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1.
Proc Natl Acad Sci U S A ; 118(1)2021 01 05.
Article in English | MEDLINE | ID: mdl-33443160

ABSTRACT

Aerobic glycolysis (AG), that is, the nonoxidative metabolism of glucose, contributes significantly to anabolic pathways, rapid energy generation, task-induced activity, and neuroprotection; yet high AG is also associated with pathological hallmarks such as amyloid-ß deposition. An important yet unresolved question is whether and how the metabolic benefits and risks of brain AG is structurally shaped by connectome wiring. Using positron emission tomography and magnetic resonance imaging techniques as well as computational models, we investigate the relationship between brain AG and the macroscopic connectome. Specifically, we propose a weighted regional distance-dependent model to estimate the total axonal projection length of a brain node. This model has been validated in a macaque connectome derived from tract-tracing data and shows a high correspondence between experimental and estimated axonal lengths. When applying this model to the human connectome, we find significant associations between the estimated total axonal projection length and AG across brain nodes, with higher levels primarily located in the default-mode and prefrontal regions. Moreover, brain AG significantly mediates the relationship between the structural and functional connectomes. Using a wiring optimization model, we find that the estimated total axonal projection length in these high-AG regions exhibits a high extent of wiring optimization. If these high-AG regions are randomly rewired, their total axonal length and vulnerability risk would substantially increase. Together, our results suggest that high-AG regions have expensive but still optimized wiring cost to fulfill metabolic requirements and simultaneously reduce vulnerability risk, thus revealing a benefit-risk balancing mechanism in the human brain.


Subject(s)
Aerobiosis/physiology , Brain/metabolism , Glycolysis/physiology , Adult , Connectome/methods , Databases, Factual , Female , Humans , Magnetic Resonance Imaging , Male , Nerve Net/metabolism , Neural Pathways , Positron-Emission Tomography
2.
Environ Res ; 220: 115240, 2023 03 01.
Article in English | MEDLINE | ID: mdl-36621544

ABSTRACT

In order to solve nitrogen pollution in environmental water, two heterotrophic nitrifying and aerobic denitrifying strains isolated from acid paddy soil were identified as Achromobacter sp. strain HNDS-1 and Enterobacter sp. strain HNDS-6 respectively. Strain HNDS-1 and strain HNDS-6 exhibited amazing ability to nitrogen removal. When (NH4)2SO4, KNO3, NaNO2 were used as nitrogen resource respectively, the NH4+-N, NO3--N, NO2--N removal efficiencies of strain HNDS-1 were 93.31%, 89.47%, and 100% respectively, while those of strain HNDS-6 were 82.39%, 96.92%, and 100%. And both of them could remove mixed nitrogen effectively in low C/N (C/N = 5). Strain HNDS-1 could remove 76.86% NH4+-N and 75.13% NO3--N. And strain HNDS-6 can remove 65.07% NH4+-N and 78.21% NO3--N. A putative ammonia monooxygenase, nitrite reductase, nitrate reductase, assimilatory nitrate reductase, nitrate/nitrite transport protein and nitric oxide reductase of strain HNDS-1, while hydroxylamine reductase, nitrite reductase, nitrate reductase, assimilatory nitrate reductase, nitrate/nitrite transport protein, and nitric oxide reductase of strain HNDS-6 were identified by genomic analysis. DNA-SIP analysis showed that genes Nxr, narG, nirK, norB, nosZ were involved in nitrogen removal pathway, which indicates that the denitrification pathway of strain HNDS-1 and strain HNDS-6 was NO3-→NO2-→NO→N2O→N2 during NH4+-N removal process. And the nitrification pathway of strain HNDS-1 and strain HNDS-6 was NO2-→NO3-, but the nitrification pathway of NH4+→ NO2- needs further studies.


Subject(s)
Achromobacter , Denitrification , Enterobacter , Nitrification , Achromobacter/genetics , Achromobacter/metabolism , Aerobiosis/genetics , Aerobiosis/physiology , Denitrification/genetics , Denitrification/physiology , Enterobacter/genetics , Enterobacter/metabolism , Nitrates/metabolism , Nitrification/genetics , Nitrification/physiology , Nitrite Reductases/metabolism , Nitrites/metabolism , Nitrogen/metabolism , Nitrogen Dioxide/metabolism
3.
Curr Issues Mol Biol ; 33: 85-100, 2019.
Article in English | MEDLINE | ID: mdl-31166186

ABSTRACT

This review is focused on recent studies of carbon metabolism in aerobic methanotrophs that specifically addressed the properties, distribution and phylogeny of some of the key enzymes involved in assimilation of carbon from methane. These include enzymes involved in sugar sythesis and cleavage, conversion of intermediates of the tricarboxylic acid cycle, as well as in osmoadaptation in halotolerant methanotrophs.


