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https://www.readbyqxmd.com/read/29345115/metatranscriptome-analysis-reveals-environmental-and-diel-regulation-of-a-heterosigma-akashiwo-raphidophyceae-bloom
#1
Nanjing Ji, Lingxiao Lin, Ling Li, Liying Yu, Yaqun Zhang, Hao Luo, Meizhen Li, Xinguo Shi, Da-Zhi Wang, Senjie Lin
Despite numerous laboratory studies on physiologies of harmful algal bloom (HAB) species, physiologies of these algae during a natural bloom are understudied. Here, we investigated a bloom of the raphidophyte Heterosigma akashiwo in the East China Sea in 2014 using metabarcode (18S rDNA) and metatranscriptome sequencing. Based on 18S rDNA analyses, the phytoplankton community shifted from high diversity in the pre-bloom stage to H. akashiwo predominance during the bloom. A sharp decrease in ambient dissolved inorganic phosphate and strong up-regulation of phosphate and dissolved organic phosphorus (DOP) uptake genes, including the rarely documented (ppGpp)ase, in H...
January 18, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29327293/overexpression-of-spot-gene-in-coccoid-forms-of-clinical-helicobacter-pylori-isolates
#2
Farkhondeh Poursina, Jamshid Fagri, Nasrin Mirzaei, Hajieh Ghasemian Safaei
Helicobacter pylori (H. pylori) can convert to coccoid form in unfavorable conditions or as a result of antibiotic treatment. In order to adapt to harsh environments, H. pylori requires a stringent response which, encoded by the spoT gene, has a bifunctional enzyme possessing both (p)ppGpp synthetic and degrading activity. Our goal in this study was to compare spoT gene expression in spiral and induced coccoid forms of H. pylori with use of amoxicillin. First, clinical isolate coccoid forms were induced with amoxicillin; then, the viability test was analyzed by flow cytometer...
January 11, 2018: Folia Microbiologica
https://www.readbyqxmd.com/read/29326162/structural-basis-for-p-ppgpp-synthesis-by-the-staphylococcus-aureus-small-alarmone-synthetase-relp
#3
Melek Cemre Manav, Jelena Beljantseva, Martin Saxtorph Bojer, Tanel Tenson, Hanne Ingmer, Vasili Hauryliuk, Ditlev Egeskov Brodersen
The stringent response is a global reprogramming of bacterial physiology that renders cells more tolerant to antibiotics and induces virulence gene expression in pathogens in response to stress. This process is driven by accumulation of the intracellular alarmone guanosine-5'-di(tri)phosphate-3'-diphosphate ([p]ppGpp), which is produced by enzymes of the RelA SpoT homologue (RSH) family. The Gram-positive Firmicute pathogen, Staphylococcus aureus, encodes three RSH enzymes: a multi-domain RSH (Rel) that senses amino acid starvation on the ribosome and two small alarmone synthetase (SAS) enzymes, RelQ (SAS1) and RelP (SAS2)...
January 11, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29311276/species-specific-interactions-of-arr-with-rplk-mediate-stringent-response-in-bacteria
#4
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
https://www.readbyqxmd.com/read/29281108/green-magic-regulation-of-the-chloroplast-stress-response-by-p-ppgpp-in-plants-and-algae
#5
Ben Field
The hyperphosphorylated nucleotides guanosine pentaphosphate and tetraphosphate (together referred to as (p)ppGpp, or magic spot) orchestrate a signalling cascade in bacteria that controls growth under optimal conditions and in response to environmental stress. (p)ppGpp is also found in the chloroplasts of plants and algae where it is has also been shown to accumulate in response to abiotic stress. Recent studies suggest that (p)ppGpp is a potent inhibitor of chloroplast gene expression in vivo, and is a significant regulator of chloroplast function that can influence both the growth and the development of plants...
