- Home
- A-Z Publications
- Annual Review of Biochemistry
- Previous Issues
- Volume 79, 2010
Annual Review of Biochemistry - Volume 79, 2010
Volume 79, 2010
- Preface
-
-
-
From Virus Structure to Chromatin: X-ray Diffraction to Three-Dimensional Electron Microscopy
Vol. 79 (2010), pp. 1–35More LessEarly influences led me first to medical school with a view to microbiology, but I felt the lack of a deeper foundation and changed to chemistry, which in turn led me to physics and mathematics. I moved to the University of Cape Town to work on the X-ray crystallography of some small organic compounds. I developed a new method of using molecular structure factors to solve the crystal structure, which won me a research studentship to Trinity College Cambridge and the Cavendish Laboratory. There I worked on the austenite-pearlite transition in steel. This is governed by the dissipation of latent heat, and I ended up numerically solving partial differential equations. I used the idea of nucleation and growth during the phase change, which had its echo when I later tackled the assembly of Tobacco mosaic virus (TMV) from its constituent RNA and protein subunits.
I wanted to move on to X-ray structure analysis of large biological molecules and obtained a Nuffield Fellowship to work in J.D. Bernal's department at Birkbeck College, London. There, I met Rosalind Franklin, who had taken up the study of TMV. I was able to interpret some of Franklin's beautiful X-ray diffraction patterns of the virus particle. From then on, my fate was sealed.
After Franklin's untimely death in 1958, I moved in 1962 to the newly built MRC Laboratory of Molecular Biology in Cambridge, which, under Max Perutz, housed the original MRC unit from the Cavendish Laboratory. I was thus privileged to join the Laboratory at an early stage in its expansion and consequently able to take advantage of, and to help build up, its then unique environment of intellectual and technological sophistication. There I have remained ever since.
-
-
-
Genomic Screening with RNAi: Results and Challenges
Vol. 79 (2010), pp. 37–64More LessRNA interference (RNAi) is an effective tool for genome-scale, high-throughput analysis of gene function. In the past five years, a number of genome-scale RNAi high-throughput screens (HTSs) have been done in both Drosophila and mammalian cultured cells to study diverse biological processes, including signal transduction, cancer biology, and host cell responses to infection. Results from these screens have led to the identification of new components of these processes and, importantly, have also provided insights into the complexity of biological systems, forcing new and innovative approaches to understanding functional networks in cells. Here, we review the main findings that have emerged from RNAi HTS and discuss technical issues that remain to be improved, in particular the verification of RNAi results and validation of their biological relevance. Furthermore, we discuss the importance of multiplexed and integrated experimental data analysis pipelines to RNAi HTS.
-
-
-
Nanomaterials Based on DNA
Vol. 79 (2010), pp. 65–87More LessThe combination of synthetic stable branched DNA and sticky-ended cohesion has led to the development of structural DNA nanotechnology over the past 30 years. The basis of this enterprise is that it is possible to construct novel DNA-based materials by combining these features in a self-assembly protocol. Thus, simple branched molecules lead directly to the construction of polyhedrons, whose edges consist of double helical DNA and whose vertices correspond to the branch points. Stiffer branched motifs can be used to produce self-assembled two-dimensional and three-dimensional periodic lattices of DNA (crystals). DNA has also been used to make a variety of nanomechanical devices, including molecules that change their shapes and molecules that can walk along a DNA sidewalk. Devices have been incorporated into two-dimensional DNA arrangements; sequence-dependent devices are driven by increases in nucleotide pairing at each step in their machine cycles.
-
-
-
Eukaryotic Chromosome DNA Replication: Where, When, and How?
Vol. 79 (2010), pp. 89–130More LessDNA replication is central to cell proliferation. Studies in the past six decades since the proposal of a semiconservative mode of DNA replication have confirmed the high degree of conservation of the basic machinery of DNA replication from prokaryotes to eukaryotes. However, the need for replication of a substantially longer segment of DNA in coordination with various internal and external signals in eukaryotic cells has led to more complex and versatile regulatory strategies. The replication program in higher eukaryotes is under a dynamic and plastic regulation within a single cell, or within the cell population, or during development. We review here various regulatory mechanisms that control the replication program in eukaryotes and discuss future directions in this dynamic field.
