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Role of a Stem-Loop Structure in Transcript Stability.
Loh JT, Lin AS, Beckett AC, McClain MS, Cover TL
(2019) Infect Immun 87:
MeSH Terms: Antigens, Bacterial, Bacterial Proteins, DNA, Bacterial, Helicobacter Infections, Helicobacter pylori, Humans, Mutagenesis, Site-Directed, RNA Stability, RNA, Messenger
Show Abstract · Added February 7, 2019
CagA is a secreted effector protein that contributes to gastric carcinogenesis. Previous studies showed that there is variation among strains in the steady-state levels of CagA and that a strain-specific motif downstream of the transcriptional start site (the +59 motif) is associated with both high levels of CagA and premalignant gastric histology. The 5' untranslated region contains a predicted stem-loop-forming structure adjacent to the +59 motif. In the current study, we investigated the effect of the +59 motif and the adjacent stem-loop on transcript levels and mRNA stability. Using site-directed mutagenesis, we found that mutations predicted to disrupt the stem-loop structure resulted in decreased steady-state levels of both the transcript and the CagA protein. Additionally, these mutations resulted in a decreased mRNA half-life. Mutagenesis of the +59 motif without altering the stem-loop structure resulted in reduced steady-state transcript and CagA protein levels but did not affect transcript stability. transcript stability was not affected by increased sodium chloride concentrations, an environmental factor known to augment transcript levels and CagA protein levels. These results indicate that both a predicted stem-loop structure and a strain-specific +59 motif in the 5' untranslated region influence the levels of expression.
Copyright © 2019 American Society for Microbiology.
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9 MeSH Terms
Amycomicin is a potent and specific antibiotic discovered with a targeted interaction screen.
Pishchany G, Mevers E, Ndousse-Fetter S, Horvath DJ, Paludo CR, Silva-Junior EA, Koren S, Skaar EP, Clardy J, Kolter R
(2018) Proc Natl Acad Sci U S A 115: 10124-10129
MeSH Terms: Anthraquinones, Anti-Bacterial Agents, DNA, Bacterial, DNA, Ribosomal, Microbial Sensitivity Tests, RNA, Ribosomal, 16S, Streptomyces coelicolor
Show Abstract · Added April 7, 2019
The rapid emergence of antibiotic-resistant pathogenic bacteria has accelerated the search for new antibiotics. Many clinically used antibacterials were discovered through culturing a single microbial species under nutrient-rich conditions, but in the environment, bacteria constantly encounter poor nutrient conditions and interact with neighboring microbial species. In an effort to recapitulate this environment, we generated a nine-strain actinomycete community and used 16S rDNA sequencing to deconvolute the stochastic production of antimicrobial activity that was not observed from any of the axenic cultures. We subsequently simplified the community to just two strains and identified sp. AA4 as the producing strain and M145 as an inducing strain. Bioassay-guided isolation identified amycomicin (AMY), a highly modified fatty acid containing an epoxide isonitrile warhead as a potent and specific inhibitor of Amycomicin targets an essential enzyme (FabH) in fatty acid biosynthesis and reduces infection in a mouse skin-infection model. The discovery of AMY demonstrates the utility of screening complex communities against specific targets to discover small-molecule antibiotics.
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MeSH Terms
Bacterial DNA is present in the fetal intestine and overlaps with that in the placenta in mice.
Martinez KA, Romano-Keeler J, Zackular JP, Moore DJ, Brucker RM, Hooper C, Meng S, Brown N, Mallal S, Reese J, Aronoff DM, Shin H, Dominguez-Bello MG, Weitkamp JH
(2018) PLoS One 13: e0197439
MeSH Terms: Amniotic Fluid, Animals, DNA, Bacterial, Female, Intestinal Mucosa, Intestines, Mice, Placenta, Pregnancy, RNA, Ribosomal, 16S, Vagina
Show Abstract · Added May 18, 2018
Bacterial DNA has been reported in the placenta and amniotic fluid by several independent groups of investigators. However, it's taxonomic overlap with fetal and maternal bacterial DNA in different sites has been poorly characterized. Here, we determined the presence of bacterial DNA in the intestines and placentas of fetal mice at gestational day 17 (n = 13). These were compared to newborn intestines (n = 15), maternal sites (mouth, n = 6; vagina, n = 6; colon, n = 7; feces, n = 8), and negative controls to rule out contamination. The V4 region of the bacterial 16S rRNA gene indicated a pattern of bacterial DNA in fetal intestine similar to placenta but with higher phylogenetic diversity than placenta or newborn intestine. Firmicutes were the most frequently assignable phylum. SourceTracker analysis suggested the placenta as the most commonly identifiable origin for fetal bacterial DNA, but also over 75% of fetal gut genera overlapped with maternal oral and vaginal taxa but not with maternal or newborn feces. These data provide evidence for the presence of bacterial DNA in the mouse fetus.
