| screen of fda-approved drug library identifies maprotiline, an antibiofilm and antivirulence compound with qsec sensor-kinase dependent activity in francisella novicida. | development of new therapeutics against select agents such as francisella is critical preparation in the event of bioterrorism. testing fda-approved drugs for this purpose may yield new activities unrelated to their intended purpose and may hasten the discovery of new therapeutics. a library of 420 fda-approved drugs was screened for antibiofilm activity against a model organism for human tularemia, francisella (f.) novicida, excluding drugs that significantly inhibited growth. the initial scree ... | 2015 | 26155740 |
| teaching old drugs new tricks: addressing resistance in francisella. | | 2015 | 26055396 |
| the atypical occurrence of two biotin protein ligases in francisella novicida is due to distinct roles in virulence and biotin metabolism. | the physiological function of biotin requires biotin protein ligase activity in order to attach the coenzyme to its cognate proteins, which are enzymes involved in central metabolism. the model intracellular pathogen francisella novicida is unusual in that it encodes two putative biotin protein ligases rather than the usual single enzyme. f. novicida bira has a ligase domain as well as an n-terminal dna-binding regulatory domain, similar to the prototypical bira protein in e. coli. however, the ... | 2015 | 26060274 |
| microinjection of francisella tularensis and listeria monocytogenes reveals the importance of bacterial and host factors for successful replication. | certain intracellular bacteria use the host cell cytosol as the replicative niche. although it has been hypothesized that the successful exploitation of this compartment requires a unique metabolic adaptation, supportive evidence is lacking. for francisella tularensis, many genes of the francisella pathogenicity island (fpi) are essential for intracellular growth, and therefore, fpi mutants are useful tools for understanding the prerequisites of intracytosolic replication. we compared the growth ... | 2015 | 26034213 |
| inflammasome priming is similar for francisella species that differentially induce inflammasome activation. | inflammasome activation is a two-step process where step one, priming, prepares the inflammasome for its subsequent activation, by step two. classically step one can be induced by lps priming followed by step two, high dose atp. furthermore, when il-18 processing is used as the inflammasome readout, priming occurs before new protein synthesis. in this context, how intracellular pathogens such as francisella activate the inflammasome is incompletely understood, particularly regarding the relative ... | 2015 | 25993107 |
| effect of enterohaemorrhagic escherichia coli o157:h7-specific enterohaemolysin on interleukin-1β production differs between human and mouse macrophages due to the different sensitivity of nlrp3 activation. | enterohaemorrhagic escherichia coli (ehec) o157:h7 infection in humans can cause acute haemorrhagic colitis and severe haemolytic uraemic syndrome. the role of enterohaemolysin (ehx) in the pathogenesis of o157:h7-mediated disease in humans remains undefined. recent studies have revealed the importance of the inflammatory response in o157:h7 pathogenesis in humans. we previously reported that ehx markedly induced interleukin-1β (il-1β) production in human macrophages. here, we investigated the d ... | 2015 | 25580516 |
| alarmin function of galectin-9 in murine respiratory tularemia. | sepsis is a complex immune disorder that is characterized by systemic hyperinflammation. alarmins, which are multifunctional endogenous factors, have been implicated in exacerbation of inflammation in many immune disorders including sepsis. here we show that galectin-9, a host endogenous β-galactoside binding lectin, functions as an alarmin capable of mediating inflammatory response during sepsis resulting from pulmonary infection with francisella novicida, a gram negative bacterial pathogen. ou ... | 2015 | 25898318 |
| drug repurposing as an alternative for the treatment of recalcitrant bacterial infections. | bacterial infection remains one of the leading causes of death worldwide, and the options for treating such infections are decreasing, due the rise of antibiotic-resistant bacteria. the pharmaceutical industry has produced few new types of antibiotics in more than a decade. researchers are taking several approaches toward developing new classes of antibiotics, including (1) focusing on new targets and processes, such as bacterial cell-cell communication that upregulates virulence; (2) designing ... | 2015 | 25914685 |
| guanylate-binding proteins promote activation of the aim2 inflammasome during infection with francisella novicida. | the aim2 inflammasome detects double-stranded dna in the cytosol and induces caspase-1-dependent pyroptosis as well as release of the inflammatory cytokines interleukin 1β (il-1β) and il-18. aim2 is critical for host defense against dna viruses and bacteria that replicate in the cytosol, such as francisella tularensis subspecies novicida (f. novicida). the activation of aim2 by f. novicida requires bacteriolysis, yet whether this process is accidental or is a host-driven immunological mechanism ... | 2015 | 25774716 |
| the transcription factor irf1 and guanylate-binding proteins target activation of the aim2 inflammasome by francisella infection. | inflammasomes are critical for mounting host defense against pathogens. the molecular mechanisms that control activation of the aim2 inflammasome in response to different cytosolic pathogens remain unclear. here we found that the transcription factor irf1 was required for activation of the aim2 inflammasome during infection with the francisella tularensis subspecies novicida (f. novicida), whereas engagement of the aim2 inflammasome by mouse cytomegalovirus (mcmv) or transfected double-stranded ... | 2015 | 25774715 |
| a more flexible lipoprotein sorting pathway. | lipoprotein biogenesis in gram-negative bacteria occurs by a conserved pathway, each step of which is considered essential. in contrast to this model, lovullo and colleagues demonstrate that the n-acyl transferase lnt is not required in francisella tularensis or neisseria gonorrhoeae. this suggests the existence of a more flexible lipoprotein pathway, likely due to a modified lol transporter complex, and raises the possibility that pathogens may regulate lipoprotein processing to modulate intera ... | 2015 | 25755190 |
| cgas and ifi204 cooperate to produce type i ifns in response to francisella infection. | type i ifn production is an important host immune response against viral and bacterial infections. however, little is known about the ligands and corresponding host receptors that trigger type i ifn production during bacterial infections. we used a model intracellular pathogen, francisella novicida, to begin characterizing the type i ifn response to bacterial pathogens. f. novicida replicates in the cytosol of host cells and elicits a robust type i ifn response that is largely tlr independent, b ... | 2015 | 25710914 |
