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- Volume 51, 2017
Annual Review of Genetics - Volume 51, 2017
Volume 51, 2017
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Witnessing Genome Evolution: Experimental Reconstruction of Endosymbiotic and Horizontal Gene Transfer
Vol. 51 (2017), pp. 1–22More LessPresent day mitochondria and plastids (chloroplasts) evolved from formerly free-living bacteria that were acquired through endosymbiosis more than a billion years ago. Conversion of the bacterial endosymbionts into cell organelles involved the massive translocation of genetic material from the organellar genomes to the nucleus. The development of transformation technologies for organellar genomes has made it possible to reconstruct this endosymbiotic gene transfer in laboratory experiments and study the mechanisms involved. Recently, the horizontal transfer of genetic information between organisms has also become amenable to experimental investigation. It led to the discovery of horizontal genome transfer as an asexual process generating new species and new combinations of nuclear and organellar genomes. This review describes experimental approaches towards studying endosymbiotic and horizontal gene transfer processes, discusses the new knowledge gained from these approaches about both the evolutionary significance of gene transfer and the underlying molecular mechanisms, and highlights exciting possibilities to exploit gene and genome transfer in biotechnology and synthetic biology.
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The Yeast Genomes in Three Dimensions: Mechanisms and Functions
Vol. 51 (2017), pp. 23–44More LessThe three-dimensional (3D) genome structure is highly ordered by a hierarchy of organizing events ranging from enhancer–promoter or gene–gene contacts to chromosomal territorial arrangement. It is becoming clear that the cohesin and condensin complexes are key molecular machines that organize the 3D genome structure. These complexes are highly conserved from simple systems, e.g., yeast cells, to the much more complex human system. Therefore, knowledge from the budding and fission yeast systems illuminates highly conserved molecular mechanisms of how cohesin and condensin establish the functional 3D genome structures. Here I discuss how these complexes are recruited across the yeast genomes, mediate distinct genome-organizing events such as gene contacts and topological domain formation, and participate in important nuclear activities including transcriptional regulation and chromosomal dynamics.
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Origin and Evolution of the Universal Genetic Code
Vol. 51 (2017), pp. 45–62More LessThe standard genetic code (SGC) is virtually universal among extant life forms. Although many deviations from the universal code exist, particularly in organelles and prokaryotes with small genomes, they are limited in scope and obviously secondary. The universality of the code likely results from the combination of a frozen accident, i.e., the deleterious effect of codon reassignment in the SGC, and the inhibitory effect of changes in the code on horizontal gene transfer. The structure of the SGC is nonrandom and ensures high robustness of the code to mutational and translational errors. However, this error minimization is most likely a by-product of the primordial code expansion driven by the diversification of the repertoire of protein amino acids, rather than a direct result of selection. Phylogenetic analysis of translation system components, in particular aminoacyl–tRNA synthetases, shows that, at a stage of evolution when the translation system had already attained high fidelity, the correspondence between amino acids and cognate codons was determined by recognition of amino acids by RNA molecules, i.e., proto-tRNAs. We propose an experimentally testable scenario for the evolution of the code that combines recognition of amino acids by unique sites on proto-tRNAs (distinct from the anticodons), expansion of the code via proto-tRNA duplication, and frozen accident.
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Regeneration Genetics
Vol. 51 (2017), pp. 63–82More LessUnderstanding how and why animals regenerate complex tissues has the potential to transform regenerative medicine. Here we present an overview of genetic approaches that have recently been applied to dissect mechanisms of regeneration. We describe new advances that relate to central objectives of regeneration biologists researching different tissues and species, focusing mainly on vertebrates. These objectives include defining the cellular sources and key cell behaviors in regenerating tissue, elucidating molecular triggers and brakes for regeneration, and defining the earliest events that control the presence of these molecular factors.
