Open Access

Transcriptional analysis of the effect of exogenous decanoic acid stress on Streptomyces roseosporus

Contributed equally
Microbial Cell Factories201312:19

https://doi.org/10.1186/1475-2859-12-19

Received: 26 December 2012

Accepted: 19 February 2013

Published: 21 February 2013

Abstract

Backgroud

Daptomycin is an important antibiotic against infections caused by drug-resistant pathogens. Its production critically depends on the addition of decanoic acid during fermentation. Unfortunately, decanoic acid (>2.5 mM) is toxic to daptomycin producer, Streptomyces roseosporus.

Results

To understand the mechanism underlying decanoic tolerance or toxicity, the responses of S. roseosporus was determined by a combination of phospholipid fatty acid analysis, reactive oxygen species (ROS) measurement and RNA sequencing. Assays using fluorescent dyes indicated a sharp increase in reactive oxygen species during decanoic acid stress; fatty acid analysis revealed a marked increase in the composition of branched-chain fatty acids by approximately 10%, with a corresponding decrease in straight-chain fatty acids; functional analysis indicated decanoic acid stress has components common to other stress response, including perturbation of respiratory functions (nuo and cyd operons), oxidative stress, and heat shock. Interestingly, our transcriptomic analysis revealed that genes coding for components of proteasome and related to treholase synthesis were up-regulated in the decanoic acid –treated cells.

Conclusion

These findings represent an important first step in understanding mechanism of decanoic acid toxicity and provide a basis for engineering microbial tolerance.

Keywords

Daptomycin Decanoic acid Toxic Tolerance Streptomyces roseosporus

Background

Daptomycin, produced by Stretomyces roseosporus, is a 10-membered cyclic lipopeptide showing excellent activity against Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (MRSA) or vancomycin-resistant Enterococci (VRE) [1]. Intensive efforts to improve daptomycin yield are carried out, including strain improvement as well as optimization of process conditions and growth media [24]. Daptomycin is the minor component of A21978C factors isolated from cultures of S. rosoesporus[5]. The mixture has a common cyclic peptide nucleus with different fatty acid moieties attached to N-terminal Trp (Figure 1). The addition of decanoic acid (DA) to the culture broth was shown to be essential for increasing daptomycin yield and productivity [6]. However, DA is highly toxic to S. rosoesporus and its feeding rate must be kept under strict control in large-scale industrial production [6]. As metabolic engineering efforts continue to increase daptomycin production titers, concomitant with addition of more DA during fermentation, it will be crucial to develop strategies for increasing DA tolerance.
Figure 1

The chemical structure of daptomycin and other A21978C factors.

The mechanism of toxicity of free fatty acids (FFA) varies with the length, branching and saturation status of the carbon backbone [7]. The degree of toxicity of a fatty acid also varies across bacteria, with some bacteria being more affected by the length of the carbon backbone while others are more affected by saturation. Their antibacterial mode of action is poorly understood, but most toxicity studies have proposed the cell membrane as the most affected target of fatty acids. In yeast, it has been proposed that DA inserts itself into the lipid bilayer of membrane and physically disturbs the membrane, resulting in increased fluidity of the membrane, leading to conformational changes in membrane proteins, the release of intracellular components [8]. It has been observed that increase of membrane fluidity induced by free fatty acid is accompanied by an increase of ROS production [9]. It can also be hypothesized that the same mechanism may be true for DA.

To elucidate the cytotoxicity mechanism of DA, we combine phospholipid fatty acid analysis, ROS measurement and RNA sequencing technologies to characterize the physiological response to DA and found that resistance to DA likely involves a functional shift of cell membrane composition, increase the gene expression involved in oxidative stress response and oxidative phospholytion. Our findings represent an important advance to understand the mechanism of DA and also provide a list of potential gene targets for further engineering DA tolerance in S. roseosporus.

