van den Brink JM

References (2)

Title : Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88 - Andersen_2011_Genome.Res_21_885
Author(s) : Andersen MR , Salazar MP , Schaap PJ , van de Vondervoort PJ , Culley D , Thykaer J , Frisvad JC , Nielsen KF , Albang R , Albermann K , Berka RM , Braus GH , Braus-Stromeyer SA , Corrochano LM , Dai Z , van Dijck PW , Hofmann G , Lasure LL , Magnuson JK , Menke H , Meijer M , Meijer SL , Nielsen JB , Nielsen ML , van Ooyen AJ , Pel HJ , Poulsen L , Samson RA , Stam H , Tsang A , van den Brink JM , Atkins A , Aerts A , Shapiro H , Pangilinan J , Salamov A , Lou Y , Lindquist E , Lucas S , Grimwood J , Grigoriev IV , Kubicek CP , Martinez D , van Peij NN , Roubos JA , Nielsen J , Baker SE
Ref : Genome Res , 21 :885 , 2011
Abstract : The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook whole-genome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi.
ESTHER : Andersen_2011_Genome.Res_21_885
PubMedSearch : Andersen_2011_Genome.Res_21_885
PubMedID: 21543515
Gene_locus related to this paper: aspna-g3y4g9 , aspna-g3yal2 , aspna-g3ycq2 , aspnc-a2qbh3 , aspnc-a2qe77 , aspnc-a2qf54 , aspnc-a2qfe9 , aspnc-a2qg33 , aspnc-a2qh76 , aspnc-a2qhe2 , aspnc-a2qi32 , aspnc-a2ql89 , aspnc-a2ql90 , aspnc-a2qla0 , aspnc-a2qmk5 , aspnc-a2qn56 , aspnc-a2qs22 , aspnc-a2qti9 , aspnc-a2qtz0 , aspnc-a2quc1 , aspnc-a2qx92 , aspnc-a2qyf0 , aspnc-a2qys7 , aspnc-a2qz72 , aspnc-a2qzn6 , aspnc-a2qzr0 , aspnc-a2qzx0 , aspnc-a2qzx4 , aspnc-a2r0p4 , aspnc-a2r1r5 , aspnc-a2r2i5 , aspnc-a2r5r4 , aspnc-a2r6h5 , aspnc-a2r8r3 , aspnc-a2r8z3 , aspnc-a2r273 , aspnc-a2r496 , aspnc-a2r502 , aspnc-a5abe5 , aspnc-a5abe8 , aspnc-a5abh9 , aspnc-a5abk1 , aspnc-axe1 , aspnc-cuti1 , aspnc-cuti2 , aspng-a2qs46 , aspng-a2qv27 , aspni-EstA , aspkw-g7y0v7 , aspnc-a2qt47 , aspnc-a2qt66 , aspna-g3xpq9 , aspnc-a2qqa1 , aspna-g3xsl3 , aspna-g3y5a6 , aspna-g3xpw9 , aspaw-a0a401kpx5 , aspnc-a2qw57 , aspaw-a0a401kcz4 , aspna-alba , aspna-azac

Title : Regulation of expression of the Aspergillus niger benzoate para-hydroxylase cytochrome P450 system - van den Brink_2000_Mol.Gen.Genet_263_601
Author(s) : van den Brink JM , Punt PJ , van Gorcom RF , van den Hondel CA
Ref : Molecular & General Genetics , 263 :601 , 2000
Abstract : Cytochrome P450 enzyme systems are found throughout nature and are involved in many different, often complex, bioconversions. In the endoplasmic reticulum of the filamentous fungus Aspergillus niger a cytochrome P450 enzyme system is present that is capable of the para-hydroxylation of benzoate. The expression of the two genes encoding the components of this system, the cytochrome P450 gene encoding benzoate para-hydroxylase (bphA) and the gene encoding cytochrome P450 reductase (cprA), is inducible by benzoate. The BPH system was used as a model system to study the mechanisms that result in co-regulation of both components of an eukaryote cytochrome P450 enzyme system. Deletion analysis of the transcription control regions of cprA and bphA resulted in the identification of a region that was involved in benzoate induction of gene expression. The functional competence of the cprA Benzoate Responsive Region thus defined was demonstrated directly by cloning this fragment upstream of a constitutively expressed mini-promoter and analysing expression of the hybrid transcription control region in a lacZ reporter system. Further analysis of cprA gene expression revealed a clear quantitative discrepancy between induction at the protein level (approximately 4-fold) and at the transcription level (> 20-fold). The majority of the transcripts observed after benzoate induction (cprAbeta) were larger then the constitutively expressed cprAalpha transcript. The difference in size between the cprAalpha and cprAbeta transcript is caused by differential promoter use. As the longer cprAbeta transcript carries a small uORF we propose that post-transcriptional regulation of CPR expression underlies the discrepancy in the degree of induction at the protein and transcriptional level. Our results show that regulation of CPR expression is particularly complex, involving regulatory promoter elements, differential promoter use and regulation at the post-transcriptional level.
ESTHER : van den Brink_2000_Mol.Gen.Genet_263_601
PubMedSearch : van den Brink_2000_Mol.Gen.Genet_263_601
PubMedID: 10852481