01989nas a2200181 4500008004100000245008700041210006900128300001400197490000800211520142000219100001901639700001801658700001801676700001501694700001501709700001701724856006601741 2014 eng d00aMolecular interactions between sugar beet and Polymyxa betae during its life cycle0 aMolecular interactions between sugar beet and Polymyxa betae dur a244–2560 v1643 aPolymyxa betae is a biotrophic obligate sugar beet parasite that belongs to plasmodiophorids. The infection of sugar beet roots by this parasite is asymptomatic, except when it transmits Beet necrotic yellow vein virus (BNYVV), the causal agent of rhizomania. To date, there has been little work on P. betae–sugar beet molecular interactions, mainly because of the obligate nature of the parasite and also because research on rhizomania has tended to focus on the virus. In this study, we investigated these interactions through differential transcript analysis, using suppressive subtractive hybridization. The analysis included 76 P. betae and 120 sugar beet expressed sequence tags (ESTs). The expression of selected ESTs from both organisms was monitored during the protist life cycle, revealing a potential role of two P. betae proteins, profilin and a Von Willebrand factor domain-containing protein, in the early phase of infection. This study also revealed an over-expression of some sugar beet genes involved in defence, such as those encoding PR proteins, stress resistance proteins or lectins, especially during the plasmodial stage of the P. betae life cycle. In addition to providing new information on the molecular aspects of P. betae–sugar beet interactions, this study also enabled previously unknown ESTs of P. betae to be sequenced, thus enhancing our knowledge of the genome of this protist.1 aDesoignies, N.1 aCarbonell, J.1 aMoreau, J.-S.1 aConesa, A.1 aDopazo, J.1 aLegrève, A. uhttp://onlinelibrary.wiley.com/doi/10.1111/aab.12095/abstract02262nas a2200193 4500008004100000245016300041210006900204520151300273100001501786700002901801700001501830700001801845700001601863700002101879700002601900700002201926700001401948856010601962 2009 eng d00aMembrane transporters and carbon metabolism implicated in chloride homeostasis differentiate salt stress responses in tolerant and sensitive Citrus rootstocks0 aMembrane transporters and carbon metabolism implicated in chlori3 a

Salinity tolerance in Citrus is strongly related to leaf chloride accumulation. Both chloride homeostasis and specific genetic responses to Cl(-) toxicity are issues scarcely investigated in plants. To discriminate the transcriptomic network related to Cl(-) toxicity and salinity tolerance, we have used two Cl(-) salt treatments (NaCl and KCl) to perform a comparative microarray approach on two Citrus genotypes, the salt-sensitive Carrizo citrange, a poor Cl(-) excluder, and the tolerant Cleopatra mandarin, an efficient Cl(-) excluder. The data indicated that Cl(-) toxicity, rather than Na(+) toxicity and/or the concomitant osmotic perturbation, is the primary factor involved in the molecular responses of citrus plant leaves to salinity. A number of uncharacterized membrane transporter genes, like NRT1-2, were differentially regulated in the tolerant and the sensitive genotypes, suggesting its potential implication in Cl(-) homeostasis. Analyses of enriched functional categories showed that the tolerant rootstock induced wider stress responses in gene expression while repressing central metabolic processes such as photosynthesis and carbon utilization. These features were in agreement with phenotypic changes in the patterns of photosynthesis, transpiration, and stomatal conductance and support the concept that regulation of transpiration and its associated metabolic adjustments configure an adaptive response to salinity that reduces Cl(-) accumulation in the tolerant genotype.

1 aBrumos, J.1 aColmenero-Flores, J., M.1 aConesa, A.1 aIzquierdo, P.1 aSanchez, G.1 aIglesias, D., J.1 aLopez-Climent, M., F.1 aGomez-Cadenas, A.1 aTalon, M. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1919094402142nas a2200253 4500008004100000245010200041210006900143300001100212490000700223520138600230653001501616653002401631100002401655700001801679700001601697700001401713700001501727700001601742700002001758700001501778700001701793700001501810856006301825 2008 eng d00aBabelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments0 aBabelomics advanced functional profiling of transcriptomics prot aW341-60 v363 a

We present a new version of Babelomics, a complete suite of web tools for the functional profiling of genome scale experiments, with new and improved methods as well as more types of functional definitions. Babelomics includes different flavours of conventional functional enrichment methods as well as more advanced gene set analysis methods that makes it a unique tool among the similar resources available. In addition to the well-known functional definitions (GO, KEGG), Babelomics includes new ones such as Biocarta pathways or text mining-derived functional terms. Regulatory modules implemented include transcriptional control (Transfac, CisRed) and other levels of regulation such as miRNA-mediated interference. Moreover, Babelomics allows for sub-selection of terms in order to test more focused hypothesis. Also gene annotation correspondence tables can be imported, which allows testing with user-defined functional modules. Finally, a tool for the ’de novo’ functional annotation of sequences has been included in the system. This allows using yet unannotated organisms in the program. Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. Babelomics is available at http://www.babelomics.org.

10ababelomics10afuntional profiling1 aAl-Shahrour, Fatima1 aCarbonell, J.1 aMinguez, P.1 aGoetz, S.1 aConesa, A.1 aTarraga, J.1 aMedina, Ignacio1 aAlloza, E.1 aMontaner, D.1 aDopazo, J. uhttp://nar.oxfordjournals.org/content/36/suppl_2/W341.long01483nas a2200133 4500008004100000245007800041210006900119300001100188490000900199520100700208100001501215700001301230856010601243 2008 eng d00aBlast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics0 aBlast2GO A Comprehensive Suite for Functional Analysis in Plant  a6198320 v20083 a

Functional annotation of novel sequence data is a primary requirement for the utilization of functional genomics approaches in plant research. In this paper, we describe the Blast2GO suite as a comprehensive bioinformatics tool for functional annotation of sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary. Blast2GO optimizes function transfer from homologous sequences through an elaborate algorithm that considers similarity, the extension of the homology, the database of choice, the GO hierarchy, and the quality of the original annotations. The tool includes numerous functions for the visualization, management, and statistical analysis of annotation results, including gene set enrichment analysis. The application supports InterPro, enzyme codes, KEGG pathways, GO direct acyclic graphs (DAGs), and GOSlim. Blast2GO is a suitable tool for plant genomics research because of its versatility, easy installation, and friendly use.