Results and discussion

The effect of decanoic acid on the growth of S. roseosporus

DA was routinely added into the cell culture during the late exponential stage to direct the biosynthesis of daptomycin. In this study, cells were subsequently grown in the presence of a wide range of DA with the FFA added at the late exponential growth phase. Growth of SR was not influenced by 0.5 mM DA. However there was a sharp boundary between sub-inhibitory and growth inhibitory concentrations of DA. A concentration of 1 M caused an approximate 48-52 h lag, followed by normal exponential growth, but a concentration of 2.5 mM halted the growth (Figure 2). The concentration of DA found to be inhibitory to S. roseosporus in this study is consistent with that to S. coelicolor (2.5 mM).
Figure 2

Cell growth profiles with the addition of 1 mM of decanoic acid at 48 h. Error bars represent the standard deviation of three biological replicates.

The concentration of DA that caused stress but not significant cell death was found to be 1 mM and was used in the other growth assay and gene expression analysis.

Effect of decanoic acid on S. roseosporus phospholipid fatty acid composition

Change in fatty acid profile is associated with FFA adaptation in bacteria [10]. To investigate whether cell membrane reorganization is involved in the DA tolerance, we compare the phospholipid fatty acid profile of S. roseosporus cells during late exponential phase growth in either TSB (control), or 1 mM DA. The anteisopentadecanoic (anteiso C15), isopalmitic (iso C16), palmitic (C16), and pentedecanoic (C16:1) fatty acids made up the majority of total phospholipid composition (Figure 3). During DA stress, the branched-chain Fatty acids (BCFA) dramatically increased, with a corresponding decrease in straight-chain fatty acids (SCFA). Especially, a significant decrease in palmitoleic acid (C16:1) content from approximately 10% to 5% was detectable, implying diminished membrane fluidity. Studies in Listeria monocytogenes have demonstrated that the increase of the ratio of BCFA/SCFA plays a significant role in tolerance to acid, temperature, and other stresses by reducing membrane fluidity and decreasing permeability [11]. Similarly, the switch to a fatty acid profile dominated by BCFA suggested a response mechanism leading to a more rigid membrane to mitigate the toxicity of DA.
Figure 3

Phospho-lipid fatty acid profiles of S. roseosporus after two hours of decanoic acid-stress. Control and stressed cell cultures were grown in triplicate. Stressed samples were exposed to1 mM decanoic acid for two hours before being harvested. Cell cultures (50 ml each) were harvested, centrifuged, washed in PBS.

Effect of decanoic on the generation of ROS in S. roseosporus

It has been observed that increase of membrane fluidity induced by FFA is accompanied by an increase of ROS production. To investigate whether ROS involved in the toxicity of DA, we compared the intracellular ROS levels of control and DA-exposed cultures. Cells were labeled with 5(and 6)-carboxy-2’,7’-dichlorodihydro-fluorescein diacetate (carboxy-H2DCFDA), a known fluorogenic marker for ROS in vivo. Cells exposed to DA showed dramatically high level of fluorescence (Figure 4). Interestingly, cells exposed to different level of DA showed almost the same level of fluorescence, implying that 1 mM DA is enough to induce the ROS generation. These results suggested that exposure to DA may cause massive oxidative stress to S. roseosporus.
Figure 4

Measurement of intracellular reactive oxygen species using carboxy-H 2 DCFDA. Stressed samples(1, 2) were exposed to 1 mM decanoic acid for 30 min. control cells treated with tertbutyl hydroperoxide (TBHP), known to produce intracellular H2O2 and serve as a positive control (PC); Cells without treatment serve as a negative control (NC). Measurements were carried out in triplicate.

Effect of decanoic acid on S. roseosporus transcriptome

To elucidate molecular mechanisms underlying tolerance, global gene expression changes during SR growth with DA were analyzed using Illumina RNA deep sequencing (RNA-seq) technology. Tanscriptome libraries were constructed using SR cells grown in the absence (control) or the presence of DA (1 mM).

RNA-seq data revealed a small subset of genes with differential transcription; 134 genes were up-regulated and 12 genes were down-regulated. The presence of DA at 1 mM resulted in transcriptional reprogramming of genes in three major discernible categories, including: energy production and conversion, posttranslational modification and protein turnover, and carbohydrate metabolism (Additional file 1).

