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.

Material Supplemental http://genome.cshlp.org/content/suppl/2011/04/07/gr.112169.110.DC1.html References http://genome.cshlp.org/content/21/6/885.full.html#ref-list-1 This article cites 63 articles, 17 of which can be accessed free at: Open Access Freely available online through the Genome Research Open Access option. service Email alerting click here top right corner of the article or Receive free email alerts when new articles cite this article sign up in the box at the

Industrial penicillin production with the filamentous fungus Penicillium chrysogenum is based on an unprecedented effort in microbial strain improvement. To gain more insight into penicillin synthesis, we sequenced the 32.19 Mb genome of P. chrysogenum Wisconsin54-1255 and identified numerous genes responsible for key steps in penicillin production. DNA microarrays were used to compare the transcriptomes of the sequenced strain and a penicillinG high-producing strain, grown in the presence and absence of the side-chain precursor phenylacetic acid. Transcription of genes involved in biosynthesis of valine, cysteine and alpha-aminoadipic acid -precursors for penicillin biosynthesis-as well as of genes encoding microbody proteins, was increased in the high-producing strain. Some gene products were shown to be directly controlling beta-lactam output. Many key cellular transport processes involving penicillins and intermediates remain to be characterized at the molecular level. Genes predicted to encode transporters were strongly overrepresented among the genes transcriptionally upregulated under conditions that stimulate penicillinG production, illustrating potential for future genomics-driven metabolic engineering.

Cigarette smoking is associated with a plethora of different diseases. Nicotine is the addictive component of cigarette but also acts onto cells of the non-neuronal system, including immune effector cells. Although nicotine itself is usually not referred to as a carcinogen, there is ongoing debate whether nicotine functions as a 'tumor enhancer.' By binding to nicotinic acetylcholine receptors, nicotine deregulates essential biological processes like angiogenesis, apoptosis, and cell-mediated immunity. Apoptosis plays critical roles in a wide variety of physiologic processes during fetal development and in adult tissue and is also a fundamental aspect of the biology of malignant diseases. This review provides an overlook how nicotine influences apoptotic processes and is thus directly involved in the etiology of pathological conditions like cancer and obstructive diseases.

Herman J Pel1, Johannes H de Winde1,2, David B Archer3, Paul S Dyer3, Gerald Hofmann4, Peter J Schaap5, Geoffrey Turner6, Ronald P de Vries7, Richard Albang8, Kaj Albermann8, Mikael R Andersen4, Jannick D Bendtsen9, Jacques A E Benen5, Marco van den Berg10, Stefaan Breestraat1, Mark X Caddick11, Roland Contreras12, Michael Cornell13, Pedro M Coutinho14, Etienne G J Danchin14, Alfons J M Debets15, Peter Dekker1, Piet W M van Dijck1, Alard van Dijk1, Lubbert Dijkhuizen16,17, Arnold J M Driessen17, Christophe d’Enfert18, Steven Geysens12, Coenie Goosen16,17, Gert S P Groot1, Piet W J de Groot19, Thomas Guillemette20, Bernard Henrissat14, Marga Herweijer1, Johannes P T W van den Hombergh1, Cees A M J J van den Hondel21, Rene T J M van der Heijden22, Rachel M van der Kaaij16,17, Frans M Klis19, Harrie J Kools5, Christian P Kubicek23, Patricia A van Kuyk21, Jürgen Lauber24, Xin Lu25, Marc J E C van der Maarel16, Rogier Meulenberg1, Hildegard Menke1, Martin A Mortimer11, Jens Nielsen4, Stephen G Oliver13, Maurien Olsthoorn1, Karoly Pal15,26, Noël N M E van Peij1, Arthur F J Ram21, Ursula Rinas25, Johannes A Roubos1, Cees M J Sagt1, Monika Schmoll23, Jibin Sun25, David Ussery27, Janos Varga26,28, Wouter Vervecken12, Peter J J van de Vondervoort21, Holger Wedler24, Han A B Wösten7, An-Ping Zeng25, Albert J J van Ooyen1, Jaap Visser29 & Hein Stam1

The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis.

