Literature DB >> 19270136

Rapid identification of genes encoding DNA polymerases by function-based screening of metagenomic libraries derived from glacial ice.

Carola Simon1, Judith Herath, Stephanie Rockstroh, Rolf Daniel.   

Abstract

Small-insert and large-insert metagenomic libraries were constructed from glacial ice of the Northern Schneeferner, which is located on the Zugspitzplatt in Germany. Subsequently, these libraries were screened for the presence of DNA polymerase-encoding genes by complementation of an Escherichia coli polA mutant. Nine novel genes encoding complete DNA polymerase I proteins or domains typical of these proteins were recovered.

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Year:  2009        PMID： 19270136      PMCID： PMC2681694          DOI： 10.1128/AEM.02644-08

Source DB:  PubMed          Journal:  Appl Environ Microbiol        ISSN： 0099-2240            Impact factor:   4.792


  21 in total

1.  Biochemical analysis of point mutations in the 5'-3' exonuclease of DNA polymerase I of Streptococcus pneumoniae. Functional and structural implications.

Authors:  M Amblar; M G de Lacoba; M A Corrales; P Lopez
Journal:  J Biol Chem       Date:  2001-03-07       Impact factor: 5.157

2.  The Y-family of DNA polymerases.

Authors:  H Ohmori; E C Friedberg; R P Fuchs; M F Goodman; F Hanaoka; D Hinkle; T A Kunkel; C W Lawrence; Z Livneh; T Nohmi; L Prakash; S Prakash; T Todo; G C Walker; Z Wang; R Woodgate
Journal:  Mol Cell       Date:  2001-07       Impact factor: 17.970

3.  Uncultured soil bacteria are a reservoir of new antibiotic resistance genes.

Authors:  Christian S Riesenfeld; Robert M Goodman; Jo Handelsman
Journal:  Environ Microbiol       Date:  2004-09       Impact factor: 5.491

4.  Sequencing genomes from single cells by polymerase cloning.

Authors:  Kun Zhang; Adam C Martiny; Nikos B Reppas; Kerrie W Barry; Joel Malek; Sallie W Chisholm; George M Church
Journal:  Nat Biotechnol       Date:  2006-05-28       Impact factor: 54.908

Review 5.  Function and structure relationships in DNA polymerases.

Authors:  C M Joyce; T A Steitz
Journal:  Annu Rev Biochem       Date:  1994       Impact factor: 23.643

6.  Selective elimination of the exonuclease activity of the deoxyribonucleic acid polymerase from Escherichia coli B by limited proteolysis.

Authors:  H Klenow; I Henningsen
Journal:  Proc Natl Acad Sci U S A       Date:  1970-01       Impact factor: 11.205

7.  Conserved sites in the 5'-3' exonuclease domain of Escherichia coli DNA polymerase.

Authors:  P D Gutman; K W Minton
Journal:  Nucleic Acids Res       Date:  1993-09-11       Impact factor: 16.971

8.  Screening of environmental DNA libraries for the presence of genes conferring Na(+)(Li(+))/H(+) antiporter activity on Escherichia coli: characterization of the recovered genes and the corresponding gene products.

Authors:  A Majerník; G Gottschalk; R Daniel
Journal:  J Bacteriol       Date:  2001-11       Impact factor: 3.490

9.  Culturable bacteria in subglacial sediments and ice from two Southern Hemisphere glaciers.

Authors:  J Foght; J Aislabie; S Turner; C E Brown; J Ryburn; D J Saul; W Lawson
Journal:  Microb Ecol       Date:  2004-03-04       Impact factor: 4.552

10.  CDD: a conserved domain database for interactive domain family analysis.

Authors:  Aron Marchler-Bauer; John B Anderson; Myra K Derbyshire; Carol DeWeese-Scott; Noreen R Gonzales; Marc Gwadz; Luning Hao; Siqian He; David I Hurwitz; John D Jackson; Zhaoxi Ke; Dmitri Krylov; Christopher J Lanczycki; Cynthia A Liebert; Chunlei Liu; Fu Lu; Shennan Lu; Gabriele H Marchler; Mikhail Mullokandov; James S Song; Narmada Thanki; Roxanne A Yamashita; Jodie J Yin; Dachuan Zhang; Stephen H Bryant
Journal:  Nucleic Acids Res       Date:  2006-11-29       Impact factor: 16.971
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  33 in total

1.  Wide variation in antibiotic resistance proteins identified by functional metagenomic screening of a soil DNA library.

Authors:  Kelly M McGarvey; Konstantin Queitsch; Stanley Fields
Journal:  Appl Environ Microbiol       Date:  2012-01-13       Impact factor: 4.792

Review 2.  Metagenomic analyses: past and future trends.

Authors:  Carola Simon; Rolf Daniel
Journal:  Appl Environ Microbiol       Date:  2010-12-17       Impact factor: 4.792

3.  Size Does Matter: Application-driven Approaches for Soil Metagenomics.

Authors:  Kavita S Kakirde; Larissa C Parsley; Mark R Liles
Journal:  Soil Biol Biochem       Date:  2010-11-01       Impact factor: 7.609

4.  Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome.

Authors:  Carola Simon; Arnim Wiezer; Axel W Strittmatter; Rolf Daniel
Journal:  Appl Environ Microbiol       Date:  2009-10-02       Impact factor: 4.792

5.  A multi-omic screening approach for the discovery of thermoactive glycoside hydrolases.

Authors:  Philip Busch; Marcel Suleiman; Christian Schäfers; Garabed Antranikian
Journal:  Extremophiles       Date:  2021-01-08       Impact factor: 2.395

Review 6.  The evolving interface between synthetic biology and functional metagenomics.

Authors:  Eric van der Helm; Hans J Genee; Morten O A Sommer
Journal:  Nat Chem Biol       Date:  2018-07-16       Impact factor: 15.040

7.  Model-enabled gene search (MEGS) allows fast and direct discovery of enzymatic and transport gene functions in the marine bacterium Vibrio fischeri.

Authors:  Shu Pan; Kiel Nikolakakis; Paul A Adamczyk; Min Pan; Edward G Ruby; Jennifer L Reed
Journal:  J Biol Chem       Date:  2017-04-26       Impact factor: 5.157

8.  WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads.

Authors:  Wolfgang Gerlach; Sebastian Jünemann; Felix Tille; Alexander Goesmann; Jens Stoye
Journal:  BMC Bioinformatics       Date:  2009-12-18       Impact factor: 3.169

Review 9.  Biocatalysts and small molecule products from metagenomic studies.

Authors:  Hala A Iqbal; Zhiyang Feng; Sean F Brady
Journal:  Curr Opin Chem Biol       Date:  2012-03-26       Impact factor: 8.822

Review 10.  Achievements and new knowledge unraveled by metagenomic approaches.

Authors:  Carola Simon; Rolf Daniel
Journal:  Appl Microbiol Biotechnol       Date:  2009-09-16       Impact factor: 4.813
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