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https://www.readbyqxmd.com/read/28098242/merr-and-chrr-mediate-blue-light-induced-photo-oxidative-stress-response-at-the-transcriptional-level-in-vibrio-cholerae
#1
Mehmet Tardu, Selma Bulut, Ibrahim Halil Kavakli
Blue light (BL) is a major environmental factor that affects the physiology, behavior, and infectivity of bacteria as it contributes to the generation of reactive oxygen species (ROS) while increasing photo-oxidative stress in cells. However, precise photo-oxidative response mechanism in non-phototrophic bacteria is yet to be elucidated. In this study, we investigated the effect of BL in Vibrio cholerae by using genetics and transcriptome profiling. Genome-wide analysis revealed that transcription of 6.3% of V...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28097055/comprehensive-transcriptome-analysis-provides-new-insights-into-nutritional-strategies-and-phylogenetic-relationships-of-chrysophytes
#2
Daniela Beisser, Nadine Graupner, Christina Bock, Sabina Wodniok, Lars Grossmann, Matthijs Vos, Bernd Sures, Sven Rahmann, Jens Boenigk
BACKGROUND: Chrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in detail at the molecular level, and no genomic and only little transcriptomic information is available. Chrysophytes exhibit different trophic modes: while phototrophic chrysophytes perform only photosynthesis, mixotrophs can gain carbon from bacterial food as well as from photosynthesis, and heterotrophs solely feed on bacteria-sized microorganisms...
2017: PeerJ
https://www.readbyqxmd.com/read/28096490/comprehensive-essentiality-analysis-of-the-mycobacterium-tuberculosis-genome-via-saturating-transposon-mutagenesis
#3
Michael A DeJesus, Elias R Gerrick, Weizhen Xu, Sae Woong Park, Jarukit E Long, Cara C Boutte, Eric J Rubin, Dirk Schnappinger, Sabine Ehrt, Sarah M Fortune, Christopher M Sassetti, Thomas R Ioerger
: For decades, identifying the regions of a bacterial chromosome that are necessary for viability has relied on mapping integration sites in libraries of random transposon mutants to find loci that are unable to sustain insertion. To date, these studies have analyzed subsaturated libraries, necessitating the application of statistical methods to estimate the likelihood that a gap in transposon coverage is the result of biological selection and not the stochasticity of insertion. As a result, the essentiality of many genomic features, particularly small ones, could not be reliably assessed...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28096446/the-rpn-yhga-like-proteins-of-escherichia-coli-k-12-and-their-contribution-to-reca-independent-horizontal-transfer
#4
Anthony W Kingston, Christine Ponkratz, Elisabeth A Raleigh
: Bacteria use a variety of DNA mobilizing enzymes to facilitate environmental niche adaptation via horizontal gene transfer. This has led to real world problems, like the spread of antibiotic resistance, yet many mobilization proteins remain undefined. Here, we investigate the uncharacterized family of YhgA-like "transposase_31" proteins (PF04754). Our primary focus was the genetic and biochemical properties of the five E. coli K-12 members of this family, which we designate RpnA-RpnE for recombination promoting nuclease...
