Oxygen-limited Environment Research Articles

Comparative insights into mitochondrial adaptations to anoxia in brain.

Numerous diseases and pathologies impair the delivery of oxygen to brain, with rapid and deleterious consequences. For example, diseases related to systemic hypoxemia (e.g., chronic pulmonary disorders, cystic fibrosis), decreased oxygen carrying capacity of blood (e.g., anemia), or decreased transport (e.g., heart attack, stroke) can all reduce or entirely prevent the delivery of oxygen to brain cells, resulting in the initiation of programmed cell death pathways, necrosis, or excitotoxic cell death in brain (Pamenter, 2014). However, oxygen-limited environments are common on earth and many organisms naturally experience periods of intermittent or prolonged hypoxia or anoxia in their daily and/or annual life cycles (Bickler and Buck, 2007). This exposure exerts a strong selective pressure that has driven the evolution of a wide range of adaptations that are neuroprotective against low oxygen stress. The brains of such hypoxia-tolerant species therefore offer a working model of neuronal survival in the absence of oxygen and their study may inform the development of novel therapeutics to protect mammalian brain against diseases and pathologies related to hypoxia.

Structural and biochemical analyses of a Clostridium perfringens sortase D transpeptidase.

The assembly and anchorage of various pathogenic proteins on the surface of Gram-positive bacteria is mediated by the sortase family of enzymes. These cysteine transpeptidases catalyze a unique sorting signal motif located at the C-terminus of their target substrate and promote the covalent attachment of these proteins onto an amino nucleophile located on another protein or on the bacterial cell wall. Each of the six distinct classes of sortases displays a unique biological role, with sequential activation of multiple sortases often observed in many Gram-positive bacteria to decorate their peptidoglycans. Less is known about the members of the class D family of sortases (SrtD), but they have a suggested role in spore formation in an oxygen-limiting environment. Here, the crystal structure of the SrtD enzyme from Clostridium perfringens was determined at 1.99 Å resolution. Comparative analysis of the C. perfringens SrtD structure reveals the typical eight-stranded β-barrel fold observed in all other known sortases, along with the conserved catalytic triad consisting of cysteine, histidine and arginine residues. Biochemical approaches further reveal the specifics of the SrtD catalytic activity in vitro, with a significant preference for the LPQTGS sorting motif. Additionally, the catalytic activity of SrtD is most efficient at 316 K and can be further improved in the presence of magnesium cations. Since C. perfringens spores are heat-resistant and lead to foodborne illnesses, characterization of the spore-promoting sortase SrtD may lead to the development of new antimicrobial agents.

Links between Anr and Quorum Sensing in Pseudomonas aeruginosa Biofilms.

In Pseudomonas aeruginosa, the transcription factor Anr controls the cellular response to low oxygen or anoxia. Anr activity is high in oxygen-limited environments, including biofilms and populations associated with chronic infections, and Anr is necessary for persistence in a model of pulmonary infection. In this study, we characterized the Anr regulon in biofilm-grown cells at 1% oxygen in the laboratory strain PAO1 and in a quorum sensing (QS)-deficient clinical isolate, J215. As expected, transcripts related to denitrification, arginine fermentation, high-affinity cytochrome oxidases, and CupA fimbriae were lower in the Δanr derivatives. In addition, we observed that transcripts associated with quorum sensing regulation, iron acquisition and storage, type VI secretion, and the catabolism of aromatic compounds were also differentially expressed in the Δanr strains. Prior reports have shown that quorum sensing-defective mutants have higher levels of denitrification, and we found that multiple Anr-regulated processes, including denitrification, were strongly inversely proportional to quorum sensing in both transcriptional and protein-based assays. We also found that in LasR-defective strains but not their LasR-intact counterparts, Anr regulated the production of the 4-hydroxy-2-alkylquinolines, which play roles in quorum sensing and interspecies interactions. These data show that Anr was required for the expression of important metabolic pathways in low-oxygen biofilms, and they reveal an expanded and compensatory role for Anr in the regulation of virulence-related genes in quorum sensing mutants, such as those commonly isolated from infections. Pseudomonas aeruginosa causes acute ocular, soft tissue, and pulmonary infections, as well as chronic infections in the airways of cystic fibrosis patients. P. aeruginosa uses quorum sensing (QS) to regulate virulence, but mutations in the gene encoding the master regulator of QS, lasR, are frequently observed in clinical isolates. We demonstrated that the regulon attributed to Anr, an oxygen-sensitive transcription factor, was more highly expressed in lasR mutants. Furthermore, we show that Anr regulates the production of several different secreted factors in lasR mutants. These data demonstrate the importance of Anr in naturally occurring quorum sensing mutants in the context of chronic infections.

