scholarly journals Key Role for Sulfur in Peptide Metabolism and in Regulation of Three Hydrogenases in the Hyperthermophilic ArchaeonPyrococcus furiosus

2001 ◽  
Vol 183 (2) ◽  
pp. 716-724 ◽  
Author(s):  
Michael W. W. Adams ◽  
James F. Holden ◽  
Angeli Lal Menon ◽  
Gerrit J. Schut ◽  
Amy M. Grunden ◽  
...  
Keyword(s):  
Growth Rates ◽  
Elemental Sulfur ◽  
Pyrococcus Furiosus ◽  
Growth Conditions ◽  
Growth Media ◽  
Hyperthermophilic Archaeon ◽  
Order Of Magnitude ◽  
Membrane Bound ◽  
Peptide Metabolism ◽  
Specific Activities

ABSTRACT The hyperthermophilic archaeon Pyrococcus furiosusgrows optimally at 100°C by the fermentation of peptides and carbohydrates. Growth of the organism was examined in media containing either maltose, peptides (hydrolyzed casein), or both as the carbon source(s), each with and without elemental sulfur (S0). Growth rates were highest on media containing peptides and S0, with or without maltose. Growth did not occur on the peptide medium without S0. S0 had no effect on growth rates in the maltose medium in the absence of peptides. Phenylacetate production rates (from phenylalanine fermentation) from cells grown in the peptide medium containing S0 with or without maltose were the same, suggesting that S0 is required for peptide utilization. The activities of 14 of 21 enzymes involved in or related to the fermentation pathways of P. furiosus were shown to be regulated under the five different growth conditions studied. The presence of S0 in the growth media resulted in decreases in specific activities of two cytoplasmic hydrogenases (I and II) and of a membrane-bound hydrogenase, each by an order of magnitude. The primary S0-reducing enzyme in this organism and the mechanism of the S0 dependence of peptide metabolism are not known. This study provides the first evidence for a highly regulated fermentation-based metabolism in P. furiosus and a significant regulatory role for elemental sulfur or its metabolites.

scholarly journals Insights into the Metabolism of Elemental Sulfur by the Hyperthermophilic Archaeon Pyrococcus furiosus: Characterization of a Coenzyme A- Dependent NAD(P)H Sulfur Oxidoreductase

2007 ◽  
Vol 189 (12) ◽  
pp. 4431-4441 ◽  
Author(s):  
Gerrit J. Schut ◽  
Stephanie L. Bridger ◽  
Michael W. W. Adams
Keyword(s):  
Gene Cluster ◽  
Elemental Sulfur ◽  
Coenzyme A ◽  
Specific Activity ◽  
Pyrococcus Furiosus ◽  
Side Reaction ◽  
Primary Response ◽  
Secondary Response ◽  
Hyperthermophilic Archaeon ◽  
Membrane Bound

ABSTRACT The hyperthermophilic archaeon Pyrococcus furiosus uses carbohydrates as a carbon source and produces acetate, CO2, and H2 as end products. When S0 is added to a growing culture, within 10 min the rate of H2 production rapidly decreases and H2S is detected. After 1 hour cells contain high NADPH- and coenzyme A-dependent S0 reduction activity (0.7 units/mg, 85°C) located in the cytoplasm. The enzyme responsible for this activity was purified to electrophoretic homogeneity (specific activity, 100 units/mg) and is termed NAD(P)H elemental sulfur oxidoreductase (NSR). NSR is a homodimeric flavoprotein (M r, 100,000) and is encoded by PF1186. This designation was previously assigned to the gene encoding an enzyme that reduces coenzyme A disulfide, which is a side reaction of NSR. Whole-genome DNA microarray and quantitative PCR analyses showed that the expression of NSR is up-regulated up to sevenfold within 10 min of S0 addition. This primary response to S0 also involves the up-regulation (>16-fold) of a 13-gene cluster encoding a membrane-bound oxidoreductase (MBX). The cluster encoding MBX is proposed to replace the homologous 14-gene cluster that encodes the ferredoxin-oxidizing, H2-evolving membrane-bound hydrogenase (MBH), which is down-regulated >12-fold within 10 min of S0 addition. Although an activity for MBX could not be demonstrated, it is proposed to conserve energy by oxidizing ferredoxin and reducing NADP, which is used by NSR to reduce S0. A secondary response to S0 is observed 30 min after S0 addition and includes the up-regulation of genes encoding proteins involved in amino acid biosynthesis and iron metabolism, as well as two so-called sulfur-induced proteins termed SipA and SipB. This novel S0-reducing system involving NSR and MBX has been found so far only in the heterotrophic Thermococcales and is in contrast to the cytochrome- and quinone-based S0-reducing system in autotrophic archaea and bacteria.

scholarly journals The Elemental Sulfur-Responsive Protein (SipA) from the Hyperthermophilic Archaeon Pyrococcus furiosus Is Regulated by Sulfide in an Iron-Dependent Manner

2010 ◽  
Vol 192 (21) ◽  
pp. 5841-5843 ◽  
Author(s):  
Sonya M. Clarkson ◽  
Elizabeth C. Newcomer ◽  
Everett G. Young ◽  
Michael W. W. Adams
Keyword(s):  
Elemental Sulfur ◽  
Iron Sulfide ◽  
Pyrococcus Furiosus ◽  
Protein A ◽  
Dependent Manner ◽  
Intracellular Iron ◽  
Hyperthermophilic Archaeon

ABSTRACT The gene (sipA) encoding the sulfur-induced protein A (PF2025) is highly upregulated during growth of Pyrococcus furiosus on elemental sulfur (S0). Expression of sipA is regulated by sulfide, the product of S0 reduction, but in an iron-dependent manner. SipA is proposed to play a role in intracellular iron sulfide detoxification.

