The spontaneous generation of distinct phenotypes within a clonal population of cells allows for both bet-hedging at the population level and the division of labor among subpopulations. This is emerging as an important theme in bacterial pathogenesis, because bacterial pathogens exhibit phenotypic heterogeneity with respect to characteristics that impact virulence. The phenomenon of persister cells and models of Salmonella enterica serovar Typhimurium pathogenesis illustrate the importance of non-genetic diversity in the disease process. Such heterogeneity can arise from specific genetic architectures amplifying stochastic fluctuations in factors affecting gene expression, which drives variation in eukaryotic cells as well. Thus reproducible variation in both host and pathogen processes affects the outcome of infection.
Regulation; Salmonella; infection; heterogeneity; bistability; bet-hedging
Bacteria must segregate their DNA and position a septum to grow and divide. In many bacteria MinD is involved in spatial regulation of the cytokinetic Z ring and ParAs are involved in chromosome and plasmid segregation. The use of the MinD/ParA family to provide positional information for spatial organization continues to expand with the recognition that orphan ParAs are required for segregating cytoplasmic protein clusters and the polar localization of chemotaxis proteins, conjugative transfer machinery, type IV pili and cellulose synthesis. Also, some bacteria lacking MinD use orphan ParAs to regulate cell division. Positioning of MinD/ParA proteins is either due to self-organization on a surface or reliance on a landmark protein which functions as a molecular beacon.
The development of efficient microbicides, the topically applied compounds that protect uninfected individuals from acquiring HIV-1, is a promising strategy to contain HIV-1 epidemics. Such microbicides should of course possess anti-HIV-1 activity, but they should also act against other genital pathogens, which facilitate HIV-1 transmission. The new trend in microbicide strategy is to use drugs currently used in HIV-1 therapy. The success of this strategy is mixed so far and is impaired by our limited knowledge of the basic mechanisms of HIV-1 transmission as well as by the inadequacy of the systems in which microbicides are tested in pre-clinical studies.
Microbicide; HIV-1; Tenofovir; Pre-exposure prophylaxis
The formation of biofilms is initiated by bacteria transitioning from the planktonic to the surface associated mode of growth. Several regulatory systems have been described to govern the initiation and subsequent formation of biofilms. Recent evidence suggests that regulatory networks governing the decision of bacteria whether to attach and form biofilms or remain as planktonic cells, are further subject to regulation by small non-coding RNAs (sRNAs). This is accomplished by sRNAs finetuning regulatory networks enabling concentration-specific responses, by sequestering, antagonizing or activating regulatory proteins in response to environmental cues, or by directly affecting the synthesis of proteins promoting/disfavoring the formation of biofilms. This review is aimed at giving an overview of the contribution of sRNAs in regulating the switch from the planktonic to the sessile bacterial lifestyle by highlighting how sRNAs converge with known regulatory systems required for biofilm formation.
Small RNAs; Biofilm; Quorum Sensing
Nearly twelve years after promising results suggested that anti-biofilm agents might be developed into novel therapeutics, there are no such products on the market. In our opinion, the reasons for this have been predominantly economic. Recent developments, however, suggest that there may still be emerging opportunities for the developments of such products.
Maturation in herpesviruses initiates in the nucleus of the infected cell with encapsidation of viral DNA to form nucleocapsids and concludes with envelopment in the cytoplasm to form infectious virions that egress the cell. The entire process of virus maturation is orchestrated by protein-protein interactions and enzymatic activities of viral and host origin. Viral tegument proteins play important roles in maintaining the structural stability of capsids and directing the acquisition of virus envelope. Envelopment occurs at modified host membranes and exploits host vesicular trafficking. In this review, we summarize the current knowledge and concepts in human cytomegalovirus (HCMV) maturation and their parallels in other herpesviruses with an emphasis on viral and host factors regulating this process.
Betaherpesviruses; replication; nuclear egress; nucleocapsids; envelope
The Human Microbiome Project (HMP) is following in the footsteps of the Human Genome Project (HGP), which will include exciting discoveries, but also potential disappointment and resentment over the lack of medical applications. There is a wiser path for the HMP. This path includes a greater attention to rare variation, an early commitment to an ethical inclusion of indigenous communities, and a recruitment strategy in which medical benefits are de-emphasized.
