scholarly journals Identification of Components of Electron Transport Chains in the Extremely Thermoacidophilic Crenarchaeon Metallosphaera sedula through Iron and Sulfur Compound Oxidation Transcriptomes

2008 ◽  
Vol 74 (24) ◽  
pp. 7723-7732 ◽  
Author(s):  
Kathryne S. Auernik ◽  
Robert M. Kelly
Keyword(s):  
Electron Transport ◽  
Ferrous Iron ◽  
Sulfur Oxidation ◽  
Open Reading Frames ◽  
Transcriptional Analysis ◽  
Sequence Information ◽  
Proton Pumps ◽  
Terminal Oxidase ◽  
Heterodisulfide Reductase ◽  
Metallosphaera Sedula

ABSTRACT The crenarchaeal order Sulfolobales collectively contain at least five major terminal oxidase complexes. Based on genome sequence information, all five complexes are found only in Metallosphaera sedula and Sulfolobus tokodaii, the two sequenced Sulfolobales capable of iron oxidization. While specific respiratory complexes in certain Sulfolobales have been characterized previously as proton pumps for maintaining intracellular pH and generating proton motive force, their contribution to sulfur and iron biooxidation has not been considered. For M. sedula growing in the presence of ferrous iron and reduced inorganic sulfur compounds (RISCs), global transcriptional analysis was used to track the response of specific genes associated with these complexes, as well as other known and putative respiratory electron transport chain elements. Open reading frames from all five terminal oxidase or bc 1-like complexes were stimulated on one or more conditions tested. Components of the fox (Msed0467 to Msed0489) and soxNL-cbsABA (Msed0500 to Msed0505) terminal/quinol oxidase clusters were triggered by ferrous iron, while the soxABCDD′ terminal oxidase cluster (Msed0285 to Msed0291) were induced by tetrathionate and S0. Chemolithotrophic electron transport elements, including a putative tetrathionate hydrolase (Msed0804), a novel polysulfide/sulfur/dimethyl sulfoxide reductase-like complex (Msed0812 to Msed0818), and a novel heterodisulfide reductase-like complex (Msed1542 to Msed1550), were also stimulated by RISCs. Furthermore, several hypothetical proteins were found to have strong responses to ferrous iron or RISCs, suggesting additional candidates in iron or sulfur oxidation-related pathways. From this analysis, a comprehensive model for electron transport in M. sedula could be proposed as the basis for examining specific details of iron and sulfur oxidation in this bioleaching archaeon.

scholarly journals Impact of Molecular Hydrogen on Chalcopyrite Bioleaching by the Extremely Thermoacidophilic Archaeon Metallosphaera sedula

2010 ◽  
Vol 76 (8) ◽  
pp. 2668-2672 ◽  
Author(s):  
Kathryne S. Auernik ◽  
Robert M. Kelly
Keyword(s):  
Energy Source ◽  
Electron Transport ◽  
Molecular Hydrogen ◽  
Electron Transport Chain ◽  
Open Reading Frames ◽  
Terminal Oxidase ◽  
Metallosphaera Sedula ◽  
Transport Chain ◽  
Heterotrophic Metabolism ◽  
Reading Frames

ABSTRACT Hydrogen served as a competitive inorganic energy source, impacting the CuFeS 2 bioleaching efficiency of the extremely thermoacidophilic archaeon Metallosphaera sedula. Open reading frames encoding key terminal oxidase and electron transport chain components were triggered by CuFeS2. Evidence of heterotrophic metabolism was noted after extended periods of bioleaching, presumably related to cell lysis.

Changes in Acidithiobacillus ferrooxidans Ability to Reduce Ferric Iron by Elemental Sulfur

2015 ◽  
Vol 1130 ◽  
pp. 97-100 ◽  
Author(s):  
Jiri Kucera ◽  
Eva Pakostova ◽  
Oldrich Janiczek ◽  
Martin Mandl
Keyword(s):  
Acidithiobacillus Ferrooxidans ◽  
Proteomic Analysis ◽  
Ferrous Iron ◽  
Iron Reduction ◽  
Elemental Sulfur ◽  
Ferric Iron ◽  
Sulfur Metabolism ◽  
Sulfur Oxidation ◽  
Quinone Reductase ◽  
Heterodisulfide Reductase