Changes in energy metabolism

Exposure to DA resulted in the up-regulation of genes encoding enzymes proteins (enzymes) involved in energy production and conversion (Table 1). nuo operon and cyd operon were among the most significantly increased transcripts during DA stress. The nuo operon encodes the NADH ubiquinone oxidoreductase (complex I), which form core components of the electron transport chain [12]. The increase in the transcript levels of 12 member of nuo operon in response to DA stress suggested that an increased requirement for energy or an impairment in the respiratory efficiency. Increases in the transcripts in the cyd operon, which encodes a terminal oxidase and gene (SSGG_06557) encoded the succinate dehydrogenase, both involved in oxidative phosphorylation, also suggested a perturbation in respiratory balance. The up-regulated expression of nuo and cyo is consistent with the recent discovery that nuo and cyo played major roles in combating against oxidative stress in E. coli exposure to exogenous n-butanol and endogenous fatty acid production [10, 13].
Table 1

Selected genes involved in energy production and conversion with significant change in expression in DA-stress relative to control

Locus

Gene description

Log2stress/control

SSGG_04165

NuoA

2.55

SSGG_04166

NuoB

2.91

SSGG_04167

NuoC

3.36

SSGG_04168

NuoD

4.09

SSGG_04169

NuoE

5.37

SSGG_04170

NuoF

3.37

SSGG_04171

NuoG

3.07

SSGG_04172

NuoH

4.33

SSGG_04173

NuoI

2.60

SSGG_04174

NuoJ

3.20

SSGG_04176

NuoL

2.61

SSGG_04178

NuoN

2.91

SSGG_03413

CydA

1.20

SSGG_03414

CydB

1.19

SSGG_04984

F0F1 ATP synthase subunit alpha

1.168

SSGG_04986

H(+)-transporting ATP synthase

1.09

SSGG_06555

cytochrome b subunit

1.67

SSGG_06557

succinate dehydrogenase iron-sulfur subunit

1.37

In addition, the increase in the transcripts in genes encoding the member of the ATP synthase complex (SSGG_04986 and SSGG_04898) was observed. ATP synthase is responsible for generation of ATP through oxidative phosphorylation . It uses energy stored in the pH and potential gradients, created by pumping of protons across the membrance by enzymes of the respiratory chian, to synthesize ATP. Similar results were observed in yeast, where exposure of cells to octanoic acid (C8) led to the activation of plasma membrane H + −ATPase [14]. These results suggested that an increased requirement for energy was required to deal with the DA stress.

Induction of oxidative stress response

Consistent with results of ROS analysis, the transcriptomic response of S. roseosporus to DA showed a massive induction of genes with a role in adaptation to oxidative stress. This response included activation of clpB (proteases), sodF and several heat shock proteins (Table 2).
Table 2

Selected genes involved in oxidative stress response with significant change in expression in DA-stress relative to control

Locus

Gene description

Log2stress/control

SSGG_00741

PafA

1.06

SSGG_00747

Pup

1.68

SSGG_00748

PafA2

1.52

SSGG_00750

Mpa

1.67

SSGG_01786

ClpB

1.59

SSGG_01803

SodF

1.18

SSGG_00191

CepB

2.58

SSGG_01307

phage shock protein A

1.45

SSGG_04333

Hsp 18

1.65

SSGG_04334

hsp60-like protein

1.81

SSGG_03360

bifunctional thioredoxin reductase/thioredoxin

1.59

SSGG_03361

thioredoxin reductase

2.02

SSGG_03856

hsp60-like protein

1.25

In addition, expression levels of genes coding for components of proteasome (pafA, pup, pfafA2, mpa) were enhanced. Bacterial proteasomes could only be found in actinomycetes [15]. Mpa assembles into a hexameric ATPase and Pup, a prokaryotic ubiquitin-like protein, is ligated by PafA to substrate proteins. Subsequently, proteins tagged with Pup were targeted for degradation by the proteasome [16]. Recently, it was shown that proteasome is important for defense against reactive nitrogen intermediates (RNI) in Mycobacterium tuberculosis[17]. Increased expression of proteasome and clpB may degrade the misfolded proteins impaired by ROS.

