scholarly journals Characterization of Bacteriophages Cp1 and Cp2, the Strain-Typing Agents for Xanthomonas axonopodis pv. citri

2013 ◽  
Vol 80 (1) ◽  
pp. 77-85 ◽  
Author(s):  
Abdelmonim Ali Ahmad ◽  
Megumi Ogawa ◽  
Takeru Kawasaki ◽  
Makoto Fujie ◽  
Takashi Yamada
Keyword(s):  
Genomic Sequence ◽  
Genomic Analysis ◽  
Citrus Canker ◽  
Open Reading Frames ◽  
Class Iii ◽  
Content Type ◽  
Xanthomonas Axonopodis ◽  
Group I ◽  
Initial Stage ◽  
Reading Frames

ABSTRACTThe strains ofXanthomonas axonopodispv. citri, the causative agent of citrus canker, are historically classified based on bacteriophage (phage) sensitivity. Nearly allX. axonopodispv. citri strains isolated from different regions in Japan are lysed by either phage Cp1 or Cp2; Cp1-sensitive (Cp1s) strains have been observed to be resistant to Cp2 (Cp2r) andvice versa. In this study, genomic and molecular characterization was performed for the typing agents Cp1 and Cp2. Morphologically, Cp1 belongs to theSiphoviridae. Genomic analysis revealed that its genome comprises 43,870-bp double-stranded DNA (dsDNA), with 10-bp 3′-extruding cohesive ends, and contains 48 open reading frames. The genomic organization was similar to that ofXanthomonasphage phiL7, but it lacked a group I intron in the DNA polymerase gene. Cp2 resembles morphologicallyEscherichia coliT7-like phages ofPodoviridae. The 42,963-bp linear dsDNA genome of Cp2 contained terminal repeats. The Cp2 genomic sequence has 40 open reading frames, many of which did not show detectable homologs in the current databases. By proteomic analysis, a gene cluster encoding structural proteins corresponding to the class III module of T7-like phages was identified on the Cp2 genome. Therefore, Cp1 and Cp2 were found to belong to completely different virus groups. In addition, we found that Cp1 and Cp2 use different molecules on the host cell surface as phage receptors and that host selection ofX. axonopodispv. citri strains by Cp1 and Cp2 is not determined at the initial stage by binding to receptors.

scholarly journals Complete Genome Sequence of Salmonella Bacteriophage SS3e

2012 ◽  
Vol 86 (18) ◽  
pp. 10253-10254 ◽  
Author(s):  
Sung-Hun Kim ◽  
Jeong-Hyun Park ◽  
Bok-Kwon Lee ◽  
Hyuk-Joon Kwon ◽  
Ji-Hyun Shin ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Sequence Analysis ◽  
Genomic Sequence ◽  
Enterobacter Cloacae ◽  
Open Reading Frames ◽  
Lytic Bacteriophage ◽  
Content Type ◽  
Double Stranded Dna ◽  
Genomic Sequence Analysis ◽  
Reading Frames

ASalmonellalytic bacteriophage, SS3e, was isolated, and its genome was sequenced completely. This phage is able to lyse not only variousSalmonellaserovars but alsoEscherichia coli,Shigella sonnei,Enterobacter cloacae, andSerratia marcescens, indicating a broad host specificity. Genomic sequence analysis of SS3e revealed a linear double-stranded DNA sequence of 40,793 bp harboring 58 open reading frames, which is highly similar toSalmonellaphages SETP13 and MB78.

scholarly journals Two Phages, phiIPLA-RODI and phiIPLA-C1C, Lyse Mono- and Dual-Species Staphylococcal Biofilms

2015 ◽  
Vol 81 (10) ◽  
pp. 3336-3348 ◽  
Author(s):  
Diana Gutiérrez ◽  
Dieter Vandenheuvel ◽  
Beatriz Martínez ◽  
Ana Rodríguez ◽  
Rob Lavigne ◽  
...  
Keyword(s):  
Phage Therapy ◽  
Gene Organization ◽  
Open Reading Frames ◽  
Group I Introns ◽  
High Similarity ◽  
Content Type ◽  
Staphylococcal Infections ◽  
Group I ◽  
Genes Encoding ◽  
Reading Frames

