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Complete Genome Sequence of Citrobacter freundii Myophage Moon Garrett B. Edwards, Adrian J. Luna, Adriana C. Hernandez, Gabriel F. Kuty Everett Center for Phage Technology, Texas A&M University, College Station, Texas, USA

Received 1 December 2014 Accepted 18 December 2014 Published 29 January 2015 Citation Edwards GB, Luna AJ, Hernandez AC, Kuty Everett GF. 2015. Complete genome sequence of Citrobacter freundii myophage Moon. Genome Announc 3(1):e01427-14. doi:10.1128/genomeA.01427-14. Copyright © 2015 Edwards et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Gabriel F. Kuty Everett, [email protected]

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itrobacter freundii is a Gram-negative bacterium found in the environment and in the intestinal tracts of animals (1). C. freundii is a pathogen of the respiratory and urinary tracts as well as the blood, and it is the cause of many opportunistic infections (2). The development of antibiotic resistance among strains of C. freundii underscores the need for alternative strategies, such as bacteriophage therapy, to fight the infections caused by this pathogenic bacterium (3–5). To that end, bacteriophage Moon, a T4-like myophage, was isolated against C. freundii. Bacteriophage Moon was isolated from a sewage sample collected in College Station, TX. The phage DNA was sequenced in an Illumina MiSeq 250-bp paired-end run, with a 550-bp insert library, at the Genomic Sequencing and Analysis Facility at the University of Texas (Austin, TX). Quality-controlled trimmed reads were assembled to a single contig at 48.1-fold coverage using Velvet version 1.2.10. The contigs were confirmed by PCR to be complete. The genes were predicted using GeneMarkS (6) and corrected using the software tools available on the Center for Phage Technology (CPT) Galaxy instance (https://cpt.tamu.edu /galaxy-public/). The morphology of Moon was determined using transmission electron microscopy performed at the Texas A&M University Microscopy and Imaging Center. Moon is a myophage with a 170,341-bp genome containing 298 coding sequences, a coding density of 95.7%, and 38.9% G⫹C content. This G⫹C content falls in the midrange for T4-like phages (35 to 43% G⫹C content) (7). Moon shares 56.1, 48.3, 59.7, and 61.1% nucleotide sequence identities with bacteriophages T4, STML-198, S16, and PG7, respectively, as shown by Emboss Stretcher (8). It falls into the T4 major subtype of the T4-like phage cluster, as defined by Grose and Casjens (9). Moon contains 9 tRNA genes compared to the 8 tRNA genes in T4. As a T4-like phage, Moon has a circularly permuted genome. It was opened to the rIIa gene by precedent (10). The core genes of T4-like phages, which encode proteins involved in replication, recombination, DNA packaging, virion morphogenesis, and lysis, were identified. The differences between Moon and T4 occur largely in the hypothetical conserved/ novel proteins of unknown function. Moon contains two standalone seg (Similar to Endonucleases encoded within Group I introns) homing endonucleases compared to the 12 seg and mob

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(mobility) homing endonucleases found in T4 (11). Moon contains a single internal protein gene homologous to ipIII of T4. It is missing a homolog to T4 EndoV (denV [UV damage-induced base excision repair] [12]). Furthermore, Moon has no homolog to T4 RepEA/B replication initiation proteins (specific for T4 oriE [13]). Presumably, it encodes origin-specific replication initiation proteins that cannot be identified by sequence homology. Moon encodes a DksA/TraR family zinc finger domain (IPR000962) containing a protein found in many T4-like phages but not in T4 itself. Additionally, Moon encodes a YgiB-like lipoprotein. The roles of these proteins within the context of the phage infection cycle are currently unknown. Nucleotide sequence accession number. The genome sequence of phage Moon was deposited in GenBank under the accession no. KM236240. ACKNOWLEDGMENTS This work was supported primarily by funding from award EF-0949351, “Whole phage genomics: a student-based approach,” from the National Science Foundation. Additional support came from the Center for Phage Technology, an Initial University Multidisciplinary Research Initiative supported by Texas A&M University and Texas AgriLife, and from the Department of Biochemistry and Biophysics. We thank the CPT staff for their advice and support. This announcement was prepared in partial fulfillment of the requirements for Bich464 Phage Genomics, an undergraduate course at Texas A&M University.