Ralstonia solanacearum uses inorganic nitrogen metabolism for virulence, ATP production, and detoxification in the oxygen-limited host xylem environment.

ABSTRACTGenomic data predict that, in addition to oxygen, the bacterial plant pathogen Ralstonia solanacearum can use nitrate (NO3−), nitrite (NO2−), nitric oxide (NO), and nitrous oxide (N2O) as terminal electron acceptors (TEAs). Genes encoding inorganic nitrogen reduction were highly expressed during tomato bacterial wilt disease, when the pathogen grows in xylem vessels. Direct measurements found that tomato xylem fluid was low in oxygen, especially in plants infected by R. solanacearum. Xylem fluid contained ~25 mM NO3−, corresponding to R. solanacearum’s optimal NO3− concentration for anaerobic growth in vitro. We tested the hypothesis that R. solanacearum uses inorganic nitrogen species to respire and grow during pathogenesis by making deletion mutants that each lacked a step in nitrate respiration (ΔnarG), denitrification (ΔaniA, ΔnorB, and ΔnosZ), or NO detoxification (ΔhmpX). The ΔnarG, ΔaniA, and ΔnorB mutants grew poorly on NO3− compared to the wild type, and they had reduced adenylate energy charge levels under anaerobiosis. While NarG-dependent NO3− respiration directly enhanced growth, AniA-dependent NO2− reduction did not. NO2− and NO inhibited growth in culture, and their removal depended on denitrification and NO detoxification. Thus, NO3− acts as a TEA, but the resulting NO2− and NO likely do not. None of the mutants grew as well as the wild type in planta, and strains lacking AniA (NO2− reductase) or HmpX (NO detoxification) had reduced virulence on tomato. Thus, R. solanacearum exploits host NO3− to respire, grow, and cause disease. Degradation of NO2− and NO is also important for successful infection and depends on denitrification and NO detoxification systems.

Stimulative mineralization of p-fluoronitrobenzene in biocathode microbial electrolysis cell with an oxygen-limited environment

p-Fluoronitrobenzene (p-FNB) is a toxic compound and tends to accumulate in the environment. p-FNB can be effectively removed and defluorinated in a single-chamber bioelectrochemical system (BES). To verify the suppositionally integrated reductive and oxidative metabolism mechanism in the BES, an oxygen-limited environment was used, with pure oxygen and nitrogen environments used as two controls. Under the oxygen-limited condition, the most excellent performance was achieved. The defluorination rate and mineralization efficiency were 0.0132h−1 and 72.99±5.68% after 96h, with 75.4% of fluorine in the form of the fluoride ion. This resulted from the unique environment that allowed conventionally integrated reductive and oxidative catabolism. Moreover, the oxidation–reduction potential (ORP) had a significant effect on microbial communities, which was also an important reason for performance diversity. These results provide a new method for complete p-FNB treatment and a control strategy by ORP regulation for optimal system performance.

