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- Volume 66, 2012
Annual Review of Microbiology - Volume 66, 2012
Volume 66, 2012
- Preface
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A Fortunate Journey on Uneven Grounds
Vol. 66 (2012), pp. 1–24More LessI was surprised to be invited to write a prefatory chapter for the Annual Review of Microbiology. Indeed, I did not feel that I belonged to that class of eminent scientists who had written such chapters. Perhaps it is because I am a kind of mutant: In spite of having experienced war, both German and Soviet occupations, repeated bombardments, dictatorships, and a revolution, I managed nonetheless to engage in scientific research, thus realizing a childhood dream. After having obtained my Doctor Rerum Naturalium degree in Budapest, Hungary, I was fortunate to meet Jacques Monod at the Pasteur Institute, and this became a turning point in my scientific career. In his laboratory, I contributed to the definition of the lactose operon promoter, uncovered intracistronic complementation in β-galactosidase, and investigated the role of cAMP in Escherichia coli. In my own laboratory, together with many gifted students and collaborators, I studied the role of adenylate cyclase in bacterial virulence. This allowed the engineering of recombinant adenylate cyclase toxin from Bordetella pertussis for the development of protective and therapeutic vaccines.
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Memories of a Senior Scientist: On Passing the Fiftieth Anniversary of the Beginning of Deciphering the Genetic Code
Vol. 66 (2012), pp. 27–38More Less2011 marked the fiftieth anniversary of breaking the genetic code in 1961. Marshall Nirenberg, the National Institutes of Health (NIH) scientist who was awarded the Nobel Prize in Physiology or Medicine in 1968 for his role in deciphering the code, wrote in 2004 a personal account of his research. The race for the code was a competition between the NIH group and Severo Ochoa's laboratory at New York University (NYU) School of Medicine, where I was a graduate student and conducted many of the experiments. I am now 83 years old. These facts prompt me to recall how I, together with Joe Speyer, an instructor in the Department of Biochemistry at NYU, unexpectedly became involved in deciphering the code, which also became the basis of my PhD thesis. Ochoa won the Nobel Prize in Physiology or Medicine in 1959 for discovering polynucleotide phosphorylase (PNP), the first enzyme found to synthesize RNA in the test tube. The story of how PNP made the deciphering of the code feasible is recalled here.
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Yeast ATP-Binding Cassette Transporters Conferring Multidrug Resistance
Vol. 66 (2012), pp. 39–63More LessOverexpression of the ATP-binding cassette (ABC) drug transporter P-glycoprotein (P-gp) is often responsible for the failure of chemotherapy as a treatment for human tumors. The presence of proteins homologous to P-gp in organisms ranging from prokaryotes to eukaryotes indicates that drug export is a general mechanism of multidrug resistance. Yeasts are no exception. They have developed a large subfamily of ABC exporters involved in pleiotropic drug resistance (PDR) and in the cellular efflux of a wide variety of drugs. The PDR transporters Pdr5p of Saccharomyces cerevisiae and Cdr1p of Candida albicans are important members of this PDR subfamily, which comprises up to 10 phylogenetic clusters in fungi. Here, we review current achievements concerning the structure, molecular mechanism, and physiological functions of yeast Pdr transporters.
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‘Gestalt,’ Composition and Function of the Trypanosoma brucei Editosome
Vol. 66 (2012), pp. 65–82More LessRNA editing describes a chemically diverse set of biomolecular reactions in which the nucleotide sequence of RNA molecules is altered. Editing reactions have been identified in many organisms and frequently contribute to the maturation of organellar transcripts. A special editing reaction has evolved within the mitochondria of the kinetoplastid protozoa. The process is characterized by the insertion and deletion of uridine nucleotides into otherwise nontranslatable messenger RNAs. Kinetoplastid RNA editing involves an exclusive class of small, noncoding RNAs known as guide RNAs. Furthermore, a unique molecular machinery, the editosome, catalyzes the process. Editosomes are megadalton multienzyme assemblies that provide a catalytic surface for the individual steps of the reaction cycle. Here I review the current mechanistic understanding and molecular inventory of kinetoplastid RNA editing and the editosome machinery. Special emphasis is placed on the molecular morphology of the editing complex in order to correlate structural features with functional characteristics.