1 aConesa, A.1 aGotz, S. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1848357201778nas a2200229 4500008004100000245010300041210006900144300001100213490000700224520087500231653007101106653013601177100001501313700001201328700002201340700001801362700001301380700001701393700001701410700001501427856010601442 2008 eng d00aDirect functional assessment of the composite phenotype through multivariate projection strategies0 aDirect functional assessment of the composite phenotype through  a373-830 v923 a

We present a novel approach for the analysis of transcriptomics data that integrates functional annotation of gene sets with expression values in a multivariate fashion, and directly assesses the relation of functional features to a multivariate space of response phenotypical variables. Multivariate projection methods are used to obtain new correlated variables for a set of genes that share a given function. These new functional variables are then related to the response variables of interest. The analysis of the principal directions of the multivariate regression allows for the identification of gene function features correlated with the phenotype. Two different transcriptomics studies are used to illustrate the statistical and interpretative aspects of the methodology. We demonstrate the superiority of the proposed method over equivalent approaches.

10aBreast Neoplasms/genetics Computational Biology/*methods Databases10aGenetic Female Gene Expression Profiling/*statistics & numerical data Humans Mathematical Computing Multivariate Analysis Phenotype1 aConesa, A.1 aBro, R.1 aGarcia-Garcia, F.1 aPrats, J., M.1 aGotz, S.1 aKjeldahl, K.1 aMontaner, D.1 aDopazo, J. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1865288802205nas a2200301 4500008004100000245007600041210006900117300001200186490000700198520130100205653001001506653002901516100001601545700002001561700001801581700002101599700001601620700001501636700002401651700002301675700001401698700001601712700002201728700001501750700001701765700001501782856010601797 2008 eng d00aGEPAS, a web-based tool for microarray data analysis and interpretation0 aGEPAS a webbased tool for microarray data analysis and interpret aW308-140 v363 a

Gene Expression Profile Analysis Suite (GEPAS) is one of the most complete and extensively used web-based packages for microarray data analysis. During its more than 5 years of activity it has continuously been updated to keep pace with the state-of-the-art in the changing microarray data analysis arena. GEPAS offers diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and functional profiling of the experiment. New options for time-course (or dose-response) experiments, microarray-based class prediction, new clustering methods and new tests for differential expression have been included. The new pipeliner module allows automating the execution of sequential analysis steps by means of a simple but powerful graphic interface. An extensive re-engineering of GEPAS has been carried out which includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. GEPAS is nowadays the most quoted web tool in its field and it is extensively used by researchers of many countries and its records indicate an average usage rate of 500 experiments per day. GEPAS, is available at http://www.gepas.org.

10agepas10amicroarray data analysis1 aTarraga, J.1 aMedina, Ignacio1 aCarbonell, J.1 aHuerta-Cepas, J.1 aMinguez, P.1 aAlloza, E.1 aAl-Shahrour, Fatima1 aVegas-Azcarate, S.1 aGoetz, S.1 aEscobar, P.1 aGarcia-Garcia, F.1 aConesa, A.1 aMontaner, D.1 aDopazo, J. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1850880603221nas a2200181 4500008004100000245010900041210006900150300000800219490000600227520260800233100001502841700001402856700001502870700001502885700001502900700001802915856010602933 2008 eng d00aLarge-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology0 aLargescale Gene Ontology analysis of plant transcriptomederived  a3470 v93 a

BACKGROUND: After 10-year-use of AFLP (Amplified Fragment Length Polymorphism) technology for DNA fingerprinting and mRNA profiling, large repertories of genome- and transcriptome-derived sequences are available in public databases for model, crop and tree species. AFLP marker systems have been and are being extensively exploited for genome scanning and gene mapping, as well as cDNA-AFLP for transcriptome profiling and differentially expressed gene cloning. The evaluation, annotation and classification of genomic markers and expressed transcripts would be of great utility for both functional genomics and systems biology research in plants. This may be achieved by means of the Gene Ontology (GO), consisting in three structured vocabularies (i.e. ontologies) describing genes, transcripts and proteins of any organism in terms of their associated cellular component, biological process and molecular function in a species-independent manner. In this paper, the functional annotation of about 8,000 AFLP-derived ESTs retrieved in the NCBI databases was carried out by using GO terminology. RESULTS: Descriptive statistics on the type, size and nature of gene sequences obtained by means of AFLP technology were calculated. The gene products associated with mRNA transcripts were then classified according to the three main GO vocabularies. A comparison of the functional content of cDNA-AFLP records was also performed by splitting the sequence dataset into monocots and dicots and by comparing them to all annotated ESTs of Arabidopsis and rice, respectively. On the whole, the statistical parameters adopted for the in silico AFLP-derived transcriptome-anchored sequence analysis proved to be critical for obtaining reliable GO results. Such an exhaustive annotation may offer a suitable platform for functional genomics, particularly useful in non-model species. CONCLUSION: Reliable GO annotations of AFLP-derived sequences can be gathered through the optimization of the experimental steps and the statistical parameters adopted. The Blast2GO software was shown to represent a comprehensive bioinformatics solution for an annotation-based functional analysis. According to the whole set of GO annotations, the AFLP technology generates thorough information for angiosperm gene products and shares common features across angiosperm species and families. The utility of this technology for structural and functional genomics in plants can be implemented by serial annotation analyses of genome-anchored fragments and organ/tissue-specific repertories of transcriptome-derived fragments.

