Papers by Andrew Kropinski
The genome of the Pseudomonas aeruginosa generalized transducing bacteriophage F116
Gene, Feb 1, 2005
F116 is a temperate, pilus-specific, generalized transducing phage belonging to the Podoviridae v... more F116 is a temperate, pilus-specific, generalized transducing phage belonging to the Podoviridae virus family. Its genome is linear, ds, TR, and CP DNA with a GC content of 63.2%. The 65 195-bp genome contains 70 putative ORFs, only 16 of which showed sequence similarity to Pseudomonas genomic or phage genes. While the current literature suggests that F116 is a non-integrating phage that maintains itself as a plasmid during the lysogenic life cycle, a putative int gene was identified. Of the phage structural genes, only the portal protein could be identified by homology. Analysis of F116 structural protein by one-dimensional SDS-PAGE revealed approximately 15 bands. MALDI-TOF MS analysis identified the gene encoding the major capsid protein. This protein appears to undergo posttranslational cleavage giving rise to a smaller capsid protein.
Lysogenic Conversion in Bacteria of Importance to the Food Industry
ASM Press eBooks, Apr 9, 2014
This chapter focuses on the exotoxins produced by Escherichia coli/Shigella, Staphylococcus, and ... more This chapter focuses on the exotoxins produced by Escherichia coli/Shigella, Staphylococcus, and Clostridium botulinum phages, as well as on changes in lipopolysaccharide (LPS) structure and membrane protein compositions brought about by E. coli-and Salmonella-specific phages; the emphasis is on phage conversion activities that affect the major food- and waterborne pathogens. Researchers isolated two converting phages, H-19A and H-19B, from strain H-19. Another research group suggested that Shiga toxins may have evolved for the purpose of bacterial antipredator defense. The staphylococcal lysogenic conversion literature includes two well-documented examples of negative conversion, where staphylococcal phages (in many cases, phages carrying additional lysogenic conversion genes) insertionally inactivate chromosomal genes that encode important exoproteins. Staphylokinase may also contribute to bacterial colonization by interacting with the immune system of the host. Over the past decade, Salmonella serovar Anatum strains transformed by plasmids carrying various ɛ15 genes have been analyzed, using a variety of biological, immunological, and biochemical assays. This work has resulted in the identification of four ɛ15 genes whose protein products influence the structure of serovar Anatum LPS, namely genes. Sections of the chapter illustrate that some proteins encoded by phage conversion genes increase host offensive weapon repertoires, while others appear to increase host defensive capabilities.
Renaming of all phage genera
Salmonella Phages and Prophages—Genomics and Practical Aspects
Methods in molecular biology, 2007
Numerous bacteriophages specific to Salmonella have been isolated or identified as part of host g... more Numerous bacteriophages specific to Salmonella have been isolated or identified as part of host genome sequencing projects. Phylogenetic analysis of the sequenced phages, based on related protein content using CoreGenes, reveals that these viruses fall into five groupings (P27-like, P2-like, lambdoid, P22-like, and T7-like) and three outliers (epsilon15, KS7, and Felix O1). The P27 group is only represented by ST64B; the P2 group contains Fels-2, SopEphi, and PSP3; the lambdoid Salmonella phages include Gifsy-1, Gifsy-2, and Fels-1. The P22-like viruses include epsilon34, ES18, P22, ST104, and ST64T. The only member of the T7-like group is SP6. The properties of each of these phages are discussed, along with their role as agents of genetic exchange and as therapeutic agents and their involvement in phage typing.
Taxonomy proposal 2019: Create one new species Flavobacterium virus FLiP, in the new genus Finnlakevirus, in the new family Finnlakeviridae
Taxonomy proposal 2019: Create one new species Flavobacterium virus FLiP, in the new genus Finnlakevirus, in the new family Finnlakeviridae: ICTV Online: International Committee on Taxonomy of Viruses (ICTV)
Coliphage T7 receptors are present in Pseudomonasaeruginosa rough lipopolysaccharides
Biochemical and Biophysical Research Communications, Apr 1, 1981
ABSTRACT
The extraction and analysis of lipopolysaccharides from <i>Pseudomonas aeruginosa</i> strain PAO, and three rough mutants
Canadian Journal of Microbiology, Mar 1, 1979
Three spontaneously arising rough mutants of Pseudomonas aeruginosa have been isolated by selecti... more Three spontaneously arising rough mutants of Pseudomonas aeruginosa have been isolated by selection for resistance to virulent lipopolysaccharide (LPS) specific bacteriophages. In addition, the first phages specific for rough mutants of P. aeruginosa were isolated. Using these phage and autoagglutination patterns in 4% NaCl and acriflavine, these mutants could be clearly distinguished from the wild-type strain and each other. Chemical analysis of the LPS together with chromatographic resolution of the polysaccharide moieties showed alterations in both O-specific side chains and core regions.