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Physiology and Diversity of Ammonia-Oxidizing Archaea
Vol. 66 (2012), pp. 83–101More LessThe discovery of ammonia-oxidizing archaea (AOA), now generally recognized to exert primary control over ammonia oxidation in terrestrial, marine, and geothermal habitats, necessitates a reassessment of the nitrogen cycle. In particular, the unusually high affinity of marine and terrestrial AOA for ammonia indicates that this group may determine the oxidation state of nitrogen available to associated micro- and macrobiota, altering our current understanding of trophic interactions. Initial comparative genomics and physiological studies have revealed a novel, and as yet unresolved, primarily copper-based pathway for ammonia oxidation and respiration distinct from that of known ammonia-oxidizing bacteria and possibly relevant to the production of atmospherically active nitrogen oxides. Comparative studies also provide compelling evidence that the lineage of Archaea with which the AOA affiliate is sufficiently divergent to justify the creation of a novel phylum, the Thaumarchaeota.
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Bacterial Persistence and Toxin-Antitoxin Loci
Vol. 66 (2012), pp. 103–123More LessBacterial persistence is caused by the presence of rare, slowly growing bacteria among populations of rapidly growing cells. The slowly growing bacteria are tolerant of antibiotics and other environmental insults, whereas their isogenic, rapidly growing siblings are sensitive. Recent research has shown that persistence of the model organism Escherichia coli depends on toxin-antitoxin (TA) loci. Deletion of type II TA loci reduces the level of persistence significantly. Lon protease but no other known ATP-dependent proteases is required for persistence. Polyphosphate and (p)ppGpp also are required for persistence. These observations led to the proposal of a simple and testable model that explains the persistence of E. coli. It is now important to challenge this model and to test whether the persistence of pathogenic bacteria also depends on TA loci.
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Activating Transcription in Bacteria
Vol. 66 (2012), pp. 125–152More LessBacteria use a variety of mechanisms to direct RNA polymerase to specific promoters in order to activate transcription in response to growth signals or environmental cues. Activation can be due to factors that interact at specific promoters, thereby increasing transcription directed by these promoters. We examine the range of architectures found at activator-dependent promoters and outline the mechanisms by which input from different factors is integrated. Alternatively, activation can be due to factors that interact with RNA polymerase and change its preferences for target promoters. We summarize the different mechanistic options for activation that are focused directly on RNA polymerase.
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Herpesvirus Transport to the Nervous System and Back Again
Vol. 66 (2012), pp. 153–176More LessHerpes simplex virus, varicella zoster virus, and pseudorabies virus are neurotropic pathogens of the Alphaherpesvirinae subfamily of the Herpesviridae. These viruses efficiently invade the peripheral nervous system and establish lifelong latency in neurons resident in peripheral ganglia. Primary and recurrent infections cycle virus particles between neurons and the peripheral tissues they innervate. This remarkable cycle of infection is the topic of this review. In addition, some of the distinguishing hallmarks of the infections caused by these viruses are evaluated in terms of their underlying similarities.
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A Virological View of Innate Immune Recognition
Vol. 66 (2012), pp. 177–196More LessThe innate immune system uses multiple strategies to detect viral infections. Because all viruses rely on host cells for their synthesis and propagation, the molecular features used to detect viral infections must be unique to viruses and absent from host cells. Research in the past decade has advanced our understanding of various cell-intrinsic and cell-extrinsic modes of virus recognition. This review examines the innate recognition from the point of view of virus invasion and replication strategies, and places innate sensors in the context of detecting viral genome, replication intermediate, transcriptional by-product, and other viral invasion strategies. On the basis of other unique features common to viral infections, undiscovered areas of virus detection are discussed.
