Substrate-specific transcription of the enigmatic GH61 family of the pathogenic white-rot fungus Heterobasidion irregulare during growth on lignocellulose

The GH61 represents the most enigmatic Glycoside Hydrolase family (GH) regarding enzymatic activity and importance in cellulose degradation. Heterobasidion irregulare is a necrotizing pathogen and white-rot fungus that causes enormous damages in conifer forests. The genome of H. irregulare allowed identification of ten HiGH61 genes. qRT-PCR analysis separate the HiGH61 members into two groups; one that show up regulation on lignocellulosic substrates (HiGH61A, HiGH61B, HiGH61D, HiGH61G, HiGH61H, and HiGH61I) and a second showing either down-regulation or constitutive expression (HiGH61C, HiGH61E, HiGH61F, and HiGH61J). HiGH61H showed up to 17,000-fold increase on spruce heartwood suggesting a pivotal role in cellulose decomposition during saprotrophic growth. Sequence analysis of these genes reveals that all GH61s except HiGH61G possess the conserved metal-binding motif essential for activity. The sequences also divide into groups having either an insert near the N terminus or an insert near the second catalytic histidine, which may represent extensions of the substrate-binding surface. Three of the HiGH61s encode cellulose-binding modules (CBM1). Interestingly, HiGH61H and HiGH61I having CBM1s are up-regulated on pure cellulose. There was a common substrate-specific induction patterns of the HiGH61s with several reference cellulolytic and hemicellulolytic GHs, this taken together with their low transcript levels on media lacking lignocellulose, reflect the concerted nature of cell wall polymer degradation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00253-012-4206-x) contains supplementary material, which is available to authorized users

Interaction of bacteriophage P1 with an epiphytic Pantoea agglomerans strain—the role of the interplay between various mobilome elements

P1 is a model, temperate bacteriophage of the 94 kb genome. It can lysogenize representatives of the Enterobacterales order. In lysogens, it is maintained as a plasmid. We tested P1 interactions with the biocontrol P. agglomerans L15 strain to explore the utility of P1 in P. agglomerans genome engineering. A P1 derivative carrying the Tn9 (cmR) transposon could transfer a plasmid from Escherichia coli to the L15 cells. The L15 cells infected with this derivative formed chloramphenicol-resistant colonies. They could grow in a liquid medium with chloramphenicol after adaptation and did not contain prophage P1 but the chromosomally inserted cmR marker of P1 Tn9 (cat). The insertions were accompanied by various rearrangements upstream of the Tn9 cat gene promoter and the loss of IS1 (IS1L) from the corresponding region. Sequence analysis of the L15 strain genome revealed a chromosome and three plasmids of 0.58, 0.18, and 0.07 Mb. The largest and the smallest plasmid appeared to encode partition and replication incompatibility determinants similar to those of prophage P1, respectively. In the L15 derivatives cured of the largest plasmid, P1 with Tn9 could not replace the smallest plasmid even if selected. However, it could replace the smallest and the largest plasmid of L15 if its Tn9 IS1L sequence driving the Tn9 mobility was inactivated or if it was enriched with an immobile kanamycin resistance marker. Moreover, it could develop lytically in the L15 derivatives cured of both these plasmids. Clearly, under conditions of selection for P1, the mobility of the P1 selective marker determines whether or not the incoming P1 can outcompete the incompatible L15 resident plasmids. Our results demonstrate that P. agglomerans can serve as a host for bacteriophage P1 and can be engineered with the help of this phage. They also provide an example of how antibiotics can modify the outcome of horizontal gene transfer in natural environments. Numerous plasmids of Pantoea strains appear to contain determinants of replication or partition incompatibility with P1. Therefore, P1 with an immobile selective marker may be a tool of choice in curing these strains from the respective plasmids to facilitate their functional analysis

Assessment of Potato Tuber Resistance Against Dry Rot

Fungi of the genus Fusarium display inter- and intraspecific variation in their pathogenic capabilities. Although no resistance genes against dry rot have been identified, some indications of the possible defense responses are noticeable, since a single isolate might cause lesions of various sizes when infecting tubers of different potato cultivars. Pathogenicity tests are routinely used to assess potato tubers resistance against dry rot; a setup of pathogenicity test performed at Młochów Research Center is described in this work

Effect of photoperiod on potato biology

Cykl życiowy wielu roślin powiązany jest z porami roku, których zmiana sygnalizowana jest przez zmieniającą się długość dnia. Roślinne fotoreceptory, reagujące na światło foto¬morfogenetycznie aktywne lub jego brak, umożliwiają roślinom odbiór sygnału o zmieniających się warunkach. Długość fotoperiodu jest istotnym czynnikiem regulującym procesy rozwojowe również w przypadku ziemniaka. W przeglądzie podsumowano wiedzę z dotychczasowych badań nad wpływem fotoperiodu na biologię rodzaju Solanum. Począwszy od udomowiania ziemniaka w odmiennych od miejsca pochodzenia szerokościach geograficznych, omówiono wpływ długości dnia na kwitnienie, tuberyzację oraz odporność na Phytophthora infestans, organizm powodujący najważniejszą pod względem ekonomicznym chorobę ziemniaka. Wybrane procesy życiowe stanowią najistotniejsze elementy biologii ziemniaka, ponieważ dotyczą jego zdolności do przetrwania i dalszego rozmnażania w zróżnicowanym środowisku.The life cycle of many plants is connected with seasons and their change is perceived by a day-length change. Plant photoreceptors responding to the presence of photomorphogenetically active light, mainly phytochromes, let plants perceive changing conditions. The length of photoperiod is also an essential factor in case of potato. In this review the knowledge obtained from previous studies on the influence of photoperiod on Solanum species was summarized. Beginning with domestication of a potato in latitudes different than the place of origin, an influence of a day-length on flowering, tuberization and resistance to Phytophthora infestans was described. The life processes chosen in this review are among the most important ones, because they allow surviving and further reproducing of potato in diverse environments