Design and Testing of Biochar Stoves

Biochar is a solid material obtained from the carbonization of biomass. Biochar is used on agricultural lands as a soil amendment to improve the fertility of the soils. Currently the most common method of producing biochar is through biochar stoves. There are two basic stove operations in the production of biochar. The first type of stove produces biochar by direct combustion of biomass. Here biomass is burnt inside a chamber in an oxygen limited environment. The resulting residue is the bio-char. The second type involves burning the biomass in one chamber and housing the biomass to be charred in the annular portion of an outer chamber. Heat is transferred from the burning fuel on the inner chamber to the material to be charred in the outer chamber. While the process of biochar production in these stoves is known, the basic principles of the stove design are not readily available. The design methodology for both the types was developed from first principles. Prototypes of both types were constructed based on the design developed and tested. The paper lists the basic principles in the design of biochar stoves and the test results.

High fatty acid oxidation capacity and phosphorylation control despite elevated leak and reduced respiratory capacity in northern elephant seal muscle mitochondria.

Northern elephant seals (Mirounga angustirostris) are extreme, hypoxia-adapted endotherms that rely largely on aerobic metabolism during extended breath-hold dives in near-freezing water temperatures. While many aspects of their physiology have been characterized to account for these remarkable feats, the contribution of adaptations in the aerobic powerhouses of muscle cells, the mitochondria, are unknown. In the present study, the ontogeny and comparative physiology of elephant seal muscle mitochondrial respiratory function was investigated under a variety of substrate conditions and respiratory states. Intact mitochondrial networks were studied by high-resolution respirometry in saponin-permeabilized fiber bundles obtained from primary swimming muscles of pup, juvenile and adult seals, and compared with fibers from adult human vastus lateralis. Results indicate that seal muscle maintains a high capacity for fatty acid oxidation despite a progressive decrease in total respiratory capacity as animals mature from pups to adults. This is explained by a progressive increase in phosphorylation control and fatty acid utilization over pyruvate in adult seals compared with humans and seal pups. Interestingly, despite higher indices of oxidative phosphorylation efficiency, juvenile and adult seals also exhibit a ~50% greater capacity for respiratory 'leak' compared with humans and seal pups. The ontogeny of this phenotype suggests it is an adaptation of muscle to the prolonged breath-hold exercise and highly variable ambient temperatures experienced by mature elephant seals. These studies highlight the remarkable plasticity of mammalian mitochondria to meet the demands for both efficient ATP production and endothermy in a cold, oxygen-limited environment.

Comprehensive proteomic profiling of outer membrane vesicles from Campylobacter jejuni.

This work demonstrates the importance of understanding vesicular proteomes from a human pathogen Campylobacter jejuni. From the secreted outer membrane vesicles (OMVs) of C. jejuni NCTC11168, we found a variety of virulence factors and essential proteins for bacterial survival. Bioinformatics analysis of these proteins predicted functional enrichment and localization. The most highly enriched were redox enzymes, which are considered to be essential for survival in oxygen-limiting environments and are predicted to be on the twin-arginine translocation (Tat) pathway suggesting a role for this pathway in the biogenesis of OMVs. This study additionally implicates a biological role for N-linked glycoproteins in OMVs. These approaches allow for a better understanding of the physiology of this important human pathogen.

Highly efficient methane biocatalysis revealed in a methanotrophic bacterium

Methane is an essential component of the global carbon cycle and one of the most powerful greenhouse gases, yet it is also a promising alternative source of carbon for the biological production of value-added chemicals. Aerobic methane-consuming bacteria (methanotrophs) represent a potential biological platform for methane-based biocatalysis. Here we use a multi-pronged systems-level approach to reassess the metabolic functions for methane utilization in a promising bacterial biocatalyst. We demonstrate that methane assimilation is coupled with a highly efficient pyrophosphate-mediated glycolytic pathway, which under oxygen limitation participates in a novel form of fermentation-based methanotrophy. This surprising discovery suggests a novel mode of methane utilization in oxygen-limited environments, and opens new opportunities for a modular approach towards producing a variety of excreted chemical products using methane as a feedstock.