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DNA Replication and Genomic Architecture of Very Large Bacteria
Vol. 66 (2012), pp. 197–212More LessLarge cell size is not restricted to a particular bacterial lifestyle, dispersal method, or cell envelope type. What is conserved among the very large bacteria are the quantity and arrangement of their genomic resources. All large bacteria described to date appear to be highly polyploid. This review focuses on Epulopiscium sp. type B, which maintains tens of thousands of genome copies throughout its life cycle. Only a tiny proportion of mother cell DNA is inherited by intracellular offspring, but surprisingly DNA replication takes place in the terminally differentiated mother cell as offspring grow. Massive polyploidy supports the acquisition of unstable genetic elements normally not seen in essential genes. Further studies of how large bacteria manage their genomic resources will provide insight into how simple cellular modifications can support unusual lifestyles and exceptional cell forms.
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Large T Antigens of Polyomaviruses: Amazing Molecular Machines
Vol. 66 (2012), pp. 213–236More LessThe large tumor antigen (T antigen) encoded by simian virus 40 is an amazing molecular machine because it orchestrates viral infection by modulating multiple fundamental viral and cellular processes. T antigen is required for viral DNA replication, transcription, and virion assembly. In addition, T antigen targets multiple cellular pathways, including those that regulate cell proliferation, cell death, and the inflammatory response. Ectopic T antigen expression results in the immortalization and transformation of many cell types in culture and T antigen induces neoplasia when expressed in rodents. The analysis of the mechanisms by which T antigen carries out its many functions has proved to be a powerful way of gaining insights into cell biology. The accelerating pace at which new polyomaviruses are being discovered provides a collection of novel T antigens that, like simian virus 40, can be used to discover and study key cellular regulatory systems.
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Peroxisome Assembly and Functional Diversity in Eukaryotic Microorganisms
Vol. 66 (2012), pp. 237–263More LessPeroxisomes are core eukaryotic organelles that generally function in lipid metabolism and detoxification of reactive oxygen species, but they are increasingly associated with taxa-specific metabolic, cellular, and developmental functions. Here, we present a brief overview of peroxisome assembly, followed by a discussion of their functional diversification. Matrix protein import occurs through a remarkable translocon that can accommodate folded and even oligomeric proteins. Metabolically specialized peroxisomes include glycosomes of trypanosomes, which have come to compartmentalize most of the glycolytic pathway and play a role in developmental signal transduction. The differentiation of physically distinct subcompartments also contributes to peroxisome diversification; in the clade of filamentous ascomycetes, dense-core Woronin bodies bud from peroxisomes to gate cell-to-cell channels. Here, the import of oligomeric cargo is central to the mechanism of subcompartment specification. In general, the acquisition of a tripeptide peroxisome targeting signal by nonperoxisomal proteins appears to be a recurrent step in the evolution of peroxisome diversity.
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Microbial Population and Community Dynamics on Plant Roots and Their Feedbacks on Plant Communities
Vol. 66 (2012), pp. 265–283More LessThe composition of the soil microbial community can be altered dramatically due to association with individual plant species, and these effects on the microbial community can have important feedbacks on plant ecology. Negative plant-soil feedback plays primary roles in maintaining plant community diversity, whereas positive plant-soil feedback may cause community conversion. Host-specific differentiation of the microbial community results from the trade-offs associated with overcoming plant defense and the specific benefits associated with plant rewards. Accumulation of host-specific pathogens likely generates negative feedback on the plant, while changes in the density of microbial mutualists likely generate positive feedback. However, the competitive dynamics among microbes depends on the multidimensional costs of virulence and mutualism, the fine-scale spatial structure within plant roots, and active plant allocation and localized defense. Because of this, incorporating a full view of microbial dynamics is essential to explaining the dynamics of plant-soil feedbacks and therefore plant community ecology.
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Bacterial Chemotaxis: The Early Years of Molecular Studies
Vol. 66 (2012), pp. 285–303More LessThis review focuses on the early years of molecular studies of bacterial chemotaxis and motility, beginning in the 1960s with Julius Adler's pioneering work. It describes key observations that established the field and made bacterial chemotaxis a paradigm for the molecular understanding of biological signaling. Consideration of those early years includes aspects of science seldom described in journals: the accidental findings, personal interactions, and scientific culture that often drive scientific progress.
