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https://www.readbyqxmd.com/read/29233894/importance-of-core-genome-functions-for-an-extreme-antibiotic-resistance-trait
#1
Larry A Gallagher, Samuel A Lee, Colin Manoil
Extreme antibiotic resistance in bacteria is associated with the expression of powerful inactivating enzymes and other functions encoded in accessory genomic elements. The contribution of core genome processes to high-level resistance in such bacteria has been unclear. In the work reported here, we evaluated the relative importance of core and accessory functions for high-level resistance to the aminoglycoside tobramycin in the nosocomial pathogen Acinetobacter baumannii Three lines of evidence establish the primacy of core functions in this resistance...
December 12, 2017: MBio
https://www.readbyqxmd.com/read/29233893/diversification-of-type-vi-secretion-system-toxins-reveals-ancient-antagonism-among-bee-gut-microbes
#2
Margaret I Steele, Waldan K Kwong, Marvin Whiteley, Nancy A Moran
Microbial communities are shaped by interactions among their constituent members. Some Gram-negative bacteria employ type VI secretion systems (T6SSs) to inject protein toxins into neighboring cells. These interactions have been theorized to affect the composition of host-associated microbiomes, but the role of T6SSs in the evolution of gut communities is not well understood. We report the discovery of two T6SSs and numerous T6SS-associated Rhs toxins within the gut bacteria of honey bees and bumble bees. We sequenced the genomes of 28 strains of Snodgrassella alvi, a characteristic bee gut microbe, and found tremendous variability in their Rhs toxin complements: altogether, these strains appear to encode hundreds of unique toxins...
December 12, 2017: MBio
https://www.readbyqxmd.com/read/29232043/an-erwinia-amylovora-yjek-mutant-exhibits-reduced-virulence-increased-chemical-sensitivity-and-numerous-environmentally-dependent-proteomic-alterations
#3
Sara Klee, Islam Mostafa, Sixue Chen, Craig Dufresne, Brian L Lehman, Judith P Sinn, Kari A Peter, Timothy W McNellis
The gram-negative bacterium Erwinia amylovora causes fire blight, an economically-important disease of apples and pears. Elongation Factor P (EF-P) is a highly conserved protein that stimulates the formation of the first peptide bond of certain proteins and facilitates translation of certain proteins, including those with polyproline motifs. YjeK and YjeA are two enzymes involved in the essential post-translational β-lysylation of EF-P at a conserved lysine residue, K34. EF-P, YjeA, and YjeK have been shown to be essential for full virulence of Escherichia coli, Salmonella species, and Agrobacterium tumefaciens, with efp, yjeA, and yjeK mutants having highly similar phenotypes...
December 12, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29230204/a-comprehensive-overview-of-online-resources-to-identify-and-predict-bacterial-essential-genes
#4
REVIEW
Chong Peng, Yan Lin, Hao Luo, Feng Gao
Genes critical for the survival or reproduction of an organism in certain circumstances are classified as essential genes. Essential genes play a significant role in deciphering the survival mechanism of life. They may be greatly applied to pharmaceutics and synthetic biology. The continuous progress of experimental method for essential gene identification has accelerated the accumulation of gene essentiality data which facilitates the study of essential genes in silico. In this article, we present some available online resources related to gene essentiality, including bioinformatic software tools for transposon sequencing (Tn-seq) analysis, essential gene databases and online services to predict bacterial essential genes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29229976/a-novel-tn1696-like-composite-transposon-tn6404-harboring-bla-imp-4-in-a-klebsiella-pneumoniae-isolate-carrying-a-rare-esbl-gene-bla-sfo-1
#5
Kai Zhou, Wei Yu, Ping Shen, Haifeng Lu, Baohong Wang, John W A Rossen, Yonghong Xiao
Genetic determinants of a clinical Klebsiella pneumoniae isolate (KP1814) coproducing IMP-4 and a rare ESBL gene SFO-1 was investigated. KP1814 belongs to a novel sequence type (ST) assigned to ST2270. WGS identified four circular DNA sequences in KP1814, including two multidrug-resistance (MDR) plasmids, one virulence plasmid, and one circular form. The MDR plasmid pKP1814-1 (299.9 Kb) is untypeable, and carries two large mosaic multiresistance regions (MRRs). bla SFO-1 and bla IMP-4 co-exists on MRR1, and bla SFO-1 is associated with an IS/Tn-independent genetic context...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29229542/random-knock-in-expression-system-for-high-yield-production-of-heterologous-protein-in-bacillus-subtilis
#6
Da-Eun Jeong, Younju So, Soo-Young Park, Seung-Hwan Park, Soo-Keun Choi
Chromosome-integrated recombinant protein expression in bacteria has advantages for the stable maintenance of genes without any use of antibiotics during large-scale fermentation. Even though different levels of gene expression were reported, depending upon their chromosomal position in bacterial species, only a limited number of integration sites have been used in B. subtilis. In this study, we randomly integrated the GFP and AprE expression cassettes into the B. subtilis genome to determine integration sites that can produce a high yield of heterologous protein expression...
