FINAL PROGRAMME

ProkaGENOMICS 2009

www.prokagenomics.org

Supporting organizations:

VAAM (Vereinigung für Allgemeine und Angewandte Mikrobiologie e.V.)

DGHM (Deutsche Gesellschaft für Hygiene und Mikrobiologie e.V.)

Akademie der Wissenschaften zu Göttingen

FEMS (Federation of European Microbiological Societies)

4th European Conference on Prokaryotic Genomics4-7 October 2009, Göttingen

ProkaGENOMICS 2009

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TABLE OF CONTENTS

COMMITTEES

Committees .................................................................. 2

Invitation ....................................................................... 3

Programme at a Glance ................................................. 4

Lecture Programme ........................................................ 7

Sunday, 4 October 2009 .......................................... 7

Monday, 5 October 2009 ......................................... 8

Tuesday, 6 October 2009 ......................................... 13

Wednesday, 7 October 2009 .................................... 18

Poster Programme ......................................................... 20

Social Programme .......................................................... 40

General Information ....................................................... 43

Imprint .......................................................................... 47

City Map ....................................................................... 48

Scientific Committee

Christoph Dehio Basel/CH Matthias Frosch Würzburg/D Gerhard Gottschalk Göttingen/D Michael Hecker Greifswald/D Dick Janssen Groningen/NL Wolfgang Liebl München/D Karl-Heinz Maurer Düsseldorf/D Alfred Pühler Bielefeld/D Christoph Sensen Calgary/CDN

Organizing Committee

Wolfgang Liebl München/D Rolf Daniel Göttingen/D Petra Ehrenreich Göttingen/D Dietrich Trzeciok Göttingen/D Matthias Frosch Würzburg/D Gabriele Gerlach Würzburg/D Alfred Pühler Bielefeld/D Werner Selbitschka Bielefeld/D

October 4-7 2009

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INVITATION

The 4th European Conference on Prokaryotic Genomics (ProkaGENOMICS 2009) will take place on 4th–7th October 2009 at the Georg-August-University Göttingen, Germany. ProkaGENOMICS 2009 is the fourth event in a series of successful conferences initiated in 2003 by the three BMBF-funded German GenoMik networks, their centers located in Göttingen, Bielefeld and Würzburg. The confe-rence addresses all basic and applied aspects of the rapidly evolving field of prokaryotic genome research. The major topics of ProkaGENOMICS 2009 are:

Prokaryotic Biotechgenomics

Prokaryotic Pathogenomics

Genomics of Plant-Associated Microorganisms

Biodiversity and Metagenomics

Synthetic Biology, Systems Biology and Bioinformatics

Reconstruction of Genomes and Reverse Genomics

The significant shortage of resources and energy, an in-creasing need for food and a growing burden on the environment due to anthropogenic pollutants are global trends which are having an ever greater influence on the world situation. Furthermore, human health is threate-ned by infectious diseases and new emerging pathogens with highly virulent properties. Research into and the use of micro-organisms offer largely unused opportuni-ties to counter these global trends and to find and im-plement solutions. ProkaGENOMICS 2009 will be an excellent occasion to review the current stage of proka-ryotic genome research in times of rapidly evolving high- throughput technologies, e.g. ultrafast sequencing and array technologies. You are cordially invited to attend the conference, listen to prominent scientists in this exciting field and to become an active part by presenting your work in short lectures or in poster sessions.

We are looking forward to welcoming you in Göttingen and to share a successful and enjoyable meeting with you.

Wolfgang Liebl and Rolf DanielChairs of the conference

ProkaGENOMICS 2009

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PROGRAMME AT A GLANCE

Sunday, 5 October

14:30Guided Sightseeing Tour

17:00

16:00Registration

21:30

18:00 Opening Session (Lecture Hall 010) W. Liebl; R. Daniel; K. von Figura; Representative of the BMBFChair: W. Goebel, München/D

18:30 Opening Lecture: P. Cossart, Paris/F19:30 Welcome Party

Monday, 5 October

Session I: Prokaryotic Biotechgenomics (Lecture Hall 010)Chair: W. Liebl, München/D

08:30 P. Dürre, Ulm/D09:00 J. L. Ramos, Granada/E09:30 N. Ogasawara, Nara/JP10:00 J. Weissenbach, Every Cedex/F10:30 Coffee Break

Session II: Synthetic Biology, Systems Biology and Bioinformatics (Lecture Hall 010)Chair: A. Pühler, Bielefeld/D

11:00 C. Sensen, Calgary/CDN11:30 S. A. Teichmann, Cambridge/UK12:00 P. Bork, Heidelberg/D12:30 Poster / Lunch14:00 D. Jahn, Braunschweig/D14:30 S. Panke, Zürich/CH15:00 Coffee Break

Short PresentationsProkaryotic Biotech- genomics (Lecture Hall 010)

Synthetic Biology, Systems Biology and Bioinformatics (Lecture Hall 009)

Chair: D. Janssen Chair: A. Goesmann15:15 T. Weber T. J. Treangen15:30 C. Monnet R. Cramm15:45 A. Angelov T. Dagan16:00 H. Falentin T. Fehér16.15 Coffee Break

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PROGRAMME AT A GLANCE

Short PresentationsProkaryotic Biotech- genomics (Lecture Hall 010)

Workshop (Lecture Hall 009)

Chair: A. Ehrenreich Chair: A. Thürmer16:30 N. Rehm „Next Generation

Sequencing – Systems and Applications“ (See page 12)

16:45 G. M. Seibold17:00 I. Ochrombel17:15 S. Schweikert17:30 P. Schweiger17:45 Postersession / Exhibition18:45 End 1st Day19:30

Welcome Reception „Old Town Hall“20:00

Tuesday, 6 October

Session III: Prokaryotic Pathogenomics (Lecture Hall 010)Chair: C. Dehio, Basel/CH

08:30 R. Rappuoli, Siena/I09:00 S. H. E. Kaufmann, Berlin/D09:30 G. Weinstock, St. Louis, MO/USA10:00 Coffee Break

Chair: M. Gilmore, Boston/USA10:30 J. Musser, Houston, TX/USA11:00 U. Nübel, Wernigerode/D

Chair: B. Friedrich, Berlin11:30 Distinguished Lecture:

G. Gottschalk, Göttingen/D12:10 Poster / Lunch

Session IV: Genomics of plant-associated microorganisms (Lecture Hall 010)Chair: M. Göttfert, Dresden/D

13:45 D. van der Lelie, Upton, NY/USA14:15 D. Capela, Castanet-Tolosan/F14:45 K. Geider, Dossenheim/D15:15 Coffee Break

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PROGRAMME AT A GLANCE

Short PresentationsProkaryotic Pathogenomics (Lecture Hall 010)

Genomics of Plant-Asso-ciated Microorganisms (Lecture Hall 009)

Chair: M. Frosch Chair: N.N.15:30 H. C. den Bakker T. Smits15:45 D. Cabanes M. Wenzel16:00 A. Rince A. Sarkar16:15 S. Engelmann B. Fan16:30 Coffee Break

Short PresentationsProkaryotic Pathogenomics (Lecture Hall 010)

Biodiversity and Metagenomics (Lecture Hall 009)

Chair: R. Hakenbeck Chair: W. Streit16:45 P. Engel T. Hurek17:00 P. Sirand-Pugnet C. Simon17:15 A. C. Schürch R. J. Siezen17:30 D. Chesnel H. Wang17:45 Postersession / Exhibition18:45 End 2nd Day19:00 Conference Dinner

Wednesday, 7 October

Session V: Biodiversity and Metagenomics (Lecture Hall 010)Chair: R. Daniel, Göttingen/D

08:30 P. O. Beja, Haifa/IL09:00 J. Jansson, Berkeley/USA09:30 U. Schwaneberg, Aachen/D10:00 J. R. van der Meer, Lausanne/CH10:30 E. Rocha, Paris/F11:00 Coffee Break

Session VI: Reconstruction of Genomes and Reverse Genomics (Lecture Hall 010)Chair: M. Hecker, Greifswald/D

11:30 J. I. Glass, Rockville, MD/USA12:00 R. Sorek, Rehovot/IL12:30 J. Vogel, Berlin/D13:00 T. Schweder, Greifswald/D13:30 Closing Remarks13:45 End of Conference

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LECTURE PROGRAMME

SUNDAY, 4 OCTOBER 2009

14:30 - 17:00 Uhr Guided Sightseeing Tour

16:00 - 21:00 Uhr Registration of participants open

Lecture Hall 010

18:00 Opening Session

Welcome Remarks W. Liebl, TU München/D; R. Daniel, Georg

August University Göttingen/D; K. von Figura, Georg August University Göttingen/D; Representative of the BMBF, Bonn/D

Session Chair: W. Goebel, München/D

18:30 Opening Lecture

The transcriptional landscape of Listeria monocytogenes: switch from saprophytism to virulence

P. Cossart, Institut Pasteur, Paris/F

19:30 Welcome Party

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MONDAY, 5 OCTOBER 2009

Session I: Prokaryotic Biotechgenomics

Lecture Hall 010

Session Chair: W. Liebl, München/D

8:30 Clostridium ljungdahlii: a biotechnological production platform from syngas

P. Dürre, Ulm University,Ulm/D

9:00 Post-genomic analysis in solvent-tolerant microbes

J. L. Ramos, Estación Experimental del Zaidín – CSIC, Granada/E

9:30 Enhanced recombinant protein productivity by genome reduction in Bacillus subtilis

