Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA sampling from a chemically diverse set of solid agar cultures of Aspergillus nidulans

ABSTRACT: In this study, we design and apply a DNA expression array for Aspergillus nidulans in combination with legacy data to form a comprehensive gene expression compendium. We apply a guilt-by-association-based analysis to predict the extent of the biosynthetic clusters for the 58 synthases active in our set of experimental conditions. A comparison with legacy data shows the method to be accurate in 13 out of 16 known clusters and nearly accurate for the remaining three. Furthermore, we apply a data clustering approach, which identifies cross-chemistry between physically separate gene clusters (super clusters), and validate this both with legacy data and experimentally by prediction and verification of a new supercluster consisting of the synthase AN1242 and the transferase AN11080. This normally requires extensive sets of combinatorial gene deletions. We have employed A. nidulansfor our method development and validation due to the wealth of available biochemical data, but the method can be applied to any fungus with a sequenced and assembled genome, thus supporting further secondary metabolite pathway elucidation in the fungal kingdom. RNA was sampled from stabbed cultures on three different solid agar-based media (CYAs, YES, CYA) after 4, 8 or 10 days, resulting in a total of 8 samples.

ORGANISM(S): Emericella nidulans

SUBMITTER: Mikael Andersen

PROVIDER: E-GEOD-39993 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Accurate prediction of secondary metabolite gene clusters in filamentous fungi.

Andersen Mikael R MR Nielsen Jakob B JB Klitgaard Andreas A Petersen Lene M LM Zachariasen Mia M Hansen Tilde J TJ Blicher Lene H LH Gotfredsen Charlotte H CH Larsen Thomas O TO Nielsen Kristian F KF Mortensen Uffe H UH

Proceedings of the National Academy of Sciences of the United States of America 20121217 1

Biosynthetic pathways of secondary metabolites from fungi are currently subject to an intense effort to elucidate the genetic basis for these compounds due to their large potential within pharmaceutics and synthetic biochemistry. The preferred method is methodical gene deletions to identify supporting enzymes for key synthases one cluster at a time. In this study, we design and apply a DNA expression array for Aspergillus nidulans in combination with legacy data to form a comprehensive gene expr ...[more]

PMID: 23248299

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Project description:It is of high importance to distinguish Tilletia caries and Tilletia laevis as causal agents of common bunt accurately from Tilletia controversa, the causal agent of dwarf bunt. All three of these wheat bunt diseases can lead to significant yield losses in crop production worldwide. But T. controversa is categorized as a quarantine pest in most areas of the world and must be discriminated from the T. caries / T. laevis complex. Usually, morphological characteristics of the teliospores are used to differentiate the three species. But due to natural hybridization and overlapping properties the discrimination is challenging. Germination behavior can also be considered for discrimination, but equivalent to their similar physiological and genetic traits the two agents of common bunt, T. caries and T. laevis could not be distinguished by this. It was suggested that the two species and maybe all three of those described Tilletia species might be conspecific. Up to now no molecular based method is available to differentiate the three species. Several studies have attempted the detection of the wheat bunt Tilletia species using PCR or other DNA-based methods. Other studies analyzed protein patterns with electrophoresis methods. But none of these approaches was able to distinguish between all of the three closely related Tilletia species. Several studies have shown that Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) is a useful tool to differentiate closely related fungal species. The aim of this study was to assess whether MALDI-TOF MS analysis is able to distinguish specimens of the three closely related pathogens T. caries, T. laevis, and T. controversa and may constitute an alternative method to the usually used morphology-based identification. Therefore MALDI-TOF MS was used to create subproteome fingerprints of the teliospores of 69 Tilletia specimens. These fingerprints were analyzed by comparing the mass spectra to each other by high-throughput multidimensional scaling (HiT-MDS ) together with hierarchical cluster analysis (HCA). The second approach was performed by discriminant analysis of principal components (DAPC). MALDI-TOF MS has proven to be a useful method for distinguishing between T. controversa and the two causal agents of common bunt, using our developed method of direct analysis of teliospores, but was unable to separate T. caries and T. laevis species. We conclude a potentially conspecific status of T. caries and T. laevis or even two morphotypes of one common species, causing identical disease symptoms and sharing the same germination requirements along with a related protein composition, shown in this study. Our developed MALDI-TOF MS method can be helpful in testing Tilletia bunt balls collected during field inspections, especially with regard to quarantine regulations or for breeding applications and may also be transferred to analyze further challenging sample material.

Dataset Information

RNA sampling from a chemically diverse set of solid agar cultures of Aspergillus nidulans

Publications

Accurate prediction of secondary metabolite gene clusters in filamentous fungi.

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