scholarly journals Pseudomonas aeruginosa transcriptome adaptations from colonization to biofilm infection of skin wounds

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Peter D’Arpa ◽  
S. L. Rajasekhar Karna ◽  
Tsute Chen ◽  
Kai P. Leung
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Carbon Source ◽  
Wound Infection ◽  
Glyoxylate Cycle ◽  
Acute Infection ◽  
Carbon Sources ◽  
Myeloid Cell ◽  
Carbon Utilization ◽  
Branched Chain ◽  
Biofilm Infection

AbstractIn burn patients Pseudomonas aeruginosa infection is a major cause of morbidity. Analysis of the pathogen’s gene expression as it transitions from colonization to acute and then biofilm wound infection may provide strategies for infection control. Toward this goal, we seeded log-phase P. aeruginosa (PAO1) into 3-day-old, full-thickness excision wounds (rabbit ear) and harvested the bacteria during colonization (Hrs 2 and 6), acute infection (Hr 24), and biofilm infection (Days 5 and 9) for transcriptome analysis (RNA-Seq). After 2–6 h in the wound, genes for metabolism and cell replication were down-regulated while wound-adaptation genes were up-regulated (vs. expression in log-phase culture). As the infection progressed from acute to biofilm infection, more genes became up-regulated than down-regulated, but the down-regulated genes enriched in more pathways, likely because the genes and pathways that bacteria already colonizing wounds up-regulate to establish biofilm infection are less known. Across the stages of infection, carbon-utilization pathways shifted. During acute infection, itaconate produced by myeloid cells appears to have been a carbon source because myeloid cell infiltration and the expression of the host gene, ACOD1, for itaconate production peaked coincidently with the expression of the PAO1 genes for itaconate transport and catabolism. Additionally, branched-chain amino acids are suggested to be a carbon source in acute infection and in biofilm infection. In biofilm infection, fatty acid degradation was also up-regulated. These carbon sources feed into the glyoxylate cycle that was coincidently up-regulated, suggesting it provided the precursors for P. aeruginosa to synthesize macromolecules in establishing wound infection.

Carbon utilization profiles of Fusarium virguliforme isolates

2010 ◽  
Vol 56 (12) ◽  
pp. 979-986 ◽  
Author(s):  
E. Tang ◽  
C.B. Hill ◽  
G.L. Hartman
Keyword(s):  
Carbon Source ◽  
Mycelial Growth ◽  
Carbon Sources ◽  
Geographic Origin ◽  
Acid Methyl Ester ◽  
Published Data ◽  
Carbon Source Utilization ◽  
Carbon Utilization ◽  
Fusarium Virguliforme ◽  
Carbon Utilization Profiles

Fusarium virguliforme is the cause of sudden death syndrome in soybean. Physiological variability among isolates of the fungus is unknown. One way to measure physiologic variability is to analyze growth on different carbon sources. The carbon source utilization profiles of 18 F. virguliforme isolates were examined using the Biolog FF 96-well microplate, which contains 95 different carbon sources. The utilization of dextrin, d-mannitol, maltotriose, d-lactic acid methyl ester, N-acetyl-d-galactosamine, salicin, d-trehalose, and l-alanine differed significantly among isolates (P = 0.05). Carbon sources were grouped into 3 clusters based on their ability to promote growth of F. virguliforme, after calculating Euclidean distances among them. About 12% of the carbon sources promoted a high amount of mycelial growth, 39% promoted a medium amount of growth, and 49% promoted a low amount of mycelial growth; the latter was not significantly different from the water blank control. A hierarchical tree diagram was produced for the 18 isolates based on their carbon source utilization profiles using Ward’s hierarchical analysis method. Two main clusters of isolates were formed. One cluster represented greater average mycelial growth on all of the carbon sources than the other cluster. In this study, variability in carbon source utilization among F. virguliforme isolates was evident, but the results were not associated with geographic origin of the isolates, year collected, or published data on aggressiveness. Additional research is needed to determine if these carbon utilization profiles are associated with other biological characteristics, like spore germination, propagule formation, and saprophytic competitiveness.

scholarly journals Effect of Denitrifying Bacterial Biomass and Carbon Sources on Nitrate Removal

2020 ◽  
Vol 14 (4) ◽  
pp. 2417-2424
Author(s):  
Essam J. Alyamani ◽  
Rayan Y. Booq ◽  
Ali H. Bahkali ◽  
Sulaiman A. Alharbi
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Carbon Source ◽  
Conventional Treatment ◽  
Nitrate Removal ◽  
Carbon Sources ◽  
Bacterial Biomass ◽  
Alkaline Ph ◽  
Biological Denitrification ◽  
Bacterial Inoculum ◽  
Denitrification Process

