scholarly journals Characterization of Lactococcus lactis Phage 949 and Comparison with Other Lactococcal Phages

2010 ◽  
Vol 76 (20) ◽  
pp. 6843-6852 ◽  
Author(s):  
Julie E. Samson ◽  
Sylvain Moineau
Keyword(s):  
Lactococcus Lactis ◽  
Defense Mechanisms ◽  
Gc Content ◽  
Tail Length ◽  
Open Reading Frames ◽  
Phage Group ◽  
Double Stranded Dna ◽  
Group I ◽  
Sds Page ◽  
Genetic Clusters

ABSTRACT The virulent Lactococcus lactis phage 949 was isolated in 1975 from cheese whey in New Zealand. This phage is a member of the Siphoviridae family and of a rare lactococcal phage group that bears its name (949 group). It has an icosahedral capsid (79-nm diameter) and a very long noncontractile tail (length, 500 nm; width, 12 nm). It infected 7 of 59 tested L. lactis strains, a somewhat expanded host range for a rare lactococcal phage. The abortive phage infection defense mechanisms AbiQ and AbiT strongly inhibited the multiplication of phage 949, but AbiK and AbiV did not. Its double-stranded DNA (dsDNA) genome of 114,768 bp is, to date, the largest among lactococcal phages. Its GC content was calculated at 32.7%, which is the lowest reported for a lactococcal phage. Its 154 open reading frames (ORFs) share limited identity with database sequences. In addition, terminal redundancy was observed as well as the presence of six tRNAs, one group I intron, and putative recombinases. SDS-PAGE coupled with mass spectrometry identified 13 structural proteins. The genomes of the members of the 10 currently known L. lactis phage groups were used to construct a proteomic tree. Each L. lactis phage group separated into distinct genetic clusters, validating the current classification scheme. Of note, members of the polythetic P335 groups were clearly separated into subgroups.

scholarly journals Isolation and characterization of bacteriophages from India, with lytic activity againstMycobacterium tuberculosis

2018 ◽  
Vol 64 (7) ◽  
pp. 483-491 ◽  
Author(s):  
Urmi Bajpai ◽  
Abhishek Kumar Mehta ◽  
Kandasamy Eniyan ◽  
Avni Sinha ◽  
Ankita Ray ◽  
...  
Keyword(s):  
Antimicrobial Agents ◽  
Sequence Similarity ◽  
Gc Content ◽  
Polymerase Chain Reaction Analysis ◽  
Open Reading Frames ◽  
Genome Maintenance ◽  
Isolation And Characterization ◽  
Virion Release ◽  
Double Stranded Dna ◽  
Transmission Electron

Bacteriophages are being considered as a promising natural resource for the development of alternative strategies against mycobacterial diseases, especially in the context of the wide-spread occurrence of drug resistance among the clinical isolates of Mycobacterium tuberculosis. However, there is not much information documented on mycobacteriophages from India. Here, we report the isolation of 17 mycobacteriophages using Mycobacterium smegmatis as the bacterial host, where 9 phages also lyse M. tuberculosis H37Rv. We present detailed analysis of one of these mycobacteriophages — PDRPv. Transmission electron microscopy and polymerase chain reaction analysis (of a conserved region within the TMP gene) show PDRPv to belong to the Siphoviridae family and B1 subcluster, respectively. The genome (69 110 bp) of PDRPv is circularly permuted double-stranded DNA with ∼66% GC content and has 106 open reading frames (ORFs). On the basis of sequence similarity and conserved domains, we have assigned function to 28 ORFs and have broadly categorized them into 6 groups that are related to replication and genome maintenance, DNA packaging, virion release, structural proteins, lysogeny-related genes and endolysins. The present study reports the occurrence of novel antimycobacterial phages in India and highlights their potential to contribute to our understanding of these phages and their gene products as potential antimicrobial agents.

scholarly journals Genome Analysis of a Novel Clade b Betabaculovirus Isolated from the Legume Pest Matsumuraeses phaseoli (Lepidoptera: Tortricidae)

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1068
Author(s):  
Ruihao Shu ◽  
Qian Meng ◽  
Lin Miao ◽  
Hongbin Liang ◽  
Jun Chen ◽  
...  
Keyword(s):  
Northeast Asia ◽  
Gc Content ◽  
Open Reading Frames ◽  
Chinese Medicinal Herb ◽  
Double Stranded Dna ◽  
Clade B ◽  
Potential Biocontrol Agent ◽  
Conserved Genes ◽  
Inhibitors Of Apoptosis Proteins ◽  
Lepidopteran Pest

