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Cell Oct 2015The microbial adaptive immune system CRISPR mediates defense against foreign genetic elements through two classes of RNA-guided nuclease effectors. Class 1 effectors...
The microbial adaptive immune system CRISPR mediates defense against foreign genetic elements through two classes of RNA-guided nuclease effectors. Class 1 effectors utilize multi-protein complexes, whereas class 2 effectors rely on single-component effector proteins such as the well-characterized Cas9. Here, we report characterization of Cpf1, a putative class 2 CRISPR effector. We demonstrate that Cpf1 mediates robust DNA interference with features distinct from Cas9. Cpf1 is a single RNA-guided endonuclease lacking tracrRNA, and it utilizes a T-rich protospacer-adjacent motif. Moreover, Cpf1 cleaves DNA via a staggered DNA double-stranded break. Out of 16 Cpf1-family proteins, we identified two candidate enzymes from Acidaminococcus and Lachnospiraceae, with efficient genome-editing activity in human cells. Identifying this mechanism of interference broadens our understanding of CRISPR-Cas systems and advances their genome editing applications.
Topics: Amino Acid Sequence; CRISPR-Cas Systems; Endonucleases; Francisella; Genetic Engineering; HEK293 Cells; Humans; Molecular Sequence Data; Nucleic Acid Conformation; RNA, Guide, CRISPR-Cas Systems; Sequence Alignment
PubMed: 26422227
DOI: 10.1016/j.cell.2015.09.038 -
Molecular Cell Feb 2019CRISPR-Cas12a (Cpf1) is an RNA-guided DNA-cutting nuclease that has been repurposed for genome editing. Upon target DNA binding, Cas12a cleaves both the target DNA in...
CRISPR-Cas12a (Cpf1) is an RNA-guided DNA-cutting nuclease that has been repurposed for genome editing. Upon target DNA binding, Cas12a cleaves both the target DNA in cis and non-target single-stranded DNAs (ssDNAs) in trans. To elucidate the molecular basis for both DNase cleavage modes, we performed structural and biochemical studies on Francisella novicida Cas12a. We show that guide RNA-target strand DNA hybridization conformationally activates Cas12a, triggering its trans-acting, non-specific, single-stranded DNase activity. In turn, cis cleavage of double-stranded DNA targets is a result of protospacer adjacent motif (PAM)-dependent DNA duplex unwinding, electrostatic stabilization of the displaced non-target DNA strand, and ordered sequential cleavage of the non-target and target DNA strands. Cas12a releases the PAM-distal DNA cleavage product and remains bound to the PAM-proximal DNA cleavage product in a catalytically competent, trans-active state. Together, these results provide a revised model for the molecular mechanisms of both the cis- and the trans-acting DNase activities of Cas12a enzymes, enabling their further exploitation as genome editing tools.
Topics: Bacterial Proteins; CRISPR-Associated Proteins; CRISPR-Cas Systems; DNA, Single-Stranded; Enzyme Activation; Francisella; Gene Editing; Models, Molecular; Nucleic Acid Conformation; Protein Conformation; RNA, Guide, CRISPR-Cas Systems; Structure-Activity Relationship; Substrate Specificity
PubMed: 30639240
DOI: 10.1016/j.molcel.2018.11.021 -
Clinical Microbiology Reviews Oct 2002Francisella tularensis is the etiological agent of tularemia, a serious and occasionally fatal disease of humans and animals. In humans, ulceroglandular tularemia is the... (Review)
Review
Francisella tularensis is the etiological agent of tularemia, a serious and occasionally fatal disease of humans and animals. In humans, ulceroglandular tularemia is the most common form of the disease and is usually a consequence of a bite from an arthropod vector which has previously fed on an infected animal. The pneumonic form of the disease occurs rarely but is the likely form of the disease should this bacterium be used as a bioterrorism agent. The diagnosis of disease is not straightforward. F. tularensis is difficult to culture, and the handling of this bacterium poses a significant risk of infection to laboratory personnel. Enzyme-linked immunosorbent assay- and PCR-based methods have been used to detect bacteria in clinical samples, but these methods have not been adequately evaluated for the diagnosis of pneumonic tularemia. Little is known about the virulence mechanisms of F. tularensis, though there is a large body of evidence indicating that it is an intracellular pathogen, surviving mainly in macrophages. An unlicensed live attenuated vaccine is available, which does appear to offer protection against ulceroglandular and pneumonic tularemia. Although an improved vaccine against tularemia is highly desirable, attempts to devise such a vaccine have been limited by the inability to construct defined allelic replacement mutants and by the lack of information on the mechanisms of virulence of F. tularensis. In the absence of a licensed vaccine, aminoglycoside antibiotics play a key role in the prevention and treatment of tularemia.
