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Methylomes of Geobacter sulfurreducens Grown on Different Terminal Electron Acceptors

ABSTRACT: The Geobacter species evolved respiratory versatility to utilize a wide range of terminal electron acceptors. To explore this adaptive mechanism, Fe(III) citrate, hydrous ferric oxide, and fumarate were selected as electron acceptors, and the methylome and metabolome of Geobacter sulfurreducens PCA grown on each electron acceptor were investigated via third-generation, single-molecule real-time DNA sequencing.Results showed that the patterns of 4-methylcytosine (m4C) and 6-methyladenine (m6A) modification were all varied in different electron acceptor cultures. Moreover, genes (e.g., GSU0466 and GSU1467) with low expression levels generally had high methylation levels. These findings suggest that m4C and m6A modifications play a role in the adaption of G. sulfurreducens to diverse electron acceptors, and DNA methylation may be involved in the adaption mainly via gene expression regulation.

ORGANISM(S): Geobacter sulfurreducens

PROVIDER: GSE157224 | GEO | 2021/08/31

REPOSITORIES: GEO

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Project description:Mahadevan2006 - Genome-scale metabolic network of Geobacter sulfurreducens (iRM588) This model is described in the article: Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling. Mahadevan R, Bond DR, Butler JE, Esteve-Nuñez A, Coppi MV, Palsson BO, Schilling CH, Lovley DR. Appl. Environ. Microbiol. 2006 Feb; 72(2): 1558-1568 Abstract: Geobacter sulfurreducens is a well-studied representative of the Geobacteraceae, which play a critical role in organic matter oxidation coupled to Fe(III) reduction, bioremediation of groundwater contaminated with organics or metals, and electricity production from waste organic matter. In order to investigate G. sulfurreducens central metabolism and electron transport, a metabolic model which integrated genome-based predictions with available genetic and physiological data was developed via the constraint-based modeling approach. Evaluation of the rates of proton production and consumption in the extracellular and cytoplasmic compartments revealed that energy conservation with extracellular electron acceptors, such as Fe(III), was limited relative to that associated with intracellular acceptors. This limitation was attributed to lack of cytoplasmic proton consumption during reduction of extracellular electron acceptors. Model-based analysis of the metabolic cost of producing an extracellular electron shuttle to promote electron transfer to insoluble Fe(III) oxides demonstrated why Geobacter species, which do not produce shuttles, have an energetic advantage over shuttle-producing Fe(III) reducers in subsurface environments. In silico analysis also revealed that the metabolic network of G. sulfurreducens could synthesize amino acids more efficiently than that of Escherichia coli due to the presence of a pyruvate-ferredoxin oxidoreductase, which catalyzes synthesis of pyruvate from acetate and carbon dioxide in a single step. In silico phenotypic analysis of deletion mutants demonstrated the capability of the model to explore the flexibility of G. sulfurreducens central metabolism and correctly predict mutant phenotypes. These results demonstrate that iterative modeling coupled with experimentation can accelerate the understanding of the physiology of poorly studied but environmentally relevant organisms and may help optimize their practical applications. This model is hosted on BioModels Database and identified by: MODEL1507180000. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Project description:The ability of Geobacter species to readily donate electrons to extracellular electron acceptors makes the study of their physiology not only important for the understanding of environmental processes, but also for industrial applications such as bioelectronics and electrosynthesis. Studies in G. sulfurreducens have shown that outer surface components, such as c-type cytochromes and conductive type IV pili play an important role in direct electron transfer to extracellular electron acceptors such as Fe(III) oxides and electrodes. However, many of these thoroughly studied outer surface components, including c-type cytochromes, are not well conserved among Geobacter species. In order to better understand which components are involved in extracellular electron transfer in Geobacter species other than G. sulfurreducens, studies were conducted with its close relative G. metallireducens. Whole-genome microarray analysis revealed that 23 of the 91 putative c-type cytochromes encoded in the G. metallireducens genome were upregulated at least 2-fold in cells grown with Fe(III) oxide compared to cells in which Fe(III) citrate was provided as the terminal electron acceptor. Protein identification with liquid-chromatography/mass spectrometry detected 6 c-type cytochromes that were more abundant in the outer surface cell fraction of cells that were grown with Fe(III) oxide as the terminal electron acceptor compared to cells grown on Fe(III) citrate. 22 genes encoding c-type cytochromes were chosen for gene deletion. Deletion of 6 genes encoding for c-type cytochromes, a gene encoding for a lipopolysaccharide biosynthesis-associated protein, and a gene encoding for a NHL- repeat containing protein inhibited growth when Fe(III) oxide was provided as the electron acceptor. This study suggests that there are different roads for extracellular electron transfer in Geobacteraceae since homologous c-type cytochromes have different functions from one species to the other, and novel components not previously found to be essential for extracellular electron transfer were identified. An eight-chip study using total RNA recovered from four separate cultures of Geobacter metallireducens GS-15 grown with acetate (10mM)-Fe(III) oxide (100 mmol l-1) (experimental condition) or with acetate (10 mM)-Fe(III) citrate (55mM) (control condition) during exponential growth. Each chip measures the expression level of 3,627 genes from Geobacter metallireducens GS-15 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