Clostridium difficile infection (CDI) has become one of the most prevalent and costly nosocomial infections. In spite of the importance of CDI, our knowledge of the pathogenesis of this infection is still rudimentary. Although previous use of antibiotics is generally considered to be the sine qua non of CDI, the mechanisms by which antibiotics render the host susceptible to C. difficile are not well defined. In this review we will explore what is known about how the indigenous microbiota acts in concert with the host to prevent colonization and virulence of C. difficile and how antibiotic administration disturbs host–microbiota homeostasis, leading to CDI.
Colonization resistance; C. difficile; microbiome; microbial ecology; antibiotics
Clinical trials testing microbicides and related biomedical interventions to block HIV transmissions have produced contradictory results and to date it is unclear why. Further elucidation of the molecular basis of mucosal HIV transmission and extensive pharmacokinetic and pharmacodynamic analyses are essential to implementing effective prevention strategies. Animal models are of critical importance to this effort and bone marrow-liver-thymus (or BLT) humanized mice have recently emerged as a powerful small animal research platform for in vivo efficacy evaluation of mucosal and parenteral HIV-1 prevention interventions. The availability of this validated system for the pre-clinical evaluation of HIV-1 prevention approaches will accelerate the implementation of the best candidate interventions into clinical trials.
humanized mice; BLT; HIV-1 prevention; efficacy evaluation; microbicides; PrEP
Bacterial pili have long been recognized as mediators of initial host-pathogen interactions important for the progression of Gram-negative bacterial diseases. An appreciation for the role of pili on Gram-positive bacteria in virulence, as well as the unique properties of their biogenesis is a rapidly emerging area of research. In this review, we focus on recent advances in one of the longest-studied Gram-negative pilus systems, the chaperone/usher assembled pili, along with the newcomer to the field, the sortase-assembled pili of Gram-positive bacteria. In both systems, a wealth of new structural and molecular details has emerged recently. In light of this, we explore similarities between chaperone/usher and sortase-assembled pilus biogenesis and highlight paradigms unique to each, with an eye toward using knowledge of each system to raise new questions and inform future studies of the other.
The blood-brain barrier (BBB) provides significant protection against microbial invasion of the brain. However, the BBB is not impenetrable, and mechanisms by which viruses breach it are becoming clearer. In vivo and in vitro model systems are enabling identification of host and viral factors contributing to breakdown of the unique BBB tight junctions. Key mechanisms of tight junction damage from inside and outside cells are disruption of the actin cytoskeleton and matrix metalloproteinase activity, respectively. Viral proteins acting in BBB disruption are described for HIV-1, currently the most studied encephalitic virus; other viruses are also discussed.
blood-brain barrier; viral encephalitis; tight junctions; matrix metalloproteinases
Legionella pneumophila proliferates within various protists and metazoan cells, where a cadre of ~300 effectors is injected into the host cell by the defect in organelle trafficking/intracellular multiplication (Dot/Icm) type IVB translocation system. Interkingdom horizontal gene transfer of genes of protists and their subsequent convergent evolution to become translocated effectors has probably enabled L. pneumophila to adapt to the intracellular life within various protists and metazoan cells through exploitation of evolutionarily eukaryotic processes, such as endoplasmic reticulum-to-Golgi vesicle traffic, phosphoinositol metabolism, AMPylation, deAMPylation, prenylation, polyubiquitination, proteasomal degradation and cytosolic amino- and oligo-peptidases. This is highlighted by the ankyrin B (AnkB) F-box effector that exploits multiple conserved eukaryotic machineries to generate high levels of free amino acids as sources of carbon and energy essential for intracellular proliferation in protists and metazoan cells and for manifestation of pulmonary disease in mammals.
prenylation; farnesylation; polyubiquitination; phosphatidylinositol; F-box; AnkB; proteasome
Candida albicans, an opportunistic fungal pathogen and a component of the gastrointestinal tract normal flora, is a frequent colonizer of humans. Is C. albicans capable of sensing the immune status of its host, a process we term immunosensing, and, if so, how? C. albicans causes serious disease only in immunocompromised hosts and therefore, the ability to immunosense would be advantageous to the organism. We propose a speculative model that, during colonization, C. albicans produces phenotypic variants that vary in relative concentration depending on host status. One variant is optimized for persistence as a commensal while the other variant has higher capacity to initiate pathogenic interactions. When the ratio of the two variants changes, the pathogenic potential of the population changes. The critical element of this model is that the C. albicans colonizing population is not uniform but is composed of subpopulations of phenotypic variants that are advantageous under different host conditions.
