Alcantara J, Mondala A, Hughey L, Shields S (2017) Direct succinic acid production from minimally pretreated biomass using sequential solid-state and slurry fermentation with mixed fungal cultures. Fermentation 3(3):30. https://doi.org/10.3390/fermentation3030030

Article  Google Scholar 

Arikawa Y, Kuroyanagi T, Shimosaka M, Muratsubaki H, Enomoto K, Kodaira R, Okazaki M (1999) Effect of gene disruptions of the TCA cycle on production of succinic acid in Saccharomyces cerevisiae. J Biosci Bioeng 87(1):28–36. https://doi.org/10.1016/S1389-1723(99)80004-8

Article  PubMed  Google Scholar 

Arst HN Jr, Peñalva MA (2003) pH regulation in Aspergillus and parallels with higher eukaryotic regulatory systems. Trends Genet 19(4):224–231. https://doi.org/10.1016/S0168-9525(03)00052-0

Article  PubMed  Google Scholar 

Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315(5819):1709–1712. https://doi.org/10.1126/science.1138140

Article  PubMed  Google Scholar 

Becker J, Wittmann C (2015) Advanced biotechnology: metabolically engineered cells for the bio-based production of chemicals and fuels, materials, and health-care products. Angewandte Chemie-International Edition 54(11):3328–3350. https://doi.org/10.1002/anie.201409033

Article  PubMed  Google Scholar 

Becker J, Lange A, Fabarius J, Wittmann C (2015) Top value platform chemicals: bio-based production of organic acids. Curr Opin Biotechnol 36:168–175. https://doi.org/10.1016/j.copbio.2015.08.022

Article  PubMed  Google Scholar 

Bhaya D, Davison M, Barrangou R (2011) CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu Rev Genet 45:273–297. https://doi.org/10.1146/annurev-genet-110410-132430

Article  PubMed  Google Scholar 

Brandl J, Aguilar-Pontes MV, Schäpe P, Noerregaard A, Arvas M, Ram AFJ, Meyer V, Tsang A, de Vries RP, Andersen MR (2018) A community-driven reconstruction of the Aspergillus niger metabolic network. Fungal Biology and Biotechnology 5(1):16. https://doi.org/10.1186/s40694-018-0060-7

Article  PubMed  PubMed Central  Google Scholar 

Brown SH, Bashkirova L, Berka R, Chandler T, Doty T, McCall K, McCulloch M, McFarland S, Thompson S, Yaver D, Berry A (2013) Metabolic engineering of Aspergillus oryzae NRRL 3488 for increased production of l-malic acid. Appl Microbiol Biotechnol 97(20):8903–8912. https://doi.org/10.1007/s00253-013-5132-2

Article  PubMed  Google Scholar 

Chai KF, Ng KR, Samarasiri M, Chen WN (2022) Precision fermentation to advance fungal food fermentations. Curr Opin Food Sci 47:100881. https://doi.org/10.1016/j.cofs.2022.100881

Article  Google Scholar 

Chakraborty J, Chaudhary AA, Khan S-U-D, Rudayni HA, Rahaman SM, Sarkar H (2022) CRISPR/Cas-based biosensor as a new age detection method for pathogenic bacteria. ACS Omega 7(44):39562–39573. https://doi.org/10.1021/acsomega.2c04513

Article  PubMed  PubMed Central  Google Scholar 

Chang P-K, Scharfenstein LL, Mahoney N, Kong Q (2023) Kojic acid gene clusters and the transcriptional activation mechanism of Aspergillus flavus KojR on expression of clustered genes. Journal of Fungi 9(2):259. https://doi.org/10.3390/jof9020259

Article  PubMed  PubMed Central  Google Scholar 

Chen JS, Ma E, Harrington LB, Da Costa M, Tian X, Palefsky JM, Doudna JA (2018) CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science 360(6387):436–439. https://doi.org/10.1126/science.aar6245

Article  PubMed  PubMed Central  Google Scholar 

Chen X, Zhou J, Ding Q, Luo Q, Liu L (2019) Morphology engineering of Aspergillus oryzae for l-malate production. Biotechnol Bioeng 116(10):2662–2673. https://doi.org/10.1002/bit.27089

Article  PubMed  Google Scholar 

Chen M-Y, Zhao F-L, Chu W-L, Bai M-R, Zhang D-M (2023) A review of tamoxifen administration regimen optimization for Cre/loxp system in mouse bone study. Biomed Pharmacother 165:115045. https://doi.org/10.1016/j.biopha.2023.115045

Article  PubMed  Google Scholar 

Chen Z, Zhang C, Pei L, Qian Q, Lu L (2023) Production of L-malic acid by metabolically engineered Aspergillus nidulans based on efficient CRISPR–Cas9 and Cre-loxP systems. J Fungi 9(7):719. https://doi.org/10.3390/jof9070719

Article  Google Scholar 

Chib S, Jamwal VL, Kumar V, Gandhi SG, Saran S (2023) Fungal production of kojic acid and its industrial applications. Appl Microbiol Biotechnol 107(7):2111–2130. https://doi.org/10.1007/s00253-023-12451-1