| type i interferons in bacterial infections: a balancing act. | defense against bacterial infections requires activation of the immune response as well as timely reestablishment of tissue and immune homeostasis. instauration of homeostasis is critical for tissue regeneration, wound healing, and host recovery. recent studies revealed that severe infectious diseases frequently result from failures in homeostatic processes rather than from inefficient pathogen eradication. type i interferons (ifn) appear to play a key role in such processes. remarkably, the inv ... | 2016 | 28082986 |
| inflammasome-independent nlrp3 restriction of a protective early neutrophil response to pulmonary tularemia. | francisella tularensis (ft) causes a frequently fatal, acute necrotic pneumonia in humans and animals. following lethal ft infection in mice, infiltration of the lungs by predominantly immature myeloid cells and subsequent myeloid cell death drive pathogenesis and host mortality. however, following sub-lethal ft challenge, more mature myeloid cells are elicited and are protective. in addition, inflammasome-dependent il-1β and il-18 are important for protection. as nlrp3 appears dispensable for r ... | 2016 | 27926940 |
| modulating endotoxin activity by combinatorial bioengineering of meningococcal lipopolysaccharide. | neisseria meningitidis contains a very potent hexa-acylated lps that is too toxic for therapeutic applications. we used systematic molecular bioengineering of meningococcal lps through deletion of biosynthetic enzymes in combination with induction of lps modifying enzymes to yield a variety of novel lps mutants with changes in both lipid a acylation and phosphorylation. mass spectrometry was used for detailed compositional determination of the lps molecular species, and stimulation of immune cel ... | 2016 | 27841285 |
| mitogen-activated protein kinases (mapks) are modulated during francisella tularensis infection, but inhibition of extracellular-signal-regulated kinases (erks) is of limited therapeutic benefit. | francisella tularensis is a gram-negative intracellular bacterium that causes the disease tularemia. the disease can be fatal if left untreated and there is currently no licenced vaccine available; the identification of new therapeutic targets is therefore required. toll-like receptors represent an interesting target for therapeutic modulation due to their essential role in generating immune responses. in this study, we analysed the in vitro expression of the key mitogen-activated protein kinase ... | 2016 | 27714591 |
| diverse functions of small rnas in different plant-pathogen communications. | rna silencing is a conserved mechanism that utilizes small rnas (srnas) to direct the regulation of gene expression at the transcriptional or post-transcriptional level. plants utilizing rna silencing machinery to defend pathogen infection was first identified in plant-virus interaction and later was observed in distinct plant-pathogen interactions. rna silencing is not only responsible for suppressing rna accumulation and movement of virus and viroid, but also facilitates plant immune responses ... | 2016 | 27757103 |
| francisella tularensis iglg belongs to a novel family of paar-like t6ss proteins and harbors a unique n-terminal extension required for virulence. | the virulence of francisella tularensis, the etiological agent of tularemia, relies on an atypical type vi secretion system (t6ss) encoded by a genomic island termed the francisella pathogenicity island (fpi). while the importance of the fpi in f. tularensis virulence is clearly established, the precise role of most of the fpi-encoded proteins remains to be deciphered. in this study, using highly virulent f. tularensis strains and the closely related species f. novicida, iglg was characterized a ... | 2016 | 27602570 |
| comparative transcriptional analyses of francisella tularensis and francisella novicida. | francisella tularensis is composed of a number of subspecies with varied geographic distribution, host ranges, and virulence. in view of these marked differences, comparative functional genomics may elucidate some of the molecular mechanism(s) behind these differences. in this study a shared probe microarray was designed that could be used to compare the transcriptomes of francisella tularensis subsp. tularensis schu s4 (ftt), francisella tularensis subsp. holarctica or960246 (fth), francisella ... | 2016 | 27537327 |
| tularemia vaccine development: paralysis or progress? | francisella tularensis (ft) is a gram-negative intercellular pathogen and category a biothreat agent. however, despite 15 years of strong government investment and intense research focused on the development of a us food and drug administration-approved vaccine against ft, the primary goal remains elusive. this article reviews research efforts focused on developing an ft vaccine, as well as a number of important factors, some only recently recognized as such, which can significantly impact the d ... | 2016 | 27200274 |
| m-cells contribute to the entry of an oral vaccine but are not essential for the subsequent induction of protective immunity against francisella tularensis. | m-cells (microfold cells) are thought to be a primary conduit of intestinal antigen trafficking. using an established neutralizing anti-rankl (receptor activator of nf-κb ligand) antibody treatment to transiently deplete m-cells in vivo, we sought to determine whether intestinal m-cells were required for the effective induction of protective immunity following oral vaccination with δiglb (a defined live attenuated francisella novicida mutant). m-cell depleted, δiglb-vaccinated mice exhibited inc ... | 2016 | 27100824 |
| nanoaerosols reduce required effective dose of liposomal levofloxacin against pulmonary murine francisella tularensis subsp. novicida infection. | the institute of theoretical and experimental biophysics in moscow recently developed a new nanoaerosol generator. this study evaluated this novel technology, which has the potential to enhance therapeutic delivery, with the goal of using the generator to treat pulmonary francisella tularensis subsp. novicida (f. novicida) infections in balb/c mice. | 2016 | 27090889 |
| francisella tularensis - immune cell activator, suppressor, or stealthy evader: the evolving view from the petri dish. | one of the hallmarks of pulmonary tularemia, which results from inhalation of francisella tularensis - a significant bioterrorism concern, is the lack of an acute th1-biased inflammatory response in the early phase of disease (days 1-3) despite significant bacterial loads. in an effort to understand this apparent hypo-responsiveness, many laboratories have utilized in vitro cell-based models as tools to probe the nature and consequences of host cell interactions with f. tularensis. the first use ... | 2016 | 27695643 |
| two parallel pathways for ferric and ferrous iron acquisition support growth and virulence of the intracellular pathogen francisella tularensis schu s4. | iron acquisition mechanisms in francisella tularensis, the causative agent of tularemia, include the francisella siderophore locus (fsl) siderophore operon and a ferrous iron-transport system comprising outer-membrane protein fupa and inner-membrane transporter feob. to characterize these mechanisms and to identify any additional iron uptake systems in the virulent subspecies tularensis, single and double deletions were generated in the fsl and feo iron acquisition systems of the strain schu s4. ... | 2016 | 26918301 |
