| membrane proteases and aminoglycoside antibiotic resistance. | we present genetic studies that help define the functional network underlying intrinsic aminoglycoside resistance in pseudomonas aeruginosa. our analysis shows that proteolysis, particularly that controlled by the membrane protease ftsh, is a major determinant of resistance. first, we examined the consequences of inactivating genes controlled by amgrs, a two-component regulator required for intrinsic tobramycin resistance. three of the gene products account for resistance: a modulator of ftsh pr ... | 2011 | 21764915 |
| intra-vacuolar proliferation of f. novicida within h. vermiformis. | francisella tularensis is a gram negative facultative intracellular bacterium that causes the zoonotic disease tularemia. free-living amebae, such as acanthamoeba and hartmannella, are environmental hosts of several intracellular pathogens. epidemiology of f. tularensis in various parts of the world is associated with water-borne transmission, which includes mosquitoes and amebae as the potential host reservoirs of the bacteria in water resources. in vitro studies showed intracellular replicatio ... | 2011 | 21747796 |
| a variety of novel lipid a structures obtained from francisella tularensis live obtained from francisella tularensis live. | f. tularensis is a gram-negative coccobacillus that causes tularemia. its lps has nominal biological activity. currently, there is controversy regarding the structure of the lipid a obtained from f. tularensis live vaccine strain (lvs). therefore, to resolve this controversy, the purification and structural identification of this lps was crucial. to achieve this, lps from f. tularensis lvs was acid hydrolyzed to obtain crude lipid a that was methylated and purified by hplc and the fractions were ... | 2011 | 21709054 |
| a variety of novel lipid a structures obtained from francisella tularensis live obtained from francisella tularensis live. | f. tularensis is a gram-negative coccobacillus that causes tularemia. its lps has nominal biological activity. currently, there is controversy regarding the structure of the lipid a obtained from f. tularensis live vaccine strain (lvs). therefore, to resolve this controversy, the purification and structural identification of this lps was crucial. to achieve this, lps from f. tularensis lvs was acid hydrolyzed to obtain crude lipid a that was methylated and purified by hplc and the fractions were ... | 2011 | 21709054 |
| toward an understanding of the perpetuation of the agent of tularemia. | the epidemiology of tularemia has influenced, perhaps incorrectly skewed, our views on the ecology of the agent of tularemia. in particular, the central role of lagomorphs needs to be reexamined. diverse observations, some incidental, and some that are more generally reproducible, have not been synthesized so that the critical elements of the perpetuation of francisella tularensis can be identified. developing a quantitative model of the basic reproduction number of f. tularensis may require sep ... | 2011 | 21687803 |
| toward an understanding of the perpetuation of the agent of tularemia. | the epidemiology of tularemia has influenced, perhaps incorrectly skewed, our views on the ecology of the agent of tularemia. in particular, the central role of lagomorphs needs to be reexamined. diverse observations, some incidental, and some that are more generally reproducible, have not been synthesized so that the critical elements of the perpetuation of francisella tularensis can be identified. developing a quantitative model of the basic reproduction number of f. tularensis may require sep ... | 2011 | 21687803 |
| tlr2 signaling contributes to rapid inflammasome activation during f. novicida infection. | background: early detection of microorganisms by the innate immune system is provided by surface-expressed and endosomal pattern recognition receptors (prrs) such as toll-like receptors (tlrs). detection of microbial components by tlrs initiates a signaling cascade leading to the expression of proinflammatory cytokines including il-6 and il-1+¦. some intracellular bacteria subvert the tlr response by rapidly escaping the phagosome and entering the cytosol. however, these bacteria may be recogniz ... | 2011 | 21698237 |
| francisella infection triggers activation of the aim2 inflammasome in murine dendritic cells. | the intracellular bacterium francisella tularensis is the causative agent of tularemia, a potentially fatal disease. in macrophages, francisella escapes the initial phagosome and replicates in the cytosol, where it is detected by the cytosolic dna sensor aim2 leading to activation of the aim2 inflammasome. however, during aerosol infection, francisella is also taken up by dendritic cells. in this study, we show that francisella novicida escapes into the cytosol of bone marrow-derived dendritic c ... | 2011 | 21902795 |
| francisella infection triggers activation of the aim2 inflammasome in murine dendritic cells. | the intracellular bacterium francisella tularensis is the causative agent of tularemia, a potentially fatal disease. in macrophages, francisella escapes the initial phagosome and replicates in the cytosol, where it is detected by the cytosolic dna sensor aim2 leading to activation of the aim2 inflammasome. however, during aerosol infection, francisella is also taken up by dendritic cells. in this study, we show that francisella novicida escapes into the cytosol of bone marrow-derived dendritic c ... | 2011 | 21902795 |
| Elevated AIM2-mediated pyroptosis triggered by hypercytotoxic Francisella mutant strains is attributed to increased intracellular bacteriolysis. | Intracellular bacterial pathogens Francisella novicida and the Live Vaccine Strain (LVS) are recognized in the macrophage cytosol by the AIM2 inflammasome, which leads to the activation of caspase-1 and the processing and secretion of active IL-1ß, IL-18 and pyroptosis. Previous studies have reported that F. novicida and LVS mutants in specific genes (e.g. FTT0584, mviN and ripA) induce elevated inflammasome activation and hypercytotoxicity in host cells, leading to the proposal that F. novicida ... | 2011 | 21883803 |
| Caspase-1-induced pyroptotic cell death. | Programmed cell death is a necessary part of development and tissue homeostasis enabling the removal of unwanted cells. In the setting of infectious disease, cells that have been commandeered by microbial pathogens become detrimental to the host. When macrophages and dendritic cells are compromised in this way, they can be lysed by pyroptosis, a cell death mechanism that is distinct from apoptosis and oncosis/necrosis. Pyroptosis is triggered by Caspase-1 after its activation by various inflamma ... | 2011 | 21884178 |
| Dermacentor andersoni transmission of Francisella tularensis subsp. novicida reflects bacterial colonization, dissemination, and replication coordinated with tick feeding. | Ticks serve as biological vectors for a wide variety of bacterial pathogens which must be able to efficiently colonize specific tick tissues prior to transmission. The bacterial determinants of tick colonization are largely unknown, a knowledge gap attributed in large part to the paucity of tools to genetically manipulate these pathogens. In this study, we demonstrated that Francisella tularensis subsp. novicida, for which a complete two-allele transposon mutant library has been constructed, ini ... | 2011 | 21930762 |