In streptomyces, the expression of genes coding for proteins involved in antioxidative defense systems was under the control of several key regulators, such as OxyR [18]. However, the homologue of OxyR, master regulator of oxidative response, was absent in S. roseosporus. FurS (SSGG_00190) is a zinc-containing redox regulator of S. reticuli which binds to an operator upstream of the furS-cepB[19]. Under oxidative stress conditions, an internal S-S bridge formed FurS abrogated its capability to block the transcription of furS-cpeB[20]. SSGG_00191 shared 80% amino acid identity to cpeB of S. reticuli and was induced during DA stress. Further studies are required to determine the roles of FurS in oxidative response.

Changes in carbohydrate transport and metabolism

Transcriptomic analysis suggested a metabolic adaptation dedicated to increase the production of trehalose (Table 3). Expression of genes coding for the putative maltose ABC transporter (SSGG_01377), and Tres (SSGG_05057) which catalyzes the conversion of maltose into Trehalose was elevated. In addition, gene expression of alpha-amylase (SSGG_05058) was induced, which degrade starch to provide the maltose for synthesis of trehalose. The accumulation of this nonreducing sugar has been previously viewed as an important osmoprotectant and stress protectant [21]. It was recently reported that trehalose played an important protective role in the cellular response to oxidative stress caused by hydrogen peroxide in Candida albicans[22]. Similarly, S. roseospous could counteract the DA stress by increasing trehalose production.
Table 3

Selected genes related to carbohydrate metabolism and transport with significant change in expression in DA-stress relative to control

Locus

Gene description

Log2stress/control

SSGG_01377

putative maltose ABC transporter permease

2.46

SSGG_05057

trehalose synthase

3.09

SSGG_05058

alpha-amylase

2.12

SSGG_03685

fructose-bisphosphate aldolase

1.37

SSGG_06343

phosphopyruvate hydratase

1.63

SSGG_01114

pyruvate kinase

1.30

SSGG_02477

phosphopyruvate hydratase

1.53

Genes encoding proteins involved in the TCA cycle were nearly unchanged. Interestingly, expression of genes involved in pyruvate production was up-regulated. Genes coding for fructose-bisphosphate aldolase (SSGG_03685), glyceraldehyde-3-phosphate dehydrogenase (SSGG_06343), phosphopyruvate hydratase (SSGG_02477) and pyruvate kinase (SSGG_01114) were upregulated after exposure to DA stress. Pyruvate is a key intermediate involved in a number of metabolic pathways. It was recently reported that pyruvate is involved into octanoic acid (C8) stress of E. coli[23]. Addition of pyruvate into media helps the cell partially recover from stress, but the exact mechanism was unclear. Similarly, enhanced production of pyruvate may help S. roseosporus to recover from DA stress.

Preliminary model for the mechanism of DA toxicity and cell response

Based on several lines of evidence, we propose a preliminary model for DA toxicity and cell’s response (Figure 5). DA incorporation into the cell membrane causes the disruption of membrane fluidity. The membrane disruption results in destabililization of membrane-bound proteins, such as NADH dehydrogenase, H-ATPase. Furthermore, DA may directly interact with and partially inhibit of components of electron transport chain, resulting in facilitating electron leakage and generation of ROS. The malfunction of those enzymes will cause inhibition of electron transport chain and lead to less ATP production. To counteract the impaired effect, S. roseosporus utilizes multiple ways to protect the cells. Cells increase the ratio of BCFA/SCFA to reduce membrane fluidity and decrease permeability; to protect against the damage caused by oxidative stress, cells activate a number of antioxidant enzymes and repair activities, such as Superoxide dismutase, catalase, and heat shock proteins; furthermore, cells produce high level of trehalose and pyruvate to alleviate the toxicity of ROS. In addition, cells increase the expression of genes encoding proteins involved in oxidative phosphoralation to supply proteins to replace the impaired proteins.
Figure 5

Illustration about hypothesis about DA toxicity mechanism and the dynamic response of S. roseosporus . DA inserted into the cell membrane disrupted the membrane integrity and induced the generation of ROS by unknown mechanisms. Cells activated expression of a number of genes coding for antioxidative systems to degrade ROS (Superoxide dismutase and catalase), to repair or degrade the disfolded proteins (heat shock proteins, Clp and proteasome). In addition, the yield of stress protectants, such as trehalose may increase to help the cell to mitigate the toxicity of DA.

