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Schully KL, Young CC, Mayo M, Connolly AL, Rigas V, Spall A, Chan AA, Salvador MG, Lawler JV, Opdyke JA, Clark DV, Currie BJ. Next-generation Diagnostics for Melioidosis: Evaluation of a Prototype i-STAT Cartridge to Detect Burkholderia pseudomallei Biomarkers. Clin Infect Dis 2020; 69:421-427. [PMID: 30403768 DOI: 10.1093/cid/ciy929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/29/2018] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Infection with the gram-negative bacterium Burkholderia pseudomallei can result in melioidosis, a life-threatening disease that can be difficult to diagnose. Culture remains the gold standard for diagnosis but requires laboratory resources not available in many endemic regions. A lateral flow immunoassay has shown promise for POC diagnostics but suffers from low sensitivity when used on blood samples. PCR also has low sensitivity on blood, attributed to the low bacterial numbers in blood observed in melioidosis patients, even when bacteraemic. METHODS A prototype i-STAT cartridge was developed to utilize the monoclonal antibody specific for the capsule of pathogenic Burkholderia species employed on the LFI. The resulting POC assay was evaluated on 414 clinical specimens from Darwin, Australia and Cambodia. RESULTS The i-STAT assay accurately distinguished Australian blood culture positive melioidosis patients from Australian patients hospitalized with other infections (AUC = 0.91, 95% CI 0.817 - 1.0). We derived an assay cutoff with 76% sensitivity and 94% specificity that correctly classified 88% (n = 74) of the Australian patients. Interestingly, only 46% (6/13) of the culture-positive melioidosis patients in Cambodia were classified correctly. Of great importance however, the assay detected capsule from blood samples for 32% of blood culture negative melioidosis patients in both cohorts and previously undiagnosed melioidosis patients in Cambodia. In addition the assay showed high sensitivity and specificity for urine, pus and sputum. CONCLUSIONS Diagnostic tools that are not dependent upon the growth kinetics or the levels of bacteremia of B. pseudomallei represent the next-generation of diagnostics and must be pursued further.
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Affiliation(s)
- Kevin L Schully
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Ft. Detrick
| | - Charles C Young
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia
| | - Amy L Connolly
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland
| | - Vanessa Rigas
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia
| | - Ammarah Spall
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Ft. Detrick
| | - Alyssa A Chan
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Ft. Detrick
| | - Mark G Salvador
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Ft. Detrick
| | - James V Lawler
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Ft. Detrick
| | - Jason A Opdyke
- Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense, Medical Countermeasure Systems, Ft. Detrick, Maryland
| | - Danielle V Clark
- Austere Environments Consortium for Enhanced Sepsis Outcomes, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Ft. Detrick
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia.,Department of Infectious Diseases and Northern Territory Medical Program, Royal Darwin Hospital, Australia
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Opdyke JA, Fozo EM, Hemm MR, Storz G. RNase III participates in GadY-dependent cleavage of the gadX-gadW mRNA. J Mol Biol 2010; 406:29-43. [PMID: 21147125 DOI: 10.1016/j.jmb.2010.12.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2010] [Revised: 12/02/2010] [Accepted: 12/03/2010] [Indexed: 10/18/2022]
Abstract
The adjacent gadX and gadW genes encode transcription regulators that are part of a complex regulatory circuit controlling the Escherichia coli response to acid stress. We previously showed that the small RNA GadY positively regulates gadX mRNA levels. The gadY gene is located directly downstream of the gadX coding sequence on the opposite strand of the chromosome. We now report that gadX is transcribed in an operon with gadW, although this full-length mRNA does not accumulate. Base pairing of the GadY small RNA with the intergenic region of the gadX-gadW mRNA results in directed processing events within the region of complementarity. The resulting two halves of the cleaved mRNA accumulate to much higher levels than the unprocessed mRNA. We examined the ribonucleases required for this processing, and found that multiple enzymes are involved in the GadY-directed cleavage including the double-strand RNA-specific endoribonuclease RNase III.