| dissection of francisella-host cell interactions in dictyostelium discoideum. | francisella bacteria cause severe disease in both vertebrates and invertebrates and include one of the most infectious human pathogens. mammalian cell lines have mainly been used to study the mechanisms by which francisella manipulates its host to replicate within a large variety of hosts and cell types, including macrophages. here, we describe the establishment of a genetically and biochemically tractable infection model: the amoeba dictyostelium discoideum combined with the fish pathogen franc ... | 2016 | 26712555 |
| biochemical and structural characterization of polyphosphate kinase 2 from the intracellular pathogen francisella tularensis. | the metabolism of polyphosphate is important for the virulence of a wide range of pathogenic bacteria and the enzymes of polyphosphate metabolism have been proposed as an anti-bacterial target. in the intracellular pathogen francisella tularensis, the product of the gene ftt1564 has been identified as a polyphosphate kinase from the polyphosphate kinase 2 (ppk2) family. the isogenic deletion mutant was defective for intracellular growth in macrophages and was attenuated in mice, indicating an im ... | 2016 | 26582818 |
| an inhibitor of gram-negative bacterial virulence protein secretion. | bacterial virulence mechanisms are attractive targets for antibiotic development because they are required for the pathogenesis of numerous global infectious disease agents. the bacterial secretion systems used to assemble the surface structures that promote adherence and deliver protein virulence effectors to host cells could comprise one such therapeutic target. in this study, we developed and performed a high-throughput screen of small molecule libraries and identified one compound, a 2-imino ... | 2008 | 18854237 |
| combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from ms-based proteomics data. | liquid chromatography-mass spectrometry-based (lc-ms) proteomics uses peak intensities of proteolytic peptides to infer the differential abundance of peptides/proteins. however, substantial run-to-run variability in intensities and observations (presence/absence) of peptides makes data analysis quite challenging. the missing observations in lc-ms proteomics data are difficult to address with traditional imputation-based approaches because the mechanisms by which data are missing are unknown a pr ... | 2010 | 20831241 |
| the role of antimicrobial peptides in preventing multidrug-resistant bacterial infections and biofilm formation. | over the last decade, decreasing effectiveness of conventional antimicrobial-drugs has caused serious problems due to the rapid emergence of multidrug-resistant pathogens. furthermore, biofilms, which are microbial communities that cause serious chronic infections and dental plaque, form environments that enhance antimicrobial resistance. as a result, there is a continuous search to overcome or control such problems, which has resulted in antimicrobial peptides being considered as an alternative ... | 2011 | 22016639 |
| liquid chromatography/tandem mass spectrometry of dolichols and polyprenols, lipid sugar carriers across evolution. | across evolution, dolichols and polyprenols serve as sugar carriers in biosynthetic processes that include protein glycosylation and lipopolysaccharide biogenesis. liquid chromatography coupled with electrospray ionization mass spectrometry offers a powerful tool for studying dolichols and polyprenols in their alcohol or glycan-modified forms in members of all three domains of life. in the following, recent examples of the how different versions of this analytical approach, namely reverse phase ... | 2011 | 21570481 |
| the origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon. | the tree of life is usually rooted between archaea and bacteria. we have previously presented three arguments that support placing the root of the tree of life in bacteria. the data have been dismissed because those who support the canonical rooting between the prokaryotic superkingdoms cannot imagine how the vast divide between the prokaryotic superkingdoms could be crossed. | 2011 | 21356104 |
| listeria monocytogenes infection causes metabolic shifts in drosophila melanogaster. | immunity and metabolism are intimately linked; manipulating metabolism, either through diet or genetics, has the power to alter survival during infection. however, despite metabolism's powerful ability to alter the course of infections, little is known about what being "sick" means metabolically. here we describe the metabolic changes occurring in a model system when listeria monocytogenes causes a lethal infection in drosophila melanogaster. l. monocytogenes infection alters energy metabolism; ... | 2012 | 23272066 |
| turning up francisella pathogenesis: the lps thermostat. | | 2012 | 23154289 |
| rapid killing of acinetobacter baumannii by polymyxins is mediated by a hydroxyl radical death pathway. | acinetobacter baumannii is an opportunistic pathogen that is a cause of clinically significant nosocomial infections. increasingly, clinical isolates of a. baumannii are extensively resistant to numerous antibiotics, and the use of polymyxin antibiotics against these infections is often the final treatment option. historically, the polymyxins have been thought to kill bacteria through membrane lysis. here, we present an alternative mechanism based on data demonstrating that polymyxins induce rap ... | 2012 | 22908157 |
| the alveolar epithelial cell chemokine response to pneumocystis requires adaptor molecule myd88 and interleukin-1 receptor but not toll-like receptor 2 or 4. | pneumocystis is an opportunistic fungal pathogen that causes pneumonia in a variety of clinical settings. an early step in pneumocystis infection involves the attachment of organisms to alveolar epithelial cells (aecs). aecs produce chemokines in response to pneumocystis stimulation, but the upstream host-pathogen interactions that activate aec signaling cascades are not well-defined. myd88 is an adaptor molecule required for activation of proinflammatory signaling cascades following toll-like r ... | 2012 | 22927048 |
| small molecules aimed at type iii secretion systems to inhibit bacterial virulence. | | 2012 | 23930198 |
| small molecules aimed at type iii secretion systems to inhibit bacterial virulence. | | 2012 | 23930198 |
| hidden evolutionary complexity of nucleo-cytoplasmic large dna viruses of eukaryotes. | the nucleo-cytoplasmic large dna viruses (ncldv) constitute an apparently monophyletic group that consists of at least 6 families of viruses infecting a broad variety of eukaryotic hosts. a comprehensive genome comparison and maximum-likelihood reconstruction of the ncldv evolution revealed a set of approximately 50 conserved, core genes that could be mapped to the genome of the common ancestor of this class of eukaryotic viruses. | 2012 | 22891861 |
| potential therapeutic drug target identification in community acquired-methicillin resistant staphylococcus aureus (ca-mrsa) using computational analysis. | the emergence of multidrug-resistant strain of community-acquired methicillin resistant staphylococcus aureus (ca-mrsa) strain has highlighted the urgent need for the alternative and effective therapeutic approach to combat the menace of this nosocomial pathogen. in the present work novel potential therapeutic drug targets have been identified through the metabolic pathways analysis. all the gene products involved in different metabolic pathways of ca-mrsa in kegg database were searched against ... | 2012 | 23055607 |