Subject(s)
Aerobiosis/physiology , Methane/metabolism , Soil Microbiology , Adaptation, Biological/genetics , Biodiversity , Carbon/metabolism , Citric Acid Cycle/genetics , Osmotic Pressure/physiology , Phylogeny
4.
Development ; 143(20): 3711-3722, 2016 10 15.
Article in English | MEDLINE | ID: mdl-27802136

ABSTRACT

During late gestation, villi extend into the intestinal lumen to dramatically increase the surface area of the intestinal epithelium, preparing the gut for the neonatal diet. Incomplete development of the intestine is the most common gastrointestinal complication in neonates, but the causes are unclear. We provide evidence in mice that Yin Yang 1 (Yy1) is crucial for intestinal villus development. YY1 loss in the developing endoderm had no apparent consequences until late gestation, after which the intestine differentiated poorly and exhibited severely stunted villi. Transcriptome analysis revealed that YY1 is required for mitochondrial gene expression, and ultrastructural analysis confirmed compromised mitochondrial integrity in the mutant intestine. We found increased oxidative phosphorylation gene expression at the onset of villus elongation, suggesting that aerobic respiration might function as a regulator of villus growth. Mitochondrial inhibitors blocked villus growth in a fashion similar to Yy1 loss, thus further linking oxidative phosphorylation with late-gestation intestinal development. Interestingly, we find that necrotizing enterocolitis patients also exhibit decreased expression of oxidative phosphorylation genes. Our study highlights the still unappreciated role of metabolic regulation during organogenesis, and suggests that it might contribute to neonatal gastrointestinal disorders.


Subject(s)
Intestinal Mucosa/metabolism , Intestines/cytology , Organogenesis/physiology , YY1 Transcription Factor/metabolism , Aerobiosis/genetics , Aerobiosis/physiology , Animals , Blotting, Western , Genotype , Immunohistochemistry , Male , Mice , Organogenesis/genetics , Oxidative Phosphorylation , Transcriptome/genetics , YY1 Transcription Factor/genetics
5.
Am J Physiol Regul Integr Comp Physiol ; 316(3): R255-R264, 2019 03 01.
Article in English | MEDLINE | ID: mdl-30601704

ABSTRACT

Purely diffusive O2 transport typically is insufficient to sustain aerobic metabolism in most multicellular organisms. In animals that are small enough, however, a high surface-to-volume ratio may allow passive diffusion alone to supply sufficient O2 transfer. The purpose of this study was to explore the impacts of internal convection on respiratory gas transfer in a small complex organism, the larval zebrafish ( Danio rerio). Specifically, we tested the hypothesis that internal convection is required for the normal transfer of the respiratory gases O2 and CO2 and maintenance of resting aerobic metabolic rate in larvae at 4 days postfertilization (dpf). Morpholino knockdown of the vascular endothelial growth factor (VEGF) or cardiac troponin T (TNNT2) proteins allowed an examination of gas transfer in two independent models lacking internal convection. With the use of a scanning micro-optrode technique to measure regional epithelial O2 fluxes ( Jo2), it was demonstrated that larvae lacking convection exhibited reduced Jo2 in regions spanning the head to the trunk. Moreover, the acute loss of internal convection caused by heart stoppage resulted in reduced rates of cutaneous Jo2, an effect that was reversed upon the restoration of internal convection. With the use of whole body respirometry, it was shown that loss of internal convection was associated with reduced resting rates of O2 consumption and CO2 excretion in larvae at 4 dpf. The results of these experiments clearly demonstrate that internal convection is required to maintain resting rates of respiratory gas transfer in larval zebrafish.


Subject(s)
Aerobiosis/physiology , Convection , Pulmonary Gas Exchange/physiology , Zebrafish/metabolism , Animals , Carbon Dioxide/metabolism , Eye/growth & development , Female , Gene Knockdown Techniques , Larva , Male , Oxygen Consumption/physiology , Respiratory Physiological Phenomena , Troponin T/metabolism , Vascular Endothelial Growth Factor A/metabolism , Zebrafish Proteins/metabolism
6.
J Exp Biol ; 222(Pt 22)2019 11 21.
Article in English | MEDLINE | ID: mdl-31628206

