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Genome organization of phages phiL7, Xop411, Xp10, and OP1. Colored arrows indicate the directions and categories of the genes (denoted below). The numbers inside or near the arrows are gene designations. The σ⁷⁰-type promoter is shown, and the black knob shows the position of a terminator predicted in phiL7.
Source publication
The lytic phage phiL7, which morphologically belongs to the Siphoviridae family, infects Xanthomonas campestris pv. campestris. Nucleotide sequence analysis has revealed that phiL7 contains a linear double-stranded DNA genome (44,080
bp, 56% G+C) with a 3′-protruding cos site (5′-TTACCGGAC-3′) and 59 possible genes. Among the deduced proteins, 32 h...
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Background
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Citations
... ORF13 in MEP401 and MEP402 contain the 3′−5′ exonuclease domain (PF01612) and the N-terminal DNA polymerase A domain (PF00476), whereas ORF15 in both phages contain the C-terminal DNA polymerase A domain (PF00476). In many phage genomes, group I introns are inserted into phage DNAP genes (42)(43)(44). Thus, it was possible that DNAP genes in MEP401 and MEP402 both phages were interrupted by an intron. ...
The marine methylotrophic OM43 clade is considered an important bacterial group in coastal microbial communities. OM43 bacteria, which are closely related to phytoplankton blooms, have small cell sizes and streamlined genomes. Bacteriophages profoundly shape the evolutionary trajectories, population dynamics, and physiology of microbes. The prevalence and diversity of several phages that infect OM43 bacteria have been reported. In this study, we isolated and sequenced two novel OM43 phages, MEP401 and MEP402. These phages share 90% of their open reading frames (ORFs) and are distinct from other known phage isolates. Furthermore, a total of 99 metagenomic viral genomes (MVGs) closely related to MEP401 and MEP402 were identified. Phylogenomic analyses suggest that MEP401, MEP402, and these identified MVGs belong to a novel subfamily in the family Zobellviridae and that they can be separated into two groups. Group I MVGs show conserved whole-genome synteny with MEP401, while group II MVGs possess the MEP401-type DNA replication module and a distinct type of morphogenesis and packaging module, suggesting that genomic recombination occurred between phages. Most members in these two groups were predicted to infect OM43 bacteria. Metagenomic read-mapping analysis revealed that the phages in these two groups are globally ubiquitous and display distinct biogeographic distributions, with some phages being predominant in cold regions, some exclusively detected in estuarine stations, and others displaying wider distributions. This study expands our knowledge of the diversity and ecology of a novel phage lineage that infects OM43 bacteria by describing their genomic diversity and global distribution patterns.
IMPORTANCE
OM43 phages that infect marine OM43 bacteria are important for host mortality, community structure, and physiological functions. In this study, two OM43 phages were isolated and characterized. Metagenomic viral genome (MVG) retrieval using these two OM43 phages as baits led to the identification of two phage groups of a new subfamily in the family Zobellviridae . We found that group I MVGs share similar genomic content and arrangement with MEP401 and MEP402, whereas group II MVGs only possess the MEP401-type DNA replication module. Metagenomic mapping analysis suggests that members in these two groups are globally ubiquitous with distinct distribution patterns. This study provides important insights into the genomic diversity and biogeography of the OM43 phages in the global ocean.
... This includes autographiviruses (10 Okabevirinae phages and 9 phages yet unassigned to any subfamily but located within the Okabevirinae clique) and six siphoviruses infecting Stenotrophomonas (BUCT603, MW934263.1) and Xanthomonas hosts (phiL7 [107], CP1 [108], OP1 [109], Xp10 [110], and Xop411 [110]). Similarities are shared through the entire replication module ( Figure S15), that is, their DNA primases, DNA helicases, DNA polymerases, DUF669-containing proteins, 5 -3 exonucleases, DNA endonucleases VII, ribonuclease H-like domain-containing proteins RNA polymerases, and lysozymes ( Figure S17). ...
