NiaA, the structural nitrate reductase gene of Phytophthora infestans: isolation, characterization and expression analysis in Aspergillus nidulans

Analysis of nitrogen source assimilation in industrial strains of Aspergillus oryzae

Nitrogen source assimilation is important for the biological functions of fungi, and its pathway has been deeply studied. Aspergillus oryzae mutants defective in nitrogen source assimilation are known to grow poorly on Czapek-Dox (CD) medium. In this study, we found an industrial strain of A. oryzae that grew very poorly on a CD medium containing sodium nitrate as a nitrogen source. We used media with various nitrogen components to examine the steps affecting the nitrogen source assimilation pathway of this strain. The strain grew well on the CD medium supplied with nitrite salt or ammonium salt, suggesting that the strain was defective in nitrate assimilation step. To ascertain the gene causing the defect of nitrate assimilation, a gene expression vector harboring either niaD or crnA of A. oryzae RIB40 was introduced into the industrial strain. The industrial strain containing the crnA vector recovered its growth. This is the first report that a mutation of crnA causes poor growth on CD medium in an industrial strain of A. oryzae, and crnA can be used as a transformation marker for crnA deficient strains.

Nitric oxide signalling in plant interactions with pathogenic fungi and oomycetes

Nitric oxide (NO) and reactive nitrogen species have emerged as crucial signalling and regulatory molecules across all organisms. In plants, fungi, and fungi-like oomycetes, NO is involved in the regulation of multiple processes during their growth, development, reproduction, responses to the external environment, and biotic interactions. It has become evident that NO is produced and used as a signalling and defence cue by both partners in multiple forms of plant interactions with their microbial counterparts, ranging from symbiotic to pathogenic modes. This review summarizes current knowledge on the role of NO in plant-pathogen interactions, focused on biotrophic, necrotrophic, and hemibiotrophic fungi and oomycetes. Actual advances and gaps in the identification of NO sources and fate in plant and pathogen cells are discussed. We review the decisive role of time- and site-specific NO production in germination, oriented growth, and active penetration by filamentous pathogens of the host tissues, as well in pathogen recognition, and defence activation in plants. Distinct functions of NO in diverse interactions of host plants with fungal and oomycete pathogens of different lifestyles are highlighted, where NO in interplay with reactive oxygen species governs successful plant colonization, cell death, and establishment of resistance.

Gene Expression and Silencing Studies in Phytophthora infestans Reveal Infection-Specific Nutrient Transporters and a Role for the Nitrate Reductase Pathway in Plant Pathogenesis

To help learn how phytopathogens feed from their hosts, genes for nutrient transporters from the hemibiotrophic potato and tomato pest Phytophthora infestans were annotated. This identified 453 genes from 19 families. Comparisons with a necrotrophic oomycete, Pythium ultimum var. ultimum, and a hemibiotrophic fungus, Magnaporthe oryzae, revealed diversity in the size of some families although a similar fraction of genes encoded transporters. RNA-seq of infected potato tubers, tomato leaves, and several artificial media revealed that 56 and 207 transporters from P. infestans were significantly up- or down-regulated, respectively, during early infection timepoints of leaves or tubers versus media. About 17 were up-regulated >4-fold in both leaves and tubers compared to media and expressed primarily in the biotrophic stage. The transcription pattern of many genes was host-organ specific. For example, the mRNA level of a nitrate transporter (NRT) was about 100-fold higher during mid-infection in leaves, which are nitrate-rich, than in tubers and three types of artificial media, which are nitrate-poor. The NRT gene is physically linked with genes encoding nitrate reductase (NR) and nitrite reductase (NiR), which mobilize nitrate into ammonium and amino acids. All three genes were coregulated. For example, the three genes were expressed primarily at mid-stage infection timepoints in both potato and tomato leaves, but showed little expression in potato tubers. Transformants down-regulated for all three genes were generated by DNA-directed RNAi, with silencing spreading from the NR target to the flanking NRT and NiR genes. The silenced strains were nonpathogenic on leaves but colonized tubers. We propose that the nitrate assimilation genes play roles both in obtaining nitrogen for amino acid biosynthesis and protecting P. infestans from natural or fertilization-induced nitrate and nitrite toxicity.