ABSTRACT

Animals that inhabit environments that fluctuate in oxygen must not only contend with disruptions to aerobic metabolism, but also the potential effects of reactive oxygen species (ROS). The goal of this study was to compare aspects of ROS metabolism in response to O2 variability (6 h hypoxia or hyperoxia, with subsequent normoxic recovery) in two species of intertidal sculpin fishes (Cottidae, Actinopterygii) that can experience O2 fluctuations in their natural environment and differ in whole-animal hypoxia tolerance. To assess ROS metabolism, we measured the ratio of glutathione to glutathione disulfide as an indicator of tissue redox environment, MitoP/MitoB ratio to assess in vivo mitochondrial ROS generation, thiobarbituric acid reactive substances (TBARS) for lipid peroxidation, and total oxidative scavenging capacity (TOSC) in the liver, brain and gill. In the brain, the more hypoxia-tolerant Oligocottusmaculosus showed large increases in TBARS levels following hypoxia and hyperoxia exposure that were generally not associated with large changes in mitochondrial H2O2 In contrast, the less-tolerant Scorpaenichthysmarmoratus showed no significant changes in TBARS or mitochondrial H2O2 in the brain. More moderate increases were observed in the liver and gill of O. maculosus exposed to hypoxia and hyperoxia with normoxic recovery, whereas S. marmoratus had a greater response to O2 variability in these tissues compared with the brain. Our results show a species- and tissue-specific relationship between hypoxia tolerance and ROS metabolism.


Subject(s)
Oxygen/metabolism , Perciformes/metabolism , Reactive Oxygen Species/metabolism , Aerobiosis/physiology , Animals , Brain/metabolism , Gills/metabolism , Hypoxia/metabolism , Lipid Peroxidation , Liver/metabolism , Oxidation-Reduction , Species Specificity
7.
J Theor Biol ; 476: 62-73, 2019 09 07.
Article in English | MEDLINE | ID: mdl-31170405

ABSTRACT

The lifeless earth was formed around 4.5 billion years ago and the first anaerobic unicellular "organisms" may have appeared half a billion years later. Despite subsequent prokaryotes (bacteria and archaea) evolving quite complex biochemistry and some eukaryote characteristics, the transition from unicellular prokaryotes to multicellular, aerobic eukaryotes took a further 2.5 billion years to begin. The key factor or factors that eventually caused this long-delayed transition is a question that has been a focus of considerable research and a topic of discussion over many years. On the basis of the extensive literature available and consideration of some of the characteristics that distinguish multicellular eukaryotes from prokaryotes, it is proposed that, as well as the development of oxygenic photosynthesis producing high levels of environmental oxygen and the formation of vital organelles such as aerobic adenosine triphosphate-generating mitochondria, the concurrent evolution of the L-ascorbic acid redox system should be considered as a key factor that led to the evolution of multicellular eukaryotes and it remains vitally involved in the maintenance of multicellularity and many other eukaryote characteristics.


Subject(s)
Ascorbic Acid/metabolism , Eukaryotic Cells/metabolism , Evolution, Molecular , Photosynthesis/physiology , Plants/metabolism , Aerobiosis/physiology , Eukaryotic Cells/cytology
8.
Mol Biol Evol ; 34(11): 2870-2878, 2017 Nov 01.
Article in English | MEDLINE | ID: mdl-28961859

ABSTRACT

Parallel evolution occurs when a similar trait emerges in independent evolutionary lineages. Although changes in protein coding and gene transcription have been investigated as underlying mechanisms for parallel evolution, parallel changes in chromatin structure have never been reported. Here, Saccharomyces cerevisiae and a distantly related yeast species, Dekkera bruxellensis, are investigated because both species have independently evolved the capacity of aerobic fermentation. By profiling and comparing genome sequences, transcriptomic landscapes, and chromatin structures, we revealed that parallel changes in nucleosome occupancy in the promoter regions of mitochondria-localized genes led to concerted suppression of mitochondrial functions by glucose, which can explain the metabolic convergence in these two independent yeast species. Further investigation indicated that similar mutational processes in the promoter regions of these genes in the two independent evolutionary lineages underlay the parallel changes in chromatin structure. Our results indicate that, despite several hundred million years of separation, parallel changes in chromatin structure, can be an important adaptation mechanism for different organisms. Due to the important role of chromatin structure changes in regulating gene expression and organism phenotypes, the novel mechanism revealed in this study could be a general phenomenon contributing to parallel adaptation in nature.


Subject(s)
Aerobiosis/genetics , Chromatin/genetics , Aerobiosis/physiology , Anaerobiosis/genetics , Biological Evolution , Chromatin/physiology , Dekkera/genetics , Dekkera/metabolism , Evolution, Molecular , Fermentation/genetics , Gene Expression/genetics , Glucose/metabolism , Phylogeny , Promoter Regions, Genetic/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism
9.
Mol Microbiol ; 104(2): 278-293, 2017 04.
Article in English | MEDLINE | ID: mdl-28118511

