Conformational changes in ezrin analyzed by Förster resonance energy transfer

Ezrin gehört zu der ERM Proteingruppe und seine Hauptfunktion besteht in der Verbindung zwischen dem Zytoskelett und der Zellmembran. Diese Arbeit demonstriert Veränderungen der Ezrin-Konformation während seiner Aktivierung und erklärt Synergismus der Aktivirungsfaktoren: Interaktion zwischen Ezrin und PIP2, Ezrin Phosphorylierung. Förster resonance energy transfer Technik wurde in dieser Arbeit angewendet.Ezrin, a member of the ERM (Ezrin-Radixin-Moesin) protein family, serves as a linker between cell membrane and cytoskeleton in the cells of all protozoans. Thereby, it is involved in cell motility, cell division, cell-cell adhesion and the maintainance of cell polarity. In resting cells ezrin exists in a so-called dormant state, where most of its binding sites are masked by an autoinhibitory association between N- and C-terminals. Ezrin activation is thought to be triggered by interaction with PIP2 and the C-terminal phosphorylation. In this study we probed ezrin’s conformational state by FRET (Förster resonance energy transfer) and showed that disruption of the N-C-terminals association occurs only when of both activating factors are applied

Emergence and Evolution of ERM Proteins and Merlin in Metazoans

Ezrin, radixin, moesin, and merlin are cytoskeletal proteins, whose functions are specific to metazoans. They participate in cell cortex rearrangement, including cell–cell contact formation, and play an important role in cancer progression. Here, we have performed a comprehensive phylogenetic analysis of the proteins spanning 87 species. The results describe a possible mechanism for the protein family origin in the root of Metazoa, paralogs diversification in vertebrates, and acquisition of novel functions, including tumor suppression. In addition, a merlin paralog, present in most vertebrates but lost in mammals, has been described here for the first time. We have also highlighted a set of amino acid variations within the conserved motifs as the candidates for determining physiological differences between ERM paralogs

Environmental adaptation of 'Acanthamoeba castellanii' and 'Entamoeba histolytica' at genome level as seen by comparative genomic analysis

Amoebozoans are in many aspects interesting research objects, as they combine features of single-cell organisms with complex signaling and defense systems, comparable to multicellular organisms. 'Acanthamoeba castellanii' is a cosmopolitan species and developed diverged feeding abilities and strong anti-bacterial resistance; 'Entamoeba histolytica' is a parasitic amoeba, who underwent massive gene loss and its genome is almost twice smaller than that of 'A. castellanii'. Nevertheless, both species prosper, demonstrating fitness to their specific environments. Here we compare transcriptomes of 'A. castellanii' and 'E. histolytica' with application of orthologs' search and gene ontology to learn how different life strategies influence genome evolution and restructuring of physiology. 'A. castellanii' demonstrates great metabolic activity and plasticity, while 'E. histolytica' reveals several interesting features in its translational machinery, cytoskeleton, antioxidant protection, and nutritional behavior. In addition, we suggest new features in 'E. histolytica' physiology that may explain its successful colonization of human colon and may facilitate medical research

NanoPipe—a web server for nanopore MinION sequencing data analysis

BACKGROUND: The fast-moving progress of the third-generation long-read sequencing technologies will soon bring the biological and medical sciences to a new era of research. Altogether, the technique and experimental procedures are becoming more straightforward and available to biologists from diverse fields, even without any profound experience in DNA sequencing. Thus, the introduction of the MinION device by Oxford Nanopore Technologies promises to “bring sequencing technology to the masses” and also allows quick and operative analysis in field studies. However, the convenience of this sequencing technology dramatically contrasts with the available analysis tools, which may significantly reduce enthusiasm of a “regular” user. To really bring the sequencing technology to every biologist, we need a set of user-friendly tools that can perform a powerful analysis in an automatic manner. FINDINGS: NanoPipe was developed in consideration of the specifics of the MinION sequencing technologies, providing accordingly adjusted alignment parameters. The range of the target species/sequences for the alignment is not limited, and the descriptive usage page of NanoPipe helps a user to succeed with NanoPipe analysis. The results contain alignment statistics, consensus sequence, polymorphisms data, and visualization of the alignment. Several test cases are used to demonstrate the efficiency of the tool. CONCLUSIONS: Freely available NanoPipe software allows effortless and reliable analysis of MinION sequencing data for experienced bioinformaticians, as well for wet-lab biologists with minimum bioinformatics knowledge. Moreover, for the latter group, we describe the basic algorithm necessary for MinION sequencing analysis from the first to last step

Somatic Functional Deletions of Upstream Open Reading Frame-Associated Initiation and Termination Codons in Human Cancer

Upstream open reading frame (uORF)-mediated translational control has emerged as an important regulatory mechanism in human health and disease. However, a systematic search for cancer-associated somatic uORF mutations has not been performed. Here, we analyzed the genetic variability at canonical (uAUG) and alternative translational initiation sites (aTISs), as well as the associated upstream termination codons (uStops) in 3394 whole-exome-sequencing datasets from patient samples of breast, colon, lung, prostate, and skin cancer and of acute myeloid leukemia, provided by The Cancer Genome Atlas research network. We found that 66.5% of patient samples were affected by at least one of 5277 recurrent uORF-associated somatic single nucleotide variants altering 446 uAUG, 347 uStop, and 4733 aTIS codons. While twelve uORF variants were detected in all entities, 17 variants occurred in all five types of solid cancer analyzed here. Highest frequencies of individual somatic variants in the TLSs of NBPF20 and CHCHD2 reached 10.1% among LAML and 8.1% among skin cancer patients, respectively. Functional evaluation by dual luciferase reporter assays identified 19 uORF variants causing significant translational deregulation of the associated main coding sequence, ranging from 1.73-fold induction for an AUG.1 > UUG variant in SETD4 to 0.006-fold repression for a CUG.6 > GUG variant in HLA-DRB1. These data suggest that somatic uORF mutations are highly prevalent in human malignancies and that defective translational regulation of protein expression may contribute to the onset or progression of cancer