Annual Review of Genetics - Volume 41, 2007

In 1962, I proposed a model for integration of λ prophage into the bacterial chromosome. The model postulated two steps (i) circularization of the linear DNA molecule that had been injected into the cell from the phage particle; (ii) reciprocal recombination between phage and bacterial DNA at specific sites on both partners. This resulted in a cyclic permutation of gene order going from phage to prophage. This contrasted with integration models current at the time, which postulated that the prophage was not inserted into the continuity of the chromosome but rather laterally attached or synapsed with it. This chapter summarizes some of the steps leading up to the model including especially the genetic characterization of specialized transducing phages (λgal) by recombinational rescue of conditionally lethal mutations.

The serendipitous discovery of the conditional lethals is also described.

Studies of endospore formation by Bacillus subtilis and fruiting body development of Myxococcus xanthus have revealed key features of regulatory networks that govern temporal and spatial gene expression in bacteria. In B. subtilis, σ factor cascades, modulated by other types of transcription factors, regulate genes in two cell types that form and communicate with each other during starvation-induced sporulation. In M. xanthus, starving cells also send signals that alter gene expression, but the cascade to emerge so far involves transcription factors other than σ factors. A hundred thousand cells coordinate their movements to build a fruiting body in which spores form. The two regulatory networks are compared, and questions that remain are identified.

Elucidation of the molecular mechanisms that underlie disease development is still a tremendous challenge for basic science, and a prerequisite to the development of new and disease-specific targeted therapies. This review focuses on the function of SNAI2, a member of the Snail family of zinc-finger transcription factors, and discusses its possible role in disease development. SNAI2 has been implicated in diseases of melanocyte development and cancer in humans. Many malignancies arise from a rare population of cells that alone have the ability to self-renew and sustain the tumor (i.e., cancer stem cells). SNAI2 controls key aspects of stem cell function in mouse and human, suggesting that similar mechanisms control normal development and cancer stem cell properties. These insights are expected to contribute significantly to the genetics of cancer and to the development of both cancer therapy and new methods for assessing treatment efficacy.

The centromere is the DNA region that ensures genetic stability and is therefore of vital importance. Paradoxically, centromere proteins and centromeric structural domains are conserved despite that fact that centromere DNA sequences are highly variable and are not conserved. Remarkably, heritable states at the centromere can be propagated independent of the underlying centromeric DNA sequences. This review describes the epigenetic mechanisms governing centromere behavior, i.e., the mechanisms that control centromere assembly and propagation. A centromeric histone variant, CenH3, and histone modifications play key roles at centromeric chromatin. Histone modifications and RNA interference are important in assembly of pericentric heterochromatin structures. The molecular machinery that is directly involved in epigenetic control of centromeres is shared with regulation of gene expression. Nucleosome remodeling factors, histone chaperones, histone-modifying enzymes, transcription factors, and even RNA polymerase II itself control epigenetic states at centromeres.

Many fully developed metazoan tissues remain in a state of flux throughout life. During physiological cell turnover, older differentiated cells are typically eliminated by apoptosis and replaced by the division progeny of adult stem cells. Independently, each of these processes has been researched extensively, yet we know very little about how cell death and stem cell division are coordinated in adult organs. Freshwater planarians are an attractive model organism for research in this area. Not only do they undergo a very high rate of somatic cell turnover throughout life, but experimental tools are now available to study this process in vivo. Together, these attributes provide an opportunity to investigate the mechanisms, functions, and regulation of cell turnover in adult tissues.

The immunoglobulin (Ig) repertoire achieves functional diversification through several somatic alterations of the Ig locus. One of these processes, somatic hypermutation (SHM), deposits point mutations into the variable region of the Ig gene to generate higher-affinity variants. Activation-induced cytidine deaminase (AID) converts cytidine to uridine to initiate the hypermutation process. Error-prone versions of DNA repair are believed to then process these lesions into a diverse spectrum of point mutations. We review the current understanding of the molecular mechanisms and regulation of SHM, and also discuss emerging ideas which merit further exploration.

Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions. In the prototypical two-component system, a sensor histidine kinase catalyzes its autophosphorylation and then subseqeuntly transfers the phosphoryl group to a response regulator, which can then effect changes in cellular physiology, often by regulating gene expression. The utility of these signaling systems is underscored by their prevalence throughout the bacterial kingdom and by the fact that many bacteria contain dozens, or sometimes hundreds, of these signaling proteins. The presence of so many highly related signaling proteins in individual cells creates both an opportunity and a challenge. Do cells take advantage of the similarity between signaling proteins to integrate signals or diversify responses, and thereby enhance their ability to process information? Conversely, how do cells prevent unwanted cross-talk and maintain the insulation of distinct pathways? Here we address both questions by reviewing the cellular and molecular mechanisms that dictate the specificity of two-component signaling pathways.

