Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens
- Carla Risso†1Email author,
- Jun Sun†2,
- Kai Zhuang3,
- Radhakrishnan Mahadevan3,
- Robert DeBoy4,
- Wael Ismail1,
- Susmita Shrivastava4,
- Heather Huot4, 5,
- Sagar Kothari4,
- Sean Daugherty4, 5,
- Olivia Bui2,
- Christophe H Schilling2,
- Derek R Lovley1 and
- Barbara A Methé4
© Risso et al; licensee BioMed Central Ltd. 2009
Received: 14 May 2009
Accepted: 22 September 2009
Published: 22 September 2009
Rhodoferax ferrireducens is a metabolically versatile, Fe(III)-reducing, subsurface microorganism that is likely to play an important role in the carbon and metal cycles in the subsurface. It also has the unique ability to convert sugars to electricity, oxidizing the sugars to carbon dioxide with quantitative electron transfer to graphite electrodes in microbial fuel cells. In order to expand our limited knowledge about R. ferrireducens, the complete genome sequence of this organism was further annotated and then the physiology of R. ferrireducens was investigated with a constraint-based, genome-scale in silico metabolic model and laboratory studies.
The iterative modeling and experimental approach unveiled exciting, previously unknown physiological features, including an expanded range of substrates that support growth, such as cellobiose and citrate, and provided additional insights into important features such as the stoichiometry of the electron transport chain and the ability to grow via fumarate dismutation. Further analysis explained why R. ferrireducens is unable to grow via photosynthesis or fermentation of sugars like other members of this genus and uncovered novel genes for benzoate metabolism. The genome also revealed that R. ferrireducens is well-adapted for growth in the subsurface because it appears to be capable of dealing with a number of environmental insults, including heavy metals, aromatic compounds, nutrient limitation and oxidative stress.
This study demonstrates that combining genome-scale modeling with the annotation of a new genome sequence can guide experimental studies and accelerate the understanding of the physiology of under-studied yet environmentally relevant microorganisms.
Rhodoferax ferrireducens is of interest because of its potentially important role in carbon and metal cycling in soils and sediments and its novel ability to convert sugars into electricity . R. ferrireducens, which was isolated from subsurface sediments in Oyster Bay, VA, is a facultative anaerobic microorganism in the Comamonadaceae family of the Betaproteobacteria . It is one of the few known facultative microorganisms that can grow anaerobically by oxidizing organic compounds to carbon dioxide with Fe(III) serving as the electron acceptor. This property, as well as its ability to grow at the low temperatures found in many subsurface environments, suggests that it could contribute to the oxidation of organic matter coupled to the reduction of Fe(III) in many soils and sediments. Microorganisms closely related to R. ferrireducens have been detected in a number of subsurface environments [3–7]. The novel ability of R. ferrireducens to oxidize sugars to carbon dioxide with quantitative electron transfer to electrodes in microbial fuel cells is of interest because of the possibility of using sugars as a renewable energy source for power production [1, 8, 9].
R. ferrireducens has a number of important physiological characteristics that distinguishes it from other members of the genus Rhodoferax. For example, it appears to be unable to grow phototrophically , a previous hallmark feature of the genus [10, 11]. Furthermore, unlike other Rhodoferax species, R. ferrireducens cannot grow anaerobically via fructose fermentation. No other Rhodoferax species have been shown to grow via anaerobic respiration, whereas R. ferrireducens can grow by oxidizing a wide variety of organic electron donors, such as acetate, lactate, propionate, pyruvate, succinate, malate and benzoate, with Fe(III) serving as the electron acceptor . In addition to Fe(III), R. ferrireducens can utilize Mn(IV) oxide, fumarate, and nitrate as electron acceptors to support anaerobic growth .
The production of linear polyesters in the form of polyhydroxyalkanoates (PHAs)  is an interesting characteristic of R. ferrireducens with important biotechnological implications. PHAs are typically synthesized in bacteria from sugars or lipids and have industrial interest due to their properties as thermoplastics and elastomers .
In order to further elucidate the physiology of R. ferrireducens, the publicly available genome sequence http://www.jcvi.org/cms/research/projects/cmr was annotated in more detail and a genome-scale metabolic model was reconstructed using the constraint-based modeling approach [13–15]. Constraint-based modeling couples stoichiometric reconstructions of all known metabolic reactions in the organism with a set of constraints on the fluxes of each of these reactions in the system. This approach unveiled a variety of previously unknown physiological features of R. ferrireducens that contributed to a better understanding of its potential role in subsurface environments and converting organic compounds to electricity.
Results and Discussion
General features of the genome
General features of the R. ferrireducens genome.
Average size of CDS (bp)
Number of rRNA operons (16S-23S-5S)
Number of tRNAs
Number of CRISPR loci
Number of conserved hypothetical proteins
Number of hypothetical proteins
Of the 319 predicted CDSs in the plasmid, BLAST searches matched only 69 to a database of Proteobacterial proteins, using the same criteria used for the chromosome (see above). These include possible conjugation proteins, 3 integrases separated by large spans of hypothetical proteins, a helicase, a DNA methylase, a gene for DNA repair protein RadA, a copy of polymerase DnaN (different from the chromosome copy), at least 6 CRISPR cas genes, a DNA ligase, a thymidine kinase, 3 secretion proteins, 2 sensor histidine kinases, and possible type 4 pilin proteins. An unusual finding was a copy of a tRNA-Ile, which is different in sequence from the identical copies in the chromosome but shares the same anticodon.
In silico constraint-based modeling as a tool to gain new insights into the physiology of R. ferrireducens
Development of the constraint-based in silico model
Characteristics of the R. ferrireducens genome-scale model.