1 aBotton, A.1 aGalla, G.1 aConesa, A.1 aBachem, C.1 aRamina, A.1 aBarcaccia, G. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1865264603447nas a2200253 4500008004100000245010700041210006900148300001200217490000700229520238400236653019002620653008902810100001402899700002402913700001702937700001602954700001502970700001602985700002403001700002603025700001703051700001903068856010603087 2008 eng d00aTime course profiling of the retinal transcriptome after optic nerve transection and optic nerve crush0 aTime course profiling of the retinal transcriptome after optic n a1050-630 v143 aPURPOSE: A time-course analysis of gene regulation in the adult rat retina after intraorbital nerve crush (IONC) and intraorbital nerve transection (IONT). METHODS: RNA was extracted from adult rat retinas undergoing either IONT or IONC at increasing times post-lesion. Affymetrix RAE230.2 arrays were hybridized and analyzed. Statistically regulated genes were annotated and functionally clustered. Arrays were validated by means of quantative reverse transcription polymerase chain reaction (qRT-PCR) on ten regulated genes at two times post-lesion. Western blotting and immunohistofluorescence for four pro-apoptotic proteins were performed on naive and injured retinas. Finally, custom signaling maps for IONT- and IONC-induced death response were generated (MetaCore, Genego Inc.). RESULTS: Here we show that over time, 3,219 sequences were regulated after IONT and 1,996 after IONC. Out of the total of regulated sequences, 1,078 were commonly regulated by both injuries. Interestingly, while IONT mainly triggers a gene upregulation-sustained over time, IONC causes a transitory downregulation. Functional clustering identified the regulation of high interest biologic processes, most importantly cell death wherein apoptosis was the most significant cluster. Ten death-related genes upregulated by both injuries were used for array validation by means of qRT-PCR. In addition, western blotting and immunohistofluorescence of total and active Caspase 3 (Casp3), tumor necrosis factor receptor type 1 associated death domain (TRADD), tumor necrosis factor receptor superfamily member 1a (TNFR1a), and c-fos were performed to confirm their protein regulation and expression pattern in naive and injured retinas. These analyses demonstrated that for these genes, protein regulation followed transcriptional regulation and that these pro-apoptotic proteins were expressed by retinal ganglion cells (RGCs). MetaCore-based death-signaling maps show that several apoptotic cascades were regulated in the retina following optic nerve injury and highlight the similarities and differences between IONT and IONC in cell death profiling. CONCLUSIONS: This comprehensive time course retinal transcriptome study comparing IONT and IONC lesions provides a unique valuable tool to understand the molecular mechanisms underlying optic nerve injury and to design neuroprotective protocols.10aAnimals Cell Death Cluster Analysis Female *Gene Expression Profiling Gene Expression Regulation *Nerve Crush Optic Nerve/*metabolism/*pathology Optic Nerve Injuries/*genetics Rats Rats10aSprague-Dawley Reproducibility of Results Retina/*metabolism/*pathology Time Factors1 aAgudo, M.1 aPerez-Marin, M., C.1 aLonngren, U.1 aSobrado, P.1 aConesa, A.1 aCanovas, I.1 aSalinas-Navarro, M.1 aMiralles-Imperial, J.1 aHallbook, F.1 aVidal-Sanz, M. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1855298002515nas a2200289 4500008004100000245007500041210006900116300001200185490000800197520143200205653002101637653001201658653007101670653010001741653010001841100002301941700001401964700001501978700001801993700002202011700002002033700001602053700001702069700001302086700002002099856010602119 2008 eng d00aTranscriptional profiling of mRNA expression in the mouse distal colon0 aTranscriptional profiling of mRNA expression in the mouse distal a2019-290 v1353 aBACKGROUND & AIMS: Intestinal epithelial cells and the myenteric plexus of the mouse gastrointestinal tract contain a circadian clock-based intrinsic time-keeping system. Because disruption of the biological clock has been associated with increased susceptibility to colon cancer and gastrointestinal symptoms, we aimed to identify rhythmically expressed genes in the mouse distal colon. METHODS: Microarray analysis was used to identify genes that were rhythmically expressed over a 24-hour light/dark cycle. The transcripts were then classified according to expression pattern, function, and association with physiologic and pathophysiologic processes of the colon. RESULTS: A circadian gene expression pattern was detected in approximately 3.7% of distal colonic genes. A large percentage of these genes were involved in cell signaling, differentiation, and proliferation and cell death. Of all the rhythmically expressed genes in the mouse colon, approximately 7% (64/906) have been associated with colorectal cancer formation (eg, B-cell leukemia/lymphoma-2 [Bcl2]) and 1.8% (18/906) with various colonic functions such as motility and secretion (eg, vasoactive intestinal polypeptide, cystic fibrosis transmembrane conductance regulator). CONCLUSIONS: A subset of genes in the murine colon follows a rhythmic expression pattern. These findings may have significant implications for colonic physiology and pathophysiology.10aAnimals Blotting10aGenetic10aInbred C57BL Microarray Analysis Proteins/*genetics/metabolism RNA10aMessenger/biosynthesis/*genetics Reverse Transcriptase Polymerase Chain Reaction *Transcription10aWestern Cell Proliferation Circadian Rhythm/*genetics Colon/cytology/*metabolism Male Mice Mice1 aHoogerwerf, W., A.1 aSinha, M.1 aConesa, A.1 aLuxon, B., A.1 aShahinian, V., B.1 aCornelissen, G.1 aHalberg, F.1 aBostwick, J.1 aTimm, J.1 aCassone, V., M. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1884855703144nas a2200277 4500008004100000245020600041210006900247300001200316490000700328520162000335653020401955653006002159653012202219653025902341100001602600700001502616700001502631700001402646700001502660700001802675700001802693700001702711700001702728700001502745856010602760 2008 eng d00aTranscriptome analysis provides new insights into liver changes induced in the rat upon dietary administration of the food additives butylated hydroxytoluene, curcumin, propyl gallate and thiabendazole0 aTranscriptome analysis provides new insights into liver changes  a2616-280 v463 aTranscriptomics was performed to gain insight into mechanisms of food additives butylated hydroxytoluene (BHT), curcumin (CC), propyl gallate (PG), and thiabendazole (TB), additives for which interactions in the liver can not be excluded. Additives were administered in diets for 28 days to Sprague-Dawley rats and cDNA microarray experiments were performed on hepatic RNA. BHT induced changes in the expression of 10 genes, including phase I (CYP2B1/2; CYP3A9; CYP2C6) and phase II metabolism (GST mu2). The CYP2B1/2 and GST expression findings were confirmed by real time RT-PCR, western blotting, and increased GST activity towards DCNB. CC altered the expression of 12 genes. Three out of these were related to peroxisomes (phytanoyl-CoA dioxygenase, enoyl-CoA hydratase; CYP4A3). Increased cyanide insensitive palmitoyl-CoA oxidation was observed, suggesting that CC is a weak peroxisome proliferator. TB changed the expression of 12 genes, including CYP1A2. In line, CYP1A2 protein expression was increased. The expression level of five genes, associated with p53 was found to change upon TB treatment, including p53 itself, GADD45alpha, DN-7, protein kinase C beta and serum albumin. These array experiments led to the novel finding that TB is capable of inducing p53 at the protein level, at least at the highest dose levels employed above the current NOAEL. The expression of eight genes changed upon PG administration. This study shows the value of gene expression profiling in food toxicology in terms of generating novel hypotheses on the mechanisms of action of food additives in relation to pathology.10aAnimals Aryl Hydrocarbon Hydroxylases/metabolism Body Weight/drug effects Butylated Hydroxytoluene/toxicity Curcumin/toxicity Cytochrome P-450 CYP1A2/metabolism Cytochrome P-450 CYP2B1/metabolism DNA10aComplementary/biosynthesis/genetics Data Interpretation10aSprague-Dawley Reverse Transcriptase Polymerase Chain Reaction Steroid Hydroxylases/metabolism Thiabendazole/toxicity10aStatistical *Diet Food Additives/*toxicity Gene Expression/drug effects *Gene Expression Profiling Glutathione Transferase/metabolism Liver/*drug effects Male Organ Size/drug effects Oxidation-Reduction Palmitoyl Coenzyme A/metabolism Propyl Gallate/toxi1 aStierum, R.1 aConesa, A.1 aHeijne, W.1 aOmmen, B.1 aJunker, K.1 aScott, M., P.1 aPrice, R., J.1 aMeredith, C.1 aLake, B., G.1 aGroten, J. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1853937703856nas a2200385 4500008004100000245011000041210006900151300000700220490000600227520253000233653016602763653002902929653009302958100001403051700001503065700002203080700001503102700001403117700001503131700001303146700001503159700001403174700001503188700002103203700001303224700001403237700001503251700001703266700001903283700001503302700001603317700001703333700001403350856010603364 2007 eng d00aAnalysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance0 aAnalysis of 13000 unique Citrus clusters associated with fruit q a310 v83 aBACKGROUND: Improvement of Citrus, the most economically important fruit crop in the world, is extremely slow and inherently costly because of the long-term nature of tree breeding and an unusual combination of reproductive characteristics. Aside from disease resistance, major commercial traits in Citrus are improved fruit quality, higher yield and tolerance to environmental stresses, especially salinity. RESULTS: A normalized full length and 9 standard cDNA libraries were generated, representing particular treatments and tissues from selected varieties (Citrus clementina and C. sinensis) and rootstocks (C. reshni, and C. sinenis x Poncirus trifoliata) differing in fruit quality, resistance to abscission, and tolerance to salinity. The goal of this work was to provide a large expressed sequence tag (EST) collection enriched with transcripts related to these well appreciated agronomical traits. Towards this end, more than 54000 ESTs derived from these libraries were analyzed and annotated. Assembly of 52626 useful sequences generated 15664 putative transcription units distributed in 7120 contigs, and 8544 singletons. BLAST annotation produced significant hits for more than 80% of the hypothetical transcription units and suggested that 647 of these might be Citrus specific unigenes. The unigene set, composed of 13000 putative different transcripts, including more than 5000 novel Citrus genes, was assigned with putative functions based on similarity, GO annotations and protein domains CONCLUSION: Comparative genomics with Arabidopsis revealed the presence of putative conserved orthologs and single copy genes in Citrus and also the occurrence of both gene duplication events and increased number of genes for specific pathways. In addition, phylogenetic analysis performed on the ammonium transporter family and glycosyl transferase family 20 suggested the existence of Citrus paralogs. Analysis of the Citrus gene space showed that the most important metabolic pathways known to affect fruit quality were represented in the unigene set. Overall, the similarity analyses indicated that the sequences of the genes belonging to these varieties and rootstocks were essentially identical, suggesting that the differential behaviour of these species cannot be attributed to major sequence divergences. This Citrus EST assembly contributes both crucial information to discover genes of agronomical interest and tools for genetic and genomic analyses, such as the development of new markers and microarrays.10aAcclimatization/*genetics Amino Acid Motifs Citrus/*genetics Cluster Analysis Expressed Sequence Tags Fruit/genetics Gene Duplication *Gene Expression Regulation10aPlant Gene Library Genes10aPlant Genomics Molecular Sequence Data Multigene Family Phylogeny *Salts/adverse effects1 aTerol, J.1 aConesa, A.1 aColmenero, J., M.1 aCercos, M.1 aTadeo, F.1 aAgusti, J.1 aAlos, E.1 aAndres, F.1 aSoler, G.1 aBrumos, J.1 aIglesias, D., J.1 aGotz, S.1 aLegaz, F.1 aArgout, X.1 aCourtois, B.1 aOllitrault, P.1 aDossat, C.1 aWincker, P.1 aMorillon, R.1 aTalon, M. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1725432702714nas a2200253 4500008004100000245009200041210006900133300001300202490000700215520168800222653010801910653001202018653001902030653005802049653012102107100001802228700001502246700002302261700002202284700001902306700001402325700001502339856010602354 2007 eng d00aDiscovering gene expression patterns in time course microarray experiments by ANOVA-SCA0 aDiscovering gene expression patterns in time course microarray e a1792-8000 v233 aMOTIVATION: Designed microarray experiments are used to investigate the effects that controlled experimental factors have on gene expression and learn about the transcriptional responses associated with external variables. In these datasets, signals of interest coexist with varying sources of unwanted noise in a framework of (co)relation among the measured variables and with the different levels of the studied factors. Discovering experimentally relevant transcriptional changes require methodologies that take all these elements into account. RESULTS: In this work, we develop the application of the Analysis of variance-simultaneous component analysis (ANOVA-SCA) Smilde et al. Bioinformatics, (2005) to the analysis of multiple series time course microarray data as an example of multifactorial gene expression profiling experiments. We denoted this implementation as ASCA-genes. We show how the combination of ANOVA-modeling and a dimension reduction technique is effective in extracting targeted signals from data by-passing structural noise. The methodology is valuable for identifying main and secondary responses associated with the experimental factors and spotting relevant experimental conditions. We additionally propose a novel approach for gene selection in the context of the relation of individual transcriptional patterns to global gene expression signals. We demonstrate the methodology on both real and synthetic datasets. AVAILABILITY: ASCA-genes has been implemented in the statistical language R and is available at http://www.ivia.es/centrodegenomica/bioinformatics.htm. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.10aAlgorithms *Analysis of Variance Computational Biology/*methods Computer Simulation Data Interpretation10aGenetic10aGenetic Models10aStatistical Gene Expression Profiling/*methods Models10aStatistical Oligonucleotide Array Sequence Analysis/*methods Principal Component Analysis Time Factors Transcription1 aNueda, M., J.1 aConesa, A.1 aWesterhuis, J., A.1 aHoefsloot, H., C.1 aSmilde, A., K.1 aTalon, M.1 aFerrer, A. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1751925000560nas a2200169 4500008004100000022001800041245005100059210005100110260005300161300001200214653001500226100001500241700001600256700001400272700001700286856008700303 2007 eng d a0-4153-7853-200aMicroarray Technology in Agricultural Research0 aMicroarray Technology in Agricultural Research bF. Falciani. Publisher: Taylor and Francis Group a173-20910ababelomics1 aConesa, A.1 aForment, J.1 aGadea, J.1 avan Dijk, J. uhttps://www.clinbioinfosspa.es/content/microarray-technology-agricultural-research02657nas a2200277 4500008004100000245007600041210006900117300001200186490000600198520157700204653011001781653008001891653001701971653001801988653005402006653006902060100001802129700002102147700001502168700001802183700001402201700001802215700002102233700001902254856010602273 2007 eng d00aSpatial differentiation in the vegetative mycelium of Aspergillus niger0 aSpatial differentiation in the vegetative mycelium of Aspergillu a2311-220 v63 aFungal mycelia are exposed to heterogenic substrates. The substrate in the central part of the colony has been (partly) degraded, whereas it is still unexplored at the periphery of the mycelium. We here assessed whether substrate heterogeneity is a main determinant of spatial gene expression in colonies of Aspergillus niger. This question was addressed by analyzing whole-genome gene expression in five concentric zones of 7-day-old maltose- and xylose-grown colonies. Expression profiles at the periphery and the center were clearly different. More than 25% of the active genes showed twofold differences in expression between the inner and outermost zones of the colony. Moreover, 9% of the genes were expressed in only one of the five concentric zones, showing that a considerable part of the genome is active in a restricted part of the colony only. Statistical analysis of expression profiles of colonies that had either been or not been transferred to fresh xylose-containing medium showed that differential expression in a colony is due to the heterogeneity of the medium (e.g., genes involved in secretion, genes encoding proteases, and genes involved in xylose metabolism) as well as to medium-independent mechanisms (e.g., genes involved in nitrate metabolism and genes involved in cell wall synthesis and modification). Thus, we conclude that the mycelia of 7-day-old colonies of A. niger are highly differentiated. This conclusion is also indicated by the fact that distinct zones of the colony grow and secrete proteins, even after transfer to fresh medium.10aAspergillus niger/*metabolism Cell Wall/metabolism Fungal Proteins/metabolism *Gene Expression Regulation10aBiological Mycelium/*metabolism Oligonucleotide Array Sequence Analysis RNA10aFungal Genes10aFungal Genome10aFungal Glucans/chemistry Maltose/chemistry Models10aFungal Time Factors Trans-Activators/metabolism Xylose/chemistry1 aLevin, A., M.1 ade Vries, R., P.1 aConesa, A.1 ade Bekker, C.1 aTalon, M.1 aMenke, H., H.1 avan Peij, N., N.1 aWosten, H., A. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1795151301951nas a2200265 4500008004100000245009000041210006900131300001200200490000800212520099700220653008201217653001201299653011301311100001501424700001501439700001601454700001401470700001601484700001501500700001501515700001901530700001501549700001501564856010601579 2007 eng d00aTranscriptional response of Citrus aurantifolia to infection by Citrus tristeza virus0 aTranscriptional response of Citrus aurantifolia to infection by  a298-3060 v3673 aChanges in gene expression of Mexican lime plants in response to infection with a severe (T305) or a mild (T385) isolate of Citrus tristeza virus (CTV) were analyzed using a cDNA microarray containing 12,672 probes to 6875 different citrus genes. Statistically significant (P<0.01) expression changes of 334 genes were detected in response to infection with isolate T305, whereas infection with T385 induced no significant change. Induced genes included 145 without significant similarity with known sequences and 189 that were classified in seven functional categories. Genes related with response to stress and defense were the main category and included 28% of the genes induced. Selected transcription changes detected by microarray analysis were confirmed by quantitative real-time RT-PCR. Changes detected in the transcriptome upon infecting lime with T305 may be associated either with symptom expression, with a strain-specific defense mechanism, or with a general response to stress.10aCitrus/*genetics/physiology/virology Closterovirus/genetics/*physiology Genes10aGenetic10aPlant Oligonucleotide Array Sequence Analysis Reverse Transcriptase Polymerase Chain Reaction *Transcription1 aGandia, M.1 aConesa, A.1 aAncillo, G.1 aGadea, J.1 aForment, J.1 aPallas, V.1 aFlores, R.1 aDuran-Vila, N.1 aMoreno, P.1 aGuerri, J. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1761743102376nas a2200229 4500008004100000245009300041210006900134300001200203490000800215520165600223653001501879100001701894700001301911700001501924700001801939700001701957700001901974700001801993700001502011700001402026856010602040 2006 eng d00aBlast2GO goes grid: developing a grid-enabled prototype for functional genomics analysis0 aBlast2GO goes grid developing a gridenabled prototype for functi a194-2040 v1203 a

