Genomes and Genes
Summary: A subdiscipline of genetics which deals with the genetic mechanisms and processes of microorganisms.
- Clark A. Toward a metabolic interpretation of genetic recombination of E. coli and its phages. Annu Rev Microbiol. 1971;25:437-64 pubmed
- Lupi O, Dadalti P, Cruz E, Goodheart C. Did the first virus self-assemble from self-replicating prion proteins and RNA?. Med Hypotheses. 2007;69:724-30 pubmed..A capsid originating from prion proteins would be a versatile and effective protection to RNA and could also explain some characteristics of virus self-assembly that are not well understood. ..
- van Soolingen D. Molecular epidemiology of tuberculosis and other mycobacterial infections: main methodologies and achievements. J Intern Med. 2001;249:1-26 pubmed..tuberculosis complex (atypical) mycobacteria. Important new insights that have been gained through molecular techniques into epidemiological aspects and diagnosis of mycobacterial diseases are highlighted. ..
- Ragan M. Detection of lateral gene transfer among microbial genomes. Curr Opin Genet Dev. 2001;11:620-6 pubmed..These complementary approaches sometimes yield inconsistent results. Not only more data but also quantitative models and simulations are needed urgently. ..
- Barth P, Beacham I, Ahmad S, Pritchard R. The inducer of the deoxynucleoside phosphorylases and deoxyriboaldolase in Escherichia coli. Biochim Biophys Acta. 1968;161:554-7 pubmed
- Randhawa G, Kumar A. Milestones in the genetical research on rhizobia. Indian J Exp Biol. 2003;41:1095-100 pubmed..Since then a large number of scientists have made efforts to understand the molecular basis of Rhizobium-legume symbiosis. The important developments of 115 years of genetical research on rhizobia have been listed in this article. ..
- Cubillos F, Louis E, Liti G. Generation of a large set of genetically tractable haploid and diploid Saccharomyces strains. FEMS Yeast Res. 2009;9:1217-25 pubmed publisher..Three versions of each strain (haploid Mat a and Mat alpha and diploid Mat a/alpha all as ura3::KanMX-Barcode) are available through the National Culture Yeast Collection...
- Lynch M. Streamlining and simplification of microbial genome architecture. Annu Rev Microbiol. 2006;60:327-49 pubmed
- Green B, Keller M. Capturing the uncultivated majority. Curr Opin Biotechnol. 2006;17:236-40 pubmed..Finally, new cultivation methods continue to be developed to improve our ability to capture a greater diversity of microorganisms within the environment. ..
- Eidell K, Burke T, Gubbels M. Development of a screen to dissect Toxoplasma gondii egress. Mol Biochem Parasitol. 2010;171:97-103 pubmed publisher..This is illustrated by a mutant generated using dithitotreitol as an egress enhancer, which displays a defect in dithitotreitol induced egress but not in Ca(2+) ionophore induced egress. ..
- Clark A, Maas W, Low B. Production of a merodiploid strain from a double male strain of E. coli K12. Mol Gen Genet. 1969;105:1-15 pubmed
- Narayanan N, Chou C. Physiological improvement to enhance Escherichia coli cell-surface display via reducing extracytoplasmic stress. Biotechnol Prog. 2008;24:293-301 pubmed publisher..Therefore, the PdegP::lacZ allele was proposed to be a suitable "sensor" for monitoring the extracytoplasmic stress and cell physiology during the course of E. coli cell-surface display. ..
- Little A, Robinson C, Peterson S, Raffa K, Handelsman J. Rules of engagement: interspecies interactions that regulate microbial communities. Annu Rev Microbiol. 2008;62:375-401 pubmed publisher..We describe current approaches to study microbial ecology and progress toward predictive modeling. ..
- Handel A, Bennett M. Surviving the bottleneck: transmission mutants and the evolution of microbial populations. Genetics. 2008;180:2193-200 pubmed publisher..We confirm our theoretical results with numerical simulations and suggest specific experiments that can be done to test our predictions. ..
- Gottesman M, Hicks M, Gellert M. Genetics and function of DNA ligase in Escherichia coli. J Mol Biol. 1973;77:531-47 pubmed
- Hofnung M, Schwartz M, Hatfield D. Complementation studies in the maltose-A region of the Escherichia coli K12 genetic map. J Mol Biol. 1971;61:681-94 pubmed
- Cundell A. Microbial identification strategies in the pharmaceutical industry. PDA J Pharm Sci Technol. 2006;60:111-23 pubmed..Emphasis in the article is given to the justification of the microbial identification program, selection of identification methods, and use of speciation in successful product failure investigations. ..
- Legout S. Jacques Monod (1910-1976) and his publications in the "Annales de l'Institut Pasteur". Res Microbiol. 2010;161:74-6 pubmed publisher..Circumstances that led him to publish in the "Annales" are recalled here. ..
