Genomic Approaches to Drug Resistance in Malaria.
Abstract Although the last two decades have seen a substantial decline in malaria incidence and mortality due to the use of insecticide-treated bed nets and artemisinin combination therapy, the threat of drug resistance is a constant obstacle to sustainable malaria control. Given that patients can die quickly from this disease, public health officials and doctors need to understand whether drug resistance exists in the parasite population, as well as how prevalent it is so they can make informed decisions about treatment. As testing for drug efficacy before providing treatment to malaria patients is impractical, r...
Source: Annual Review of Microbiology - September 8, 2020 Category: Microbiology Authors: Rocamora F, Winzeler EA Tags: Annu Rev Microbiol Source Type: research

Introduction.
PMID: 32905750 [PubMed - as supplied by publisher] (Source: Annual Review of Microbiology)
Source: Annual Review of Microbiology - September 8, 2020 Category: Microbiology Authors: Gottesman S Tags: Annu Rev Microbiol Source Type: research

Ape Origins of Human Malaria.
Abstract African apes harbor at least twelve Plasmodium species, some of which have been a source of human infection. It is now well established that Plasmodium falciparum emerged following the transmission of a gorilla parasite, perhaps within the last 10,000 years, while Plasmodium vivax emerged earlier from a parasite lineage that infected humans and apes in Africa before the Duffy-negative mutation eliminated the parasite from humans there. Compared to their ape relatives, both human parasites have greatly reduced genetic diversity and an excess of nonsynonymous mutations, consistent with severe genetic bottle...
Source: Annual Review of Microbiology - September 8, 2020 Category: Microbiology Authors: Sharp PM, Plenderleith LJ, Hahn BH Tags: Annu Rev Microbiol Source Type: research

Prospects and Pitfalls: Next-Generation Tools to Control Mosquito-Transmitted Disease.
los G Abstract Mosquito-transmitted diseases, including malaria and dengue, are a major threat to human health around the globe, affecting millions each year. A diverse array of next-generation tools has been designed to eliminate mosquito populations or to replace them with mosquitoes that are less capable of transmitting key pathogens. Many of these new approaches have been built on recent advances in CRISPR/Cas9-based genome editing. These initiatives have driven the development of pathogen-resistant lines, new genetics-based sexing methods, and new methods of driving desirable genetic traits into mosquito popu...
Source: Annual Review of Microbiology - September 8, 2020 Category: Microbiology Authors: Caragata EP, Dong S, Dong Y, Simões ML, Tikhe CV, Dimopoulos G Tags: Annu Rev Microbiol Source Type: research

Surface Sensing and Adaptation in Bacteria.
Abstract Bacteria thrive both in liquids and attached to surfaces. The concentration of bacteria on surfaces is generally much higher than in the surrounding environment, offering bacteria ample opportunity for mutualistic, symbiotic, and pathogenic interactions. To efficiently populate surfaces, they have evolved mechanisms to sense mechanical or chemical cues upon contact with solid substrata. This is of particular importance for pathogens that interact with host tissue surfaces. In this review we discuss how bacteria are able to sense surfaces and how they use this information to adapt their physiology and beha...
Source: Annual Review of Microbiology - September 8, 2020 Category: Microbiology Authors: Laventie BJ, Jenal U Tags: Annu Rev Microbiol Source Type: research

The Influence of Bacteria on Animal Metamorphosis.
Abstract The swimming larvae of many marine animals identify a location on the seafloor to settle and undergo metamorphosis based on the presence of specific surface-bound bacteria. While bacteria-stimulated metamorphosis underpins processes such as the fouling of ship hulls, animal development in aquaculture, and the recruitment of new animals to coral reef ecosystems, little is known about the mechanisms governing this microbe-animal interaction. Here we review what is known and what we hope to learn about how bacteria and the factors they produce stimulate animal metamorphosis. With a few emerging model systems...
Source: Annual Review of Microbiology - September 8, 2020 Category: Microbiology Authors: Cavalcanti GS, Alker AT, Delherbe N, Malter KE, Shikuma NJ Tags: Annu Rev Microbiol Source Type: research

Clostridioides difficile Spore Formation and Germination: New Insights and Opportunities for Intervention.
Abstract Spore formation and germination are essential for the bacterial pathogen Clostridioides difficile to transmit infection. Despite the importance of these developmental processes to the infection cycle of C. difficile, the molecular mechanisms underlying how this obligate anaerobe forms infectious spores and how these spores germinate to initiate infection were largely unknown until recently. Work in the last decade has revealed that C. difficile uses a distinct mechanism for sensing and transducing germinant signals relative to previously characterized spore formers. The C. difficile spore assembly pathway...
Source: Annual Review of Microbiology - September 8, 2020 Category: Microbiology Authors: Shen A Tags: Annu Rev Microbiol Source Type: research

