Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Functional Divergence of Two Secreted Immune Proteases of Tomato
    Ilyas, M. ; Hörger, A.C. ; Bozkurt, T.O. ; Burg, H.A. van den; Kaschani, F. ; Kaiser, M. ; Belhaj, K. ; Smoker, M. ; Joosten, M. ; Kamoun, S. ; Hoorn, R.A.L. van der - \ 2015
    Current Biology 25 (2015)17. - ISSN 0960-9822 - p. 2300 - 2306.
    cf-2-dependent disease resistance - pathogen effectors - transcription factors - provides insights - genome sequence - plant-pathogens - gene - defense - target - specialization
    Rcr3 and Pip1 are paralogous secreted papain-like proteases of tomato. Both proteases are inhibited by Avr2 from the fungal pathogen Cladosporium fulvum, but only Rcr3 acts as a co-receptor for Avr2 recognition by the tomato Cf-2 immune receptor [ 1, 2, 3 and 4]. Here, we show that Pip1-depleted tomato plants are hyper-susceptible to fungal, bacterial, and oomycete plant pathogens, demonstrating that Pip1 is an important broad-range immune protease. By contrast, in the absence of Cf-2, Rcr3 depletion does not affect fungal and bacterial infection levels but causes increased susceptibility only to the oomycete pathogen Phytophthora infestans. Rcr3 and Pip1 reside on a genetic locus that evolved over 36 million years ago. These proteins differ in surface-exposed residues outside the substrate-binding groove, and Pip1 is 5- to 10-fold more abundant than Rcr3. We propose a model in which Rcr3 and Pip1 diverged functionally upon gene duplication, possibly driven by an arms race with pathogen-derived inhibitors or by coevolution with the Cf-2 immune receptor detecting inhibitors of Rcr3, but not of Pip1.
    Large-scale evolutionary analysis of genes and supergene clusters from terpenoid modular pathways provides insights into metabolic diversification in flowering plants.
    Hofberger, J.A. ; Ramirez, A.M. ; Bergh, E. van den; Zhu, X. ; Bouwmeester, H.J. ; Schuurink, R.C. ; Schranz, M.E. - \ 2015
    PLoS ONE 10 (2015)6. - ISSN 1932-6203 - 37 p.
    isopentenyl diphosphate isomerases - disease resistance genes - arabidopsis-thaliana - genome sequence - whole-genome - protein families - draft genome - isoprenoid biosynthesis - secondary metabolism - oxidosqualene cyclase
    An important component of plant evolution is the plethora of pathways producing more than 200,000 biochemically diverse specialized metabolites with pharmacological, nutritional and ecological significance. To unravel dynamics underlying metabolic diversification, it is critical to determine lineage-specific gene family expansion in a phylogenomics framework. However, robust functional annotation is often only available for core enzymes catalyzing committed reaction steps within few model systems. In a genome informatics approach, we extracted information from early-draft gene-space assemblies and non-redundant transcriptomes to identify protein families involved in isoprenoid biosynthesis. Isoprenoids comprise terpenoids with various roles in plant-environment interaction, such as pollinator attraction or pathogen defense. Combining lines of evidence provided by synteny, sequence homology and Hidden-Markov-Modelling, we screened 17 genomes including 12 major crops and found evidence for 1,904 proteins associated with terpenoid biosynthesis. Our terpenoid genes set contains evidence for 840 core terpene-synthases and 338 triterpene-specific synthases. We further identified 190 prenyltransferases, 39 isopentenyl-diphosphate isomerases as well as 278 and 219 proteins involved in mevalonate and methylerithrol pathways, respectively. Assessing the impact of gene and genome duplication to lineage-specific terpenoid pathway expansion, we illustrated key events underlying terpenoid metabolic diversification within 250 million years of flowering plant radiation. By quantifying Angiosperm-wide versatility and phylogenetic relationships of pleiotropic gene families in terpenoid modular pathways, our analysis offers significant insight into evolutionary dynamics underlying diversification of plant secondary metabolism. Furthermore, our data provide a blueprint for future efforts to identify and more rapidly clone terpenoid biosynthetic genes from any plant species.
