Physiological Roles of ArcA, Crp, and EtrA and Their Interactive Control on Aerobic and Anaerobic Respiration in Shewanella oneidensis

Gao, Haichun; Wang, Xiaohu; Yang, Zamin K.; Chen, Jingrong; Liang, Yili; Chen, Haijiang; Palzkill, Timothy; Zhou, Jizhong

doi:10.1371/journal.pone.0015295

Cited by 70 publications

(176 citation statements)

References 49 publications

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“…The same result was obtained from sequencing the same region of 5 new suppressor strains generated from a new round of the experiment, implying a role for the deletion in suppression. To test if the fabF1 gene is associated with the suppression, we placed the fabF1 gene under the control of the arcA promoter (P arcA ), which is constitutively active at levels similar to those for the fabB promoter (11,18). Expression of the fabF1 gene driven by P arcA largely corrected the growth defect of the ⌬desA ⌬fabB strain (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Plasmid pHG102, which carries the constitutively active S. oneidensis arcA promoter, was used in genetic complementation of fabB, fabF1, and fabF2 mutants (18,19). After being verified by sequencing, the vectors were introduced into the relevant mutants for phenotypic assays.…”

Section: Methodsmentioning

confidence: 99%

“…This unexpected observation is likely due to accumulation of C 14 fatty acids and the overall reduction in UFA production because the loss of FabB (in contrast to that of FabA) does not stimulate DesA production (11). In addition to playing an important role in the elongation of C 14 -ACP in S. oneidensis, FabB when overabundant is inhibitory to growth by generating C 18 and even longer fatty acids (11). Based on these differences, it is clear that S. oneidensis FabB and its E. coli counterpart differ from each other in that the former is much more effective in catalyzing elongation of C 14 to C 16 and C 16 to C 18 species.…”

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confidence: 95%

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Suppression of fabB Mutation by fabF1 Is Mediated by Transcription Read-through in Shewanella oneidensis

Quanfei

et al. 2016

J Bacteriol

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As type II fatty acid synthesis is essential for the growth of Escherichia coli, its many components are regarded as potential targets for novel antibacterial drugs. Among them, ␤-ketoacyl-acyl carrier protein (ACP) synthase (KAS) FabB is the exclusive factor for elongation of the cis-3-decenoyl-ACP (cis-3-C 10 -ACP). In our previous study, we presented evidence to suggest that this may not be the case in Shewanella oneidensis, an emerging model gammaproteobacterium renowned for its respiratory versatility. Here, we identified FabF1, another KAS, as a functional replacement for FabB in S. oneidensis. In fabB ؉ or desA ؉ (encoding a desaturase) cells, which are capable of making unsaturated fatty acids (UFA), FabF1 is barely produced. However, UFA auxotroph mutants devoid of both fabB and desA genes can be spontaneously converted to suppressor strains, which no longer require exogenous UFAs for growth. Suppression is caused by a TGTTTT deletion in the region upstream of the fabF1 gene, resulting in enhanced FabF1 production. We further demonstrated that the deletion leads to transcription read-through of the terminator for acpP, an acyl carrier protein gene immediately upstream of fabF1. There are multiple tandem repeats in the region covering the terminator, and the TGTTTT deletion, as well as others, compromises the terminator efficacy. In addition, FabF2 also shows an ability to complement the FabB loss, albeit substantially less effectively than FabF1. IMPORTANCEIt has been firmly established that FabB for UFA synthesis via type II fatty acid synthesis in FabA-containing bacteria such as E. coli is essential. However, S. oneidensis appears to be an exception. In this bacterium, FabF1, when sufficiently expressed, is able to fully complement the FabB loss. Importantly, such a capability can be obtained by spontaneous mutations, which lead to transcription read-through. Therefore, our data, by identifying the functional overlap between FabB and FabFs, provide new insights into the current understanding of KAS and help reveal novel ways to block UFA synthesis for therapeutic purposes. The de novo fatty acid synthesis (FAS) pathway, namely, type II, is the predominant, if not exclusive, route for endogenous production of fatty acids (1). The FAS pathway, the current knowledge of which derives mainly from the model organism Escherichia coli, is highly conserved in bacteria. Central to the pathway are reactions catalyzed by ␤-ketoacyl-acyl carrier protein (ACP) synthases (KAS), including FabH, FabB, and FabF. FabH is responsible for the condensation of an acyl coenzyme A (acylCoA) unit and a malonyl-acyl carrier protein (malonyl-ACP) unit, but cannot work with acetyl-ACP, the substrate of FabB and FabF; as a consequence, FabH could not function as a replacement for FabB or FabF (1). While FabB and FabF are exchangeable in elongation of saturated intermediates, each catalyzes a reaction with the unsaturated branch that the other cannot or at least much less effectively (2) (Fig. 1). The key reaction catalyze...