The vast amount in complexity of data generated in Genomic Research implies that new dedicated and powerful computational tools need to be developed to meet their analysis requirements. Blast2GO (B2G) is a bioinformatics tool for Gene Ontology-based DNA or protein sequence annotation and function-based data mining. The application has been developed with the aim of affering an easy-to-use tool for functional genomics research. Typical B2G users are middle size genomics labs carrying out sequencing, ETS and microarray projects, handling datasets up to several thousand sequences. In the current version of B2G. The power and analytical potential of both annotation and function data-mining is somehow restricted to the computational power behind each particular installation. In order to be able to offer the possibility of an enhanced computational capacity within this bioinformatics application, a Grid component is being developed. A prototype has been conceived for the particular problem of speeding up the Blast searches to obtain fast results for large datasets. Many efforts have been done in the literature concerning the speeding up of Blast searches, but few of them deal with the use of large heterogeneous production Grid Infrastructures. These are the infrastructures that could reach the largest number of resources and the best load balancing for data access. The Grid Service under development will analyse requests based on the number of sequences, splitting them accordingly to the available resources. Lower-level computation will be performed through MPIBLAST. The software architecture is based on the WSRF standard.

10ababelomics1 aAparicio, G.1 aGotz, S.1 aConesa, A.1 aSegrelles, D.1 aBlanquer, I.1 aGarcia, J., M.1 aHernandez, V.1 aRobles, M.1 aTalon, M. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1682313802539nas a2200265 4500008004100000245016000041210006900201300001200270490000700282520126500289653009401554653019301648653013501841653002601976100002102002700001702023700001902040700002002059700001502079700001502094700002002109700001802129700002002147856010602167 2006 eng d00aDevelopment of the GENIPOL European flounder (Platichthys flesus) microarray and determination of temporal transcriptional responses to cadmium at low dose0 aDevelopment of the GENIPOL European flounder Platichthys flesus  a6479-880 v403 aWe have constructed a high density, 13 270-clone cDNA array for the sentinel fish species European flounder (Platichthys flesus), combining clones from suppressive subtractive hybridization and a liver cDNA library; DNA sequences of 5211 clones were determined. Fish were treated by single intraperitoneal injection with 50 micrograms cadmium chloride per kilogram body weight, a dose relevant to environmental exposures, and hepatic gene expression changes were determined at 1, 2, 4, 8, and 16 days postinjection in comparison to saline-treated controls. Gene expression responses were confirmed by real-time reverse transcription polymerase chain reaction (RT-PCR). Blast2GO gene ontology analysis highlighted a general induction of the unfolded protein response, response to oxidative stress, protein synthesis, transport, and degradation pathways, while apoptosis, cell cycle, cytoskeleton, and cytokine genes were also affected. Transcript levels of cytochrome P450 1A (CYP1A) were repressed and vitellogenin altered, real-time PCR showed induction of metallothionein. We thus describe the establishment of a useful resource for ecotoxicogenomics and the determination of the temporal molecular responses to cadmium, a prototypical heavy metal pollutant.10aAnimals Cadmium Chloride/administration & dosage/*pharmacology Dose-Response Relationship10aDevelopmental/drug effects Liver/drug effects/growth & development/metabolism Oligonucleotide Array Sequence Analysis/*methods Reverse Transcriptase Polymerase Chain Reaction Transcription10aDrug Environmental Monitoring/methods Flounder/*genetics/growth & development Gene Expression Profiling Gene Expression Regulation10aGenetic/*drug effects1 aWilliams, T., D.1 aDiab, A., M.1 aGeorge, S., G.1 aGodfrey, R., E.1 aSabine, V.1 aConesa, A.1 aMinchin, S., D.1 aWatts, P., C.1 aChipman, J., K. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1712058401934nas a2200193 4500008004100000245012000041210006900161300001300230490000700243520110800250653010701358653001901465653008801484100001501572700001801587700001501605700001401620856010601634 2006 eng d00amaSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments0 amaSigPro a method to identify significantly differential express a1096-1020 v223 aMOTIVATION: Multi-series time-course microarray experiments are useful approaches for exploring biological processes. In this type of experiments, the researcher is frequently interested in studying gene expression changes along time and in evaluating trend differences between the various experimental groups. The large amount of data, multiplicity of experimental conditions and the dynamic nature of the experiments poses great challenges to data analysis. RESULTS: In this work, we propose a statistical procedure to identify genes that show different gene expression profiles across analytical groups in time-course experiments. The method is a two-regression step approach where the experimental groups are identified by dummy variables. The procedure first adjusts a global regression model with all the defined variables to identify differentially expressed genes, and in second a variable selection strategy is applied to study differences between groups and to find statistically significant different profiles. The methodology is illustrated on both a real and a simulated microarray dataset.10a*Algorithms Computer Simulation Gene Expression/*physiology Gene Expression Profiling/*methods *Models10aGenetic Models10aStatistical Oligonucleotide Array Sequence Analysis/*methods *Software Time Factors1 aConesa, A.1 aNueda, M., J.1 aFerrer, A.1 aTalon, M. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1648133301401nas a2200193 4500008004100000245010600041210006900147300001100216490000700227520075600234653001500990100001501005700001301020700002501033700001401058700001401072700001501086856010601101 2005 eng d00aBlast2GO: a universal tool for annotation, visualization and analysis in functional genomics research0 aBlast2GO a universal tool for annotation visualization and analy a3674-60 v213 a