January 17, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28096329/tissue-dual-rna-seq-allows-fast-discovery-of-infection-specific-functions-and-riboregulators-shaping-host-pathogen-transcriptomes
#5
Aaron M Nuss, Michael Beckstette, Maria Pimenova, Carina Schmühl, Wiebke Opitz, Fabio Pisano, Ann Kathrin Heroven, Petra Dersch
Pathogenic bacteria need to rapidly adjust their virulence and fitness program to prevent eradication by the host. So far, underlying adaptation processes that drive pathogenesis have mostly been studied in vitro, neglecting the true complexity of host-induced stimuli acting on the invading pathogen. In this study, we developed an unbiased experimental approach that allows simultaneous monitoring of genome-wide infection-linked transcriptional alterations of the host and colonizing extracellular pathogens. Using this tool for Yersinia pseudotuberculosis-infected lymphatic tissues, we revealed numerous alterations of host transcripts associated with inflammatory and acute-phase responses, coagulative activities, and transition metal ion sequestration, highlighting that the immune response is dominated by infiltrating neutrophils and elicits a mixed TH17/TH1 response...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28095919/ancient-bacteria-of-the-%C3%A3-tzi-s-microbiome-a-genomic-tale-from-the-copper-age
#6
Gabriele Andrea Lugli, Christian Milani, Leonardo Mancabelli, Francesca Turroni, Chiara Ferrario, Sabrina Duranti, Douwe van Sinderen, Marco Ventura
BACKGROUND: Ancient microbiota information represents an important resource to evaluate bacterial evolution and to explore the biological spread of infectious diseases in history. The soft tissue of frozen mummified humans, such as the Tyrolean Iceman, has been shown to contain bacterial DNA that is suitable for population profiling of the prehistoric bacteria that colonized such ancient human hosts. RESULTS: Here, we performed a microbial cataloging of the distal gut microbiota of the Tyrolean Iceman, which highlights a predominant abundance of Clostridium and Pseudomonas species...
January 17, 2017: Microbiome
https://www.readbyqxmd.com/read/28095778/the-pangenome-of-antarctic-pseudoalteromonas-bacteria-evolutionary-and-functional-insights
#7
Emanuele Bosi, Marco Fondi, Valerio Orlandini, Elena Perrin, Isabel Maida, Donatella de Pascale, Maria Luisa Tutino, Ermenegilda Parrilli, Angelina Lo Giudice, Alain Filloux, Renato Fani
BACKGROUND: Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production...
January 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28095753/a-functional-endonuclease-q-exists-in-the-bacterial-domain-identification-and-characterization-of-endonuclease-q-from-bacillus-pumilus
#8
Miyako Shiraishi, Sonoko Ishino, Isaac Cann, Yoshizumi Ishino
DNA base deamination occurs spontaneously under physiological conditions and is promoted by high temperature. Therefore, hyperthermophiles are expected to have efficient repair systems of the deaminated bases in their genomes. Endonuclease Q (EndoQ) was originally identified from the hyperthermophlic archaeon, Pyrococcus furiosus, as a hypoxanthine-specific endonuclease recently. Further biochemical analyses revealed that EndoQ also recognizes uracil, xanthine, and the AP site in DNA, and is probably involved in a specific repair process for damaged bases...
January 18, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28094982/bacterial-genome-editing-via-a-designed-toxin-antitoxin-cassette
#9
Jie Wu, Aihua Deng, Qinyun Sun, Hua Bai, Zhaopeng Sun, Xiuling Shang, Yun Zhang, Qian Liu, Yong Liang, Shuwen Liu, Yongsheng Che, Tingyi Wen
Manipulating the bacterial genomes in an efficient manner is essential to biological and biotechnological research. Despite usage of various modules for genomic editing with counter-selectable markers including the toxin genes, an easy-to-use and highly designable toxin-antitoxin (TA) cassette without causing any leakages is urgently needed for efficient genome editing of the Gram-positive bacteria. Here, we reprogramed the bacterial TA systems as a toxin counter-selectable cassette regulated by an antitoxin switch (TCCRAS) for genetic modifications in the extensively studied and utilized Gram-positive bacteria, B...
January 17, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28094796/the-evolution-of-no-cost-resistance-at-sub-mic-concentrations-of-streptomycin-in-streptomyces-coelicolor
#10
Sanne Westhoff, Tim Marijn van Leeuwe, Omar Qachach, Zheren Zhang, Gilles Philippus van Wezel, Daniel Eric Rozen
At the high concentrations used in medicine, antibiotics exert strong selection on bacterial populations for the evolution of resistance. However, these lethal concentrations may not be representative of the concentrations bacteria face in soil, a recognition that has led to questions of the role of antibiotics in soil environments as well as the dynamics of resistance evolution during sublethal challenge. Here we examine the evolution of resistance to sub-minimal inhibitory concentrations (sub-MIC) of streptomycin in the filamentous soil bacterium Streptomyces coelicolor...