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Affiliation(s)
- Jason A Opdyke
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and HumanDevelopment, Bethesda, MD 20892, USA
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Storz G, Opdyke JA, Fozo EM, Waters LS, Kawano M, Zhang A. Varied functions of small, non‐coding RNAs in bacteria. FASEB J 2008. [DOI: 10.1096/fasebj.22.1_supplement.97.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Gisela Storz
- Cell Biology and Metabolism BranchNICHDNIHBethesdaMD
| | | | | | | | - Mitsuoki Kawano
- Cell Biology and Metabolism BranchNICHDNIHBethesdaMD
- Genome Exploration Research GroupRIKEN Yokohama InstituteKanagawaJapan
| | - Aixia Zhang
- Cell Biology and Metabolism BranchNICHDNIHBethesdaMD
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Abstract
In recent years, the combinations of computational and molecular approaches have led to the identification of an increasing number of small, noncoding RNAs encoded by bacteria and their plasmids and phages. Most of the characterized small RNAs have been shown to operate at a posttranscriptional level, modulating mRNA stability or translation by base-pairing with the 5' regions of the target mRNAs. However, a subset of small RNAs has been found to regulate transcription. One example is the abundant 6S RNA that has been proposed to compete for DNA binding of RNA polymerase by mimicking the open conformation of promoter DNA. Other small RNAs affect transcription termination via base-pairing interactions with sequences in the mRNA. Here, we discuss current understanding and questions regarding the roles of small RNAs in regulating transcription.
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Affiliation(s)
- G Storz
- Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, Bethesda, Maryland 20892-5430, USA
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Wang X, Mukhopadhyay P, Wood MJ, Outten FW, Opdyke JA, Storz G. Mutational analysis to define an activating region on the redox-sensitive transcriptional regulator OxyR. J Bacteriol 2006; 188:8335-42. [PMID: 17012382 PMCID: PMC1698235 DOI: 10.1128/jb.01318-06] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The OxyR transcription factor is a key regulator of the Escherichia coli response to oxidative stress. Previous studies showed that OxyR binding to a target promoter enhances RNA polymerase binding and vice versa, suggesting a direct interaction between OxyR and RNA polymerase. To identify the region of OxyR that might contact RNA polymerase, we carried out alanine scanning and random mutagenesis of oxyR. The combination of these approaches led to the identification of several mutants defective in the activation of an OxyR target gene. A subset of the mutations map to the DNA-binding domain, other mutations appear to affect dimerization of the regulatory domain, while another group is suggested to affect disulfide bond formation. The two mutations, D142A and R273H, giving the most dramatic phenotype are located in a patch on the surface of the oxidized OxyR protein and possibly define an activating region on OxyR.
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Affiliation(s)
- Xunde Wang
- Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892-5430, USA
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Abstract
Many small, noncoding RNAs in bacteria act as post-transcriptional regulators by basepairing with target mRNAs. While the number of characterized small RNAs (sRNAs) has steadily increased, only a limited number of the corresponding mRNA targets have been identified. Here we present a program, TargetRNA, that predicts the targets of these bacterial RNA regulators. The program was evaluated by assessing whether previously known targets could be identified. The program was then used to predict targets for the Escherichia coli RNAs RyhB, OmrA, OmrB and OxyS, and the predictions were compared with changes in whole genome expression patterns observed upon expression of the sRNAs. Our results show that TargetRNA is a useful tool for finding mRNA targets of sRNAs, although its rate of success varies between sRNAs.
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Affiliation(s)
- Brian Tjaden
- Computer Science Department, Wellesley College, Wellesley, MA 02481, USA.
