Showing papers in "Nature Reviews Microbiology in 2009"
TL;DR: Pyroptosis, or caspase 1-dependent cell death, is inherently inflammatory, is triggered by various pathological stimuli, such as stroke, heart attack or cancer, and is crucial for controlling microbial infections.
Abstract: Eukaryotic cells can initiate several distinct programmes of self-destruction, and the nature of the cell death process (non-inflammatory or proinflammatory) instructs responses of neighbouring cells, which in turn dictates important systemic physiological outcomes Pyroptosis, or caspase 1-dependent cell death, is inherently inflammatory, is triggered by various pathological stimuli, such as stroke, heart attack or cancer, and is crucial for controlling microbial infections Pathogens have evolved mechanisms to inhibit pyroptosis, enhancing their ability to persist and cause disease Ultimately, there is a competition between host and pathogen to regulate pyroptosis, and the outcome dictates life or death of the host
2,326 citations
TL;DR: The molecular epidemiology of the epidemic waves of peniillin- and methicillin-resistant strains of S. aureus that have occurred since 1940 are reviewed, with a focus on the clinical and molecular epidemiological of CA-MRSA.
Abstract: Staphylococcus aureus is notorious for its ability to become resistant to antibiotics. Infections that are caused by antibiotic-resistant strains often occur in epidemic waves that are initiated by one or a few successful clones. Methicillin-resistant S. aureus (MRSA) features prominently in these epidemics. Historically associated with hospitals and other health care settings, MRSA has now emerged as a widespread cause of community infections. Community or community-associated MRSA (CA-MRSA) can spread rapidly among healthy individuals. Outbreaks of CA-MRSA infections have been reported worldwide, and CA-MRSA strains are now epidemic in the United States. Here, we review the molecular epidemiology of the epidemic waves of penicillin- and methicillin-resistant strains of S. aureus that have occurred since 1940, with a focus on the clinical and molecular epidemiology of CA-MRSA.
2,222 citations
TL;DR: This Progress article explores the underlying reasons for exocellular electron transfer, including cellular respiration and possible cell–cell communication, to understand bacterial versatility in mechanisms used for current generation.
Abstract: The use of microbial fuel cells to generate electrical current is increasingly being seen as a viable source of renewable energy production In this Progress article, Bruce Logan highlights recent advances in our understanding of the mechanisms used by exoelectrogenic bacteria to generate electrical current and the important factors to consider in microbial fuel cell design There has been an increase in recent years in the number of reports of microorganisms that can generate electrical current in microbial fuel cells Although many new strains have been identified, few strains individually produce power densities as high as strains from mixed communities Enriched anodic biofilms have generated power densities as high as 69 W per m2 (projected anode area), and therefore are approaching theoretical limits To understand bacterial versatility in mechanisms used for current generation, this Progress article explores the underlying reasons for exocellular electron transfer, including cellular respiration and possible cell–cell communication
2,045 citations
TL;DR: This Review focuses on recent advances in the understanding of the mechanisms of coronavirus replication, interactions with the host immune response and disease pathogenesis and the recent identification of numerous novel coronaviruses.
Abstract: Although coronaviruses were first identified nearly 60 years ago, they only received notoriety in 2003 when one of their members was identified as the aetiological agent of severe acute respiratory syndrome. Previously these viruses were known to be important agents of respiratory and enteric infections of domestic and companion animals and to cause approximately 15% of all cases of the common cold. This Review focuses on recent advances in our understanding of the mechanisms of coronavirus replication, interactions with the host immune response and disease pathogenesis. It also highlights the recent identification of numerous novel coronaviruses and the propensity of this virus family to cross species barriers.
1,431 citations
TL;DR: The molecular basis of the commensal and infectious lifestyles of S. epidermidis is discussed, beginning to comprehend the roles in balancing the epithelial microflora and serving as a reservoir of resistance genes.
Abstract: Although nosocomial infections by Staphylococcus epidermidis have gained much attention, this skin-colonizing bacterium has apparently evolved not to cause disease, but to maintain the commonly benign relationship with its host. Accordingly, S. epidermidis does not produce aggressive virulence determinants. Rather, factors that normally sustain the commensal lifestyle of S. epidermidis seem to give rise to additional benefits during infection. Furthermore, we are beginning to comprehend the roles of S. epidermidis in balancing the epithelial microflora and serving as a reservoir of resistance genes. In this Review, I discuss the molecular basis of the commensal and infectious lifestyles of S. epidermidis.
