scholarly journals Amino Acid Catabolism in Staphylococcus aureus and the Function of Carbon Catabolite Repression

mBio ◽  
2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Cortney R. Halsey ◽  
Shulei Lei ◽  
Jacqueline K. Wax ◽  
Mckenzie K. Lehman ◽  
Austin S. Nuxoll ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Soft Tissue ◽  
Carbon Source ◽  
Carbon Sources ◽  
Atp Synthesis ◽  
Gene Coding ◽  
Organ Systems ◽  
Available Carbon ◽  
Glutamate Synthesis

ABSTRACT Staphylococcus aureus must rapidly adapt to a variety of carbon and nitrogen sources during invasion of a host. Within a staphylococcal abscess, preferred carbon sources such as glucose are limiting, suggesting that S. aureus survives through the catabolism of secondary carbon sources. S. aureus encodes pathways to catabolize multiple amino acids, including those that generate pyruvate, 2-oxoglutarate, and oxaloacetate. To assess amino acid catabolism, S. aureus JE2 and mutants were grown in complete defined medium containing 18 amino acids but lacking glucose (CDM). A mutation in the gudB gene, coding for glutamate dehydrogenase, which generates 2-oxoglutarate from glutamate, significantly reduced growth in CDM, suggesting that glutamate and those amino acids generating glutamate, particularly proline, serve as the major carbon source in this medium. Nuclear magnetic resonance (NMR) studies confirmed this supposition. Furthermore, a mutation in the ackA gene, coding for acetate kinase, also abrogated growth of JE2 in CDM, suggesting that ATP production from pyruvate-producing amino acids is also critical for growth. In addition, although a functional respiratory chain was absolutely required for growth, the oxygen consumption rate and intracellular ATP concentration were significantly lower during growth in CDM than during growth in glucose-containing media. Finally, transcriptional analyses demonstrated that expression levels of genes coding for the enzymes that synthesize glutamate from proline, arginine, and histidine are repressed by CcpA and carbon catabolite repression. These data show that pathways important for glutamate catabolism or ATP generation via Pta/AckA are important for growth in niches where glucose is not abundant, such as abscesses within skin and soft tissue infections. IMPORTANCE S. aureus is a significant cause of both morbidity and mortality worldwide. This bacterium causes infections in a wide variety of organ systems, the most common being skin and soft tissue. Within a staphylococcal abscess, levels of glucose, a preferred carbon source, are limited due to the host immune response. Therefore, S. aureus must utilize other available carbon sources such as amino acids or peptides to proliferate. Our results show that glutamate and amino acids that serve as substrates for glutamate synthesis, particularly proline, function as major carbon sources during growth, whereas other amino acids that generate pyruvate are important for ATP synthesis via substrate-level phosphorylation in the Pta-AckA pathway. Our data support a model whereby certain amino acid catabolic pathways, and acquisition of those particular amino acids, are crucial for growth in niches where glucose is not abundant. IMPORTANCE S. aureus is a significant cause of both morbidity and mortality worldwide. This bacterium causes infections in a wide variety of organ systems, the most common being skin and soft tissue. Within a staphylococcal abscess, levels of glucose, a preferred carbon source, are limited due to the host immune response. Therefore, S. aureus must utilize other available carbon sources such as amino acids or peptides to proliferate. Our results show that glutamate and amino acids that serve as substrates for glutamate synthesis, particularly proline, function as major carbon sources during growth, whereas other amino acids that generate pyruvate are important for ATP synthesis via substrate-level phosphorylation in the Pta-AckA pathway. Our data support a model whereby certain amino acid catabolic pathways, and acquisition of those particular amino acids, are crucial for growth in niches where glucose is not abundant.