Fungal Volatile Organic Compounds: More Than Just a Funky Smell?
Abstract Many volatile organic compounds (VOCs) associated with industry cause adverse health effects, but less is known about the physiological effects of biologically produced volatiles. This review focuses on the VOCs emitted by fungi, which often have characteristic moldy or "mushroomy" odors. One of the most common fungal VOCs, 1-octen-3-ol, is a semiochemical for many arthropod species and also serves as a developmental hormone for several fungal groups. Other fungal VOCs are flavor components of foods and spirits or are assayed in indirect methods for detecting the presence of mold in stored agric...
Source: Annual Review of Microbiology - September 8, 2020 Category: Microbiology Authors: Inamdar AA, Morath S, Bennett JW Tags: Annu Rev Microbiol Source Type: research

Molecular Mechanisms of Drug Resistance in Plasmodium falciparum Malaria.
Abstract Understanding and controlling the spread of antimalarial resistance, particularly to artemisinin and its partner drugs, is a top priority. Plasmodium falciparum parasites resistant to chloroquine, amodiaquine, or piperaquine harbor mutations in the P. falciparum chloroquine resistance transporter (PfCRT), a transporter resident on the digestive vacuole membrane that in its variant forms can transport these weak-base 4-aminoquinoline drugs out of this acidic organelle, thus preventing these drugs from binding heme and inhibiting its detoxification. The structure of PfCRT, solved by cryogenic electron micro...
Source: Annual Review of Microbiology - September 8, 2020 Category: Microbiology Authors: Wicht KJ, Mok S, Fidock DA Tags: Annu Rev Microbiol Source Type: research

Implications of the Evolutionary Trajectory of Centromeres in the Fungal Kingdom.
Abstract Chromosome segregation during the cell cycle is an evolutionarily conserved, fundamental biological process. Dynamic interaction between spindle microtubules and the kinetochore complex that assembles on centromere DNA is required for faithful chromosome segregation. The first artificial minichromosome was constructed by cloning the centromere DNA of the budding yeast Saccharomyces cerevisiae. Since then, centromeres have been identified in>60 fungal species. The DNA sequence and organization of the sequence elements are highly diverse across these fungal centromeres. In this article, we provide a comp...
Source: Annual Review of Microbiology - July 24, 2020 Category: Microbiology Authors: Guin K, Sreekumar L, Sanyal K Tags: Annu Rev Microbiol Source Type: research

Structural Basis of Hydrogenotrophic Methanogenesis.
Abstract Most methanogenic archaea use the rudimentary hydrogenotrophic pathway-from CO2 and H2 to methane-as the terminal step of microbial biomass degradation in anoxic habitats. The barely exergonic process that just conserves sufficient energy for a modest lifestyle involves chemically challenging reactions catalyzed by complex enzyme machineries with unique metal-containing cofactors. The basic strategy of the methanogenic energy metabolism is to covalently bind C1 species to the C1 carriers methanofuran, tetrahydromethanopterin, and coenzyme M at different oxidation states. The four reduction reactions from ...
Source: Annual Review of Microbiology - July 21, 2020 Category: Microbiology Authors: Shima S, Huang G, Wagner T, Ermler U Tags: Annu Rev Microbiol Source Type: research

How Food Affects Colonization Resistance Against Enteropathogenic Bacteria.
Abstract Food has a major impact on all aspects of health. Recent data suggest that food composition can also affect susceptibility to infections by enteropathogenic bacteria. Here, we discuss how food may alter the microbiota as well as mucosal defenses and how this can affect infection. Salmonella Typhimurium diarrhea serves as a paradigm, and complementary evidence comes from other pathogens. We discuss the effects of food composition on colonization resistance, host defenses, and the infection process as well as the merits and limitations of mouse models and experimental foods, which are available to decipher ...
Source: Annual Review of Microbiology - July 21, 2020 Category: Microbiology Authors: Kreuzer M, Hardt WD Tags: Annu Rev Microbiol Source Type: research

The Ingenuity of Bacterial Genomes.
Abstract The genomes of bacteria contain fewer genes and substantially less noncoding DNA than those of eukaryotes, and as a result, they have much less raw material to invent new traits. Yet, bacteria are vastly more taxonomically diverse, numerically abundant, and globally successful in colonizing new habitats than eukaryotes. Although bacterial genomes are generally considered to be optimized for efficient growth and rapid adaptation, nonadaptive processes have played a major role in shaping the size, contents, and compact organization of bacterial genomes and have allowed the establishment of deleterious trait...
Source: Annual Review of Microbiology - July 21, 2020 Category: Microbiology Authors: Kirchberger PC, Schmidt M, Ochman H Tags: Annu Rev Microbiol Source Type: research