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RNA Interference Pathways in Fungi: Mechanisms and Functions
Vol. 66 (2012), pp. 305–323More LessRNA interference (RNAi) is a conserved eukaryotic gene regulatory mechanism that uses small noncoding RNAs to mediate posttranscriptional/transcriptional gene silencing. The fission yeast Schizosaccharomyces pombe and the filamentous fungus Neurospora crassa have served as important model systems for RNAi research. Studies on these two organisms and other fungi have contributed significantly to our understanding of the mechanisms and functions of RNAi in eukaryotes. In addition, surprisingly diverse RNAi-mediated processes and small RNA biogenesis pathways have been discovered in fungi. In this review, we give an overview of different fungal RNAi pathways with a focus on their mechanisms and functions.
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Evolution of Two-Component Signal Transduction Systems
Vol. 66 (2012), pp. 325–347More LessTo exist in a wide range of environmental niches, bacteria must sense and respond to a variety of external signals. A primary means by which this occurs is through two-component signal transduction pathways, typically composed of a sensor histidine kinase that receives the input stimuli and then phosphorylates a response regulator that effects an appropriate change in cellular physiology. Histidine kinases and response regulators have an intrinsic modularity that separates signal input, phosphotransfer, and output response; this modularity has allowed bacteria to dramatically expand and diversify their signaling capabilities. Recent work has begun to reveal the molecular basis by which two-component proteins evolve. How and why do orthologous signaling proteins diverge? How do cells gain new pathways and recognize new signals? What changes are needed to insulate a new pathway from existing pathways? What constraints are there on gene duplication and lateral gene transfer? Here, we review progress made in answering these questions, highlighting how the integration of genome sequence data with experimental studies is providing major new insights.
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The Unique Paradigm of Spirochete Motility and Chemotaxis
Vol. 66 (2012), pp. 349–370More LessSpirochete motility is enigmatic: It differs from the motility of most other bacteria in that the entire bacterium is involved in translocation in the absence of external appendages. Using the Lyme disease spirochete Borrelia burgdorferi (Bb) as a model system, we explore the current research on spirochete motility and chemotaxis. Bb has periplasmic flagella (PFs) subterminally attached to each end of the protoplasmic cell cylinder, and surrounding the cell is an outer membrane. These internal helix-shaped PFs allow the spirochete to swim by generating backward-moving waves by rotation. Exciting advances using cryoelectron tomography are presented with respect to in situ analysis of cell, PF, and motor structure. In addition, advances in the dynamics of motility, chemotaxis, gene regulation, and the role of motility and chemotaxis in the life cycle of Bb are summarized. The results indicate that the motility paradigms of flagellated bacteria do not apply to these unique bacteria.
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Vaginal Microbiome: Rethinking Health and Disease
Vol. 66 (2012), pp. 371–389More LessVaginal microbiota form a mutually beneficial relationship with their host and have a major impact on health and disease. In recent years our understanding of vaginal bacterial community composition and structure has significantly broadened as a result of investigators using cultivation-independent methods based on the analysis of 16S ribosomal RNA (rRNA) gene sequences. In asymptomatic, otherwise healthy women, several kinds of vaginal microbiota exist, the majority often dominated by species of Lactobacillus, while others are composed of a diverse array of anaerobic microorganisms. Bacterial vaginosis is the most common vaginal condition and is vaguely characterized as the disruption of the equilibrium of the normal vaginal microbiota. A better understanding of normal and healthy vaginal ecosystems that is based on their true function and not simply on their composition would help better define health and further improve disease diagnostics as well as the development of more personalized regimens to promote health and treat diseases.
