PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Genome, Archaeal”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources
PubMed2003

Remarkable sequence signatures in archaeal genomes.

Complete archaeal genomes were probed for the presence of long (> or = 25 bp) oligonucleotide repeats (words). We detected the presence of many words distributed in tandem with narrow ranges of periodicity (i.e., spacer length between repeats). Similar words were not identified in genomes of non-archaeal species, namely Escherichia coli, Bacillus subtilis, Haemophilus influenzae, Mycoplasma genitalium and Mycoplasma pneumoniae. BLAST similarity searches against the GenBank nucleotide sequence database revealed that these words were archaeal species-specific, indicating that they are of a signature character. Sequence analysis and genome viewing tools showed these repeats to be restricted to non-coding regions. Thus, archaea appear to possess a non-coding genomic signature that is absent in bacterial species. The identification of a species-specific genomic signature would be of great value to archaeal genome mapping, evolutionary studies and analyses of genome complexity.

Base Sequence↗
PubMed2006

The UCSC Archaeal Genome Browser.

As more archaeal genomes are sequenced, effective research and analysis tools are needed to integrate the diverse information available for any given locus. The feature-rich UCSC Genome Browser, created originally to annotate the human genome, can be applied to any sequenced organism. We have created a UCSC Archaeal Genome Browser, available at http://archaea.ucsc.edu/, currently with 26 archaeal genomes. It displays G/C content, gene and operon annotation from multiple sources, sequence motifs (promoters and Shine-Dalgarno), microarray data, multi-genome alignments and protein conservation across phylogenetic and habitat categories. We encourage submission of new experimental and bioinformatic analysis from contributors. The purpose of this tool is to aid biological discovery and facilitate greater collaboration within the archaeal research community.

Archaeal Proteins↗
PubMed2005

Genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomes.

Bacterial, archaeal, yeast, and fly genomes are compared with respect to predicted highly expressed (PHX) genes and several genomic properties. There is a striking difference in the status of PHX ribosomal protein (RP) genes where the archaeal genome generally encodes more RP genes and fewer PHX RPs compared with bacterial genomes. The increase in RPs in archaea and eukaryotes compared with that in bacteria may reflect a more complex set of interactions in archaea and eukaryotes in regulating translation, e.g., differences in structure requiring scaffolding of longer rRNA molecules, expanded interactions with the chaperone machinery, and, in eukaryotic interactions with endoplasmic reticulum components. The yeast genome is similar to fast-growing bacteria in PHX genes but also features several cytoskeletal genes, including actin and tropomyosin, and several signal transduction regulatory proteins from the 14.3.3 family. The most PHX genes of Drosophila encode cytoskeletal and exoskeletal proteins. We found that the preference of a microorganism for an anaerobic metabolism correlates with the number of PHX enzymes of the glycolysis pathway that well exceeds the number of PHX enzymes acting in the tricarboxylic acid cycle. Conversely, if the number of PHX enzymes of the tricarboxylic acid cycle well exceeds the PHX enzymes of glycolysis, an aerobic metabolism is preferred. Where the numbers are approximately commensurate, a facultative growth behavior prevails.

Animals↗
PubMed2001

Lineage-specific gene expansions in bacterial and archaeal genomes.

Gene duplication is an important mechanistic antecedent to the evolution of new genes and novel biochemical functions. In an attempt to assess the contribution of gene duplication to genome evolution in archaea and bacteria, clusters of related genes that appear to have expanded subsequent to the diversification of the major prokaryotic lineages (lineage-specific expansions) were analyzed. Analysis of 21 completely sequenced prokaryotic genomes shows that lineage-specific expansions comprise a substantial fraction (approximately 5%-33%) of their coding capacities. A positive correlation exists between the fraction of the genes taken up by lineage-specific expansions and the total number of genes in a genome. Consistent with the notion that lineage-specific expansions are made up of relatively recently duplicated genes, >90% of the detected clusters consists of only two to four genes. The more common smaller clusters tend to include genes with higher pairwise similarity (as reflected by average score density) than larger clusters. Regardless of size, cluster members tend to be located more closely on bacterial chromosomes than expected by chance, which could reflect a history of tandem gene duplication. In addition to the small clusters, almost all genomes also contain rare large clusters of size > or =20. Several examples of the potential adaptive significance of these large clusters are explored. The presence or absence of clusters and their related genes was used as the basis for the construction of a similarity graph for completely sequenced prokaryotic genomes. The topology of the resulting graph seems to reflect a combined effect of common ancestry, horizontal transfer, and lineage-specific gene loss.

Chromosomes, Bacterial↗
PubMed2002

Mobile elements in archaeal genomes.

