Genomic and Transcriptomic Comparison of Aspergillus Oryzae Strains: a Case Study in Soy Sauce Koji Fermentation

Overview

Journal J Ind Microbiol Biotechnol

Publisher Oxford University Press

Specialty Biotechnology

Date 2018 Jul 7

PMID 29978373

Citations 17

Authors

Yiyi Zhong

Xi Lu

Lei Xing

Shiu Woon Allen Ho

Hoi Shan Kwan

Affiliations

Soon will be listed here.

Abstract

The filamentous fungus Aspergillus oryzae is used in soy sauce koji making due to its high productivity of hydrolytic enzymes. In this study, we compared the genomes and transcriptomes of an industrial strain RD2 and a strain with decreased fermentation performance TS2, aiming to explain their phenotypic differences at the molecular level. Under the regulation of conidiation and fermentation conditions, the enhanced hydrolytic enzyme production and flavor precursor formation in RD2 described a complete expression profile necessary to maintain desirable fermentation performance. By contrast, central carbon metabolism was up-regulated in TS2 for fast growth, suggesting a conflicting relationship between mycelium growth and fermentation performance. Accumulation of mutations also lowered the fermentation performance of TS2. Our study has deepened the understanding of the metabolism and related regulatory mechanisms in desirable koji fermentation. A list of potential molecular markers identified here could facilitate targeted strain maintenance and improvement for better koji fermentation.

Citing Articles

Adaptive Changes and Genetic Mechanisms in Organisms Under Controlled Conditions: A Review.

Guo Y, Liu Y, Huang P, Rong M, Wei W, Xu Y Int J Mol Sci. 2025; 26(5).

PMID: 40076752 PMC: 11900562. DOI: 10.3390/ijms26052130.

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.

Revealing salt concentration for microbial balance and metabolite enrichment in secondary fortified fermented soy sauce: A multi-omics perspective.

Zhang L, Zhang Z, Huang J, Zhou R, Wu C Food Chem X. 2024; 23:101722.

PMID: 39229615 PMC: 11369399. DOI: 10.1016/j.fochx.2024.101722.

Exploring the Potential of for Sustainable Mycoprotein Production Using Okara and Soy Whey as Cost-Effective Substrates.

Devanthi P, Pratama F, Pramanda I, Bani M, Kadar A, Kho K J Fungi (Basel). 2024; 10(8).

PMID: 39194881 PMC: 11355589. DOI: 10.3390/jof10080555.

References

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

Wang B, Guo G, Wang C, Lin Y, Wang X, Zhao M . Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucleic Acids Res. 2010; 38(15):5075-87. PMC: 2926611. DOI: 10.1093/nar/gkq256. View

Gruben B, Zhou M, Wiebenga A, Ballering J, Overkamp K, Punt P . Aspergillus niger RhaR, a regulator involved in L-rhamnose release and catabolism. Appl Microbiol Biotechnol. 2014; 98(12):5531-40. DOI: 10.1007/s00253-014-5607-9. View

te Biesebeke R, van Biezen N, de Vos W, van den Hondel C, Punt P . Different control mechanisms regulate glucoamylase and protease gene transcription in Aspergillus oryzae in solid-state and submerged fermentation. Appl Microbiol Biotechnol. 2005; 67(1):75-82. DOI: 10.1007/s00253-004-1807-z. View

Liang Y, Pan L, Lin Y . Analysis of extracellular proteins of Aspergillus oryzae grown on soy sauce koji. Biosci Biotechnol Biochem. 2009; 73(1):192-5. DOI: 10.1271/bbb.80500. View

Mendes-Pinto M . Carotenoid breakdown products the-norisoprenoids-in wine aroma. Arch Biochem Biophys. 2009; 483(2):236-45. DOI: 10.1016/j.abb.2009.01.008. View

Adams T, Wieser J, Yu J . Asexual sporulation in Aspergillus nidulans. Microbiol Mol Biol Rev. 1998; 62(1):35-54. PMC: 98905. DOI: 10.1128/MMBR.62.1.35-54.1998. 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

MacPherson S, Larochelle M, Turcotte B . A fungal family of transcriptional regulators: the zinc cluster proteins. Microbiol Mol Biol Rev. 2006; 70(3):583-604. PMC: 1594591. DOI: 10.1128/MMBR.00015-06. View

10.

Maeda H, Sano M, Maruyama Y, Tanno T, Akao T, Totsuka Y . Transcriptional analysis of genes for energy catabolism and hydrolytic enzymes in the filamentous fungus Aspergillus oryzae using cDNA microarrays and expressed sequence tags. Appl Microbiol Biotechnol. 2004; 65(1):74-83. DOI: 10.1007/s00253-004-1608-4. View

11.

Zhao G, Hou L, Yao Y, Wang C, Cao X . Comparative proteome analysis of Aspergillus oryzae 3.042 and A. oryzae 100-8 strains: Towards the production of different soy sauce flavors. J Proteomics. 2012; 75(13):3914-24. DOI: 10.1016/j.jprot.2012.04.056. View

12.

Kobayashi T, Abe K, Asai K, Gomi K, Juvvadi P, Kato M . Genomics of Aspergillus oryzae. Biosci Biotechnol Biochem. 2007; 71(3):646-70. DOI: 10.1271/bbb.60550. View

13.

Kaminski E, Stawicki S, Wasowicz E . Volatile Flavor Compounds Produced by Molds of Aspergillus, Penicillium, and Fungi imperfecti. Appl Microbiol. 1974; 27(6):1001-4. PMC: 380197. DOI: 10.1128/am.27.6.1001-1004.1974. View

14.

te Biesebeke R, Record E, van Biezen N, Heerikhuisen M, Franken A, Punt P . Branching mutants of Aspergillus oryzae with improved amylase and protease production on solid substrates. Appl Microbiol Biotechnol. 2005; 69(1):44-50. DOI: 10.1007/s00253-005-1968-4. View

15.

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley D . Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012; 7(3):562-78. PMC: 3334321. DOI: 10.1038/nprot.2012.016. View

16.

Otoole D . The role of microorganisms in soy sauce production. Adv Appl Microbiol. 2019; 108:45-113. DOI: 10.1016/bs.aambs.2019.07.002. View

17.

Ogawa M, Kobayashi T, Koyama Y . ManR, a novel Zn(II)2Cys6 transcriptional activator, controls the β-mannan utilization system in Aspergillus oryzae. Fungal Genet Biol. 2012; 49(12):987-95. DOI: 10.1016/j.fgb.2012.09.006. View

18.

Chambergo F, Bonaccorsi E, Ferreira A, Ramos A, Ferreira Junior J, Abrahao-Neto J . Elucidation of the metabolic fate of glucose in the filamentous fungus Trichoderma reesei using expressed sequence tag (EST) analysis and cDNA microarrays. J Biol Chem. 2002; 277(16):13983-8. DOI: 10.1074/jbc.M107651200. View

19.

Xu D, Pan L, Zhao H, Zhao M, Sun J, Liu D . Breeding and identification of novel koji molds with high activity of acid protease by genome recombination between Aspergillus oryzae and Aspergillus niger. J Ind Microbiol Biotechnol. 2010; 38(9):1255-65. DOI: 10.1007/s10295-010-0904-5. View

20.

Steinhaus P, Schieberle P . Characterization of the key aroma compounds in soy sauce using approaches of molecular sensory science. J Agric Food Chem. 2007; 55(15):6262-9. DOI: 10.1021/jf0709092. View