Description of Alicyclobacillus montanus sp. nov., a mixotrophic bacterium isolated from acidic hot springs

Three morphologically similar thermo-acidophilic strains, USBA-GBX-501, USBA-GBX-502 and USBA-GBX-503^T, were isolated from acidic thermal springs at the National Natural Park Los Nevados (Colombia). All isolates were spore-forming, Gram-stain-positive and motile, growing aerobically at 25-55 °C (optimum ~45 °C) and at pH 1.5-4.5 (optimum pH ~3.0). Phylogenetic analysis of the 16S rRNA gene sequences of these isolates showed an almost identical sequence (99.0 % similarity) and they formed a robust cluster with the closest relative Alicyclobacillus tolerans DSM 16297^T with a sequence similarity of 99.0 %. Average similarity to other species of the genus Alicyclobacillus was 93.0 % and average similarity to species of the genus Effusibacillus was 90 %. In addition, the level of DNA-DNA hybridization between strain USBA-GBX-503^T and Alicyclobacillus tolerans DSM 16297^T was 31.7 %. The genomic DNA G+C content of strain USBA-GBX-503^T was 44.6 mol%. The only menaquinone was MK-7 (100.0 %). No ω-alicyclic fatty acids were detected in strain USBA-GBX-503^T, and the major cellular fatty acids were C18 : 1ω7c, anteiso-C17 : 0 and iso-C17 : 0. Based on phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA-DNA relatedness values, along with low levels of identity at the whole genome level (ANIb and ANIm values of <67.0 and <91.0 %, respectively), it can be concluded that strain USBA-GBX-503^T represents a novel species of the genus Alicyclobacillus, for which the name Alicyclobacillus montanus sp. nov. is proposed. The type strain is USBA-GBX-503^T (=CMPUJ UGB U503^T=CBMAI1927^T).

The genome of the obligately intracellular bacterium Ehrlichia canis reveals themes of complex membrane structure and immune evasion strategies

Ehrlichia canis, a small obligately intracellular, tick-transmitted, gram-negative, alpha-proteobacterium, is the primary etiologic agent of globally distributed canine monocytic ehrlichiosis. Complete genome sequencing revealed that the E. canis genome consists of a single circular chromosome of 1,315,030 bp predicted to encode 925 proteins, 40 stable RNA species, 17 putative pseudogenes, and a substantial proportion of noncoding sequence (27%). Interesting genome features include a large set of proteins with transmembrane helices and/or signal sequences and a unique serine-threonine bias associated with the potential for O glycosylation that was prominent in proteins associated with pathogen-host interactions. Furthermore, two paralogous protein families associated with immune evasion were identified, one of which contains poly(G-C) tracts, suggesting that they may play a role in phase variation and facilitation of persistent infections. Genes associated with pathogen-host interactions were identified, including a small group encoding proteins (n = 12) with tandem repeats and another group encoding proteins with eukaryote-like ankyrin domains (n = 7).

Experimental determination and system level analysis of essential genes in Escherichia coli MG1655

Defining the gene products that play an essential role in an organism's functional repertoire is vital to understanding the system level organization of living cells. We used a genetic footprinting technique for a genome-wide assessment of genes required for robust aerobic growth of Escherichia coli in rich media. We identified 620 genes as essential and 3,126 genes as dispensable for growth under these conditions. Functional context analysis of these data allows individual functional assignments to be refined. Evolutionary context analysis demonstrates a significant tendency of essential E. coli genes to be preserved throughout the bacterial kingdom. Projection of these data over metabolic subsystems reveals topologic modules with essential and evolutionarily preserved enzymes with reduced capacity for error tolerance.

Analysis of the Thermotoga maritima genome combining a variety of sequence similarity and genome context tools

The proliferation of genome sequence data has led to the development of a number of tools and strategies that facilitate computational analysis. These methods include the identification of motif patterns, membership of the query sequences in family databases, metabolic pathway involvement and gene proximity. We re-examined the completely sequenced genome of Thermotoga maritima by employing the combined use of the above methods. By analyzing all 1877 proteins encoded in this genome, we identified 193 cases of conflicting annotations (10%), of which 164 are new function predictions and 29 are amendments of previously proposed assignments. These results suggest that the combined use of existing computational tools can resolve inconclusive sequence similarities and significantly improve the prediction of protein function from genome sequence.