| the acid phosphatase acpa is secreted in vitro and in macrophages by francisella spp. | francisella tularensis is a remarkably infectious facultative intracellular pathogen that causes the zoonotic disease tularemia. essential to f. tularensis spp. pathogenesis is its ability to escape the destructive phagosomal environment and inhibit the host cell respiratory burst. f. tularensis spp. encode a series of acid phosphatases, which have been reported to play important roles in francisella phagosomal escape, inhibition of the respiratory burst and intracellular survival. however, rigo ... | 2011 | 22184418 |
| uncoupling of pyrin-only protein 2 (pop2)-mediated dual regulation of nf-κb and the inflammasome. | activation of transcription factor nf-κb and inflammasome-directed caspase-1 cleavage of il-1β are key processes in the inflammatory response to pathogen or host-derived signals. pyrin-only proteins (pops) are restricted to old world monkeys, apes, and humans and have previously been shown to impair inflammasome assembly and/or nf-κb p65 transcriptional activity in transfected epithelial cells. however, the biological role of pop2 and the molecular basis for its observed functions are not well u ... | 2011 | 21976665 |
| listeria monocytogenes infection in macrophages induces vacuolar-dependent host mirna response. | listeria monocytogenes is a gram-positive facultative intracellular pathogen, causing serious illness in immunocompromised individuals and pregnant women. upon detection by macrophages, which are key players of the innate immune response against infection, l. monocytogenes induces specific host cell responses which need to be tightly controlled at transcriptional and post-transcriptional levels. here, we ask whether and how host mirnas, which represent an important mechanism of post-transcriptio ... | 2011 | 22114673 |
| the biochemical properties of the francisella pathogenicity island (fpi)-encoded proteins igla, iglb, iglc, pdpb and dotu suggest roles in type vi secretion. | the francisella pathogenicity island (fpi) encodes proteins thought to compose a type vi secretion system (t6ss) that is required for the intracellular growth of francisella novicida. in this work we used deletion mutagenesis and genetic complementation to determine that the intracellular growth of f. novicida was dependent on 14 of the 18 genes in the fpi. the products of the iglabcd operon were localized by the biochemical fractionation of f. novicida, and francisella tularensis lvs. sucrose g ... | 2011 | 21980115 |
| the murine caecal microrna signature depends on the presence of the endogenous microbiota. | the intestinal messenger rna expression signature is affected by the presence and composition of the endogenous microbiota, with effects on host physiology. the intestine is also characterized by a distinctive micronome. however, it is not known if microbes also impact intestinal gene expression epigenetically. we investigated if the murine caecal microrna expression signature depends on the presence of the microbiota, and the potential implications of this interaction on intestinal barrier func ... | 2012 | 22211115 |
| the murine caecal microrna signature depends on the presence of the endogenous microbiota. | the intestinal messenger rna expression signature is affected by the presence and composition of the endogenous microbiota, with effects on host physiology. the intestine is also characterized by a distinctive micronome. however, it is not known if microbes also impact intestinal gene expression epigenetically. we investigated if the murine caecal microrna expression signature depends on the presence of the microbiota, and the potential implications of this interaction on intestinal barrier func ... | 2012 | 22211115 |
| francisella tularensis uses cholesterol and clathrin-based endocytic mechanisms to invade hepatocytes. | francisella tularensis are highly infectious microbes that cause the disease tularemia. although much of the bacterial burden is carried in non-phagocytic cells, the strategies these pathogens use to invade these cells remains elusive. to examine these mechanisms we developed two in vitro francisella-based infection models that recapitulate the non-phagocytic cell infections seen in livers of infected mice. using these models we found that francisella novicida exploit clathrin and cholesterol de ... | 2011 | 22355707 |
| production of outer membrane vesicles and outer membrane tubes by francisella novicida. | francisella spp. are highly infectious and virulent bacteria that cause the zoonotic disease tularemia. knowledge is lacking for the virulence factors expressed by francisella and how these factors are secreted and delivered to host cells. gram-negative bacteria constitutively release outer membrane vesicles (omv), which may function in the delivery of virulence factors to host cells. we identified growth conditions under which francisella novicida produces abundant omv. purification of the vesi ... | 2012 | 23264574 |
| a structure-based classification of class a β-lactamases, a broadly diverse family of enzymes. | for medical biologists, sequencing has become a commonplace technique to support diagnosis. rapid changes in this field have led to the generation of large amounts of data, which are not always correctly listed in databases. this is particularly true for data concerning class a β-lactamases, a group of key antibiotic resistance enzymes produced by bacteria. many genomes have been reported to contain putative β-lactamase genes, which can be compared with representative types. we analyzed several ... | 2016 | 26511485 |
| a structure-based classification of class a β-lactamases, a broadly diverse family of enzymes. | for medical biologists, sequencing has become a commonplace technique to support diagnosis. rapid changes in this field have led to the generation of large amounts of data, which are not always correctly listed in databases. this is particularly true for data concerning class a β-lactamases, a group of key antibiotic resistance enzymes produced by bacteria. many genomes have been reported to contain putative β-lactamase genes, which can be compared with representative types. we analyzed several ... | 2016 | 26511485 |
| abc transporters involved in export of cell surface glycoconjugates. | complex glycoconjugates play critical roles in the biology of microorganisms. despite the remarkable diversity in glycan structures and the bacteria that produce them, conserved themes are evident in the biosynthesis-export pathways. one of the primary pathways involves representatives of the atp-binding cassette (abc) transporter superfamily. these proteins are responsible for the export of a wide variety of cell surface oligo- and polysaccharides in both gram-positive and gram-negative bacteri ... | 2010 | 20805402 |
| stress wars: the direct role of host and bacterial molecular chaperones in bacterial infection. | | 2006 | 16790742 |
| silencing the alarm: insights into the interaction between host and pathogen. conference on microbial pathogenesis: mechanisms of infectious disease. | | 2007 | 18084188 |