Stress granule; Antiviral response; Translation silencing; G3BP; TIA-1; eIF4G; PKR
Recent advances in liquid chromatography and mass spectrometry have enabled the highly parallel, quantitative measurement of metabolites within a cell and the ability to trace their biochemical fates. In Mycobacterium tuberculosis (Mtb), these advances have highlighted major gaps in our understanding of central carbon metabolism (CCM) that have prompted fresh interpretations of the composition and structure of its metabolic pathways and the phenotypes of Mtb strains in which CCM genes have been deleted. High-throughput screens have demonstrated that small chemical compounds can selectively inhibit some enzymes of Mtb’s CCM while sparing homologs in the host. Mtb’s CCM has thus emerged as a frontier for both fundamental and translational research.
Activation of innate immune signaling pathways through cytosolic RIG-I like receptors (RLR) is a critical response that is antagonized by many viruses. A variety of RNA related pathogen associated molecular patterns have been identified and their role in RLR activation has been examined. Recent studies suggest that several virally encoded components that antagonize RLR signaling interact with and inhibit the interferon (IFN)-α/β activation pathway using both RNA-dependent and RNA-independent mechanisms. The structural basis for these RLR inhibitory mechanisms, as well as the multifunctional nature of viral RLR antagonists, is reviewed in the context of recent biochemical and structural studies.
innate immune inhibition; RIG-I; MDA-5; PRRs; PAMPs; viral inhibitors; IFNs
For many infectious diseases, novel treatment options are needed to address problems with cost, toxicity and resistance to current drugs. Systems biology tools can be used to gain valuable insight into pathogenic processes and aid in expediting drug discovery. In the past decade, constraint-based modeling of genome-scale metabolic networks has become widely used. Focusing on pathogen metabolic networks, we review in silico strategies to identify effective drug targets, and we highlight recent successes as well as limitations associated with such computational analyses. We further discuss how accounting for the host environment and even targeting the host may offer new therapeutic options. These systems-level approaches are beginning to provide novel avenues for drug targeting against infectious agents.
systems biology; metabolic network reconstruction; flux balance analysis; drug targeting; computational biology; microbial pathogens
GB virus C (GBV-C) is a lymphotropic human virus discovered in 1995 that is related to hepatitis C virus (HCV). GBV-C infection has not been convincingly associated with any disease; however, several studies found an association between persistent GBV-C infection and improved survival in HIV-positive individuals. GBV-C infection modestly alters T cell homeostasis in vivo through various mechanisms, including modulation of chemokine and cytokine release and receptor expression, and by diminution of T cell activation, proliferation and apoptosis, all of which may contribute to improved HIV clinical outcomes. In vitro studies confirm these clinical observations and demonstrate an anti-HIV replication effect of GBV-C. This review summarizes existing data on potential mechanisms by which GBV-C interferes with HIV, and the research needed to capitalize on this epidemiological observation.
GBV-C; HIV; T cell; activation; IL-2
How we classify the genes, products, and complexes that are present or absent in genomes, transcriptomes, proteomes, and other datasets helps us place biological objects into subsystems with common functions, see how molecular functions are used to implement biological processes, and compare the biology of different species and strains. Gene Ontology (GO) is one of the most successful systems for classifying biological function. Although GO is widely used for eukaryotic genomics, it has not yet been widely used for bacterial systems. The potential applications of GO are currently limited by the need to improve the annotation of bacterial genomes with GO and to improve how prokaryotic biology is represented in the ontology. In this review, we will discuss why GO should be adopted by microbiologists, and describe recent efforts to build and maintain high-quality GO annotation for Escherichia coli as a model system.
