scholarly journals An Archaeal Chromosomal Autonomously Replicating Sequence Element from an Extreme Halophile, Halobacterium sp. Strain NRC-1

2003 ◽  
Vol 185 (20) ◽  
pp. 5959-5966 ◽  
Author(s):  
Brian R. Berquist ◽  
Shiladitya DasSarma
Keyword(s):  
Inverted Repeat ◽  
Halophilic Archaea ◽  
Extreme Halophile ◽  
Haloarcula Marismortui ◽  
Sequence Element ◽  
Autonomously Replicating Sequence ◽  
Autonomous Replication ◽  
Repeat Structure ◽  
Translational Start ◽  
Plasmid Recovery

ABSTRACT We report on the identification and first cloning of an autonomously replicating sequence element from the chromosome of an archaeon, the extreme halophile Halobacterium strain NRC-1. The putative replication origin was identified by association with the orc7 gene and replication ability in the host strain, demonstrated by cloning into a nonreplicating plasmid. Deletion analysis showed that sequences located up to 750 bp upstream of the orc7 gene translational start, plus the orc7 gene and 50 bp downstream, are sufficient to endow the plasmid with replication ability, as judged by expression of a plasmid-encoded mevinolin resistance selectable marker and plasmid recovery after transformation. Sequences located proximal to the two other chromosomally carried haloarchaeal orc genes (orc6 and orc8) are not able to promote efficient autonomous replication. Located within the 750-bp region upstream of orc7 is a nearly perfect inverted repeat of 31 bp, which flanks an extremely AT-rich (44%) stretch of 189 bp. The replication ability of the plasmid was lost when one copy of the inverted repeat was deleted. Additionally, the inverted repeat structure near orc7 homologs in the genomic sequences of two other halophiles, Haloarcula marismortui and Haloferax volcanii, is highly conserved. Our results indicate that, in halophilic archaea, a chromosomal origin of replication is physically linked to orc7 homologs and that this element is sufficient to promote autonomous replication. We discuss the finding of a functional haloarchaeal origin in relation to the large number of orc1-cdc6 homologs identified in the genomes of all haloarchaea to date.

scholarly journals Methylomes of Two Extremely Halophilic Archaea Species, Haloarcula marismortui and Haloferax mediterranei

2019 ◽  
Vol 8 (27) ◽  
Author(s):  
Shiladitya DasSarma ◽  
Alexey Fomenkov ◽  
Satyajit L. DasSarma ◽  
Tamas Vincze ◽  
Priya DasSarma ◽  
...  
Keyword(s):  
Single Molecule ◽  
Gene Annotation ◽  
Halophilic Archaea ◽  
Restriction Enzymes ◽  
Haloferax Mediterranei ◽  
Haloarcula Marismortui ◽  
Content Type ◽  
Extremely Halophilic Archaea ◽  
Large Plasmids ◽  
Methyl Cytosine

ABSTRACT The genomes of two extremely halophilic Archaea species, Haloarcula marismortui and Haloferax mediterranei, were sequenced using single-molecule real-time sequencing. The ∼4-Mbp genomes are GC rich with multiple large plasmids and two 4-methyl-cytosine patterns. Methyl transferases were incorporated into the Restriction Enzymes Database (REBASE), and gene annotation was incorporated into the Haloarchaeal Genomes Database (HaloWeb).

scholarly journals Organization of replication of ribosomal DNA in Saccharomyces cerevisiae.

1988 ◽  
Vol 8 (11) ◽  
pp. 4927-4935 ◽  
Author(s):  
M H Linskens ◽  
J A Huberman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Ribosomal Dna ◽  
Repeat Unit ◽  
Replication Forks ◽  
Sequence Element ◽  
Autonomously Replicating Sequence ◽  
Nontranscribed Spacer ◽  
Precursor Rna ◽  
Mapping Techniques ◽  
Region Ii

Using recently developed replicon mapping techniques, we have analyzed the replication of the ribosomal DNA in Saccharomyces cerevisiae. The results show that (i) the functional origin of replication colocalizes with an autonomously replicating sequence element previously mapped to the nontranscribed spacer region, (ii) only a fraction of the potential origins are utilized in a single S phase, and (iii) the replication forks moving counter to the direction of transcription of the 37S precursor RNA stop at or near the termination site of transcription. Consequently, most ribosomal DNA is replicated unidirectionally by forks moving in the direction of transcription and most replicons are larger than the repeat unit. The significance of this finding for the replication of abundantly transcribed genes is discussed.

Instability of integrated hepatitis B virus DNA with inverted repeat structure in a transgenic mouse

1989 ◽  
Vol 37 (2) ◽  
pp. 273-278 ◽  
Author(s):  
Okio Hino ◽  
Kimie Nomura ◽  
Keiko Ohtake ◽  
Tokuich Kawaguchi ◽  
Haruo Sugano ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Transgenic Mouse ◽  
Inverted Repeat ◽  
Hepatitis B Virus Dna ◽  
Repeat Structure ◽  
B Virus

scholarly journals Characterization of a Mobile clpL Gene from Lactobacillus rhamnosus

2005 ◽  
Vol 71 (4) ◽  
pp. 2061-2069 ◽  
Author(s):  
Aki Suokko ◽  
Kirsi Savijoki ◽  
Erja Malinen ◽  
Airi Palva ◽  
Pekka Varmanen
Keyword(s):  
Elevated Temperature ◽  
Binding Sites ◽  
Inverted Repeat ◽  
Promoter Region ◽  
Lactobacillus Rhamnosus ◽  
Sequence Analyses ◽  
Promoter Regions ◽  
Repeat Structure ◽  
Genes Encoding