| silencing the alarm: insights into the interaction between host and pathogen. conference on microbial pathogenesis: mechanisms of infectious disease. | | 2007 | 18084188 |
| repression of bacterial lipoprotein production by francisella novicida facilitates evasion of innate immune recognition. | innate recognition systems, including the toll-like receptors (tlrs), play a critical role in activating host defences and proinflammatory pathways in response to infection. pathogens have developed strategies to subvert tlrs in order to survive and replicate within the host. the model intracellular pathogen, francisella novicida, modulates host defences to promote survival and replication in macrophages. tlr2, which recognizes bacterial lipoproteins (blps), is critical for activating host defen ... | 2012 | 22632124 |
| inborn errors of human stat1: allelic heterogeneity governs the diversity of immunological and infectious phenotypes. | the genetic dissection of various human infectious diseases has led to the definition of inborn errors of human stat1 immunity of four types, including (i) autosomal recessive (ar) complete stat1 deficiency, (ii) ar partial stat1 deficiency, (iii) autosomal dominant (ad) stat1 deficiency, and (iv) ad gain of stat1 activity. the two types of ar stat1 defect give rise to a broad infectious phenotype with susceptibility to intramacrophagic bacteria (mostly mycobacteria) and viruses (herpes viruses ... | 2012 | 22651901 |
| cyclic di-gmp: the first 25 years of a universal bacterial second messenger. | twenty-five years have passed since the discovery of cyclic dimeric (3'→5') gmp (cyclic di-gmp or c-di-gmp). from the relative obscurity of an allosteric activator of a bacterial cellulose synthase, c-di-gmp has emerged as one of the most common and important bacterial second messengers. cyclic di-gmp has been shown to regulate biofilm formation, motility, virulence, the cell cycle, differentiation, and other processes. most c-di-gmp-dependent signaling pathways control the ability of bacteria t ... | 2013 | 23471616 |
| mechanisms of antimicrobial peptide resistance in gram-negative bacteria. | cationic antimicrobial peptides (camps) are important innate immune defenses that inhibit colonization by pathogens and contribute to clearance of infections. gram-negative bacterial pathogens are a major target, yet many of them have evolved mechanisms to resist these antimicrobials. these resistance mechanisms can be critical contributors to bacterial virulence and are often crucial for survival within the host. here, we summarize methods used by gram-negative bacteria to resist camps. underst ... | 2014 | 25927010 |
| mechanisms of antimicrobial peptide resistance in gram-negative bacteria. | cationic antimicrobial peptides (camps) are important innate immune defenses that inhibit colonization by pathogens and contribute to clearance of infections. gram-negative bacterial pathogens are a major target, yet many of them have evolved mechanisms to resist these antimicrobials. these resistance mechanisms can be critical contributors to bacterial virulence and are often crucial for survival within the host. here, we summarize methods used by gram-negative bacteria to resist camps. underst ... | 2014 | 25927010 |
| thermal control of virulence factors in bacteria: a hot topic. | pathogenic bacteria sense environmental cues, including the local temperature, to control the production of key virulence factors. thermal regulation can be achieved at the level of dna, rna or protein and although many virulence factors are subject to thermal regulation, the exact mechanisms of control are yet to be elucidated in many instances. understanding how virulence factors are regulated by temperature presents a significant challenge, as gene expression and protein production are often ... | 2014 | 25494856 |
| benchmarking of methods for genomic taxonomy. | one of the first issues that emerges when a prokaryotic organism of interest is encountered is the question of what it is--that is, which species it is. the 16s rrna gene formed the basis of the first method for sequence-based taxonomy and has had a tremendous impact on the field of microbiology. nevertheless, the method has been found to have a number of shortcomings. in the current study, we trained and benchmarked five methods for whole-genome sequence-based prokaryotic species identification ... | 2014 | 24574292 |
| revisiting the gram-negative lipoprotein paradigm. | the processing of lipoproteins (lpps) in gram-negative bacteria is generally considered an essential pathway. mature lipoproteins in these bacteria are triacylated, with the final fatty acid addition performed by lnt, an apolipoprotein n-acyltransferase. the mature lipoproteins are then sorted by the lol system, with most lpps inserted into the outer membrane (om). we demonstrate here that the lnt gene is not essential to the gram-negative pathogen francisella tularensis subsp. tularensis strain ... | 2015 | 25755189 |
| outer-inner membrane vesicles naturally secreted by gram-negative pathogenic bacteria. | outer-inner membrane vesicles (o-imvs) were recently described as a new type of membrane vesicle secreted by the antarctic bacterium shewanella vesiculosa m7t. their formation is characterized by the protrusion of both outer and plasma membranes, which pulls cytoplasmic components into the vesicles. to demonstrate that this is not a singular phenomenon in a bacterium occurring in an extreme environment, the identification of o-imvs in pathogenic bacteria was undertaken. with this aim, a structur ... | 2015 | 25581302 |
| from in vitro to in vivo models of bacterial biofilm-related infections. | the influence of microorganisms growing as sessile communities in a large number of human infections has been extensively studied and recognized for 30-40 years, therefore warranting intense scientific and medical research. nonetheless, mimicking the biofilm-life style of bacteria and biofilm-related infections has been an arduous task. models used to study biofilms range from simple in vitro to complex in vivo models of tissues or device-related infections. these different models have progressi ... | 2013 | 25437038 |
| structural basis of pam-dependent target dna recognition by the cas9 endonuclease. | the crispr-associated protein cas9 is an rna-guided endonuclease that cleaves double-stranded dna bearing sequences complementary to a 20-nucleotide segment in the guide rna. cas9 has emerged as a versatile molecular tool for genome editing and gene expression control. rna-guided dna recognition and cleavage strictly require the presence of a protospacer adjacent motif (pam) in the target dna. here we report a crystal structure of streptococcus pyogenes cas9 in complex with a single-molecule gui ... | 2014 | 25079318 |
| mouse genome engineering via crispr-cas9 for study of immune function. | clustered regularly interspaced palindromic repeats (crispr)-associated (cas9) technology has proven a formidable addition to our armory of approaches for genomic editing. derived from pathways in archaea and bacteria that mediate the resistance to exogenous genomic material, the crispr-cas9 system utilizes a short single guide rna (sgrna) to direct the endonuclease cas9 to virtually anywhere in the genome. upon targeting, cas9 generates dna double-strand breaks (dsbs) and facilitates the repair ... | 2015 | 25607456 |
