3,354 research outputs found
Neurospora 2018 - Program and Abstracts
Program and abstracts from Neurospora 2018, October 18-2
Regulation of stress induced metabolic rearrangements in plants : from model species to crops
In nature, plants are exposed to continuous changes in the environment. To ensure their growth and survival, plants have evolved intrincate molecular machinery that allows rapid adjustments in cellular functions in response to a variety of biotic and abiotic cues. Mechanisms that integrate stress-induced signals include cascades of protein kinases and phosphatases, which mediate and direct the signals to elicit appropriate cellular responses. Among defensive measures, changes in the contents of specialized metabolites play an important role in plant-environment interactions. Plant-derived specialized metabolites are of great value to humans, since they offer nutritional benefits and a rich resource of raw material for pharmaceutical industries. The aim of this doctoral dissertation was therefore to elucidate how environmental changes affect metabolic rearrangements in the model plant Arabidopsis thaliana, and to translate this knowledge into applications on crop species. Work on Arabidopsis thaliana identified protein phosphatase 2A as an important regulator of the activated methyl cycle and the associated glucosinolate metabolism, more specifically the formation of a specialized metabolite called 4-methoxy-indol-3-yl-methyl glucosinolate (4MO-I3M GSL). Further analysis with kale (Brassica oleracea convar. acephala) varieties revealed that formation of specific health-promoting glucosinolates, including 2-phenylethyl glucosinolate (2PE GSL) and 4-methylsulfinyl butenyl (4MSB GSL) could be significantly influenced by light conditions in brassica crops. Collectively, the findings highlighted that plant specialized metabolism is highly responsive to environmental factors, and that exposure to potentially stressful growth light conditions could be utilized to improve the nutritional value of crops.Kasvit altistuvat luonnossa kasvaessaan alati vaihteleville kasvuympÀristön muutoksille. Kasveille on kuitenkin evoluution kuluessa kehittynyt molekyylitason mekanismeja, joiden avulla ne voivat sopeuttaa aineenvaihduntaansa vallitsevien olosuhteiden mukaisesti. Erityisesti proteiinikinaasien ja -fosfataasien vÀlittÀmÀt soluviestinnÀn signaalit ovat tÀrkeitÀ kasvien elintoimintoja sÀÀteleviÀ tekijöitÀ. Erilaisten kemiallisten suojayhdisteiden kertyminen kasvin lehtiin taas on tyypillinen sopeutumisvaste, joka havaitaan ympÀristöstressille altistuneissa kasveissa. Monet kasvien suojayhdisteet ovat arvokkaita myös ihmiselle, sillÀ ne voivat vaikuttaa syötÀvien kasvien ravitsemukselliseen laatuun tai toimivat raaka-aineina lÀÀketeollisuudessa. TÀmÀn vÀitöskirjan tavoitteena oli kasvibiologian mallikasvina tunnettua lituruohoa (Arabidopsis thaliana) hyödyntÀen selvittÀÀ miten ympÀristössÀ tapahtuvat muutokset vaikuttavat kasvien aineenvaihduntaan. LisÀksi tutkimuksessa etsittiin keinoja soveltaa tutkimustietoa hyötykasvien viljelyyn liittyvissÀ sovelluksissa. Lituruoholla tehty työ osoitti, ettÀ proteiinifosfataasi 2A sÀÀtelee kasvien metyylisykliÀ ja siihen liittyvÀÀ glukosinolaattiyhdisteiden biosynteesiÀ. Lehtikaaleilla (Brassica oleracea convar. acephala) suoritetut kokeet puolestaan osoittivat, ettÀ kasvun aikana vallitsevat valo-olosuhteet muokkaavat kaalikasvien glukosinolaattikoostumusta. Erityisesti kirkkaan valon havaittiin lisÀÀvÀn tiettyjen terveyttÀ edistÀvien glukosinolaattiyhdisteiden kertymistÀ lehtikaalien lehtiin. Tutkimus osoitti, ettÀ kasvien aineenvaihduntakoneisto reagoi herkÀsti vallitsevissa olosuhteissa tapahtuviin muutoksiin, ja ettÀ kasvien tarkoituksellinen altistaminen valostressille voisi toimia työkaluna lehtimÀisten vihannesten terveellisyyden parantamiseksi. Tutkimustiedon hyödyntÀminen voi tulevaisuudessa edesauttaa kasvien ravitsemuksellisen arvon muokkausta ja ekologisesti kestÀvien viljelytekniikoiden kehitystÀ
To Gibberellins and Beyond! Surveying the Evolution of (Di)Terpenoid Metabolism
The diterpenoids are classically defined by their composition, four isoprenyl units (20 carbons), and are generally derived from [E,E,E]-geranylgeranyl diphosphate (GGPP). Such metabolism seems to be ancient and has been extensively diversified, with ~12,000 diterpenoid natural products known. Particularly notable are the gibberellin phytohormones, whose requisite biosynthesis has provided a genetic reservoir giving rise to not only a large super-family of ~7,000 diterpenoids, but to some degree all plant terpenoid natural products. This review focuses on the diterpenoids, particularly the defining biosynthetic characteristics of the major superfamilies defined by the cyclization and/or rearrangement of GGPP catalyzed by diterpene synthases/ cyclases, although some discussion also is provided of the important subsequent elaboration in those few cases where molecular genetic information is available. In addition, the array of biological activity providing the selective pressure driving the observed gene family expansion and diversification, along with biosynthetic gene clustering, will be discussed as well
