Dataset Information

Genome sequence and transcriptome analyses of the thermophilic zygomycete fungus Rhizomucor miehei.

ABSTRACT: BACKGROUND: The zygomycete fungi like Rhizomucor miehei have been extensively exploited for the production of various enzymes. As a thermophilic fungus, R. miehei is capable of growing at temperatures that approach the upper limits for all eukaryotes. To date, over hundreds of fungal genomes are publicly available. However, Zygomycetes have been rarely investigated both genetically and genomically. RESULTS: Here, we report the genome of R. miehei CAU432 to explore the thermostable enzymatic repertoire of this fungus. The assembled genome size is 27.6-million-base (Mb) with 10,345 predicted protein-coding genes. Even being thermophilic, the G + C contents of fungal whole genome (43.8%) and coding genes (47.4%) are less than 50%. Phylogenetically, R. miehei is more closerly related to Phycomyces blakesleeanus than to Mucor circinelloides and Rhizopus oryzae. The genome of R. miehei harbors a large number of genes encoding secreted proteases, which is consistent with the characteristics of R. miehei being a rich producer of proteases. The transcriptome profile of R. miehei showed that the genes responsible for degrading starch, glucan, protein and lipid were highly expressed. CONCLUSIONS: The genome information of R. miehei will facilitate future studies to better understand the mechanisms of fungal thermophilic adaptation and the exploring of the potential of R. miehei in industrial-scale production of thermostable enzymes. Based on the existence of a large repertoire of amylolytic, proteolytic and lipolytic genes in the genome, R. miehei has potential in the production of a variety of such enzymes.

SUBMITTER: Zhou P

PROVIDER: S-EPMC4023604 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Genome sequence and transcriptome analyses of the thermophilic zygomycete fungus Rhizomucor miehei.

Zhou Peng P Zhang Guoqiang G Chen Shangwu S Jiang Zhengqiang Z Tang Yanbin Y Henrissat Bernard B Yan Qiaojuan Q Yang Shaoqing S Chen Chin-Fu CF Zhang Bing B Du Zhenglin Z

BMC genomics 20140421

<h4>Background</h4>The zygomycete fungi like Rhizomucor miehei have been extensively exploited for the production of various enzymes. As a thermophilic fungus, R. miehei is capable of growing at temperatures that approach the upper limits for all eukaryotes. To date, over hundreds of fungal genomes are publicly available. However, Zygomycetes have been rarely investigated both genetically and genomically.<h4>Results</h4>Here, we report the genome of R. miehei CAU432 to explore the thermostable e ...[more]

PMID: 24746234

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Project description:BACKGROUND:?-Mannanase randomly cleaves the ?-1,4-linked mannan backbone of hemicellulose, which plays the most important role in the enzymatic degradation of mannan. Although the industrial applications of ?-mannanase have tremendously expanded in recent years, the wild-type ?-mannanases are still defective for some industries. The glycoside hydrolase (GH) family 5 ?-mannanase (RmMan5A) from Rhizomucor miehei shows many outstanding properties, such as high specific activity and hydrolysis property. However, owing to the low catalytic activity in acidic and thermophilic conditions, the application of RmMan5A to the biorefinery of mannan biomasses is severely limited. RESULTS:To overcome the limitation, RmMan5A was successfully engineered by directed evolution. Through two rounds of screening, a mutated ?-mannanase (mRmMan5A) with high catalytic activity in acidic and thermophilic conditions was obtained, and then characterized. The mutant displayed maximal activity at pH 4.5 and 65 °C, corresponding to acidic shift of 2.5 units in optimal pH and increase by 10 °C in optimal temperature. The catalytic efficiencies (kcat/Km) of mRmMan5A towards many mannan substrates were enhanced more than threefold in acidic and thermophilic conditions. Meanwhile, the high specific activity and excellent hydrolysis property of RmMan5A were inherited by the mutant mRmMan5A after directed evolution. According to the result of sequence analysis, three amino acid residues were substituted in mRmMan5A, namely Tyr233His, Lys264Met, and Asn343Ser. To identify the function of each substitution, four site-directed mutations (Tyr233His, Lys264Met, Asn343Ser, and Tyr233His/Lys264Met) were subsequently generated, and the substitutions at Tyr233 and Lys264 were found to be the main reason for the changes of mRmMan5A. CONCLUSIONS:Through directed evolution of RmMan5A, two key amino acid residues that controlled its catalytic efficiency under acidic and thermophilic conditions were identified. Information about the structure-function relationship of GH family 5 ?-mannanase was acquired, which could be used for modifying ?-mannanases to enhance the feasibility in industrial application, especially in biorefinery process. This is the first report on a ?-mannanase from zygomycete engineered by directed evolution.

Dataset Information

Genome sequence and transcriptome analyses of the thermophilic zygomycete fungus Rhizomucor miehei.

Publications

Genome sequence and transcriptome analyses of the thermophilic zygomycete fungus Rhizomucor miehei.

Similar Datasets

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