- Wijsman H, Pafort H. Pleiotropic mutations in Escherichia coli conferring tolerance to glycine and sensitivity to penicillin. Mol Gen Genet. 1974;128:349-57 pubmed
- ..However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered as a community property. ..
- Fiil N, Friesen J. Isolation of "relaxed" mutants of Escherichia coli. J Bacteriol. 1968;95:729-31 pubmed
- Ye Y, Tang H. An ORFome assembly approach to metagenomics sequences analysis. J Bioinform Comput Biol. 2009;7:455-71 pubmed..This improvement is especially useful for metagenomic projects when the genome assembly does not work because of the low sequence coverage. ..
- Iankovskii N. [Sos Isaakovich Alikhanyan and All-Russia Research Institute of Genetics and Selection of Industrial Microorganisms: a perspective from a student to a head of laboratory]. Genetika. 2006;42:1475-80 pubmed
- Relman D. The human body as microbial observatory. Nat Genet. 2002;30:131-3 pubmed
- Fradkin J, Fraenkel D. 2-keto-3-deoxygluconate 6-phosphate aldolase mutants of Escherichia coli. J Bacteriol. 1971;108:1277-83 pubmed..KDGP is probably the inducer of KDGP aldolase. ..
- Schueller C, Quinn F, Haas A. The Afipia toolbox and its use to isolate flagellar mutants. FEMS Microbiol Lett. 2010;302:203-10 pubmed publisher..Insertion loci for two selected mutants were located in the genes for flagellin and flagellin biosynthesis FlhA, confirming the validity of the approach...
- Merkl R. AMIGOS: a method for the inspection of genomic organisation or structure and its application to characterise conserved gene arrangements. In Silico Biol. 2006;6:281-306 pubmed..In addition, cons(CL) values provide a sound basis for non-homologous gene annotation. Based on cons(CL) values, examples of conserved clusters containing annotated genes and single ones with unknown function are given. ..
- Ullrich S, Schüler D. Cre-lox-based method for generation of large deletions within the genomic magnetosome island of Magnetospirillum gryphiswaldense. Appl Environ Microbiol. 2010;76:2439-44 pubmed publisher..The method will facilitate future functional analysis of magnetosome genes and also can be utilized for large-scale genome engineering in magnetotactic bacteria...
- Medjahed H, Singh A. Genetic manipulation of Mycobacterium abscessus. Curr Protoc Microbiol. 2010;Chapter 10:Unit 10D.2 pubmed publisher..M. abscessus is a Biosafety Level 2 (BSL-2) bacterium, and working considerations are also discussed. ..
- Mattern I, Pittard J. Regulation of tyrosine biosynthesis in Escherichia coli K-12: isolation and characterization of operator mutants. J Bacteriol. 1971;107:8-15 pubmed..The mutant allele aroK is not recessive to aroK(+) and aroK/aroK(+) strains exhibit the aroK phenotype of resistance to 4-aminophenylalanine. It is proposed that aroK is an operator locus for an aroF tyrA operon. ..
- Banerjee S, Fraenkel D. Glucose-6-phosphate dehydrogenase from Escherichia coli and from a "high-level" mutant. J Bacteriol. 1972;110:155-60 pubmed..The two enzymes are the same in all characteristics studied thus far: specific activity, kinetics, specificity, and subunit size. ..
- Donch J, Greenberg J. Genetic analysis of lon mutants of strain K-12 of Escherichia coli. Mol Gen Genet. 1968;103:105-15 pubmed
- Helling R. Selection of a mutant of Escherichia coli which has high mutation rates. J Bacteriol. 1968;96:975-80 pubmed..This mutation (mut-2) and the Treffers' mutation (mutT1) mapped at approximately the same position to the right of leu. Specificity studies showed that the two mutations differ in rates of mutation produced. ..
- Peyru G, Fraenkel D. Genetic mapping of loci for glucose-6-phosphate dehydrogenase, gluconate-6-phosphate dehydrogenase, and gluconate-6-phosphate dehydrase in Escherichia coli. J Bacteriol. 1968;95:1272-8 pubmed..They are in the same region of the chromosome, and their order is gnd-his-(edd, zwf)-aroD; gnd and his are cotransduceable, as are zwf and edd. The position of gnd in Salmonella typhimurium was shown to be similar to that in E. coli. ..
- Boyce N. An ocean of genes. Speed-reading all the DNA in the sea--and the gut--could reveal worlds of unknown organisms. US News World Rep. 2003;134:62 pubmed
- Gellert M, Little J, Oshinsky C, Zimmerman S. Joining of DNA strands by DNA ligase of E. coli. Cold Spring Harb Symp Quant Biol. 1968;33:21-6 pubmed
- Ramirez M, Don M, Merkier A, Bistué A, Zorreguieta A, Centron D, et al. Naturally competent Acinetobacter baumannii clinical isolate as a convenient model for genetic studies. J Clin Microbiol. 2010;48:1488-90 pubmed publisher..A. baumannii A118 took up a fluorophore-labeled oligonucleotide analog. These characteristics make this isolate a convenient model for genetic studies. ..