December 21, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29273811/the-stringent-response-promotes-biofilm-dispersal-in-pseudomonas-putida
#6
Carlos Díaz-Salazar, Patricia Calero, Rocío Espinosa-Portero, Alicia Jiménez-Fernández, Lisa Wirebrand, María G Velasco-Domínguez, Aroa López-Sánchez, Victoria Shingler, Fernando Govantes
Biofilm dispersal is a genetically programmed response enabling bacterial cells to exit the biofilm in response to particular physiological or environmental conditions. In Pseudomonas putida biofilms, nutrient starvation triggers c-di-GMP hydrolysis by phosphodiesterase BifA, releasing inhibition of protease LapG by the c-di-GMP effector protein LapD, and resulting in proteolysis of the adhesin LapA and the subsequent release of biofilm cells. Here we demonstrate that the stringent response, a ubiquitous bacterial stress response, is accountable for relaying the nutrient stress signal to the biofilm dispersal machinery...
December 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29241543/ppgpp-controls-global-gene-expression-in-light-and-in-darkness-in-s-%C3%A2-elongatus
#7
Anna M Puszynska, Erin K O'Shea
The bacterial and plant stringent response involves production of the signaling molecules guanosine tetraphosphate and guanosine pentaphosphate ((p)ppGpp), leading to global reorganization of gene expression. The function of the stringent response has been well characterized in stress conditions, but its regulatory role during unstressed growth is less studied. Here, we demonstrate that (p)ppGpp-deficient strains of S. elongatus have globally deregulated biosynthetic capacity, with increased transcription rate, translation rate, and cell size in unstressed conditions in light and impaired viability in darkness...
December 12, 2017: Cell Reports
https://www.readbyqxmd.com/read/29233898/prophages-and-growth-dynamics-confound-experimental-results-with-antibiotic-tolerant-persister-cells
#8
Alexander Harms, Cinzia Fino, Michael A Sørensen, Szabolcs Semsey, Kenn Gerdes
Bacterial persisters are phenotypic variants that survive antibiotic treatment in a dormant state and can be formed by multiple pathways. We recently proposed that the second messenger (p)ppGpp drives Escherichia coli persister formation through protease Lon and activation of toxin-antitoxin (TA) modules. This model found considerable support among researchers studying persisters but also generated controversy as part of recent debates in the field. In this study, we therefore used our previous work as a model to critically examine common experimental procedures to understand and overcome the inconsistencies often observed between results of different laboratories...
December 12, 2017: MBio
https://www.readbyqxmd.com/read/29158241/polyphosphate-kinase-antagonizes-virulence-gene-expression-in-francisella-tularensis
#9
Amy E Rohlfing, Kathryn M Ramsey, Simon L Dove
The alarmone ppGpp is a critical regulator of virulence gene expression in Francisella tularensis In this intracellular pathogen ppGpp is thought to work in concert with the putative DNA-binding protein PigR and the SspA protein family members MglA and SspA to control a common set of genes. MglA and SspA form a complex that interacts with RNA polymerase (RNAP) and PigR functions by interacting with the RNAP-associated MglA-SspA complex. Prior work suggested that ppGpp exerts its regulatory effects in F. tularensis indirectly by promoting the accumulation of polyphosphate in the cell, which in turn was required for formation of the MglA-SspA complex...
November 20, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/29157236/monitoring-of-nutrient-limitation-in-growing-e-coli-a-mathematical-model-of-a-ppgpp-based-biosensor
#10
Alexandra Pokhilko
BACKGROUND: E. coli can be used as bacterial cell factories for production of biofuels and other useful compounds. The efficient production of the desired products requires careful monitoring of growth conditions and the optimization of metabolic fluxes. To avoid nutrient depletion and maximize product yields we suggest using a natural mechanism for sensing nutrient limitation, related to biosynthesis of an intracellular messenger - guanosine tetraphosphate (ppGpp). RESULTS: We propose a design for a biosensor, which monitors changes in the intracellular concentration of ppGpp by coupling it to a fluorescent output...
