The PHY Domain Dimer Interface of Bacteriophytochromes Mediates Cross-talk between Photosensory Modules and Output Domains

Protein dynamics play a major role for the catalytic function of enzymes, the interaction of protein complexes or signal integration in regulatory proteins. In the context of multi-domain proteins involved in light-regulation of enzymatic effectors, the central role of conformational dynamics is well established. Light activation of sensory modules is followed by long-range signal transduction to different effectors; rather than domino-style structural rearrangements, a complex interplay of functional elements is required to maintain functionality. One family of such sensor-effector systems are red-light-regulated phytochromes that control diguanylate cyclases involved in cyclic-dimeric-GMP formation. Based on structural and functional studies of one prototypic family member, the central role of the coiled-coil sensor-effector linker was established. Interestingly, subfamilies with different linker lengths feature strongly varying biochemical characteristics. The dynamic interplay of the domains involved, however, is presently not understood. Here we show that the PHY domain dimer interface plays an essential role in signal integration, and that a functional coupling with the coiled-coil linker element is crucial. Chimaeras of two biochemically different family members highlight the phytochrome-spanning helical spine as an essential structural element involved in light-dependent upregulation of enzymatic turnover. However, isolated structural elements can frequently not be assigned to individual characteristics, which further emphasises the importance of global conformational dynamics. Our results provide insights into the intricate processes at play during light signal integration and transduction in these photosensory systems and thus provide additional guidelines for a more directed design of novel sensor-effector combinations with potential applications as optogenetic tools.     

The Geography of Evolution and the Evolution of Geography

Insights into the geography of life have played a fundamental role in motivating major developments in evolutionary biology. The focus here is on outlining some of these major developments, specifically in the context of paleontology, by emphasizing the significance of geographic isolation and allopatric speciation, punctuated equilibria, and the Turnover Pulse Hypothesis to evolutionary theory. One of the major debates in evolution concerns the relative contributions of abiotic and biotic factors to macroevolution, and each one of these developments increasingly suggested that it was climatic and geologic factors, rather than competition, that played the primary role in motivating macroevolution. New technical developments, including in the area of Geographic Information Systems, allow continued detailed testing of the relative roles that biotic as opposed to abiotic factors play in causing evolution, and some of the work in this area will also be described.     

On the origin and evolution of major morphological characters

Although the mathematical principles underpinning population-level evolution are now well studied, the origin and evolution of morphological novelties has received far less attention. Here, a broad but general theory for how this sort of change takes place is outlined, relying on functional continuity, least-constrained components of morphology, redundancy and preadaptation. At least four distinct sorts of redundancy are identified: (i) redundancy arising through duplication (amplification); (ii) redundancy arising through regionalisation (parcellation); (iii) redundancy arising through functional convergence; and (iv) redundancy arising from shared function (functional degeneracy). Although organisms are here recognised to be functionally constrained ("burdened", in Riedl's terminology), these constraints can be overcome through the combination of the four principles given above. Contrary to its common treatment, functional constraint is neither an ever-increasing restriction on the scope of evolution, nor does it require drastic events to overcome or "break" it. Rather, it is an evolutionary quantity, subject to selection at some level. The rules that govern morphological evolution are the primary controls on what is allowed to happen in the evolution of the overall genotype-phenotype system, suggesting strong controls on the sorts of developmental changes that might be associated with macroevolution. This model, then, sees organism functionality as the primary control on evolvability, with exact genetic make-up being of secondary importance. It should prove possible to recast traditional notions of body-plan evolution into the formulations of complex system analysis, which in the future may prove a unifying discipline for fields as disparate as palaeontology and gene regulatory networks. In particular, understanding how morphology can evolve may provide the critical link between the ecological and morphological networks that are currently the intense focus of evolutionary investigations.     

