Oded Yarden - Academia.edu (original) (raw)

Papers by Oded Yarden

Physiological and Molecular Plant Pathology, 2011

The Fusarium oxysporum f. sp. melonis (FOM) Snt2 transcription factor is related to pathogenesis.... more The Fusarium oxysporum f. sp. melonis (FOM) Snt2 transcription factor is related to pathogenesis. In FOM and Neurospora crassa Dsnt2 strains, hydrogen peroxide-induced SOD activity was impaired. The expression of fe,mn sod genes in the Dsnt2 mutants, was up-regulated following hydrogen peroxide induction, indicative of a mitochondrial function defect. Furthermore, cytochrome-dependent oxidation in FOM and N. crassa was affected, leading to reduced oxygen consumption in the mutants, linking snt2 to regulation of fungal aerobic respiration. This was accompanied by increased expression of an alternative oxidase gene, suggesting the presence of a compensatory mechanism or the potential presence of a direct link between snt2 and regulation of alternative oxidation.

Molecular Microbiology, 2009

Dysfunction of the Neurospora crassa nuclear Dbf2related kinase COT1 leads to cessation of tip ex... more Dysfunction of the Neurospora crassa nuclear Dbf2related kinase COT1 leads to cessation of tip extension and massive induction of new sites of growth. To determine the role phosphorylation plays in COT1 function, we mutated COT1 residues corresponding to positions of highly conserved nuclear Dbf2-related phosphorylation sites. Analyses of the point-mutation cot-1 strains (mimicking non-and constitutively phosphorylated states) indicate the involvement of COT1 phosphorylation in the regulation of hyphal elongation and branching as well as asexual development by altering cell wall integrity and actin organization. Phosphorylation of COT1's activation segment (at Ser417) is required for proper in vitro kinase activity, but has only a limited effect on hyphal growth. In marked contrast, even though phosphorylation of the C-terminal hydrophobic motif (at Thr589) is crucial for all COT1 functions in vivo, the lack of Thr589 phosphorylation did not significantly affect in vitro COT1 kinase activity. Nevertheless, its regulatory role has been made evident by the significant increase observed in COT1 kinase activity when this residue was substituted in a manner mimicking constitutive phosphorylation. We conclude that COT1 regulates elongation and branching in an indepen-dent manner, which is determined by its phosphorylation state. Fig. 5. COT1 is involved in the regulation of conidiation. A. SEM imaging of conidiation in the different mutants. Bar = 20 mm. B. Conidial abundance in the different mutants. C. Abundance of arthroconidia in the different mutants. D. Calcoflour staining of conidial chains of cot-1(S417A) and the myc-cot-1 control. Arrows mark the connective between adjacent conidia. Bar = 10 mm. 980 C. Ziv et al.

Phytopathology, 1993

ABSTRACT Three phenotypes were identified among benomyl-resistant strains of Botrytis cinerea in ... more ABSTRACT Three phenotypes were identified among benomyl-resistant strains of Botrytis cinerea in Israel when tested for sensitivity to carbendazim (M BC) and diethofencarb (NPC): Ben(HR)NPC(S) = highly resistant to MBC (50% effective concentration [EC(50)] > 50 mu g/ml) and sensitive to 0.5 mu g/ml NPC; Ben(MR)NPC(R) = moderately resistant to MBC (10 less than or equal to EC(50) < 20 mu g/ml) and resistant to 10 mu g/ml NPC; and Ben(HR)NPC(R) = highly resistant to MBC and resistant to NPC. A 1-kb fragment of the wild-type gene encoding for beta-tubulin (designated benA) in B. cinerea was cloned and sequenced. The deduced partial amino acid sequence of the B. cinerea beta-tubulin showed a high degree of similarity to beta-tubulins of other filamentous fungi. A polymerase chain reaction approach was used to amplify and sequence 992-bp benA fragments from strains representing the three phenotypes. in the eight Ben(R) strains analyzed, three single base-pair mutations were identified and found to correlate with the different phenotypes: codon 198, encoding glutamic acid in the wild type, was changed to an alanine codon in the Ben(HR)NPC(S) phenotype or to a lysine codon in the Ben(HR)NPC(R) phenotype; codon 200, encoding phenylalanine, was changed to a tyrosine codon in the Ben(MR)NPC(R) phenotype. These mutations were similar to those identified in benomyl-resistant field strains of other phytopathogenic fungi.

