Aklujkar, Muktak

Butler, Jessica E

Lovley, Derek R

Young, Nelson D

BMC Genomics

English

PubMed

Background A new strain of Geobacter sulfurreducens, strain KN400, produces more electrical current in microbial fuel cells and reduces insoluble Fe(III) oxides much faster than the wildtype strain, PCA. The genome of KN400 was compared to wildtype with the goal of discovering how the network for extracellular electron transfer has changed and how these two strains evolved. Results Both genomes were re-annotated, resulting in 14 fewer genes (net) in the PCA genome; 28 fewer (net) in the KN400 genome; and ca. 400 gene start and stop sites moved. 96% of genes in KN400 had clear orthologs with conserved synteny in PCA. Most of the remaining genes were in regions of genomic mobility and were strain-specific or conserved in other Geobacteraceae, indicating that the changes occurred post-divergence. There were 27,270 single nucleotide polymorphisms (SNP) between the genomes. There was significant enrichment for SNP locations in non-coding or synonymous amino acid sites, indicating significant selective pressure since the divergence. 25% of orthologs had sequence differences, and this set was enriched in phosphorylation and ATP-dependent enzymes. Substantial sequence differences (at least 12 non-synonymous SNP/kb) were found in 3.6% of the orthologs, and this set was enriched in cytochromes and integral membrane proteins. Genes known to be involved in electron transport, those used in the metabolic cell model, and those that exhibit changes in expression during growth in microbial fuel cells were examined in detail

Butler, Jessica

Young, Nelson

Lovley, Derek

ScholarWorks@UMass Amherst

Comparative genomic analysis of Geobacter sulfurreducens KN400, a strain with enhanced capacity for extracellular electron transfer and electricity production

Jessica E Butler

Nelson D Young

Muktak Aklujkar

Derek R Lovley

Springer - Publisher Connector

Aberdeen University Research

Crossref

Abstract Background A new strain of Geobacter sulfurreducens, strain KN400, produces more electrical current in microbial fuel cells and reduces insoluble Fe(III) oxides much faster than the wildtype strain, PCA. The genome of KN400 was compared to wildtype with the goal of discovering how the network for extracellular electron transfer has changed and how these two strains evolved. Results Both genomes were re-annotated, resulting in 14 fewer genes (net) in the PCA genome; 28 fewer (net) in the KN400 genome; and ca. 400 gene start and stop sites moved. 96% of genes in KN400 had clear orthologs with conserved synteny in PCA. Most of the remaining genes were in regions of genomic mobility and were strain-specific or conserved in other Geobacteraceae, indicating that the changes occurred post-divergence. There were 27,270 single nucleotide polymorphisms (SNP) between the genomes. There was significant enrichment for SNP locations in non-coding or synonymous amino acid sites, indicating significant selective pressure since the divergence. 25% of orthologs had sequence differences, and this set was enriched in phosphorylation and ATP-dependent enzymes. Substantial sequence differences (at least 12 non-synonymous SNP/kb) were found in 3.6% of the orthologs, and this set was enriched in cytochromes and integral membrane proteins. Genes known to be involved in electron transport, those used in the metabolic cell model, and those that exhibit changes in expression during growth in microbial fuel cells were examined in detail. Conclusions The improvement in external electron transfer in the KN400 strain does not appear to be due to novel gene acquisition, but rather to changes in the common metabolic network. The increase in electron transfer rate and yield in KN400 may be due to changes in carbon flux towards oxidation pathways and to changes in ATP metabolism, both of which indicate that the overall energy state of the cell may be different. The electrically conductive pili appear to be unchanged, but cytochrome folding, localization, and redox potentials may all be affected, which would alter the electrical connection between the cell and the substrate.</p

Butler Jessica E

Young Nelson D

Aklujkar Muktak

Lovley Derek R

Directory of Open Access Journals

Comparative genomic analysis of <it>Geobacter sulfurreducens</it> KN400, a strain with enhanced capacity for extracellular electron transfer and electricity production

Butler, JE

Arkin AP: MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res 2010, 38(Database issue):D396–D400.

