| effects of ribosomes and intracellular solutes on activities and stabilities of elongation factor 2 proteins from psychrotolerant and thermophilic methanogens. | low-temperature-adapted archaea are abundant in the environment, yet little is known about the thermal adaptation of their proteins. we have previously compared elongation factor 2 (ef-2) proteins from antarctic (methanococcoides burtonii) and thermophilic (methanosarcina thermophila) methanogens and found that the m. burtonii ef-2 had greater intrinsic activity at low temperatures and lower thermal stability at high temperatures (t. thomas and r. cavicchioli, j. bacteriol. 182:1328-1332, 2000). ... | 2001 | 11222595 |
| low temperature regulated dead-box rna helicase from the antarctic archaeon, methanococcoides burtonii. | dead-box rna helicases, by unwinding duplex rna in bacteria and eukaryotes, are involved in essential cellular processes, including translation initiation and ribosome biogenesis, and have recently been implicated in enabling bacteria to survive cold-shock and grow at low temperature. despite these critical physiological roles, they have not been characterized in archaea. due to their presumed importance in removing cold-stabilised secondary structures in mrna, we have characterised a putative d ... | 2000 | 10731411 |
| microbial diversity in sediments collected from the deepest cold-seep area, the japan trench. | : the japan trench land slope at a depth of 6,400 m is the deepest cold-seep environment with calyptogena communities. sediment samples from inside and beside the calyptogena communities were collected, and the microbial diversity in the sediment samples was studied by molecular phylogenetic techniques. from dna extracted directly from the sediment samples, 16s rdnas were amplified by the polymerase chain reaction method. the sequences of the amplified 16s rdnas selected by restriction fragment ... | 1999 | 10489418 |
| phylogenomic analysis of proteins that are distinctive of archaea and its main subgroups and the origin of methanogenesis. | the archaea are highly diverse in terms of their physiology, metabolism and ecology. presently, very few molecular characteristics are known that are uniquely shared by either all archaea or the different main groups within archaea. the evolutionary relationships among different groups within the euryarchaeota branch are also not clearly understood. | 2007 | 17394648 |
| detection of methanogenic archaea in seawater particles and the digestive tract of a marine fish species. | a methanogen-specific nested pcr approach was used to detect methanogenic archaea in seawater particles of the north sea and the feces and the digestive tract of flounder (platichthys flesus), a fish found in the north sea. a number of 16s rdna sequences with 97.6-99.5% similarity to methanococcoides methylutens were found in the seawater particles as well as the digestive tract and fecal samples. | 1999 | 10220894 |
| phylogenetic diversity of archaea in sediment samples from a coastal salt marsh. | the archaea present in salt marsh sediment samples from a tidal creek and from an adjacent area of vegetative marshland, both of which showed active methanogenesis and sulfate reduction, were sampled by using 16s rrna gene libraries created with archaea-specific primers. none of the sequences were the same as reference sequences from cultured taxa, although some were closely related to sequences from methanogens previously isolated from marine sediments. a wide range of euryarchaeota sequences w ... | 1997 | 9406392 |
| taxonomic description of methanococcoides euhalobius and its transfer to the methanohalophilus genus. | a sequence analysis of the 16s-rrna of methanococcoides euhalobius revealed that this organism was highly related to members of the genus methanohalophilus. on the basis of sequence data, an oligonucleotide probe specific to methanohalophilus species was designed. hybridization studies with this probe confirmed close relationship of methanococcoides euhalobius to methanohalophilus species. therefore, we propose that methanococcoides euhalobius should be transferred to the genus methanohalophilus ... | 1997 | 9195005 |
| characterization of the biosynthetic pathway of glucosylglycerate in the archaeon methanococcoides burtonii. | the pathway for the synthesis of the organic solute glucosylglycerate (gg) is proposed based on the activities of the recombinant glucosyl-3-phosphoglycerate synthase (gpgs) and glucosyl-3-phosphoglycerate phosphatase (gpgp) from methanococcoides burtonii. a mannosyl-3-phosphoglycerate phosphatase gene homologue (mpgp) was found in the genome of m. burtonii (http://www.jgi.doe.gov), but an mpgs gene coding for mannosyl-3-phosphoglycerate synthase (mpgs) was absent. the gene upstream of the mpgp ... | 2006 | 16428406 |