| crispr-mediated epigenome editing. | mounting evidence has called into question our understanding of the role that the central dogma of molecular biology plays in human pathology. the conventional view that elucidating the mechanisms for translating genes into proteins can account for a panoply of diseases has proven incomplete. landmark studies point to epigenetics as a missing piece of the puzzle. however, technological limitations have hindered the study of specific roles for histone post-translational modifications, dna modific ... | 2016 | 28018139 |
| mining high-throughput experimental data to link gene and function. | nearly 2200 genomes that encode around 6 million proteins have now been sequenced. around 40% of these proteins are of unknown function, even when function is loosely and minimally defined as 'belonging to a superfamily'. in addition to in silico methods, the swelling stream of high-throughput experimental data can give valuable clues for linking these unknowns with precise biological roles. the goal is to develop integrative data-mining platforms that allow the scientific community at large to ... | 2011 | 21310501 |
| genomes of model organisms: know thy tools. | | 2008 | 18474084 |
| interaction of leptospira elongation factor tu with plasminogen and complement factor h: a metabolic leptospiral protein with moonlighting activities. | the elongation factor tu (ef-tu), an abundant bacterial protein involved in protein synthesis, has been shown to display moonlighting activities. known to perform more than one function at different times or in different places, it is found in several subcellular locations in a single organism, and may serve as a virulence factor in a range of important human pathogens. here we demonstrate that leptospira ef-tu is surface-exposed and performs additional roles as a cell-surface receptor for host ... | 2013 | 24312361 |
| phosphate groups of lipid a are essential for salmonella enterica serovar typhimurium virulence and affect innate and adaptive immunity. | lipid a is a key component of the outer membrane of gram-negative bacteria and stimulates proinflammatory responses via the toll-like receptor 4 (tlr4)-md2-cd14 pathway. its endotoxic activity depends on the number and length of acyl chains and its phosphorylation state. in salmonella enterica serovar typhimurium, removal of the secondary laurate or myristate chain in lipid a results in bacterial attenuation and growth defects in vitro. however, the roles of the two lipid a phosphate groups in b ... | 2012 | 22753374 |
| identification of a novel francisella tularensis factor required for intramacrophage survival and subversion of innate immune response. | francisella tularensis, the causative agent of tularemia, is one of the deadliest agents of biological warfare and bioterrorism. extremely high virulence of this bacterium is associated with its ability to dampen or subvert host innate immune response. the objectives of this study were to identify factors and understand the mechanisms of host innate immune evasion by f. tularensis. we identified and explored the pathogenic role of a mutant interrupted at gene locus ftl_0325, which encodes an omp ... | 2012 | 22654100 |
| activity and crystal structure of arabidopsis thaliana udp-n-acetylglucosamine acyltransferase. | the udp-n-acetylglucosamine (udp-glcnac) acyltransferase, encoded by lpxa, catalyzes the first step of lipid a biosynthesis in gram-negative bacteria, the (r)-3-hydroxyacyl-acp-dependent acylation of the 3-oh group of udp-glcnac. recently, we demonstrated that the arabidopsis thaliana orthologs of six enzymes of the bacterial lipid a pathway produce lipid a precursors with structures similar to those of escherichia coli lipid a precursors [li, c., et al. (2011) proc. natl. acad. sci. u.s.a. 108, ... | 2012 | 22545860 |
| ceg: a database of essential gene clusters. | essential genes are indispensable for the survival of living entities. they are the cornerstones of synthetic biology, and are potential candidate targets for antimicrobial and vaccine design. | 2013 | 24209780 |
| the origin of 8-amino-3,8-dideoxy-d-manno-octulosonic acid (kdo8n) in the lipopolysaccharide of shewanella oneidensis. | lipopolysaccharide (lps; endotoxin) is an essential component of the outer monolayer of nearly all gram-negative bacteria. lps is composed of a hydrophobic anchor, known as lipid a, an inner core oligosaccharide, and a repeating o-antigen polysaccharide. in nearly all species, the first sugar bridging the hydrophobic lipid a and the polysaccharide domain is 3-deoxy-d-manno-octulosonic acid (kdo), and thus it is critically important for lps biosynthesis. modifications to lipid a have been shown t ... | 2013 | 23413030 |
| kdo2 -lipid a: structural diversity and impact on immunopharmacology. | 3-deoxy-d-manno-octulosonic acid-lipid a (kdo2 -lipid a) is the essential component of lipopolysaccharide in most gram-negative bacteria and the minimal structural component to sustain bacterial viability. it serves as the active component of lipopolysaccharide to stimulate potent host immune responses through the complex of toll-like-receptor 4 (tlr4) and myeloid differentiation protein 2. the entire biosynthetic pathway of escherichia coli kdo2 -lipid a has been elucidated and the nine enzymes ... | 2014 | 24838025 |
| kdo2 -lipid a: structural diversity and impact on immunopharmacology. | 3-deoxy-d-manno-octulosonic acid-lipid a (kdo2 -lipid a) is the essential component of lipopolysaccharide in most gram-negative bacteria and the minimal structural component to sustain bacterial viability. it serves as the active component of lipopolysaccharide to stimulate potent host immune responses through the complex of toll-like-receptor 4 (tlr4) and myeloid differentiation protein 2. the entire biosynthetic pathway of escherichia coli kdo2 -lipid a has been elucidated and the nine enzymes ... | 2014 | 24838025 |
| haemophilus ducreyi hfq contributes to virulence gene regulation as cells enter stationary phase. | to adapt to stresses encountered in stationary phase, gram-negative bacteria utilize the alternative sigma factor rpos. however, some species lack rpos; thus, it is unclear how stationary-phase adaptation is regulated in these organisms. here we defined the growth-phase-dependent transcriptomes of haemophilus ducreyi, which lacks an rpos homolog. compared to mid-log-phase organisms, cells harvested from the stationary phase upregulated genes encoding several virulence determinants and a homolog ... | 2014 | 24520065 |
| lipid a as a drug target and therapeutic molecule. | in this review, lipid a, from its discovery to recent findings, is presented as a drug target and therapeutic molecule. first, the biosynthetic pathway for lipid a, the raetz pathway, serves as a good drug target for antibiotic development. several assay methods used to screen for inhibitors of lipid a synthesis will be presented, and some of the promising lead compounds will be described. second, utilization of lipid a biosynthetic pathways by various bacterial species can generate modified lip ... | 2015 | 26535075 |