Denitrification based on immobilized microbial cellulose may offer an economical replacement for conventional treatment for nitrate removal. The environmental and bacterial biomass may influence the rate of biological denitrification processes. This study aimed to investigate the factors that affect denitrification rates, including carbon sources, pH, and bacterial inoculum. Different inoculum biomass of Pseudomonas aeruginosa and various carbon sources of glucose, sucrose, and cellulose with different concentrations were tested to assimilate 100 mg/L of KNO3 as nitrate source. Additionally, five additional inoculations, five different incubation time, and seven different pH levels were studied. The Pseudomonas aeruginosa isolates used different mineral media with three carbon sources, glucose, sucrose, and cellulose, with different concentrations at different rates to denitrify nitrate. The highest denitrification rate was with glucose after 18 hrs and was after 24 hrs when sucrose and cellulose were used, respectively. The bacterial biomass denitrification level was the highest, between 0.8% and 1% of OD600=1. Nitrate removal by Pseudomonas aeruginosa was the highest at pH 7, 8, and 9. This report suggests that when glucose is used as a carbon source, at neutral to alkaline pH, and 1% of denitrifying bacterial biomass, the highest level of biological denitrification process may be achieved.

scholarly journals Carbon Catabolite Control in Candida albicans: New Wrinkles in Metabolism

mBio ◽  
2013 ◽  
Vol 4 (1) ◽  
Author(s):  
Michael C. Lorenz
Keyword(s):  
Candida Albicans ◽  
Carbon Source ◽  
Phosphoenolpyruvate Carboxykinase ◽  
Isocitrate Lyase ◽  
Glyoxylate Cycle ◽  
Carbon Sources ◽  
Fungal Species ◽  
Content Type ◽  
Catabolite Control

ABSTRACTMost microorganisms maintain strict control of nutrient assimilation pathways to ensure that they preferentially use compounds that generate the most energy or are most efficiently catabolized. In doing so, they avoid potentially inefficient conflicts between parallel catabolic and metabolic pathways. The regulation of carbon source utilization in a wide array of bacterial and fungal species involves both transcriptional and posttranscriptional mechanisms, and while the details can vary significantly, carbon catabolite control is widely conserved. In many fungi, the posttranslational aspect (carbon catabolite inactivation [CCI]) involves the ubiquitin-mediated degradation of catabolic enzymes for poor carbon sources when a preferred one (glucose) becomes available. A recent article presents evidence for a surprising exception to CCI in the fungal pathogenCandida albicans, an organism that makes use of gluconeogenic carbon sources during infection (D. Sandai, Z. Yin, L. Selway, D. Stead, J. Walker, M. D. Leach, I. Bohovych, I. V. Ene, S. Kastora, S. Budge, C. A. Munro, F. C. Odds, N. A. Gow, and A. J. Brown,mBio3[6]:e00495-12).In vitro, addition of glucose to cells grown in a poor carbon source rapidly represses transcripts encoding gluconeogenic and glyoxylate cycle enzymes, such as phosphoenolpyruvate carboxykinase (Pck1p) and isocitrate lyase (Icl1p), in bothC. albicansandSaccharomyces cerevisiae. Yet, uniquely, theC. albicansproteins persist, permitting parallel assimilation of multiple carbon sources, likely because they lack consensus ubiquitination sites found in the yeast homologs. Indeed, the yeast proteins are rapidly degraded when expressed inC. albicans, indicating a conservation of the machinery needed for CCI. How this surprising metabolic twist contributes to fungal commensalism or pathogenesis remains an open question.

scholarly journals Mutations in Alternative Carbon Utilization Pathways in Candida albicans Attenuate Virulence and Confer Pleiotropic Phenotypes

2006 ◽  
Vol 6 (2) ◽  
pp. 280-290 ◽  
Author(s):  
Melissa A. Ramírez ◽  
Michael C. Lorenz
Keyword(s):  
Candida Albicans ◽  
Carbon Metabolism ◽  
Innate Immune System ◽  
Glyoxylate Cycle ◽  
Transcriptional Profiling ◽  
Carbon Sources ◽  
Innate Immune ◽  
Carbon Utilization ◽  
The Glyoxylate Cycle