Little is known of how plant pathogens adapt to different growth conditions and host tissues. To understand the interaction between the filamentous eukaryotic microbe Phytophthora infestans and its potato and tomato hosts, we mined the genome for genes encoding proteins involved in nutrient uptake and measured their expression in leaves, tubers, and three artificial media. We observed dynamic changes between the growth conditions, and identified transporters expressed mainly in the biotrophic stage, leaves, tubers, or artificial media. When we blocked the expression of a nitrate transporter and two other genes involved in assimilating nitrate, we observed that those genes were required for successful colonization of nitrate-rich leaves but not nitrate-poor tissues, and that nitrate had become toxic to the silenced strains. We therefore hypothesize that the nitrate assimilation pathway may help the pathogen use inorganic nitrogen for nutrition and/or detoxify nitrate when its levels may become damaging.

Phylogenetic relationships of Phytophthora andina, a new species from the highlands of Ecuador that is closely related to the Irish potato famine pathogen Phytophthora infestans

Phylogenetic relationships of Phytophthora infestans sensu lato in the Andean highlands of South America were examined. Three clonal lineages (US-1, EC-1, EC-3) and one heterogeneous lineage (EC-2) were found in association with different host species in genus Solanum. The EC-2 lineage includes two mitochondrial (mtDNA) haplotypes, Ia and Ic. Isolates of P. infestans sensu lato EC-2 fit the morphological description of P. infestans but are different from any genotypes of P. infestans described to date. All isolates of P. infestans sensu lato from Ecuador were amplified by a P. infestans specific primer (PINF), and restriction fragment length patterns were identical in isolates amplified with ITS primers 4 and 5. The EC-1 clonal lineage of P. infestans sensu lato from S. andreanum, S. columbianum, S. paucijugum, S. phureja, S. regularifolium, S. tuberosum and S. tuquerense was confirmed to be P. infestans based on sequences of the cytochrome oxidase I (cox I) gene and intron 1 of ras gene. The EC-2 isolates with the Ic haplotype formed a distinct branch in the same clade with P. infestans and P. mirabilis, P. phaseoli and P. ipomoeae for both cox I and ras intron 1 phylogenies and were identified as the newly described species P. andina. Ras intron 1 sequence data suggests that P. andina might have arisen via hybridization between P. infestans and P. mirabilis.

Phytophthora infestans-triggered response of growth- and defense-related genes in potato cultivars with different levels of resistance under the influence of nitrogen availability

The effects of high and low N concentrations on the Solanum tuberosum-Phytophthora infestans interaction were studied in the potato cultivars Bettina, New York 121, Indira and Arkula, which exhibited different levels of resistance. Aboveground biomass and Chl and N content were significantly higher in all cultivars grown in higher N environments, while C:N ratios were lower, confirming successful application of N. High availability of N significantly increased susceptibility of three of the four potato cultivars, and amounts of pathogen within the infected leaflets determined in a quantitative real-time reverse transcriptase-polymerase chain reaction reflected this. Differential gene expression of P. infestans-induced and -repressed genes derived from three subtracted cDNA libraries at 0, 24, 48 and 72 h post-inoculation was studied in parallel. P. infestans attack led to an induction of defense-related and at the same time repression of growth-related potato genes mainly encoding photosynthetic genes. High N supply led to higher transcript abundance of photosynthetic genes such as Chl a/b-binding protein and ribulose bisphosphate carboxylase. N-dependent suppression of defense-related compounds in absence of the pathogen was not observed. Better N nutrition appeared to allow the plants to invest more resources in defense reactions.

