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https://www.readbyqxmd.com/read/27924916/insights-into-functional-and-evolutionary-analysis-of-carbaryl-metabolic-pathway-from-pseudomonas-sp-strain-c5pp
#1
Vikas D Trivedi, Pramod Kumar Jangir, Rakesh Sharma, Prashant S Phale
Carbaryl (1-naphthyl N-methylcarbamate) is a most widely used carbamate pesticide in the agriculture field. Soil isolate, Pseudomonas sp. strain C5pp mineralizes carbaryl via 1-naphthol, salicylate and gentisate, however the genetic organization and evolutionary events of acquisition and assembly of pathway have not yet been studied. The draft genome analysis of strain C5pp reveals that the carbaryl catabolic genes are organized into three putative operons, 'upper', 'middle' and 'lower'. The sequence and functional analysis led to identification of new genes encoding: i) hitherto unidentified 1-naphthol 2-hydroxylase, sharing a common ancestry with 2,4-dichlorophenol monooxygenase; ii) carbaryl hydrolase, a member of a new family of esterase; and iii) 1,2-dihydroxy naphthalene dioxygenase, uncharacterized type-II extradiol dioxygenase...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27923578/characterization-of-antibiotic-resistance-genes-in-representative-organic-solid-wastes-food-waste-recycling-wastewater-manure-and-sewage-sludge
#2
Jangwoo Lee, Seung Gu Shin, Hyun Min Jang, Young Beom Kim, Joonyeob Lee, Young Mo Kim
In this research, the distribution of antibiotic resistance genes (ARGs) was characterized in representative organic solid waste (OSW) in Korea: food waste-recycling wastewater (FRW), manure, and sewage sludge. The amounts of total ARG (gene copies/16S rRNA gene copies) was greatest in manure followed by sewage sludge and FRW. Interestingly, there were significantly different patterns in the diversity and mechanisms of ARGs. For example, a significant proportion of ARGs were tetracycline resistant genes in all the OSW (40...
December 3, 2016: Science of the Total Environment
https://www.readbyqxmd.com/read/27923069/characterization-in-helicobacter-pylori-of-a-nickel-transporter-essential-for-colonization-that-was-acquired-during-evolution-by-gastric-helicobacter-species
#3
Frédéric Fischer, Marie Robbe-Saule, Evelyne Turlin, Francesco Mancuso, Valérie Michel, Pierre Richaud, Frédéric J Veyrier, Hilde De Reuse, Daniel Vinella
Metal acquisition is crucial for all cells and for the virulence of many bacterial pathogens. In particular, nickel is a virulence determinant for the human gastric pathogen Helicobacter pylori as it is the cofactor of two enzymes essential for in vivo colonization, urease and a [NiFe] hydrogenase. To import nickel despite its scarcity in the human body, H. pylori requires efficient uptake mechanisms that are only partially defined. Indeed, alternative ways of nickel entry were predicted to exist in addition to the well-described NixA permease...
December 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27922601/the-effect-of-extrinsic-mortality-on-genome-size-evolution-in-prokaryotes
#4
Piotr Bentkowski, Cock van Oosterhout, Ben Ashby, Thomas Mock
Mortality has a significant role in prokaryotic ecology and evolution, yet the impact of variations in extrinsic mortality on prokaryotic genome evolution has received little attention. We used both mathematical and agent-based models to reveal how variations in extrinsic mortality affect prokaryotic genome evolution. Our results suggest that the genome size of bacteria increases with increased mortality. A high extrinsic mortality increases the pool of free resources and shortens life expectancy, which selects for faster reproduction, a phenotype we called 'scramblers'...
December 6, 2016: ISME Journal
https://www.readbyqxmd.com/read/27922269/genomic-study-of-the-type-ivc-secretion-system-in-clostridium-difficile-understanding-c-difficile-evolution-via-horizontal-gene-transfer
#5
Wen Zhang, Ying Cheng, Pengcheng Du, Yuanyuan Zhang, Hongbing Jia, Xianping Li, Jing Wang, Na Han, Yujun Qiang, Chen Chen, Jinxing Lu
Clostridium difficile, the etiological agent of Clostridium difficile infection (CDI), is a gram-positive, spore-forming bacillus that is responsible for ∼20% of antibiotic-related cases of diarrhea and nearly all cases of pseudomembranous colitis. Previous data have shown that a substantial proportion (11%) of the C. difficile genome consists of mobile genetic elements, including seven conjugative transposons. However, the mechanism underlying the formation of a mosaic genome in C. difficile is unknown. The type-IV secretion system (T4SS) is the only secretion system known to transfer DNA segments among bacteria...