| control of gene expression by crispr-cas systems. | clustered regularly interspaced short palindromic repeats (crispr) loci and their associated cas (crispr-associated) genes provide adaptive immunity against viruses (phages) and other mobile genetic elements in bacteria and archaea. while most of the early work has largely been dominated by examples of crispr-cas systems directing the cleavage of phage or plasmid dna, recent studies have revealed a more complex landscape where crispr-cas loci might be involved in gene regulation. in this review, ... | 2013 | 24273648 |
| elucidation of a novel lipid a α-(1,1)-gala transferase gene (rgtf) from mesorhizobium loti: heterologous expression of rgtf causes rhizobium etli to synthesize lipid a with α-(1,1)-gala. | an unusual α-(1,1)-galacturonic acid (gala) lipid a modification has been reported in the lipopolysaccharide of a number of interesting gram-negative bacteria, including the nitrogen-fixing bacteria azospirillum lipoferum, mesorhizobium huakuii and m. loti, the stalk-forming bacterium caulobacter crescentus and the hyperthermophilic bacterium aquifex aeolicus. however, the α-(1,1)-gala transferase (galat) gene, which we have named rgtf, was not identified. species of the rhizobium genera produce ... | 2013 | 23283001 |
| differences in carbon source utilisation distinguish campylobacter jejuni from campylobacter coli. | campylobacter jejuni and c. coli are human intestinal pathogens that are the most frequent causes of bacterial foodborne gastroenteritis in humans in the uk. in this study, we aimed to characterise the metabolic diversity of both c. jejuni and c. coli using a diverse panel of clinical strains isolated from the uk, pakistan and thailand, thereby representing both the developed and developing world. our aim was to apply multi genome analysis and biolog phenotyping to determine differences in carbo ... | 2014 | 25348335 |
| [bacterial biofilms: their importance in animal health and public health]. | bacterial biofilms are structured communities of bacterial cells enclosed in a self-produced polymer matrix that is attached to a surface. biofilms protect and allow bacteria to survive and thrive in hostile environments. bacteria within biofilms can withstand host immune responses, and are much less susceptible to antibiotics and disinfectants when compared to their planktonic counterparts. the ability to form biofilms is now considered an attribute of many microorganisms. diseases associated w ... | 2014 | 24688172 |
| the renaissance of bacillosamine and its derivatives: pathway characterization and implications in pathogenicity. | prokaryote-specific sugars, including n,n'-diacetylbacillosamine (dinacbac) and pseudaminic acid, have experienced a renaissance in the past decade because of their discovery in glycans related to microbial pathogenicity. dinacbac is found at the reducing end of oligosaccharides of n- and o-linked bacterial protein glycosylation pathways of gram-negative pathogens, including campylobacter jejuni and neisseria gonorrhoeae. further derivatization of dinacbac results in the nonulosonic acid known a ... | 2014 | 24383882 |
| the bacteriophage carrier state of campylobacter jejuni features changes in host non-coding rnas and the acquisition of new host-derived crispr spacer sequences. | incorporation of self-derived crispr dna protospacers in campylobacter jejuni pt14 occurs in the presence of bacteriophages encoding a crispr-like cas4 protein. this phenomenon was evident in carrier state infections where both bacteriophages and host are maintained for seemingly indefinite periods as stable populations following serial passage. carrier state cultures of c. jejuni pt14 have greater aerotolerance in nutrient limited conditions, and may have arisen as an evolutionary response to s ... | 2016 | 27047470 |
| the role of crispr-cas systems in virulence of pathogenic bacteria. | clustered regularly interspaced short palindromic repeats (crispr) and crispr-associated (cas) genes are present in many bacterial and archaeal genomes. since the discovery of the typical crispr loci in the 1980s, well before their physiological role was revealed, their variable sequences have been used as a complementary typing tool in diagnostic, epidemiologic, and evolutionary analyses of prokaryotic strains. the discovery that crispr spacers are often identical to sequence fragments of mobil ... | 2014 | 24600041 |
| contribution of amino acid catabolism to the tissue specific persistence of campylobacter jejuni in a murine colonization model. | campylobacter jejuni is a major cause of food-borne disease in industrialized countries. carbohydrate utilization by c. jejuni is severely restricted, and knowledge about which substrates fuel c. jejuni infection and growth is limited. some amino acids have been shown to serve as carbon sources both in vitro and in vivo. in the present study we investigated the contribution of serine and proline catabolism to the invitro and invivo growth of c. jejuni 81-176. we confirmed that the serine transpo ... | 2012 | 23226358 |
| identification of essential genes of the periodontal pathogen porphyromonas gingivalis. | porphyromonas gingivalis is a gram-negative anaerobic bacterium associated with periodontal disease onset and progression. genetic tools for the manipulation of bacterial genomes allow for in-depth mechanistic studies of metabolism, physiology, interspecies and host-pathogen interactions. analysis of the essential genes, protein-coding sequences necessary for survival of p. gingivalis by transposon mutagenesis has not previously been attempted due to the limitations of available transposon syste ... | 2012 | 23114059 |
| the lipopolysaccharide from capnocytophaga canimorsus reveals an unexpected role of the core-oligosaccharide in md-2 binding. | capnocytophaga canimorsus is a usual member of dog's mouths flora that causes rare but dramatic human infections after dog bites. we determined the structure of c. canimorsus lipid a. the main features are that it is penta-acylated and composed of a "hybrid backbone" lacking the 4' phosphate and having a 1 phosphoethanolamine (p-etn) at 2-amino-2-deoxy-d-glucose (glcn). c. canimorsus lps was 100 fold less endotoxic than escherichia coli lps. surprisingly, c. canimorsus lipid a was 20,000 fold le ... | 2012 | 22570611 |
| crispr-cas immunity against phages: its effects on the evolution and survival of bacterial pathogens. | | 2013 | 24348245 |
| phylogeny of cas9 determines functional exchangeability of dual-rna and cas9 among orthologous type ii crispr-cas systems. | the crispr-cas-derived rna-guided cas9 endonuclease is the key element of an emerging promising technology for genome engineering in a broad range of cells and organisms. the dna-targeting mechanism of the type ii crispr-cas system involves maturation of tracrrna:crrna duplex (dual-rna), which directs cas9 to cleave invading dna in a sequence-specific manner, dependent on the presence of a protospacer adjacent motif (pam) on the target. we show that evolution of dual-rna and cas9 in bacteria pro ... | 2013 | 24270795 |