Stoichiometry of the electron transport chain
It is interesting to point out that the obtained NGAM for the R. ferrireducens genome-scale model is similar to that of G. sulfurreducens, another acetate-oxidizing Fe(III) reducer  often found in the same microbial niche [3–7]. Both R. ferrireducens and G. sulfurreducens in silico models have an H+/2e- ratio of 2 for the NADH dehydrogenase of the electron transfer chains. However, the H+/2e-ratio for cytochrome reductase is 2 in R. ferrireducens as opposed to 1 in G. sulfurreducens . Such a difference between the two models implies that the electron transfer chain of R. ferrireducens is more efficient than that of G. sulfurreducens. The evolution of electron transport chains with different efficiencies suggests that microorganisms could adapt to different lifestyles within the same community. Additional modeling studies on microbial community competition have shown that G. sulfurreducens is better adapted to acetate-rich environments, whereas R. ferrireducens thrives in nutrient-depleted environments (K. Zhuang, personal communication). Understanding these survival strategies is crucial for modeling complex microbial communities.
R. ferrireducens possesses a full tricarboxylic acids (TCA) cycle and pentose phosphate pathway. Oxaloacetate is likely replenished by the combined action of PEP carboxylase (Rfer_1714) and pyruvate phosphate dikinase (Rfer_0088). Genes coding for the enzymes of the glyoxylate cycle and a glyoxylate oxidase (Rfer_0480-81) are present, which allow this organism to utilize glycolate as the sole electron and carbon source (data not shown).
The versatility in donor utilization is reflected by the existence of several pathways and their associated enzymes by which the key intermediate pyruvate can be produced. These include the enzymes of the glycolytic pathway, L-lactate dehydrogenase (cytochrome) [Rfer_2351, EC 220.127.116.11], and the pyruvate-oxidoreductase (POR) complex. Likewise, the genome provides multiple alternatives for generating acetyl-CoA: pyruvate dehydrogenase, aldehyde dehydrogenase/acetaldehyde dehydrogenase, acetate-CoA ligase and acetate kinase/phosphate acetyltransferase. Notably, of these enzymes only the pyruvate dehydrogenase and acetate kinase/phosphate acetyltransferase are shared by G. sulfurreducens.
No fermentative growth with sugars was observed in R. ferrireducens, which contrasts with other Rhodoferax species [2, 10, 11]. Fermentative growth on glucose was simulated with the in silico model and the result confirmed the experimental observation. Detailed analysis of the metabolic network suggested that the lack of fermentative growth of R. ferrireducens with glucose is likely due to its inability to recycle reduced NADH generated from glycolysis for redox balance without an electron acceptor. Compared to the E. coli metabolic model, the R. ferrireducens model lacks several reactions, including the reversible lactate dehydrogenase (LdhA), the pyruvate formate lyase (PflA), and the acetaldehyde CoA dehydrogenase/alcohol dehydrogenase (AdhE). These reactions are important to the E. coli fermentative growth that produces acetate, ethanol, lactate, and formate to allow the balance of the reducing equivalents generated during glycolysis . Simulations with the R. ferrireducens model predicted that introducing any one of these enzymes into R. ferrireducens should support the fermentation of glucose (data not shown).
R. ferrireducens differs from most other acetate-oxidizing Fe(III) reducers in its ability to completely oxidize sugars to carbon dioxide with electron transfer to Fe(III) and electrodes . The genome contains genes coding for the Entner-Doudoroff glycolytic pathway, typical of Pseudomonads and Comamonas. Sugars are likely to be imported into the bacterial cells by a homolog of a general hexose phosphotransferase system (Rfer_0601-03). In addition, several ABC transporters might be related to sugar transport. For instance, Rfer_0952-55 have weak similarity to ABC-type sugar transporters and are surrounded by genes related to carbohydrate metabolism (see Additional file 2). A larger cluster comprising CDSs Rfer_1094 to Rfer_1113 contains at least two putative sugar ABC transporters as well as other genes involved in sugar metabolism. R. ferrireducens is able to oxidize other sugars such as fructose, sucrose and mannose, but not lactose (not shown). The presence of two putative betaglucosidases in the genome (Rfer_1102 and Rfer_1111) suggested that R. ferrireducens might also be able to metabolize cellobiose, a fact confirmed in subsequent growth studies (see Additional file 3). Cellobiose degradation is of biotechnological interest because of the potential of turning common cellulosic waste products into energy. The in silico R. ferrireducens model includes the pathway for cellobiose degradation and predicts growth on this substrate.
Citrate tested negative as an electron donor in the initial description of Rhodoferax ferrireducens . However, other members of the Rhodoferax genus are able to utilize citrate , and examination of the genome suggests that it might be the case for R. ferrireducens as well. Rfer_2412 (CitT) is 44% identical to a putative citrate transporter from E. coli CFT073  and is located in a cluster of genes also associated with citrate metabolism. Further experimental evaluation confirmed that R. ferrireducens could utilize citrate as electron donor and carbon source with Fe(III) or nitrate as the electron acceptor (see Additional file 4). Even though other Betaproteobacteria can also use citrate , BLAST-based analyses revealed that these R. ferrireducens citrate-related proteins are more closely related to Gammaproteobacteria and Alphaproteobacteria homologs (see Additional file 5). An exception is isocitrate dehydrogenase (Rfer_2411), for which there is a lineage-specific gene duplication in the R. ferrireducens genome (Rfer_2380, 97% identity) that resembles homologs of the Betaproteobacteria. Rfer_3489, annotated as a CitB, a citrate-utilization protein, might also be involved in this metabolism.
Degradation of aromatic compounds
In the absence of oxygen, the first step in benzoate catabolism is the production of benzoyl-CoA. The fact that there is only one gene for benzoate-CoA ligase in the R. ferrireducens genome (Rfer_0216) suggests that benzoyl-CoA formation is catalyzed by the same enzyme under both aerobic and anaerobic conditions, as observed in the denitrifying organism Thauera aromatica . In facultative anaerobes, benzoyl-CoA is reductively dearomatized by an ATP-dependent benzoyl-CoA reductase, but the genes coding for this enzyme could not be found in the R. ferrireducens genome. It has been recently postulated that benzoyl-CoA reduction in obligate anaerobes like Geobacter metallireducens is mediated by a novel ATP-independent enzyme complex encoded by the genes bamB-I [32, 33]. The genome of R. ferrireducens contains several genes whose products are moderately similar (based on percent similarity at protein-level) to some bam genes of G. metallireducens (see Additional file 6), but they do not appear to form a cluster. The possibility of R. ferrireducens having a novel system for benzoyl-CoA reduction cannot be excluded. The full elucidation of these pathways warrants further study. The R. ferrireducens model contains a pathway for benzoate degradation, and predicts the growth of R. ferrireducens on benzoate with Fe(III) as an electron acceptor.
