Genomes and Genes
Summary: The heritable modification of the properties of a competent bacterium by naked DNA from another source. The uptake of naked DNA is a naturally occuring phenomenon in some bacteria. It is often used as a GENE TRANSFER TECHNIQUE.
- Wilharm G, Lepka D, Faber F, Hofmann J, Kerrinnes T, Skiebe E. A simple and rapid method of bacterial transformation. J Microbiol Methods. 2010;80:215-6 pubmed publisherRecently, a unique method for bacterial transformation using nanofibers to inoculate DNA has been developed by Naoto Yoshida and colleagues...
- Lartigue C, Vashee S, Algire M, Chuang R, Benders G, Ma L, et al. Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science. 2009;325:1693-6 pubmed publisher..mycoides. These methods allow the construction of strains that could not be produced with genetic tools available for this bacterium...
- Gulig P, Tucker M, Thiaville P, Joseph J, Brown R. USER friendly cloning coupled with chitin-based natural transformation enables rapid mutagenesis of Vibrio vulnificus. Appl Environ Microbiol. 2009;75:4936-49 pubmed publisher..The methods and genetic tools that we developed should be of general use to those performing molecular genetic analysis and manipulation of other gram-negative bacteria. ..
- Levine S, Lin E, Emara W, Kang J, DiBenedetto M, Ando T, et al. Plastic cells and populations: DNA substrate characteristics in Helicobacter pylori transformation define a flexible but conservative system for genomic variation. FASEB J. 2007;21:3458-67 pubmed..pylori population biology. ..
- Tadesse S, Graumann P. DprA/Smf protein localizes at the DNA uptake machinery in competent Bacillus subtilis cells. BMC Microbiol. 2007;7:105 pubmed..Our data show that DprA/Smf acts downstream of the DNA uptake machinery, and support the idea that Smf protects incoming ssDNA, possibly in conjunction with RecA. ..
- Yasui K, Kano Y, Tanaka K, Watanabe K, Shimizu Kadota M, Yoshikawa H, et al. Improvement of bacterial transformation efficiency using plasmid artificial modification. Nucleic Acids Res. 2009;37:e3 pubmed publisher..In the case of Lactococcus lactis IO-1, by using PAM with a putative Type I methyltransferase system, hsdMS1, the transformation efficiency was improved by a factor of seven over that without PAM. ..
- Blokesch M, Schoolnik G. Serogroup conversion of Vibrio cholerae in aquatic reservoirs. PLoS Pathog. 2007;3:e81 pubmed..cholerae variants that are better adapted for survival in environmental niches or more pathogenic for humans. ..
- Bhattacharjee M, Fine D, Figurski D. tfoX (sxy)-dependent transformation of Aggregatibacter (Actinobacillus) actinomycetemcomitans. Gene. 2007;399:53-64 pubmed..The cloning and induction of tfoX makes it possible to transform nearly any strain of A. actinomycetemcomitans, and allelic exchange has proven to be important for site-directed mutagenesis. ..
- Szöllosi G, Derényi I, Vellai T. The maintenance of sex in bacteria is ensured by its potential to reload genes. Genetics. 2006;174:2173-80 pubmed..These findings imply that the primary role of NGT is not to serve the cell with food, but to provide homologous sequences for restoring genes that have disappeared from or become degraded in the local population. ..
- Smits W, Eschevins C, Susanna K, Bron S, Kuipers O, Hamoen L. Stripping Bacillus: ComK auto-stimulation is responsible for the bistable response in competence development. Mol Microbiol. 2005;56:604-14 pubmed
- Guiral S, Mitchell T, Martin B, Claverys J. Competence-programmed predation of noncompetent cells in the human pathogen Streptococcus pneumoniae: genetic requirements. Proc Natl Acad Sci U S A. 2005;102:8710-5 pubmed..We propose that allolysis constitutes a competence-programmed mechanism of predation of noncompetent cells, which benefits to the competent cells and contributes to virulence by coordinating the release of virulence factors. ..