-
-
-
Regulators of the Cohesin Network
Vol. 79 (2010), pp. 131–153More LessChromosome cohesion is the term used to describe the cellular process in which sister chromatids are held together from the time of their replication until the time of separation at the metaphase to anaphase transition. In this capacity, chromosome cohesion, especially at centromeric regions, is essential for chromosome segregation. However, cohesion of noncentromeric DNA sequences has been shown to occur during double-strand break (DSB) repair and the transcriptional regulation of genes. Cohesion for the purposes of accurate chromosome segregation, DSB repair, and gene regulation are all achieved through a similar network of proteins, but cohesion for each purpose may be regulated differently. In this review, we focus on recent developments regarding the regulation of this multipurpose network for tying DNA sequences together. In particular, regulation via effectors and posttranslational modifications are reviewed. A picture is emerging in which complex regulatory networks are capable of differential regulation of cohesion in various contexts.
-
-
-
Reversal of Histone Methylation: Biochemical and Molecular Mechanisms of Histone Demethylases
Vol. 79 (2010), pp. 155–179More LessThe importance of histone methylation in gene regulation was suggested over 40 years ago. Yet, the dynamic nature of this histone modification was recognized only recently, with the discovery of the first histone demethylase nearly five years ago. Since then, our insight into the mechanisms, structures, and macromolecular complexes of these enzymes has grown exponentially. Overall, the evidence strongly supports a key role for histone demethylases in eukaryotic transcription and other chromatin-dependent processes. Here, we examine these and related facets of histone demethylases discovered to date, focusing on their biochemistry, structure, and enzymology.
-
-
-
The Mechanism of Double-Strand DNA Break Repair by the Nonhomologous DNA End-Joining Pathway
Vol. 79 (2010), pp. 181–211More LessDouble-strand DNA breaks are common events in eukaryotic cells, and there are two major pathways for repairing them: homologous recombination (HR) and nonhomologous DNA end joining (NHEJ). The various causes of double-strand breaks (DSBs) result in a diverse chemistry of DNA ends that must be repaired. Across NHEJ evolution, the enzymes of the NHEJ pathway exhibit a remarkable degree of structural tolerance in the range of DNA end substrate configurations upon which they can act. In vertebrate cells, the nuclease, DNA polymerases, and ligase of NHEJ are the most mechanistically flexible and multifunctional enzymes in each of their classes. Unlike repair pathways for more defined lesions, NHEJ repair enzymes act iteratively, act in any order, and can function independently of one another at each of the two DNA ends being joined. NHEJ is critical not only for the repair of pathologic DSBs as in chromosomal translocations, but also for the repair of physiologic DSBs created during variable (diversity) joining [V(D)J] recombination and class switch recombination (CSR). Therefore, patients lacking normal NHEJ are not only sensitive to ionizing radiation (IR), but also severely immunodeficient.
-
-
-
The Discovery of Zinc Fingers and Their Applications in Gene Regulation and Genome Manipulation
Vol. 79 (2010), pp. 213–231More LessAn account is given of the discovery of the classical Cys2His2 zinc finger, arising from the interpretation of biochemical studies on the interaction of the Xenopus protein transcription factor IIIA with 5S RNA, and of structural studies on its structure and its interaction with DNA. The finger is a self-contained domain stabilized by a zinc ion ligated to a pair of cysteines and a pair of histidines, and by an inner hydrophobic core. This discovery showed not only a new protein fold but also a novel principle of DNA recognition. Whereas other DNA binding proteins generally make use of the two-fold symmetry of the double helix, zinc fingers can be linked linearly in tandem to recognize nucleic acid sequences of varying lengths. This modular design offers a large number of combinatorial possibilities for the specific recognition of DNA (or RNA). It is therefore not surprising that the zinc finger is found widespread in nature, including 3% of the genes of the human genome.
The zinc finger design is ideally suited for engineering proteins to target specific genes. In the first example of their application in 1994, a three-finger protein was constructed to block the expression of an oncogene transformed into a mouse cell line. In addition, a reporter gene was activated by targeting an inserted zinc finger promoter. Thus, by fusing zinc finger peptides to repression or activation domains, genes can be selectively switched off or on. It was also suggested that by combining zinc fingers with other effector domains, e.g., from nucleases or integrases, to form chimeric proteins, genomes could be manipulated or modified. Several applications of such engineered zinc finger proteins are described here, including some of therapeutic importance.