ABSTRACT

The metabolism of the purple non-sulfur bacterium Rhodobacter sphaeroides is versatile and it can grow under various conditions. Here, we report evidence that the anaerobic photosynthetic metabolism of R. sphaeroides is regulated by protein lysine acetylation. Using a proteomic approach, 59 acetylated peptides were detected. Among them is the global anaerobic transcription factor FnrL, which regulates the biosynthetic pathway of tetrapyrroles and synthesis of the photosynthetic apparatus. Lysine 223 of FnrL was identified as acetylated. We show that all three lysines in the DNA binding domain (K223, K213 and K175) of FnrL can be acetylated by acetyl-phosphate in vitro. A bacterial deacetylase homolog, RsCobB can deacetylate FnrL in vitro. The transcription of genes downstream of FnrL decreased when the DNA binding domain of FnrL was acetylated, as revealed by chromatin immunoprecipitation and acetylation-mimicking mutagenesis. An increasing number of acetylated lysines resulted in a further decrease in DNA binding ability. These results demonstrate that the lysine acetylation can fine tune the function of the oxygen-sensitive FnrL; thus, it might regulate anaerobic photosynthetic metabolism of R. sphaeroides.


Subject(s)
Bacterial Proteins/metabolism , Bacterial Proteins/physiology , Trans-Activators/metabolism , Trans-Activators/physiology , Acetylation , Aerobiosis/physiology , Anaerobiosis/physiology , Bacterial Proteins/genetics , Chromatin Immunoprecipitation , DNA, Bacterial/metabolism , Gene Expression Regulation, Bacterial/genetics , Genes, Bacterial , Lysine/metabolism , Photosynthesis/genetics , Proteomics , Rhodobacter sphaeroides/genetics , Rhodobacter sphaeroides/metabolism , Tetrapyrroles/metabolism , Trans-Activators/genetics , Transcription Factors/metabolism
10.
Respir Res ; 19(1): 9, 2018 01 15.
Article in English | MEDLINE | ID: mdl-29334947

ABSTRACT

Dysregulation of VEGF-A bioavailability has been implicated in the development of lung injury/fibrosis, exemplified by Idiopathic Pulmonary Fibrosis (IPF). VEGF-A is a target of the hypoxic response via its translational regulation by HIF-1α. The role of hypoxia and hyperoxia in the development and progression of IPF has not been explored. In normal lung (NF) and IPF-derived fibroblasts (FF) VEGF-Axxxa protein expression was upregulated by hypoxia, mediated through activation of VEGF-Axxxa gene transcription. VEGF-A receptors and co-receptors were differentially expressed by hypoxia and hyperoxia. Our data supports a potential role for hypoxia, hyperoxia and VEGF-Axxxa isoforms as drivers of fibrogenesis.


Subject(s)
Idiopathic Pulmonary Fibrosis/metabolism , Lung/metabolism , Receptors, Vascular Endothelial Growth Factor/biosynthesis , Vascular Endothelial Growth Factor A/biosynthesis , Aerobiosis/physiology , Cell Hypoxia/physiology , Cells, Cultured , Fibroblasts/metabolism , Fibroblasts/pathology , Gene Expression , Humans , Idiopathic Pulmonary Fibrosis/pathology , Lung/pathology , Protein Isoforms/biosynthesis , Protein Isoforms/genetics , Receptors, Vascular Endothelial Growth Factor/genetics , Vascular Endothelial Growth Factor A/genetics
11.
J Biol Regul Homeost Agents ; 32(3): 649-654, 2018.
Article in English | MEDLINE | ID: mdl-29921394

ABSTRACT

Saccharomyces cerevisiae can utilize a wide range of carbon sources; however, in the presence of glucose the use of alternate carbon sources would be repressed. Several genes involved in the metabolic pathways exert these effects. Among them, the zinc finger protein, Mig1 (multicopy inhibitor of GAL gene expression) plays important roles in glucose repression of Saccharomyces cerevisiae. To investigate whether the alleviation of glucose effect would result in a switch to oxidative production pathway, MIG1 were disrupted in a haploid laboratory strain (2805) of S. cerevisiae. The impact of this disruption was studied under fully aerobic conditions when glucose was the sole carbon source. Our results showed that glucose repression was partly alleviated; i.e., ethanol, as a significant fermentation marker, and acetate productions were respectively decreased by 14.13% and 43.71% compared to the wild type. In ΔMIG1 strain, the metabolic shifting on the aerobic pathway and a significant increase in pyruvate and glycerol production suggested it as an optimally productive industrial yeast strain. However, further studies are needed to confirm these findings.