The MSDIN family in amanitin-producing mushrooms and evolution of the prolyl oligopeptidase genes
The biosynthetic pathway for amanitins and related cyclic peptides in deadly Amanita (Amanitace ae) mushrooms represents the first known ribosomal cyclic peptide pathway in the Fungi. Amanitins are found outside of the genus in distantly related agarics Galerina (Strophariaceae) and Lepiota (Agaricaceae). A long-standing question in the field persists: why is this pathway present in these phylogenetically disjunct agarics? Two deadly mushrooms, A. pallidorosea and A. subjunquillea, were deep sequenced, and sequences of biosynthetic genes encoding MSDINs (cyclic peptide presursor) and prolyl oligopeptidases (POPA and POPB) were obtained. The two Amanita species yielded 20 and 18 MSDINs, respectively. In addition, two MSDIN sequences were cloned from L. brunneoincarnata basidiomes. The toxin MSDIN genes encoding amatoxins or phallotoxins from the three genera were compared, and a phylogenetic tree constructed. Prolyl oligopeptidase B (POPB), a key enzyme in the biosynthetic pathway, was used in phylogenetic reconstruction to infer the evolutionary history of the genes. Phylogenenies of POPB and POPA based on both coding and amino acid sequences showed very different results: while POPA genes clearly reflected the phylogeny of the host species, POPB did not; strikingly, it formed a well supported monophyletic clade, despite that the species belong to different genera in disjunct families. POPA, a known house-keeping gene, was shown to be restricted in a branch containing on Amanita species and the phylogeny resembled that of those Amanita species. Phylogenetic analyses of MSDIN and POPB genes showed tight coordination and disjunct disdistribution. A POPB gene tree was compared with a corresponding species tree, and distances and substitution rates were compared. The results suggested POPB genes have significant smaller distances and substitution rates were compared. The result suggested POPB genes have significant smaller distances and rates than the house-keeping rpb2, discounting massive gene loss. Under this assumption, the consistently cluster Galerina and Amantia POPB genes, while Lepiota POPB is distant. Our result suggests that horizontal gene transfer (HGT), at least between Amanita and Galerian, was invovled in the acquisition of POPB genes, which may shed light on the evolution of the a-amanitin biosynthetic pathway
Ecosystem type drives soil eukaryotic diversity and composition in Europe
Soil eukaryotes play a crucial role in maintaining ecosystem functions and services, yet the factors driving their diversity and distribution remain poorly understood. While many studies focus on some eukaryotic groups (mostly fungi), they are limited in their spatial scale. Here, we analyzed an unprecedented amount of observational data of soil eukaryomes at continental scale (787 sites across Europe) to gain further insights into the impact of a wide range of environmental conditions (climatic and edaphic) on their community composition and structure. We found that the diversity of fungi, protists, rotifers, tardigrades, nematodes, arthropods, and annelids was predominantly shaped by ecosystem type (annual and permanent croplands, managed and unmanaged grasslands, coniferous and broadleaved woodlands), and higher diversity of fungi,
protists, nematodes, arthropods, and annelids was observed in croplands than in less intensively managed systems, such as coniferous and broadleaved woodlands. Also in croplands, we found more specialized eukaryotes, while the composition between croplands was more homogeneous compared to the composition of other ecosystems. The observed high proportion of overlapping taxa between ecosystems also indicates that DNA has accumulated from previous land uses, hence mimicking the land transformations occurring in Europe in the last decades. This strong ecosystem-type influence was linked to soil properties, and particularly, soil pH was driving the richness of fungi, rotifers, and annelids, while plant-available phosphorus drove the richness of protists, tardigrades, and nematodes. Furthermore, the soil organic carbon to total nitrogen ratio crucially explained the richness of fungi, protists, nematodes, and