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Conditional Degrons for Controlling Protein Expression at the Protein Level
Vol. 51 (2017), pp. 83–102More LessThe conditional depletion of a protein of interest (POI) is useful not only for loss-of-function studies, but also for the modulation of biological pathways. Technologies that work at the level of DNA, mRNA, and protein are available for temporal protein depletion. Compared with technologies targeting the pretranslation steps, direct protein depletion (or protein knockdown approaches) is advantageous in terms of specificity, reversibility, and time required for depletion, which can be achieved by fusing a POI with a protein domain called a degron that induces rapid proteolysis of the fusion protein. Conditional degrons can be activated or inhibited by temperature, small molecules, light, or the expression of another protein. The conditional degron-based technologies currently available are described and discussed.
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Mas-Related G Protein–Coupled Receptors and the Biology of Itch Sensation
Vol. 51 (2017), pp. 103–121More LessChronic, persistent itch is a devastating symptom that causes much suffering. In recent years, there has been great progress made in understanding the molecules, cells, and circuits underlying itch sensation. Once thought to be carried by pain-sensing neurons, itch is now believed to be capable of being transmitted by dedicated sensory labeled lines. Members of the Mas-related G protein–coupled receptor (Mrgpr) family demarcate an itch-specific labeled line in the peripheral nervous system. In the spinal cord, the expression of other proteins identifies additional populations of itch-dedicated sensory neurons. However, as evidence for labeled-line coding has mounted, studies promoting alternative itch-coding strategies have emerged, complicating our understanding of the neural basis of itch. In this review, we cover the molecules, cells, and circuits related to understanding the neural basis of itch, with a focus on the role of Mrgprs in mediating itch sensation.
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Mosaicism in Cutaneous Disorders
Vol. 51 (2017), pp. 123–141More LessGenetic mosaicism arises when a zygote harbors two or more distinct genotypes, typically due to de novo, somatic mutation during embryogenesis. The clinical manifestations largely depend on the differentiation status of the mutated cell; earlier mutations target pluripotent cells and generate more widespread disease affecting multiple organ systems. If gonadal tissue is spared—as in somatic genomic mosaicism—the mutation and its effects are limited to the proband, whereas mosaicism also affecting the gametes, such as germline or gonosomal mosaicism, is transmissible. Mosaicism is easily appreciated in cutaneous disorders, as phenotypically distinct mutant cells often give rise to lesions in patterns determined by the affected cell type. Genetic investigation of cutaneous mosaic disorders has identified pathways central to disease pathogenesis, revealing novel therapeutic targets. In this review, we discuss examples of cutaneous mosaicism, approaches to gene discovery in these disorders, and insights into molecular pathobiology that have potential for clinical translation.
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Transcriptional Regulation in Archaea: From Individual Genes to Global Regulatory Networks
Vol. 51 (2017), pp. 143–170More LessArchaea are major contributors to biogeochemical cycles, possess unique metabolic capabilities, and resist extreme stress. To regulate the expression of genes encoding these unique programs, archaeal cells use gene regulatory networks (GRNs) composed of transcription factor proteins and their target genes. Recent developments in genetics, genomics, and computational methods used with archaeal model organisms have enabled the mapping and prediction of global GRN structures. Experimental tests of these predictions have revealed the dynamical function of GRNs in response to environmental variation. Here, we review recent progress made in this area, from investigating the mechanisms of transcriptional regulation of individual genes to small-scale subnetworks and genome-wide global networks. At each level, archaeal GRNs consist of a hybrid of bacterial, eukaryotic, and uniquely archaeal mechanisms. We discuss this theme from the perspective of the role of individual transcription factors in genome-wide regulation, how these proteins interact to compile GRN topological structures, and how these topologies lead to emergent, high-level GRN functions. We conclude by discussing how systems biology approaches are a fruitful avenue for addressing remaining challenges, such as discovering gene function and the evolution of GRNs.