ABSTRACT The interaction between Candida albicans and cells of the innate immune system is a key determinant of disease progression. Transcriptional profiling has revealed that C. albicans has a complex response to phagocytosis, much of which is similar to carbon starvation. This suggests that nutrient limitation is a significant stress in vivo, and we have shown that glyoxylate cycle mutants are less virulent in mice. To examine whether other aspects of carbon metabolism are important in vivo during an infection, we have constructed strains lacking FOX2 and FBP1, which encode key components of fatty acid β-oxidation and gluconeogenesis, respectively. As expected, fox2Δ mutants failed to utilize several fatty acids as carbon sources. Surprisingly, however, these mutants also failed to grow in the presence of several other carbon sources, whose assimilation is independent of β-oxidation, including ethanol and citric acid. Mutants lacking the glyoxylate enzyme ICL1 also had more severe carbon utilization phenotypes than were expected. These results suggest that the regulation of alternative carbon metabolism in C. albicans is significantly different from that in other fungi. In vivo, fox2Δ mutants show a moderate but significant reduction in virulence in a mouse model of disseminated candidiasis, while disruption of the glyoxylate cycle or gluconeogenesis confers a severe attenuation in this model. These data indicate that C. albicans often encounters carbon-poor conditions during growth in the host and that the ability to efficiently utilize multiple nonfermentable carbon sources is a virulence determinant. Consistent with this in vivo requirement, C. albicans uniquely regulates carbon metabolism in a more integrated manner than in Saccharomyces cerevisiae, such that defects in one part of the machinery have wider impacts than expected. These aspects of alternative carbon metabolism may then be useful as targets for therapeutic intervention.

scholarly journals Contextual flexibility in Pseudomonas aeruginosa central carbon metabolism during growth in single carbon sources

2019 ◽  
Author(s):  
Stephen K. Dolan ◽  
Michael Kohlstedt ◽  
Stephen Trigg ◽  
Pedro Vallejo Ramirez ◽  
Christoph Wittmann ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Carbon Source ◽  
Metabolic Flux ◽  
Antimicrobial Agents ◽  
Carbon Sources ◽  
Aerobic Denitrification ◽  
Human Pathogen ◽  
Opportunistic Human Pathogen

AbstractPseudomonas aeruginosa is an opportunistic human pathogen, particularly noted for causing infections in the lungs of people with cystic fibrosis (CF). Previous studies have shown that the gene expression profile of P. aeruginosa appears to converge towards a common metabolic program as the organism adapts to the CF airway environment. However, at a systems level, we still have only a limited understanding of how these transcriptional changes impact on metabolic flux. To address this, we analysed the transcriptome, proteome and fluxome of P. aeruginosa grown on glycerol or acetate. These carbon sources were chosen because they are the primary breakdown products of airway surfactant, phosphatidylcholine, which is known to be a major carbon source for P. aeruginosa in the CF airways. We show that the flux of carbon through central metabolism is radically different on each carbon source. For example, the newly-recognised EDEMP cycle plays an important role in supplying NADPH during growth on glycerol. By contrast, the EDEMP cycle is attenuated during growth on acetate, and instead, NADPH is primarily supplied by the isocitrate dehydrogenase(s)-catalyzed reaction. Perhaps more importantly, our proteomic and transcriptomic analyses reveal a global remodelling of gene expression during growth on the different carbon sources, with unanticipated impacts on aerobic denitrification, electron transport chain architecture, and the redox economy of the cell. Collectively, these data highlight the remarkable metabolic plasticity of P. aeruginosa; a plasticity which allows the organism to seamlessly segue between different carbon sources, maximising the energetic yield from each.ImportancePseudomonas aeruginosa is an opportunistic human pathogen, well-known for causing infections in the airways of people with cystic fibrosis. Although it is clear that P. aeruginosa is metabolically well-adapted to life in the CF lung, little is currently known about how the organism metabolises the nutrients available in the airways. In this work, we use a combination of gene expression and isotope tracer (“fluxomic”) analyses to find out exactly where the input carbon goes during growth on two CF-relevant carbon sources, acetate and glycerol (derived from the breakdown of lung surfactant). We find that carbon is routed (“fluxed”) through very different pathways during growth on these substrates, and that this is accompanied by an unexpected remodelling of the cell’s electron transfer pathways. Having access to this “blueprint” is important because the metabolism of P. aeruginosa is increasingly being recognised as a target for the development of much-needed antimicrobial agents.