Ferric iron may act as a thermodynamically favourable electron acceptor during elemental sulfur oxidation byAcidithiobacillus ferrooxidansin extremely acidic anoxic environments. A loss of anaerobic ferric iron reduction ability has been observed in ferrous iron-grownA. ferrooxidansCCM 4253 after aerobic passaging on elemental sulfur. In this study, iron-oxidising cells aerobically adapted from ferrous iron to elemental sulfur were still able to anaerobically reduce ferric iron, however, following aerobic passage on elemental sulfur it could not. Preliminary quantitative proteomic analysis of whole cell lysates of the passage that lost anaerobic ferric iron-reducing activity resulted in 150 repressed protein spots in comparison with the antecedent culture, which retained the activity. Identification of selected protein spots by tandem mass spectrometry revealed physiologically important proteins including rusticyanin and outer-membrane cytochrome Cyc2, which are involved in iron oxidation. Other proteins were associated with sulfur metabolism such as sulfide-quinone reductase and proteins encoded by the thiosulfate dehydrogenase and heterodisulfide reductase complex operons. Furthermore, proteomic analysis identified proteins directly related to anaerobiosis. The results indicate the importance of iron-oxidising system components for anaerobic sulfur oxidation in the studied microbial strain.

scholarly journals The oxidation of nicotinic acid by Pseudomonas ovalis Chester. The terminal oxidase

1972 ◽  
Vol 129 (3) ◽  
pp. 755-761 ◽  
Author(s):  
M. V. Jones ◽  
D. E. Hughes
Keyword(s):  
Electron Transport ◽  
Nicotinic Acid ◽  
Electron Transport Chain ◽  
Acid Oxidase ◽  
Terminal Oxidase ◽  
Difference Spectra ◽  
Terminal Oxidases ◽  
Cytochrome O ◽  
Transport Chain ◽  
Terminal Oxidation

In cell-free extracts of Pseudomonas ovalis nicotinic acid oxidase is confined to the wallmembrane fraction. It is associated with an electron-transport chain comprising b- and c-type cytochromes only, differing proportions of which are reduced by nicotinate and NADH. CO difference-spectra show two CO-binding pigments, cytochrome o (absorption maximum at 417nm) and another component absorbing maximally at 425nm. Cytochrome o is not reduced by NADH or by succinate but is by nicotinate, which can also reduce the ‘425’ CO-binding pigment. The effects of inhibitors of terminal oxidation support the idea of two terminal oxidases and a scheme involving the ‘425’ CO-binding pigment and the other components of the electron-transport chain is proposed.

Comparative studies on succinate and terminal oxidase activity in microbial and mammalian electron-transport systems

1969 ◽  
Vol 15 (7) ◽  
pp. 797-807 ◽  
Author(s):  
Peter Jurtshuk ◽  
Ann K. May ◽  
Leodocia M. Pope ◽  
Patricia R. Aston
Keyword(s):  
Electron Transport ◽  
Cytochrome C ◽  
Comparative Studies ◽  
Azotobacter Vinelandii ◽  
Transport Systems ◽  
Terminal Oxidase ◽  
Succinate Oxidation ◽  
State Reduction ◽  
Hydroxy Quinoline ◽  
Terminal Oxidation

A comparative study was undertaken to examine the succinate and terminal oxidase activities of the electron-transport systems of Azotobacter vinelandii and mammalian mitochondria. For succinate oxidation, both systems exhibited similar relative specificities for the electron acceptors phenazine methosulfate, O2, methylene blue, K3Fe(CN)6, nitrotetrazolium blue, 2,6-dichlorophenolindophenol (DCIP), and cytochrome c. They differed in that DCIP and cytochrome c were less active in the Azotobacter electron-transport system (R3 fraction) than in the bovine mitochondrial system. Comparative studies with known inhibitors of mammalian mitochondrial electron-transport demonstrated that the succinoxidase activity of the Azotobacter R3 fraction was, at least, 2000 times less sensitive to antimycin A, 700 times less sensitive to thenoyl-trifluoroacetone, and 30 times less sensitive to 2-n-heptyl-4-hydroxy-quinoline-N-oxide. Both systems were equally sensitive to KCN, p-chloromercuribenzoic acid, and chlorpromazine.The ability of the two systems to use tetramethyl-p-phenylenediamine (TMPD) and its derivatives as electron donors, for terminal oxidation, was also similar. Studies on steady state reduction revealed that in the Azotobacter R3 fraction, the cytochromes (a2, a1, b1, c4 + c5) and flavoprotein components were reduced substantially by succinate as well as by TMPD in the presence of ascorbate. Ultrastructure analyses of the Azotobacter R3 electron-transport fraction revealed the vesicular membranous components identified as oxidosomes according to the terminology used by DeLey and contained spherical headpiece units of 80 Å in diameter which appeared to be morphologically identical with the tripartite units or the elementary particles described by Green and associates, viz., Kopaczyk et al., and by Fernandez-Moran et al.