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11 MeSH Terms
Structure of a DNA glycosylase that unhooks interstrand cross-links.
Mullins EA, Warren GM, Bradley NP, Eichman BF
(2017) Proc Natl Acad Sci U S A 114: 4400-4405
MeSH Terms: Anti-Bacterial Agents, Bacterial Proteins, DNA Glycosylases, DNA, Bacterial, Gene Expression Regulation, Bacterial, Gene Expression Regulation, Enzymologic, Models, Molecular, Mutation, Naphthalenes, Peptides, Protein Binding, Protein Conformation, Protein Folding, Streptomyces
Show Abstract · Added August 26, 2019
DNA glycosylases are important editing enzymes that protect genomic stability by excising chemically modified nucleobases that alter normal DNA metabolism. These enzymes have been known only to initiate base excision repair of small adducts by extrusion from the DNA helix. However, recent reports have described both vertebrate and microbial DNA glycosylases capable of unhooking highly toxic interstrand cross-links (ICLs) and bulky minor groove adducts normally recognized by Fanconi anemia and nucleotide excision repair machinery, although the mechanisms of these activities are unknown. Here we report the crystal structure of AlkZ (previously Orf1), a bacterial DNA glycosylase that protects its host by excising ICLs derived from azinomycin B (AZB), a potent antimicrobial and antitumor genotoxin. AlkZ adopts a unique fold in which three tandem winged helix-turn-helix motifs scaffold a positively charged concave surface perfectly shaped for duplex DNA. Through mutational analysis, we identified two glutamine residues and a β-hairpin within this putative DNA-binding cleft that are essential for catalytic activity. Additionally, we present a molecular docking model for how this active site can unhook either or both sides of an AZB ICL, providing a basis for understanding the mechanisms of base excision repair of ICLs. Given the prevalence of this protein fold in pathogenic bacteria, this work also lays the foundation for an emerging role of DNA repair in bacteria-host pathogenesis.
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DNA Transfer and Toll-like Receptor Modulation by Helicobacter pylori.
Varga MG, Peek RM
(2017) Curr Top Microbiol Immunol 400: 169-193
MeSH Terms: Animals, DNA, Bacterial, Gastric Mucosa, Helicobacter Infections, Helicobacter pylori, Humans, Toll-Like Receptors
Show Abstract · Added April 6, 2017
Helicobacter pylori is the most common bacterial infection worldwide, and virtually all infected persons develop co-existing gastritis. H. pylori is able to send and receive signals from the gastric mucosa, which enables both host and microbe to engage in a dynamic equilibrium. In order to persist within the human host, H. pylori has adopted dichotomous strategies to both induce inflammation as a means of liberating nutrients while simultaneously tempering the immune response to augment its survival. Toll-like receptors (TLRs) and Nod proteins are innate immune receptors that are present in epithelial cells and represent the first line of defense against pathogens. To ensure persistence, H. pylori manipulates TLR-mediated defenses using strategies that include rendering its LPS and flagellin to be non-stimulatory to TLR4 and TLR5, respectively; translocating peptidoglycan into host cells to induce NOD1-mediated anti-inflammatory responses; and translocating DNA into host cells to induce TLR9 activation.
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7 MeSH Terms
A Catalytic Role for C-H/π Interactions in Base Excision Repair by Bacillus cereus DNA Glycosylase AlkD.
