Aspergillus westerdijkiae polyketide synthase gene “aoks1” is involved in the biosynthesis of ochratoxin A

OchratoxinA (OTA) is a potential nephrotoxic, teratogenic, immunogenic, hepatotoxic and carcinogenic mycotoxin, produced by Aspergillus westerdijkiae NRRL 3174. Herein we describe the characterization of a putative OTA-polyketide synthasegene “aoks1”, cloned by using gene walking approach. The predicted amino acid sequence of the 2 kb clone display 34–60% similarities to different polyketide synthasegenes including lovastatine biosynthesis gene “lovb” in A. terreus, compactin biosynthesis gene “mlcA” in Penicillium citrinum and OTA biosynthesis gene “otapksPN” in P. nordicum. Based on the reverse transcription PCR and kinetic secondary metabolites production studies, aoks1 expression was found to be associated with OTA biosynthesis. Further a mutant, in which the aoks1gene was inactivated by Escherichia coli hygromycin B phosphotransferase gene, lost the capacity to produce OTA, but still producing mellein. To our knowledge this report describes for the first time characterization of a gene involved in OTA biosynthesis, with the information about mellein which was proposed in the literature to be an intermediate OTA. This study also suggests that aoks1 may be the second polyketide synthase gene required for OTA biosynthesis in A. westerdijkiae NRRL 3174

Cloning and characterization of novel methylsalicylic acid synthase gene involved in the biosynthesis of isoasperlactone and asperlactone in Aspergillus westerdijkiae

Aspergillus westerdijkiae is the main producer of several biologically active polyketide metabolites including isoasperlactone and asperlactone. A 5298 bp polyketide synthase gene ‘‘aomsas” has been cloned in Aspergillus westerdijkiae by using gene walking approach and RACE-PCR. The predicted amino acid sequence of aomsas shows an identity of 40–56% with different methylsalicylic acid synthase genes found in Byssochlamys nivea, P. patulum, A. terreus and Streptomyces viridochromogenes. Based on the reverse transcription PCR and kinetic secondary metabolites production studies, aomsas expression was found to be associated with the biosynthesis of isoasperlactone and asperlactone. Moreover an aomsas knockout mutant ‘‘aoDmsas” of A. westerdijkiae, not only lost the capacity to produce isoasperlactone and asperlactone,but also 6-methylsalicylic acid. The genetically complemented mutant ao+msas restored the biosynthesis of all the missing metabolites. Chemical complementation through the addition of 6-methylsalicylic acid, aspyrone and diepoxide to growing culture of aoDmsas mutant revealed that these compounds play intermediate roles in the biosynthesis of asperlactone and isoasperlactone

Digital search trees and chaos game representation

In this paper, we consider a possible representation of a DNA sequence in a quaternary tree, in which on can visualize repetitions of subwords. The CGR-tree turns a sequence of letters into a digital search tree (DST), obtained from the suffixes of the reversed sequence. Several results are known concerning the height and the insertion depth for DST built from i.i.d. successive sequences. Here, the successive inserted wors are strongly dependent. We give the asymptotic behaviour of the insertion depth and of the length of branches for the CGR-tree obtained from the suffixes of reversed i.i.d. or Markovian sequence. This behaviour turns out to be at first order the same one as in the case of independent words. As a by-product, asymptotic results on the length of longest runs in a Markovian sequence are obtained

Moments of the Count of a Regular Expression in a Heterogeneous Random Sequence

International audienceWe focus here on the distribution of the random count N of a regular expression in a multi-state random sequence generated by a heterogenous Markov source. We first briefly recall how classical Markov chain embedding techniques allow reducing the problem to the count of specific transitions in a (heterogenous) order 1 Markov chain over a deterministic finite automaton state space. From this result we derive the expression of both the mgf/pgf of N as well as the factorial and non-factorial moments of N. We then introduce the notion of evidence-based constraints in this context. Following the classical forward/backward algorithm in hidden Markov models, we provide explicit recursions allowing to compute the mgf/pgf of N under the evidence constraint. All the results presented are illustrated with a toy example

Effective p-value computations using Finite Markov Chain Imbedding (FMCI): application to local score and to pattern statistics

The technique of Finite Markov Chain Imbedding (FMCI) is a classical approach to complex combinatorial problems related to sequences. In order to get efficient algorithms, it is known that such approaches need to be first rewritten using recursive relations. We propose here to give here a general recursive algorithms allowing to compute in a numerically stable manner exact Cumulative Distribution Function (CDF) or complementary CDF (CCDF). These algorithms are then applied in two particular cases: the local score of one sequence and pattern statistics. In both cases, asymptotic developments are derived. For the local score, our new approach allows for the very first time to compute exact p-values for a practical study (finding hydrophobic segments in a protein database) where only approximations were available before. In this study, the asymptotic approximations appear to be completely unreliable for 99.5% of the considered sequences. Concerning the pattern statistics, the new FMCI algorithms dramatically outperform the previous ones as they are more reliable, easier to implement, faster and with lower memory requirements