Subject(s)
Ethanol/metabolism , Glucose/metabolism , Glycerol/metabolism , Pyruvic Acid/metabolism , Repressor Proteins/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Aerobiosis/physiology , Fermentation/physiology , Oxidation-Reduction , Repressor Proteins/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/genetics
12.
Antonie Van Leeuwenhoek ; 111(12): 2473-2484, 2018 Dec.
Article in English | MEDLINE | ID: mdl-30066210

ABSTRACT

An elliptical to cucumber-shaped methanotroph with large cells was isolated from a rice rhizosphere in Western India. Strain Sn10-6 is one of the first methanotrophs to be isolated from Indian rice fields. Cells of Sn10-6 are Gram-negative, motile, large in size (3-6 µm × 1.5-2 µm) and contain intracellular cytoplasmic membrane stacks. Colonies of Sn10-6 and liquid cultures have a pale pink colour. Strain Sn10-6 was initially isolated under micro-oxic conditions but later adapted to grow under fully oxic conditions. The major fatty acids present were identified as C16:1ω6c, C16:1ω7c and C16:0 and ubiquinone was found to be the major quinone. The 16S rRNA gene sequence of strain Sn10-6 displays high similarity to the genes of Methylovulum psychrotolerans Sph1T (93.6%) followed by Methylosarcina fibrata AML-C10T (93.5%) and about 90-93% similarity to the genes of known species of Type I methanotrophic genera from the family Methylococcaceae. The draft genome information indicated that the G + C content of strain Sn10-6 is 43.9 mol%. Phylogenetic trees using 16S rRNA gene and the particulate methane mono-oxygenase sequences unequivocally placed Sn10-6 close to the genus Methylovulum. Based on the 16S rRNA gene differences, morphological characters and draft genome information, strain Sn10-6 (=MCC 3492 =KCTC 15683) is described here as the type strain of a novel species within a new genus, 'Candidatus Methylocucumis oryzae'.


Subject(s)
DNA, Bacterial/genetics , Genome, Bacterial , Methylococcaceae/genetics , Oryza/microbiology , Phylogeny , RNA, Ribosomal, 16S/genetics , Aerobiosis/physiology , Bacterial Typing Techniques , Base Composition , Color , Crops, Agricultural/microbiology , Fatty Acids/biosynthesis , Genotype , India , Methane/metabolism , Methylococcaceae/classification , Methylococcaceae/isolation & purification , Methylococcaceae/metabolism , Phenotype , Rhizosphere , Ubiquinone/biosynthesis
13.
J Neurosci ; 36(6): 1871-8, 2016 Feb 10.
Article in English | MEDLINE | ID: mdl-26865611

ABSTRACT

Aerobic glycolysis and lactate production in the brain plays a key role in memory, yet the role of this metabolism in the cognitive decline associated with Alzheimer's disease (AD) remains poorly understood. Here we examined the relationship between cerebral lactate levels and memory performance in an APP/PS1 mouse model of AD, which progressively accumulates amyloid-ß. In vivo (1)H-magnetic resonance spectroscopy revealed an age-dependent decline in lactate levels within the frontal cortex of control mice, whereas lactate levels remained unaltered in APP/PS1 mice from 3 to 12 months of age. Analysis of hippocampal interstitial fluid by in vivo microdialysis revealed a significant elevation in lactate levels in APP/PS1 mice relative to control mice at 12 months of age. An age-dependent decline in the levels of key aerobic glycolysis enzymes and a concomitant increase in lactate transporter expression was detected in control mice. Increased expression of lactate-producing enzymes correlated with improved memory in control mice. Interestingly, in APP/PS1 mice the opposite effect was detected. In these mice, increased expression of lactate producing enzymes correlated with poorer memory performance. Immunofluorescent staining revealed localization of the aerobic glycolysis enzymes pyruvate dehydrogenase kinase and lactate dehydrogenase A within cortical and hippocampal neurons in control mice, as well as within astrocytes surrounding amyloid plaques in APP/PS1 mice. These observations collectively indicate that production of lactate, via aerobic glycolysis, is beneficial for memory function during normal aging. However, elevated lactate levels in APP/PS1 mice indicate perturbed lactate processing, a factor that may contribute to cognitive decline in AD. SIGNIFICANCE STATEMENT: Lactate has recently emerged as a key metabolite necessary for memory consolidation. Lactate is the end product of aerobic glycolysis, a unique form of metabolism that occurs within certain regions of the brain. Here we detected an age-dependent decline in the expression of aerobic glycolysis enzymes and a concomitant decrease in lactate levels within the frontal cortex of wild-type mice. Improved memory performance in wild-type mice correlated with elevated expression of aerobic glycolysis enzymes. Surprisingly, lactate levels remained elevated with age and increased aerobic glycolysis enzyme expression correlated with poorer memory performance in APP/PS1 mice. These findings suggest that while lactate production is beneficial for memory in the healthy aging brain, it might be detrimental in an Alzheimer's disease context.


