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Journal of Bacteriology

Katherine J Fenstermacher, Vasudevan Achuthan, Thomas D Schneider, Jeffrey J DeStefano
DNA polymerases (DNAPs) recognize 3' recessed termini on duplex DNA and carry out nucleotide catalysis. Unlike promoter-specific RNA polymerases (RNAPs), no sequence specificity is required for binding or initiation of catalysis. Despite this, previous results indicate that viral reverse transcriptases bind much more tightly to DNA primers that mimic the polypurine tract. In the current report, primer sequences that bind with high affinity to Taq and Klenow polymerases were identified using a modified Selective Evolution of Ligands by Exponential Enrichment (SELEX) approach...
January 16, 2018: Journal of Bacteriology
Jeong-A Kim, Mi-Ae Lee, You-Chul Jung, Bo-Ram Jang, Kyu-Ho Lee
Septicemia-causing Vibrio vulnificus produces at least three exoproteases, VvpE, VvpS and VvpM, all of which participate in interactions with human cells. Expression of VvpE and VvpS is induced in the stationary phase by multiple transcription factors including Sigma S, SmcR, and cAMP-CRP complex. Distinct roles of VvpM, such as induction of apoptosis, lead us to hypothesize VvpM expression is different from that of the other exoproteases. Its transcription, which was found to be independent of Sigma S, is induced at the early exponential phase and then became negligible upon entry into the stationary phase...
January 16, 2018: Journal of Bacteriology
Tino Krell
Two-component systems (TCS) exist in bacteria and archaea. In contrast to bacterial TCSs little information is available on their archaeal counterparts. In this issue Galperin and coworkers present a bioinformatics analysis of TCS genes from archaeal genome sequences. This study identified different aspects in which bacterial and archaeal TCS mediated signaling differ and forms a sound basis for the experimental design of studies to increase our knowledge on this poorly investigated protein family.
January 16, 2018: Journal of Bacteriology
Alex J McCarthy, Richard A Stabler, Peter W Taylor
Escherichia coli K1 strains are major causative agents of invasive disease of the new born. The age dependency of infection can be reproduced in the neonatal rat. Colonization of the small intestine following oral administration of K1 bacteria leads rapidly to invasion of the blood circulation; bacteria that avoid capture by the mesenteric lymphatic system and evade antibacterial mechanisms in the blood may disseminate to cause organ-specific infections such as meningitis. Some E. coli K1 surface constituents, in particular the polysialic acid capsule, are known to contribute to invasive potential but a comprehensive picture of the factors that determine the fully virulent phenotype has not so far emerged...
January 16, 2018: Journal of Bacteriology
Zhe Lyu, Chau-Wen Chou, Hao Shi, Liangliang Wang, Robel Ghebreab, Dennis Phillips, Yajun Yan, Evert C Duin, William B Whitman
Methyl-coenzyme M reductase (MCR) is a complex enzyme that catalyzes the final step in biological methanogenesis. To better understand its assembly, the recombinant MCR from the thermophile Methanothermococcus okinawensis (rMCRok) was expressed in the mesophile Methanococcus maripaludis The rMCRok was post-translationally modified correctly and contained McrD and the unique nickel tetrapyrrole coenzyme F430 Subunits of the native M. maripaludis (MCRmar) were largely absent, suggesting that the recombinant enzyme was formed by an assembly of co-transcribed subunits...
January 16, 2018: Journal of Bacteriology
Lindsey R Lyman, Eric D Peng, Michael P Schmitt
Corynebacterium diphtheriae utilizes various heme-containing proteins, including hemoglobin (Hb) and the hemoglobin-haptoglobin complex (Hb-Hp), as iron sources during growth in iron-depleted environments. The ability to utilize Hb-Hp as an iron source requires the surface anchored proteins HtaA and either ChtA or ChtC. The ability to bind hemin, Hb and Hb-Hp by each of these C. diphtheriae proteins requires the previously characterized Conserved Region (CR) domain. In this study, we identified an Hb-Hp binding protein, HbpA (38...
January 8, 2018: Journal of Bacteriology
Kurt M Dahlstrom, Alan J Collins, Georgia Doing, Jaclyn N Taroni, Timothy J Gauvin, Casey S Greene, Deborah A Hogan, George A O'Toole
The Pseudomonas fluorescens genome encodes for 50+ proteins predicted to be involved in c-di-GMP signaling. Here, we demonstrate that when tested across 188 nutrients, these enzymes and effectors appear capable of impacting biofilm formation. Transcriptional analysis of network members across ∼50 nutrient conditions indicates that altered gene expression can explain a subset, but not all, of biofilm-formation responses to the nutrients. Additional organization of the network is likely achieved through physical interaction, as determined via probing ∼2000 interactions by bacterial two-hybrid assays...