| betaine fermentation and oxidation by marine desulfuromonas strains. | two bacterial strains were dominant in anaerobic enrichment cultures with betaine (n,n,n-trimethylglycine) as a substrate and intertidal mud as an inoculum. one was a coccoid bacterium which was a trimethylamine (tma)-fermenting methanogen similar to methanococcoides methylutens. the other strain, a rod-shaped, gram-negative, motile bacterium, fermented betaine. on the basis of its ability to oxidize acetate and ethanol to co(2) with sulfur as an electron acceptor, its inability to reduce sulfat ... | 1989 | 16347897 |
| isolation and characterization of a methylotrophic marine methanogen, methanococcoides methylutens gen. nov., sp. nov. | a new genus of marine methanogenic bacteria is described that utilizes trimethylamine, diethylamine, monomethylamine, and methanol as substrates for growth and methanogenesis. methane was not produced from h(2)-co(2), sodium formate, or sodium acetate. growth on trimethylamine was stimulated by yeast extract, trypticase (bbl microbiology systems, cockeysville, md.), rumen fluid, or b vitamins. the optimal growth temperature was 30 to 35 degrees c. the maximum growth rate was between ph 7.0 and 7 ... | 1983 | 16346215 |
| isolation and characterization of methylotrophic methanogens from anoxic marine sediments in skan bay, alaska: description of methanococcoides alaskense sp. nov., and emended description of methanosarcina baltica. | three novel strains of methylotrophic methanogens were isolated from skan bay, alaska, by using anaerobic cultivation techniques. the water was 65 m deep at the sampling site. strains ak-4 (=ocm 774), ak-5t (=ocm 775t=dsm 17273t) and ak-9 (=ocm 793) were isolated from the sulfate-reducing zone of the sediments. each of the strains was a non-motile coccus and occurred singly. cells grew with trimethylamine as a catabolic substrate and strain ak-4 could also catabolize methanol. yeast extract and ... | 2005 | 16280522 |
| methanogen diversity evidenced by molecular characterization of methyl coenzyme m reductase a (mcra) genes in hydrothermal sediments of the guaymas basin. | the methanogenic community in hydrothermally active sediments of guaymas basin (gulf of california, mexico) was analyzed by pcr amplification, cloning, and sequencing of methyl coenzyme m reductase (mcra) and 16s rrna genes. members of the methanomicrobiales and methanosarcinales dominated the mcra and 16s rrna clone libraries from the upper 15 cm of the sediments. within the h2/co2- and formate-utilizing family methanomicrobiales, two mcra and 16s rrna lineages were closely affiliated with cult ... | 2005 | 16085853 |
| tetramethylammonium:coenzyme m methyltransferase system from methanococcoides sp | a methanogen (strain nat1) that belongs to the family of methanosarcinaceae and that can grow on tetramethylammonium as the sole energy source has recently been isolated. we report here that cell extracts of the archaeon catalyze the formation of methyl-coenzyme m from coenzyme m and tetramethylammonium. the activity was dependent on the presence of ti(iii) citrate and atp, and was rapidly lost under oxic conditions. anoxic chromatography on deae-sepharose revealed that two fractions, fractions ... | 1998 | 9732435 |
| isolation and characterization of methanomethylovorans hollandica gen. nov., sp. nov., isolated from freshwater sediment, a methylotrophic methanogen able to grow on dimethyl sulfide and methanethiol. | a newly isolated methanogen, strain dms1(t), is the first obligately anaerobic archaeon which was directly enriched and isolated from a freshwater sediment in defined minimal medium containing dimethyl sulfide (dms) as the sole carbon and energy source. the use of a chemostat with a continuous dms-containing gas stream as a method of enrichment, followed by cultivation in deep agar tubes, resulted in a pure culture. since the only substrates utilized by strain dms1(t) are methanol, methylamines, ... | 1999 | 10427061 |
| diversity and distribution of methanotrophic archaea at cold seeps. | in this study we investigated by using 16s rrna-based methods the distribution and biomass of archaea in samples from (i) sediments above outcropping methane hydrate at hydrate ridge (cascadia margin off oregon) and (ii) massive microbial mats enclosing carbonate reefs (crimea area, black sea). the archaeal diversity was low in both locations; there were only four (hydrate ridge) and five (black sea) different phylogenetic clusters of sequences, most of which belonged to the methanotrophic archa ... | 2005 | 15640223 |