Article  PubMed  Google Scholar 

Djukić-Vuković A, Mladenović D, Ivanović J, Pejin J, Mojović L (2019) Towards sustainability of lactic acid and poly-lactic acid polymers production. Renew Sustain Energy Rev 108:238–252. https://doi.org/10.1016/j.rser.2019.03.050

Article  Google Scholar 

Elmore JR, Dexter GN, Salvachúa D, Martinez-Baird J, Hatmaker EA, Huenemann JD, Klingeman DM, Peabody GL, Peterson DJ, Singer C, Beckham GT, Guss AM (2021) Production of itaconic acid from alkali pretreated lignin by dynamic two stage bioconversion. Nat Commun 12(1):2261. https://doi.org/10.1038/s41467-021-22556-8

Article  PubMed  PubMed Central  Google Scholar 

Hamilton DL, Abremski K (1984) Site-specific recombination by the bacteriophage P1 lox-Cre system: Cre-mediated synapsis of two lox sites. J Mol Biol 178(2):481–486. https://doi.org/10.1016/0022-2836(84)90154-2

Article  PubMed  Google Scholar 

Hossain AH, Li A, Brickwedde A, Wilms L, Caspers M, Overkamp K, Punt PJ (2016) Rewiring a secondary metabolite pathway towards itaconic acid production in Aspergillus niger. Microb Cell Fact 15(1):130. https://doi.org/10.1186/s12934-016-0527-2

Article  PubMed  PubMed Central  Google Scholar 

Hossain AH, van Gerven R, Overkamp KM, Lübeck PS, Taşpınar H, Türker M, Punt PJ (2019) Metabolic engineering with ATP-citrate lyase and nitrogen source supplementation improves itaconic acid production in Aspergillus niger. Biotechnol Biofuels 12(1):233. https://doi.org/10.1186/s13068-019-1577-6

Article  PubMed  PubMed Central  Google Scholar 

Hossain GS, Saini M, Miyake R, Ling H, Chang MW (2020) Genetic biosensor design for natural product biosynthesis in microorganisms. Trends Biotechnol 38(7):797–810. https://doi.org/10.1016/j.tibtech.2020.03.013

Article  PubMed  Google Scholar 

Hou L, Liu L, Zhang H, Zhang L, Zhang L, Zhang J, Gao Q, Wang D (2018) Functional analysis of the mitochondrial alternative oxidase gene (aox1) from Aspergillus niger CGMCC 10142 and its effects on citric acid production. Appl Microbiol Biotechnol 102(18):7981–7995. https://doi.org/10.1007/s00253-018-9197-9

Article  PubMed  Google Scholar 

Huang X, Men P, Tang S, Lu X (2021) Aspergillus terreus as an industrial filamentous fungus for pharmaceutical biotechnology. Curr Opin Biotechnol 69:273–280. https://doi.org/10.1016/j.copbio.2021.02.004

Article  PubMed  Google Scholar 

Huang Z, Tian D, Liu Y, Lin Z, Lyon CJ, Lai W, Fusco D, Drouin A, Yin X, Hu T, Ning B (2020) Ultra-sensitive and high-throughput CRISPR-p owered COVID-19 diagnosis. Biosensors and Bioelectronics 164. https://doi.org/10.1016/j.bios.2020.112316

Iyyappan J, Bharathiraja B, Baskar G, Kamalanaban E (2019) Process optimization and kinetic analysis of malic acid production from crude glycerol using Aspergillus niger. Biores Technol 281:18–25. https://doi.org/10.1016/j.biortech.2019.02.067

Article  Google Scholar 

Jia X, Song J, Wu Y, Feng S, Sun Z, Hu Y, Yu M, Han R, Zeng B (2024) Strategies for the enhancement of secondary metabolite production via biosynthesis gene cluster regulation in Aspergillus oryzae. Journal of Fungi 10(5):312. https://doi.org/10.3390/jof10050312

Article  PubMed  PubMed Central  Google Scholar 

Kadooka C, Nakamura E, Mori K, Okutsu K, Yoshizaki Y, Takamine K, Goto M, Tamaki H, Futagami T (2020) LaeA controls citric acid production through regulation of the citrate exporter-encoding cexA gene in Aspergillus luchuensis mut. kawachii. Appl Environ Microbiol. https://doi.org/10.1128/aem.01950-19

Article  PubMed  PubMed Central  Google Scholar 

Kanaar R, Hoeijmakers JHJ, Van Gent DC (1998) Molecular mechanisms of DNA double-strand break repair. Trends Cell Biol 8(12):483–489. https://doi.org/10.1016/S0962-8924(98)01383-X

Article  PubMed  Google Scholar 

Katayama T, Tanaka Y, Okabe T, Nakamura H, Fujii W, Kitamoto K, Maruyama J-i (2016) Development of a genome editing technique using the CRISPR/Cas9 system in the industrial filamentous fungus Aspergillus oryzae. Biotech Lett 38(4):637–642. https://doi.org/10.1007/s10529-015-2015-x

Article  Google Scholar