August 30, 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/27922098/comparison-of-432-pseudomonas-strains-through-integration-of-genomic-functional-metabolic-and-expression-data
#6
Jasper J Koehorst, Jesse C J van Dam, Ruben G A van Heck, Edoardo Saccenti, Vitor A P Martins Dos Santos, Maria Suarez-Diez, Peter J Schaap
Pseudomonas is a highly versatile genus containing species that can be harmful to humans and plants while others are widely used for bioengineering and bioremediation. We analysed 432 sequenced Pseudomonas strains by integrating results from a large scale functional comparison using protein domains with data from six metabolic models, nearly a thousand transcriptome measurements and four large scale transposon mutagenesis experiments. Through heterogeneous data integration we linked gene essentiality, persistence and expression variability...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27919802/integrative-view-of-2-oxoglutarate-fe-ii-dependent-oxygenase-diversity-and-functions-in-bacteria
#7
Baolei Jia, Xiaomeng Jia, Kyung Hyun Kim, Che Ok Jeon
BACKGROUND: The 2-oxoglutarate/Fe(II)-dependent oxygenase (2OG oxygenase) superfamily is extremely diverse and includes enzymes responsible for protein modification, DNA and mRNA repair, and synthesis of secondary metabolites. METHODS: To investigate the evolutionary relationship and make functional inferences within this remarkably diverse superfamily in bacteria, we used a protein sequence similarity network and other bioinformatics tools to analyze the bacterial proteins in the superfamily...
December 2, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27917926/clonal-spread-of-mcr-1-in-pmqr-carrying-st34-salmonella-isolates-from-animals-in-china
#8
Xing-Ping Li, Liang-Xing Fang, Jia-Qi Song, Jing Xia, Wei Huo, Jin-Tao Fang, Xiao-Ping Liao, Ya-Hong Liu, Youjun Feng, Jian Sun
Since initial identification in China, the widespread geographical occurrence of plasmid-mediated colistin resistance gene mcr-1 in Enterobacteriaceae has been of great concern. In this study, a total of 22 Salmonella enterica were resistant to colistin, while only five isolates which belonged to ST34 Salmonella enterica serovar Typhimurium (S. Typhimurium) were mcr-1 positive. Four of them shared nearly identical PFGE type, although they were from different host species and diverse geographical locations. All the mcr-1-positive S...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27917155/aerobic-lineage-of-the-oxidative-stress-response-protein-rubrerythrin-emerged-in-an-ancient-microaerobic-hyper-thermophilic-environment
#9
Juan P Cardenas, Raquel Quatrini, David S Holmes
Rubrerythrins (RBRs) are non-heme di-iron proteins belonging to the ferritin-like superfamily. They are involved in oxidative stress defense as peroxide scavengers in a wide range of organisms. The vast majority of RBRs, including classical forms of this protein, contain a C-terminal rubredoxin-like domain involved in electron transport that is used during catalysis in anaerobic conditions. Rubredoxin is an ancient and large protein family of short length (<100 residues) that contains a Fe-S center involved in electron transfer...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27915286/presence-of-diverse-rhizobial-communities-responsible-for-nodulation-of-common-bean-phaseolus-vulgaris-in-south-african-and-mozambican-soils
#10
Mwazuma K Zinga, Sanjay K Jaiswal, Felix D Dakora
The diversity and phylogeny of root-nodule bacteria isolated from common bean grown in Mozambique and different provinces of South Africa was studied by restriction fragment length polymorphism and phylogenetic analysis. The combined restriction banding pattern of 16S rRNA and nifH profile-generated dendrogram grouped all test isolates into four major clusters with XXI restriction group and three clusters with the VIII restriction groups. Location-based clustering was observed with the 16S-RFLP analysis. Phylogenetic analysis of 16S rRNA, glnII, gyrB and gltA sequences showed that common bean was nodulated specifically by Rhizobium etli in Mozambican soils, and by diverse of group of Rhizobium species in South African soils (e...
