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Bacterial genomics

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https://www.readbyqxmd.com/read/29140998/using-whole-genome-sequencing-to-study-american-foulbrood-epidemiology-in-honeybees
#1
Joakim Ågren, Marc Oliver Schäfer, Eva Forsgren
American foulbrood (AFB), caused by Paenibacillus larvae, is a devastating disease in honeybees. In most countries, the disease is controlled through compulsory burning of symptomatic colonies causing major economic losses in apiculture. The pathogen is endemic to honeybees world-wide and is readily transmitted via the movement of hive equipment or bees. Molecular epidemiology of AFB currently largely relies on placing isolates in one of four ERIC-genotypes. However, a more powerful alternative is multi-locus sequence typing (MLST) using whole-genome sequencing (WGS), which allows for high-resolution studies of disease outbreaks...
2017: PloS One
https://www.readbyqxmd.com/read/29140975/natural-variation-of-a-sensor-kinase-controlling-a-conserved-stress-response-pathway-in-escherichia-coli
#2
Manuela Roggiani, Srujana S Yadavalli, Mark Goulian
Previous studies have shown that exponentially growing Escherichia coli can detect mild acidity (~pH 5.5) and, in response, synthesize enzymes that protect against severe acid shock. This adaptation is controlled by the EvgS/EvgA phosphorelay, a signal transduction system present in virtually every E. coli isolate whose genome has been sequenced. Here we show that, despite this high level of conservation, the EvgS/EvgA system displays a surprising natural variation in pH-sensing capacity, with some strains entirely non-responsive to low pH stimulus...
November 15, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29139347/aestuariicoccus-marinus-gen-nov-sp-nov-isolated-from-sea-tidal-flat-sediment
#3
Tingye Feng, Sang Eun Jeong, Kyung Hyun Kim, Hye Yoon Park, Che Ok Jeon
A Gram-stain-negative, strictly aerobic and halotolerant bacterial strain, designated strain NAP41(T), was isolated from a sea tidal flat in the Yellow Sea of South Korea. Cells were non-motile cocci showing oxidase- and catalase-positive activities. Growth of strain NAP41(T) was observed at 15-40 °C (optimum, 37 °C), at pH 6.5-9.0 (optimum, pH 7.0-7.5) and in the presence of 0.5-12 % (w/v) NaCl (optimum, 2 %). Strain NAP41(T) contained summed feature 8 (comprising C18 : ω7c/C18 : 1ω6c) and C18 : 0 as the major fatty acids and ubiquinone-10 as the sole isoprenoid quinone...
November 15, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29139344/aeropyrum-pernix-membrane-topology-of-protein-vkor-promotes-protein-disulfide-bond-formation-in-two-subcellular-compartments
#4
Stijntje Hibender, Cristina Landeta, Mehmet Berkmen, Jon Beckwith, Dana Boyd
Disulfide bonds confer stability and activity to proteins. Bioinformatic approaches allow predictions of which organisms make protein disulfide bonds and in which subcellular compartments disulfide bond formation takes place. Such an analysis, along with biochemical and protein structural data, suggests that many of the extremophile Crenarachaea make protein disulfide bonds in both the cytoplasm and the cell envelope. We have sought to determine the oxidative folding pathways in the sequenced genomes of the Crenarchaea, by seeking homologues of the enzymes known to be involved in disulfide bond formation in bacteria...
November 15, 2017: Microbiology
https://www.readbyqxmd.com/read/29138307/microdiversity-of-an-abundant-terrestrial-bacterium-encompasses-extensive-variation-in-ecologically-relevant-traits
#5
Alexander B Chase, Ulas Karaoz, Eoin L Brodie, Zulema Gomez-Lunar, Adam C Martiny, Jennifer B H Martiny
Much genetic diversity within a bacterial community is likely obscured by microdiversity within operational taxonomic units (OTUs) defined by 16S rRNA gene sequences. However, it is unclear how variation within this microdiversity influences ecologically relevant traits. Here, we employ a multifaceted approach to investigate microdiversity within the dominant leaf litter bacterium, Curtobacterium, which comprises 7.8% of the bacterial community at a grassland site undergoing global change manipulations. We use cultured bacterial isolates to interpret metagenomic data, collected in situ over 2 years, together with lab-based physiological assays to determine the extent of trait variation within this abundant OTU...
