Nucleotide sequence of ISH11, a new<i>Halobacterium halobium</i>insertion element isolated from the plasmid pGRB1

Krebs, Mark P.; RajBhandary, U L; Khorana, H G

doi:10.1093/nar/18.22.6699

Cited by 15 publications

(5 citation statements)

References 11 publications

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“…ISH11, from H. salinarium, was observed as an insertion into plasmid pGRB1. It is 1,068 bp long, with 15-bp terminal IRs, and was flanked by 7-bp direct target repeats (43). It exhibits a single long ORF of 334 aa.…”

Section: Spontaneous Mutation In the Extreme Halophilesmentioning

confidence: 99%

Insertion Sequence Diversity in Archaea

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Chandler

2007

Microbiol Mol Biol Rev

133

134

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SUMMARY Insertion sequences (ISs) can constitute an important component of prokaryotic (bacterial and archaeal) genomes. Over 1,500 individual ISs are included at present in the ISfinder database (www-is.biotoul.fr ), and these represent only a small portion of those in the available prokaryotic genome sequences and those that are being discovered in ongoing sequencing projects. In spite of this diversity, the transposition mechanisms of only a few of these ubiquitous mobile genetic elements are known, and these are all restricted to those present in bacteria. This review presents an overview of ISs within the archaeal kingdom. We first provide a general historical summary of the known properties and behaviors of archaeal ISs. We then consider how transposition might be regulated in some cases by small antisense RNAs and by termination codon readthrough. This is followed by an extensive analysis of the IS content in the sequenced archaeal genomes present in the public databases as of June 2006, which provides an overview of their distribution among the major archaeal classes and species. We show that the diversity of archaeal ISs is very great and comparable to that of bacteria. We compare archaeal ISs to known bacterial ISs and find that most are clearly members of families first described for bacteria. Several cases of lateral gene transfer between bacteria and archaea are clearly documented, notably for methanogenic archaea. However, several archaeal ISs do not have bacterial equivalents but can be grouped into Archaea-specific groups or families. 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.

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Section: Spontaneous Mutation In the Extreme Halophilesmentioning

confidence: 99%

Insertion Sequence Diversity in Archaea

Filée

Siguier

Chandler

2007

Microbiol Mol Biol Rev

133

134

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“…In rare cases, the abolishment of bop can be attributed to spontaneous insertions either in bop itself or in the brp gene. Since the early 1980s, several insertion sequences (IS) have been identified in bop from various PM-deficient Halobacterium strains ( Simsek et al, 1982 ; DasSarma et al, 1983 ; Ovchinnikov et al, 1984 ; Pfeiffer et al, 1984 ; Pfeiffer and Betlach, 1985 ; Ebert et al, 1987 ). Typically, the IS called ISH 1 (1 118 bp in size) integrates into a single site in the bop gene and ISH 2 (520 bp in size) at several sites of bop .…”

Section: Discussionmentioning

confidence: 99%

Complex Effects of Cytochrome P450 Monooxygenase on Purple Membrane and Bacterioruberin Production in an Extremely Halophilic Archaeon: Genetic, Phenotypic, and Transcriptomic Analyses

et al. 2018

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Halophilic archaea are known to produce a diverse array of pigments for phototrophy and photoprotection. The aim of this paper was to determine the role of a Halobacterium gene encoding the predicted cytochrome P450 monooxygenase (CYP174A1) in pigment synthesis through a combined genetic, phenotypic, and transcriptomic approach. We report on the observed phenotype changes [increased bacterioruberin levels and the loss of purple membrane (PM)] between the Halobacterium salinarum R1 and its CYP174A1-deletion mutant. In addition, we report on the whole-genome DNA microarray analysis, which supports the phenotype of PM loss. This work expands our understanding of the bop-gene regulon, and its relation to carotenoid biosynthesis, and sheds light on our broader understanding of the role (s) of CYP174A1 in archaeal pigment synthesis. To date, this is the first study in which the physiological role of any cytochrome P450 monooxygenase (CYP450) in extremely halophilic archaea has been reported.

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“…strain AS-7901, and pZMX201 from Natrinema sp. strain CX2021, belong to superfamily I RCR plasmids (see Table S2 in the supplemental material) (38,39,(209)(210)(211)(212)(213). Some of these plasmids were isolated decades ago have not been characterized further.…”

Section: Replication Mechanismsmentioning

confidence: 99%

Archaeal Extrachromosomal Genetic Elements

Wang

Peng

Shah

et al. 2015

Microbiol Mol Biol Rev

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SUMMARY Research on archaeal extrachromosomal genetic elements (ECEs) has progressed rapidly in the past decade. To date, over 60 archaeal viruses and 60 plasmids have been isolated. These archaeal viruses exhibit an exceptional diversity in morphology, with a wide array of shapes, such as spindles, rods, filaments, spheres, head-tails, bottles, and droplets, and some of these new viruses have been classified into one order, 10 families, and 16 genera. Investigation of model archaeal viruses has yielded important insights into mechanisms underlining various steps in the viral life cycle, including infection, DNA replication and transcription, and virion egression. Many of these mechanisms are unprecedented for any known bacterial or eukaryal viruses. Studies of plasmids isolated from different archaeal hosts have also revealed a striking diversity in gene content and innovation in replication strategies. Highly divergent replication proteins are identified in both viral and plasmid genomes. Genomic studies of archaeal ECEs have revealed a modular sequence structure in which modules of DNA sequence are exchangeable within, as well as among, plasmid families and probably also between viruses and plasmids. In particular, it has been suggested that ECE-host interactions have shaped the coevolution of ECEs and their archaeal hosts. Furthermore, archaeal hosts have developed defense systems, including the innate restriction-modification (R-M) system and the adaptive CRISPR (clustered regularly interspaced short palindromic repeats) system, to restrict invasive plasmids and viruses. Together, these interactions permit a delicate balance between ECEs and their hosts, which is vitally important for maintaining an innovative gene reservoir carried by ECEs. In conclusion, while research on archaeal ECEs has just started to unravel the molecular biology of these genetic entities and their interactions with archaeal hosts, it is expected to accelerate in the next decade.

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Nucleotide sequence of ISH11, a newHalobacterium halobiuminsertion element isolated from the plasmid pGRB1

Cited by 15 publications

References 11 publications

Insertion Sequence Diversity in Archaea

Insertion Sequence Diversity in Archaea

Complex Effects of Cytochrome P450 Monooxygenase on Purple Membrane and Bacterioruberin Production in an Extremely Halophilic Archaeon: Genetic, Phenotypic, and Transcriptomic Analyses

Archaeal Extrachromosomal Genetic Elements

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