- Hahn J, Maier B, Haijema B, Sheetz M, Dubnau D. Transformation proteins and DNA uptake localize to the cell poles in Bacillus subtilis. Cell. 2005;122:59-71 pubmed..The results suggest the regulated assembly and disassembly of a DNA-uptake machine at the cell poles. ..
- Thomas C, Nielsen K. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol. 2005;3:711-21 pubmed..However, if a gene moves onto a broad-host-range plasmid it might be able to spread without the need for recombination. There are barriers to both these processes but they reduce, rather than prevent, gene acquisition. ..
- Redfield R, Cameron A, Qian Q, Hinds J, Ali T, Kroll J, et al. A novel CRP-dependent regulon controls expression of competence genes in Haemophilus influenzae. J Mol Biol. 2005;347:735-47 pubmed..Natural selection has united these 25 genes under a common regulatory mechanism. Elucidating this mechanism, and the functions of the genes, will provide a valuable window into the evolutionary function of natural competence. ..
- Blaise F, Remy E, Meyer M, Zhou L, Narcy J, Roux J, et al. A critical assessment of Agrobacterium tumefaciens-mediated transformation as a tool for pathogenicity gene discovery in the phytopathogenic fungus Leptosphaeria maculans. Fungal Genet Biol. 2007;44:123-38 pubmed..The preferential insertion into gene-rich regions along with the high ratio of tagged mutants renders ATMT a tool of choice for large-scale gene discovery in L. maculans. ..
- Pietramellara G, Ceccherini M, Ascher J, Nannipieri P. Persistence of transgenic and not transgenic extracellular DNA in soil and bacterial transformation. Riv Biol. 2006;99:37-68 pubmed..Anyway the importance of transformation in evolutionary terms, represents a valid reason to continue the investigation on the fate of extracellular DNA in soil. ..
- Maamar H, Dubnau D. Bistability in the Bacillus subtilis K-state (competence) system requires a positive feedback loop. Mol Microbiol. 2005;56:615-24 pubmed..We further address the source of the noise that results in the stochastic selection of cells that will express comK. A revised model for the regulation of comK expression is proposed that partially explains bistability. ..
- Hamilton H, Dillard J. Natural transformation of Neisseria gonorrhoeae: from DNA donation to homologous recombination. Mol Microbiol. 2006;59:376-85 pubmed..Here we review these recent developments and address the implications of natural transformation in the evolution and pathogenesis N. gonorrhoeae. ..
- Wang J, Sarov M, Rientjes J, Fu J, Hollak H, Kranz H, et al. An improved recombineering approach by adding RecA to lambda Red recombination. Mol Biotechnol. 2006;32:43-53 pubmed
- Meibom K, Blokesch M, Dolganov N, Wu C, Schoolnik G. Chitin induces natural competence in Vibrio cholerae. Science. 2005;310:1824-7 pubmed
- Baldridge G, Burkhardt N, Herron M, Kurtti T, Munderloh U. Analysis of fluorescent protein expression in transformants of Rickettsia monacensis, an obligate intracellular tick symbiont. Appl Environ Microbiol. 2005;71:2095-105 pubmed..monacensis. We demonstrated that our vectors provide a means to study rickettsia-host cell interactions by visualizing GFPuv-fluorescent R. monacensis associated with actin tails in tick host cells. ..
- Pyndiah S, M nard A, Zerbib F, M graud F. Evaluation of the homologous recombination in Helicobacter pylori. Helicobacter. 2005;10:185-92 pubmed publisher..For example, they could be useful in performing protein fusion for a better understanding of the virulence factor's mechanism...
- Kraft C, Suerbaum S. Mutation and recombination in Helicobacter pylori: mechanisms and role in generating strain diversity. Int J Med Microbiol. 2005;295:299-305 pubmed..In this review article, we discuss the genetic variability of H. pylori, the mechanisms that generate diversity, and the potential relevance of genetic variability to colonization and pathogenicity. ..
- Takata T, Ando T, Israel D, Wassenaar T, Blaser M. Role of dprA in transformation of Campylobacter jejuni. FEMS Microbiol Lett. 2005;252:161-8 pubmed..pylori>H. influenzae) restored electro-transformation. Thus, C. jejuni expresses a DprA ortholog that functionally most closely resembles that of H. pylori and is involved in DNA transformation. ..