| infection of primary bovine macrophages with mycobacterium avium subspecies paratuberculosis suppresses host cell apoptosis. | mycobacterium avium subspecies paratuberculosis (map) is able to survive intracellularly in macrophages by preventing normal phagosome maturation processes utilized to destroy bacteria. infected macrophages often undergo apoptotic cell death to efficiently present bacterial antigens to the host adaptive immune system in a process known as efferocytosis. recent studies with mycobacterium tuberculosis (mtb) showed that macrophages infected with mtb are less likely to undergo apoptosis than control ... | 2012 | 22833736 |
| caspase-1 activity is required to bypass macrophage apoptosis upon salmonella infection. | here we report awp28, an activity-based probe that can be used to biochemically monitor caspase-1 activation in response to proinflammatory stimuli. using awp28, we show that apoptosis is triggered upon salmonella enterica var. typhimurium infection in primary mouse bone marrow macrophages lacking caspase-1. furthermore, we report that upon salmonella infection, inflammasome-mediated caspase-1 activity is required to bypass apoptosis in favor of proinflammatory pyroptotic cell death. | 2012 | 22797665 |
| caspase-11 promotes the fusion of phagosomes harboring pathogenic bacteria with lysosomes by modulating actin polymerization. | inflammasomes are multiprotein complexes that include members of the nlr (nucleotide-binding domain leucine-rich repeat containing) family and caspase-1. once bacterial molecules are sensed within the macrophage, the inflammasome is assembled, mediating the activation of caspase-1. caspase-11 mediates caspase-1 activation in response to lipopolysaccharide and bacterial toxins, and yet its role during bacterial infection is unknown. here, we demonstrated that caspase-11 was dispensable for caspas ... | 2012 | 22658523 |
| the role of inflammasome modulation in virulence. | pathogens frequently exist in an immunological balancing act with their host. pathogens must not only replicate within a host but also transmit effectively between hosts to perpetuate their species. on the other hand, the host seeks to maintain homeostasis by clearing pathogens. the inflammasome is a multi-protein complex that can induce cell death and processes il-1β and additional proinflammatory substrates. in this review we discuss the pathogen specific modulation of inflammasome activation ... | 2012 | 22546900 |
| assessment of pseudomonas aeruginosa n5,n10-methylenetetrahydrofolate dehydrogenase-cyclohydrolase as a potential antibacterial drug target. | the bifunctional enzyme methylenetetrahydrofolate dehydrogenase - cyclohydrolase (fold) is identified as a potential drug target in gram-negative bacteria, in particular the troublesome pseudomonas aeruginosa. in order to provide a comprehensive and realistic assessment of the potential of this target for drug discovery we generated a highly efficient recombinant protein production system and purification protocol, characterized the enzyme, carried out screening of two commercial compound librar ... | 2012 | 22558288 |
| mining genomes of marine cyanobacteria for elements of zinc homeostasis. | zinc is a recognized essential element for the majority of organisms, and is indispensable for the correct function of hundreds of enzymes and thousands of regulatory proteins. in aquatic photoautotrophs including cyanobacteria, zinc is thought to be required for carbonic anhydrase and alkaline phosphatase, although there is evidence that at least some carbonic anhydrases can be cambialistic, i.e., are able to acquire in vivo and function with different metal cofactors such as co(2+) and cd(2+). ... | 2012 | 22514551 |
| genotype-phenotype associations in a nonmodel prokaryote. | to help define the biological functions of nonessential genes of francisella novicida, we measured the growth of arrayed members of a comprehensive transposon mutant library under a variety of nutrition and stress conditions. mutant phenotypes were identified for 37% of the genes, corresponding to ten carbon source utilization pathways, nine amino acid- and nucleotide-biosynthetic pathways, ten intrinsic antibiotic resistance traits, and six other stress resistance traits. the greatest surprise ... | 2012 | 22434848 |
| architecture and conservation of the bacterial dna replication machinery, an underexploited drug target. | new antibiotics with novel modes of action are required to combat the growing threat posed by multi-drug resistant bacteria. over the last decade, genome sequencing and other high-throughput techniques have provided tremendous insight into the molecular processes underlying cellular functions in a wide range of bacterial species. we can now use these data to assess the degree of conservation of certain aspects of bacterial physiology, to help choose the best cellular targets for development of n ... | 2012 | 22206257 |
| activation of the pyrin inflammasome by intracellular burkholderia cenocepacia. | burkholderia cenocepacia is an opportunistic pathogen that causes chronic infection and induces progressive respiratory inflammation in cystic fibrosis patients. recognition of bacteria by mononuclear cells generally results in the activation of caspase-1 and processing of il-1β, a major proinflammatory cytokine. in this study, we report that human pyrin is required to detect intracellular b. cenocepacia leading to il-1β processing and release. this inflammatory response involves the host adapte ... | 2012 | 22368275 |
| the protein sdha maintains the integrity of the legionella-containing vacuole. | legionella pneumophila directs the formation of a specialized vacuole within host cells, dependent on protein substrates of the icm/dot translocation system. survival of the host cell is essential for intracellular replication of l. pneumophila. strains lacking the translocated substrate sdha are defective for intracellular replication and activate host cell death pathways in primary macrophages. to understand how sdha promotes evasion of death pathways, we performed a mutant hunt to identify ba ... | 2012 | 22308473 |
| sec-mediated secretion by coxiella burnetii. | coxiella burnetii is a gram-negative intracellular bacterial pathogen that replicates within a phagolysosome-like parasitophorous vacuole (pv) of macrophages. pv formation requires delivery of effector proteins directly into the host cell cytoplasm by a type ivb secretion system. however, additional secretion systems are likely responsible for modification of the pv lumen microenvironment that promote pathogen replication. | 2013 | 24093460 |
| lipoproteins of slow-growing mycobacteria carry three fatty acids and are n-acylated by apolipoprotein n-acyltransferase bcg_2070c. | lipoproteins are virulence factors of mycobacterium tuberculosis. bacterial lipoproteins are modified by the consecutive action of preprolipoprotein diacylglyceryl transferase (lgt), prolipoprotein signal peptidase (lspa) and apolipoprotein n- acyltransferase (lnt) leading to the formation of mature triacylated lipoproteins. lnt homologues are found in gram-negative and high gc-rich gram-positive, but not in low gc-rich gram-positive bacteria, although n-acylation is observed. in fast-growing my ... | 2013 | 24093492 |
