Showing papers in "Annual Review of Biochemistry in 2006"
TL;DR: The relative importance of the common main-chain and side-chain interactions in determining the propensities of proteins to aggregate is discussed and some of the evidence that the oligomeric fibril precursors are the primary origins of pathological behavior is described.
Abstract: Peptides or proteins convert under some conditions from their soluble forms into highly ordered fibrillar aggregates. Such transitions can give rise to pathological conditions ranging from neurodegenerative disorders to systemic amyloidoses. In this review, we identify the diseases known to be associated with formation of fibrillar aggregates and the specific peptides and proteins involved in each case. We describe, in addition, that living organisms can take advantage of the inherent ability of proteins to form such structures to generate novel and diverse biological functions. We review recent advances toward the elucidation of the structures of amyloid fibrils and the mechanisms of their formation at a molecular level. Finally, we discuss the relative importance of the common main-chain and side-chain interactions in determining the propensities of proteins to aggregate and describe some of the evidence that the oligomeric fibril precursors are the primary origins of pathological behavior.
5,897 citations
TL;DR: The recent biochemical, molecular, cellular, and physiological functions of histone methylation and ubiquitination involved in the regulation of gene expression as determined by a combination of enzymological, structural, and genetic methodologies are highlighted.
Abstract: It is more evident now than ever that nucleosomes can transmit epigenetic information from one cell generation to the next. It has been demonstrated during the past decade that the posttranslational modifications of histone proteins within the chromosome impact chromatin structure, gene transcription, and epigenetic information. Multiple modifications decorate each histone tail within the nucleosome, including some amino acids that can be modified in several different ways. Covalent modifications of histone tails known thus far include acetylation, phosphorylation, sumoylation, ubiquitination, and methylation. A large body of experimental evidence compiled during the past several years has demonstrated the impact of histone acetylation on transcriptional control. Although histone modification by methylation and ubiquitination was discovered long ago, it was only recently that functional roles for these modifications in transcriptional regulation began to surface. Highlighted in this review are the recent biochemical, molecular, cellular, and physiological functions of histone methylation and ubiquitination involved in the regulation of gene expression as determined by a combination of enzymological, structural, and genetic methodologies.
1,119 citations
TL;DR: Present knowledge of Hsp90 structure and function gleaned from crystallographic studies of individual domains and recent progress in obtaining a structure for the ATP-bound conformation of the intact dimeric chaperone are discussed.
Abstract: Heat shock protein 90 (Hsp90) is a molecular chaperone essential for activating many signaling proteins in the eukaryotic cell. Biochemical and structural analysis of Hsp90 has revealed a complex mechanism of ATPase-coupled conformational changes and interactions with cochaperone proteins, which facilitate activation of Hsp90's diverse "clientele." Despite recent progress, key aspects of the ATPase-coupled mechanism of Hsp90 remain controversial, and the nature of the changes, engendered by Hsp90 in client proteins, is largely unknown. Here, we discuss present knowledge of Hsp90 structure and function gleaned from crystallographic studies of individual domains and recent progress in obtaining a structure for the ATP-bound conformation of the intact dimeric chaperone. Additionally, we describe the roles of the plethora of cochaperones with which Hsp90 cooperates and growing insights into their biochemical mechanisms, which come from crystal structures of Hsp90 cochaperone complexes.
1,028 citations
TL;DR: In gram-negative bacteria, it is proposed that biosynthesis and translocation of capsular polysaccharides to the cell surface are temporally and spatially coupled by multiprotein complexes that span the cell envelope.
Abstract: Capsules are protective structures on the surfaces of many bacteria. The remarkable structural diversity in capsular polysaccharides is illustrated by almost 80 capsular serotypes in Escherichia coli. Despite this variation, the range of strategies used for capsule biosynthesis and assembly is limited, and E. coli isolates provide critical prototypes for other bacterial species. Related pathways are also used for synthesis and export of other bacterial glycoconjugates and some enzymes/processes have counterparts in eukaryotes. In gram-negative bacteria, it is proposed that biosynthesis and translocation of capsular polysaccharides to the cell surface are temporally and spatially coupled by multiprotein complexes that span the cell envelope. These systems have an impact on both a general understanding of membrane trafficking in bacteria and on bacterial pathogenesis.