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Regulation by 3′-Untranslated Regions
Vol. 51 (2017), pp. 171–194More Less3′-untranslated regions (3′-UTRs) are the noncoding parts of mRNAs. Compared to yeast, in humans, median 3′-UTR length has expanded approximately tenfold alongside an increased generation of alternative 3′-UTR isoforms. In contrast, the number of coding genes, as well as coding region length, has remained similar. This suggests an important role for 3′-UTRs in the biology of higher organisms. 3′-UTRs are best known to regulate diverse fates of mRNAs, including degradation, translation, and localization, but they can also function like long noncoding or small RNAs, as has been shown for whole 3′-UTRs as well as for cleaved fragments. Furthermore, 3′-UTRs determine the fate of proteins through the regulation of protein–protein interactions. They facilitate cotranslational protein complex formation, which establishes a role for 3′-UTRs as evolved eukaryotic operons. Whereas bacterial operons promote the interaction of two subunits, 3′-UTRs enable the formation of protein complexes with diverse compositions. All of these 3′-UTR functions are accomplished by effector proteins that are recruited by RNA-binding proteins that bind to 3′-UTR cis-elements. In summary, 3′-UTRs seem to be major players in gene regulation that enable local functions, compartmentalization, and cooperativity, which makes them important tools for the regulation of phenotypic diversity of higher organisms.
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Integration of Agrobacterium T-DNA into the Plant Genome
Vol. 51 (2017), pp. 195–217More LessAgrobacterium strains transfer a single-strand form of T-DNA (T-strands) and Virulence (Vir) effector proteins to plant cells. Following transfer, T-strands likely form complexes with Vir and plant proteins that traffic through the cytoplasm and enter the nucleus. T-strands may subsequently randomly integrate into plant chromosomes and permanently express encoded transgenes, a process known as stable transformation. The molecular processes by which T-strands integrate into the host genome remain unknown. Although integration resembles DNA repair processes, the requirement of known DNA repair pathways for integration is controversial. The configuration and genomic position of integrated T-DNA molecules likely affect transgene expression, and control of integration is consequently important for basic research and agricultural biotechnology applications. This article reviews our current knowledge of the process of T-DNA integration and proposes ways in which this knowledge may be manipulated for genome editing and synthetic biology purposes.
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Genetics and Evolution of Social Behavior in Insects
Vol. 51 (2017), pp. 219–239More LessThe study of insect social behavior has offered tremendous insight into the molecular mechanisms mediating behavioral and phenotypic plasticity. Genomic applications to the study of eusocial insect species, in particular, have led to several hypotheses for the processes underlying the molecular evolution of behavior. Advances in understanding the genetic control of social organization have also been made, suggesting an important role for supergenes in the evolution of divergent behavioral phenotypes. Intensive study of social phenotypes across species has revealed that behavior and caste are controlled by an interaction between genetic and environmentally mediated effects and, further, that gene expression and regulation mediate plastic responses to environmental signals. However, several key methodological flaws that are hindering progress in the study of insect social behavior remain. After reviewing the current state of knowledge, we outline ongoing challenges in experimental design that remain to be overcome in order to advance the field.
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Human Genetic Determinants of Viral Diseases
Vol. 51 (2017), pp. 241–263More LessMuch progress has been made in the identification of specific human gene variants that contribute to enhanced susceptibility or resistance to viral diseases. Herein we review multiple discoveries made with genome-wide or candidate gene approaches that have revealed significant insights into virus–host interactions. Genetic factors that have been identified include genes encoding virus receptors, receptor-modifying enzymes, and a wide variety of innate and adaptive immunity-related proteins. We discuss a range of pathogenic viruses, including influenza virus, respiratory syncytial virus, human immunodeficiency virus, human T cell leukemia virus, human papilloma virus, hepatitis B and C viruses, herpes simplex virus, norovirus, rotavirus, parvovirus, and Epstein-Barr virus. Understanding the genetic underpinnings that affect infectious disease outcomes should allow tailored treatment and prevention approaches in the future.
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Sex Determination in the Mammalian Germline
Vol. 51 (2017), pp. 265–285More LessSexual reproduction crucially depends on the production of sperm in males and oocytes in females. Both types of gamete arise from the same precursor, the germ cells. We review the events that characterize the development of germ cells during fetal life as they commit to, and prepare for, oogenesis or spermatogenesis. In females, fetal germ cells enter meiosis, whereas in males they delay meiosis and instead lose pluripotency, activate an irreversible program of prospermatogonial differentiation, and temporarily cease dividing. Both pathways involve sex-specific molecular signals from the somatic cells of the developing gonads and a suite of intrinsic receptors, signal transducers, transcription factors, RNA stability factors, and epigenetic modulators that act in complex, interconnected positive and negative regulatory networks. Understanding these networks is important in the contexts of the etiology, diagnosis, and treatment of infertility and gonadal cancers, and in efforts to augment human and animal fertility using stem cell approaches.
