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Here, we identify RBM41 as a novel unique protein component of the minor spliceosome. RBM41 has no previously recognized cellular function but has been identified as a paralog of U11/U12-65K, a known unique component of the U11/U12 di-snRNP. Both proteins use their highly similar C-terminal RRMs to bind to 3′-terminal stem-loops in U12 and U6atac snRNAs with comparable affinity. Our BioID data indicate that the unique N-terminal domain of RBM41 is necessary for its association with complexes containing DHX8, an RNA helicase, which in the major spliceosome drives the release of mature mRNA from the spliceosome. Consistently, we show that RBM41 associates with excised U12-type intron lariats, is present in the U12 mono-snRNP, and is enriched in Cajal bodies, together suggesting that RBM41 functions in the post-splicing steps of the minor spliceosome assembly/disassembly cycle. This contrasts with U11/U12-65K, which uses its N-terminal region to interact with U11 snRNP during intron recognition. Finally, while RBM41 knockout cells are viable, they show alterations in U12-type 3′ splice site usage. Together, our results highlight the role of the 3′-terminal stem-loop of U12 snRNA as a dynamic binding platform for the U11/U12-65K and RBM41 proteins, which function at distinct stages of the assembly/disassembly cycle.

De deelnemers van het project Natuurinclusief Betuws Boeren hebben de afgelopen jaren ervaring opgedaan met de diverse toepassingen van natuurinclusieve landbouw in de boomteelt (incl. de spillenteelt). Deze kennis, resultaten en ervaringen uit de praktijk zijn gebundeld in deze leaflet.

De deelnemers van het project Natuurinclusief Betuws Boeren hebben de afgelopen jaren ervaring opgedaan met het toepassen van natuurinclusieve maatregelen. Deze kennis, resultaten en ervaringen uit de praktijk zijn gebundeld in deze leaflet.

De deelnemers van N de afgelopen jaren ervaring opgedaan met het toepassen van natuurinclusieve maatregelen. Deze kennis, resultaten en ervaringen uit de praktijk zijn gebundeld in deze leaflet.

De deelnemers van het natuurinclusief Betuws Boeren hebben de afgelopen jaren op verschillende vlakken ervaring opgedaan met het toepassen van natuurinclusieve maatregelen in de fruiteelt. Deze kennis, resultaten en ervaringen uit praktijk zijn gebundeld in deze leaflet.

The term eukaryote refers to organisms with cells that contain a nucleus. This is a special cellular compartment in which the DNA is stored. Animals, plants, fungi and protists are all eukaryotes. There are two other domains of life that do not correspond to nucleated cells. These are the bacteria and archeae, collectively referred to as prokaryotes. Current research indicates that eukaryotes have evolved from a merger between an archeum and a bacterium during a long process called eukaryogenesis. Eukaryotic cells are quite complex compared to prokaryotic cells. Apart from the nucleus they also universally contain many other features that are largely absent from prokaryotic cells. An example is the endomembrane system, which is a set of membranes and cellular compartments that collectively transport and process the molecular components of the cell. How exactly eukaryogenesis took place is still a mystery because all eukaryotic cells have descended from a single ancestor and all intermediate forms of life have gone extinct. This makes it difficult to determine the order in which different cellular features evolved, and the evolutionary pressures that caused them to evolve. Sometimes a prokaryotic species harbors a feature that is very similar to a eukaryotic feature. We can, by comparing the two, use these prokaryotic features to learn about the process of eukaryogenesis. Often these prokaryotes have only one such feature which allows scientists to study it in isolation, rather than in a complex eukaryotic cell. A complex endomembrane, for instance, also occurs in the bacterium G. obscuriglobus. In this literature thesis we show many examples of cellular features that occur in a prokaryote and are very similar to a eukaryotic feature. We than show how these parallel features can be used to form hypotheses about the process of eukaryogenesis. There is a great diversity of prokaryotic organisms on the planet. Only an incredibly small fraction of these has been investig

Eukaryogenesis is one of the most enigmatic evolutionary transitions, during which simple prokaryotic cells gave rise to complex eukaryotic cells. While evolutionary intermediates are lacking, gene duplications provide information on the order of events by which eukaryotes originated. Here we use a phylogenomics approach to reconstruct successive steps during eukaryogenesis. We find that gene duplications roughly doubled the proto-eukaryotic gene repertoire, with families inherited from the Asgard archaea-related host being duplicated most. By relatively timing events using phylogenetic distances, we inferred that duplications in cytoskeletal and membrane-trafficking families were among the earliest events, whereas most other families expanded predominantly after mitochondrial endosymbiosis. Altogether, we infer that the host that engulfed the proto-mitochondrion had some eukaryote-like complexity, which drastically increased upon mitochondrial acquisition. This scenario bridges the signs of complexity observed in Asgard archaeal genomes to the proposed role of mitochondria in triggering eukaryogenesis.