Comparative Enzymology of Sulfite Oxidation in Thiocapsa roseopersicina Strains 6311, M1 and BBS under Chemotrophic and Phototrophic Conditions

1989 ◽  
Vol 44 (7-8) ◽  
pp. 617-622 ◽  
Author(s):  
Christiane Dahl ◽  
Hans G. Trüper
Keyword(s):  
Growth Conditions ◽  
Reduced Sulfur Compounds ◽  
Atp Sulfurylase ◽  
Purple Sulfur Bacterium ◽  
Sulfite Oxidation ◽  
Aps Reductase ◽  
Comparative Enzymology ◽  
Membrane Bound ◽  
Specific Activities ◽  
Phototrophic Growth

The purple sulfur bacterium T. roseopersicina is able to grow chemoautotrophically in the dark under micro- to semiaerobic conditions. Under the latter cell yield and growth rate are considerably reduced. During chemo- and phototrophic growth reduced sulfur compounds are metabolized by the same pathway, i.e. oxidized to sulfate via adenylylsulfate. APS reductase (EC 1.8.99.2), ADP sulfurylase (EC 2.7.7.5) and ATP sulfurylase (EC 2.7.7.4) could be shown in all the strains tested, whereas only strain BBS contained an AMP independent sulfite-oxidizing activity under photo- as well as under chemotrophic conditions. Not only ADP but also ATP sulfurylase perform a dissimilatory function proven by their high specific activities. In contrast to the enzyme of T. roseopersicina strain 6311 APS reductases from strains M1 and BBS are strictly membrane-bound. The enzyme from strain M1 was solubilized, enriched and characterized. While the KM values of purified APS reductase remain unaffected, specific activities of APS reductase, ATP and ADP sulfurylase are increased substantially under chemotrophic growth conditions.

scholarly journals Features of Rhodobacter sphaeroides CcmFH

2003 ◽  
Vol 185 (2) ◽  
pp. 422-431 ◽  
Author(s):  
Carlos Rios-Velazquez ◽  
Ryan Coller ◽  
Timothy J. Donohue
Keyword(s):  
Rhodobacter Sphaeroides ◽  
Signal Sequence ◽  
Critical Role ◽  
Growth Conditions ◽  
Anaerobic Growth ◽  
Growth Media ◽  
Thiol Compounds ◽  
Membrane Bound ◽  
Electron Carriers

ABSTRACT In this study, the in vivo function and properties of two cytochrome c maturation proteins, CcmF and CcmH from Rhodobacter sphaeroides, were analyzed. Strains lacking CcmH or both CcmF and CcmH are unable to grow under anaerobic conditions where c-type cytochromes are required, demonstrating their critical role in the assembly of these electron carriers. Consistent with this observation, strains lacking both CcmF and CcmH are deficient in c-type cytochromes when assayed under permissive growth conditions. In contrast, under permissive growth conditions, strains lacking only CcmH contain several soluble and membrane-bound c-type cytochromes, albeit at reduced levels, suggesting that this bacterium has a CcmH-independent route for their maturation. In addition, the function of CcmH that is needed to support anaerobic growth can be replaced by adding cysteine or cystine to growth media. The ability of exogenous thiol compounds to replace CcmH provides the first physiological evidence for a role of this protein in thiol chemistry during c-type cytochrome maturation. The properties of R. sphaeroides cells containing translational fusions between CcmF and CcmH and either Escherichia coli alkaline phosphatase or β-galactosidase suggest that they are each integral cytoplasmic membrane proteins with their presumed catalytic domains facing the periplasm. Analysis of CcmH shows that it is synthesized as a higher-molecular-weight precursor protein with an N-terminal signal sequence.

scholarly journals Defining Genes in the Genome of the Hyperthermophilic Archaeon Pyrococcus furiosus: Implications for All Microbial Genomes

2005 ◽  
Vol 187 (21) ◽  
pp. 7325-7332 ◽  
Author(s):  
Farris L. Poole ◽  
Brian A. Gerwe ◽  
Robert C. Hopkins ◽  
Gerrit J. Schut ◽  
Michael V. Weinberg ◽  
...  
Keyword(s):  
Pyrococcus Furiosus ◽  
Growth Conditions ◽  
Open Reading Frames ◽  
Genomic Research ◽  
Bacterial Genomes ◽  
Microbial Genomes ◽  
Hyperthermophilic Archaeon ◽  
The Public ◽  
Heat Stable ◽  
Original Genome