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The Genetics of Plant Metabolism
Vol. 51 (2017), pp. 287–310More LessPlant metabolic studies have traditionally focused on the role and regulation of the enzymes catalyzing key reactions within specific pathways. Within the past 20 years, reverse genetic approaches have allowed direct determination of the effects of the deficiency, or surplus, of a given protein on the biochemistry of a plant. In parallel, top-down approaches have also been taken, which rely on screening broad, natural genetic diversity for metabolic diversity. Here, we compare and contrast the various strategies that have been adopted to enhance our understanding of the natural diversity of metabolism. We also detail how these approaches have enhanced our understanding of both specific and global aspects of the genetic regulation of metabolism. Finally, we discuss how such approaches are providing important insights into the evolution of plant secondary metabolism.
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Genetic and Structural Analyses of RRNPP Intercellular Peptide Signaling of Gram-Positive Bacteria
Vol. 51 (2017), pp. 311–333More LessBacteria use diffusible chemical messengers, termed pheromones, to coordinate gene expression and behavior among cells in a community by a process known as quorum sensing. Pheromones of many gram-positive bacteria, such as Bacillus and Streptococcus, are small, linear peptides secreted from cells and subsequently detected by sensory receptors such as those belonging to the large family of RRNPP proteins. These proteins are cytoplasmic pheromone receptors sharing a structurally similar pheromone-binding domain that functions allosterically to regulate receptor activity. X-ray crystal structures of prototypical RRNPP members have provided atomic-level insights into their mechanism and regulation by pheromones. This review provides an overview of RRNPP prototype signaling; describes the structure–function of this protein family, which is spread widely among gram-positive bacteria; and suggests approaches to target RRNPP systems in order to manipulate beneficial and harmful bacterial behaviors.
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Genetic Networks in Plant Vascular Development
Vol. 51 (2017), pp. 335–359More LessUnderstanding the development of vascular tissues in plants is crucial because the evolution of vasculature enabled plants to thrive on land. Various systems and approaches have been used to advance our knowledge about the genetic regulation of vasculature development, from the scale of single genes to networks. In this review, we provide a perspective on the major approaches used in studying plant vascular development, and we cover the mechanisms and genetic networks underlying vascular tissue specification, patterning, and differentiation.
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Big Lessons from Little Yeast: Budding and Fission Yeast Centrosome Structure, Duplication, and Function
Vol. 51 (2017), pp. 361–383More LessCentrosomes are a functionally conserved feature of eukaryotic cells that play an important role in cell division. The conserved γ-tubulin complex organizes spindle and astral microtubules, which, in turn, separate replicated chromosomes accurately into daughter cells. Like DNA, centrosomes are duplicated once each cell cycle. Although in some cell types it is possible for cell division to occur in the absence of centrosomes, these divisions typically result in defects in chromosome number and stability. In single-celled organisms such as fungi, centrosomes [known as spindle pole bodies (SPBs)] are essential for cell division. SPBs also must be inserted into the membrane because fungi undergo a closed mitosis in which the nuclear envelope (NE) remains intact. This poorly understood process involves events similar or identical to those needed for de novo nuclear pore complex assembly. Here, we review how analysis of fungal SPBs has advanced our understanding of centrosomes and NE events.
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Noncoding RNAs in Polycomb and Trithorax Regulation: A Quantitative Perspective
Vol. 51 (2017), pp. 385–411More LessThe question of how noncoding RNAs are involved in Polycomb group (PcG) and Trithorax group (TrxG) regulation has been on an extraordinary journey over the last three decades. Favored models have risen and fallen, and healthy debates have swept back and forth. The field has recently reached a critical mass of compelling data that throws light on several previously unresolved issues. The time is ripe for a fruitful combination of these findings with two other long-running avenues of research, namely the biochemical properties of the PcG/TrxG system and the application of theoretical mathematical models toward an understanding of the system's regulatory properties. I propose that integrating our current knowledge of noncoding RNA into a quantitative biochemical and theoretical framework for PcG and TrxG regulation has the potential to reconcile several apparently conflicting models and identifies fascinating questions for future research.