| phylogeny of cas9 determines functional exchangeability of dual-rna and cas9 among orthologous type ii crispr-cas systems. | the crispr-cas-derived rna-guided cas9 endonuclease is the key element of an emerging promising technology for genome engineering in a broad range of cells and organisms. the dna-targeting mechanism of the type ii crispr-cas system involves maturation of tracrrna:crrna duplex (dual-rna), which directs cas9 to cleave invading dna in a sequence-specific manner, dependent on the presence of a protospacer adjacent motif (pam) on the target. we show that evolution of dual-rna and cas9 in bacteria pro ... | 2013 | 24270795 |
| deg 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements. | the combination of high-density transposon-mediated mutagenesis and high-throughput sequencing has led to significant advancements in research on essential genes, resulting in a dramatic increase in the number of identified prokaryotic essential genes under diverse conditions and a revised essential-gene concept that includes all essential genomic elements, rather than focusing on protein-coding genes only. deg 10, a new release of the database of essential genes (available at http://www.essenti ... | 2013 | 24243843 |
| deg 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements. | the combination of high-density transposon-mediated mutagenesis and high-throughput sequencing has led to significant advancements in research on essential genes, resulting in a dramatic increase in the number of identified prokaryotic essential genes under diverse conditions and a revised essential-gene concept that includes all essential genomic elements, rather than focusing on protein-coding genes only. deg 10, a new release of the database of essential genes (available at http://www.essenti ... | 2013 | 24243843 |
| (non-)translational medicine: targeting bacterial rna. | the rise and spread of antibiotic resistance is among the most severe challenges facing modern medicine. despite this fact, attempts to develop novel classes of antibiotic have been largely unsuccessful. the traditional mechanisms by which antibiotics work are subject to relatively rapid bacterial resistance via mutation, and hence have a limited period of efficacy. one promising strategy to ameliorate this problem is to shift from the use of chemical compounds targeting protein structures and p ... | 2013 | 24265632 |
| alternative roles for crispr/cas systems in bacterial pathogenesis. | | 2013 | 24146613 |
| unique structural modifications are present in the lipopolysaccharide from colistin-resistant strains of acinetobacter baumannii. | acinetobacter baumannii is a nosocomial opportunistic pathogen that can cause severe infections, including hospital-acquired pneumonia, wound infections, and sepsis. multidrug-resistant (mdr) strains are prevalent, further complicating patient treatment. due to the increase in mdr strains, the cationic antimicrobial peptide colistin has been used to treat a. baumannii infections. colistin-resistant strains of a. baumannii with alterations to the lipid a component of lipopolysaccharide (lps) have ... | 2013 | 23877686 |
| degeneration of a crispr/cas system and its regulatory target during the evolution of a pathogen. | crispr/cas systems are bacterial rna-guided endonuclease machineries that target foreign nucleic acids. recently, we demonstrated that the cas protein cas9 controls gene expression and virulence in francisella novicida by altering the stability of the mrna for an immunostimulatory bacterial lipoprotein (blp). genomic analyses, however, revealed that francisella species with increased virulence harbor degenerated crispr/cas systems. we hypothesize that crispr/cas degeneration removed a barrier ag ... | 2013 | 24100224 |
| feob-mediated uptake of iron by francisella tularensis. | francisella tularensis, the bacterial cause of tularemia, infects the liver and replicates in hepatocytes in vivo and in vitro. however, the factors that govern adaptation of f. tularensis to the intrahepatocytic niche have not been identified. using cdna microarrays, we determined the transcriptional profile of the live vaccine strain (lvs) of f. tularensis grown in the fl83b murine hepatocytic cell line compared to that of f. tularensis cultured in broth. the fslc gene of the fsl operon was th ... | 2013 | 23716605 |
| a crispr/cas system mediates bacterial innate immune evasion and virulence. | crispr/cas (clustered regularly interspaced palindromic repeats/crispr-associated) systems are a bacterial defence against invading foreign nucleic acids derived from bacteriophages or exogenous plasmids. these systems use an array of small crispr rnas (crrnas) consisting of repetitive sequences flanking unique spacers to recognize their targets, and conserved cas proteins to mediate target degradation. recent studies have suggested that these systems may have broader functions in bacterial phys ... | 2013 | 23584588 |
| the tracrrna and cas9 families of type ii crispr-cas immunity systems. | crispr-cas is a rapidly evolving rna-mediated adaptive immune system that protects bacteria and archaea against mobile genetic elements. the system relies on the activity of short mature crispr rnas (crrnas) that guide cas protein(s) to silence invading nucleic acids. a set of crispr-cas, type ii, requires a trans-activating small rna, tracrrna, for maturation of precursor crrna (pre-crrna) and interference with invading sequences. following co-processing of tracrrna and pre-crrna by rnase iii, ... | 2013 | 23563642 |
| nuclease activity of legionella pneumophila cas2 promotes intracellular infection of amoebal host cells. | legionella pneumophila, the primary agent of legionnaires' disease, flourishes in both natural and man-made environments by growing in a wide variety of aquatic amoebae. recently, we determined that the cas2 protein of l. pneumophila promotes intracellular infection of acanthamoeba castellanii and hartmannella vermiformis, the two amoebae most commonly linked to cases of disease. the cas2 family of proteins is best known for its role in the bacterial and archeal clustered regularly interspaced s ... | 2014 | 25547789 |
| nuclease activity of legionella pneumophila cas2 promotes intracellular infection of amoebal host cells. | legionella pneumophila, the primary agent of legionnaires' disease, flourishes in both natural and man-made environments by growing in a wide variety of aquatic amoebae. recently, we determined that the cas2 protein of l. pneumophila promotes intracellular infection of acanthamoeba castellanii and hartmannella vermiformis, the two amoebae most commonly linked to cases of disease. the cas2 family of proteins is best known for its role in the bacterial and archeal clustered regularly interspaced s ... | 2014 | 25547789 |
| transcriptional regulation of bacterial virulence gene expression by molecular oxygen and nitric oxide. | molecular oxygen (o2) and nitric oxide (no) are diatomic gases that play major roles in infection. the host innate immune system generates reactive oxygen species and no as bacteriocidal agents and both require o2 for their production. furthermore, the ability to adapt to changes in o2 availability is crucial for many bacterial pathogens, as many niches within a host are hypoxic. pathogenic bacteria have evolved transcriptional regulatory systems that perceive these gases and respond by reprogra ... | 2014 | 25603427 |