Conclusions

Multiple mechanisms are involved in the mitigation of the toxicity of DA. The relative contribution of particular mechanism to the toxicity of fatty acid remains elusive. Taken together, our study provided insights into the toxicity or tolerance mechanism underlying DA exposure and several candidates that may be targeted for further engineering to mitigate the toxicity of DA.

Methods

Culture conditions

For toxicity assays, Streptomyces roseosporus (NRRL11579) was grown in TSB medium. To determine the effect of DA on S. roseosporus growth, wide range of concentrations was tested first (data not shown) and then narrowed to a range that caused stress but not significant cell death. Growth assays to test the effect of different concentrations of DA on S. roseosporus were performed in 250 ml shake flasks with 25 ml of TSB medium with a 2% inoculation culturing at 200 rpm at 28°C. Unless specified otherwise, all subsequent DA assays were conducted at 1 mM DA.

Phospholipid fatty acid analysis

Cells were harvested in control culture and DA-stressed S. rosoeporus cultures (2 h after exposure to 1 mM DA) of growth by centrifugation at 3000 × g and 4 for 15 min, and the pellet was washed three times with distilled water. The fatty acids in the cells (40–50 mg in wet weight) were saponified and methylated. The methyl ester mixtures were separated using an Agilent 5890 dual tower gas chromatograph. Fatty acids were identified by the MIDI microbial identification system (Sherlock 4.5 microbial identification system) [24]. Minor fatty acids (<0.6% of the total) are not reported.

Reactive oxygen species assay

Control and DA-stressed S. rosoeporus cultures were grown in TSB medium as described with various concentrations of DA. Positive controls for oxidative stressed cells were prepared by adding 10 ul of 7.78 M tert-butyl hydroperoxide (TBHP) (Invitrogen, USA) to one set of control cells before incubation. Ten microliters of 25 mM carboxy-H2DCFDA was added to all cells. Florescence at 535 nm was measured after 30 min.

RNA extraction

S. roseosprous was cultured in TSB to exponential phase (48 h). DA was added to a final concentration of 1 mM, and biomass was collected after treatment of 30 min. the cultures were centrifuged at 3000 × g and 4 for 15 min, and cell pellets were immediately frozen in liquid nitrogen and stored at −80 for subsequent RNA isolation. Total RNA was extracted using Trizol (Invitrogen), following manufacturer’s protocols. RNA preparations were treated with RNase-free DNase (Promega) and the integrity of the RNA was determined using Bioanalyzer 2100 (Agilent Technologies). mRNA was enriched by removing the rRNAs using MICROBExpress kit. The mRNA remaining in the supernatant was recovered by ethanol precipitation and quantified by Bioanalyzer 2100. A cDNA library was constructed and sequenced by Illumina Hiseq™ 2000 [25].

Data processing and analysis

Raw sequencing reads were mapped against the S. roseosprous genome. Reads that mapped to more than one region of the genome (5 to 8% of the total) failed to be unambiguously mapped were excluded for subsequent analyses. Analyses of differential expression including FDR calculations were performed using DESeq [26, 27]. Only P values of <0.01, FDR ≤ 0.01 were considered to be significant.

Notes

Declarations

Acknowledgements

This work was supported by grants from National Natural Science Foundation of China (Grant No. 31100069), the Natural Science Foundation Project of CQ CSTC (cstc2012jjA10149) and the Fundamental Research Funds for the Central Universities (XDJK2013A010), New Century Excellent Talents in Universities (NCET-11-0703).