Fossil evidence for the escalation and origin of marine mutualisms

Mutualism is an interactive, mutually beneficial relationship between two or rarely more unrelated taxa. It is ubiquitous in most environments. In the marine environment it is most likely to occur in shallow marine, oligotrophic regions, the open marine photic zone and oxygen-limited environments. Whereas the eukaryote cell is of some antiquity, other mutualisms may have been acquired during the Phanerozoic. The fossil record provides inferential evidence for the minimum time of origin and occurrence of mutualisms. This suggests that a variety of mutualisms may have occurred during the Palaeozoic with most apparently being terminated by the Permian mass extinction. Tracing back the origin of extant mutualisms suggests that the majority of these began in the Mesozoic or Cenozoic and indicate an increase to the present day. Whether the increase in mutualisms is a product of increased biodiversity or whether mutualisms may have partly driven biodiversity is unclear.

Oxygen, pH, and mitochondrial oxidative phosphorylation

The oxygen dependence of mitochondrial oxidative phosphorylation was measured in suspensions of isolated rat liver mitochondria using recently developed methods for measuring oxygen and cytochrome c reduction. Cytochrome-c oxidase (energy conservation site 3) activity of the mitochondrial respiratory chain was measured using an artificial electron donor (N,N,N',N'-tetramethyl-p-phenylenediamine) and ascorbate to directly reduce the cytochrome c, bypassing sites 1 and 2. For mitochondrial suspensions with added ATP, metabolic conditions approximating those in intact cells and decreasing oxygen pressure both increased reduction of cytochrome c and decreased respiratory rate. The kinetic parameters [K(M) and maximal rate (V(M))] for oxygen were determined from the respiratory rates calculated for 100% reduction of cytochrome c. At 22°C, the K(M) for oxygen is near 3 Torr (5 μM), 12 Torr (22 μM), and 18 Torr (32 μM) at pH 6.9, 7.4, and 7.9, respectively, and V(M) corresponds to a turnover number for cytochrome c at 100% reduction of near 80/s and is independent of pH. Uncoupling oxidative phosphorylation increased the respiratory rate at saturating oxygen pressures by twofold and decreased the K(M) for oxygen to <2 Torr at all tested pH values. Mitochondrial oxidative phosphorylation is an important oxygen sensor for regulation of metabolism, nutrient delivery to tissues, and cardiopulmonary function. The decrease in K(M) for oxygen with acidification of the cellular environment impacts many tissue functions and may give transformed cells a significant survival advantage over normal cells at low-pH, oxygen-limited environment in growing tumors.

Do Globins in Microaerophilic Campylobacter jejuni Confer Nitrosative Stress Tolerance Under Oxygen Limitation?

The microaerophilic pathogen Campylobacter jejuni possesses inducible systems for resisting NO. Two globins--Cgb (a single-domain globin) and Ctb (a truncated globin)--are up-regulated in response to NO via the positively acting transcription factor NssR. Our aims were to determine whether these oxygen-binding globins also function in severely oxygen-limited environments, as in the host. At growth-limiting oxygen transfer rates, bacteria were more S-nitrosoglutathione (GSNO) sensitive, irrespective of the presence of Cgb, Ctb, or NssR. Pregrowth of cells with GSNO enhanced GSNO resistance, even in nssR and cgb mutants, but transcriptomic profiling of oxygen-limited, NO-exposed cells failed to reveal the NssR regulon. Nevertheless, globin expression in an Escherichia coli mutant lacking the NO-detoxifying flavohemoglobin Hmp showed that Cgb and Ctb consume NO aerobically or anoxically and offer some protection to respiratory inhibition by NO. The constitutively expressed nitrite reductase NrfA does not provide resistance under oxygen-limited conditions. We, therefore, hypothesize that, although Cgb and NrfA can detoxify NO, even anoxically, they are neither up-regulated nor functional under physiologically relevant oxygen-limited conditions and, second, responses to NO do not stem from trancriptional regulation.