946 citations
TL;DR: The identification and characterization of yeast mutants defective either in the biogenesis of peroxisomes or in one of its metabolic functions, notably fatty acid beta-oxidation, combined with the recognition of a group of genetic diseases in man, wherein these processes are also defective, have provided new insights in all aspects of perxisomes.
Abstract: In this review, we describe the current state of knowledge about the biochemistry of mammalian peroxisomes, especially human peroxisomes. The identification and characterization of yeast mutants defective either in the biogenesis of peroxisomes or in one of its metabolic functions, notably fatty acid beta-oxidation, combined with the recognition of a group of genetic diseases in man, wherein these processes are also defective, have provided new insights in all aspects of peroxisomes. As a result of these and other studies, the indispensable role of peroxisomes in multiple metabolic pathways has been clarified, and many of the enzymes involved in these pathways have been characterized, purified, and cloned. One aspect of peroxisomes, which has remained ill defined, is the transport of metabolites across the peroxisomal membrane. Although it is clear that mammalian peroxisomes under in vivo conditions are closed structures, which require the active presence of metabolite transporter proteins, much remains to be learned about the permeability properties of mammalian peroxisomes and the role of the four half ATP-binding cassette (ABC) transporters therein.
871 citations
TL;DR: Understanding the mechanisms involved in modulating skeletal muscle phenotypes can potentiate the development of new therapeutic measures to ameliorate muscular diseases.
Abstract: Skeletal muscle is comprised of heterogeneous muscle fibers that differ in their physiological and metabolic parameters. It is this diversity that enables different muscle groups to provide a variety of functional properties. In response to environmental demands, skeletal muscle remodels by activating signaling pathways to reprogram gene expression to sustain muscle performance. Studies have been performed using exercise, electrical stimulation, transgenic animal models, disease states, and microgravity to show genetic alterations and transitions of muscle fibers in response to functional demands. Various components of calcium-dependent signaling pathways and multiple transcription factors, coactivators and corepressors have been shown to be involved in skeletal muscle remodeling. Understanding the mechanisms involved in modulating skeletal muscle phenotypes can potentiate the development of new therapeutic measures to ameliorate muscular diseases.
762 citations
TL;DR: This review addresses the structure, function, and stability of cold-adapted enzymes, highlighting the challenges for immediate and future consideration.
Abstract: By far the largest proportion of the Earth's biosphere is comprised of organisms that thrive in cold environments (psychrophiles). Their ability to proliferate in the cold is predicated on a capacity to synthesize cold-adapted enzymes. These enzymes have evolved a range of structural features that confer a high level of flexibility compared to thermostable homologs. High flexibility, particularly around the active site, is translated into low-activation enthalpy, low-substrate affinity, and high specific activity at low temperatures. High flexibility is also accompanied by a trade-off in stability, resulting in heat lability and, in the few cases studied, cold lability. This review addresses the structure, function, and stability of cold-adapted enzymes, highlighting the challenges for immediate and future consideration. Because of the unique properties of cold-adapted enzymes, they are not only an important focus in extremophile biology, but also represent a valuable model for fundamental researc...
749 citations
TL;DR: The data suggest that LKB1 functions as a tumor suppressor by not only inhibiting proliferation, but also by exerting profound effects on cell polarity and, most unexpectedly, on the ability of a cell to detect and respond to low cellular energy levels.