Protein interaction maps for complete genomes based on gene fusion events

A large-scale effort to measure, detect and analyse protein-protein interactions using experimental methods is under way. These include biochemistry such as co-immunoprecipitation or crosslinking, molecular biology such as the two-hybrid system or phage display, and genetics such as unlinked noncomplementing mutant detection. Using the two-hybrid system, an international effort to analyse the complete yeast genome is in progress. Evidently, all these approaches are tedious, labour intensive and inaccurate. From a computational perspective, the question is how can we predict that two proteins interact from structure or sequence alone. Here we present a method that identifies gene-fusion events in complete genomes, solely based on sequence comparison. Because there must be selective pressure for certain genes to be fused over the course of evolution, we are able to predict functional associations of proteins. We show that 215 genes or proteins in the complete genomes of Escherichia coli, Haemophilus influenzae and Methanococcus jannaschii are involved in 64 unique fusion events. The approach is general, and can be applied even to genes of unknown function.

Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide

GOLD (Genomes On Line Database) is a World Wide Web resource for comprehensive access to information regarding complete and ongoing genome projects around the world.

AVAILABILITY

GOLD is based at the University of Illinois at Urbana-Champaign and is available at http://geta.life.uiuc.edu/ approximately nikos/genomes. html. It is also mirrored at the European Bioinformatics Institute at http://www.ebi.ac.uk/research/cgg/genomes.html.

CONTACT

genomes@ebi.ac.uk

Transcription in archaea

Using the sequences of all the known transcription-associated proteins from Bacteria and Eucarya (a total of 4,147), we have identified their homologous counterparts in the four complete archaeal genomes. Through extensive sequence comparisons, we establish the presence of 280 predicted transcription factors or transcription-associated proteins in the four archaeal genomes, of which 168 have homologs only in Bacteria, 51 have homologs only in Eucarya, and the remaining 61 have homologs in both phylogenetic domains. Although bacterial and eukaryotic transcription have very few factors in common, each exclusively shares a significantly greater number with the Archaea, especially the Bacteria. This last fact contrasts with the obvious close relationship between the archaeal and eukaryotic transcription mechanisms per se, and in particular, basic transcription initiation. We interpret these results to mean that the archaeal transcription system has retained more ancestral characteristics than have the transcription mechanisms in either of the other two domains.

Identification of protein-tyrosine phosphatases in Archaea

Protein-tyrosine dephosphorylation is a major mechanism in cellular regulation. A large number of protein-tyrosine phosphatases is known from Eukarya, and more recently bacterial homologues have also been identified. By employing conserved sequence patterns from both eukaryotic and bacterial protein-tyrosine phosphatases, we have identified three homologous sequences in two of the four complete archaeal genomes. Two hypothetical open reading frames in the genome of Methanococcus jannaschii (MJ0215 and MJECL20) and one in the genome of Pyrococcus horikoshii (PH1732) clearly bear all the conserved residues of this family. No homologues were found in the genomes of Archaeoglobus fulgidus and Methanobacterium thermoautotrophicum. This is the first report of protein-tyrosine phosphatase sequences in Archaea.

Methanococcus jannaschii genome: revisited

Analysis of genomic sequences is necessarily an ongoing process. Initial gene assignments tend (wisely) to be on the conservative side (Venter, 1996). The analysis of the genome then grows in an iterative fashion as additional data and more sophisticated algorithms are brought to bear on the data. The present report is an emendation of the original gene list of Methanococcus jannaschii (Bult et al., 1996). By using a somewhat more updated database and more relaxed (and operator-intensive) pattern matching methods, we were able to add significantly to, and in a few cases amend, the gene identification table originally published by Bult et al. (1996).