Topics: Animals; Bacterial Vaccines; Disease Models, Animal; Francisella tularensis; Gene Expression Regulation, Bacterial; Humans; Tularemia; Virulence
PubMed: 12364373
DOI: 10.1128/CMR.15.4.631-646.2002 -
Frontiers in Cellular and Infection... 2019Bacteria alter gene expression in response to changes in their environment through various mechanisms that include signal transduction systems. These signal transduction... (Review)
Review
Bacteria alter gene expression in response to changes in their environment through various mechanisms that include signal transduction systems. These signal transduction systems use membrane histidine kinase with sensing domains to mediate phosphotransfer to DNA-binding proteins that alter the level of gene expression. Such regulators are called two-component systems (TCSs). TCSs integrate external signals and information from stress pathways, central metabolism and other global regulators, thus playing an important role as part of the overall regulatory network. This review will focus on the knowledge of TCSs in the Gram-negative bacterium, , a biothreat agent with a wide range of potential hosts and a significant ability to cause disease. While TCSs have been well-studied in several bacterial pathogens, they have not been well-studied in non-model organisms, such as and its subspecies, whose canonical TCS content surprisingly ranges from few to none. Additionally, of those TCS genes present, many are orphan components, including KdpDE, QseC, QseB/PmrA, and an unnamed two-component system (FTN_1452/FTN_1453). We discuss recent advances in this field related to the role of TCSs in physiology and pathogenesis and compare the TCS genes present in human virulent versus. environmental species and subspecies of .
Topics: Animals; Bacterial Proteins; DNA-Binding Proteins; Francisella tularensis; Gene Expression Regulation, Bacterial; Histidine Kinase; Humans; Protein Domains; Signal Transduction; Tularemia; Virulence
PubMed: 31263682
DOI: 10.3389/fcimb.2019.00198 -
Emerging Microbes & Infections 2019is a Gram-negative, intracellular bacterium causing the zoonosis tularemia. This highly infectious microorganism is considered a potential biological threat agent.... (Review)
Review
is a Gram-negative, intracellular bacterium causing the zoonosis tularemia. This highly infectious microorganism is considered a potential biological threat agent. Humans are usually infected through direct contact with the animal reservoir and tick bites. However, tularemia cases also occur after contact with a contaminated hydro-telluric environment. Water-borne tularemia outbreaks and sporadic cases have occurred worldwide in the last decades, with specific clinical and epidemiological traits. These infections represent a major public health and military challenge. Human contaminations have occurred through consumption or use of -contaminated water, and various aquatic activities such as swimming, canyoning and fishing. In addition, in Sweden and Finland, mosquitoes are primary vectors of tularemia due to infection of mosquito larvae in contaminated aquatic environments. The mechanisms of survival in water may include the formation of biofilms, interactions with free-living amoebae, and the transition to a 'viable but nonculturable' state, but the relative contribution of these possible mechanisms remains unknown. Many new aquatic species of have been characterized in recent years. likely shares with these species an ability of long-term survival in the aquatic environment, which has to be considered in terms of tularemia surveillance and control.
