The evolution of domain arrangements in proteins and interaction networks

Proteins are composed of domains, which are conserved evolutionary units that often also correspond to functional units and can frequently be detected with reasonable reliability using computational methods. Most proteins consist of two or more domains, giving rise to a variety of combinations of domains. Another level of complexity arises because proteins themselves can form complexes with small molecules, nucleic acids and other proteins. The networks of both domain combinations and protein interactions can be conceptualised as graphs, and these graphs can be analysed conveniently by computational methods. In this review we summarise facts and hypotheses about the evolution of domains in multi-domain proteins and protein complexes, and the tools and data resources available to study them.Received 20 September 2004; received after revision 23 October 2004; accepted 1 November 2004     

Oxygen consumption and the evolution of order: negentropy criteria applied to the evolution of ants

Optimization of energy use by evolving organisms, predicted by theoretical extensions of the neo-Darwinian theory, i. contrasted with that of irreversible thermodynamics, which predicts an increase in orderliness and thus an increase in energy consumption per unit of biomass. We compared this index with estimates of social complexity among ant genera and species. Our results show that simple optimization models cannot explain experimental data, and that social complexity correlates differently with negentropy at different levels of analysis. Comparing the genera among Formicidae, workers (not colonies) from genera with highly social species are less negentropic than those of socially primitive ones. At the sub-generic level, social complexity correlated positively with negentropy among species, for major workers inAcromyrmex and for minor workers inAtta. The results illustrate the complexity of thermodynamic criteria in the study of evolution but also hint at their usefulness. In this case, they show that two different evolutionary routes to the complex Attini ant societies may exist.     

Genetic ecology: A new interdisciplinary science,fundamental for evolution,biodiversity and biosafety evaluations

Genetic ecology is the extension of our modern knowledge in molecular genetics to studies of viability, gene expression and gene movements in natural environments like soils, aquifers and digestive tracts. In such milieux, the horizontal transfer of plasmid-borne genes between phylogenetically distant species has already been found to be much more frequent than had been expected from laboratory experience. For the study of exchanges involving chromosomally-located genes, more has to be learned about the behaviour of transposons in such environments. The results expected from studies in genetic ecology are relevant for considerations of evolution, biodiversity and biosafety. The role of this new field of research in restoring popular confidence in science and in its biotechnological applications is stressed.     

Ancient origin of reggie (flotillin), reggie-like, and other lipid-raft proteins: convergent evolution of the SPFH domain

Reggies (flotillins) are detergent-resistant microdomains involved in the scaffolding of large heteromeric complexes that signal across the plasma membrane. Based on the presence of an evolutionarily widespread motif, reggies/flotillins have been included within the SPFH (stomatin-prohibitin-flotillin-HflC/K) protein superfamily. To better understand the origin and evolution of reggie/flotillin structure and function, we searched databases for reggie/flotillin and SPFH-like proteins in organisms at the base and beyond the animal kingdom, and used the resulting dataset to compare their structural and functional domains. Our analysis shows that the SPFH grouping has little phylogenetic support, probably due to convergent evolution of its members. We also find that reggie/flotillin homologues are highly conserved among metazoans but are absent in plants, fungi and bacteria, where only proteins with ‘reggie-like’ domains can be found. However, despite their low sequence similarities, reggie/flotillin and ‘reggie-like’ domains appear to subserve related functions, suggesting that their basic biological role was acquired independently during evolution. Received 21 September 2005; received after revision 14 November 2005; accepted 21 November 2005     

The postpharyngeal glands and the cuticle of Formicidae contain the same characteristic hydrocarbons

Summary Comparison of the contents of the postpharyngeal gland and cuticular hydrocarbons of five species of ant have shown them to contain the same compounds and to be characteristic of the species. For four species (Formica selysi, Camponotus lateralis, Camponotus vagus andManica rubida), quantitative similarity was very close, but more divergent in the fifth (Myrmica rubra). Glands and cuticle ofM. rubra queens were shown to be closely similar to those of workers, except the glands of queens are larger, but the cuticle of larvae was different from that of adult cuticle and postpharyngeal glands.     