December 8, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/29228556/riemerella-anatipestifer-m949_0459-gene-is-responsible-for-the-bacterial-resistance-to-tigecycline
#7
Tao Li, Min Shan, Jing He, Xiaolan Wang, Shaohui Wang, Mingxing Tian, Jingjing Qi, Tingrong Luo, Yonghong Shi, Chan Ding, Shengqing Yu
Based on its important role in last-line therapeutics against multidrug-resistant bacteria, tigecycline has been increasingly important in treating infections. However, mounting reports on tigecycline-resistant bacterial strains isolated from different sources are of concern, and molecular mechanisms regarding tigecycline resistance are poorly understood. Riemerella anatipestifer is a Gram-negative, non-motile, non-spore-forming, rod-shaped bacterium, which causes fibrinous pericarditis, perihepatitis, and meningitis in infected ducks...
November 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228286/cut-and-paste-transposons-in-fungi-with-diverse-lifestyles
#8
Anna Muszewska, Kamil Steczkiewicz, Marta Stepniewska-Dziubinska, Krzysztof Ginalski
Transposons (TEs) shape genomes via recombination and transposition, lead to chromosomal rearrangements, create new gene neighbourhoods and alter gene expression. They play key roles in adaptation either to symbiosis in Amanita genus or to pathogenicity in Pyrenophora tritici-repentis. Despite growing evidence of their importance, the abundance and distribution of mobile elements replicating in a "cut and paste" fashion is barely described so far. In order to improve our knowledge on this old and ubiquitous class of transposable elements, 1,730 fungal genomes were scanned using both de novo and homology-based approaches...
December 8, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29228229/variable-plasmid-fitness-effects-and-mobile-genetic-element-dynamics-across-pseudomonas-species
#9
Anastasia Kottara, James P J Hall, Ellie Harrison, Michael A Brockhurst
Mobile genetic elements (MGE) such as plasmids and transposons mobilise genes within and between species, playing a crucial role in bacterial evolution via horizontal gene transfer (HGT). Currently we lack data on variation in MGE dynamics across bacterial host species. We tracked the dynamics of a large conjugative plasmid, pQBR103, and its Tn5042 mercury resistance transposon, in five diverse Pseudomonas species in environments with and without mercury selection. Plasmid fitness effects and stability varied extensively between host species and environments, as did the propensity for chromosomal capture of the Tn5042 mercury resistance transposon associated with loss of the plasmid...
December 4, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29226517/natural-selection-beyond-genes-identification-and-analyses-of-evolutionarily-conserved-elements-in-the-genome-of-the-collared-flycatcher-ficedula-albicollis
#10
Rory J Craig, Alexander Suh, Mi Wang, Hans Ellegren
It is becoming increasingly clear that a significant proportion of the functional sequence within eukaryotic genomes is noncoding. However, since the identification of conserved elements (CEs) has been restricted to a limited number of model organisms, the dynamics and evolutionary character of the genomic landscape of conserved, and hence likely functional, sequence is poorly understood in most species. Moreover, identification and analysis of the full suite of functional sequence is particularly important for the understanding of the genetic basis of trait loci identified in genome scans or quantitative trait locus mapping efforts...