ABSTRACTPhage therapy is a promising option for fighting against staphylococcal infections. Two lytic phages, vB_SauM_phiIPLA-RODI (phiIPLA-RODI) and vB_SepM_phiIPLA-C1C (phiIPLA-C1C), belonging to theMyoviridaefamily and exhibiting wide host ranges, were characterized in this study. The complete genome sequences comprised 142,348 bp and 140,961 bp and contained 213 and 203 open reading frames, respectively. The gene organization was typical ofSpounavirinaemembers, with long direct terminal repeats (LTRs), genes grouped into modules not clearly separated from each other, and several group I introns. In addition, four genes encoding tRNAs were identified in phiIPLA-RODI. Comparative DNA sequence analysis showed high similarities with two phages, GH15 and 676Z, belonging to theTwort-like virusgenus (nucleotide identities of >84%); for phiIPLA-C1C, a high similarity with phage phiIBB-SEP1 was observed (identity of 80%). Challenge assays of phages phiIPLA-RODI and phiIPLA-C1C against planktonic staphylococcal cells confirmed their lytic ability, as they were able to remove 5 log units in 8 h. Exposure of biofilms to phages phiIPLA-RODI and phiIPLA-C1C reduced the amount of adhered bacteria to about 2 log units in both monospecies and dual-species biofilms, but phiIPLA-RODI turned out to be as effective as the mixture of both phages. Moreover, the frequencies of bacteriophage-insensitive mutants (BIMs) ofStaphylococcus aureusandS. epidermidiswith resistance to phiIPLA-RODI and phiIPLA-C1C were low, at 4.05 × 10−7± 2.34 × 10−9and 1.1 × 10−7± 2.08 × 10−9, respectively. Overall, a generally reduced fitness in the absence of phages was observed for BIMs, which showed a restored phage-sensitive phenotype in a few generations. These results confirm that lytic bacteriophages can be efficient biofilm-disrupting agents, supporting their potential as antimicrobials against staphylococcal infections.

scholarly journals Comparative Genomic Analysis of Acinetobacter oleivorans DR1 To Determine Strain-Specific Genomic Regions and Gentisate Biodegradation

2011 ◽  
Vol 77 (20) ◽  
pp. 7418-7424 ◽  
Author(s):  
Jaejoon Jung ◽  
Eugene L. Madsen ◽  
Che Ok Jeon ◽  
Woojun Park
Keyword(s):  
Metabolic Pathways ◽  
Genomic Analysis ◽  
Metal Resistance ◽  
Genomic Region ◽  
Open Reading Frames ◽  
Comparative Genomic ◽  
Content Type ◽  
Large Size ◽  
Genomic Regions ◽  
Reading Frames

ABSTRACTThe comparative genomics ofAcinetobacter oleivoransDR1 assayed withA. baylyiADP1,A. calcoaceticusPHEA-2, andA. baumanniiATCC 17978 revealed that the incorporation of phage-related genomic regions and the absence of transposable elements have contributed to the large size (4.15 Mb) of the DR1 genome. A horizontally transferred genomic region and a higher proportion of transcriptional regulator- and signal peptide-coding genes were identified as characteristics of the DR1 genome. Incomplete glucose metabolism, metabolic pathways of aromatic compounds, biofilm formation, antibiotics and metal resistance, and natural competence genes were conserved in four compared genomes. Interestingly, only strain DR1 possesses gentisate 1,2-dioxygenase (nagI) and grows on gentisate, whereas other species cannot. Expression of thenagIgene was upregulated during gentisate utilization, and four downstream open reading frames (ORFs) were cotranscribed, supporting the notion that gentisate metabolism is a unique characteristic of strain DR1. The genomic analysis of strain DR1 provides additional insights into the function, ecology, and evolution ofAcinetobacterspecies.

scholarly journals Genomic Sequence of Bacteriophage ATCC 8074-B1 and Activity of Its Endolysin and Engineered Variants against Clostridium sporogenes

2012 ◽  
Vol 78 (10) ◽  
pp. 3685-3692 ◽  
Author(s):  
Melinda J. Mayer ◽  
Michael J. Gasson ◽  
Arjan Narbad
Keyword(s):  
Catalytic Domain ◽  
Genomic Sequence ◽  
Open Reading Frames ◽  
Clostridium Tyrobutyricum ◽  
Lytic Bacteriophage ◽  
Clostridium Sporogenes ◽  
Content Type ◽  
Terminal Domain ◽  
Content Sequencing ◽  
Reading Frames