REFERENCES 1. Wang JT, Chang SC, Chen YC, Luh KT. 2000. Comparison of antimicrobial susceptibility of Citrobacter freundii isolates in two different time periods. J Microbiol Immunol Infect 33:258 –262. 2. Whalen JG, Mully TW, English JC III. 2007. Spontaneous Citrobacter freundii infection in an immunocompetent patient. Arch Dermatol 143: 124 –125. http://dx.doi.org/10.1001/archderm.143.1.124. 3. Poirel L, Ros A, Carricajo A, Berthelot P, Pozzetto B, Bernabeu S, Nordmann P. 2011. Extremely drug-resistant Citrobacter freundii isolate producing NDM-1 and other carbapenemases identified in a patient returning from India. Antimicrob Agents Chemother 55:447– 448. http:// dx.doi.org/10.1128/AAC.01305-10. 4. Abedon ST, Kuhl SJ, Blasdel BG, Kutter EM. 2011. Phage treatment of human infections. Bacteriophage 1:66 – 85. http://dx.doi.org/10.4161/ bact.1.2.15845.

Genome Announcements

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Citrobacter freundii and other Gram-negative opportunistic pathogens necessitate concern from the public health sector. Bacteriophages that kill such pathogens may be useful in the control and containment of these infections. Here, we describe the genome of a newly isolated T4-like myophage of C. freundii, Moon, and present its features.

Edwards et al.

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bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae. Virology 468 – 470C:421– 443. http://dx.doi.org/10.1016/ j.virol.2014.08.024. Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Rüger W. 2003. Bacteriophage T4 genome. Microbiol Mol Biol Rev 67:86 –156, table of contents. http://dx.doi.org/10.1128/MMBR.67.1.86-156.2003. Edgell DR, Gibb EA, Belfort M. 2010. Mobile DNA elements in T4 and related phages. Virol J 7:290. http://dx.doi.org/10.1186/1743-422X-7-290. McMillan S, Edenberg HJ, Radany EH, Friedberg RC, Friedberg EC. 1981. denV gene of bacteriophage T4 codes for both pyrimidine dimer-DNA glycosylase and apyrimidinic endonuclease activities. J Virol 40:211–223. Vaiskunaite R, Miller A, Davenport L, Mosig G. 1999. Two new early bacteriophage T4 genes, repEA and repEB, that are important for DNA replication initiated from origin E. J Bacteriol 181:7115–7125.

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5. Samonis G, Ho DH, Gooch GF, Rolston KV, Bodey GP. 1987. In vitro susceptibility of Citrobacter species to various antimicrobial agents. Antimicrob Agents Chemother 31:829 – 830. http://dx.doi.org/10.1128/ AAC.31.5.829. 6. Besemer J, Lomsadze A, Borodovsky M. 2001. GeneMarkS: a selftraining method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29:2607–2618. http://dx.doi.org/10.1093/nar/29.12.2607. 7. Liao WC, Ng WV, Lin IH, Syu WJ, Liu TT, Chang CH. 2011. T4-like genome organization of the Escherichia coli O157:H7 lytic phage AR1. J Virol 85:6567– 6578. http://dx.doi.org/10.1128/JVI.02378-10. 8. Myers EW, Miller W. 1988. Optimal alignments in linear space. Comput Appl Biosci 4:11–17. http://dx.doi.org/10.1093/bioinformatics/4.1.11. 9. Grose JH, Casjens SR. 2014. Understanding the enormous diversity of

Complete Genome Sequence of Citrobacter freundii Myophage Moon.

Citrobacter freundii and other Gram-negative opportunistic pathogens necessitate concern from the public health sector. Bacteriophages that kill such ...
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