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Bacteria AND essential genes

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https://www.readbyqxmd.com/read/28096490/comprehensive-essentiality-analysis-of-the-mycobacterium-tuberculosis-genome-via-saturating-transposon-mutagenesis
#1
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/28096329/tissue-dual-rna-seq-allows-fast-discovery-of-infection-specific-functions-and-riboregulators-shaping-host-pathogen-transcriptomes
#2
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/28095319/autophagy-and-autoimmunity
#3
REVIEW
Dennis J Wu, Iannis E Adamopoulos
Autophagy is a highly conserved protein degradation pathway from yeasts to humans that is essential for removing protein aggregates and misfolded proteins in healthy cells. Recently, autophagy-related genes polymorphisms have been implicated in several autoimmune diseases including systemic lupus erythematosus, rheumatoid arthritis, psoriasis, and multiple sclerosis. Numerous studies reveal autophagy and autophagy-related proteins also participate in immune regulation. Conditional deletions of autophagy-related proteins in mice have rendered protection from experimental autoimmune encephalomyelitis, and TNF-mediated joint destruction in animal models of multiple sclerosis and experimental arthritis respectively...
January 14, 2017: Clinical Immunology: the Official Journal of the Clinical Immunology Society
https://www.readbyqxmd.com/read/28094982/bacterial-genome-editing-via-a-designed-toxin-antitoxin-cassette
#4
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/28094221/synthesis-biological-evaluation-and-molecular-docking-analysis-of-2-phenyl-benzofuran-3-carboxamide-derivatives-as-potential-inhibitors-of-staphylococcus-aureus-sortase-a
#5
Wan He, Yong Zhang, Jian Bao, Xinxian Deng, Jennifer Batara, Shawn Casey, Qiuyuan Guo, Faqin Jiang, Lei Fu
In Gram-positive bacteria, Sortase A (Srt A) is a critical cysteine transpeptidase that is responsible for recognizing and assembling surface virulence proteins through the recognition of a LPXTG (leucine, proline, X, threonine, and glycine, where X is any amino acid) signal. Mutants lacking genes for Srt A attenuate infections without affecting microbial viability. Here a series of 2-phenyl-benzofuran-3-carboxamide derivatives were synthesized and identified as potent Srt A inhibitors. Activity assays revealed that multiple compounds exhibited excellent inhibitory activity against Srt A compared with known Sortase A inhibitor pHMB (IC50=130μM)...
December 25, 2016: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28091931/identifying-anti-host-effectors-in-photorhabdus
#6
Andrea J Dowling
The death of the insect host is an essential part of the life cycle of Photorhabdus, and as a result, this bacterium comes equipped with a dazzlingly large array of toxins and virulence factors that ensure rapid insect death. Elucidation of the key players in insect infection and mortality has therefore proved difficult using traditional microbiological techniques such as individual gene knockouts due to the high level of functional redundancy displayed by Photorhabdus virulence factors. Thus, knockout of any individual toxin gene may serve to delay time to death but not to render the bacteria avirulent due to the continued presence of an array of other toxins and virulence factors in the single-gene mutant...
December 28, 2016: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/28091524/formate-simultaneously-reduces-oxidase-activity-and-enhances-respiration-in-campylobacter-jejuni
#7
Issmat I Kassem, Rosario A Candelero-Rueda, Kawthar A Esseili, Gireesh Rajashekara
The foodborne microaerophilic pathogen, Campylobacter jejuni, possesses a periplasmic formate dehydrogenase and two terminal oxidases, which serve to metabolize formate and facilitate the use of oxygen as a terminal electron acceptor, respectively. Formate, a primary energy source for C. jejuni, inhibits oxidase activity in other bacteria. Here, we hypothesized that formate might affect both energy metabolism and microaerobic survival in C. jejuni. Subsequently, we showed that C. jejuni 81-176 (wildtype) exhibited enhanced chemoattraction to and respiration of formate in comparison to other organic acids...
January 16, 2017: Scientific Reports
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
#8
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/28088479/three-dimensional-structure-of-full-length-ntrx-an-unusual-member-of-the-ntrc-family-of-response-regulators
#9
Ignacio Fernández, Irina Cornaciu, Mariela Del Carmen Carrica, Emiko Uchikawa, Guillaume Hoffmann, Rodrigo Sieira, José Antonio Márquez, Fernando A Goldbaum
Bacteria sense and adapt to environmental changes using two-component systems (TCS). These signaling pathways are formed by a histidine kinase (HK) that phosphorylates a response regulator (RR), which finally modulates the transcription of target genes. The bacterium Brucella abortus codes for a TCS formed by the HK NtrY and the RR NtrX that participates in sensing low oxygen tension and in generating an adaptive response. NtrX is a modular protein with REC, AAA+ and DNA binding domains, an architecture that classifies it among the NtrC subfamily of RRs...