In this study, we isolated and characterized three novel virulent Autographiviridae bacteriophages, vB_AspA_Bolek, vB_AspA_Lolek, and vB_AspA_Tola, which infect different Aeromonas strains. These three host–pathogen pairs were derived from the same sampling location—the arsenic-containing microbial mats of the Zloty Stok gold mine. Functional analysis showed they are psychrotolerant (4–25 °C), albeit with a much wider temperature range of propagation for the hosts (≤37 °C). Comparative genomic analyses revealed a high nucleotide and amino acid sequence similarity of vB_AspA_Bolek and vB_AspA_Lolek, with significant differences exclusively in the C-terminal region of their tail fibres, which might explain their host range discrimination. The protein-based phage network, together with a phylogenetic analysis of the marker proteins, allowed us to assign vB_AspA_Bolek and vB_AspA_Lolek to the Beijerinckvirinae and vB_AspA_Tola to the Colwellvirinae subfamilies, but as three novel species, due to their low nucleotide sequence coverage and identity with other known phage genomes. Global comparative analysis showed that the studied phages are also markedly different from most of the 24 Aeromonas autographiviruses known so far. Finally, this study provides in-depth insight into the diversity of the Autographiviridae phages and reveals genomic similarities between selected groups of this family as well as between autographiviruses and their relatives of other Caudoviricetes families.
... oryzae [23] P4L Cf Temperate/carrier state X. citri [84] φL7 Lytic X. campestris pv. campestris [95] that catalyzes the direct methylation of deoxycytidine monophosphate (dCMP) to 5-methylcytosine, in the presence of tetrahydrofolic acid [107,108]. Modification of phosphorylation occurs during Xanthomonas phage infection. ...
Phytopathogenic bacteria are economically important because they affect crop yields and threaten the livelihoods of farmers worldwide. The genus Xanthomonas is particularly significant because it is associated with some plant diseases that cause tremendous loss in yields of globally essential crops. Current management practices are ineffective, unsustainable and harmful to natural ecosystems. Bacteriophage (phage) biocontrol for plant disease management has been of particular interest from the early nineteenth century to date. Xanthomonas phage research for plant disease management continues to demonstrate promising results under laboratory and field conditions. AgriPhage has developed phage products for the control of Xanthomonas campestris pv. vesicatoria and Xanthomonas citri subsp. citri. These are causative agents for tomato, pepper spot and speck disease as well as citrus canker disease.
Phage-mediated biocontrol is becoming a viable option because phages occur naturally and are safe for disease control and management. Thorough knowledge of biological characteristics of Xanthomonas phages is vital for developing effective biocontrol products. This review covers Xanthomonas phage research highlighting aspects of their ecology, biology and biocontrol applications.
... The studies of genomic analysis of bacteriophage CP1 and CP2 have reported that the CP1 DNA sequence was detected in the genome sequence of X. campestris bacteriophage phiL7 (GenBank accession number EU717894), X. oryzae bacteriophage OP1 (GenBank accession number AP008979) and Xanthomonas bacteriophage Xp10 (GenBank accession number AY299121) [45]. In addition, a sequence in the genomic contig of the Ralstonia-related blood disease bacterium R229 (GenBank accession number FR854082) was related to spacer Xcc_31; this sequence encodes a DNAdependent DNA polymerase with homology to DNA polymerases of the Xanthomonas-specific bacteriophages phiL7, OP1 and Xp10 [58][59][60]. Possibly, the genomic sequence of the blood disease bacterium R229 corresponds to a prophage with similarity to Xanthomonas-specific bacteriophages. Therefore, spacer Xcc_31 was likely acquired from a bacteriophage. ...
Background: Xanthomonads are an important clade of Gram-negative bacteria infecting a plethora of economically important host plants, including citrus. Knowledge about the pathogen’s diversity and population structure are prerequisite for epidemiological surveillance and efficient disease management. Rapidly evolving genetic loci, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are of special interest to develop new molecular typing tools.
Results: We analyzed CRISPR loci of 56 Xanthomonas citri pv. citri strains of world-wide origin, a regulated pathogen causing Asiatic citrus canker in several regions of the world. With one exception, 23 unique sequences built up the repertoire of spacers, suggesting that this set of strains originated from a common ancestor that already harbored these 23 spacers. One isolate originating from Pakistan contained a string of 14 additional, probably more recently acquired spacers indicating that this genetic lineage has or had until recently the capacity to acquire new spacers. Comparison of CRISPR arrays with previously obtained molecular typing data, such as amplified fragment length polymorphisms (AFLP), variable-number of tandem-repeats (VNTR) and genome-wide single-nucleotide polymorphisms (SNP), demonstrated that these methods reveal similar evolutionary trajectories. Notably, genome analyses allowed to generate a model for CRISPR array evolution in X. citri pv. citri, which provides a new framework for the genealogy of the citrus canker pathogen.