    Karyotype evolution in apomictic Boechera and the origin of the aberrant chromosomes
    Mandáková, T. ; Schranz, M.E. ; Sharbel, T.F. ; Jong, J.H.S.G.M. de; Lysak, M. - \ 2015
    The Plant Journal 82 (2015)5. - ISSN 0960-7412 - p. 785 - 793.
    holboellii complex - genus boechera - genome sequence - centric fission - brassicaceae - arabidopsis - centromere - phylogeny - arabis - reproduction
    Chromosome rearrangements may result in both decrease and increase of chromosome numbers. Here we have used comparative chromosome painting (CCP) to reconstruct the pathways of descending and ascending dysploidy in the genus Boechera (tribe Boechereae, Brassicaceae). We describe the origin and structure of three Boechera genomes and establish the origin of the previously described aberrant Het and Del chromosomes found in Boechera apomicts with euploid (2n = 14) and aneuploid (2n = 15) chromosome number. CCP analysis allowed us to reconstruct the origin of seven chromosomes in sexual B. stricta and apomictic B. divaricarpa from the ancestral karyotype (n = 8) of Brassicaceae lineage I. Whereas three chromosomes (BS4, BS6, and BS7) retained their ancestral structure, five chromosomes were reshuffled by reciprocal translocations to form chromosomes BS1-BS3 and BS5. The reduction of the chromosome number (from x = 8 to x = 7) was accomplished through the inactivation of a paleocentromere on chromosome BS5. In apomictic 2n = 14 plants, CCP identifies the largely heterochromatic chromosome (Het) being one of the BS1 homologues with the expansion of pericentromeric heterochromatin. In apomictic B. polyantha (2n = 15), the Het has undergone a centric fission resulting in two smaller chromosomes – the submetacentric Het' and telocentric Del. Here we show that new chromosomes can be formed by a centric fission and can be fixed in populations due to the apomictic mode of reproduction.
    Immunomodulatory Properties of Streptococcus and Veillonella Isolates from the Human Small Intestine Microbiota
    Bogert, B. van den; Meijerink, M. ; Zoetendal, E.G. ; Wells, J.M. ; Kleerebezem, M. - \ 2014
    PLoS ONE 9 (2014)12. - ISSN 1932-6203 - 20 p.
    segmented filamentous bacteria - tight junction proteins - patch dendritic cells - gut microbiota - lactobacillus-plantarum - ly6c(hi) monocytes - genome sequence - oral tolerance - immune-system - in-vivo
    The human small intestine is a key site for interactions between the intestinal microbiota and the mucosal immune system. Here we investigated the immunomodulatory properties of representative species of commonly dominant small-intestinal microbial communities, including six streptococcal strains (four Streptococcus salivarius, one S. equinus, one S. parasanguinis) one Veillonella parvula strain, one Enterococcus gallinarum strain, and Lactobacillus plantarum WCFS1 as a bench mark strain on human monocyte-derived dendritic cells. The different streptococci induced varying levels of the cytokines IL-8, TNF-a, and IL-12p70, while the V. parvula strain showed a strong capacity to induce IL-6. E. gallinarum strain was a potent inducer of cytokines and TLR2/6 signalling. As Streptococcus and Veillonella can potentially interact metabolically and frequently co-occur in ecosystems, immunomodulation by pair-wise combinations of strains were also tested for their combined immunomodulatory properties. Strain combinations induced cytokine responses in dendritic cells that differed from what might be expected on the basis of the results obtained with the individual strains. A combination of (some) streptococci with Veillonella appeared to negate IL-12p70 production, while augmenting IL-8, IL-6, IL-10, and TNF-a responses. This suggests that immunomodulation data obtained in vitro with individual strains are unlikely to adequately represent immune responses to mixtures of gut microbiota communities in vivo. Nevertheless, analysing the immune responses of strains representing the dominant species in the intestine may help to identify immunomodulatory mechanisms that influence immune homeostasis.
    Horizontal transmission dynamics of White spot syndrome virus by cohabitation trials in juvenile Penaeus monodon and P. vannamei
    Ngo Xuan, T. ; Verreth, J.A.J. ; Vlak, J.M. ; Jong, M.C.M. de - \ 2014
    Preventive Veterinary Medicine 117 (2014)1. - ISSN 0167-5877 - p. 286 - 294.