| cytoplasmic lps activates caspase-11: implications in tlr4-independent endotoxic shock. | inflammatory caspases, such as caspase-1 and -11, mediate innate immune detection of pathogens. caspase-11 induces pyroptosis, a form of programmed cell death, and specifically defends against bacterial pathogens that invade the cytosol. during endotoxemia, however, excessive caspase-11 activation causes shock. we report that contamination of the cytoplasm by lipopolysaccharide (lps) is the signal that triggers caspase-11 activation in mice. specifically, caspase-11 responds to penta- and hexa-a ... | 2013 | 24031018 |
| the organisational structure of protein networks: revisiting the centrality-lethality hypothesis. | protein networks, describing physical interactions as well as functional associations between proteins, have been unravelled for many organisms in the recent past. databases such as the string provide excellent resources for the analysis of such networks. in this contribution, we revisit the organisation of protein networks, particularly the centrality-lethality hypothesis, which hypothesises that nodes with higher centrality in a network are more likely to produce lethal phenotypes on removal, ... | 2013 | 24592293 |
| the organisational structure of protein networks: revisiting the centrality-lethality hypothesis. | protein networks, describing physical interactions as well as functional associations between proteins, have been unravelled for many organisms in the recent past. databases such as the string provide excellent resources for the analysis of such networks. in this contribution, we revisit the organisation of protein networks, particularly the centrality-lethality hypothesis, which hypothesises that nodes with higher centrality in a network are more likely to produce lethal phenotypes on removal, ... | 2013 | 24592293 |
| molecular mechanisms of crispr-mediated microbial immunity. | bacteriophages (phages) infect bacteria in order to replicate and burst out of the host, killing the cell, when reproduction is completed. thus, from a bacterial perspective, phages pose a persistent lethal threat to bacterial populations. not surprisingly, bacteria evolved multiple defense barriers to interfere with nearly every step of phage life cycles. phages respond to this selection pressure by counter-evolving their genomes to evade bacterial resistance. the antagonistic interaction betwe ... | 2013 | 23959171 |
| molecular mechanisms of crispr-mediated microbial immunity. | bacteriophages (phages) infect bacteria in order to replicate and burst out of the host, killing the cell, when reproduction is completed. thus, from a bacterial perspective, phages pose a persistent lethal threat to bacterial populations. not surprisingly, bacteria evolved multiple defense barriers to interfere with nearly every step of phage life cycles. phages respond to this selection pressure by counter-evolving their genomes to evade bacterial resistance. the antagonistic interaction betwe ... | 2013 | 23959171 |
| geptop: a gene essentiality prediction tool for sequenced bacterial genomes based on orthology and phylogeny. | integrative genomics predictors, which score highly in predicting bacterial essential genes, would be unfeasible in most species because the data sources are limited. we developed a universal approach and tool designated geptop, based on orthology and phylogeny, to offer gene essentiality annotations. in a series of tests, our geptop method yielded higher area under curve (auc) scores in the receiver operating curves than the integrative approaches. in the ten-fold cross-validations among random ... | 2013 | 23977285 |
| salmonella require the fatty acid regulator pparδ for the establishment of a metabolic environment essential for long-term persistence. | host-adapted salmonella strains are responsible for a number of disease manifestations in mammals, including an asymptomatic chronic infection in which bacteria survive within macrophages located in systemic sites. however, the host cell physiology and metabolic requirements supporting bacterial persistence are poorly understood. in a mouse model of long-term infection, we found that s. typhimurium preferentially associates with anti-inflammatory/m2 macrophages at later stages of infection. furt ... | 2013 | 23954156 |
| the contribution of pmrab to the virulence of a clinical isolate of escherichia coli. | previous data from our laboratory suggest a relationship between increased pmrab expression and virulence in an escherichia coli mouse infection model of pyelonephritis. competitive infections with wild type and pmrab mutants showed that disruption of pmrab caused decreased persistence of e. coli within the mouse kidney. these results were confirmed with plasmid-mediated complementation of the pmrab mutant. additionally, increased expression of pmrab from this complementing plasmid in a previous ... | 2013 | 23921442 |
| transcriptional abundance is not the single force driving the evolution of bacterial proteins. | despite rapid progress in understanding the mechanisms that shape the evolution of proteins, the relative importance of various factors remain to be elucidated. in this study, we have assessed the effects of 16 different biological features on the evolutionary rates (ers) of protein-coding sequences in bacterial genomes. | 2013 | 23914835 |
| propionibacterium acnes induces il-1β secretion via the nlrp3 inflammasome in human monocytes. | propionibacterium acnes induction of inflammatory responses is a major etiological factor contributing to the pathogenesis of acne vulgaris. in particular, the il-1 family of cytokines has a critical role in both initiation of acne lesions and in the inflammatory response in acne. in this study, we demonstrated that human monocytes respond to p. acnes and secrete mature il-1β partially via the nlrp3-mediated pathway. when monocytes were stimulated with live p. acnes, caspase-1 and caspase-5 gene ... | 2013 | 23884315 |
| propionibacterium acnes induces il-1β secretion via the nlrp3 inflammasome in human monocytes. | propionibacterium acnes induction of inflammatory responses is a major etiological factor contributing to the pathogenesis of acne vulgaris. in particular, the il-1 family of cytokines has a critical role in both initiation of acne lesions and in the inflammatory response in acne. in this study, we demonstrated that human monocytes respond to p. acnes and secrete mature il-1β partially via the nlrp3-mediated pathway. when monocytes were stimulated with live p. acnes, caspase-1 and caspase-5 gene ... | 2013 | 23884315 |
| crisprs extending their reach: prokaryotic rnai protein cas9 recruited for gene regulation. | a cas protein from the crispr defence system against foreign dna, also functions in endogenous gene regulation. sampson et al (2013) have revealed that in pathogenic francisella bacteria, the cas9 protein guided by small rnas represses the mrna of a lipoprotein. this novel mechanism of post-transcriptional regulation enables the infecting bacteria to evade the tlr2-based innate immune response of its host. thus, reminiscent of eukaryotic rnai where some proteins facilitate both genome defence an ... | 2013 | 23756465 |