January 8, 2018: Journal of Bacteriology
Benjamin R Pursley, Michael M Maiden, Meng-Lun Hsieh, Nicolas Fernandez, Geoffrey B Severin, Christopher M Waters
Cyclic di-GMP (c-di-GMP) is a bacterial second messenger molecule that is a key global regulator in Vibrio cholerae, but the molecular mechanisms by which this molecule regulates downstream phenotypes have not been fully characterized. One such regulatory factor that may respond to c-di-GMP is the Vc2 c-di-GMP-binding riboswitch that is hypothesized to control the expression of the downstream putative transcription factor TfoY. Although much is known about the physical and structural properties of the Vc2 riboswitch aptamer, the nature of its expression and function in V...
January 8, 2018: Journal of Bacteriology
Eric Markel, Hollie Dalenberg, Caroline L Monteil, Boris A Vinatzer, Bryan Swingle
Production of bacterial flagella is controlled by a multi-tiered regulatory system that coordinates expression of 40-50 subunits and ordered assembly of these elaborate structures. Flagellar expression is environmentally controlled, presumably to optimize the benefits and liabilities of having these organelles with cell growth and survival. We recently reported a global survey of AlgU-dependent regulation and binding in Pseudomonas syringae pv. tomato DC3000 that included evidence for strong down-regulation of many flagellar and chemotaxis motility genes...
January 8, 2018: Journal of Bacteriology
Sue Zanne Tan, Christopher R Reisch, Kristala L J Prather
Pseudomonas spp. are widely used model organisms in different areas of research. Despite its relevance in many applications, protein depletion tools in this host remain limited. Here, we developed the CRISPR interference system for gene repression in Pseudomonas spp. using the Streptococcus pasteurianus dCas9. We demonstrate a robust and titratable gene depletion system with up to 100-fold repression in β-galactosidase activity in P. aeruginosa and 300-fold repression in pyoverdine production in P. putida This inducible system enables the study of essential genes, as shown by ftsZ depletions in P...
January 8, 2018: Journal of Bacteriology
David J Lemon, Derek A Schutzman, Anthony G Garza
Biofilm-forming bacteria typically deposit a layer of polysaccharide on the surfaces they inhabit; hence, polysaccharide is their immediate environment on such surfaces. Previously, we showed that many biofilm-forming bacteria preferentially spread in the direction of aligned and densely packed polysaccharide fibers in compressed substrates, a behavior we referred to as polymertropism. This arrangement of polysaccharide fibers is likely to be similar to that found in the "slime" trails deposited by many biofilm-forming bacteria and would explain previous observations that bacteria tend to follow these trails of polysaccharide...
January 8, 2018: Journal of Bacteriology
Katherine J Wu, Jenna Zhang, Catherine Baranowski, Vivian Leung, E Hesper Rego, Yasu S Morita, Eric J Rubin, Cara C Boutte
Septation in bacteria requires coordinated regulation of cell wall biosynthesis and hydrolysis enzymes so that new septal cross-wall can be appropriately constructed without compromising the integrity of the existing cell wall. Bacteria with different modes of growth and different types of cell wall require different regulators to mediate cell growth and division processes. Mycobacteria have both a cell wall structure and mode of growth that are distinct from well-studied model organisms and use several different regulatory mechanisms...
January 8, 2018: Journal of Bacteriology
Priyanka Agrawal, Rajagopal Varada, Shivjee Sah, Souvik Bhattacharyya, Umesh Varshney
Bacteria respond to stressful growth conditions through a conserved phenomenon of 'stringent response' mediated by synthesis of stress alarmones, ppGpp or pppGpp [referred to as (p)ppGpp]. The (p)ppGpp synthesis is known to occur by ribosome associated RelA. In addition, a dual function protein SpoT (with both the synthetase and hydrolase activities) maintains (p)ppGpp homeostasis. The presence of (p)ppGpp is also known to contribute to antibiotic resistance in bacteria. Mycobacterium smegmatis possesses Arr, which inactivates rifampicin by its ADP-ribosylation...
