Complete Genome Sequence of Klebsiella pneumoniae Phage JD001

Cui, Zelin; Shen, Wenbin; Wang, Zheng; Zhang, Haotian; Me, Rao; Wang, Yanchun; Zeng, Lieguang; Zhu, Yongzhang; Qin, Jinhong; He, Ping; Guo, Xia

doi:10.1128/jvi.02435-12

Cited by 14 publications

(13 citation statements)

References 11 publications

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“…Basic Local Alignment Search Tool (BLAST) (http://www.ncbi.nlm.nih.gov/BLAST/) was used to identify putative proteins sharing similarities with the predicted phage proteins through the Blastp program, and select the results with an E value less than e-5 based on the actual situation to define the function of the gene. Putative tRNA-encoding genes were analyzed using tRNAscan-SE 1.21 (http://lowelab.ucsc.edu/ tRNAscan-SE/) [6,25]. We used the CpG islands function from the European bioinformatics institute of EMBL-EBI website (http://www.ebi.ac.uk/emboss/cpgplot), and the CpGFinder PROMOTER softberry website options (finder GC-islands) function (http://www.softberry.com/berry.phtml) to analyze the distribution of phage genome GC.…”

Section: Whole-genome Bioinformatic Analysismentioning

confidence: 99%

Isolation and Characterization of AbTJ, an Acinetobacter baumannii Phage, and Functional Identification of Its Receptor-Binding Modules

Kang

et al. 2020

Viruses

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A. baumannii is an opportunistic pathogen and a major cause of various community-acquired infections. Strains of this species can be resistant to multiple antimicrobial agents, leaving limited therapeutic options, also lacking in methods for accurate and prompt diagnosis. In this context, AbTJ, a novel phage that infects A. baumannii MDR-TJ, was isolated and characterized, together with its two tail fiber proteins. Morphological analysis revealed that it belongs to Podoviridae family. Its host range, growth characteristics, stability under various conditions, and genomic sequence, were systematically investigated. Bioinformatic analysis showed that AbTJ consists of a circular, double-stranded 42670-bp DNA molecule which contains 62 putative open reading frames (ORFs). Genome comparison revealed that the phage AbTJ is related to the Acinetobacter phage Ab105-1phi (No. KT588074). Tail fiber protein (TFPs) gp52 and gp53 were then identified and confirmed as species-specific proteins. By using a combination of bioluminescent methods and magnetic beads, these TFPs exhibit excellent specificity to detect A. baumannii. The findings of this study can be used to help control opportunistic infections and to provide pathogen-binding modules for further construction of engineered bacteria of diagnosis and treatment.

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Section: Whole-genome Bioinformatic Analysismentioning

confidence: 99%

Isolation and Characterization of AbTJ, an Acinetobacter baumannii Phage, and Functional Identification of Its Receptor-Binding Modules

Kang

et al. 2020

Viruses

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“…This information suggests that viral Sir2/cobB proteins of Vibrio “schizoT4like” phages can act similarly to the bacterial and are able to deacetylase acetyl-lysines of enzymes, like ACS , and subsequently activate them. The Sir2/cobB protein is also conserved at the genomes of E. coli bacteriophage T5 (Wang et al, 2005), at Salmonella phage SPC35 (Kim and Ryu, 2011), at Cronobacter phage vB_CsaM_GAP32 (Abbasifar et al, 2014), at Pectobacter phage My1 (Lee et al, 2012) and at Klebsiella phage JD001 (Cui et al, 2012). …”

Section: Resultsmentioning

confidence: 99%

Comparative Functional Genomic Analysis of Two Vibrio Phages Reveals Complex Metabolic Interactions with the Host Cell

et al. 2016

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Sequencing and annotation was performed for two large double stranded DNA bacteriophages, φGrn1 and φSt2 of the Myoviridae family, considered to be of great interest for phage therapy against Vibrios in aquaculture live feeds. In addition, phage–host metabolic interactions and exploitation was studied by transcript profiling of selected viral and host genes. Comparative genomic analysis with other large Vibrio phages was also performed to establish the presence and location of homing endonucleases highlighting distinct features for both phages. Phylogenetic analysis revealed that they belong to the “schizoT4like” clade. Although many reports of newly sequenced viruses have provided a large set of information, basic research related to the shift of the bacterial metabolism during infection remains stagnant. The function of many viral protein products in the process of infection is still unknown. Genome annotation identified the presence of several viral open reading frames (ORFs) participating in metabolism, including a Sir2/cobB (sirtuin) protein and a number of genes involved in auxiliary NAD+ and nucleotide biosynthesis, necessary for phage DNA replication. Key genes were subsequently selected for detail study of their expression levels during infection. This work suggests a complex metabolic interaction and exploitation of the host metabolic pathways and biochemical processes, including a possible post-translational protein modification, by the virus during infection.

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“…). Two of them were isolated from marine bacteria ( Edwardsiella phage MSW-3 and Klebsiella phage JDOO1) [ 92 , 93 ] and most of them were lytic phages, except for Vibrio phage CP-T1 that is known to be temperate (i.e., capable of forming a lysogen; [ 94 ]). Although DNA polymerases have been suggested to be good phylogenetic markers for investigating viral phylogeny since they offer the greatest number of viral homologs [ 95 ], our results showed that this gene’s phylogeny may be incongruent with electron microscopy- and genome-based taxonomy.…”

Section: Resultsmentioning

confidence: 99%

Life-Style and Genome Structure of Marine Pseudoalteromonas Siphovirus B8b Isolated from the Northwestern Mediterranean Sea

et al. 2015

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Marine viruses (phages) alter bacterial diversity and evolution with impacts on marine biogeochemical cycles, and yet few well-developed model systems limit opportunities for hypothesis testing. Here we isolate phage B8b from the Mediterranean Sea using Pseudoalteromonas sp. QC-44 as a host and characterize it using myriad techniques. Morphologically, phage B8b was classified as a member of the Siphoviridae family. One-step growth analyses showed that this siphovirus had a latent period of 70 min and released 172 new viral particles per cell. Host range analysis against 89 bacterial host strains revealed that phage B8b infected 3 Pseudoalteromonas strains (52 tested, >99.9% 16S rRNA gene nucleotide identity) and 1 non-Pseudoaltermonas strain belonging to Alteromonas sp. (37 strains from 6 genera tested), which helps bound the phylogenetic distance possible in a phage-mediated horizontal gene transfer event. The Pseudoalteromonas phage B8b genome size was 42.7 kb, with clear structural and replication modules where the former were delineated leveraging identification of 16 structural genes by virion structural proteomics, only 4 of which had any similarity to known structural proteins. In nature, this phage was common in coastal marine environments in both photic and aphotic layers (found in 26.5% of available viral metagenomes), but not abundant in any sample (average per sample abundance was 0.65% of the reads). Together these data improve our understanding of siphoviruses in nature, and provide foundational information for a new ‘rare virosphere’ phage–host model system.

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Complete Genome Sequence of Klebsiella pneumoniae Phage JD001

Cited by 14 publications

References 11 publications

Isolation and Characterization of AbTJ, an Acinetobacter baumannii Phage, and Functional Identification of Its Receptor-Binding Modules

Isolation and Characterization of AbTJ, an Acinetobacter baumannii Phage, and Functional Identification of Its Receptor-Binding Modules

Comparative Functional Genomic Analysis of Two Vibrio Phages Reveals Complex Metabolic Interactions with the Host Cell

Life-Style and Genome Structure of Marine Pseudoalteromonas Siphovirus B8b Isolated from the Northwestern Mediterranean Sea

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