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Transposon mutagenesis

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https://www.readbyqxmd.com/read/27909217/the-small-foxp1-isoform-predominantly-expressed-in-activated-b-cell-like-diffuse-large-b-cell-lymphoma-and-full-length-foxp1-exert-similar-oncogenic-and-transcriptional-activity-in-human-b-cells
#1
Martine van Keimpema, Leonie J Grüneberg, Esther J M Schilder-Tol, Monique E C M Oud, Esther Beuling, Paul J Hensbergen, Johann de Jong, Steven T Pals, Marcel Spaargaren
The forkhead transcription factor FOXP1 is generally regarded as an oncogene in activated B cell-like diffuse large B-cell lymphoma. Previous studies have suggested that a small isoform of FOXP1 (FOXP1-iso), rather than full-length FOXP1 (FOXP1-FL), may possess this oncogenic activity. Corroborating those studies, we here show that activated B cell-like diffuse large B-cell lymphoma cell-lines and primary activated B cell-like diffuse large B-cell lymphoma cells predominantly express FOXP1-iso and that the 5-end of the Foxp1 gene is a common insertion site in murine lymphomas in leukaemia virus- and transposon-mediated insertional mutagenesis screens...
December 1, 2016: Haematologica
https://www.readbyqxmd.com/read/27895128/characterization-of-the-pathogenicity-of-streptococcus-intermedius-tyg1620-isolated-from-a-human-brain-abscess-based-on-the-complete-genome-sequence-with-transcriptome-analysis-and-transposon-mutagenesis-in-a-murine-subcutaneous-abscess-model
#2
Noriko Hasegawa, Tsuyoshi Sekizuka, Yutaka Sugi, Nobuhiro Kawakami, Yumiko Ogasawara, Kengo Kato, Akifumi Yamashita, Fumihiko Takeuchi, Makoto Kuroda
Streptococcus intermedius is known to cause periodontitis and pyogenic infections in the brain and liver. Here we report the complete genome sequence of strain TYG1620 (genome size: 2,006,877 bp; GC content: 37.6%; 2,020 predicted ORFs) isolated from a brain abscess in an infant. Comparative genome analysis of S. intermedius genome sequences suggested that TYG1620 carries a notable type VII secretion system (T7SS), two long-repeat regions and 19 ORFs for cell-wall-anchored proteins (CWAPs). To elucidate genes responsible for the pathogenicity of TYG1620, transcriptome analysis was performed in a murine subcutaneous abscess model...
November 28, 2016: Infection and Immunity
https://www.readbyqxmd.com/read/27884113/disrupting-ros-protection-mechanism-allows-hydrogen-peroxide-to-accumulate-and-oxidize-sb-iii-to-sb-v-in-pseudomonas-stutzeri-ts44
#3
Dan Wang, Fengqiu Zhu, Qian Wang, Christopher Rensing, Peng Yu, Jing Gong, Gejiao Wang
BACKGROUND: Microbial antimonite [Sb(III)] oxidation converts toxic Sb(III) into less toxic antimonate [Sb(V)] and plays an important role in the biogeochemical Sb cycle. Currently, little is known about the mechanisms underlying bacterial Sb(III) resistance and oxidation. RESULTS: In this study, Tn5 transposon mutagenesis was conducted in the Sb(III)-oxidizing strain Pseudomonas stutzeri TS44 to isolate the genes responsible for Sb(III) resistance and oxidation...
November 25, 2016: BMC Microbiology
https://www.readbyqxmd.com/read/27881418/environmental-pseudomonads-inhibit-cystic-fibrosis-patient-derived-pseudomonas-aeruginosa
#4
Payel Chatterjee, Elizabeth Davis, Fengan Yu, Sarah James, Julia H Wildschutte, Daniel D Wiegmann, David H Sherman, Robert M McKay, John J LiPuma, Hans Wildschutte
: Pseudomonas aeruginosa is an opportunistic pathogen which is evolving resistance to many currently used antibiotics. While much research has been devoted to the roles of pathogenic P. aeruginosa in cystic fibrosis (CF) patients, less is known of its ecological properties. P. aeruginosa dominate the lungs during chronic infection in CF patients, yet its abundance in some environments is less compared to other diverse groups of pseudomonads. Here, we sought to determine if clinical isolates of P...