January 17, 2017: ISME Journal
https://www.readbyqxmd.com/read/28094347/endozoicomonas-genomes-reveal-functional-adaptation-and-plasticity-in-bacterial-strains-symbiotically-associated-with-diverse-marine-hosts
#11
Matthew J Neave, Craig T Michell, Amy Apprill, Christian R Voolstra
Endozoicomonas bacteria are globally distributed and often abundantly associated with diverse marine hosts including reef-building corals, yet their function remains unknown. In this study we generated novel Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora pistillata, Pocillopora verrucosa, and Acropora humilis. We then compared these culture-independent genomes to existing genomes of bacterial isolates acquired from a sponge, sea slug, and coral to examine the functional landscape of this enigmatic genus...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28092693/pathogenic-streptococcus-strains-employ-novel-escape-strategy-to-inhibit-bacteriostatic-effect-mediated-by-mammalian-peptidoglycan-recognition-protein
#12
Jing Wang, Youjun Feng, Changjun Wang, Swaminath Srinivas, Chen Chen, Hui Liao, Elaine He, Shibo Jiang, Jiaqi Tang
Pathogenic streptococcal species are responsible for some of the most lethal and prevalent animal and human infections. Previous reports have identified a candidate pathogenicity island (PAI) in two highly virulent clinical isolates of Streptococcus suis type 2 (SS2), a causative agent of high-mortality streptococcal toxic shock syndrome (STSS). This PAI contains a Type-IVC secretion system C subgroup (Type-IVC secretion system) that is involved in the secretion of unknown pathogenic effectors that are responsible for STSS caused by highly virulent strains of SS2...
January 16, 2017: Cellular Microbiology
https://www.readbyqxmd.com/read/28092263/transcription-leads-to-pervasive-replisome-instability-in-bacteria
#13
Sarah Mangiameli, Christopher N Merrikh, Paul A Wiggins, Houra Merrikh
The canonical model of DNA replication describes a highly-processive and largely continuous process by which the genome is duplicated. This continuous model is based upon in vitro reconstitution and in vivo ensemble experiments. Here, we characterize the replisome-complex stoichiometry and dynamics with single-molecule resolution in bacterial cells. Strikingly, the stoichiometries of the replicative helicase, DNA polymerase, and clamp loader complexes are consistent with the presence of only one active replisome in a significant fraction of cells (>40%)...
January 16, 2017: ELife
https://www.readbyqxmd.com/read/28092137/isolation-and-characterization-of-rhizobium-sp-strain-ys-1r-that-degrades-lignin-in-plant-biomass
#14
Colin A Jackson, Matthew B Couger, Madhu Prabhakaran, Karthikeyan D Ramachandriya, Patricia Canaan, Babu Z Fathepure
AIMS: The aim of this work was to isolate novel lignin degrading organisms. METHODS AND RESULTS: Several pure cultures of bacteria that degrade lignin were isolated from bacterial consortia developed from decaying biomass. Among the isolates, Rhizobium sp. strain YS-1r (closest relative of Rhizobium petrolearium Strain SL-1) was explored for its lignin degrading ability. Microcosm studies showed that strain YS-1r was able to degrade a variety of lignin monomers, dimers, and also native lignin in switchgrass and alfalfa...
January 16, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28091882/identification-of-some-main-streptococcus-iniae-associated-proteins-relationship
#15
Fatima El Aamri, José Ángel Guillén, Daniel Padilla, Félix Acosta, Fernando Real
The surface-associated proteins play a key role in bacterial physiology and pathogenesis, and are the major targets in the development of new vaccines. These proteins contribute to the adaptation of bacteria to different hosts and environments. To study differences at the genomic level, we first sequenced the whole genome of Streptococcus iniae from fish (IUSA-1 strain) and compared it to Streptococcus iniae from human (9117 strain), revealing a high similitude between both strains. To gain further insights into host- and environment-specific differences, we then studied proteins in silico and by High Performance Liquid Chromatography...