    yellow head virus - litopenaeus-vannamei - experimental-infection - baculovirus wsbv - commodity shrimp - genome sequence - oral routes - wssv - japonicus - histopathology
    White spot syndrome virus (WSSV), a rod-shaped double-stranded DNA virus, is an infectious agent causing fatal disease in shrimp farming around the globe. Within shrimp populations WSSV is transmitted very fast, however, the modes and dynamics of transmission of this virus are not well understood. In the current study the dynamics of disease transmission of WSSV were investigated in small, closed populations of Penaeus monodon and Penaeus vannamei. Pair cohabitation experiments using PCR as a readout for virus infection were used to estimate transmission parameters for WSSV in these two species. The mortality rate of contact-infected shrimp in P. monodon was higher than the rate in P. vannamei. The transmission rate parameters for WSSV were not different between the two species. The relative contribution of direct and indirect transmission rates of WSSV differed between the two species. For P. vannamei the direct contact transmission rate of WSSV was significantly lower than the indirect environmental transmission rate, but for P. monodon, the opposite was found. The reproduction ratio R0 for WSSV for these two species of shrimp was estimated to be above one: 2.07 (95%CI 1.53, 2.79) for P. monodon and 1.51 (95%CI 1.12, 2.03) for P. vannamei. The difference in R0 between the two species is due to a lower host mortality and hence a longer infectious period of WSSV in P. monodon.
    Profiling the secretome and extracellular proteome of the potato late blight pathogen Phytophthora infestans
    Meijer, H.J.G. ; Mancuso, F.M. ; Espadas, G. ; Seidl, M.F. ; Chiva, C. ; Govers, F. ; Sabido, E. - \ 2014
    Molecular and Cellular Proteomics 13 (2014)8. - ISSN 1535-9476 - p. 2101 - 2113.
    phosphate kinase domain - amino-acid-sequence - cell-wall proteins - coupled receptors - genome sequence - identification - family - infection - virulence - effectors
    Oomycetes are filamentous organisms that cause notorious diseases, several of which have a high economic impact. Well known is Phytophthora infestans, the causal agent of potato late blight. Previously, in silico analyses of the genome and transcriptome of P. infestans resulted in the annotation of a large number of genes encoding proteins with an N-terminal signal peptide. This set is collectively referred to as the secretome and comprises proteins involved in, for example, cell wall growth and modification, proteolytic processes, and the promotion of successful invasion of plant cells. So far, proteomic profiling in oomycetes was primarily focused on subcellular, intracellular or cell wall fractions; the extracellular proteome has not been studied systematically. Here we present the first comprehensive characterization of the in vivo secretome and extracellular proteome of P. infestans. We have used mass spectrometry to analyze P. infestans proteins present in seven different growth media with mycelial cultures and this resulted in the consistent identification of over two hundred proteins. Gene ontology classification pinpointed proteins involved in cell wall modifications, pathogenesis, defense responses, and proteolytic processes. Moreover, we found members of the RXLR and CRN effector families as well as several proteins lacking an obvious signal peptide. The latter were confirmed to be bona fide extracellular proteins and this suggests that, similar to other organisms, oomycetes exploit non-conventional secretion mechanisms to transfer certain proteins to the extracellular environment.
    vanI: a novel d-Ala-d-Lac vancomycin resistance gene cluster found in Desulfitobacterium hafniense
    Kruse, T. ; Levisson, M. ; Vos, W.M. de; Smidt, H. - \ 2014
    Microbial Biotechnology 7 (2014)5. - ISSN 1751-7907 - p. 456 - 466.