The recent availability of several archaeal genome sequences has provided a basis for detailed analyses of the frequency, location and phylogeny of archaeal mobile elements. All the known elements fall into two main types, autonomous insertion sequence (IS) elements and the non-autonomous miniature inverted repeat element (MITE)-like elements. Both classes are considered to be mobilized via transposases that are encoded by the IS elements, although mobility has only been demonstrated experimentally for a few elements. The number, and diversity, of the elements differs greatly between the genomes. At one extreme Sulfolobus solfataricus P2 and Halobacterium NRC-1 are very rich in elements while Methanobacterium thermoautotrophicum contains none. The former also show examples of complex clusters of interwoven elements. An analysis of the genomic distribution in S. solfataricus suggests that the putative oriC and terC regions act as barriers for the mobility of both IS and MITE-like elements. Moreover, the very high level of truncated IS elements in the genomes of S. solfataricus, Sulfolobus tokodaii and Thermoplasma volcanium suggests that there may be a cellular mechanism for selectively inactivating IS elements at a point when they become too numerous and disadvantageous for the cell. Phylogenetically, archaeal IS elements are confined to 11 of the 17 known families of bacterial and eukaryal IS elements where some generate distinct subgroups. Finally, DNA viruses, plasmids and DNA fragments can also be inserted into, and excised from, archaeal genomes by means of an integrase-mediated mechanism that has special archaeal characteristics.

Crenarchaeota↗
PubMed1997

A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure.

Representative genomes from each of the three kingdoms of life are compared in terms of protein structure, in particular, those of Haemophilus influenzae (a bacteria), Methanococcus jannaschii (an archaeon), and yeast (a eukaryote). The comparison is in the form of a census (or comprehensive accounting) of the relative occurrence of secondary and tertiary structures in the genomes, which particular emphasis on patterns of supersecondary structure. Comparison of secondary structure shows that the three genomes have nearly the same overall secondary-structure content, although they differ markedly in amino acid composition. Comparison of super-secondary structure, using a novel "frequent-words" approach, shows that yeast has a preponderance of consecutive strands (e.g. beta-beta-beta patterns), Haemophilus, consecutive helices (alpha-alpha-alpha), and Methanococcus, alternating helix-strand structures (beta-alpha-beta). Yeast also has significantly more helical membrane proteins than the other two genomes, with most of the differences concentrated in proteins containing two transmembrane segments. Comparison of tertiary structure (by sequence matching and domain-level clustering) highlights the substantial duplication in each genome (approximately 30% to 50%), with the degree of duplication following similar patterns in all three. Many sequence families are shared among the genomes, with the degree of overlap between any two genomes being roughly similar. In total, the three genomes contain 148 of the approximately 300 known protein folds. Forty-five of these 148 that are present in all three genomes are especially enriched in mixed super-secondary structures (alpha/beta). Moreover, the five most common of these 45 (the "top-5") have a remarkably similar super-secondary structure architecture, containing a central sheet of parallel strands with helices packed onto at least one face and beta-alpha-beta connections between adjacent strands. These most basic molecular parts, which, presumably, were present in the last common ancestor to the three Kingdoms, include the TIM-barrel, Rossmann, flavodoxin, thiamin-binding, and P-loop-hydrolase folds.

Archaea↗
PubMed2003

Gene recognition from questionable ORFs in bacterial and archaeal genomes.

The ORFs of microbial genomes in annotation files are usually classified into two groups: the first corresponds to known genes; whereas the second includes 'putative', 'probable', 'conserved hypothetical', 'hypothetical', 'unknown' and 'predicted' ORFs etc. Since the annotation is not 100% accurate, it is essential to confirm which ORF of the latter group is coding and which is not. Starting from known genes in the former, this paper describes an improved Z curve method to recognize genes in the latter. Ten-fold cross-validation tests show that the average accuracy of the algorithm is greater than 99% for recognizing the known genes in 57 bacterial and archaeal genomes. The method is then applied to recognize genes of the latter group. The likely non-coding ORFs in each of the 57 bacterial or archaeal genomes studied here are recognized and listed at the website http://tubic.tju.edu.cn/ZCURVE_C_html/noncoding.html. The working mechanism of the algorithm has been discussed in details. A computer program, called ZCURVE_C, was written to calculate a coding score called Z-curve score for ORFs in the above 57 bacterial and archaeal genomes. Coding/non-coding is simply determined by the criterion of Z-curve score > 0/ Z-curve score < 0. A website has been set up to provide the service to calculate the Z-curve score. A user may submit the DNA sequence of an ORF to the server at http://tubic.tju.edu.cn/ZCURVE_C/Default.cgi, and the Z-curve score of the ORF is calculated and returned to the user immediately.

Algorithms↗
PubMed1999

Novel coding regions in four complete archaeal genomes.

