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Snapshot of iron response in Shewanella oneidensis by gene network reconstruction.

Yang Y, Harris DP, Luo F, Xiong W, Joachimiak M, Wu L, Dehal P, Jacobsen J, Yang Z, Palumbo AV, Arkin AP, Zhou J - BMC Genomics (2009)

Bottom Line: Disruption of a novel transcriptional factor (SO1415) caused deficiency in both anaerobic iron reduction and growth with thiosulfate or TMAO as an electronic acceptor, suggesting that SO1415 is required for specific branches of anaerobic energy metabolism pathways.Using a reconstructed gene network, we identified major biological pathways that were differentially expressed during iron depletion and repletion.Genetic studies not only demonstrated the importance of iron acquisition and protein degradation for iron depletion, but also characterized a novel transcriptional factor (SO1415) with a role in anaerobic energy metabolism.

View Article: PubMed Central - HTML - PubMed

Affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. yangy@ornl.gov

ABSTRACT

Background: Iron homeostasis of Shewanella oneidensis, a gamma-proteobacterium possessing high iron content, is regulated by a global transcription factor Fur. However, knowledge is incomplete about other biological pathways that respond to changes in iron concentration, as well as details of the responses. In this work, we integrate physiological, transcriptomics and genetic approaches to delineate the iron response of S. oneidensis.

Results: We show that the iron response in S. oneidensis is a rapid process. Temporal gene expression profiles were examined for iron depletion and repletion, and a gene co-expression network was reconstructed. Modules of iron acquisition systems, anaerobic energy metabolism and protein degradation were the most noteworthy in the gene network. Bioinformatics analyses suggested that genes in each of the modules might be regulated by DNA-binding proteins Fur, CRP and RpoH, respectively. Closer inspection of these modules revealed a transcriptional regulator (SO2426) involved in iron acquisition and ten transcriptional factors involved in anaerobic energy metabolism. Selected genes in the network were analyzed by genetic studies. Disruption of genes encoding a putative alcaligin biosynthesis protein (SO3032) and a gene previously implicated in protein degradation (SO2017) led to severe growth deficiency under iron depletion conditions. Disruption of a novel transcriptional factor (SO1415) caused deficiency in both anaerobic iron reduction and growth with thiosulfate or TMAO as an electronic acceptor, suggesting that SO1415 is required for specific branches of anaerobic energy metabolism pathways.

Conclusion: Using a reconstructed gene network, we identified major biological pathways that were differentially expressed during iron depletion and repletion. Genetic studies not only demonstrated the importance of iron acquisition and protein degradation for iron depletion, but also characterized a novel transcriptional factor (SO1415) with a role in anaerobic energy metabolism.

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(A) Growth curves of S. oneidensis MR-1 in liquid LB medium with different concentrations of iron chelator (2,2'-dipyridyl). Triplicates of cells grown to mid-log phase were diluted 1:100 in fresh LB liquid medium, and cell density was measured every half hour for five consecutive days. The standard deviations are shown as error bars. (B) When MR-1 cultures were grown to mid-log phase (O.D.600 nm = 0.6), 160 μM 2,2'-dipyridyl was added to inhibit bacterial growth, which was subsequently reversed by repleting iron with 200 μM FeSO4. The arrows represents the time when 2,2'-dipyridyl or iron was added. Data are averages for triplicate cultures.
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Figure 1: (A) Growth curves of S. oneidensis MR-1 in liquid LB medium with different concentrations of iron chelator (2,2'-dipyridyl). Triplicates of cells grown to mid-log phase were diluted 1:100 in fresh LB liquid medium, and cell density was measured every half hour for five consecutive days. The standard deviations are shown as error bars. (B) When MR-1 cultures were grown to mid-log phase (O.D.600 nm = 0.6), 160 μM 2,2'-dipyridyl was added to inhibit bacterial growth, which was subsequently reversed by repleting iron with 200 μM FeSO4. The arrows represents the time when 2,2'-dipyridyl or iron was added. Data are averages for triplicate cultures.

Mentions: To examine the iron response of S. oneidensis, the wild-type strain MR-1 was grown in LB medium with different concentrations of the iron chelator 2,2'-dipyridyl used to deplete iron. LB medium, a rich source of iron (~17 μM) [26], was used to provide sufficient biomass for the following microarray experiments. Iron depletion imposed a challenge to cell proliferation and survival, resulting in an extended lag phase, slower growth rate at mid-log phase, and lower cell density at stationary phase (Fig. 1A). While 80 μM 2,2'-dipyridyl had a marginal effect on the growth rate of MR-1, the cells displayed clear growth inhibition with 160 μM and 240 μM 2,2'-dipyridyl. When 320 μM 2,2'-dipyridyl was used, cell growth was completely arrested throughout five days of observation.