The establishment of the photosynthetic organelle (plastid) in eukaryotes and the diversification of algae and plants were landmark evolutionary events because these taxa form the base of the food chain for many ecosystems on our planet. The plastid originated via a putative single, ancient primary endosymbiosis in which a heterotrophic protist engulfed and retained a cyanobacterium in its cytoplasm. Once successfully established, this plastid spread into other protist lineages through eukaryote-eukaryote (secondary and tertiary) endosymbioses. This process of serial cell capture and enslavement explains the diversity of photosynthetic eukaryotes. Recent genomic and phylogenomic approaches have significantly clarified plastid genome evolution, the movement of endosymbiont genes to the “host” nuclear genome (endosymbiotic gene transfer), and plastid spread throughout the eukaryotic tree of life. Here we review these aspects of plastid evolution with a focus on understanding early events in plastid endosymbiosis.

Chromosomal fragile sites are specific loci that preferentially exhibit gaps and breaks on metaphase chromosomes following partial inhibition of DNA synthesis. Their discovery has led to novel findings spanning a number of areas of genetics. Rare fragile sites are seen in a small proportion of individuals and are inherited in a Mendelian manner. Some, such as FRAXA in the FMR1 gene, are associated with human genetic disorders, and their study led to the identification of nucleotide-repeat expansion as a frequent mutational mechanism in humans. In contrast, common fragile sites are present in all individuals and represent the largest class of fragile sites. Long considered an intriguing component of chromosome structure, common fragile sites have taken on novel significance as regions of the genome that are particularly sensitive to replication stress and that are frequently rearranged in tumor cells. In recent years, much progress has been made toward understanding the genomic features of common fragile sites and the cellular processes that monitor and influence their stability. Their study has merged with that of cell cycle checkpoints and DNA repair, and common fragile sites have provided insight into understanding the consequences of replication stress on DNA damage and genome instability in cancer cells.

Candida albicans is a species of fungus that typically resides in the gastrointestinal tracts of humans and other warm-blooded animals. It is also the most common human fungal pathogen, causing a variety of skin and soft tissue infections in healthy people and more virulent invasive and disseminated diseases in patients with compromised immune systems. How this microorganism manages to persist in healthy hosts but also to cause a spectrum of disease states in the immunocompromised host are questions of significant biological interest as well as major clinical and economic importance. In this review, we describe recent developments in population genetics, the mating process, and gene disruption technology that are providing much needed experimental insights into the biology of C. albicans.

Stably maintaining specific states of gene expression during cell division is crucial for cellular differentiation. In fission yeast, such patterns result from directed gene rearrangements and chromosomally inherited epigenetic gene control mechanisms that control mating cell type. Recent advances have shown that a specific DNA strand at the mat1 locus is “differentiated” by a novel strand-specific imprint so that nonequivalent sister chromatids are produced. Therefore, cellular differentiation is a natural consequence of the fact that DNA strands are complementary and nonequivalent. Another epigenetic control that “silences” library copies of mat-information is due to heterochromatin organization. This is a clear case where Mendel’s gene is composed of DNA plus the associated epigenetic moiety. Following up on initial genetic studies with more recent molecular investigations, this system has become one of the prominent models to understand mechanisms of gene regulation, genome integrity, and cellular differentiation. By applying lessons learned from these studies, such epigenetic gene control mechanisms, which must be installed in somatic cells, might explain mechanisms of cellular differentiation and development in higher eukaryotes.

Eukaryotic DNA replication is regulated to ensure all chromosomes replicate once and only once per cell cycle. Replication begins at many origins scattered along each chromosome. Except for budding yeast, origins are not defined DNA sequences and probably are inherited by epigenetic mechanisms. Initiation at origins occurs throughout the S phase according to a temporal program that is important in regulating gene expression during development. Most replication proteins are conserved in evolution in eukaryotes and archaea, but not in bacteria. However, the mechanism of initiation is conserved and consists of origin recognition, assembly of prereplication (pre-RC) initiative complexes, helicase activation, and replisome loading. Cell cycle regulation by protein phosphorylation ensures that pre-RC assembly can only occur in G1 phase, whereas helicase activation and loading can only occur in S phase. Checkpoint regulation maintains high fidelity by stabilizing replication forks and preventing cell cycle progression during replication stress or damage.

The acronym Mhc, major histocompatibility complex, is customarily not allied with topics in evolutionary biology. Here, however, we attempt to demonstrate that the Mhc has much to offer to this discipline and intimate that evolutionary biologists who ignore its contributions miss out on a chance of applying a new approach to vexing questions. One aspect of the Mhc in particular affords a fresh look at the population processes that transform one species into another: the trans-species polymorphism, the passage of allelic lineages from ancestral to descendant species. We provide examples of using the Mhc polymorphism in estimating the size of the founding population of new species, and of analyzing the long-term population demographies of phylogenetic lineages. We then extend the concept of trans-species polymorphism to other genes, even those not evolving under balancing selection, and argue that the phenomenon is widespread between closely related species. On the example of the cichlid fishes of Lake Victoria, we demonstrate how the concept changes the interpretation of this so-called “species flock.” We contend that the conclusions reached regarding the cichlid fishes apply also to other examples of adaptive radiation, for example that of Darwin's finches, and so provide new insights into the nature of speciation in general.