November 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29135333/challenges-of-ligand-identification-for-the-second-wave-of-orphan-riboswitch-candidates
#11
Etienne B Greenlee, Shira Stav, Ruben M Atilho, Kenneth I Brewer, Kimberly A Harris, Sarah N Malkowski, Gayan Mirihana Arachchilage, Kevin R Perkins, Madeline E Sherlock, Ronald R Breaker
Orphan riboswitch candidates are noncoding RNA motifs whose representatives are believed to function as genetic regulatory elements, but whose target ligands have yet to be identified. The study of certain orphans, particularly classes that have resisted experimental validation for many years, has led to the discovery of important biological pathways and processes once their ligands were identified. Previously, we highlighted details for four of the most common and intriguing orphan riboswitch candidates. This facilitated the validation of riboswitches for the signaling molecules c-di-AMP, ZTP, and ppGpp, the metal ion Mn(2+), and the metabolites guanidine and PRPP...
November 14, 2017: RNA Biology
https://www.readbyqxmd.com/read/29061665/dksa-and-ppgpp-regulate-the-%C3%AF-s-stress-response-by-activating-promoters-for-the-small-rna-dsra-and-the-anti-adapter-protein-irap
#12
Mary E Girard, Saumya Gopalkrishnan, Elicia D Grace, Jennifer A Halliday, Richard L Gourse, Christophe Herman
σ(S) is an alternative sigma factor, encoded by the rpoS gene, that redirects cellular transcription to a large family of genes in response to stressful environmental signals. This so-called σ(S) general stress response is necessary for survival in many bacterial species and is controlled by a complex, multifactorial pathway that regulates σ(S) levels transcriptionally, translationally, and post-translationally in Escherichia coli It was shown previously that the transcription factor DksA and its cofactor ppGpp are among the many factors governing σ(S) synthesis, thus playing an important role in activation of the σ(S) stress response...
October 23, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/29034854/whole-genome-transcriptomics-reveals-global-effects-including-up-regulation-of-francisella-pathogenicity-island-gene-expression-during-active-stringent-response-in-the-highly-virulent-francisella-tularensis-subsp-tularensis-schu-s4
#13
Amber L Murch, Paul J Skipp, Peter L Roach, Petra C F Oyston
During conditions of nutrient limitation bacteria undergo a series of global gene expression changes to survive conditions of amino acid and fatty acid starvation. Rapid reallocation of cellular resources is brought about by gene expression changes coordinated by the signalling nucleotides' guanosine tetraphosphate or pentaphosphate, collectively termed (p)ppGpp and is known as the stringent response. The stringent response has been implicated in bacterial virulence, with elevated (p)ppGpp levels being associated with increased virulence gene expression...
October 16, 2017: Microbiology
https://www.readbyqxmd.com/read/29027458/the-stringent-response-induced-by-phosphate-limitation-promotes-purine-salvage-in-agrobacterium-fabrum
#14
Smitha Sivapragasam, Dinesh K Deochand, Jacob K Meariman, Anne Grove
Agrobacterium fabrum induces tumor growth in susceptible plant species. The upregulation of virulence genes that occurs when the bacterium senses plant-derived compounds is enhanced by acidic pH and limiting inorganic phosphate. Nutrient starvation may also trigger the stringent response, and purine salvage is among the pathways expected to be favored under such conditions. We show here that phosphate limitation induces the stringent response, as evidenced by production of (p)ppGpp, and that the xdhCSML operon encoding the purine salvage enzyme xanthine dehydrogenase is upregulated ∼15-fold...
