Genomes and Genes
Summary: Deoxyribonucleic acid that makes up the genetic material of archaea.
- Galand P, Casamayor E, Kirchman D, Potvin M, Lovejoy C. Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing. ISME J. 2009;3:860-9 pubmed publisher..Our results unveiled for the first time an archaeal community dominated by group III Euryarchaeota and show biogeographical traits for marine Arctic Archaea. ..
- Schomacher L, Schürer K, Ciirdaeva E, McDermott P, Chong J, Kramer W, et al. Archaeal DNA uracil repair via direct strand incision: A minimal system reconstituted from purified components. DNA Repair (Amst). 2010;9:438-47 pubmed publisher..Finally, DNA ligase seals the resulting nick. This defines mechanism and minimal enzymatic requirements of DNA-U repair in this organism. ..
- Mosier A, Francis C. Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary. Environ Microbiol. 2008;10:3002-16 pubmed publisher..Overall, this study significantly enhances our understanding of estuarine ammonia-oxidizing microbial communities and highlights the environmental conditions and niches under which different AOA and beta-AOB phylotypes may thrive. ..
- Zhang T, Jin T, Yan Q, Shao M, Wells G, Criddle C, et al. Occurrence of ammonia-oxidizing Archaea in activated sludges of a laboratory scale reactor and two wastewater treatment plants. J Appl Microbiol. 2009;107:970-7 pubmed publisher..AOA communities found in this study were significantly different from those found in other places. To retrieve diverse AOA communities from environmental samples, a combination of different primers for the amoA gene is needed. ..
- Chen Y, Lin Y, Yoshinaga A, Chhotani B, Lorenzini J, Crofts A, et al. Molecular analyses of a three-subunit euryarchaeal clamp loader complex from Methanosarcina acetivorans. J Bacteriol. 2009;191:6539-49 pubmed publisher..Mutational analysis, however, suggested that the similarity between the two clamp loaders does not translate into the complete conservation of the functions of individual subunits within the RFC(Ma) complex...
- Nicholson M, Evans P, Joblin K. Analysis of methanogen diversity in the rumen using temporal temperature gradient gel electrophoresis: identification of uncultured methanogens. Microb Ecol. 2007;54:141-50 pubmed..may be the predominant methanogens in the rumen. The TTGE method presented in this article provides a new opportunity for characterizing methanogen populations in the rumen microbial ecosystem...
- Imamura K, Fukunaga K, Kawarabayasi Y, Ishino Y. Specific interactions of three proliferating cell nuclear antigens with replication-related proteins in Aeropyrum pernix. Mol Microbiol. 2007;64:308-18 pubmedProliferating cell nuclear antigen (PCNA) is a well-known multifunctional protein involved in eukaryotic and archaeal DNA transactions...
- Lin L, Yoshinaga A, Lin Y, Guzman C, Chen Y, Mei S, et al. Molecular analyses of an unusual translesion DNA polymerase from Methanosarcina acetivorans C2A. J Mol Biol. 2010;397:13-30 pubmed publisher..acetivorans cells. ..
- Salonen A, Nikkilä J, Jalanka Tuovinen J, Immonen O, Rajilić Stojanović M, Kekkonen R, et al. Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J Microbiol Methods. 2010;81:127-34 pubmed publisher..The assessment of performance differences between different methodologies serves as a concrete step towards the comparison and reliable meta-analysis of the results obtained in different laboratories. ..
- Kozobay Avraham L, Hosid S, Bolshoy A. Involvement of DNA curvature in intergenic regions of prokaryotes. Nucleic Acids Res. 2006;34:2316-27 pubmed..Our hypothesis is that DNA curvature could affect transcription termination in many prokaryotes either directly, through contacts with RNA polymerase, or indirectly, via contacts with some regulatory proteins. ..
- Stewart J, Chadwick V, Murray A. Carriage, quantification, and predominance of methanogens and sulfate-reducing bacteria in faecal samples. Lett Appl Microbiol. 2006;43:58-63 pubmed..To determine carriage rates and densities of methanogens and sulfate-reducing bacteria in adults and children using molecular methods, and to also determine if a reciprocal relationship exists between these organisms...