Phylogenetic Analysis of Proteins Associated in the Four Major Energy Metabolism Systems: Photosynthesis, Aerobic Respiration, Denitrification, and Sulfur Respiration

The four electron transfer energy metabolism systems, photosynthesis, aerobic respiration, denitrification, and sulfur respiration, are thought to be evolutionarily related because of the similarity of electron transfer patterns and the existence of some homologous proteins. How these systems have evolved is elusive. We therefore conducted a comprehensive homology search using PSI-BLAST, and phylogenetic analyses were conducted for the three homologous groups (groups 1-3) based on multiple alignments of domains defined in the Pfam database. There are five electron transfer types important for catalytic reaction in group 1, and many proteins bind molybdenum. Deletions of two domains led to loss of the function of binding molybdenum and ferredoxin, and these deletions seem to be critical for the electron transfer pattern changes in group 1. Two types of electron transfer were found in group 2, and all its member proteins bind siroheme and ferredoxin. Insertion of the pyridine nucleotide disulfide oxidoreductase domain seemed to be the critical point for the electron transfer pattern change in this group. The proteins belonging to group 3 are all flavin enzymes, and they bind flavin adenine dinucleotide (FAD) or flavin mononucleotide (FMN). Types of electron transfer in this group are divergent, but there are two common characteristics. NAD(P)H works as an electron donor or acceptor, and FAD or FMN transfers electrons from/to NAD(P)H. Electron transfer functions might be added to these common characteristics by the addition of functional domains through the evolution of group 3 proteins. Based on the phylogenetic analyses in this study and previous studies, we inferred the phylogeny of the energy metabolism systems as follows: photosynthesis (and possibly aerobic respiration) and the sulfur/nitrogen assimilation system first diverged, then the sulfur/nitrogen dissimilation system was produced from the latter system.

Characterization of the glucose-6-phosphate isomerase gene in Phytophthora infestans reveals the presence of multiple alleles

Glucose-6-phosphate isomerase (GPI) plays a key role in both glycolysis and gluconeogenesis. Isoforms of GPI are common, and therefore, its isozyme pattern is widely used to characterize isolates of Phytophthora infestans. Despite the importance of GPI in P. infestans studies, the gene encoding this enzyme has not yet been characterized. Furthermore, it has been suggested that P. infestans contains multiple copies of the gene but this hypothesis remains to be demonstrated. We have cloned and characterized GPI in various isolates of P. infestans as well as in several species of the genus Phytophthora. The gene contains 1671bp and encodes a protein with a predicted molecular weight of 60.8kDa. Multiple different alleles were identified and Southern analysis indicated certain P. infestans isolates carry several copies of the gene. Phylogenetic analysis revealed that P. infestans GPI is most closely related to sequences from Toxoplasma gondii, Arabidopsis thaliana, and Clarkia lewisii.

Genetic Structure of Peruvian Populations of Phytophthora infestans

ABSTRACT Isolates of the late blight pathogen Phytophthora infestans (n = 327) from the central to southern Peruvian Andes were systematically collected in 1997 to 1999 and analyzed to determine the pathogen's population structure at its host's center of diversity. No isolates of the A2 mating type were detected. Cluster analysis of DNA fingerprinting data indicated that the collection consisted of five major groups that were interpreted to be clonal lineages. Two of the lineages (US-1 and EC-1) have been previously described, and three (PE-3, 5, and 6) are described here for the first time. Collections from three areas in the central Peruvian Andes, including two key sites used in an international potato breeding program, consisted of isolates of the EC-1 lineage, which has been reported to dominate the pathogen population in Andean countries to the north of Peru. The collections from Cusco and Puno were more diverse. More than one lineage was detected in 10 of the 20 fields sampled in Cusco. Data on virulence, metalaxyl sensitivity, and band data for allozymes, mitochondrial DNA, and ipiB1 suggested that PE-3 may have been produced through recombination events between US-1 and EC-1. Restriction fragment length polymorphism and amplified fragment length polymorphism marker data were not consistent with this hypothesis.