December 2, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27915087/genetically-unrelated-multidrug-and-carbapenem-resistant-citrobacter-freundii-detected-in-outpatients-admitted-to-a-portuguese-hospital
#11
Cátia Santos, Elmano Ramalheira, Gabriela Da Silva, Sónia Mendo
OBJECTIVES: Non-clonal, carbapenem- and multidrug-resistant Citrobacter freundii isolates were collected from unrelated outpatients admitted to a Portuguese hospital emergency department. One patient lived in a nursing home and was never hospitalised, whereas the other patient was repeatedly hospitalised in this hospital. The aim of this study was to unveil the molecular mechanisms associated with the carbapenem resistance of these isolates and to assess its potential dissemination. METHODS: Isolate identification was performed by VITEK(®)2 and was confirmed by 16S rDNA sequencing...
November 15, 2016: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/27914300/structure-based-analysis-of-bacilli-and-plasmid-dihydrofolate-reductase-evolution
#12
Mona Alotaibi, Ben Delos Reyes, Tin Le, Phuong Luong, Faramarz Valafar, Robert P Metzger, Gary B Fogel, David Hecht
Dihydrofolate reductase (DHFR), a key enzyme in tetrahydrofolate-mediated biosynthetic pathways, has a structural motif known to be highly conserved over a wide range of organisms. Given its critical role in purine and amino acid synthesis, DHFR is a well established therapeutic target for treating a wide range of prokaryotic and eukaryotic infections as well as certain types of cancer. Here we present a structural-based computer analysis of bacterial (Bacilli) and plasmid DHFR evolution. We generated a structure-based sequence alignment using 7 wild-type DHFR x-ray crystal structures obtained from the RCSB Protein Data Bank and 350 chromosomal and plasmid homology models we generated from sequences obtained from the NCBI Protein Database...
November 22, 2016: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/27913727/regulated-complex-assembly-safeguards-the-fidelity-of-sleeping-beauty-transposition
#13
Yongming Wang, Diana Pryputniewicz-Dobrinska, Enikö Éva Nagy, Christopher D Kaufman, Manvendra Singh, Steve Yant, Jichang Wang, Anna Dalda, Mark A Kay, Zoltán Ivics, Zsuzsanna Izsvák
The functional relevance of the inverted repeat structure (IR/DR) in a subgroup of the Tc1/mariner superfamily of transposons has been enigmatic. In contrast to mariner transposition, where a topological filter suppresses single-ended reactions, the IR/DR orchestrates a regulatory mechanism to enforce synapsis of the transposon ends before cleavage by the transposase occurs. This ordered assembly process shepherds primary transposase binding to the inner 12DRs (where cleavage does not occur), followed by capture of the 12DR of the other transposon end...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27913675/motility-and-adhesion-through-type-iv-pili-in-gram-positive-bacteria
#14
REVIEW
Kurt H Piepenbrink, Eric J Sundberg
Type IV pili are hair-like bacterial surface appendages that play a role in diverse processes such as cellular adhesion, colonization, twitching motility, biofilm formation, and horizontal gene transfer. These extracellular fibers are composed exclusively or primarily of many copies of one or more pilin proteins, tightly packed in a helix so that the highly hydrophobic amino-terminus of the pilin is buried in the pilus core. Type IV pili have been characterized extensively in Gram-negative bacteria, and recent advances in high-throughput genomic sequencing have revealed that they are also widespread in Gram-positive bacteria...
December 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27912842/the-rapid-spread-of-carbapenem-resistant-enterobacteriaceae
#15
REVIEW
Robert F Potter, Alaric W D'Souza, Gautam Dantas
Carbapenems, our one-time silver bullet for multidrug resistant bacterial infections, are now threatened by widespread dissemination of carbapenem-resistant Enterobacteriaceae (CRE). Successful expansion of Enterobacteriaceae clonal groups and frequent horizontal gene transfer of carbapenemase expressing plasmids are causing increasing carbapenem resistance. Recent advances in genetic and phenotypic detection facilitate global surveillance of CRE diversity and prevalence. In particular, whole genome sequencing enabled efficient tracking, annotation, and study of genetic elements colocalized with carbapenemase genes on chromosomes and on plasmids...