Plant Pathology, Mar 1, 1985

ABSTRACT A simple and rapid bioassay for the direct determination of carbendazim residues in soil... more ABSTRACT A simple and rapid bioassay for the direct determination of carbendazim residues in soil was developed. Pellets composed of mixtures of soil (200–500 mg) and agar were placed on an agar medium pre–inoculated with the test organism Penicillium digitatum. After cold pre–incubation followed by incubation at 27°C, the size of the inhibition zone was determined. The lowest detectable concentrations of carbendazim and thiabendazole in a sandy soil were 0.25 and 10 μg/g, respectively. The lowest detectable concentration was higher in heavy soils. In a study of carbendazim degradation in soil, chemical analysis and the pellet bioassay technique yielded similar results. This technique requires only small quantities of soil, without the need for soil extraction.

Canadian Journal of Microbiology, 1995

The considerable industrial interest in the qualitative and quantitative production of polyhydrox... more The considerable industrial interest in the qualitative and quantitative production of polyhydroxyalkanoates in microorganisms has led to the characterization of those synthesized in the nitrogen-fixing bacteria Azospirillum brasilense and Azotobacter paspali. In contrast to some other bacterial species, Azospirillum brasilense does not produce copolymers of hydroxyalkanoates when grown under the different carbon sources assayed, namely n-alkanoic acids, hydroxyalkanoates, and sugars with varying C:N ratios. Rather, only homopolymers of polyhydroxybutyrate were detected, comprising up to 70% of the cell dry mass. No copolymers were detected in Azotobacter paspali. Quantitative analyses of poly(P-hydroxybutyrate) are also presented.

Fungal Genetics and Biology, Apr 30, 1998

European Journal of Biochemistry, Feb 29, 1996

Despite numerous demonstrations of protein degradation in chloroplasts of higher plants, little i... more Despite numerous demonstrations of protein degradation in chloroplasts of higher plants, little is known about the identity of the proteases involved in these reactions. To identify chloroplast proteases by immunological means, we investigated two proteins : ClpP, a protein similar to the proteolytic subunit of the bacterial ATP-dependent Clp protease, for which a gene is found in the chloroplast genome [Maurizi, M. R.. We expressed the clpP gene from rice in Escherichia coli, purified its product, and generated antibodies against the product. Western blot analysis revealed the ClpP protein in different leaf extracts. Analysis of fractionated barley chloroplasts revealed that the protein was associated with the stromal fraction. The expression of ClpP is light independent and tissue specific, as it was found in green and etiolated barley leaves, but not in roots. A second protein, similar to the cyanobacterial protease PrcA, was also detected in chloroplasts. Antibody against this protease recognized proteins in various leaf extracts. When pea chloroplasts were fractionated, the antibody only recognized a stromal protein. The expression of this protein is regulated by light, as it was found in green leaves but not in etiolated leaves. The tissue specificity of PrcA was similar to that of ClpP in that it could not be detected in root extracts.