The genome of R. ferrireducens also contains a putative pathway for the anaerobic catabolism of phenylalanine that includes a transaminase (Rfer_2174), a phenylpyruvate decarboxylase (Rfer_0518) and phenylacetaldehyde dehydrogenase (Rfer_0598). The end product of this pathway, phenylacetate, could be converted into benzoyl-CoA by the successive action of putative phenylacetate-CoA ligase (Rfer_3536) , phenylacetyl-CoA: acceptor oxidoreductase (Rfer_3093, Rfer_3094) and phenylglyoxylate:acceptor oxidoreductase (Rfer_2184-87) .
The complete oxidation of benzoate requires an elevated Fe(III):substrate ratio. This suggests that benzoate or other aromatic compounds could be a good feedstock for R. ferrireducens based microbial fuel cells to generate electricity. Thus, using aromatic waste stream for R. ferrireducens based microbial fuel cells could be an attractive idea that can achieve both bioremediation of aromatic compound contaminants and generation of electricity.
Analysis of substrate efficiency
Photosynthesis and autotrophic growth
Although other members of the Rhodoferax genus are capable of autotrophic growth [10, 11], this is not the case for R. ferrireducens . No evidence of photosystems I or II was found in the genome. However, incomplete pathways associated with CO2 fixation are present. For instance, there is a gene coding for the large subunit of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RuBisCO) (Rfer_1391), but not the small subunit. Some genes encoding enzymes for the Calvin-Benson-Bassham cycle are present as well, but genes for phosphoketolase and seduheptulose-bisphosphatase are missing. The reductive carboxylate cycle, present in many photosynthetic bacteria, is also incomplete as a gene for the key enzyme ATP citrate synthase, is missing.
Well-studied Fe(III)-reducing microorganisms such as Shewanella and Geobacter species have abundant c-type cytochromes that are essential for extracellular electron transfer [36, 37]. R. ferrireducens also has an abundance of c-type cytochrome genes (see Additional file 7). Based on matches to Prosite and hidden Markov Model (HMM) profiles, the R. ferrireducens genome possess 69 putative c-type cytochromes, of which 45 have matched above the high confidence scores to the Prosite profiles for the Cytochrome c family (PS51007) and multiheme cytochrome c family profiles (PS51008). Of the R. ferrireducens putative c-type cytochrome complement, approximately 45% (31/69) possess a homolog to a c-type cytochrome indentified in a previously sequenced Geobacter spp. genome and the majority appears to reside in the periplasm or outer membrane based on the presence of predicted signal peptides. One c-type cytochrome gene in R. ferrireducens, Rfer_0244, is a homolog of OmcE, an outer-membrane c-type cytochrome that is essential for Fe(III) oxide reduction in G. sulfurreducens . However, there are no homologs to several other cytochromes shown to be important in G. sulfurreducens Fe(III) oxide reduction (and electricity generation) including OmcB, OmcC, OmcF, OmcS, OmcT and OmcZ [38–40]. These results suggest that c-type cytochrome complements can vary in Fe(III) oxide reducing (and electricity producing) prokaryotes. However, whether or not a subset of c-type cytochromes essential to Fe(III) oxide reduction (or electricity generation) exists within the set shared between Rhodoferax and other Fe(III) oxide reducing prokaryotes remains to be determined. This may not be surprising as there is poor conservation of cytochromes even among Geobacter species (J. Butler, personal communication).
R. ferrireducens also contains assimilatory forms of nitrate reductase (Rfer_2559) and nitrite reductase NAD(P)H (Rfer_2557-2558) that allow growth on nitrate without the addition of ammonia, although the growth rate was higher in the ammonia-amended cultures (Figure 9A).
The R. ferrireducens model contains reactions that account for nitrate utilization as electron acceptor and nitrogen source. It predicts a 20% faster growth rate if ammonium is added to the medium, in agreement with actual experimental results (Figure 9A and 9C). The model also accurately predicted the proportion of nitrate converted to nitrite, ca. 80% (Figure 9B and 9D). The rest is likely converted to ammonium, of which 60% is predicted to be assimilated into biomass, probably via glutamine synthetase.
Metalloid and metal resistance
The R. ferrireducens genome contains a cluster of genes related to arsenic metabolism (see Additional file 8). The gene cluster Rfer_3663-3665 encode respectively: a putative arsenite efflux pump; an arsenite-activated ATPase and a arsenate reductase which are likely to be involved in removing arsenic from the cell. However, tolerance to arsenic has yet to be evaluated.
The genome contains two genes, Rfer_2447 and Rfer_2824, which have 30% and 27% identity respectively to the characterized chromate transporter homolog, ChrA, in P. aeruginosa . ChrB (Rfer_2446), on the other hand, is 58% identical to the Cr(VI)-sensing regulator ChrB in Ochrobactrum triciti, an Alphaproteobacteria isolated from chromium-contaminated sludge and able to grow in the presence of high concentrations of chromium [43–45]. A chromate reductase (ChrR) homolog was not evident. The R. ferrireducens genome also encodes a heavy metal efflux pump CzcA (Rfer_0411), which might confer resistance to Cd, Zn and Co . Other genes encoding proteins involved in metal resistance are four putative copper-translocating P-type ATPases (Rfer_0024, Rfer_0418, Rfer_1144 and Rfer_1927) and a periplasmic copper-binding protein (Rfer_3200).