    comparative-analysis system - antibiotic-resistance - enterococcus-faecium - genome sequence - streptomyces-coelicolor - bacteria - enrichment - evolution - resistome - alignment
    The glycopeptide vancomycin was until recently considered a drug of last resort against Gram-positive bacteria. Increasing numbers of bacteria, however, are found to carry genes that confer resistance to this antibiotic. So far, 10 different vancomycin resistance clusters have been described. A chromosomal vancomycin resistance gene cluster was previously described for the anaerobic Desulfitobacterium hafniense Y51. We demonstrate that this gene cluster, characterized by its d-Ala-d-Lac ligase-encoding vanI gene, is present in all strains of D.¿hafniense, D.¿chlororespirans and some strains of Desulfosporosinus spp. This gene cluster was not found in vancomycin-sensitive Desulfitobacterium or Desulfosporosinus spp., and we show that this antibiotic resistance can be exploited as an intrinsic selection marker for Desulfitobacterium hafniense and D.¿chlororespirans. The gene cluster containing vanI is phylogenetically only distantly related with those described from soil and gut bacteria, but clusters instead with vancomycin resistance genes found within the phylum Actinobacteria that include several vancomycin-producing bacteria. It lacks a vanH homologue, encoding a D-lactate dehydrogenase, previously thought to always be present within vancomycin resistance gene clusters. The location of vanH outside the resistance gene cluster likely hinders horizontal gene transfer. Hence, the vancomycin resistance cluster in D.¿hafniense should be regarded a novel one that we here designated vanI after its unique d-Ala-d-Lac ligase
    Regulation of reductive dehalogenase gene transcription in Dehalococcoides mccartyi
    Wagner, A. ; Segler, L. ; Kleinsteuber, S. ; Sawers, G. ; Smidt, H. ; Lechner, U. - \ 2013
    Philosophical Transactions of the Royal Society B. Biological sciences 368 (2013)1616. - ISSN 0962-8436
    sp strain cbdb1 - vinyl-chloride reductase - escherichia-coli - desulfitobacterium-hafniense - response regulators - bacillus-subtilis - genome sequence - marr family - ethenogenes - expression
    The remarkable capacity of the genus Dehalococcoides to dechlorinate a multitude of different chlorinated organic compounds reflects the number and diversity of genes in the genomes of Dehalococcoides species encoding reductive dehalogenase homologues (rdh). Most of these genes are located in the vicinity of genes encoding multiple antibiotic resistance regulator (MarR)-type or two-component system regulators. Here, the transcriptional response of rdhA genes (coding for the catalytic subunit) to 2,3- and 1,3-dichlorodi-benzo-p-dioxin (DCDD) was studied in Dehalococcoides mccartyi strain CBDB1. Almost all rdhA genes were transcribed in the presence of 2,3-DCDD, albeit at different levels as shown for the transcripts of cbrA, cbdbA1453, cbdbA1624 and cbdbA1588. By contrast, 1,3-DCDD did not induce rdhA transcription. The putative MarR CbdbA1625 was heterologously produced and its ability to bind in vitro to the overlapping promoter regions of the genes cbdbA1624 and cbdbA1625 was demonstrated. To analyse regulation in vivo, single-copy transcriptional promoter-lacZ fusions of different rdhA genes and of cbdbA1625 were constructed and introduced into the heterologous host Escherichia coli, and expression levels of the fusions were measured. The cbdbA1625 gene was cloned into a vector allowing a regulation of expression by arabinose and it was transformed into the strains containing the rdh-promoter-lacZ fusion derivatives. CbdbA1625 was shown to downregulate transcription from its own promoter resulting in a 40-50% reduction in the beta-galactosidase activity, giving the first hint that it acts as a repressor.
    Functional analysis of potato genes involved in quantitative resistance to Phytophthora infestans
    Du, J. ; Tian, Z.D. ; Liu, J. ; Vleeshouwers, V.G.A.A. ; Shi, X.L. ; Xie, C.H. - \ 2013
    Molecular Biology Reports 40 (2013)2. - ISSN 0301-4851 - p. 957 - 967.
    systemic acquired-resistance - beta-aminobutyric acid - late blight - disease resistance - nicotiana-benthamiana - anionic peroxidase - durable resistance - genome sequence - virus - plant
    The most significant threat to potato production worldwide is the late blight disease, which is caused by the oomycete pathogen Phytophthora infestans. Based on previous cDNA microarrays and cDNA-amplified fragment length polymorphism analysis, 63 candidate genes that are expected to contribute to developing a durable resistance to late blight were selected for further functional analysis. We performed virus-induced gene silencing (VIGS) to these candidate genes on both Nicotiana benthamiana and potato, subsequently inoculated detached leaves and assessed the resistance level. Ten genes decreased the resistance to P. infestans after VIGS treatment. Among those, a lipoxygenase (LOX; EC 1.13.11.12) and a suberization-associated anionic peroxidase affected the resistance in both N. benthamiana and potato. Our results identify genes that may play a role in quantitative resistance mechanisms to late blight.