October 31, 2017: Biochemistry
https://www.readbyqxmd.com/read/29021784/synthetic-peptides-to-target-stringent-response-controlled-virulence-in-a-pseudomonas-aeruginosa-murine-cutaneous-infection-model
#15
Daniel Pletzer, Heidi Wolfmeier, Manjeet Bains, Robert E W Hancock
Microorganisms continuously monitor their surroundings and adaptively respond to environmental cues. One way to cope with various stress-related situations is through the activation of the stringent stress response pathway. In Pseudomonas aeruginosa this pathway is controlled and coordinated by the activity of the RelA and SpoT enzymes that metabolize the small nucleotide secondary messenger molecule (p)ppGpp. Intracellular ppGpp concentrations are crucial in mediating adaptive responses and virulence. Targeting this cellular stress response has recently been the focus of an alternative approach to fight antibiotic resistant bacteria...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28986449/mfd-translocase-is-necessary-and-sufficient-for-transcription-coupled-repair-in-escherichia-coli
#16
Ogun Adebali, Aziz Sancar, Christopher P Selby
Nucleotide excision repair in Escherichia coli is stimulated by transcription, specifically in the transcribed strand. Previously, it was shown that this transcription-coupled repair (TCR) is mediated by the Mfd translocase. Recently, it was proposed that in fact the majority of TCR in E. coli is catalyzed by a second pathway ("backtracking-mediated TCR") that is dependent on the UvrD helicase and the guanosine pentaphosphate (ppGpp) alarmone/stringent response regulator. Recently, we reported that as measured by the excision repair-sequencing (XR-seq), UvrD plays no role in TCR genome-wide...
November 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28986375/stringent-response-regulators-contribute-to-the-recovery-from-glucose-phosphate-stress-in-escherichia-coli
#17
Julie R Kessler, Brandi L Cobe, Gregory R Richards
In enteric bacteria like Escherichia coli, the transcription factor SgrR and the small RNA SgrS regulate the response to glucose-phosphate stress, a metabolic dysfunction that results in growth inhibition and stems from the intracellular accumulation of sugar-phosphates. SgrR activates transcription of sgrS, and SgrS helps to rescue cells from stress in part by inhibiting uptake of stressor sugar-phosphates. While the regulatory targets of this stress response are well described, less is known about how the SgrR-SgrS response itself is regulated...
October 6, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28979246/variable-persister-gene-interactions-with-p-ppgpp-for-persister-formation-in-escherichia-coli
#18
Shuang Liu, Nan Wu, Shanshan Zhang, Youhua Yuan, Wenhong Zhang, Ying Zhang
Persisters comprise a group of phenotypically heterogeneous metabolically quiescent bacteria with multidrug tolerance and contribute to the recalcitrance of chronic infections. Although recent work has shown that toxin-antitoxin (TA) system HipAB depends on stringent response effector (p)ppGppin persister formation, whether other persister pathways are also dependent on stringent response has not been explored. Here we examined the relationship of (p)ppGpp with 15 common persister genes (dnaK, clpB, rpoS, pspF, tnaA, sucB, ssrA, smpB, recA, umuD, uvrA, hipA, mqsR, relE, dinJ) using Escherichia coli as a model...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28965178/integration-of-multiple-stimuli-sensing-systems-to-regulate-hrps-and-type-iii-secretion-system-in-erwinia-amylovora
#19
Jae Hoon Lee, Youfu Zhao
The bacterial enhancer binding protein (bEBP) HrpS is essential for Erwinia amylovora virulence by activating the type III secretion system (T3SS). However, how the hrpS gene is regulated remains poorly understood in E. amylovora. In this study, 5' rapid amplification of cDNA ends and promoter deletion analyses showed that the hrpS gene contains two promoters driven by HrpX/HrpY and the Rcs phosphorelay system, respectively. Electrophoretic mobility shift and gene expression assays demonstrated that integration host factor IHF positively regulates hrpS expression through directly binding the hrpX promoter and positively regulating hrpX/hrpY expression...
September 30, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28948393/within-and-beyond-the-stringent-response-rsh-and-p-ppgpp-in-plants
#20
REVIEW
Justyna Boniecka, Justyna Prusińska, Grażyna B Dąbrowska, Anna Goc
Plant RSH proteins are able to synthetize and/or hydrolyze unusual nucleotides called (p)ppGpp or alarmones. These molecules regulate nuclear and chloroplast transcription, chloroplast translation and plant development and stress response. Homologs of bacterial RelA/SpoT proteins, designated RSH, and products of their activity, (p)ppGpp-guanosine tetra-and pentaphosphates, have been found in algae and higher plants. (p)ppGpp were first identified in bacteria as the effectors of the stringent response, a mechanism that orchestrates pleiotropic adaptations to nutritional deprivation and various stress conditions...
November 2017: Planta
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