Relationship between carbon source and susceptibility of Cephalosporium acremonium to selected amino acid analogues

1979 ◽  
Vol 25 (7) ◽  
pp. 818-821 ◽  
Author(s):  
R. J. Mehta ◽  
C. H. Nash
Keyword(s):  
Amino Acid ◽  
Carbon Source ◽  
Carbon Sources ◽  
Soluble Starch ◽  
Cephalosporium Acremonium ◽  
Specific Amino Acid ◽  
Minimal Inhibitory Concentrations ◽  
Amino Acid Analogues ◽  
Resistant Mutants

The susceptibility of Cephalosporium acremonium to selected amino acid analogues was markedly influenced by the carbon source used in the test media. Lysine hydroxamate, β-hydroxy norvaline, and hexafluorovaline were toxic when tested with ribose, ribose or fructose, and ribose or galactose, respectively. In contrast, thialysine and thiaisoleucine inhibited C. acremonium with glucose, fructose, galactose, sucrose, mannitol, sorbitol, and soluble starch. Neither of these analogues was toxic at levels tested when glycerol was used as a carbon source. The minimal inhibitory concentrations (MIC) of thialysine, homoserine, and α-methylserine were > 1000, > 1000, and 250 μg/mL, respectively, with glycerol. In contrast, the MIC values for the same three analogues were 31, 62, and 125 μg/mL, respectively, with mannitol. The matching of the carbon sources with the specific amino acid analogues expands the number of analogues useful for selecting derepressed mutants. Thialysine-resistant mutants (tlysR) of C. acremonium which excrete lysine were isolated on a medium containing mannitol.

scholarly journals Gene expression noise can promote the fixation of beneficial mutations in fluctuating environments

2020 ◽  
Vol 16 (10) ◽  
pp. e1007727 ◽  
Author(s):  
Michael Schmutzer ◽  
Andreas Wagner
Keyword(s):  
Transcription Factor ◽  
Carbon Source ◽  
Carbon Sources ◽  
High Growth ◽  
Population Bottlenecks ◽  
Gene Expression Noise ◽  
Fluctuating Environments ◽  
Speed Up ◽  
Available Carbon ◽  
Beneficial Allele

Nongenetic phenotypic variation can either speed up or slow down adaptive evolution. We show that it can speed up evolution in environments where available carbon and energy sources change over time. To this end, we use an experimentally validated model of Escherichia coli growth on two alternative carbon sources, glucose and acetate. On the superior carbon source (glucose), all cells achieve high growth rates, while on the inferior carbon source (acetate) only a small fraction of the population manages to initiate growth. Consequently, populations experience a bottleneck when the environment changes from the superior to the inferior carbon source. Growth on the inferior carbon source depends on a circuit under the control of a transcription factor that is repressed in the presence of the superior carbon source. We show that noise in the expression of this transcription factor can increase the probability that cells start growing on the inferior carbon source. In doing so, it can decrease the severity of the bottleneck and increase mean population fitness whenever this fitness is low. A modest amount of noise can also enhance the fitness effects of a beneficial allele that increases the fraction of a population initiating growth on acetate. Additionally, noise can protect this allele from extinction, accelerate its spread, and increase its likelihood of going to fixation. Central to the adaptation-enhancing principle we identify is the ability of noise to mitigate population bottlenecks, particularly in environments that fluctuate periodically. Because such bottlenecks are frequent in fluctuating environments, and because periodically fluctuating environments themselves are common, this principle may apply to a broad range of environments and organisms.

Biodegradation of RDX-contaminated wastes in a nitrogen-deficient environment

1998 ◽  
Vol 38 (4-5) ◽  
pp. 219-224 ◽  
Author(s):  
Z. Ronen ◽  
A. Brenner ◽  
A. Abeliovich
Keyword(s):  
Carbon Source ◽  
Carbon Sources ◽  
Cost Effective ◽  
Complete Removal ◽  
Chemical Treatments ◽  
Carbon Adsorption ◽  
Physico Chemical ◽  
Cost Effective Alternative ◽  
Available Carbon ◽  
Waste Mixture

A feasible biological treatment process for RDX-contaminated wastes was demonstrated in a bench-scale system, using real wastewater of a munitions factory. The wastewater mixture tested included the nitramine RDX together with high levels of nitrate and various organic solvents such as cyclohexanone and acetone. The purpose of the study was to remove both RDX and nitrate in order to prevent groundwater contamination. A two-stage reactor system including an anoxic stage followed by an aerobic one was tested. The anoxic stage was aimed at removing nitrate by denitrification, using available carbon sources present in the waste mixture. Additional supply of carbon source (acetone) was required to support complete removal of nitrate. Further removal of residual organic was achieved in the aerobic stage together with total mineralization of RDX. Complete removal of nitrate in the anoxic stage was found to be crucial to RDX mineralization in the aerobic stage, since RDX was used solely as a nitrogen source. Additional carbon source (cyclohexanone) was also required in the aerobic stage to assure complete removal of RDX. The treatment scheme tested may be a cost-effective alternative to physico-chemical treatments such as carbon adsorption and UV destruction, commonly applied for explosives-contaminated wastes.