arthropods, possibly linked to decades of agricultural inputs. Our results highlighted the importance of long-term environmental variables rather than variables measured at the time of the sampling in shaping soil eukaryotic communities, which reinforces the need to include those variables in addition to ecosystem type in future monitoring programs and conservation efforts.Collaborative Doctoral Partnership JRC and Universidade de Vigo | Ref. n. 35533Universidade de Vigo/CISUG | Ref. acceso abiert
Comparative analysis of diversity and environmental niches of soil bacterial, archaeal, fungal and protist communities reveal niche divergences along environmental gradients in the Alps
Although widely used in ecology, comparative analyses of diversity and niche properties are still lacking for microorganisms, especially focusing on niche variations. Quantifying the niches of microbial taxa is necessary to then forecast how taxa and the communities they compose might respond to environmental changes. In this study, we first identified important topoclimatic, edaphic, spatial and biotic drivers of the alpha and beta di-versity of bacterial, archaeal, fungal and protist communities. Then, we calculated the niche breadth and position of each taxon along the important environmental gradients to determine how these vary within and among the taxonomic groups. We found that edaphic properties were the most important drivers of both, community di-versity and composition, for all microbial groups. Protists and bacteria presented the largest niche breadths on average, followed by archaea, with fungi displaying the smallest. Niche breadth generally decreased towards environmental extremes, especially along edaphic gradients, suggesting increased specialization of microbial taxa in highly selective environments. Overall, we showed that microorganisms have well defined niches, as do macro-organisms, likely driving part of the observed spatial patterns of community variations. Assessing niche variation more widely in microbial ecology should open new perspectives, especially to tackle global change effects on microbes.Peer reviewe
An integrated âomicsâ approach to unravel the impact of root symbionts on tomato direct and indirect defenses against insect herbivores
As sessile organisms, plants are constantly under attack by insect herbivores. To defend themselves, they have developed a broad array of direct and indirect defense mechanisms. Plants can also build mutualistic relationships with several microbes that are hosted in their rhizosphere. These microbes provide their hosts with essential services, such as improved mineral uptake, nitrogen fixation, growth promotion, and protection from pathogens and insect herbivores. Among these beneficial microbes, the arbuscular mycorrhizal fungus (AMF) Rhizophagus irregularis and the plant growth-promoting fungus (PGPF) Trichoderma harzianum have been broadly studied. In the present doctoral study, tomato (Solanum lycopersicum) was used as a model plant to investigate the effect of R. irregularis and T. harzianum on modulating tomatoâs direct and indirect defenses against insect herbivores. Overall, the study aims to explore the potential of using beneficial root fungi in protecting crop plants against insect herbivores. In this frame, a series of experiments, comprising transcriptomic and metabolomic approaches, was conducted aiming to illuminate aspects of plant-microbe-insect interactions that are less studied and contribute to the transformation of conventional to sustainable Agriculture. Conclusively, the results presented in this doctoral thesis indicate that the beneficial root fungi R. irregularis and T. harzianum mediate plant-insect interactions and can trigger important effects over the three trophic levels: namely the plant, its herbivores, and their natural enemies. Therefore, these findings reinforce the potential of beneficial root fungi to be used in Agriculture as a promising alternative tool to reduce the use of chemical insecticides, ensure crop productivity and food security, and protect human health as well as the environment
Characterization of CYP76M5â8 Indicates Metabolic Plasticity within a Plant Biosynthetic Gene Cluster
Recent reports have revealed genomic clustering of enzymatic genes for particular biosynthetic pathways in plant specialized/secondary metabolism. Rice (Oryza sativa) carries two such clusters for production of antimicrobial diterpenoid phytoalexins, with the cluster on chromosome 2 containing four closely related/homologous members of the cytochrome P450 CYP76M subfamily (CYP76M5â8). Notably, the underlying evolutionary expansion of these CYP appears to have occurred after assembly of the ancestral biosynthetic gene cluster, suggesting separate roles. It has been demonstrated that CYP76M7 catalyzes C11α-hydroxylation of ent-cassadiene, and presumably mediates an early step in biosynthesis of the derived phytocassane class of phytoalexins. Here we report biochemical characterization of CYP76M5, -6, and -8. Our results indicate that CYP76M8 is a