on A. arachidicola morphological, genetic and chemotype similarities with A. flavus and A. parasiticus, sequencing the genome of A. arachidicola will contribute to our understanding of the evolutionary relatedness among aflatoxigenic fungi.
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Affiliation(s)
- Geromy G. Moore
- Southern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 1100 Robert E Lee Blvd, New Orleans, Louisiana, 70124 USA
| | - Brian M. Mack
- Southern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 1100 Robert E Lee Blvd, New Orleans, Louisiana, 70124 USA
| | - Shannon B. Beltz
- Southern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 1100 Robert E Lee Blvd, New Orleans, Louisiana, 70124 USA
| | - Olivier Puel
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
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14
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Hua SST, Parfitt DE, Sarreal SBL, Lee BG, Wood DF. First report of an atypical new Aspergillus parasiticus isolates with nucleotide insertion in aflR gene resembling to A. sojae. Mycotoxin Res 2018; 34:151-157. [PMID: 29464607 DOI: 10.1007/s12550-018-0309-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 02/01/2018] [Accepted: 02/06/2018] [Indexed: 11/30/2022]
Abstract
Aflatoxins are toxic and carcinogenic secondary metabolites produced primarily by the filamentous fungi Aspergillus flavus and Aspergillus parasiticus and cause toxin contamination in food chain worldwide. Aspergillus oryzae and Aspergillus sojae are highly valued as koji molds in the traditional preparation of fermented foods, such as miso, sake, and shoyu. Koji mold species are generally perceived of as being nontoxigenic and are generally recognized as safe (GRAS). Fungal isolates were collected from a California orchard and a few were initially identified to be A. sojae using β-tubulin gene sequences blasted against NCBI data base. These new isolates all produced aflatoxins B1, B2, G1, and G2 and were named as Pistachio Winter Experiment (PWE) strains. Thus, it is very important to further characterize these strains for food safety purposes. The full length of aflR gene of these new isolates was sequenced. Comparison of aflR DNA sequences of PWE, A. parasiticus and A. sojae, showed that the aflatoxigenic PWE strains had the six base insertion (CTCATG) similar to domesticated A. sojae, but a pre-termination codon TGA at nucleotide positions 1153-1155 was absent due to a nucleotide codon change from T to C. Colony morphology and scanning microscopic imaging of spore surfaces showed similarity of PWE strains to both A. parasiticus and A. sojae. Concordance analysis of multi locus DNA sequences indicated that PWE strains were closely linked between A. parasiticus and A. sojae. The finding documented the first report that such unique strains have been found in North America and in the world.
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Affiliation(s)
- Sui Sheng T Hua
- US Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA.
| | - Dan E Parfitt
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Siov Bouy L Sarreal
- US Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Bertram G Lee
- US Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Delilah F Wood
- US Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
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Chang PK, Scharfenstein LL, Solorzano CD, Abbas HK, Hua SST, Jones WA, Zablotowicz RM. High sequence variations in the region containing genes encoding a cellular morphogenesis protein and the repressor of sexual development help to reveal origins of Aspergillus oryzae. Int J Food Microbiol 2015; 200:66-71. [PMID: 25689355 DOI: 10.1016/j.ijfoodmicro.2015.01.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 01/21/2015] [Accepted: 01/28/2015] [Indexed: 01/28/2023]
Abstract
Aspergillus oryzae and Aspergillus flavus are closely related fungal species. The A. flavus morphotype that produces numerous small sclerotia (S strain) and aflatoxin has a unique 1.5 kb deletion in the norB-cypA region of the aflatoxin gene cluster (i.e. the S genotype). Phylogenetic studies have indicated that an isolate of the nonaflatoxigenic A. flavus with the S genotype is the ancestor of A. oryzae. Genome sequence comparison between A. flavus NRRL3357, which produces large sclerotia (L strain), and S-strain A. flavus 70S identified a region (samA-rosA) that was highly variable in the two morphotypes. A third type of samA-rosA region was found in A. oryzae RIB40. The three samA-rosA types were later revealed to be commonly present in A. flavus L-strain populations. Of the 182 L-strain A. flavus field isolates examined, 46%, 15% and 39% had the samA-rosA type of NRRL3357, 70S and RIB40, respectively. The three types also were found in 18 S-strain A. flavus isolates with different proportions. For A. oryzae, however, the majority (80%) of the 16 strains examined had the RIB40 type and none had the NRRL3357 type. The results suggested that A. oryzae strains in the current culture collections were mostly derived from the samA-rosA/RIB40 lineage of the nonaflatoxigenic A. flavus with the S genotype.
