Functional Genomics of : Strategies and Progress

Overview

Journal Microorganisms

Specialty Microbiology

Date 2019 Apr 13

PMID 30974907

Citations 18

Authors

Bin He

Yayi Tu

Chunmiao Jiang

Zhe Zhang

Yongkai Li

Bin Zeng

Affiliations

Soon will be listed here.

Abstract

has been used for the production of traditional fermentation and has promising potential to produce primary and secondary metabolites. Due to the tough cell walls and high drug resistance of , functional genomic characterization studies are relatively limited. The exploitation of selection markers and genetic transformation methods are critical for improving fermentative strains. In this review, we describe the genome sequencing of various strains. Recently developed selection markers and transformation strategies are also described in detail, and the advantages and disadvantages of transformation methods are presented. Lastly, we introduce the recent progress on highlighted topics in functional genomics including conidiation, protein secretion and expression, and secondary metabolites, which will be beneficial for improving the application of to industrial production.

Citing Articles

Locust Pathogen XJ1 Is Different from and Based on Genomics Comparisons.

You Y, Xu X, Liu H, Zhang L Microorganisms. 2025; 12(12.

PMID: 39770704 PMC: 11727900. DOI: 10.3390/microorganisms12122501.

The postbiotic potential of - a narrative review.

Seidler Y, Rimbach G, Luersen K, Vinderola G, Ipharraguerre I Front Microbiol. 2024; 15:1452725.

PMID: 39507340 PMC: 11538067. DOI: 10.3389/fmicb.2024.1452725.

Construction of an Aspergillus oryzae △nptB△pyrG Host for Homologous Expression of Lipase and Catalytic Property Characterization of Recombinant Lipase.

Zhang Y, Nie H, Zhang F, Jin M, Wang Z, Zheng J Appl Biochem Biotechnol. 2024; 197(2):873-890.

PMID: 39325292 DOI: 10.1007/s12010-024-05064-5.

Strategies for the Enhancement of Secondary Metabolite Production via Biosynthesis Gene Cluster Regulation in .

Jia X, Song J, Wu Y, Feng S, Sun Z, Hu Y J Fungi (Basel). 2024; 10(5).

PMID: 38786667 PMC: 11121810. DOI: 10.3390/jof10050312.

The ancient koji mold (Aspergillus oryzae) as a modern biotechnological tool.

Daba G, Mostafa F, Elkhateeb W Bioresour Bioprocess. 2024; 8(1):52.

PMID: 38650252 PMC: 10992763. DOI: 10.1186/s40643-021-00408-z.

References

Zhong Y, Lu X, Xing L, Ho S, Kwan H . Genomic and transcriptomic comparison of Aspergillus oryzae strains: a case study in soy sauce koji fermentation. J Ind Microbiol Biotechnol. 2018; 45(9):839-853. PMC: 6105210. DOI: 10.1007/s10295-018-2059-8. View

Zhu L, Maruyama J, Kitamoto K . Further enhanced production of heterologous proteins by double-gene disruption (ΔAosedD ΔAovps10) in a hyper-producing mutant of Aspergillus oryzae. Appl Microbiol Biotechnol. 2013; 97(14):6347-57. DOI: 10.1007/s00253-013-4795-z. View

Nodvig C, Nielsen J, Kogle M, Mortensen U . A CRISPR-Cas9 System for Genetic Engineering of Filamentous Fungi. PLoS One. 2015; 10(7):e0133085. PMC: 4503723. DOI: 10.1371/journal.pone.0133085. View

Machida M, Yamada O, Gomi K . Genomics of Aspergillus oryzae: learning from the history of Koji mold and exploration of its future. DNA Res. 2008; 15(4):173-83. PMC: 2575883. DOI: 10.1093/dnares/dsn020. View

Jin F, Maruyama J, Juvvadi P, Arioka M, Kitamoto K . Adenine auxotrophic mutants of Aspergillus oryzae: development of a novel transformation system with triple auxotrophic hosts. Biosci Biotechnol Biochem. 2004; 68(3):656-62. DOI: 10.1271/bbb.68.656. View

Lee J, Jo E, Hong E, Kim K, Lee I . Safety evaluation of filamentous fungi isolated from industrial doenjang koji. J Microbiol Biotechnol. 2014; 24(10):1397-404. DOI: 10.4014/jmb.1403.03007. View