Archaeal translation initiation revisited: the initiation factor 2 and eukaryotic initiation factor 2B alpha-beta-delta subunit families

As the amount of available sequence data increases, it becomes apparent that our understanding of translation initiation is far from comprehensive and that prior conclusions concerning the origin of the process are wrong. Contrary to earlier conclusions, key elements of translation initiation originated at the Universal Ancestor stage, for homologous counterparts exist in all three primary taxa. Herein, we explore the evolutionary relationships among the components of bacterial initiation factor 2 (IF-2) and eukaryotic IF-2 (eIF-2)/eIF-2B, i.e., the initiation factors involved in introducing the initiator tRNA into the translation mechanism and performing the first step in the peptide chain elongation cycle. All Archaea appear to posses a fully functional eIF-2 molecule, but they lack the associated GTP recycling function, eIF-2B (a five-subunit molecule). Yet, the Archaea do posses members of the gene family defined by the (related) eIF-2B subunits alpha, beta, and delta, although these are not specifically related to any of the three eukaryotic subunits. Additional members of this family also occur in some (but by no means all) Bacteria and even in some eukaryotes. The functional significance of the other members of this family is unclear and requires experimental resolution. Similarly, the occurrence of bacterial IF-2-like molecules in all Archaea and in some eukaryotes further complicates the picture of translation initiation. Overall, these data lend further support to the suggestion that the rudiments of translation initiation were present at the Universal Ancestor stage.

Universally conserved translation initiation factors

The process by which translation is initiated has long been considered similar in Bacteria and Eukarya but accomplished by a different unrelated set of factors in the two cases. This not only implies separate evolutionary histories for the two but also implies that at the universal ancestor stage, a translation initiation mechanism either did not exist or was of a different nature than the extant processes. We demonstrate herein that (i) the "analogous" translation initiation factors IF-1 and eIF-1A are actually related in sequence, (ii) the "eukaryotic" translation factor SUI1 is universal in distribution, and (iii) the eukaryotic/archaeal translation factor eIF-5A is homologous to the bacterial translation factor EF-P. Thus, the rudiments of translation initiation would seem to have been present in the universal ancestor stage. However, significant development and refinement subsequently occurred independently on both the bacterial lineage and on the archaeal/eukaryotic line.

ThiD-TenA: a gene pair fusion in eukaryotes

Computational analysis of the hypothetical open reading frame MJ0236 from Methanococcus jannaschii reveals its membership to a family of bacterial and eukaryotic proteins, predicted to be the HMP-P kinases involved in thiamin biosyntheis (ThiD). The eukaryotic members of this family contain a C-terminal extension similar to a bacterial transcriptional activator (TenA), thus pointing to a fusion event that took place during cellular evolution. The C-terminal domain is absent from M. jannaschii. The significance of this observation is two-fold: first, this is a case where a fusion protein contains two domains with an unusual phylogenetic distribution, and second, the TenA domain is a rare case of a gene family involved in transcription present both in bacteria and eukaryotes.

The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

Archaeoglobus fulgidus is the first sulphur-metabolizing organism to have its genome sequence determined. Its genome of 2,178,400 base pairs contains 2,436 open reading frames (ORFs). The information processing systems and the biosynthetic pathways for essential components (nucleotides, amino acids and cofactors) have extensive correlation with their counterparts in the archaeon Methanococcus jannaschii. The genomes of these two Archaea indicate dramatic differences in the way these organisms sense their environment, perform regulatory and transport functions, and gain energy. In contrast to M. jannaschii, A. fulgidus has fewer restriction-modification systems, and none of its genes appears to contain inteins. A quarter (651 ORFs) of the A. fulgidus genome encodes functionally uncharacterized yet conserved proteins, two-thirds of which are shared with M. jannaschii (428 ORFs). Another quarter of the genome encodes new proteins indicating substantial archaeal gene diversity.