November 23, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27872077/identification-of-inca-c-plasmid-replication-and-maintenance-genes-and-development-of-a-plasmid-multi-locus-sequence-typing-scheme
#5
Steven J Hancock, Minh-Duy Phan, Kate M Peters, Brian M Forde, Teik Min Chong, Wai-Fong Yin, Kok-Gan Chan, David L Paterson, Timothy R Walsh, Scott A Beatson, Mark A Schembri
Plasmids of incompatibility group IncA/C are becoming increasingly prevalent within pathogenic Enterobacteriaceae. They are associated with the dissemination of multiple clinically relevant resistance genes, including blaCMY and blaNDM Current typing methods for IncA/C plasmids offer limited resolution. In this study, we present the complete sequence of a blaNDM-1-positive IncA/C plasmid, pMS6198A, isolated from a multi-drug resistant uropathogenic Escherichia coli strain. Hyper-saturated transposon mutagenesis, coupled with transposon directed insertion site sequencing (TraDIS) was employed to identify conserved genetic elements required for replication and maintenance of pMS6198A...
November 21, 2016: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/27849608/transposon-mutagenesis-identifies-genes-that-cooperate-with-mutant-pten-in-breast-cancer-progression
#6
Roberto Rangel, Song-Choon Lee, Kenneth Hon-Kim Ban, Liliana Guzman-Rojas, Michael B Mann, Justin Y Newberg, Takahiro Kodama, Leslie A McNoe, Luxmanan Selvanesan, Jerrold M Ward, Alistair G Rust, Kuan-Yew Chin, Michael A Black, Nancy A Jenkins, Neal G Copeland
Triple-negative breast cancer (TNBC) has the worst prognosis of any breast cancer subtype. To better understand the genetic forces driving TNBC, we performed a transposon mutagenesis screen in a phosphatase and tensin homolog (Pten) mutant mice and identified 12 candidate trunk drivers and a much larger number of progression genes. Validation studies identified eight TNBC tumor suppressor genes, including the GATA-like transcriptional repressor TRPS1 Down-regulation of TRPS1 in TNBC cells promoted epithelial-to-mesenchymal transition (EMT) by deregulating multiple EMT pathway genes, in addition to increasing the expression of SERPINE1 and SERPINB2 and the subsequent migration, invasion, and metastasis of tumor cells...
November 14, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27849596/genome-wide-screen-identifies-host-colonization-determinants-in-a-bacterial-gut-symbiont
#7
J Elijah Powell, Sean P Leonard, Waldan K Kwong, Philipp Engel, Nancy A Moran
Animal guts are often colonized by host-specialized bacterial species to the exclusion of other transient microorganisms, but the genetic basis of colonization ability is largely unknown. The bacterium Snodgrassella alvi is a dominant gut symbiont in honey bees, specialized in colonizing the hindgut epithelium. We developed methods for transposon-based mutagenesis in S. alvi and, using high-throughput DNA sequencing, screened genome-wide transposon insertion (Tn-seq) and transcriptome (RNA-seq) libraries to characterize both the essential genome and the genes facilitating host colonization...
November 14, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27834373/in-vivo-protein-interaction-network-analysis-reveals-porin-localized-antibiotic-inactivation-in-acinetobacter-baumannii-strain-ab5075
#8
Xia Wu, Juan D Chavez, Devin K Schweppe, Chunxiang Zheng, Chad R Weisbrod, Jimmy K Eng, Ananya Murali, Samuel A Lee, Elizabeth Ramage, Larry A Gallagher, Hemantha D Kulasekara, Mauna E Edrozo, Cassandra N Kamischke, Mitchell J Brittnacher, Samuel I Miller, Pradeep K Singh, Colin Manoil, James E Bruce
The nosocomial pathogen Acinetobacter baumannii is a frequent cause of hospital-acquired infections worldwide and is a challenge for treatment due to its evolved resistance to antibiotics, including carbapenems. Here, to gain insight on A. baumannii antibiotic resistance mechanisms, we analyse the protein interaction network of a multidrug-resistant A. baumannii clinical strain (AB5075). Using in vivo chemical cross-linking and mass spectrometry, we identify 2,068 non-redundant cross-linked peptide pairs containing 245 intra- and 398 inter-molecular interactions...
November 11, 2016: Nature Communications
https://www.readbyqxmd.com/read/27830190/phenotypic-screens-identify-parasite-genetic-factors-associated-with-malarial-fever-response-in-plasmodium-falciparum-piggybac-mutants
#9
Phaedra Thomas, Jennifer Sedillo, Jenna Oberstaller, Suzanne Li, Min Zhang, Naresh Singh, Chengqi C Q Wang, Kenneth Udenze, Rays H Y Jiang, John H Adams
Malaria remains one of the most devastating parasitic diseases worldwide, with 90% of the malaria deaths in Africa in 2013 attributable to Plasmodium falciparum. The clinical symptoms of malaria include cycles of fever, corresponding to parasite rupture from red blood cells every 48 h. Parasite pathways involved in the parasite's ability to survive the host fever response, and indeed, the functions of ~40% of P. falciparum genes as a whole, are still largely unknown. Here, we evaluated the potential of scalable forward-genetic screening methods to identify genes involved in the host fever response...