ABSTRACTLytic bacteriophage ATCC 8074-B1 produces large plaques on its hostClostridium sporogenes. Sequencing of the 47,595-bp genome allowed the identification of 82 putative open reading frames, including those encoding proteins for head and tail morphogenesis and lysis. However, sequences commonly associated with lysogeny were absent. ORF 22 encodes an endolysin, CS74L, that shows homology toN-acetylmuramoyl-l-alanine amidases, and when expressed inEscherichia coli, the protein causes effective lysis ofC. sporogenescells when added externally. CS74L was also active onClostridium tyrobutyricumandClostridium acetobutylicum. The catalytic domain expressed alone (CS74L1–177) exhibited a similar activity and the same host range as the full-length endolysin. A chimeric endolysin consisting of the CS74L catalytic domain fused to the C-terminal domain of endolysin CD27L, derived fromClostridium difficilebacteriophage ΦCD27, was produced. This chimera (CSCD) lysedC. sporogenescells with an activity equivalent to that of the catalytic domain alone. In contrast, the CD27L C-terminal domain reduced the efficacy of the CS74L catalytic domain when tested againstC. tyrobutyricum. The addition of the CD27L C-terminal domain did not enable the lysin to targetC. difficileor other CD27L-sensitive bacteria.

scholarly journals Mitochondrial Intronic Open Reading Frames in Podospora: Mobility and Consecutive Exonic Sequence Variations

Genetics ◽  
1996 ◽  
Vol 143 (2) ◽  
pp. 777-788 ◽  
Author(s):  
Carole H Sellem ◽  
Yves d'Aubenton-Carafa ◽  
Michèle Rossignol ◽  
Léon Belcour
Keyword(s):  
Mitochondrial Genome ◽  
Open Reading Frames ◽  
Nucleotide Substitutions ◽  
Sequence Comparisons ◽  
Modular Evolution ◽  
Group I ◽  
Sequence Variations ◽  
Type Strains ◽  
Reading Frames ◽  
Adjacent Exon

Abstract The mitochondrial genome of 23 wild-type strains belonging to three different species of The mitochondrial genome the filamentous fungus Podospora was examined. Among the 15 optional sequences identified are two intronic reading frames, nad1-i4-orf1 and cox1-i7-orf2. We show that the presence of these sequences was strictly correlated with tightly clustered nucleotide substitutions in the adjacent exon. This correlation applies to the presence or absence of closely related open reading frames (ORFs), found at the same genetic locations, in all the Pyrenomycete genera examined. The recent gain of these optional ORFs in the evolution of the genus Podospora probably account for such sequence differences. In the homoplasmic progeny from heteroplasmons constructed between Podospora strains differing by the presence of these optional ORFs, nad1-i4-orf1 and cox1-i7-orf2 appeared highly invasive. Sequence comparisons in the nad1-i4 intron of various strains of the Pyrenomycete family led us to propose a scenario of its evolution that includes several events of loss and gain of intronic ORFs. These results strongly reinforce the idea that group I intronic ORFs are mobile elements and that their transfer, and comcomitant modification of the adjacent exon, could participate in the modular evolution of mitochondrial genomes.

scholarly journals Characterization and Genome Analysis of Staphylococcus aureus Podovirus CSA13 and Its Anti-Biofilm Capacity

Viruses ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 54 ◽  
Author(s):  
Yoyeon Cha ◽  
Jihwan Chun ◽  
Bokyung Son ◽  
Sangryeol Ryu
Keyword(s):  
Staphylococcus Aureus ◽  
Biocontrol Agent ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Experimental Setting ◽  
Human Pathogens ◽  
Bacteriophage Therapy ◽  
Chromosomal Structure ◽  
Inhibition Effect ◽  
Reading Frames

Staphylococcus aureus is one of the notable human pathogens that can be easily encountered in both dietary and clinical surroundings. Among various countermeasures, bacteriophage therapy is recognized as an alternative method for resolving the issue of antibiotic resistance. In the current study, bacteriophage CSA13 was isolated from a chicken, and subsequently, its morphology, physiology, and genomics were characterized. This Podoviridae phage displayed an extended host inhibition effect of up to 23 hours of persistence. Its broad host spectrum included methicillin susceptible S. aureus (MSSA), methicillin resistant S. aureus (MRSA), local S. aureus isolates, as well as non-aureus staphylococci strains. Moreover, phage CSA13 could successfully remove over 78% and 93% of MSSA and MRSA biofilms in an experimental setting, respectively. Genomic analysis revealed a 17,034 bp chromosome containing 18 predicted open reading frames (ORFs) without tRNAs, representing a typical chromosomal structure of the staphylococcal Podoviridae family. The results presented here suggest that phage CSA13 can be applicable as an effective biocontrol agent against S. aureus.