scholarly journals The Fungal Pathogen Candida albicans Autoinduces Hyphal Morphogenesis by Raising Extracellular pH

mBio ◽  
2011 ◽  
Vol 2 (3) ◽  
Author(s):  
Slavena Vylkova ◽  
Aaron J. Carman ◽  
Heather A. Danhof ◽  
John R. Collette ◽  
Huaijin Zhou ◽  
...  
Keyword(s):  
Amino Acids ◽  
Candida Albicans ◽  
Amino Acid ◽  
Carbon Source ◽  
Fungal Pathogen ◽  
Host Cells ◽  
Acid Uptake ◽  
Content Type ◽  
Virulence Trait ◽  
Ph Adaptation

ABSTRACTpH homeostasis is critical for all organisms; in the fungal pathogenCandida albicans, pH adaptation is critical for virulence in distinct host niches. We demonstrate that beyond adaptation,C. albicansactively neutralizes the environment from either acidic or alkaline pHs. Under acidic conditions, this species can raise the pH from 4 to >7 in less than 12 h, resulting in autoinduction of the yeast-hyphal transition, a critical virulence trait. Extracellular alkalinization has been reported to occur in several fungal species, but under the specific conditions that we describe, the phenomenon is more rapid than previously observed. Alkalinization is linked to carbon deprivation, as it occurs in glucose-poor media and requires exogenous amino acids. These conditions are similar to those predicted to exist inside phagocytic cells, and we find a strong correlation between the use of amino acids as a cellular carbon source and the degree of alkalinization. Genetic and genomic approaches indicate an emphasis on amino acid uptake and catabolism in alkalinizing cells. Mutations in four genes,STP2, a transcription factor regulating amino acid permeases,ACH1(acetyl-coenzyme A [acetyl-CoA] hydrolase),DUR1,2(urea amidolyase), andATO5, a putative ammonia transporter, abolish or delay neutralization. The pH changes are the result of the extrusion of ammonia, as observed in other fungi. We propose that nutrient-deprivedC. albicanscells catabolize amino acids as a carbon source, excreting the amino nitrogen as ammonia to raise environmental pH and stimulate morphogenesis, thus directly contributing to pathogenesis.IMPORTANCECandida albicansis the most important fungal pathogen of humans, causing disease at multiple body sites. The ability to switch between multiple morphologies, including a rounded yeast cell and an elongated hyphal cell, is a key virulence trait in this species, as this reversible switch is thought to promote dissemination and tissue invasion in the host. We report here thatC. albicanscan actively alter the pH of its environment and induce its switch to the hyphal form. The change in pH is caused by the release of ammonia from the cells produced during the breakdown of amino acids. This phenomenon is unprecedented in a human pathogen and may substantially impact host physiology by linking morphogenesis, pH adaptation, carbon metabolism, and interactions with host cells, all of which are critical for the ability ofC. albicansto cause disease.

scholarly journals The regulation of NADL-glutamate dehydrogenase inAspergillus nidulans

1974 ◽  
Vol 23 (1) ◽  
pp. 119-124 ◽  
Author(s):  
J. R. Kinghorn ◽  
J. A. Pateman
Keyword(s):  
Amino Acids ◽  
Linkage Group ◽  
Carbon Source ◽  
Glutamate Dehydrogenase ◽  
Aspergillus Nidulans ◽  
Dehydrogenase Activity ◽  
Carbon Sources ◽  
Wild Type ◽  
Group Iii ◽  
Glutamate Dehydrogenase Activity

SummaryWild-type cells ofAspergillus nidulanshave undetectable NADL-glutamate dehydrogenase activity when utilizing glucose and high levels of NADL-glutamate dehydrogenase when utilizing certain amino acids as sole carbon sources.A mutant, designatedgdhCl, has appreciable NAD-GDH activity when utilizing glucose as a carbon source. ThegdhC1mutation is semi-dominant and is located in linkage group III.

scholarly journals Assessment of Carbon Substrate Catabolism Pattern and Functional Metabolic Pathway for Microbiota of Limestone Caves

