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Peter Williams

No longer a member of F1000[ 24-JUL-2001 - 25-JUL-2008 ]
[ Biography ] [ Evaluations ]
Biography

I graduated with a Chemistry degree and a D.Phil. in Physical Biochemistry from the University of Oxford in 1966. From there I moved directly to the University of Wales, Bangor as a lecturer in what was then the Department of Biochemistry & Soil Science. The professorial Head of Department was W.Charles Evans who was one of the initiators of the study of aromatic catabolism in bacteria, having started in the late 1930s. It was his research which really stimulated my chemistsl palate by introducing me to bacteria growing on such exotica as chloroacetic acid, naphthalene, phenoxyacetate herbicides etc. I tentatively entered the field and was lucky enough to be working with Pseudomonas putida mt-2 at the time catabolic plasmids were first reported fom Gunsalus'' laboratory. Some of the behaviour of mt-2 fitted well with the presence of a transmissible and cureable plasmid carrying its catabolic genes for aromatics, what we termed the TOL plasmid. Since then plasmids and aromatic catabolism have been the daily task of my laboratory. Currently I have a personal chair in what is now the School of Biological Sciences at UWB and am a Fellow of the American Academy of Microbiology and one of the three Editors of Applied & Environmental Microbiology based in Europe, handling papers mainly covering biodegradation and aspects of microbial ecology.

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Evaluations

Mutational activation of niche-specific genes provides insight into regulatory networks and bacterial function in a complex environment.
Giddens SR, Jackson RW, …, Gehrig SM, Rainey PB
Proc Natl Acad Sci U S A 2007 Nov 13 104(46):18247-52 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Peter Williams
Evaluated 29 Nov 2007

Conjugative transfer of the IncP-7 carbazole degradative plasmid, pCAR1, in river water samples.
Shintani M, Fukushima N, …, Yamane H, Nojiri H
Biotechnol Lett 2008 Jan 30(1):117-22 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Peter Williams
Evaluated 15 Oct 2007

Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol.
Hristova KR, Schmidt R, …, Scow KM, Kane SR
Appl Environ Microbiol 2007 Nov 73(22):7347-57 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Peter Williams
Evaluated 15 Oct 2007

Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere.
Matilla MA, Espinosa-Urgel M, …, Ramos JL, Ramos-González MI
Genome Biol 2007 8(9):R179 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 17 Sep 2007

Genomics of IncP-1 antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool.
Schlüter A, Szczepanowski R, Pühler A, Top EM
FEMS Microbiol Rev 2007 Jul 31(4):449-77 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Peter Williams
Evaluated 25 Jun 2007

Characterization of the last step of the aerobic phenylacetic acid degradation pathway.
Nogales J, Macchi R, …, Bertoni G, Díaz E
Microbiology 2007 Feb 153(Pt 2):357-65 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Peter Williams
Evaluated 9 Feb 2007

Effects of temperature and biostimulation on oil-degrading microbial communities in temperate estuarine waters.
Coulon F, McKew BA, …, McGenity TJ, Timmis KN
Environ Microbiol 2007 Jan 9(1):177-86 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Peter Williams
Evaluated 9 Feb 2007

Unraveling adaptive evolution: how a single point mutation affects the protein coregulation network.
Knight CG, Zitzmann N, …, Hebestreit H, Rainey PB
Nat Genet 2006 Sep 38(9):1015-22 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Mark D Adams / Joshua Akey / Fergal O'Gara / Peter Williams
Evaluated 6 Dec 2006

Coping with polychlorinated biphenyl (PCB) toxicity: Physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB-mediated stress.
Parnell JJ, Park J, …, Quensen J, Tiedje JM
Appl Environ Microbiol 2006 Oct 72(10):6607-14 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Kevin Sowers / Peter Williams
Evaluated 30 Nov 2006

The RpoT regulon of Pseudomonas putida DOT-T1E and its role in stress endurance against solvents.
Duque E, Rodríguez-Herva JJ, …, Muñoz-Rojas J, Ramos JL
J Bacteriol 2007 Jan 189(1):207-19 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 30 Nov 2006

Plasmids from freshwater environments capable of IncQ retrotransfer are diverse and include pQKH54, a new IncP-1 subgroup archetype.
Haines AS, Akhtar P, …, Day MJ, Fry JC
Microbiology 2006 Sep 152(Pt 9):2689-701 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 14 Sep 2006

Comparison of mechanisms of alkane metabolism under sulfate-reducing conditions among two bacterial isolates and a bacterial consortium.
Callaghan AV, Gieg LM, …, Suflita JM, Young LY
Appl Environ Microbiol 2006 Jun 72(6):4274-82 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 12 Jul 2006