| biology of the cold adapted archaeon, methanococcoides burtonii determined by proteomics using liquid chromatography-tandem mass spectrometry. | genome sequence data of the cold-adapted archaeon, methanococcoides burtonii, was linked to liquid chromatography-mass spectrometry analysis of the expressed-proteome to define the key biological processes functioning at 4 degrees c. 528 proteins ranging in pi from 3.5 to 13.2, and 3.5-230 kda, were identified. 133 identities were for hypothetical proteins, and the analysis of these is described separately (goodchild et al. manuscript in preparation). dna replication and cell division involves e ... | 2004 | 15595725 |
| effect of temperature on stability and activity of elongation factor 2 proteins from antarctic and thermophilic methanogens. | despite the presence and abundance of archaea in low-temperature environments, little information is available regarding their physiological and biochemical properties. in order to investigate the adaptation of archaeal proteins to low temperatures, we purified and characterized the elongation factor 2 (ef-2) protein from the antarctic methanogen methanococcoides burtonii, which was expressed in escherichia coli, and compared it to the recombinant ef-2 protein from a phylogenetically related the ... | 2000 | 10671454 |
| cold adaptation of the antarctic archaeon, methanococcoides burtonii assessed by proteomics using icat. | using isotope coded affinity tag (icat) chromatography and liquid chromatography-mass spectrometry, 163 proteins were identified from the cold-adapted archaeon, methanococcoides burtonii. 14 proteins were differentially expressed during growth at 4 degrees c and 23 degrees c. knowledge of protein abundance, protein identity and gene arrangement was used to determine mechanisms of cold adaptation. growth temperature was found to affect proteins involved in energy generation and biosynthesis linke ... | 2005 | 15822924 |
| influence of temperature on trna modification in archaea: methanococcoides burtonii (optimum growth temperature [topt], 23 degrees c) and stetteria hydrogenophila (topt, 95 degrees c). | we report the first study of trna modification in psychrotolerant archaea, specifically in the archaeon methanococcoides burtonii grown at 4 and 23 degrees c. for comparison, unfractionated trna from the archaeal hyperthermophile stetteria hydrogenophila cultured at 93 degrees c was examined. analysis of modified nucleosides using liquid chromatography-electrospray ionization mass spectrometry revealed striking differences in levels and identities of trna modifications between the two organisms. ... | 2003 | 12949100 |
| mechanisms of thermal adaptation revealed from the genomes of the antarctic archaea methanogenium frigidum and methanococcoides burtonii. | we generated draft genome sequences for two cold-adapted archaea, methanogenium frigidum and methanococcoides burtonii, to identify genotypic characteristics that distinguish them from archaea with a higher optimal growth temperature (ogt). comparative genomics revealed trends in amino acid and trna composition, and structural features of proteins. proteins from the cold-adapted archaea are characterized by a higher content of noncharged polar amino acids, particularly gln and thr and a lower co ... | 2003 | 12805271 |
| analysis of the sulfate-reducing bacterial and methanogenic archaeal populations in contrasting antarctic sediments. | the distribution and activity of communities of sulfate-reducing bacteria (srb) and methanogenic archaea in two contrasting antarctic sediments were investigated. methanogenesis dominated in freshwater lake heywood, while sulfate reduction dominated in marine shallow bay. slurry experiments indicated that 90% of the methanogenesis in lake heywood was acetoclastic. this finding was supported by the limited diversity of clones detected in a lake heywood archaeal clone library, in which most clones ... | 2003 | 12788715 |
| cold adaptation of archaeal elongation factor 2 (ef-2) proteins. | cell growth at low temperature is dependent on the ability of cells to perform protein synthesis. cold adapted micro-organisms (psychrophilic or psychrotolerant) have a superior ability to perform translation at low temperature. this review addresses cold adaptation of protein synthesis in archaea by examining what is presently known about thermal adaptation of elongation factor 2 (ef-2) proteins from archaea. despite the knowledge that archaea are abundant in cold environments (e.g. the ocean), ... | 2002 | 12188905 |