Recent studies have identified ancient virus genomes preserved as fossils within diverse animal genomes. These fossils have led to the revelation that a broad range of mammalian virus families are older and more ubiquitous than previously appreciated. Long-term interactions between viruses and their hosts often develop into genetic arms races, where both parties continually jockey for evolutionary dominance. It is difficult to imagine how mammalian hosts have kept pace in the evolutionary race against rapidly evolving viruses over large expanses of time, given their much slower evolutionary rates. However, recent data has begun to reveal the evolutionary strategy of slowly-evolving hosts. We review these data, and suggest a modified arms race model where the evolutionary possibilities of viruses are relatively constrained. Such a model could allow more accurate forecasting of virus evolution.
Budding yeasts adhere to biotic or abiotic surfaces and aggregate to form biofilms, using wall-anchored glycoprotein adhesins. The process is paradoxical: adhesins often show weak binding to specific ligands, yet mediate remarkably strong adherence. Single-molecule atomic force microscopy, genomics, biochemistry, and cell biology have recently explained the puzzle, with Candida albicans Als adhesins as the paradigm. The strength of adhesion results partly from force-activated amyloid-like clustering of hundreds of adhesin molecules to form arrays of ordered multimeric binding sites. The various protein domains of eukaryotic adhesins cooperate to facilitate this fascinating new mechanism of activation.
Amyloid is a distinct β-sheet-rich fold that many proteins can acquire. Frequently associated with neurodegenerative diseases in humans, including Alzheimer’s, Parkinson’s and Huntington’s, amyloids are traditionally considered the product of protein misfolding. However, the amyloid fold is now recognized as a ubiquitous part of normal cellular biology. ‘Functional’ amyloids have been identified in nearly all facets of cellular life, with microbial functional amyloids leading the way. Unlike disease-associated amyloids, functional amyloids are assembled by dedicated, directed pathways and ultimately perform a physiological function that benefits the organism. The evolved amyloid assembly and disassembly pathways of microbes have provided novel insights into how cells have harnessed the amyloid assembly process for productive means. Understanding functional amyloid biogenesis promises to provide a fresh perspective on the molecular events that underlie disease-associated amyloidogenesis. Here, we review functional microbial amyloids with an emphasis on curli fibers and their role in promoting biofilm formation and other community behaviors.
Pathogenic viral infections have exerted selection pressure on their hosts to evolve cellular antiviral inhibitors referred to as restriction factors. Examples of such molecules are APOBEC3G, APOBEC3F and TRIM5α. APOBEC3G and APOBEC3F are cytidine deaminases that are able to strongly inhibit retroviral replication by at least two mechanisms. They are counteracted by the lentiviral Vif protein. TRIM5α binds to sensitive, incoming retroviruses via its C-terminal PRY/SPRY domain and rapidly recruits them to the proteasome before significant viral DNA synthesis can occur. Both of these proteins robustly block retroviral replication in a species-specific way. It remains an open but important question as to whether innate restriction factors such as these can be harnessed to inhibit HIV-1 replication in humans.
Adaptation has a crucial role in the gradient-sensing mechanism that underlies bacterial chemotaxis. The Escherichia coli chemotaxis pathway uses a single adaptation system involving reversible receptor methylation. In Bacillus subtilis, the chemotaxis pathway seems to use three adaptation systems. One involves reversible receptor methylation, although quite differently than in E. coli. The other two involve CheC, CheD and CheV, which are chemotaxis proteins not found in E. coli. Remarkably, no one system is absolutely required for adaptation or is independently capable of generating adaptation. In this review, we discuss these three novel adaptation systems in B. subtilis and propose a model for their integration.
Brucella is an important zoonotic pathogen for which no human vaccine exists. In an infected host, Brucella resides in macrophages but must coordinate expression of multiple virulence factors for successful cell entry and trafficking to acquire this replicative niche. Brucella responds to environmental signals to regulate virulence strategies that circumvent or blunt the host immune response. The Brucella quorum sensing system is a nexus of control for several Brucella virulence factors including flagellar genes and the type IV secretion system. Other sensory transduction systems, such as BvrRS and the newly described LOV-HK, sense environmental factors to control virulence. Here, we examine the contributions of various regulatory systems to Brucella virulence.