Genomic Analysis of Anaerobic Respiration in the Archaeon Halobacterium sp. Strain NRC-1: Dimethyl Sulfoxide and Trimethylamine N-Oxide as Terminal Electron Acceptors

ABSTRACT We have investigated anaerobic respiration of the archaeal model organism Halobacterium sp. strain NRC-1 by using phenotypic and genetic analysis, bioinformatics, and transcriptome analysis. NRC-1 was found to grow on either dimethyl sulfoxide (DMSO) or trimethylamine N-oxide (TMAO) as the sole terminal electron acceptor, with a doubling time of 1 day. An operon, dmsREABCD, encoding a putative regulatory protein, DmsR, a molybdopterin oxidoreductase of the DMSO reductase family (DmsEABC), and a molecular chaperone (DmsD) was identified by bioinformatics and confirmed as a transcriptional unit by reverse transcriptase PCR analysis. dmsR, dmsA, and dmsD in-frame deletion mutants were individually constructed. Phenotypic analysis demonstrated that dmsR, dmsA, and dmsD are required for anaerobic respiration on DMSO and TMAO. The requirement for dmsR, whose predicted product contains a DNA-binding domain similar to that of the Bat family of activators (COG3413), indicated that it functions as an activator. A cysteine-rich domain was found in the dmsR gene, which may be involved in oxygen sensing. Microarray analysis using a whole-genome 60-mer oligonucleotide array showed that the dms operon is induced during anaerobic respiration. Comparison of dmsR + and ΔdmsR strains by use of microarrays showed that the induction of the dmsEABCD operon is dependent on a functional dmsR gene, consistent with its action as a transcriptional activator. Our results clearly establish the genes required for anaerobic respiration using DMSO and TMAO in an archaeon for the first time.

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Production and consumption of nitrous oxide in nitrate-ammonifying Wolinella succinogenes cells

Microbiology ◽

10.1099/mic.0.079293-0 ◽

2014 ◽

Vol 160 (8) ◽

pp. 1749-1759 ◽

Cited By ~ 17

Author(s):

Monique Luckmann ◽

Daniel Mania ◽

Melanie Kern ◽

Lars R. Bakken ◽

Åsa Frostegård ◽

...

Keyword(s):

Nitrous Oxide ◽

Nitrosative Stress ◽

Stratospheric Ozone ◽

Anaerobic Respiration ◽

Model Organism ◽

Wolinella Succinogenes ◽

Terminal Electron Acceptor ◽

Production And Consumption ◽

Public Consciousness ◽

Nitrate And Nitrite

Global warming is moving more and more into the public consciousness. Besides the commonly mentioned carbon dioxide and methane, nitrous oxide (N2O) is a powerful greenhouse gas in addition to its contribution to depletion of stratospheric ozone. The increasing concern about N2O emission has focused interest on underlying microbial energy-converting processes and organisms harbouring N2O reductase (NosZ), such as denitrifiers and ammonifiers of nitrate and nitrite. Here, the epsilonproteobacterial model organism Wolinella succinogenes is investigated with regard to its capacity to produce and consume N2O during growth by anaerobic nitrate ammonification. This organism synthesizes an unconventional cytochrome c nitrous oxide reductase (cNosZ), which is encoded by the first gene of an atypical nos gene cluster. However, W. succinogenes lacks a nitric oxide (NO)-producing nitrite reductase of the NirS- or NirK-type as well as an NO reductase of the Nor-type. Using a robotized incubation system, the wild-type strain and suitable mutants of W. succinogenes that either produced or lacked cNosZ were analysed as to their production of NO, N2O and N2 in both nitrate-sufficient and nitrate-limited growth medium using formate as electron donor. It was found that cells growing in nitrate-sufficient medium produced small amounts of N2O, which derived from nitrite and, most likely, from the presence of NO. Furthermore, cells employing cNosZ were able to reduce N2O to N2. This reaction, which was fully inhibited by acetylene, was also observed after adding N2O to the culture headspace. The results indicate that W. succinogenes cells are competent in N2O and N2 production despite being correctly grouped as respiratory nitrate ammonifiers. N2O production is assumed to result from NO detoxification and nitrosative stress defence, while N2O serves as a terminal electron acceptor in anaerobic respiration. The ecological implications of these findings are discussed.