| predicted roles for hypothetical proteins in the low-temperature expressed proteome of the antarctic archaeon methanococcoides burtonii. | using liquid chromatography-mass spectrometry, 528 proteins were identified that are expressed during growth at 4 degrees c in the cold adapted archaeon, methanococcoides burtonii. of those, 135 were annotated previously as unique or conserved hypothetical proteins. we have performed a comprehensive, integrated analysis of the latter proteins using threading, interproscan, predicted subcellular localization and visualization of conserved gene context across multiple prokaryotic genomes. function ... | 2005 | 15822923 |
| metabolite and enzyme profiles of glycogen metabolism in methanococcoides methylutens. | when a buffered anaerobic cell suspension of methanococcoides methylutens was maintained under methanol-limited conditions, intracellular glycogen and hexose phosphates were consumed rapidly and a very small amount of methane formed at 4 h of a starvation period. when methanol was supplemented after a total of 20 h of starvation, a reverse pattern was observed: the glycogen level and the hexose phosphate pool increased, and formation of methane took place after a lag period of 90 min. a consider ... | 2001 | 11325549 |
| cold adaptation in the antarctic archaeon methanococcoides burtonii involves membrane lipid unsaturation. | direct analysis of membrane lipids by liquid chromatography-electrospray mass spectrometry was used to demonstrate the role of unsaturation in ether lipids in the adaptation of methanococcoides burtonii to low temperature. a proteomics approach using two-dimensional liquid chromatography-mass spectrometry was used to identify enzymes involved in lipid biosynthesis, and a pathway for lipid biosynthesis was reconstructed from the m. burtonii draft genome sequence. the major phospholipids were arch ... | 2004 | 15576801 |
| proteomic and computational analysis of secreted proteins with type i signal peptides from the antarctic archaeon methanococcoides burtonii. | lc-ms/ms was used to identify secreted proteins in the antarctic archaeon methanococcoides burtonii. seven proteins possessing a classical class 1 signal peptide were identified in the supernatant from cultures grown at 4 and 23 degrees c. the proteins included a putative s-layer cell surface protein, cell surface protein involved with cell adhesion, and trypsin-like serine protease. protease activity was detected in the secreted fraction, and the signal peptide cleavage site of the protease was ... | 2006 | 16944959 |
| glucosylglycerate biosynthesis in the deepest lineage of the bacteria: characterization of the thermophilic proteins gpgs and gpgp from persephonella marina. | the pathway for the synthesis of glucosylglycerate (gg) in the thermophilic bacterium persephonella marina is proposed based on the activities of recombinant glucosyl-3-phosphoglycerate (gpg) synthase (gpgs) and glucosyl-3-phosphoglycerate phosphatase (gpgp). the sequences of gpgs and gpgp from the cold-adapted bacterium methanococcoides burtonii were used to identify the homologues in the genome of p. marina, which were separately cloned and overexpressed as his-tagged proteins in escherichia c ... | 2007 | 17189358 |
| analysis of the aaa+ chaperone clpb gene and stress-response expression in the halophilic methanogenic archaeon methanohalophilus portucalensis. | clpb is a member of the protein-disaggregating chaperone machinery belonging to the aaa+ superfamily. this paper describes a new clpb gene from the halophilic methanoarchaeon methanohalophilus portucalensis, which has not been reported previously in archaea. the partial sequence of clpb was identified from the investigation of the salt-stress response of meh. portucalensis by differential-display rt-pcr (ddrt-pcr). furthermore, the complete clpb sequence (2610 nt) and its upstream genes encoding ... | 2007 | 17660421 |
| methanogenic community composition and anaerobic carbon turnover in submarine permafrost sediments of the siberian laptev sea. | the siberian laptev sea shelf contains submarine permafrost, which was formed by flooding of terrestrial permafrost with ocean water during the holocene sea level rise. this flooding resulted in a warming of the permafrost to temperatures close below 0 degrees c. the impact of these environmental changes on methanogenic communities and carbon dynamics in the permafrost was studied in a submarine permafrost core of the siberian laptev sea shelf. total organic carbon (toc) content varied between 0 ... | 2009 | 19278451 |