Conclusions: CRISPR-based typing will further improve the accuracy of the genetic identification of X. citri pv. citri outbreak strains in molecular epidemiology analyses, especially when used concomitantly with another genotyping method.
... The studies of genomic analysis of bacteriophage CP1and CP2 have reported that the CP1 DNA sequence was detected in the genome sequence of X. campestris bacteriophage phiL7 (GenBank accession number EU717894), X. oryzae bacteriophage OP1 (GenBank accession number AP008979) and Xanthomonas bacteriophage Xp10 (GenBank accession number AY299121) [45]. In addition, a sequence in the genomic contig of the Ralstonia-related blood disease bacterium R229 (GenBank accession number FR854082) was related to spacer Xcc_31; this sequence encodes a DNA-dependent DNA polymerase with homology to DNA polymerases of the Xanthomonas-speci c bacteriophages phiL7, OP1 and Xp10 [58, 59,60]. Possibly, the genomic sequence of the blood disease bacterium R229 corresponds to a prophage with similarity to Xanthomonas-speci c bacteriophages. ...
Background Xanthomonads are an important clade of Gram-negative bacteria infecting a plethora of economically important host plants, including citrus. Knowledge about the pathogen’s diversity and population structure are prerequisite for epidemiological surveillance and efficient disease management. Rapidly evolving genetic loci, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are of special interest to develop new molecular typing tools. Results We analyzed CRISPR loci of 56 Xanthomonas citri pv. citri strains of world-wide origin, a regulated pathogen causing Asiatic citrus canker in several regions of the world. With one exception, 23 unique sequences built up the repertoire of spacers, suggesting that this set of strains originated from a common ancestor that already harbored these 23 spacers. One isolate originating from Pakistan contained a string of 14 additional, probably more recently acquired spacers indicating that this genetic lineage has or had until recently the capacity to acquire new spacers. Comparison of CRISPR arrays with previously obtained molecular typing data, such as amplified fragment length polymorphisms (AFLP), variable-number of tandem-repeats (VNTR) and genome-wide single-nucleotide polymorphisms (SNP), demonstrated that these methods reveal similar evolutionary trajectories. Notably, genome analyses allowed to generate a model for CRISPR array evolution in X. citri pv. citri, which provides a new framework for the genealogy of the citrus canker pathogen. Conclusions CRISPR-based typing will further improve the accuracy of the genetic identification of X. citri pv. citri outbreak strains in molecular epidemiology analyses, especially when used concomitantly with another genotyping method.
... Also, Wakimoto (1960) grouped phages infecting Xoo into OP1 and OP2 based on morphological and serological properties. Lee et al. (2009) reported that Xoo phage OP2 belong to family Caudoviridae. Furthermore, results from several groups proposed that Xoo phage OP2 should be classified in the new genus Bcep781likevirus, family Myoviridae (Lavigne et al. 2009;Adams and Carstens 2012). ...
Bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most severe bacterial diseases of rice. This study identified and characterized five Xoo bacteriophages X1, X2, X3, X4, and X5, isolated from diseased rice leaves in China as potential biocontrol agents. Electron microscopy showed that the five phages have contractile tails thus all belong to the family Myoviridae possessing icosahedral heads, necks and base plates with tail fibres. The head diameters ranged from 57.49 to 85.27 nm, while the tail lengths ranged from 75.88 to 112.47 nm. It was confirmed that the phages had the expected double-stranded DNA genomes. Phylogenetic analysis of DNAP gene indicated that the five phages could be clustered into one group with phage OP2, but were well separated from other Xoo phages. Significant physiological changes were observed in Xoo after infection by these phages, which differed in their host range and infection ability. Phage X3 had the broadest host range, lysing 22 out of the 23 Xoo strains tested, and had the longest latent period of 40 min with a burst size of 50-plaque forming units per infected cell. It caused 53% degradation of exopolysaccharide production, 43% degradation of biofilm, while the highest rate of bacteriophage-resistant bacterial colonies emerged at log 4 PFU/ml of strain Gz 0011. Application of phage X3 decreased disease severity in vivo: it was more effective (83.1% decrease) if applied by spraying before pathogen inoculation rather than after (28.9–73.9%), and seed treatment was also very effective (95.4% decrease).