Journal of Clinical Microbiology, May 1, 1989
The lipopolysaccharide (LPS) of Pseudomonas aeruginosa PAO1 contains two species of O polysacchar... more The lipopolysaccharide (LPS) of Pseudomonas aeruginosa PAO1 contains two species of O polysaccharide termed A and B bands. The high-molecular-weight B-band LPS determines the O specificity of the bacterium, while the antigenically distinct A-band LPS consists of only shorter-chain polysaccharides. Seven hybridomas secreting A-band-specific monoclonal antibodies were produced and used to study the LPS of standard and clinical strains. Although A-band antibodies did not agglutinate any of the serotype strains presently in the International Antigenic Typing Scheme, Western immunoblots revealed that Il of the 17 serotype strains possessed A-band LPS. In a group of 250 clinical isolates from patients with cystic fibrosis, 170 (68%) had A-band LPS on the basis of agglutination tests, but in silver-stained gels all were shown to be deficient in O-antigen-containing B band. Investigation of serial isolates from a single patient revealed a pattern of antigenic variation. During the course of the infection, serotypeable isolates became nontypeable, and the O antigen was replaced with A band as the major LPS antigen. These results suggest that A-band LPS may be the major LPS antigen in nontypeable clinical isolates and a common antigen among other P. aeruginosa strains.
Molecular and applied aspects
Preface Contributors Introduction Section 1: Bacteriophage Genomics 1. Preparation of Bacteriopha... more Preface Contributors Introduction Section 1: Bacteriophage Genomics 1. Preparation of Bacteriophage Lysates and Pure DNA Derek John Juan Pickard 2. Approaches to the Compositional Analysis of DNA Richard A. Manderville and Andrew M. Kropinski 3. Determination of Bacteriophage Genome Size by Pulsed-Field Gel Electrophoresis Erika Lingohr, Shelley Frost, and Roger P. Johnson 4. Preparation of a Phage DNA Fragment Library for Whole Genome Shotgun Sequencing Elizabeth J. Summer 5. PCR and Partial Sequencing of Bacteriophage Genomes Martha R. J. Clokie 6. In Silico Identification of Genes in Bacteriophage DNA Andrew M. Kropinski, Mark Borodovsky, Tim J. Carver, Ana M. Cerdeno-Tarraga, Aaron Darling, Alexandre Lomsadze, Padmanabhan Mahadevan, Paul Stothard, Donald Seto, Gary Van Domselaar, and David S. Wishart 7. Determining DNA Packaging Strategy by Analysis of the Termini of the Chromosomes in Tailed-Bacteriophage Virions Sherwood R. Casjens and Eddie B. Gilcrease 8. In silico Characterization of DNA Motifs with Particular Reference to Promoters and Terminators Rob Lavigne, Andre Villegas, and Andrew M. Kropinksi 9. Molecular Phylogenetics: Testing Evolutionary Hypotheses David A. Walsh and Adrian K. Sharma Section 2: Bacteriophage Transcriptomics and Proteomics 10. Preparation of RNA from Bacteria Infected with Bacteriophages: A Case Study from the Marine Unicellular Synechococcus sp. WH7803 Infected by Phage S-PM2 Jinyu Shan and Martha R. J. Clokie 11. Quantification of Host and Phage mRNA Expression during Infection Using Real-Time PCR Martha R. J. Clokie 12. Oligonucleotide Microarrays for Bacteriophage Expression Studies Andrew D.Millard and Bella Tiwari 13. Purification of Bacteriophages and SDS-PAGE Analysis of Phage Structural Proteins from Ghost Particles Pascale Boulanger 14. Phage Proteomics: Applications of Mass Spectrometry Rob Lavigne, Pieter-Jan Ceyssens, and J. Robben Section 3: Community Bacteriophage Approaches 15. Isolation Independent Methods of Characterizing Phage Communities 1: Strain Typing Using Fingerprinting Methods Clemens Pausz, Jessica L. Clasen, and Curtis A. Suttle 16. Isolation Independent Methods of Characterizing Phage Communities 2: Characterizing a Metagenome K. Eric Wommack, Shellie R. Bench, Jaysheel Bhavsar, David Mead, and Tom Hanson Section 4: Applied Aspects of Bacteriophage Biology 17. Phage Typing Irina Chirakadze, Ann Perets, and Rafiq Ahmed 18. A Genetic Screen to Identify Bacteriophage Lysins Raymond Schuch, Vincent A. Fischetti, and Daniel Nelson 19. General M13 Phage Display: M13 Phage Display in Identification and Characterization of Protein-Protein Interactions Kirsten Hertveldt, Tim Belien, and Guido Volckaert 20. Isolation of Monoclonal Antibody Fragments from Phage Display Libraries Mehdi Arbabi-Ghahroudi, Jamshid Tanha, and Roger MacKenzie 21. Internet Resources of Interest to Bacteriophage Workers Andrew M. Kropinski
This paper is dedicated to Hans-Wolfgang Ackermann, a pioneer of prokaryotic virus electron micro... more This paper is dedicated to Hans-Wolfgang Ackermann, a pioneer of prokaryotic virus electron microscopy and taxonomy, who died on February 12 th , 2017, at the age of 80. He was involved in the early stages of this study, and his input is dearly missed.
