Two domains of superfamily I helicases may exist as separate proteins

Koonin, Eugene V.; Rudd, Kenneth E.

doi:10.1002/pro.5560050124

Cited by 31 publications

(22 citation statements)

References 29 publications

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“…However, despite the well-studied nature of the Pho regulon and the presence of phoH genes in a wide array of phage genomes, the function of PhoH remains unknown. The gene product is likely an ATPase, given its conserved nucleoside triphosphate hydrolase domain (24,30,38,66). If PhoH hydrolyzes ATP, the resulting reaction would release energy to drive another reaction, presumably to assist in the uptake of phosphate by the cell.…”

Section: Resultsmentioning

confidence: 99%

Development of phoH as a Novel Signature Gene for Assessing Marine Phage Diversity

Goldsmith

Crosti

Dwivedi

et al. 2011

Appl Environ Microbiol

133

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Phages play a key role in the marine environment by regulating the transfer of energy between trophic levels and influencing global carbon and nutrient cycles. The diversity of marine phage communities remains difficult to characterize because of the lack of a signature gene common to all phages. Recent studies have demonstrated the presence of host-derived auxiliary metabolic genes in phage genomes, such as those belonging to the Pho regulon, which regulates phosphate uptake and metabolism under low-phosphate conditions. Among the completely sequenced phage genomes in GenBank, this study identified Pho regulon genes in nearly 40% of the marine phage genomes, while only 4% of nonmarine phage genomes contained these genes. While several Pho regulon genes were identified, phoH was the most prevalent, appearing in 42 out of 602 completely sequenced phage genomes. Phylogenetic analysis demonstrated that phage phoH sequences formed a cluster distinct from those of their bacterial hosts. PCR primers designed to amplify a region of the phoH gene were used to determine the diversity of phage phoH sequences throughout a depth profile in the Sargasso Sea and at six locations worldwide. phoH was present at all sites examined, and a high diversity of phoH sequences was recovered. Most phoH sequences belonged to clusters without any cultured representatives. Each depth and geographic location had a distinct phoH composition, although most phoH clusters were recovered from multiple sites. Overall, phoH is an effective signature gene for examining phage diversity in the marine environment.Marine viruses merit study not only because of their sheer abundance but also because of the critical roles they play in the Earth's biogeochemical cycles (11). The majority of these viruses are phages (viruses that infect bacteria). Because phages are host-specific predators that influence the composition of the bacterial community (9, 47), it is essential to understand the diversity of marine phages. Microscopy-based methods have only limited resolution for analyzing marine phage diversity, and therefore genetic methods are preferable. However, identification of phages in environmental samples is hampered by the lack of a single gene found in all phages (50). Nonetheless, some genes are shared within groups of phages, and these "signature genes" can be used as markers to examine the diversity of a phage group of interest (70). Several signature genes have been developed to examine the diversity of phages in the marine environment, including structural genes (61,64,86), replication genes (10, 33), and auxiliary metabolic genes (14,54,60,68,80).Auxiliary metabolic genes (AMGs) are phage-borne metabolic genes that were typically thought to be restricted to cellular genomes yet have been identified in phage genomes through sequencing (11). Numerous AMGs involved in photosynthesis, carbon metabolism, and nucleotide metabolism have been identified in marine phages (14,35,36,42,43,65,68,78,80). In addition, marine phages carry AMGs involved in nut...

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Section: Resultsmentioning

confidence: 99%

Development of phoH as a Novel Signature Gene for Assessing Marine Phage Diversity

Goldsmith

Crosti

Dwivedi

et al. 2011

Appl Environ Microbiol

133

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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%

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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“…Samples were collected at the indicated times. LacZ protein levels were determined using SDS-10% PAGE separation, followed by Western blotting with mouse anti-LacZ antibodies (top panel), and lacZ transcript levels were measured using real time RT-PCR as described in Materials and Methods (bottom panel (16,17). Positional coupling of this family with neighboring genes points to its involvement in putative metal dependent RNA modification (16).…”

Section: Discussionmentioning

confidence: 99%

“…Positional coupling of this family with neighboring genes points to its involvement in putative metal dependent RNA modification (16). The N terminus of YbeZ has homology to the N-terminal domains of superfamily I RNA helices (17). According to studies of the E. coli interactome, YbeZ interacts with YbeY and, in addition, interacts with many ribosomal proteins (4).…”

Section: Discussionmentioning

confidence: 99%

YbeY, a Heat Shock Protein Involved in Translation in Escherichia coli

et al. 2009

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Here we provide evidence that YbeY, a conserved heat shock protein with unknown function, is involved in the translation process. ybeY deletion mutants are temperature sensitive and have a significantly reduced thermotolerance. Nonetheless, there appears to be no damage of the protein quality control of mature polypeptides, as the levels of chaperones and proteases are normal and there is no accumulation of aggregates. Rather, the mutation results in a significant reduction in the level of polysomes, and upon a shift to a restrictive temperature (42°C), there is an immediate and severe slowdown of translation. Taken together, the data indicate that YbeY is an important factor for bacterial translation even at 37°C but becomes essential at high temperatures.Heat shock results in a dramatic increase in the rate of synthesis of a set of proteins called heat shock proteins (30), many of which are chaperones (3) and proteases (14, 34), protecting cells against damage induced by protein unfolding. Heat shock proteins are also induced by conditions that lead to protein unfolding even at low temperatures, such as exposure to heavy metals, denaturing alcohols (30), or amino acid analogs (12).Recently, microarray experiments defining the heat shock regulon in Escherichia coli (7,20,23,26,32,39) revealed the existence of novel heat shock genes. These experiments led to the characterization of heat shock proteins that function in different stages of the translation process (2,5,6,18,19,21,35). As with chaperones and proteases, the function of these genes is important under all growth conditions but is more critical at higher temperatures.One of the genes identified as a heat shock gene by global transcriptional analysis is ybeY, whose function has not yet been determined. YbeY is a 17-kDa protein, highly conserved among bacteria, that belongs to the UPF0054 family. The sequence similarity of YbeY to metal-dependent hydrolases suggests a potential hydrolytic function. The structures of YbeY in E. coli (38), Aquifex aeolicus (24), and Haemophilus influenzae (36) was determined and suggest that YbeY is a metalloprotein with an active site located at the C terminus of the protein. In A. aeolicus (24), YbeY structure homology analysis showed similarity to eukaryotic extracelleular proteinases such as colagenase and gelatinase. However, in vitro YbeY did not have colagenease or gelatinase activity, and no other hydrolase activity could be detected.Recently, a mutant with a deletion of SMc01113, the Sinorhizobium meliloti homolog of ybeY, was characterized in vivo (9). The SMc01113 protein is required for symbiosis of S. meliloti with Medicago sativa (alfalfa) and the SMc01113 deletion mutant is sensitive to UV, oxidative stress, and cell wall inhibitors.Here we show that ybeY deletion mutants have a severe growth defect at higher temperatures and essentially no thermotolerance at lethal temperatures. However, the mutants do not appear to be defective in protein quality control of mature polypeptides. Instead, the mutants are impa...

show abstract

Two domains of superfamily I helicases may exist as separate proteins

Cited by 31 publications

References 29 publications

Development of phoH as a Novel Signature Gene for Assessing Marine Phage Diversity

Development of phoH as a Novel Signature Gene for Assessing Marine Phage Diversity

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

YbeY, a Heat Shock Protein Involved in Translation in Escherichia coli

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