    CRISPRTarget: bioinformatic prediction and analysis of crRNA targets
    Biswas, A. ; Gagnon, J.N. ; Brouns, S.J.J. ; Fineran, P.C. ; Brown, C.M. - \ 2013
    RNA Biology 10 (2013)5. - ISSN 1547-6286 - p. 817 - 827.
    short palindromic repeats - bacterial immune-system - cas systems - pectobacterium-atrosepticum - streptococcus-thermophilus - salmonella-enterica - dynamic properties - antiviral defense - adaptive immunity - genome sequence
    The bacterial and archaeal CRISPR/Cas adaptive immune system targets specific protospacer nucleotide sequences in invading organisms. This requires base pairing between processed CRISPR RNA and the target protospacer. For type I and II CRISPR/Cas systems, protospacer adjacent motifs (PAM) are essential for target recognition, and for type III, mismatches in the flanking sequences are important in the antiviral response. In this study, we examine the properties of each class of CRISPR. We use this information to provide a tool (CRISPRTarget) that predicts the most likely targets of CRISPR RNAs (http://bioanalysis.otago.ac.nz/CRISPRTarget). This can be used to discover targets in newly sequenced genomic or metagenomic data. To test its utility, we discover features and targets of well-characterized Streptococcus thermophilus and Sulfolobus solfataricus type II and III CRISPR/Cas systems. Finally, in Pectobacterium species, we identify new CRISPR targets and propose a model of temperate phage exposure and subsequent inhibition by the type I CRISPR/Cas systems
    Functional analysis of the ComK protein of Bacillus coagulans
    Kovács, Á.T. ; Eckhardt, T.H. ; Hartskamp, M. van; Kranenburg, R. van; Kuipers, O.P. - \ 2013
    PLoS ONE 8 (2013)1. - ISSN 1932-6203
    competence transcription factor - gram-positive bacteria - subtilis k-state - gene-expression - natural competence - biofilm formation - genome sequence - lactic-acid - dna uptake - transformation
    The genes for DNA uptake and recombination in Bacilli are commonly regulated by the transcriptional factor ComK. We have identified a ComK homologue in Bacillus coagulans, an industrial relevant organism that is recalcitrant for transformation. Introduction of B. coagulans comK gene under its own promoter region into Bacillus subtilis comK strain results in low transcriptional induction of the late competence gene comGA, but lacking bistable expression. The promoter regions of B. coagulans comK and the comGA genes are recognized in B. subtilis and expression from these promoters is activated by B. subtilis ComK. Purified ComK protein of B. coagulans showed DNA-binding ability in gel retardation assays with B. subtilis- and B. coagulans-derived probes. These experiments suggest that the function of B. coagulans ComK is similar to that of ComK of B. subtilis. When its own comK is overexpressed in B. coagulans the comGA gene expression increases 40-fold, while the expression of another late competence gene, comC is not elevated and no reproducible DNA-uptake could be observed under these conditions. Our results demonstrate that B. coagulans ComK can recognize several B.subtilis comK-responsive elements, and vice versa, but indicate that the activation of the transcription of complete sets of genes coding for a putative DNA uptake apparatus in B. coagulans might differ from that of B. subtilis
    Development and growth of fruit bodies and crops of the button mushroom, Agaricus bisporus
    Straatsma, G. ; Sonnenberg, A.S.M. ; Griensven, L.J.L.D. van - \ 2013
    Fungal Biology 117 (2013)10. - ISSN 1878-6146 - p. 697 - 707.
    morphogenetic cell-death - cultivated mushroom - primordium formation - mathematical-model - genome sequence - histogenesis - sporophores - initiation - substrate - mycelium
    We studied the appearance of fruit body primordia, the growth of individual fruit bodies and the development of the consecutive flushes of the crop. Relative growth, measured as cap expansion, was not constant. It started extremely rapidly, and slowed down to an exponential rate with diameter doubling of 1.7 d until fruit bodies showed maturation by veil breaking. Initially many outgrowing primordia were arrested, indicating nutritional competition. After reaching 10 mm diameter, no growth arrest occurred; all growing individuals, whether relatively large or small, showed an exponential increase of both cap diameter and biomass, until veil breaking. Biomass doubled in 0.8 d. Exponential growth indicates the absence of competition. Apparently there exist differential nutritional requirements for early growth and for later, continuing growth. Flushing was studied applying different picking sizes. An ordinary flushing pattern occurred at an immature picking size of 8 mm diameter (picking mushrooms once a day with a diameter above 8 mm). The smallest picking size yielded the highest number of mushrooms picked, confirming the competition and arrested growth of outgrowing primordia: competition seems less if outgrowing primordia are removed early. The flush duration (i.e. between the first and last picking moments) was not affected by picking size. At small picking size, the subsequent flushes were not fully separated in time but overlapped. Within 2 d after picking the first individuals of the first flush, primordia for the second flush started outgrowth. Our work supports the view that the acquisition of nutrients by the mycelium is demand rather than supply driven. For formation and early outgrowth of primordia, indications were found for an alternation of local and global control, at least in the casing layer. All these data combined, we postulate that flushing is the consequence of the depletion of some unknown specific nutrition required by outgrowing primordia.