Abstract: This review focuses on remarkable recent findings concerning the mechanism by which the LKB1 protein kinase that is mutated in Peutz-Jeghers cancer syndrome operates as a tumor suppressor. We discuss evidence that the cellular localization and activity of LKB1 is controlled through its interaction with a catalytically inactive protein resembling a protein kinase, termed STRAD, and an armadillo repeat-containing protein, named mouse protein 25 (MO25). The data suggest that LKB1 functions as a tumor suppressor by not only inhibiting proliferation, but also by exerting profound effects on cell polarity and, most unexpectedly, on the ability of a cell to detect and respond to low cellular energy levels. Genetic and biochemical findings indicate that LKB1 exerts its effects by phosphorylating and activating 14 protein kinases, all related to the AMP-activated protein kinase. The work described in this review shows how a study of an obscure cancer syndrome can uncover new and important regulatory pathways, relevant to the understanding of multiple human diseases.
730 citations
TL;DR: The coupling mechanism of complex I most likely involves semiquinone intermediates that drive proton pumping through redox-linked conformational changes.
Abstract: NADH:quinone oxidoreductase (complex I) pumps protons across the inner membrane of mitochondria or the plasma membrane of many bacteria. Human complex I is involved in numerous pathological conditions and degenerative processes. With 14 central and up to 32 accessory subunits, complex I is among the largest membrane-bound protein assemblies. The peripheral arm of the L-shaped molecule contains flavine mononucleotide and eight or nine iron-sulfur clusters as redox prosthetic groups. Seven of the iron-sulfur clusters form a linear electron transfer chain between flavine and quinone. In most organisms, the seven most hydrophobic subunits forming the core of the membrane arm are encoded by the mitochondrial genome. Most central subunits have evolved from subunits of different hydrogenases and bacterial Na+/H+ antiporters. This evolutionary origin is reflected in three functional modules of complex I. The coupling mechanism of complex I most likely involves semiquinone intermediates that drive proton pumping through redox-linked conformational changes.
725 citations
TL;DR: Evidence is provided of the propensity of rhodopsin and, most likely, other GPCRs to dimerize, a property that may be pertinent to their function.
Abstract: The rhodopsin crystal structure provides a structural basis for understanding the function of this and other G protein–coupled receptors (GPCRs). The major structural motifs observed for rhodopsin are expected to carry over to other GPCRs, and the mechanism of transformation of the receptor from inactive to active forms is thus likely conserved. Moreover, the high expression level of rhodopsin in the retina, its specific localization in the internal disks of the photoreceptor structures [termed rod outer segments (ROS)], and the lack of other highly abundant membrane proteins allow rhodopsin to be examined in the native disk membranes by a number of methods. The results of these investigations provide evidence of the propensity of rhodopsin and, most likely, other GPCRs to dimerize, a property that may be pertinent to their function.
708 citations
TL;DR: The chemical mechanism of sirtuins provides novel opportunities for signaling and metabolic regulation of protein deacetylation and the biological, chemical, and structural characteristics of these unusual enzymes are discussed.
Abstract: Sirtuins are a family of NAD+-dependent protein deacetylases widely distributed in all phyla of life. Accumulating evidence indicates that sirtuins are important regulators of organism life span. In yeast, these unique enzymes regulate gene silencing by histone deacetylation and via formation of the novel compound 2′-O-acetyl-ADP-ribose. In multicellular organisms, sirtuins deacetylate histones and transcription factors that regulate stress, metabolism, and survival pathways. The chemical mechanism of sirtuins provides novel opportunities for signaling and metabolic regulation of protein deacetylation. The biological, chemical, and structural characteristics of these unusual enzymes are discussed in this review.
TL;DR: This review examines the linkage between protein conformational motions and enzyme catalysis in the context of two enzymes that catalyze hydride transfer, namely dihydrofolate reductase and liver alcohol dehydrogenase.
Abstract: This review examines the linkage between protein conformational motions and enzyme catalysis. The fundamental issues related to this linkage are probed in the context of two enzymes that catalyze hydride transfer, namely dihydrofolate reductase and liver alcohol dehydrogenase. The extensive experimental and theoretical studies addressing the role of protein conformational changes in these enzyme reactions are summarized. Evidence is presented for a network of coupled motions throughout the protein fold that facilitate the chemical reaction. This network is comprised of fast thermal motions that are in equilibrium as the reaction progresses along the reaction coordinate and that lead to slower equilibrium conformational changes conducive to the chemical reaction.