Storage capabilities: Polyhydroxyalkanoates
Many organisms have the ability to trigger the production of carbon storage compounds under unfavorable conditions such as limited or inaccessible electron acceptors and/or lack of key nutrients (e.g., nitrogen or sulfate) . Some of these polymers have attractive physical properties that make them relevant for industrial use, particularly in biodegradable materials . Genome analysis indentified three genes well characterized for their involvement in PHA synthesis present in a putative operon in the R. ferrireducens genome: Acetoacetyl-CoA reductase (Rfer_2560), Acetyl-CoA acetyltransferase (Rfer_2561) and PHA synthase (Rfer_2562). Even though production of PHAs has been previously observed in R. ferrireducens , the in silico model does not account for this pathway. It is expected to be included once experimental data are available.
Response to environmental challenges
R. ferrireducens is a psychrotolerant organism that can withstand temperatures as low as 4°C, which might confer a competitive advantage in certain environments . Notably, no genes coding for major cold shock proteins (Csp) (as identified by matches above trusted cutoffs to PF00313: cold-shock DNA-binding domain or TIGR02381: cold shock domain protein CspD) could be identified in the R. ferrireducens genome or other members of the Comamonadaceae whose genomes have been sequenced (Polaromonas spp. and Acidovorax sp. JS42). Other members of the Betaproteobacteria for which whole genome sequence is available (from the genera Burkholderias, Azoarcus, Nitrobacter and Ralstonia) possess these Csp homologs. This suggests that other cold shock proteins or other mechanisms for surviving cold shock events have yet to be identified in R. ferrireducens.
R. ferrireducens is a facultative organism and can utilize atmospheric oxygen as a terminal electron acceptor. The genome contains a cytochrome c-oxidase and also several genes coding for enzymes related to the oxidative stress response, such as superoxide dismutase (Rfer_3151) and several alkylhydroxyperoxidases (see Additional file 9).
Examination of the R. ferrireducens genome revealed that this organism has potential to respond to a wide variety of stimuli, with over 30 genes coding for putative sensor histidine kinases, 23 methyl-accepting chemotaxis proteins (MCPs) and 32 DNA-binding response regulator elements. The genes coding for sensor proteins and response regulators (possibly two-component systems) are often found in pairs, and at least 47 such pairs were found in the R. ferrireducens genome (see Additional file 10). Homologs of CheA, CheW, CheV and CheY are also present, though the chemotactic behavior of R. ferrireducens is largely unknown.
R. ferrireducens is motile by means of one polar flagellum . Genes coding for flagellin-like proteins have been identified (Rfer_0630 and Rfer_0631) that cluster with genes coding for a flagellar hook-associated protein (Rfer_0632) and for flagellin-specific chaperons FliS and FliT . At least 35 genes are directly (components of the flagellar apparatus) or indirectly (specific chaperones, regulators) related to flagellar motility and are grouped in two clusters in the genome.
CRISPR sequences and immunity to phage attack
A 5.7 kb array of clustered regularly interspaced short palindromic repeats (CRISPR) was identified in the chromosome of R. ferrireducens, using the CRISPR Recognition Tool . It has been previously shown in a different bacterial system that new CRISPR spacer sequences derived from phage genomic DNA are added after viral challenge . The presence of these sequences in the host genome was shown to confer phage-resistance, in association with the cas genes. Thus, the CRISPR locus in the chromosome of R. ferrireducens may protect against phage attack. In addition, there is a 1.5 kb CRISPR array in the plasmid, encoding 24 spacer sequences of 32 bp. The CRISPRs in the chromosome and plasmid are 37 bp and 32 bp respectively, and these two loci are associated with separate sets of cas genes. Thus, the plasmid-encoded CRISPR appears independent of the chromosome-encoded CRISPR. Spacer sequences in both loci have no significant matches to entries in the NCBI databases (except to themselves). The results suggest that a significant cache of horizontally transferrable genetic elements which the R. ferrireducens chromosome and plasmid have encountered previously have yet to be sequenced and identified. Alternatively, if the horizontal acquisition of these elements occurred a long time ago in terms of R. ferrireducens evolution and selective pressure to maintain the original sequence is low, these spacer regions may have been ameliorated to such a degree that homology to the original sequence is no longer detectable.
Bacterial strains and culturing conditions
Rhodoferax ferrireducens strain DMS 15236 (ATCC BAA-621)  was obtained from our laboratory collection. A defined freshwater medium was used to culture and propagate this bacterium . Electron donors were added as follows: acetate 10 mM, lactate 0.1%, glycolate 10 mM, citrate 10 mM, glucose 0.1%, mannose 0.1%, sucrose 0.1%, cellobiose 0.1%. Electron acceptors were added as follows: fumarate 30 mM, ferric citrate 56 mM, Fe(III)NTA 5 mM, nitrate 20 mM.
Determination of growth yields
Rhodoferax ferrireducens cells were collected at stationary phase, centrifuged at 4000 RPM for 15 minutes at 4°C and washed with isotonic buffer . Any remaining liquid was carefully removed with a pipette and the pellets were flash-frozen for storage at -80°C. Cell pellets were subsequently resuspended in 5% SDS and boiled for 10 minutes. Protein concentrations were determined with the bicinchoninic acid (BCA) method using bovine serum albumin as standard . Dry weight was calculated assuming that protein accounts for 55% of the cell mass according to the biomass equation derived from E. coli model . Biomass yield from published acetate and Fe(III) data  was calculated using the value from E. coli (10-12 g/cell).
Growth of fumarate cultures was assessed by measuring optical density at 600 nm with a Genesys 2 spectrophotometer (Spectronic Instruments, Rochester, NY). The organic acid content of the culture medium was determined by high-pressure liquid chromatography (HPLC) using an LC-10AT high-pressure liquid chromatograph (Shimadzu, Kyoto, Japan) equipped with an Aminex HPX-87H column (300 by 7.8 mm; Bio-Rad, Hercules, CA). Organic acids were eluted in 8 mM H2SO4 and quantitated with an SPD-10VP UV detector (Shimadzu, Kyoto, Japan) set at 215 nm. Nitrate and nitrite concentrations were determined with a Dionex DX-100 ion chromatograph. Fe(II) concentrations were determined with the ferrozine assay as previously described .