Parallel origins of the nucleosome core and eukaryotic transcription from Archaea

Computational sequence analysis of 10 available archaean histone-like proteins has shown that this family is not only divergently related to the eukaryotic core histones H2A/B, H3, and H4, but also to the central domain of subunits A and C of the CCAAT-binding factor (CBF), a transcription factor associated with eukaryotic promoters. Despite the low sequence identity, it is unambiguously shown that the core histone fold shares a common evolutionary history. Archaean histones and the two CBF families show a remarkable variability in contrast to eukaryotic core histones. Conserved residues shared between families are identified, possibly being responsible for the functional versatility of the core histone fold. The H4 subfamily is most similar to archaean proteins and may be the progenitor of the other core histones in eukaryotes. While it is not clear whether archaean histones are more actively involved in transcription regulation, the present observations link two processes, nucleosomal packing and transcription in a unique way. Both these processes, evidently hybrid in Archaea, have originated before the ermergence of the eukaryotic cell.

Nucleic acid-binding metabolic enzymes: living fossils of stereochemical interactions?

Recently, a series of intriguing observations expanded the list of a number of metabolic enzymes known to be associated with various forms of nucleic acids, including single- and double-stranded DNA, cognate and noncognate RNAs, and specific tRNAs. There is no clear reason why such a phenomenon should take place in contemporary cell physiology, or, further, why such a property has evolved at all. Sixteen known cases are presented in an attempt to delineate any common features of these enzymes. Apart from their ancient nature, as judged by their wide distribution and their participation in fundamental biochemical pathways, it appears that these enzymes do not share any structural or functional characteristics. Given that most of these proteins require nucleotide-based cofactors for their activity, it is proposed that they may represent genuine molecular fossils of the transition from an RNA to a protein world. Their nucleic acid-binding properties are in keeping with previously proposed hypotheses regarding the origins and evolution of nucleotide-based cofactors. The mode of interaction between these proteins and their nucleic acid substrates remains unclear, but it may represent an extended form of stereochemical interactions that have been proposed for the origins of the genetic code.

On the evolution of arginases and related enzymes

Sequence analysis of the arginase/agmatine ureohydrolase family, important enzymes in arginine/agmatine metabolism and the urea cycle, reveals the similarity of arginases to formiminoglutamate hydrolase (hutG) in Klebsiella aerogenes and to a previously unidentified open reading frame adjacent to the HMf locus of the archaebacterium Methanothermus fervidus. The gene structure and distribution of these homologous proteins across primary kingdoms suggest that this family is another example of a primordial enzyme possibly present in the universal common ancestor and that can be used as phylogenetic marker.

Reverse interpretation: a hypothetical selection mechanism for adaptive mutagenesis based on autoregulated mRNA stability

The problem of adaptive mutagenesis is examined under the assumption that selection occurs through the interaction of cognate mRNA and protein molecules, a phenomenon that has been considered to lead to differential mRNA decay (Kyrpides & Ouzounis, 1993, J. theor. Biol. 163, 373-392). Based on the stereochemical hypothesis, we speculate that the origin of this process relies on an extended form of molecular interactions. This mechanism, termed reverse interpretation, predicts the selective amplification of successful molecular forms with the capability of their immortalization through reverse transcription, in a manner that resembles, but is not equivalent to, reverse translation. Finally, we argue that the proposed mechanism conforms with the Darwinian view of evolutionary change, if variability is considered to be a property of molecular and not cellular populations.

Mechanisms of specificity in mRNA degradation: autoregulation and cognate interactions

Autoregulation of gene expression is a common control mechanism for a large number of transcriptional units. Cases of self-regulation of the stability of various messenger RNAs (mRNAs) are re-evaluated here, and a general hypothesis for the origins and the mechanism of this process is presented. It is proposed that post-transcriptional autoregulation and mRNA stability are closely associated processes that might represent a general class of gene regulation mechanisms, with special regard to mRNA-protein cognate interactions. Generalizing from known examples, autoregulation is here considered to induce the decay of certain messenger RNAs through a yet undiscovered mechanism. Autoregulation via cognate interactions might be the vestigial process of a primitive world, where protein-nucleic acid interactions originated. The model can therefore serve as a framework to study the origins of the genetic code in particular, and gene expression in general.