scholarly journals Ferrous Iron- and Sulfur-Induced Genes in Sulfolobus metallicus

2007 ◽  
Vol 73 (8) ◽  
pp. 2491-2497 ◽  
Author(s):  
Stephan Bathe ◽  
Paul R. Norris
Keyword(s):  
Reverse Transcription ◽  
Ferrous Iron ◽  
Subtractive Hybridization ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
Reverse Transcription Pcr ◽  
Genes Encoding ◽  
Induced Genes ◽  
Reading Frames ◽  
Sulfur Oxygenase Reductase

ABSTRACT Genes of Sulfolobus metallicus that appeared to be upregulated in relation to growth on either ferrous iron or sulfur were identified using subtractive hybridization of cDNAs. The genes upregulated during growth on ferrous iron were found in a cluster, and most were predicted to encode membrane proteins. Quantitative reverse transcription-PCR of cDNA showed upregulation of most of these genes during growth on ferrous iron and pyrite compared to results during growth on sulfur. The highest expression levels observed included those for genes encoding proteins with similarities to cytochrome c oxidase subunits and a CbsA-like cytochrome. The genes identified here that may be involved in oxidation of ferrous iron by S. metallicus are termed fox genes. Of three available genomes of Sulfolobus species (S. tokodaii, S. acidocaldarius, and S. solfataricus), only that of S. tokodaii has a cluster of highly similar open reading frames, and only S. tokodaii of these three species was also able to oxidize ferrous iron. A gene encoding sulfur oxygenase-reductase was identified as the source of the dominant transcript in sulfur-grown cells of S. metallicus, with the predicted protein showing high identities to the previously described examples from S. tokodaii and species of Acidianus.

scholarly journals DNA Microarray Analysis of Central Carbohydrate Metabolism: Glycolytic/Gluconeogenic Carbon Switch in the Hyperthermophilic Crenarchaeum Thermoproteus tenax

2008 ◽  
Vol 190 (6) ◽  
pp. 2231-2238 ◽  
Author(s):  
Melanie Zaparty ◽  
Alexander Zaigler ◽  
Claudia Stamme ◽  
Jörg Soppa ◽  
Reinhard Hensel ◽  
...  
Keyword(s):  
Carbohydrate Metabolism ◽  
Dna Microarray ◽  
Transcript Level ◽  
Open Reading Frames ◽  
Transcriptional Analysis ◽  
Heterotrophic Growth ◽  
Thermoproteus Tenax ◽  
Central Carbohydrate Metabolism ◽  
Reading Frames

ABSTRACT In order to unravel the role of regulation on transcript level in central carbohydrate metabolism (CCM) of Thermoproteus tenax, a focused DNA microarray was constructed by using 85 open reading frames involved in CCM. A transcriptional analysis comparing heterotrophic growth on glucose versus autotrophic growth on CO2-H2 was performed.

scholarly journals Transcriptomes of the Extremely Thermoacidophilic Archaeon Metallosphaera sedula Exposed to Metal “Shock” Reveal Generic and Specific Metal Responses

2016 ◽  
Vol 82 (15) ◽  
pp. 4613-4627 ◽  
Author(s):  
Garrett H. Wheaton ◽  
Arpan Mukherjee ◽  
Robert M. Kelly
Keyword(s):  
Metal Toxicity ◽  
Cellular Response ◽  
Sulfur Metabolism ◽  
Metal Resistance ◽  
Open Reading Frames ◽  
Copper Resistance ◽  
Natural Environments ◽  
Cluster Assembly ◽  
Content Type ◽  
Metallosphaera Sedula

