This Déjà Vu Feeling—Analysis of Multidomain Protein Evolution in Eukaryotic Genomes

Evolutionary innovation in eukaryotes and especially animals is at least partially driven by genome rearrangements and the resulting emergence of proteins with new domain combinations, and thus potentially novel functionality. Given the random nature of such rearrangements, one could expect that proteins with particularly useful multidomain combinations may have been rediscovered multiple times by parallel evolution. However, existing reports suggest a minimal role of this phenomenon in the overall evolution of eukaryotic proteomes. We assembled a collection of 172 complete eukaryotic genomes that is not only the largest, but also the most phylogenetically complete set of genomes analyzed so far. By employing a maximum parsimony approach to compare repertoires of Pfam domains and their combinations, we show that independent evolution of domain combinations is significantly more prevalent than previously thought. Our results indicate that about 25% of all currently observed domain combinations have evolved multiple times. Interestingly, this percentage is even higher for sets of domain combinations in individual species, with, for instance, 70% of the domain combinations found in the human genome having evolved independently at least once in other species. We also show that previous, much lower estimates of this rate are most likely due to the small number and biased phylogenetic distribution of the genomes analyzed. The process of independent emergence of identical domain combination is widespread, not limited to domains with specific functional categories. Besides data from large-scale analyses, we also present individual examples of independent domain combination evolution. The surprisingly large contribution of parallel evolution to the development of the domain combination repertoire in extant genomes has profound consequences for our understanding of the evolution of pathways and cellular processes in eukaryotes and for comparative functional genomics.     

Déjà vu in proteomics. A hit parade of repeatedly identified differentially expressed proteins

After reading many 2-DE-based articles featuring lists of the differentially expressed proteins, one starts experiencing a disturbing déjà vu. The same proteins seem to predominate regardless of the experiment, tissue or species. To quantify the occurrence of individual differentially expressed proteins in 2-DE experiment reports, we compiled the identities of differentially expressed proteins identified in human, mouse, and rat tissues published in three recent volumes of Proteomics and calculated the appearance of the most predominant proteins in the dataset. The most frequently identified protein is a highly abundant glycolytic enzyme enolase 1, differentially expressed in nearly every third experiment on both human and rodent tissues. Heat-shock protein 27 (HSP27) and heat-shock protein 60 (HSP60) were differentially expressed in about 30 percent of human and rodent samples, respectively. Considering protein families as units, keratins and peroxiredoxins are the most frequently identified molecules, with at least one member of the group being differentially expressed in about 40 percent of all experiments. We suggest that the frequent identification of these proteins must be considered in the interpretation of any 2-DE studies. We consider if these commonly observed changes represent common cellular stress responses or are a reflection of the technical limitations of 2-DE.     

Café Scientifique--déjà vu

Is the Café Scientifique a fashionable by-product of a comfortable age or an indicator of the changing relationship between science and society?     

It's Déjà Vu All Over Again: The Intelligent Design Movement's Recycling of Creationist Strategies

The intelligent design (ID) creationist movement is now a quarter of a century old. ID proponents at the Discovery Institute, headquartered in Seattle, WA, USA, insist that ID is not creationism. However, it is the direct descendant of the creation science movement that began in the 1960s and continued until the definitive ruling against creationism by the US Supreme Court in Edwards v. Aguillard 1987, which struck down laws that required balancing the teaching of evolution with creationism in public schools. Already anticipating in the early 1980s that Arkansas and Louisiana “balanced treatment” laws would be declared unconstitutional, a group of creationists led by Charles Thaxton began laying the groundwork for what is now the ID movement. After Edwards, Thaxton and his associates promoted ID aggressively until it, too, was declared unconstitutional by a federal judge in Kitzmiller et al. v. Dover Area School District 2005. Subsequently, in 2008, the Discovery Institute began its multistate promotion of model “academic freedom” legislation that bears striking parallels to the 1980s balanced treatment laws. Because of Kitzmiller, ID proponents have written their model legislation in code language in an effort to avoid another court challenge. Yet despite attempting to evade the legal constraints imposed by Edwards, they are merely recycling earlier creationist tactics that date back to the late 1970s and early 1980s. The tactics that ID creationists now use—promoting legislation, publishing “educational” materials, establishing a “research” institute, and sanitizing their terminology—are the recycled tactics of their creation science predecessors.     