ABSTRACT Two genes encoding ClpL ATPase proteins were identified in a probiotic Lactobacillus rhamnosus strain, E-97800. Sequence analyses revealed that the genes, designated clpL1 and clpL2, share 80% identity. The clpL2 gene showed the highest degree of identity (98.5%) to a clpL gene from Lactobacillus plantarum WCFSI, while it was not detected in three other L. rhamnosus strains studied. According to Northern analyses, the expression of clpL1 and the clpL2 were induced during heat shock by >20- and 3-fold, respectively. The functional promoter regions were determined by primer extension analyses, and the clpL1 promoter was found to be overlapped by an inverted repeat structure identical to the conserved CIRCE element, indicating that clpL1 belongs to the HrcA regulon in L. rhamnosus. No consensus binding sites for HrcA or CtsR could be identified in the clpL2 promoter region. Interestingly, the clpL2 gene was found to be surrounded by truncated transposase genes and flanked by inverted repeat structures nearly identical to the terminal repeats of the ISLpl1 from L. plantarum HN38. Furthermore, clpL2 was shown to be mobilized during prolonged cultivation at elevated temperature. The presence of a gene almost identical to clpL2 in L. plantarum and its absence in other L. rhamnosus strains suggest that the L. rhamnosus E-97800 has acquired the clpL2 gene via horizontal transfer. No change in the stress tolerance of the ClpL2-deficient derivative of E-97800 compared to the parental strain was observed.

scholarly journals Characterization of the proteasome from the extremely halophilic archaeonHaloarcula marismortui

Archaea ◽  
2002 ◽  
Vol 1 (1) ◽  
pp. 53-61 ◽  
Author(s):  
B. Franzetti ◽  
G. Schoehn ◽  
D. Garcia ◽  
R. W. H. Ruigrok ◽  
G. Zaccai
Keyword(s):  
Three Dimensional ◽  
Halophilic Archaea ◽  
20S Proteasome ◽  
Misfolded Protein ◽  
Haloarcula Marismortui ◽  
Low Salt ◽  
Dimensional Reconstruction ◽  
The Stability

A 20S proteasome, comprising two subunits α and β, was purified from the extreme halophilic archaeonHaloarcula marismortui, which grows only in saturated salt conditions. The three-dimensional reconstruction of theH. marismortuiproteasome (Hm proteasome), obtained from negatively stained electron micrographs, is virtually identical to the structure of a thermophilic proteasome filtered to the same resolution. The stability of the Hm proteasome was found to be less salt-dependent than that of other halophilic enzymes previously described. The proteolytic activity of the Hm proteasome was investigated using the malate dehydrogenase fromH. marismortui(HmMalDH) as a model substrate. The HmMalDH denatures when the salt concentration is decreased below 2 M. Under these conditions, the proteasome efficiently cleaves HmMalDH during its denaturation process, but the fully denatured HmMalDH is poorly degraded. These in vitro experiments show that, at low salt concentrations, the 20S proteasome from halophilic archaea eliminates a misfolded protein.

scholarly journals Identification of the Polyhydroxyalkanoate (PHA)-Specific Acetoacetyl Coenzyme A Reductase among Multiple FabG Paralogs in Haloarcula hispanica and Reconstruction of the PHA Biosynthetic Pathway in Haloferax volcanii

2009 ◽  
Vol 75 (19) ◽  
pp. 6168-6175 ◽  
Author(s):  
Jing Han ◽  
Qiuhe Lu ◽  
Ligang Zhou ◽  
Hailong Liu ◽  
Hua Xiang
Keyword(s):  
Biosynthetic Pathway ◽  
Coenzyme A ◽  
Reductase Activity ◽  
Halophilic Archaea ◽  
Haloferax Volcanii ◽  
Pha Synthase ◽  
Haloarcula Marismortui ◽  
Coa Reductase ◽  
Haloarcula Hispanica ◽  
Acetoacetyl Coa Reductase

ABSTRACT Genome-wide analysis has revealed abundant FabG (β-ketoacyl-ACP reductase) paralogs, with uncharacterized biological functions, in several halophilic archaea. In this study, we identified for the first time that the fabG1 gene, but not the other five fabG paralogs, encodes the polyhydroxyalkanoate (PHA)-specific acetoacetyl coenzyme A (acetoacetyl-CoA) reductase in Haloarcula hispanica. Although all of the paralogous fabG genes were actively transcribed, only disruption or knockout of fabG1 abolished PHA synthesis, and complementation of the ΔfabG1 mutant with the fabG1 gene restored both PHA synthesis capability and the NADPH-dependent acetoacetyl-CoA reductase activity. In addition, heterologous coexpression of the PHA synthase genes (phaEC) together with fabG1, but not its five paralogs, reconstructed the PHA biosynthetic pathway in Haloferax volcanii, a PHA-defective haloarchaeon. Taken together, our results indicate that FabG1 in H. hispanica, and possibly its counterpart in Haloarcula marismortui, has evolved the distinct function of supplying precursors for PHA biosynthesis, like PhaB in bacteria. Hence, we suggest the renaming of FabG1 in both genomes as PhaB, the PHA-specific acetoacetyl-CoA reductase of halophilic archaea.

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