November 14, 2017: MBio
https://www.readbyqxmd.com/read/29138003/serine-threonine-protein-kinases-from-bacteria-archaea-and-eukarya-share-a-common-evolutionary-origin-deeply-rooted-in-the-tree-of-life
#6
Ivan Andreas Stancik, Martin Sebastijan Šestak, Boyang Ji, Marina Axelson-Fisk, Damjan Franjevic, Carsten Jers, Tomislav Domazet-Lošo, Ivan Mijakovic
The main family of serine/threonine/tyrosine protein kinases present in eukarya was defined and described by Hanks et al. in 1988. It was initially believed that these kinases do not exist in bacteria, but extensive genome sequencing revealed their existence in many bacteria. For historical reasons, the term "eukaryotic-type kinases" propagated in the literature to describe bacterial members of this protein family. Here, we argue that this term should be abandoned as a misnomer, and we provide several lines of evidence to support this claim...
November 11, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29136536/on-the-bright-side-of-a-forest-pest-the-metabolic-potential-of-bark-beetles-bacterial-associates
#7
Anna Fabryová, Martin Kostovčík, Alexandra Díez-Méndez, Alejandro Jiménez-Gómez, Lorena Celador-Lera, Zaki Saati-Santamaría, Hana Sechovcová, Esther Menéndez, Miroslav Kolařik, Paula García-Fraile
Bark beetles reproduce and overwinter under the bark of trees, and are associated with bacteria that may influence the fitness of their hosts. As regard the aim of this study was to test the metabolic potential of bacterial strains, isolated from the bark beetle species Cryphalus piceae, Ips typographus and Pityophthorus pityophthorus and collected in the Czech Republic from fir, spruce and pine trees, respectively, to degrade plant cell compounds. The bacterial strains were identified as belonging to the genera Curtobacterium, Erwinia, Pantoea, Pseudomonas, Rahnella, Staphylococcus, and Yersinia...
November 11, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29136200/prodoric2-the-bacterial-gene-regulation-database-in-2018
#8
Denitsa Eckweiler, Christian-Alexander Dudek, Juliane Hartlich, David Brötje, Dieter Jahn
Bacteria adapt to changes in their environment via differential gene expression mediated by DNA binding transcriptional regulators. The PRODORIC2 database hosts one of the largest collections of DNA binding sites for prokaryotic transcription factors. It is the result of the thoroughly redesigned PRODORIC database. PRODORIC2 is more intuitive and user-friendly. Besides significant technical improvements, the new update offers more than 1000 new transcription factor binding sites and 110 new position weight matrices for genome-wide pattern searches with the Virtual Footprint tool...
November 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29134709/light-sensing-by-opsins-and-fungal-ecology-nop-1-modulates-entry-into-sexual-reproduction-in-response-to-environmental-cues
#9
Zheng Wang, Junrui Wang, Ning Li, Jigang Li, Frances Trail, Jay C Dunlap, Jeffrey P Townsend
Understanding the genetic basis of the switch from asexual to sexual lifestyles in response to sometimes rapid environmental changes is one of the major challenges in fungal ecology. Light appears to play a critical role in the switch-but fungal genomes harbor diverse light sensors. Fungal opsins are homologous to bacterial green-light sensory rhodopsins, and their organismal functions in fungi have not been well understood. Three of these opsin-like proteins were widely distributed across fungal genomes, but homologs of the Fusarium opsin-like protein CarO were present only in plant-associated fungi...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29134663/multiple-plasmid-borne-virulence-genes-of-clavibacter-michiganensis-ssp-capsici-critical-for-disease-development-in-pepper
#10
In Sun Hwang, Eom-Ji Oh, Donghyuk Kim, Chang-Sik Oh
Clavibacter michiganensis ssp. capsici is a Gram-positive plant-pathogenic bacterium causing bacterial canker disease in pepper. Virulence genes and mechanisms of C. michiganensis ssp. capsici in pepper have not yet been studied. To identify virulence genes of C. michiganensis ssp. capsici, comparative genome analyses with C. michiganensis ssp. capsici and its related C. michiganensis subspecies, and functional analysis of its putative virulence genes during infection were performed. The C. michiganensis ssp...
