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Journal of Bacteriology

Tyler Boone, Adam Driks
Despite over a century of research into the mystery of bacterial spore dormancy and germination, a key question remains unresolved: is protein synthesis required for germination? The development of more sophisticated techniques for assessing and preventing protein synthesis has renewed interest in this long-standing question in recent years. In this issue of Journal of Bacteriology, Korza et al address this with a novel approach. We discuss their results in the context of recently published data.
October 10, 2016: Journal of Bacteriology
Matthew A Richards, Thomas J Lie, Juan Zhang, Stephen W Ragsdale, John A Leigh, Nathan D Price
: Hydrogenotrophic methanogenesis occurs in multiple environments ranging from the intestinal tracts of animals to anaerobic sediments and hot springs. Energy conservation in hydrogenotrophic methanogens was long a mystery; only within the last decade, it was reported that net energy conservation for growth depends on electron bifurcation. In this work we focus on Methanococcus maripaludis, a well-studied hydrogenotrophic marine methanogen. To better understand hydrogenotrophic methanogenesis and compare it with methylotrophic methanogenesis that utilizes oxidative phosphorylation rather than electron bifurcation, we have built iMR539, a genome scale metabolic reconstruction that accounts for 539 of the 1722 protein-coding genes of M...
October 10, 2016: Journal of Bacteriology
Josué Flores-Kim, Andrew J Darwin
: The Phage shock protein (Psp) system is a widely conserved cell envelope stress response that is essential for the virulence of some bacteria, including Yersinia enterocolitica Recruitment of PspA by the inner membrane PspB•PspC complex characterizes the activated state of this response. The PspB•PspC complex has been proposed to be a stress-responsive switch, changing from an OFF to an ON state in response to an inducing stimulus. In the OFF state, PspA cannot access its binding site in the C-terminal cytoplasmic domain of PspC (PspC(CT)) because this site is bound to PspB...
October 3, 2016: Journal of Bacteriology
Laurel D Wright, Alan D Grossman
: Integrative and conjugative elements (ICEs), also known as conjugative transposons, are self-transferable elements that are widely distributed among bacterial phyla and are important drivers of horizontal gene transfer. Many ICEs carry genes that confer antibiotic resistances to their host cells and are involved in the dissemination of these resistance genes. ICEs reside in host chromosomes, but under certain conditions can excise to form a plasmid that is typically the substrate for transfer...
October 3, 2016: Journal of Bacteriology
Susanne Müller, Sarah N Strack, Sarah E Ryan, Mary Shawgo, Abigail Walling, Susanna Harris, Chris Chambers, Jennifer Boddicker, John R Kirby
: Soil bacteria engage each other in competitive and cooperative ways to determine their microenvironments. In this study we report the identification of a large number of genes required for Myxococcus xanthus to engage Bacillus subtilis in a predator-prey relationship. We generated and tested over 6000 individual transposon insertion mutants of M. xanthus and found many new factors required to promote efficient predation, including the specialized metabolite myxoprincomide, an ATP-binding cassette (ABC) transporter permease and a CRISPR locus encoding bacterial immunity...
October 3, 2016: Journal of Bacteriology
James P R Connolly, Andrew J Roe
: We recently discovered that exposure of enterohaemorrhagic Escherichia coli (EHEC) to D-serine resulted in accumulation of this unusual amino acid, induction of the SOS regulon and downregulation of type III secretion that is essential for efficient colonization of the host. Here, we have investigated the physiological relevance of this elevated SOS response, which is of particular interest given the presence of Stx-toxin carrying lysogenic prophages on the EHEC chromosome that are activated during the SOS response...
October 3, 2016: Journal of Bacteriology
Víctor M Ayala-García, Luz I Valenzuela-García, Peter Setlow, Mario Pedraza-Reyes
: Aag from B. subtilis has been implicated in in vitro removal of hypoxanthine and alkylated bases from DNA. The regulation of expression of aag in B. subtilis, and the resistance to genotoxic agents and mutagenic properties of an Aag-deficient strain were studied here. A strain with a transcriptional aag-lacZ fusion expressed low levels of β-galactosidase during growth and early sporulation but exhibited increased transcription during late stages of this developmental process. Notably, aag-lacZ expression was higher inside the forespore than in the mother cell compartment and this expression was abolished in a sigG-deficient background suggesting a forespore-specific mechanism of aag transcription...