2021 ◽  
Author(s):  
Suprokash Koner ◽  
Jung-Sheng Chen ◽  
Bing-Mu Hsu ◽  
Chao-Wen Tan ◽  
Cheng-Wei Fan ◽  
...  
Keyword(s):  
Amino Acids ◽  
Microbial Community ◽  
Amino Acid ◽  
Calcium Carbonate ◽  
Energy Metabolism ◽  
Carbon Source ◽  
16S Rrna ◽  
Bacterial Communities ◽  
Utilization Rate ◽  
Biolog Ecoplate

Abstract Microbially induced calcium carbonate precipitation (MICP), a widespread biochemical process involving heterotopic bacterial communities, generally occurs in organic matter-rich environments. Limestone caves, whose oligotrophic conditions result from the absence of sunlight, are considered an extreme environment. In such environments, bacteria have the potential to form calcium carbonate. In this study, the microbial community diversity and taxonomical structure outside and inside a limestone cave was investigated with their community-level carbon source by fingerprinting and functional metabolic pathway prediction using 16S rRNA amplicon sequencing analysis. The Biolog EcoPlate™ assay revealed that microbes from outside the cave were metabolically highly active, resulting in a rising carbon source utilization rate curve. Conversely, the microbial community within the cave was not very active in consuming the carbon substrates of Biolog EcoPlate™. Although major carbon sources were found to be used by microbial communities both inside and outside the cave, the microbial utilization rate of carbon bacteria inside was much lower than for bacteria outside the cave. The taxonomic classification of microbial diversity using 16S rRNA metagenomic analysis revealed eight predominant bacterial phyla associated with both sampling areas: Proteobacteria, Acidobacteria, Actinobacteria, Planctomycetes, Nitrospirae, Chloroflexi, Gemmatimonadetes, and Cyanobacteria. Among these, Planctomycetes, Proteobacteria, Cyanobacteria, and Nitrospirae were predominantly associated with external cave samples, whereas Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes were associated with internal cave samples. Functional prediction analysis showed that bacterial communities both inside and outside the cave were functionally involved in the metabolism of carbohydrates, amino acids, other amino acid, lipids, xenobiotic compounds, energy metabolism, and environmental information processing. However, the amino acid and carbohydrate metabolic pathways were predominantly linked to the external cave samples, while xenobiotic compounds, lipids, other amino acids, and energy metabolism were associated with internal cave samples. Overall, a positive correlation was observed between Biolog EcoPlate™ assay carbon utilization and metagenomically observed metabolic function.

scholarly journals Bomb Carbon as a Tracer of Dietary Carbon Sources in Omnivorous Mammals

Radiocarbon ◽  
2001 ◽  
Vol 43 (2B) ◽  
pp. 711-721 ◽  
Author(s):  
Nancy Beavan-Athfield ◽  
Rodger J Sparks
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Essential Amino Acid ◽  
Carbon Sources ◽  
Essential Amino Acids ◽  
Metabolic Effects ◽  
C Value ◽  
The Creation ◽  
Carbon Contribution

We have isolated amino acid groups from modern bone hydrolysates and compared their relative Δ14C value to assess the carbon contribution of diet to the overall radiocarbon signal in bone. We find that both essential and non-essential amino acids may produce widely varying 14C, relative to other amino acid groups in the hydrolysate and to the original whole bone protein. We hypothesize that the 14C variations in non-essential amino acids may be due to metabolic effects that utilize essential amino acid carbon skeletons in the creation of non-essential amino acids.

scholarly journals Novel OXA-10-Derived Extended-Spectrum β-Lactamases Selected In Vivo or In Vitro

1998 ◽  
Vol 42 (12) ◽  
pp. 3113-3116 ◽  
Author(s):  
P. Mugnier ◽  
I. Casin ◽  
A. T. Bouthors ◽  
E. Collatz
Keyword(s):  
Amino Acids ◽  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Clavulanic Acid ◽  
Extended Spectrum ◽  
Gene Coding ◽  
Lactamase Gene

ABSTRACT A clinical isolate of Pseudomonas aeruginosa, PAe191, was found to be highly resistant to all anti-Pseudomonasβ-lactam antibiotics (except imipenem) and resistant also to aminoglycosides. It produced a β-lactamase (with an apparent pI of 7.6) which was not inhibited by clavulanic acid. Cloning and characterization of the β-lactamase gene showed that it coded for a novel extended-spectrum OXA-10 variant, called OXA-19, which differed from OXA-10 by nine amino acids and from OXA-13 by two, i.e., Asn in position 73 (Asn73) instead of Ser and Asp157 instead of Gly. Asparagine in position 157 is implicated in resistance to ceftazidime, while the amino acid in position 73, in this variant, seems to condition the level of resistance to penicillins. The oxa19gene was found to be inserted, in a typical integron structure, immediately downstream from anaac(6′)-Ib gene coding for an aminoglycoside acetyltransferase variant, which was called AAC(6′)-Ib9.