September 2016: MSphere
https://www.readbyqxmd.com/read/27824878/high-throughput-parallel-sequencing-to-measure-fitness-of-leptospira-interrogans-transposon-insertion-mutants-during-acute-infection
#10
Kristel Lourdault, James Matsunaga, David A Haake
Pathogenic species of Leptospira are the causative agents of leptospirosis, a zoonotic disease that causes mortality and morbidity worldwide. The understanding of the virulence mechanisms of Leptospira spp is still at an early stage due to the limited number of genetic tools available for this microorganism. The development of random transposon mutagenesis in pathogenic strains a decade ago has contributed to the identification of several virulence factors. In this study, we used the transposon sequencing (Tn-Seq) technique, which combines transposon mutagenesis with massive parallel sequencing, to study the in vivo fitness of a pool of Leptospira interrogans mutants...
November 2016: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/27824140/random-mutagenesis-of-the-hyperthermophilic-archaeon-pyrococcus-furiosus-using-in-vitro-mariner-transposition-and-natural-transformation
#11
Natalia Guschinskaya, Romain Brunel, Maxime Tourte, Gina L Lipscomb, Michael W W Adams, Philippe Oger, Xavier Charpentier
Transposition mutagenesis is a powerful tool to identify the function of genes, reveal essential genes and generally to unravel the genetic basis of living organisms. However, transposon-mediated mutagenesis has only been successfully applied to a limited number of archaeal species and has never been reported in Thermococcales. Here, we report random insertion mutagenesis in the hyperthermophilic archaeon Pyrococcus furiosus. The strategy takes advantage of the natural transformability of derivatives of the P...
November 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27792127/identifying-cancer-driver-genes-using-replication-incompetent-retroviral-vectors
#12
REVIEW
Victor M Bii, Grant D Trobridge
Identifying novel genes that drive tumor metastasis and drug resistance has significant potential to improve patient outcomes. High-throughput sequencing approaches have identified cancer genes, but distinguishing driver genes from passengers remains challenging. Insertional mutagenesis screens using replication-incompetent retroviral vectors have emerged as a powerful tool to identify cancer genes. Unlike replicating retroviruses and transposons, replication-incompetent retroviral vectors lack additional mutagenesis events that can complicate the identification of driver mutations from passenger mutations...
October 25, 2016: Cancers
https://www.readbyqxmd.com/read/27790711/transposon-mutagenesis-identifies-candidate-genes-that-cooperate-with-loss-of-transforming-growth-factor-beta-signaling-in-mouse-intestinal-neoplasms
#13
Shelli M Morris, Jerry Davison, Kelly T Carter, Rachele M O'Leary, Patty Trobridge, Sue E Knoblaugh, Lois L Myeroff, Sanford D Markowitz, Benjamin T Brett, Todd E Scheetz, Adam J Dupuy, Timothy K Starr, William M Grady
Colorectal cancer (CRC) results from the accumulation of gene mutations and epigenetic alterations in colon epithelial cells, which promotes CRC formation through deregulating signaling pathways. One of the most commonly deregulated signaling pathways in CRC is the transforming growth factor β (TGF-β) pathway. Importantly, the effects of TGF-β signaling inactivation in CRC are modified by concurrent mutations in the tumor cell, and these concurrent mutations determine the ultimate biological effects of impaired TGF-β signaling in the tumor...