The Embo Journal, Jun 1, 1992

Neurospora crassa is a filamentous fungus that grows on semisolid media by forming spreading colo... more Neurospora crassa is a filamentous fungus that grows on semisolid media by forming spreading colonies. Mutations at several loci prevent this spreading growth. cot-i is a temperature sensitive mutant of N.crassa that exhibits restricted colonial growth. At temperatures above 32'C colonies are compact while at lower temperatures growth is indistinguishable from that of the wild type. Restricted colonial growth is due to a defect in hyphal tip elongation and a concomitant increase in hyphal branching. We have isolated a genomic cosmid clone containing the wild type allele of cot-i by complementation. Sequence analyses suggested that cot-i encodes a member of the cAMP-dependent protein kinase family. Strains in which we disrupted cot-i are viable but display restricted colonial growth. Duplication, by ectopic integration of a promoter-containing fragment which includes the first one-third (209 codons) of the structural gene, unexpectedly resulted in restricted colonial growth. Our results suggest that an active COTi kinase is required for one or more events essential for hyphal elongation.

Applied Bioinformatics, Feb 1, 2005

managing a local repository of sequence information linked to DNA clones. This tool is designed t... more managing a local repository of sequence information linked to DNA clones. This tool is designed to assist in high-throughput sequence and gene expression projects, providing a link between both types of information. The unique feature of the application is the automation of batch sequence annotation following BLAST ® searches, which is supported by easy-to-use web interfaces. Furthermore, any set of sequences can be annotated against any sequence database. This replaces the need to perform and analyse individual web BLAST ® searches or the need to learn how to produce batch searches and perform analysis in a UNIX ® operating system. BioCloneDB is open-source software that can be installed on Linux or UNIX ® operating systems. To test the application, we used 1400 expressed sequence tags obtained from the filamentous fungus Neurospora crassa. The results were analysed and compared with published results and they show a significant change due to the accumulation of the data in the nr database (ftp://ftp.ncbi.nih.gov/blast/db/). Availability: BioCloneDB is available for academic use along with documentation, screenshots, database scheme and readme files at http://bioclonedb.agri.huji.ac.il/ Contact: Oded Yarden (Oded.Yarden@huji.ac.il)

Journal of Agricultural and Food Chemistry, 2009

Ten beta-trifluoroalkyl aminovinyl ketone derivatives were synthesized, and their inhibitory effe... more Ten beta-trifluoroalkyl aminovinyl ketone derivatives were synthesized, and their inhibitory effects on several phytopathogenic fungi, an oomycete and plants were assessed. The various compounds were fungitoxic at the 10-100 microM range, with (Z)-3-amino-4,4,4-trifluoro-1-(4-chlorophenyl)but-2-en-1-one exhibiting the highest inhibitory effect on most of the test pathogens. Alternaria alternata and Neurospora crassa were the most tolerant and sensitive fungi to the compounds, respectively. We propose that (Z)-3-amino-4,4,4-trifluoro-1-phenylbut-2-en-1-one is the minimal structural requirement for a beta-trifluoroalkyl aminovinyl ketone fungitoxic derivative.

J Nat Prod, 2005

Fractionation of the ethyl acetate extract of a Cladosporium sp., isolated from the Red Sea spong... more Fractionation of the ethyl acetate extract of a Cladosporium sp., isolated from the Red Sea sponge Niphates rowi, yielded a new hexaketide, pandangolide 1a (1), together with its known diastereomer pandangolide 1 (2) and the known iso-cladospolide B (3). The structures of the compounds were determined by 1D and 2D NMR techniques and mass spectrometric data. The absolute configurations of the stereocenters in these compounds were determined by Riguera's method and circular dichroism. a 400 MHz, δ in ppm. b 500 MHz δ in ppm.

Curr Genetics, 1995

A PCR approach, employing the use of degenerate oligonucleotide mixtures, was used to isolate pph... more A PCR approach, employing the use of degenerate oligonucleotide mixtures, was used to isolate pph-1, a type-2A protein phosphatase (catalytic subunit)-encoding gene, from Neurospora crassa. The isolated singlecopy gene is 1327 nucleotides in length, contains four putative introns and encodes a 310 amino-acid polypeptide. pph-1 is located between pdx-1 and col-4 on the right arm of N. crassa linkage group IV. pph-1 transcript levels are highest during the first hours of conidial germination. Failure to obtain viable progeny in which pph-1 had been inactivated via the repeat-induced point (RIP) mutation process, and evidence that nuclei harboring a disrupted pph-1 gene could only be maintained in a heterokaryon, indicated that a functional pph-1 gone is essential for fungal growth. This is the first report providing evidence that inactivation of a single type-2A protein phosphatase gene results in a lethal phenotype in fungi.