ABSTRACTThe extremely thermoacidophilic archaeonMetallosphaera sedulamobilizes metals by novel membrane-associated oxidase clusters and, consequently, requires metal resistance strategies. This issue was examined by “shocking”M. sedulawith representative metals (Co2+, Cu2+, Ni2+, UO22+, Zn2+) at inhibitory and subinhibitory levels. Collectively, one-quarter of the genome (554 open reading frames [ORFs]) responded to inhibitory levels, and two-thirds (354) of the ORFs were responsive to a single metal. Cu2+(259 ORFs, 106 Cu2+-specific ORFs) and Zn2+(262 ORFs, 131 Zn2+-specific ORFs) triggered the largest responses, followed by UO22+(187 ORFs, 91 UO22+-specific ORFs), Ni2+(93 ORFs, 25 Ni2+-specific ORFs), and Co2+(61 ORFs, 1 Co2+-specific ORF). While one-third of the metal-responsive ORFs are annotated as encoding hypothetical proteins, metal challenge also impacted ORFs responsible for identifiable processes related to the cell cycle, DNA repair, and oxidative stress. Surprisingly, there were only 30 ORFs that responded to at least four metals, and 10 of these responded to all five metals. This core transcriptome indicated induction of Fe-S cluster assembly (Msed_1656-Msed_1657), tungsten/molybdenum transport (Msed_1780-Msed_1781), and decreased central metabolism. Not surprisingly, a metal-translocating P-type ATPase (Msed_0490) associated with a copper resistance system (Cop) was upregulated in response to Cu2+(6-fold) but also in response to UO22+(4-fold) and Zn2+(9-fold). Cu2+challenge uniquely induced assimilatory sulfur metabolism for cysteine biosynthesis, suggesting a role for this amino acid in Cu2+resistance or issues in sulfur metabolism. The results indicate thatM. sedulaemploys a range of physiological and biochemical responses to metal challenge, many of which are specific to a single metal and involve proteins with yet unassigned or definitive functions.IMPORTANCEThe mechanisms by which extremely thermoacidophilic archaea resist and are negatively impacted by metals encountered in their natural environments are important to understand so that technologies such as bioleaching, which leverage microbially based conversion of insoluble metal sulfides to soluble species, can be improved. Transcriptomic analysis of the cellular response to metal challenge provided both global and specific insights into how these novel microorganisms negotiate metal toxicity in natural and technological settings. As genetics tools are further developed and implemented for extreme thermoacidophiles, information about metal toxicity and resistance can be leveraged to create metabolically engineered strains with improved bioleaching characteristics.

scholarly journals High-throughput subcellular protein localization using cell arrays

2005 ◽  
Vol 33 (6) ◽  
pp. 1407-1408 ◽  
Author(s):  
Y.-H. Hu ◽  
D. Vanhecke ◽  
H. Lehrach ◽  
M. Janitz
Keyword(s):  
High Throughput ◽  
Cellular Localization ◽  
Fluorescent Protein ◽  
Protein Localization ◽  
Open Reading Frames ◽  
Expression Vectors ◽  
Sequence Information ◽  
Cell Array ◽  
Single Experiment ◽  
Cell Arrays

Accomplishment of the human and mouse genome projects resulted in accumulation of extensive gene sequence information. However, the information about the biological functions of the identified genes remains a bottleneck of the post-genomic era. Hence, assays providing simple functional information, such as localization of the protein within the cell, can be very helpful in the elucidation of its function. Transfected cell arrays offer a robust platform for protein localization studies. Open reading frames of unknown genes can be linked to a His6-tag or GFP (green fluorescent protein) reporter in expression vectors and subsequently transfected using the cell array. Cellular localization of the transfected proteins is detected either by specific anti-His-tag antibodies or directly by fluorescence of the GFP fusion protein and by counterstaining with organelle-specific dyes. The high throughput of the method in terms of information provided for every single experiment makes this approach superior to classical immunohistological methods for protein localization.

scholarly journals Molecular Organization of Intrinsic Restriction and Modification Genes BsuM of Bacillus subtilis Marburg

2002 ◽  
Vol 184 (2) ◽  
pp. 381-389 ◽  
Author(s):  
Hideyuki Ohshima ◽  
Satoshi Matsuoka ◽  
Kei Asai ◽  
Yoshito Sadaie
Keyword(s):  
Bacillus Subtilis ◽  
Dna Methyltransferases ◽  
Open Reading Frames ◽  
Molecular Organization ◽  
Transcriptional Analysis ◽  
Logarithmic Phase ◽  
Modification System ◽  
Target Sequences ◽  
Reading Frames ◽  
Classical Mutant

