Genomes and Genes
Summary: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.
- Benelli D, Maone E, Londei P. Two different mechanisms for ribosome/mRNA interaction in archaeal translation initiation. Mol Microbiol. 2003;50:635-43 pubmed
- Grissa I, Vergnaud G, Pourcel C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics. 2007;8:172 pubmed..Subsequent analyses of the intra-species CRISPR polymorphism will be facilitated by CRISPRFinder and the dictionary creator. CRISPRdb is accessible at http://crispr.u-psud.fr/crispr. ..
- Hallam S, Konstantinidis K, Putnam N, Schleper C, Watanabe Y, Sugahara J, et al. Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc Natl Acad Sci U S A. 2006;103:18296-301 pubmed..In total, the C. symbiosum genome was remarkably distinct from those of other known Archaea and shared many core metabolic features in common with its free-living planktonic relatives...
- Ulrich L, Zhulin I. MiST: a microbial signal transduction database. Nucleic Acids Res. 2007;35:D386-90 pubmed..Newly available, complete genomes are loaded into the database each month. MiST is the only comprehensive and up-to-date electronic catalog of the signaling machinery in microbial genomes. ..
- 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
- Beiko R, Harlow T, Ragan M. Highways of gene sharing in prokaryotes. Proc Natl Acad Sci U S A. 2005;102:14332-7 pubmed..The inferred relationships suggest a pattern of inheritance that is largely vertical, but with notable exceptions among closely related taxa, and among distantly related organisms that live in similar environments. ..
- Sugahara J, Yachie N, Arakawa K, Tomita M. In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs. RNA. 2007;13:671-81 pubmed..Moreover, the candidates completely complemented all the codons of two archaeal species of uncultured methanogenic archaeon, RC-I and Thermofilum pendens Hrk 5, with novel candidates that were not detectable by tRNAscan-SE alone. ..
- Schleper C, Jurgens G, Jonuscheit M. Genomic studies of uncultivated archaea. Nat Rev Microbiol. 2005;3:479-88 pubmed..Here, we review genomic studies of uncultivated archaea within a framework of the phylogenetic diversity and ecological distribution of this domain. ..
- Gophna U, Doolittle W, Charlebois R. Weighted genome trees: refinements and applications. J Bacteriol. 2005;187:1305-16 pubmed..Comparisons of results obtained with different methods can provide further clues to major events and processes in genome evolution. ..
- Ulrich L, Koonin E, Zhulin I. One-component systems dominate signal transduction in prokaryotes. Trends Microbiol. 2005;13:52-6 pubmed..One-component systems are evolutionarily older, more widely distributed among bacteria and archaea, and display a greater diversity of domains than two-component systems. ..
- Markowitz V, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen I, et al. The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res. 2008;36:D528-33 pubmed..IMG is provided by the DOE-Joint Genome Institute (JGI) and is available from http://img.jgi.doe.gov. ..
- Liolios K, Chen I, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz V, et al. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2010;38:D346-54 pubmed publisher..GOLD is available at: http://www.genomesonline.org and has a mirror site at the Institute of Molecular Biology and Biotechnology, Crete, Greece, at: http://gold.imbb.forth.gr/ ..
- Waters E, Hohn M, Ahel I, Graham D, Adams M, Barnstead M, et al. The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci U S A. 2003;100:12984-8 pubmed..equitans has few pseudogenes or extensive regions of noncoding DNA. This organism represents a basal archaeal lineage and has a highly reduced genome. ..
- Aziz R, Bartels D, Best A, DeJongh M, Disz T, Edwards R, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75 pubmed publisher..By providing accurate, rapid annotation freely to the community we have created an important community resource. The service has now been utilized by over 120 external users annotating over 350 distinct genomes. ..
- Puigbò P, Romeu A, Garcia Vallve S. HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection. Nucleic Acids Res. 2008;36:D524-7 pubmed..The HEG-DB is freely available at http://genomes.urv.cat/HEG-DB. ..
- Huber H, Hohn M, Stetter K, Rachel R. The phylum Nanoarchaeota: present knowledge and future perspectives of a unique form of life. Res Microbiol. 2003;154:165-71 pubmed..Growth occurs only in coculture with a new chemolithoautotrophic Ignicoccus species...
- ..Since organization results from cellular processes, a better understanding of chromosome organization will help unravel the underlying cellular processes and their diversity...
- Galperin M. Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J Bacteriol. 2006;188:4169-82 pubmed..The complete list of response regulators encoded in each of the 200 analyzed genomes is available online at http://www.ncbi.nlm.nih.gov/Complete_Genomes/RRcensus.html. ..