To rename all (523) existing bacterial virus and 2 archaeal virus species
Inexpensive protease source for improving the specificity of DNA hybridizations
PubMed, Feb 1, 1993
Complete genome sequence analysis of temperateErwiniabacteriophages 49 and 59
Journal of Basic Microbiology, Jun 6, 2019
To date, a small number of temperate phages are known to infect members of the genus Erwinia. In ... more To date, a small number of temperate phages are known to infect members of the genus Erwinia. In this study, the genomes of temperate phages vB_EhrS_49 and vB_EhrS_59 infecting Erwinia horticola, the causative agent of beech black bacteriosis in Ukraine, were sequenced and annotated. Their genomes reveal no significant similarity to that of any previously reported viruses of Enterobacteriaceae. At the same time, phages 49 and 59 share extensive nucleotide sequence identity across the regions encoding head assembly, DNA packaging, and lysis. Despite significant homology between structural modules, the organization of distal tail morphogenesis genes is different. Furthermore, a number of putative morons and DNA methylases have been found in both phage genomes. Due to the revealed synteny as well as the structure of lysogeny module, phages 49 and 59 are suggested to be novel members of the lambdoid phage group. Conservative structural genes together with varying homology across the nonstructural region of the genomes make phages 49 and 59 highly promising objects for studying the genetic recombination and evolution of microbial viruses. The obtained data may as well be helpful for better understanding of relationships among Erwinia species.
Campylobacter is recognized worldwide as the major etiologic agent in human diarrheoal disease, w... more Campylobacter is recognized worldwide as the major etiologic agent in human diarrheoal disease, with Campylobacter jejuni and Campylobacter coli being the most prevalent species. The reason for this high incidence is that once Campylobacter is introduced into a flock, infection spreads rapidly by environmental contamination and coprophagy. The problem of Campylobacter contamination of poultry is exacerbated following slaughter by cross-contamination from Campylobacter-positive to Campylobacter-negative carcasses during processing in the abattoir, showing that standard biosecurity measures on the processing plant are ineffective. Even if it were possible to reduce the level of carcass contamination, such measures would be costly, difficult to maintain and restrictive. Consequently, another strategy is to operate control measures on the farm and thus significantly reduce colonization with Campylobacter prior to slaughter.
Fems Microbiology Letters, Nov 1, 1984
A bacterium, as yet unidentified, has been isolated from floor dust by direct selection on minima... more A bacterium, as yet unidentified, has been isolated from floor dust by direct selection on minimal agar using L-glucitol (D-gulitol) as the sole carbon energy source. The bacterium possesses a constitutive enzyme which catalyzes the reaction: L-glucitol + NAD + ---, D-sorbose + NADH + H + . A new species of enzyme has been induced by L-arabinitol or ribitol, but not L-or D-glucito1, and the induction is only partially counteracted by the glucose-repression effect. The constitutive enzyme was purified by fractionation on Sephadex G-200 gel and chromatography on DEAE Biogel A. The enzyme required NAD +, but not NADP +, as a cofactor. It oxidizes also ribitol, xylitol and Larabinitol, but not D-arabinitol, lactitol or a variety of other commercially available alditols. The enzyme is not inhibited by 10 mM sodium azide but is totally inhibited by 0.1 mM potassium ferricyanide.
