The DNA-recognition fold of Sso7c4 suggests a new member of SpoVT-AbrB superfamily from archaea

Hsu, Chun‐Hua; Wang, Andrew H.-J.

doi:10.1093/nar/gkr283

Cited by 15 publications

(16 citation statements)

References 29 publications

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“…6C). How ORF4 regulates the stability of SNJ1 is not clear, but sequence analysis suggests that it belongs to the SpoVT/ AbrB family of transcription regulators (66). It is possible that ORF4 regulates the expression of proteins required for the partitioning of SNJ1.…”

Section: Discussionmentioning

confidence: 99%

Identification, Characterization, and Application of the Replicon Region of the Halophilic Temperate Sphaerolipovirus SNJ1

Wang

Sima

et al. 2016

J Bacteriol

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The temperate haloarchaeal virus SNJ1 displays lytic and lysogenic life cycles. During the lysogenic cycle, the virus resides in its host, Natrinema sp. strain J7-1, in the form of an extrachromosomal circular plasmid, pHH205. In this study, a 3.9-kb region containing seven predicted genes organized in two operons was identified as the minimal replicon of SNJ1. Only RepA, encoded by open reading frame 11-12 (ORF11-12), was found to be essential for replication, and its expression increased during the lytic cycle. Sequence analysis suggested that RepA is a distant homolog of HUH endonucleases, a superfamily that includes rollingcircle replication initiation proteins from various viruses and plasmids. In addition to RepA, two genetic elements located within both termini of the 3.9-kb replicon were also required for SNJ1 replication. SNJ1 genome and SNJ1 replicon-based shuttle vectors were present at 1 to 3 copies per chromosome. However, the deletion of ORF4 significantly increased the SNJ1 copy number, suggesting that the product of ORF4 is a negative regulator of SNJ1 abundance. Shuttle vectors based on the SNJ1 replicon were constructed and validated for stable expression of heterologous proteins, both in J7 derivatives and in Natrinema pallidum JCM 8980 T , suggesting their broad applicability as genetic tools for Natrinema species. IMPORTANCEArchaeal viruses exhibit striking morphological diversity and unique gene content. In this study, the minimal replicon of the temperate haloarchaeal virus SNJ1 was identified. A number of ORFs and genetic elements controlling virus genome replication, maintenance, and copy number were characterized. In addition, based on the replicon, a novel expression shuttle vector has been constructed and validated for protein expression and purification in Natrinema sp. CJ7 and Natrinema pallidum JCM 8980 T . This study not only provided mechanistic and functional insights into SNJ1 replication but also led to the development of useful genetic tools to investigate SNJ1 and other viruses infecting Natrinema species as well as their hosts. Haloarchaea are the dominant microbes in hypersaline environments, such as salt lakes and salterns. Viruses infecting haloarchaea outnumber their hosts by several orders of magnitude (1). It has been speculated that in such a harsh environment with no other predators, interactions between viruses and their hosts constitute the main evolutionary driving force (2). About 90 haloarchaeal viruses have been discovered so far, a relatively small number compared to the ϳ6,200 reported bacteriophages (3, 4). Given that the characterization of bacterial and eukaryotic viruses has yielded remarkable insights into the physiology and cell biology of their hosts, studies on haloarchaeal viruses are expected to be equally revealing. However, thus far, research has been limited by the scarcity of suitable and genetically tractable virus-host models. Consequently, most of the current knowledge on viral entry, transcription, genome replication, assembly, and ...

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Section: Discussionmentioning

confidence: 99%

Identification, Characterization, and Application of the Replicon Region of the Halophilic Temperate Sphaerolipovirus SNJ1

Wang

Sima

et al. 2016

J Bacteriol

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“…The N-terminal domains of the AbrB dimmer form a novel fold that was previously called the "looped-hinge helix" (45) and renamed later as the "swapped-hairpin barrel" (34). In addition to various bacteria, this AbrB-like DNA recognition fold is present in archaea, such as the putative chromatin-associated protein Sso7c4 protein in Sulfolobus solfataricus (46). The AbrB-like domain of H. mediterranei PhaR is highly conserved in its archaeal homologs.…”

Section: Discussionmentioning

confidence: 99%

A Novel DNA-Binding Protein, PhaR, Plays a Central Role in the Regulation of Polyhydroxyalkanoate Accumulation and Granule Formation in the Haloarchaeon Haloferax mediterranei

