真菌功能基因组学：可调式敲除-敲入表达及标记策略
Fungal functional genomics: tunable knockout-knock-in expression and tagging strategies.
作者信息
Larrondo Luis F, Colot Hildur V, Baker Christopher L, Loros Jennifer J, Dunlap Jay C
机构信息
Department of Genetics, Dartmouth Medical School, Hanover, NH 03755, USA.
出版信息
Eukaryot Cell. 2009 May;8(5):800-4. doi: 10.1128/EC.00072-09. Epub 2009 Mar 13.
Abstract
Strategies for promoting high-efficiency homologous gene replacement have been developed and adopted for many filamentous fungal species. The next generation of analysis requires the ability to manipulate gene expression and to tag genes expressed from their endogenous loci. Here we present a suite of molecular tools that provide versatile solutions for fungal high-throughput functional genomics studies based on locus-specific modification of any target gene. Additionally, case studies illustrate caveats to presumed overexpression constructs. A tunable expression system and different tagging strategies can provide valuable phenotypic information for uncharacterized genes and facilitate the analysis of essential loci, an emerging problem in systematic deletion studies of haploid organisms.
摘要
促进高效同源基因置换的策略已被开发并应用于许多丝状真菌物种。下一代分析需要具备操纵基因表达以及标记从其内源位点表达的基因的能力。在此，我们展示了一套分子工具，这些工具基于对任何目标基因的位点特异性修饰，为真菌高通量功能基因组学研究提供了通用的解决方案。此外，案例研究说明了假定的过表达构建体存在的问题。一个可调节的表达系统和不同的标记策略可以为未表征的基因提供有价值的表型信息，并有助于分析必需位点，这是单倍体生物系统缺失研究中一个新出现的问题。
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1
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FEMS Microbiol Lett. 2008 Dec;289(2):225-32. doi: 10.1111/j.1574-6968.2008.01388.x.
2
Gene targeting in a nonhomologous end joining deficient Hypocrea jecorina.
J Biotechnol. 2009 Jan 15;139(2):146-51. doi: 10.1016/j.jbiotec.2008.10.007. Epub 2008 Nov 5.
3
A circadian clock in Neurospora: how genes and proteins cooperate to produce a sustained, entrainable, and compensated biological oscillator with a period of about a day.
Cold Spring Harb Symp Quant Biol. 2007;72:57-68. doi: 10.1101/sqb.2007.72.072.
4
Gene deletion and allelic replacement in the filamentous fungus Podospora anserina.
Curr Genet. 2008 Apr;53(4):249-58. doi: 10.1007/s00294-008-0180-3. Epub 2008 Feb 12.
5
e-Fungi: a data resource for comparative analysis of fungal genomes.
BMC Genomics. 2007 Nov 20;8:426. doi: 10.1186/1471-2164-8-426.
6
Insights from sequencing fungal and oomycete genomes: what can we learn about plant disease and the evolution of pathogenicity?
Plant Cell. 2007 Nov;19(11):3318-26. doi: 10.1105/tpc.107.056663. Epub 2007 Nov 16.
7
Regulation of hyphal morphogenesis by cdc42 and rac1 homologues in Aspergillus nidulans.
Mol Microbiol. 2007 Dec;66(6):1579-96. doi: 10.1111/j.1365-2958.2007.06021.x. Epub 2007 Nov 13.
8
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9
The band mutation in Neurospora crassa is a dominant allele of ras-1 implicating RAS signaling in circadian output.
Genes Dev. 2007 Jun 15;21(12):1494-505. doi: 10.1101/gad.1551707.
10
Use of a nonhomologous end joining deficient strain (Deltaku70) of the ergot fungus Claviceps purpurea for identification of a nonribosomal peptide synthetase gene involved in ergotamine biosynthesis.
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