Phenol degradation in bio-electrochemical cells

A bio-electrochemical cell (BEC) was constructed as a typical two-chamber microbial fuel cell (MFC), except that it was operated under external voltage instead of constant resistance as in an MFC. The anode chamber contained a pure culture of Cupriavidus basilensis grown in a medium containing phenol as the sole carbon source. Operating the BEC under an external voltage of 125 mV led to an increase in bacterial cell growth to 0.53 OD600 nm, while the control (open circuit potential) BEC reached only 0.24 OD. The total dry weight of the bacterial cells in the poised potential BEC was 48% higher than in the control BEC. The peak current generated in the poised potential BEC was 478 mA m−2. The level of residual phenol in the control potential BEC was between 47% and 78% higher than that in the poised potential BEC. The rate of phenol degradation as a function of 0.1 OD was about 0.36 mg phenol l−1 h−1. Cyclic voltammetry examination at the end of the experiment demonstrated an oxidation peak above −0.06 V. In conclusion, operating the BEC at 125 mV enabled growth of a pure culture of C. basilensis, current formation, and phenol degradation even in an oxygen-limited environment.

Significance of the Cgl1427 gene encoding cytidylate kinase in microaerobic growth of Corynebacterium glutamicum

The Cgl1427 gene was previously found to be relevant to the microaerobic growth of Corynebacterium glutamicum (Ikeda et al. Biosci Biotechnol Biochem 73:2806-2808, 2009). In the present work, Cgl1427 was identified as a cytidylate kinase gene (cmk) by homology analysis of its deduced amino acid sequence with that of other bacterial cytidylate kinases (CMP kinases) and on the basis of findings that deletion of Cgl1427 results in loss of CMP kinase activity. Deletion of the cmk gene significantly impaired the growth of C. glutamicum in oxygen-limiting static culture, and the impaired growth was restored by introducing a plasmid containing the cmk gene, suggesting that this gene plays an important role in the microaerobic growth of C. glutamicum. On the other hand, in the main culture with aerobic shaking, a prolonged lag phase was observed in the cmk disruptant, despite an unchanged growth rate, compared to the behavior of the wild-type strain. The prolongation was observed when using seed culture grown to later growth stages in which oxygen limitation occurred, but it was not observed when using seed culture grown to an earlier growth stage in which oxygen remained relatively plentiful. Since nucleotide biosynthesis in C. glutamicum requires oxygen, we hypothesized that the ability of the cmk disruptant to synthesize nucleotides was influenced by oxygen limitation in the later growth stages of the seed culture, which caused the prolongation of the lag phase in the following shaken culture. To verify this hypothesis, a plasmid containing genes encoding all components of a homologous ribonucleotide reductase, a key enzyme for nucleotide synthesis that requires oxygen for its reaction, was introduced into the cmk disruptant, which significantly ameliorated the lag phase prolongation. Furthermore, this experimental setup almost completely restored the growth of the cmk disruptant in the oxygen-limiting static culture. These results indicate that CMP kinase plays an important role in normal nucleotide biosynthesis under an oxygen-limiting environment.

Effect of shear rate and oxygen stresses on the survival of Lactococcus lactis during the atomization and drying stages of spray drying: A laboratory and pilot scale study

The effect of shear rate and oxygen injury during atomization and the combination of these factors on the survival of Lactococcus lactis subsp. cremoris in spray drying was studied using laboratory and pilot scale spray dryers. The atomization was carried out using a two-fluid nozzle in the laboratory study and a two-fluid nozzle or rotary atomizer in the pilot scale study. The extent of oxygen-induced death was determined using ascorbic acid in the feed and atomizing the feed with gaseous nitrogen. The lowest levels of bacterial death were observed at lowest characteristic shear rate and in the presence of nitrogen and ascorbic acid. Quantitative analysis showed that lower shear rate, creating an oxygen-limiting environment during atomization and drying, and using oxygen scavengers in the feed were successful in enhancing bacterial survival in spray drying. We also report for the first time that, at least for L. lactis, the extent of death during the atomization stage far outweighs death during the drying stage, and that the majority of bacterial death (up to 93%) occurs during the atomization stage. The death of bacteria was found to be less when using a rotary atomizer or when using a two-fluid nozzle atomizer at lower flow rate. This work shows that bacterial death during spray drying can be minimized by using oxygen scavengers such as ascorbic acid and/or an anaerobic atomizing medium (such as nitrogen), and by altering the spraying conditions.