October 3, 2016: Journal of Bacteriology
David A Hufnagel, Margery L Evans, Sarah E Greene, Jerry S Pinkner, Scott J Hultgren, Matthew R Chapman
The extracellular matrix protects Escherichia coli from immune cells, oxidative stress, predation, and other environmental stresses. Production of the E. coli extracellular matrix is regulated by transcription factors that are tuned to environmental conditions. The biofilm master-regulator protein CsgD upregulates curli and cellulose, the two major polymers in the extracellular matrix of uropathogenic E. coli (UPEC) biofilms. Here, we found that cAMP regulates curli, cellulose, and UPEC biofilms through csgD The alarmone cAMP is produced by adenylate cyclase (CyaA) and deletion of cyaA resulted in lower extracellular matrix production and biofilm formation...
October 3, 2016: Journal of Bacteriology
Todd A Cameron, Nicholas R De Lay
: Gene regulation by base-pairing between small non-coding RNAs (sRNAs) and their mRNA targets is an important mechanism that allows bacteria to maintain homeostasis and respond to dynamic environments. In Gram negative bacteria, sRNA pairing and regulation is mediated by several RNA-binding proteins, including the sRNA chaperone Hfq and polynucleotide phosphorylase (PNPase). PNPase and its homolog RNase PH together represent the two 3' -5' phosphorolytic exoribonucleases found in Escherichia coli; however, a role for RNase PH in sRNA regulation has not yet been explored and reported...
October 3, 2016: Journal of Bacteriology
Brittany Barreto, Elizabeth Rogers, Jun Xia, Ryan L Frisch, Megan Richters, Devon M Fitzgerald, Susan M Rosenberg
: Microbes and human cells possess mechanisms of mutagenesis activated by stress responses. Stress-inducible mutagenesis mechanisms may provide important models for mutagenesis that drives host-pathogen interactions, antibiotic resistance, and possibly much of evolution generally. In Escherichia coli, repair of DNA double-strand breaks is switched to a mutagenic mode, using error-prone DNA polymerases, via the SOS DNA-damage and the general (σ(S)) stress responses. We investigated small RNA (sRNA) clients of Hfq, an RNA chaperone that promotes mutagenic break repair (MBR), and found that GcvB promotes MBR by allowing a robust σ(S) response, achieved via opposing the membrane stress (σ(E)) response...
October 3, 2016: Journal of Bacteriology
Lauren R Walling, J Scott Butler
: Toxin-antitoxin (TA) systems are ubiquitous in bacteria and archaea, where they play a pivotal role in the establishment and maintenance of dormancy. Under normal growth conditions, the antitoxin neutralizes the toxin. However, under conditions of stress, such as nutrient starvation or antibiotic treatment, cellular proteases degrade the antitoxin, and the toxin functions to arrest bacterial growth. We characterized the specificity determinants of the interactions between VapB antitoxins and VapC toxins from nontypeable Haemophilus influenzae (NTHi) in an effort to gain a better understanding of how antitoxins control toxin activity and bacterial persistence...
September 26, 2016: Journal of Bacteriology
Christina C Saak, Karine A Gibbs
Proteus mirabilis is a social bacterium that is capable of self (kin) versus non-self recognition. Swarming colonies of this bacterium expand outward on surfaces at centimeter-scale distances due to the collective motility of individual cells. Colonies of genetically distinct populations remain separate while those of identical populations merge. Ids proteins are essential for this recognition behavior. Two of these proteins, IdsD and IdsE, encode identity information for each strain. These two proteins bind in vitro in an allele-restrictive manner, and IdsD-IdsE binding is correlated with populations merging whereas a lack of binding correlates with populations separating...
September 26, 2016: Journal of Bacteriology
Pauline Moulin, Kévin Patron, Camille Cano, Mohamed Amine Zorgani, Emilie Camiade, Elise Borezée-Durant, Agnès Rosenau, Laurent Mereghetti, Aurélia Hiron
: The Lmb protein of Streptococcus agalactiae is described as an adhesin that binds laminin, a component of the human extracellular matrix. In this study, we reveal a new role for this protein in zinc uptake. We also identified two Lmb homologs, AdcA and AdcAII, redundant binding proteins that combine with the AdcCB translocon to form a zinc-ABC transporter. Expression of this transporter is controlled by the zinc concentration of the medium through the zinc-dependent regulator AdcR. Triple deletion of lmb, adcA, and adcAII, or that of the adcCB encoding genes, impaired growth and cell separation in a zinc-restricted environment...