The cephalopod heart: The evolution of a high-performance invertebrate pump

Cephalopods typically have high metabolic rates. They have blood in which the oxygen carrier is haemocyanin, a pigment that is found only in solution and which never seems to be present in concentrations that will transport more than 4–5 vols % of oxygen. Their hearts must in consequence have very high cardiac outputs. In this account the performance of the heart ofNautilus, the only surviving ectocochleate, is contrasted with the performance of the hearts of coleoids,Octopus which has a relatively low metabolic rate (for a coleoid) and squids which have very high oxygen uptakes by any standards. In all these animals, heartbeat frequency is temperature-dependent and the additional oxygen demand in exercise is met very largely by a 2–3-fold increase in stroke volume. With the exception ofNautilus, cephalopods tend to utilise nearly all of the oxygen transported in the blood even at rest; they show very limited factorial scopes. Specific power output has, however, increased dramatically from 2.7 mWg^–1 in an activeNautilus to 5.5 mWg^–1 inOctopus and up to 20 or 30 mWg^–1 in species ofLoligo. The increase is almost entirely due to a 10-fold increase in heartbeat frequency. It is argued that frequency cannot be used as a means of responding to extra demand in an animal that must also carry automatic compensation for changes in metabolic rate dependent upon the ambient temperature, and that the use of frequency in some squid may be associated with a reduced temperature tolerance. Cephalopod systemic hearts do not scale directly with body mass, like the hearts of fish and the higher vertebrates. Smaller cephalopods have relatively larger hearts (as Mass^0.9). A typical 100-g coleoid would have a heart mass of 0.15 g. Oegopsid squids appear to be exceptional with hearts twice as large.     

Chemical and tactile communication between the root aphid parasitoidParalipsis enervis and trophobiotic ants: consequences for parasitoid survival

Females of the aphid parasitoidParalipsis enervis received liquid food by regurgitation (trophallaxis) from workers of the ant speciesLasius niger, but were not fed by workers ofMyrmica laevinodis andTetramorium caespitum. WhileP. enervis was not treated aggressively by workers of any of these species,Lasius flavus workers killed the parasitoid. This different ant behaviour resulted in a different parasitoid longevity. WhileP. enervis survived for only 10 min in the presence ofL. flavus (due to ant aggression) or for approximately one day in the presence ofT. caespitum andM. laevinodis (due to lack of trophallaxis), survival increased significantly to more than five days in the presence ofL. niger, which provided food regularly to the parasitoids. Our study suggests thatP. enervis mimics behavioural signals ofL. niger, as well as odor cues of its host aphidAnoecia corni, to avoid aggression byL. niger.     

Ubiquitin-like and ubiquitin-associated domain proteins: significance in proteasomal degradation

The ubiquitin–proteasome pathway of protein degradation is one of the major mechanisms that are involved in the maintenance of the proper levels of cellular proteins. The regulation of proteasomal degradation thus ensures proper cell functions. The family of proteins containing ubiquitin-like (UbL) and ubiquitin-associated (UBA) domains has been implicated in proteasomal degradation. UbL–UBA domain containing proteins associate with substrates destined for degradation as well as with subunits of the proteasome, thus regulating the proper turnover of proteins.     

Sex pheromone communication in the lepidoptera: New research progress

Summary Significant progress has been made recently in research on lepidopterous sex pheromones. Advances in understanding the biochemical, neurobiological, and behavioral events that results in both successful and unsuccessful pheromone communication have allowed researchers to gain new insights into the genetic control and evolution of phermone systems.     

SET domain protein lysine methyltransferases: Structure, specificity and catalysis

Site- and state-specific lysine methylation of histones is catalyzed by a family of proteins that contain the evolutionarily conserved SET domain and plays a fundamental role in epigenetic regulation of gene activation and silencing in all eukaryotes. The recently determined three-dimensional structures of the SET domains from chromosomal proteins reveal that the core SET domain structure contains a two-domain architecture, consisting of a conserved anti-parallel β-barrel and a structurally variable insert that surround a unusual knot-like structure that comprises the enzyme active site. These structures of the SET domains, either in the free state or when bound to cofactor S-adenosyl-L-homocysteine and/or histone peptide, mimicking an enzyme/cofactor/substrate complex, further yield the structural insights into the molecular basis of the substrate specificity, methylation multiplicity and the catalytic mechanism of histone lysine methylation. Received 10 June 2006; accepted 22 August 2006     

The value-ladenness of transparency in science: Lessons from Lyme disease

Both philosophers and scientists have recently promoted transparency as an important element of responsible scientific practice. Philosophers have placed particular emphasis on the ways that transparency can assist with efforts to manage value judgments in science responsibly. This paper examines a potential challenge to this approach, namely, that efforts to promote transparency can themselves be value-laden. This is particularly problematic when transparency incorporates second-order value judgments that are underwritten by the same values at stake in the desire for transparency about the first-order value judgments involved in scientific research. The paper uses a case study involving research on Lyme disease to illustrate this worry, but it responds by elucidating a range of scenarios in which transparency can still play an effective role in managing value judgments responsibly.     