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Zinc limitation in Klebsiella pneumoniae profiled by quantitative proteomics influences transcriptional regulation and cation transporter-associated capsule production

BMC Microbiology ◽

10.1186/s12866-021-02091-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

A. Sukumaran ◽

S. Pladwig ◽

J. Geddes-McAlister

Keyword(s):

Klebsiella Pneumoniae ◽

Metal Ion ◽

Ion Homeostasis ◽

Cellular Protein ◽

Pcr Analysis ◽

Phenotypic Analysis ◽

Metal Ion Homeostasis ◽

Capsule Production ◽

The Impact

Abstract Background Microbial organisms encounter a variety of environmental conditions, including changes to metal ion availability. Metal ions play an important role in many biological processes for growth and survival. As such, microbes alter their cellular protein levels and secretion patterns in adaptation to a changing environment. This study focuses on Klebsiella pneumoniae, an opportunistic bacterium responsible for nosocomial infections. By using K. pneumoniae, we aim to determine how a nutrient-limited environment (e.g., zinc depletion) modulates the cellular proteome and secretome of the bacterium. By testing virulence in vitro, we provide novel insight into bacterial responses to limited environments in the presence of the host. Results Analysis of intra- and extracellular changes identified 2380 proteins from the total cellular proteome (cell pellet) and 246 secreted proteins (supernatant). Specifically, HutC, a repressor of the histidine utilization operon, showed significantly increased abundance under zinc-replete conditions, which coincided with an expected reduction in expression of genes within the hut operon from our validating qRT-PCR analysis. Additionally, we characterized a putative cation transport regulator, ChaB that showed significantly higher abundance under zinc-replete vs. -limited conditions, suggesting a role in metal ion homeostasis. Phenotypic analysis of a chaB deletion strain demonstrated a reduction in capsule production, zinc-dependent growth and ion utilization, and reduced virulence when compared to the wild-type strain. Conclusions This is first study to comprehensively profile the impact of zinc availability on the proteome and secretome of K. pneumoniae and uncover a novel connection between zinc transport and capsule production in the bacterial system.

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The contribution of nitrate respiration to the energy budget of the symbiont-containing clam Lucinoma aequizonata: a calorimetric study

Journal of Experimental Biology ◽

10.1242/jeb.199.2.427 ◽

1996 ◽

Vol 199 (2) ◽

pp. 427-433

Author(s):

U Hentschel ◽

S Hand ◽

H Felbeck

Keyword(s):

Heat Production ◽

Sea Water ◽

Anaerobic Respiration ◽

Gill Tissue ◽

Nitrate Respiration ◽

Heat Output ◽

Marine Bivalve ◽

Calorimetric Study ◽

Perfusion Medium ◽

Terminal Electron Acceptor

Heat production and nitrate respiration rates were measured simultaneously in the gill tissue of Lucinoma aequizonata. This marine bivalve contains chemoautotrophic, intracellular, bacterial symbionts in its gill tissue. The symbionts show constitutive anaerobic respiration, using nitrate instead of oxygen as a terminal electron acceptor. An immediate increase in heat production was observed after the addition of nitrate to the perfusion medium of the calorimeter and this was accompanied by the appearance of nitrite in the effluent sea water. The nitrate-stimulated heat output was similar under aerobic and anaerobic conditions, which is consistent with the constitutive nature of nitrate respiration. The amount of heat released was dependent on the concentration of nitrate in the perfusion medium. At nitrate concentrations between 0.5 and 5 mmol l-1, the total heat production was increased over twofold relative to unstimulated baseline values. A mean (±s.e.m.) experimental enthalpy of -130±22.6 kJ mol-1 nitrite (N=13) was measured for this concentration range.

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Altered renal hemodynamics is associated with glomerular lipid accumulation in obese Dahl salt-sensitive leptin receptor mutant rats

AJP Renal Physiology ◽

10.1152/ajprenal.00438.2019 ◽

2020 ◽

Vol 318 (4) ◽

pp. F911-F921 ◽

Cited By ~ 2

Author(s):

Kasi C. McPherson ◽

Corbin A. Shields ◽

Bibek Poudel ◽

Ashley C. Johnson ◽

Lateia Taylor ◽

...