The basal transcription factor TFIID is central for RNA polymerase II-dependent transcription. Human TFIID is endowed with chromatin reader and DNA-binding domains and protein interaction surfaces. Fourteen TFIID TATA-binding protein (TBP)-associated factor (TAF) subunits assemble into the holocomplex, which shares subunits with the Spt–Ada–Gcn5–acetyltransferase (SAGA) coactivator. Here, we discuss the structural and functional evolution of TFIID and its divergence from SAGA. Our orthologous tree and domain analyses reveal dynamic gains and losses of epigenetic readers, plant-specific functions of TAF1 and TAF4, the HEAT2-like repeat in TAF2, and, importantly, the pre-LECA origin of TFIID and SAGA. TFIID evolution exemplifies the dynamic plasticity in transcription complexes in the eukaryotic lineage.

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Rijenbemesting met dierlijke mest in mais is een methode om de nutriënten uit de mest beter te benutten. Waar moet je op letten?

Aangepast voer kan de ammoniakuitstoot verlagen. Maar hoe realistisch zijn acht basisrantsoenen? DLV deed een haalbaarheidsstudie.

The origin of life on early Earth is unresolved still. Two approaches to the problem dominate the debate. Replicator-first proponents search for the very first replicator molecule. A much envisioned molecule in this regard is RNA. Metabolism-first adherents deem it unlikely that a replicator molecule emerged de novo on early Earth, and instead search for a network of small molecules that could have seeded modern life. Three metabolism-first scenarios are discussed. The elaborate lipid world scenario proclaims the Darwinian selection of early metabolic networks. It is shown that even though persisting entities may have come into existence, heredity in ensemble replicators is probably too inaccurate to allow for their selection, and even if accurate enough inherently attractor based, posing severe problems for their subsequent evolution. The problems are exemplary for scenarios that pose the evolution of metabolic networks. The only demonstration to date of the accumulation of novel mutations in ensemble replicators is provided in a far-off from real chemistry polymer model. The evolutionary dynamics encountered in the model depend heavily on the combinatorial chemistry of polymers, and cannot be generalised with the same success to monomer models. Moreover, many open questions remain. It is concluded that the standing of Darwinian selection in metabolism-first scenarios is problematic. The proposition that life started with the reverse tricarboxylic acid cycle that arose due to geochemical ordering is discussed as an example of a preparatory metabolism theory. As yet, it has not been shown that the cycle arises spontaneously in geothermal environments. The repertoire of catalysis by small organic molecules and mineral surfaces seems to be a crucial factor. A thermodynamic framework for non-equilibrium systems is lacking. However, experiments in hydrothermal reactors might provide the answer: the possibility that part of metabolic complexity is merely the result of th

Transposable elements (TEs) were originally discovered in Zea mays in the 1950s by Barbara McClintock (MCCLINTOCK 1956). In essence, they are genetic elements that are mobile and can move from one position to another within genomes. This concept fundamentally changed the view on genomes. Instead of rather static entities, it suggested that genomes are actually highly dynamic (Georgiev 1984). The draft of the human genome revealed that nearly half of the human genome is derived from transposable elements (Jurka et al. 2005; Lander et al. 2001). Britten and Davidson hypothesized that repetitive elements can act to distribute regulatory sequences throughout the genome, and thereby enriching, possibly even creating, whole pathways (Britten and Davidson 1971). The adoption of a TE to a new function by the genome is called “exaptation” (Gould and Vrba 1982), and would enhance genetic innovation. In this sense, they can be viewed as catalysts of evolution because their contribution to variation might have increased the speed of evolution on the human lineage (Britten 2010). Here, I will present an overview of the role of TEs in the human genome and their suggested influences on human evolution. In summary, it is obvious that TEs are really an integrated part of our genomes. It seems that the reduction of effective population size during evolution enabled the accumulation of TEs in most of the eukaryotic organisms. TEs provided the necessary base pairs which were needed to generate new genes and to acquire regulatory functions. They had probably the most profound influences on genome architecture in the early times of evolution and during moments of rapid population expansions. During following evolutionary periods TE derived fragments may have evolved slowly into functional elementsIn addition to effects caused by direct insertion, it seems that TEs had a profound impact on genome evolution by recombination events. The immense TE copy number within the human genome increas

Sugar signalling in plants is crucial to distribute available energy and respond appropriately to energy deprivation induced by nutrient shortage or environmental and biotic stresses. Several regulatory systems are involved in sugar signalling in plants. Orthologs of components of these systems are often already studied in non-plant eukaryotes. Knowledge about the function of these orthologous systems can contribute to unravelling sugar signalling pathways in plants. Differences between sugar signalling in different species might increase our understanding of the way in which evolution dealt with characteristics of these species that influence their regulation of metabolism. In order to better understand the function and evolutionary history of two sugar signalling components in plants, the SnRK1 kinase complex and trehalose 6-phosphate, their regulation and downstream effects were compared between plants, yeast and mammals. Current knowledge on the evolution of these systems was also collected. Together these data point out interesting directions for future research on sugar signalling in plants and its evolution.