Amyloid Signaling in Filamentous Fungi and Bacteria.
Abstract Amyloids are implicated in many protein misfolding diseases. Amyloid folds, however, also display a range of functional roles particularly in the microbial world. The templating ability of these folds endows them with specific properties allowing their self-propagation and protein-to-protein transmission in vivo. This property, the prion principle, is exploited by specific signaling pathways that use transmission of the amyloid fold as a way to convey information from a receptor to an effector protein. I describe here amyloid signaling pathways involving fungal nucleotide binding and oligomerization domai...
Source: Annual Review of Microbiology - July 20, 2020 Category: Microbiology Authors: Saupe SJ Tags: Annu Rev Microbiol Source Type: research

Conflict, Competition, and Cooperation Regulate Social Interactions in Filamentous Fungi.
G, Glass NL Abstract Social cooperation impacts the development and survival of species. In higher taxa, kin recognition occurs via visual, chemical, or tactile cues that dictate cooperative versus competitive interactions. In microbes, the outcome of cooperative versus competitive interactions is conferred by identity at allorecognition loci, so called kind recognition. In syncytial filamentous fungi, the acquisition of multicellularity is associated with somatic cell fusion within and between colonies. However, such intraspecific cooperation entails risks, as fusion can transmit deleterious genotypes or infectio...
Source: Annual Review of Microbiology - July 20, 2020 Category: Microbiology Authors: Gonçalves AP, Heller J, Rico-Ramírez AM, Daskalov A, Rosenfield G, Glass NL Tags: Annu Rev Microbiol Source Type: research

Epigenetic Regulation of Virulence and Immunoevasion by Phase-Variable Restriction-Modification Systems in Bacterial Pathogens.
We present and discuss examples of phasevarion systems in the major human pathogens Haemophilus influenzae, Neisseria meningitidis, Neisseria gonorrhoeae, Helicobacter pylori, Moraxella catarrhalis, and Streptococcus pneumoniae. Expected final online publication date for the Annual Review of Microbiology, Volume 74 is September 8, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates. PMID: 32689914 [PubMed - as supplied by publisher] (Source: Annual Review of Microbiology)
Source: Annual Review of Microbiology - July 20, 2020 Category: Microbiology Authors: Seib KL, Srikhanta YN, Atack JM, Jennings MP Tags: Annu Rev Microbiol Source Type: research

Defining and Disrupting Species Boundaries in Saccharomyces.
Abstract The genus Saccharomyces is an evolutionary paradox. On the one hand, it is composed of at least eight clearly phylogenetically delineated species; these species are reproductively isolated from each other, and hybrids usually cannot complete their sexual life cycles. On the other hand, Saccharomyces species have a long evolutionary history of hybridization, which has phenotypic consequences for adaptation and domestication. A variety of cellular, ecological, and evolutionary mechanisms are responsible for this partial reproductive isolation among Saccharomyces species. These mechanisms have caused the evo...
Source: Annual Review of Microbiology - July 20, 2020 Category: Microbiology Authors: Ono J, Greig D, Boynton PJ Tags: Annu Rev Microbiol Source Type: research

Membrane Dynamics in Phototrophic Bacteria.
Abstract Photosynthetic membranes are typically densely packed with proteins, and this is crucial for their function in efficient trapping of light energy. Despite being crowded with protein, the membranes are fluid systems in which proteins and smaller molecules can diffuse. Fluidity is also crucial for photosynthetic function, as it is essential for biogenesis, electron transport, and protein redistribution for functional regulation. All photosynthetic membranes seem to maintain a delicate balance between crowding, order, and fluidity. How does this work in phototrophic bacteria? In this review, we focus on two ...
Source: Annual Review of Microbiology - July 20, 2020 Category: Microbiology Authors: Mullineaux CW, Liu LN Tags: Annu Rev Microbiol Source Type: research

From Input to Output: The Lap/c-di-GMP Biofilm Regulatory Circuit.
Abstract Biofilms are the dominant bacterial lifestyle. The regulation of the formation and dispersal of bacterial biofilms has been the subject of study in many organisms. Over the last two decades, the mechanisms of Pseudomonas fluorescens biofilm formation and regulation have emerged as among the best understood of any bacterial biofilm system. Biofilm formation by P. fluorescens occurs through the localization of an adhesin, LapA, to the outer membrane via a variant of the classical type I secretion system. The decision between biofilm formation and dispersal is mediated by LapD, a c-di-GMP receptor, and LapG,...
Source: Annual Review of Microbiology - July 20, 2020 Category: Microbiology Authors: Collins AJ, Smith TJ, Sondermann H, O'Toole GA Tags: Annu Rev Microbiol Source Type: research