1,429 citations
TL;DR: Recent advances in the development of vaccines and therapeutics based on the S protein are highlighted, which plays key parts in the induction of neutralizing-antibody and T-cell responses, as well as protective immunity, during infection with SARS-CoV.
Abstract: Severe acute respiratory syndrome (SARS) is a newly emerging infectious disease caused by a novel coronavirus, SARS-coronavirus (SARS-CoV). The SARS-CoV spike (S) protein is composed of two subunits; the S1 subunit contains a receptor-binding domain that engages with the host cell receptor angiotensin-converting enzyme 2 and the S2 subunit mediates fusion between the viral and host cell membranes. The S protein plays key parts in the induction of neutralizing-antibody and T-cell responses, as well as protective immunity, during infection with SARS-CoV. In this Review, we highlight recent advances in the development of vaccines and therapeutics based on the S protein.
1,404 citations
TL;DR: Since 2001, the prevalence and severity of C. difficile infection has increased significantly, which has led to increased research interest and the discovery of new virulence factors, and has expanded and focused the development of new treatment and prevention regimens.
Abstract: Clostridium difficile is now considered to be one of the most important causes of health care-associated infections. C. difficile infections are also emerging in the community and in animals used for food, and are no longer viewed simply as unpleasant complications that follow antibiotic therapy. Since 2001, the prevalence and severity of C. difficile infection has increased significantly, which has led to increased research interest and the discovery of new virulence factors, and has expanded and focused the development of new treatment and prevention regimens. This Review summarizes the recent epidemiological changes in C. difficile infection, our current knowledge of C. difficile virulence factors and the clinical outcomes of C. difficile infection.
1,339 citations
TL;DR: This Review focuses on emerging principles of c-di-GMP signalling using selected systems in different bacteria as examples.
Abstract: On the stage of bacterial signal transduction and regulation, bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) has long played the part of Sleeping Beauty. c-di-GMP was first described in 1987, but only recently was it recognized that the enzymes that 'make and break' it are not only ubiquitous in the bacterial world, but are found in many species in huge numbers. As a key player in the decision between the motile planktonic and sedentary biofilm-associated bacterial 'lifestyles', c-di-GMP binds to an unprecedented range of effector components and controls diverse targets, including transcription, the activities of enzymes and larger cellular structures. This Review focuses on emerging principles of c-di-GMP signalling using selected systems in different bacteria as examples.
1,337 citations
TL;DR: The biology of latent tuberculosis is discussed as part of a broad range of responses that occur following infection with Mycobacterium tuberculosis, which result in the formation of physiologically distinct granulomatous lesions that provide microenvironments with differential ability to support or suppress the persistence of viable bacteria.
Abstract: Immunological tests provide evidence of latent tuberculosis in one third of the global population, which corresponds to more than two billion individuals. Latent tuberculosis is defined by the absence of clinical symptoms but carries a risk of subsequent progression to clinical disease, particularly in the context of co-infection with HIV. In this Review we discuss the biology of latent tuberculosis as part of a broad range of responses that occur following infection with Mycobacterium tuberculosis, which result in the formation of physiologically distinct granulomatous lesions that provide microenvironments with differential ability to support or suppress the persistence of viable bacteria. We then show how this model can be used to develop a rational programme to discover effective drugs for the eradication of M. tuberculosis infection.
1,254 citations
TL;DR: The transfer of hydrogen and formate between bacteria and archaea that helps to sustain growth in syntrophic methanogenic communities is reviewed and the process of reverse electron transfer is described, which is a key requirement in obligately syntrophic interactions.
Abstract: Interspecies electron transfer is a key process in methanogenic and sulphate-reducing environments. Bacteria and archaea that live in syntrophic communities take advantage of the metabolic abilities of their syntrophic partner to overcome energy barriers and break down compounds that they cannot digest by themselves. Here, we review the transfer of hydrogen and formate between bacteria and archaea that helps to sustain growth in syntrophic methanogenic communities. We also describe the process of reverse electron transfer, which is a key requirement in obligately syntrophic interactions. Anaerobic methane oxidation coupled to sulphate reduction is also carried out by syntrophic communities of bacteria and archaea but, as we discuss, the exact mechanism of this syntrophic interaction is not yet understood.