Microbial dioxygenase gene population shifts during polycyclic aromatic hydrocarbon biodegradation.
Ní Chadhain SM, Norman RS, …, Kukor JJ, Zylstra GJ
Appl Environ Microbiol 2006 Jun 72(6):4078-87 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 10 Jul 2006

Generation of novel-substrate-accepting biphenyl dioxygenases through segmental random mutagenesis and identification of residues involved in enzyme specificity.
Zielinski M, Kahl S, …, Seeger M, Hofer B
Appl Environ Microbiol 2006 Mar 72(3):2191-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 7 Apr 2006

Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400.
Denef VJ, Klappenbach JA, …, Eltis LD, Tiedje JM
Appl Environ Microbiol 2006 Jan 72(1):585-95 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 20 Jan 2006

Native folding of aggregation-prone recombinant proteins in Escherichia coli by osmolytes, plasmid- or benzyl alcohol-overexpressed molecular chaperones.
de Marco A, Vigh L, Diamant S, Goloubinoff P
Cell Stress Chaperones 2005 10(4):329-39 [abstract on PubMed] [related articles] [order article]
Selected by | Peter Williams
Evaluated 19 Jan 2006

Genetically modified organisms for the environment: stories of success and failure and what we have learned from them.
Cases I, de Lorenzo V
Int Microbiol 2005 Sep 8(3):213-22 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 25 Oct 2005

Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin.
Bolotin A, Quinquis B, Sorokin A, Ehrlich SD
Microbiology 2005 Aug 151(Pt 8):2551-61 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams / Camilla Nesbo
Evaluated 22 Sep 2005

The effect of a bacteriophage on diversification of the opportunistic bacterial pathogen, Pseudomonas aeruginosa.
Brockhurst MA, Buckling A, Rainey PB
Proc Biol Sci 2005 Jul 7 272(1570):1385-91 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 22 Jul 2005

Structure of the terminal oxygenase component of angular dioxygenase, carbazole 1,9a-dioxygenase.
Nojiri H, Ashikawa Y, …, Habe H, Omori T
J Mol Biol 2005 Aug 12 351(2):355-70 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Peter Williams
Evaluated 18 Jul 2005

The origin and evolution of operons: the piecewise building of the proteobacterial histidine operon.
Fani R, Brilli M, Liò P
J Mol Evol 2005 Mar 60(3):378-90 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Peter Williams
Evaluated 13 May 2005

Substrate-dependent regulation of anaerobic degradation pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1.
Kühner S, Wöhlbrand L, …, Reinhardt R, Rabus R
J Bacteriol 2005 Feb 187(4):1493-503 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 1 Apr 2005

The evolution of pTF-FC2 and pTC-F14, two related plasmids of the IncQ-family.
Rawlings DE
Plasmid 2005 Mar 53(2):137-47 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Peter Williams
Evaluated 30 Mar 2005

Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1.
Warren R, Hsiao WW, …, Davies J, Eltis LD
J Bacteriol 2004 Nov 186(22):7783-95 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 24 Jan 2005

Role of the bacterial organomercury lyase (MerB) in controlling methylmercury accumulation in mercury-contaminated natural waters.
Schaefer JK, Yagi J, …, Tel-Or S, Barkay T
Environ Sci Technol 2004 Aug 15 38(16):4304-11 [abstract on PubMed] [related articles] [order article]
Selected by | Peter Williams
Evaluated 8 Oct 2004

Proteome analysis of Pseudomonas sp. K82 biodegradation pathways.
Kim SI, Kim JY, …, Leem SH, Lee C
Proteomics 2004 Nov 4(11):3610-21 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Peter Williams
Evaluated 5 Oct 2004

Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways.
Trefault N, De la Iglesia R, …, Stuardo M, González B
Environ Microbiol 2004 Jul 6(7):655-68 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Peter Williams
Evaluated 1 Jul 2004

Characterization of transcriptional regulatory genes for biphenyl degradation in Rhodococcus sp. strain RHA1.
Takeda H, Yamada A, …, Masai E, Fukuda M
J Bacteriol 2004 Apr 186(7):2134-46 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 1 Jul 2004

Selenocysteine-containing proteins in anaerobic benzoate metabolism of Desulfococcus multivorans.
Peters F, Rother M, Boll M
J Bacteriol 2004 Apr 186(7):2156-63 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 30 Jun 2004

Gene amplification involves site-specific short homology-independent illegitimate recombination in Acinetobacter sp. strain ADP1.
Reams AB, Neidle EL
J Mol Biol 2004 May 7 338(4):643-56 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Peter Williams
Evaluated 30 Jun 2004