- Meyerdierks A, Kube M, Lombardot T, Knittel K, Bauer M, Glöckner F, et al. Insights into the genomes of archaea mediating the anaerobic oxidation of methane. Environ Microbiol. 2005;7:1937-51 pubmed
- Andersson A, Bernander R, Nilsson P. Dual-genome primer design for construction of DNA microarrays. Bioinformatics. 2005;21:325-32 pubmed..3. The software is freely available at http://www.biotech.kth.se/molbio/microarray/. ..
- Snel B, Huynen M, Dutilh B. Genome trees and the nature of genome evolution. Annu Rev Microbiol. 2005;59:191-209 pubmed..We expect such sophisticated methods to help us resolve the branching order between the main bacterial phyla. ..
- Baliga N, Bonneau R, Facciotti M, Pan M, Glusman G, Deutsch E, et al. Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res. 2004;14:2221-34 pubmed..Finally, as expected from the larger genome, H. marismortui encodes many more functions and seems to have fewer nutritional requirements for survival than does Halobacterium sp. NRC-1...
- Roberts R, Vincze T, Posfai J, Macelis D. REBASE--a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res. 2010;38:D234-6 pubmed publisher..The contents of REBASE may be browsed from the web (http://rebase.neb.com) and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email. ..
- Anderson I, Ulrich L, Lupa B, Susanti D, Porat I, Hooper S, et al. Genomic characterization of methanomicrobiales reveals three classes of methanogens. PLoS ONE. 2009;4:e5797 pubmed publisher..While these organisms appear to be more closely related to the Methanosarcinales in ribosomal-based phylogenetic analyses, they are metabolically more similar to Class I methanogens...
- Chang B, Halgamuge S, Tang S. Analysis of SD sequences in completed microbial genomes: non-SD-led genes are as common as SD-led genes. Gene. 2006;373:90-9 pubmed
- Mackwan R, Carver G, Kissling G, Drake J, Grogan D. The rate and character of spontaneous mutation in Thermus thermophilus. Genetics. 2008;180:17-25 pubmed publisher..thermophilus resembled those of the thermoacidophilic archaeon Sulfolobus acidocaldarius, despite important molecular differences between these two thermophiles and their genomes...
- Poole F, Gerwe B, Hopkins R, Schut G, Weinberg M, Jenney F, et al. Defining genes in the genome of the hyperthermophilic archaeon Pyrococcus furiosus: implications for all microbial genomes. J Bacteriol. 2005;187:7325-32 pubmed..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. ..
- Brugger K, Chen L, Stark M, Zibat A, Redder P, Ruepp A, et al. The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 degrees C. Archaea. 2007;2:127-35 pubmed..This suggests that the genome structure is quite stable, possibly reflecting a constant, and relatively uncompetitive, natural environment...
- Sandberg R, Bränden C, Ernberg I, Cöster J. Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content. Gene. 2003;311:35-42 pubmed..This was performed in order to illustrate the feasibility of a hierarchical classification scheme in future applications of the described classification methodology in screening for horizontal gene transfer and biodiversity studies. ..
- Azad R, Borodovsky M. Probabilistic methods of identifying genes in prokaryotic genomes: connections to the HMM theory. Brief Bioinform. 2004;5:118-30 pubmed
- Torarinsson E, Klenk H, Garrett R. Divergent transcriptional and translational signals in Archaea. Environ Microbiol. 2005;7:47-54 pubmed..High levels of leaderless transcripts are found in the longer branched Archaea. ..
- Soppa J. From genomes to function: haloarchaea as model organisms. Microbiology. 2006;152:585-90 pubmed..Taken together, the wealth of techniques available make haloarchaea excellent archaeal model species...
- Redder P, Garrett R. Mutations and rearrangements in the genome of Sulfolobus solfataricus P2. J Bacteriol. 2006;188:4198-206 pubmed..The results underline the caution required in working experimentally with an organism such as S. solfataricus with a continually changing genome. ..
- Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007;35:W52-7 pubmed..CRISPRFinder is freely accessible at http://crispr.u-psud.fr/Server/CRISPRfinder.php. ..