Influence of RpoN on isocitrate lyase activity in Pseudomonas aeruginosa

Microbiology ◽  
2010 ◽  
Vol 156 (4) ◽  
pp. 1201-1210 ◽  
Author(s):  
Jessica M. Hagins ◽  
Jessica A. Scoffield ◽  
Sang-Jin Suh ◽  
Laura Silo-Suh
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Metabolic Pathways ◽  
Isocitrate Lyase ◽  
Tricarboxylic Acid Cycle ◽  
Acute Infection ◽  
Carbon Sources ◽  
Pulmonary Infections ◽  
Lyase Activity ◽  
Glyoxylate Pathway ◽  
Knockout Mutation

Pseudomonas aeruginosa is the major aetiological agent of chronic pulmonary infections in patients with cystic fibrosis (CF). The metabolic pathways utilized by P. aeruginosa during these infections, which can persist for decades, are poorly understood. Several lines of evidence suggest that the glyoxylate pathway, which utilizes acetate or fatty acids to replenish intermediates of the tricarboxylic acid cycle, is an important metabolic pathway for P. aeruginosa adapted to the CF lung. Isocitrate lyase (ICL) is one of two major enzymes of the glyoxylate pathway. In a previous study, we determined that P. aeruginosa is dependent upon aceA, which encodes ICL, to cause disease on alfalfa seedlings and in rat lungs. Expression of aceA in PAO1, a P. aeruginosa isolate associated with acute infection, is regulated by carbon sources that utilize the glyoxyate pathway. In contrast, expression of aceA in FRD1, a CF isolate, is constitutively upregulated. Moreover, this deregulation of aceA occurs in other P. aeruginosa isolates associated with chronic infection, suggesting that high ICL activity facilitates adaptation of P. aeruginosa to the CF lung. Complementation of FRD1 with a PAO1 clone bank identified that rpoN negatively regulates aceA. However, the deregulation of aceA in FRD1 was not due to a knockout mutation of rpoN. Regulation of the glyoxylate pathway by RpoN is likely to be indirect, and represents a unique regulatory role for this sigma factor in bacterial metabolism.

Effect of carbon source on Phenobarbital metabolism by Rhizopus stolonifer

2010 ◽  
Vol 3 (2) ◽  
pp. 1022-1027
Author(s):  
Kavitha K ◽  
Asha S ◽  
Hima Bindu T.V.L ◽  
Vidyavathi M
Keyword(s):  
Carbon Source ◽  
High Performance ◽  
Carbon Sources ◽  
In Vitro Models ◽  
Rhizopus Stolonifer ◽  
Safety And Efficacy ◽  
Alternative Systems ◽  
Toxicological Studies ◽  
Microbial Model

The safety and efficacy of a drug is based on its metabolism or metabolite formed. The metabolism of drugs can be studied by different in vitro models, among which microbial model became popular. In the present study, eight microbes were screened for their ability to metabolize phenobarbital in a manner comparable to humans with a model to develop alternative systems to study human drug metabolism. Among the different microbes screened, a filamentous fungi Rhizopus stolonifer metabolized phenobarbital to its metabolite which is used for further pharmacological and toxicological studies. The transformation of phenobarbital was identified by high- performance liquid chromatography (HPLC). Interestingly, Rhizopus stolonifer sample showed an extra metabolite peak at 3.11min. compared to its controls. The influence of different carbon sources in media used for growth of fungus, on metabolite production was studied, to find its effect in production of metabolite as the carbon source may influence the growth of the cell.

Application of Phenotype Microarray for Profiling Carbon Sources Utilization between Biofilm and Non-Biofilm of Pseudomonas aeruginosa from Clinical Isolates

2020 ◽  
Vol 21 (14) ◽  
pp. 1539-1550
Author(s):  
Nur S. Ismail ◽  
Suresh K. Subbiah ◽  
Niazlin M. Taib
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Carbon Sources ◽  
Anaerobic Respiration ◽  
Regulatory System ◽  
Negative Control ◽  
High Morbidity ◽  
Metabolic Profiles ◽  
Phenotype Microarray ◽  
Diverse Environment ◽  
Phenotype Microarrays