Parsons ZD, Bland JM, Mullins EA, Eichman BF
(2016) J Am Chem Soc 138: 11485-8
MeSH Terms: Bacillus cereus, Biocatalysis, DNA Glycosylases, DNA Repair, DNA, Bacterial
Show Abstract · Added April 7, 2017
DNA glycosylases protect genomic integrity by locating and excising aberrant nucleobases. Substrate recognition and excision usually take place in an extrahelical conformation, which is often stabilized by π-stacking interactions between the lesion nucleobase and aromatic side chains in the glycosylase active site. Bacillus cereus AlkD is the only DNA glycosylase known to catalyze base excision without extruding the damaged nucleotide from the DNA helix. Instead of contacting the nucleobase itself, the AlkD active site interacts with the lesion deoxyribose through a series of C-H/π interactions. These interactions are ubiquitous in protein structures, but evidence for their catalytic significance in enzymology is lacking. Here, we show that the C-H/π interactions between AlkD and the lesion deoxyribose participate in catalysis of glycosidic bond cleavage. This is the first demonstration of a catalytic role for C-H/π interactions as intermolecular forces important to DNA repair.
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5 MeSH Terms
Pathogenic Helicobacter pylori strains translocate DNA and activate TLR9 via the cancer-associated cag type IV secretion system.
Varga MG, Shaffer CL, Sierra JC, Suarez G, Piazuelo MB, Whitaker ME, Romero-Gallo J, Krishna US, Delgado A, Gomez MA, Good JA, Almqvist F, Skaar EP, Correa P, Wilson KT, Hadjifrangiskou M, Peek RM
(2016) Oncogene 35: 6262-6269
MeSH Terms: Bacterial Proteins, Biological Transport, Carcinogenesis, DNA, Bacterial, Helicobacter Infections, Helicobacter pylori, Humans, Mutation, Stomach Neoplasms, Toll-Like Receptor 9, Type IV Secretion Systems
Show Abstract · Added May 15, 2016
Helicobacter pylori (H. pylori) is the strongest identified risk factor for gastric cancer, the third most common cause of cancer-related death worldwide. An H. pylori constituent that augments cancer risk is the strain-specific cag pathogenicity island, which encodes a type IV secretion system (T4SS) that translocates a pro-inflammatory and oncogenic protein, CagA, into epithelial cells. However, the majority of persons colonized with CagA H. pylori strains do not develop cancer, suggesting that other microbial effectors also have a role in carcinogenesis. Toll-like receptor 9 (TLR9) is an endosome bound, innate immune receptor that detects and responds to hypo-methylated CpG DNA motifs that are most commonly found in microbial genomes. High-expression tlr9 polymorphisms have been linked to the development of premalignant lesions in the stomach. We now demonstrate that levels of H. pylori-mediated TLR9 activation and expression are directly related to gastric cancer risk in human populations. Mechanistically, we show for the first time that the H. pylori cancer-associated cag T4SS is required for TLR9 activation and that H. pylori DNA is actively translocated by the cag T4SS to engage this host receptor. Activation of TLR9 occurs through a contact-dependent mechanism between pathogen and host, and involves transfer of microbial DNA that is both protected as well as exposed during transport. These results indicate that TLR9 activation via the cag island may modify the risk for malignancy within the context of H. pylori infection and provide an important framework for future studies investigating the microbial-epithelial interface in gastric carcinogenesis.
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11 MeSH Terms
Molecular Analysis of Sarcoidosis Granulomas Reveals Antimicrobial Targets.
Rotsinger JE, Celada LJ, Polosukhin VV, Atkinson JB, Drake WP
(2016) Am J Respir Cell Mol Biol 55: 128-34
MeSH Terms: Adolescent, Adult, Aged, Anti-Infective Agents, Case-Control Studies, DNA, Bacterial, Demography, Female, Granuloma, Humans, In Situ Hybridization, Male, Middle Aged, Molecular Targeted Therapy, Mycobacterium, Real-Time Polymerase Chain Reaction, Sarcoidosis, Young Adult
Show Abstract · Added February 4, 2016
Sarcoidosis is a granulomatous disease of unknown cause. Prior molecular and immunologic studies have confirmed the presence of mycobacterial virulence factors, such as catalase peroxidase and superoxide dismutase A, within sarcoidosis granulomas. Molecular analysis of granulomas can identify targets of known antibiotics classes. Currently, major antibiotics are directed against DNA synthesis, protein synthesis, and cell wall formation. We conducted molecular analysis of 40 sarcoidosis diagnostic specimens and compared them with 33 disease control specimens for the presence of mycobacterial genes that encode antibiotic targets. We assessed for genes involved in DNA synthesis (DNA gyrase A [gyrA] and DNA gyrase B), protein synthesis (RNA polymerase subunit β), cell wall synthesis (embCAB operon and enoyl reductase), and catalase peroxidase. Immunohistochemical analysis was conducted to investigate the locale of mycobacterial genes such as gyrA within 12 sarcoidosis specimens and 12 disease controls. Mycobacterial DNA was detected in 33 of 39 sarcoidosis specimens by quantitative real-time polymerase chain reaction compared with 2 of 30 disease control specimens (P < 0.001, two-tailed Fisher's test). Twenty of 39 were positive for three or more mycobacterial genes, compared with 1 of 30 control specimens (P < 0.001, two-tailed Fisher's test). Immunohistochemistry analysis localized mycobacterial gyrA nucleic acids to sites of granuloma formation in 9 of 12 sarcoidosis specimens compared with 1 of 12 disease controls (P < 0.01). Microbial genes encoding enzymes that can be targeted by currently available antimycobacterial antibiotics are present in sarcoidosis specimens and localize to sites of granulomatous inflammation. Use of antimicrobials directed against target enzymes may be an innovative treatment alternative.