In the process of analysing the four available complete archaeal genomes, we have noted that certain regions characterised as 'non-coding' exhibit significant sequence similarity to other protein sequences from Archaea and other species. Using established technology, we have identified a number of potential protein coding regions in these putative 'non-coding' regions. We have detected 524 such cases, of which 113 regions appear to code for proteins present in archaeal or other species, while the remaining 411 regions are mostly start/stop definition conflicts. Of the 113 protein coding regions, only 21 code for proteins with homologues of known function. The number of novel coding sequences identified herein amounts to 1. 5% of the total genome entries, while the conflicting cases represent an additional 5%. The observed differences between the four complete archaeal genomes seem to reflect disparate approaches to genome annotation. Genome sequence collections should be regularly checked to improve gene prediction by sequence similarity and greater effort is required to make gene definitions consistent across related species.

Archaeal Proteins↗
PubMed2003

ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes.

A new system, ZCURVE 1.0, for finding protein- coding genes in bacterial and archaeal genomes has been proposed. The current algorithm, which is based on the Z curve representation of the DNA sequences, lays stress on the global statistical features of protein-coding genes by taking the frequencies of bases at three codon positions into account. In ZCURVE 1.0, since only 33 parameters are used to characterize the coding sequences, it gives better consideration to both typical and atypical cases, whereas in Markov-model-based methods, e.g. Glimmer 2.02, thousands of parameters are trained, which may result in less adaptability. To compare the performance of the new system with that of Glimmer 2.02, both systems were run, respectively, for 18 genomes not annotated by the Glimmer system. Comparisons were also performed for predicting some function-known genes by both systems. Consequently, the average accuracy of both systems is well matched; however, ZCURVE 1.0 has more accurate gene start prediction, lower additional prediction rate and higher accuracy for the prediction of horizontally transferred genes. It is shown that the joint applications of both systems greatly improve gene-finding results. For a typical genome, e.g. Escherichia coli, the system ZCURVE 1.0 takes approximately 2 min on a Pentium III 866 PC without any human intervention. The system ZCURVE 1.0 is freely available at: http://tubic. tju.edu.cn/Zcurve_B/.

Algorithms↗
PubMed1999

Archaeal genomics.

Four euryarchaeal genomes have been completely sequenced and are publicly available: Methanococcus jannaschii, Methanobacterium thermoautotrophicum, Pyrococcus horikoshii and Archaeoglobus fulgidus. Four more genome sequences, two crenarchaeal and two pyrococci, will soon be released. In addition, seven more archaeal genome sequencing projects are under way, including two halophiles, two Thermoplasma, and a methanogen. These projects cover all branches of the archaeal domain and will lead to new insights into archaeal metabolism, DNA processing, and evolutionary relationships with the Bacteria and Eukarya.

Archaea↗
PubMed2005

Biosynthesis of ribose-5-phosphate and erythrose-4-phosphate in archaea: a phylogenetic analysis of archaeal genomes.

A phylogenetic analysis of the genes encoding enzymes in the pentose phosphate pathway (PPP), the ribulose monophosphate (RuMP) pathway, and the chorismate pathway of aromatic amino acid biosynthesis, employing data from 13 complete archaeal genomes, provides a potential explanation for the enigmatic phylogenetic patterns of the PPP genes in archaea. Genomic and biochemical evidence suggests that three archaeal species (Methanocaldococcus jannaschii, Thermoplasma acidophilum and Thermoplasma volcanium) produce ribose-5-phosphate via the nonoxidative PPP (NOPPP), whereas nine species apparently lack an NOPPP but may employ a reverse RuMP pathway for pentose synthesis. One species (Halobacterium sp. NRC-1) lacks both the NOPPP and the RuMP pathway but may possess a modified oxidative PPP (OPPP), the details of which are not yet known. The presence of transketolase in several archaeal species that are missing the other two NOPPP genes can be explained by the existence of differing requirements for erythrose-4-phosphate (E4P) among archaea: six species use transketolase to make E4P as a precursor to aromatic amino acids, six species apparently have an alternate biosynthetic pathway and may not require the ability to make E4P, and one species (Pyrococcus horikoshii) probably does not synthesize aromatic amino acids at all.

Amino Acids, Aromatic↗
PubMed2005

Identification of replication origins in archaeal genomes based on the Z-curve method.