1,052 citations
TL;DR: The process that is currently used to achieve comprehensive network reconstructions is described and how these reconstructions are curated and validated is discussed to aid the growing number of researchers who are carrying out reconstructions for particular target organisms.
Abstract: Systems analysis of metabolic and growth functions in microbial organisms is rapidly developing and maturing. Such studies are enabled by reconstruction, at the genomic scale, of the biochemical reaction networks that underlie cellular processes. The network reconstruction process is organism specific and is based on an annotated genome sequence, high-throughput network-wide data sets and bibliomic data on the detailed properties of individual network components. Here we describe the process that is currently used to achieve comprehensive network reconstructions and discuss how these reconstructions are curated and validated. This Review should aid the growing number of researchers who are carrying out reconstructions for particular target organisms.
TL;DR: An overview of the antimicrobial defences of the host cell is presented, with emphasis on macrophages, for which phagocytosis has been studied most extensively and some of the evasive strategies used by bacteria are described.
Abstract: Professional phagocytes have a vast and sophisticated arsenal of microbicidal features. They are capable of ingesting and destroying invading organisms, and can present microbial antigens on their surface, eliciting acquired immune responses. To survive this hostile response, certain bacterial species have developed evasive strategies that often involve the secretion of effectors to co-opt the cellular machinery of the host. In this Review, we present an overview of the antimicrobial defences of the host cell, with emphasis on macrophages, for which phagocytosis has been studied most extensively. In addition, using Mycobacterium tuberculosis, Listeria monocytogenes, Legionella pneumophila and Coxiella burnetii as examples, we describe some of the evasive strategies used by bacteria.
TL;DR: This work shows how functional genomics approaches are providing new insight into the genetic control of plant infection by M. oryzae, and looks ahead to the key questions that need to be addressed to provide a better understanding of the molecular processes that lead to plant disease and the prospects for sustainable control of rice blast.
Abstract: The filamentous fungus Magnaporthe oryzae causes rice blast, the most serious disease of cultivated rice. Cellular differentiation of M. oryzae forms an infection structure called the appressorium, which generates enormous cellular turgor that is sufficient to rupture the plant cuticle. Here, we show how functional genomics approaches are providing new insight into the genetic control of plant infection by M. oryzae. We also look ahead to the key questions that need to be addressed to provide a better understanding of the molecular processes that lead to plant disease and the prospects for sustainable control of rice blast.
TL;DR: This Review summarizes the current knowledge of P. aeruginosa type III secretion, including the secretion and translocation machinery, the regulation of this machinery, and the associated chaperones and effector proteins.
Abstract: Pseudomonas aeruginosauses a type III secretion system to proliferate within the host. Here, Alan Hauser describes the regulation of the formation of this secretion system, the components that allow the transfer of effectors into the host and the activity of these effectors. The Gram-negative bacterium Pseudomonas aeruginosa uses a complex type III secretion apparatus to inject effector proteins into host cells. The configuration of this secretion machinery, the activities of the proteins that are injected by it and the consequences of this process for infection are now being elucidated. This Review summarizes our current knowledge of P. aeruginosa type III secretion, including the secretion and translocation machinery, the regulation of this machinery, and the associated chaperones and effector proteins. The features of this interesting secretion system have important implications for the pathogenesis of P. aeruginosa infections and for other type III secretion systems.
TL;DR: The interaction of a diverse repertoire of accessory proteins with FtsZ contributes to the formation of a functional division machine that is responsive to cell cycle status and environmental stress.
Abstract: Bacterial cell division is orchestrated by a tubulin homologue, FtsZ, which polymerizes to form a ring-like structure that is both a scaffold for the assembly of the bacterial cytokinetic machinery and, at least in part, a source of the energy for constriction. FtsZ assembly is tightly regulated, and a diverse repertoire of accessory proteins contributes to the formation of a functional division machine that is responsive to cell cycle status and environmental stress. In this Review, we describe the interaction of these proteins with FtsZ and discuss recent advances in our understanding of Z ring assembly.