Ogawa M, Tokuoka M, Jin F, Takahashi T, Koyama Y . Genetic analysis of conidiation regulatory pathways in koji-mold Aspergillus oryzae. Fungal Genet Biol. 2009; 47(1):10-8. DOI: 10.1016/j.fgb.2009.10.004. View

Frisvad J, Moller L, Larsen T, Kumar R, Arnau J . Safety of the fungal workhorses of industrial biotechnology: update on the mycotoxin and secondary metabolite potential of Aspergillus niger, Aspergillus oryzae, and Trichoderma reesei. Appl Microbiol Biotechnol. 2018; 102(22):9481-9515. PMC: 6208954. DOI: 10.1007/s00253-018-9354-1. View

Katayama T, Tanaka Y, Okabe T, Nakamura H, Fujii W, Kitamoto K . Development of a genome editing technique using the CRISPR/Cas9 system in the industrial filamentous fungus Aspergillus oryzae. Biotechnol Lett. 2015; 38(4):637-42. DOI: 10.1007/s10529-015-2015-x. View

10.

Zhang S, Ban A, Ebara N, Mizutani O, Tanaka M, Shintani T . Self-excising Cre/mutant lox marker recycling system for multiple gene integrations and consecutive gene deletions in Aspergillus oryzae. J Biosci Bioeng. 2016; 123(4):403-411. DOI: 10.1016/j.jbiosc.2016.11.001. View

11.

Hatakeyama R, Nakahama T, Higuchi Y, Kitamoto K . Light represses conidiation in koji mold Aspergillus oryzae. Biosci Biotechnol Biochem. 2007; 71(8):1844-9. DOI: 10.1271/bbb.60713. View

12.

Yoon J, Maruyama J, Kitamoto K . Disruption of ten protease genes in the filamentous fungus Aspergillus oryzae highly improves production of heterologous proteins. Appl Microbiol Biotechnol. 2010; 89(3):747-59. DOI: 10.1007/s00253-010-2937-0. View

13.

Piers K, Heath J, Liang X, Stephens K, Nester E . Agrobacterium tumefaciens-mediated transformation of yeast. Proc Natl Acad Sci U S A. 1996; 93(4):1613-8. PMC: 39990. DOI: 10.1073/pnas.93.4.1613. View

14.

Liu H, Jiao X, Wang Y, Yang X, Sun W, Wang J . Fast and efficient genetic transformation of oleaginous yeast Rhodosporidium toruloides by using electroporation. FEMS Yeast Res. 2017; 17(2). DOI: 10.1093/femsyr/fox017. View

15.

Machida M, Asai K, Sano M, Tanaka T, Kumagai T, Terai G . Genome sequencing and analysis of Aspergillus oryzae. Nature. 2005; 438(7071):1157-61. DOI: 10.1038/nature04300. View

16.

Yokota J, Shiro D, Tanaka M, Onozaki Y, Mizutani O, Kakizono D . Cellular responses to the expression of unstable secretory proteins in the filamentous fungus Aspergillus oryzae. Appl Microbiol Biotechnol. 2017; 101(6):2437-2446. DOI: 10.1007/s00253-016-8086-3. View

17.

Yoon J, Aishan T, Maruyama J, Kitamoto K . Enhanced production and secretion of heterologous proteins by the filamentous fungus Aspergillus oryzae via disruption of vacuolar protein sorting receptor gene Aovps10. Appl Environ Microbiol. 2010; 76(17):5718-27. PMC: 2935050. DOI: 10.1128/AEM.03087-09. View

18.

Jiang D, Zhu W, Wang Y, Sun C, Zhang K, Yang J . Molecular tools for functional genomics in filamentous fungi: recent advances and new strategies. Biotechnol Adv. 2013; 31(8):1562-74. DOI: 10.1016/j.biotechadv.2013.08.005. View

19.

Yao G, Zhang F, Nie X, Wang X, Yuan J, Zhuang Z . Essential APSES Transcription Factors for Mycotoxin Synthesis, Fungal Development, and Pathogenicity in . Front Microbiol. 2017; 8:2277. PMC: 5702001. DOI: 10.3389/fmicb.2017.02277. View

20.

Kitamoto K . Cell biology of the Koji mold Aspergillus oryzae. Biosci Biotechnol Biochem. 2015; 79(6):863-9. DOI: 10.1080/09168451.2015.1023249. View