-
-
-
Origins of Specificity in Protein-DNA Recognition
Vol. 79 (2010), pp. 233–269More LessSpecific interactions between proteins and DNA are fundamental to many biological processes. In this review, we provide a revised view of protein-DNA interactions that emphasizes the importance of the three-dimensional structures of both macromolecules. We divide protein-DNA interactions into two categories: those when the protein recognizes the unique chemical signatures of the DNA bases (base readout) and those when the protein recognizes a sequence-dependent DNA shape (shape readout). We further divide base readout into those interactions that occur in the major groove from those that occur in the minor groove. Analogously, the readout of the DNA shape is subdivided into global shape recognition (for example, when the DNA helix exhibits an overall bend) and local shape recognition (for example, when a base pair step is kinked or a region of the minor groove is narrow). Based on the >1500 structures of protein-DNA complexes now available in the Protein Data Bank, we argue that individual DNA-binding proteins combine multiple readout mechanisms to achieve DNA-binding specificity. Specificity that distinguishes between families frequently involves base readout in the major groove, whereas shape readout is often exploited for higher resolution specificity, to distinguish between members within the same DNA-binding protein family.
-
-
-
Transcript Elongation by RNA Polymerase II
Vol. 79 (2010), pp. 271–293More LessUntil recently, it was generally assumed that essentially all regulation of transcription takes place via regions adjacent to the coding region of a gene—namely promoters and enhancers—and that, after recruitment to the promoter, the polymerase simply behaves like a machine, quickly “reading the gene.” However, over the past decade a revolution in this thinking has occurred, culminating in the idea that transcript elongation is extremely complex and highly regulated and, moreover, that this process significantly affects both the organization and integrity of the genome. This review addresses basic aspects of transcript elongation by RNA polymerase II (RNAPII) and how it relates to other DNA-related processes.
-
-
-
Biochemical Principles of Small RNA Pathways
Qinghua Liu, and Zain ParooVol. 79 (2010), pp. 295–319More LessThe discovery of RNA interference (RNAi) is among the most significant biomedical breakthroughs in recent history. Multiple classes of small RNA, including small-interfering RNA (siRNA), micro-RNA (miRNA), and piwi-interacting RNA (piRNA), play important roles in many fundamental biological and disease processes. Collective studies in multiple organisms, including plants, Drosophila, Caenorhabditis elegans, and mammals indicate that these pathways are highly conserved throughout evolution. Thus, scientists across disciplines have found novel pathways to unravel, new insights in probing pathology, and nascent technologies to develop. The field of RNAi also provides a clear framework for understanding fundamental principles of biochemistry. The current review highlights elegant, reason-based experimentation in discovering RNA-directed biological phenomena and the importance of robust assay development in translating these observations into mechanistic understanding. This biochemical template also provides a conceptual framework for overcoming emerging challenges in the field and for understanding an expanding small RNA world.
-
-
-
Functions and Regulation of RNA Editing by ADAR Deaminases
Vol. 79 (2010), pp. 321–349More LessOne type of RNA editing converts adenosines to inosines (A→I editing) in double-stranded RNA (dsRNA) substrates. A→I RNA editing is mediated by adenosine deaminase acting on RNA (ADAR) enzymes. A→I RNA editing of protein-coding sequences of a limited number of mammalian genes results in recoding and subsequent alterations of their functions. However, A→I RNA editing most frequently targets repetitive RNA sequences located within introns and 5′ and 3′ untranslated regions (UTRs). Although the biological significance of noncoding RNA editing remains largely unknown, several possibilities, including its role in the control of endogenous short interfering RNAs (esiRNAs), have been proposed. Furthermore, recent studies have revealed that the biogenesis and functions of certain microRNAs (miRNAs) are regulated by the editing of their precursors. Here, I review the recent findings that indicate new functions for A→I editing in the regulation of noncoding RNAs and for interactions between RNA editing and RNA interference mechanisms.
-
-
-
Regulation of mRNA Translation and Stability by microRNAs
Vol. 79 (2010), pp. 351–379More LessMicroRNAs (miRNAs) are small noncoding RNAs that extensively regulate gene expression in animals, plants, and protozoa. miRNAs function posttranscriptionally by usually base-pairing to the mRNA 3′-untranslated regions to repress protein synthesis by mechanisms that are not fully understood. In this review, we describe principles of miRNA-mRNA interactions and proteins that interact with miRNAs and function in miRNA-mediated repression. We discuss the multiple, often contradictory, mechanisms that miRNAs have been reported to use, which cause translational repression and mRNA decay. We also address the issue of cellular localization of miRNA-mediated events and a role for RNA-binding proteins in activation or relief of miRNA repression.