A Bacterial Tower of Babel: Quorum-Sensing Signaling Diversity and Its Evolution.
Abstract Quorum sensing is a process in which bacteria secrete and sense a diffusible molecule, thereby enabling bacterial groups to coordinate their behavior in a density-dependent manner. Quorum sensing has evolved multiple times independently, utilizing different molecular pathways and signaling molecules. A common theme among many quorum-sensing families is their wide range of signaling diversity-different variants within a family code for different signal molecules with a cognate receptor specific to each variant. This pattern of vast allelic polymorphism raises several questions-How do different signaling va...
Source: Annual Review of Microbiology - July 17, 2020 Category: Microbiology Authors: Aframian N, Eldar A Tags: Annu Rev Microbiol Source Type: research

Polymorphic Toxins and Their Immunity Proteins: Diversity, Evolution, and Mechanisms of Delivery.
Abstract All bacteria must compete for growth niches and other limited environmental resources. These existential battles are waged at several levels, but one common strategy entails the transfer of growth-inhibitory protein toxins between competing cells. These antibacterial effectors are invariably encoded with immunity proteins that protect cells from intoxication by neighboring siblings. Several effector classes have been described, each designed to breach the cell envelope of target bacteria. Although effector architectures and export pathways tend to be clade specific, phylogenetically distant species often ...
Source: Annual Review of Microbiology - July 17, 2020 Category: Microbiology Authors: Ruhe ZC, Low DA, Hayes CS Tags: Annu Rev Microbiol Source Type: research

Toxoplasma Mechanisms for Delivery of Proteins and Uptake of Nutrients Across the Host-Pathogen Interface.
j JPJ Abstract Many intracellular pathogens, including the protozoan parasite Toxoplasma gondii, live inside a vacuole that resides in the host cytosol. Vacuolar residence provides these pathogens with a defined niche for replication and protection from detection by host cytosolic pattern recognition receptors. However, the limiting membrane of the vacuole, which constitutes the host-pathogen interface, is also a barrier for pathogen effectors to reach the host cytosol and for the acquisition of host-derived nutrients. This review provides an update on the specialized secretion and trafficking systems used by Toxo...
Source: Annual Review of Microbiology - July 17, 2020 Category: Microbiology Authors: Wang Y, Sangaré LO, Paredes-Santos TC, Saeij JPJ Tags: Annu Rev Microbiol Source Type: research

Assembly of Bacterial Capsular Polysaccharides and Exopolysaccharides.
Abstract Polysaccharides are dominant features of most bacterial surfaces and are displayed in different formats. Many bacteria produce abundant long-chain capsular polysaccharides, which can maintain a strong association and form a capsule structure enveloping the cell and/or take the form of exopolysaccharides that are mostly secreted into the immediate environment. These polymers afford the producing bacteria protection from a wide range of physical, chemical, and biological stresses, support biofilms, and play critical roles in interactions between bacteria and their immediate environments. Their biological an...
Source: Annual Review of Microbiology - July 17, 2020 Category: Microbiology Authors: Whitfield C, Wear SS, Sande C Tags: Annu Rev Microbiol Source Type: research

Bacterial Volatile Compounds: Functions in Communication, Cooperation, and Competition.
We present work showing the ability of volatile compounds to modulate nutrient availability in the environment; alter the growth, development, and motility of bacteria and fungi; influence protist and arthropod behavior; and impact plant and animal health. We further discuss the benefits associated with using volatile compounds for communication and competition, alongside the challenges of studying these molecules and their functional roles. Finally, we address the opportunities these compounds present from commercial, clinical, and agricultural perspectives. Expected final online publication date for the Annual Review of ...
Source: Annual Review of Microbiology - July 15, 2020 Category: Microbiology Authors: Netzker T, Shepherdson EMF, Zambri MP, Elliot MA Tags: Annu Rev Microbiol Source Type: research

Bacterial Quorum Sensing During Infection.
Abstract Bacteria are highly interactive and possess an extraordinary repertoire of intercellular communication and social behaviors, including quorum sensing (QS). QS has been studied in detail at the molecular level, so mechanistic details are well understood in many species and are often involved in virulence. The use of different animal host models has demonstrated QS-dependent control of virulence determinants and virulence in several human pathogenic bacteria. QS also controls virulence in several plant pathogenic species. Despite the role QS plays in virulence during animal and plant laboratory-engineered i...
Source: Annual Review of Microbiology - July 13, 2020 Category: Microbiology Authors: Azimi S, Klementiev AD, Whiteley M, Diggle SP Tags: Annu Rev Microbiol Source Type: research