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Affiliation(s)
- Perng-Kuang Chang
- Southern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, New Orleans, LA 70124, United States.
| | - Leslie L Scharfenstein
- Southern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, New Orleans, LA 70124, United States
| | - Cesar D Solorzano
- Biological Control of Pests Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Stoneville, MS 38776, United States
| | - Hamed K Abbas
- Biological Control of Pests Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Stoneville, MS 38776, United States
| | - Sui-Sheng T Hua
- Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, 94710, United States
| | - Walker A Jones
- Biological Control of Pests Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Stoneville, MS 38776, United States
| | - Robert M Zablotowicz
- Crop Production Systems Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Stoneville, MS 38776, United States
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Zhang F, Guo Z, Zhong H, Wang S, Yang W, Liu Y, Wang S. RNA-Seq-based transcriptome analysis of aflatoxigenic Aspergillus flavus in response to water activity. Toxins (Basel) 2014; 6:3187-207. [PMID: 25421810 PMCID: PMC4247253 DOI: 10.3390/toxins6113187] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 10/27/2014] [Accepted: 11/13/2014] [Indexed: 01/06/2023] Open
Abstract
Aspergillus flavus is one of the most important producers of carcinogenic aflatoxins in crops, and the effect of water activity (aw) on growth and aflatoxin production of A. flavus has been previously studied. Here we found the strains under 0.93 aw exhibited decreased conidiation and aflatoxin biosynthesis compared to that under 0.99 aw. When RNA-Seq was used to delineate gene expression profile under different water activities, 23,320 non-redundant unigenes, with an average length of 1297 bp, were yielded. By database comparisons, 19,838 unigenes were matched well (e-value < 10−5) with known gene sequences, and another 6767 novel unigenes were obtained by comparison to the current genome annotation of A. flavus. Based on the RPKM equation, 5362 differentially expressed unigenes (with |log2Ratio| ≥ 1) were identified between 0.99 aw and 0.93 aw treatments, including 3156 up-regulated and 2206 down-regulated unigenes, suggesting that A. flavus underwent an extensive transcriptome response during water activity variation. Furthermore, we found that the expression of 16 aflatoxin producing-related genes decreased obviously when water activity decreased, and the expression of 11 development-related genes increased after 0.99 aw treatment. Our data corroborate a model where water activity affects aflatoxin biosynthesis through increasing the expression of aflatoxin producing-related genes and regulating development-related genes.
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Affiliation(s)
- Feng Zhang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of the Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zhenni Guo
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of the Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Hong Zhong
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of the Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Sen Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of the Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Weiqiang Yang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of the Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yongfeng Liu
- Shenzhen Key Laboratory of Bioenergy, BGI-Shenzhen, Shenzhen 518083, China.
| | - Shihua Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of the Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Ehrlich KC, Mack BM. Comparison of expression of secondary metabolite biosynthesis cluster genes in Aspergillus flavus, A. parasiticus, and A. oryzae. Toxins (Basel) 2014; 6:1916-28. [PMID: 24960201 PMCID: PMC4073137 DOI: 10.3390/toxins6061916] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 06/09/2014] [Accepted: 06/13/2014] [Indexed: 12/28/2022] Open
Abstract
Fifty six secondary metabolite biosynthesis gene clusters are predicted to be in the Aspergillus flavus genome. In spite of this, the biosyntheses of only seven metabolites, including the aflatoxins, kojic acid, cyclopiazonic acid and aflatrem, have been assigned to a particular gene cluster. We used RNA-seq to compare expression of secondary metabolite genes in gene clusters for the closely related fungi A. parasiticus, A. oryzae, and A. flavus S and L sclerotial morphotypes. The data help to refine the identification of probable functional gene clusters within these species. Our results suggest that A. flavus, a prevalent contaminant of maize, cottonseed, peanuts and tree nuts, is capable of producing metabolites which, besides aflatoxin, could be an underappreciated contributor to its toxicity.
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Affiliation(s)
- Kenneth C Ehrlich
- Southern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, New Orleans, LA 70124, USA.
| | - Brian M Mack
- Southern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, New Orleans, LA 70124, USA.
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18
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Modelling Aspergillus flavus growth and aflatoxins production in pistachio nuts. Food Microbiol 2012; 32:378-88. [DOI: 10.1016/j.fm.2012.07.018] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 06/16/2012] [Accepted: 07/30/2012] [Indexed: 11/20/2022]
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