Annotation and comparative genomic analyses
The R. ferrireducens genome was originally sequenced and annotated at the DOE Joint Genome Institute (JGI) http://www.jgi.doe.gov/ and assigned GenBank accession number CP000267 and CP000268 for the chromosome and plasmid, respectively. In order to enhance our ability to perform comparative genomic analyses and to generate a more accurate in silico constraints based model, further manual curation of the original genome assembly (chromosome and plasmid) was completed at the J. Craig Venter Institute (JCVI) as indicated in the following description. Results of the manual curation (as well as the original annotation from the JGI) are available at the Comprehensive Microbial Resource http://www.jcvi.org/cms/research/projects/cmr maintained by the JCVI. An initial set of CDSs that likely encode proteins was identified using GLIMMER 3 and those shorter than 90 base pairs (bp) as well as some of those with overlaps eliminated. There are 4451 CDSs that have been predicted on the main chromosome and 319 on the plasmid for a total of 4770 CDSs in the genome. 4333 CDSs from the JCVI annotation mapped to JGI annotation in GenBank. For clarity and ease of access to data, locus tags as assigned by GenBank are used to indicate CDSs referred to specifically in the work presented here unless otherwise indicated. For clarity and ease of access to data, locus tags as assigned by GenBank are used to indicate CDSs referred to specifically in the work presented here unless otherwise indicated.
CDSs were searched against a non-redundant protein database as previously described . Frameshifts and point mutations were detected and corrected where appropriate. Remaining frameshifts and point mutations are considered authentic and corresponding regions were annotated as 'authentic frameshift' or 'authentic point mutation', respectively. The CDS prediction and gene family identifications were completed as follows. Two sets of HMMs were used to determine CDS membership in families and superfamilies. These included 721 HMMs from Pfam v22.0 and 631 HMMs from the TIGR ortholog resource. TMHMM  was used to identify membrane-spanning domains (MSD) in proteins. Manual annotation, included adjustment of start sites, gene names and assignment to putative functional role categories.
Criteria for the identification of cytochrome genes used the Perl script "ps_scan.pl" and 3 Prosite profiles: PS51007 cytochrome c family profile, PS51008 multiheme cytochrome c family profile, and PS51009 cytochrome c class II profile. A gene scoring a low confidence cutoff (level = -1) was qualified as "putative" compared to a gene scoring above the reliable cutoff (level = 0). Additional HMM evidence and matches to a database of experimentally characterized genes maintained in house sometimes provided greater specificity to the corresponding gene name.
All predicted proteins from the R. ferrireducens genome were compared using bidirectional BLASTP to those from all other completed Proteobacterial genomes. Significant BLAST matches were scored for each CDS using cutoffs of 10-5 for the P value, and 70% for the length of the alignment compared to both query and database proteins. CDSs with a top match to another R. ferrireducens protein rather than to a protein in another species were considered candidates for which recent lineage-specific duplication events have occurred.
Metabolic network reconstruction
The R. ferrireducens metabolic network was reconstructed in SimPheny (Genomatica, Inc., CA) by modifying previously published procedures . The annotated genes of the R. ferrireducens genome as well as genes from several high-quality genome-scale metabolic models, including previously published Escherichia coli , Geobacter sulfurreducens , and Bacillus subtilis  models, were utilized for BLASTP sequence similarity search to generate a draft network as a starting point for model reconstruction. Among the base models used, E. coli was the phylogenetically closest to R. ferrireducens and provided about half of all reactions in the draft model, which captured significant portions of central metabolism, biosynthetic pathways for amino acids, nucleotides, and lipids. The reactions and their gene associations in the draft model of R. ferrireducens were evaluated manually based on gene annotations, published biochemical and physiological information, and external references as previously described  The remaining genes were also reviewed for inclusion in the reconstructed network. During this process, reactions and pathways not in the base models were identified, validated, and added into the R. ferrireducens model. A biomass demand reaction based on biomass compositions of the published E. coli model  was used in the R. ferrireducens model (See Additional file 1 for details). Exchange reactions for all extracellular compounds were added. The resulting reconstructed network was then subjected to the gap filling process where gaps were identified and filled manually through simulations to allow biomass formation under physiological growth conditions that include growth with Fe(III)-NTA, nitrate and oxygen as electron acceptors and acetate, propionate, lactate, pyruvate, malate, succinate, benzoate and glucose as electron donors [1, 2].
Estimation of energy parameters of the metabolic model
Energy parameters of the metabolic model including GAM, NGAM and proton translocation stoichiometry were estimated as follows. The GAM requirement for the R. ferrireducens model was assumed to be the same as the E. coli model at 59.81 mmol ATP/gdw h  based on their similar biomass compositions. The NGAM requirement and the proton translocation stoichiometry (H+/2e-, number of protons per pair of electrons) for NADH dehydrogenase and cytochrome reductase were estimated by iterating for optimization between in silico-predicted and experimentally determined growth yields. Observed experimental growth rates were all less than 0.04 h-1, so all in silico simulations were constrained with a growth rate less than 0.04 h-1. The experimental data used to determine the energetic parameters were obtained from three independent experiments where R. ferrireducens was cultivated in batch under the following conditions: a) acetate and fumarate, b) citrate and Fe(III), and c) acetate and Fe(III) .
In silico analysis of metabolism
The metabolic capabilities of the R. ferrireducens network were calculated using flux balance analysis and linear optimization  in SimPheny. Biomass synthesis was selected as the objective function to be maximized in growth simulations, and ATP consumption was selected as the objective function to be maximized in energy requirement simulations. The simulations resulted in flux values in units of mmol/gdw h. The following external metabolites were allowed to freely enter and leave the network for simulations of anaerobic growth on minimal media: CO2, H+, H2O, K+, Mg2+, NH4+, phosphate, and sulfate. A minimal amount of oxygen was allowed for biomass component requirements. The electron donors or acceptors tested were allowed a maximum uptake rate into the network of 5 mmol/gdw h or as specified in the results. All other external metabolites were only allowed to leave the system.