Topics: Animals; Culicidae; Francisella tularensis; Humans; Tularemia; Waterborne Diseases; Zoonoses
PubMed: 31287787
DOI: 10.1080/22221751.2019.1638734 -
Frontiers in Cellular and Infection... 2022is an obligate hematophagous parasitic arthropod that is responsible for the transmission of a wide range of zoonotic pathogens including spirochetes of the genus... (Review)
Review
is an obligate hematophagous parasitic arthropod that is responsible for the transmission of a wide range of zoonotic pathogens including spirochetes of the genus spp., , and , which are part the tick´s microbiome. Most of the studies focus on "pathogens" and only very few elucidate the role of "non-pathogenic" symbiotic microorganisms in . While most of the members of the microbiome are leading an intracellular lifestyle, they are able to complement tick´s nutrition and stress response having a great impact on tick´s survival and transmission of pathogens. The composition of the tick´s microbiome is not consistent and can be tied to the environment, tick species, developmental stage, or specific organ or tissue. Ovarian tissue harbors a stable microbiome consisting mainly but not exclusively of endosymbiotic bacteria, while the microbiome of the digestive system is rather unstable, and together with salivary glands, is mostly comprised of pathogens. The most prevalent endosymbionts found in ticks are spp., spp., -like and -like endosymbionts, spp. and Midichloria spp. Since microorganisms can modify ticks' behavior, such as mobility, feeding or saliva production, which results in increased survival rates, we aimed to elucidate the potential, tight relationship, and interaction between bacteria of the microbiome. Here we show that endosymbionts including -like spp., can provide with different types of vitamin B (B2, B6, B7, B9) essential for eukaryotic organisms. Furthermore, we hypothesize that survival of spp., or the bacterial pathogen can be supported by the tick itself since coinfection with symbiotic provides with complete metabolic pathway of folate biosynthesis necessary for DNA synthesis and cell division. Manipulation of tick´s endosymbiotic microbiome could present a perspective way of control and regulation of spread of emerging bacterial pathogens.
Topics: Animals; Ixodes; Microbiota; Coxiella; Symbiosis; Rickettsia; Francisella tularensis
PubMed: 36467722
DOI: 10.3389/fcimb.2022.990889 -
PloS One 2022Francisella tularensis, the bacterium that causes the zoonosis tularemia, and its genetic near neighbor species, can be difficult or impossible to cultivate from complex...
Francisella tularensis, the bacterium that causes the zoonosis tularemia, and its genetic near neighbor species, can be difficult or impossible to cultivate from complex samples. Thus, there is a lack of genomic information for these species that has, among other things, limited the development of robust detection assays for F. tularensis that are both specific and sensitive. The objective of this study was to develop and validate approaches to capture, enrich, sequence, and analyze Francisella DNA present in DNA extracts generated from complex samples. RNA capture probes were designed based upon the known pan genome of F. tularensis and other diverse species in the family Francisellaceae. Probes that targeted genomic regions also present in non-Francisellaceae species were excluded, and probes specific to particular Francisella species or phylogenetic clades were identified. The capture-enrichment system was then applied to diverse, complex DNA extracts containing low-level Francisella DNA, including human clinical tularemia samples, environmental samples (i.e., animal tissue and air filters), and whole ticks/tick cell lines, which was followed by sequencing of the enriched samples. Analysis of the resulting data facilitated rigorous and unambiguous confirmation of the detection of F. tularensis or other Francisella species in complex samples, identification of mixtures of different Francisella species in the same sample, analysis of gene content (e.g., known virulence and antimicrobial resistance loci), and high-resolution whole genome-based genotyping. The benefits of this capture-enrichment system include: even very low target DNA can be amplified; it is culture-independent, reducing exposure for research and/or clinical personnel and allowing genomic information to be obtained from samples that do not yield isolates; and the resulting comprehensive data not only provide robust means to confirm the presence of a target species in a sample, but also can provide data useful for source attribution, which is important from a genomic epidemiology perspective.