January 11, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28076662/vps13f-links-bacterial-recognition-and-intracellular-killing-in-dictyostelium
#10
Jade Leiba, Ayman Sabra, Romain Bodinier, Anna Marchetti, Wanessa C Lima, Astrid Melotti, Jackie Perrin, Frederic Burdet, Marco Pagni, Thierry Soldati, Emmanuelle Lelong, Pierre Cosson
Bacterial sensing, ingestion and killing by phagocytic cells are essential processes to protect the human body from infectious microorganisms. The cellular mechanisms involved in intracellular killing, their relative importance, and their specificity towards different bacteria are however poorly defined. In this study, we used Dictyostelium discoideum, a phagocytic cell model amenable to genetic analysis, to identify new gene products involved in intracellular killing. A random genetic screen led us to identify the role of Vps13F in intracellular killing of Klebsiella pneumoniae...
January 11, 2017: Cellular Microbiology
https://www.readbyqxmd.com/read/28073944/a-novel-bifunctional-transcriptional-regulator-of-riboflavin-metabolism-in-archaea
#11
Irina A Rodionova, Matthew W Vetting, Xiaoqing Li, Steven C Almo, Andrei L Osterman, Dmitry A Rodionov
Riboflavin (vitamin B2) is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide, which are essential coenzymes in all free-living organisms. Riboflavin biosynthesis in many Bacteria but not in Archaea is controlled by FMN-responsive riboswitches. We identified a novel bifunctional riboflavin kinase/regulator (RbkR), which controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain...
January 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28073812/the-conserved-hypothetical-protein-pspto_3957-is-essential-for-virulence-in-the-plant-pathogen-pseudomonas-syringae-pv-tomato-dc3000
#12
Katherine D'Amico, Melanie J Filiatrault
The plant pathogen Pseudomonas syringae accounts for substantial crop losses and is considered an important agricultural issue. To better manage disease in the field, it is important to have an understanding of the underlying genetic mechanisms that mediate virulence. There are a substantial number of genes in sequenced bacterial genomes, including P. syringae, that encode for conserved hypothetical proteins; some of these have been functionally characterized in other Pseudomonads and have been demonstrated to play important roles in disease...
January 10, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28065920/pamps-prrs-effectors-and-r-genes-associated-with-citrus-pathogen-interactions
#13
REVIEW
Ronaldo J D Dalio, Diogo M Magalhães, Carolina M Rodrigues, Gabriella D Arena, Tiago S Oliveira, Reinaldo R Souza-Neto, Simone C Picchi, Paula M M Martins, Paulo J C Santos, Heros J Maximo, Inaiara S Pacheco, Alessandra A De Souza, Marcos A Machado
BACKGROUND: Recent application of molecular-based technologies has considerably advanced our understanding of complex processes in plant-pathogen interactions and their key components such as PAMPs, PRRs, effectors and R-genes. To develop novel control strategies for disease prevention in citrus, it is essential to expand and consolidate our knowledge of the molecular interaction of citrus plants with their pathogens. SCOPE: This review provides an overview of our understanding of citrus plant immunity, focusing on the molecular mechanisms involved in the interactions with viruses, bacteria, fungi, oomycetes and vectors related to the following diseases: tristeza, psorosis, citrus variegated chlorosis, citrus canker, huanglongbing, brown spot, post-bloom, anthracnose, gummosis and citrus root rot...
January 8, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28042081/two-short-peptidoglycan-recognition-proteins-from-crassostrea-gigas-with-similar-structure-exhibited-different-pamp-binding-activity
#14
Chuanyan Yang, Lingling Wang, Zhihao Jia, Qilin Yi, Qingsong Xu, Weilin Wang, Changhao Gong, Conghui Liu, Linsheng Song
Peptidoglycan recognition protein (PGRP) is an essential molecule in innate immunity for both invertebrates and vertebrates, owing to its prominent ability in specifically recognizing bacterial peptidoglycan (PGN) and eliminating the invading bacteria. In the present study, the full length cDNA of two PGRP genes, CgPGRPS2 and CgPGRPS4, were cloned from oyster Crassostrea gigas. Their amino acid sequences both contained one signal peptide, one typical PGRP/amidase domain with conserved catalytic residues responsible for amidase activity (55H, 90Y, 164H, 172C in CgPGRPS2, and 98H, 133Y, 207H, 215C in CgPGRPS4), and specific PGN recognition (84R, 85W, 104R, 109V in CgPGRPS2, and 127G, 128W, 147R, 152V in CgPGRPS4), and they shared 55...
