Homing endonuclease structure and function

Homing endonucleases are encoded by open reading frames that are embedded within group I, group II and archael introns, as well as inteins (intervening sequences that are spliced and excised post-translationally). These enzymes initiate transfer of those elements (and themselves) by generating strand breaks in cognate alleles that lack the intervening sequence, as well as in additional ectopic sites that broaden the range of intron and intein mobility. Homing endonucleases can be divided into several unique families that are remarkable in several respects: they display extremely high DNA-binding specificities which arise from long DNA target sites (14-40 bp), they are tolerant of a variety of sequence variations in these sites, and they display disparate DNA cleavage mechanisms. A significant number of homing endonucleases also act as maturases (highly specific cofactors for the RNA splicing reactions of their cognate introns). Of the known homing group I endonuclease families, two (HNH and His-Cys box enzymes) appear to be diverged from a common ancestral nuclease. While crystal structures of several representatives of the LAGLIDADG endonuclease family have been determined, only structures of single members of the HNH (I-HmuI), His-Cys box (I-PpoI) and GIY-YIG (I-TevI) families have been elucidated. These studies provide an important source of information for structure-function relationships in those families, and are the centerpiece of this review. Finally, homing endonucleases are significant targets for redesign and selection experiments, in hopes of generating novel DNA binding and cutting reagents for a variety of genomic applications.     

Rapid rise and fall of selfish sex-ratio X chromosomes in Drosophila simulans: spatiotemporal analysis of phenotypic and molecular data

Sex-ratio drive, which has been documented in several Drosophila species, is induced by X-linked segregation distorters. Contrary to Mendel's law of independent assortment, the sex-ratio chromosome (X(SR)) is inherited by more than half the offspring of carrier males, resulting in a female-biased sex ratio. This segregation advantage allows X(SR) to spread in populations, even if it is not beneficial for the carriers. In the cosmopolitan species D. simulans, the Paris sex-ratio is caused by recently emerged selfish X(SR) chromosomes. These chromosomes have triggered an intragenomic conflict, and their propagation has been halted over a large area by the evolution of complete drive suppression. Previous molecular population genetics analyses revealed a selective sweep indicating that the invasion of X(SR) chromosomes was very recent in Madagascar (likely less than 100 years ago). Here, we show that X(SR) chromosomes are now declining at this location as well as in Mayotte and Kenya. Drive suppression is complete in the three populations, which display little genetic differentiation and share swept haplotypes, attesting to a common and very recent ancestry of the X(SR) chromosomes. Patterns of DNA sequence variation also indicate a fitness cost of the segmental duplication involved in drive. The data suggest that X(SR) chromosomes started declining first on the African continent, then in Mayotte, and finally in Madagascar and strongly support a scenario of rapid cycling of X chromosomes. Once drive suppression has evolved, standard X(ST) chromosomes locally replace costly X(SR) chromosomes in a few decades.     

Making waves: the rise and fall and rise of quantitative developmental biology

The tenth annual RIKEN Center for Developmental Biology symposium 'Quantitative Developmental Biology' held in March 2012 covered a range of topics from coat colour patterning to the mechanics of morphogenesis. The studies presented shared a common theme in which a combination of physical theory, quantitative analysis and experiment was used to understand a specific cellular process in development. This report highlights these innovative studies and the long-standing questions in developmental biology that they seek to answer.     

Homing endonuclease I-TevIII: dimerization as a means to a double-strand break

Homing endonucleases are unusual enzymes, capable of recognizing lengthy DNA sequences and cleaving site-specifically within genomes. Many homing endonucleases are encoded within group I introns, and such enzymes promote the mobility reactions of these introns. Phage T4 has three group I introns, within the td, nrdB and nrdD genes. The td and nrdD introns are mobile, whereas the nrdB intron is not. Phage RB3 is a close relative of T4 and has a lengthier nrdB intron. Here, we describe I-TevIII, the H–N–H endonuclease encoded by the RB3 nrdB intron. In contrast to previous reports, we demonstrate that this intron is mobile, and that this mobility is dependent on I-TevIII, which generates 2-nt 3′ extensions. The enzyme has a distinct catalytic domain, which contains the H–N–H motif, and DNA-binding domain, which contains two zinc fingers required for interaction with the DNA substrate. Most importantly, I-TevIII, unlike the H–N–H endonucleases described so far, makes a double-strand break on the DNA homing site by acting as a dimer. Through deletion analysis, the dimerization interface was mapped to the DNA-binding domain. The unusual propensity of I-TevIII to dimerize to achieve cleavage of both DNA strands underscores the versatility of the H–N–H enzyme family.     

Social insects and selfish genes

Sometimes science advances because of a new idea. Sometimes, it's because of a new technique. When both occur together, exciting times result. In the study of social insects, DNA-based methods for measuring relatedness now allow increasingly detailed tests of Hamilton's theory of kin selection.     

Foxa2: the rise and fall of dopamine neurons

Understanding the development and maintenance of dopamine neurons is essential to establish novel stem cell therapies and animal models of Parkinson's disease. A recent PLoS Biology report (Kittappa et al., 2007) reveals that Foxa2 regulates dopamine neuron generation and differentiation, and that aging foxa2(+/-) mice spontaneously develop Parkinsonism.     

The rise and fall of SRY

Comparisons between species reveal when and how SRY, the testis-determining gene, evolved. SRY is younger than the Y chromosome, and so was probably not the original mammal sex-determining gene that defined the Y. SRY is typical of genes on the Y chromosome. It arose from a gene on the proto-sex chromosome pair with a function (possibly brain-determination) in both sexes. It has been buffeted in evolution, and shows variation in copy number, structure and expression. And it is dispensable, having been lost at least twice independently in different rodent lineages. At the observed rate of attrition, the human Y chromosome will be gone in 5-10 million years. This could lead to the extinction of our species or to a burst of hominid speciation.     