Subject(s)
Amyloid beta-Protein Precursor/genetics , Amyloidosis/genetics , Amyloidosis/metabolism , Frontal Lobe/metabolism , Glycolysis/physiology , Memory/physiology , Presenilin-1/genetics , Psychomotor Performance/physiology , Aerobiosis/physiology , Aging/metabolism , Animals , Astrocytes/enzymology , Astrocytes/metabolism , Brain Chemistry/genetics , Hippocampus/growth & development , Hippocampus/metabolism , Lactic Acid/metabolism , Magnetic Resonance Spectroscopy , Mice, Inbred C57BL , Mice, Transgenic , Monocarboxylic Acid Transporters/metabolism
14.
J Biol Chem ; 291(30): 15653-62, 2016 07 22.
Article in English | MEDLINE | ID: mdl-27288412

ABSTRACT

The bacterium Bradyrhizobium japonicum USDA110 does not synthesize siderophores for iron utilization in aerobic environments, and the mechanism of iron uptake within symbiotic soybean root nodules is unknown. An mbfA bfr double mutant defective in iron export and storage activities cannot grow aerobically in very high iron medium. Here, we found that this phenotype was suppressed by loss of function mutations in the feoAB operon encoding ferrous (Fe(2+)) iron uptake proteins. Expression of the feoAB operon genes was elevated under iron limitation, but mutants defective in either gene were unable to grow aerobically over a wide external ferric (Fe(3+)) iron (FeCl3) concentration range. Thus, FeoAB accommodates iron acquisition under iron limited and iron replete conditions. Incorporation of radiolabel from either (55)Fe(2+) or (59)Fe(3+) into cells was severely defective in the feoA and feoB strains, suggesting Fe(3+) reduction to Fe(2+) prior to traversal across the cytoplasmic membrane by FeoAB. The feoA or feoB deletion strains elicited small, ineffective nodules on soybean roots, containing few bacteria and lacking nitrogen fixation activity. A feoA(E40K) mutant contained partial iron uptake activity in culture that supported normal growth and established an effective symbiosis. The feoA(E40K) strain had partial iron uptake activity in situ within nodules and in isolated cells, indicating that FeoAB is the iron transporter in symbiosis. We conclude that FeoAB supports iron acquisition under limited conditions of soil and in the iron-rich environment of a symbiotic nodule.


Subject(s)
Bacterial Proteins/metabolism , Bradyrhizobium/metabolism , Glycine max/microbiology , Membrane Transport Proteins/metabolism , Root Nodules, Plant/microbiology , Symbiosis/physiology , Aerobiosis/physiology , Bacterial Proteins/genetics , Bradyrhizobium/genetics , Iron/metabolism , Membrane Transport Proteins/genetics , Root Nodules, Plant/metabolism
15.
Biochim Biophys Acta ; 1857(3): 190-7, 2016 Mar.
Article in English | MEDLINE | ID: mdl-26546715

ABSTRACT

Aerobic respiratory chains from all life kingdoms are composed by several complexes that have been deeply characterized in their isolated form. These membranous complexes link the oxidation of reducing substrates to the reduction of molecular oxygen, in a process that conserves energy by ion translocation between both sides of the mitochondrial or prokaryotic cytoplasmatic membranes. In recent years there has been increasing evidence that those complexes are organized as supramolecular structures, the so-called supercomplexes and respirasomes, being available for eukaryotes strong data namely obtained by electron microscopy and single particle analysis. A parallel study has been developed for prokaryotes, based on blue native gels and mass spectrometry analysis, showing that in these more simple unicellular organisms such supercomplexes also exist, involving not only typical aerobic-respiration associated complexes, but also anaerobic-linked enzymes. After a short overview of the data on eukaryotic supercomplexes, we will analyse comprehensively the different types of prokaryotic aerobic respiratory supercomplexes that have been thus far suggested, in both bacteria and archaea. This article is part of a Special Issue entitled Organization and dynamics of bioenergetic systems in bacteria, edited by Prof Conrad Mullineaux.


Subject(s)
Bacteria/enzymology , Bacterial Proteins/metabolism , Cell Membrane/enzymology , Electron Transport Chain Complex Proteins/metabolism , Proton-Motive Force/physiology , Aerobiosis/physiology , Electron Transport/physiology
16.
Environ Microbiol ; 19(10): 4326-4348, 2017 10.
Article in English | MEDLINE | ID: mdl-28892295