RNA templating of molecular assembly and covalent modification patterning in early molecular evolution and modern biosystems

The Direct RNA Template (DRT) hypothesis proposes that an early stage of genetic code evolution involved RNA molecules acting as stereochemical recognition templates for assembly of specific amino acids in sequence-ordered arrays, providing a framework for directed covalent peptide bond formation. It is hypothesized here that modern biological precedents may exist for RNA-based structural templating with functional analogies to hypothetical DRT systems. Beyond covalent molecular assembly, an extension of the DRT concept can include RNA molecules acting as dynamic structural template guides for the specific non-covalent assembly of multi-subunit complexes, equivalent to structural assembly chaperones. However, despite numerous precedents for RNA molecules acting as scaffolds for protein complexes, true RNA-mediated assembly chaperoning appears to be absent in modern biosystems. Another level of function with parallels to a DRT system is possible if RNA structural motifs dynamically guided specific patterns of catalytic modifications within multiple target sites in a pre-formed polymer or macromolecular complex. It is suggested that this type of structural RNA templating could logically play a functional role in certain areas of biology, one of which is the glycome of complex organisms. If any such RNA templating processes are shown to exist, they would share no necessary evolutionary relationships with events during early molecular evolution, but may promote understanding of the practical limits of biological RNA functions now and in the ancient RNA World. Awareness of these formal possibilities may also assist in the current search for functions of extensive non-coding RNAs in complex organisms, or for efforts towards artificial rendering of DRT systems.     

The Staminal Lever Mechanism in Salvia L. (Lamiaceae) - a Review

Abstract: The genus Salvia encompasses about 900 species distributed world-wide. It is characterized by the famous staminal lever mechanism of the flower which is one of the best known examples of a nototribic pollination mechanism. We hypothesize that structure and functioning of the staminal levers play a major role as key structures in speciation. To cope with the complex evolutionary processes involved, a number of different methodological approaches are needed. The present paper summarizes the literature referring to structural and functional diversity, breeding systems, systematics and evolution in Salvia.     

A role for lipids in the functional and structural properties of the rat liver aminoacyl-tRNA synthetase complex

The high molecular weight aminoacyl-tRNA synthetase complexes found in extracts of many eukaryotic cells often contain lipids and other non-protein components. Since hydrophobic interactions play an important role in maintaining synthetases in the complex, it has been suggested that the lipids present may also participate in its functional and structural integrity. In order to learn more about the role of lipids in the complex, we have compared the properties of the normal complex to one which has been delipidated by treatment with Triton X-114. Delipidation does not affect the size or activity of the aminoacyl-tRNA synthetase complex, but a variety of functional and structural properties of individual synthetases in the complex are altered dramatically. These include sensitivity to salts plus detergents, temperature inactivation, hydrophobicity, and sensitivity to protease digestion. In the latter case, removal of lipids also affects the low molecular weight products released by protease digestion. Purification of the synthetase complex by various chromatographic procedures can remove the lipids and lead to a structure that behaves like the delipidated complex prepared by detergent treatment. The significance of these findings for the intracellular location of aminoacyl-tRNA synthetases and for the study of purified complexes are discussed.     

The concept of macroevolution in view of modern data

Macroevolution, or evolution of superspecies taxa is the process of transformation of “organismal” life flows on the Earth during its geological history. In the present study, this process is analyzed with using the system and evolutionarily?ecological approaches. Based on modern paleontological, evolutionary biological, molecular, and genetic data, mostly on vertebrates and hominins, the major factors and patterns of macroevolution and also the role of macroevolution in the biosphere evolution are discussed. The fundamental bases of the concept of macroevolution, the problems of methodology and methods of the study of organismal evolution are considered. It is shown that the processes at the macroevolutionary level agree with the epigenetic theory of evolution.     

Patterns of heterochrony in the fossil record

Recent analyses of the fossil record have revealed that heterochrony has played a significant role in the evolution of most marine invertebrate groups. Recognition of several different heterochronic processes has allowed their influence under different ecological regimes to be assessed. Furthermore, recent research has demonstrated significant differences in frequencies of these processes between groups and at their different stages of phylogenetic development. The fossil record shows that heterochron y has been an important component in the generation of evolutionary trends. Heterochrony is an important factor in macroevolution because it can result in relatively abrupt morphological change with only minimum alteration of the genome.     

Examining the Interaction of Acceptance and Understanding: How Does the Relationship Change with a Focus on Macroevolution?

