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Liis Andresen, Erik Holmqvist
RNA-protein interactions are at the heart of many central cellular processes, and RNA-binding proteins (RBPs) associate with virtually all RNA molecules in a cell. In bacteria, global RBPs, often in conjunction with small regulatory RNAs, affect physiology and virulence by controlling transcription, translation, and RNA decay. To understand how these regulatory proteins orchestrate global gene expression, detailed maps of their cellular RNA binding sites are required. To this end, cross-linking and immunoprecipitation followed by deep sequencing (CLIP-seq) has revolutionized RBP studies by providing knowledge about global recognition patterns of RBPs in both eukaryotic and bacterial cells...
2018: Methods in Enzymology
Naoto F Ishikawa, Yu Itahashi, Thomas M Blattmann, Yoshinori Takano, Nanako O Ogawa, Masako Yamane, Yusuke Yokoyama, Toshi Nagata, Minoru Yoneda, Negar Haghipour, Timothy I Eglinton, Naohiko Ohkouchi
We have improved a method for isolation and purification of individual amino acids for compound-specific radiocarbon analysis (CSRA). To remove high-performance liquid chromatography (HPLC) eluent blanks from isolated amino acid fractions prior to the radiocarbon (Δ14 C) measurement, each fraction was filtered through a membrane filter and then washed with diethyl ether twice. Radiocarbon measurements on standard amino acids processed and purified with the above method using elemental analyzer-accelerator mass spectrometry resulted in Δ14 C values that were in strong agreement ( R2 = 0...
October 1, 2018: Analytical Chemistry
Binru Yin, Lixian Zhu, Yimin Zhang, Pengcheng Dong, Yanwei Mao, Rongrong Liang, Lebao Niu, Xin Luo
The biofilm formation behavior of Salmonella isolated from beef processing plants was investigated under varying temperatures (4°C, 10°C, 25°C, 37°C, and 42°C) and pH (4.5, 5.0, 5.5, 6.0, 7.0, and 8.0). The relationships between the presence of biofilm-related genes and the biofilm formation capacity were evaluated. A total of 77 Salmonella strains in 8 different serotypes were assessed: Salmonella Agona (n = 43), Salmonella Senftenberg (n = 13), Salmonella Meleagridis (n = 8), Salmonella Derby (n = 7), Salmonella Kottbus (n = 2), Salmonella Calabar (n = 2), Salmonella Kingston (n = 1), and Salmonella Typhimurium (n = 1)...
September 8, 2018: Foodborne Pathogens and Disease
William K Arnold, Christina R Savage, Kathryn G Lethbridge, Trever C Smith, Catherine A Brissette, Janakiram Seshu, Brian Stevenson
Borrelia burgdorferi, the causative agent of Lyme disease, survives in nature through a cycle that alternates between ticks and vertebrates. To facilitate this defined lifestyle, B. burgdorferi has evolved a gene regulatory network that ensures transmission between those hosts, along with specific adaptations to niches within each host. Several regulatory proteins are known to be essential for the bacterium to complete these critical tasks, but interactions between regulators had not previously been investigated in detail, due to experimental uses of different strain backgrounds and growth conditions...
2018: PloS One
Jiaqi Li, Connor J Gulbronson, Marek Bogacz, David R Hendrixson, Stuart A Thompson
Campylobacter jejuni is an important human pathogen that causes 96 million cases of acute diarrheal disease worldwide each year. We have shown that C. jejuni CsrA is involved in the post-transcriptional regulation of more than 100 proteins, and altered expression of these proteins is presumably involved in the altered virulence-related phenotypes of a csrA mutant. Mutation of fliW results in C. jejuni cells that have greatly truncated flagella, are less motile, less able to form biofilms, and exhibit a reduced ability to colonize chicks...
August 16, 2018: Microbiology
Yaron S Feldheim, Tal Zusman, Anya Kapach, Gil Segal
The intracellular pathogen Legionella pneumophila translocates more than 300 effector proteins into host cells during infection. The PmrAB two-component system (TCS) has been shown to activate the expression of a large pool of these effector-encoding genes (EEGs) and the LetAS TCS, as part of the LetAS-RsmYZ-CsrA cascade, has been shown to repress the expression of another pool of EEGs. We identified a single-domain response regulator (SDRR), named LerC, which functions as a connector protein between the PmrAB and the LetAS TCSs...