K. Ara, Biological Science Laboratories, Kao Corporation, Tokio/JP and N. Ogasawara, Nara Institute of Science and Technology, Nara/JP

10:00 Exploring the metabolic biodiversity of prokaryotes in genomes and metagenomes

J. Weissenbach, Genoscope-CNS, Evry Cedex/F

10:30 Coffee Break

Session II: Synthetic Biology, Systems Biology and Bioinformatics

Lecture Hall 010

Session Chair: A. Pühler, Bielefeld/D

11:00 From Mycoplasma capricolum to 1 000 com-plete microbial genomes: Building genome analysis and annotation tools for 15 years

C. Sensen, University of Calgary/CDN

11:30 Prokaryotic Transcriptional Regulatory Networks

S. A. Teichmann, MRC Laboratory of Molecular Biology, Cambridge/UK

12:00 Comparative Metagenomics P. Bork, EMBL Heidelberg/D

12:30 Poster / Lunch

LECTURE PROGRAMME

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LECTURE PROGRAMME

14:00 Systems biology of pathogenic and biotechnologically relevant bacteria

D. Jahn, TU Braunschweig/D

14:30 Title to be announced S. Panke, ETH Zürich/CH

15:00 Coffee Break

Short Presentations: Prokaryotic Biotechgenomics

Lecture Hall 010

Session Chair: D. Janssen, Groningen/NL

15:15 Kirromycin biosynthesis in Streptomyces collinus Tü 365 - a genomic approach

T. Weber1, E. Pross1, E. Musiol1, T. Laiple1, A. Textor2, S. Grond2, S. Pelzer3, W. Wohlleben1 1University of Tübingen/D, 2University of Göttin-gen/D, 3Merlion Pharmaceuticals GmbH, Berlin/D

15:30 Genome sequence of Arthrobacter arilaitensis RE117, one of the bacteria essential for the ripening of smear cheeses

C. Monnet1, F. Irlinger1, E. Spinnler1, V. Loux2, J. F. Gibrat2, V. Barbe3, B. Vacherie3, F. Gavory3, P. Siguier4, E. Simonnot4, M. Chandler4, R. Elleuch5, T. Vallaeys6

1INRA-AgroParisTech, Thiverval-Grignon/F; 2INRA, Jouy-en-Josas/F; 3Genoscope, Evry/F; 4CNRS-Université Paul Sabatier, Toulouse/F; 5Université des Sciences de Sfax, Sfax/F; 6CNRS - Université Montpellier II, Montpellier/F

15:45 Genome sequence of the polysaccharide-degrading, thermophilic anaerobe Spirochaeta thermophila

A. Angelov1, S. Liebl1, H. Liesegang2, W. Liebl1 1Technical University Munich, Freising/D; 2

University of Göttingen/D

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16:00 Propionibacterium freudenreichii: sequencing and post-genomic approach

H. Falentin1, S. M. Deutsch1, P. Le Bivic1, F. BagliniËre1, S. Parayre1, M. B. Maillard1, J. Dherbécourt1, G. Jan1, A. Thierry1, V. Loux2, A. Couloux3, V. Barbe3, S. Lortal1

1INRA UMR STLO, Rennes/F; 2INRA MIG, Jouy/F; 3Genoscope, Evry/F

16:15 Coffee Break

Session Chair: A. Ehrenreich, München/D

16:30 Nitrogen control of Corynebacterium glutamicum: impact on glutamine metabolism

N. Rehm1, E. Hiery1, T. Georgi2, M. Bott2, A. Burkovski1 1University of Erlangen-Nuremberg, Erlangen/D; 2Forschungszentrum Jülich/D

16:45 The transcriptional regulators RamA and RamB are involved in the regulation of glycogen synthesis in Corynebacterium glutamicum

G. M. Seibold1, C. Hagmann2, M. Schietzel2, D. Emer2, M. Auchter2, B. J. Eikmanns2 1University of Cologne/D; 2University of Ulm/D

17:00 Functional genomics of pH homeostasis in Corynebacterium glutamicum revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis

I. Ochrombel1, M. Follmann1, R. Kraemer1, C. Troetschel2, A. Poetsch2, C. Rueckert3, A. Hueser3, M. Persicke3, J. Kalinowski3, K. Marin1 1University of Cologne/D; 2University of Bochum/D; 3University of Bielefeld/D

17:15 The repertoire of DNA-binding transcriptional regulators in Gluconobacter oxydans 621H

S. Schweikert, T. Polen, S. Bringer, M. Bott Forschungszentrum Jülich/D

17:30 Using the genome of Gluconobacter oxydans for the analysis of novel oxidoreductases

P. Schweiger, U. Deppenmeier; University of Bonn/D

LECTURE PROGRAMME

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17:45 Postersession / Exhibition

18:45 End of 1st Day

19:30 Welcome Reception „Old Town Hall“

Short Presentations: Synthetic Biology, Systems Biology and Bioinformatics

Lecture Hall 009

Session Chair: A. Goesmann, Bielefeld/D

15:15 M-GCAT & Repeatoire: tools for detecting unique and repeated regions in closely related prokaryote genomes

T. J. Treangen1, E. P. Rocha1

1Univ. Pierre et Marie Curie, Paris/F

15:30 Comprehensive analysis of denitrification by a combined proteomics/transcriptomics approach

R. Cramm1, Y. Kohlmann1, A. Pohlmann1, C. Döring2, A. Ehrenreich2, D. Zühlke3, B. Voigt3, D. Becher3, M. Hecker3, B. Friedrich1, E. Schwartz1 1Humboldt-University, Berlin/D; 2University of Göttingen/D; 3University of Greifswald/D

15:45 A reconstructed network of detectable lateral gene transfers in prokaryotes reveals barriers for transfer between different taxonomic groups

O. Popa1, G. Landan2, W. Martin1, T. Dagan1 1Heinrich-Heine-University, Düsseldorf/D; 2University of Houston/USA

16:00 Removal of the flexible gene pool of Escherichia coli is accompanied by loss of adaptability

K. Umenhoffer1, T. Fehér1, I. Karcagi1, B. Csörgö1, G. Draskovits1, G. Balikû1, Z. Györfy1, F. R. Blattner2, G. Pûsfai1 1Hungarian Academy of Sciences, Szeged/HU; 2Scarab Genomics LLC, Madison/USA

16:15 Coffee Break

LECTURE PROGRAMME

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Workshop „Next Generation Sequencing: Systems and Applications“

Lecture Hall 009

Session Chair: A. Thürmer, Göttingen/D

16:30 High through-sequencing of bacteria – one run – one scaffold

M. Dröge, Roche Diagnostics GmbH, Penzberg/D

16:40 Illumina Genome Analyzer System The most widely adopted next generation sequencing system

S. Brooking, Illumina UK Ltd., Essex/UK

16:50 The SOLiD system – recent developments in high throughput sequencing

F. Freund, Applied Biosystems Deutschland GmbH, Darmstadt/D

17:00 Sequencing and transcriptional analysis of bacterial genomes

G. Gradl, A. Strittmatter; Eurofins MWG Operon, Ebersberg/D

17:10 Complete analysis of procaryots with Next Gen sequencing technologies: De novo-, re- and transcriptome sequencing including bioinformatic service

K. A. Stangier, GATC Biotech AG, Konstanz/D

17:20 Roche 454 Sequencing! a novel approach to whole transcriptom sequencing

G. Nyakatura, AGOWA genomics, Berlin/D

17:30 Break

17:45 Postersession / Exhibition

18:45 End of 1st Day

19:30 Welcome Reception „Old Town Hall“

LECTURE PROGRAMME

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TUESDAY, 6 OCTOBER 2009

Session III: Prokaryotic Pathogenomics

Lecture Hall 010

Session Chair: C. Dehio, Basel/CH

8:30 From reverse vaccinology to pathogenesis R. Rappuoli, Novartis Vaccines & Diagnostics,

Siena/I

9:00 Towards a better understanding of the crosstalk between Mycobacterium tuberculosis and its host

S. H. E. Kaufmann, Max Planck Institute for Infection Biology, Berlin/D

9:30 New insights into pathogens and commensals with next-generation sequencing

G. Weinstock, Washington University, St. Louis, MO/USA

10:00 Coffee Break

Session Chair: M. Gilmore, Boston/USA

10:30 Molecular architecture of group A streptococcus epidemics

J. Musser, The Methodist Hospital, Houston, TX/USA

11:00 Genome-wide SNPs reveal the evolutionary history of methicillin-resistant Staphylococcus aureus

U. Nübel, Robert Koch Institute, Wernigerode/D

Distinguished Lecture

Lecture Hall 010

Session Chair: B. Friedrich, Berlin/D

11:30 Wanderings through microbial genomes G. Gottschalk, Georg August University

Göttingen/D

12:10 Poster / Lunch

LECTURE PROGRAMME

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Session IV: Genomics of Plant-Associated Microorganisms