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Abstract
A previous bioinformatics-based search for small RNAs in Escherichia coli identified a novel RNA named IS183. The gene encoding this small RNA is located between and on the opposite strand of genes encoding two transcriptional regulators of the acid response, gadX (yhiX) and gadW (yhiW). Given that IS183 is encoded in the gad gene cluster and because of its role in regulating acid response genes reported here, this RNA has been renamed GadY. We show that GadY exists in three forms, a long form consisting of 105 nucleotides and two processed forms, consisting of 90 and 59 nucleotides. The expression of this small RNA is highly induced during stationary phase in a manner that is dependent on the alternative sigma factor sigmaS. Overexpression of the three GadY RNA forms resulted in increased levels of the mRNA encoding the GadX transcriptional activator, which in turn caused increased levels of the GadA and GadB glutamate decarboxylases. A promoter mutation which abolished gadY expression resulted in a reduction in the amount of gadX mRNA during stationary phase. The gadY gene was shown to overlap the 3' end of the gadX gene, and this overlap region was found to be necessary for the GadY-dependent accumulation of gadX mRNA. We suggest that during stationary phase, GadY forms base pairs with the 3'-untranslated region of the gadX mRNA and confers increased stability, allowing for gadX mRNA accumulation and the increased expression of downstream acid resistance genes.
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Affiliation(s)
- Jason A Opdyke
- Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Abstract
Recent studies have led to the identification of more than 50 small regulatory RNAs in Escherichia coli. Only a subset of these RNAs has been characterized. However, it is clear that many of the RNAs, such as the MicF, OxyS, DsrA, Spot42 and RyhB RNAs, act by basepairing to activate or repress translation or to destabilize mRNAs. Basepairing between these regulatory RNAs and their target mRNAs requires the Sm-like Hfq protein which most likely functions as an RNA chaperone to increase RNA unfolding or local target RNA concentration. Here we summarize the physiological roles of the basepairing RNAs, examine their prevalence in bacteria and discuss unresolved questions regarding their mechanisms of action.
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Affiliation(s)
- Gisela Storz
- Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-5430, USA.
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Abstract
Secondary RNA polymerase sigma factors in many bacteria are responsible for regulating a vast range of processes including virulence. A protein (sigma(X)) in the gram-positive human pathogen Streptococcus pyogenes (the group A Streptococcus or GAS) was recently shown to function in vitro as a secondary sigma factor. We report here the isolation of a mutant in which both sigX genes are inactivated, show that sigma(X) functions in GAS cells, and show that the amount of sigma(X) is controlled at two levels. Primer extension analysis indicates that sigX transcription is low in GAS cells grown in Todd-Hewitt yeast broth, and immunoblot assays with a sigma(X)-specific polyclonal antibody demonstrate that the protein does not accumulate in these cells. To increase the level of sigX transcription in GAS, we constructed a strain that constitutively expresses the sigX gene from a heterologous promoter. Expression of sigX from this promoter led to transcription of the sigma(X)-dependent cinA promoter in GAS cells. We found that expression of the sigX gene in a clpP mutant strain resulted in greater accumulation of sigma(X) protein, which resulted in higher levels of transcription from the sigma(X)-dependent promoters cinA, smf, and cglA. In addition, a clpP mutant containing sigX only at its wild-type loci on the chromosome generated more transcription from the sigma(X)-dependent cinA promoter than did the wild-type parental strain. Therefore, sigma(X) activity in GAS is limited by low-level transcription of the sigX structural genes and by clpP, which appears to negatively regulate sigma(X) accumulation.
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Affiliation(s)
- Jason A Opdyke
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Abstract
The important human pathogen Streptococcus pyogenes (the group A streptococcus or GAS) causes diseases ranging from mild, self-limiting pharyngitis to severe invasive infections. Regulation of the expression of GAS genes in response to specific environmental differences within the host is probably key in determining the course of the infectious process, however, little is known of global regulators of gene expression in GAS. Although secondary RNA polymerase sigma factors act as global regulators of gene expression in many other bacteria, none has yet been isolated from the GAS. The newly available GAS genome sequence indicates that the only candidate secondary sigma factor is encoded by two identical open reading frames (ORFS). These ORFS encode a protein that is 40% identical to the transcription factor ComX, believed to act as an RNA polymerase sigma factor in Streptococcus pneumoniae. To test whether the GAS ComX homologue functions as a sigma factor, we cloned and purified it from Escherichia coli. We found that in vitro, this GAS protein, which we call sigmaX, directed core RNA polymerase from Bacillus subtilis to transcribe from two GAS promoters that contain the cin-box region, required for transcription by S. pneumoniae ComX in vivo. On the other hand, GAS sigmaX did not promote transcription of a GAS promoter (hasA) expected to be dependent on sigmaA, the housekeeping or primary RNA polymerase sigma factor. Addition of monoclonal antibody that inhibited sigmaA-directed transcription had no effect on sigmaX-directed transcription, showing that the latter was not the result of contaminating sigmaA. Transcription of both cin-box-containing promoters initiated downstream of the cin-box and two different single basepair substitutions in the cin-box of the cinA promoter each caused a severe reduction of sigmaX-directed transcription in vitro. Thus, the cin-box is required for sigmaX-directed transcription.
