Genome sequence and characterization of a novel Pseudomonas putida phage, MiCath

Jaryenneh, James; Schoeniger, Joseph S.; Mageeney, Catherine M.

doi:10.1038/s41598-023-48634-z

Genome sequence and characterization of a novel Pseudomonas putida phage, MiCath

Journal Article · Fri Dec 08 23:00:00 EST 2023 · Scientific Reports

DOI:https://doi.org/10.1038/s41598-023-48634-z· OSTI ID:2229501

Jaryenneh, James; Schoeniger, Joseph S.; Mageeney, Catherine M.

Abstract

Pseudomonads are ubiquitous bacteria with importance in medicine, soil, agriculture, and biomanufacturing. We report a novel Pseudomonas putida phage, MiCath, which is the first known phage infecting P. putida S12, a strain increasingly used as a synthetic biology chassis. MiCath was isolated from garden soil under a tomato plant using P. putida S12 as a host and was also found to infect four other P. putida strains. MiCath has a ~ 61 kbp double-stranded DNA genome which encodes 97 predicted open reading frames (ORFs); functions could only be predicted for 48 ORFs using comparative genomics. Functions include structural phage proteins, other common phage proteins (e.g., terminase), a queuosine gene cassette, a cas4 exonuclease, and an endosialidase. Restriction digestion analysis suggests the queuosine gene cassette encodes a pathway capable of modification of guanine residues. When compared to other phage genomes, MiCath shares at most 74% nucleotide identity over 2% of the genome with any sequenced phage. Overall, MiCath is a novel phage with no close relatives, encoding many unique gene products.

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Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI ID:: 2229501

Alternate ID(s):: OSTI ID: 2311498

Journal Information:: Scientific Reports, Journal Name: Scientific Reports Journal Issue: 1 Vol. 13; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (40)