Lecture Hall 010

Session Chair: M. Göttfert, Dresden/D

13:45 Genomics of endophytic bacteria associated with poplar – functions to improve plant establishment, biomass production and phytoremediation

D. van der Lelie, Brookhaven National Labora-tory, Upton, NY/USA

14:15 Genomics of rhizobia: from diversity to experimental evolution

D. Capela, INRA-CNRS, Castanet-Tolosan/F

14:45 Genome comparison and virulence regions of plant-associated bacteria in the genus Erwinia

K. Geider, Biologische Bundesanstalt, JKI Dossenheim/D

15:15 Coffee Break

Short Presentations: Prokaryotic Pathogenomics

Lecture Hall 010

Session Chair: M. Frosch, Würzburg/D

15:30 Rapid, short-read sequencing and comparison of 8 different Listeria strains

H. C. den Bakker1, P. Vatta2, M. Barker2, L. Degoricija2, C. Cummings2, O. Petrauskene2, M. Furtado2, M. Wiedmann1 1Cornell University, Ithaca, NY/USA; 2Applied Biosystems, CA/USA

15:45 In vivo transcriptional profiling of Listeria monocytogenes and mutagenesis identify new virulence factors involved in infection

A. Camejo1, C. Buchrieser2, E. Couvé2, F. Carvalho1, O. Reis1, P. Ferreira1, S. Sousa1, P. Cossart2, D. Cabanes1 1IBMC, Porto/PT; 2Institut Pasteur, Paris/F

LECTURE PROGRAMME

October 4-7 2009

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16:00 Analysis of the regulome of Enterococcus faecalis: connection to stress response and virulence

A. Rince, J. C. Giard, A. Benachour, N. Verneuil, V. Pichereau, Y. Auffray, A. Hartke University of Caen/F

16:15 The impact of the redox sensor Rex on anaerobic gene expression in Staphylococcus aureus

S. Fuchs1, M. Pagels1, J. Pané-Farré1, C. Kohler1, L. Menschner1, R. A. Proctor2, M. Hecker1, S. Engelmann1 1University of Greifswald/D; 2University of Wisconsin-Madison, Madison, WI/USA

16:30 Coffee Break

Session Chair: R. Hakenbeck, Kaiserslautern/D

16:45 Lineage-specific diversification of VirB Type IV secretion systems confers host adaptability in the genus Bartonella

P. Engel1, W. Salzburger1, C. Lanz2, S. C. Schuster3, C. Dehio1 1University of Basel/CH; 2Max Planck Institute, Tübingen/D; 3PennState University, Philadelphia, PA/USA

17:00 Gene exchange among mycoplasmas: acquiring new potentials in a general context of massive gene loss

P. Sirand-Pugnet1, C. Citti2, A. Barre1, A. Blanchard1 1University of Bordeaux/F; 2INRA, Toulouse/F

17:15 Unveiling exact transmission chains in a large tuberculosis outbreak by integration of genome sequencing data

A. C. Schürch1, K. Kremer1, O. Daviena1, A. Kiers2, M. J. Boeree3, R. Siezen4, D. van Soolin-gen1 1RIVM, Bilthoven/NL; 2GGD Fryslân, Leeuwarden/NL; 3Radboud University Nijmegen Medical Cen-tre, Nijmegen/NL; 4Radboud University Nijmegen Medical Centre / NCMLS, Nijmegen/NL

LECTURE PROGRAMME

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17:30 The EMBL repository for M. tuberculosis targets for structural and functional characterization

D. Chesnel, M. Wilmanns, A. Geerlof, J. Mueller-Dieckmann, Y. Song, P. Tucker, M. Weiss; EMBL, Hamburg/D

17:45 Postersession / Exhibition

18:45 End of 2nd Day

19:00 Conference Dinner (Mensa am Turm)

Short Presentations: Genomics of Plant-Associated Microorganisms

Lecture Hall 009

Session Chair: N.N.

15:30 Comparative functional genomics to elucidate virulence factors in virulent Erwinia spp. and biocontrol features in Pantoea agglomerans

T. Smits1, J. E. Frey1, A. Goesmann2, F. Rezzonico1, B. Duffy1 1Agroscope Changins-Wädenswil ACW, Wädenswil/CH; 2University of Bielefeld/D

15:45 Analysis of a novel flavonoid-dependent regulatory pathway in Bradyrhizobium japonicum

M. Wenzel, K. Lang, T. Günther, A. Bhandari, K. Mäbert, M. Göttfert; TU Dresden/D

16:00 Expression profile analysis of nitrogen and oxygen responses in the diazotrophic endophytic BETA-proteobacterium Azoarcus sp. BH72 by genome-wide microarray

A. Sarkar1, A. Becker2, B. Reinhold-Hurek1 1University of Bremen/D; 2University of Freiburg/D

16:15 Transcriptional profiling of Bacillus amyloliquefaciens FZB42 in response to root exudates

B. Fan1, A. Becker2, B. Baumgarth2, X. H. Chen1, R. Borriss1 1Humoldt-University Berlin/D; 2University of Bielefeld/D

16:30 Coffee Break

LECTURE PROGRAMME

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LECTURE PROGRAMME

Short Presentations: Biodiversity and Metagenomics

Lecture Hall 009

Session Chair: W. Streit, Hamburg/D

16:45 The rice endophyte metagenome A. Sessitsch1, P. Hardoim2, J. Döring3,

A. Krause3, S. G. Tringe4, A. Weilharter1, B. Mitter1, L. Hauberg3, F. Friedrich3, M. Rahalkar3, T. Hurek3, L. van Overbeek5, L. Bodrossy1, D. Brar6, J. van Elsas2, B. Reinhold-Hurek3 1ARC Seibersdorf research GmbH, Seibersdorf/D; 2University of Groningen/D; 3University of Bremen/D; 4Joint Genome Institute, Walnut Creek, CA/USA; 5Plant Research International B.V, Wageningen/NL; 6IRRI, Manila/PH

17:00 Metagenomic analyses of glacier ice C. Simon, A. Wiezer, S. Rockstroh, J. Herath,

R. Daniel University of Göttingen/D

17:15 Genotype-phenotypic matching of diversity in Lactococcus lactis and Lactobacillus plantarum strains

R. J. Siezen1, V. A. Tzeneva2, G. E. Felis3, M. Wels2, J. L. Rademaker2, M. J. Starrenburg2, J. Bayjanov1, D. Molenaar2, J. E. van Hylckama Vlieg2, S. A. van Hijum2

1Radboud University Medical Centre, Nijmegen/NL; 2TI Food & Nutrition, Ede/NL; 3University of Verona/I

17:30 Comparative genomic analysis of two toxic bloom-forming Anabaena strains

H. Wang1, L. Rouhiainen1, D. P. Fewer1, G. Corti2, E. Rizzi2, G. De Bellis2, Z. Li3, B. Liu3, K. Sivonen1 1University of Helsinki/FI; 2National Research Council, Milan/I; 3Beijing Genomics Institute, Beijing/in/CN

17:45 Postersession / Exhibition

18:45 End of 2nd Day

19:00 Conference Dinner (Mensa am Turm)

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LECTURE PROGRAMME

WEDNESDAY, 7 OCTOBER 2009

Session V: Biodiversity and Metagenomics

Lecture Hall 010

Session Chair: R. Daniel, Göttingen/D

8:30 Metagenomics & viral photosynthesis O. Beja, Technion – Israel Institute of Technology,

Haifa/IL

9:00 Studying the human gut microbiome (in health and disease) using a variety of „omics“ approaches

J. Jansson, Lawrence Berkeley National Laboratory, Berkeley, CA/USA

9:30 Steering directed protein evolution by managing the combinatorial complexity of mutant libraries

U. Schwaneberg, RWTH Aachen University/D

10:00 The plasmid mobilome in wastewater treatment plant

J. R. van der Meer, University of Lausanne/CH

10:30 Comparative genomics at the edge of evolutionary ecology

E. Rocha, Institut Pasteur, Paris/F

11:00 Coffee Break

Session VI: Reconstruction of Genomes and Reverse Genomics

Lecture Hall 010

Session Chair: M. Hecker, Greifswald/D

11:30 Transplantation of genomes across branches of life: from bacteria to a eukaryote and back again to bacteria

J. I. Glass, J. Craig Venter Institute, Rockville, MD/USA

12:00 Deep sequencing of microbial transcriptomes R. Sorek, Weizman Institute of Science,

Rehovot/IL

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LECTURE PROGRAMME

12:30 Discovery and functional analysis of small noncoding RNAs in bacteria

J. Vogel, Max Planck Institute for Infection Biology, Berlin/D

13:00 Reverse genomics of Bacilli T. Schweder, Ernst Moritz Arndt University of

Greifswald/D

13:30 Closing Remarks

13:45 End of Conference

ProkaGENOMICS 2009

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Prokaryotic Biotechgenomics

1 Bacterium exometabolite regulatory functions

N. Chalisova, Pavlov Institute of Physiology of Russian Academy of Sciences, St. Petersburg/RU

2 NtcA, a negative regulator of chivosazol biosynthesis in Sorangium cellulosum

S. Rachid1, K. Gerth2, R. Müller1 1University of Saarland, Saarbruecken/D; 2Helmholtz Center for Infection Research, Braunschweig/D