| the genome sequence of the psychrophilic archaeon, methanococcoides burtonii: the role of genome evolution in cold adaptation. | psychrophilic archaea are abundant and perform critical roles throughout the earth's expansive cold biosphere. here we report the first complete genome sequence for a psychrophilic methanogenic archaeon, methanococcoides burtonii. the genome sequence was manually annotated including the use of a five-tiered evidence rating (er) system that ranked annotations from er1 (gene product experimentally characterized from the parent organism) to er5 (hypothetical gene product) to provide a rapid means o ... | 2009 | 19404327 |
| comparison of the molecular diversity of the methanogenic community at the brackish and marine ends of a uk estuary. | abstract the 16s rrna sequence diversity of the euryarchaeal community in a predominately freshwater sediment at east hill bridge (ehb) on the river colne estuary, essex, uk was investigated and compared to that from marine sediments at the mouth of the river (colne point). the east hill bridge sediments appear to support the full range of methanogen phenotypes with some genotypes similar to those previously detected at colne point. however, no marine benthic group d or halophilic archaeal genot ... | 2002 | 19709180 |
| substrate-induced assembly of methanococcoides burtonii d-ribulose-1,5-bisphosphate carboxylase/oxygenase dimers into decamers. | like many enzymes, the biogenesis of the multi-subunit co(2)-fixing enzyme ribulose-1,5-bisphosphate (rubp) carboxylase/oxygenase (rubisco) in different organisms requires molecular chaperones. when expressed in escherichia coli, the large (l) subunits of the rubisco from the archaeabacterium methanococcoides burtonii assemble into functional dimers (l(2)). however, further assembly into pentamers of l(2) (l(10)) occurs when expressed in tobacco chloroplasts or e. coli producing rubp. in vitro a ... | 2009 | 19837658 |
| recombinant production, crystallization and preliminary x-ray analysis of pcna from the psychrophilic archaeon methanococcoides burtonii dsm 6242. | proliferating cell nuclear antigen (pcna) is a dna-clamping protein that is responsible for increasing the processivity of the replicative polymerases during dna replication and repair. the pcna from the eurypsychrophilic archaeon methanococcoides burtonii dsm 6242 (mbpcna) has been targeted for protein structural studies. a recombinant expression system has been created that overproduces mbpcna with an n-terminal hexahistidine affinity tag in escherichia coli. as a result, recombinant mbpcna wi ... | 2009 | 19923734 |
| global proteomic analysis of the insoluble, soluble, and supernatant fractions of the psychrophilic archaeon methanococcoides burtonii. part ii: the effect of different methylated growth substrates. | methanococcoides burtonii is a cold-adapted methanogenic archaeon from ace lake in antarctica. methanol and methylamines are the only substrates it can use for carbon and energy. we carried out quantitative proteomics using itraq of m. burtonii cells grown on different substrates (methanol in defined media or trimethylamine in complex media), using techniques that enriched for secreted and membrane proteins in addition to cytoplasmic proteins. by integrating proteomic data with the complete, man ... | 2010 | 19947665 |
| analyzing the hydrophobic proteome of the antarctic archaeon methanococcoides burtonii using differential solubility fractionation. | proteomic studies have proven useful for studying the antarctic archaeon methanococcoides burtonii; however, little has been learned about the hydrophobic and membrane proteins, despite knowledge of their biological importance. in this study, new methods were developed to analyze and maximize the coverage of the hydrophobic proteome. central to the analysis was a differential solubility fractionation (dsf) procedure using n-octyl-beta-d-glucopyranoside. the study achieved a significant increase ... | 2010 | 19968327 |
| a proteomic determination of cold adaptation in the antarctic archaeon, methanococcoides burtonii. | a global view of the biology of the cold-adapted archaeon methanococcoides burtonii was achieved using proteomics. proteins specific to growth at 4 degrees c versus t(opt) (23 degrees c) were identified by mass spectrometry using the draft genome sequence of m. burtonii. mrna levels were determined for all genes identified by proteomics, and specific enzyme assays confirmed the protein expression results. key aspects of cold adaptation related to transcription, protein folding and metabolism, in ... | 2004 | 15225324 |