Isolation, Identification and Preservation of Fusarium SPP. Causing Dry Rot of Potato Tubers

Fungi of the genus Fusarium cause dry rot, a potato disease which develops during long-term storage of tubers. The disease-inducing capabilities differ among Fusarium spp., but may also vary within species uni-versally considered main dry rot agents. Identification of Fusarium spp. present on diseased tubers in a surveyed area can help minimize crop losses and mycotoxin contamination by, for example, applying proper fungicides or planning crop rotation. Here, we present a procedure of obtaining single spore colonies of Fusarium spp. from potato tubers infected by dry rot, their identification using molecular methods and ways of preservation

Quantitative Trait Loci for Resistance to Potato Dry Rot Caused by Fusarium sambucinum

Tuber dry rot is an important disease of potato caused by soil and seed-borne pathogens of the Fusarium genus leading to losses that may reach 60% of the yield. The goal of this work was to study the inheritance of the dry rot resistance in two diploid potato hybrid populations (11–36 and 12–3) with complex pedigrees, including several wild Solanum spp. We used an aggressive isolate of F. sambucinum for phenotyping both progenies, parents, and standard potato cultivars in laboratory tuber tests, in three subsequent years. The QTL for dry rot resistance were mapped by interval mapping on existing genetic maps of both mapping populations. The most important and reproducible QTL for this trait was mapped on chromosome I and additional year- and population-specific QTL were mapped on chromosomes II, VII, IX, XI, and XII, confirming polygenic control of this resistance. This is the first study mapping the loci affecting tuber dry rot resistance in potato genome that can contribute to better understanding of potato-F. sambucinum interaction and to more efficient breeding of resistant potato cultivars

Resistance of Phytophthora infestans in three Solanum nigrum F3 families

Solanum nigrum is a self-pollinating, hexaploid weed and one of a few Solanaceae species native to Europe. It used to be described as a non-host  for Phytophthora infestans. However, now it is known that, like its distant relatives: potato (Solanum tuberosum L.) and tomato (Solanum lycopersicum L.), S. nigrum can suffer from potato late blight caused by this pathogen. Both susceptible and resistant S. nigrum genotypes  have been previously identified and inheritance of resistance originating from one accession has been described based on population of F2 plants and 15 F3 lines. The goal of this study was to evaluate resistance of three families of F3 lines, originating from crosses between  a susceptible and three different  resistant  S. nigrum accessions  followed  by two self-pollinations.  Parental  acces- sions were tested for the spectrum of late blight resistance against 48 P. infestans isolates. The three families consisted of 106, 96 and 115 F3 lines, respectively, and from each line 20 plants were tested for resistance to P. infestans. Laboratory  detached leaf assays were  performed in two dates and two replications  of three leaves  each.  Segregation  of the trait  within the line  allowed  us  to distinguish hetero- and homozygous lines. In one F3 family, the ratio of resistant homozygotes: heterozygotes: susceptible  homozygotes  was 1:2:1, indicating  that  a single  gene is  most likely  underlying  the late blight resistance in this case. In the other two, observed segregations of the trait significantly deviated from this model suggesting more complex inheritance patterns

eQTL mapping of the 12S globulin cruciferin gene PGCRURSE5 as a novel candidate associated with starch content in potato tubers

Abstract Tuber starch content (TSC) is a very important trait in potato (Solanum tuberosum L.). This study is the first to use expression quantitative trait loci (eQTL) mapping of transcript-derived markers for TSC in potato. Thirty-four differentially expressed genes were selected by comparing the RNA-seq data of contrasting bulked segregants. For the 11 candidate genes, we determined their relative expression levels across the segregating diploid potato population using RT-qPCR. We detected 36 eQTL as candidate genes distributed on all twelve potato chromosomes, and nine of them overlapped with QTL for TSC. Peaks for two eQTL, eAGPaseS-a and ePGRCRURSE5, were close to the corresponding loci of the large subunit of ADP-glucose pyrophosphorylase (AGPaseS-a) and the 12S globulin cruciferin gene (PGCRURSE5), respectively. The eQTL peaks for AGPaseS-a and PGRCRURSE5 explained 41.0 and 28.3% of the phenotypic variation at the transcript level. We showed the association of the DNA markers for AGPaseS-a and PGRCRURSE5 with QTL for TSC, and significant correlation between the expression level of PGRCRURSE5 and TSC. We did not observe a significant correlation between the expression level of AGPaseS-a and TSC. We concluded that the cruciferin gene PGRCRURSE5 is a novel candidate involved in the regulation of starch content in potato tubers