| inflammasome-mediated pyroptotic and apoptotic cell death, and defense against infection. | cell death is an effective strategy to limit intracellular infections. canonical inflammasomes, including nlrp3, nlrc4, and aim2, recruit and activate caspase-1 in response to a range of microbial stimuli and endogenous danger signals. caspase-1 then promotes the secretion of il-1β and il-18 and a rapid form of lytic programmed cell death termed pyroptosis. a second inflammatory caspase, mouse caspase-11, mediates pyroptotic death through an unknown non-canonical inflammasome system in response ... | 2013 | 23707339 |
| type i ifn triggers rig-i/tlr3/nlrp3-dependent inflammasome activation in influenza a virus infected cells. | influenza a virus (iav) triggers a contagious and potentially lethal respiratory disease. a protective il-1β response is mediated by innate receptors in macrophages and lung epithelial cells. nlrp3 is crucial in macrophages; however, which sensors elicit il-1β secretion in lung epithelial cells remains undetermined. here, we describe for the first time the relative roles of the host innate receptors rig-i (ddx58), tlr3, and nlrp3 in the il-1β response to iav in primary lung epithelial cells. to ... | 2013 | 23592984 |
| minor modifications to the phosphate groups and the c3' acyl chain length of lipid a in two bordetella pertussis strains, bp338 and 18-323, independently affect toll-like receptor 4 protein activation. | lipopolysaccharides (lps) of bordetella pertussis are important modulators of the immune system. interaction of the lipid a region of lps with the toll-like receptor 4 (tlr4) complex causes dimerization of tlr4 and activation of downstream nuclear factor κb (nfκb), which can lead to inflammation. we have previously shown that two strains of b. pertussis, bp338 (a tohama i-derivative) and 18-323, display two differences in lipid a structure. 1) bp338 can modify the 1- and 4'-phosphates by the add ... | 2013 | 23467413 |
| the evolutionary rate of antibacterial drug targets. | one of the major issues in the fight against infectious diseases is the notable increase in multiple drug resistance in pathogenic species. for that reason, newly acquired high-throughput data on virulent microbial agents attract the attention of many researchers seeking potential new drug targets. many approaches have been used to evaluate proteins from infectious pathogens, including, but not limited to, similarity analysis, reverse docking, statistical 3d structure analysis, machine learning, ... | 2013 | 23374913 |
| spontaneous cardiac calcinosis in balb/cbyj mice. | balb/c mice are predisposed to dystrophic cardiac calcinosis-the mineralization of cardiac tissues, especially the right ventricular epicardium. in previous reports, the disease appeared in aged animals and had an unknown etiology. in the current study, we report a substrain of balb/c mice (balb/cbyj) that develops disease early and with high frequency. here we analyzed hearts grossly to identify the presence and measure the severity of disease and to compare balb/c substrains. histologic analys ... | 2013 | 23561935 |
| construction of monophosphoryl lipid a producing escherichia coli mutants and comparison of immuno-stimulatory activities of their lipopolysaccharides. | the lipid a moiety of escherichia coli lipopolysaccharide is a hexaacylated disaccharide of glucosamine phosphorylated at the 1- and 4'-positions. it can be recognized by the tlr4/md-2 complex of mammalian immune cells, leading to release of proinflammatory cytokines. the toxicity of lipid a depends on its structure. in this study, two e. coli mutants, hw001 and hw002, were constructed by deleting or integrating key genes related to lipid a biosynthesis in the chromosome of e. coli w3110. hw001 ... | 2013 | 23434832 |
| an archaeal crispr type iii-b system exhibiting distinctive rna targeting features and mediating dual rna and dna interference. | crispr-cas systems provide a small rna-based mechanism to defend against invasive genetic elements in archaea and bacteria. to investigate the in vivo mechanism of rna interference by two type iii-b systems (cmr-α and cmr-β) in sulfolobus islandicus, a genetic assay was developed using plasmids carrying an artificial mini-crispr (ac) locus with a single spacer. after pac plasmids were introduced into different strains, northern analyses confirmed that mature crrnas were produced from the plasmid ... | 2014 | 25505143 |
| an archaeal crispr type iii-b system exhibiting distinctive rna targeting features and mediating dual rna and dna interference. | crispr-cas systems provide a small rna-based mechanism to defend against invasive genetic elements in archaea and bacteria. to investigate the in vivo mechanism of rna interference by two type iii-b systems (cmr-α and cmr-β) in sulfolobus islandicus, a genetic assay was developed using plasmids carrying an artificial mini-crispr (ac) locus with a single spacer. after pac plasmids were introduced into different strains, northern analyses confirmed that mature crrnas were produced from the plasmid ... | 2014 | 25505143 |
| tlr signaling that induces weak inflammatory response and ship1 enhances osteogenic functions. | toll-like receptor (tlr)-mediated inflammatory response could negatively affect bone metabolism. in this study, we determined how osteogenesis is regulated during inflammatory responses that are downstream of tlr signaling. human primary osteoblasts were cultured in collagen gels. pam3csk4 (p3c) and escherichia coli lipopolysaccharide (eclps) were used as tlr2 and tlr4 ligand respectively. porphyromonas gingivalis lps having tlr2 activity with either tlr4 agonism (pg1690) or tlr4 antagonism (pg1 ... | 2014 | 26273527 |
| regulation of gene expression in diverse cyanobacterial species by using theophylline-responsive riboswitches. | cyanobacteria are photosynthetic bacteria that are currently being developed as biological production platforms. they derive energy from light and carbon from atmospheric carbon dioxide, and some species can fix atmospheric nitrogen. one advantage of developing cyanobacteria for renewable production of biofuels and other biological products is that they are amenable to genetic manipulation, facilitating bioengineering and synthetic biology. to expand the currently available genetic toolkit, we h ... | 2014 | 25149516 |
| rational considerations about development of live attenuated yersinia pestis vaccines. | the risk of plague as a bioweapon has prompted increasing research efforts to develop plague vaccines due to its extreme virulence and the ease of its transmission. subunit vaccines that contain f1 and lcrv antigens of y. pestis have been tested for safety and immunogenicity, but doubts have been raised about whether subunit vaccines that engender antibody responses will protect against pneumonic plague, which requires both humeral and cellular immune responses for protection. the live, attenuat ... | 2014 | 24372254 |