Advances of External Carbon Source in Denitrification

2012 ◽  
Vol 518-523 ◽  
pp. 2319-2323 ◽  
Author(s):  
Guang Ying Liu ◽  
Huan Zhen Zhang ◽  
Wei Li ◽  
Xin Zhang
Keyword(s):  
Carbon Source ◽  
Slow Release ◽  
Removal Rate ◽  
Nitrate Removal ◽  
Carbon Sources ◽  
Electron Donors ◽  
Primary Sludge ◽  
External Carbon Source ◽  
The Media ◽  
Available Carbon

Carbon source used as electron donors is critical to heterotrophic denitrification. Addition of external carbon source is necessary when internal organics are deficient. A review was conducted on the use of external carbon source in denitrification. Traditional carbon sources such as methanol and ethanol, alternative carbon sources such as cellulose-rich materials, biodegradable polymers and primary sludge are included in external carbon sources. Present situation and problems of its biodegradability and effects in denitrification are summarized. Focus in external carbon source includes further study on the biodegradation mechanism of the media, slow release performance and nitrate removal rate of available carbon source and continuous research on new kinds of substrates. Recommendations on further study of carbon source are put forward.

scholarly journals Two Pathways for Glutamate Biosynthesis in the Syntrophic Bacterium Syntrophus aciditrophicus

2015 ◽  
Vol 81 (24) ◽  
pp. 8434-8444 ◽  
Author(s):  
Marie Kim ◽  
Huynh M. Le ◽  
Xiulan Xie ◽  
Xueyang Feng ◽  
Yinjie J. Tang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Citrate Synthase ◽  
Carbon Sources ◽  
Krebs Cycle ◽  
Content Type ◽  
Cell Extracts ◽  
Cyclohexane Carboxylate ◽  
Glutamate Synthesis ◽  
Glutamate Biosynthesis ◽  
Syntrophus Aciditrophicus

ABSTRACTThe anaerobic metabolism of crotonate, benzoate, and cyclohexane carboxylate bySyntrophus aciditrophicusgrown syntrophically withMethanospirillum hungateiprovides a model to study syntrophic cooperation. Recent studies revealed thatS. aciditrophicuscontainsRe-citrate synthase but lacks the commonSi-citrate synthase. To establish whether theRe-citrate synthase is involved in glutamate synthesis via the oxidative branch of the Krebs cycle, we have used [1-13C]acetate and [1-14C]acetate as well as [13C]bicarbonate as additional carbon sources during axenic growth ofS. aciditrophicuson crotonate. Our analyses showed that labeled carbons were detected in at least 14 amino acids, indicating the global utilization of acetate and bicarbonate. The labeling patterns of alanine and aspartate verified that pyruvate and oxaloacetate were synthesized by consecutive carboxylations of acetyl coenzyme A (acetyl-CoA). The isotopomer profile and13C nuclear magnetic resonance (NMR) spectroscopy of the obtained [13C]glutamate, as well as decarboxylation of [14C]glutamate, revealed that this amino acid was synthesized by two pathways. Unexpectedly, only the minor route usedRe-citrate synthase (30 to 40%), whereas the majority of glutamate was synthesized via the reductive carboxylation of succinate. This symmetrical intermediate could have been formed from two acetates via hydration of crotonyl-CoA to 4-hydroxybutyryl-CoA. 4-Hydroxybutyrate was detected in the medium ofS. aciditrophicuswhen grown on crotonate, but an active hydratase could not be measured in cell extracts, and the annotated 4-hydroxybutyryl-CoA dehydratase (SYN_02445) lacks key amino acids needed to catalyze the hydration of crotonyl-CoA. BesidesClostridium kluyveri, this study reveals the second example of a microbial species to employ two pathways for glutamate synthesis.

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