-
-
-
Structure and Dynamics of a Processive Brownian Motor: The Translating Ribosome
Vol. 79 (2010), pp. 381–412More LessThere is mounting evidence indicating that protein synthesis is driven and regulated by mechanisms that direct stochastic, large-scale conformational fluctuations of the translational apparatus. This mechanistic paradigm implies that a free-energy landscape governs the conformational states that are accessible to and sampled by the translating ribosome. This scenario presents interdependent opportunities and challenges for structural and dynamic studies of protein synthesis. Indeed, the synergism between cryogenic electron microscopic and X-ray crystallographic structural studies, on the one hand, and single-molecule fluorescence resonance energy transfer (smFRET) dynamic studies, on the other, is emerging as a powerful means for investigating the complex free-energy landscape of the translating ribosome and uncovering the mechanisms that direct the stochastic conformational fluctuations of the translational machinery. In this review, we highlight the principal insights obtained from cryogenic electron microscopic, X-ray crystallographic, and smFRET studies of the elongation stage of protein synthesis and outline the emerging themes, questions, and challenges that lie ahead in mechanistic studies of translation.
-
-
-
Adding New Chemistries to the Genetic Code
Vol. 79 (2010), pp. 413–444More LessThe development of new orthogonal aminoacyl-tRNA synthetase/tRNA pairs has led to the addition of approximately 70 unnatural amino acids (UAAs) to the genetic codes of Escherichia coli, yeast, and mammalian cells. These UAAs represent a wide range of structures and functions not found in the canonical 20 amino acids and thus provide new opportunities to generate proteins with enhanced or novel properties and probes of protein structure and function.
-
-
-
Bacterial Nitric Oxide Synthases
Vol. 79 (2010), pp. 445–470More LessNitric oxide synthases (NOSs) are multidomain metalloproteins first identified in mammals as being responsible for the synthesis of the wide-spread signaling and protective agent nitric oxide (NO). Over the past 10 years, prokaryotic proteins that are homologous to animal NOSs have been identified and characterized, both in terms of enzymology and biological function. Despite some interesting differences in cofactor utilization and redox partners, the bacterial enzymes are in many ways similar to their mammalian NOS (mNOS) counterparts and, as such, have provided insight into the structural and catalytic properties of the NOS family. In particular, spectroscopic studies of thermostable bacterial NOSs have revealed key oxyheme intermediates involved in the oxidation of substrate L-arginine (Arg) to product NO. The biological functions of some bacterial NOSs have only more recently come to light. These studies disclose new roles for NO in biology, such as taking part in toxin biosynthesis, protection against oxidative stress, and regulation of recovery from radiation damage.
-
-
-
Enzyme Promiscuity: A Mechanistic and Evolutionary Perspective
Vol. 79 (2010), pp. 471–505More LessMany, if not most, enzymes can promiscuously catalyze reactions, or act on substrates, other than those for which they evolved. Here, we discuss the structural, mechanistic, and evolutionary implications of this manifestation of infidelity of molecular recognition. We define promiscuity and related phenomena and also address their generality and physiological implications. We discuss the mechanistic enzymology of promiscuity—how enzymes, which generally exert exquisite specificity, catalyze other, and sometimes barely related, reactions. Finally, we address the hypothesis that promiscuous enzymatic activities serve as evolutionary starting points and highlight the unique evolutionary features of promiscuous enzyme functions.
-
-
-
Hydrogenases from Methanogenic Archaea, Nickel, a Novel Cofactor, and H2 Storage
Vol. 79 (2010), pp. 507–536More LessMost methanogenic archaea reduce CO2 with H2 to CH4. For the activation of H2, they use different [NiFe]-hydrogenases, namely energy-converting [NiFe]-hydrogenases, heterodisulfide reductase-associated [NiFe]-hydrogenase or methanophenazine-reducing [NiFe]-hydrogenase, and F420-reducing [NiFe]-hydrogenase. The energy-converting [NiFe]-hydrogenases are phylogenetically related to complex I of the respiratory chain. Under conditions of nickel limitation, some methanogens synthesize a nickel-independent [Fe]-hydrogenase (instead of F420-reducing [NiFe]-hydrogenase) and by that reduce their nickel requirement. The [Fe]-hydrogenase harbors a unique iron-guanylylpyridinol cofactor (FeGP cofactor), in which a low-spin iron is ligated by two CO, one C(O)CH2-, one S-CH2-, and a sp2-hybridized pyridinol nitrogen. Ligation of the iron is thus similar to that of the low-spin iron in the binuclear active-site metal center of [NiFe]- and [FeFe]-hydrogenases. Putative genes for the synthesis of the FeGP cofactor have been identified. The formation of methane from 4 H2 and CO2 catalyzed by methanogenic archaea is being discussed as an efficient means to store H2.