| programmable rna recognition and cleavage by crispr/cas9. | the crispr-associated protein cas9 is an rna-guided dna endonuclease that uses rna-dna complementarity to identify target sites for sequence-specific double-stranded dna (dsdna) cleavage. in its native context, cas9 acts on dna substrates exclusively because both binding and catalysis require recognition of a short dna sequence, known as the protospacer adjacent motif (pam), next to and on the strand opposite the twenty-nucleotide target site in dsdna. cas9 has proven to be a versatile tool for ... | 2014 | 25274302 |
| pleiotropic role of the rna chaperone protein hfq in the human pathogen clostridium difficile. | clostridium difficile is an emergent human pathogen and the most common cause of nosocomial diarrhea. our recent data strongly suggest the importance of rna-based mechanisms for the control of gene expression in c. difficile. in an effort to understand the function of the rna chaperone protein hfq, we constructed and characterized an hfq-depleted strain in c. difficile. hfq depletion led to a growth defect, morphological changes, an increased sensitivity to stresses, and a better ability to spor ... | 2014 | 24982306 |
| purification, crystallization and preliminary x-ray crystallographic analysis of tssl from vibrio cholerae. | the type vi secretion system (t6ss) is a macromolecular complex that is conserved in gram-negative bacteria. the t6ss secretes effector proteins into recipient cells in a contact-dependent manner in order to accomplish cooperative and competitive interactions with the cells. although the composition and mechanism of the t6ss have been intensively investigated across many gram-negative bacteria, to date structural information on t6ss components from the important pathogen vibrio cholerae has been ... | 2014 | 25195905 |
| identification of multifaceted binding modes for pyrin and asc pyrin domains gives insights into pyrin inflammasome assembly. | inflammasomes are macromolecular complexes that mediate inflammatory and cell death responses to pathogens and cellular stress signals. dysregulated inflammasome activation is associated with autoinflammatory syndromes and several common diseases. during inflammasome assembly, oligomerized cytosolic pattern recognition receptors recruit procaspase-1 and procaspase-8 via the adaptor protein asc. inflammasome assembly is mediated by pyrin domains (pyds) and caspase recruitment domains, which are p ... | 2014 | 25006247 |
| antimicrobial peptides in reptiles. | reptiles are among the oldest known amniotes and are highly diverse in their morphology and ecological niches. these animals have an evolutionarily ancient innate-immune system that is of great interest to scientists trying to identify new and useful antimicrobial peptides. significant work in the last decade in the fields of biochemistry, proteomics and genomics has begun to reveal the complexity of reptilian antimicrobial peptides. here, the current knowledge about antimicrobial peptides in re ... | 2014 | 24918867 |
| development and applications of crispr-cas9 for genome engineering. | recent advances in genome engineering technologies based on the crispr-associated rna-guided endonuclease cas9 are enabling the systematic interrogation of mammalian genome function. analogous to the search function in modern word processors, cas9 can be guided to specific locations within complex genomes by a short rna search string. using this system, dna sequences within the endogenous genome and their functional outputs are now easily edited or modulated in virtually any organism of choice. ... | 2014 | 24906146 |
| bdla, dipa and induced dispersion contribute to acute virulence and chronic persistence of pseudomonas aeruginosa. | the human pathogen pseudomonas aeruginosa is capable of causing both acute and chronic infections. differences in virulence are attributable to the mode of growth: bacteria growing planktonically cause acute infections, while bacteria growing in matrix-enclosed aggregates known as biofilms are associated with chronic, persistent infections. while the contribution of the planktonic and biofilm modes of growth to virulence is now widely accepted, little is known about the role of dispersion in vir ... | 2014 | 24901523 |
| crispr-cas systems: prokaryotes upgrade to adaptive immunity. | clustered regularly interspaced short palindromic repeats (crispr), and associated proteins (cas) comprise the crispr-cas system, which confers adaptive immunity against exogenic elements in many bacteria and most archaea. crispr-mediated immunization occurs through the uptake of dna from invasive genetic elements such as plasmids and viruses, followed by its integration into crispr loci. these loci are subsequently transcribed and processed into small interfering rnas that guide nucleases for s ... | 2014 | 24766887 |
| sepsis in old age: review of human and animal studies. | sepsis is a serious problem among the geriatric population as its incidence and mortality rates dramatically increase with advanced age. despite a large number of ongoing clinical and basic research studies, there is currently no effective therapeutic strategy that rescues elderly patients with severe sepsis. recognition of this problem is relatively low as compared to other age-associated diseases. the disparity between clinical and basic studies is a problem, and this is likely due, in part, t ... | 2014 | 24729938 |
| fha interaction with phosphothreonine of tssl activates type vi secretion in agrobacterium tumefaciens. | the type vi secretion system (t6ss) is a widespread protein secretion system found in many gram-negative bacteria. t6sss are highly regulated by various regulatory systems at multiple levels, including post-translational regulation via threonine (thr) phosphorylation. the ser/thr protein kinase ppka is responsible for this thr phosphorylation regulation, and the forkhead-associated (fha) domain-containing fha-family protein is the sole t6ss phosphorylation substrate identified to date. here we d ... | 2014 | 24626341 |
| crystal structure of cas9 in complex with guide rna and target dna. | the crispr-associated endonuclease cas9 can be targeted to specific genomic loci by single guide rnas (sgrnas). here, we report the crystal structure of streptococcus pyogenes cas9 in complex with sgrna and its target dna at 2.5 å resolution. the structure revealed a bilobed architecture composed of target recognition and nuclease lobes, accommodating the sgrna:dna heteroduplex in a positively charged groove at their interface. whereas the recognition lobe is essential for binding sgrna and dna, ... | 2014 | 24529477 |
| alveolar macrophages infected with ames or sterne strain of bacillus anthracis elicit differential molecular expression patterns. | alveolar macrophages (ams) phagocytose bacillus anthracis following inhalation and induce the production of pro-inflammatory cytokines and chemokines to mediate the activation of innate immunity. ames, the virulent strain of b. anthracis, contains two plasmids that encode the antiphagocytic poly-γ-d-glutamic acid capsule and the lethal toxin. the attenuated sterne strain of b. anthracis, which lacks the plasmid encoding capsule, is widely adapted as a vaccine strain. although differences in the ... | 2014 | 24516547 |