| systems biology perspectives on minimal and simpler cells. | the concept of the minimal cell has fascinated scientists for a long time, from both fundamental and applied points of view. this broad concept encompasses extreme reductions of genomes, the last universal common ancestor (luca), the creation of semiartificial cells, and the design of protocells and chassis cells. here we review these different areas of research and identify common and complementary aspects of each one. we focus on systems biology, a discipline that is greatly facilitating the c ... | 2014 | 25184563 |
| motif depletion in bacteriophages infecting hosts with crispr systems. | crispr is a microbial immune system likely to be involved in host-parasite coevolution. it functions using target sequences encoded by the bacterial genome, which interfere with invading nucleic acids using a homology-dependent system. the system also requires protospacer associated motifs (pams), short motifs close to the target sequence that are required for interference in crispr types i and ii. here, we investigate whether pams are depleted in phage genomes due to selection pressure to escap ... | 2014 | 25103210 |
| protein localization analysis of essential genes in prokaryotes. | essential genes, those critical for the survival of an organism under certain conditions, play a significant role in pharmaceutics and synthetic biology. knowledge of protein localization is invaluable for understanding their function as well as the interaction of different proteins. however, systematical examination of essential genes from the aspect of the localizations of proteins they encode has not been explored before. here, a comprehensive protein localization analysis of essential genes ... | 2014 | 25105358 |
| nild crispr rna contributes to xenorhabdus nematophila colonization of symbiotic host nematodes. | the bacterium xenorhabdus nematophila is a mutualist of entomopathogenic steinernema carpocapsae nematodes and facilitates infection of insect hosts. x. nematophila colonizes the intestine of s. carpocapsae which carries it between insects. in the x. nematophila colonization-defective mutant nild6::tn5, the transposon is inserted in a region lacking obvious coding potential. we demonstrate that the transposon disrupts expression of a single crispr rna, nild rna. a variant nild rna also is expres ... | 2014 | 25041533 |
| a crispr-cas system enhances envelope integrity mediating antibiotic resistance and inflammasome evasion. | clustered, regularly interspaced, short palindromic repeats-crispr associated (crispr-cas) systems defend bacteria against foreign nucleic acids, such as during bacteriophage infection and transformation, processes which cause envelope stress. it is unclear if these machineries enhance membrane integrity to combat this stress. here, we show that the cas9-dependent crispr-cas system of the intracellular bacterial pathogen francisella novicida is involved in enhancing envelope integrity through th ... | 2014 | 25024199 |
| classification and evolution of type ii crispr-cas systems. | the crispr-cas systems of archaeal and bacterial adaptive immunity are classified into three types that differ by the repertoires of crispr-associated (cas) genes, the organization of cas operons and the structure of repeats in the crispr arrays. the simplest among the crispr-cas systems is type ii in which the endonuclease activities required for the interference with foreign deoxyribonucleic acid (dna) are concentrated in a single multidomain protein, cas9, and are guided by a co-processed dua ... | 2014 | 24728998 |
| crispr-cas systems: new players in gene regulation and bacterial physiology. | crispr-cas systems are bacterial defenses against foreign nucleic acids derived from bacteriophages, plasmids or other sources. these systems are targeted in an rna-dependent, sequence-specific manner, and are also adaptive, providing protection against previously encountered foreign elements. in addition to their canonical function in defense against foreign nucleic acid, their roles in various aspects of bacterial physiology are now being uncovered. we recently revealed a role for a cas9-based ... | 2014 | 24772391 |
| association of clustered regularly interspaced short palindromic repeat (crispr) elements with specific serotypes and virulence potential of shiga toxin-producing escherichia coli. | shiga toxin-producing escherichia coli (stec) strains (n = 194) representing 43 serotypes and e. coli k-12 were examined for clustered regularly interspaced short palindromic repeat (crispr) arrays to study genetic relatedness among stec serotypes. a subset of the strains (n = 81) was further analyzed for subtype i-e cas and virulence genes to determine a possible association of crispr elements with potential virulence. four types of crispr arrays were identified. crispr1 and crispr2 were presen ... | 2014 | 24334663 |
| polyphosphate kinases modulate campylobacter jejuni outer membrane constituents and alter its capacity to invade and survive in intestinal epithelial cells in vitro. | campylobacter jejuni is the most prevalent cause of bacterial gastroenteritis worldwide. polyphosphate kinases 1 and 2 (ppk1 and ppk2) regulate several cellular processes, including the biosynthesis of the bacterial cell wall. despite their importance, whether ppk1 and ppk2 modulate the composition of c. jejuni outer membrane constituents (omcs) and consequently impact its interaction with host cells remains unknown. our comparative analysis between c. jejuni wild type, δppk1, and δppk2 strains ... | 2015 | 26714783 |
| statistical analysis of hurst exponents of essential/nonessential genes in 33 bacterial genomes. | methods for identifying essential genes currently depend predominantly on biochemical experiments. however, there is demand for improved computational methods for determining gene essentiality. in this study, we used the hurst exponent, a characteristic parameter to describe long-range correlation in dna, and analyzed its distribution in 33 bacterial genomes. in most genomes (31 out of 33) the significance levels of the hurst exponents of the essential genes were significantly higher than for th ... | 2015 | 26067107 |
| clustered regularly interspaced short palindromic repeat-dependent, biofilm-specific death of pseudomonas aeruginosa mediated by increased expression of phage-related genes. | the clustered regularly interspaced short palindromic repeat (crispr)/crispr-associated (crispr/cas) system is an adaptive immune system present in many archaea and bacteria. crispr/cas systems are incredibly diverse, and there is increasing evidence of crispr/cas systems playing a role in cellular functions distinct from phage immunity. previously, our laboratory reported one such alternate function in which the type 1-f crispr/cas system of the opportunistic pathogen pseudomonas aeruginosa str ... | 2015 | 25968642 |
| crispr-cas: biology, mechanisms and relevance. | prokaryotes have evolved several defence mechanisms to protect themselves from viral predators. clustered regularly interspaced short palindromic repeats (crispr) and their associated proteins (cas) display a prokaryotic adaptive immune system that memorizes previous infections by integrating short sequences of invading genomes-termed spacers-into the crispr locus. the spacers interspaced with repeats are expressed as small guide crispr rnas (crrnas) that are employed by cas proteins to target i ... | 2016 | 27672148 |