ABSTRACT Transcriptional analysis and disruption of five open reading frames (ORFs), ydiO, ydiP, ydiR, ydiS, and ydjA, in the prophage 3 region of the chromosome of Bacillus subtilis Marburg revealed that they are component genes of the intrinsic BsuM restriction and modification system of this organism. The classical mutant strain RM125, which lacks the restriction and modification system of B. subtilis Marburg, lacks the prophage 3 region carrying these five ORFs. These ORFs constitute two operons, the ydiO-ydiP operon and the ydiR-ydiS-ydjA operon, both of which are expressed during the logarithmic phase of growth. The predicted gene products YdiO and YdiP are the orthologues of cytosine DNA methyltransferases. The predicted YdiS product is an orthologue of restriction nucleases, while the predicted YdiR and YdjA products have no apparent paralogues and orthologues whose functions are known. Disruption of the ydiR-ydiS-ydjA operon resulted in enhanced transformation by plasmid DNA carrying multiple BsuM target sequences. Disruption of ydiO or ydiP function requires disruption of at least one of the following genes on the chromosome: ydiR, ydiS, and ydjA. The degrees of methylation of the BsuM target sequences on chromosomal DNAs were estimated indirectly by determining the susceptibility to digestion with XhoI (an isoschizomer of BsuM) of DNAs extracted from the disruptant strains. Six XhoI (BsuM) sites were examined. XhoI digested at the XhoI sites in the DNAs from disruptants with disruptions in both operons, while XhoI did not digest at the XhoI sites in the DNAs from the wild-type strain or from the disruptants with disruptions in the ydiR-ydiS-ydjA operon. Therefore, the ydiO-ydiP operon and the ydiR-ydiS-ydjA operon are considered operons that are responsible for BsuM modification and BsuM restriction, respectively.

scholarly journals Vibrio cholerae VciB Mediates Iron Reduction

2017 ◽  
Vol 199 (12) ◽  
Author(s):  
Eric D. Peng ◽  
Shelley M. Payne
Keyword(s):  
Electron Transport ◽  
Vibrio Cholerae ◽  
Ferrous Iron ◽  
Electron Transport Chain ◽  
Iron Reduction ◽  
Iron Transport ◽  
Ferric Iron ◽  
Transport Systems ◽  
Content Type ◽  
Transport Chain

ABSTRACT Vibrio cholerae is the causative agent of the severe diarrheal disease cholera. V. cholerae thrives within the human host, where it replicates to high numbers, but it also persists within the aquatic environments of ocean and brackish water. To survive within these nutritionally diverse environments, V. cholerae must encode the necessary tools to acquire the essential nutrient iron in all forms it may encounter. A prior study of systems involved in iron transport in V. cholerae revealed the existence of vciB, which, while unable to directly transport iron, stimulates the transport of iron through ferrous (Fe2+) iron transport systems. We demonstrate here a role for VciB in V. cholerae in which VciB stimulates the reduction of Fe3+ to Fe2+, which can be subsequently transported into the cell with the ferrous iron transporter Feo. Iron reduction is independent of functional iron transport but is associated with the electron transport chain. Comparative analysis of VciB orthologs suggests a similar role for other proteins in the VciB family. Our data indicate that VciB is a dimer located in the inner membrane with three transmembrane segments and a large periplasmic loop. Directed mutagenesis of the protein reveals two highly conserved histidine residues required for function. Taken together, our results support a model whereby VciB reduces ferric iron using energy from the electron transport chain. IMPORTANCE Vibrio cholerae is a prolific human pathogen and environmental organism. The acquisition of essential nutrients such as iron is critical for replication, and V. cholerae encodes a number of mechanisms to use iron from diverse environments. Here, we describe the V. cholerae protein VciB that increases the reduction of oxidized ferric iron (Fe3+) to the ferrous form (Fe2+), thus promoting iron acquisition through ferrous iron transporters. Analysis of VciB orthologs in Burkholderia and Aeromonas spp. suggest that they have a similar activity, allowing a functional assignment for this previously uncharacterized protein family. This study builds upon our understanding of proteins known to mediate iron reduction in bacteria.

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