In situ iron isotope analyses of pyrite and organic carbon isotope ratios in the Fortescue Group: Metabolic variations of a Late Archean ecosystem

The biogeochemical cycle of the Late Archean ocean is important for understanding the relationships between biological activity and oxygenation of the atmosphere and ocean. Based on the detailed geological survey of the Fortescue Group in the Redmont area in Pilbara Craton, Western Australia, we carefully selected 44 samples for iron isotope analyses, which consist of sandstones, stromatolitic carbonate rocks, alternating mudstone/sandstone rocks, mudstones and cherts. Our in situ analyses of δ56Fe values of 210 pyrite grains in these samples show a large variation from −4.2‰ to +3.0‰. We also analyzed 128 and 40 carbon isotope compositions of organic (δ13Corg: −51.8 to −10.3‰) and inorganic (δ13Ccarb: −6.1 to 0.6‰) carbons, respectively.Microscopic observations show obvious relationships between pyrite grain morphology and iron isotope ratio. Most pyrite grains with positive δ56Fe values show hexagonal, rectangular, and parallelogram shapes, which may replace former iron-oxide crystal systems: hematite, magnetite, and goethite, respectively. In contrast, more than half the pyrite grains with negative δ56Fe values show irregular forms. The correlation allows the possibility to solve the origin and the formation process of each grain of pyrite. The positive δ56Fe values suggest the partial oxidation of iron in an oxygen-limited environment. Some pyrites show very lower δ56Fe values below −2.2‰ suggesting a biological origin, probably due to microbial iron reduction.On the other hand, the pyrite is accompanied by isotopically very light organic carbon (δ13Corg: −51.8‰ to −40‰), which indicates aerobic or anaerobic methanotrophy. The coexistence of the low δ56Fe values and low δ13C values in the some rocks suggests anoxic oxidation of methane by iron-reduction (AOM/IR). The iron and carbon isotopes demonstrate the metabolic variations of microorganisms in a Late Archean shallow marine environment.

Ammonia transformations and abundance of ammonia oxidizers in a clay soil underlying a manure pond

Unlined manure ponds are constructed on clay soil worldwide to manage farm waste. Seepage of ammonia-rich liquor into underlying soil layers contributes to groundwater contamination by nitrate. To identify the possible processes that lead to the production of nitrate from ammonia in this oxygen-limited environment, we studied the diversity and abundance of ammonia-transforming microorganisms under an unlined manure pond. The numbers of ammonia-oxidizing bacteria and anammox bacteria were most abundant in the top of the soil profile and decreased significantly with depth (0.5 m), correlating with soil pore-water ammonia concentrations and soil ammonia concentrations, respectively. On the other hand, the numbers of ammonia-oxidizing archaea were relatively constant throughout the soil profile (10(7) amoA copies per g(soil)). Nitrite-oxidizing bacteria were detected mainly in the top 0.2 m. The results suggest that nitrate accumulation in the vadose zone under the manure pond could be the result of complete aerobic nitrification (ammonia oxidation to nitrate) and could exist as a byproduct of anammox activity. While the majority of the nitrogen was removed within the 0.5-m soil section, possibly by combined anammox and heterotrophic denitrification, a fraction of the produced nitrate leached into the groundwater.