scholarly journals Genomic Sequence of Rhesus Cytomegalovirus 180.92: Insights into the Coding Potential of Rhesus Cytomegalovirus

2006 ◽  
Vol 80 (8) ◽  
pp. 4179-4182 ◽  
Author(s):  
Pierre Rivailler ◽  
Amitinder Kaur ◽  
R. Paul Johnson ◽  
Fred Wang
Keyword(s):  
Genomic Sequence ◽  
Open Reading Frames ◽  
Rhesus Cytomegalovirus ◽  
Human Cmv ◽  
Coding Capacity ◽  
Coding Potential ◽  
Reading Frames ◽  
Genetic Rearrangements

ABSTRACT A pathogenic isolate of rhesus cytomegalovirus (rhCMV 180.92) was cloned, sequenced, and annotated. Comparisons with the published rhCMV 68.1 genome revealed 8 open reading frames (ORFs) in isolate 180.92 that are absent in 68.1, 10 ORFs in 68.1 that are absent in 180.92, and 34 additional ORFs that were not previously annotated. Most of the differences appear to be due to genetic rearrangements in both isolates from a region that is frequently altered in human CMV (hCMV) during in vitro passage. These results indicate that the rhCMV ORF repertoire is larger than previously recognized. Like hCMV, understanding of the complete coding capacity of rhCMV is complicated by genomic instability and may require comparisons with additional isolates in vitro and in vivo.

scholarly journals Two Unrelated 8-Vinyl Reductases Ensure Production of Mature Chlorophylls in Acaryochloris marina

2016 ◽  
Vol 198 (9) ◽  
pp. 1393-1400 ◽  
Author(s):  
Guangyu E. Chen ◽  
Andrew Hitchcock ◽  
Philip J. Jackson ◽  
Roy R. Chaudhuri ◽  
Mark J. Dickman ◽  
...  
Keyword(s):  
Transcriptional Control ◽  
Sequence Similarity ◽  
Open Reading Frames ◽  
High Sequence Similarity ◽  
Content Type ◽  
Ethyl Group ◽  
Acaryochloris Marina ◽  
Vinyl Group ◽  
Vinyl Reductase ◽  
Reading Frames

ABSTRACTThe major photopigment of the cyanobacteriumAcaryochloris marinais chlorophylld, while its direct biosynthetic precursor, chlorophylla, is also present in the cell. These pigments, along with the majority of chlorophylls utilized by oxygenic phototrophs, carry an ethyl group at the C-8 position of the molecule, having undergone reduction of a vinyl group during biosynthesis. Two unrelated classes of 8-vinyl reductase involved in the biosynthesis of chlorophylls are known to exist, BciA and BciB. The genome ofAcaryochloris marinacontains open reading frames (ORFs) encoding proteins displaying high sequence similarity to BciA or BciB, although they are annotated as genes involved in transcriptional control (nmrA) and methanogenesis (frhB), respectively. These genes were introduced into an 8-vinyl chlorophylla-producing ΔbciBstrain ofSynechocystissp. strain PCC 6803, and both were shown to restore synthesis of the pigment with an ethyl group at C-8, demonstrating their activities as 8-vinyl reductases. We propose thatnmrAandfrhBbe reassigned asbciAandbciB, respectively; transcript and proteomic analysis ofAcaryochloris marinareveal that bothbciAandbciBare expressed and their encoded proteins are present in the cell, possibly in order to ensure that all synthesized chlorophyll pigment carries an ethyl group at C-8. Potential reasons for the presence of two 8-vinyl reductases in this strain, which is unique for cyanobacteria, are discussed.IMPORTANCEThe cyanobacteriumAcaryochloris marinais the best-studied phototrophic organism that uses chlorophylldfor photosynthesis. Unique among cyanobacteria sequenced to date, its genome contains ORFs encoding two unrelated enzymes that catalyze the reduction of the C-8 vinyl group of a precursor molecule to an ethyl group. Carrying a reduced C-8 group may be of particular importance to organisms containing chlorophylld. Plant genomes also contain orthologs of both of these genes; thus, the bacterial progenitor of the chloroplast may also have contained bothbciAandbciB.