Keyword(s):

Mean Arterial Pressure ◽

Arterial Pressure ◽

Mutant Strain ◽

Early Development ◽

Lipid Accumulation ◽

Leptin Receptor ◽

Regulatory Protein ◽

Pcr Analysis ◽

Glomerular Injury ◽

Receptor Mutant

The present study examined whether development of renal injury in the nondiabetic obese Dahl salt-sensitive leptin receptor mutant (SSLepRmutant) strain is associated with elevations in glomerular filtration rate and renal lipid accumulation. Baseline mean arterial pressure at 6 wk of age was similar between Dahl salt-sensitive wild-type (SSWT) and SSLepRmutant rats. However, by 18 wk of age, the SSLepRmutant strain developed hypertension, while the elevation in mean arterial pressure was not as severe in SSWT rats (192 ± 4 and 149 ± 6 mmHg, respectively). At baseline, proteinuria was fourfold higher in SSLepRmutant than SSWT rats and remained elevated throughout the study. The early development of progressive proteinuria was associated with renal hyperfiltration followed by a decline in renal function over the course of study in the SSLepRmutant compared with SSWT rats. Kidneys from the SSLepRmutant strain displayed more glomerulosclerosis and glomerular lipid accumulation than SSWT rats. Glomeruli were isolated from the renal cortex of both strains at 6 and 18 wk of age, and RNA sequencing was performed to identify genes and pathways driving glomerular injury. We observed significant increases in expression of the influx lipid transporters, chemokine (C-X-C motif) ligand 16 (Cxcl16) and scavenger receptor and fatty acid translocase (Cd36), respectively, and a significant decrease in expression of the efflux lipid transporter, ATP-binding cassette subfamily A member 2 ( Abca2; cholesterol efflux regulatory protein 2), in SSLepRmutant compared with SSWT rats at 6 and 18 wk of age, which were validated by RT-PCR analysis. These data suggest an association between glomerular hyperfiltration and glomerular lipid accumulation during the early development of proteinuria associated with obesity.

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Role for Outer Membrane Cytochromes OmcA and OmcB of Shewanella putrefaciens MR-1 in Reduction of Manganese Dioxide

Applied and Environmental Microbiology ◽

10.1128/aem.67.1.260-269.2001 ◽

2001 ◽

Vol 67 (1) ◽

pp. 260-269 ◽

Cited By ~ 175

Author(s):

Judith M. Myers ◽

Charles R. Myers

Keyword(s):

Outer Membrane ◽

Anaerobic Respiration ◽

Shewanella Putrefaciens ◽

Gene Replacement ◽

Electron Acceptors ◽

Ferric Citrate ◽

Disulfonic Acid ◽

Pcr Analysis ◽

Western Blots ◽

Reverse Transcription Pcr

ABSTRACT Shewanella putrefaciens MR-1 can use a wide variety of terminal electron acceptors for anaerobic respiration, including certain insoluble manganese and iron oxides. To examine whether the outer membrane (OM) cytochromes of MR-1 play a role in Mn(IV) and Fe(III) reduction, mutants lacking the OM cytochrome OmcA or OmcB were isolated by gene replacement. Southern blotting and PCR confirmed replacement of the omcA and omcB genes, respectively, and reverse transcription-PCR analysis demonstrated loss of the respective mRNAs, whereas mRNAs for upstream and downstream genes were retained. The omcA mutant (OMCA1) resembled MR-1 in its growth on trimethylamine N-oxide (TMAO), dimethyl sulfoxide, nitrate, fumarate, thiosulfate, and tetrathionate and its reduction of nitrate, nitrite, ferric citrate, FeOOH, and anthraquinone-2,6-disulfonic acid. Similarly, the omcBmutant (OMCB1) grew on fumarate, nitrate, TMAO, and thiosulfate and reduced ferric citrate and FeOOH. However, OMCA1 and OMCB1 were 45 and 75% slower than MR-1, respectively, at reducing MnO2. OMCA1 lacked only OmcA. While OMCB1 lacked OmcB, other OM cytochromes were also missing or markedly depressed. The total cytochrome content of the OM of OMCB1 was less than 15% of that of MR-1. Western blots demonstrated that OMCB1 still synthesized OmcA, but most of it was localized in the cytoplasmic membrane and soluble fractions rather than in the OM. OMCB1 had therefore lost the ability to properly localize multiple OM cytochromes to the OM. Together, the results suggest that the OM cytochromes of MR-1 participate in the reduction of Mn(IV) but are not required for the reduction of Fe(III) or other electron acceptors.