Applied and Environmental Microbiology, 2016

Although Mn(2+) is the most abundant substrate of versatile peroxidases (VPs), repression of Pleu... more Although Mn(2+) is the most abundant substrate of versatile peroxidases (VPs), repression of Pleurotus osteatus vp1 expression occurred in Mn(2+) sufficient medium. This seems to be a &amp;quot;biological contradiction&amp;quot;. The aim of this study was to explore the mechanism of direct oxidation by VP1 under Mn(2+)-deficient conditions, as it was found to be the predominant enzyme during fungal growth in the presence of synthetic and natural substrates. The native VP1 was purified and characterized using three substrates: Mn(2+), Orange II (OII) and Reactive Black 5 (RB5), each oxidized by a different active site in the enzyme. While the pH optimum for Mn(2+) oxidation is 5, the optimum pH for direct oxidation of both dyes was found to be 3. Indeed, effective in vivo decolorization occurred in media without addition of Mn(2+) only under acidic conditions. We have determined that Mn(2+) inhibits in vitro the direct oxidation of both OII and RB5 while RB5 stabilizes both Mn(2+) and OII oxidation. Furthermore, OII was found to inhibit the oxidation of both Mn(2+) and RB5. In addition, we could demonstrate that VP1 can cleave OII in two different modes. Under Mn(2+)-mediated oxidation conditions, VP1 was able to cleave the azo-bond only in an asymmetric mode while at the optimum conditions for direct oxidation (absence of Mn(2+) at pH 3) both symmetric and asymmetric cleavages. We concluded that the oxidation mechanism of aromatic compounds by VP1 is controlled by Mn(2+) and pH levels both in the growth medium and in the reaction mixture. Versatile peroxidases 1 (VP1) is a member of the ligninolytic heme peroxidase gene family of the white rot fungus Pleurotus ostreatus and plays fundamental role in biodegradation. This enzyme exhibit versatile nature as it can oxidize different substrate under altered environmental conditions. VPs are highly interesting enzymes due to the fact that they contain unique active sites which are responsible for direct oxidation of various aromatic compounds including lignin, in addition to the well-known Mn(2+) binding active site. This study demonstrates the limits of versatility of P. ostreatus VP1 which harbors multiple active sites, exhibiting a broad range of enzymatic activities, but perform differently under distinct conditions. The versatility of P. ostreatus and its enzymes is an advantageous factor in the fungal ability to adapt to changing environments. This trait expands the possibilities for potential utilization of P. ostreatus and other WRF.

Journal of Natural Products, Mar 1, 2011

The new tetraglycosylceramide neurosporaside (1a) has been isolated from the fungus Neurospora cr... more The new tetraglycosylceramide neurosporaside (1a) has been isolated from the fungus Neurospora crassa. Neurosporaside is a tetraglycosylated glycosphingolipid characterized by a sugar chain unprecedented among natural glycoconjugates. The structure of neurosporaside was elucidated by extensive spectroscopic analysis and microscale degradation analysis, which allowed full structure elucidation using less than 1 mg of compound.