August 13, 2018: Molecular Microbiology
Lara M Stepleman, Jiby Yohannan, Samantha M Scott, Lauren L Titus, Joan Walker, Eliot J Lopez, Lauren Wooten Smith, Alexis L Rossi, Thomas M Toomey, Elizabeth D Eldridge
The 2016 Municipal Equality Index rated Augusta, the largest city in the Central Savannah River Area (CSRA), as one of the least lesbian, gay, bisexual, and transgender (LGBT) friendly cities in America. To understand the context of our region in relation to LGBT wellness, we conducted the first LGBT health needs assessment of the CSRA, assessing physical and mental health status and health care needs and experiences in the community. Participants (N = 436) were recruited using venue and snowball sampling and completed an anonymous online survey...
August 10, 2018: Journal of Homosexuality
Rebecca B Stone, Yunmi Chung, Benjamin E Ansa
There has been an alarming resurgence of early syphilis since 2000, especially in the southeast region, which has one of the highest rates of primary and secondary syphilis in the United States of America (USA). Although the Central Savannah River Area (CSRA) is the second most populous area in Georgia with a large presence of health care facilities, its counties have one of the lowest overall rankings in health outcomes. This study examined the syphilis rates and trends in the CSRA. Data from the Centers for Disease Control and Prevention (CDC) National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention's AtlasPlus was used...
July 31, 2018: Journal of Clinical Medicine
Leidy Patricia Bedoya-Pérez, Luis Felipe Muriel-Millán, Soledad Moreno, Elva Quiroz-Rocha, Nancy Rivera-Gómez, Guadalupe Espín
In bacteria, the 5'-end-dependent RNA degradation is triggered by the RNA pyrophosphohydrolase RppH converting tri/diphosphate to monophosphate transcripts. This study shows that in the soil bacterium Azotobacter vinelandii, inactivation of rppH gene negatively affected the production of bioplastic poly-β-hydroxybutyrate (PHB) by reducing the expression at the translational level of PhbR, the specific transcriptional activator of the phbBAC biosynthetic operon. The effect of RppH on the translation of phbR seemed to be exerted through the translational repressor RsmA, as the inactivation of rsmA in the rppH mutant restored the phbR expression...
September 2018: Microbiological Research
A N Leistra, G Gelderman, S W Sowa, A Moon-Walker, H M Salis, L M Contreras
Bacterial global post-transcriptional regulators execute hundreds of interactions with targets that display varying molecular features while retaining specificity. Herein, we develop, validate, and apply a biophysical, statistical thermodynamic model of canonical target mRNA interactions with the CsrA global post-transcriptional regulator to understand the molecular features that contribute to target regulation. Altogether, we model interactions of CsrA with a pool of 236 mRNA: 107 are experimentally regulated by CsrA and 129 are suspected interaction partners...
July 2, 2018: Scientific Reports
Kayley H Janssen, Manisha R Diaz, Cindy J Gode, Matthew C Wolfgang, Timothy L Yahr
The Gram-negative opportunistic pathogen Pseudomonas aeruginosa has distinct genetic programs that favor either acute or chronic virulence gene expression. Acute virulence is associated with twitching and swimming motility, expression of a type III secretion system (T3SS), and the absence of alginate, Psl, or Pel polysaccharide production. Traits associated with chronic infection include growth as a biofilm, reduced motility, and expression of a type VI secretion system (T6SS). The Rsm posttranscriptional regulatory system plays important roles in the inverse control of phenotypes associated with acute and chronic virulence...
August 15, 2018: Journal of Bacteriology
Huawei Gu, Haonan Qi, Shuyi Chen, Kan Shi, Haiying Wang, Jufang Wang
The carbon storage regulator CsrA is a global regulator that controls multiple virulence-associated processes including host cell invasion, virulence secretion, quorum sensing, biofilm formation, and motility in many pathogenic bacteria. However, the roles of CsrA in Clostridium difficile still remain unclear. In this study, a C. difficile strain overexpressing csrA was constructed to investigate its effects on multiple virulence associated processes. Overexpression of csrA resulted in flagella defect and poor motility in C...
August 2018: Microbial Pathogenesis
B Z Cvetković, G Salazar, D Kunz, S Szidat, E Wieland
The combination of ion chromatography (IC) with accelerator mass spectrometry (AMS) was developed to determine the speciation of 14C-(radiocarbon) bearing organic compounds in the femto to pico molar concentration range. The development of this compound-specific radiocarbon analysis (CSRA) of carboxylic acids is reported and the application of the method on a leaching solution from neutron-irradiated steel is demonstrated. The background and the dynamic range of the AMS-based method were quantified. On using 14C-labelled standards, the measurements demonstrate the repeatability of the analytical method and the reproducible recovery of the main target carboxylic acids (i...