December 11, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29223450/pesticide-degrading-natural-multidrug-resistance-bacterial-flora
#11
REVIEW
Kirubakaran Rangasamy, Murugan Athiappan, Natarajan Devarajan, Gopinath Samykannu, Javid A Parray, K N Aruljothi, Nowsheen Shameem, Abdulaziz A Alqarawi, Abeer Hashem, Elsayed Fathi Abd Allah
Multidrug-resistant (MDR) bacteria are a growing threat to humans across the world. Antibiotic resistance is a global problem that has developed through continuous antibiotic use, combinatorial antibiotic use, pesticide-antibiotic cross-resistance, and horizontal gene transfer, as well as various other modes. Pesticide-antibiotic cross-resistance and the subsequent expansion of drug-resistant bacteria are critically documented in this review, the primary focus of which is to assess the impact of indiscriminate pesticide use on the development of microbial communities with parallel pesticide and multidrug resistance...
December 6, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29216827/comparative-genomic-analysis-of-brevibacterium-strains-insights-into-key-genetic-determinants-involved-in-adaptation-to-the-cheese-habitat
#12
Nguyen-Phuong Pham, Séverine Layec, Eric Dugat-Bony, Marie Vidal, Françoise Irlinger, Christophe Monnet
BACKGROUND: Brevibacterium strains are widely used for the manufacturing of surface-ripened cheeses, contributing to the breakdown of lipids and proteins and producing volatile sulfur compounds and red-orange pigments. The objective of the present study was to perform comparative genomic analyses in order to better understand the mechanisms involved in their ability to grow on the cheese surface and the differences between the strains. RESULTS: The genomes of 23 Brevibacterium strains, including twelve strains isolated from cheeses, were compared for their gene repertoire involved in salt tolerance, iron acquisition, bacteriocin production and the ability to use the energy compounds present in cheeses...
December 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29211718/pirna-mediated-regulation-of-transposon-alternative-splicing-in-the-soma-and-germ-line
#13
Felipe Karam Teixeira, Martyna Okuniewska, Colin D Malone, Rémi-Xavier Coux, Donald C Rio, Ruth Lehmann
Transposable elements can drive genome evolution, but their enhanced activity is detrimental to the host and therefore must be tightly regulated. The Piwi-interacting small RNA (piRNA) pathway is vital for the regulation of transposable elements, by inducing transcriptional silencing or post-transcriptional decay of mRNAs. Here we show that piRNAs and piRNA biogenesis components regulate precursor mRNA splicing of P-transposable element transcripts in vivo, leading to the production of the non-transposase-encoding mature mRNA isoform in Drosophila germ cells...
December 6, 2017: Nature
https://www.readbyqxmd.com/read/29211708/selective-silencing-of-euchromatic-l1s-revealed-by-genome-wide-screens-for-l1-regulators
#14
Nian Liu, Cameron H Lee, Tomek Swigut, Edward Grow, Bo Gu, Michael Bassik, Joanna Wysocka
Transposable elements (TEs) are now recognized not only as parasitic DNA, whose spread in the genome must be controlled by the host, but also as major players in genome evolution and regulation1-6. Long INterspersed Element-1 (LINE-1 or L1), the only currently autonomous mobile transposon in humans, occupies 17% of the genome and continues to generate inter- and intra-individual genetic variation, in some cases resulting in disease1-7. Nonetheless, how L1 activity is controlled and what function L1s play in host gene regulation remain incompletely understood...
December 6, 2017: Nature
https://www.readbyqxmd.com/read/29209580/the-pht4-1-3-mutant-line-contains-a-loss-of-function-allele-in-the-fatty-acid-desaturase-7-gene-caused-by-a-remnant-inactivated-selection-marker-a-cautionary-tale
#15
Anders K Nilsson, Mats X Andersson
A striking and unexpected biochemical phenotype was found in an insertion mutant line in the model plant Arabidopsis thaliana. One of two investigated insertion mutant lines in the gene encoding the phosphate transporter PHT4;1 demonstrated a prominent loss of trienoic fatty acids, whereas the other insertion line was indistinguishable from wild type in this aspect. We demonstrate that the loss of trienoic fatty acids was due to a remnant inactive negative selection marker gene in this particular transposon tagged line, pht4;1-3...