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Electromicrobiology
Vol. 66 (2012), pp. 391–409More LessElectromicrobiology deals with the interactions between microorganisms and electronic devices and with the novel electrical properties of microorganisms. A diversity of microorganisms can donate electrons to, or accept electrons from, electrodes without the addition of artificial electron shuttles. However, the mechanisms for microbe-electrode electron exchange have been seriously studied in only a few microorganisms. Shewanella oneidensis interacts with electrodes primarily via flavins that function as soluble electron shuttles. Geobacter sulfurreducens makes direct electrical contacts with electrodes via outer-surface, c-type cytochromes. G. sulfurreducens is also capable of long-range electron transport along pili, known as microbial nanowires, that have metallic-like conductivity similar to that previously described in synthetic conducting polymers. Pili networks confer conductivity to G. sulfurreducens biofilms, which function as a conducting polymer, with supercapacitor and transistor functionalities. Conductive microorganisms and/or their nanowires have a number of potential practical applications, but additional basic research will be necessary for rational optimization.
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Origin and Diversification of Eukaryotes
Vol. 66 (2012), pp. 411–427More LessThe bulk of the diversity of eukaryotic life is microbial. Although the larger eukaryotes—namely plants, animals, and fungi—dominate our visual landscapes, microbial lineages compose the greater part of both genetic diversity and biomass, and contain many evolutionary innovations. Our understanding of the origin and diversification of eukaryotes has improved substantially with analyses of molecular data from diverse lineages. These data have provided insight into the nature of the genome of the last eukaryotic common ancestor (LECA). Yet, the origin of key eukaryotic features, namely the nucleus and cytoskeleton, remains poorly understood. In contrast, the past decades have seen considerable refinement in hypotheses on the major branching events in the evolution of eukaryotic diversity. New insights have also emerged, including evidence for the acquisition of mitochondria at the time of the origin of eukaryotes and data supporting the dynamic nature of genomes in LECA.
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Genomic Insights into Syntrophy: The Paradigm for Anaerobic Metabolic Cooperation
Vol. 66 (2012), pp. 429–452More LessSyntrophy is a tightly coupled mutualistic interaction between hydrogen-/formate-producing and hydrogen-/formate-using microorganisms that occurs throughout the microbial world. Syntrophy is essential for global carbon cycling, waste decomposition, and biofuel production. Reverse electron transfer, e.g., the input of energy to drive critical redox reactions, is a defining feature of syntrophy. Genomic analyses indicate multiple systems for reverse electron transfer, including ion-translocating ferredoxin:NAD+ oxidoreductase and hydrogenases, two types of electron transfer flavoprotein:quinone oxidoreductases, and other quinone reactive complexes. Confurcating hydrogenases that couple the favorable production of hydrogen from reduced ferredoxin with the unfavorable production of hydrogen from NADH are present in almost all syntrophic metabolizers, implicating their critical role in syntrophy. Transcriptomic analysis shows upregulation of many genes without assigned functions in the syntrophic lifestyle. High-throughput technologies provide insight into the mechanisms used to establish and maintain syntrophic consortia and conserve energy from reactions that operate close to thermodynamic equilibrium.
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Structure and Regulation of the Type VI Secretion System
Vol. 66 (2012), pp. 453–472More LessThe type VI secretion system (T6SS) is a complex and widespread gram-negative bacterial export pathway with the capacity to translocate protein effectors into a diversity of target cell types. Current structural models of the T6SS indicate that the apparatus is composed of at least two complexes, a dynamic bacteriophage-like structure and a cell-envelope-spanning membrane-associated assembly. How these complexes interact to promote effector secretion and cell targeting remains a major question in the field. As a contact-dependent pathway with specific cellular targets, the T6SS is subject to tight regulation. Thus, the identification of regulatory elements that control T6S expression continues to shape our understanding of the environmental circumstances relevant to its function. This review discusses recent progress toward characterizing T6S structure and regulation.
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Network News: The Replication of Kinetoplast DNA
Vol. 66 (2012), pp. 473–491More LessOne of the most fascinating and unusual features of trypanosomatids, parasites that cause disease in many tropical countries, is their mitochondrial DNA. This genome, known as kinetoplast DNA (kDNA), is organized as a single, massive DNA network formed of interlocked DNA rings. In this review, we discuss recent studies on kDNA structure and replication, emphasizing recent developments on replication enzymes, how the timing of kDNA synthesis is controlled during the cell cycle, and the machinery for segregating daughter networks after replication.