3 Oxaloacetate decarboxylase of Corynebacterium glutamicum

S. Klaffl, B. J. Eikmanns Ulm University/D

4 13C-Labeling study with D-glucose-grown Gluconobacter oxydans 621H

T. Hanke, S. Noack, M. Oldiges, K. Nöh, S. Bringer, H. Sahm, M. Bott, W. Wiechert

Forschungszentrum Jülich/D

5 Functional annotation of unknown proteins by enzymatic screening and structural proteomics

A. Yakunin, E. Kuznetsova, G. Brown, N. Beloglazova, R. Flick, S. Kochinyan, A. Tchigvintsev, A. Savchenko

University of Toronto/CA

6 Examination of the physiological role of deglycating enzymes in Bacillus subtilis

V. M. Deppe1, T. O‘Connell1, J. Bongaerts1, F. Meinhardt2, K. H. Maurer1

1Henkel AG & Co. KGaA, Düsseldorf/D; 2University of Münster/D

7 Functional genome analysis of the purine-utilising bacterium Clostridium acidiurici

K. Hartwich, G. Gottschalk, R. Daniel University of Göttingen/D8 Screening for molecules interfering with

quorum sensing for use in biotechnology N. Weiland, N. Pinnow, F. Symanowski, R. A. Schmitz-Streit; CAU Kiel/D

POSTER PROGRAMME

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POSTER PROGRAMME

9 DNA-Transfer into Bacillus licheniformis by trans-conjugation

M. Rachinger1, J. Bongaerts2, R. Daniel1, W. Liebl3, H. Liesegang1, A. Ehrenreich3

University of Göttingen/D; 2Henkel AG & Co. KGaA, Düsseldorf/D; 3TU Munich/D

10 Nitrogen regulation of Corynebacterium glutamicum: influence of mutations on metabolome and trancriptome profiles

N. Rehm1, J. Strösser2, S. Buchinger2, S. Hans3, A. Burkovski1 1University Erlangen-Nuremberg/D; 2University of Cologne/D; 3Evonik-Degussa GmbH, Halle-Kün-sebeck/D

11 Isolation and characterization of a steroid degrading bacterial strain from the Baltic Sea at Kiel Germany

G. Xiong, T. Zhang, Y. Sang, E. Maser University of Kiel/D

12 A novel system for the functional expression of heterologous membrane proteins

A. Heck, S. Arvani, F. Circolone, K. E. Jaeger, N. Katzke, J. Potzkei, V. Svensson, T. Drepper Heinrich-Heine-University Düsseldorf/D

13 A novel system for the functional expression of clustered genes

A. Loeschcke, A. Markert, F. Rosenau, S. Wilhelm, K. E. Jaeger, T. Drepper

Heinrich-Heine-University Düsseldorf/D

14 Development of novel fluorescent proteins that do not require oxygen

F. Circolone1, J. Potzkei1, S. Endres1, A. Heck1, M. G. Puls2, K. E. Jaeger1, T. Drepper1 1Heinrich-Heine-University Düsseldorf/D; 2evocatal GmbH, Düsseldorf/D

15 Biotenside production and biofilm formation of Burkholderia glumae depends on a functional type II secretion system

J. Knorr1, S. Isenhardt1, S. Wilhelm1, S. Voget2, K. E. Jaeger1, F. Rosenau1 1Heinrich-Heine-University Düsseldorf/D; 2University of Göttingen/D

ProkaGENOMICS 2009

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16 Production of a new two-peptide lantibiotic by Bacillus licheniformis DSM13

J. Dischinger, M. Josten, H. G. Sahl, G. Bierbaum University of Bonn/D

17 The complete genome sequence of Corynebacterium glycinophilum

J. Milse, J. Kalinowski, A. Pühler, C. Rückert University of Bielefeld/D

18 Cell harvesting for metabolome analysis in C. glutamicum by size exclusion chromatography

M. Persicke, J. Plassmeier, H. Neuweger, A. Pühler, J. Kalinowski University of Bielefeld/D

19 Transcriptional analysis of continuous cultures during the metabolic switch from acidogenesis to solventogenesis

C. Doering1, D. Krauße2, A. Ehrenreich1,2 1University of Göttingen/D; 2TU Munich, Freising/D

20 Identification and characterization of an L-cystine uptake system in Corynebacterium glutamicum ATCC13032

A. Lömker1, T. Radespiel2, K. Marin2, A. Pühler1, J. Kalinowski1, C. Rückert1 1University of Bielefeld/D; 2University of Cologne/D

21 Genome & transcriptome analysis: maximising the benefits of next-generation sequencing by combining technologies

K. Stangier, U. Schoeck, Y. Kumar, C. Bauser GATC Biotech AG, Konstanz/D

22 Regulation of ethanol metabolism in Corynebacterium glutamicum by the transcriptional regulator Cg0146

M. Auchter1, C. Fleischer1, L. Schiller1, A. Arndt1, L. Gaigalat2, B. J. Eikmanns1 1University of Ulm/D; 2University of Bielefeld/D

POSTER PROGRAMME

October 4-7 2009

23

23 The role of the aco- and acu genes during growth of Bacillus licheniformis on amino acids

M. Bauch1, M. Schwarzer2, J. Bongaerts3, S. Evers3, W. Liebl1, A. Ehrenreich1 1TU Munich, Freising/D; 2University of Göttingen/D; 3Henkel AG & Co. KGaA, Düsseldorf/D

24 A search for new enzymes of the purine degradation pathway in the soil bacterium Acinetobacter baylyi ADP1

C. Fischer, A. Papeil, V. de Berardinis, M. Bes-nard, N. Perchat, A. Kreimeyer, C. Lechaplais, C. Pelle, A. Perret, A. Pinet, B. Segurens, S. Tricot, J. Weissenbach, M. Salanoubat Genoscope, Evry/F

25 Deletion of membrane bound dehydrogenases in Gluconobacter oxydans DSM 7145

J. Voss1, A. Junker2, A. Ehrenreich2, W. Liebl2 1University of Göttingen/D; 2TU Munich, Freising/D

26 Clostridium ljungdahlii - insight in the metabolism of a homoacetogenic Clostridium

C. Held1, M. Köpke2, W. Liebl1, A. Ehrenreich1, P. Dürre2 1TU Munich, Freising/D; 2University of Ulm/D

27 The response of B. licheniformis cells to environmental stress

B. Voigt1, R. Schroeter1, D. Albrecht1, D. Becher1, B. Jürgen1, S. Evers2, K. H. Maurer2, T. Mascher3, T. Schweder1, M. Hecker1 1University of Greifswald/D; 2Henkel AG & Co. KGaA,Düsseldorf/D; 3University of Karlsruhe/D

28 Comparative genome analysis of the potential production strain Burkholderia glumae PG1

S. Voget1, F. Rosenau2, A. Wollherr1, H. Liesegang1, A. Poehlein1, W. R. Streit3, G. Gottschalk1, R. Daniel1, K. E. Jäger2 1University of Göttingen/D; 2University of Düsseldorf/D; 3University of Hamburg/D

POSTER PROGRAMME

ProkaGENOMICS 2009

24

29 A cloning and enzymatic screening platform for large-scale functional genomic studies and discovery of novel biocatalysts

V. de Berardinis1, M. Anissimova1, A. Perret1, P. Marliere2, M. Salanoubat1, J. Weissenbach1 1Genoscope, Evry/F; 2Isthmus, Evry/F

30 Living on hydrogen and carbon dioxide – a functional genomics analysis of lithoautotrophy

Y. Kohlmann1, A. Pohlmann1, R. Cramm1, A. Otto2, D. Becher2, M. Hecker2, B. Friedrich1 1Humboldt-University of Berlin/D; 2University of Greifswald/D

31 Regulation of autotrophy and the Entner-Doudoroff pathway in Ralstonia eutropha H16

B. Kusian1, A. Näther1, V. Halacheva1, R. Budinova1, A. Dimitrova1, S. Peykov1, G. Stahlhut1, A. Ehrenreich2, B. Bowien1 1University of Göttingen/D; 2TU Munich/D

32 Insights into the energy metabolism of Acetobacterium woodii from its genome analysis

A. Poehlein1, J. Vollmers1, E. Biegel2, S. Schmidt2, M. Goenrich3, A. Thürmer1, R. Daniel1, G. Gottschalk1, R. K. Thauer3, V. Müller2 1University of Göttingen; 2Goethe-University Frankfurt/D; 3Max Planck Institute for Terrestrial Microbiology, Marburg/D

33 Genome-wide transcriptome analyses of the ‚Knallgas‘ bacterium Ralstonia eutropha H16 particularly with regard to PHA metabolism

K. Peplinski1, A. Ehrenreich2, C. Döring2, M. Bömeke2, A. Steinbüchel1 1University of Münster/D; 2University of Göttingen