- Ashelford K, Chuzhanova N, Fry J, Jones A, Weightman A. New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol. 2006;72:5734-41 pubmed..Mallard is freely available from our website at http://www.cardiff.ac.uk/biosi/research/biosoft/. ..
- Webster G, Parkes R, Cragg B, Newberry C, Weightman A, Fry J. Prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin. FEMS Microbiol Ecol. 2006;58:65-85 pubmed..This study clearly demonstrates that the deep subsurface sediments of the Peru Margin have a large diverse and metabolically active prokaryotic population. ..
- Andersson A, Lundgren M, Eriksson S, Rosenlund M, Bernander R, Nilsson P. Global analysis of mRNA stability in the archaeon Sulfolobus. Genome Biol. 2006;7:R99 pubmed..Here, we present a microarray-based analysis of mRNA half-lives in the hyperthermophilic crenarchaea Sulfolobus solfataricus and Sulfolobus acidocaldarius, constituting the first genome-wide study of RNA decay in archaea...
- Barry E, Bell S. DNA replication in the archaea. Microbiol Mol Biol Rev. 2006;70:876-87 pubmedThe archaeal DNA replication machinery bears striking similarity to that of eukaryotes and is clearly distinct from the bacterial apparatus...
- Lundgren M, Bernander R. Genome-wide transcription map of an archaeal cell cycle. Proc Natl Acad Sci U S A. 2007;104:2939-44 pubmed
- Vianna M, Conrads G, Gomes B, Horz H. Identification and quantification of archaea involved in primary endodontic infections. J Clin Microbiol. 2006;44:1274-82 pubmed..e., bacteria plus archaea). Our findings show that archaea can be intimately connected with infectious diseases and thus support the hypothesis that members of the domain Archaea may have a role as human pathogens. ..
- Nishida H, Kiyonari S, Ishino Y, Morikawa K. The closed structure of an archaeal DNA ligase from Pyrococcus furiosus. J Mol Biol. 2006;360:956-67 pubmed publisher..This sequence is also conserved exclusively among the covalent nucleotidyltransferases, even including mRNA-capping enzymes with similar helical extensions at the C termini...
- Park H, Wells G, Bae H, Criddle C, Francis C. Occurrence of ammonia-oxidizing archaea in wastewater treatment plant bioreactors. Appl Environ Microbiol. 2006;72:5643-7 pubmed
- Sharp K, Eam B, Faulkner D, Haygood M. Vertical transmission of diverse microbes in the tropical sponge Corticium sp. Appl Environ Microbiol. 2007;73:622-9 pubmed
- Herfort L, Schouten S, Abbas B, Veldhuis M, Coolen M, Wuchter C, et al. Variations in spatial and temporal distribution of Archaea in the North Sea in relation to environmental variables. FEMS Microbiol Ecol. 2007;62:242-57 pubmed
- Park Y, Yoon S, Lee H. A novel thermostable arylesterase from the archaeon Sulfolobus solfataricus P1: purification, characterization, and expression. J Bacteriol. 2008;190:8086-95 pubmed publisher..solfataricus arylesterase in Escherichia coli. Together, our results show that the enzyme is a serine esterase belonging to the A-esterases and contains a catalytic triad composed of Ser156, Asp251, and His281 in the active site...
- Mikkelsen D, Kappler U, McEwan A, Sly L. Probing the archaeal diversity of a mixed thermophilic bioleaching culture by TGGE and FISH. Syst Appl Microbiol. 2009;32:501-13 pubmed publisher..These results highlight the importance of using more than one molecular technique when investigating the archaeal diversity of complex bioleaching reactor samples. ..
- Nettmann E, Bergmann I, Mundt K, Linke B, Klocke M. Archaea diversity within a commercial biogas plant utilizing herbal biomass determined by 16S rDNA and mcrA analysis. J Appl Microbiol. 2008;105:1835-50 pubmed publisher..Therein the hydrogenotrophic methanogenesis seems to be the major pathway of methane formation. These results are in contrast with the common thesis that in biogas fermentations the primary substrate for methanogenesis is acetate. ..