Shaping an Endospore: Architectural Transformations During Bacillus subtilis Sporulation.
Abstract Endospore formation in Bacillus subtilis provides an ideal model system for studying development in bacteria. Sporulation studies have contributed a wealth of information about the mechanisms of cell-specific gene expression, chromosome dynamics, protein localization, and membrane remodeling, while helping to dispel the early view that bacteria lack internal organization and interesting cell biological phenomena. In this review, we focus on the architectural transformations that lead to a profound reorganization of the cellular landscape during sporulation, from two cells that lie side by side to the endo...
Source: Annual Review of Microbiology - July 13, 2020 Category: Microbiology Authors: Khanna K, Lopez-Garrido J, Pogliano K Tags: Annu Rev Microbiol Source Type: research

The Bacterial Ro60 Protein and Its Noncoding Y RNA Regulators.
Abstract Ro60 ribonucleoproteins (RNPs), composed of the ring-shaped Ro 60-kDa (Ro60) protein and noncoding RNAs called Y RNAs, are present in all three domains of life. Ro60 was first described as an autoantigen in patients with rheumatic disease, and Ro60 orthologs have been identified in 3% to 5% of bacterial genomes, spanning the majority of phyla. Their functions have been characterized primarily in Deinococcus radiodurans, the first sequenced bacterium with a recognizable ortholog. In D. radiodurans, the Ro60 ortholog enhances the ability of 3'-to-5' exoribonucleases to degrade structured RNA during several ...
Source: Annual Review of Microbiology - July 13, 2020 Category: Microbiology Authors: Sim S, Hughes K, Chen X, Wolin SL Tags: Annu Rev Microbiol Source Type: research

Toward a Fully Resolved Fungal Tree of Life.
Abstract In this review, we discuss the current status and future challenges for fully elucidating the fungal tree of life. In the last 15 years, advances in genomic technologies have revolutionized fungal systematics, ushering the field into the phylogenomic era. This has made the unthinkable possible, namely access to the entire genetic record of all known extant taxa. We first review the current status of the fungal tree and highlight areas where additional effort will be required. We then review the analytical challenges imposed by the volume of data and discuss methods to recover the most accurate species tre...
Source: Annual Review of Microbiology - July 13, 2020 Category: Microbiology Authors: James TY, Stajich JE, Hittinger CT, Rokas A Tags: Annu Rev Microbiol Source Type: research

Iron-Only and Vanadium Nitrogenases: Fail-Safe Enzymes or Something More?
Abstract The enzyme molybdenum nitrogenase converts atmospheric nitrogen gas to ammonia and is of critical importance for the cycling of nitrogen in the biosphere and for the sustainability of life. Alternative vanadium and iron-only nitrogenases that are homologous to molybdenum nitrogenases are also found in archaea and bacteria, but they have a different transition metal, either vanadium or iron, at their active sites. So far alternative nitrogenases have only been found in microbes that also have molybdenum nitrogenase. They are less widespread than molybdenum nitrogenase in bacteria and archaea, and they are ...
Source: Annual Review of Microbiology - July 13, 2020 Category: Microbiology Authors: Harwood CS Tags: Annu Rev Microbiol Source Type: research

Chemical Mediators at the Bacterial-Fungal Interface.
Abstract Interactions among microbes are key drivers of evolutionary progress and constantly shape ecological niches. Microorganisms rely on chemical communication to interact with each other and surrounding organisms. They synthesize natural products as signaling molecules, antibiotics, or modulators of cellular processes that may be applied in agriculture and medicine. Whereas major insight has been gained into the principles of intraspecies interaction, much less is known about the molecular basis of interspecies interplay. In this review, we summarize recent progress in the understanding of chemically mediated...
Source: Annual Review of Microbiology - July 13, 2020 Category: Microbiology Authors: Scherlach K, Hertweck C Tags: Annu Rev Microbiol Source Type: research

Structure and Function of the Mycobacterial Type VII Secretion Systems.
Abstract Bacteria have evolved intricate secretion machineries for the successful delivery of large molecules across their cell envelopes. Such specialized secretion systems allow a variety of bacteria to thrive in specific host environments. In mycobacteria, type VII secretion systems (T7SSs) are dedicated protein transport machineries that fulfill diverse and crucial roles, ranging from metabolite uptake to immune evasion and subversion to conjugation. Since the discovery of mycobacterial T7SSs about 15 y ago, genetic, structural, and functional studies have provided insight into the roles and functioning of the...
Source: Annual Review of Microbiology - July 13, 2020 Category: Microbiology Authors: Bunduc CM, Bitter W, Houben ENG Tags: Annu Rev Microbiol Source Type: research