| temperature-dependent global gene expression in the antarctic archaeon methanococcoides burtonii. | methanococcoides burtonii is a member of the archaea that was isolated from ace lake in antarctica and is a valuable model for studying cold adaptation. low temperature transcriptional regulation of global gene expression, and the arrangement of transcriptional units in cold-adapted archaea has not been studied. we developed a microarray for determing which genes are expressed in operons, and which are differentially expressed at low (4°c) or high (23°c) temperature. approximately 55% of genes w ... | 2010 | 21059163 |
| the rna polymerase subunits e/f from the antarctic archaeon methanococcoides burtonii bind to specific species of mrna. | rna polymerase in archaea is composed of 11 or 12 subunits - 9 or 10 that form the core, and a heterodimer formed from subunits e and f that associates with the core and can interact with general transcription factors and facilitate transcription. while the ability of the heterodimer to bind rna has been demonstrated, it has not been determined whether it can recognize specific rna targets. in this study we used a recombinant archaeal mbrpoe/f to capture cellular mrna in vitro and a microarray t ... | 2010 | 21108724 |
| archaeal populations in hypersaline sediments underlying orange microbial mats in the napoli mud volcano. | microbial mats in marine cold seeps are known to be associated with ascending sulfide- and methane-rich fluids. hence, they could be visible indicators of anaerobic oxidation of methane (aom) and methane cycling processes in underlying sediments. the napoli mud volcano is situated in the olimpi area that lies on saline deposits; from there, brine fluids migrate upward to the seafloor. sediments associated with a brine pool and microbial orange mats of the napoli mud volcano were recovered during ... | 2011 | 21335391 |
| thermodynamic activation properties of elongation factor 2 (ef-2) proteins from psychrotolerant and thermophilic archaea. | in this study, the thermodynamic activation parameters of cold-adapted proteins from archaeaa are described for the first time for the irreversible protein unfolding and ribosome-dependent gtpase activity of elongation factor 2 (ef-2) from the psychrotolerant methanococcoides burtonii and the thermophilic methanosarcina thermophila. thermolability of methanococcoides burtonii ef-2 was demonstrated by a low activation free-energy of unfolding as a result of low activation-enthalpy. although struc ... | 2002 | 12013435 |
| distribution, structure and diversity of "bacterial" genes encoding two-component proteins in the euryarchaeota. | the publicly available annotated archaeal genome sequences (23 complete and three partial annotations, october 2005) were searched for the presence of potential two-component open reading frames (orfs) using gene category lists and blastp. a total of 489 potential two-component genes were identified from the gene category lists and blastp. two-component genes were found in 14 of the 21 euryarchaeal sequences (october 2005) and in neither the crenarchaeota nor the nanoarchaeota. a total of 20 pre ... | 2006 | 16877318 |
| global proteomic analysis of the insoluble, soluble, and supernatant fractions of the psychrophilic archaeon methanococcoides burtonii. part i: the effect of growth temperature. | the response of the cold-adapted (psychrophilic) methanogenic archaeon methanococcoides burtonii to growth temperature was investigated using differential proteomics (postincorporation isobaric labeling) and tandem liquid chromatography-mass spectrometry (lc/lc-ms/ms). this is the first proteomic study of m. burtonii to include techniques that specifically enrich for both surface and membrane proteins and to assess the effects of growth temperature (4 vs 23 degrees c) and carbon source (trimethy ... | 2010 | 20039705 |
| a modulator domain controlling thermal stability in the group ii chaperonins of archaea. | archaeal group ii chaperonins (cpns) are strongly conserved, considering that their growth temperatures range from 23 to 122°c. the c-terminal 15-25 residues are hypervariable, and highly charged in thermophilic species. our hypothesis is that the c-terminal is a key determinant of stabilization of the cpn complex. the c-terminus of the cpn from the hyperthermophile pyrococcus furiosus was mutated to test this hypothesis. c-terminal deletions and replacement of charged residues resulted in desta ... | 2011 | 21600187 |
| cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor. | microbial methanogenesis in subseafloor sediments is a key process in the carbon cycle on the earth. however, the cultivation-dependent evidences have been poorly demonstrated. here we report the cultivation of a methanogenic microbial consortium from subseafloor sediments using a continuous-flow-type bioreactor with polyurethane sponges as microbial habitats, called down-flow hanging sponge (dhs) reactor. we anaerobically incubated methane-rich core sediments collected from off shimokita penins ... | 2011 | 21654849 |