January 14, 2017: Veterinary Research Communications
https://www.readbyqxmd.com/read/28091681/microbial-rrna-sequencing-analysis-of-evaporative-cooler-indoor-environments-located-in-the-great-basin-desert-region-of-the-united-states
#16
Angela R Lemons, Mary Beth Hogan, Ruth A Gault, Kathleen Holland, Edward Sobek, Kimberly A Olsen-Wilson, Yeonmi Park, Ju-Hyeong Park, Ja Kook Gu, Michael L Kashon, Brett J Green
Recent studies conducted in the Great Basin Desert region of the United States have shown that skin test reactivity to fungal and dust mite allergens are increased in children with asthma or allergy living in homes with evaporative coolers (EC). The objective of this study was to determine if the increased humidity previously reported in EC homes leads to varying microbial populations compared to homes with air conditioners (AC). Children with physician-diagnosed allergic rhinitis living in EC or AC environments were recruited into the study...
January 16, 2017: Environmental Science. Processes & Impacts
https://www.readbyqxmd.com/read/28090080/you-are-where-you-live
#17
Samuel E Kidman, Josephine M Bryant
This month's Genome Watch discusses how whole-genome sequencing of bacteria from several body sites has provided insights into the spatial diversity of bacteria within patients.
January 16, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28088723/discovery-and-metagenomic-analysis-of-an-anammox-bacterial-enrichment-related-to-candidatus-brocadia-caroliniensis-in-a-full-scale-glycerol-fed-nitritation-denitritation-separate-centrate-treatment-process
#18
Hongkeun Park, Ariane C Brotto, Mark C M van Loosdrecht, Kartik Chandran
A distinctive red biofilm was observed in a glycerol-fed digester liquid effluent treatment process coupling partial nitrification (nitritation) and partial denitrification (denitritation) processes. Based on initial phylogenetic screening using 16S rRNA clone libraries and quantitative polymerase chain reaction, the biofilm was enriched in novel anaerobic ammonium oxidizing bacteria (AMX/anammox) closely related to Candidatus "Brocadia caroliniensis". The metabolic functionality of the C. "Brocadia caroliniensis" enrichment was further explored using high-throughput sequencing and de novo metagenome assembly...
January 6, 2017: Water Research
https://www.readbyqxmd.com/read/28088165/genomic-characterization-of-ensifer-aridi-a-proposed-new-species-of-nitrogen-fixing-rhizobium-recovered-from-asian-african-and-american-deserts
#19
Antoine Le Quéré, Nisha Tak, Hukam Singh Gehlot, Celine Lavire, Thibault Meyer, David Chapulliot, Sonam Rathi, Ilham Sakrouhi, Guadalupe Rocha, Marine Rohmer, Dany Severac, Abdelkarim Filali-Maltouf, Jose-Antonio Munive
BACKGROUND: Nitrogen fixing bacteria isolated from hot arid areas in Asia, Africa and America but from diverse leguminous plants have been recently identified as belonging to a possible new species of Ensifer (Sinorhizobium). In this study, 6 strains belonging to this new clade were compared with Ensifer species at the genome-wide level. Their capacities to utilize various carbon sources and to establish a symbiotic interaction with several leguminous plants were examined. RESULTS: Draft genomes of selected strains isolated from Morocco (Merzouga desert), Mexico (Baja California) as well as from India (Thar desert) were produced...
January 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28087584/emergence-of-klebsiella-variicola-positive-for-ndm-9-a-variant-of-new-delhi-metallo-%C3%AE-lactamase-in-an-urban-river-in-south-korea
#20
Doris Y W Di, Jeonghwan Jang, Tatsuya Unno, Hor-Gil Hur
OBJECTIVES: To examine the presence of pathogenic bacteria carrying New Delhi metallo-β-lactamase in the environment and to characterize the genome structures of these strains. METHODS: Phenotypic screening of antimicrobial susceptibility and WGS were conducted on three Klebsiella variicola strains possessing NDM-9 isolated from an urban river. RESULTS: Three carbapenem-resistant K. variicola isolated from Gwangju tributary were found to possess blaNDM-9 genes...
January 12, 2017: Journal of Antimicrobial Chemotherapy
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