TL;DR: This work focuses on the question of how the remarkably diverse array of eukaryotic signaling circuits may have evolved and shows that such modular systems can be exploited to engineer nonnatural signaling proteins and pathways with novel behavior.
Abstract: Living cells display complex signal processing behaviors, many of which are mediated by networks of proteins specialized for signal transduction. Here we focus on the question of how the remarkably diverse array of eukaryotic signaling circuits may have evolved. Many of the mechanisms that connect signaling proteins into networks are highly modular: The core catalytic activity of a signaling protein is physically and functionally separable from molecular domains or motifs that determine its linkage to both inputs and outputs. This high degree of modularity may make these systems more evolvable—in principle, novel circuits, and therefore highly innovative regulatory behaviors, can arise from relatively simple genetic events such as recombination, deletion, or insertion. In support of this hypothesis, recent studies show that such modular systems can be exploited to engineer nonnatural signaling proteins and pathways with novel behavior.
TL;DR: The structure and integrity of telomeres are essential for genome stability and regulation by RNA-DNA, TERT- DNA, Tert-RNA, TTERT interactions, and TERN-associated proteins; and the relationship between telomerase enzymology and telomere maintenance is discussed.
Abstract: The structure and integrity of telomeres are essential for genome stability. Telomere dysregulation can lead to cell death, cell senescence, or abnormal cell proliferation. The maintenance of telomere repeats in most eukaryotic organisms requires telomerase, which consists of a reverse transcriptase (RT) and an RNA template that dictates the synthesis of the G-rich strand of telomere terminal repeats. Structurally, telomerase reverse transcriptase (TERT) contains unique and variable N- and C-terminal extensions that flank a central RTlike domain. The enzymology of telomerase includes features that are both similar to and distinct from those characteristic of other RTs. Two distinguishing features of TERT are its stable association with the telomerase RNA and its ability to repetitively reverse transcribe the template segment of RNA. Here we discuss TERT structure and function; its regulation by RNA-DNA, TERT-DNA, TERT-RNA, TERT-TERT interactions, and TERT-associated proteins; and the relationship between telomerase enzymology and telomere maintenance.
TL;DR: The mechanism underlying cytokinesis, the final step in cell division, remains one of the major unsolved questions in basic cell biology and thanks to advances in functional genomics and proteomics, a "parts list" of proteins involved in cytokines is assembled.
Abstract: The mechanism underlying cytokinesis, the final step in cell division, remains one of the major unsolved questions in basic cell biology. Thanks to advances in functional genomics and proteomics, we are now able to assemble a “parts list” of proteins involved in cytokinesis. In this review, we discuss how to relate this parts list to biological mechanism. For easier analysis, we split cytokinesis into discrete steps: cleavage plane specification, rearrangement of microtubule structures, contractile ring assembly, ring ingression, and completion. We report on the advances that have been made to understand these steps and how they can be integrated into a global understanding of cytokinesis. We also discuss the extent to which classic questions have been answered and identify major outstanding questions.
TL;DR: This review presents a thorough structural analysis of the DAPk kinases, discusses methods of regulation, clarifies their cellular targets and functions, and shows how these functions are integrated.
Abstract: Death-associated protein kinase (DAPk) is the founding member of a newly classified family of Ser/Thr kinases, whose members not only possess significant homology in their catalytic domains, but also share cell death–associated functions. The realization that DAPk is a tumor suppressor gene, whose expression is lost in multiple tumor types, has spurred a flurry of interest in the kinase family and produced an impressive body of literature concerning its function, regulation, and connection to disease. The DAPk family has been linked to several cell death–related signaling pathways, and functions other than cell death have also been proposed. This review presents a thorough structural analysis of the kinases, discusses methods of regulation, clarifies their cellular targets and functions, and shows how these functions are integrated. Although many gaps in our knowledge still remain, the data generated to date can be combined to delineate a place for the DAPk family within the general cell death-signaling network.