multifunctional/promiscuous hydroxylase, with CYP76M5 and -7 seeming to provide only redundant activity, while CYP76M6 seems to provide both redundant and novel activity, relative to CYP76M8. RNAi-mediated double knockdown of CYP76M7 and -8 suppresses elicitor inducible phytocassane production, indicating a role for these monooxygenases in phytocassane biosynthesis. In addition, our data suggests that CYP76M5, -6, and -8 may play redundant roles in production of the oryzalexin class of phytoalexins as well. Intriguingly, the preceding diterpene synthase for oryzalexin biosynthesis, unlike that for the phytocassanes, is not found in the chromosome 2 diterpenoid biosynthetic gene cluster. Accordingly, our results not only uncover a complex evolutionary history, but also further suggest some intriguing differences between plant biosynthetic gene clusters and the seemingly similar microbial operons. The implications for the underlying metabolic evolution of plants are then discussed
HooghÀnnaliste (Collembola) ja nendega seotud seeneliikide molekulaarne mÀÀramine
VĂ€itekirja elektrooniline versioon ei sisalda publikatsiooneMuld on mitmekesine elupaik, mis hĂ”lmab suurt mikroobide ja loomade liigirikkust. Rikkalik mullaelustik on olulisel kohal paljudes looduslikes protsessides alates mulla kujundamisest ja lagundamisprotsessidest kuni mikrokliima reguleerimiseni. Molekulaarsete identifitseerimismeetodite areng on kaasa aidanud mullaorganismide tuvastamisele, mis vĂ”imaldavad mÀÀrata liike nii indiviidi kui ka koosluste tasemel. Oma doktoritöös uurisin ITS2 rakendatavust hooghĂ€nnaliste (Collembola) mÀÀramisel, kuna vastava DNA lĂ”iguga on potentsiaalselt vĂ”imalik mullaproovidest mÀÀrata samaaegselt mitmesugused eukarĂŒootide rĂŒhmad liigi tasemele. Kuna hooghĂ€nnalised on tihedalt seotud seenekooslustega (seened moodustavad olulise osa nende toidust), siis uurisin oma doktoritöös ka hooghĂ€nnalistega seotud seenekoosluste ruumilist ja ajalist struktuuri kasutades nii seente kultuurides kasvatamise kui ka mass-sekveneerimise (HTS) meetodit. Vastavate HTS andmete lihtsaks ja kiireks bioinformaatiliste analĂŒĂŒside teostamiseks oli vaja vĂ€lja töötada mass-sekveneerimisandmete töötlemise töölaud. Doktoritöö peamised tulemused ja jĂ€reldused on jĂ€rgmised: 1) ITS2 lĂ”ik omab piisavat liikidevahelist erinevust, et eristada hooghĂ€nnaliste liike; 2) hooghĂ€nnalistega seotud seeneliikide tuvastamine on tĂ”husam mass-sekveneerimise meetodiga, mis tĂ”i esile, et hooghĂ€nnalised on seotud palju rohkemate seeneliikidega kui seni traditsiooniliste meetoditega kindlaks mÀÀratud; 3) tulenevalt seenekoosluste suktsessioonist on hooghĂ€nnalistega seotud seenekoosluste struktuur ja liigirikkus mĂ”jutatud nii sesoonist kui aastast; 4) töös kasutatud hooghĂ€nnaliste liikide vahel ei tuvastatud toitumiseelistusi seente osas; 5) koostatud HTS andmete töötlemise programm vĂ”imaldas kiiret ja tĂ”husat DNA jĂ€rjestuste töötlust.Microbial and faunal communities are highly diverse in soils where they play fundamental roles in several ecosystem processes ranging from soil formation to microclimate regulation. The identification of small soil organisms has benefited from the development of molecular methods that enable identification of single species to whole communities. In this thesis, I examined the usefulness of the rDNA ITS2 subregion for identification purposes of Collembola, because of its potential for simultaneous use in metabarcoding surveys of multiple taxa. Moreover, this thesis addresses the spatial and temporal structure of Collembola-associated fungal communities as based on culturing and high-throughput sequencing (HTS). To simplify the HTS data analyses, one of the objectives of this thesis was the compilation of a user-friendly and flexible platform for bioinformatics analysis of custom high-throughput amplicon sequencing data. The main results and conclusions are the following: 1) the ITS2 barcoding marker provides sufficient resolution for discriminating among Collembola species; 2) HTS outperformed the culturing method in terms of recovering Collembola-associated fungal species, and it revealed that collembolans are associated with much higher diversity of fungi than previously anticipated; 3) the Collembola-associated fungal richness and community structure exhibited significant variation in different temporal scales, which probably reflects the succession of the litter fungal community; 4) diet specialization among the studied Collembola species was not evident, suggesting that these arthropods possess relatively opportunistic feeding behavior; 5) the compiled high-throughput amplicon sequencing data analysis platform enabled efficient bioinformatics workflow for the analysis of fungal ITS2 amplicons in soil and Collembola-associated samples
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