TL;DR: It is proposed that the disappearance of these ancestral indigenous organisms, which are intimately involved in human physiology, is not entirely beneficial and has consequences that might include post-modern conditions such as obesity and asthma.
Abstract: Humans and our ancestors have evolved since the most ancient times with a commensal microbiota. The conservation of indicator species in a niche-specific manner across all of the studied human population groups suggests that the microbiota confer conserved benefits on humans. Nevertheless, certain of these organisms have pathogenic properties and, through medical practices and lifestyle changes, their prevalence in human populations is changing, often to an extreme degree. In this Essay, we propose that the disappearance of these ancestral indigenous organisms, which are intimately involved in human physiology, is not entirely beneficial and has consequences that might include post-modern conditions such as obesity and asthma.
TL;DR: Metal sensors, transporters and stores perform a broader role in microbial physiology: they allow cells to overcome inadequate protein metal affinities to populate large numbers of metalloproteins with the right metals.
Abstract: Protein metal-coordination sites are richly varied and exquisitely attuned to their inorganic partners, yet many metalloproteins still select the wrong metals when presented with mixtures of elements. Cells have evolved elaborate mechanisms to scavenge for sufficient metal atoms to meet their needs and to adjust their needs to match supply. Metal sensors, transporters and stores have often been discovered as metal-resistance determinants, but it is emerging that they perform a broader role in microbial physiology: they allow cells to overcome inadequate protein metal affinities to populate large numbers of metalloproteins with the right metals.
TL;DR: The life cycle of the bacterium, the recent advances in understanding and the implications for the future prevention of leptospirosis are discussed.
Abstract: Leptospirosis is a zoonotic disease that has emerged as an important cause of morbidity and mortality among impoverished populations. One hundred years after the discovery of the causative spirochaetal agent, little is understood about Leptospira spp. pathogenesis, which in turn has hampered the development of new intervention strategies to address this neglected disease. However, the recent availability of complete genome sequences for Leptospira spp. and the discovery of genetic tools for their transformation have led to important insights into the biology of these pathogens and their pathogenesis. We discuss the life cycle of the bacterium, the recent advances in our understanding and the implications for the future prevention of leptospirosis.
TL;DR: This Review focuses on the strategies that L. pneumophila uses to establish intracellular growth and evaluates why this microorganism has accumulated an unprecedented number of translocated substrates that are targeted at host cells.
Abstract: The pathogenesis of Legionella pneumophila is derived from its growth within lung macrophages after aerosols are inhaled from contaminated water sources. Interest in this bacterium stems from its ability to manipulate host cell vesicular-trafficking pathways and establish a membrane-bound replication vacuole, making it a model for intravacuolar pathogens. Establishment of the replication compartment requires a specialized translocation system that transports a large cadre of protein substrates across the vacuolar membrane. These substrates regulate vesicle traffic and survival pathways in the host cell. This Review focuses on the strategies that L. pneumophila uses to establish intracellular growth and evaluates why this microorganism has accumulated an unprecedented number of translocated substrates that are targeted at host cells.
TL;DR: The versatility of the bacteria in the genus Stenotrophomonas is discussed and the insight that comparative genomic analysis of clinical and endophytic isolates of S. maltophilia has brought to the understanding of the adaptation of this genus to various niches is discussed.
Abstract: The genus Stenotrophomonas comprises at least eight species. These bacteria are found throughout the environment, particularly in close association with plants. Strains of the most predominant species, Stenotrophomonas maltophilia, have an extraordinary range of activities that include beneficial effects for plant growth and health, the breakdown of natural and man-made pollutants that are central to bioremediation and phytoremediation strategies and the production of biomolecules of economic value, as well as detrimental effects, such as multidrug resistance, in human pathogenic strains. Here, we discuss the versatility of the bacteria in the genus Stenotrophomonas and the insight that comparative genomic analysis of clinical and endophytic isolates of S. maltophilia has brought to our understanding of the adaptation of this genus to various niches.
TL;DR: This work proposes the constant-diversity dynamics model, in which the diversity of prokaryotic populations is preserved by phage predation, and provides supporting evidence for this model from metagenomics, mathematical analysis and computer simulations.
