Molecular analysis of the phoH gene, belonging to the phosphate regulon in Escherichia coli

Kim, Soo-Ki; Makino, Kozo; Amemura, Mitsuko; Shinagawa, Hideo; Nakata, Atsuo

doi:10.1128/jb.175.5.1316-1324.1993

Cited by 112 publications

(92 citation statements)

References 36 publications

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“…Thymidylate synthase, the gp134 of PVP-SE1, is the enzyme that catalyzes the conversion of dUMP to TMP, and to accomplish this task, like ribonucleotide reductases, it requires the NAD ϩ cofactor (36,46,53). Further, the codification of a protein involved in phosphate transport (gp147) might enable the phage to grow even under conditions of phosphate depletion (37,50).…”

Section: Resultsmentioning

confidence: 99%

Genomic and Proteomic Characterization of the Broad-Host-Range Salmonella Phage PVP-SE1: Creation of a New Phage Genus

Santos

Kropinski

Ceyssens

et al. 2011

J Virol

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(Bacterio)phage PVP-SE1, isolated from a German wastewater plant, presents a high potential value as a biocontrol agent and as a diagnostic tool, even compared to the well-studied typing phage Felix 01, due to its broad lytic spectrum against different Salmonella strains. Sequence analysis of its genome (145,964 bp) shows it to be terminally redundant and circularly permuted. Its G؉C content, 45.6 mol%, is lower than that of its hosts (50 to 54 mol%). We found a total of 244 open reading frames (ORFs), representing 91.6% of the coding capacity of the genome. Approximately 46% of encoded proteins are unique to this phage, and 22.1% of the proteins could be functionally assigned. This myovirus encodes a large number of tRNAs (n ‫؍‬ 24), reflecting its lytic capacity and evolution through different hosts. Tandem mass spectrometric analysis using electron spray ionization revealed 25 structural proteins as part of the mature phage particle. The genome sequence was found to share homology with 140 proteins of the Escherichia coli bacteriophage rV5. Both phages are unrelated to any other known virus, which suggests that an "rV5-like virus" genus should be created within the Myoviridae to contain these two phages.

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Section: Resultsmentioning

confidence: 99%

Genomic and Proteomic Characterization of the Broad-Host-Range Salmonella Phage PVP-SE1: Creation of a New Phage Genus

Santos

Kropinski

Ceyssens

et al. 2011

J Virol

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“…PhoH is part of the Pho regulon and is expressed in response to phosphate starvation (81). Little is known about its function, but it is similar to the N-terminal domain of superfamily I helicases (81,82). Interestingly, Pho regulon genes have been found in more than 40% of marine phages but in only 4% of nonmarine phages, with phoH being the most prevalent of these genes (83).…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

The Genomes, Proteomes, and Structures of Three Novel Phages That Infect the Bacillus cereus Group and Carry Putative Virulence Factors

Grose

Belnap

Jensen

et al. 2014

J Virol

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This article reports the results of studying three novel bacteriophages, JL, Shanette, and Basilisk, which infect the pathogen Bacillus cereus and carry genes that may contribute to its pathogenesis. We analyzed host range and superinfection ability, mapped their genomes, and characterized phage structure by mass spectrometry and transmission electron microscopy (TEM). The JL and Shanette genomes were 96% similar and contained 217 open reading frames (ORFs) and 220 ORFs, respectively, while Basilisk has an unrelated genome containing 138 ORFs. Mass spectrometry revealed 23 phage particle proteins for JL and 15 for Basilisk, while only 11 and 4, respectively, were predicted to be present by sequence analysis. Structural protein homology to wellcharacterized phages suggested that JL and Shanette were members of the family Myoviridae, which was confirmed by TEM. The third phage, Basilisk, was similar only to uncharacterized phages and is an unrelated siphovirus. Cryogenic electron microscopy of this novel phage revealed a T‫9؍‬ icosahedral capsid structure with the major capsid protein (MCP) likely having the same fold as bacteriophage HK97 MCP despite the lack of sequence similarity. Several putative virulence factors were encoded by these phage genomes, including TerC and TerD involved in tellurium resistance. Host range analysis of all three phages supports genetic transfer of such factors within the B. cereus group, including B. cereus, B. anthracis, and B. thuringiensis. This study provides a basis for understanding these three phages and other related phages as well as their contributions to the pathogenicity of B. cereus group bacteria. IMPORTANCEThe Bacillus cereus group of bacteria contains several human and plant pathogens, including B. cereus, B. anthracis, and B. thuringiensis. Phages are intimately linked to the evolution of their bacterial hosts and often provide virulence factors, making the study of B. cereus phages important to understanding the evolution of pathogenic strains. Herein we provide the results of detailed study of three novel B. cereus phages, two highly related myoviruses (JL and Shanette) and an unrelated siphovirus (Basilisk). The detailed characterization of host range and superinfection, together with results of genomic, proteomic, and structural analyses, reveal several putative virulence factors as well as the ability of these phages to infect different pathogenic species.