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18 MeSH Terms
The nucleoid-associated protein HU enhances 8-oxoguanine base excision by the formamidopyrimidine-DNA glycosylase.
Le Meur R, Culard F, Nadan V, Goffinont S, Coste F, Guerin M, Loth K, Landon C, Castaing B
(2015) Biochem J 471: 13-23
MeSH Terms: DNA Breaks, Double-Stranded, DNA Repair, DNA, Bacterial, DNA-Binding Proteins, DNA-Formamidopyrimidine Glycosylase, Escherichia coli, Escherichia coli Proteins, Guanine
Show Abstract · Added January 11, 2016
The nucleoid-associated protein HU is involved in numerous DNA transactions and thus is essential in DNA maintenance and bacterial survival. The high affinity of HU for SSBs (single-strand breaks) has suggested its involvement in DNA protection, repair and recombination. SSB-containing DNA are major intermediates transiently generated by bifunctional DNA N-glycosylases that initiate the BER (base excision repair) pathway. Enzyme kinetics and DNA-binding experiments demonstrate that HU enhances the 8-oxoguanine-DNA glycosylase activity of Fpg (formamidopyrimidine-DNA glycosylase) by facilitating the release of the enzyme from its final DNA product (one nucleoside gap). We propose that the displacement of Fpg from its end-DNA product by HU is an active mechanism in which HU recognizes the product when it is still bound by Fpg. Through DNA binding, the two proteins interplay to form a transient ternary complex Fpg/DNA/HU which results in the release of Fpg and the molecular entrapment of SSBs by HU. These results support the involvement of HU in BER in vivo.
© 2015 Authors; published by Portland Press Limited.
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8 MeSH Terms
Facilitated diffusion framework for transcription factor search with conformational changes.
Cartailler J, Reingruber J
(2015) Phys Biol 12: 046012
MeSH Terms: DNA, DNA, Bacterial, Escherichia coli, Facilitated Diffusion, Lac Repressors, Models, Genetic, Nucleic Acid Conformation, Promoter Regions, Genetic, Protein Conformation, Transcription Factors
Show Abstract · Added May 16, 2017
Cellular responses often require the fast activation or repression of specific genes, which depends on transcription factors (TFs) that have to quickly find the promoters of these genes within a large genome. TFs search for their DNA promoter target by alternating between bulk diffusion and sliding along the DNA, a mechanism known as facilitated diffusion. We study a facilitated diffusion framework with switching between three search modes: a bulk mode and two sliding modes triggered by conformational changes between two protein conformations. In one conformation (search mode) the TF interacts unspecifically with the DNA backbone resulting in fast sliding. In the other conformation (recognition mode) it interacts specifically and strongly with DNA base pairs leading to slow displacement. From the bulk, a TF associates with the DNA at a random position that is correlated with the previous dissociation point, which implicitly is a function of the DNA structure. The target affinity depends on the conformation. We derive exact expressions for the mean first passage time (MFPT) to bind to the promoter and the conditional probability to bind before detaching when arriving at the promoter site. We systematically explore the parameter space and compare various search scenarios. We compare our results with experimental data for the dimeric Lac repressor search in E. coli bacteria. We find that a coiled DNA conformation is absolutely necessary for a fast MFPT. With frequent spontaneous conformational changes, a fast search time is achieved even when a TF becomes immobilized in the recognition state due to the specific bindings. We find a MFPT compatible with experimental data in presence of a specific TF-DNA interaction energy that has a Gaussian distribution with a large variance.
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10 MeSH Terms