34 Heterologous production of L-pipecolic acid in Corynebacterium glutamicum

N. Wagner, A. Steinkämper, R. Biener, D. Schwartz University of Applied Sciences, Esslingen/D

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October 4-7 2009

25

35 Regulation of friulimicin production in Actinoplanes friuliensis

N. Wagner, A. Steinkämper, R. Biener, D. Schwartz University of Applied Sciences, Esslingen/D

36 The genome of Burkholderia rhizoxinica reveals secrets of an endofungal toxin factory

G. Lackner, L. P. Partida-Martínez, C. Hertweck Hans-Knöll-Institute, Jena/D

37 Transcriptional analysis of continuous cultures during the metabolic switch from acidogenesis to solventogenesis in Clostridium acetobutylicum

C. Döring1, D. Krauße2, A. Ehrenreich2 1Unversity of Göttingen/D; 2TU Munich/D

Prokaryotic Pathogenomics

38 Comparative genomic analyses of clinical Bordetella pertussis isolates: Insights in the genomic content of strains isolated in different countries

A. J. King, S. van der Lee, F. R. Mooi RIVM, Bilthoven/NL

39 Structural and functional characterization of type III effectors using a structural proteomics pipeline

A. U. Singer1, T. Skarina1, R. Lam2, N. Y. Chirgadze2, C. Parsot3, A. Savchenko1

1University of Toronto/CA; 2University Health Net-work, Toronto/CA; 3Institute Pasteur, Paris/F

40 Transfer of a putative hyaluronidase hylEfm and distribution of its putative pathogenicity island among different Enterococcus faecium isolates

J. Laverde-Gomez, C. Fleige, G. Werner Robert Koch Institute, Wernigerode/D

41 Chromosomal transfer of the Enterococcus faecalis pathogenicity island

J. Laverde-Gomez, C. Fleige, G. Werner Robert Koch Institute, Wernigerode/D

POSTER PROGRAMME

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26

42 The Burkholderia cepacia complex RNA chaperone Hfq is required for stress resistance and virulence to the nematode Caenorhabditis elegans

S. A. Sousa, C. G. Ramos, L. M. Moreira, J. H. Leitão IBB-Institute for Biotechnology and Bioengineering, Lisboa/PT

43 Comparison of one- and two-color array CGH analyses of 30 Neisseria meningitidis strains across serogroups: Quantifying the cost-quality-tradeoff

R. Schwarz, B. Joseph, A. Schramm-Glück, K. Engelhard, M. Frosch, T. Müller, C. Schoen University of Würzburg/D

44 The transcriptome of meningococci under in vivo mimicking conditions

B. Joseph1, M. Dondrup2, D. Esser3, R. Schwarz1, H. Neuweger2, S. Jaenicke2, A. Goesmann2, M. Frosch1, C. Schoen1 1University of Würzburg/D; 2University of Bielefeld/D; 3GATC Biotech, Konstanz/D

45 Antibiotic stress triggers the transposition frequency of IS256r in Staphylococcus aureus

M. Nagel, G. Bierbaum University of Bonn/D

46 (Re-)Sequencing of Pseudomonas aeruginosa PAO1 sublines

J. Klockgether, C. F. Davenport, L. Wiehlmann, B. Tuemmler Hanover Medical School, Hanover/D

47 Sequencing of low-copy IncN plasmids mediating cephalosporin resistance

A. Danschke, W. Witte Robert-Koch Institute, Wernigerode/D

48 Microevolution of Staphylococcus aureus clonal complex 5 investigated on the basis of whole genome sequences

J. Dordel, W. Witte, U. Nuebel Robert Koch Institute, Wernigerode/D

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October 4-7 2009

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49 Mycobacterium tuberculosis: reactivation from latency

B. Tizzano1, D. Chesnel1, H. Rachman2, S. H. Kaufmann2, M. Wilmanns1 1EMBL Hamburg/D; 2Max Planck Institute, Berlin/D

50 Transcriptomic variability delineate the phylogeny of Mycobacterium tuberculosis complex

S. Homolka1, S. Niemann1, D. Russell2, K. Rohde2 1Research Center Borstel/D; 2Cornell University, Ithaca, NY/USA

51 Species-specific evolutionary strategies revealed from genome and transcriptome of Streptococcus pyogenes and S. mutans

F. Maruyama1, H. Mori1, C. Aikawa2, T. Nozawa2, K. Kurokawa1, I. Nakagawa2 1Tokyo Institute of Technology, Yokohama/JP; 2Tokyo Med Dent University, Tokyo/JP

52 Sequencing of the two canine Helicobacter species: H. bizzozeronii and H.salomonis

T. Raitila, L. Paulin, P. Auvinen, M. Hänninen University of Helsinki/FI

53 Genome-wide screen of in vivo expressed genes in the opportunistic pathogen Enterococcus faecalis

A. Hanin1, N. Sauvageot1, I. Sava2, Y. Bao2, A. Rince1, J. Huebner2, A. Hartke1, Y. Auffray1 1University of Caen/F; 2University Medical Center, Freiburg/D

54 Population structure of Pseudomonas aeruginosa in CF and COPD

L. Wiehlmann, E. Rakhimova, S. Horatzek, N. Cramer, A. Pelnikevich, B. Tümmler Hanover Medical School, Hanover/D

55 A large number of small non-coding RNAs are controlled by the two-component regulatory system CiaRH in various streptococci

R. Brückner, P. Marx, M. Kovács, R. Hakenbeck University of Kaiserslautern/D

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28

56 Adaptations of Pseudomonas aeruginosa during the infection of chronic wounds

M. Hogardt1, S. Schmoldt2, I. Oezkaya1, M. Schobert3, J. Heesemann1 1Ludwig-Maximilians-University Munich/D; 2Institut für Mikrobiologie der Bundeswehr, Munich/D; 3TU Braunschweig/D

57 The virulence of Pseudomonas aeruginosa is triggered by the conditions in the urinary tract

N. Rosner, M. Schobert, D. Jahn, P. Tielen TU Braunschweig/D

58 Use of large scale genomic deletions and in vivo models to identify genomic islands encoding virulence factors in Pseudomonas aeruginosa

M. Crosatti, E. Harrison, B. Rieck, K. Rajakumar University of Leicester/D

59 The complete genome sequence of asymptomatic bacteriuria strain 83972 of Escherichia coli: Insights into reductive evolution of a pathogen towards a commensal of the urinary tract

E. Brzuszkiewicz1, J. Zdziarski2, C. Svanborg3, J. Hacker4, U. Dobrindt2, G. Gottschalk1 1University of Göttingen/D; 2University of Würz-burg/D; 3Lund University, Lund/SE; 4Robert Koch Institute, Berlin/D

60 Transcriptomic analysis of a Staphylococcus aureus Rex mutant

G. Sander1, J. Seggewiss1, R. A. Proctor2, G. Peters1, K. Becker1, C. von Eiff1 1University of Münster/D; 2University of Madison, WI/USA

61 Pathogenomics of Burkholderia genus: insights in the adaptation to a pathogenic lifestyle

I. Maida, E. Perrin, M. C. Papaleo, R. Fani, M. Fondi; University of Florence/I

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October 4-7 2009

29

62 Genomic comparison of oral streptococci by DNA-microarray analysis

Y. Schähle, R. Hakenbeck, D. Denapaite University of Kaiserslautern/D

63 Comparative genome analysis of 17 non-typhoidal Salmonella enterica isolates from twelve serotypes

F. Fricke1, P. F. McDermott2, D. G. White2, M. K. Mammel3, J. E. LeClerc3, J. Ravel1, T. A. Cebula4 1University of Maryland, Baltimore, MD/USA; 2Center for Veterinary Medicine (CVM-FDA), Laurel, MD/USA; 3Center for Food Safety and Applied Nutrition (CVM-FDA), Laurel, MD/USA; 4Johns Hopkins University, Baltimore, MD/USA

64 Complete genome sequencing of the stone fruit quarantine pathogen Xanthomonas arboricola pv. pruni

J. F. Pothier1, S. Theo H. M.1, F. J. Vorhölter2, R. Szczepanowski2, A. Goesmann2, A. Pühler2, B. Duffy1 1Agroscope Changins-Wädenswil ACW, Wädens-wil/CH; 2University of Bielefeld/D

65 Analysis of intestinal flora in Clostridium difficile positive and negative fecal samples from humans and animals

J. Skraban1, M. Rupnik2 1Institute of Public Health, Maribor/SI; 2University of Maribor/SI

66 Variability of Clostridium difficile toxin co-ding region PaLoc

A. Kocuvan, M. Rupnik University of Maribor/SI

67 Comparative genome analysis of Enterococcus faecalis isolates

K. Palmer1, D. Gevers2, M. Gilmore1 1Harvard Medical School, Boston, MA/USA; 2Broad Institute, Cambridge/UK

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Genomics of Plant-Associated Microorganisms

68 Analysis of the transport and the biochemical properties of the type III-secreted effector NopE1 of Bradyrhizobium japonicum

S. Zehner, M. Wenzel, L. Friedrich, M. Göttfert TU Dresden/D

69 High through-put analysis of plant growth promotion genes in plant-associated Bacillus strains by M-CGH and direct genome sequencing