Authors’ Affiliations

(1)
Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, School of life sciences, School of Pharmaceutical Sciences Southwest University,

References

  1. Baltz RH: Daptomycin: mechanisms of action and resistance, and biosynthetic engineering. Curr Opin Chem Biol. 2009, 13: 144-151. 10.1016/j.cbpa.2009.02.031.View ArticleGoogle Scholar
  2. Wang L, Zhao Y, Liu Q, Huang Y, Hu C, Liao G: Improvement of A21978C production in Streptomyces roseosporus by reporter-guided rpsL mutation selection. J Appl Microbiol. 2012, 112: 1095-1101. 10.1111/j.1365-2672.2012.05302.x.View ArticleGoogle Scholar
  3. Yu G, Jia X, Wen J, Lu W, Wang G, Caiyin Q, Chen Y: Strain improvement of Streptomyces roseosporus for daptomycin production by rational screening of He-Ne laser and NTG induced mutants and kinetic modeling. Appl Biochem Biotechnol. 2011, 163: 729-743. 10.1007/s12010-010-9078-x.View ArticleGoogle Scholar
  4. Lu W, Fan J, Wen J, Xia Z, Caiyin Q: Kinetic analysis and modeling of daptomycin batch fermentation by Streptomyces roseosporus. Appl Biochem Biotechnol. 2011, 163: 453-462. 10.1007/s12010-010-9053-6.View ArticleGoogle Scholar
  5. Debono M, Abbott BJ, Molloy RM, Fukuda DS, Hunt AH, Daupert VM, Counter FT, Ott JL, Carrell CB, Howard LC: Enzymatic and chemical modifications of lipopeptide antibiotic A21978C: the synthesis and evaluation of daptomycin (LY146032). J Antibiot (Tokyo). 1988, 41: 1093-1105. 10.7164/antibiotics.41.1093.View ArticleGoogle Scholar
  6. Huber FM, Pieper RL, Tietz AJ: The formation of daptomycin by supplying decanoic acid to Streptomyces roseosporus cultures producing the antibiotic complex A21978C. J Biotechnol. 1988, 7: 283-292. 10.1016/0168-1656(88)90040-5.View ArticleGoogle Scholar
  7. Desbois AP, Smith VJ: Antibacterial free fatty acids: activities, mechanisms of action and biotechnological potential. Appl Microbiol Biotechnol. 2010, 85: 1629-1642. 10.1007/s00253-009-2355-3.View ArticleGoogle Scholar
  8. Alexandre H, Mathieu B, Charpentier C: Alteration in membrane fluidity and lipid composition, and modulation of H(+)-ATPase activity in Saccharomyces cerevisiae caused by decanoic acid. Microbiology. 1996, 142 (Pt 3): 469-475.View ArticleGoogle Scholar
  9. Heiskanen KM, Savolainen KM: Erucic acid and erucic acid anilide-induced oxidative burst in human polymorphonuclear leukocytes. Free Radic Res. 1997, 27: 477-485. 10.3109/10715769709065787.View ArticleGoogle Scholar
  10. Lennen RM, Kruziki MA, Kumar K, Zinkel RA, Burnum KE, Lipton MS, Hoover SW, Ranatunga DR, Wittkopp TM, Marner WD, Pfleger BF: Membrane stresses induced by overproduction of free fatty acids in Escherichia coli. Appl Environ Microbiol. 2011, 77: 8114-8128. 10.1128/AEM.05421-11.View ArticleGoogle Scholar
  11. Giotis ES, McDowell DA, Blair IS, Wilkinson BJ: Role of branched-chain fatty acids in pH stress tolerance in Listeria monocytogenes. Appl Environ Microbiol. 2007, 73: 997-1001. 10.1128/AEM.00865-06.View ArticleGoogle Scholar
  12. Ingledew WJ, Poole RK: The respiratory chains of Escherichia coli. Microbiol Rev. 1984, 48: 222-271.Google Scholar
  13. Rutherford BJ, Dahl RH, Price RE, Szmidt HL, Benke PI, Mukhopadhyay A, Keasling JD: Functional genomic study of exogenous n-butanol stress in Escherichia coli. Appl Environ Microbiol. 2010, 76: 1935-1945. 10.1128/AEM.02323-09.View ArticleGoogle Scholar