-
-
-
Copper Metallochaperones
Vol. 79 (2010), pp. 537–562More LessThe current state of knowledge on how copper metallochaperones support the maturation of cuproproteins is reviewed. Copper is needed within mitochondria to supply the CuA and intramembrane CuB sites of cytochrome oxidase, within the trans-Golgi network to supply secreted cuproproteins and within the cytosol to supply superoxide dismutase 1 (Sod1). Subpopulations of copper-zinc superoxide dismutase also localize to mitochondria, the secretory system, the nucleus and, in plants, the chloroplast, which also requires copper for plastocyanin. Prokaryotic cuproproteins are found in the cell membrane and in the periplasm of gram-negative bacteria. Cu(I) and Cu(II) form tight complexes with organic molecules and drive redox chemistry, which unrestrained would be destructive. Copper metallochaperones assist copper in reaching vital destinations without inflicting damage or becoming trapped in adventitious binding sites. Copper ions are specifically released from copper metallochaperones upon contact with their cognate cuproproteins and metal transfer is thought to proceed by ligand substitution.
-
Previous Volumes
-
Volume 93 (2024)
-
Volume 92 (2023)
-
Volume 91 (2022)
-
Volume 90 (2021)
-
Volume 89 (2020)
-
Volume 88 (2019)
-
Volume 87 (2018)
-
Volume 86 (2017)
-
Volume 85 (2016)
-
Volume 84 (2015)
-
Volume 83 (2014)
-
Volume 82 (2013)
-
Volume 81 (2012)
-
Volume 80 (2011)
-
Volume 79 (2010)
-
Volume 78 (2009)
-
Volume 77 (2008)
-
Volume 76 (2007)
-
Volume 75 (2006)
-
Volume 74 (2005)
-
Volume 73 (2004)
-
Volume 72 (2003)
-
Volume 71 (2002)
-
Volume 70 (2001)
-
Volume 69 (2000)
-
Volume 68 (1999)
-
Volume 67 (1998)
-
Volume 66 (1997)
-
Volume 65 (1996)
-
Volume 64 (1995)
-
Volume 63 (1994)
-
Volume 62 (1993)
-
Volume 61 (1992)
-
Volume 60 (1991)
-
Volume 59 (1990)
-
Volume 58 (1989)
-
Volume 57 (1988)
-
Volume 56 (1987)
-
Volume 55 (1986)
-
Volume 54 (1985)
-
Volume 53 (1984)
-
Volume 52 (1983)
-
Volume 51 (1982)
-
Volume 50 (1981)
-
Volume 49 (1980)
-
Volume 48 (1979)
-
Volume 47 (1978)
-
Volume 46 (1977)
-
Volume 45 (1976)
-
Volume 44 (1975)
-
Volume 43 (1974)
-
Volume 42 (1973)
-
Volume 41 (1972)
-
Volume 40 (1971)
-
Volume 39 (1970)
-
Volume 38 (1969)
-
Volume 37 (1968)
-
Volume 36 (1967)
-
Volume 35 (1966)
-
Volume 34 (1965)
-
Volume 33 (1964)
-
Volume 32 (1963)
-
Volume 31 (1962)
-
Volume 30 (1961)
-
Volume 29 (1960)
-
Volume 28 (1959)
-
Volume 27 (1958)
-
Volume 26 (1957)
-
Volume 25 (1956)
-
Volume 24 (1955)
-
Volume 23 (1954)
-
Volume 22 (1953)
-
Volume 21 (1952)
-
Volume 20 (1951)
-
Volume 19 (1950)
-
Volume 18 (1949)
-
Volume 17 (1948)
-
Volume 16 (1947)
-
Volume 15 (1946)
-
Volume 14 (1945)
-
Volume 13 (1944)
-
Volume 12 (1943)
-
Volume 11 (1942)
-
Volume 10 (1941)
-
Volume 9 (1940)
-
Volume 8 (1939)
-
Volume 7 (1938)
-
Volume 6 (1937)
-
Volume 5 (1936)
-
Volume 4 (1935)
-
Volume 3 (1934)
-
Volume 2 (1933)
-
Volume 1 (1932)
-
Volume 0 (1932)