N-acyl-l-homoserine lactones (AHLs) affect microbial community composition and function in activated sludge.
Valle A, Bailey MJ, Whiteley AS, Manefield M
Environ Microbiol 2004 Apr 6(4):424-33 [abstract on PubMed] [related articles] [order article]
Selected by | Ian M Head / Peter Williams
Evaluated 25 Mar 2004

Monitoring intracellular levels of XylR in Pseudomonas putida with a single-chain antibody specific for aromatic-responsive enhancer-binding proteins.
Fraile S, Roncal F, Fernández LA, de Lorenzo V
J Bacteriol 2001 Oct 183(19):5571-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 3 Mar 2004

Trends between gene content and genome size in prokaryotic species with larger genomes.
Konstantinidis KT, Tiedje JM
Proc Natl Acad Sci U S A 2004 Mar 2 101(9):3160-5 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams / Jonathan A Eisen / Christos Ouzounis
Evaluated 3 Mar 2004

The biphenyl- and 4-chlorobiphenyl-catabolic transposon Tn4371, a member of a new family of genomic islands related to IncP and Ti plasmids.
Toussaint A, Merlin C, …, Mergeay M, Springael D
Appl Environ Microbiol 2003 Aug 69(8):4837-45 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 26 Sep 2003

Unusual integrase gene expression on the clc genomic island in Pseudomonas sp. strain B13.
Sentchilo V, Ravatn R, …, Zehnder AJ, van der Meer JR
J Bacteriol 2003 Aug 185(15):4530-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 6 Aug 2003

The gene cassette metagenome is a basic resource for bacterial genome evolution.
Holmes AJ, Gillings MR, …, Nevalainen KM, Stokes HW
Environ Microbiol 2003 May 5(5):383-94 [abstract on PubMed] [related articles] [order article]
Selected by | Peter Williams
Evaluated 26 Jun 2003

Degradation of polycyclic aromatic hydrocarbons at low temperature under aerobic and nitrate-reducing conditions in enrichment cultures from northern soils.
Eriksson M, Sodersten E, …, Dalhammar G, Mohn WW
Appl Environ Microbiol 2003 Jan 69(1):275-84 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 25 Jun 2003

Degradation and transformability of DNA from transgenic leaves.
Ceccherini M, Poté J, …, Vogel TM, Simonet P
Appl Environ Microbiol 2003 Jan 69(1):673-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 25 Jun 2003

Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440.
Nelson KE, Weinel C, …, Tümmler B, Fraser CM
Environ Microbiol 2002 Dec 4(12):799-808 [abstract on PubMed] [related articles] [order article]
Selected by | Peter Williams
Evaluated 27 Feb 2003

Evolution of a chlorobenzene degradative pathway among bacteria in a contaminated groundwater mediated by a genomic island in Ralstonia.
Müller TA, Werlen C, Spain J, Van Der Meer JR
Environ Microbiol 2003 Mar 5(3):163-73 [abstract on PubMed] [related articles] [order article]
Selected by | Peter Williams
Evaluated 24 Feb 2003

Biodegradation of an alicyclic hydrocarbon by a sulfate-reducing enrichment from a gas condensate-contaminated aquifer.
Rios-Hernandez LA, Gieg LM, Suflita JM
Appl Environ Microbiol 2003 Jan 69(1):434-43 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 24 Feb 2003

Genes coding for a new pathway of aerobic benzoate metabolism in Azoarcus evansii.
Gescher J, Zaar A, …, Schägger H, Fuchs G
J Bacteriol 2002 Nov 184(22):6301-15 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 24 Feb 2003

RNA stable isotope probing, a novel means of linking microbial community function to phylogeny.
Manefield M, Whiteley AS, Griffiths RI, Bailey MJ
Appl Environ Microbiol 2002 Nov 68(11):5367-73 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams / Ian M Head / Michael Wagner
Evaluated 5 Nov 2002

A real-time polymerase chain reaction method for monitoring anaerobic, hydrocarbon-degrading bacteria based on a catabolic gene.
Beller HR, Kane SR, Legler TC, Alvarez PJ
Environ Sci Technol 2002 Sep 15 36(18):3977-84 [abstract on PubMed] [related articles] [order article]
Selected by | Peter Williams
Evaluated 4 Nov 2002

The ICESt1 element of Streptococcus thermophilus belongs to a large family of integrative and conjugative elements that exchange modules and change their specificity of integration.
Burrus V, Pavlovic G, Decaris B, Guédon G
Plasmid 2002 Sep 48(2):77-97 [abstract on PubMed] [related articles] [order article]
Selected by | Peter Williams
Evaluated 4 Nov 2002