Background: This is the fastest work in obtaining the metabolic profiles of Pseudomonas aeruginosa in order to combat the infection diseases which leads to high morbidity and mortality rates. Pseudomonas aeruginosa is a high versatility of gram-negative bacteria that can undergo aerobic and anaerobic respiration. Capabilities in deploying different carbon sources, energy metabolism and regulatory system, ensure the survival of this microorganism in the diverse environment condition. Determination of differences in carbon sources utilization among biofilm and non-biofilm of Pseudomonas aeruginosa provides a platform in understanding the metabolic activity of the microorganism. Methods: The study was carried out from September 2017 to February 2019. Four archive isolates forming strong and intermediate biofilm and non-biofilms producer were subcultured from archive isolates. ATCC 27853 P. aeruginosa was used as a negative control or non-biofilm producing microorganism. Biofilm formation was confirmed by Crystal Violet Assay (CVA) and Congo Red Agar (CRA). Metabolic profiles of the biofilm and non-biofilms isolates were determined by phenotype microarrays (Biolog Omnilog). Results and Discussion: In this study, Pseudomonas aeruginosa biofilm isolates utilized uridine, L-threonine and L-serine while non-biofilm utilized adenosine, inosine, monomethyl, sorbic acid and succinamic acid. Conclusion: The outcome of this result will be used for future studies to improve detection or inhibit the growth of P. aeruginosa biofilm and non-biofilm respectively.

scholarly journals Denitrification Control in a Recirculating Aquaculture System—A Simulation Study

Processes ◽  
2020 ◽  
Vol 8 (10) ◽  
pp. 1306
Author(s):  
Pedro Almeida ◽  
Laurent Dewasme ◽  
Alain Vande Wouwer
Keyword(s):  
Carbon Source ◽  
Carbon Sources ◽  
Aquatic Organisms ◽  
Operating Conditions ◽  
Toxic Substances ◽  
Recirculating Aquaculture System ◽  
Treatment Technology ◽  
Tuning Method ◽  
Recirculating Aquaculture ◽  
Aquaculture System

The recirculating aquaculture system (RAS) is a land-based water treatment technology, which allows for farming aquatic organisms, such as fish, by reusing the water in the production (often less than 5%). This technology is based on the use of filters, either mechanical or biological, and can, in principle, be used for any species grown in aquaculture. Due to the low recirculation rate, ammonia accumulates in the system and must be converted into nitrate using nitrification reactors. Although less toxic for fish, nitrate can also be further reduced into nitrogen gas by the use of denitrification biofilters which may create several issues, such as incomplete denitrification, resulting in toxic substances, such as nitrite and nitric oxide, or a waste of carbon source in excess. Control of the added quantity of carbon source in the denitrification biofilter is then mandatory to keep nitrate/nitrite concentrations under toxic levels for fish and in accordance with local effluent regulations, and to reduce costs related to wasted organic carbon sources. This study therefore investigates the application of different control methodologies to a denitrification reactor in a RAS. To this end, a numerical simulator is built to predict the RAS behavior and to allow for the comparison of different control approaches, in the presence of changes in the operating conditions, such as fish density and biofilter removal efficiency. First, a classical proportional-integral-derivative (PID) controller was designed, based on an SIMC tuning method depending on the amount of ammonia excreted by fish. Then, linearizing and cascade controllers were considered as possible alternatives.

scholarly journals The carbon source-dependent pattern of antimicrobial activity and gene expression in Pseudomonas donghuensis P482

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marta Matuszewska ◽  
Tomasz Maciąg ◽  
Magdalena Rajewska ◽  
Aldona Wierzbicka ◽  
Sylwia Jafra
Keyword(s):  
Gene Expression ◽  
Antimicrobial Activity ◽  
Carbon Source ◽  
Reference Genes ◽  
Plant Pathogens ◽  
Plant Protection ◽  
Carbon Sources ◽  
Unknown Compound ◽  
Fungal Plant Pathogens ◽  
The Impact

AbstractPseudomonas donghuensis P482 is a tomato rhizosphere isolate with the ability to inhibit growth of bacterial and fungal plant pathogens. Herein, we analysed the impact of the carbon source on the antibacterial activity of P482 and expression of the selected genes of three genomic regions in the P482 genome. These regions are involved in the synthesis of pyoverdine, 7-hydroxytropolone (7-HT) and an unknown compound (“cluster 17”) and are responsible for the antimicrobial activity of P482. We showed that the P482 mutants, defective in these regions, show variations and contrasting patterns of growth inhibition of the target pathogen under given nutritional conditions (with glucose or glycerol as a carbon source). We also selected and validated the reference genes for gene expression studies in P. donghuensis P482. Amongst ten candidate genes, we found gyrB, rpoD and mrdA the most stably expressed. Using selected reference genes in RT-qPCR, we assessed the expression of the genes of interest under minimal medium conditions with glucose or glycerol as carbon sources. Glycerol was shown to negatively affect the expression of genes necessary for 7-HT synthesis. The significance of this finding in the light of the role of nutrient (carbon) availability in biological plant protection is discussed.

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