2017: PeerJ
https://www.readbyqxmd.com/read/29209072/free-sepf-interferes-with-recruitment-of-late-cell-division-proteins
#16
Yongqiang Gao, Michaela Wenzel, Martijs J Jonker, Leendert W Hamoen
The conserved cell division protein SepF aligns polymers of FtsZ, the key cell division protein in bacteria, during synthesis of the (Fts)Z-ring at midcell, the first stage in cytokinesis. In addition, SepF acts as a membrane anchor for the Z-ring. Recently, it was shown that SepF overexpression in Mycobacterium smegmatis blocks cell division. Why this is the case is not known. Surprisingly, we found in Bacillus subtilis that SepF overproduction does not interfere with Z-ring assembly, but instead blocks assembly of late division proteins responsible for septum synthesis...
December 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29208130/novel-large-scale-chromosomal-transfer-in-bacteroides-fragilis-contributes-to-its-pan-genome-and-rapid-environmental-adaptation
#17
Fasahath Husain, Kevin Tang, Yaligara Veeranagouda, Renata Boente, Sheila Patrick, Garry Blakely, Hannah M Wexler
Bacteroides fragilis, an important component of the human gastrointestinal microbiota, can cause lethal extra-intestinal infection upon escape from the gastrointestinal tract. We demonstrated transfer and recombination of large chromosomal segments from B. fragilis HMW615, a multidrug resistant clinical isolate, to B. fragilis 638R. In one example, the transfer of a segment of ~435 Kb/356 genes replaced ~413 Kb/326 genes of the B. fragilis 638R chromosome. In addition to transfer of antibiotic resistance genes, these transfers (1) replaced complete divergent polysaccharide biosynthesis loci; (2) replaced DNA inversion-controlled intergenic shufflons (that control expression of genes encoding starch utilization system outer membrane proteins) with more complex, divergent shufflons; and (3) introduced additional intergenic shufflons encoding divergent Type 1 restriction/modification systems...
November 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29208119/comparative-analysis-of-the-burkholderia-cenocepacia-k56-2-essential-genome-reveals-cell-envelope-functions-that-are-uniquely-required-for-survival-in-species-of-the-genus-burkholderia
#18
April S Gislason, Keith Turner, Mike Domaratzki, Silvia T Cardona
Burkholderia cenocepacia K56-2 belongs to the Burkholderia cepacia complex, a group of Gram-negative opportunistic pathogens that have large and dynamic genomes. In this work, we identified the essential genome of B. cenocepacia K56-2 using high-density transposon mutagenesis and insertion site sequencing (Tn-seq circle). We constructed a library of one million transposon mutants and identified the transposon insertions at an average of one insertion per 27 bp. The probability of gene essentiality was determined by comparing of the insertion density per gene with the variance of neutral datasets generated by Monte Carlo simulations...
November 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29205551/regulatory-genes-coordinating-antibiotic-induced-changes-in-promoter-activity-and-early-transcriptional-termination-of-the-mycobacterial-intrinsic-resistance-gene-whib7
#19
Ján Burian, Charles J Thompson
Diseases caused by various Mycobacterium sp., especially Mycobacterium tuberculosis, are a major burden on global health care. Due to high intrinsic antibiotic resistance, treatment options are severely limited. In mycobacteria, WhiB7 coordinates intrinsic resistance to a broad range of antibiotics. While WhiB7 has been established as an auto-regulatory transcriptional activator, the signals and genes needed to induce its expression are poorly understood. Using Mycobacterium smegmatis as a model, we coupled transposon mutagenesis and next generation sequencing with WhiB7-specific antibiotic selection to identify genes that contribute to WhiB7 regulation and function...
December 4, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/29201017/characterization-of-metagenomes-in-urban-aquatic-compartments-reveals-high-prevalence-of-clinically-relevant-antibiotic-resistance-genes-in-wastewaters
#20
Charmaine Ng, Martin Tay, Boonfei Tan, Thai-Hoang Le, Laurence Haller, Hongjie Chen, Tse H Koh, Timothy M S Barkham, Karina Y-H Gin
The dissemination of antimicrobial resistance (AMR) is an escalating problem and a threat to public health. Comparative metagenomics was used to investigate the occurrence of antibiotic resistant genes (ARGs) in wastewater and urban surface water environments in Singapore. Hospital and municipal wastewater (n = 6) were found to have higher diversity and average abundance of ARGs (303 ARG subtypes, 197,816 x/Gb) compared to treated wastewater effluent (n = 2, 58 ARG subtypes, 2,692 x/Gb) and surface water (n = 5, 35 subtypes, 7,985 x/Gb)...
2017: Frontiers in Microbiology
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