- Barry E, Bell S. DNA replication in the archaea. Microbiol Mol Biol Rev. 2006;70:876-87 pubmed
- Veloso F, Riadi G, Aliaga D, Lieph R, Holmes D. Large-scale, multi-genome analysis of alternate open reading frames in bacteria and archaea. OMICS. 2005;9:91-105 pubmed
- Ettema T, Makarova K, Jellema G, Gierman H, Koonin E, Huynen M, et al. Identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism. J Bacteriol. 2004;186:7754-62 pubmed publisher..The newly identified atPEPC, with its distinct properties, constitutes yet another example of the versatility of the enzymes of the central carbon metabolic pathways in the archaeal domain...
- Urbonavicius J, Auxilien S, Walbott H, Trachana K, Golinelli Pimpaneau B, Brochier Armanet C, et al. Acquisition of a bacterial RumA-type tRNA(uracil-54, C5)-methyltransferase by Archaea through an ancient horizontal gene transfer. Mol Microbiol. 2008;67:323-35 pubmed..This functional shift probably occurred in an ancestor of all Thermococcales. This study also provides new evidence in favour of a close relationship between Thermococcales and Nanoarchaea...
- Pertea M, Ayanbule K, Smedinghoff M, Salzberg S. OperonDB: a comprehensive database of predicted operons in microbial genomes. Nucleic Acids Res. 2009;37:D479-82 pubmed publisher..The new database is updated regularly as additional genomes become available in public archives. OperonDB can be accessed at: http://operondb.cbcb.umd.edu. ..
- Noguchi H, Park J, Takagi T. MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res. 2006;34:5623-30 pubmed..Applied to the Sargasso Sea dataset, MetaGene predicted almost all of the annotated genes and a notable number of novel genes. MetaGene can be applied to wide variety of metagenomic projects and expands the utility of metagenomics. ..
- Manzan A, Pfeiffer G, Hefferin M, Lang C, Carney J, Hopfner K. MlaA, a hexameric ATPase linked to the Mre11 complex in archaeal genomes. EMBO Rep. 2004;5:54-9 pubmed..Our data suggest that the archaeal Mre11 complex is associated with a novel hexameric ATPase that could be required for the processing of DNA double-stranded breaks and recombination intermediates. ..
- Guo F, Wang J, Zhang C. Gene recognition based on nucleotide distribution of ORFs in a hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. DNA Res. 2004;11:361-70 pubmed..Annotation information of re-recognized genes and their AZ scores are available at: http://tubic.tju.edu.cn/Aper/...
- Koonin E, Wolf Y. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res. 2008;36:6688-719 pubmed publisherThe first bacterial genome was sequenced in 1995, and the first archaeal genome in 1996...
- Omelchenko M, Makarova K, Wolf Y, Rogozin I, Koonin E. Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. Genome Biol. 2003;4:R55 pubmed..These findings also emphasize that not all aspects of operon evolution are selfish, with operon integrity maintained by purifying selection at the organism level. ..
- Filee J, Siguier P, Chandler M. Insertion sequence diversity in archaea. Microbiol Mol Biol Rev. 2007;71:121-57 pubmed..In addition to ISs, we identify and list nonautonomous IS-derived elements, such as miniature inverted-repeat transposable elements. Finally, we present a possible scenario for the evolutionary history of ISs in the Archaea. ..
- Siebers B, Tjaden B, Michalke K, Dörr C, Ahmed H, Zaparty M, et al. Reconstruction of the central carbohydrate metabolism of Thermoproteus tenax by use of genomic and biochemical data. J Bacteriol. 2004;186:2179-94 pubmed..Almost all genes necessary for glycogen and trehalose metabolism were identified in the T. tenax genome...
- Singer G, Hickey D. Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content. Gene. 2003;317:39-47 pubmed..In addition to these multiple selective effects, however, the genomes of both thermophiles and mesophiles are often subject to superimposed large changes in composition due to mutational bias. ..
- McCann A, Cotton J, McInerney J. The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods. BMC Evol Biol. 2008;8:312 pubmed publisher..We conclude that genome phylogenies need to be interpreted differently, depending on the method used to construct them. ..
- Makarova K, Koonin E. Filling a gap in the central metabolism of archaea: prediction of a novel aconitase by comparative-genomic analysis. FEMS Microbiol Lett. 2003;227:17-23 pubmed..The prediction of aconitase X completes the TCA cycle for Methanothermobacter thermoautotrophicus and Archaeoglobus fulgidus and suggests that most archaea have a full TCA cycle. ..
- Bryson K, Loux V, Bossy R, Nicolas P, Chaillou S, van de Guchte M, et al. AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Res. 2006;34:3533-45 pubmed..AGMIAL is currently being used by several INRA laboratories to analyze genomes of bacteria relevant to the food-processing industry, and is distributed under an open source license. ..