TL;DR: Recent findings in lipid-induced functional impairments in the major peripheral organs that control energy flux are reviewed, placing emphasis on adipose tissue, the liver, skeletal muscle, and the pancreas.
Abstract: An epidemic surge in the incidence of obesity has occurred worldwide over the past two decades. This alarming trend has been triggered by lifestyle habits that encourage overconsumption of energy-rich foods while also discouraging regular physical activity. These environmental influences create a chronic energy imbalance that leads to persistent weight gain in the form of body fat and a host of other abnormalities in metabolic homeostasis. As adiposity increases, so does the risk of developing comorbidities such as diabetes, hypertension, and cardiovascular disease. The intimate association between obesity and systemic metabolic dysregulation has inspired a new area of biochemistry research in which scientists are seeking to understand the molecular mechanisms that link chronic lipid oversupply to tissue dysfunction and disease development. The purpose of this chapter is to review recent findings in this area, placing emphasis on lipid-induced functional impairments in the major peripheral organs that control energy flux: adipose tissue, the liver, skeletal muscle, and the pancreas.
TL;DR: When a telomere becomes unprotected or if only one end of a chromosomal double-strand break succeeds in recombining with a template sequence, DNA can be repaired by a recombination-dependent DNA replication process termed break-induced replication (BIR).
Abstract: When a telomere becomes unprotected or if only one end of a chromosomal double-strand break succeeds in recombining with a template sequence, DNA can be repaired by a recombination-dependent DNA replication process termed break-induced replication (BIR). In budding yeasts, there are two BIR pathways, one dependent on the Rad51 recombinase protein and one Rad51 independent; these two repair processes lead to different types of survivors in cells lacking the telomerase enzyme that is required for normal telomere maintenance. Recombination at telomeres is triggered by either excessive telomere shortening or disruptions in the function of telomere-binding proteins. Telomere elongation by BIR appears to often occur through a "roll and spread" mechanism. In this process, a telomeric circle produced by recombination at a dysfunctional telomere acts as a template for a rolling circle BIR event to form an elongated telomere. Additional BIR events can then copy the elongated sequence to all other telomeres.
TL;DR: Structural, experimental, and theoretical evidence supports the model of long-distance proton transfer via hydrogen-bonded water chains in proteins as well as the basic concept that proton uptake and release in a redox-driven pump are driven by charge changes at the membrane-embedded centers.
Abstract: A series of metalloprotein complexes embedded in a mitochondrial or bacterial membrane utilize electron transfer reactions to pump protons across the membrane and create an electrochemical potential (ΔμH+) Current understanding of the principles of electron-driven proton transfer is discussed, mainly with respect to the wealth of knowledge available from studies of cytochrome c oxidase Structural, experimental, and theoretical evidence supports the model of long-distance proton transfer via hydrogen-bonded water chains in proteins as well as the basic concept that proton uptake and release in a redox-driven pump are driven by charge changes at the membrane-embedded centers Key elements in the pumping mechanism may include bound water, carboxylates, and the heme propionates, arginines, and associated water above the hemes There is evidence for an important role of subunit III and proton backflow, but the number and nature of gating mechanisms remain elusive, as does the mechanism of physiologic
TL;DR: Not only are these transport systems crucial to maintain neuronal viability and differentiation, but considerable experimental evidence suggests that failure of axonal transport may play a role in the development or progression of neurological diseases such as Alzheimer's disease.
Abstract: In contrast to most eukaryotic cells, neurons possess long, highly branched processes called axons and dendrites. In large mammals, such as humans, some axons reach lengths of over 1 m. These lengths pose a major challenge to the movement of proteins, vesicles, and organelles between presynaptic sites and cell bodies. To overcome this challenge axons and dendrites rely upon specialized transport machinery consisting of cytoskeletal motor proteins generating directed movements along cytoskeletal tracks. Not only are these transport systems crucial to maintain neuronal viability and differentiation, but considerable experimental evidence suggests that failure of axonal transport may play a role in the development or progression of neurological diseases such as Alzheimer's disease.
