The information transfer system of halophilic archaea

Capes, Melinda D.; Coker, James; Gessler, Rachael; Grinblat-Huse, Valerie; DasSarma, Satyajit L.; Jacob, Christopher G; Kim, Jong‐Myoung; DasSarma, Priya; DasSarma, Shiladitya

doi:10.1016/j.plasmid.2010.11.005

Cited by 45 publications

(55 citation statements)

References 121 publications

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“…Proteins in the COG3413 family are also found in Sulfolobus and Thermoplasma spp. (7,8), which, like haloarchaea, are facultative anaerobes that can grow aerobically using organic compounds. These observations suggest that the COG3413 family may be involved in oxygen/redox regulation in other clades of facultative anaerobic Archaea.…”

Section: Discussionmentioning

confidence: 99%

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Genome-Wide Responses of the Model Archaeon Halobacterium sp. Strain NRC-1 to Oxygen Limitation

et al. 2012

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As part of a comprehensive postgenomic investigation of the model archaeon Halobacterium sp. strain NRC-1, we used wholegenome DNA microarrays to compare transcriptional profiles of cells grown under anaerobic or aerobic conditions. When anaerobic growth supported by arginine fermentation was compared to aerobic growth, genes for arginine fermentation (arc) and anaerobic respiration (dms), using trimethylamine N-oxide (TMAO) as the terminal electron acceptor, were highly upregulated, as was the bop gene, required for phototrophic growth. When arginine fermentation was compared to anaerobic respiration with TMAO, the arc and dms genes were both induced with arginine, while TMAO induced the bop gene and major gas vesicle protein (gvpAC) genes specifying buoyant gas vesicles. Anaerobic conditions with either TMAO or arginine also upregulated the cba genes, encoding one of three cytochrome oxidases. In-frame deletion of two COG3413 family regulatory genes, bat and dmsR, showed downregulation of the bop gene cluster and loss of purple membrane synthesis and downregulation of the dms operon and loss of anaerobic respiration capability, respectively. Bioinformatic analysis identified additional regulatory and sensor genes that are likely involved in the full range of cellular responses to oxygen limitation. Our results show that the Halobacterium sp. has evolved a carefully orchestrated set of responses to oxygen limitation. As conditions become more reducing, cells progressively increase buoyancy, as well as capabilities for phototrophy, scavenging of molecular oxygen, anaerobic respiration, and fermentation.

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Section: Discussionmentioning

confidence: 99%

“…To determine the differentially expressed genes that were statistically significant, a P value of Ͻ0.05 and a fold change cutoff threshold of Ն2 were used. Local clusters of proteins developed using reciprocal blasting (7,8) as well as the COG cluster at NCBI were utilized to identify conserved proteins and domains. Membrane analysis.…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Responses of the Model Archaeon Halobacterium sp. Strain NRC-1 to Oxygen Limitation

et al. 2012

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“…Haloarchaeal genomes are generally composed of multiple genetic elements (chromosome, minichromosome, and megaplasmids) with multiple Cdc6 homologs (Capes et al, 2011), which is suggestive of the occurrence of multiple replication origins. Recently, multiple replication origins were predicted in 15 completely sequenced haloarchaeal genomes by searching for putative ORBs associated with cdc6 genes (Wu et al, 2012), and active replication origins have been experimentally studied in three model systems, Halobacterium sp.…”

Section: Identification (Mapping) Of Replication Originsmentioning

confidence: 99%

“…Both the ORBs within oriC1 and the oriC1 -associated Cdc6 homologs are highly conserved. In addition, gene order analysis found that genes around oriC1 are highly syntenic among haloarchaea ( Figure 2 ; Capes et al, 2011). Notably, other studies (Robinson et al, 2004; Coker et al, 2009) and our results indicated that the oriC1 replication origin is broadly conserved in archaea, in terms of both function and structure, which strongly suggested that the ancestral chromosome was dependent on oriC1 .…”

Section: Evolution Of Multiple Replication Origins In Archaeamentioning

confidence: 99%

DNA replication origins in archaea

Wu¹,

Liu²,

Yang³

et al. 2014

Front. Microbiol.

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DNA replication initiation, which starts at specific chromosomal site (known as replication origins), is the key regulatory stage of chromosome replication. Archaea, the third domain of life, use a single or multiple origin(s) to initiate replication of their circular chromosomes. The basic structure of replication origins is conserved among archaea, typically including an AT-rich unwinding region flanked by several conserved repeats (origin recognition box, ORB) that are located adjacent to a replication initiator gene. Both the ORB sequence and the adjacent initiator gene are considerably diverse among different replication origins, while in silico and genetic analyses have indicated the specificity between the initiator genes and their cognate origins. These replicator–initiator pairings are reminiscent of the oriC-dnaA system in bacteria, and a model for the negative regulation of origin activity by a downstream cluster of ORB elements has been recently proposed in haloarchaea. Moreover, comparative genomic analyses have revealed that the mosaics of replicator-initiator pairings in archaeal chromosomes originated from the integration of extrachromosomal elements. This review summarizes the research progress in understanding of archaeal replication origins with particular focus on the utilization, control and evolution of multiple replication origins in haloarchaea.

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“…Generally, haloarchaeal genomes contain extrachromosomal elements, such as large megaplasmids or minichromosomes (Capes et al, 2011). Genome sequence analysis is required to understand halophilic archaea, and the analysis of their functional gene information will be important for ecological research and industrialization.…”

Section: Introductionmentioning

confidence: 99%