The chordate amphioxus: an emerging model organism for developmental biology

The cephalochordate amphioxus is the closest living invertebrate relative of the vertebrates. It is vertebrate-like in having a dorsal, hollow nerve cord, notochord, segmental muscles, pharyngeal gill slits and a post-anal tail that develops from a tail bud. However, amphioxus is less complex than vertebrates, lacking neural crest and having little or no mesenchyme. The genetic programs patterning the amphioxus embryo are also similar to those patterning vertebrate embryos, although the amphioxus genome lacks the extensive gene duplications characteristic of vertebrates. This relative structural and genomic simplicity in a vertebrate-like organism makes amphioxus ideal as a model organism for understanding mechanisms of vertebrate development.Received 18 February 2004; received after revision 9 April 2004; accepted 19 April 2004     

The accessory gland proteins in maleDrosophila: structural,reproductive, and evolutionary aspects

Recent results from biochemical and molecular genetic studies of the accessory gland proteins in maleDrosophila are reviewed. The most prominent feature is the species-specific variability. However, the analysis of the sex peptide inD. melanogaster shows that there is a strong homology in the molecular structure to the closely related sibling species, and that divergence increases with increasing phylogenetic distance. For this reason the sex peptide, after being transferred to the female genital tract during copulation, reduces receptivity and increases oviposition only in virgin females belonging to the same species group and subgroup. Even though studies were hitherto limited to a small number of the secretory components, it is evident that the accessory gland proteins play a key role in reproductive success of the fruit fly by changing female sexual behavior, supporting sperm transfer, storage and displacement. Thus, genes encoding the accessory gland proteins are apparently under strong evolutionary selection.     

Asexual reproduction: Genetics and evolutionary aspects

Reproduction is essential to all organisms if they are to contribute to the next generation. There are various means and ways of achieving this goal. This review focuses on the role of asexual reproduction for eukaryotic organisms and how its integration in a life cycle can influence their population genetics and evolution. An important question for evolutionary biologists as to why some organisms reproduce sexually, as opposed to asexually, is addressed. We also discuss the economic and medical importance of asexual organisms. Received 4 December 2006; received after revision 25 January 2007; accepted 20 February 2007     

Scientific patronage in the age of Darwin: The curious case of William Boyd Dawkins

This essay examines the curious relationship between Charles Darwin and the palaeontologist William Boyd Dawkins (1837–1929). Dawkins was a beneficiary of Darwin's patronage and styled himself as a Darwinian to Darwin and the public, yet viciously attacked Darwin and his theory in anonymous reviews. This has confused historians who have misunderstood the exact nature of Dawkins's attitude towards evolution and his relationship to Darwin. The present study explains both the reasons for Dawkins's contradictory statements and his relationship with Darwin. I introduce Batesian mimicry as a conceptual framework to make sense of Dawkins's actions, suggesting that Dawkins mimicked a Darwinian persona in order to secure advancement in the world of Victorian science. Dawkins's pro-Darwinian stance, therefore, was a façade, an act of mimicry. I argue that Dawkins exploited Darwin for his patronage – which took the form of advice, support from Darwin's well-placed friends, and monetary assistance – while safely expressing his dissent from Darwinian orthodoxy in the form of anonymous reviews. This is, therefore, a case study in how scientific authority and power could be gained and maintained in Victorian science by professing allegiance to Darwin and Darwinism.     

Analysis and prediction of the population in Spain: 1910-2000

"The starting hypothesis of this paper was the actual occurrence of important interactions between demographic and socio-economic factors when trying to reach population forecasts that may be more efficient than those obtained by mere extrapolative methods. In order to be able to implement this approach to the Spanish case it has been necessary to reconstruct first the Spanish population series by age and sex groups from 1910 to 1980. Later, we proceed to obtain population forecasts using alternative modeling strategies and comment on the potential problems that the new demographic situation may have for future public policy."