The rise and fall of photomutagenesis

UV is the most abundant human carcinogen, and protection from extensive exposure to it is a widespread human health issue. The use of chemicals (sunscreens) for protection is intuitive and efficacious. However, these chemicals may become activated to reactive intermediates when absorbing energy from UV, thus producing damage themselves, which may manifest itself in phototoxic, photoallergenic or photocarcinogenic reactions in humans. The development of safe sunscreens for humans is of high interest. Similar issues have been observed for some therapeutically used principles such as PUVA therapy for psoriasis or porphyrins for phototherapy of human cancers. Photoactivation has also been reported as a side effect of various pharmaceuticals such as the antibacterial fluoroquinolones. In this context, the authors have been involved over more than 20 years in the development and refinement of assays to test for photomutagenicity as an unwanted side effect of UV-mediated activation of such chemicals for cosmetic or pharmaceutical use. The initial years of great hopes for simple mammalian cell-based assays for photomutagenicity to screen out substances of concern for human use were followed by many years of collaborative trials to achieve standardization. However, it is now realized that this topic, albeit of human safety relevance, is highly complex and subject to many artificial modifiers, especially in vitro in mammalian cell culture. Thus, it is not really suitable for being engineered into a general testing framework within cosmetic or pharmaceutical testing guidelines. Much knowledge has been generated over the years to arrive at the conclusion that yes, photomutagenicity does exist with the use of chemicals, but how to best test for it will require a sophisticated case-by-case approach. Moreover, in comparison to the properties and risks of exposure to UV itself, it remains a comparatively minor human safety risk to address. In considering risks and benefits, we should also acknowledge beneficial effects of UV on human health, including an essential role in the production of Vitamin D. Thus, the interrelationships between UV, chemicals and human health remain a fascinating topic of research.     

Isolation and characterization of endonuclease J: a sequence-specific endonuclease cleaving immunoglobulin genes.

An endonuclease activity which cleaves close to the recombination sites of the immunoglobulin JK segments was found in extracts of chicken bursa of Fabricius and characterized after partial purification. The enzyme preparation also cleaved a VK segment at its 3' end. A similar activity was found in mouse liver, mouse myelomas and Hela cells. The enzyme designated as endonuclease J introduces double-stranded cleavages preferentially at sequences containing G clusters of pBR322 as well as the JK segments. However, not all the G clusters were cleaved by endonuclease J, suggesting that the enzyme recognizes additional sequences. Deletion of the conserved nonamer (GGTTTTTGT) located immediately 5' to the JK4 segment drastically reduced the cleavage activity of its immediate downstream G cluster. Although biological function of endonuclease J is not clear at this stage, the possibilities of its involvement in the immunoglobulin gene recombination and general recombination were discussed.     

The rise and fall of forensic hypnosis

This paper examines the fortunes of the controversial use of hypnosis to ‘enhance’ autobiographical memories in postwar America. From the 1950s through the early 1980s, hypnosis became increasingly popular as a means to exhume information thought to be buried within the mind. This practice was encouraged by lay understandings of memory drawn from a material culture full of new recording devices (motion pictures, tape and then video recorders); and during the years when the practice was becoming most popular and accepted, academic psychologists developed a contrary, reconstructive, account of memory that was put to use in a series of battles meant to put an end to hypnotic recall. But popular commitment to the idea of permanent memory ‘recordings’ sustained the practice and the assumptions about memory and self that were associated with it, and in the face of a culture of academic psychology fully committed to the idea of ‘reconstructive’, malleable memory, a tidal wave of ‘enhanced’ memories swept America in the late 1980s and 1990s, in the so-called ‘memory wars’. These, in turn, provoked academic psychologists to research the claims and counter claims central to the memory wars. The paper will also make an argument about the importance of lay knowledge in the psychological sciences explored in this paper: that popular psychological beliefs played a significant, even formative role in defining the nature of forensic psychological expertise, and also the framing of elite academic psychological research.     

The rise and fall of mutator bacteria

Bacteria with elevated mutation rates are frequently found among natural isolates. This is probably because of their ability to generate genetic variability, the substrate for natural selection. However, such high mutation rates can lead to the loss of vital functions. The evolution of bacterial populations may happen through alternating periods of high and low mutation rates. The cost and benefits of high mutation rates in the course of bacterial adaptive evolution are reviewed.     

Modelling and the fall and rise of the handicap principle

The story of the fall and rise of Zahavi??s handicap principle is one of a battle between models. Early attempts at formal modeling produced negative results and, unsurprisingly, scepticism about the principle. A major change came in 1990 with Grafen??s production of coherent models of a handicap mechanism of honest signalling. This paper??s first claim is that acceptance of the principle, and its dissemination into other disciplines, has been driven principally by that, and subsequent modeling, rather than by empirical results. Secondly, there is a vast literature on biological signalling but few studies that make all of the observations necessary to diagnose the handicap mechanism. My final claim is that many of the applications of ??costly signalling theory?? in other disciplines are conceptually confused. Misinterpretations of what is meant by ??costly signalling?? are common. Demonstrating that a signal is costly is insufficient and is not always necessary in order to prove that, and explain why, a signal is honest. In addition to the biological modelling of signals, there is an economic literature on the same subject. The two run in parallel in the sense that they have had little mutual interaction. Additionally, it is the biological modelling that has been picked up, and often misapplied, by other disciplines.