The Yersinia Type III Secretion System as a Tool for Studying Cytosolic Innate Immune Surveillance.
Abstract Microbial pathogens have evolved complex mechanisms to interface with host cells in order to evade host defenses and replicate. However, mammalian innate immune receptors detect the presence of molecules unique to the microbial world or sense the activity of virulence factors, activating antimicrobial and inflammatory pathways. We focus on how studies of the major virulence factor of one group of microbial pathogens, the type III secretion system (T3SS) of human pathogenic Yersinia, have shed light on these important innate immune responses. Yersinia are largely extracellular pathogens, yet they insert T3...
Source: Annual Review of Microbiology - July 13, 2020 Category: Microbiology Authors: Schubert KA, Xu Y, Shao F, Auerbuch V Tags: Annu Rev Microbiol Source Type: research

Microbes as Biosensors.
Abstract The ability to detect disease early and deliver precision therapy would be transformative for the treatment of human illnesses. To achieve these goals, biosensors that can pinpoint when and where diseases emerge are needed. Rapid advances in synthetic biology are enabling us to exploit the information-processing abilities of living cells to diagnose disease and then treat it in a controlled fashion. For example, living sensors could be designed to precisely sense disease biomarkers, such as by-products of inflammation, and to respond by delivering targeted therapeutics in situ. Here, we provide an overvie...
Source: Annual Review of Microbiology - July 13, 2020 Category: Microbiology Authors: Inda ME, Lu TK Tags: Annu Rev Microbiol Source Type: research

What Is Metagenomics Teaching Us, and What Is Missed?
Abstract Shotgun metagenomic sequencing has revolutionized our ability to detect and characterize the diversity and function of complex microbial communities. In this review, we highlight the benefits of using metagenomics as well as the breadth of conclusions that can be made using currently available analytical tools, such as greater resolution of species and strains across phyla and functional content, while highlighting challenges of metagenomic data analysis. Major challenges remain in annotating function, given the dearth of functional databases for environmental bacteria compared to model organisms, and the...
Source: Annual Review of Microbiology - June 30, 2020 Category: Microbiology Authors: New FN, Brito IL Tags: Annu Rev Microbiol Source Type: research

Assembly and Dynamics of the Bacterial Flagellum.
Abstract The bacterial flagellar motor is the most complex structure in the bacterial cell, driving the ion-driven rotation of the helical flagellum. The ordered expression of the regulon and the assembly of the series of interacting protein rings, spanning the inner and outer membranes to form the ∼45-50-nm protein complex, have made investigation of the structure and mechanism a major challenge since its recognition as a rotating nanomachine about 40 years ago. Painstaking molecular genetics, biochemistry, and electron microscopy revealed a tiny electric motor spinning in the bacterial membrane. Over the las...
Source: Annual Review of Microbiology - June 30, 2020 Category: Microbiology Authors: Armitage JP, Berry RM Tags: Annu Rev Microbiol Source Type: research

Cyclic di-AMP Signaling in Bacteria.
l;ger L Abstract The second messenger molecule cyclic di-AMP (c-di-AMP) is formed by many bacteria and archaea. In many species that produce c-di-AMP, this second messenger is essential for viability on rich medium. Recent research has demonstrated that c-di-AMP binds to a large number of proteins and riboswitches, which are often involved in potassium and osmotic homeostasis. c-di-AMP becomes dispensable if the bacteria are cultivated on minimal media with low concentrations of osmotically active compounds. Thus, the essentiality of c-di-AMP does not result from an interaction with a single essential target but r...
Source: Annual Review of Microbiology - June 30, 2020 Category: Microbiology Authors: Stülke J, Krüger L Tags: Annu Rev Microbiol Source Type: research

The Plant Microbiome: From Ecology to Reductionism and Beyond.
gl JL Abstract Methodological advances over the past two decades have propelled plant microbiome research, allowing the field to comprehensively test ideas proposed over a century ago and generate many new hypotheses. Studying the distribution of microbial taxa and genes across plant habitats has revealed the importance of various ecological and evolutionary forces shaping plant microbiota. In particular, selection imposed by plant habitats strongly shapes the diversity and composition of microbiota and leads to microbial adaptation associated with navigating the plant immune system and utilizing plant-derived res...
Source: Annual Review of Microbiology - June 12, 2020 Category: Microbiology Authors: Fitzpatrick CR, Salas-González I, Conway JM, Finkel OM, Gilbert S, Russ D, Teixeira PJPL, Dangl JL Tags: Annu Rev Microbiol Source Type: research