- Imachi H, Sakai S, Nagai H, Yamaguchi T, Takai K. Methanofollis ethanolicus sp. nov., an ethanol-utilizing methanogen isolated from a lotus field. Int J Syst Evol Microbiol. 2009;59:800-5 pubmed publisher..nov. is proposed. The type strain is HASU(T) (=NBRC 104120(T)=JCM 15103(T)=DSM 21041(T))...
- Manerkar M, Seena S, Bärlocher F. Q-RT-PCR for assessing archaea, bacteria, and fungi during leaf decomposition in a stream. Microb Ecol. 2008;56:467-73 pubmed publisher..b>Archaeal DNA was consistently present at low levels...
- Bardavid R, Mana L, Oren A. Haloplanus natans gen. nov., sp. nov., an extremely halophilic, gas-vacuolate archaeon isolated from Dead Sea-Red Sea water mixtures in experimental outdoor ponds. Int J Syst Evol Microbiol. 2007;57:780-3 pubmed..The name Haloplanus natans gen. nov., sp. nov. is proposed for this novel organism. The type strain of Haloplanus natans is RE-101(T) (=DSM 17983(T)=JCM 14081(T)). ..
- Qiu G, Wan M, Qian L, Huang Z, Liu K, Liu X, et al. Archaeal diversity in acid mine drainage from Dabaoshan Mine, China. J Basic Microbiol. 2008;48:401-9 pubmed publisher..The high temperature of the sampling sites was one of the factors that could explain why archaea belonging to the Thermoplasmatales were abundant in the analyzed AMD samples while those belonging to the Sulfolobales were absent. ..
- Sandman K, Louvel H, Samson R, Pereira S, Reeve J. Archaeal chromatin proteins histone HMtB and Alba have lost DNA-binding ability in laboratory strains of Methanothermobacter thermautotrophicus. Extremophiles. 2008;12:811-7 pubmed publisher..The loss of DNA binding by HMtB(I19) does not therefore prevent HMtB from participating in DNA interactions as one partner of an archaeal histone heterodimer. ..
- Gieg L, Duncan K, Suflita J. Bioenergy production via microbial conversion of residual oil to natural gas. Appl Environ Microbiol. 2008;74:3022-9 pubmed publisher..Such microbe-based methane production holds promise for producing a clean-burning and efficient form of energy from underutilized hydrocarbon-bearing resources. ..
- Kim M, Bae S, Seol M, Lee J, Oh Y. Monitoring nutrient impact on bacterial community composition during bioremediation of anoxic PAH-contaminated sediment. J Microbiol. 2008;46:615-23 pubmed publisher..These results suggest a possible contribution of methanogenic community to PAH degradation and give us more insights on how to effectively remediate PAH-contaminated sediments. ..
- Peng J, Lu Z, Rui J, Lu Y. Dynamics of the methanogenic archaeal community during plant residue decomposition in an anoxic rice field soil. Appl Environ Microbiol. 2008;74:2894-901 pubmed publisher..The in situ concentration of acetate (and possibly of H(2)) seems to be the key factor that regulates the shift of methanogenic community...
- Hardy C, Martin P. Biochemical characterization of DNA-binding proteins from Pyrobaculum aerophilum and Aeropyrum pernix. Extremophiles. 2008;12:235-46 pubmed..Finally, we present the equilibrium affinity constants and kinetic association constants of each protein for single-stranded and double-stranded DNA...
- Li Z, Lu S, Hou G, Ma X, Sheng D, Ni J, et al. Hjm/Hel308A DNA helicase from Sulfolobus tokodaii promotes replication fork regression and interacts with Hjc endonuclease in vitro. J Bacteriol. 2008;190:3006-17 pubmed publisher..These results may suggest that the Hjm/Hel308 family helicases, in association with Hjc endonucleases, are involved in processing of stalled replication forks...
- Lipscomb G, Keese A, Cowart D, Schut G, Thomm M, Adams M, et al. SurR: a transcriptional activator and repressor controlling hydrogen and elemental sulphur metabolism in Pyrococcus furiosus. Mol Microbiol. 2009;71:332-49 pubmed publisher..Herein we give evidence for the role of SurR in both mediating the primary response to S(0) and controlling hydrogen production in P. furiosus. ..