The goal of this research was to illuminate the relationship between students’ acceptance and understanding of macroevolution. Our research questions were: (1) Is there a relationship between knowledge of macroevolution and acceptance of the theory of evolution?; (2) Is there a relationship between the amount of college level biology course work and acceptance of evolutionary theory and knowledge of macroevolution?; and (3) Can college student acceptance of the theory of evolution and knowledge of macroevolution change over the course of a semester? The research participants included 667 students from a first-semester biology course and 74 students from the evolutionary biology course. Data were collected using both the MATE (a measure of the acceptance of evolutionary theory) and the MUM (a measure of understanding of macroevolution). Pre-instruction data were obtained for the introductory biology course, and pre- and post-data were obtained for the evolutionary biology course. Analysis revealed acceptance of evolution (as measured by the MATE) was correlated to understanding of macroevolution, and the number of biology courses was significantly correlated to acceptance and knowledge of macroevolution. Finally, there was a statistically significant change in students’ understanding of macroevolution and acceptance of evolution after the one-semester evolutionary biology course. Significance of these findings is discussed.     

Trends in the sand: Directional evolution in the shell shape of recessing scallops (Bivalvia: Pectinidae)

Directional evolution is one of the most compelling evolutionary patterns observed in macroevolution. Yet, despite its importance, detecting such trends in multivariate data remains a challenge. In this study, we evaluate multivariate evolution of shell shape in 93 bivalved scallop species, combining geometric morphometrics and phylogenetic comparative methods. Phylomorphospace visualization described the history of morphological diversification in the group; revealing that taxa with a recessing life habit were the most distinctive in shell shape, and appeared to display a directional trend. To evaluate this hypothesis empirically, we extended existing methods by characterizing the mean directional evolution in phylomorphospace for recessing scallops. We then compared this pattern to what was expected under several alternative evolutionary scenarios using phylogenetic simulations. The observed pattern did not fall within the distribution obtained under multivariate Brownian motion, enabling us to reject this evolutionary scenario. By contrast, the observed pattern was more similar to, and fell within, the distribution obtained from simulations using Brownian motion combined with a directional trend. Thus, the observed data are consistent with a pattern of directional evolution for this lineage of recessing scallops. We discuss this putative directional evolutionary trend in terms of its potential adaptive role in exploiting novel habitats.     

Lessons from the deep: mechanisms behind diversification of eukaryotic protein complexes

Genetic variation is the major mechanism behind adaptation and evolutionary change. As most proteins operate through interactions with other proteins, changes in protein complex composition and subunit sequence provide potentially new functions. Comparative genomics can reveal expansions, losses and sequence divergence within protein-coding genes, but in silico analysis cannot detect subunit substitutions or replacements of entire protein complexes. Insights into these fundamental evolutionary processes require broad and extensive comparative analyses, from both in silico and experimental evidence. Here, we combine data from both approaches and consider the gamut of possible protein complex compositional changes that arise during evolution, citing examples of complete conservation to partial and total replacement by functional analogues. We focus in part on complexes in trypanosomes as they represent one of the better studied non-animal/non-fungal lineages, but extend insights across the eukaryotes by extensive comparative genomic analysis. We argue that gene loss plays an important role in diversification of protein complexes and hence enhancement of eukaryotic diversity.     

Taxic evolutionary paleoecology and the ecological context of macroevolutionary change

Summary A traditional focus of evolutionary paleoecology has been the reconstruction of the selective forces that have affected evolving lineages through time. If the history of those lineages is dominated by stasis and punctuation, however, this is at best an inadequate and at worst a misdirected research strategy for macroevolution, because long-term stasis implies that environmental factors may have less influence on evolving lineages than previously believed. Such reasoning has led some proponents of punctuated views to reject ecological interactions as predominant or even significant forces in evolution. This is not a necessary conclusion. It is possible to accept the empirical predominance of stasis in evolution and at the same time the importance of ecology in affecting the course of evolutionary trends within lineages. If stasis prevails, ecology matters in the evolution of lineages if either (1) stabilizing selection is an important cause of stasis or (2) ecological interactions play an important role in controlling the speciation process. Viewing allopatric speciation explicitly as a three-stage process (consisting of formation, persistence and differentiation of isolated populations) clarifies testing of the role of ecology in speciation and may redirect clade-specific evolutionary paleoecology towards more enlightening interaction with other areas of macroevolutionary study.     

What is macroevolution?