List of Abbreviations
grams of dry weight
malic enzyme (NADP)
pyruvate oxidoreductase complex
pyruvate phosphate dikinase
This research was supported by the Office of Science (BER), U. S. Department of Energy, Cooperative Agreement No. DE-FC02-02ER63446.
We thank the Department of Energy Joint Genome Institute for completing and making publicly available the genome sequence and automated annotation that was used as the starting material for further analyses presented in this manuscript.
- Chaudhuri SK, Lovley DR: Electricity generation by direct oxidation of glucose in mediatorless microbial fuel cells. Nat Biotechnol. 2003, 21 (10): 1229-1232. 10.1038/nbt867.View ArticlePubMedGoogle Scholar
- Finneran KT, Johnsen CV, Lovley DR: Rhodoferax ferrireducens sp. nov., a psychrotolerant, facultatively anaerobic bacterium that oxidizes acetate with the reduction of Fe(III). Int J Syst Evol Microbiol. 2003, 53 (Pt 3): 669-673. 10.1099/ijs.0.02298-0.View ArticlePubMedGoogle Scholar
- Davis JA, Curtis GP, Wilkins MJ, Kohler M, Fox P, Naftz DL, Lloyd JR: Processes affecting transport of uranium in a suboxic aquifer. Physics and Chemistry of the Earth. 2006, 31 (10-14): 548-555.View ArticleGoogle Scholar
- Hwang C, Wu W, Gentry TJ, Carley J, Corbin GA, Carroll SL, Watson DB, Jardine PM, Zhou J, Criddle CS, et al: Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths. ISME J. 2009, 3 (1): 47-64. 10.1038/ismej.2008.77.View ArticlePubMedGoogle Scholar
- Suzuki Y, Kelly SD, Kemner KM, Banfield JF: Direct microbial reduction and subsequent preservation of uranium in natural near-surface sediment. Appl Environ Microbiol. 2005, 71 (4): 1790-1797. 10.1128/AEM.71.4.1790-1797.2005.PubMed CentralView ArticlePubMedGoogle Scholar
- Wilkins MJ, Livens FR, Vaughan DJ, Beadle I, Lloyd JR: The influence of microbial redox cycling on radionuclide mobility in the subsurface at a low-level radioactive waste storage site. Geobiology. 2007, 5 (3): 293-301. 10.1111/j.1472-4669.2007.00101.x.View ArticleGoogle Scholar
- Mouser PJ, N'Guessan LA, Elifantz H, Holmes DE, Williams KH, Wilkins MJ, Long PE, Lovley DR: Influence of ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater. Environmental Science & Technology. 2009, 43 (12): 4386-4392. 10.1021/es8031055.View ArticleGoogle Scholar
- Lovley DR: Bug juice: harvesting electricity with microorganisms. Nature reviews. 2006, 4 (7): 497-508. 10.1038/nrmicro1442.PubMedGoogle Scholar
- Lovley DR: The microbe electric: conversion of organic matter to electricity. Curr Opin Biotechnol. 2008, 19 (6): 564-571. 10.1016/j.copbio.2008.10.005.View ArticlePubMedGoogle Scholar
- Madigan MT, Jung DO, Woese CR, Achenbach LA: Rhodoferax antarcticus sp. nov., a moderately psychrophilic purple nonsulfur bacterium isolated from an Antarctic microbial mat. Arch Microbiol. 2000, 173 (4): 269-277. 10.1007/s002030000140.View ArticlePubMedGoogle Scholar
- Hiraishi AHY, Satoh T: Rhodoferax fermentans gen. nov., and sp. nov., a phototrophic purple nonsulfur bacterium previously referred to as the "Rhodocyclus gelatinous-like" group. Arch Microbiol. 1991, 153: 330-336.Google Scholar
- Anderson AJ, Dawes EA: Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates. Microbiol Mol Biol Rev. 1990, 54 (4): 450-472.Google Scholar
- Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BO: Reconstruction of biochemical networks in microorganisms. Nature reviews. 2009, 7 (2): 129-143. 10.1038/nrmicro1949.PubMed CentralPubMedGoogle Scholar
- Price ND, Reed JL, Palsson BO: Genome-scale models of microbial cells: evaluating the consequences of constraints. Nature reviews. 2004, 2 (11): 886-897. 10.1038/nrmicro1023.PubMedGoogle Scholar
- Reed JL, Palsson BO: Thirteen years of building constraint-based in silico models of Escherichia coli. J Bacteriol. 2003, 185 (9): 2692-2699. 10.1128/JB.185.9.2692-2699.2003.PubMed CentralView ArticlePubMedGoogle Scholar
- Joint Genome Institute. [http://www.jgi.doe.gov/]
- Irgens RL, Gosink JJ, Staley JT: Polaromonas vacuolata gen. nov., sp. nov., a psychrophilic, marine, gas vacuolate bacterium from Antarctica. Int J Syst Bacteriol. 1996, 46 (3): 822-826.View ArticlePubMedGoogle Scholar
- Jeon CO, Park W, Ghiorse WC, Madsen EL: Polaromonas naphthalenivorans sp. nov., a naphthalene-degrading bacterium from naphthalene-contaminated sediment. Int J Syst Evol Microbiol. 2004, 54 (Pt 1): 93-97. 10.1099/ijs.0.02636-0.View ArticlePubMedGoogle Scholar
- Kampfer P, Busse HJ, Falsen E: Polaromonas aquatica sp. nov., isolated from tap water. Int J Syst Evol Microbiol. 2006, 56 (Pt 3): 605-608. 10.1099/ijs.0.63963-0.View ArticlePubMedGoogle Scholar