October 28, 2016: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/27774087/identification-of-genes-involved-in-indole-3-acetic-acid-biosynthesis-by-gluconacetobacter-diazotrophicus-pal5-strain-using-transposon-mutagenesis
#14
Elisete P Rodrigues, Cleiton de Paula Soares, Patrícia G Galvão, Eddie L Imada, Jean L Simões-Araújo, Luc F M Rouws, André L M de Oliveira, Márcia S Vidal, José I Baldani
Gluconacetobacter diazotrophicus is a beneficial nitrogen-fixing endophyte found in association with sugarcane plants and other important crops. Beneficial effects of G. diazotrophicus on sugarcane growth and productivity have been attributed to biological nitrogen fixation process and production of phytohormones especially indole-3-acetic acid (IAA); however, information about the biosynthesis and function of IAA in G. diazotrophicus is still scarce. Therefore, the aim of this work was to identify genes and pathways involved in IAA biosynthesis in this bacterium...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27768890/rickettsia-sca4-reduces-vinculin-mediated-intercellular-tension-to-promote-spread
#15
Rebecca L Lamason, Effie Bastounis, Natasha M Kafai, Ricardo Serrano, Juan C Del Álamo, Julie A Theriot, Matthew D Welch
Spotted fever group (SFG) rickettsiae are human pathogens that infect cells in the vasculature. They disseminate through host tissues by a process of cell-to-cell spread that involves protrusion formation, engulfment, and vacuolar escape. Other bacterial pathogens rely on actin-based motility to provide a physical force for spread. Here, we show that SFG species Rickettsia parkeri typically lack actin tails during spread and instead manipulate host intercellular tension and mechanotransduction to promote spread...
October 20, 2016: Cell
https://www.readbyqxmd.com/read/27762102/multiple-roles-for-a-novel-rnd-type-efflux-system-in-acinetobacter-baumannii-ab5075
#16
Kyle A Tipton, Marjan Farokhyfar, Philip N Rather
Colony opacity phase variation in Acinetobacter baumannii strain AB5075 is regulated by a reversible high-frequency switch. Transposon mutagenesis was used to generate mutations that decreased the opaque to translucent switch and a gene encoding a predicted periplasmic membrane fusion component of a resistance-nodulation-cell division (RND)-type efflux system was isolated. This gene was designated arpA and immediately downstream was a gene designated arpB that encodes a predicted membrane transporter of RND-type systems...
October 19, 2016: MicrobiologyOpen
https://www.readbyqxmd.com/read/27729512/no-go-zones-for-mariner-transposition
#17
Brian J Akerley
The property of transposons to randomly insert into target DNA has long been exploited for generalized mutagenesis and forward genetic screens. Newer applications that monitor the relative abundance of each transposon insertion in large libraries of mutants can be used to evaluate the roles in cellular fitness of all genes of an organism, provided that transposition is in fact random across all genes. In a recent article, Kimura and colleagues identified an important exception to the latter assumption [S. Kimura, T...
October 11, 2016: MBio
https://www.readbyqxmd.com/read/27729044/retroviral-vectors-and-transposons-for-stable-gene-therapy-advances-current-challenges-and-perspectives
#18
José Eduardo Vargas, Leonardo Chicaybam, Renato Tetelbom Stein, Amilcar Tanuri, Andrés Delgado-Cañedo, Martin H Bonamino
Gene therapy protocols require robust and long-term gene expression. For two decades, retrovirus family vectors have offered several attractive properties as stable gene-delivery vehicles. These vectors represent a technology with widespread use in basic biology and translational studies that require persistent gene expression for treatment of several monogenic diseases. Immunogenicity and insertional mutagenesis represent the main obstacles to a wider clinical use of these vectors. Efficient and safe non-viral vectors are emerging as a promising alternative and facilitate clinical gene therapy studies...
October 12, 2016: Journal of Translational Medicine
https://www.readbyqxmd.com/read/27709585/genome-wide-transposon-mutagenesis-in-mycobacterium-tuberculosis-and-mycobacterium-smegmatis
#19
Gaurav Majumdar, Rendani Mbau, Vinayak Singh, Digby F Warner, Marte Singsås Dragset, Raju Mukherjee
TnSeq, or transposon (Tn) insertion sequencing, is a powerful method for identifying the essential-as well as conditionally essential-regions in a genome, both coding and noncoding. The advent of accessible massively parallel DNA sequencing technologies in particular has resulted in the increased use of TnSeq-based approaches to elucidate various aspects of bacterial physiology and metabolism. Moreover, the availability of detailed protocols has enabled even nonspecialist laboratories to adapt and develop TnSeq approaches to address specific research questions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27709584/transposon-insertion-mutagenesis-for-archaeal-gene-discovery
#20
Saija Kiljunen, Maria I Pajunen, Harri Savilahti
Archaea constitute the third domain of life, but studies on their physiology and other features have lagged behind bacteria and eukarya, largely due to the challenging biology of archaea and concomitant difficulties in methods development. The use of genome-wide en masse insertion mutagenesis is one of the most efficient means to discover the genes behind various biological functions, and such a methodology is described in this chapter for a model archaeon Haloferax volcanii. The strategy successfully employs efficient in vitro transposition in combination with gene targeting in vivo via homologous recombination...
2017: Methods in Molecular Biology
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