Definitions of macroevolution fall into three categories: (1) evolution of taxa of supraspecific rank; (2) evolution on the grand time-scale; and (3) evolution that is guided by sorting of interspecific variation (as opposed to sorting of intraspecific variation in microevolution). Here, it is argued that only definition 3 allows for a consistent separation of macroevolution and microevolution. Using this definition, speciation has both microevolutionary and macroevolutionary aspects: the process of morphological transformation is microevolutionary, but the variation among species that it produces is macroevolutionary, as is the rate at which speciation occurs. Selective agents may have differential effects on intraspecific and interspecific variation, with three possible situations: effect at one level only, effect at both levels with the same polarity but potentially different intensity, and effects that oppose between levels. Whereas the impact of all selective agents is direct in macroevolution, microevolution requires intraspecific competition as a mediator between selective agents and evolutionary responses. This mediating role of intraspecific competition occurs in the presence of sexual reproduction and has therefore no analogue at the macroevolutionary level where species are the evolutionary units. Competition between species manifests both on the microevolutionary and macroevolutionary level, but with different effects. In microevolution, interspecific competition spurs evolutionary divergence, whereas it is a potential driver of extinction at the macroevolutionary level. Recasting the Red Queen hypothesis in a macroevolutionary framework suggests that the effects of interspecific competition result in a positive correlation between origination and extinction rates, confirming empirical observations herein referred to as Stanley's rule.     

A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae

The presence of multiple membrane-bound intracellular compartments is a major feature of eukaryotic cells. Many of the proteins required for formation and maintenance of these compartments share an evolutionary history. Here, we identify the SEA (Seh1-associated) protein complex in yeast that contains the nucleoporin Seh1 and Sec13, the latter subunit of both the nuclear pore complex and the COPII coating complex. The SEA complex also contains Npr2 and Npr3 proteins (upstream regulators of TORC1 kinase) and four previously uncharacterized proteins (Sea1-Sea4). Combined computational and biochemical approaches indicate that the SEA complex proteins possess structural characteristics similar to the membrane coating complexes COPI, COPII, the nuclear pore complex, and, in particular, the related Vps class C vesicle tethering complexes HOPS and CORVET. The SEA complex dynamically associates with the vacuole in vivo. Genetic assays indicate a role for the SEA complex in intracellular trafficking, amino acid biogenesis, and response to nitrogen starvation. These data demonstrate that the SEA complex is an additional member of a family of membrane coating and vesicle tethering assemblies, extending the repertoire of protocoatomer-related complexes.     

In search of the biological significance of modular structures in protein networks

Many complex networks such as computer and social networks exhibit modular structures, where links between nodes are much denser within modules than between modules. It is widely believed that cellular networks are also modular, reflecting the relative independence and coherence of different functional units in a cell. While many authors have claimed that observations from the yeast protein–protein interaction (PPI) network support the above hypothesis, the observed structural modularity may be an artifact because the current PPI data include interactions inferred from protein complexes through approaches that create modules (e.g., assigning pairwise interactions among all proteins in a complex). Here we analyze the yeast PPI network including protein complexes (PIC network) and excluding complexes (PEC network). We find that both PIC and PEC networks show a significantly greater structural modularity than that of randomly rewired networks. Nonetheless, there is little evidence that the structural modules correspond to functional units, particularly in the PEC network. More disturbingly, there is no evolutionary conservation among yeast, fly, and nematode modules at either the whole-module or protein-pair level. Neither is there a correlation between the evolutionary or phylogenetic conservation of a protein and the extent of its participation in various modules. Using computer simulation, we demonstrate that a higher-than-expected modularity can arise during network growth through a simple model of gene duplication, without natural selection for modularity. Taken together, our results suggest the intriguing possibility that the structural modules in the PPI network originated as an evolutionary byproduct without biological significance.     

Evolutionary dynamics of complex biomechanical systems: an example using the four-bar mechanism

Like many phenotypic traits, biomechanical systems are defined by both an underlying morphology and an emergent functional property. The relationship between these levels may have a profound impact on how selection for functional performance is translated into morphological evolution. In particular, complex mechanical systems are likely to be highly redundant, because many alternative morphologies yield equivalent functions. We suggest that this redundancy weakens the relationship between morphological and functional diversity, and we illustrate this effect using an evolutionary model of the four-bar lever system of labrid fishes. Our results demonstrate that, when traits are complex, the morphological diversity of a clade may only weakly predict its mechanical diversity. Furthermore, parallel or convergent selection on function does not necessarily produce convergence in morphology. Empirical observations suggest that this weak form-function relationship has contributed to the morphological diversity of labrid fishes, as functionally equivalent species may nevertheless possess morphologically distinct jaws. We suggest that partial decoupling of morphology and mechanics due to redundancy is a major factor in morphological diversification.     