Effect of external voltage on Pseudomonas putida F1 in a bio electrochemical cell using toluene as sole carbon and energy source

A bio electrochemical cell (BEC) was constructed as a typical two-chamber microbial fuel cell (MFC), except that it was operated under external voltage instead of constant resistance as in an MFC. The anode chamber contained a pure culture of Pseudomonas putida F1 grown in a minimal medium containing toluene as the sole carbon and energy source. Operating the BEC under external voltages of 75, 125, 175, 250 and 500 mV (versus an Ag/AgCl reference electrode) led to increased bacterial cell growth to an OD(600) of 0.62-0.75, while the control BEC, which was not connected to external voltage, reached an OD(600) of only 0.3. Examination of the current generated under external voltages of 75, 125, 175, 250 and 500 mV showed that the maximal currents were 11, 23, 28, 54 and 94 mA m(-2), respectively. Cyclic voltammetry experiments demonstrated an anodic peak at 270 mV, which may imply oxidation of a vital molecule. The average residual toluene concentration after 147 h in the BEC operated under external voltage was 22 %, whereas in the control BEC it was 81 %. Proteome analysis of bacterial cells grown in the BEC (125 mV) revealed two groups of proteins, which are ascribed to charge transfer in the bacterial cells and from the cell to the electrode. In conclusion, operating the BEC at 75-500 mV enabled growth of a pure culture of P. putida F1 and toluene degradation even in an oxygen-limited environment.

Metabolomics-on-a-chip and metabolic flux analysis for label-free modeling of the internal metabolism of HepG2/C3A cells

In vitro microfluidic systems are increasingly used as an alternative to standard Petri dishes in bioengineering and metabolomic investigations, as they are expected to provide cellular environments close to the in vivo conditions. In this work, we combined the recently developed "metabolomics-on-a-chip" approach with metabolic flux analysis to model the metabolic network of the hepatoma HepG2/C3A cell line and to infer the distribution of intracellular metabolic fluxes in standard Petri dishes and microfluidic biochips. A high pyruvate reduction to lactate was observed in both systems, suggesting that the cells operate in oxygen-limited environments. Our results also indicate that HepG2/C3A cells in the biochip are characterized by a higher consumption rate of oxygen, presumably due to a higher oxygenation rate in the microfluidic environment. This leads to a higher entry of the ultimate glycolytic product, acetyl-CoA, into the Krebs cycle. These findings are supported by the transcriptional activity of HepG2/C3A cells in both systems since we observed that genes regulated by a HIF-1 (hypoxia-regulated factor-1) transcriptional factor were over expressed under the Petri conditions, but to a lesser extent in the biochip.

Genomic Expression Analysis Reveals Strategies of Burkholderia cenocepacia to Adapt to Cystic Fibrosis Patients' Airways and Antimicrobial Therapy

Pulmonary colonization of cystic fibrosis (CF) patients with Burkholderia cenocepacia or other bacteria of the Burkholderia cepacia complex (Bcc) is associated with worse prognosis and increased risk of death. During colonization, the bacteria may evolve under the stressing selection pressures exerted in the CF lung, in particular, those resulting from challenges of the host immune defenses, antimicrobial therapy, nutrient availability and oxygen limitation. Understanding the adaptive mechanisms that promote successful colonization and long-term survival of B. cenocepacia in the CF lung is essential for an improved therapeutic outcome of chronic infections. To get mechanistic insights into these adaptive strategies a transcriptomic analysis, based on DNA microarrays, was explored in this study. The genomic expression levels in two clonal variants isolated during long-term colonization of a CF patient who died from the cepacia syndrome were compared. One of the isolates examined, IST439, is the first B. cenocepacia isolate retrieved from the patient and the other isolate, IST4113, was obtained three years later and is more resistant to different classes of antimicrobials. Approximately 1000 genes were found to be differently expressed in the two clonal variants reflecting a marked reprogramming of genomic expression. The up-regulated genes in IST4113 include those involved in translation, iron uptake (in particular, in ornibactin biosynthesis), efflux of drugs and in adhesion to epithelial lung tissue and to mucin. Alterations related with adaptation to the nutritional environment of the CF lung and to an oxygen-limited environment are also suggested to be a key feature of transcriptional reprogramming occurring during long-term colonization, antibiotic therapy and the progression of the disease.