Matsumuraeses phaseoli is a Lepidopteran pest that primarily feeds on numerous species of cultivated legumes, such as Glycine and Phaseolus. It is widely distributed in northeast Asia. A novel granulovirus, designated as Matsumuraeses phaseoli granulovirus (MaphGV), was isolated from pathogenic M. phaseoli larvae that dwell in rolled leaves of Astragalus membranaceus, a Chinese medicinal herb. In this study, using next-generation sequencing, we report the complete genome of MaphGV. MaphGV genome comprises a double-stranded DNA of 116,875 bp, with 37.18% GC content. It has 128 hypothetical open reading frames (ORFs). Among them, 38 are baculovirus core genes, 18 are lepidopteran baculovirus conserved genes, and 5 are unique to Baculoviridae. MaphGV has one baculovirus repeat ORF (bro) and three inhibitors of apoptosis proteins (iap), including a newfound iap-6. We found two atypical baculoviral homologous regions (hrs) and four direct repeats (drs) in the MaphGV genome. Based on phylogenetic analysis, MaphGV belongs to Clade b of Betabaculovirus and is closely related to Cydia pomonellagranulovirus (CpGV) and Cryptophlebia leucotretagranulovirus (CrleGV). This novel baculovirus discovery and sequencing are invaluable in understanding the evolution of baculovirus and MaphGV may be a potential biocontrol agent against the bean ravaging pest.

scholarly journals A Virulent Phage Infecting Lactococcus garvieae, with Homology to Lactococcus lactis Phages

2015 ◽  
Vol 81 (24) ◽  
pp. 8358-8365 ◽  
Author(s):  
Giovanni Eraclio ◽  
Denise M. Tremblay ◽  
Alexia Lacelle-Côté ◽  
Simon J. Labrie ◽  
Maria Grazia Fortina ◽  
...  
Keyword(s):  
Lactococcus Lactis ◽  
Common Ancestor ◽  
Burst Size ◽  
Open Reading Frames ◽  
Content Type ◽  
Virulent Phage ◽  
Lactococcus Garvieae ◽  
Double Stranded Dna ◽  
Compost Soil ◽  
Reading Frames

ABSTRACTA new virulent phage belonging to theSiphoviridaefamily and able to infectLactococcus garvieaestrains was isolated from compost soil. Phage GE1 has a prolate capsid (56 by 38 nm) and a long noncontractile tail (123 nm). It had a burst size of 139 and a latent period of 31 min. Its host range was limited to only twoL. garvieaestrains out of 73 tested. Phage GE1 has a double-stranded DNA genome of 24,847 bp containing 48 predicted open reading frames (ORFs). Putative functions could be assigned to only 14 ORFs, and significant matches in public databases were found for only 17 ORFs, indicating that GE1 is a novel phage and its genome contains several new viral genes and encodes several new viral proteins. Of these 17 ORFs, 16 were homologous to deduced proteins of virulent phages infecting the dairy bacteriumLactococcus lactis, including previously characterized prolate-headed phages. Comparative genome analysis confirmed the relatedness ofL. garvieaephage GE1 toL. lactisphages c2 (22,172 bp) and Q54 (26,537 bp), although its genome organization was closer to that of phage c2. Phage GE1 did not infect any of the 58L. lactisstrains tested. This study suggests that phages infecting different lactococcal species may have a common ancestor.

scholarly journals Mitochondrial genome evolution of placozoans: gene rearrangements and repeat expansions

2020 ◽  
Author(s):  
Hideyuki Miyazawa ◽  
Hans-Jürgen Osigus ◽  
Sarah Rolfes ◽  
Kai Kamm ◽  
Bernd Schierwater ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gc Content ◽  
Distribution Patterns ◽  
Sister Group ◽  
Open Reading Frames ◽  
Mitochondrial Genomes ◽  
Inverted Repeats ◽  
Protein Coding ◽  
Group I ◽  
Phylogenomic Analyses