Metabolic biomarkers for monitoring anaerobic naphthalene biodegradation in situ.
Phelps CD, Battistelli J, Young LY
Environ Microbiol 2002 Sep 4(9):532-7 [abstract on PubMed] [related articles] [order article]
Selected by | Peter Williams
Evaluated 4 Nov 2002

Biodegradation of 1,2,3-trichloropropane through directed evolution and heterologous expression of a haloalkane dehalogenase gene.
Bosma T, Damborský J, Stucki G, Janssen DB
Appl Environ Microbiol 2002 Jul 68(7):3582-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 1 Aug 2002

Origins of the 2,4-dinitrotoluene pathway.
Johnson GR, Jain RK, Spain JC
J Bacteriol 2002 Aug 184(15):4219-32 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 31 Jul 2002

Importance of different tfd genes for degradation of chloroaromatics by Ralstonia eutropha JMP134.
Plumeier I, Pérez-Pantoja D, …, González B, Pieper DH
J Bacteriol 2002 Aug 184(15):4054-64 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 31 Jul 2002

Functional analysis of alkane hydroxylases from gram-negative and gram-positive bacteria.
Smits TH, Balada SB, Witholt B, van Beilen JB
J Bacteriol 2002 Mar 184(6):1733-42 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 8 May 2002

Development and characterization of a green fluorescent protein-based bacterial biosensor for bioavailable toluene and related compounds.
Stiner L, Halverson LJ
Appl Environ Microbiol 2002 Apr 68(4):1962-71 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams / Bruce Rittmann
Evaluated 8 May 2002

Biodegradation of atrazine and related s-triazine compounds: from enzymes to field studies.
Wackett LP, Sadowsky MJ, Martinez B, Shapir N
Appl Microbiol Biotechnol 2002 Jan 58(1):39-45 [abstract on PubMed] [related articles] [order article]
Selected by | Peter Williams
Evaluated 8 May 2002

Strain characterization and 16S-23S probe development for differentiating geographically dispersed isolates of the phytopathogen Ralstonia solanacearum.
Timms-Wilson TM, Bryant K, Bailey MJ
Environ Microbiol 2001 Dec 3(12):785-97 [abstract on PubMed] [related articles] [order article]
Selected by | Peter Williams
Evaluated 25 Feb 2002

Integration of global regulation of two aromatic-responsive sigma(54)-dependent systems: a common phenotype by different mechanisms.
Sze CC, Bernardo LM, Shingler V
J Bacteriol 2002 Feb 184(3):760-70 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 22 Feb 2002

Functional versatility and molecular diversity of the metabolic map of Escherichia coli.
Tsoka S, Ouzounis CA
Genome Res 2001 Sep 11(9):1503-10 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 28 Jan 2002

Laboratory evolution of toluene dioxygenase to accept 4-picoline as a substrate.
Sakamoto T, Joern JM, Arisawa A, Arnold FH
Appl Environ Microbiol 2001 Sep 67(9):3882-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 28 Jan 2002

In vivo UV laser footprinting of the Pseudomonas putidasigma 54Pu promoter reveals that integration host factor couples transcriptional activity to growth phase.
Valls M, Buckle M, de Lorenzo V
J Biol Chem 2002 Jan 18 277(3):2169-75 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 23 Jan 2002

Selection of a plant-bacterium pair as a novel tool for rhizostimulation of polycyclic aromatic hydrocarbon-degrading bacteria.
Kuiper I, Bloemberg GV, Lugtenberg BJ
Mol Plant Microbe Interact 2001 Oct 14(10):1197-205 [abstract on PubMed] [related articles] [order article]
Selected by | Peter Williams
Evaluated 27 Nov 2001

A novel replication element from an Antarctic plasmid as a tool for the expression of proteins at low temperature.
Tutino ML, Duilio A, …, Sannia G, Marino G
Extremophiles 2001 Aug 5(4):257-64 [abstract on PubMed] [related articles] [order article]
Selected by | Peter Williams
Evaluated 27 Nov 2001

Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays.
Cho JC, Tiedje JM
Appl Environ Microbiol 2001 Aug 67(8):3677-82 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 12 Sep 2001

Molecular characterization of a deletion/duplication rearrangement in tfd genes from Ralstonia eutropha JMP134(pJP4) that improves growth on 3-chlorobenzoic acid but abolishes growth on 2,4-dichlorophenoxyacetic acid.
Clément P, Pieper DH, González B
Microbiology 2001 Aug 147(Pt 8):2141-8 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Peter Williams
Evaluated 7 Sep 2001

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