We report the complete sequence of an extreme halophile, Halobacterium sp. NRC-1, harboring a dynamic 2,571,010-bp genome containing 91 insertion sequences representing 12 families and organized into a large chromosome and 2 related minichromosomes. The Halobacterium NRC-1 genome codes for 2,630 predicted proteins, 36% of which are unrelated to any previously reported. Analysis of the genome sequence shows the presence of pathways for uptake and utilization of amino acids, active sodiumproton antiporter and potassium uptake systems, sophisticated photosensory and signal transduction pathways, and DNA replication, transcription, and translation systems resembling more complex eukaryotic organisms. Whole proteome comparisons show the definite archaeal nature of this halophile with additional similarities to the Gram-positive Bacillus subtilis and other bacteria. The ease of culturing Halobacterium and the availability of methods for its genetic manipulation in the laboratory, including construction of gene knockouts and replacements, indicate this halophile can serve as an excellent model system among the archaea.

Background Haloferax volcanii is an easily culturable moderate halophile that grows on simple defined media, is readily transformable, and has a relatively stable genome. This, in combination with its biochemical and genetic tractability, has made Hfx. volcanii a key model organism, not only for the study of halophilicity, but also for archaeal biology in general.Methodology/Principal FindingsWe report here the sequencing and analysis of the genome of Hfx. volcanii DS2, the type strain of this species. The genome contains a main 2.848 Mb chromosome, three smaller chromosomes pHV1, 3, 4 (85, 438, 636 kb, respectively) and the pHV2 plasmid (6.4 kb).Conclusions/SignificanceThe completed genome sequence, presented here, provides an invaluable tool for further in vivo and in vitro studies of Hfx. volcanii.

Nop56p and Nop58p are two core proteins of the box C/D snoRNPs that interact concurrently with fibrillarin and snoRNAs to function in enzyme assembly and catalysis. Here we report the 2.9 A resolution co-crystal structure of an archaeal homolog of Nop56p/Nop58p, Nop5p, in complex with fibrillarin from Archaeoglobus fulgidus (AF) and the methyl donor S-adenosyl-L-methionine. The N-terminal domain of Nop5p forms a complementary surface to fibrillarin that serves to anchor the catalytic subunit and to stabilize cofactor binding. A coiled coil in Nop5p mediates dimerization of two fibrillarin-Nop5p heterodimers for optimal interactions with bipartite box C/D RNAs. Structural analysis and complementary biochemical data demonstrate that the conserved C-terminal domain of Nop5p harbors RNA-binding sites. A model of box C/D snoRNP assembly is proposed based on the presented structural and biochemical data.

Major advances have recently been made in understanding the molecular biology of the archaebacteria. In this review, we compare the structure of protein and stable RNA-encoding genes cloned and sequenced from each of the major classes of archaebacteria: the methanogens, extreme halophiles, and acid thermophiles. Protein-encoding genes, including some encoding proteins directly involved in methanogenesis and photoautotrophy, are analyzed on the basis of gene organization and structure, transcriptional control signals, codon usage, and evolutionary conservation. Stable RNA-encoding genes are compared for gene organization and structure, transcriptional signals, and processing events involved in RNA maturation, including intron removal. Comparisons of archaebacterial structures and regulatory systems are made with their eubacterial and eukaryotic homologs.

Methanobacterium thermoautotrophicum and Methanobacterium formicicum, and five in Methanococcus and Charles J. Daniels Department of Microbiology jannaschii, two of which are plasmid-encoded (Bult et al., 1996;Grayling et al., 1996). In most cases, the pri-Ohio State University Columbus, Ohio 43210 mary sequences of the archaeal histones within one species are more similar to each other than to the sequences of histones in other Archaea, indicating that the original histone gene has undergone different num-The packaging of nuclear DNA by histones into nucleobers of duplications during the divergence of different somes and chromatin is a feature as definitive of the euryarchaeal lineages. To date, only histone-like DNA-Eucarya as the nuclear membrane, and determining how binding proteins have been identified in members of the eucaryal RNA polymerases access promoters buried Crenarchaeota (Grayling et al., 1996). Fifteen complete within nucleosomes and initiate transcription is currently archaeal histone sequences are available, and the resi-an area of considerable research interest. Bacteria condues on the interacting hydrophobic faces of their ␣ tain "histone-like" proteins (Schmid, 1990), but despite helix 2s are very highly conserved (-A15---L14A15--L12---this designation, these are not histone-like and do not A 13 --I 12 A 13 --A 14 V 13 --A 15 --A 15 -[hyphens indicate amino acid form DNA-protein complexes structurally related to the residues between the identified residues; see Figure 1]), nucleosome. Bacterial RNA polymerases do not, theresuggesting that all homodimer and heterodimer partner-fore, appear to face the same promoter-access problem, ships may still be possible, although some partnerships and bacterial RNA polymerases are structurally simpler may be preferred, or may even have been fixed. The than their eucaryal counterparts. What about Archaea?residues at these positions in the eucaryal core histones As detailed below, although Archaea lack a nuclear are hydrophobic, but they are more variable and gener-membrane, they do contain histones that compact DNA ally bulkier, and space and interaction constraints iminto nucleosome-related structures, and archaeal RNA posed by these different R groups presumably direct polymerases have the multisubunit complexity of eucarthe correct eucaryal histone heterodimerization and pre-yal RNA polymerases (Langer et al., 1995). They also clude homodimerization. require the participation of homologs of eucaryal TATA-Histone-fold domains do not occur exclusively in his-binding protein (TBP) and transcription initiation factor tones but have also been identified in both positive and IIB (TFIIB) to initiate transcription.negative transcription regulators (Burley et al., 1997). Histone sequences and the structure of the nucleo-The subunits of the CCAAT-binding transcriptional actisome are universally conserved in Eucarya, and histones vators, CBF-A (HAP3 in yeast) and CBFC (HAP5), associ-and their method of DNA compaction must therefore ate through histone-fold pairin...