Abstract Placozoans, non-bilaterian animals with the simplest known metazoan bauplan, are currently classified into 20 haplotypes belonging to three genera, Polyplacotoma, Trichoplax, and Hoilungia. The latter two comprise two and five clades, respectively. In Trichoplax and Hoilungia, previous studies on six haplotypes belonging to four different clades have shown that their mtDNA are circular chromosomes of 32-43 kbp in size, which encode 12 protein-coding genes, 24 tRNAs, and 2 rRNAs. These mitochondrial genomes (mitogenomes) also show unique features rarely seen in other metazoans, including open reading frames (ORFs) of unknown function, and group I and II introns. Here, we report seven new mitogenomes, covering the five previously described haplotypes H2, H17, H19, H9, and H11, as well as two new haplotypes, H23 (clade III) and H24 (clade VII). The overall gene content is shared between all placozoan mitochondrial genomes, but genome sizes, gene orders, and several exon-intron boundaries vary among clades. Phylogenomic analyses strongly support a tree topology different from previous 16S rRNA analyses, with clade VI as the sister group to all other Hoilungia clades. We found small inverted repeats in all 13 mitochondrial genomes of the Trichoplax and Hoilungia genera and evaluated their distribution patterns among haplotypes. Since P. mediterranea (H0), the sister to the remaining haplotypes, has a small mitochondrial genome with few small inverted repeats and ORFs, we hypothesized that the proliferation of inverted repeats and ORFs substantially contributed to the observed increase in the size and GC content of the Trichoplax and Hoilungia mitochondrial genomes.

scholarly journals Three Novel Virophage Genomes Discovered from Yellowstone Lake Metagenomes

2014 ◽  
Vol 89 (2) ◽  
pp. 1278-1285 ◽  
Author(s):  
Jinglie Zhou ◽  
Dawei Sun ◽  
Alyson Childers ◽  
Timothy R. McDermott ◽  
Yongjie Wang ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Evolutionary Relationship ◽  
Gc Content ◽  
Open Reading Frames ◽  
Lake Ecosystem ◽  
Photic Zone ◽  
Yellowstone Lake ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Unique Distribution

ABSTRACTVirophages are a unique group of circular double-stranded DNA viruses that are considered parasites of giant DNA viruses, which in turn are known to infect eukaryotic hosts. In this study, the genomes of three novel Yellowstone Lake virophages (YSLVs)—YSLV5, YSLV6, and YSLV7—were identified from Yellowstone Lake through metagenomic analyses. The relative abundance of these three novel virophages and previously identified Yellowstone Lake virophages YSLV1 to -4 were determined in different locations of the lake, revealing that most of the sampled locations in the lake, including both mesophilic and thermophilic habitats, had multiple virophage genotypes. This likely reflects the diverse habitats or diversity of the eukaryotic hosts and their associated giant viruses that serve as putative hosts for these virophages. YSLV5 has a 29,767-bp genome with 32 predicted open reading frames (ORFs), YSLV6 has a 24,837-bp genome with 29 predicted ORFs, and YSLV7 has a 23,193-bp genome with 26 predicted ORFs. Based on multilocus phylogenetic analysis, YSLV6 shows a close evolutionary relationship with YSLV1 to -4, whereas YSLV5 and YSLV7 are distantly related to the others, and YSLV7 represents the fourth novel virophage lineage. In addition, the genome of YSLV5 has a G+C content of 51.1% that is much higher than all other known virophages, indicating a unique host range for YSLV5. These results suggest that virophages are abundant and have diverse genotypes that likely mirror diverse giant viral and eukaryotic hosts within the Yellowstone Lake ecosystem.IMPORTANCEThis study discovered novel virophages present within the Yellowstone Lake ecosystem using a conserved major capsid protein as a phylogenetic anchor for assembly of sequence reads from Yellowstone Lake metagenomic samples. The three novel virophage genomes (YSLV5 to -7) were completed by identifying specific environmental samples containing these respective virophages, and closing gaps by targeted PCR and sequencing. Most of the YSLV genotypes were associated primarily with photic-zone and nonhydrothermal samples; however, YSLV5 had a unique distribution with an occurrence in vent samples similar to that in photic-zone samples and with a higher GC content that suggests a distinct host and habitat compared to other YSLVs. In addition, genome content and phylogenetic analyses indicate that YSLV5 and YSLV7 are distinct from known virophages and that additional as-yet-uncharacterized virophages are likely present within the Yellowstone Lake ecosystem.