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Calmodulin and Calmodulin Binding Proteins in Dictyostelium: A Primer

International Journal of Molecular Sciences ◽

10.3390/ijms21041210 ◽

2020 ◽

Vol 21 (4) ◽

pp. 1210

Author(s):

Danton H. O’Day ◽

Ryan J. Taylor ◽

Michael A. Myre

Keyword(s):

Conformational Changes ◽

Calcium Binding ◽

Binding Proteins ◽

Regulatory Protein ◽

Model Organism ◽

Ion Binding ◽

Calcium Dependent ◽

Calmodulin Binding ◽

Human Counterpart ◽

Ef Hands

Dictyostelium discoideum is gaining increasing attention as a model organism for the study of calcium binding and calmodulin function in basic biological events as well as human diseases. After a short overview of calcium-binding proteins, the structure of Dictyostelium calmodulin and the conformational changes effected by calcium ion binding to its four EF hands are compared to its human counterpart, emphasizing the highly conserved nature of this central regulatory protein. The calcium-dependent and -independent motifs involved in calmodulin binding to target proteins are discussed with examples of the diversity of calmodulin binding proteins that have been studied in this amoebozoan. The methods used to identify and characterize calmodulin binding proteins is covered followed by the ways Dictyostelium is currently being used as a system to study several neurodegenerative diseases and how it could serve as a model for studying calmodulinopathies such as those associated with specific types of heart arrythmia. Because of its rapid developmental cycles, its genetic tractability, and a richly endowed stock center, Dictyostelium is in a position to become a leader in the field of calmodulin research.

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Complete Genome Assembly of Yersinia pseudotuberculosis IP2666pIB1

Microbiology Resource Announcements ◽

10.1128/mra.01592-18 ◽

2019 ◽

Vol 8 (7) ◽

Cited By ~ 1

Author(s):

Adam Zoubeidi ◽

Leah Schwiesow ◽

Victoria Auerbuch ◽

Hanh N. Lam

Keyword(s):

Yersinia Pestis ◽

Genome Assembly ◽

Complete Genome ◽

Yersinia Pseudotuberculosis ◽

Model Organism ◽

Genomic Analysis ◽

Bacterial Pathogenesis ◽

Bacterial Virulence ◽

Human Pathogen ◽

Content Type

Yersinia pseudotuberculosis, closely related to Yersinia pestis, is a human pathogen and model organism for studying bacterial pathogenesis. To aid in genomic analysis and understanding bacterial virulence, we sequenced and assembled the complete genome of the human pathogen Yersinia pseudotuberculosis IP2666pIB1.

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Host-Derived Metabolites Modulate Transcription ofSalmonellaGenes Involved in L-Lactate Utilization during Gut Colonization

Infection and Immunity ◽

10.1128/iai.00773-18 ◽

2019 ◽

Vol 87 (4) ◽

Cited By ~ 5

Author(s):

Caroline C. Gillis ◽

Maria G. Winter ◽

Rachael B. Chanin ◽

Wenhan Zhu ◽

Luisella Spiga ◽

...

Keyword(s):

Cell Metabolism ◽

Regulatory Protein ◽

Transcriptional Level ◽

Lactate Oxidation ◽

Terminal Electron Acceptor ◽

Content Type ◽

Gut Colonization ◽

Serovar Typhimurium ◽

Lactate Utilization

ABSTRACTDuringSalmonella entericaserovar Typhimurium infection, host inflammation alters the metabolic environment of the gut lumen to favor the outgrowth of the pathogen at the expense of the microbiota. Inflammation-driven changes in host cell metabolism lead to the release ofl-lactate and molecular oxygen from the tissue into the gut lumen.Salmonellautilizes lactate as an electron donor in conjunction with oxygen as the terminal electron acceptor to support gut colonization. Here, we investigated transcriptional regulation of the respiratoryl-lactate dehydrogenase LldDin vitroand in mouse models ofSalmonellainfection. The two-component system ArcAB repressed transcription ofl-lactate utilization genes under anaerobic conditionsin vitro. The ArcAB-mediated repression oflldDtranscription was relieved under microaerobic conditions. Transcription oflldDwas induced byl-lactate but notd-lactate. A mutant lacking the regulatory protein LldR failed to inducelldDtranscription in response tol-lactate. Furthermore, thelldRmutant exhibited reduced transcription ofl-lactate utilization genes and impaired fitness in murine models of infection. These data provide evidence that the host-derived metabolites oxygen andl-lactate serve as cues forSalmonellato regulate lactate oxidation metabolism on a transcriptional level.