    FLOWERING LOCUS C in monocots and the tandem origin of angiosperm specific MADS-box genes
    Ruelens, P. ; Maagd, R.A. de; Proost, S. ; Theissen, G. ; Geuten, K. ; Kaufmann, K. - \ 2013
    Nature Communications 4 (2013). - ISSN 2041-1723
    genome sequence - brachypodium-distachyon - epigenetic regulation - floral repressor - core eudicots - vernalization - evolution - arabidopsis - flc - protein
    MADS-domain transcription factors have been shown to act as key repressors or activators of the transition to flowering and as master regulators of reproductive organ identities. Despite their important roles in plant development, the origin of several MADS-box subfamilies has remained enigmatic so far. Here we demonstrate, through a combination of genome synteny and phylogenetic reconstructions, the origin of three major, apparently angiosperm-specific MADS-box gene clades: FLOWERING LOCUS C- (FLC-), SQUAMOSA- (SQUA-) and SEPALLATA- (SEP-) -like genes. We find that these lineages derive from a single ancestral tandem duplication in a common ancestor of extant seed plants. Contrary to common belief, we show that FLC-like genes are present in cereals where they can also act as floral repressors responsive to prolonged cold or vernalization. This opens a new perspective on the translation of findings from Arabidopsis to cereal crops, in which vernalization was originally described.
    The xylem as battleground for plant hosts and vascular wilt pathogens
    Yadeta, K.A. ; Thomma, B.P.H.J. - \ 2013
    Frontiers in Plant Science 4 (2013). - ISSN 1664-462X
    xa21-mediated innate immunity - dutch elm disease - campestris pv. campestris - verticillium-albo-atrum - pit membrane porosity - rich repeat domain - fusarium-oxysporum - genome sequence - ralstonia-solanacearum - arabidopsis-thaliana
    Vascular wilts are among the most destructive plant diseases that occur in annual crops as well as in woody perennials. These diseases are generally caused by soil-borne bacteria, fungi, and oomycetes that infect through the roots and enter the water-conducting xylem vessels where they proliferate and obstruct the transportation of water and minerals. As a consequence, leaves wilt and die, which may lead to impairment of the whole plant and eventually to death of the plant. Cultural, chemical, and biological measures to control this group of plant pathogens are generally ineffective, and the most effective control strategy is the use of genetic resistance. Owing to the fact that vascular wilt pathogens live deep in the interior of their host plants, studies into the biology of vascular pathogens are complicated. However, to design novel strategies to combat vascular wilt diseases, understanding the (molecular) biology of vascular pathogens and the molecular mechanisms underlying plant defense against these pathogens is crucial. In this review, we discuss the current knowledge on interactions of vascular wilt pathogens with their host plants, with emphasis on host defense responses against this group of pathogens.
    GK4, a G-protein-coupled receptor with a phosphatidylinositol phosphate kinase domain in Phytophthora infestans, is involved in sporangia development and virulence
    Hua, C. ; Meijer, H.J.G. ; Keijzer, J. de; Zhao, W. ; Wang, Y. ; Govers, F. - \ 2013
    Molecular Microbiology 88 (2013)2. - ISSN 0950-382X - p. 352 - 370.
    heterotrimeric g-protein - pollen-tube growth - escherichia-coli - nicotiana-tabacum - genome sequence - alpha-subunit - arabidopsis - gene - topology - fungi
    For dispersal and host infection plant pathogens largely depend on asexual spores. Pathogenesis and sporulation are complex processes that are governed by cellular signalling networks including G-protein and phospholipid signalling. Oomycetes possess a family of novel proteins called GPCR-PIPKs (GKs) that are composed of a seven-transmembrane spanning (7-TM) domain fused to a phosphatidylinositol phosphate kinase (PIPK) domain. Based on this domain structure GKs are anticipated to link G-protein and phospholipid signal pathways; however, their functions are currently unknown. Expression analyses of the 12 GK genes in Phytophthora infestans and their orthologues in Phytophthora sojae, revealed differential expression during asexual development. PiGK1 and PiGK4 were fused to monomeric red fluorescent protein (mRFP) and ectopically expressed in P.¿infestans. In growing hyphae different subcellular distribution patterns were observed indicating that these two GKs act independently during development. We focused on the functional analyses of PiGK4. Its localization suggested involvement in cell differentiation and elongation and its 7-TM domain showed a canonical GPCR membrane topology. Silencing of GK4 and overexpression of full-length and truncated constructs in P.¿infestans revealed that PiGK4 is not only involved in spore germination and hyphal elongation but also in sporangia cleavage and infection.