  14. Viegas CA, Almeida PF, Cavaco M, Sa-Correia I: The H(+)-ATPase in the plasma membrane of Saccharomyces cerevisiae is activated during growth latency in octanoic acid-supplemented medium accompanying the decrease in intracellular pH and cell viability. Appl Environ Microbiol. 1998, 64: 779-783.Google Scholar
  15. De Mot R, Nagy I, Walz J, Baumeister W: Proteasomes and other self-compartmentalizing proteases in prokaryotes. Trends Microbiol. 1999, 7: 88-92. 10.1016/S0966-842X(98)01432-2.View ArticleGoogle Scholar
  16. Darwin KH: Prokaryotic ubiquitin-like protein (Pup), proteasomes and pathogenesis. Nat Rev Microbiol. 2009, 7: 485-491. 10.1038/nrmicro2148.View ArticleGoogle Scholar
  17. Darwin KH, Ehrt S, Gutierrez-Ramos JC, Weich N, Nathan CF: The proteasome of Mycobacterium tuberculosis is required for resistance to nitric oxide. Science. 2003, 302: 1963-1966. 10.1126/science.1091176.View ArticleGoogle Scholar
  18. Hahn JS, Oh SY, Roe JH: Role of OxyR as a peroxide-sensing positive regulator in Streptomyces coelicolor A3(2). J Bacteriol. 2002, 184: 5214-5222. 10.1128/JB.184.19.5214-5222.2002.View ArticleGoogle Scholar
  19. Ortiz De Orue Lucana D, Schrempf H: The DNA-binding characteristics of the Streptomyces reticuli regulator FurS depend on the redox state of its cysteine residues. Mol Gen Genet. 2000, 264: 341-353. 10.1007/s004380000328.View ArticleGoogle Scholar
  20. Ortiz De Orue Lucana D, Troller M, Schrempf H: Amino acid residues involved in reversible thiol formation and zinc ion binding in the Streptomyces reticuli redox regulator FurS. Mol Genet Genomics. 2003, 268: 618-627.Google Scholar
  21. Benaroudj N, Lee DH, Goldberg AL: Trehalose accumulation during cellular stress protects cells and cellular proteins from damage by oxygen radicals. J Biol Chem. 2001, 276: 24261-24267. 10.1074/jbc.M101487200.View ArticleGoogle Scholar
  22. Cao Y, Wang Y, Dai B, Wang B, Zhang H, Zhu Z, Xu Y, Jiang Y, Zhang G: Trehalose is an important mediator of Cap1p oxidative stress response in Candida albicans. Biol Pharm Bull. 2008, 31: 421-425. 10.1248/bpb.31.421.View ArticleGoogle Scholar
  23. Fu Y: Metabolic flux analysis of Escherichia coli MG1655 under octanoic acid (C8) stress. 2011, Iowa State University: Department of Chemical and Biological EngineeringGoogle Scholar
  24. Li Y, Florova G, Reynolds KA: Alteration of the fatty acid profile of Streptomyces coelicolor by replacement of the initiation enzyme 3-ketoacyl acyl carrier protein synthase III (FabH). J Bacteriol. 2005, 187: 3795-3799. 10.1128/JB.187.11.3795-3799.2005.View ArticleGoogle Scholar
  25. Mandlik A, Livny J, Robins WP, Ritchie JM, Mekalanos JJ, Waldor MK: RNA-Seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression. Cell Host Microbe. 2011, 10: 165-174. 10.1016/j.chom.2011.07.007.View ArticleGoogle Scholar
  26. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5: R80- 10.1186/gb-2004-5-10-r80.View ArticleGoogle Scholar
  27. Khudyakov JI, D'Haeseleer P, Borglin SE, Deangelis KM, Woo H, Lindquist EA, Hazen TC, Simmons BA, Thelen MP: Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus. Proc Natl Acad Sci USA. 2012, 109: E2173-2182. 10.1073/pnas.1112750109.View ArticleGoogle Scholar

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© Liao et al.; licensee BioMed Central Ltd. 2013

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.

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