Project description:Whole-genome DNA microarray analysis of Geobacter sulfurreducens cells grown on Fe(III)-oxide or Mn(IV)-oxide versus cells grown on soluble Fe(III) citrate indicated that there were significant differences in transcription patterns during growth on the insoluble metal oxides compared to growth on soluble Fe(III). Many of the genes that appeared to be up-regulated during growth on the metal hydroxides were involved in electron transport. The most highly up-regulated genes for both conditions were omcS and omcT, which encode co-transcribed c-type cytochromes exposed on the outer surface of the cell that are known to be required for Fe(III) and Mn(IV)-oxide reduction. Other electron transport genes that were up-regulated on both insoluble metals included the gene coding for the outer membrane c-type cytochrome, OmcG, genes for the outer membrane proteins, OmpB and OmpC, and the gene that codes for the structural protein of electrically conductive pili, PilA. Genes that were up-regulated in cells grown on Fe(III)-oxide but not Mn(IV)-oxide, included outer membrane c-type cytochromes including OmcE, a putative DMSO reductase protein, and proteins from the cytochrome bc1 complex. Electron transport genes that were only up-regulated in Mn(IV)-oxide grown cells included the genes that code for the outer membrane c-type cytochromes, OmcZ and OmcB, the periplasmic c-type cytochrome, MacA, and fumarate reductase. Genetic studies indicated that the c-type cytochrome proteins, PpcH, OmcJ, OmcM, OmcV, MacA, OmcF, OmcI, and OmcQ, and the iron sulfur subunit of the cytochrome b/b6 complex, QcrA, are important for reduction of insoluble Fe(III)-oxides but do not appear to be important for Mn(IV) reduction. These results demonstrate that the physiology of Fe(III) reducing bacteria differ significantly during growth on insoluble electron and soluble electron acceptors and emphasizes the importance of c-type cytochromes in extracellular electron transfer in G. sulfurreducens. Geobacter sulfurreducens cells were grown with acetate (5 mM) provided as the electron donor and either Fe(III) oxide or Fe(III) citrate provided as the electron acceptor. Cells were harvested at mid-log and total RNA was extracted. Total RNA (0.5 M-NM-<g) was amplified using the MessageAmp II-Bacteria Kit (Ambion, Foster City, CA) according to the manufacturers instructions. Ten micrograms of amplified RNA (aRNA) was chemically labeled with Cy3 (for the control or soluble electron acceptor condition) or Cy5 (for the experimental or insoluble electron acceptor condition) dye using the MicroMax ASAP RNA Labeling Kit (Perkin Elmer, Wellesley, MA) according to the manufacturerM-bM-^@M-^Ys instructions. RNA samples from three biological replicates were hybridized in duplicate on 12K Combimatrix antisense-detecting arrays. The experimental condition (DL1 grown with Mn(IV) oxide as acceptor) was labeled with cy5, the control condition (DL1 grown with Fe(III) citrate as acceptor) was labeled with cy3

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Methylomes of Geobacter sulfurreducens Grown on Different Terminal Electron Acceptors

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