SUMMARY: We present here Blast2GO (B2G), a research tool designed with the main purpose of enabling Gene Ontology (GO) based data mining on sequence data for which no GO annotation is yet available. B2G joints in one application GO annotation based on similarity searches with statistical analysis and highlighted visualization on directed acyclic graphs. This tool offers a suitable platform for functional genomics research in non-model species. B2G is an intuitive and interactive desktop application that allows monitoring and comprehension of the whole annotation and analysis process. AVAILABILITY: Blast2GO is freely available via Java Web Start at http://www.blast2go.de. SUPPLEMENTARY MATERIAL: http://www.blast2go.de -> Evaluation.

10ababelomics1 aConesa, A.1 aGotz, S.1 aGarcia-Gomez, J., M.1 aTerol, J.1 aTalon, M.1 aRobles, M. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1608147403705nas a2200805 4500008004100000245010800041210006900149300001100218490000700229520133100236653002501567653010901592653000801701653010501709653007501814100001601889700001401905700001501919700001701934700001501951700001501966700001301981700001501994700001602009700002002025700001502045700002102060700001502081700001802096700001502114700002902129700001502158700001702173700001502190700002802205700001502233700001602248700001402264700002602278700001602304700001502320700002102335700001602356700001902372700002002391700001702411700002702428700001702455700001502472700001602487700001502503700002502518700002002543700001302563700001602576700002202592700001302614700001602627700001402643700001402657700001402671700001402685700001502699700001502714700001602729700001402745700001702759700001702776856010602793 2005 eng d00aDevelopment of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies0 aDevelopment of a citrus genomewide EST collection and cDNA micro a375-910 v573 aA functional genomics project has been initiated to approach the molecular characterization of the main biological and agronomical traits of citrus. As a key part of this project, a citrus EST collection has been generated from 25 cDNA libraries covering different tissues, developmental stages and stress conditions. The collection includes a total of 22,635 high-quality ESTs, grouped in 11,836 putative unigenes, which represent at least one third of the estimated number of genes in the citrus genome. Functional annotation of unigenes which have Arabidopsis orthologues (68% of all unigenes) revealed gene representation in every major functional category, suggesting that a genome-wide EST collection was obtained. A Citrus clementina Hort. ex Tan. cv. Clemenules genomic library, that will contribute to further characterization of relevant genes, has also been constructed. To initiate the analysis of citrus transcriptome, we have developed a cDNA microarray containing 12,672 probes corresponding to 6875 putative unigenes of the collection. Technical characterization of the microarray showed high intra- and inter-array reproducibility, as well as a good range of sensitivity. We have also validated gene expression data achieved with this microarray through an independent technique such as RNA gel blot analysis.10aCitrus/*genetics DNA10aComplementary/chemistry/genetics *Expressed Sequence Tags Gene Expression Profiling Gene Library *Genome10aDNA10aPlant Genomics/*methods Molecular Sequence Data Oligonucleotide Array Sequence Analysis/*methods RNA10aPlant/genetics/metabolism Reproducibility of Results Sequence Analysis1 aForment, J.1 aGadea, J.1 aHuerta, L.1 aAbizanda, L.1 aAgusti, J.1 aAlamar, S.1 aAlos, E.1 aAndres, F.1 aArribas, R.1 aBeltran, J., P.1 aBerbel, A.1 aBlazquez, M., A.1 aBrumos, J.1 aCanas, L., A.1 aCercos, M.1 aColmenero-Flores, J., M.1 aConesa, A.1 aEstables, B.1 aGandia, M.1 aGarcia-Martinez, J., L.1 aGimeno, J.1 aGisbert, A.1 aGomez, G.1 aGonzalez-Candelas, L.1 aGranell, A.1 aGuerri, J.1 aLafuente, M., T.1 aMadueno, F.1 aMarcos, J., F.1 aMarques, M., C.1 aMartinez, F.1 aMartinez-Godoy, M., A.1 aMiralles, S.1 aMoreno, P.1 aNavarro, L.1 aPallas, V.1 aPerez-Amador, M., A.1 aPerez-Valle, J.1 aPons, C.1 aRodrigo, I.1 aRodriguez, P., L.1 aRoyo, C.1 aSerrano, R.1 aSoler, G.1 aTadeo, F.1 aTalon, M.1 aTerol, J.1 aTrenor, M.1 aVaello, L.1 aVicente, O.1 aVidal, Ch1 aZacarias, L.1 aConejero, V. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1583012802305nas a2200205 4500008004100000245007400041210006900115300001200184490000800196520129400204653014101498653005201639653021501691653002601906100001101932700001501943700001701958700001801975856010601993 2003 eng d00aExamining the role of glutamic acid 183 in chloroperoxidase catalysis0 aExamining the role of glutamic acid 183 in chloroperoxidase cata a13855-90 v2783 aSite-directed mutagenesis has been used to investigate the role of glutamic acid 183 in chloroperoxidase catalysis. Based on the x-ray crystallographic structure of chloroperoxidase, Glu-183 is postulated to function on distal side of the heme prosthetic group as an acid-base catalyst in facilitating the reaction between the peroxidase and hydrogen peroxide with the formation of Compound I. In contrast, the other members of the heme peroxidase family use a histidine residue in this role. Plasmids have now been constructed in which the codon for Glu-183 is replaced with a histidine codon. The mutant recombinant gene has been expressed in Aspergillus niger. An analysis of the produced mutant gene shows that the substitution of Glu-183 with a His residue is detrimental to the chlorination and dismutation activity of chloroperoxidase. The activity is reduced by 85 and 50% of wild type activity, respectively. However, quite unexpectedly, the epoxidation activity of the mutant enzyme is significantly enhanced approximately 2.5-fold. These results show that Glu-183 is important but not essential for the chlorination activity of chloroperoxidase. It is possible that the increased epoxidation of the mutant enzyme is based on an increase in the hydrophobicity of the active site.10aAspergillus niger/metabolism Catalase/metabolism Catalysis Chloride Peroxidase/*chemistry/*metabolism Chlorine/metabolism Chromatography10aIon Exchange Circular Dichroism Crystallography10aPolyacrylamide Gel Fungi/enzymology Glutamic Acid/*chemistry Histidine/chemistry/metabolism Hydrogen-Ion Concentration Immunoblotting Isoelectric Focusing Mutation Oxidoreductases/metabolism Plasmids/metabolism10aX-Ray Electrophoresis1 aYi, X.1 aConesa, A.1 aPunt, P., J.1 aHager, L., P. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1257647702286nas a2200193 4500008004100000245009100041210006900132300001100201490000700212520140500219653025701624653001201881100001501893700001501908700001901923700002701942700001701969856010601986 2002 eng d00aCalnexin overexpression increases manganese peroxidase production in Aspergillus niger0 aCalnexin overexpression increases manganese peroxidase productio a846-510 v683 aHeme-containing peroxidases from white rot basidiomycetes, in contrast to most proteins of fungal origin, are poorly produced in industrial filamentous fungal strains. Factors limiting peroxidase production are believed to operate at the posttranslational level. In particular, insufficient availability of the prosthetic group which is required for peroxidase biosynthesis has been proposed to be an important bottleneck. In this work, we analyzed the role of two components of the secretion pathway, the chaperones calnexin and binding protein (BiP), in the production of a fungal peroxidase. Expression of the Phanerochaete chrysosporium manganese peroxidase (MnP) in Aspergillus niger resulted in an increase in the expression level of the clxA and bipA genes. In a heme-supplemented medium, where MnP was shown to be overproduced to higher levels, induction of clxA and bipA was also higher. Overexpression of these two chaperones in an MnP-producing strain was analyzed for its effect on MnP production. Whereas bipA overexpression seriously reduced MnP production, overexpression of calnexin resulted in a four- to fivefold increase in the extracellular MnP levels. However, when additional heme was provided in the culture medium, calnexin overexpression had no synergistic effect on MnP production. The possible function of these two chaperones in MnP maturation and production is discussed.10aAspergillus niger/*enzymology/genetics Calcium-Binding Proteins/*metabolism Calnexin Culture Media *Fungal Proteins HSP70 Heat-Shock Proteins/metabolism Heme/metabolism Peroxidases/*biosynthesis/genetics Phanerochaete/enzymology/genetics Transformation10aGenetic1 aConesa, A.1 aJeenes, D.1 aArcher, D., B.1 avan den Hondel, C., A.1 aPunt, P., J. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1182322701632nas a2200193 4500008004100000245007600041210006900117300001000186490000700196520078800203653023600991100001701227700001901244700001501263700001501278700001601293700002301309856010601332 2002 eng d00aFilamentous fungi as cell factories for heterologous protein production0 aFilamentous fungi as cell factories for heterologous protein pro a200-60 v203 aFilamentous fungi have been used as sources of metabolites and enzymes for centuries. For about two decades, molecular genetic tools have enabled us to use these organisms to express extra copies of both endogenous and exogenous genes. This review of current practice reveals that molecular tools have enabled several new developments. But it has been process development that has driven the final breakthrough to achieving commercially relevant quantities of protein. Recent research into gene expression in filamentous fungi has explored their wealth of genetic diversity with a view to exploiting them as expression hosts and as a source of new genes. Inevitably, the progress in the ’genomics’ technology will further develop high-throughput technologies for these organisms.10aFermentation/genetics/physiology Fungi/*genetics/*metabolism Humans Interleukin-6/analysis/*biosynthesis/genetics Peroxidases/analysis/*biosynthesis/genetics Protein Conformation Recombinant Proteins/analysis/*biosynthesis/genetics1 aPunt, P., J.1 avan Biezen, N.1 aConesa, A.1 aAlbers, A.1 aMangnus, J.1 avan den Hondel, C. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1194337501436nas a2200157 4500008004100000245005900041210005800100300001100158490000700169520072900176653020800905100001501113700001701128700002701145856010601172 2002 eng d00aFungal peroxidases: molecular aspects and applications0 aFungal peroxidases molecular aspects and applications a143-580 v933 aPeroxidases are oxidoreductases that utilize hydrogen peroxide to catalyze oxidative reactions. A large number of peroxidases have been identified in fungal species and are being characterized at the molecular level. In this manuscript we review the current knowledge on the molecular aspects of this type of enzymes. We present an overview of the research efforts undertaken in deciphering the structural basis of the catalytic properties of fungal peroxidases and discuss molecular genetics and protein homology aspects of this enzyme class. Finally, we summarize the potential biotechnological applications of these enzymes and evaluate recent advances on their expression in heterologous systems for production purposes.10aAmino Acid Sequence Binding Sites Biotechnology Catalysis Fungi/*enzymology Molecular Sequence Data Peroxidases/chemistry/*genetics/metabolism Recombinant Proteins Sequence Homology Substrate Specificity1 aConesa, A.1 aPunt, P., J.1 avan den Hondel, C., A. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1173872101688nas a2200169 4500008004100000245010100041210006900142300001100211490000800222520084700230653026001077100001501337700001601352700002701368700001701395856010601412 2001 eng d00aC-terminal propeptide of the Caldariomyces fumago chloroperoxidase: an intramolecular chaperone?0 aCterminal propeptide of the Caldariomyces fumago chloroperoxidas a117-200 v5033 aThe Caldariomyces fumago chloroperoxidase (CPO) is synthesised as a 372-aa precursor which undergoes two proteolytic processing events: removal of a 21-aa N-terminal signal peptide and of a 52-aa C-terminal propeptide. The Aspergillus niger expression system developed for CPO was used to get insight into the function of this C-terminal propeptide. A. niger transformants expressing a CPO protein from which the C-terminal propeptide was deleted failed in producing any extracellular CPO activity, although the CPO polypeptide was synthesised. Expression of the full-length gene in an A. niger strain lacking the KEX2-like protease PclA also resulted in the production of CPO cross-reactive material into the culture medium, but no CPO activity. Based on these results, a function of the C-terminal propeptide in CPO maturation is indicated.10aAmino Acid Sequence Ascomycota/*enzymology/genetics Aspergillus niger/genetics Base Sequence Chloride Peroxidase/biosynthesis/*chemistry/genetics DNA Primers/genetics Enzyme Precursors/biosynthesis/chemistry/genetics Gene Expression Molecular Chaperones/b1 aConesa, A.1 aWeelink, G.1 avan den Hondel, C., A.1 aPunt, P., J. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1151386601692nas a2200193 4500008004100000245012800041210006900169300001300238490000800251520081300259653019901072100001501271700002101286700002101307700002001328700002701348700001701375856010601392 2001 eng d00aExpression of the Caldariomyces fumago chloroperoxidase in Aspergillus niger and characterization of the recombinant enzyme0 aExpression of the Caldariomyces fumago chloroperoxidase in Asper a17635-400 v2763 aThe Caldariomyces fumago chloroperoxidase was successfully expressed in Aspergillus niger. The recombinant enzyme was produced in the culture medium as an active protein and could be purified by a three-step purification procedure. The catalytic behavior of recombinant chloroperoxidase (rCPO) was studied and compared with that of native CPO. The specific chlorination activity (47 units/nmol) of rCPO and its pH optimum (pH 2.75) were very similar to those of native CPO. rCPO catalyzes the oxidation of various substrates in comparable yields and selectivities to native CPO. Indole was oxidized to 2-oxindole with 99% selectivity and thioanisole to the corresponding R-sulfoxide (enantiomeric excess >98%). Incorporation of (18)O from labeled H(2)18O(2) into the oxidized products was 100% in both cases.10aAspergillus niger/enzymology/genetics Catalysis Chloride Peroxidase/biosynthesis/*genetics Fungal Proteins/biosynthesis/*genetics Recombinant Proteins/biosynthesis/genetics Substrate Specificity1 aConesa, A.1 avan De Velde, F.1 avan Rantwijk, F.1 aSheldon, R., A.1 avan den Hondel, C., A.1 aPunt, P., J. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1127870101536nas a2200169 4500008004100000245007200041210006700113300001100180490000700191520084500198653014001043100001501183700001701198700001801215700002701233856010601260 2001 eng d00aThe secretion pathway in filamentous fungi: a biotechnological view0 asecretion pathway in filamentous fungi a biotechnological view a155-710 v333 aThe high capacity of the secretion machinery of filamentous fungi has been widely exploited for the production of homologous and heterologous proteins; however, our knowledge of the fungal secretion pathway is still at an early stage. Most of the knowledge comes from models developed in yeast and higher eukaryotes, which have served as reference for the studies on fungal species. In this review we compile the data accumulated in recent years on the molecular basis of fungal secretion, emphasizing the relevance of these data for the biotechnological use of the fungal cell and indicating how this information has been applied in attempts to create improved production strains. We also present recent emerging approaches that promise to provide answers to fundamental questions on the molecular genetics of the fungal secretory pathway.10aAnimals Biotechnology/*methods Fungal Proteins/*genetics/*metabolism Fungi/*genetics/*metabolism Humans Recombinant Proteins/metabolism1 aConesa, A.1 aPunt, P., J.1 avan Luijk, N.1 avan den Hondel, C., A. uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11495573