- FERNANDEZ ROBLEDO J, Lin Z, Vasta G. Transfection of the protozoan parasite Perkinsus marinus. Mol Biochem Parasitol. 2008;157:44-53 pubmed
- Epstein W, Jewett S, Fox C. Isolation and mapping of phosphotransferase mutants in Escherichia coli. J Bacteriol. 1970;104:793-7 pubmed..These two genes lie between the purC and supN markers in the order: strA... guaB-purC-ptsI-ptsH-supN-dsdA... his. ..
- Lomax M, Greenberg G. Characteristics of the deo operon: role in thymine utilization and sensitivity to deoxyribonucleosides. J Bacteriol. 1968;96:501-14 pubmed..The inhibition of respiration in deoC strains and the induction of thymidine phosphorylase and deoxyribose 5-phosphate aldolase in the wild-type organism are considered to result from the accumulation of deoxyribose 5-phosphate. ..
- Podar M, Reysenbach A. New opportunities revealed by biotechnological explorations of extremophiles. Curr Opin Biotechnol. 2006;17:250-5 pubmed..More recently, innovative culturing approaches, environmental genome sequencing and whole genome sequencing have provided new opportunities for the biotechnological exploration of extremophiles. ..
- Kaplarevic M, Murray A, Cary S, Gao G. EnGenIUS -- Environmental Genome Informational Utility System. J Bioinform Comput Biol. 2008;6:1193-211 pubmed..A fully browsable EnGenIUS portal is available at (http://ocean.dbi.udel.edu/) (access code: "guest"). The scope of this paper covers the implementation details and technical aspects of the EnGenIUS toolset. ..
- Brown C, Hogg R. A second transport system for L-arabinose in Escherichia coli B-r controlled by the araC gene. J Bacteriol. 1972;111:606-13 pubmed..These observations support a role for the binding protein in l-arabinose uptake. ..
- Tsukagoshi N, Fox C. Abortive assembly of the lactose transport system in Escherichia coli. Biochemistry. 1973;12:2816-22 pubmed
- Sayut D, Niu Y, Sun L. Construction and enhancement of a minimal genetic and logic gate. Appl Environ Microbiol. 2009;75:637-42 pubmed publisher..In addition, detailed characterizations of the AND gate's responses shed light on how LuxR, LacI, and RNA polymerase interact to activate gene expression. ..
- Stockert E, Old L, Boyse E. The G-IX system. A cell surface allo-antigen associated with murine leukemia virus; implications regarding chromosomal integration of the viral genome. J Exp Med. 1971;133:1334-55 pubmed..But there is a good prospect that further genetic analysis will provide the answer and so elucidate the special relationship of leukemia viruses to the cells of their natural hosts...
- Boucher Y, Nesbø C, Doolittle W. Microbial genomes: dealing with diversity. Curr Opin Microbiol. 2001;4:285-9 pubmed..Surprisingly, even strains of the same species can differ by as much as 20% in gene content. Conceptual and methodological approaches for dealing with such diversity are now being developed, and should transform microbial genomics. ..
- Oxender D. Membrane transport. Annu Rev Biochem. 1972;41:777-814 pubmed
- Huse S, Huber J, Morrison H, Sogin M, Welch D. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 2007;8:R143 pubmed..75% or better. By using objective criteria to eliminate low quality data, the quality of individual GS20 sequence reads in molecular ecological applications can surpass the accuracy of traditional capillary methods. ..
- Allers T, Barak S, Liddell S, Wardell K, Mevarech M. Improved strains and plasmid vectors for conditional overexpression of His-tagged proteins in Haloferax volcanii. Appl Environ Microbiol. 2010;76:1759-69 pubmed publisher..We also deleted the mrr restriction endonuclease gene, thereby allowing direct transformation without the need to passage DNA through an Escherichia coli dam mutant. ..
- DeLong E. Microbial population genomics and ecology. Curr Opin Microbiol. 2002;5:520-4 pubmed..Genome-enabled approaches are now significantly advancing current knowledge of genome content, diversity, population biology and evolution in natural microbial populations. ..
- Wright M. Mutants of Escherichia coli lacking endonuclease I, ribonuclease I, or ribonuclease II. J Bacteriol. 1971;107:87-94 pubmed..Most end mutations, called endA, are also cotransducible with serA and are located between serA and strA. One end mutation, called endB, is located between purE and trp (i.e., between 13 and 25 min on the genetic map). ..