Comparative analysis of barophily-related amino acid content in protein domains of Pyrococcus abyssi and Pyrococcus furiosus.

Amino acid substitution patterns between the nonbarophilic Pyrococcus furiosus and its barophilic relative P. abyssi confirm that hydrostatic pressure asymmetry indices reflect the extent to which amino acids are preferred by barophilic archaeal organisms. Substitution patterns in entire protein sequences, shared protein domains defined at fold superfamily level, domains in homologous sequence pairs, and domains of very ancient and very recent origin now provide further clues about the environment that led to the genetic code and diversified life. The pyrococcal proteomes are very similar and share a very early ancestor. Relative amino acid abundance analyses showed that biases in the use of amino acids are due to their shared fold superfamilies. Within these repertoires, only two of the five amino acids that are preferentially barophilic, aspartic acid and arginine, displayed this preference significantly and consistently across structure and in domains appearing in the ancestor. The more primordial asparagine, lysine and threonine displayed a consistent preference for nonbarophily across structure and in the ancestor. Since barophilic preferences are already evident in ancient domains that are at least ~3 billion year old, we conclude that barophily is a very ancient trait that unfolded concurrently with genetic idiosyncrasies in convergence towards a universal code.

Putative lateral inhibition in sensory processing for directional turns.

Computing targeted responses is a general problem in goal-directed behaviors. We sought the sensory template for directional turning in the predatory sea slug Pleurobranchaea californica, which calculates precise turn angles by averaging multiple stimulus sites on its chemotactile oral veil (Yafremava LS, Anthony CW, Lane L, Campbell JK, Gillette R. J Exp Biol 210: 561-569, 2007). Spiking responses to appetitive chemotactile stimulation were recorded in the two bilateral pairs of oral veil nerves, the large oral veil nerve (LOVN) and the tentacle nerve (TN). The integrative abilities of the peripheral nervous system were significant. Nerve spiking responses to punctate, one-site stimulation of the oral veil followed sigmoid relations as stimuli moved between lateral tentacle and the midline. Receptive fields of LOVN and TN were unilateral, overlapping, and oppositely weighted for responsiveness across the length of oral veil. Simultaneous two-site stimulation caused responses of amplitudes markedly smaller than the sum of corresponding one-site responses. Plots of two-site nerve responses against the summed approximate distances from midline of each site were markedly linear. Thus the sensory paths in the peripheral nervous system show reciprocal occlusion similar to lateral inhibition. This outcome suggests a novel neural function for lateral inhibitory mechanisms, distinct from simple contrast enhancement, in computation of both sensory maps and targeted motor actions.

The origin and evolution of modern metabolism.

One fundamental goal of current research is to understand how complex biomolecular networks took the form that we observe today. Cellular metabolism is probably one of the most ancient biological networks and constitutes a good model system for the study of network evolution. While many evolutionary models have been proposed, a substantial body of work suggests metabolic pathways evolve fundamentally by recruitment, in which enzymes are drawn from close or distant regions of the network to perform novel chemistries or use different substrates. Here we review how structural and functional genomics has impacted our knowledge of evolution of modern metabolism and describe some approaches that merge evolutionary and structural genomics with advances in bioinformatics. These include mining the data on structure and function of enzymes for salient patterns of enzyme recruitment. Initial studies suggest modern metabolism originated in enzymes of nucleotide metabolism harboring the P-loop hydrolase fold, probably in pathways linked to the purine metabolic subnetwork. This gateway of recruitment gave rise to pathways related to the synthesis of nucleotides and cofactors for an ancient RNA world. Once the TIM beta/alpha-barrel fold architecture was discovered, it appears metabolic activities were recruited explosively giving rise to subnetworks related to carbohydrate and then amino acid metabolism. Remarkably, recruitment occurred in a layered system reminiscent of Morowitz's prebiotic shells, supporting the notion that modern metabolism represents a palimpsest of ancient metabolic chemistries.

Origins and evolution of modern biochemistry: insights from genomes and molecular structure.

The survey of components in living systems at different levels of organization enables an evolutionary exploration of patterns and processes in macromolecules, networks, and genomic repertoires. Here we discuss how phylogenetic strategies that generate intrinsically rooted phylogenies impact the evolutionary study of RNA and protein components of the macromolecular machinery that is responsible for biological function. We used these methods to generate timelines of discovery of components in systems, such as substructures in RNA molecules, architectures in proteomes, domains in multi-domain proteins, enzymes in metabolic networks, and protein architectures in proteomes. These timelines unfolded remarkable patterns of origin and evolution of molecules, repertoires and networks, showing episodes of both functional specialization (e.g., rise of domains with specialized functions) and molecular simplification (e.g., reductive tendencies in molecules and proteomes). These observations have important evolutionary implications for origins of translation, the genetic code, modules in the protein world, and diversification of life, and suggest early evolution of modern biochemistry was driven by recruitment of both RNA and protein catalysts in an ancient community of complex organisms.