Invertebrate memory: honeybees with a sense of déjà vu

Recent studies of visual sequence learning in honeybees have investigated the bees' ability to perform delayed-matching-to-sample and their short-term memory during such tasks. The insect's successful performance raises questions about the underlying mechanisms.     

HCV versus HIV drug discovery: Déjà vu all over again?

Efforts to address HIV infection have been highly successful, enabling chronic suppression of viral replication with once-daily regimens. More recent research into HCV therapeutics have also resulted in very promising clinical candidates. This Digest explores similarities and differences in the two fields and compares the chronology of drug discovery relative to the availability of enabling tools, and concludes that safe and convenient, once-daily regimens are likely to reach approval much more rapidly for HCV than was the case for HIV.     

Déjà vu all over again: finding and analyzing protein structure similarities

Structure comparison is a crucial aspect of structural biology today. The field of structure comparison is developing rapidly, with the development of new algorithms, similarity scores, and statistical scores. The predicted large increase of experimental structures and structural models made possible by high-throughput efforts means that structural comparison and searching of structural databases using automated methods will become increasingly common. This Ways & Means article is meant to guide the structural biologist in the basics of structural alignment, and to provide an overview of the available software tools. The main purpose is to encourage users to gain some understanding of the strengths and limitations of structural alignment, and to take these factors into account when interpreting the results of different programs.     

Investigating the Role of Assessment Method on Reports of Déjà Vu and Tip-of-the-Tongue States during Standard Recognition Tests

Déjà vu and tip-of-the-tongue (TOT) are retrieval-related subjective experiences whose study relies on participant self-report. In four experiments (ns = 224, 273, 123 and 154), we explored the effect of questioning method on reported occurrence of déjà vu and TOT in experimental settings. All participants carried out a continuous recognition task, which was not expected to induce déjà vu or TOT, but were asked about their experiences of these subjective states. When presented with contemporary definitions, between 32% and 58% of participants nonetheless reported experiencing déjà vu or TOT. Changing the definition of déjà vu or asking participants to bring to mind a real-life instance of déjà vu or TOT before completing the recognition task had no impact on reporting rates. However, there was an indication that changing the method of requesting subjective reports impacted reporting of both experiences. More specifically, moving from the commonly used retrospective questioning (e.g. “Have you experienced déjà vu?”) to free report instructions (e.g. “Indicate whenever you experience déjà vu.”) reduced the total number of reported déjà vu and TOT occurrences. We suggest that research on subjective experiences should move toward free report assessments. Such a shift would potentially reduce the presence of false alarms in experimental work, thereby reducing the overestimation of subjective experiences prevalent in this area of research.     

The integrated Michaelis-Menten rate equation: déjà vu or vu jàdé?

A recent article of Johnson and Goody (Biochemistry, 2011;50:8264–8269) described the almost-100-years-old paper of Michaelis and Menten. Johnson and Goody translated this classic article and presented the historical perspective to one of incipient enzyme-reaction data analysis, including a pioneering global fit of the integrated rate equation in its implicit form to the experimental time-course data. They reanalyzed these data, although only numerical techniques were used to solve the model equations. However, there is also the still little known algebraic rate-integration equation in a closed form that enables direct fitting of the data. Therefore, in this commentary, I briefly present the integral solution of the Michaelis-Menten rate equation, which has been largely overlooked for three decades. This solution is expressed in terms of the Lambert W function, and I demonstrate here its use for global nonlinear regression curve fitting, as carried out with the original time-course dataset of Michaelis and Menten.     

Targeting B cells in systemic lupus erythematosus: not just déjà vu all over again

Epratuzumab (anti-CD22) is a humanized monoclonal antibody that recognizes a pan-B-cell marker. It potentially downregulates B cell activity through negative signaling, as well as depleting B cells moderately. The uncontrolled series discussed by Dörner and colleagues in this issue of Arthritis Research &; Therapy suggests that epratuzumab may be safe and efficacious for systemic lupus erythematosus. A randomized controlled trial is currently active to test this possibility.