    In-silico-driven metabolic engineering of Pseudomonas putida for enhanced production of poly-hydroxyalkanoates
    Poblete-Castro, I. ; Binger, D. ; Rodrigues, A. ; Becker, J. ; Martins Dos Santos, V.A.P. ; Wittmann, C. - \ 2013
    Metabolic Engineering 15 (2013). - ISSN 1096-7176 - p. 113 - 123.
    chain-length polyhydroxyalkanoates - gram-negative bacteria - fed-batch culture - genome sequence - escherichia-coli - kt2440 - pathways - acid - poly(3-hydroxyalkanoates) - biosynthesis
    Here, we present systems metabolic engineering driven by in-silico modeling to tailor Pseudomonas putida for synthesis of medium chain length PHAs on glucose. Using physiological properties of the parent wild type as constraints, elementary flux mode analysis of a large-scale model of the metabolism of P. putida was used to predict genetic targets for strain engineering. Among a set of priority ranked targets, glucose dehydrogenase (encoded by gcd) was predicted as most promising deletion target. The mutant P. putida ¿gcd, generated on basis of the computational design, exhibited 100% increased PHA accumulation as compared to the parent wild type, maintained a high specific growth rate and exhibited an almost unaffected gene expression profile, which excluded detrimental side effects of the modification. A second mutant strain, P. putida ¿pgl, that lacked 6-phosphogluconolactonase, exhibited a substantially decreased PHA synthesis, as was also predicted by the model. The production potential of P. putida ¿gcd was assessed in batch bioreactors. The novel strain showed an increase of the PHA yield (+80%), the PHA titer (+100%) and cellular PHA content (+50%) and revealed almost unaffected growth and diminished by-product formation. It was thus found superior in all relevant criteria towards industrial production. Beyond the contribution to more efficient PHA production processes at reduced costs that might replace petrochemical plastics in the future, the study illustrates the power of computational prediction to tailor microbial strains for enhanced biosynthesis of added-value compounds
    Marker2sequence, mine your QTL regions for candidate genes
    Chibon, P.Y.F.R.P. ; Schoof, H. ; Visser, R.G.F. ; Finkers, H.J. - \ 2012
    Bioinformatics 28 (2012)14. - ISSN 1367-4803 - p. 1921 - 1922.
    genome sequence - tomato - web
    Marker2sequence (M2S) aims at mining quantitative trait loci (QTLs) for candidate genes. For each gene, within the QTL region, M2S uses data integration technology to integrate putative gene function with associated gene ontology terms, proteins, pathways and literature. As a typical QTL region easily contains several hundreds of genes, this gene list can then be further filtered using a keyword-based query on the aggregated annotations. M2S will help breeders to identify potential candidate genes for their traits of interest.
    Viral diseases of wild and farmed European eel Anguilla anguilla with particular reference to the Netherlands
    Beurden, S.J. van; Engelsma, M.Y. ; Roozenburg, I. ; Voorbergen-Laarman, H.A. ; Tulden, P.W. van; Kerkhoff, S. ; Nieuwstadt, A. ; Davidse, A. ; Haenen, O.L.M. - \ 2012
    Diseases of Aquatic Organisms 101 (2012). - ISSN 0177-5103 - p. 69 - 86.