scholarly journals Morphology, Genome Sequence, and Structural Proteome of Type Phage P335 from Lactococcus lactis

2008 ◽  
Vol 74 (15) ◽  
pp. 4636-4644 ◽  
Author(s):  
Simon J. Labrie ◽  
Jytte Josephsen ◽  
Horst Neve ◽  
Finn K. Vogensen ◽  
Sylvain Moineau
Keyword(s):  
Lactococcus Lactis ◽  
Open Reading Frames ◽  
Comparative Genomic ◽  
Double Stranded Dna ◽  
Virulent Type ◽  
Liquid Chromatography Tandem Mass ◽  
Late Transcription ◽  
Type Phage ◽  
Conserved Gene ◽  
High Level

ABSTRACT Lactococcus lactis phage P335 is a virulent type phage for the species that bears its name and belongs to the Siphoviridae family. Morphologically, P335 resembled the L. lactis phages TP901-1 and Tuc2009, except for a shorter tail and a different collar/whisker structure. Its 33,613-bp double-stranded DNA genome had 50 open reading frames. Putative functions were assigned to 29 of them. Unlike other sequenced genomes from lactococcal phages belonging to this species, P335 did not have a lysogeny module. However, it did carry a dUTPase gene, the most conserved gene among this phage species. Comparative genomic analyses revealed a high level of identity between the morphogenesis modules of the phages P335, ul36, TP901-1, and Tuc2009 and two putative prophages of L. lactis SK11. Differences were noted in genes coding for receptor-binding proteins, in agreement with their distinct host ranges. Sixteen structural proteins of phage P335 were identified by liquid chromatography-tandem mass spectrometry. A 2.8-kb insertion was recognized between the putative genes coding for the activator of late transcription (Alt) and the small terminase subunit (TerS). Four genes within this region were autonomously late transcribed and possibly under the control of Alt. Three of the four deduced proteins had similarities with proteins from Streptococcus pyogenes prophages, suggesting that P335 acquired this module from another phage genome. The genetic diversity of the P335 species indicates that they are exceptional models for studying the modular theory of phage evolution.

scholarly journals Complete Genome Analysis of a Novel Alcaligenes Faecalis Phage vB_Af_QDWS595

2021 ◽  
Author(s):  
Yujie Jing ◽  
Hong Lin ◽  
Houqi Ning ◽  
Jingxue Wang
Keyword(s):  
Genome Analysis ◽  
Gc Content ◽  
Alcaligenes Faecalis ◽  
Open Reading Frames ◽  
Lytic Phage ◽  
Double Stranded Dna ◽  
Phylogeny Analysis ◽  
The Family ◽  
Complete Genome Analysis ◽  
Reading Frames

Abstract A novel lytic phage named vB_Af_QDWS595 against Alcaligenes faecalis was isolated and characterized in this study. The genome of phage vB_Af_QDWS595 was sequenced and analyzed, and the result revealed that the phage contained a 88,795 bp of circular double-stranded DNA with 41.12% of GC content. There were 74 putative open reading frames (ORFs) and 11 tRNAs predicted in genome of phage vB_Af_QDWS595. Phenotype and phylogeny analysis indicated that this phage might be a new member within the family Schitoviridae. Phage vB_Af_QDWS595 is the first sequenced phage against Alcaligenes faecalis to the best of our knowledge.

scholarly journals Genome Organization and Characterization of the Virulent Lactococcal Phage 1358 and Its Similarities to Listeria Phages

2010 ◽  
Vol 76 (5) ◽  
pp. 1623-1632 ◽  
Author(s):  
Marie-�ve Dupuis ◽  
Sylvain Moineau
Keyword(s):  
Burst Size ◽  
Gc Content ◽  
Open Reading Frames ◽  
Structural Proteins ◽  
Origin And Evolution ◽  
Sds Page ◽  
Liquid Chromatography Tandem Mass ◽  
Icosahedral Capsid ◽  
Rare Group