September 26, 2016: Journal of Bacteriology
Peter E Burby, Taylor M Nye, Jeremy W Schroeder, Lyle A Simmons
Few discoveries have been more transformative to the biological sciences than the development of DNA sequencing technologies. The rapid advancement of sequencing and bioinformatics tools has revolutionized bacterial genetics, deepening our understanding of model and clinically relevant organisms. Although application of newer sequencing technologies to studies in bacterial genetics is increasing, the implementation of DNA sequencing technologies and development of the bioinformatics tools required for analyzing the large data sets generated remains a challenge for many...
September 26, 2016: Journal of Bacteriology
Andreas Matern, Danielle Pedrolli, Stephanie Großhennig, Jörgen Johansson, Matthias Mack
The riboflavin analogs roseoflavin (RoF) and 8-demethyl-8-aminoriboflavin (AF) are produced by the bacteria Streptomyces davawensis and Streptomyces cinnabarinus Riboflavin analogs have the potential to be used as broad-spectrum antibiotics and we therefore studied the metabolism of riboflavin (vitamin B2), RoF and AF in the human pathogen Listeria monocytogenes, a bacterium which is a riboflavin auxotroph. We show that the L. monocytogenes protein Lmo1945 is responsible for uptake of riboflavin, RoF and AF...
September 26, 2016: Journal of Bacteriology
Oren Mayer, Paras Jain, Torin Weisbrod, Daniel Biro, Libby Ho, Deborah Jacobs-Sera, Graham F Hatfull, William R Jacobs
: Mycobacteriophage DS6A is unique amongst the more than 8000 isolated mycobacteriophages due to its ability to form plaques exclusively on mycobacteria belonging to the Mycobacterium tuberculosis Complex (MTBC). Speculation surrounding this specificity has led to unsupported assertions in published studies and patents that non-tuberculous mycobacteria (NTM) are wholly resistant to DS6A infection. In this study, we identified two independent, nonessential regions in the DS6A genome and replaced them with an mVenus-expressing plasmid to generate fluorescent reporter phages Φ(2)GFP12 and Φ(2)GFP13...
September 26, 2016: Journal of Bacteriology
Amit Pathania, Arvind Kumar Gupta, Swati Dubey, Balasubramanian Gopal, Abhijit A Sardesai
: ArgO and LysE are members of the LysE family of exporter proteins and ordinarily mediate export of L-arginine (Arg) in Escherichia coli and L-lysine (Lys) and Arg in Corynebacterium glutamicum respectively. Under certain conditions ArgO also mediates Lys export. To delineate the arrangement of ArgO in the cytoplasmic membrane of E. coli we have employed a combination of cysteine accessibility in situ, alkaline phosphatase fusion reporters and protein modelling, to arrive at a topological model for ArgO...
September 19, 2016: Journal of Bacteriology
Brian A Renda, Cindy Chan, Kristin N Parent, Jeffrey E Barrick
: Bacterial genomes commonly contain prophage sequences as a result of past infections with lysogenic phages. Many of these integrated viral sequences are believed to be cryptic, but prophage genes are sometimes co-opted by the host, and some prophages may be re-activated to form infectious particles when cells are stressed or mutate. We found that a previously uncharacterized filamentous phage emerged from the genome of Acinetobacter baylyi ADP1 during a laboratory evolution experiment...
September 19, 2016: Journal of Bacteriology
Christian Lorenz, Thomas J Dougherty, Stephen Lory
: In Gram-negative bacteria a dedicated machinery, consisting of LolABCDE components targets lipoproteins to the outer membrane. We used a previously identified small molecule inhibitor of the LolCDE complex of Escherichia coli to assess the global transcriptional consequences of interference with lipoprotein transport. Exposure of E. coli to the LolCDE inhibitor at concentrations leading to minimal and significant growth inhibition, followed by RNA-seq, identified a small group of genes, whose transcripts were decreased and a larger group where mRNA levels increased 10-100 fold when compared to untreated cells...
September 19, 2016: Journal of Bacteriology
Etsuko Sugawara, Seiji Kojima, Hiroshi Nikaido
: Klebsiella pneumoniae, one of the most important nosocomial pathogens, is becoming a major problem in health care because of its resistance to multiple antibiotics including cephalosporins of the latest generation and more recently even carbapenems. This is largely due to the spread of plasmid-coded extended spectrum β-lactamases. However, antimicrobial agents must first penetrate through the outer membrane barrier in order to reach their targets, and hydrophilic and charged β-lactams presumably diffuse through the porin channels...
September 19, 2016: Journal of Bacteriology
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