scholarly journals First Staphylococcal Cassette ChromosomemecContaining amecB-Carrying Gene Complex Independent of Transposon Tn6045in a Macrococcus caseolyticus Isolate from a Canine Infection

2015 ◽  
Vol 59 (8) ◽  
pp. 4577-4583 ◽  
Author(s):  
Elena Gómez-Sanz ◽  
Sybille Schwendener ◽  
Andreas Thomann ◽  
Stefanie Gobeli Brawand ◽  
Vincent Perreten
Keyword(s):  
Integration Site ◽  
Direct Repeat ◽  
Open Reading Frames ◽  
Gene Complex ◽  
Direct Repeats ◽  
Content Type ◽  
Canine Infection ◽  
The Right ◽  
Lactamase Gene ◽  
Reading Frames

ABSTRACTA methicillin-resistantmecB-positiveMacrococcus caseolyticus(strain KM45013) was isolated from the nares of a dog with rhinitis. It contained a novel 39-kb transposon-defective completemecB-carrying staphylococcal cassette chromosomemecelement (SCCmecKM45013). SCCmecKM45013contained 49 coding sequences (CDSs), was integrated at the 3′ end of the chromosomalorfXgene, and was delimited at both ends by imperfect direct repeats functioning as integration site sequences (ISSs). SCCmecKM45013presented two discontinuous regions of homology (SCCmeccoverage of 35%) to the chromosomal and transposon Tn6045-associated SCCmec-like element ofM. caseolyticusJCSC7096: (i) themecgene complex (98.8% identity) and (ii) theccr-carrying segment (91.8% identity). Themecgene complex, located at the right junction of the cassette, also carried the β-lactamase geneblaZm(mecRm-mecIm-mecB-blaZm). SCCmecKM45013contained two cassette chromosome recombinase genes,ccrAm2andccrBm2, which shared 94.3% and 96.6% DNA identity with those of the SCCmec-like element of JCSC7096 but shared less than 52% DNA identity with the staphylococcalccrABandccrCgenes. Three distinct extrachromosomal circularized elements (the entire SCCmecKM45013, ΨSCCmecKM45013lacking theccrgenes, and SCCKM45013lackingmecB) flanked by one ISS copy, as well as the chromosomal regions remaining after excision, were detected. An unconventional circularized structure carrying themecBgene complex was associated with two extensive direct repeat regions, which enclosed two open reading frames (ORFs) (ORF46 and ORF51) flanking the chromosomalmecB-carrying gene complex. This study revealedM. caseolyticusas a potential disease-associated bacterium in dogs and also unveiled an SCCmecelement carryingmecBnot associated with Tn6045in the genusMacrococcus.

scholarly journals Bacteriophages LIMElight and LIMEzero of Pantoea agglomerans, Belonging to the “phiKMV-Like Viruses”

2011 ◽  
Vol 77 (10) ◽  
pp. 3443-3450 ◽  
Author(s):  
Evelien M. Adriaenssens ◽  
Pieter-Jan Ceyssens ◽  
Vincent Dunon ◽  
Hans-Wolfgang Ackermann ◽  
Johan Van Vaerenbergh ◽  
...  
Keyword(s):  
Soil Samples ◽  
Pantoea Agglomerans ◽  
Open Reading Frames ◽  
Human Pathogen ◽  
Content Type ◽  
Host Diversity ◽  
Double Stranded Dna ◽  
Opportunistic Human Pathogen ◽  
Reading Frames

ABSTRACTPantoea agglomeransis a common soil bacterium used in the biocontrol of fungi and bacteria but is also an opportunistic human pathogen. It has been described extensively in this context, but knowledge of bacteriophages infecting this species is limited. Bacteriophages LIMEzero and LIMElight ofP. agglomeransare lytic phages, isolated from soil samples, belonging to thePodoviridaeand are the firstPantoeaphages of this family to be described. The double-stranded DNA (dsDNA) genomes (43,032 bp and 44,546 bp, respectively) encode 57 and 55 open reading frames (ORFs). Based on the presence of an RNA polymerase in their genomes and their overall genome architecture, these phages should be classified in the subfamily of theAutographivirinae, within the genus of the “phiKMV-like viruses.” Phylogenetic analysis of all the sequenced members of theAutographivirinaesupports the classification of phages LIMElight and LIMEzero as members of the “phiKMV-like viruses” and corroborates the subdivision into the different genera. These data expand the knowledge ofPantoeaphages and illustrate the wide host diversity of phages within the “phiKMV-like viruses.”

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