Molecular Plant Pathology, Jun 1, 2011

The soil-borne, asexual fungus Fusarium oxysporum f.sp. melonis (FOM) is a causal agent of muskme... more The soil-borne, asexual fungus Fusarium oxysporum f.sp. melonis (FOM) is a causal agent of muskmelon wilt disease. The current study focused on the most virulent race of FOM-race 1,2. The tagged mutant D122, generated by Agrobacterium tumefaciens-mediated transformation, caused the delayed appearance of initial wilt disease symptoms, as well as a 75% reduction in pathogenicity. D122 was impaired in the gene product homologous to the Snt2-like transcription factor of Schizosaccharomyces pombe. Involvement of snt2 in the early stage of FOM pathogenesis and its requirement for host colonization were confirmed by targeted disruption followed by quantitative reverse transcription-polymerase chain reaction analysis of snt2 expression in planta. Δsnt2 mutants of FOM and Neurospora crassa exhibited similar morphological abnormalities, including a reduction in conidia production and biomass accumulation, slower vegetative growth and frequent hyphal septation. In N. crassa, snt-2 is required for sexual development, as Δsnt-2 mutants were unable to produce mature perithecia. Suppressive subtraction hybridization analysis of the D122 mutant versus wild-type isolate detected four genes (idi4, pdc, msf1, eEF1G) that were found previously in association with the target of rapamycin (TOR) kinase pathway. Expression of the autophagy-related idi4 and pdc genes was found to be up-regulated in the Δsnt2 FOM mutant. In N. crassa, disruption of snt-2 also conferred a significant over-expression of idi4.

Mol Gen Genet, 1996

Colletotrichum trifolii is a fungal pathogen which is responsible for anthracnose disease of alfa... more Colletotrichum trifolii is a fungal pathogen which is responsible for anthracnose disease of alfalfa. To initiate research on molecular communication in this fungus, a kinase-encoding gene (TB3) and the corresponding cDNA were cloned and sequenced. The deduced amino acid sequence of TB3 closely resembles that of a Neurospora crassa serine/threonine protein kinase, COT1, required for hyphal elongation and branching. The C-terminal catalytic domains of TB3 and COT1 are highly conserved but the N-terminal regions are divergent, particularly in the homopolymeric glutamine repeats of TB3. Northern analysis indicated that TB3 expression was highest 1 h after inducing conidial germination and 1 h before germ tubes were first observed. Expression of TB3 transcripts returned to constitutive levels by 4 h after induction of germination. TB3 complemented the cot-1 mutant of Neurospora crassa, demonstrating the functional conservation of this kinase between a pathogenic and a saprophytic fungus.

Molecular Plant Microbe Interactions Mpmi, Oct 1, 2003

Plant pathology has made significant progress over the years, a process that involved overcoming ... more Plant pathology has made significant progress over the years, a process that involved overcoming a variety of conceptual and technological hurdles. Descriptive mycology and the advent of chemical plant-disease management have been followed by biochemical and physiological studies of fungi and their hosts. The later establishment of biochemical genetics along with the introduction of DNA-mediated transformation have set the stage for dissection of gene function and advances in our understanding of fungal cell biology and plant-fungus interactions. Currently, with the advent of high-throughput technologies, we have the capacity to acquire vast data sets that have direct relevance to the numerous subdisciplines within fungal biology and pathology. These data provide unique opportunities for basic research and for engineering solutions to important agricultural problems. However, we also are faced with the challenge of data organization and mining to analyze the relationships between fungal and plant genomes and to elucidate the physiological function of pertinent DNA sequences. We present our perspective of fungal biology and agriculture, including administrative and political challenges to plant protection research.

Bba Protein Struct Mol Enzym, 1998

The gene and cDNA of a novel protein phosphatase were cloned from Neurospora crassa. The pzl-1 ge... more The gene and cDNA of a novel protein phosphatase were cloned from Neurospora crassa. The pzl-1 gene encompasses three introns and is localized to the left arm of chromosome I between cyt-21 and Fsr-12. It encodes a protein of 58.3 kDa containing a Ser/Pro rich N-terminal segment, and a C-terminal domain that is similar to the catalytic subunit of type 1 protein phosphatases. The first 51 amino acid residues, including a potential N-myristoylation site, as well as the C-terminal domain (about 300 residues) have a high level of sequence identity with yeast PPZ phosphatases. However, residues 52–208 do not share high similarity with other proteins. The mRNA of pzl-1 was detected in all phases of asexual development of the filamentous fungus.