Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites.
Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites.
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DOI：
10.1371/journal.ppat.1003475
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发表时间：
2013
期刊：
影响因子：
6.7
通讯作者：
Tudzynski B
中科院分区：
文献类型：
--
作者：
Wiemann P;Sieber CM;von Bargen KW;Studt L;Niehaus EM;Espino JJ;Huß K;Michielse CB;Albermann S;Wagner D;Bergner SV;Connolly LR;Fischer A;Reuter G;Kleigrewe K;Bald T;Wingfield BD;Ophir R;Freeman S;Hippler M;Smith KM;Brown DW;Proctor RH;Münsterkötter M;Freitag M;Humpf HU;Güldener U;Tudzynski B
真菌藤井镰刀菌因其产生赤霉素(GAs)的能力而引起水稻的“恶臭”病，但它也因产生有害的真菌毒素而闻名。然而，所有天然化合物的遗传能力以及它们在真菌与水稻相互作用中的作用尚不清楚。在这里，我们提出了一个高质量的Fujikuroi的基因组序列，它被组装成12个支架，对应于为这种真菌描述的12条染色体。我们使用基因组序列以及芯片序列、转录组、蛋白质组和基于高效液相-FTMS的代谢组分析来识别潜在的次生代谢物生物合成基因簇，并研究它们对氮素有效性和植物信号的调控。结果表明，大多数但不是所有基因簇的表达与蛋白质组和芯片序列数据相关。Fujikuroi的基因组与其他6个镰刀菌的基因组比较发现，这些物种中只有少量的基因簇是保守的，从而为了解镰刀菌属次生代谢的差异提供了新的见解。值得注意的是，GA生物合成基因在一些相关物种中存在，但GA生物合成仅限于Fujikuroi，这表明这在侵染寄主植物水稻时提供了选择性优势。在所分析的基因组序列中，一个包含多酮合成酶基因(PKS19)的簇和另一个包含非核糖体多肽合成酶基因(NRPS31)的簇是Fujikuroi所独有的。通过基于高效液相色谱-傅立叶变换红外光谱对过量表达簇基因的藤井氏杆菌工程菌株的分析，鉴定了来自这些簇的代谢物。在植物表达方面，研究表明PKS19衍生产物在水稻侵染过程中具有特定的作用。因此，我们的结果表明，结合比较基因组学和全基因组实验分析，确定了有助于Fujikuroi作为水稻病原菌进化成功的新基因和次生代谢物。真菌产生许多“次生代谢物”(Sms)，这些物质对生命不是必需的，但在自然条件下，例如在真菌与宿主的相互作用中，可以提供优势。在这里，我们利用镰刀菌进行了迄今为止最全面的真菌次生代谢分析。这种真菌引起水稻的“恶臭”病，并以其产生赤霉素(GAs)的能力而闻名。我们的研究表明，赤霉素GA的产生仅限于Fujikuroi菌株，并且在寄主植物水稻侵染过程中提供了选择性优势。一个高质量的新镰刀菌基因组序列的产生和分析，结合与其他六个镰刀菌基因组的比较，发现存在45个大多未知的SM基因簇。我们提供了广泛的实验数据，包括在不同氮和pH条件下的表观遗传学、转录、蛋白质组和化学产物分析。其中两个SM簇(PKS19和NRPS31)不存在于任何其他已测序的真菌基因组中。在植物中的表达研究表明，原本沉默的PKS19簇在水稻上被诱导，但在玉米上不被诱导，这表明PKS19衍生产物在水稻侵染过程中具有特定的作用。综上所述，我们的结果证明了单一真菌物种产生多样化的绿色荧光物质的巨大潜力，这可能有助于适应环境变化。
The fungus Fusarium fujikuroi causes “bakanae” disease of rice due to its ability to produce gibberellins (GAs), but it is also known for producing harmful mycotoxins. However, the genetic capacity for the whole arsenal of natural compounds and their role in the fungus' interaction with rice remained unknown. Here, we present a high-quality genome sequence of F. fujikuroi that was assembled into 12 scaffolds corresponding to the 12 chromosomes described for the fungus. We used the genome sequence along with ChIP-seq, transcriptome, proteome, and HPLC-FTMS-based metabolome analyses to identify the potential secondary metabolite biosynthetic gene clusters and to examine their regulation in response to nitrogen availability and plant signals. The results indicate that expression of most but not all gene clusters correlate with proteome and ChIP-seq data. Comparison of the F. fujikuroi genome to those of six other fusaria revealed that only a small number of gene clusters are conserved among these species, thus providing new insights into the divergence of secondary metabolism in the genus Fusarium. Noteworthy, GA biosynthetic genes are present in some related species, but GA biosynthesis is limited to F. fujikuroi, suggesting that this provides a selective advantage during infection of the preferred host plant