January 8, 2018: Journal of Bacteriology
Anna C Hughes, Sundharraman Subramanian, Charles E Dann, Daniel B Kearns
SwrA is the master activator of flagellar biosynthesis in Bacillus subtilis and SwrA activity is restricted by regulatory proteolysis in liquid environments. SwrA is proteolyzed by the LonA protease but requires a proteolytic adaptor protein, SmiA. Here we show that SwrA and SmiA interact directly. To better understand SwrA activity, SwrA was randomly mutagenized and loss-of-function and gain-of-function mutants were localized primarily to the predicted unstructured C-terminal region. Loss-of-function mutations impaired swarming motility and activation from the Pfla-che promoter...
January 8, 2018: Journal of Bacteriology
Amanda K Rudat, Arya Pokhrel, Todd J Green, Michael J Gray
Bacteria synthesize inorganic polyphosphate (polyP) in response to a wide variety of stresses, and production of polyP is essential for stress response and survival in many important pathogens and bacteria used in biotechnological processes. However, surprisingly little is known about the molecular mechanisms that control polyP synthesis. We have therefore developed a novel genetic screen that specifically links growth of Escherichia coli to polyP synthesis, allowing us to isolate mutations leading to enhanced polyP production...
January 8, 2018: Journal of Bacteriology
Martina Trokter, Gabriel Waksman
Bacterial conjugation, a mechanism of horizontal gene transfer, is the major means by which antibiotic resistance spreads among bacteria (1, 2). Conjugative plasmids are transferred from one bacterium to another through a type IV secretion system (T4SS) in a form of single-stranded DNA covalently attached to a protein called relaxase. The relaxase is fully functional both in a donor cell (prior to conjugation) and recipient cell (after conjugation). Here we demonstrate that the protein substrate has to unfold for efficient translocation through the conjugative T4SS...
January 8, 2018: Journal of Bacteriology
Hardik M Zatakia, Timofey D Arapov, Veronika M Meier, Birgit E Scharf
The chemosensory system in Sinorhizobium meliloti has several important deviations from the widely studied enterobacterial paradigm. To better understand the differences between the two systems and how they are optimally tuned, we determined the cellular stoichiometry of the methyl-accepting chemotaxis proteins (MCPs) and the histidine kinase CheA in S. meliloti Quantitative immunoblotting was used to determine the total amount of MCPs and CheA per cell in S. meliloti The MCPs are present in the cell in high abundance (McpV), low abundance (IcpA, McpU, McpX, and McpW), and very low abundance (McpY and McpZ), whereas McpT was below detection limit...
December 20, 2017: Journal of Bacteriology
Michael Y Galperin, Kira S Makarova, Yuri I Wolf, Eugene V Koonin
The two-component signal transduction (TCS) machinery is a key mechanism of sensing environmental changes in the prokaryotic world. The TCS systems have been thoroughly characterized in bacteria but to a much lesser extent, in archaea. Here, we provide an updated census of more than 2,000 histidine kinases and response regulators encoded in 218 complete archaeal genomes as well as unfinished genomes available from metagenomic data. We describe the domain architectures of the archaeal TCS components, including several novel output domains, and discuss the evolution of the archaeal TCS machinery...
December 20, 2017: Journal of Bacteriology
Samvel A Nazaretyan, Neda Savic, Michael Sadek, Brandy J Hackert, Justin Courcelle, Charmain T Courcelle
In both prokaryotes and eukaryotes, hydroxyurea is suggested to inhibit DNA replication by inactivating ribonucleotide reductase and depleting deoxyribonucleoside triphosphate pools. In this study, we show that the inhibition of replication in Escherichia coli is transient even at concentrations of 0.1 M hydroxyurea and that replication rapidly recovers and continues in its presence. The recovery of replication does not require the alternative ribonucleotide reductases, NrdEF and NrdDG, or translesion DNA polymerases, Pol II, Pol IV, or Pol V...
December 20, 2017: Journal of Bacteriology
Manisha Vaish, Alexa Price-Whelan, Tamara Reyes-Robles, Jun Liu, Amyeo Jereen, Stephanie Christie, Francis Alonzo, Meredith A Benson, Victor J Torres, Terry A Krulwich
Staphylococcus aureus has three types of cation/proton antiporters. The type three family includes two multi-subunit Na+/H+ (Mnh) antiporters, Mnh1 and Mnh2. These antiporters are clusters of seven hydrophobic membrane bound protein subunits. Mnh antiporters play important roles in maintaining cytoplasmic pH in prokaryotes, enabling their survival under extreme environmental stress. In this study, we investigated the physiological roles and catalytic properties of Mnh1 and Mnh2 in S. aureus Both Mnh1 and Mnh2 were cloned separately into a pGEM3Z+ vector in the antiporter deficient KNabc E...
December 20, 2017: Journal of Bacteriology
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