Snapshot of iron response in Shewanella oneidensis by gene network reconstruction.

Yang Y, Harris DP, Luo F, Xiong W, Joachimiak M, Wu L, Dehal P, Jacobsen J, Yang Z, Palumbo AV, Arkin AP, Zhou J - BMC Genomics (2009)

(A) Growth curves of S. oneidensis MR-1 in liquid LB medium with different concentrations of iron chelator (2,2'-dipyridyl). Triplicates of cells grown to mid-log phase were diluted 1:100 in fresh LB liquid medium, and cell density was measured every half hour for five consecutive days. The standard deviations are shown as error bars. (B) When MR-1 cultures were grown to mid-log phase (O.D.600 nm = 0.6), 160 μM 2,2'-dipyridyl was added to inhibit bacterial growth, which was subsequently reversed by repleting iron with 200 μM FeSO4. The arrows represents the time when 2,2'-dipyridyl or iron was added. Data are averages for triplicate cultures.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2667191&req=5

Figure 1: (A) Growth curves of S. oneidensis MR-1 in liquid LB medium with different concentrations of iron chelator (2,2'-dipyridyl). Triplicates of cells grown to mid-log phase were diluted 1:100 in fresh LB liquid medium, and cell density was measured every half hour for five consecutive days. The standard deviations are shown as error bars. (B) When MR-1 cultures were grown to mid-log phase (O.D.600 nm = 0.6), 160 μM 2,2'-dipyridyl was added to inhibit bacterial growth, which was subsequently reversed by repleting iron with 200 μM FeSO4. The arrows represents the time when 2,2'-dipyridyl or iron was added. Data are averages for triplicate cultures.
Mentions: To examine the iron response of S. oneidensis, the wild-type strain MR-1 was grown in LB medium with different concentrations of the iron chelator 2,2'-dipyridyl used to deplete iron. LB medium, a rich source of iron (~17 μM) [26], was used to provide sufficient biomass for the following microarray experiments. Iron depletion imposed a challenge to cell proliferation and survival, resulting in an extended lag phase, slower growth rate at mid-log phase, and lower cell density at stationary phase (Fig. 1A). While 80 μM 2,2'-dipyridyl had a marginal effect on the growth rate of MR-1, the cells displayed clear growth inhibition with 160 μM and 240 μM 2,2'-dipyridyl. When 320 μM 2,2'-dipyridyl was used, cell growth was completely arrested throughout five days of observation.

Bottom Line: Disruption of a novel transcriptional factor (SO1415) caused deficiency in both anaerobic iron reduction and growth with thiosulfate or TMAO as an electronic acceptor, suggesting that SO1415 is required for specific branches of anaerobic energy metabolism pathways.Using a reconstructed gene network, we identified major biological pathways that were differentially expressed during iron depletion and repletion.Genetic studies not only demonstrated the importance of iron acquisition and protein degradation for iron depletion, but also characterized a novel transcriptional factor (SO1415) with a role in anaerobic energy metabolism.

View Article: PubMed Central - HTML - PubMed

Affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. yangy@ornl.gov

ABSTRACT

Background: Iron homeostasis of Shewanella oneidensis, a gamma-proteobacterium possessing high iron content, is regulated by a global transcription factor Fur. However, knowledge is incomplete about other biological pathways that respond to changes in iron concentration, as well as details of the responses. In this work, we integrate physiological, transcriptomics and genetic approaches to delineate the iron response of S. oneidensis.

Results: We show that the iron response in S. oneidensis is a rapid process. Temporal gene expression profiles were examined for iron depletion and repletion, and a gene co-expression network was reconstructed. Modules of iron acquisition systems, anaerobic energy metabolism and protein degradation were the most noteworthy in the gene network. Bioinformatics analyses suggested that genes in each of the modules might be regulated by DNA-binding proteins Fur, CRP and RpoH, respectively. Closer inspection of these modules revealed a transcriptional regulator (SO2426) involved in iron acquisition and ten transcriptional factors involved in anaerobic energy metabolism. Selected genes in the network were analyzed by genetic studies. Disruption of genes encoding a putative alcaligin biosynthesis protein (SO3032) and a gene previously implicated in protein degradation (SO2017) led to severe growth deficiency under iron depletion conditions. Disruption of a novel transcriptional factor (SO1415) caused deficiency in both anaerobic iron reduction and growth with thiosulfate or TMAO as an electronic acceptor, suggesting that SO1415 is required for specific branches of anaerobic energy metabolism pathways.

Conclusion: Using a reconstructed gene network, we identified major biological pathways that were differentially expressed during iron depletion and repletion. Genetic studies not only demonstrated the importance of iron acquisition and protein degradation for iron depletion, but also characterized a novel transcriptional factor (SO1415) with a role in anaerobic energy metabolism.

Show MeSH