December 30, 2016: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28040177/regulation-of-the-synthesis-of-pulp-degrading-enzymes-in-bacillus-isolated-from-cocoa-fermentation
#15
Honoré G Ouattara, Sylvie Reverchon, Sébastien L Niamke, William Nasser
Pectin degrading enzymes are essential for quality of product from cocoa fermentation. Previously, we studied purified pectate lyases (Pel) produced by Bacillus strains from fermenting cocoa and characterized the cloned pel genes. This study aims to search for biological signals that modulates Pel production and regulators that influence pel gene expression. Strains were grown to the end of exponential phase in media containing various carbon sources. Pel enzymes production in Bacillus was unaffected by simple sugar content variation up to 2%...
May 2017: Food Microbiology
https://www.readbyqxmd.com/read/28038357/streptococcus-gordonii-induces-nitric-oxide-production-through-its-lipoproteins-stimulating-toll-like-receptor-2-in-murine-macrophages
#16
Hyun Young Kim, Jung Eun Baik, Ki Bum Ahn, Ho Seong Seo, Cheol-Heui Yun, Seung Hyun Han
Streptococcus gordonii, a Gram-positive commensal in the oral cavity, is an opportunistic pathogen that can cause endodontic and systemic infections resulting in infective endocarditis. Lipoteichoic acid (LTA) and lipoprotein are major virulence factors of Gram-positive bacteria that are preferentially recognized by Toll-like receptor 2 (TLR2) on immune cells. In the present study, we investigated the effect of S. gordonii LTA and lipoprotein on the production of the representative inflammatory mediator nitric oxide (NO) by the mouse macrophages...
December 27, 2016: Molecular Immunology
https://www.readbyqxmd.com/read/28036248/functional-analysis-of-a-biosynthetic-cluster-essential-for-production-of-4-formylaminooxyvinylglycine-a-germination-arrest-factor-from-pseudomonas-fluorescens-wh6
#17
Rachel A Okrent, Kristin Trippe, Maciej Maselko, Viola A Manning
Rhizosphere-associated Pseudomonas fluorescens WH6 produces the germination-arrest factor, 4-formylaminooxyvinylglycine (FVG). FVG has previously been shown to both arrest the germination of weedy grasses and to inhibit the growth of the bacterial plant pathogen Erwinia amylovora. Very little is known about the mechanism by which FVG is produced. Although a previous study identified a region of the genome that may be involved in FVG biosynthesis, it has not yet been determined which genes within that region are sufficient and necessary for FVG production...
December 30, 2016: Microbiology
https://www.readbyqxmd.com/read/28028880/metapopulation-theory-identifies-biogeographical-patterns-among-core-and-satellite-marine-bacteria-scaling-from-tens-to-thousands-of-kilometers
#18
Markus V Lindh, Johanna Sjöstedt, Börje Ekstam, Michele Casini, Daniel Lundin, Luisa W Hugerth, Yue O O Hu, Anders F Andersson, Agneta Andersson, Catherine Legrand, Jarone Pinhassi
Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations...
December 28, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/28028487/exploring-the-cockatiel-nymphicus-hollandicus-fecal-microbiome-bacterial-inhabitants-of-a-worldwide-pet
#19
Luis David Alcaraz, Apolinar M Hernández, Mariana Peimbert
BACKGROUND: Cockatiels (Nymphicus hollandicus) were originally endemic to Australia; now they are popular pets with a global distribution. It is now possible to conduct detailed molecular studies on cultivable and uncultivable bacteria that are part of the intestinal microbiome of healthy animals. These studies show that bacteria are an essential part of the metabolic capacity of animals. There are few studies on bird microbiomes and, to the best of our knowledge, this is the first report on the cockatiel microbiome...
2016: PeerJ
https://www.readbyqxmd.com/read/28027024/whop-a-genomic-region-associated-with-woody-hosts-in-the-pseudomonas-syringae-complex-contributes-to-the-virulence-and-fitness-of-pseudomonas-savastanoi-pv-savastanoi-in-olive-plants
#20
Eloy Caballo-Ponce, Pieter van Dillewijn, Regina-Michaela Wittich, Cayo Ramos
Bacteria from the Pseudomonas syringae complex belonging to phylogroups 1 (PG1) and 3 (PG3) isolated from woody hosts share a genomic region herein referred to as WHOP (from woody host and Pseudomonas), which is absent in strains infecting herbaceous organs. In this work, we show that this region is also encoded in P. syringae pv. actinidifoliorum (PG1) and six additional members of PG3: Pseudomonas savastanoi pv. retacarpa, three P. syringae pathovars, Pseudomonas meliae and Pseudomonas amygdali. Partial conservation of the WHOP occurs in only a few PG2 strains...
December 27, 2016: Molecular Plant-microbe Interactions: MPMI
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