ABSTRACT

Campylobacter jejuni, the most frequent cause of food-borne bacterial gastroenteritis worldwide, is a microaerophile that has to survive high environmental oxygen tensions, adapt to oxygen limitation in the intestine and resist host oxidative attack. Here, oxygen-dependent changes in C. jejuni physiology were studied at constant growth rate using carbon (serine)-limited continuous chemostat cultures. We show that a perceived aerobiosis scale can be calibrated by the acetate excretion flux, which becomes zero when metabolism is fully aerobic (100% aerobiosis). Transcriptome changes in a downshift experiment from 150% to 40% aerobiosis revealed many novel oxygen-regulated genes and highlighted re-modelling of the electron transport chains. A label-free proteomic analysis showed that at 40% aerobiosis, many proteins involved in host colonisation (e.g., PorA, CadF, FlpA, CjkT) became more abundant. PorA abundance increased steeply below 100% aerobiosis. In contrast, several citric-acid cycle enzymes, the peptide transporter CstA, PEB1 aspartate/glutamate transporter, LutABC lactate dehydrogenase and PutA proline dehydrogenase became more abundant with increasing aerobiosis. We also observed a co-ordinated response of oxidative stress protection enzymes and Fe-S cluster biogenesis proteins above 100% aerobiosis. Our approaches reveal key virulence factors that respond to restricted oxygen availability and specific transporters and catabolic pathways activated with increasing aerobiosis.


Subject(s)
Aerobiosis/physiology , Campylobacter jejuni/metabolism , Campylobacter jejuni/pathogenicity , Oxidative Stress/physiology , Oxygen/metabolism , Campylobacter Infections/microbiology , Campylobacter jejuni/genetics , Humans , Oxidation-Reduction , Proteome/metabolism , Proteomics , Transcriptome/genetics , Virulence Factors/genetics , Virulence Factors/metabolism
17.
Metab Eng ; 44: 100-107, 2017 11.
Article in English | MEDLINE | ID: mdl-28951266

ABSTRACT

Adaptive laboratory evolution (ALE) is a widely-used method for improving the fitness of microorganisms in selected environmental conditions. It has been applied previously to Escherichia coli K-12 MG1655 during aerobic exponential growth on glucose minimal media, a frequently used model organism and growth condition, to probe the limits of E. coli growth rate and gain insights into fast growth phenotypes. Previous studies have described up to 1.6-fold increases in growth rate following ALE, and have identified key causal genetic mutations and changes in transcriptional patterns. Here, we report for the first time intracellular metabolic fluxes for six such adaptively evolved strains, as determined by high-resolution 13C-metabolic flux analysis. Interestingly, we found that intracellular metabolic pathway usage changed very little following adaptive evolution. Instead, at the level of central carbon metabolism the faster growth was facilitated by proportional increases in glucose uptake and all intracellular rates. Of the six evolved strains studied here, only one strain showed a small degree of flux rewiring, and this was also the strain with unique genetic mutations. A comparison of fluxes with two other wild-type (unevolved) E. coli strains, BW25113 and BL21, showed that inter-strain differences are greater than differences between the parental and evolved strains. Principal component analysis highlighted that nearly all flux differences (95%) between the nine strains were captured by only two principal components. The distance between measured and flux balance analysis predicted fluxes was also investigated. It suggested a relatively wide range of similar stoichiometric optima, which opens new questions about the path-dependency of adaptive evolution.


Subject(s)
Directed Molecular Evolution , Escherichia coli K12/growth & development , Escherichia coli K12/genetics , Aerobiosis/physiology
18.
Metab Eng ; 39: 9-18, 2017 01.
Article in English | MEDLINE | ID: mdl-27840237

ABSTRACT

Glucose and xylose are the two most abundant sugars derived from the breakdown of lignocellulosic biomass. While aerobic glucose metabolism is relatively well understood in E. coli, until now there have been only a handful of studies focused on anaerobic glucose metabolism and no 13C-flux studies on xylose metabolism. In the absence of experimentally validated flux maps, constraint-based approaches such as MOMA and RELATCH cannot be used to guide new metabolic engineering designs. In this work, we have addressed this critical gap in current understanding by performing comprehensive characterizations of glucose and xylose metabolism under aerobic and anaerobic conditions, using recent state-of-the-art techniques in 13C metabolic flux analysis (13C-MFA). Specifically, we quantified precise metabolic fluxes for each condition by performing parallel labeling experiments and analyzing the data through integrated 13C-MFA using the optimal tracers [1,2-13C]glucose, [1,6-13C]glucose, [1,2-13C]xylose and [5-13C]xylose. We also quantified changes in biomass composition and confirmed turnover of macromolecules by applying [U-13C]glucose and [U-13C]xylose tracers. We demonstrated that under anaerobic growth conditions there is significant turnover of lipids and that a significant portion of CO2 originates from biomass turnover. Using knockout strains, we also demonstrated that ß-oxidation is critical for anaerobic growth on xylose. Quantitative analysis of co-factor balances (NADH/FADH2, NADPH, and ATP) for different growth conditions provided new insights regarding the interplay of energy and redox metabolism and the impact on E. coli cell physiology.