November 14, 2017: New Phytologist
https://www.readbyqxmd.com/read/29134604/muprints-and-whole-genome-insertion-scans-methods-for-investigating-chromosome-accessibility-and-dna-dynamics-using-bacteriophage-mu
#11
N Patrick Higgins
Bacteriophage Mu infects a broad range of gram-negative bacteria. After infection, Mu amplifies its DNA through a coupled transposition/replication cycle that inserts copies of Mu throughout all domains of the folded chromosome. Mu has the most relaxed target specificity of the known transposons (Manna et al., J Bacteriol 187: 3586-3588, 2005) and the Mu DNA packaging process, called "headful packaging", incorporates 50-150 bp of host sequences covalently bound to its left end and 2 kb of host DNA linked to its right end into a viral capsid...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134602/applications-of-the-bacteriophage-mu-in-vitro-transposition-reaction-and-genome-manipulation-via-electroporation-of-dna-transposition-complexes
#12
Saija Haapa-Paananen, Harri Savilahti
The capacity of transposable elements to insert into the genomes has been harnessed during the past decades to various in vitro and in vivo applications. This chapter describes in detail the general protocols and principles applicable for the Mu in vitro transposition reaction as well as the assembly of DNA transposition complexes that can be electroporated into bacterial cells to accomplish efficient gene delivery. These techniques with their modifications potentiate various gene and genome modification applications, which are discussed briefly here, and the reader is referred to the original publications for further details...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134601/transposable-bacteriophages-as-genetic-tools
#13
Ariane Toussaint
Phage Mu is the paradigm of a growing family of bacteriophages that infect a wide range of bacterial species and replicate their genome by replicative transposition. This molecular process, which is used by other mobile genetic elements to move within genomes, involves the profound rearrangement of the host genome [chromosome(s) and plasmid(s)] and can be exploited for the genetic analysis of the host bacteria and the in vivo cloning of host genes. In this chapter we review Mu-derived constructs that optimize the phage as a series of genetic tools that could inspire the development of similarly efficient tools from other transposable phages for a large spectrum of bacteria...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134599/phage-genome-annotation-using-the-rast-pipeline
#14
Katelyn McNair, Ramy Karam Aziz, Gordon D Pusch, Ross Overbeek, Bas E Dutilh, Robert Edwards
Phages are complex biomolecular machineries that have to survive in a bacterial world. Phage genomes show many adaptations to their lifestyle such as shorter genes, reduced capacity for redundant DNA sequences, and the inclusion of tRNAs in their genomes. In addition, phages are not free-living, they require a host for replication and survival. These unique adaptations provide challenges for the bioinformatics analysis of phage genomes. In particular, ORF calling, genome annotation, noncoding RNA (ncRNA) identification, and the identification of transposons and insertions are all complicated in phage genome analysis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134596/preparing-cdna-libraries-from-lytic-phage-infected-cells-for-whole-transcriptome-analysis-by-rna-seq
#15
Bob Blasdel, Pieter-Jan Ceyssens, Rob Lavigne
Whole genome wide analysis of transcription using RNA-Seq methods is a powerful way to elucidate differential expression of gene features in bacteria across different conditions as well as for discovering previously exotic RNA species. Indeed, RNA sequencing has revolutionized the study of bacterial transcription with the diversity and quantity of small noncoding RNA elements that have been found and its ability to clearly define operons, promoters , and terminators . We discuss our experience with applying RNA sequencing technology to analyzing the lytic cycle, including extraction, processing, and a guide to the customized statistical analysis necessary for analyzing differential host and phage transcription...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134117/identification-of-nonserotypeable-shigella-spp-using-genome-sequencing-a-step-forward
#16
Muthuirulandi Sethuvel Dhiviya Prabaa, Devanga Ragupathi Naveen Kumar, Inbanathan Francis Yesurajan, Shalini Anandan, Walia Kamini, Veeraraghavan Balaji
Aim: Sequencing technology has replaced conventional methods in identifying and characterizing bacterial pathogens. We characterized 23 nonserotypeable Shigella that biochemically resembled Shigella spp. using whole genome sequencing. Materials & methods: Genome sequences were analyzed using online tools based on 16S rRNA, k-mer, gyrB sequences and analysis of O-antigen arrangement was done using PATRIC database for species identification. Sequence types, plasmid types, antimicrobial resistance and virulence genes were also investigated...
