Krushkal J, Yan B, DiDonato LN, Puljic M, Nevin KP, Woodard TL et al.. Genome-wide expression profiling in Geobacter sulfurreducens: identification of Fur and RpoS transcription regulatory sites in a relGsu mutant. Funct Integr Genomics 7: 229-255
Rel(Gsu) is the single Geobacter sulfurreducens homolog of RelA and SpoT proteins found in many organisms. These proteins are involved in the regulation of levels of guanosine 3', 5' bispyrophosphate, ppGpp, a molecule that signals slow growth and stress response under nutrient limitation in bacteria. We used information obtained from genome-wide expression profiling of the rel(Gsu) deletion mutant to identify putative regulatory sites involved in transcription networks modulated by Rel(Gsu) or ppGpp. Differential gene expression in the rel(Gsu) deletion mutant, as compared to the wild type, was available from two growth conditions, steady state chemostat cultures and stationary phase batch cultures. Hierarchical clustering analysis of these two datasets identified several groups of operons that are likely co-regulated. Using a search for conserved motifs in the upstream regions of these co-regulated operons, we identified sequences similar to Fur- and RpoS-regulated sites. These findings suggest that Fur- and RpoS-dependent gene expression in G. sulfurreducens is affected by Rel(Gsu)-mediated signaling.
"If OmcB is more abundant in upper sections of the electrode-grown biofilm, then what could cells be responding to? Expression of omcB is affected by the stress-related sigma factor RpoS – and the stringent response , . More relevant to growth in these biofilms, which were under constant electron donor levels and nutrient conditions, is the fact that expression of omcB increases when G. sulfurreducens is limited for Fe(III) as an electron acceptor , . "
[Show abstract][Hide abstract] ABSTRACT: When Geobacter sulfurreducens utilizes an electrode as its electron acceptor, cells embed themselves in a conductive biofilm tens of microns thick. While environmental conditions such as pH or redox potential have been shown to change close to the electrode, less is known about the response of G. sulfurreducens to growth in this biofilm environment. To investigate whether respiratory protein abundance varies with distance from the electrode, antibodies against an outer membrane multiheme cytochrome (OmcB) and cytoplasmic acetate kinase (AckA) were used to determine protein localization in slices spanning ∼25 µm-thick G. sulfurreducens biofilms growing on polished electrodes poised at +0.24 V (vs. Standard Hydrogen Electrode). Slices were immunogold labeled post-fixing, imaged via transmission electron microscopy, and digitally reassembled to create continuous images allowing subcellular location and abundance per cell to be quantified across an entire biofilm. OmcB was predominantly localized on cell membranes, and 3.6-fold more OmcB was detected on cells 10-20 µm distant from the electrode surface compared to inner layers (0-10 µm). In contrast, acetate kinase remained constant throughout the biofilm, and was always associated with the cell interior. This method for detecting proteins in intact conductive biofilms supports a model where the utilization of redox proteins changes with depth.
PLoS ONE 08/2014; 9(8):e104336. DOI:10.1371/journal.pone.0104336 · 3.23 Impact Factor
"Operon organization and gene annotation Operon organization of the F. placidus genome was predicted using the commercial version of the FGENESB software (V Solovyev and A Salamov, unpublished data; Softberry Inc., Mount Kisco, NY, USA; 2003–2009), as previously described for the genomes of various Geobacteraceae (Krushkal et al., 2007; Mahadevan et al., 2008; Tran et al., 2008). "
[Show abstract][Hide abstract] ABSTRACT: Insight into the mechanisms for the anaerobic metabolism of aromatic compounds by the hyperthermophilic archaeon Ferroglobus placidus is expected to improve understanding of the degradation of aromatics in hot (>80° C) environments and to identify enzymes that might have biotechnological applications. Analysis of the F. placidus genome revealed genes predicted to encode enzymes homologous to those previously identified as having a role in benzoate and phenol metabolism in mesophilic bacteria. Surprisingly, F. placidus lacks genes for an ATP-independent class II benzoyl-CoA (coenzyme A) reductase (BCR) found in all strictly anaerobic bacteria, but has instead genes coding for a bzd-type ATP-consuming class I BCR, similar to those found in facultative bacteria. The lower portion of the benzoate degradation pathway appears to be more similar to that found in the phototroph Rhodopseudomonas palustris, than the pathway reported for all heterotrophic anaerobic benzoate degraders. Many of the genes predicted to be involved in benzoate metabolism were found in one of two gene clusters. Genes for phenol carboxylation proceeding through a phenylphosphate intermediate were identified in a single gene cluster. Analysis of transcript abundance with a whole-genome microarray and quantitative reverse transcriptase polymerase chain reaction demonstrated that most of the genes predicted to be involved in benzoate or phenol metabolism had higher transcript abundance during growth on those substrates vs growth on acetate. These results suggest that the general strategies for benzoate and phenol metabolism are highly conserved between microorganisms living in moderate and hot environments, and that anaerobic metabolism of aromatic compounds might be analyzed in a wide range of environments with similar molecular targets.
The ISME Journal 07/2011; 6(1):146-57. DOI:10.1038/ismej.2011.88 · 9.30 Impact Factor
"Operon organization of the Geobacteraceae genomes was predicted using the commercial version of the FGENESB software (V. Solovyev and A. Salamov, unpublished; Softberry , Inc., 2003–2009), as described earlier (Krushkal et al., 2007; Mahadevan et al., 2008; Tran et al., 2008). For the G. sulfurreducens genome sequence (GenBank accession number AE017180), operon annotation version of March 2007 was employed in analysis. "
[Show abstract][Hide abstract] ABSTRACT: Members of the TetR family of bacterial transcriptional regulators affect expression of genes whose products are involved in a variety of important functions, including osmotic stress, catabolic pathways, homeostasis, biosynthesis of antibiotics, expression of efflux pumps, multidrug resistance, and virulence of pathogenic bacteria. We used genome sequence information to carry out phylogenetic classification of 864 TetR family members with a special focus on TetR regulators in Geobacteraceae, an environmentally important family of delta-Proteobacteria. The genome of Geobacter sulfurreducens, a model representative of Geobacteraceae, contains nine genes from the tetR family. Several of these genes are located immediately upstream of operons encoding functionally important c-type cytochromes. Computational analyses identified the presence of conserved promoters and other regulatory binding sites upstream of several G. sulfurreducens tetR genes. This suggests the possibility of an intermediary role of TetR family proteins in Geobacteraceae in regulatory cascades involving a variety of sigma factors. In order to understand the role of the TetR regulatory family in Geobacteraceae, we have inferred phylogenetic relationships among the Geobacteraceae TetR proteins and their homologs in other microbial species.
Omics: a journal of integrative biology 06/2011; 15(7-8):495-506. DOI:10.1089/omi.2010.0117 · 2.36 Impact Factor
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