Smoking is associated with different serious diseases, including cancer. The fact that only a minority of smokers develops tobacco-associated diseases suggests the contribution of other individual factors, which are still far from understood. New technologies that can be referred to as 'molecular profiling' allow for investigating the deregulation of thousands of genes simultaneously. Numerous such studies have investigated in vitro and in vivo the effects of smoking in different cell types aiming at a better understanding of smoking-induced diseases and the detection of new biomarkers of exposure and harm. This review is a short survey of these investigations and how they have contributed to the detection of new biomarkers and to a better understanding of smoking-induced harm.

Uropathogenic Escherichia coli (UPEC) strain 536 (O6:K15:H31) is one of the model organisms of extraintestinal pathogenic E. coli (ExPEC). To analyze this strain's genetic basis of urovirulence, we sequenced the entire genome and compared the data with the genome sequence of UPEC strain CFT073 (O6:K2:H1) and to the available genomes of nonpathogenic E. coli strain MG1655 (K-12) and enterohemorrhagic E. coli. The genome of strain 536 is ≈292 kb smaller than that of strain CFT073. Genomic differences between both UPEC are mainly restricted to large pathogenicity islands, parts of which are unique to strain 536 or CFT073. Genome comparison underlines that repeated insertions and deletions in certain parts of the genome contribute to genome evolution. Furthermore, 427 and 432 genes are only present in strain 536 or in both UPEC, respectively. The majority of the latter genes is encoded within smaller horizontally acquired DNA regions scattered all over the genome. Several of these genes are involved in increasing the pathogens' fitness and adaptability. Analysis of virulence-associated traits expressed in the two UPEC O6 strains, together with genome comparison, demonstrate the marked genetic and phenotypic variability among UPEC. The ability to accumulate and express a variety of virulence-associated genes distinguishes ExPEC from many commensals and forms the basis for the individual virulence potential of ExPEC. Accordingly, instead of a common virulence mechanism, different ways exist among ExPEC to cause disease.

In this paper, we present the Functional Catalogue (FunCat), a hierarchically structured, organism-independent, flexible and scalable controlled classification system enabling the functional description of proteins from any organism. FunCat has been applied for the manual annotation of prokaryotes, fungi, plants and animals. We describe how FunCat is implemented as a highly efficient and robust tool for the manual and automatic annotation of genomic sequences. Owing to its hierarchical architecture, FunCat has also proved to be useful for many subsequent downstream bioinformatic applications. This is illustrated by the analysis of large-scale experiments from various investigations in transcriptomics and proteomics, where FunCat was used to project experimental data into functional units, as 'gold standard' for functional classification methods, and also served to compare the significance of different experimental methods. Over the last decade, the FunCat has been established as a robust and stable annotation scheme that offers both, meaningful and manageable functional classification as well as ease of perception.

The methylotrophic yeast Hansenula polymorpha is a recognised model system for investigation of peroxisomal function, special metabolic pathways like methanol metabolism, of nitrate assimilation or thermostability. Strain RB11, an odc1 derivative of the particular H. polymorpha isolate CBS4732 (synonymous to ATCC34438, NRRL-Y-5445, CCY38-22-2) has been developed as a platform for heterologous gene expression. The scientific and industrial significance of this organism is now being met by the characterisation of its entire genome. The H. polymorpha RB11 genome consists of approximately 9.5 Mb and is organised as six chromosomes ranging in size from 0.9 to 2.2 Mb. Over 90% of the genome was sequenced with concomitant high accuracy and assembled into 48 contigs organised on eight scaffolds (supercontigs). After manual annotation 4767 out of 5933 open reading frames (ORFs) with significant homologies to a non-redundant protein database were predicted. The remaining 1166 ORFs showed no significant similarity to known proteins. The number of ORFs is comparable to that of other sequenced budding yeasts of similar genome size.