November 2016: Drug Resistance Updates: Reviews and Commentaries in Antimicrobial and Anticancer Chemotherapy
https://www.readbyqxmd.com/read/27911777/siderophore-based-microbial-adaptations-to-iron-scarcity-across-the-eastern-pacific-ocean
#16
Rene M Boiteau, Daniel R Mende, Nicholas J Hawco, Matthew R McIlvin, Jessica N Fitzsimmons, Mak A Saito, Peter N Sedwick, Edward F DeLong, Daniel J Repeta
Nearly all iron dissolved in the ocean is complexed by strong organic ligands of unknown composition. The effect of ligand composition on microbial iron acquisition is poorly understood, but amendment experiments using model ligands show they can facilitate or impede iron uptake depending on their identity. Here we show that siderophores, organic compounds synthesized by microbes to facilitate iron uptake, are a dynamic component of the marine ligand pool in the eastern tropical Pacific Ocean. Siderophore concentrations in iron-deficient waters averaged 9 pM, up to fivefold higher than in iron-rich coastal and nutrient-depleted oligotrophic waters, and were dominated by amphibactins, amphiphilic siderophores with cell membrane affinity...
December 1, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27908230/dna-import-into-mitochondria
#17
REVIEW
Yu M Konstantinov, A Dietrich, F Weber-Lotfi, N Ibrahim, E S Klimenko, V I Tarasenko, T A Bolotova, M V Koulintchenko
In recent decades, it has become evident that the condition for normal functioning of mitochondria in higher eukaryotes is the presence of membrane transport systems of macromolecules (proteins and nucleic acids). Natural competence of the mitochondria in plants, animals, and yeasts to actively uptake DNA may be directly related to horizontal gene transfer into these organelles occurring at much higher rate compared to the nuclear and chloroplast genomes. However, in contrast with import of proteins and tRNAs, little is known about the biological role and molecular mechanism underlying import of DNA into eukaryotic mitochondria...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27906133/the-plastid-genome-of-some-eustigmatophyte-algae-harbours-a-bacteria-derived-six-gene-cluster-for-biosynthesis-of-a-novel-secondary-metabolite
#18
Tatiana Yurchenko, Tereza Ševčíková, Hynek Strnad, Anzhelika Butenko, Marek Eliáš
Acquisition of genes by plastid genomes (plastomes) via horizontal gene transfer (HGT) seems to be a rare phenomenon. Here, we report an interesting case of HGT revealed by sequencing the plastomes of the eustigmatophyte algae Monodopsis sp. MarTras21 and Vischeria sp. CAUP Q 202. These plastomes proved to harbour a unique cluster of six genes, most probably acquired from a bacterium of the phylum Bacteroidetes, with homologues in various bacteria, typically organized in a conserved uncharacterized putative operon...
November 2016: Open Biology
https://www.readbyqxmd.com/read/27905116/unparalleled-replacement-of-native-mitochondrial-genes-by-foreign-homologs-in-a-holoparasitic-plant
#19
M Virginia Sanchez-Puerta, Laura E García, Josefina Wohlfeiler, Luis F Ceriotti
Horizontal gene transfer (HGT) among flowering plant mitochondria occurs frequently and, in most cases, leads to nonfunctional transgenes in the recipient genome. Parasitic plants are particularly prone to this phenomenon, but their mitochondrial genomes (mtDNA) have been largely unexplored. We undertook a large-scale mitochondrial genomic study of the holoparasitic plant Lophophytum mirabile (Balanophoraceae). Comprehensive phylogenetic analyses were performed to address the frequency, origin, and impact of HGT...
November 30, 2016: New Phytologist
https://www.readbyqxmd.com/read/27904954/the-mathematics-of-xenology-di-cographs-symbolic-ultrametrics-2-structures-and-tree-representable-systems-of-binary-relations
#20
Marc Hellmuth, Peter F Stadler, Nicolas Wieseke
The concepts of orthology, paralogy, and xenology play a key role in molecular evolution. Orthology and paralogy distinguish whether a pair of genes originated by speciation or duplication. The corresponding binary relations on a set of genes form complementary cographs. Allowing more than two types of ancestral event types leads to symmetric symbolic ultrametrics. Horizontal gene transfer, which leads to xenologous gene pairs, however, is inherent asymmetric since one offspring copy "jumps" into another genome, while the other continues to be inherited vertically...
November 30, 2016: Journal of Mathematical Biology
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