TL;DR: This review discusses the birth of the concept of generating targeted, nontoxic signal transduction inhibitors, the potential to utilize PTK inhibitors/tyrphostins to attenuate nonmalignant pathological conditions, such as immune disorders, tissue rejection, and restenosis.
Abstract: The development of tyrosine phosphorylation inhibitors has transformed the approach to cancer therapy and is likely to affect other fields of medicine. In spite of the conservation among protein tyrosine kinases (PTKs), one can develop small molecules that block the activity of a narrow spectrum of PTKs and that exhibit much less toxicity than the currently used chemotherapeutic agents. In this review, we discuss principles for inhibiting specific PTKs. We discuss (a) the birth of the concept of generating targeted, nontoxic signal transduction inhibitors, (b) the potential of substrate-competitive versus the more common ATP-competitive PTK inhibitors, (c) the combination of PTK inhibitors with other signal transduction inhibitors to induce apoptosis—the best way to induce the demise of the cancer cell, and (d) the potential to utilize PTK inhibitors/tyrphostins to attenuate nonmalignant pathological conditions, such as immune disorders, tissue rejection, and restenosis.
TL;DR: Bacterial cells contain a variety of structural filamentous proteins necessary for the spatial regulation of cell shape, cell division, and chromosome segregation, analogous to the eukaryotic cytoskeleton proteins.
Abstract: Bacterial cells contain a variety of structural filamentous proteins necessary for the spatial regulation of cell shape, cell division, and chromosome segregation, analogous to the eukaryotic cytoskeletal proteins. The molecular mechanisms by which these proteins function are beginning to be revealed, and these proteins show numerous three-dimensional structural features and biochemical properties similar to those of eukaryotic actin and tubulin, revealing their evolutionary relationship. Recent technological advances have illuminated links between cell division and chromosome segregation, suggesting a higher complexity and organization of the bacterial cell than was previously thought.
TL;DR: The first successful, mechanism-based efforts to prepare and characterize nanomolar ASNS inhibitors are discussed, together with the implications of these studies for future efforts to develop useful drugs.
Abstract: Modern clinical treatments of childhood acute lymphoblastic leukemia (ALL) employ enzyme-based methods for depletion of blood asparagine in combination with standard chemotherapeutic agents. Significant side effects can arise in these protocols and, in many cases, patients develop drug-resistant forms of the disease that may be correlated with up-regulation of the enzyme glutamine-dependent asparagine synthetase (ASNS). Though the precise molecular mechanisms that result in the appearance of drug resistance are the subject of active study, potent ASNS inhibitors may have clinical utility in treating asparaginase-resistant forms of childhood ALL. This review provides an overview of recent developments in our understanding of (a) the structure and catalytic mechanism of ASNS, and (b) the role that ASNS may play in the onset of drug-resistant childhood ALL. In addition, the first successful, mechanism-based efforts to prepare and characterize nanomolar ASNS inhibitors are discussed, together with the...
TL;DR: Crystal structures and their implications for function are described for the energy transducing hetero-oligomeric dimeric cytochrome b6f complex of oxygenic photosynthesis from the thermophilic cyanobacterium, Mastigocladus laminosus, and the green alga.
Abstract: Crystal structures and their implications for function are described for the energy transducing hetero-oligomeric dimeric cytochrome b 6 f complex of oxygenic photosynthesis from the thermophilic cyanobacterium, Mastigocladus laminosus, and the green alga, Chlamydomonas reinhardtii. The complex has a cytochrome b core and a central quinone exchange cavity, defined by the two monomers that are very similar to those in the respiratory cytochrome bc 1 complex. The pathway of quinol/quinone (Q/QH2) transfer emphasizes the labyrinthine internal structure of the complex, including an 11×12 A portal through which Q/QH2, containing a 45-carbon isoprenoid chain, must pass. Three prosthetic groups are present in the b 6 f complex that are not found in the related bc 1 complex: a chlorophyll (Chl) a, a β-carotene, and a structurally unique covalently bound heme that does not possess amino acid side chains as axial ligands. It is hypothesized that this heme, exposed to the cavity and a neighboring plastoquino...