June 25, 2018: Analyst
Erik Holmqvist, Lei Li, Thorsten Bischler, Lars Barquist, Jörg Vogel
The conserved RNA-binding protein ProQ has emerged as the centerpiece of a previously unknown third large network of post-transcriptional control in enterobacteria. Here, we have used in vivo UV crosslinking and RNA sequencing (CLIP-seq) to map hundreds of ProQ binding sites in Salmonella enterica and Escherichia coli. Our analysis of these binding sites, many of which are conserved, suggests that ProQ recognizes its cellular targets through RNA structural motifs found in small RNAs (sRNAs) and at the 3' end of mRNAs...
June 7, 2018: Molecular Cell
Anthony C Otigbu, Anna M Clarke, Justine Fri, Emmanuel O Akanbi, Henry A Njom
Campylobacter jejuni (CJ) is a zoonotic microbe and a major causative organism of diarrheal infection in humans that often has its functional characteristics inactivated in stressed conditions. The current study assessed the correlation between recovered CJ and water quality parameters and the drug sensitivity patterns of the pathogen to frontline antibiotics in human and veterinary medicine. Water samples ( n = 244) from rivers/estuarines were collected from April⁻September 2016, and physicochemical conditions were recorded on-site...
May 6, 2018: International Journal of Environmental Research and Public Health
Alexandra Götz, Matthias Lechner, Andreas Mader, Benedikt von Bronk, Erwin Frey, Madeleine Opitz
The bacterial SOS response is a cellular reaction to DNA damage, that, among other actions, triggers the expression of colicin - toxic bacteriocins in Escherichia coli that are released to kill close relatives competing for resources. However, it is largely unknown, how the complex network regulating toxin expression controls the time-point of toxin release to prevent premature release of inefficient protein concentrations. Here, we study how different regulatory mechanisms affect production and release of the bacteriocin ColicinE2 in Escherichia coli...
April 25, 2018: Scientific Reports
Anastasia H Potts, Yuanyuan Leng, Paul Babitzke, Tony Romeo
The Csr global regulatory system coordinates gene expression in response to metabolic status. This system utilizes the RNA binding protein CsrA to regulate gene expression by binding to transcripts of structural and regulatory genes, thus affecting their structure, stability, translation, and/or transcription elongation. CsrA activity is controlled by sRNAs, CsrB and CsrC, which sequester CsrA away from other transcripts. CsrB/C levels are partly determined by their rates of turnover, which requires CsrD to render them susceptible to RNase E cleavage...
March 29, 2018: Scientific Reports
Svetlana Durica-Mitic, Yvonne Göpel, Boris Görke
Survival of bacteria in ever-changing habitats with fluctuating nutrient supplies requires rapid adaptation of their metabolic capabilities. To this end, carbohydrate metabolism is governed by complex regulatory networks including posttranscriptional mechanisms that involve small regulatory RNAs (sRNAs) and RNA-binding proteins. sRNAs limit the response to substrate availability and set the threshold or time required for induction and repression of carbohydrate utilization systems. Carbon catabolite repression (CCR) also involves sRNAs...
March 2018: Microbiology Spectrum
Tony Romeo, Paul Babitzke
The sequence-specific RNA binding protein CsrA is employed by diverse bacteria in the posttranscriptional regulation of gene expression. Its binding interactions with RNA have been documented at atomic resolution and shown to alter RNA secondary structure, RNA stability, translation, and/or Rho-mediated transcription termination through a growing number of molecular mechanisms. In Gammaproteobacteria , small regulatory RNAs (sRNAs) that contain multiple CsrA binding sites compete with mRNA for binding to CsrA, thereby sequestering and antagonizing this protein...
March 2018: Microbiology Spectrum
Fei Ye, Fanli Yang, Ruijie Yu, Xi Lin, Jianxun Qi, Zhujun Chen, Yu Cao, Yuquan Wei, George F Gao, Guangwen Lu
The T3SS chaperone CesT is recently shown to interact with the post-transcriptional regulator CsrA to modulate post-attachment signaling in enteropathogenic and enterohemorrhagic Escherichia coli. The molecular basis of the CesT/CsrA binding, however, remains elusive. Here, we show that CesT and CsrA both created two ligand binding sites in their homodimers, forming irregular multimeric complexes in solution. Through construction of a recombinant CsrA-dimer (Re-CsrA) that contains a single CesT binding site, the atomic binding features between CesT and CsrA are delineated via the structure of the CesT/Re-CsrA complex...
March 22, 2018: Nature Communications
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