X. Chen1, C. Rückert2, B. Baumgarth2, A. Becker2, R. Borriss1 1Humboldt-University Berlin/D; 2Bielefeld University/D

70 Microarray analysis of stress response networks in Bradyrhizobium japonicum

K. Lang, J. Schirrmeister, M. Göttfert TU Dresden/D

71 Proteome of plant growth promoting rhizobacterium Bacillus amyloliquefaciens FZB42

K. Kierul1, B. Voigt2, X. Chen1, R. Borriss1 1Humboldt-University Berlin/D; 2University of Greifswald/D

72 Functional genomics of Roseobacter litoralis – a seaweed associated marine bacterium

D. Kalhoefer1, S. Voget2, H. Liesegang2, R. Daniel2, T. Brinkhoff1, R. Rabus1, M. Simon1 1University of Oldenburg/D; 2University of Göttingen/D

73 Functional genome analysis of Phaeobacter gallaeciensis

S. Thole1, S. Voget2, H. Liesegang2, R. Daniel2, R. Rabus1, T. Brinkhoff1, M. Simon1 1Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg/D; 2University of Göttingen/D

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October 4-7 2009

31

74 Novel quorum quenching clones from Rhizobium sp. NGR234

D. Krysciak1, C. Schmeisser1, J. Steiger1, M. Quitschau2, S. Grond2, W. Streit1 1University of Hamburg/D; 2University of Göttingen/D

75 Proteomic and transcriptomic approaches for the molecular characterisation of a novel quorum sensing system in the diazotrophic grass endophyte Azoarcus sp. strain BH72

L. Hauberg1, C. Scharf2, U. Völker2, B. Reinhold-Hurek1 1University of Bremen/D; 2University of Greifs-wald/D

76 Computer based and experimental approaches to elucidate the role of TonB-dependent receptors in the endophytic life of Azoarcus sp. BH72

A. Krause, A. Klindworth, L. Hauberg, J. Oetjen, F. Battistoni, B. Reinhold-Hurek

University of Bremen/D

77 Structure and transport of the endogenous siderophore of Herbaspirillum seropedicae Z67 in comparison to the Burkholderia spp. ornibactin mediated iron uptake system

F. Rosconi1, J. A. Abin1, D. Davyt2, F. Pedrosa3, E. M. Souza3, E. Fabiano1 1Instituto Clemente Estable, Montevideo/UY; 2Facultad de QuÌmica, Montevideo/UY; 3Universidade Federal do Paran, Curitiba/BR

78 A novel type of transcriptional regulator involved in iron response in S. meliloti

V. Amarelle1, F. Rosconi1, U. Koziol1, F. Noya1, M. R. O‘Brian2, E. Fabiano1 1Instituto Clemente Estable, Montevideo/UY; 2State University of New York at Buffalo, NY/USA

79 Complete genome sequencing of Pantoea agglomerans C9-1, an effective antagonist of the fire blight bacterium Erwinia amylovora

T. Smits1, C. Pelludat1, J. E. Frey1, A. Goesmann2, F. Rezzonico1, B. Duffy1

1Agroscope Changins-Wädenswil ACW, Wädenswil/CH; 2University of Bielefeld/D

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32

80 Effect of maize root exudates collected under different nutritional deficiencies on global gene expression in plant-associated Bacillus amyloliquefaciens FZB42 L

L. Costa Carvalhais1, N. von Wirén2, D. Fedoseyenko3, X. Chen1, O. Makarewicz1, B. Baumgarth4, A. Becker5, R. Borriss1

1Humboldt-University Berlin/D; 2Leibniz Institute of Plant Genetics and Crop Plant Re-search, Gatersleben/D; 3Hohenheim University, Stuttgart/D; 4Bielefeld University, Bielefeld/D; 5Freiburg University, Freiburg/D

Biodiversity and Metagenomics

81 Developing genetic tools to study and monitor degradation of pollutants in anaerobic soils with chlorate as electron acceptor

M. Oosterkamp University of Wageningen/NL

82 A proteogenomic comparison of bacterial endosymbionts from the deep sea tube worms Tevnia jerichonana and Riftia pachyptila

A. Gardebrecht1, S. Markert1, H. Felbeck2, A. Thürmer3, H. Liesegang3, D. Albrecht4, R. Daniel3, S. Sievert5, M. Hecker4, T. Schweder1 1Institute of Marine Biotechnology, Greifswald/D; 2Scripps Institution of Oceanography, La Jolla, CA/USA; 3University of Göttingen/D; 4University of Greifswald/D; 5Woods Hole Oceanographic Institution, Woods Hole, MA/USA

83 Comparative genomics of representative members of the Roseobacter-clade: the genus Octadecabacter

J. Vollmers1, S. Voget1, A. Wollherr1, H. Liesegang1, T. Brinkhoff2, M. Simon2, R. Daniel1

1University of Göttingen/D; 2University of Oldenburg/D

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October 4-7 2009

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84 Deep inside the biodiversity of superoxide reductases

C. Lucchetti-Miganeh, D. Thybert, S. Aavner, F. Barloy-Hubler UMR CNRS 6026, Rennes/F

85 Synthesis of the compatible solute hydroxyectoine: physiology, biochemistry and the crystal structure of the ectoine hydroxylase EctD

M. Pittelkow, J. Bursy, A. Pierik, A. Heine, K. Reuter, E. Bremer University of Marburg/D

86 Uptake and metabolism of the compatible solutes ectoine and hydroxyectoine by the marine bacterium Silicibacter pomeroyi DSS-3

A. Rolbetzki1, M. Pittelkow1, J. Bursy1, T. Bönig1, J. Lecher2, S. Zobel2, S. Smits2, L. Schmitt2, E. Bremer1 1University of Marburg/D; 2University of Düsseldorf/D

87 Assessment of the functional diversity of soil microbial communities in grassland and forest areas of the German Biodiversity Exploratory Hainich-Dün by metagenomics

C. Will, R. Daniel University of Göttingen/D

88 Dependence of the soil microbial community structure on tree species

B. Pfeiffer, R. Daniel University of Göttingen/D

89 Identification and characterization of microbial key functions in soils of the German Biodiversity Exploratories Schorfheide-Chorin and Swabian Alb representing different land-use gradients

H. Nacke, S. Herzog, R. Daniel University of Göttingen/D

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90 Metatie – Accurate, flexible and fast taxonomic assignment for ultra-short metagenomic reads

C. Davenport1, J. Klockgether1, B. Langmead2, B. Tümmler1 1Hanover Medical School, Hannover/D; 2University of Maryland, MD/USA

91 Proteomics of the bacterial endosymbiont from the deep sea tube worm Riftia pachyptila

S. Markert1, A. Gardebrecht1, H. Felbeck2, A. Thürmer3, H. Liesegang3, D. Becher1, R. Daniel3, S. M. Sievert4, M. Hecker1, T. Schweder1 1University of Greifswald/D; 2Scripps Institution of Oceanography, San Diego, CA/USA; 3University of Göttingen/D; 4Woods Hole Oceanographic Institution, Woods Hole, MA/USA

92 New insights into the lysine fermentation pathway

A. Perret, A. Kreimeyer, C. Lechapelais, C. Pellé, N. Perchat, S. Tricot, D. Vallenet, C. Médigue, M. Salanoubat, J. Weissenbach Genoscope, Evry/F

93 A conserved gene cluster rules anaerobic oxidative degradation of L-Ornithine

N. Fonknechten, A. Perret, N. Perchat, S. Tricot, C. Lechapelais, D. Vallenet, C. Vergne, D. Le Paslier, A. Zaparucha, J. Weissenbach, M. Salanoubat Genoscope, Evry/F

94 Metagenomic analysis of rotting flies D. Schneider, S. Rockstroh, R. Daniel

University of Göttingen/D

95 A metagenome approach to find new quorum sensing inhibitors

T. Pirch1, C. Anetzberger1, B. Schalkhaußer1, D. Rädler1, N. Weiland2, R. Schmitz-Streit2, K. Jung1 1University of Munich, Planegg-Martinsried/D; 2University of Kiel/D

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96 A visualization tool for comparative community analyses using nearest relatives

H. Mori, F. Maruyama, K. Kurokawa Tokyo Institute of Technology, Yokohama/JP

97 Genomic analysis of a pool of plasmids isolated from several carotenoid-producing strains of Paracoccus spp.

A. Klicka, L. Dziewit, D. Bartosik University of Warsaw/PL

98 Identification of a novel non-autonomous transposable element in Pseudomonas sp. UW12 and search for the transposase responsible for its mobility

M. Szuplewska1, M. Warsinska2, A. Klicka1, D. Bartosik1 1University of Warsaw/PL; 2Institute of Bioche-mistry and Biophysics, Warsaw/PL

99 New cellulolytic and hemicellulolytic enzymes derived from a thermophilic microbial community

M. Mientus1, S. Wittenberg2, J. Schuldes2, A. Angelov1, R. Daniel2, W. Liebl1 1Technical University of Munich, Freising/D; 2University of Göttingen/D

100 Metagenome-derived quorum-quenching clones interfering with P.aeruginosa biofilm formation

C. Hornung1, P. Bijtenhoorn1, C. Vollstedt1, M. Quitschau2, S. Grond2, W. Streit1 1University of Hamburg/D; 2University of Göttingen/D