Circos: an information aesthetic for comparative genomics. Genome Res

CL: De novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads. PLoS One

CM: Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science

DJ: A genomic perspective on protein families. Science

DR: Identification of an extracellular polysaccharide network essential for cytochrome anchoring and biofilm formation in Geobacter sulfurreducens.

DR: NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007, 35(Database issue):D61–D65.

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet

Hederstedt L: Composition and function of cytochrome c biogenesis System II.

KH: Polyphasic characterization of the genus Leptothrix: New descriptions of Leptothrix mobilis sp. nov. and Leptothrix discophora sp. nov. nom. rev. and emended description of Leptothrix cholodnii emend. Syst Appl Microbiol

KP: Geobacter: the microbe electric's physiology, ecology, and practical applications. Adv Microb Physiol

KP: Microbial fuel cells, a current review. Energies

Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res

Loewen PC: Diversity of structures and properties among catalases. Cell Mol Life Sci

Lovley DR: A novel Geobacteraceae-specific outer membrane protein J (OmpJ) is essential for electron transport to Fe(III) and Mn(IV) oxides in Geobacter sulfurreducens.

Lovley DR: Alignment of the c-type cytochrome OmcS along pili of Geobacter sulfurreducens. Appl Environ Microbiol

Lovley DR: Anode biofilm transcriptomics reveals outer surface components essential for high density current production in Geobacter sulfurreducens fuel cells. PLoS One

Lovley DR: Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling. Appl Environ Microbiol

Lovley DR: Computational and experimental analysis of redundancy in the central metabolism of Geobacter sulfurreducens. PLoS Comput Biol

Lovley DR: Electricity production by Geobacter sulfurreducens attached to electrodes. Appl Environ Microbiol

Lovley DR: Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes.

Lovley DR: Extracellular electron transfer via microbial nanowires. Nature

Lovley DR: Genes for two multicopper proteins required for Fe(III) oxide reduction in Geobacter sulfurreducens have different expression patterns both in the subsurface and on energy-harvesting electrodes. Microbiology

Lovley DR: Interference with histidyl-tRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of Pelobacter carbinolicus.

Lovley DR: Microarray and genetic analysis of electron transfer to electrodes in Geobacter sulfurreducens. Environ Microbiol

Lovley DR: Power output and columbic efficiencies from biofilms of Geobacter sulfurreducens comparable to mixed community microbial fuel cells. Environ Microbiol

Lovley DR: Selection of a variant of Geobacter sulfurreducens with enhanced capacity for current production in microbial fuel cells. Biosens Bioelectron

Lovley DR: Tunable metallic-like conductivity in microbial nanowire networks.

MJ: Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism. Appl Environ Microbiol

NL: CueR (YbbI) of Escherichia coli is a MerR family regulator controlling expression of the copper exporter CopA. Mol Microbiol 2001, 39(2):502–511. Butler et al.

NT: Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res

Pathways of oxidative damage. Annu Rev Microbiol

Salgueiro CA: Thermodynamic characterization of the redox centres in a representative domain of a novel c-type multihaem cytochrome.

SH: CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res 2009, 37(Database issue):

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc

T: A putative multicopper protein secreted by an atypical type II secretion system involved in the reduction of insoluble electron acceptors in Geobacter sulfurreducens.

Terns RM: CRISPR-based adaptive immune systems.

Waldor MK: Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat Rev Microbiol

WC: The iProClass integrated database for protein functional analysis. Comput Biol Chem

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Comparative genomic analysis of Geobacter sulfurreducens KN400, a strain with enhanced capacity for extracellular electron transfer and electricity production

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ScholarWorks@UMass Amherst

Springer - Publisher Connector

Aberdeen University Research

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Directory of Open Access Journals

ScholarWorks@UMass Amherst