Subject(s)
Carbon-13 Magnetic Resonance Spectroscopy/methods , Escherichia coli/metabolism , Glucose/metabolism , Lipid Metabolism/physiology , Metabolic Flux Analysis/methods , Oxygen/metabolism , Xylose/metabolism , Aerobiosis/physiology , Anaerobiosis/physiology , Carbon Isotopes/pharmacokinetics , Escherichia coli Proteins/metabolism , Metabolic Networks and Pathways/physiology , Models, Biological
19.
Am J Physiol Regul Integr Comp Physiol ; 313(6): R740-R753, 2017 Dec 01.
Article in English | MEDLINE | ID: mdl-28877871

ABSTRACT

Muscle contraction requires the physiology to adapt rapidly to meet the surge in energy demand. To investigate the shift in metabolic control, especially between oxygen and metabolism, researchers often depend on near-infrared spectroscopy (NIRS) to measure noninvasively the tissue O2 Because NIRS detects the overlapping myoglobin (Mb) and hemoglobin (Hb) signals in muscle, interpreting the data as an index of cellular or vascular O2 requires deconvoluting the relative contribution. Currently, many in the NIRS field ascribe the signal to Hb. In contrast, 1H NMR has only detected the Mb signal in contracting muscle, and comparative NIRS and NMR experiments indicate a predominant Mb contribution. The present study has examined the question of the NIRS signal origin by measuring simultaneously the 1H NMR, 31P NMR, and NIRS signals in finger flexor muscles during the transition from rest to contraction, recovery, ischemia, and reperfusion. The experiment results confirm a predominant Mb contribution to the NIRS signal from muscle. Given the NMR and NIRS corroborated changes in the intracellular O2, the analysis shows that at the onset of muscle contraction, O2 declines immediately and reaches new steady states as contraction intensity rises. Moreover, lactate formation increases even under quite aerobic condition.


Subject(s)
Exercise/physiology , Fingers , Magnetic Resonance Spectroscopy/methods , Muscle, Skeletal/metabolism , Oxygen Consumption/physiology , Spectroscopy, Near-Infrared/methods , Adult , Aerobiosis/physiology , Energy Metabolism/physiology , Ergometry , Hemoglobins/metabolism , Humans , Ischemia , Male , Muscle Contraction/physiology , Muscle, Skeletal/blood supply , Myoglobin/metabolism , Oxygen/blood , Regional Blood Flow
20.
Am J Physiol Regul Integr Comp Physiol ; 312(1): R93-R100, 2017 01 01.
Article in English | MEDLINE | ID: mdl-27856415

ABSTRACT

Deteriorated aerobic response to moderate exercise might precede the manifestation of clinical symptoms of noncommunicable diseases. The purpose of the current study was to verify that the use of current wearable technologies for analysis of pulmonary oxygen uptake (V̇o2) dynamics during a pseudorandom ternary sequence (PRTS) over-ground walking protocol is a suitable procedure for the investigation of the aerobic response in more realistic settings. A wearable accelerometer located at the hip assessed the magnitude of the input changes delivered to the aerobic system. Eight adults (24 ± 4 yr old, 174 ± 7 cm, and 71.4 ± 7.4 kg) performed two identical PRTS over-ground walking protocols. In addition, they performed on the cycle ergometer two identical pseudorandom binary sequence (PRBS) protocols and one incremental protocol for maximal V̇o2 determination. In the frequency domain, mean normalized gain amplitude (MNG in %) quantified V̇o2 dynamics. The MNG during PRTS was correlated (r = -0.80, P = 0.01) with the V̇o2 time constant (τ) obtained during cycling. The MNG estimated during PRBS was similar to the MNG estimated during PRTS (r = 0.80, P = 0.01). The maximal V̇o2 correlated with the MNG obtained during the PRBS (r = 0.79, P = 0.01) and PRTS (r = 0.78, P = 0.02) protocols. In conclusion, PRTS over-ground walking protocol can be used to evaluate the aerobic system dynamics by the simultaneous measurement of V̇o2 and hip acceleration. In addition, the aerobic response dynamics from PRBS and PRTS were correlated to maximal V̇o2 This study has shown that wearable technologies in combination with assessment of MNG, a novel indicator of system dynamics, open new possibilities to monitor cardiorespiratory health under conditions that better simulate activities of daily living than cardiopulmonary exercise testing performed in a medical environment.


Subject(s)
Accelerometry/methods , Gait/physiology , Hip Joint/physiology , Models, Biological , Oxygen Consumption/physiology , Walking/physiology , Acceleration , Aerobiosis/physiology , Computer Simulation , Exercise Test/methods , Humans , Male , Monitoring, Ambulatory/methods , Reproducibility of Results , Sensitivity and Specificity , Young Adult
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