- Chen I, Christie P, Dubnau D. The ins and outs of DNA transfer in bacteria. Science. 2005;310:1456-60 pubmed..All or nearly all the machine components involved in transformation and conjugation have been identified, and here we present models for their roles in DNA transport. ..
- Gioia J, Qin X, Jiang H, Clinkenbeard K, Lo R, Liu Y, et al. The genome sequence of Mannheimia haemolytica A1: insights into virulence, natural competence, and Pasteurellaceae phylogeny. J Bacteriol. 2006;188:7257-66 pubmed..haemolytica, Actinobacillus pleuropneumoniae, and Haemophilus ducreyi form a lineage distinct from other Pasteurellaceae. This observation was supported by a phylogenetic analysis using sequences of predicted housekeeping genes...
- Karnholz A, Hoefler C, Odenbreit S, Fischer W, Hofreuter D, Haas R. Functional and topological characterization of novel components of the comB DNA transformation competence system in Helicobacter pylori. J Bacteriol. 2006;188:882-93 pubmed..comB2, comB3, and comB4 are organized as a separate operon. Thus, for the H. pylori comB system, all T4SS core components have been identified except for homologues to VirB1, VirD4, VirB5, and VirB11. ..
- Frandsen R, Nielsen N, Maolanon N, Sørensen J, Olsson S, Nielsen J, et al. The biosynthetic pathway for aurofusarin in Fusarium graminearum reveals a close link between the naphthoquinones and naphthopyrones. Mol Microbiol. 2006;61:1069-80 pubmed..Gip1, a putative laccase, is proposed to be responsible for the dimerization of two oxidized rubrofusarin molecules resulting in the formation of aurofusarin. ..
- Nakajima O, Koyano S, Akiyama H, Sawada J, Teshima R. Confirmation of a predicted lack of IgE binding to Cry3Bb1 from genetically modified (GM) crops. Regul Toxicol Pharmacol. 2010;56:306-11 pubmed publisher..Our study provides additional information that confirms the predicted lack of IgE binding to Cry3Bb1 in people with existing food allergies. ..
- Kim J, Wang Y, Park M, Ji G. Improvement of transformation efficiency through in vitro methylation and SacII site mutation of plasmid vector in Bifidobacterium longum MG1. J Microbiol Biotechnol. 2010;20:1022-6 pubmed..The result showed that R-M system is a factor to limit introduction of exogenous DNA and in vitro modification was a convenient method to overcome barrier of R-M system for transformation. ..
- Jacquelín D, Martina M, Argaraña C, Barra J. Plasmid expression of mutS, -L and/or -H gene in Escherichia coli dam cells results in strains that display reduced mutation frequency. Mutat Res. 2008;637:197-204 pubmed..Transformed strains are also more susceptible to killing by the base analogue 2-aminopurine. However, dam and dam transformed cells have similar duplication time, proportion of live/dead cells and morphology. ..
- Oddone G, Mills D, Block D. Incorporation of nisI-mediated nisin immunity improves vector-based nisin-controlled gene expression in lactic acid bacteria. Plasmid. 2009;61:151-8 pubmed publisher..Therefore, the incorporation of nisI in the pMSP3535H3 NICE system described here unveils new ranges of induction parameters to be studied in the course of optimizing recombinant protein expression in LAB. ..
- Matsui T, Saeki H, Shinzato N, Matsuda H. Analysis of the 7.6-kb cryptic plasmid pNC500 from Rhodococcus rhodochrous B-276 and construction of Rhodococcus-E. coli shuttle vector. Appl Microbiol Biotechnol. 2007;74:169-75 pubmed..ORFs 3 and 4 containing a pNC5403 derivative, pN5DXB, was stably maintained for over 80 generations in the absence of antibiotic selective conditions. ..
- Okinaga T, Xie Z, Niu G, Qi F, Merritt J. Examination of the hdrRM regulon yields insight into the competence system of Streptococcus mutans. Mol Oral Microbiol. 2010;25:165-77 pubmed publisher..This suggests that S. mutans has multiple parallel input sensory systems that control the same output response: the induction of natural competence and concurrent production of bacteriocins. ..