When eukaryotic cells encounter double-stranded RNA, genes of matching sequence are silenced through RNA interference. Surprisingly, in some animals and plants, the same gene is specifically silenced even in cells that did not encounter the double-stranded RNA, due to the transport of a gene-specific silencing signal between cells. This silencing signal likely has an RNA component that gives it sequence-specificity, however its precise identity remains unknown. Studies in the worm Caenorhabditis elegans and in plants have revealed parts of a complex protein machinery that transports this silencing signal. Some of these proteins are conserved in vertebrates, including mammals, raising the possibility that higher animals can communicate gene-specific silencing information between cells. Such communication provides antiviral immunity in plants and perhaps in C. elegans. Identifying the transported silencing signal and deciphering the evolutionarily selected role of the transport machinery are some of the key challenges for the future.

Transposable elements are mobile genetic units that exhibit broad diversity in their structure and transposition mechanisms. Transposable elements occupy a large fraction of many eukaryotic genomes and their movement and accumulation represent a major force shaping the genes and genomes of almost all organisms. This review focuses on DNA-mediated or class 2 transposons and emphasizes how this class of elements is distinguished from other types of mobile elements in terms of their structure, amplification dynamics, and genomic effect. We provide an up-to-date outlook on the diversity and taxonomic distribution of all major types of DNA transposons in eukaryotes, including Helitrons and Mavericks. We discuss some of the evolutionary forces that influence their maintenance and diversification in various genomic environments. Finally, we highlight how the distinctive biological features of DNA transposons have contributed to shape genome architecture and led to the emergence of genetic innovations in different eukaryotic lineages.

Our understanding of the details of mammalian meiotic recombination has recently advanced significantly. Sperm typing technologies, linkage studies, and computational inferences from population genetic data have together provided information in unprecedented detail about the location and activity of the sites of crossing-over in mice and humans. The results show that the vast majority of meiotic recombination events are localized to narrow DNA regions (hot spots) that constitute only a small fraction of the genome. The data also suggest that the molecular basis of hot spot activity is unlikely to be strictly determined by specific DNA sequence motifs in cis. Further molecular studies are needed to understand how hot spots originate, function and evolve.

Cholesterol is an essential component of mammalian cell membranes and is required for proper membrane permeability, fluidity, organelle identity, and protein function. Cells maintain sterol homeostasis by multiple feedback controls that act through transcriptional and posttranscriptional mechanisms. The membrane-bound transcription factor sterol regulatory element binding protein (SREBP) is the principal regulator of both sterol synthesis and uptake. In mammalian cells, the ER membrane protein Insig has emerged as a key component of homeostatic regulation by controlling both the activity of SREBP and the sterol-dependent degradation of the biosynthetic enzyme HMG-CoA reductase. In this review, we focus on recent advances in our understanding of the molecular mechanisms of the regulation of sterol synthesis. A comparative analysis of SREBP and HMG-CoA reductase regulation in mammals, yeast, and flies points toward an equilibrium model for how lipid signals regulate the activity of sterol-sensing proteins and their downstream effectors.

The dynamic range of a bacterial species’ natural environment is reflected in the complexity of its systems that control cell cycle progression and its range of adaptive responses. We discuss the genetic network and integrated three-dimensional sensor/response systems that regulate the cell cycle and asymmetric cell division in the bacterium Caulobacter crescentus. The cell cycle control circuitry is tied closely to chromosome replication and morphogenesis by multiple feedback pathways from the modular functions that implement the cell cycle. The sophistication of the genetic regulatory circuits and the elegant integration of temporally controlled transcription and protein synthesis with spatially dynamic phosphosignaling and proteolysis pathways, and epigenetic regulatory mechanisms, form a remarkably robust living system.

Although the role of biotin in metabolic reactions has long been recognized, its influence on transcription has only recently been discovered. A key protein in biotin-mediated transcription regulation is the biotin protein ligase, the enzyme responsible for catalyzing covalent linkage of the vitamin to biotin-dependent carboxylases. In the biotin regulatory system of Escherichia coli, the best characterized of the biotin-sensing systems, the biotin protein ligase functions both as the biotinylating enzyme and as a transcription repressor. Detailed mechanistic studies of this system are reviewed. In addition, recent studies have revealed other biotin-sensing systems in organisms ranging from bacteria to humans. These systems and the central role of the biotin protein ligase in each are also reviewed.

In recent years, it has become clear that all of the organisms on the Earth are related to each other in ways that can be documented by molecular sequence comparison. In this review, we focus on the evolutionary relationships among the proteins of the eukaryotes, especially those that allow inference of function from one species to another. Data and illustrations are derived from specific comparison of eight species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Caenorhabditis elegans, Danio rerio, Saccharomyces cerevisiae, and Plasmodium falciparum.