| characterization and spatial distribution of methanogens and methanogenic biosignatures in hypersaline microbial mats of baja california. | well-developed hypersaline cyanobacterial mats from guerrero negro, baja california sur, sustain active methanogenesis in the presence of high rates of sulfate reduction. very little is known about the diversity and distribution of the microorganisms responsible for methane production in these unique ecosystems. applying a combination of 16s rrna and metabolic gene surveys, fluorescence in situ hybridization, and lipid biomarker analysis, we characterized the diversity and spatial relationships ... | 2008 | 18564187 |
| engineering of functional replication protein a homologs based on insights into the evolution of oligonucleotide/oligosaccharide-binding folds. | the bacterial single-stranded dna-binding protein (ssb) and the archaeal/eukaryotic functional homolog, replication protein a (rpa), are essential for most aspects of dna metabolism. structural analyses of the architecture of ssb and rpa suggest that they are composed of different combinations of a module called the oligonucleotide/oligosaccharide-binding (ob) fold. members of the domains bacteria and eukarya, in general, contain one type of ssb or rpa. in contrast, organisms in the archaeal dom ... | 2008 | 18586938 |
| defining the response of a microorganism to temperatures that span its complete growth temperature range (-2°c to 28°c) using multiplex quantitative proteomics. | the growth of all microorganisms is limited to a specific temperature range. however, it has not previously been determined to what extent global protein profiles change in response to temperatures that incrementally span the complete growth temperature range of a microorganism. as a result it has remained unclear to what extent cellular processes (inferred from protein abundance profiles) are affected by growth temperature and which, in particular, constrain growth at upper and lower temperatur ... | 2011 | 21443741 |
| diversity of methanogenic archaea in a mangrove sediment and isolation of a new methanococcoides strain. | mangrove forest sediments produce significant amounts of methane, but the diversity of methanogenic archaea is not well known at present. therefore, 16s rrna gene libraries were made using archaea-specific primers and dna extracted directly from tanzanian mangrove sediment samples as a template. analysis of sequence data showed phylotypes closely related to cultivated methylotrophic methanogenic archaea from the marine environment, or distantly related to acetoclastic and hydrogenotrophic methan ... | 2009 | 19146579 |
| chaperonins from an antarctic archaeon are predominantly monomeric: crystal structure of an open state monomer. | archaea are abundant in permanently cold environments. the antarctic methanogen, methanococcoides burtonii, has proven an excellent model for studying molecular mechanisms of cold adaptation. methanococcoides burtonii contains three group ii chaperonins that diverged prior to its closest orthologues from mesophilic methanosarcina spp. the relative abundance of the three chaperonins shows little dependence on organism growth temperature, except at the highest temperatures, where the most thermall ... | 2011 | 21477108 |
| methanogenic diversity and activity in hypersaline sediments of the centre of the napoli mud volcano, eastern mediterranean sea. | submarine mud volcanoes are a significant source of methane to the atmosphere. the napoli mud volcano, situated in the brine-impacted olimpi area of the eastern mediterranean sea, emits mainly biogenic methane particularly at the centre of the mud volcano. temperature gradients support the suggestion that napoli is a cold mud volcano with moderate fluid flow rates. biogeochemical and molecular genetic analyses were carried out to assess the methanogenic activity rates, pathways and diversity in ... | 2011 | 21382146 |
| chaperone action of a versatile small heat shock protein from methanococcoides burtonii, a cold adapted archaeon. | the methanococcoides burtonii small heat shock protein (mb-shsp) is an alphab-crystallin homolog that delivers protein stabilizing and protective functions to model enzymes, presumably reflecting its role as a molecular chaperone in vivo. although the gene encoding mb-shsp was cloned from a cold-adapted microorganism, the mb-shsp is an efficient protein chaperone at temperatures far above the optimum growth temperature of m. burtonii. we show that mb-shsp can prevent aggregation in e. coli cell ... | 2009 | 18951410 |