- Chen L, Lin J, Li B, Lin J, Liu X. Method development for electrotransformation of Acidithiobacillus caldus. J Microbiol Biotechnol. 2010;20:39-44 pubmed..Optimizations were made and the transformation efficiency was increased from 0.8 to 3.6 x 104 transfomants/microng plasmid DNA. The developed electrotransformation method was convenient in introducing foreign genes into A. caldus...
- L thje P, von K ckritz Blickwede M, Schwarz S. Identification and characterization of nine novel types of small staphylococcal plasmids carrying the lincosamide nucleotidyltransferase gene lnu(A). J Antimicrob Chemother. 2007;59:600-6 pubmed publisher..Structurally different lnu(A)-carrying plasmids were detected in various CoNS species. The detection of the same lnu(A) gene in different plasmid backbones suggested the exchange of the gene via interplasmid recombinational events...
- Choi K, Schweizer H. mini-Tn7 insertion in bacteria with secondary, non-glmS-linked attTn7 sites: example Proteus mirabilis HI4320. Nat Protoc. 2006;1:170-8 pubmed..Vectors are available for gene complementation and expression, gene fusion analyses and tagging with a green fluorescent protein (GFP)-encoding reporter gene. ..
- Hily J, Singer S, Yang Y, Liu Z. A transformation booster sequence (TBS) from Petunia hybrida functions as an enhancer-blocking insulator in Arabidopsis thaliana. Plant Cell Rep. 2009;28:1095-104 pubmed publisher..We demonstrate that the TBS MAR element, but not the ADH1 or Rb7 MARs, is able to block interactions between the 35S enhancer and AGIP without compromising the function of either with elements from which they are not insulated. ..
- Campos I, Darrieux M, Ferreira D, Miyaji E, Silva D, Arêas A, et al. Nasal immunization of mice with Lactobacillus casei expressing the Pneumococcal Surface Protein A: induction of antibodies, complement deposition and partial protection against Streptococcus pneumoniae challenge. Microbes Infect. 2008;10:481-8 pubmed publisher..In addition, an increase in survival of immunized mice after a systemic challenge with a virulent pneumococcal strain was observed...
- Zolotarev A, Unnikrishnan M, Shmukler B, Clark J, Vandorpe D, Grigorieff N, et al. Increased sulfate uptake by E. coli overexpressing the SLC26-related SulP protein Rv1739c from Mycobacterium tuberculosis. Comp Biochem Physiol A Mol Integr Physiol. 2008;149:255-66 pubmed publisher..Our data show that facilitation of bacterial sulfate uptake by Rv1739c requires CysA and its associated sulfate permease activity, and suggest that Rv1739c may be a CysTWA-dependent sulfate transporter...
- Monier J, Bernillon D, Kay E, Faugier A, Rybalka O, Dessaux Y, et al. Detection of potential transgenic plant DNA recipients among soil bacteria. Environ Biosafety Res. 2007;6:71-83 pubmed..were able to integrate exogenous plasmid DNA by electro-transformation and natural transformation, respectively. Our data suggest that transplastomic plant DNA recipients might be present in soil bacterial communities. ..
- Wang A, Su Y, Cheng T, Zou Z, Wang J. [Soluble expression and purification of human alpha-defensin-5 in Escherichia coli]. Sheng Wu Gong Cheng Xue Bao. 2008;24:291-6 pubmed..5 microg/mL rmHD-5 in the media. These results indicate that the strategy of soluble expression of fusion protein in E. coli can be a useful and practical way to produce bioactive defensins. ..
- Yamane K, Wachino J, Suzuki S, Kimura K, Shibata N, Kato H, et al. New plasmid-mediated fluoroquinolone efflux pump, QepA, found in an Escherichia coli clinical isolate. Antimicrob Agents Chemother. 2007;51:3354-60 pubmed publisher..coli was first identified. Surveillance of the qepA-harboring clinical isolates should be encouraged to minimize further dissemination of the kind of plasmid-dependent FQ resistance determinants among pathogenic microbes...