Structures and Strategies of Anti-CRISPR-Mediated Immune Suppression.
Abstract More than 50 protein families have been identified that inhibit CRISPR (clustered regularly interspaced short palindromic repeats)-Cas-mediated adaptive immune systems. Here, we analyze the available anti-CRISPR (Acr) structures and describe common themes and unique mechanisms of stoichiometric and enzymatic suppressors of CRISPR-Cas. Stoichiometric inhibitors often function as molecular decoys of protein-binding partners or nucleic acid targets, while enzymatic suppressors covalently modify Cas ribonucleoprotein complexes or degrade immune signaling molecules. We review mechanistic insights that have bee...
Source: Annual Review of Microbiology - June 5, 2020 Category: Microbiology Authors: Wiegand T, Karambelkar S, Bondy-Denomy J, Wiedenheft B Tags: Annu Rev Microbiol Source Type: research

Archaeal DNA Replication.
Abstract It is now well recognized that the information processing machineries of archaea are far more closely related to those of eukaryotes than to those of their prokaryotic cousins, the bacteria. Extensive studies have been performed on the structure and function of the archaeal DNA replication origins, the proteins that define them, and the macromolecular assemblies that drive DNA unwinding and nascent strand synthesis. The results from various archaeal organisms across the archaeal domain of life show surprising levels of diversity at many levels-ranging from cell cycle organization to chromosome ploidy to r...
Source: Annual Review of Microbiology - June 5, 2020 Category: Microbiology Authors: Greci MD, Bell SD Tags: Annu Rev Microbiol Source Type: research

A Tale of Good Fortune in the Era of DNA.
Abstract Two strains of good fortune in my career were to stumble upon the Watson-Gilbert laboratory at Harvard when I entered graduate school in 1964, and to study gene regulation in bacteriophage λ when I was there. λ was almost entirely a genetic item a few years before, awaiting biochemical incarnation. Throughout my career I was a relentless consumer of the work of previous and current generations of λ geneticists. Empowered by this background, my laboratory made contributions in two areas. The first was regulation of early gene transcription in λ, the study of which bega...
Source: Annual Review of Microbiology - May 26, 2020 Category: Microbiology Authors: Roberts J Tags: Annu Rev Microbiol Source Type: research

Bacterial Persisters and Infection: Past, Present, and Progressing.
Abstract Persisters are nongrowing, transiently antibiotic-tolerant bacteria within a clonal population of otherwise susceptible cells. Their formation is triggered by environmental cues and involves the main bacterial stress response pathways that allow persisters to survive many harsh conditions, including antibiotic exposure. During infection, bacterial pathogens are exposed to a vast array of stresses in the host and form nongrowing persisters that survive both antibiotics and host immune responses, thereby most likely contributing to the relapse of many infections. While antibiotic persisters have been extens...
Source: Annual Review of Microbiology - September 8, 2019 Category: Microbiology Authors: Gollan B, Grabe G, Michaux C, Helaine S Tags: Annu Rev Microbiol Source Type: research

Introduction: Remembering Olaf Schneewind.
PMID: 31500533 [PubMed - in process] (Source: Annual Review of Microbiology)
Source: Annual Review of Microbiology - September 8, 2019 Category: Microbiology Authors: Gottesman S Tags: Annu Rev Microbiol Source Type: research

The Way It Was.
Abstract Mary Osborn was a native Californian. She was an undergraduate at the University of California, Berkeley, where she worked in the laboratory of I.L. Chaikoff. She received her PhD at the University of Washington, where her work on the role of folic acid coenzymes in one-carbon metabolism revealed the mechanism of action of methotrexate. After postdoctoral training with Bernard Horecker in the Department of Microbiology at New York University (NYU), she embarked on her research career as a faculty member in the NYU Department of Microbiology and in the Department of Molecular Biology at Albert Einstein Col...
Source: Annual Review of Microbiology - September 8, 2019 Category: Microbiology Authors: Osborn MJ Tags: Annu Rev Microbiol Source Type: research

Diversity, Genomics, and Distribution of Phytoplankton-Cyanobacterium Single-Cell Symbiotic Associations.
Abstract Cyanobacteria are common in symbiotic relationships with diverse multicellular organisms (animals, plants, fungi) in terrestrial environments and with single-celled heterotrophic, mixotrophic, and autotrophic protists in aquatic environments. In the sunlit zones of aquatic environments, diverse cyanobacterial symbioses exist with autotrophic taxa in phytoplankton, including dinoflagellates, diatoms, and haptophytes (prymnesiophytes). Phototrophic unicellular cyanobacteria related to Synechococcus and Prochlorococcus are associated with a number of groups. N2-fixing cyanobacteria are symbiotic with diatoms...
Source: Annual Review of Microbiology - September 8, 2019 Category: Microbiology Authors: Foster RA, Zehr JP Tags: Annu Rev Microbiol Source Type: research

