BACKGROUND: Departures from the standard genetic code in eukaryotic nuclear genomes are known for only a handful of lineages and only a few genetic code variants seem to exist outside the ciliates, the most creative group in this regard. Most frequent code modifications entail reassignment of the UAG and UAA codons, with evidence for at least 13 independent cases of a coordinated change in the meaning of both codons. However, no change affecting each of the two codons separately has been documented, suggesting the existence of underlying evolutionary or mechanistic constraints. RESULTS: Here, we present the discovery of two new variants of the nuclear genetic code, in which UAG is translated as an amino acid while UAA is kept as a termination codon (along with UGA). The first variant occurs in an organism noticed in a (meta)transcriptome from the heteropteran Lygus hesperus and demonstrated to be a novel insect-dwelling member of Rhizaria (specifically Sainouroidea). This first documented case of a rhizarian with a non-canonical genetic code employs UAG to encode leucine and represents an unprecedented change among nuclear codon reassignments. The second code variant was found in the recently described anaerobic flagellate Iotanema spirale (Metamonada: Fornicata). Analyses of transcriptomic data revealed that I. spirale uses UAG to encode glutamine, similarly to the most common variant of a non-canonical code known from several unrelated eukaryotic groups, including hexamitin diplomonads (also a lineage of fornicates). However, in these organisms, UAA also encodes glutamine, whereas it is the primary termination codon in I. spirale. Along with phylogenetic evidence for distant relationship of I. spirale and hexamitins, this indicates two independent genetic code changes in fornicates. CONCLUSIONS: Our study documents, for the first time, that evolutionary changes of the meaning of UAG and UAA codons in nuclear genomes can be decoupled and that the interpretation of the two codons by the cytoplasmic translation apparatus is mechanistically separable. The latter conclusion has interesting implications for possibilities of genetic code engineering in eukaryotes. We also present a newly developed generally applicable phylogeny-informed method for inferring the meaning of reassigned codons.

• MeSH
• buněčné jádro genetika   MeSH
• Ciliophora genetika   MeSH
• fylogeneze MeSH
• genetický kód * MeSH
• glutamin genetika   MeSH
• hmyz parazitologie   MeSH
• kodon genetika   MeSH
• leucin genetika   MeSH
• molekulární evoluce MeSH
• otevřené čtecí rámce genetika   MeSH
• Rhizaria genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Algae frequently get a bad press. Pond slime is a problem in garden pools, algal blooms can produce toxins that incapacitate or kill animals and humans and even the term seaweed is pejorative - a weed being a plant growing in what humans consider to be the wrong place. Positive aspects of algae are generally less newsworthy - they are the basis of marine food webs, supporting fisheries and charismatic marine megafauna from albatrosses to whales, as well as consuming carbon dioxide and producing oxygen. Here we consider what algae are, their diversity in terms of evolutionary origin, size, shape and life cycles, and their role in the natural environment and in human affairs.

• MeSH
• Apicomplexa genetika   fyziologie   MeSH
• biodiverzita * MeSH
• Chlorophyta klasifikace   genetika   fyziologie   MeSH
• Cryptophyta genetika   fyziologie   MeSH
• Dinoflagellata genetika   fyziologie   MeSH
• Eukaryota klasifikace   genetika   fyziologie   MeSH
• Glaucophyta klasifikace   genetika   fyziologie   MeSH
• Haptophyta genetika   fyziologie   MeSH
• Heterokontophyta genetika   fyziologie   MeSH
• parožnatky genetika   fyziologie   MeSH
• Rhizaria genetika   fyziologie   MeSH
• Rhodophyta klasifikace   genetika   fyziologie   MeSH
• rozmnožování fyziologie   MeSH
• sinice klasifikace   genetika   fyziologie   MeSH
• symbióza fyziologie   MeSH
• Publikační typ
• časopisecké články MeSH

Plasmodiophora brassicae is a soil-borne pathogen that belongs to Rhizaria, an almost unexplored eukaryotic organism group. This pathogen requires a living host for growth and multiplication, which makes molecular analysis further complicated. To broaden our understanding of a plasmodiophorid such as P. brassicae, we here chose to study immunophilins, a group of proteins known to have various cellular functions, including involvement in plant defense and pathogen virulence. Searches in the P. brassicae genome resulted in 20 putative immunophilins comprising of 11 cyclophilins (CYPs), 7 FK506-binding proteins (FKBPs) and 2 parvulin-like proteins. RNAseq data showed that immunophilins were differentially regulated in enriched life stages such as germinating spores, maturing spores, and plasmodia, and infected Brassica hosts (B. rapa, B. napus and B. oleracea). PbCYP3 was highly induced in all studied life stages and during infection of all three Brassica hosts, and hence was selected for further analysis. PbCYP3 was heterologously expressed in Magnaporthe oryzae gene-inactivated ΔCyp1 strain. The new strain ΔCyp1+ overexpressing PbCYP3 showed increased virulence on rice compared to the ΔCyp1 strain. These results suggest that the predicted immunophilins and particularly PbCYP3 are activated during plant infection. M. oryzae is a well-studied fungal pathogen and could be a valuable tool for future functional studies of P. brassicae genes, particularly elucidating their role during various infection phases.

• MeSH
• Brassica klasifikace   parazitologie   MeSH
• cyklofiliny klasifikace   genetika   metabolismus   MeSH
• fylogeneze MeSH
• imunofiliny genetika   metabolismus   MeSH
• interakce hostitele a patogenu MeSH
• kořeny rostlin parazitologie   MeSH
• nemoci rostlin parazitologie   MeSH
• Plasmodiophorida genetika   metabolismus   fyziologie   MeSH
• protozoální proteiny genetika   metabolismus   MeSH
• regulace genové exprese MeSH
• sekvence aminokyselin MeSH
• sekvenční homologie aminokyselin MeSH
• spory protozoální genetika   MeSH
• stanovení celkové genové exprese metody   MeSH
• Publikační typ
• časopisecké články MeSH

A central challenge in ecology is to understand the relative importance of processes that shape diversity patterns. Compared with aboveground biota, little is known about spatial patterns and processes in soil organisms. Here we examine the spatial structure of communities of small soil eukaryotes to elucidate the underlying stochastic and deterministic processes in the absence of environmental gradients at a local scale. Specifically, we focus on the fine-scale spatial autocorrelation of prominent taxonomic and functional groups of eukaryotic microbes. We collected 123 soil samples in a nested design at distances ranging from 0.01 to 64 m from three boreal forest sites and used 454 pyrosequencing analysis of Internal Transcribed Spacer for detecting Operational Taxonomic Units of major eukaryotic groups simultaneously. Among the main taxonomic groups, we found significant but weak spatial variability only in the communities of Fungi and Rhizaria. Within Fungi, ectomycorrhizas and pathogens exhibited stronger spatial structure compared with saprotrophs and corresponded to vegetation. For the groups with significant spatial structure, autocorrelation occurred at a very fine scale (<2 m). Both dispersal limitation and environmental selection had a weak effect on communities as reflected in negative or null deviation of communities, which was also supported by multivariate analysis, that is, environment, spatial processes and their shared effects explained on average <10% of variance. Taken together, these results indicate a random distribution of soil eukaryotes with respect to space and environment in the absence of environmental gradients at the local scale, reflecting the dominant role of drift and homogenizing dispersal.

• MeSH
• ekologie MeSH
• Eukaryota klasifikace   MeSH
• houby klasifikace   genetika   izolace a purifikace   MeSH
• lesy MeSH
• půdní mikrobiologie * MeSH
• společenstvo * MeSH
• stromy mikrobiologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Estonsko MeSH