Predicting protein function with hierarchical phylogenetic profiles: The Gene3D phylo-tuner method applied to eukaryotic Genomes

"Phylogenetic profiling'' is based on the hypothesis that during evolution functionally or physically interacting genes are likely to be inherited or eliminated in a codependent manner. Creating presence-absence profiles of orthologous genes is now a common and powerful way of identifying functionally associated genes. In this approach, correctly determining orthology, as a means of identifying functional equivalence between two genes, is a critical and nontrivial step and largely explains why previous work in this area has mainly focused on using presence-absence profiles in prokaryotic species. Here, we demonstrate that eukaryotic genomes have a high proportion of multigene families whose phylogenetic profile distributions are poor in presence-absence information content. This feature makes them prone to orthology mis-assignment and unsuited to standard profile-based prediction methods. Using CATH structural domain assignments from the Gene3D database for 13 complete eukaryotic genomes, we have developed a novel modification of the phylogenetic profiling method that uses genome copy number of each domain superfamily to predict functional relationships. In our approach, superfamilies are subclustered at ten levels of sequence identity from 30% to 100% - and phylogenetic profiles built at each level. All the profiles are compared using normalised Euclidean distances to identify those with correlated changes in their domain copy number. We demonstrate that two protein families will "auto-tune'' with strong co-evolutionary signals when their profiles are compared at the similarity levels that capture their functional relationship. Our method finds functional relationships that are not detectable by the conventional presence - absence profile comparisons, and it does not require a priori any fixed criteria to define orthologous genes

What is Life?

In searching for life in extraterrestrial space, it is essential to act based on an unequivocal definition of life. In the twentieth century, life was defined as cells that self-replicate, metabolize, and are open for mutations, without which genetic information would remain unchangeable, and evolution would be impossible. Current definitions of life derive from statistical mechanics, physics, and chemistry of the twentieth century in which life is considered to function machine like, ignoring a central role of communication. Recent observations show that context-dependent meaningful communication and network formation (and control) are central to all life forms. Evolutionary relevant new nucleotide sequences now appear to have originated from social agents such as viruses, their parasitic relatives, and related RNA networks, not from errors. By applying the known features of natural languages and communication, a new twenty-first century definition of life can be reached in which communicative interactions are central to all processes of life. A new definition of life must integrate the current empirical knowledge about interactions between cells, viruses, and RNA networks to provide a better explanatory power than the twentieth century narrative

STDP-driven networks and the \emph{C. elegans} neuronal network

We study the dynamics of the structure of a formal neural network wherein the strengths of the synapses are governed by spike-timing-dependent plasticity (STDP). For properly chosen input signals, there exists a steady state with a residual network. We compare the motif profile of such a network with that of a real neural network of \emph{C. elegans} and identify robust qualitative similarities. In particular, our extensive numerical simulations show that this STDP-driven resulting network is robust under variations of the model parameters.Comment: 16 pages, 14 figure

Artificial and Natural Genetic Information Processing

Conventional methods of genetic engineering and more recent genome editing techniques focus on identifying genetic target sequences for manipulation. This is a result of historical concept of the gene which was also the main assumption of the ENCODE project designed to identify all functional elements in the human genome sequence. However, the theoretical core concept changed dramatically. The old concept of genetic sequences which can be assembled and manipulated like molecular bricks has problems in explaining the natural genome-editing competences of viruses and RNA consortia that are able to insert or delete, combine and recombine genetic sequences more precisely than random-like into cellular host organisms according to adaptational needs or even generate sequences de novo. Increasing knowledge about natural genome editing questions the traditional narrative of mutations (error replications) as essential for generating genetic diversity and genetic content arrangements in biological systems. This may have far-reaching consequences for our understanding of artificial genome editing

Characterisation of components and mechanisms involved in redox-regulation of protein import into chloroplasts

The vast majority of chloroplast proteins is encoded in the nucleus and thus has to be posttranslationally imported into the organelle, a process that is facilitated by two multimeric protein machineries, the Toc and Tic complexes (translocon at the outer/inner envelope of chloroplasts). Regulation of protein import, e.g. by redox signals, is a crucial step to adapt the protein content to the biochemical requirements of the organelle. In particular, one subunit of the Tic complex, Tic62, has been proposed as a redox sensor, whose possible function is to regulate protein import by sensing and reacting to the redox state of the organelle. To elucidate a potential redox regulation of protein import, structural features, redox-dependent properties and the evolutional origin of Tic62 were investigated. The results show that Tic62 consists of two very different modules: the N-terminal part was found to be mainly -helical and possesses dehydrogenase activity in vitro. It is furthermore an evolutionary ancient domain, as it is highly conserved in all photosynthetic organisms from flowering plants to cyanobacteria and even green sulfur bacteria. In contrast to this, the C-terminus is largely disordered and interacts specifically with ferredoxin-NADP+ oxidoreductase (FNR), a key enzyme in photosynthetic electron transfer reactions. Moreover, this domain was found to exist only in flowering plants, and thus the full-length Tic62 protein seems to be one of the evolutionary youngest Tic components. The results of this study make also clear that Tic62 is a target of redox regulation itself, as its localization and interaction properties depend on the metabolic redox state: oxidized conditions lead to fast membrane binding and interaction with the Tic complex, whereas reduced conditions cause solubilization of Tic62 into the stroma and increased interaction with FNR. This novel shuttling behaviour indicates a dynamic composition of the Tic complex. The NADP+/NADPH ratio was furthermore found to be able to influence the import efficiency of many precursor proteins. Interestingly, the import of not all preproteins depends on the stromal redox state. Hence it was proposed that not a single stable Tic translocon exists, but several Tic subcomplexes with different subunit compositions, which might mediate the import of different precursor groups in a redox-dependent or -independent fashion. Another redox signal that was analyzed in regard to an impact on protein import is the reversible reduction of disulfide bridges, which was found to affect the channel and receptor proteins of the Toc complex. The import of all proteins that use the Toc translocon for entering the chloroplast was shown to be influenced by disulfide bridge formation. Thus it can be concluded that a variety of redox signals, acting both on the Toc and Tic complexes, are able to influence chloroplast protein import

Second Symposium on Chemical Evolution and the Origin of Life

Recent findings by NASA Exobiology investigators are reported. Scientific papers are presented in the following areas: cosmic evolution of biogenic compounds, prebiotic evolution (planetary and molecular), early evolution of life (biological and geochemical), evolution of advanced life, solar system exploration, and the Search for Extraterrestrial Intelligence (SETI)

Satisfiability, sequence niches, and molecular codes in cellular signaling

Biological information processing as implemented by regulatory and signaling networks in living cells requires sufficient specificity of molecular interaction to distinguish signals from one another, but much of regulation and signaling involves somewhat fuzzy and promiscuous recognition of molecular sequences and structures, which can leave systems vulnerable to crosstalk. This paper examines a simple computational model of protein-protein interactions which reveals both a sharp onset of crosstalk and a fragmentation of the neutral network of viable solutions as more proteins compete for regions of sequence space, revealing intrinsic limits to reliable signaling in the face of promiscuity. These results suggest connections to both phase transitions in constraint satisfaction problems and coding theory bounds on the size of communication codes