Random Loss and Selective Fusion of Bones Originate Morphological Complexity Trends in Tetrapod Skull Networks

The tetrapod skull has undergone a reduction in number of bones in all major lineages since the origin of vertebrates, an evolutionary trend known as Williston’s Law. Using connectivity relations between bones as a proxy for morphological complexity we showed that this reduction in number of bones generated an evolutionary trend toward more complex skulls. This would imply that connectivity patterns among bones impose structural constraints on bone loss and fusion that increase bone burden due to the formation of new functional and developmental dependencies; thus, the higher the number of connections, the higher the burden. Here, we test this hypothesis by exploring plausible evolutionary scenarios based on selective versus random processes of bone loss and fusion. To do this, we have built a computational model that reduces iteratively the number of bones by loss and fusion, starting from hypothetical ancestral skulls represented as Gabriel networks in which bones are nodes and suture connections are links. Simulation results indicate that losses and fusions of bones affect skull structure differently whether they target bones at random or selectively depending on the number of bone connections. Our findings support a mixed scenario for Williston’s Law: the random loss of poorly connected bones and the selective fusion of the most connected ones. This evolutionary scenario offers a new explanation for the increase of morphological complexity in the tetrapod skull by reduction of bones during development.     

Modular antenna of photosystem I in secondary plastids of red algal origin: a <Emphasis Type="Italic">Nannochloropsis oceanica</Emphasis> case study

Photosystem I (PSI) is a multi-subunit integral pigment–protein complex that performs light-driven electron transfer from plastocyanin to ferredoxin in the thylakoid membrane of oxygenic photoautotrophs. In order to achieve the optimal photosynthetic performance under ambient irradiance, the absorption cross section of PSI is extended by means of peripheral antenna complexes. In eukaryotes, this role is played mostly by the pigment–protein complexes of the LHC family. The structure of the PSI-antenna supercomplexes has been relatively well understood in organisms harboring the primary plastid: red algae, green algae and plants. The secondary endosymbiotic algae, despite their major ecological importance, have so far received less attention. Here we report a detailed structural analysis of the antenna-PSI association in the stramenopile alga Nannochloropsis oceanica (Eustigmatophyceae). Several types of PSI-antenna assemblies are identified allowing for identification of antenna docking sites on the PSI core. Instances of departure of the stramenopile system from the red algal model of PSI-Lhcr structure are recorded, and evolutionary implications of these observations are discussed.     

Macroevolution is more than repeated rounds of microevolution

SUMMARY Arguments over macroevolution versus microevolution have waxed and waned through most of the twentieth century. Initially, paleontologists and other evolutionary biologists advanced a variety of non-Darwinian evolutionary processes as explanations for patterns found in the fossil record, emphasizing macroevolution as a source of morphologic novelty. Later, paleontologists, from Simpson to Gould, Stanley, and others, accepted the primacy of natural selection but argued that rapid speciation produced a discontinuity between micro- and macroevolution. This second phase emphasizes the sorting of innovations between species. Other discontinuities appear in the persistence of trends (differential success of species within clades), including species sorting, in the differential success between clades and in the origination and establishment of evolutionary novelties. These discontinuities impose a hierarchical structure to evolution and discredit any smooth extrapolation from allelic substitution to large-scale evolutionary patterns. Recent developments in comparative developmental biology suggest a need to reconsider the possibility that some macroevolutionary discontinuites may be associated with the origination of evolutionary innovation. The attractiveness of macroevolution reflects the exhaustive documentation of large-scale patterns which reveal a richness to evolution unexplained by microevolution. If the goal of evolutionary biology is to understand the history of life, rather than simply document experimental analysis of evolution, studies from paleontology, phylogenetics, developmental biology, and other fields demand the deeper view provided by macroevolution.