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

详细信息    查看全文

• 作者：Peng Zhou ; Guoqiang Zhang ; Shangwu Chen ; Zhengqiang Jiang ; Yanbin Tang…
• 关键词：Rhizomucor miehei ; Genome ; Transcriptome ; Thermophilic fungus ; Thermostable enzymes
• 刊名：BMC Genomics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：15
• 期：1
• 全文大小：908 KB
• 参考文献：1. Mora, C, Tittensor, DP, Adl, S, Simpson, AG, Worm, B (2011) How many species are there on Earth and in the ocean?. PLoS Biol 9: pp. e1001127 CrossRef
  2. Hibbett, DS, Binder, M, Bischoff, JF, Blackwell, M, Cannon, PF, Eriksson, OE, Huhndorf, S, James, T, Kirk, PM, Lucking, R, Thorsten Lumbsch, H, Lutzoni, F, Matheny, PB, McLaughlin, DJ, Powell, MJ, Redhead, S, Schoch, CL, Spatafora, JW, Stalpers, JA, Vilgalys, R, Aime, MC, Aptroot, A, Bauer, R, Begerow, D, Benny, GL, Castlebury, LA, Crous, PW, Dai, YC, Gams, W, Geiser, DM (2007) A higher-level phylogenetic classification of the Fungi. Mycol Res 111: pp. 509-547 CrossRef
  3. Morgenstern, I, Powlowski, J, Ishmael, N, Darmond, C, Marqueteau, S, Moisan, MC, Quennevillea, G, Tsang, A (2012) A molecular phylogeny of thermophilic fungi. Fungal Biol 116: pp. 489-502 CrossRef
  4. Schipper, MAA (1978) On the genera Rhizomucor and Parasitella. Stud Mycol 17: pp. 53-71
  5. de Hoog, GS, Guarra, J, Gené, J, Figueras, MJ (2000) Atlas of clinical fungi. Centralbureau voor Schimmelcultures; Universitat Rovira i Virgili, Utrecht, The Nederlands; Reus, Spain
  6. Maheshwari, R, Bharadwaj, G, Bhat, MK (2000) Thermophilic fungi: their physiology and enzymes. Microbiol Mol Biol Rev 64: pp. 461-488 CrossRef
  7. Rao, MB, Tanksale, AM, Ghatge, MS, Deshpande, VV (1998) Molecular and biotechnological aspects of microbial proteases. Microbiol Mol Biol Rev 62: pp. 597-635
  8. Rodrigues, RC, Fernandez-Lafuente, R (2010) Lipase from Rhizomucor miehei as an industrial biocatalyst in chemical process. J Mol Catal B: Enzymatic 64: pp. 1-22 CrossRef
  9. Harboe, MK (1998) Rhizomucor miehei aspartic proteinases having improved properties. Adv Exp Med Biol 436: pp. 293-296 CrossRef
  10. Ali, UF, Ibrahim, ZM (2008) Production and some properties of fibrinolytic enzyme from Rhizomucor miehei (Cooney & Emerson) Schipper. J Appl Sci Res 4: pp. 892-899
  11. Tang, Y, Yang, S, Yan, Q, Zhou, P, Cui, J, Jiang, Z (2012) Purification and characterization of a novel β-1,3-1,4-glucanase (lichenase) from thermophilic Rhizomucor miehei with high specific activity and its gene sequence. J Agric Food Chem 60: pp. 2354-2361 CrossRef
  12. Fawzi, EM (2010) Highly thermostable purified xylanase from Rhizomucor miehei NRRL 3169. Ann Microbiol 60: pp. 363-368 CrossRef
  13. Liu, Y, Xu, H, Yan, Q, Yang, S, Duan, X, Jiang, Z (2013) Biochemical characterization of a first fungal esterase from Rhizomucor miehei showing high efficiency of ester synthesis. PLoS ONE 8: pp. e77856 CrossRef
  14. Galagan, JE, Calvo, SE, Borkovich, KA, Selker, EU, Read, ND, Jaffe, D, FitzHugh, W, Ma, LJ, Smirnov, S, Purcell, S, Rehman, B, Elkins, T, Engels, R, Wang, S, Nielsen, CB, Butler, J, Endrizzi, M, Qui, D, Ianakiev, P, Bell-Pedersen, D, Nelson, MA, Werner-Washburne, M, Selitrennikoff, CP, Kinsey, JA, Braun, EL, Zelter, A, Schulte, U, Kothe, GO, Jedd, G, Mewes, W (2003) The genome sequence of the filamentous fungus Neurospora crassa. Nature 422: pp. 859-868 CrossRef
  15. Martinez, D, Larrondo, LF, Putnam, N, Gelpke, MD, Huang, K, Chapman, J, Helfenbein, KG, Ramaiya, P, Detter, JC, Larimer, F, Coutinho, PM, Henrissat, B, Berka, R, Cullen, D, Rokhsar, D (2004) Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat Biotechnol 22: pp. 695-700 CrossRef
  16. Nierman, WC, Pain, A, Anderson, MJ, Wortman, JR, Kim, HS, Arroyo, J, Berriman, M, Abe, K, Archer, DB, Bermejo, C, Bennett, J, Bowyer, P, Chen, D, Collins, M, Coulsen, R, Davies, R, Dyer, PS, Farman, M, Fedorova, N, Fedorova, N, Feldblyum, TV, Fischer, R, Fosker, N, Fraser
• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

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.