| survival and evolution of crispr-cas system in prokaryotes and its applications. | prokaryotes have developed numerous innate immune mechanisms in order to fend off bacteriophage or plasmid attack. one of these immune systems is clustered regularly interspaced short palindromic repeats (crispr). crispr-associated proteins play a key role in survival of prokaryotes against invaders, as these systems cleave dna of foreign genetic elements. beyond providing immunity, these systems have significant impact in altering the bacterial physiology in term of its virulence and pathogenic ... | 2016 | 27725818 |
| an approach for predicting essential genes using multiple homology mapping and machine learning algorithms. | investigation of essential genes is significant to comprehend the minimal gene sets of cell and discover potential drug targets. in this study, a novel approach based on multiple homology mapping and machine learning method was introduced to predict essential genes. we focused on 25 bacteria which have characterized essential genes. the predictions yielded the highest area under receiver operating characteristic (roc) curve (auc) of 0.9716 through tenfold cross-validation test. proper features w ... | 2016 | 27660763 |
| drug target identification and prioritization for treatment of ovine foot rot: an in silico approach. | ovine foot rot is an infection of the feet of sheep, mainly caused by dichelobacter nodosus. in its virulent form, it is highly contagious and debilitating, causing significant losses in the form of decline in wool growth and quality and poor fertility. current methods of treatment are ineffective in complete eradication. effective antibiotic treatment of foot rot is hence necessary to ensure better outcomes during control phases by reduction in culling count and the possibility of carriers of t ... | 2016 | 27379247 |
| comparative genomic analysis of mannheimia haemolytica from bovine sources. | bovine respiratory disease is a common health problem in beef production. the primary bacterial agent involved, mannheimia haemolytica, is a target for antimicrobial therapy and at risk for associated antimicrobial resistance development. the role of m. haemolytica in pathogenesis is linked to serotype with serotypes 1 (s1) and 6 (s6) isolated from pneumonic lesions and serotype 2 (s2) found in the upper respiratory tract of healthy animals. here, we sequenced the genomes of 11 strains of m. hae ... | 2016 | 26926339 |
| myxobacteria produce outer membrane-enclosed tubes in unstructured environments. | myxobacteria are social microbes that exhibit complex multicellular behaviors. by use of fluorescent reporters, we show that myxococcus xanthus isolates produce long narrow filaments that are enclosed by the outer membrane (om) and contain proteins. we show that these om tube (omt) structures are produced at surprisingly high levels when cells are placed in liquid medium or buffer without agitation. omts can be long and easily exceed multiple cell lengths. when viewed by transmission electron mi ... | 2014 | 24391054 |
| antimicrobial strategies centered around reactive oxygen species--bactericidal antibiotics, photodynamic therapy, and beyond. | reactive oxygen species (ros) can attack a diverse range of targets to exert antimicrobial activity, which accounts for their versatility in mediating host defense against a broad range of pathogens. most ros are formed by the partial reduction in molecular oxygen. four major ros are recognized comprising superoxide (o2•-), hydrogen peroxide (h2o2), hydroxyl radical (•oh), and singlet oxygen ((1)o2), but they display very different kinetics and levels of activity. the effects of o2•- and h2o2 ar ... | 2013 | 23802986 |
| a crispr with roles in myxococcus xanthus development and exopolysaccharide production. | the gram-negative soil bacterium myxococcus xanthus utilizes its social (s) gliding motility to move on surfaces during its vegetative and developmental cycles. it is known that s motility requires the type iv pilus (t4p) and the exopolysaccharide (eps) to function. the t4p is the s motility motor, and it powers cell movement by retraction. as the key regulator of the s motor, eps is proposed to be the anchor and trigger for t4p retraction. the production of eps is regulated in turn by the t4p i ... | 2014 | 25201946 |
| a subset of the diverse cog0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life. | cog0523 proteins are, like the nickel chaperones of the ureg family, part of the g3e family of gtpases linking them to metallocenter biosynthesis. even though the first cog0523-encoding gene, cobw, was identified almost 20 years ago, little is known concerning the function of other members belonging to this ubiquitous family. | 2009 | 19822009 |
| transcriptome of dickeya dadantii infecting acyrthosiphon pisum reveals a strong defense against antimicrobial peptides. | the plant pathogenic bacterium dickeya dadantii has recently been shown to be able to kill the aphid acyrthosiphon pisum. while the factors required to cause plant disease are now well characterized, those required for insect pathogeny remain mostly unknown. to identify these factors, we analyzed the transcriptome of the bacteria isolated from infected aphids. more than 150 genes were upregulated and 300 downregulated more than 5-fold at 3 days post infection. no homologue to known toxin genes c ... | 2013 | 23342088 |
| temperature-sensitive salmonella enterica serovar enteritidis pt13a expressing essential proteins of psychrophilic bacteria. | synthetic genes based on deduced amino acid sequences of the nad-dependent dna ligase (liga) and ctp synthetase (pyrg) of psychrophilic bacteria were substituted for their native homologues in the genome of salmonella enterica serovar enteritidis phage type 13a (pt13a). the resulting strains were rendered temperature sensitive (ts) and did not revert to temperature resistance at a detectable level. at permissive temperatures, ts strains grew like the parental strain in broth medium and in macrop ... | 2015 | 26187965 |
| temperature sensitivity conferred by liga alleles from psychrophilic bacteria upon substitution in mesophilic bacteria and a yeast species. | we have assembled a collection of 13 psychrophilic liga alleles that can serve as genetic elements for engineering mesophiles to a temperature-sensitive (ts) phenotype. when these liga alleles were substituted into francisella novicida, they conferred a ts phenotype with restrictive temperatures between 33 and 39°c. when the f. novicida liga hybrid strains were plated above their restrictive temperatures, eight of them generated temperature-resistant variants. for two alleles, the mutations that ... | 2016 | 26773080 |
| tetr-based gene regulation systems for francisella tularensis. | there are a number of genetic tools available for studying francisella tularensis, the etiological agent of tularemia; however, there is no effective inducible or repressible gene expression system. here, we describe inducible and repressible gene expression systems for f. tularensis based on the tet repressor, tetr. for the inducible system, a tet operator sequence was cloned into a modified f. tularensis groesl promoter sequence and carried in a plasmid that constitutively expressed tetr. to m ... | 2012 | 22820330 |