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Auxological and endocrine phenotype in a population-based cohort of patients with PROP1 gene defects

Acta Endocrinologica ◽

10.1530/eje.1.01989 ◽

2005 ◽

Vol 153 (3) ◽

pp. 389-396 ◽

Cited By ~ 41

Author(s):

Jan Lebl ◽

Jan Vosáhlo ◽

Roland W Pfaeffle ◽

Heike Stobbe ◽

Jana Černá ◽

...

Keyword(s):

Genomic Analysis ◽

Population Based ◽

Hormone Deficiency ◽

Heterozygous Mutation ◽

Pituitary Hormone ◽

Phenotypic Analysis ◽

Phenotypic Data ◽

Sibling Pairs ◽

Pituitary Development ◽

Gene Defects

Objective: Multiple pituitary hormone deficiency (MPHD) may result from defects of transcription factors that govern early pituitary development. We aimed to establish the prevalence of HESX1, PROP1, and POU1F1 gene defects in a population-based cohort of patients with MPHD and to analyse the phenotype of affected individuals. Design and methods: Genomic analysis was carried out on 74 children and adults with MPHD from the Czech Republic (including four sibling pairs). Phenotypic data were collected from medical records and referring physicians. Results: One patient carried a heterozygous mutation of POU1F1 (71C > T), and 18 patients (including three sibling pairs) had a PROP1 mutation (genotypes 150delA/301delGA/9/, 301delGA/301-delGA/8/, or 301delGA/349T > A/1/). A detailed longitudinal phenotypic analysis was performed for patients with PROP1 mutations (n = 17). The mean ( ±s.d.) birth length SDS of these patients (0.12 ± 0.76) was lower than expected based on their mean ( ±s.d.) birth weight SDS (0.63 ± 1.27; P = 0.01). Parental heights were normal. The patients’ mean ( ±s.d.) height SDS declined to −1.5 ± 0.9, −3.6 ± 1.3 and −4.1 ± 1.2 at 1.5, 3 and 5 years of age, respectively. GH therapy, initiated at 6.8 ± 3.2 years of age (mean dose: 0.022 mg/kg per day), led to substantial growth acceleration in all patients. Mean adult height (n = 7) was normal when adjusted for mid-parental height. ACTH deficiency developed in two out of seven young adult patients. Conclusions: PROP1 defects are a prevalent cause of MPHD. We suggest that testing for PROP1 mutations in patients with MPHD might become standard practice in order to predict risk of additional pituitary hormone deficiencies.

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Identification of Anaerobic Selenate-Respiring Bacteria from Aquatic Sediments

Applied and Environmental Microbiology ◽

10.1128/aem.02737-06 ◽

2007 ◽

Vol 73 (11) ◽

pp. 3519-3527 ◽

Cited By ~ 69

Author(s):

Priya Narasingarao ◽

Max M. Häggblom

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Anaerobic Respiration ◽

Pseudomonas Stutzeri ◽

Elemental Selenium ◽

Rrna Gene ◽

Terminal Electron Acceptor ◽

Isolation And Characterization ◽

Anaerobic Biotransformation ◽

Gene Similarity

ABSTRACT The diversity population of microorganisms with the capability to use selenate as a terminal electron acceptor, reducing it to selenite and elemental selenium by the process known as dissimilatory selenate reduction, is largely unknown. The overall objective of this study was to gain an in-depth understanding of anaerobic biotransformation of selenium in the environment, particularly anaerobic respiration, and to characterize the microorganisms catalyzing this process. Here, we demonstrate the isolation and characterization of four novel anaerobic dissimilatory selenate-respiring bacteria enriched from a variety of sources, including sediments from three different water bodies in Chennai, India, and a tidal estuary in New Jersey. Strains S5 and S7 from India, strain KM from the Meadowlands, NJ, and strain pn1, categorized as a laboratory contaminant, were all phylogenetically distinct, belonging to various phyla in the bacterial domain. The 16S rRNA gene sequence shows that strain S5 constitutes a new genus belonging to Chrysiogenetes, while strain S7 belongs to the Deferribacteres, with greater than 98% 16S rRNA gene similarity to Geovibrio ferrireducens. Strain KM is related to Malonomonas rubra, Pelobacter acidigallici, and Desulfuromusa spp., with 96 to 97% 16S rRNA gene similarity. Strain pn1 is 99% similar to Pseudomonas stutzeri. Strains S5, S7, and KM are obligately anaerobic selenate-respiring microorganisms, while strain pn1 is facultatively anaerobic. Besides respiring selenate, all these strains also respire nitrate.

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