Cloning and characterization of sulfite dehydrogenase, two c-type cytochromes, and a flavoprotein of Paracoccus denitrificans GB17: essential role of sulfite dehydrogenase in lithotrophic sulfur oxidation

A 13-kb genomic region of Paracoccus dentrificans GB17 is involved in lithotrophic thiosulfate oxidation. Adjacent to the previously reported soxB gene (C. Wodara, S. Kostka, M. Egert, D. P. Kelly, and C. G. Friedrich, J. Bacteriol. 176:6188-6191, 1994), 3.7 kb were sequenced. Sequence analysis revealed four additional open reading frames, soxCDEF. soxC coded for a 430-amino-acid polypeptide with an Mr of 47,339 that included a putative signal peptide of 40 amino acids (Mr of 3,599) with a RR motif present in periplasmic proteins with complex redox centers. The mature soxC gene product exhibited high amino acid sequence similarity to the eukaryotic molybdoenzyme sulfite oxidase and to nitrate reductase. We constructed a mutant, GBsoxC delta, carrying an in-frame deletion in soxC which covered a region possibly coding for the molybdenum cofactor binding domain. GBsoxC delta was unable to grow lithoautotrophically with thiosulfate but grew well with nitrate as a nitrogen source or as an electron acceptor. Whole cells and cell extracts of mutant GBsoxC delta contained 10% of the thiosulfate-oxidizing activity of the wild type. Only a marginal rate of sulfite-dependent cytochrome c reduction was observed from cell extracts of mutant GBsoxC delta. These results demonstrated that sulfite dehydrogenase was essential for growth with thiosulfate of P. dentrificans GB17. soxD coded for a periplasmic diheme c-type cytochrome of 384 amino acids (Mr of 39,983) containing a putative signal peptide with an Mr of 2,363. soxE coded for a periplasmic monoheme c-type cytochrome of 236 amino acids (Mr of 25,926) containing a putative signal peptide with an Mr of 1,833. SoxD and SoxE were highly identical to c-type cytochromes of P. denitrificans and other organisms. soxF revealed an incomplete open reading frame coding for a peptide of 247 amino acids with a putative signal peptide (Mr of 2,629). The deduced amino acid sequence of soxF was 47% identical and 70% similar to the sequence of the flavoprotein of flavocytochrome c of Chromatium vinosum, suggesting the involvement of the flavoprotein in thiosulfate oxidation of P. denitrificans GB17.

Sequence analysis and expression of the Penicillium chrysogenum nitrate reductase encoding gene (niaD)

The nitrate reductase gene (niaD) of the filamentous fungus Penicillium chrysogenum encodes a protein of 864 amino acids. The derived protein sequence shows 78% and 72% sequence identity to the corresponding Aspergillus niger and A. nidulans proteins, respectively. The coding region of the Penicillium gene is interrupted by six small introns, as deduced by comparison with the niaD sequences of A. niger and A. nidulans, whereby the positions of the introns are perfectly conserved between these three fungal genes. Northern blot analysis indicated a 2.8 kb transcript and showed that expression of this gene is controlled at the level of mRNA accumulation depending on both induction by nitrate and nitrogen metabolite derepression. Induction of transcription of niaD was found to be paralleled by expression of the major nitrogen regulatory gene nre.

Cloning and characterization of the nitrate reductase-encoding gene from Chlorella vulgaris: structure and identification of transcription start points and initiator sequences

The reduction of nitrate to nitrite catalyzed by nitrate reductase (NR) is considered to be the rate-limiting and regulated step of nitrate assimilation, a major metabolic pathway occurring in a wide range of organisms which in turn supply the nutritional nitrogen requirements for other forms of life. Chlorella vulgaris NR mRNA levels are very responsive to changes in nitrogen source. In the presence of ammonia as the sole nitrogen source, under repressed conditions, NR mRNA is undetectable. Under inducing conditions, the removal of ammonia and addition of nitrate, rapid NR mRNA synthesis occurs. We are studying the elements involved in regulating the expression of this important gene. Two overlapping genomic clones (NRS1 and NR5') were isolated from a cosmid library. The two clones were sequenced and their sequences were aligned with that of a full-length NR cDNA. The gene is approximately 8 kb long and consists of 19 exons and 18 introns. Unlike NR isolated from other species, the exons which code for the functional domains of C. vulgaris are separated by introns. Two transcription start points (tsp) were identified and each is surrounded by potential initiator sequences. No TATA, CAAT or GC-rich promoter elements were located. A time course of NR induction revealed that while transcription initiation from one tsp remains at a constant level from the point of induction through steady state, the level of initiation from another tsp is high upon induction, but decreases as steady state is attained.