    pancreatic necrosis virus - pillar cell necrosis - herpesvirus-anguillae - japanese eel - japonica temminck - phylogenetic-relationships - rhabdoviral dermatitis - taxonomic position - genome sequence - rainbow-trout
    Diseases are an important cause of losses and decreased production rates in freshwater eel farming, and have been suggested to play a contributory role in the worldwide decline in wild freshwater eel stocks. Three commonly detected pathogenic viruses of European eel Anguilla anguilla are the aquabirnavirus eel virus European (EVE), the rhabdovirus eel virus European X (EVEX), and the alloherpesvirus anguillid herpesvirus 1 (AngHV1). In general, all 3 viruses cause a nonspecific haemorrhagic disease with increased mortality rates. This review provides an overview of the current knowledge on the aetiology, prevalence, clinical signs and gross pathology of these 3 viruses. Reported experimental infections showed the temperature dependency and potential pathogenicity of these viruses for eels and other fish species. In addition to the published literature, an overview of the isolation of pathogenic viruses from wild and farmed A. anguilla in the Netherlands during the past 2 decades is given. A total of 249 wild A. anguilla, 39 batches of glass eels intended for farming purposes, and 239 batches of farmed European eels were necropsied and examined virologically. AngHV1 was isolated from wild A. anguilla yellow and silver eels from the Netherlands from 1998 until the present, while EVEX was only found sporadically, and EVE was never isolated. In farmed A. anguilla AngHV1 was also the most commonly isolated virus, followed by EVE and EVEX.
    A multicomponent sugar phosphate sensor system specifically induced in Bacillus cereus during infection of the insect gut
    Song, F. ; Peng, Q. ; Brillard, J. ; Buisson, C. ; Been, M.W.H.J. de; Abee, T. ; Broussolle, V. ; Huang, D. ; Zhang, J. ; Lereclus, D. ; Nielsen-LeRoux, C. - \ 2012
    FASEB Journal 26 (2012)8. - ISSN 0892-6638 - p. 3336 - 3350.
    2-component signal-transduction - gram-positive bacteria - plcr virulence regulon - low-gc-content - escherichia-coli - in-vivo - functional-analysis - histidine kinases - genome sequence - gene-expression
    Using a previously developed Bacillus cereus in vivo expression technology (IVET) promoter trap system, we showed that spsA, a gene of unknown function, was specifically expressed in the larval gut during infection. Search for gut-related compounds inducing spsA transcription identified glucose-6-phosphate (G6P) as an activation signal. Analysis of the spsA-related 5-gene cluster indicated that SpsA is part of a new sugar phosphate sensor system composed of a 2-component system (TCS) encoded by spsR and spsK, and 2 additional downstream genes, spsB and spsC. In B. cereus, American Type Culture Collection (ATCC) 14579, spsRK, and spsABC are separate transcriptional units, of which only spsABC was activated by extracellular G6P. lacZ transcriptional fusions tested in mutant and complemented strains showed that SpsRK, SpsA, and SpsB are essential for the transcription of spsABC. Deletion mutant analysis showed that SpsC is essential for the G6P uptake. gfp-transcriptional fusions showed that these genes are required for host-activated expression, as well. This sugar phosphate sensor and transport system is found in pathogenic Bacillus group and Clostridia bacteria and may be important for host adaptation. Our findings provide new insights into the function of 2-component sensor systems in host-pathogen interactions, specifically in the gut.—Song, F., Peng, Q., Brillard, J., Buisson, C., de Been, M., Abee, T., Broussolle, V., Huang, D., Zhang, J., Lereclus, D., Nielsen-LeRoux, C. A multicomponent sugar phosphate sensor system specifically induced in Bacillus cereus during infection of the insect gut.
    Translational plant proteomics: A perspective
    Agrawal, G.K. ; Pedreschi, R. ; Barkla, B.J. ; Bindschedler, L.V. ; Cramer, R. ; Sarkar, A. ; Renaut, J. ; Job, D. ; Rakwal, R. - \ 2012
    Journal of Proteomics 75 (2012)15. - ISSN 1874-3919 - p. 4588 - 4601.
    2-dimensional gel-electrophoresis - botrytis-cinerea infection - champagne wine proteins - pyrus-communis l. - non-model plants - mass-spectrometry - liquid-chromatography - genome sequence - rice genome - posttranslational modifications
    Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic values of plants, food security and safety, and energy sustainability. In this review, we highlight the substantial progress reached in plant proteomics during the past decade which has paved the way for translational plant proteomics. Increasing proteomics knowledge in plants is not limited to model and non-model plants, proteogenomics, crop improvement, and food analysis, safety, and nutrition but to many more potential applications. Given the wealth of information generated and to some extent applied, there is the need for more efficient and broader channels to freely disseminate the information to the scientific community. This article is part of a Special Issue entitled: Translational Proteomics.
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