| structures of cas9 endonucleases reveal rna-mediated conformational activation. | type ii crispr (clustered regularly interspaced short palindromic repeats)-cas (crispr-associated) systems use an rna-guided dna endonuclease, cas9, to generate double-strand breaks in invasive dna during an adaptive bacterial immune response. cas9 has been harnessed as a powerful tool for genome editing and gene regulation in many eukaryotic organisms. we report 2.6 and 2.2 angstrom resolution crystal structures of two major cas9 enzyme subtypes, revealing the structural core shared by all cas9 ... | 2014 | 24505130 |
| a pnpase dependent crispr system in listeria. | the human bacterial pathogen listeria monocytogenes is emerging as a model organism to study rna-mediated regulation in pathogenic bacteria. a class of non-coding rnas called crisprs (clustered regularly interspaced short palindromic repeats) has been described to confer bacterial resistance against invading bacteriophages and conjugative plasmids. crispr function relies on the activity of crispr associated (cas) genes that encode a large family of proteins with nuclease or helicase activities a ... | 2014 | 24415952 |
| exploiting crispr/cas systems for biotechnology. | the cas9 endonuclease is the central component of the type ii crispr/cas system, a prokaryotic adaptive restriction system against invading nucleic acids, such as those originating from bacteriophages and plasmids. recently, this rna-directed dna endonuclease has been harnessed to target dna sequences of interest. here, we review the development of cas9 as an important tool to not only edit the genomes of a number of different prokaryotic and eukaryotic species, but also as an efficient system f ... | 2014 | 24323919 |
| synthetic promoters functional in francisella novicida and escherichia coli. | in this work, we describe the identification of synthetic, controllable promoters that function in the bacterial pathogen francisella novicida, a model facultative intracellular pathogen. synthetic dna fragments consisting of the tetracycline operator (teto) flanked by a random nucleotide sequence were inserted into a francisella novicida shuttle plasmid upstream of a promoterless artificial operon containing the reporter genes cat and lacz. fragments able to promote transcription were selected ... | 2014 | 24141126 |
| a cellular genome-wide association study reveals human variation in microtubule stability and a role in inflammatory cell death. | pyroptosis is proinflammatory cell death that occurs in response to certain microbes. activation of the protease caspase-1 by molecular platforms called inflammasomes is required for pyroptosis. we performed a cellular genome-wide association study (gwas) using salmonella typhimurium infection of human lymphoblastoid cell lines as a means of dissecting the genetic architecture of susceptibility to pyroptosis and identifying unknown regulatory mechanisms. cellular gwas revealed that a common huma ... | 2014 | 24173717 |
| immuno-stimulatory activity of escherichia coli mutants producing kdo2-monophosphoryl-lipid a or kdo2-pentaacyl-monophosphoryl-lipid a. | lipid a is the active center of lipopolysaccharide which also known as endotoxin. monophosphoryl-lipid a (mpla) has less toxicity but retains potent immunoadjuvant activity; therefore, it can be developed as adjuvant for improving the strength and duration of the immune response to antigens. however, mpla cannot be chemically synthesized and can only be obtained by hydrolyzing lipopolysaccharide (lps) purified from gram-negative bacteria. purifying lps is difficult and time-consuming and can dam ... | 2015 | 26710252 |
| pore-forming toxins induce macrophage necroptosis during acute bacterial pneumonia. | necroptosis is a highly pro-inflammatory mode of cell death regulated by rip (or ripk)1 and rip3 kinases and mediated by the effector mlkl. we report that diverse bacterial pathogens that produce a pore-forming toxin (pft) induce necroptosis of macrophages and this can be blocked for protection against serratia marcescens hemorrhagic pneumonia. following challenge with s. marcescens, staphylococcus aureus, streptococcus pneumoniae, listeria monocytogenes, uropathogenic escherichia coli (upec), a ... | 2015 | 26659062 |
| the cpf1 crispr-cas protein expands genome-editing tools. | crispr-cas systems have immense biotechnological utility. a recent study reveals the potential of the cpf1 nuclease to complement and extend the existing crispr-cas9 genome-editing tools. | 2015 | 26578176 |
| interferon-γ inhibits ebola virus infection. | ebola virus outbreaks, such as the 2014 makona epidemic in west africa, are episodic and deadly. filovirus antivirals are currently not clinically available. our findings suggest interferon gamma, an fda-approved drug, may serve as a novel and effective prophylactic or treatment option. using mouse-adapted ebola virus, we found that murine interferon gamma administered 24 hours before or after infection robustly protects lethally-challenged mice and reduces morbidity and serum viral titers. furt ... | 2015 | 26562011 |
| inflammasomes coordinate pyroptosis and natural killer cell cytotoxicity to clear infection by a ubiquitous environmental bacterium. | defective neutrophils in patients with chronic granulomatous disease (cgd) cause susceptibility to extracellular and intracellular infections. microbes must first be ejected from intracellular niches to expose them to neutrophil attack, so we hypothesized that inflammasomes detect certain cgd pathogens upstream of neutrophil killing. here, we identified one such ubiquitous environmental bacterium, chromobacterium violaceum, whose extreme virulence was fully counteracted by the nlrc4 inflammasome ... | 2015 | 26572063 |
| diversity of crispr-cas immune systems and molecular machines. | bacterial adaptive immunity hinges on crispr-cas systems that provide dna-encoded, rna-mediated targeting of exogenous nucleic acids. a plethora of crispr molecular machines occur broadly in prokaryotic genomes, with a diversity of cas nucleases that can be repurposed for various applications. | 2015 | 26549499 |
| current and future prospects for crispr-based tools in bacteria. | crispr-cas systems have rapidly transitioned from intriguing prokaryotic defense systems to powerful and versatile biomolecular tools. this article reviews how these systems have been translated into technologies to manipulate bacterial genetics, physiology, and communities. recent applications in bacteria have centered on multiplexed genome editing, programmable gene regulation, and sequence-specific antimicrobials, while future applications can build on advances in eukaryotes, the rich natural ... | 2015 | 26460902 |
| current and future prospects for crispr-based tools in bacteria. | crispr-cas systems have rapidly transitioned from intriguing prokaryotic defense systems to powerful and versatile biomolecular tools. this article reviews how these systems have been translated into technologies to manipulate bacterial genetics, physiology, and communities. recent applications in bacteria have centered on multiplexed genome editing, programmable gene regulation, and sequence-specific antimicrobials, while future applications can build on advances in eukaryotes, the rich natural ... | 2015 | 26460902 |
| no time to waste--the ethical challenges created by crispr: crispr/cas, being an efficient, simple, and cheap technology to edit the genome of any organism, raises many ethical and regulatory issues beyond the use to manipulate human germ line cells. | | 2015 | 26450575 |