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The Relationship Between the Human Genome and Microbiome Comes into View
Vol. 51 (2017), pp. 413–433More LessThe body's microbiome, composed of microbial cells that number in the trillions, is involved in human health and disease in ways that are just starting to emerge. The microbiome is assembled at birth, develops with its host, and is greatly influenced by environmental factors such as diet and other exposures. Recently, a role for human genetic variation has emerged as also influential in accounting for interpersonal differences in microbiomes. Thus, human genes may influence health directly or by promoting a beneficial microbiome. Studies of the heritability of gut microbiotas reveal a subset of microbes whose abundances are partly genetically determined by the host. However, the use of genome-wide association studies (GWASs) to identify human genetic variants associated with microbiome phenotypes has proven challenging. Studies to date are small by GWAS standards, and cross-study comparisons are hampered by differences in analytical approaches. Nevertheless, associations between microbes or microbial genes and human genes have emerged that are consistent between human populations. Most notably, higher levels of beneficial gut bacteria called Bifidobacteria are associated with the human lactase nonpersister genotype, which typically confers lactose intolerance, in several different human populations. It is time for the microbiome to be incorporated into studies that quantify interactions among genotype, environment, and the microbiome in order to predict human disease susceptibility.
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Combining Traditional Mutagenesis with New High-Throughput Sequencing and Genome Editing to Reveal Hidden Variation in Polyploid Wheat
Vol. 51 (2017), pp. 435–454More LessInduced mutations have been used to generate novel variation for breeding purposes since the early 1900s. However, the combination of this old technology with the new capabilities of high-throughput sequencing has resulted in powerful reverse genetic approaches in polyploid crops. Sequencing genomes or exomes of large mutant populations can generate extensive databases of mutations for most genes. These mutant collections, together with genome editing, are being used in polyploid species to combine mutations in all copies of a gene (homoeologs), and to expose phenotypic variation that was previously hidden by functional redundancy among homoeologs. This redundancy is more extensive in recently formed polyploids such as wheat, which can now benefit from the deployment of useful recessive mutations previously identified in its diploid relatives. Sequenced mutant populations and genome editing have changed the paradigm of what is possible in functional genetic analysis of wheat.
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Previous Volumes
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Volume 58 (2024)
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Volume 57 (2023)
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Volume 56 (2022)
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Volume 55 (2021)
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Volume 54 (2020)
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Volume 53 (2019)
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Volume 52 (2018)
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Volume 51 (2017)
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Volume 50 (2016)
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Volume 49 (2015)
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Volume 48 (2014)
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Volume 47 (2013)
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Volume 46 (2012)
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Volume 45 (2011)
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Volume 44 (2010)
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Volume 43 (2009)
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Volume 42 (2008)
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Volume 41 (2007)
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Volume 40 (2006)
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Volume 39 (2005)
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Volume 38 (2004)
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Volume 37 (2003)
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Volume 36 (2002)
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Volume 35 (2001)
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Volume 34 (2000)
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Volume 33 (1999)
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Volume 32 (1998)
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Volume 31 (1997)
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Volume 30 (1996)
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Volume 29 (1995)
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Volume 28 (1994)
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Volume 27 (1993)
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Volume 26 (1992)
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Volume 25 (1991)
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Volume 24 (1990)
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Volume 23 (1989)
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Volume 22 (1988)
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Volume 21 (1987)
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Volume 20 (1986)
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Volume 19 (1985)
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Volume 18 (1984)
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Volume 17 (1983)
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Volume 16 (1982)
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Volume 15 (1981)
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Volume 14 (1980)
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Volume 13 (1979)
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Volume 12 (1978)
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Volume 11 (1977)
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Volume 10 (1976)
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Volume 9 (1975)
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Volume 8 (1974)
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Volume 7 (1973)
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Volume 6 (1972)
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Volume 5 (1971)
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Volume 4 (1970)
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Volume 3 (1969)
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Volume 2 (1968)
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Volume 1 (1967)
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Volume 0 (1932)