Abstract: Not all isolates of a species contain the same set of genes. In this Opinion article, Rodriguez-Valera and colleagues propose the constant-diversity model to account for these differences. In this model, predation by phages promotes bacterial diversity and allows more efficient use of the nutrients in the environment. The remarkable differences that have been detected by metagenomics in the genomes of strains of the same bacterial species are difficult to reconcile with the widely accepted paradigm that periodic selection within bacterial populations will regularly purge genomic diversity by clonal replacement. We have found that many of the genes that differ between strains affect regions that are potential phage recognition targets. We therefore propose the constant-diversity dynamics model, in which the diversity of prokaryotic populations is preserved by phage predation. We provide supporting evidence for this model from metagenomics, mathematical analysis and computer simulations. Periodic selection and phage predation dynamics are not mutually exclusive; we compare their predictions to shed light on the ecological circumstances under which each type of dynamics could predominate.
TL;DR: Strong membrane-binding and micromolar therapeutic concentrations of AMPs indicate that membrane-bound concentrations may be reached that are higher than intuitively expected, triggering disruptive effects on bacteria.
Abstract: An increasing amount of information on the action of antimicrobial peptides (AMPs) at the molecular level has not yet been translated into a comprehensive understanding of effects in bacteria. Although some biophysical attributes of AMPs have been correlated with macroscopic features, the physiological relevance of other properties has not yet been addressed. Pertinent and surprising conclusions have therefore been left unstated. Strong membrane-binding and micromolar therapeutic concentrations of AMPs indicate that membrane-bound concentrations may be reached that are higher than intuitively expected, triggering disruptive effects on bacteria.
TL;DR: During the life cycle of the filamentous bacteria Streptomyces, morphological differentiation is closely integrated with fundamental growth and cell-cycle processes, as well as with truly complex multicellular behaviour that involves hormone-like extracellular signalling and coordination with an extraordinarily diverse secondary metabolism.
Abstract: During the life cycle of the filamentous bacteria Streptomyces, morphological differentiation is closely integrated with fundamental growth and cell-cycle processes, as well as with truly complex multicellular behaviour that involves hormone-like extracellular signalling and coordination with an extraordinarily diverse secondary metabolism. Not only are the bacterial cytoskeleton and the machineries for cell-wall assembly, cell division and chromosome segregation reorganized during sporulation, but the developmental programme of these fascinating organisms also has many unusual elements, including the formation of a sporulating aerial mycelium and the production of a surfactant peptide and a hydrophobic sheath that allow cells to escape from the surface tension of the growth medium.
TL;DR: Advances that will help to unravel how interactions between the host, the bacterial pathogen and the lytic bacteriophage might propel and quench cholera outbreaks in endemic settings and in emergent epidemic regions such as Zimbabwe are highlighted.
Abstract: Zimbabwe offers the most recent example of the tragedy that befalls a country and its people when cholera strikes The 2008–2009 outbreak rapidly spread across every province and brought rates of mortality similar to those witnessed as a consequence of cholera infections a hundred years ago In this Review we highlight the advances that will help to unravel how interactions between the host, the bacterial pathogen and the lytic bacteriophage might propel and quench cholera outbreaks in endemic settings and in emergent epidemic regions such as Zimbabwe
TL;DR: The regulation of PrfA and its role in the L. monocytogenes transition from the saprophytic stage to the virulent intracellular stage is described.
Abstract: Bacteria need to adjust as they move between different environments. In this Progress article, Freitag, Port and Miner describe howListeria monocytogenesregulates the transition from saprophyte to human pathogen. Listeria monocytogenes is a bacterium that lives in the soil as a saprophyte but is capable of making the transition into a pathogen following its ingestion by susceptible humans or animals. Recent studies suggest that L. monocytogenes mediates its saprophyte-to-cytosolic-parasite transition through the careful modulation of the activity of a virulence regulatory protein known as PrfA, using a range of environmental cues that include available carbon sources. In this Progress article we describe the regulation of PrfA and its role in the L. monocytogenes transition from the saprophytic stage to the virulent intracellular stage.
TL;DR: The role of galectins in microbial infection is discussed, with particular emphasis on adaptations of pathogens to evasion or subversion of host galectin-mediated immune responses.