A general framework of persistence strategies for biological systems helps explain domains of life.

The nature and cause of the division of organisms in superkingdoms is not fully understood. Assuming that environment shapes physiology, here we construct a novel theoretical framework that helps identify general patterns of organism persistence. This framework is based on Jacob von Uexküll's organism-centric view of the environment and James G. Miller's view of organisms as matter-energy-information processing molecular machines. Three concepts describe an organism's environmental niche: scope, umwelt, and gap. Scope denotes the entirety of environmental events and conditions to which the organism is exposed during its lifetime. Umwelt encompasses an organism's perception of these events. The gap is the organism's blind spot, the scope that is not covered by umwelt. These concepts bring organisms of different complexity to a common ecological denominator. Ecological and physiological data suggest organisms persist using three strategies: flexibility, robustness, and economy. All organisms use umwelt information to flexibly adapt to environmental change. They implement robustness against environmental perturbations within the gap generally through redundancy and reliability of internal constituents. Both flexibility and robustness improve survival. However, they also incur metabolic matter-energy processing costs, which otherwise could have been used for growth and reproduction. Lineages evolve unique tradeoff solutions among strategies in the space of what we call "a persistence triangle." Protein domain architecture and other evidence support the preferential use of flexibility and robustness properties. Archaea and Bacteria gravitate toward the triangle's economy vertex, with Archaea biased toward robustness. Eukarya trade economy for survivability. Protista occupy a saddle manifold separating akaryotes from multicellular organisms. Plants and the more flexible Fungi share an economic stratum, and Metazoa are locked in a positive feedback loop toward flexibility.

Orienting and avoidance turning are precisely computed by the predatory sea-slug Pleurobranchaea californica McFarland.

Computing the direction and amplitude of orienting and avoidance turns is fundamental to prey pursuit and risk avoidance in motile foragers. We examined computation of turns in the predatory sea-slug Pleurobranchaea californica, observing orienting and aversive turn responses to chemotactile stimuli applied to the chemosensory oral veil. We made seven observations: (1) the relation of turn angle/stimulus site on the oral veil was linear; (2) turn amplitudes increased with stimulus strength; (3) turn responses markedly overshot the target stimulus; (4) responses to two simultaneous stimuli at different loci were averaged to an intermediate angle; (5) stimuli could induce sequential turns in which the angles of the first and third turns were similar, a form of working memory; (6) turn direction was affected by appetitive state, so that animals with higher feeding thresholds tended to avoid appetitive stimuli; and (7) avoidance turns induced by mildly noxious stimuli were computed similarly to orienting, while differing in direction. These observations appear to outline a framework of behavior that could be employed for efficient tracking of odor trails, and which is regulated by decision mechanisms that integrate sensation, internal state and experience.

Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world.

The repertoire of protein architectures in proteomes is evolutionarily conserved and capable of preserving an accurate record of genomic history. Here we use a census of protein architecture in 185 genomes that have been fully sequenced to generate genome-based phylogenies that describe the evolution of the protein world at fold (F) and fold superfamily (FSF) levels. The patterns of representation of F and FSF architectures over evolutionary history suggest three epochs in the evolution of the protein world: (1) architectural diversification, where members of an architecturally rich ancestral community diversified their protein repertoire; (2) superkingdom specification, where superkingdoms Archaea, Bacteria, and Eukarya were specified; and (3) organismal diversification, where F and FSF specific to relatively small sets of organisms appeared as the result of diversification of organismal lineages. Functional annotation of FSF along these architectural chronologies revealed patterns of discovery of biological function. Most importantly, the analysis identified an early and extensive differential loss of architectures occurring primarily in Archaea that segregates the archaeal lineage from the ancient community of organisms and establishes the first organismal divide. Reconstruction of phylogenomic trees of proteomes reflects the timeline of architectural diversification in the emerging lineages. Thus, Archaea undertook a minimalist strategy using only a small subset of the full architectural repertoire and then crystallized into a diversified superkingdom late in evolution. Our analysis also suggests a communal ancestor to all life that was molecularly complex and adopted genomic strategies currently present in Eukarya.