The Z-curve is a three-dimensional curve that constitutes a unique representation of a DNA sequence, i.e., both the Z-curve and the given DNA sequence can be uniquely reconstructed from the other. We employed Z-curve analysis to identify one replication origin in the Methanocaldococcus jannaschii genome, two replication origins in the Halobacterium species NRC-1 genome and one replication origin in the Methanosarcina mazei genome. One of the predicted replication origins of Halobacterium species NRC-1 is the same as a replication origin later identified by in vivo experiments. The Z-curve analysis of the Sulfolobus solfataricus P2 genome suggested the existence of three replication origins, which is also consistent with later experimental results. This review aims to summarize applications of the Z-curve in identifying replication origins of archaeal genomes, and to provide clues about the locations of as yet unidentified replication origins of the Aeropyrum pernix K1, Methanococcus maripaludis S2, Picrophilus torridus DSM 9790 and Pyrobaculum aerophilum str. IM2 genomes.

Archaea↗
PubMed1998

Archaeal genomics: do archaea have a mixed heritage?

A third complete archaeal genome sequence, replete with eukaryote-like genes for replication, transcription and translation, has appeared. The sequence also shows bacteria-like features. It is time to come to grips with this evidence for a mixed heritage.

Archaea↗
PubMed2004

MlaA, a hexameric ATPase linked to the Mre11 complex in archaeal genomes.

We identify and characterize MlaA, a novel protein, which is found in a conserved operon with Mre11 and Rad50 in archaeal genomes. MlaA is fused with Mre11 in Methanobacter thermoautotrophicus, suggesting the MlaA is functionally linked to the Mre11 complex. MlaA preferentially and cooperatively binds double-stranded and secondary structure containing DNA and has double-stranded but not single-stranded DNA-stimulated ATPase activity. Electron microscopy reveals that MlaA forms a 360-kDa hexameric ring structure with a central hole. 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.

Adenosine Triphosphatases↗
PubMed2003

Circular codes in archaeal genomes.

A new statistical method associating each trinucleotide with a frame is developed for identifying circular codes. Its sensibility allows the detection of several circular codes in the (protein coding) genes of archaeal genomes. Several properties of these circular codes are described, in particular the lengths of the minimal windows to retrieve the construction frames, a new definition of a parameter for measuring some probabilities of words generated by the circular codes, and the types of nucleotides in the trinucleotide sites. Some biological consequences are presented in Discussion.

Archaea↗
PubMed2005

Predicted highly expressed genes in archaeal genomes.

Based primarily on 16S rRNA sequence comparisons, life has been broadly divided into the three domains of Bacteria, Archaea, and Eukarya. Archaea is further classified into Crenarchaea and Euryarchaea. Archaea generally thrive in extreme environments as assessed by temperature, pH, and salinity. For many prokaryotic organisms, ribosomal proteins (RP), transcription/translation factors, and chaperone genes tend to be highly expressed. A gene is predicted highly expressed (PHX) if its codon usage is rather similar to the average codon usage of at least one of the RP, transcription/translation factors, and chaperone gene classes and deviates strongly from the average gene of the genome. The thermosome (Ths) chaperonin family represents the most salient PHX genes among Archaea. The chaperones Trigger factor and HSP70 have overlapping functions in the folding process, but both of these proteins are lacking in most archaea where they may be substituted by the chaperone prefoldin. Other distinctive PHX proteins of Archaea, absent from Bacteria, include the proliferating cell nuclear antigen PCNA, a replication auxiliary factor responsible for tethering the catalytic unit of DNA polymerase to DNA during high-speed replication, and the acidic RP P0, which helps to initiate mRNA translation at the ribosome. Other PHX genes feature Cell division control protein 48 (Cdc48), whereas the bacterial septation proteins FtsZ and minD are lacking in Crenarchaea. RadA is a major DNA repair and recombination protein of Archaea. Archaeal genomes feature a strong Shine-Dalgarno ribosome-binding motif more pronounced in Euryarchaea compared with Crenarchaea.

Archaea↗
PubMed2000

An archaeal genomic signature.

Comparisons of complete genome sequences allow the most objective and comprehensive descriptions possible of a lineage's evolution. This communication uses the completed genomes from four major euryarchaeal taxa to define a genomic signature for the Euryarchaeota and, by extension, the Archaea as a whole. The signature is defined in terms of the set of protein-encoding genes found in at least two diverse members of the euryarchaeal taxa that function uniquely within the Archaea; most signature proteins have no recognizable bacterial or eukaryal homologs. By this definition, 351 clusters of signature proteins have been identified. Functions of most proteins in this signature set are currently unknown. At least 70% of the clusters that contain proteins from all the euryarchaeal genomes also have crenarchaeal homologs. This conservative set, which appears refractory to horizontal gene transfer to the Bacteria or the Eukarya, would seem to reflect the significant innovations that were unique and fundamental to the archaeal "design fabric." Genomic protein signature analysis methods may be extended to characterize the evolution of any phylogenetically defined lineage. The complete set of protein clusters for the archaeal genomic signature is presented as supplementary material (see the PNAS web site, www.pnas.org).

Archaeal Proteins↗