101 Overexpression and purification of novel metagenome derived thermoactive lipases affiliated to Thermaceae-species

J. Chow1, C. Vollstedt1, O. Thum2, W. R. Streit1 1University of Hamburg/D; 2Evonik Goldschmidt GmbH, Essen/D

102 The standard genetic code is ubiquitous in environmental samples

B. E. Dutilh Radboud University Nijmegen Medical Centre, Nijmegen/NL

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103 Genetic diversity between Campylobacter jejuni strains using Random Amplified Polymorphic DNA (RAPD)

J. Petrov Medical Faculty, Skopje/MK

104 Chemical analysis of biofilm inhibition (ChemBiofilm)

M. Quitschau1, S. Grond1, W. Streit2, C. Schipper2 1University of Göttingen/D; 2University of Hamburg/D

105 Novel bacterial laccases and a xylanase from environmental samples

N. Stößer, N. Schreiber, G. Antranikian TU Hamburg-Harburg, Hamburg/D

106 Introgression of an antibiotic resistance gene into a naturally transformable bacterial population

O. Wikmark1,2, J. L. Ray1, K. Harms2, I. Starikova1, P. J. Johnsen1, K. M. Nielsen1,2

1University of Tromsø/NO; 2GenØk – Centre of Biosafety, Tromsø/NO

107 Novel shuttle vectors to construct metagenomic libraries

S. Tröschel, C. Real, S. Wilhelm, F. Rosenau, K. E. Jäger University of Düsseldorf/D

Reconstruction of Genomes and Reverse Genomics

108 Genomic feature analyses of Serratia odorifera

A. Thürmer1, M. Kai2, R. Daniel1, B. Piechulla2, G. Gottschalk1 1University of Göttingen/D; 2University of Rostock/D

109 Comparative genomics of non-O157 enterohemorrhagic Escherichia coli (EHEC)

J. Schuldes1, E. Brzuszkiewicz1, A. Mellmann2, S. Bletz2, A. Liebchen2, M. A. Schmidt2, H. Karch2, R. Daniel1, G. Gottschalk1 1University of Göttingen/D; 2University of Münster/D

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Synthetic Biology, Systems Biology and Bioinformatics

110 Development of the web-based ECF sigma factor identification and classification tool ECFfinder based on Hidden Markov models

S. Dietrich University of Göttingen/D

111 BiBag – a softwaretool for identification of bacterial pan and core genomes based on bidirectional blast

A. Wollherr, H. Liesegang University of Göttingen/D

112 Gene-to-gene and gene-to-metabolite network analysis based on the time lag between gene and metabolite in Escherichia coli

H. Takahashi1, R. Morioka2, K. Kai3, D. Ohta3, T. Oshima1, M. Altaf-Ul-Amin1, N. Ogasawara1, S. Kanaya1 1Nara Institute of Science and Technology, Ikoma/JP; 2Computational Biology Research Center, Tokyo/JP; 3Osaka Prefecture University, Sakai/JP

113 Reprogramming of the metabolic network in a Bacillus subtilis strain depleted of 874 kb of the genomic sequence

T. Morimoto1, Y. Kageyama1, K. Manabe1, K. Ara1, K. Ozaki1, N. Ogasawara2 1KAO Co., Ichikai/JP; 2Nara Institute of Science and Technology, Ikoma/JP

114 GenoList and GenoScript: two microbial integrated databases

P. Lechat, S. Rousseau, J. Torrent, P. Ventadour, I. Moszer Institut Pasteur, Paris/F

115 NCBI reference sequence targeted loci project – 16S ribosomal RNA

W. Klimke, A. Badretdin, S. Ciufo, B. Fedorov, K. O‘Neill, L. Zaslavsky, T. Tatusova NIH, NCBI/NLM, Bethesda, MD/USA

POSTER PROGRAMME

ProkaGENOMICS 2009

38

116 SNiPer: Hunting for small differences between sequences

B. Chane-Woon-Ming, V. Barbe, C. Médigue, S. Cruveiller CEA – Institut de Génomique, Evry/F

117 Growth phase-dependent global protein and metabolite profiles of Phaeobacter gallaeciensis DSM 17395, a member of the marine Roseobacter-clade

H. Zech1, S. Thole1, K. Schreiber2, D. Kalhöfer1, S. Voget3, T. Brinkhoff1, M. Simon1, D. Schomburg2, R. Rabus1 1University of Oldenburg/D; 2TU Braunschweig/D; 3University of Göttingen/D

118 Genome sequence of Bacillus megaterium DSM319 - chances for a new model organism in systems biotechnology

B. Bunk1, R. Biedendieck1, P. S. Vary2, J. Ravel3, M. Johns2, M. Eppinger3, M. Gamer1, S. Stammen1, R. Münch1, D. Jahn1 1TU Braunschweig/D; 2Northern Illinois University, DeKalb, IL/USA; 3University of Maryland, Baltimore, MD/USA

119 P2CS: a two-component system resource for prokaryotic signal transduction research

M. Barakat1, P. Ortet1, C. Jourlin-Castelli2, M. Ansaldi2, V. Méjean2, D. E. Whitworth3 1CEA, Saint-Paul Lez-Durance/F; 2CNRS, Marseille/F; 3Aberystwyth University, Ceredigion/UK

120 Orphelia: a web server for predicting genes in metagenomic sequencing reads

K. J. Hoff, P. Meinicke, M. Tech University of Göttingen/D

121 Novel promoter for short RNA synthesis in the Escherichia coli uxuR locus

M. N. Tutukina, K. S. Shavkunov, O. N. Ozoline ICB RAS, Pushchino/RU

POSTER PROGRAMME

October 4-7 2009

39

122 Metabolomics reveals a link between phosphate starvation and glycogen metabolism in Corynebacterium glutamicum

H. M. Woo1, G. Seibold2, M. Brocker1, B. J. Eikmanns2, M. Bott1 1Research Center Jülich/D; 2University of Ulm/D

123 Jumping Anti-Sense RNA S. Findeiß1, C. Schubert2, P. F. Stadler1,

U. Bonas2 1Bioinformatics University Leipzig/D; 2Institute for Biology, Halle/D

124 Exploring the evolutionary dynamics of plasmids: the Acinetobacter plasmidome

M. Fondi1, M. C. Papaleo1, A. Mengoni2, G. Bacci1, M. Brilli3, R. Fani1 1University of Florence/I; 2Laboratoire de Biometrie et Biologie Evolutive, Florence/I; 3Laboratoire de Biometrie et Biologie Evolutive, Lyon/F

125 Transcriptional response of the photoheterotrophic marine bacterium Dinoroseobacter shibae to light

J. Tomasch1, B. Bunk2, R. Münch2, I. Wagner-Döbler1 1Helmholtz-Center for Infection Research, Braunschweig/D; 2TU Braunschweig/D

Please note that all posters must be placed on the as-signed boards by Monday, 5 October, 2009 at 11:00 a.m. at the latest.

All authors are requested to be present at their posters during the Poster Sessions on

Monday, 5 October 2009, 12.30 p.m. - 2.00 p.m. (after lunch) and 5.45 p.m. - 6.45 p.m.

Tuesday, 6 October 2009, 12.10 p.m. - 1.45 p.m. (after lunch) and 5.45 p.m. - 6.45 p.m.

Posters will also be viewed and discussed during the coffee breaks.

POSTER PROGRAMME

ProkaGENOMICS 2009

40

SOCIAL PROGRAMME

History of Göttingen

First mentioned by Emperor Otto I. in a deed dated 953, Göttingen enjoys a rich his-tory spanning more than a millennium. Around the year 1200 Göttingen re-ceived town status. It fl ou-rished, as a member of the Hanseatic eague, in the 14th and 15th centuries. In later years, war torn and prey to political battles, this once blos-soming centre of trade became a sleepy provincial town.

Göttingen experienced a revival in 1734 as the result of the foundation of the Georgia Augusta University by King George August II, Elector of Hanover and King of Great Britain. The university rapidy grew into one of the lar-gest academic institutions in Europe. The „Zentrales Hör-saalgebäude“ is located in Platz der Göttinger Sieben, a reference to the „Göttinger Seven“, a group of professors who protested against King Ernst August‘s infringement of the Hanoverian constitution in 1837. As a result they were suspended from their positions, some of them even being banned from the state of Hanover. Nowadays, however, life at the university proceeds more conventionally.

Guided Sightseeing Tour:Old Botanical Garden and historical city of Göttingen

Sunday, October 4, 2009, 2.30 p.m. – 5.00 p.m.

The almost 300 year-old Botanical Garden welcomes its visitors. With over 10 000 species, it is one of the most important botanical gardens in Germany. You can fi nd a great collection of tropical ferns in the 150 year-old fern-house or waterplants like the famous water lily „victoria“.

With the alpinum, the Ar-boreum and the Garden of Evolution, it is a great place to look, to learn and to re-lax.

The centre of Göttingen is not, however, a museum or collection of half-timbe-

to look, to learn and to re-

The centre of Göttingen is

or collection of half-timbe-

October 4-7 2009

41

SOCIAL PROGRAMME

red houses. Instead, each epoch has left its characteristics on the city. This can be seen at the Old Town Hall, St. Jacob‘s Church or the old and new buildings of the university. If Georg August, Elector of Hanover and King of Great Britain, had not made its am-bition to found a university in Göttin-gen, the history of this town would have evolved very differently. When the fi rst lecture was held in October 1734 in a building, which was then „presumably a storage room for fruit and cereals“, things started to pick up in this once unimportant little town.