rice. Among the genome sequences analyzed, one cluster that includes a polyketide synthase gene (PKS19) and another that includes a non-ribosomal peptide synthetase gene (NRPS31) are unique to F. fujikuroi. The metabolites derived from these clusters were identified by HPLC-FTMS-based analyses of engineered F. fujikuroi strains overexpressing cluster genes. In planta expression studies suggest a specific role for the PKS19-derived product during rice infection. Thus, our results indicate that combined comparative genomics and genome-wide experimental analyses identified novel genes and secondary metabolites that contribute to the evolutionary success of F. fujikuroi as a rice pathogen. Fungi produce numerous “secondary metabolites” (SMs) that are not essential for life but can provide an advantage under natural conditions, e.g. in fungal-host interactions. Here, we conducted the most comprehensive analysis to date of secondary metabolism in fungi using Fusarium fujikuroi. This fungus causes “bakanae” disease of rice and is best known for its ability to produce gibberellins (GAs). We show that GA production is limited to F. fujikuroi and provides a selective advantage during infection of the preferred host plant rice. Generation and analysis of a high-quality de novo F. fujikuroi genome sequence combined with comparisons to six other Fusarium genomes revealed the presence of 45 mostly unknown SM gene clusters. We provide a broad spectrum of experimental data including epigenetic, transcriptional, proteomic and chemical product analyses under different nitrogen and pH conditions. Two of the SM clusters (PKS19 and NRPS31) are not present in any other sequenced fungal genome. In planta expression studies revealed that the otherwise silent PKS19 cluster is induced on rice, but not on maize, suggesting a specific role for the PKS19-derived product during rice infection. Together, our results demonstrate the tremendous potential of a single fungal species to produce a diversity of SMs that likely contributes to adaptation to environmental changes.
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影响因子：
6.5
作者：
Aguileta, G.;Marthey, S.;Giraud, T.
通讯作者：
Giraud, T.
影响因子：
3
作者：
Brown, Daren W.;Butchko, Robert A. E.;Proctor, Robert H.
通讯作者：
Proctor, Robert H.
影响因子：
5.3
作者：
BURGER, G;STRAUSS, J;LANG, BF
通讯作者：
LANG, BF
影响因子：
4.5
作者：
Coleman JJ;Rounsley SD;Rodriguez-Carres M;Kuo A;Wasmann CC;Grimwood J;Schmutz J;Taga M;White GJ;Zhou S;Schwartz DC;Freitag M;Ma LJ;Danchin EG;Henrissat B;Coutinho PM;Nelson DR;Straney D;Napoli CA;Barker BM;Gribskov M;Rep M;Kroken S;Molnár I;Rensing C;Kennell JC;Zamora J;Farman ML;Selker EU;Salamov A;Shapiro H;Pangilinan J;Lindquist E;Lamers C;Grigoriev IV;Geiser DM;Covert SF;Temporini E;Vanetten HD
通讯作者：
Vanetten HD
影响因子：
14.8
作者：
Bok, Jin Woo;Chiang, Yi-Ming;Szewczyk, Edyta;Reyes-Domingez, Yazmid;Davidson, Ashley D.;Sanchez, James F.;Lo, Hsien-Chun;Watanabe, Kenji;Strauss, Joseph;Oakley, Berl R.;Wang, Clay C. C.;Keller, Nancy P.
通讯作者：
Keller, Nancy P.