We describe a genome-wide characterization of mRNA transcript levels in yeast grown on the fatty acid oleate, determined using Serial Analysis of Gene Expression (SAGE). Comparison of this SAGE library with that reported for glucose grown cells revealed the dramatic adaptive response of yeast to a change in carbon source. A major fraction (>20%) of the 15,000 mRNA molecules in a yeast cell comprised differentially expressed transcripts, which were derived from only 2% of the total number of approximately 6300 yeast genes. Most of the mRNAs that were differentially expressed code for enzymes or for other proteins participating in metabolism (e.g., metabolite transporters). In oleate-grown cells, this was exemplified by the huge increase of mRNAs encoding the peroxisomal beta-oxidation enzymes required for degradation of fatty acids. The data provide evidence for the existence of redox shuttles across organellar membranes that involve peroxisomal, cytoplasmic, and mitochondrial enzymes. We also analyzed the mRNA profile of a mutant strain with deletions of the PIP2 and OAF1 genes, encoding transcription factors required for induction of genes encoding peroxisomal proteins. Induction of genes under the immediate control of these factors was abolished; other genes were up-regulated, indicating an adaptive response to the changed metabolism imposed by the genetic impairment. We describe a statistical method for analysis of data obtained by SAGE.

SACCHAROMYCES CEREVISIAE – OVERVIEW EXAMPLES ade5 cdc28 CUP1 SPC105 act1-606 his2-1 Ade5p Cdc28p Cup1p Spc105p Arg – (cf. wild type Arg +) SWI SWI1 SWI3 SWI5 etc. YKL025C (a) ade6::URA4 (b) ade6-∆1 (c) ade6⌬::URA4 SUP4 SUF1 sup35 suf11 SUF1 or suf1 (a) ssn1 (b) srn1 (c) suh1 SUP4-o SUP4-a sup4-o-1 Gene symbols comprise three italic lowercase letters, and an Arabic number (full gene names are not controlled by the nomenclature system). Symbols are styled according to the phenotype of the identifying mutation or for the function of the wild-type gene (see 'Genes' and 'Alleles' for more details): lowercase italic for recessive, uppercase italic for dominant. ALLELES Allele designations consist of the gene symbol, a hyphen and an italic Arabic number. PROTEINS Proteins are referred to by the relevant gene symbol, non-italic, initial letter uppercase and with the suffix 'p' (to avoid confusion with the phenotype, see below). If unambiguous, the suffix can be omitted e.g. 'the Ade5 protein'. PHENOTYPES Phenotypes are designated by a non-italic three-letter abbreviation corresponding to the gene symbol, initial letter uppercase. Wild-type or mutant status is indicated by a superscript plus or minus sign, respectively, e.g. a strain requiring arginine. GENES As mentioned above, for genes defined by mutation, upper-and lowercase designations are used for dominant and recessive alleles, respectively. However, because a given allele can be dominant in one cross and recessive in another, this can lead to some difficulty. On the genetic and physical maps, the convention is to use the mapped allele to decide which form of the name is used. Genes with related properties are usually given the same three-letter name and different numbers, e.g. there are multiple genes that have functions in mating-type switching. Open reading frame (ORF) designations are not gene names but 'location holders' on the genetic map until a gene name is assigned. ORF names are always three non-italic uppercase letters, a number and a letter: Y (for yeast unknown sequence); A, B to P (for chromosome I, II through XVI); R or L (for right or left arm); a number corresponding to the order of the ORF (counting from the centromere), and W or C to designate Watson or Crick strand (the Watson strand is 5Ј→3Ј left telomere to right telomere), e.g. the 25th ORF on the left arm of chromosome XI. Mitochondrial mutations should, in general, be designated following the rules outlined above, but well-known symbols, …