November 2017: Future Science OA
https://www.readbyqxmd.com/read/29133883/pseudomonas-aeruginosa-defends-against-phages-through-type-iv-pilus-glycosylation
#17
Hanjeong Harvey, Joseph Bondy-Denomy, Hélène Marquis, Kristina M Sztanko, Alan R Davidson, Lori L Burrows
Since phages present a major challenge to survival in most environments, bacteria express a battery of anti-phage defences including CRISPR-Cas, restriction-modification and abortive infection systems (1-4) . Such strategies are effective, but the phage genome-which encodes potentially inhibitory gene products-is still allowed to enter the cell. The safest way to preclude phage infection is to block initial phage adsorption to the cell. Here, we describe a cell-surface modification that blocks infection by certain phages...
November 13, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29132331/adaptation-of-the-goldenbraid-modular-cloning-system-and-creation-of-a-toolkit-for-the-expression-of-heterologous-proteins-in-yeast-mitochondria
#18
Ana Pérez-González, Ryan Kniewel, Marcel Veldhuizen, Hemant K Verma, Mónica Navarro-Rodríguez, Luis M Rubio, Elena Caro
BACKGROUND: There is a need for the development of synthetic biology methods and tools to facilitate rapid and efficient engineering of yeast that accommodates the needs of specific biotechnology projects. In particular, the manipulation of the mitochondrial proteome has interesting potential applications due to its compartmentalized nature. One of these advantages resides in the fact that metalation occurs after protein import into mitochondria, which contains pools of iron, zinc, copper and manganese ions that can be utilized in recombinant metalloprotein metalation reactions...
November 13, 2017: BMC Biotechnology
https://www.readbyqxmd.com/read/29132318/bugmat-and-findneighbour-command-line-and-server-applications-for-investigating-bacterial-relatedness
#19
Oriol Mazariegos-Canellas, Trien Do, Tim Peto, David W Eyre, Anthony Underwood, Derrick Crook, David H Wyllie
BACKGROUND: Large scale bacterial sequencing has made the determination of genetic relationships within large sequence collections of bacterial genomes derived from the same microbial species an increasingly common task. Solutions to the problem have application to public health (for example, in the detection of possible disease transmission), and as part of divide-and-conquer strategies selecting groups of similar isolates for computationally intensive methods of phylogenetic inference using (for example) maximal likelihood methods...
November 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29132315/comprehensive-genomic-analysis-of-the-cngc-gene-family-in-brassica-oleracea-novel-insights-into-synteny-structures-and-transcript-profiles
#20
Kaleem U Kakar, Zarqa Nawaz, Khadija Kakar, Essa Ali, Abdulwareth A Almoneafy, Raqeeb Ullah, Xue-Liang Ren, Qing-Yao Shu
BACKGROUND: The cyclic nucleotide-gated ion channel (CNGC) family affects the uptake of cations, growth, pathogen defence, and thermotolerance in plants. However, the systematic identification, origin and function of this gene family has not been performed in Brassica oleracea, an important vegetable crop and genomic model organism. RESULTS: In present study, we identified 26 CNGC genes in B. oleracea genome, which are non-randomly localized on eight chromosomes, and classified into four major (I-IV) and two sub-groups (i...
November 13, 2017: BMC Genomics
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