Abstract: Galectins, which were first characterized in the mid-1970s, were assigned a role in the recognition of endogenous ('self') carbohydrate ligands in embryogenesis, development and immune regulation. Recently, however, galectins have been shown to bind glycans on the surface of potentially pathogenic microorganisms, and function as recognition and effector factors in innate immunity. Some parasites subvert the recognition roles of the vector or host galectins to ensure successful attachment or invasion. This Review discusses the role of galectins in microbial infection, with particular emphasis on adaptations of pathogens to evasion or subversion of host galectin-mediated immune responses.
TL;DR: The current knowledge about the mode of action of ACTs, their pharmacological properties and the proposed mechanisms of drug resistance are discussed.
Abstract: Plasmodium falciparum resistance to chloroquine and sulphadoxine-pyrimethamine has led to the recent adoption of artemisinin-based combination therapies (ACTs) as the first line of treatment against malaria. ACTs comprise semisynthetic artemisinin derivatives paired with distinct chemical classes of longer acting drugs. These artemisinins are exceptionally potent against the pathogenic asexual blood stages of Plasmodium parasites and also act on the transmissible sexual stages. These combinations increase the rates of clinical and parasitological cures and decrease the selection pressure for the emergence of antimalarial resistance. This Review article discusses our current knowledge about the mode of action of ACTs, their pharmacological properties and the proposed mechanisms of drug resistance.
TL;DR: Recent data on the structure and functional properties of the protein families that are involved in c-di-GMP signalling are reviewed and the mechanistic implications are discussed.
Abstract: Bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) is a ubiquitous second messenger that regulates cell surface-associated traits in bacteria. Components of this regulatory network include GGDEF and EAL domain-containing proteins that determine the cellular concentrations of c-di-GMP by mediating its synthesis and degradation, respectively. Crystal structure analyses in combination with functional studies have revealed the catalytic mechanisms and regulatory principles involved. Downstream, c-di-GMP is recognized by PilZ domain-containing receptors that can undergo large-scale domain rearrangements on ligand binding. Here, we review recent data on the structure and functional properties of the protein families that are involved in c-di-GMP signalling and discuss the mechanistic implications.
TL;DR: Developments in molecular transfection technology, including the ability to generate deletion mutants and to introduce fluorescent reporter proteins that track the locations and dynamics of parasite proteins, have increased understanding of the processes and machinery for export of proteins in P. falciparum-infected erythrocytes and has provided insights into the functions of the parasite protein exportome.
Abstract: Exported proteins of the malaria parasite Plasmodium falciparum interact with proteins of the erythrocyte membrane and induce substantial changes in the morphology, physiology and function of the host cell. These changes underlie the pathology that is responsible for the deaths of 1-2 million children every year due to malaria infections. The advent of molecular transfection technology, including the ability to generate deletion mutants and to introduce fluorescent reporter proteins that track the locations and dynamics of parasite proteins, has increased our understanding of the processes and machinery for export of proteins in P. falciparum-infected erythrocytes and has provided us with insights into the functions of the parasite protein exportome. We review these developments, focusing on parasite proteins that interact with the erythrocyte membrane skeleton or that promote delivery of the major virulence protein, PfEMP1, to the erythrocyte membrane.
TL;DR: The ideal microorganism for biofuel production will possess high substrate utilization and processing capacities, fast and deregulated pathways for sugar transport, good tolerance to inhibitors and product, and high metabolic fluxes and will produce a single fermentation product.
Abstract: Production of biofuels is becoming increasingly important. In this Review, Alper and Stephanopoulos describe the advantages and disadvantages of the use of native strains and engineered model microorganisms for the production of biofuels. The ideal microorganism for biofuel production will possess high substrate utilization and processing capacities, fast and deregulated pathways for sugar transport, good tolerance to inhibitors and product, and high metabolic fluxes and will produce a single fermentation product. It is unclear whether such an organism will be engineered using a native, isolated strain or a recombinant, model organism as the starting point. The choice between engineering natural function and importing biosynthetic capacity is affected by current progress in metabolic engineering and synthetic biology. This Review highlights some of the factors influencing the above decision, in light of current advances.