TL;DR: The functional mechanisms, nucleotide recognition, and conformational changes for the transport, suggested from the structure, are discussed along with the large body of biochemical and functional results.
Abstract: Import and export of metabolites through mitochondrial membranes are vital processes that are highly controlled and regulated at the level of the inner membrane. Proteins of the mitochondrial carrier family ( MCF ) are embedded in this membrane, and each member of the family achieves the selective transport of a specific metabolite. Among these, the ADP/ATP carrier transports ADP into the mitochondrial matrix and exports ATP toward the cytosol after its synthesis. Because of its natural abundance, the ADP/ATP carrier is the best characterized within MCF, and a high-resolution structure of one conformation is known. The overall structure is basket shaped and formed by six transmembrane helices that are not only tilted with respect to the membrane, but three of them are also kinked at the level of prolines. The functional mechanisms, nucleotide recognition, and conformational changes for the transport, suggested from the structure, are discussed along with the large body of biochemical and functional results.
TL;DR: The work presented here on the ADP/ATP carrier, rhodopsin, and the cytochrome b6f complex represents incredible progress in this now blossoming field of membrane proteins.
Abstract: In our review, we introduce an organizational scheme for membrane protein function. It is the relationship between structure, dynamics, and environment that endows the membrane and its constituents with remarkable sensitivity and robustness. Our understanding begins with landmark advances like those presented in the following chapters. Membrane proteins are notoriously difficult to study, and so the work presented here on the ADP/ATP carrier [Nury et al. (2)], rhodopsin [Palczewski (24)], and the cytochrome b 6 f complex [Cramer et al. (35)] represents incredible progress in this now blossoming field.
TL;DR: The fundamental problems in duplicating and transmitting genetic information posed by the geometric and topological features of DNA, combined with its large size, are qualitatively similar for prokaryotic and eukaryotic chromosomes and plasmids.
Abstract: The fundamental problems in duplicating and transmitting genetic information posed by the geometric and topological features of DNA, combined with its large size, are qualitatively similar for prokaryotic and eukaryotic chromosomes. The evolutionary solutions to these problems reveal common themes. However, depending on differences in their organization, ploidy, and copy number, chromosomes and plasmids display distinct segregation strategies as well. In bacteria, chromosome duplication, likely mediated by a stationary replication factory, is accompanied by rapid, directed migration of the daughter duplexes with assistance from DNA-compacting and perhaps translocating proteins. The segregation of unit-copy or low-copy bacterial plasmids is also regulated spatially and temporally by their respective partitioning systems. Eukaryotic chromosomes utilize variations of a basic pairing and unpairing mechanism for faithful segregation during mitosis and meiosis. Rather surprisingly, the yeast plasmid 2-m...
TL;DR: I am a member of what has been called, perhaps too grandiosely, "The Greatest Generation." I grew up during the Great Depression and served in the U.S. Army during World War II, and later, graduate school, where I studied enzymes that are critical to the understanding of DNA replication, repair, and recombination.
Abstract: I am a member of what has been called, perhaps too grandiosely, “The Greatest Generation.” I grew up during the Great Depression and served in the U.S. Army during World War II. Because of my military service and the benefits of the GI Bill, I was able to attend college and, later, graduate school. Early in my graduate studies, I became fascinated with enzymes and the biochemical reactions that they catalyze. This fascination has never left me during the 50 years I have been a “DNA enzymologist.” I was fortunate to have had as a mentor Arthur Kornberg, one of the great biochemists of the twentieth century, and a splendid group of postdocs and graduate students. I have studied DNA polymerases, DNA nucleases, DNA ligases, and DNA recombinases, enzymes that are critical to our understanding of DNA replication, repair, and recombination. Most recently, I have been studying herpes virus replication and inadvertently wandered into an entirely new area—viral latency.