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“…Other genes involved in P acquisition are also present in all 6 marine cyanobacterial genomes, including the genes involved in internal polyphosphate metabolism (ppK and ppX), consistent with the ability of the strains tested to grow with PPP i as the sole source of P (Table 1), and the P-starvationinduced protein, phoH, believed to be an RNA helicase that is highly conserved in bacteria (Kim et al 1993). Another gene for a P-starvation-induced protein, psip1 (N. J.…”

Section: Genomic Comparisonsmentioning

confidence: 99%

Ecotypic variation in phosphorus-acquisition mechanisms within marine picocyanobacteria

Moore¹,

Ostrowski²,

Scanlan³

et al. 2005

Aquat. Microb. Ecol.

166

196

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Prochlorococcus and Synechococcus are major prokaryotic primary producers in the oligotrophic oceans that may be affected by the climate-related increases in nitrogen fixation and subsequent phosphorus (P) limitation in some parts of the oceans. Evidence that Prochlorococcus populations in the North Pacific subtropical gyre (NPSG) have increased over the past decades, possibly due to having a competitive advantage under conditions of P limitation, suggests aspects of their P physiology that are important for dictating their in situ success. Here, we compared the physiology of P acquisition and response to P stress (indicated by alkaline phosphatase activity, APA) among isolates of Prochlorococcus and Synechococcus representing different genotypic clades within the marine picophytoplankton lineage (sensu Urbach et al. 1998: J Mol Evol 46:188-201). The 2 Synechococcus isolates examined (WH 8102 and WH 7803) can utilize a wide variety of organic P sources. Of the 3 Prochlorococcus isolates examined, only the HLI genotype, MED4, is capable of growth on a variety of organic P sources. Under conditions of P starvation the 2 Synechococcus strains and Prochlorococcus MED4 exhibit significant increases in APA, above their measurable constitutive activities. The genomes of the Synechococcus strains and Prochlorococcus MED4 indicate the presence of many P-uptake and -regulatory genes required under conditions of P stress, including the phoA gene that encodes for an alkaline phosphatase enzyme. The other isolates of Prochlorococcus, HLII MIT 9312 and LLIV MIT 9313, have distinctly different P-stress responses. MIT 9312, which contains the same P-uptake and -regulatory genes as MED4, except for psip1 and ptrA, has no constitutive APA, but does exhibit measurable, albeit very low, activity when P starved. MIT 9313, which lacks phoA and a functional phosphate-sensing histidine kinase gene, phoR, exhibits low constitutive activity that decreases when the cells become P-starved. These results show variability in P utilization and in P-stress response between the 2 genera of marine unicellular cyanobacteria, and marked differences among Prochlorococcus genotypes, implying that only certain eco/genotypes of these marine cyanobacteria will have an ecological advantage under conditions of P limitation in the oceans. This further points to the critical need to continue developing genotypic-or cell-specific tools to assess the response of the picophytoplankton community to large-scale changes in nutrient conditions in the oceans.

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Molecular analysis of the phoH gene, belonging to the phosphate regulon in Escherichia coli

Cited by 112 publications

References 36 publications

Genomic and Proteomic Characterization of the Broad-Host-Range Salmonella Phage PVP-SE1: Creation of a New Phage Genus

Genomic and Proteomic Characterization of the Broad-Host-Range Salmonella Phage PVP-SE1: Creation of a New Phage Genus

The Genomes, Proteomes, and Structures of Three Novel Phages That Infect the Bacillus cereus Group and Carry Putative Virulence Factors

Ecotypic variation in phosphorus-acquisition mechanisms within marine picocyanobacteria

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