Multiple Roles of c-di-GMP Signaling in Bacterial Pathogenesis.
Abstract The intracellular signaling molecule cyclic di-GMP (c-di-GMP) regulates the lifestyle of bacteria and controls many key functions and mechanisms. In the case of bacterial pathogens, a wide variety of virulence lifestyle factors have been shown to be regulated by c-di-GMP. Evidence of the importance of this molecule for bacterial pathogenesis has become so great that new antimicrobial agents are tested for their capacity of targeting c-di-GMP signaling. This review summarizes the current knowledge on this topic and reveals its application for the development of new antivirulence intervention strategies. ...
Source: Annual Review of Microbiology - September 8, 2019 Category: Microbiology Authors: Valentini M, Filloux A Tags: Annu Rev Microbiol Source Type: research

Coordination of the Cell Cycle in Trypanosomes.
Abstract Trypanosomes have complex life cycles within which there are both proliferative and differentiation cell divisions. The coordination of the cell cycle to achieve these different divisions is critical for the parasite to infect both host and vector. From studying the regulation of the proliferative cell cycle of the Trypanosoma brucei procyclic life cycle stage, three subcycles emerge that control the duplication and segregation of (a) the nucleus, (b) the kinetoplast, and (c) a set of cytoskeletal structures. We discuss how the clear dependency relationships within these subcycles, and the potential for c...
Source: Annual Review of Microbiology - September 8, 2019 Category: Microbiology Authors: Wheeler RJ, Gull K, Sunter JD Tags: Annu Rev Microbiol Source Type: research

Chromatic Acclimation in Cyanobacteria: A Diverse and Widespread Process for Optimizing Photosynthesis.
Abstract Chromatic acclimation (CA) encompasses a diverse set of molecular processes that involve the ability of cyanobacterial cells to sense ambient light colors and use this information to optimize photosynthetic light harvesting. The six known types of CA, which we propose naming CA1 through CA6, use a range of molecular mechanisms that likely evolved independently in distantly related lineages of the Cyanobacteria phylum. Together, these processes sense and respond to the majority of the photosynthetically relevant solar spectrum, suggesting that CA provides fitness advantages across a broad range of light co...
Source: Annual Review of Microbiology - September 8, 2019 Category: Microbiology Authors: Sanfilippo JE, Garczarek L, Partensky F, Kehoe DM Tags: Annu Rev Microbiol Source Type: research

Signaling Cascades Governing Entry into and Exit from Host Cells by Toxoplasma gondii.
Abstract The Apicomplexa phylum includes a large group of obligate intracellular protozoan parasites responsible for important diseases in humans and animals. Toxoplasma gondii is a widespread parasite with considerable versatility, and it is capable of infecting virtually any warm-blooded animal, including humans. This outstanding success can be attributed at least in part to an efficient and continuous sensing of the environment, with a ready-to-adapt strategy. This review updates the current understanding of the signals governing the lytic cycle of T. gondii, with particular focus on egress from infected cells,...
Source: Annual Review of Microbiology - September 8, 2019 Category: Microbiology Authors: Bisio H, Soldati-Favre D Tags: Annu Rev Microbiol Source Type: research

Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens.
Krause J Abstract The last century has witnessed progress in the study of ancient infectious disease from purely medical descriptions of past ailments to dynamic interpretations of past population health that draw upon multiple perspectives. The recent adoption of high-throughput DNA sequencing has led to an expanded understanding of pathogen presence, evolution, and ecology across the globe. This genomic revolution has led to the identification of disease-causing microbes in both expected and unexpected contexts, while also providing for the genomic characterization of ancient pathogens previously believed to be...
Source: Annual Review of Microbiology - July 5, 2019 Category: Microbiology Authors: Bos KI, Kühnert D, Herbig A, Esquivel-Gomez LR, Valtueña AA, Barquera R, Giffin K, Kumar Lankapalli A, Nelson EA, Sabin S, Spyrou MA, Krause J Tags: Annu Rev Microbiol Source Type: research

The Metabolic Basis of Pathogenesis and Host Adaptation in Rice Blast.
Abstract The blast disease, caused by the ascomycete Magnaporthe oryzae, poses a great threat to rice production worldwide. Increasing use of fungicides and/or blast-resistant varieties of rice (Oryza sativa) has proved to be ineffective in long-term control of blast disease under field conditions. To develop effective and durable resistance to blast, it is important to understand the cellular mechanisms underlying pathogenic development in M. oryzae. In this review, we summarize the latest research in phototropism, autophagy, nutrient and redox signaling, and intrinsic phytohormone mimics in M. oryzae for cellula...
Source: Annual Review of Microbiology - July 5, 2019 Category: Microbiology Authors: Deng YZ, Naqvi NI Tags: Annu Rev Microbiol Source Type: research