The gene composition of present-day genomes has been shaped by a complicated evolutionary history, resulting in diverse distributions of genes across genomes. The pattern of presence and absence of a gene in different genomes is called its phylogenetic profile. It has been shown that proteins whose encoding genes have highly similar profiles tend to be functionally related: As these genes were gained and lost together, their encoded proteins can probably only perform their full function if both are present. However, a large proportion of genes encoding interacting proteins do not have matching profiles. In this study, we analysed one possible reason for this, namely that phylogenetic profiles can be affected by multi-functional proteins such as shared subunits of two or more protein complexes. We found that by considering triplets of proteins, of which one protein is multi-functional, a large fraction of disturbed co-occurrence patterns can be explained.

Background - Associations between proteins are essential to understand cell biology. While this complex interplay between proteins has been studied in model organisms, it has not yet been described for the oomycete late blight pathogen Phytophthora infestans. Results - We present an integrative probabilistic functional gene network that provides associations for 37 percent of the predicted P. infestans proteome. Our method unifies available genomic, transcriptomic and comparative genomic data into a single comprehensive network using a Bayesian approach. Enrichment of proteins residing in the same or related subcellular localization validates the biological coherence of our predictions. The network serves as a framework to query existing genomic data using network-based methods, which thus far was not possible in Phytophthora. We used the network to study the set of interacting proteins that are encoded by genes co-expressed during sporulation. This identified potential novel roles for proteins in spore formation through their links to proteins known to be involved in this process such as the phosphatase Cdc14. Conclusions - The functional association network represents a novel genome-wide data source for P. infestans that also acts as a framework to interrogate other system-wide data. In both capacities it will improve our understanding of the complex biology of P. infestans and related oomycete pathogens

Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ecosystems. We have sequenced the 63 Mb genome of the fresh water fish pathogen, Saprolegnia parasitica. Approximately 1/3 of the assembled genome exhibits loss of heterozygosity, indicating an efficient mechanism for revealing new variation. Comparison of S. parasitica with plant pathogenic oomycetes suggests that during evolution the host cellular environment has driven distinct patterns of gene expansion and loss in the genomes of plant and animal pathogens. S. parasitica possesses one of the largest repertoires of proteases (270) among eukaryotes that are deployed in waves at different points during infection as determined from RNA-Seq data. In contrast, despite being capable of living saprotrophically, parasitism has led to loss of inorganic nitrogen and sulfur assimilation pathways, strikingly similar to losses in obligate plant pathogenic oomycetes and fungi. The large gene families that are hallmarks of plant pathogenic oomycetes such as Phytophthora appear to be lacking in S. parasitica, including those encoding RXLR effectors, Crinkler's, and Necrosis Inducing-Like Proteins (NLP). S. parasitica also has a very large kinome of 543 kinases, 10% of which is induced upon infection. Moreover, S. parasitica encodes several genes typical of animals or animal-pathogens and lacking from other oomycetes, including disintegrins and galactose-binding lectins, whose expression and evolutionary origins implicate horizontal gene transfer in the evolution of animal pathogenesis in S. parasitica.

Item does not contain fulltext, Mass spectrometry (MS)-based proteome analysis relies heavily on the presence of complete protein databases. Such a strategy is extremely powerful, albeit not adequate in the analysis of unpredicted postgenome events, such as posttranslational modifications, which exponentially increase the search space. Therefore, it is of interest to explore "database-free" approaches. Here, we sampled the ostrich and human proteomes with a method facilitating de novo sequencing, utilizing the protease Lys-N in combination with electron transfer dissociation. By implementing several validation steps, including the combined use of collision-induced dissociation/electron transfer dissociation data and a cross-validation with conventional database search strategies, we identified approximately 2,500 unique de novo peptide sequences from the ostrich sample with over 900 peptides generating full backbone sequence coverage. This dataset allowed the appropriate positioning of ostrich in the evolutionary tree. The described database-free sequencing approach is generically applicable and has great potential in important proteomics applications such as in the analysis of variable parts of endogenous antibodies or proteins modified by a plethora of complex posttranslational modifications.