Protein Sequence Analysis Using the MPI Bioinformatics Toolkit Gabler, Felix; Nam, Seung‐Zin; Till, Sebastian Current Protocols in Bioinformatics, Vol. 72, Issue 1 https://doi.org/10.1002/cpbi.108	journal	December 2020
Endosialidases: Versatile Tools for the Study of Polysialic Acid Jakobsson, Elina; Schwarzer, David; Jokilammi, Anne Topics in Current Chemistry https://doi.org/10.1007/128_2012_349	book	January 2012
Pseudomonas putida—a versatile host for the production of natural products Loeschcke, Anita; Thies, Stephan Applied Microbiology and Biotechnology, Vol. 99, Issue 15 https://doi.org/10.1007/s00253-015-6745-4	journal	June 2015
Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee Turner, Dann; Shkoporov, Andrey N.; Lood, Cédric Archives of Virology, Vol. 168, Issue 2 https://doi.org/10.1007/s00705-022-05694-2	journal	January 2023
Frequency of morphological phage descriptions in the year 2000 Ackermann, H. -W. Archives of Virology, Vol. 146, Issue 5 https://doi.org/10.1007/s007050170120	journal	May 2001
A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core Zimmermann, Lukas; Stephens, Andrew; Nam, Seung-Zin Journal of Molecular Biology, Vol. 430, Issue 15 https://doi.org/10.1016/j.jmb.2017.12.007	journal	July 2018
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/s0022-2836(05)80360-2	journal	October 1990
Identification of protein coding regions by database similarity search Gish, Warren; States, David J. Nature Genetics, Vol. 3, Issue 3 https://doi.org/10.1038/ng0393-266	journal	March 1993
Fast gapped-read alignment with Bowtie 2 Langmead, Ben; Salzberg, Steven L. Nature Methods, Vol. 9, Issue 4 https://doi.org/10.1038/nmeth.1923	journal	March 2012
NIH Image to ImageJ: 25 years of image analysis Schneider, Caroline A.; Rasband, Wayne S.; Eliceiri, Kevin W. Nature Methods, Vol. 9, Issue 7 https://doi.org/10.1038/nmeth.2089	journal	June 2012
7-Deazaguanine modifications protect phage DNA from host restriction systems Hutinet, Geoffrey; Kot, Witold; Cui, Liang Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13384-y	journal	November 2019
Clades of huge phages from across Earth’s ecosystems Al-Shayeb, Basem; Sachdeva, Rohan; Chen, Lin-Xing Nature, Vol. 578, Issue 7795 https://doi.org/10.1038/s41586-020-2007-4	journal	February 2020
Restriction and modification of deoxyarchaeosine (dG+)-containing phage 9 g DNA Tsai, Rebecca; Corrêa, Ivan R.; Xu, Michael Y. Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-08864-4	journal	August 2017
Genome sequence and characterization of Streptomyces phage Pablito, representing a new species within the genus Janusvirus Ongenae, Véronique; Azeredo, Joana; Kropinski, Andrew M. Scientific Reports, Vol. 12, Issue 1 https://doi.org/10.1038/s41598-022-22784-y	journal	October 2022
The Growth of Bacteriophage Ellis, E. L. The Journal of General Physiology, Vol. 22, Issue 3 https://doi.org/10.1085/jgp.22.3.365	journal	January 1939
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry Journal of Computational Biology, Vol. 19, Issue 5 https://doi.org/10.1089/cmb.2012.0021	journal	May 2012
INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes Cook, Ryan; Brown, Nathan; Redgwell, Tamsin PHAGE, Vol. 2, Issue 4 https://doi.org/10.1089/phage.2021.0007	journal	December 2021
Identifying bacterial genes and endosymbiont DNA with Glimmer Delcher, Arthur L.; Bratke, Kirsten A.; Powers, Edwin C. Bioinformatics, Vol. 23, Issue 6 https://doi.org/10.1093/bioinformatics/btm009	journal	January 2007
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates Ecale Zhou, Carol L.; Malfatti, Stephanie; Kimbrel, Jeffrey Bioinformatics, Vol. 35, Issue 21 https://doi.org/10.1093/bioinformatics/btz258	journal	May 2019
PHANOTATE: a novel approach to gene identification in phage genomes McNair, Katelyn; Zhou, Carol; Dinsdale, Elizabeth A. Bioinformatics, Vol. 35, Issue 22 https://doi.org/10.1093/bioinformatics/btz265	journal	April 2019
Comparative Genomics of Bacteriophage of the Genus Seuratvirus Sazinas, Pavelas; Redgwell, Tamsin; Rihtman, Branko Genome Biology and Evolution, Vol. 10, Issue 1 https://doi.org/10.1093/gbe/evx275	journal	December 2017
An Improved General Amino Acid Replacement Matrix Le, S. Q.; Gascuel, O. Molecular Biology and Evolution, Vol. 25, Issue 7 https://doi.org/10.1093/molbev/msn067	journal	April 2008
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy Parks, Donovan H.; Chuvochina, Maria; Rinke, Christian Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab776	journal	September 2021
GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses Besemer, J.; Borodovsky, M. Nucleic Acids Research, Vol. 33, Issue Web Server https://doi.org/10.1093/nar/gki487	journal	July 2005
Diversity, specificity and molecular evolution of the lytic arsenal of Pseudomonas phages: in silico perspective Valero‐Rello, Ana Environmental Microbiology, Vol. 21, Issue 11 https://doi.org/10.1111/1462-2920.14767	journal	October 2019
Variability in progeny production and virulence of cyanophages determined at the single‐cell level Kirzner, Shay; Barak, Efrat; Lindell, Debbie Environmental Microbiology Reports, Vol. 8, Issue 5 https://doi.org/10.1111/1758-2229.12409	journal	May 2016
Large Pseudomonas phages isolated from barley rhizosphere Campbell, Joan I. A.; Albrechtsen, Merete; Sørensen, Jan FEMS Microbiology Ecology, Vol. 18, Issue 1 https://doi.org/10.1111/j.1574-6941.1995.tb00164.x	journal	January 2006
Complete Genome Sequence of Streptococcus pneumoniae Virulent Phage MS1 Kot, Witold; Sabri, Mourad; Gingras, Hélène Genome Announcements, Vol. 5, Issue 28 https://doi.org/10.1128/genomeA.00333-17	journal	July 2017
Complete Genome Sequences of Four Novel Escherichia coli Bacteriophages Belonging to New Phage Groups Carstens, Alexander B.; Kot, Witold; Hansen, Lars H. Genome Announcements, Vol. 3, Issue 4 https://doi.org/10.1128/genomeA.00741-15	journal	August 2015
Genomic and Biochemical Characterization of Acinetobacter Podophage Petty Reveals a Novel Lysis Mechanism and Tail-Associated Depolymerase Activity Hernandez-Morales, A. C.; Lessor, L. L.; Wood, T. L. Journal of Virology, Vol. 92, Issue 6 https://doi.org/10.1128/jvi.01064-17	journal	March 2018
Search for destruction factors of bacterial biofilms: Comparison of phage properties in a group of Pseudomonas putida bacteriophages and specificity of their halo-formation products Shaburova, O. V.; Krylov, S. V.; Veiko, V. P. Russian Journal of Genetics, Vol. 45, Issue 2 https://doi.org/10.1134/S1022795409020057	journal	February 2009
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
MUSCLE: a multiple sequence alignment method with reduced time and space complexity Edgar, Robert C. BMC Bioinformatics, Vol. 5, Issue 1, p. 113 https://doi.org/10.1186/1471-2105-5-113	journal	August 2004
Phylogenomics of Cas4 family nucleases Hudaiberdiev, Sanjarbek; Shmakov, Sergey; Wolf, Yuri I. BMC Evolutionary Biology, Vol. 17, Issue 1 https://doi.org/10.1186/s12862-017-1081-1	journal	November 2017
Pseudomonas 2.0: genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression Martínez-García, Esteban; Nikel, Pablo I.; Aparicio, Tomás Microbial Cell Factories, Vol. 13, Issue 1 https://doi.org/10.1186/s12934-014-0159-3	journal	November 2014
Four principles to establish a universal virus taxonomy Simmonds, Peter; Adriaenssens, Evelien M.; Zerbini, F. Murilo PLOS Biology, Vol. 21, Issue 2 https://doi.org/10.1371/journal.pbio.3001922	journal	February 2023
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010
Pf16 and phiPMW: Expanding the realm of Pseudomonas putida bacteriophages Magill, Damian J.; Krylov, Victor N.; Shaburova, Olga V. PLOS ONE, Vol. 12, Issue 9 https://doi.org/10.1371/journal.pone.0184307	journal	September 2017
Root inoculation with Pseudomonas putida KT2440 induces transcriptional and metabolic changes and systemic resistance in maize plants Planchamp, Chantal; Glauser, Gaetan; Mauch-Mani, Brigitte Frontiers in Plant Science, Vol. 5 https://doi.org/10.3389/fpls.2014.00719	journal	January 2015
VIRIDIC—A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses Moraru, Cristina; Varsani, Arvind; Kropinski, Andrew M. Viruses, Vol. 12, Issue 11 https://doi.org/10.3390/v12111268	journal	November 2020

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