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Affiliation(s)
- J A Opdyke
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
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Abstract
During endospore formation in Bacillus subtilis, the DNA binding protein GerE stimulates transcription from several promoters that are used by RNA polymerase containing sigmaK. GerE binds to a site on one of these promoters, cotX, that overlaps its -35 region. We tested the model that GerE interacts with sigmaK at the cotX promoter by seeking amino acid substitutions in sigmaK that interfered with GerE-dependent activation of the cotX promoter but which did not affect utilization of the sigmaK-dependent, GerE-independent promoter gerE. We identified two amino acid substitutions in sigmaK, E216K and H225Y, that decrease cotX promoter utilization but do not affect gerE promoter activity. Alanine substitutions at these positions had similar effects. We also examined the effects of the E216A and H225Y substitutions in sigmaK on transcription in vitro. We found that these substitutions specifically reduced utilization of the cotX promoter. These and other results suggest that the amino acid residues at positions 216 and 225 are required for GerE-dependent cotX promoter activity, that the histidine at position 225 of sigmaK may interact with GerE at the cotX promoter, and that this interaction may facilitate the initial binding of sigmaK RNA polymerase to the cotX promoter. We also found that the alanine substitutions at positions 216 and 225 of sigmaK had no effect on utilization of the GerE-dependent promoter cotD, which contains GerE binding sites that do not overlap with its -35 region.
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Affiliation(s)
- K H Wade
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Abstract
Brazilian purpuric fever (BPF)-associated Haemophilus influenzae biogroup aegyptius strain F3031 contains two identical copies of a five gene cluster (hifA to hifE) encoding pili similar to well-characterized Hif fimbriae of H. influenzae type b. HifE, the putative pilus tip adhesin of F3031, shares only 40% amino acid sequence similarity with the same molecule from type b strains, whereas the other four proteins have 75 to 95% identity. To determine whether pilus cluster duplication and the hifE(F3031) allele were special features of BPF-associated bacteria, we analyzed a collection of H. influenzae strains by PCR with hifA- and hifE-specific oligonucleotides, by Southern hybridization with a hifC gene probe, and by nucleotide sequencing. The presence of two pilus clusters was limited to some H. influenzae biogroup aegyptius strains. The hifE(F3031) allele was limited to H. influenzae biogroup aegyptius. Two strains contained one copy of hifE(F3031) and one copy of a variant hifE allele. We determined the nucleotide sequences of four hifE genes from H. influenzae biogroup aegyptius and H. influenzae capsule serotypes a and c. The predicted proteins produced by these genes demonstrated only 35 to 70% identity to the three published HifE proteins from nontypeable H. influenzae, serotype b, and BPF strains. The C-terminal third of the molecules implicated in chaperone binding was the most highly conserved region. Three conserved domains in the otherwise highly variable N-terminal putative receptor-binding region of HifE were similar to conserved portions in the N terminus of Neisseria pilus adhesin PilC. We concluded that two pilus clusters and hifE(F3031) were not specific for BPF-causing H. influenzae, and we also identified portions of HifE possibly involved in binding mammalian cell receptors.
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Affiliation(s)
- T D Read
- Veterans Affairs Medical Center and Department of Medicine, Emory University School of Medicine, Decatur, Georgia 30033, USA
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