- Letain T, Kane S, Legler T, Salazar E, Agron P, Beller H. Development of a genetic system for the chemolithoautotrophic bacterium Thiobacillus denitrificans. Appl Environ Microbiol. 2007;73:3265-71 pubmed..The availability of a genetic system in T. denitrificans will facilitate our understanding of the genetics and biochemistry underlying its unusual metabolism. ..
- Zakataeva N, Nikitina O, Gronskiy S, Romanenkov D, Livshits V. A simple method to introduce marker-free genetic modifications into the chromosome of naturally nontransformable Bacillus amyloliquefaciens strains. Appl Microbiol Biotechnol. 2010;85:1201-9 pubmed publisher..This approach can be used as a routine method for the investigation of complex physiological pathways and for the metabolic engineering of food-grade industrial B. amyloliquefaciens and other Bacillus strains. ..
- Oyarzabal O, Rad R, Backert S. Conjugative transfer of chromosomally encoded antibiotic resistance from Helicobacter pylori to Campylobacter jejuni. J Clin Microbiol. 2007;45:402-8 pubmed..The significance of this DNA uptake by C. jejuni in the context of acquiring antibiotic resistance is discussed. ..
- Banu L, Conrads G, Rehrauer H, Hussain H, Allan E, van der Ploeg J. The Streptococcus mutans serine/threonine kinase, PknB, regulates competence development, bacteriocin production, and cell wall metabolism. Infect Immun. 2010;78:2209-20 pubmed publisher..Real-time reverse transcriptase PCR (RT-PCR) showed that genes downregulated in the pknB mutant were upregulated in the pppL mutant, indicating that PppL serves to counteract PknB...
- Cameron A, Volar M, Bannister L, Redfield R. RNA secondary structure regulates the translation of sxy and competence development in Haemophilus influenzae. Nucleic Acids Res. 2008;36:10-20 pubmed..Thus, mRNA secondary structure is responsive to conditions where DNA uptake will be favorable, and transcription of sxy is simultaneously enhanced if CRP activation signals that energy supplies are limited. ..
- Solleti S, Bakshi S, Sahoo L. Additional virulence genes in conjunction with efficient selection scheme, and compatible culture regime enhance recovery of stable transgenic plants in cowpea via Agrobacterium tumefaciens-mediated transformation. J Biotechnol. 2008;135:97-104 pubmed publisher..The presence, integration, expression and inheritance of transgenes were confirmed by molecular analysis. The protocol developed for cultivar Pusa Komal will facilitate the transfer of desirable traits into cowpea. ..
- Fierfort N, Samain E. Genetic engineering of Escherichia coli for the economical production of sialylated oligosaccharides. J Biotechnol. 2008;134:261-5 pubmed publisher..This high concentration and low cost of fermentation medium should make possible to use sialylated oligosaccharides in new fields such as the food industry...
- Nakajima K, Inatsu S, Mizote T, Nagata Y, Aoyama K, Fukuda Y, et al. Possible involvement of put A gene in Helicobacter pylori colonization in the stomach and motility. Biomed Res. 2008;29:9-18 pubmed..DeltaputA had lost its ability to colonize the stomach of nude mice, an ability possessed by the wild-type. These findings indicate that put A may play an important role in H. pylori colonization on the gastric mucus layer. ..
- Itaya M, Kaneko S. Integration of stable extracellular DNA released from Escherichia coli into the Bacillus subtilis genome vector by culture mix method. Nucleic Acids Res. 2010;38:2551-7 pubmed publisher..This technique should facilitate giant DNA cloning in the BGM vector and allow its application to other hosts that can undergo natural transformation. ..
- Yu H, Seo J, Kim J, Han K, Shim W, Yun S, et al. Functional analyses of heterotrimeric G protein G alpha and G beta subunits in Gibberella zeae. Microbiology. 2008;154:392-401 pubmed publisher..Our study shows that G. zeae heterotrimeric G protein subunits can regulate vegetative growth, sexual development, toxin production and pathogenicity...