bioRxiv (Cold Spring Harbor Laboratory), Nov 16, 2017
It is almost a cliché that tailed bacteriophages of the order Caudovirales are the most abundant ... more It is almost a cliché that tailed bacteriophages of the order Caudovirales are the most abundant and diverse viruses in the world. Yet, their taxonomy still consists of a single order with just three families: Myoviridae , Siphoviridae , and Podoviridae . Thousands of newly discovered phage genomes have recently challenged this morphology-based classification, revealing that tailed bacteriophages are genomically even more diverse than once thought. Here, we evaluate a range of methods for bacteriophage taxonomy by using a particularly challenging group as an example, the Bacillus phage SPO1-related viruses of the myovirid subfamily Spounavirinae . Exhaustive phylogenetic and phylogenomic analyses indicate that the spounavirins are consistent with the taxonomic rank of family and should be divided into at least five subfamilies. This work is a case study for virus genomic taxonomy and the first step in an impending massive reorganization of the tailed bacteriophage taxonomy.
Genome Announcements, Aug 28, 2014
The complete genome of an Erwinia amylovora bacteriophage, vB_EamM_Ea35-70 (Ea35-70), is 271,084 ... more The complete genome of an Erwinia amylovora bacteriophage, vB_EamM_Ea35-70 (Ea35-70), is 271,084 bp, encodes 318 putative proteins, and contains one tRNA. Comparative analysis with other Myoviridae genomes suggests that Ea35-70 is related to the Phikzlikevirus genus within the family Myoviridae, since 26% of Ea35-70 proteins share homology to proteins in Pseudomonas phage KZ.
ICTV Virus Taxonomy Profile: Herelleviridae
Journal of General Virology, Apr 1, 2020
Members of the family Herelleviridae are bacterial viruses infecting members of the phylum Firmic... more Members of the family Herelleviridae are bacterial viruses infecting members of the phylum Firmicutes. The virions have myovirus morphology and virus genomes comprise a linear dsDNA of 125-170 kb. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Herelleviridae, which is available at ictv.global/report/herelleviridae.
Journal of Virology, Nov 1, 1981
We investigated the 4)PLS27 receptor in Pseudomonas aeruginosa strain PAO lipopolysaccharide (LPS... more We investigated the 4)PLS27 receptor in Pseudomonas aeruginosa strain PAO lipopolysaccharide (LPS) by analyzing a resistant mutant. This mutant, which was designated AK1282, had the most defective LPS yet reported for a P. aeruginosa rough mutant; this LPS contained only lipid A, 2-keto-3-deoxyoctonate, heptose, and alanine as major components. In addition, this LPS lacked galactosamine, which is present in the inner core of the LPS of other rough mutants. The loss of galactosamine but only a small decrease in the alanine content indicated that the core of strain PAO LPS differed from the core structure which has been suggested for the LPS of other well-characterized P. aeruginosa strains. Our analysis also indicated that galactosamine residues may be crucial for 4PLS27 receptor activity of the LPS. Electrodialysis of LPS and conversion to salt forms (sodium or triethylamine) influenced the phage-inactivating capacity of the LPS, as did the medium in which the inactivation occurred; experiments performed in 1/10-strength broth resulted in much lower PhIo (concentration of LPS causing a 50% decrease in the titer of phage during 1 h of incubation at 370C) values than experiments performed in regular-strength broth. Sonication of the LPS also increased the phage-inactivating capacities of the LPS prepara- tions. To try to resolve some of the controversy surrounding the role of Pseudomonas aerugi- nosa lipopolysaccharide (LPS) in pathogenesis, as well as in other properties of this organism, we isolated several LPS-specific phages (22, 23, 25, 28) and used them to enrich for a number of LPS-defective mutants (24, 27, 29). However, the most LPS-defective mutants (strains AK43 and AK1012) that we isolated by phage selection still contained 2-keto-3-deoxyoctonate (KDO), heptose, galactosamine, and alanine in the core polysaccharide (24, 25). This led to the success- ful search for a rough LPS-specific phage, des- ignated 4PLS27, which lysed these mutants and, in addition, was inactivated specifically by the isolated rough LPS (25). In this work we used 4PLS27 to isolate the most defective LPS mutant thus far described for P. aeruginosa. The LPS of this mutant lacks galactosamine, and this information is the first indication that the location of alanine in strain PAO LPS is different from the location of alanine in the LPS of other P. aeruginosa strains ). An analysis of the LPS of 4PLS27sensitive and 4PLS-resistant cells indicated that
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Papers by Andrew Kropinski