Open Access Research article

Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae

Darlene D Wagner1, Laura A Hug2, Janet K Hatt3, Melissa R Spitzmiller3, Elizabeth Padilla-Crespo4, Kirsti M Ritalahti46, Elizabeth A Edwards5, Konstantinos T Konstantinidis13 and Frank E Löffler467*

Author Affiliations

1 School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA, 30332, USA

2 Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada

3 School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA, 30332, USA

4 Department of Microbiology, University of Tennessee, M409 Walters Life Science Building, 1414 Cumberland Avenue, Knoxville, TN, 37996, USA

5 Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada

6 Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Bethel Valley Road, Building 1520, Oak Ridge, TN, 37831, USA

7 Department of Civil and Environmental Engineering, University of Tennessee, 223 Perkins Hall, Knoxville, TN, 37996, USA

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BMC Genomics 2012, 13:200  doi:10.1186/1471-2164-13-200

Published: 22 May 2012

Additional files

Additional file 1:

Unrooted 16S rRNA gene tree showing organohalide-respiring δ-Proteobacteriafrom isolates or mixed cultures. Selected related non-dechlorinating organisms (non-highlighted branches) are added to show divergence within genera.

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Additional file 2:

Codon usage of pce-genes and adjacent genes encoded on the Pce genomic island in comparison to all strain SZ chromosomal genes using the codon adaptation index (CAI). Normalized CAI < 1.00 (red font) indicates a possible laterally acquired gene and is scored below genomic expected CAI at a 5% level of significance (genomes.urv.es/CAIcal/E-CAI).

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Additional file 3:

Circular genome map of theG. lovleyistrain SZ chromosome (CP001089). From outside to center: COG categories of genes on forward strand, COG categories of genes on reverse strand, percent GC content, GC skew, and percent blastx identity of strain SZ ORFs to ORFs on the chromosomes of Pelobacter propionicus (CP000482), G. uraniireducens, and G. sulfurreducens. Genomic island regions, six in all, are indicated by pink arcs and are characterized by genes lacking blast matches in a majority of other Geobacter/Pelobacter spp. genomes (e.g. the three innermost circles), suggesting horizontal gene transfer. The genomic island Pce harbors the pce-gene cluster, encoding the PCE reductive dehalogenases, and exhibits nucleotide sequence deviations in GC% and GC-skew relative to the entire strain SZ chromosome. The chromosome map was generated using GenomeViz [81].

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Additional file 4:

Codon usage of predicted F-factor conjugative pilustra-genes in comparison to all strain SZ chromosomal genes using the codon adaptation index (CAI). A majority of genes in the tra-pilus cluster have normalized CAI < 1.00 (red font), but are interspersed with genes having normalized CAI > 1.00, indicating sufficient residence time in strain SZ for the cluster to partially ameliorate to chromosomal codon usage.

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Additional file 5:

Inferredc-type cytochrome genes on theG. lovleyistrain SZ chromosome.

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Additional file 6:

Inferred c-type cytochrome genes inPelobacter propionicusDSM 2379.

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Additional file 7:

Electron-transfer proteins encoded on theG. lovleyistrain SZ chromosome.

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Additional file 8:

Inferred reactive-oxygen-species-responsive or oxygen-reducing genes inG. lovleyistrain SZ.

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Additional file 9:

Circular genome map of theG. lovleyistrain SZ plasmid pSZ77 (CP001090). From outside to center: COG categories of genes on forward strand, COG categories of genes on reverse strand, percent GC content, GC skew, percent blastx identity of SZ ORFs to plasmids of Pelobacter propionicus (CP000483 and CP000484), and percent blastx identity to the chromosomes of Pelobacter propionicus (CP000482), Geobacter uraniireducens, and G. sulfurreducens. The plasmid map was generated using Genome Viz [81].

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Additional file 10:

pSZ77 genes related to plasmid replication, maintenance, and recombination.

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Additional file 11:

Inferred cobalamin-dependent genes on theG. lovleyistrain SZ chromosome.

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Additional file 12:

Codon usage of pSZ77 genes in comparison to strain SZ chromosomal genes using the codon adaptation index (CAI). Out of 79 total predicted plasmid genes, 42 have normalized CAI > 1.00, indicating that over half of pSZ77 genes have resided in the strain SZ genome for sufficient time to ameliorate their codon usage to the chromosome. The predicted replication/maintenance genes repA and parA have normalized CAI < 1.00 (red font) [82].

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Additional file 13:

DNA sequence differences between the pSZ77 and the KB-1 plasmid assemblies.

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Additional file 14:

Detection of the pSZ77repAgene andGeobacteraceaespp. 16S rRNA genes in pure and mixed cultures containing Geobacter strains with specific PCR primers. Top row: repA gene-targeted PCR (565 bp amplicon) and bottom row Geobacteraceae 16S rRNA gene-targeted PCR (312 bp amplicon). The arrows indicate the expected PCR amplicons. Lane 1: 1 kb Plus DNA ladder (Invitrogen), Lane 2: no template (negative control), Lane 3: G. lovleyi strain SZ (positive control), Lanes 4 and 5: consortium BDI, Lane 6: consortium KB-1, Lane 7: Ft. Lewis isolate 7.1, Lane 8: Ft. Lewis isolate 7.2, Lane 9: Ft. Lewis isolate 7.3, Lane 10: Ft. Lewis isolate 7.4, Lane 11: G. thiogenes.

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