Topics: Animals; Anti-Infective Agents; DNA, Bacterial; Francisella tularensis; Genomics; Humans; Phylogeny; RNA; Tularemia
PubMed: 36223396
DOI: 10.1371/journal.pone.0273273 -
Frontiers in Cellular and Infection... 2017, the causative agent of tularemia, is a Gram-negative bacterium that infects a variety of cell types including macrophages, and propagates with great efficiency in the... (Review)
Review
, the causative agent of tularemia, is a Gram-negative bacterium that infects a variety of cell types including macrophages, and propagates with great efficiency in the cytoplasm. Iron, essential for key enzymatic and redox reactions, is among the nutrients required to support this pathogenic lifestyle and the bacterium relies on specialized mechanisms to acquire iron within the host environment. Two distinct pathways for iron acquisition are encoded by the genome- a siderophore-dependent ferric iron uptake system and a ferrous iron transport system. Genes of the Fur-regulated operon direct the production and transport of the siderophore rhizoferrin. Siderophore biosynthesis involves enzymes FslA and FslC, while export across the inner membrane is mediated by FslB. Uptake of the rhizoferrin- ferric iron complex is effected by the siderophore receptor FslE in the outer membrane in a TonB-independent process, and FslD is responsible for uptake across the inner membrane. Ferrous iron uptake relies largely on high affinity transport by FupA in the outer membrane, while the Fur-regulated FeoB protein mediates transport across the inner membrane. FslE and FupA are paralogous proteins, sharing sequence similarity and possibly sharing structural features as well. This review summarizes current knowledge of iron acquisition in this organism and the critical role of these uptake systems in bacterial pathogenicity.
Topics: Animals; Biological Transport; Disease Models, Animal; Ferric Compounds; Ferrous Compounds; Francisella tularensis; Humans; Iron; Metabolic Networks and Pathways; Virulence
PubMed: 28421167
DOI: 10.3389/fcimb.2017.00107 -
Veterinary Research 2005Francisella tularensis is a gram-negative coccobacillus and the etiologic agent of the zoonotic disease tularemia. First described in 1911 in Tulare County, California,... (Review)
Review
Francisella tularensis is a gram-negative coccobacillus and the etiologic agent of the zoonotic disease tularemia. First described in 1911 in Tulare County, California, it has since been reported throughout the Northern Hemisphere, with natural infections reported among an unusually wide range of vertebrates and invertebrates. In recent years, tularemia has emerged in new geographic locations, populations, and settings. This review will serve to highlight mechanisms contributing to the recent emergence of tularemia as well as a repertoire of diagnostic tools useful for detecting and diagnosing disease.
Topics: Animals; Communicable Diseases, Emerging; Disease Outbreaks; Francisella tularensis; Global Health; Humans; Tularemia
PubMed: 15845234
DOI: 10.1051/vetres:2005006 -
Frontiers in Cellular and Infection... 2018Tularemia is a zoonotic disease caused by the facultative intracellular bacterium . This microorganism can infect a plethora of animal species and its ecology is... (Review)
Review
Tularemia is a zoonotic disease caused by the facultative intracellular bacterium . This microorganism can infect a plethora of animal species and its ecology is particularly complex. Much research was performed to understand its biology but many questions are still open, especially concerning the life cycle of this bacterium in the environment related to physical and biological parameters. Numerous animals are major hosts of but precise reservoir species are not yet well defined. Moreover, the exact range of species susceptible to tularemia is not clear and is complicated by the differences in virulence and ecology observed among the subspecies of . Indeed, different life cycles in nature, including the animal species concerned, were previously described for subsp. and subsp. . Recently, molecular techniques showing adequate discrimination between strains were developed, leading to the possibility to investigate links between phylogenetic lineages and infection in animals. New perspectives in research are now possible thanks to the information available and the simplicity of the molecular procedures. Current studies are unfolding the evolution of and these developments will lead to the elucidation of geographical and ecological differences observed by veterinarians, microbiologists and conservation biologists. However, systematic, coordinated collection of data and extensive sampling are important to efficiently assemble the findings of future research.
Topics: Animals; Francisella tularensis; Phylogeny; Tularemia
PubMed: 30109216
DOI: 10.3389/fcimb.2018.00258