ABSTRACT Virulent phage 1358 is the reference member of a rare group of phages infecting Lactococcus lactis. Electron microscopy revealed a typical icosahedral capsid connected to one of the smallest noncontractile tails found in a lactococcal phage of the Siphoviridae family. Microbiological characterization identified a burst size of 72 virions released per infected host cell and a latent period of 90 min. The host range of phage 1358 was limited to 3 out of the 60 lactococcal strains tested. Moreover, this phage was insensitive to four Abi systems (AbiK, AbiQ, AbiT, and AbiV). The genome of phage 1358 consisted of a linear, double-stranded, 36,892-bp DNA molecule containing 43 open reading frames (ORFs). At least 14 ORFs coded for structural proteins, as identified by SDS-PAGE coupled to liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses. The genomic organization was similar to those of other siphophages. All genes were on the same coding strand and in the same orientation. This lactococcal phage was unique, however, in its 51.4% GC content, much higher than those of other phages infecting this low-GC Gram-positive host. A bias for GC-rich codons was also observed. Comparative analyses showed that several phage 1358 structural proteins shared similarity with two Listeria monocytogenes phages, P35 and P40. The possible origin and evolution of lactococcal phage 1358 is discussed.

scholarly journals Evolution of Lactococcus lactis Phages within a Cheese Factory

2009 ◽  
Vol 75 (16) ◽  
pp. 5336-5344 ◽  
Author(s):  
Geneviève M. Rousseau ◽  
Sylvain Moineau
Keyword(s):  
Lactococcus Lactis ◽  
High Performance ◽  
Core Genome ◽  
Open Reading Frames ◽  
Structural Proteins ◽  
Tandem Mass ◽  
Double Stranded Dna ◽  
Chromatography Tandem Mass Spectrometry ◽  
Liquid Chromatography Tandem Mass ◽  
Reading Frames

ABSTRACT We have sequenced the double-stranded DNA genomes of six lactococcal phages (SL4, CB13, CB14, CB19, CB20, and GR7) from the 936 group that were isolated over a 9-year period from whey samples obtained from a Canadian cheese factory. These six phages infected the same two industrial Lactococcus lactis strains out of 30 tested. The CB14 and GR7 genomes were found to be 100% identical even though they were isolated 14 months apart, indicating that a phage can survive in a cheese plant for more than a year. The other four genomes were related but notably different. The length of the genomes varied from 28,144 to 32,182 bp, and they coded for 51 to 55 open reading frames. All five genomes possessed a 3′ overhang cos site that was 11 nucleotides long. Several structural proteins were also identified by nano-high-performance liquid chromatography-tandem mass spectrometry, confirming bioinformatic analyses. Comparative analyses suggested that the most recently isolated phages (CB19 and CB20) were derived, in part, from older phage isolates (CB13 and CB14/GR7). The organization of the five distinct genomes was similar to the previously sequenced lactococcal phage genomes of the 936 group, and from these sequences, a core genome was determined for lactococcal phages of the 936 group.

scholarly journals Comparison of Enterococcus faecalis Biofilm Removal Efficiency among Bacteriophage PBEF129, Its Endolysin, and Cefotaxime

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 426
Author(s):  
Hyun Keun Oh ◽  
Yoon Jung Hwang ◽  
Hye-Won Hong ◽  
Heejoon Myung
Keyword(s):  
Enterococcus Faecalis ◽  
Gc Content ◽  
Bacterial Biofilm ◽  
Open Reading Frames ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Biofilm Removal ◽  
Query Coverage ◽  
Encoding Genes

Enterococcus faecalis is a Gram-positive pathogen which colonizes human intestinal surfaces, forming biofilms, and demonstrates a high resistance to many antibiotics. Especially, antibiotics are less effective for eradicating biofilms and better alternatives are needed. In this study, we have isolated and characterized a bacteriophage, PBEF129, infecting E. faecalis. PBEF129 infected a variety of strains of E. faecalis, including those exhibiting antibiotic resistance. Its genome is a linear double-stranded DNA, 144,230 base pairs in length. Its GC content is 35.9%. The closest genomic DNA sequence was found in Enterococcus phage vB_EfaM_Ef2.3, with a sequence identity of 99.06% over 95% query coverage. Furthermore, 75 open reading frames (ORFs) were functionally annotated and five tRNA-encoding genes were found. ORF 6 was annotated as a phage endolysin having an L-acetylmuramoyl-l-alanine amidase activity. We purified the enzyme as a recombinant protein and confirmed its enzymatic activity. The endolysin’s host range was observed to be wider than its parent phage PBEF129. When applied to bacterial biofilm on the surface of in vitro cultured human intestinal cells, it demonstrated a removal efficacy of the same degree as cefotaxime, but much lower than its parent bacteriophage.

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