- Sizova M, Panikov N: Polaromonas hydrogenivorans sp. nov., a psychrotolerant hydrogen-oxidizing bacterium from Alaskan soil. Int J Syst Evol Microbiol. 2007, 57 (Pt 3): 616-619. 10.1099/ijs.0.64350-0.View ArticlePubMedGoogle Scholar
- Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO: A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol. 2007, 3: 121-10.1038/msb4100155.PubMed CentralView ArticlePubMedGoogle Scholar
- Mahadevan R, Bond DR, Butler JE, Esteve-Nunez A, Palsson ABO, Schilling CH, Coppi MV, Lovley DR: Characterization of metabolism in the Fe(III) reducing organism, Geobacter sulfurreducens, by constraint-based modeling. Appl Environ Microbiol. 2006, 72: 1558-1568. 10.1128/AEM.72.2.1558-1568.2006.PubMed CentralView ArticlePubMedGoogle Scholar
- Clark DP: The fermentation pathways of Escherichia coli. FEMS Microbiol Rev. 1989, 5 (3): 223-234. 10.1016/0168-6445(89)90033-8.PubMedGoogle Scholar
- Zaunmuller T, Kelly DJ, Glockner FO, Unden G: Succinate dehydrogenase functioning by a reverse redox loop mechanism and fumarate reductase in sulphate-reducing bacteria. Microbiology. 2006, 152 (Pt 8): 2443-2453. 10.1099/mic.0.28849-0.View ArticlePubMedGoogle Scholar
- Ullmann R, Gross R, Simon J, Unden G, Kroger A: Transport of C(4)-dicarboxylates in Wolinella succinogenes. J Bacteriol. 2000, 182 (20): 5757-5764. 10.1128/JB.182.20.5757-5764.2000.PubMed CentralView ArticlePubMedGoogle Scholar
- Welch RA, Burland V, Plunkett G, Redford P, Roesch P, Rasko D, Buckles EL, Liou SR, Boutin A, Hackett J, et al: Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci USA. 2002, 99 (26): 17020-17024. 10.1073/pnas.252529799.PubMed CentralView ArticlePubMedGoogle Scholar
- Garrity GMBJA, Lilburn T: Class II. Betaproteobacteria class. nov. Bergey's Manual of Systematic Bacteriology. Edited by: G. Garrity DJB, Krieg NR, Staley JT. 2005, The Proteobacteria (Part C): Springer, Two: 575-600.View ArticleGoogle Scholar
- Zaar A, Eisenreich W, Bacher A, Fuchs G: A novel pathway of aerobic benzoate catabolism in the bacteria Azoarcus evansii and Bacillus stearothermophilus. J Biol Chem. 2001, 276 (27): 24997-25004. 10.1074/jbc.M100291200.View ArticlePubMedGoogle Scholar
- Gescher J, Zaar A, Mohamed M, Schagger H, Fuchs G: Genes coding for a new pathway of aerobic benzoate metabolism in Azoarcus evansii. J Bacteriol. 2002, 184 (22): 6301-6315. 10.1128/JB.184.22.6301-6315.2002.PubMed CentralView ArticlePubMedGoogle Scholar
- Fuchs G: Anaerobic metabolism of aromatic compounds. Ann N Y Acad Sci. 2008, 82-99. 1125
- Breese K, Boll M, Alt-Morbe J, Schagger H, Fuchs G: Genes coding for the benzoyl-CoA pathway of anaerobic aromatic metabolism in the bacterium Thauera aromatica. Eur J Biochem. 1998, 256 (1): 148-154. 10.1046/j.1432-1327.1998.2560148.x.View ArticlePubMedGoogle Scholar
- Wischgoll S, Heintz D, Peters F, Erxleben A, Sarnighausen E, Reski R, Van Dorsselaer A, Boll M: Gene clusters involved in anaerobic benzoate degradation of Geobacter metallireducens. Mol Microbiol. 2005, 58 (5): 1238-1252.View ArticlePubMedGoogle Scholar
- Butler JE, He Q, Nevin KP, He Z, Zhou J, Lovley DR: Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site. BMC Genomics. 2007, 8: 180-10.1186/1471-2164-8-180.PubMed CentralView ArticlePubMedGoogle Scholar
- Rhee SK, Fuchs G: Phenylacetyl-CoA:acceptor oxidoreductase, a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. Eur J Biochem. 1999, 262 (2): 507-515. 10.1046/j.1432-1327.1999.00399.x.View ArticlePubMedGoogle Scholar
- Hirsch W, Schagger H, Fuchs G: Phenylglyoxylate:NAD+ oxidoreductase (CoA benzoylating), a new enzyme of anaerobic phenylalanine metabolism in the denitrifying bacterium Azoarcus evansii. Eur J Biochem. 1998, 251 (3): 907-915. 10.1046/j.1432-1327.1998.2510907.x.View ArticlePubMedGoogle Scholar
- Lovley DR: Extracellular electron transfer: wires, capacitors, iron lungs, and more. Geobiology. 2008, 6 (3): 225-231. 10.1111/j.1472-4669.2008.00148.x.View ArticlePubMedGoogle Scholar
- Shi L, Squier TC, Zachara JM, Fredrickson JK: Respiration of metal (hydr)oxides by Shewanella and Geobacter : a key role for multihaem c-type cytochromes. Mol Microbiol. 2007, 65 (1): 12-20. 10.1111/j.1365-2958.2007.05783.x.PubMed CentralView ArticlePubMedGoogle Scholar
- Mehta T, Coppi MV, Childers SE, Lovley DR: Outer membrane c-type cytochromes required for Fe(III) and Mn(IV) oxide reduction in Geobacter sulfurreducens. Appl Environ Microbiol. 2005, 71 (12): 8634-8641. 10.1128/AEM.71.12.8634-8641.2005.PubMed CentralView ArticlePubMedGoogle Scholar
- Kim BC, Leang C, Ding YH, Glaven RH, Coppi MV, Lovley DR: OmcF, a putative c-type monoheme outer membrane cytochrome required for the expression of other outer membrane cytochromes in Geobacter sulfurreducens. J Bacteriol. 2005, 187 (13): 4505-4513. 10.1128/JB.187.13.4505-4513.2005.PubMed CentralView ArticlePubMedGoogle Scholar