ABSTRACT The original genome annotation of the hyperthermophilic archaeon Pyrococcus furiosus contained 2,065 open reading frames (ORFs). The genome was subsequently automatically annotated in two public databases by the Institute for Genomic Research (TIGR) and the National Center for Biotechnology Information (NCBI). Remarkably, more than 500 of the originally annotated ORFs differ in size in the two databases, many very significantly. For example, more than 170 of the predicted proteins differ at their N termini by more than 25 amino acids. Similar discrepancies were observed in the TIGR and NCBI databases with the other archaeal and bacterial genomes examined. In addition, the two databases contain 60 (NCBI) and 221 (TIGR) ORFs not present in the original annotation of P. furiosus. In the present study we have experimentally assessed the validity of 88 previously unannotated ORFs. Transcriptional analyses showed that 11 of 61 ORFs examined were expressed in P. furiosus when grown at either 95 or 72°C. In addition, 7 of 54 ORFs examined yielded heat-stable recombinant proteins when they were expressed in Escherichia coli, although only one of the seven ORFs was expressed in P. furiosus under the growth conditions tested. It is concluded that the P. furiosus genome contains at least 17 ORFs not previously recognized in the original annotation. This study serves to highlight the discrepancies in the public databases and the problems of accurately defining the number and sizes of ORFs within any microbial genome.

scholarly journals Pyrobaculum calidifontissp. nov., a novel hyperthermophilic archaeon that grows in atmospheric air

Archaea ◽  
2002 ◽  
Vol 1 (2) ◽  
pp. 113-121 ◽  
Author(s):  
Taku Amo ◽  
Maria Luz F. Paje ◽  
Akiko Inagaki ◽  
Satoshi Ezaki ◽  
Haruyuki Atomi ◽  
...  
Keyword(s):  
Cell Growth ◽  
Electron Acceptor ◽  
Elemental Sulfur ◽  
Growth Conditions ◽  
The Philippines ◽  
Aerobic Growth ◽  
Hyperthermophilic Archaeon ◽  
Atmospheric Air ◽  
Final Electron ◽  
Final Electron Acceptor

A novel, facultatively aerobic, heterotrophic hyperthermophilic archaeon was isolated from a terrestrial hot spring in the Philippines. Cells of the new isolate, strain VA1, were rod-shaped with a length of 1.5 to 10 μm and a width of 0.5 to 1.0 μm. Isolate VA1 grew optimally at 90 to 95 °C and pH 7.0 under atmospheric air. Oxygen served as a final electron acceptor under aerobic growth conditions, and vigorous shaking of the medium significantly enhanced growth. Elemental sulfur inhibited cell growth under aerobic growth conditions, whereas thiosulfate stimulated cell growth. Under anaerobic growth conditions, nitrate served as a final electron acceptor, but nitrite or sulfur-containing compounds such as elemental sulfur, thiosulfate, sulfate and sulfite could not act as final electron acceptors. The G+C content of the genomic DNA was 51 mol%. Phylogenetic analysis based on 16S rRNA sequences indicated that strain VA1 exhibited close relationships to species of the genusPyrobaculum. A DNA–DNA hybridization study revealed a low level of similarity (≤ 18%) between strain VA1 and previously described members of the genusPyrobaculum. Physiological characteristics also indicated that strain VA1 was distinct from thesePyrobaculumspecies. Our results indicate that isolate VA1 represents a novel species, namedPyrobaculum calidifontis.

scholarly journals Mutability of demographic noise in microbial range expansions

2021 ◽  
Author(s):  
QinQin Yu ◽  
Matti Gralka ◽  
Marie-Cécilia Duvernoy ◽  
Megan Sousa ◽  
Arbel Harpak ◽  
...  
Keyword(s):  
Gene Deletion ◽  
Genetic Manipulation ◽  
Single Gene ◽  
Population Level ◽  
Growth Conditions ◽  
Establishment Probability ◽  
In The Wild ◽  
Order Of Magnitude ◽  
Demographic Noise ◽  
Single Gene Deletion

AbstractDemographic noise, the change in the composition of a population due to random birth and death events, is an important driving force in evolution because it reduces the efficacy of natural selection. Demographic noise is typically thought to be set by the population size and the environment, but recent experiments with microbial range expansions have revealed substantial strain-level differences in demographic noise under the same growth conditions. Many genetic and phenotypic differences exist between strains; to what extent do single mutations change the strength of demographic noise? To investigate this question, we developed a high-throughput method for measuring demographic noise in colonies without the need for genetic manipulation. By applying this method to 191 randomly-selected single gene deletion strains from the E. coli Keio collection, we find that a typical single gene deletion mutation decreases demographic noise by 8% (maximal decrease: 81%). We find that the strength of demographic noise is an emergent trait at the population level that can be predicted by colony-level traits but not cell-level traits. The observed differences in demographic noise from single gene deletions can increase the establishment probability of beneficial mutations by almost an order of magnitude (compared to in the wild type). Our results show that single mutations can substantially alter adaptation through their effects on demographic noise and suggest that demographic noise can be an evolvable trait of a population.

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