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 95%

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Suppression of fabB Mutation by fabF1 Is Mediated by Transcription Read-through in Shewanella oneidensis

Quanfei

et al. 2016

J Bacteriol

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“…All mutants from previous studies were successfully complemented by a copy of the corresponding gene on plasmids pHG101 and pHG102 (Table 1) (24,25). In this study, these complementation vectors were used with similar results.…”

Section: Methodsmentioning

confidence: 99%

A Matter of Timing: Contrasting Effects of Hydrogen Sulfide on Oxidative Stress Response in Shewanella oneidensis

Wan

et al. 2015

J Bacteriol

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Hydrogen sulfide (H 2 S), well known for its toxic properties, has recently become a research focus in bacteria, in part because it has been found to prevent oxidative stress caused by treatment with some antibiotics. H 2 S has the ability to scavenge reactive oxygen species (ROS), thus preventing oxidative stress, but it is also toxic, leading to conflicting reports of its effects in different organisms. Here, with Shewanella oneidensis as a model, we report that the effects of H 2 S on the response to oxidative stress are time dependent. When added simultaneously with H 2 O 2 , H 2 S promoted H 2 O 2 toxicity by inactivating catalase, KatB, a hemecontaining enzyme involved in H 2 O 2 degradation. Such an inhibitory effect may apply to other heme-containing proteins, such as cytochrome cbb 3 oxidase. When H 2 O 2 was supplied 20 min or later after the addition of H 2 S, the oxidative-stress-responding regulator OxyR was activated, resulting in increased resistance to H 2 O 2 . The activation of OxyR was likely triggered by the influx of iron, a response to lowered intracellular iron due to the iron-sequestering property of H 2 S. Given that Shewanella bacteria thrive in redox-stratified environments that have abundant sulfur and iron species, our results imply that H 2 S is more important for bacterial survival in such environmental niches than previously believed. IMPORTANCE Previous studies have demonstrated that H 2 S is either detrimental or beneficial to bacterial cells. While it can act as a growth-inhibiting molecule by damaging DNA and denaturing proteins, it helps cells to combat oxidative stress. Here we report that H 2 S indeed has these contrasting biological functions and that its effects are time dependent. Immediately after H 2 S treatment, there is growth inhibition due to damage of heme-containing proteins, at least to catalase and cytochrome c oxidase. In contrast, when added a certain time later, H 2 S confers an enhanced ability to combat oxidative stress by activating the H 2 O 2 -responding regulator OxyR. Our data reconcile conflicting observations about the functions of H 2 S.

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“…A complete list of the genes with identified CRP-binding motifs can be found in Table S4 in the supplemental material. A larger proportion of the identified putative CRP-binding motifs were located upstream of genes in clusters 2 and 4 (genes with increased expression) than in clusters 1 and 3 (genes with decreased expression). Among the genes identified to have potential CRP-binding motifs are genes with known CRP-binding sites, such as mtrC and omcA (51). Also included are genes encoding other cytochromes (e.g., so_0939, cctA, and mtrA), genes important for cytochrome maturation (e.g., sirE), genes involved in heme biosynthesis (e.g., hemH), and other electron transfer-related genes.…”

Section: Fig 6 Representation Of the Alignment Of Known E Coli Crp-bmentioning

confidence: 99%

Regulation of Gene Expression in Shewanella oneidensis MR-1 during Electron Acceptor Limitation and Bacterial Nanowire Formation

Barchinger

Pirbadian

Sambles

et al. 2016

Appl Environ Microbiol

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In limiting oxygen as an electron acceptor, the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1 rapidly forms nanowires, extensions of its outer membrane containing the cytochromes MtrC and OmcA needed for extracellular electron transfer. RNA sequencing (RNA-Seq) analysis was employed to determine differential gene expression over time from triplicate chemostat cultures that were limited for oxygen. We identified 465 genes with decreased expression and 677 genes with increased expression. The coordinated increased expression of heme biosynthesis, cytochrome maturation, and transport pathways indicates that S. oneidensis MR-1 increases cytochrome production, including the transcription of genes encoding MtrA, MtrC, and OmcA, and transports these decaheme cytochromes across the cytoplasmic membrane during electron acceptor limitation and nanowire formation. In contrast, the expression of the mtrA and mtrC homologs mtrF and mtrD either remains unaffected or decreases under these conditions. The ompW gene, encoding a small outer membrane porin, has 40-fold higher expression during oxygen limitation, and it is proposed that OmpW plays a role in cation transport to maintain electrical neutrality during electron transfer. The genes encoding the anaerobic respiration regulator cyclic AMP receptor protein (CRP) and the extracytoplasmic function sigma factor RpoE are among the transcription factor genes with increased expression. RpoE might function by signaling the initial response to oxygen limitation. Our results show that RpoE activates transcription from promoters upstream of mtrC and omcA. The transcriptome and mutant analyses of S. oneidensis MR-1 nanowire production are consistent with independent regulatory mechanisms for extending the outer membrane into tubular structures and for ensuring the electron transfer function of the nanowires. IMPORTANCEShewanella oneidensis MR-1 has the capacity to transfer electrons to its external surface using extensions of the outer membrane called bacterial nanowires. These bacterial nanowires link the cell's respiratory chain to external surfaces, including oxidized metals important in bioremediation, and explain why S. oneidensis can be utilized as a component of microbial fuel cells, a form of renewable energy. In this work, we use differential gene expression analysis to focus on which genes function to produce the nanowires and promote extracellular electron transfer during oxygen limitation. Among the genes that are expressed at high levels are those encoding cytochrome proteins necessary for electron transfer. Shewanella coordinates the increased expression of regulators, metabolic pathways, and transport pathways to ensure that cytochromes efficiently transfer electrons along the nanowires.

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Physiological Roles of ArcA, Crp, and EtrA and Their Interactive Control on Aerobic and Anaerobic Respiration in Shewanella oneidensis

Cited by 70 publications

References 49 publications

Suppression of fabB Mutation by fabF1 Is Mediated by Transcription Read-through in Shewanella oneidensis

Suppression of fabB Mutation by fabF1 Is Mediated by Transcription Read-through in Shewanella oneidensis

A Matter of Timing: Contrasting Effects of Hydrogen Sulfide on Oxidative Stress Response in Shewanella oneidensis

Regulation of Gene Expression in Shewanella oneidensis MR-1 during Electron Acceptor Limitation and Bacterial Nanowire Formation

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