- Leang C, Coppi MV, Lovley DR: OmcB, a c-type polyheme cytochrome, involved in Fe(III) reduction in Geobacter sulfurreducens. J Bacteriol. 2003, 185 (7): 2096-2103. 10.1128/JB.185.7.2096-2103.2003.PubMed CentralView ArticlePubMedGoogle Scholar
- Mahne I, Tiedje JM: Criteria and Methodology for Identifying Respiratory Denitrifiers. Appl Environ Microbiol. 1995, 61 (3): 1110-1115.PubMed CentralPubMedGoogle Scholar
- Alvarez AH, Moreno-Sanchez R, Cervantes C: Chromate Efflux by Means of the ChrA Chromate Resistance Protein from Pseudomonas aeruginosa. J Bacteriol. 1999, 181 (23): 7398-7400.PubMed CentralPubMedGoogle Scholar
- Francisco R, Alpoim MC, Morais PV: Diversity of chromium-resistant and -reducing bacteria in a chromium-contaminated activated sludge. J Appl Microbiol. 2002, 92 (5): 837-843. 10.1046/j.1365-2672.2002.01591.x.View ArticlePubMedGoogle Scholar
- Branco R, Alpoim MC, Morais PV: Ochrobactrum tritici strain 5bvl1 - characterization of a Cr(VI)-resistant and Cr(VI)-reducing strain. Can J Microbiol. 2004, 50 (9): 697-703. 10.1139/w04-048.View ArticlePubMedGoogle Scholar
- Branco R, Chung AP, Johnston T, Gurel V, Morais P, Zhitkovich A: The chromate-inducible chrBACF operon from the transposable element TnOtChr confers resistance to chromium(VI) and superoxide. J Bacteriol. 2008, 190 (21): 6996-7003. 10.1128/JB.00289-08.PubMed CentralView ArticlePubMedGoogle Scholar
- Max Mergeay SM, Vallaeys Tatiana, Auquier Vanessa, Benotmane Abderrafi, Bertin Philippe, Taghavi Safiyh, Dunn John, Lelie Daniel, Wattiez Ruddy: Ralstonia metallidurans, a bacterium specifically adapted to toxic metals: towards a catalogue of metal-responsive genes. FEMS Microbiology Reviews. 2003, 27 (2-3): 385-410. 10.1016/S0168-6445(03)00045-7.View ArticlePubMedGoogle Scholar
- Valappil SP, Rai R, Bucke C, Roy I: Polyhydroxyalkanoate biosynthesis in Bacillus cereus SPV under varied limiting conditions and an insight into the biosynthetic genes involved. Journal of Applied Microbiology. 2008, 104 (6): 1624-1635. 10.1111/j.1365-2672.2007.03678.x.View ArticlePubMedGoogle Scholar
- Evans LD, Stafford GP, Ahmed S, Fraser GM, Hughes C: An escort mechanism for cycling of export chaperones during flagellum assembly. Proc Natl Acad Sci USA. 2006, 103 (46): 17474-17479. 10.1073/pnas.0605197103.PubMed CentralView ArticlePubMedGoogle Scholar
- Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P: CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007, 8: 209-10.1186/1471-2105-8-209.PubMed CentralView ArticlePubMedGoogle Scholar
- Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P: CRISPR provides acquired resistance against viruses in prokaryotes. Science. 2007, 315 (5819): 1709-1712. 10.1126/science.1138140.View ArticlePubMedGoogle Scholar
- Lovley DR, Giovannoni SJ, White DC, Champine JE, Phillips EJ, Gorby YA, Goodwin S: Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals. Arch Microbiol. 1993, 159 (4): 336-344. 10.1007/BF00290916.View ArticlePubMedGoogle Scholar
- Risso C, Van Dien SJ, Orloff A, Lovley DR, Coppi MV: Elucidation of an alternate isoleucine biosynthesis pathway in Geobacter sulfurreducens. J Bacteriol. 2008, 190 (7): 2266-2274. 10.1128/JB.01841-07.PubMed CentralView ArticlePubMedGoogle Scholar
- Smith PK, Krohn RI, Hermanson GT, Mallia AK, Gartner FH, Provenzano MD, Fujimoto EK, Goeke NM, Olson BJ, Klenk DC: Measurement of protein using bicinchoninic acid. Anal Biochem. 1985, 150 (1): 76-85. 10.1016/0003-2697(85)90442-7.View ArticlePubMedGoogle Scholar
- Lovley DR, Phillips EJP: Organic matter mineralization with the reduction of ferric iron in anaerobic sediments. Appl Environ Microbiol. 1986, 51: 683-689.PubMed CentralPubMedGoogle Scholar
- Fouts DE, Tyler HL, DeBoy RT, Daugherty S, Ren Q, Badger JH, Durkin AS, Huot H, Shrivastava S, Kothari S, et al: Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice. PLoS Genet. 2008, 4 (7): e1000141-10.1371/journal.pgen.1000141.PubMed CentralView ArticlePubMedGoogle Scholar
- Edwards JS, Palsson BO: The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci USA. 2000, 97 (10): 5528-5533. 10.1073/pnas.97.10.5528.PubMed CentralView ArticlePubMedGoogle Scholar
- Oh YK, Palsson BO, Park SM, Schilling CH, Mahadevan R: Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J Biol Chem. 2007, 282 (39): 28791-28799. 10.1074/jbc.M703759200.View ArticlePubMedGoogle Scholar
- Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BO: Metabolic modeling of microbial strains in silico. Trends Biochem Sci. 2001, 26 (3): 179-186. 10.1016/S0968-0004(00)01754-0.View ArticlePubMedGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.