During the tour our guides will acquaint you with the his-tory of the Georgia Augusta University, show you the im-portant historical sites of the alma mater and bring back memories of some renowned scholars.

Starting point: Entrance of the Old Botanical Garden, Untere Karspüle 2

End point: Old Town Hall

Costs: 9.50 EUR p.p.

Registration necessary

Welcome Party

Sunday, October 4, 2009, 7.30 p.m. – 9.00 p.m.

There will be an informal gathering at the Central Lecture Hall of the Göttingen Uni-versity to welcome the con-ference participants and to give them an opportunity to meet. Drinks and snacks are complimentary.

Venue: Central Lecture Hall

Free of charge, Registration necessary

ProkaGENOMICS 2009

42

Welcome Reception by invitation of the Mayor of Göttingen

Monday, October 5, 2009, 7.30 p.m.

The Mayor of the City of Göttingen, Mr Wolfgang Meyer, takes pleasure in inviting all participants and their accom-panying persons to a recep-tion at the „Altes Rathaus“, the old town hall of the city of Göttingen. Beverages will be served by invitation of the Mayor of Göttingen.

Venue: Old Town Hall

Free of charge, including a welcome drink. Registration ne-cessary. Maximum persons per participant: 2

Conference Dinner

Tuesday, October 6, 2009, 7.00 p.m. – 11.00 p.m.

Plenty of time to meet, to talk, to enjoy delicious food and to listen to good music. The conference dinner will be at the „Mensa am Turm“, a few steps from the Central Lecture Hall.

Venue: Mensa am Turm, Goßlerstraße 12b

Costs: 43.00 EUR p.p., dinner buffet and beverages included

Poster Sessions

Monday, October 5, 200912.30 p.m. – 2.00 p.m. and 5.45 p.m. – 6.45 p.m.

Tuesday, October 6, 200912.10 p.m. – 1.45 p.m. and 5.45 p.m. – 6.45 p.m.

In order to give each participant adequate opportunity for an intensive discussion of the posters, informal poster ses-sion will take place. Poster authors are requested to be present at their posters. Drinks and snacks will be served by the organizer.

SOCIAL PROGRAMME

October 4-7 2009

43

GENERAL INFORMATION

Last Minute Posters

You can submit last minute posters online via the confe-rence website – www.prokagenomics.org – from June 25 until August 10. The abstracts will be reviewed by the Or-ganizing Committee.

For further information about abstract submission, please contact the conference secretariat:

vokativ GmbHphone +49.(0)551.488 57 409email prokagenomics@vokativ.de

Exhibition

The conference will be accompanied by an exhibition to demonstrate recent developments in the field of miniatu-risation for chemical, pharmaceutical and biotchnological applications. Industrial companies, research institutes and universities are invited to participate in the exhibition. Pre-sent your latest results, products and manufacturing equip-ment for chemical, pharmaceutical and biotechnological applications and meet the leading experts in prokaryotic genomics.

For further information, please contact the conference secretariat:

vokativ GmbH, Göttingen/Dphone +49.(0)551.488 57 409email prokagenomics@vokativ.de

Registered Exhibitors as of June 2009:

Advalytix, Munich/DAGOWA GmbH, Berlin/DApplied Biosystems Deutschland GmbH, Darmstadt/DEurofins MWG operon, Ebersberg/DIllumina Ltd., Essex/UKRoche Diagnostics GmbH, Mannheim/D

Conference Site

University of GöttingenCentral Lecture Hall (Zentrales Hörsaalgebäude)Platz der Göttinger Sieben37073 Göttingen/D

ProkaGENOMICS 2009

44

Conference Secretariat

vokativ GmbHNikolaistraße 2937073 Göttingen/Dphone +49.(0)551.488 57 409fax +49.(0)551.488 57 79email prokagenomics@vokativ.de

Registration

To attend the ProkaGENOMICS 2009 conference, please register online via the conference website www.prokage-nomics.org. The online registration will be open until Sep-tember 25, 2009.

For registration after September 25, please register onsite at the conference office. Please note: registrations made after September 25, 2009 are not guaranteed to appear in the list of participants.

Registration Fees

Members* OtherParticipants from Academia € 165.00 € 180.00Participants from Industry € 370.00 € 385.00Students/Pensioners** € 65.00 € 80.00

* VAAM / DGHM members. Proof required.** Proof required.

In accordance to § 4.22 UStG, VAT is not applicable.

The registration fee includes admission to all sessions, the exhibition, the poster programme, the Welcome Reception on October 5, 2009, soft drinks during the breaks, lunch on October 5 and 6, 2009, drinks during the poster ses-sions, the list of participants and the book of conference abstracts.

Remittance of Fees

For administrative costs 30.00 Euro will be charged for cancellations received by September 4, 2009. Thereafter 80 percent of the registration fee will be invoiced; however the book of abstracts will be mailed. Only written cancella-tions will be accpeted.

GENERAL INFORMATION

October 4-7 2009

45

Visa Formalities

Participants from a number of countries may need an entry visa for Germany. It is recommended that the visa should be applied as soon as possible before the meeting.

Insurance

The organizers are not responsible for loss or damage to the private property of participants and accompanying per-sons which may occur either during or arising from the conference. Participants should therefore take whatever steps they consider necessary for their insurance.

Accomodation

You can book hotel rooms online via the conference web-site www.prokagenomics.org. For enquiries regarding ac-comodation, please contact:

Tourist Information GöttingenMs Christiane von SchliebenAltes Rathaus, Markt 937073 Göttingen/Dphone +49.(0)551.499 80 20fax +49.(0)551.499 80 10email zimmerreservierung@goettingen.de

Public Transport in Göttingen

You can buy a reduced ticket, the „GöCard“, for public transport which gives you free transfer on all municipal bu-ses troughout town, reduced admission to the Municipal Museum, Göttingen‘s theatres, the Badeparadies Eiswiese (in and outdoor swimming pools), exhibitions held at the Old Town Hall, etc. The GöCard is available at the tourist information in the Old Town Hall.

Price for 3 days: 12.00 EUR

GENERAL INFORMATION

ProkaGENOMICS 2009

46

Travel Information

By plane

You can either fly to Frankfurt/Main, Hanover or Berlin.

By train

Göttingen is served by the ICE High Speed Trains. On weekdays, these trains run on an hourly schedule. More information, especially regarding the timetable, is available at www.bahn.de.

The conference will take place in the „Zentrales Hörsaal-gebäude“ (ZHG/Central Lecture Hall) of the University of Göttingen, about 10 minutes walk from the railway station (please refer to the map). Taxis are available at both exits of the railway station.

Travel time by train

Frankfurt/M. Airp. to Göttingen: approx. 2 hours 20 min.Hanover Airport to Göttingen: approx. 1 hour 20 minutesBerlin Airport to Göttingen: approx. 3 hours

By car

Göttingen is served by the A7 motorway (Autobahn). Lea-ve the A7 at exit 73 (Ausfahrt Göttingen / Dransfeld) or exit 72 (Ausfahrt Göttingen Nord). Please refer to the map.

On campus there is public parking available close to the Central Lecture Hall of the University of Göttingen (please refer to the map).

Local buses

The Central Lecture Hall is connected to different local bus lines. There are four bus stopps close to campus:

Auditorium (Weender Landstraße): line 2, 3, 10, 12, 14Auditorium (Nikolausberger Weg): line 5 and 9Blauer Turm: line 10 and 12Campus: line 5

Detailed information is available at the customer center (Weender Straße 80-82) or at the Tourist-Information in the Old Town Hall (www.goettingen-tourismus.de).

See also „Public transport in Göttingen“ (page 45).

GENERAL INFORMATION

October 4-7 2009

47

Publisher

BiotechGenoMik Network GöttingenInstitute of Microbiology and GeneticsGeorg-August-University of GöttingenGrisebachstr. 837077 Göttingen, Germanywww.genomik.uni-goettingen.de

Concept, Design & Editorial Matter

vokativ GmbHNikolaistr. 2937073 Göttingen, Germanyphone +49.(0)551.488 570email info@vokativ.dewww.vokativ.de

Copyright

Layout/Title: vokativ GmbH info@vokativ.de, www.vokativ.de

page 40: Fremdenverkehrsverein Göttingen e.V., Photograph: Alciro Theodoro da Silva (top right), Torsten Krüger (bottom left)

page 41: (top right) Fremdenverkehrsverein Göt-tingen e.V., Photograph: Torsten Krüger; (down right) University of Göttingen – press office

page 42: Fremdenverkehrsverein Göttingen e.V., Photograph: Torsten Krüger (top right), Alciro Theodoro da Silva (bottom right)

page 48: Göttingen Tourismus e.V.

IMPRINT

1 Central Lecture Hall2 Mensa am Turm3 Train Station4 Entrance Old Botanical Garden5 Old Town Hall6 Gebhard‘s Hotel7 Eden Hotel8 Kasseler Landstraße, Direction A7, exit „Göttingen Dransfeld“

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