Cai

Zhao

et al. 2015

Appl Environ Microbiol

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c Polyhydroxyalkanoates (PHAs) are synthesized and assembled as PHA granules that undergo well-regulated formation in many microorganisms. However, this regulation remains unclear in haloarchaea. In this study, we identified a PHA granule-associated regulator (PhaR) that negatively regulates the expression of both its own gene and the granule structural gene phaP in the same operon (phaRP) in Haloferax mediterranei. Chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) assays demonstrated a significant interaction between PhaR and the phaRP promoter in vivo. Scanning mutagenesis of the phaRP promoter revealed a specific cis-element as the possible binding position of the PhaR. The haloarchaeal homologs of the PhaR contain a novel conserved domain that belongs to a swapped-hairpin barrel fold family found in AbrB-like proteins. Amino acid substitution indicated that this AbrB-like domain is critical for the repression activity of PhaR. In addition, the phaRP promoter had a weaker activity in the PHA-negative strains, implying a function of the PHA granules in titration of the PhaR. Moreover, the H. mediterranei strain lacking phaR was deficient in PHA accumulation and produced granules with irregular shapes. Interestingly, the PhaR itself can promote PHA synthesis and granule formation in a PhaP-independent manner. Collectively, our results demonstrated that the haloarchaeal PhaR is a novel bifunctional protein that plays the central role in the regulation of PHA accumulation and granule formation in H. mediterranei. P olyhydroxyalkanoates (PHAs) are biodegradable polyesters synthesized by most genera of bacteria (1, 2) and some archaea (3-5). PHAs are accumulated as storage compounds of energy and carbon under imbalanced growth conditions (i.e., when nutrients such as nitrogen, phosphorus, or oxygen are limited but the carbon sources are in excess) (6).PHAs are often deposited in the cytoplasm as water-insoluble inclusions that are called PHA granules (6). Native PHA granules are found to be composed of 97.5% PHA, 2% proteins, and likely some amount of lipids (7). At least four types of proteins were found to be the PHA granule-associated proteins (PGAPs) in bacteria: PHA synthases, PHA depolymerases, regulators, and structural proteins (phasins [PhaPs]) (8, 9). In recent years, increasing new roles have been found for the PGAPs. Besides the classical phasin role of preventing PHA granules from coalescing, two distinct phasin-like proteins, PhaM and PhaF, have also been characterized as being crucial for granule distribution during cell division (10, 11).The PGAPs play important roles in PHA synthesis, PHA utilization, and granule formation and distribution (8, 9, 12), among which the regulatory proteins are responsible for ensuring the proper formation of PHA granules by influencing the expression of both phasins and themselves (13)(14)(15)(16)(17). A classic regulation model was presented in a poly(3-hydroxybutyrate) (PHB [a type of PHA])-accumulating bacterium, Ralstonia eutropha H16 (9). Briefly, the cy...

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“…In bacterial firmicutes, AbrB regulates the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation (59,60). While AbrB homologs have been reported in Sulfolobus and its viruses (61,62), their functional roles are unclear.…”

Section: Figmentioning

confidence: 99%

Expanding the Limits of Thermoacidophily in the Archaeon Sulfolobus solfataricus by Adaptive Evolution

McCarthy

Johnson

Pavlik

et al. 2016

Appl Environ Microbiol

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Extremely thermoacidophilic Crenarchaeota belonging to the order Sulfolobales flourish in hot acidic habitats that are strongly oxidizing. The pH extremes of these habitats, however, often exceed the acid tolerance of type species and strains. Here, adaptive laboratory evolution was used over a 3-year period to test whether such organisms harbor additional thermoacidophilic capacity. Three distinct cell lines derived from a single type species were subjected to high-temperature serial passage while culture acidity was gradually increased. A 178-fold increase in thermoacidophily was achieved after 29 increments of shifted culture pH resulting in growth at pH 0.8 and 80°C. These strains were named super-acid-resistant Crenarchaeota (SARC). Mathematical modeling using growth parameters predicted the limits of acid resistance, while genome resequencing and transcriptome resequencing were conducted for insight into mechanisms responsible for the evolved trait. Among the mutations that were detected, a set of eight nonsynonymous changes may explain the heritability of increased acid resistance despite an unexpected lack of transposition. Four multigene components of the SARC transcriptome implicated oxidative stress as a primary challenge accompanying growth at acid extremes. These components included accelerated membrane biogenesis, induction of the mer operon, and an increased capacity for the generation of energy and reductant.

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The DNA-recognition fold of Sso7c4 suggests a new member of SpoVT-AbrB superfamily from archaea

Cited by 15 publications

References 29 publications

Identification, Characterization, and Application of the Replicon Region of the Halophilic Temperate Sphaerolipovirus SNJ1

Identification, Characterization, and Application of the Replicon Region of the Halophilic Temperate Sphaerolipovirus SNJ1

A Novel DNA-Binding Protein, PhaR, Plays a Central Role in the Regulation of Polyhydroxyalkanoate Accumulation and Granule Formation in the Haloarchaeon Haloferax mediterranei

Expanding the Limits of Thermoacidophily in the Archaeon Sulfolobus solfataricus by Adaptive Evolution

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