- Bose A, Pritchett M, Metcalf W. Genetic analysis of the methanol- and methylamine-specific methyltransferase 2 genes of Methanosarcina acetivorans C2A. J Bacteriol. 2008;190:4017-26 pubmed publisher..mtaA2 was expressed at very low levels on all substrates. The mtaA1 transcript had a large 5' untranslated region (UTR) (275 bp), while the 5' UTR of the mtbA transcript was only 28 bp long...
- Mardanov A, Ravin N, Svetlitchnyi V, Beletsky A, Miroshnichenko M, Bonch Osmolovskaya E, et al. Metabolic versatility and indigenous origin of the archaeon Thermococcus sibiricus, isolated from a siberian oil reservoir, as revealed by genome analysis. Appl Environ Microbiol. 2009;75:4580-8 pubmed publisher..Considering that agarose and laminarin are components of algae, the encoded enzymes and the substrate spectrum of T. sibiricus indicate the ability to metabolize the buried organic matter from the original oceanic sediment. ..
- Thummes K, Kampfer P, Jäckel U. Temporal change of composition and potential activity of the thermophilic archaeal community during the composting of organic material. Syst Appl Microbiol. 2007;30:418-29 pubmed..Likewise, compost may act as a potential carrier for thermophilic methanogens in temperate soils because it is widely used as a soil amendment. ..
- Vissers E, Bodelier P, Muyzer G, Laanbroek H. A nested PCR approach for improved recovery of archaeal 16S rRNA gene fragments from freshwater samples. FEMS Microbiol Lett. 2009;298:193-8 pubmed publisher..The nested PCR-DGGE method presented here is therefore a reliable tool to analyze the archaeal diversity in freshwater habitats, revealing even more widespread diversity of the archaea. ..
- O Reilly J, Chinalia F, Mahony T, Collins G, Wu J, O Flaherty V. Cultivation of low-temperature (15 degrees C), anaerobic, wastewater treatment granules. Lett Appl Microbiol. 2009;49:421-6 pubmed publisher..Granulation underpins high-rate anaerobic waste treatment bioreactors. Most LT bioreactor trials have employed mesophilic seed sludge, and granulation <20 degrees C was not previously documented. ..
- Angellotti M, Bhuiyan S, Chen G, Wan X. CodonO: codon usage bias analysis within and across genomes. Nucleic Acids Res. 2007;35:W132-6 pubmed..Here we present a CodonO webserver service as a user-friendly tool for codon usage bias analyses across and within genomes in real time. The webserver is available at http//www.sysbiology.org/CodonO. firstname.lastname@example.org. ..
- Herrera A, Cockell C. Exploring microbial diversity in volcanic environments: a review of methods in DNA extraction. J Microbiol Methods. 2007;70:1-12 pubmed..Finally, we discuss these approaches in the wider context of modern work to understand the microbial diversity of volcanic environments. ..
- Wilson C, Murthy S, Fang Y, Novak J. The effect of temperature on the performance and stability of thermophilic anaerobic digestion. Water Sci Technol. 2008;57:297-304 pubmed publisher..5 degrees C are likely due to temperature limitations of thermophilic aceticlastic methanogens. ..
- Song Z, Chen J, Jiang H, Zhou E, Tang S, Zhi X, et al. Diversity of Crenarchaeota in terrestrial hot springs in Tengchong, China. Extremophiles. 2010;14:287-96 pubmed publisher..Crenarchaeotal diversity in moderate-temperature (59-77 degrees C) hot springs was the highest, indicating that the moderately hot-temperature springs may provide optimal conditions for speciation of Crenarchaeota...
- Happonen L, Redder P, Peng X, Reigstad L, Prangishvili D, Butcher S. Familial relationships in hyperthermo- and acidophilic archaeal viruses. J Virol. 2010;84:4747-54 pubmed publisher..A combination of genomic and proteomic analyses revealed important new insights into the structural organization of these viruses and added to our limited knowledge of archaeal virus life cycles and host-cell interactions...
- Heijs S, Laverman A, Forney L, Hardoim P, van Elsas J. Comparison of deep-sea sediment microbial communities in the Eastern Mediterranean. FEMS Microbiol Ecol. 2008;64:362-77 pubmed publisher..The data supported the notion of (1) uniqueness of each habitat at fine taxonomic levels, (2) stratification in depth and (3) conservation of function in the sediments. ..