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Pseudomonas aeruginosa Twitching Motility: Type IV Pili in Action
Vol. 66 (2012), pp. 493–520More LessType IV pili (T4P) are one of the most common forms of bacterial and archaeal surface structures, involved in adherence, motility, competence for DNA uptake, and pathogenesis. Pseudomonas aeruginosa has emerged as one of the key model systems for the investigation of T4P structure and function. Although its reputation as a serious nosocomial and opportunistic pathogen is well deserved, its facile growth requirements and the ready availability of molecular tools have allowed for rapid advances in our understanding of how T4P are assembled; their contributions to motility, biofilm formation and virulence; and their complex regulation. This review covers recent findings concerning the three different types of T4P found in P. aeruginosa (type IVa, type IVb, and Tad) and provides details about the modes of translocation mediated by T4aP, the architecture and function of the T4aP assembly system, and the complex regulation of T4aP biogenesis and function.
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Postgenomic Approaches to Using Corynebacteria as Biocatalysts
Vol. 66 (2012), pp. 521–550More LessCorynebacterium glutamicum exhibits numerous ideal intrinsic attributes as a factory of primary and secondary metabolites. The versatile capabilities of this organism have long been implemented at the industrial scale to produce an array of amino acids at high yields and conversion rates, thereby enabling the development of an entire industry. The postgenomic era provides a new technological platform not only to further optimize the intrinsic attributes of C. glutamicum whole cells as biocatalysts, but also to dramatically expand the product portfolio that can be manufactured by this organism, from amino acids to commodity chemicals. This review addresses the methods and strain optimization strategies enabled by genomic information and associated techniques. Their implementation has provided important additional incremental improvements to the economics of industry-scale manufacturing in which C. glutamicum and its episomal elements are used as a performing host-vector system.
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Previous Volumes
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Volume 77 (2023)
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Volume 76 (2022)
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Volume 75 (2021)
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Volume 74 (2020)
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Volume 73 (2019)
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Volume 72 (2018)
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Volume 71 (2017)
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Volume 70 (2016)
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Volume 69 (2015)
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Volume 68 (2014)
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Volume 67 (2013)
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Volume 66 (2012)
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Volume 65 (2011)
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Volume 64 (2010)
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Volume 63 (2009)
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Volume 62 (2008)
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Volume 61 (2007)
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Volume 60 (2006)
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Volume 59 (2005)
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Volume 58 (2004)
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Volume 57 (2003)
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Volume 56 (2002)
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Volume 55 (2001)
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Volume 54 (2000)
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Volume 53 (1999)
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Volume 52 (1998)
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Volume 51 (1997)
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Volume 50 (1996)
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Volume 49 (1995)
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Volume 48 (1994)
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Volume 47 (1993)
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Volume 46 (1992)
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Volume 45 (1991)
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Volume 44 (1990)
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Volume 43 (1989)
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Volume 42 (1988)
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Volume 41 (1987)
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Volume 40 (1986)
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Volume 39 (1985)
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Volume 38 (1984)
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Volume 37 (1983)
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Volume 36 (1982)
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Volume 35 (1981)
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Volume 34 (1980)
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Volume 33 (1979)
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Volume 32 (1978)
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Volume 31 (1977)
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Volume 30 (1976)
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Volume 29 (1975)
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Volume 28 (1974)
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Volume 27 (1973)
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Volume 26 (1972)
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Volume 25 (1971)
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Volume 24 (1970)
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Volume 23 (1969)
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Volume 22 (1968)
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Volume 21 (1967)
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Volume 20 (1966)
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Volume 19 (1965)
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Volume 18 (1964)
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Volume 17 (1963)
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Volume 16 (1962)
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Volume 15 (1961)
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Volume 14 (1960)
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Volume 13 (1959)
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Volume 12 (1958)
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Volume 11 (1957)
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Volume 10 (1956)
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Volume 9 (1955)
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Volume 8 (1954)
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Volume 7 (1953)
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Volume 6 (1952)
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Volume 5 (1951)
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Volume 4 (1950)
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Volume 3 (1949)
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Volume 2 (1948)
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Volume 1 (1947)
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Volume 0 (1932)