... Also, Wakimoto (1960) grouped phages infecting Xoo into OP1 and OP2 based on morphological and serological properties. Lee et al. (2009) reported that Xoo phage OP2 belong to family Caudoviridae. Furthermore, results from several groups proposed that Xoo phage OP2 should be classified in the new genus Bcep781likevirus, family Myoviridae (Lavigne et al. 2009;Adams and Carstens 2012). ...
Bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most severe bacterial diseases of rice. This study identified and characterized five Xoo bacteriophages X1, X2, X3, X4, and X5, isolated from diseased rice leaves in China as potential biocontrol agents. Electron microscopy showed that the five phages have contractile tails thus all belong to the family Myoviridae possessing icosahedral heads, necks and base plates with tail fibres. The head diameters ranged from 57.49 to 85.27 nm, while the tail lengths ranged from 75.88 to 112.47 nm. It was confirmed that the phages had the expected double-stranded DNA genomes. Phylogenetic analysis of DNAP gene indicated that the five phages could be clustered into one group with phage OP2, but were well separated from other Xoo phages. Significant physiological changes were observed in Xoo after infection by these phages, which differed in their host range and infection ability. Phage X3 had the broadest host range, lysing 22 out of the 23 Xoo strains tested, and had the longest latent period of 40 min with a burst size of 50-plaque forming units per infected cell. It caused 53% degradation of exopolysaccharide production, 43% degradation of biofilm, while the highest rate of bacteriophage-resistant bacterial colonies emerged at log 4 PFU/ml of strain Gz 0011. Application of phage X3 decreased disease severity in vivo: it was more effective (83.1% decrease) if applied by spraying before pathogen inoculation rather than after (28.9-73.9%), and seed treatment was also very effective (95.4% decrease).
... The Xanthomonas phage phiL7 is a lytic phage, which has a long tail and belongs to the Siphoviridae family. It infects the plant pathogen Xanthomonas campestris [48]. ...
Bacteriophages are viruses that infect bacteria, and consequently they have a major impact on the development of a microbial population. In this study, the genome of a novel broad host range bacteriophage, Aquamicrobium phage P14, isolated from a wastewater treatment plant, was analyzed. The Aquamicrobium phage P14 was found to infect members of different Proteobacteria classes (Alphaproteobacteria and Betaproteobacteria). This phage contains a 40,551 bp long genome and 60% of its genes had blastx hits. Furthermore, the bacteriophage was found to share more than 50% of its genes with several podoviruses and has the same gene order as other polyvalent bacteriophages. The results obtained in this study led to the conclusion that indeed general features of the genome of the Aquamicrobium phage P14 are shared with other broad host range bacteriophages, however further analysis of the genome is needed in order to identify the specific mechanisms which enable the bacteriophage to infect both Alphaproteobacteria and Betaproteobacteria.
... Images of different stages of phage cycle were captured starting from attachment of phage to the host cells to its absorption, release of nucleic acid to bursting stage (Fig 1a-f). PhiL7 phage of Xcc (Lee et al., 2009) was also found to have an icosahedral capsid ...
Soil and plant samples from black rot infected fields were processed to isolate wild type Xanthomonas campestris pv. campestris (Xcc) bacteriophages by overlay agar method. Various Xcc strains were employed as indicator hosts. The aim of this study was to isolate and purify potential bacteriophages for their ability to lyse plant pathogenic strains of Xcc in vitro. Bacteriophages were purified and selected for further characterization based on their ability to produce clear lysis on plaque assay. Seventeen strains of pathogenic Xcc were tested for sensitivity to 31 phages isolated during the study. Lysis was graded subjectively as per standard. A virulent phage Xcc9SH3 isolated from soil sample from Lucknow was found to lyse all tested strains of Xcc in vitro. Characterization of Xcc9SH3 was done based on plaque morphology, phage titre, organic solvent sensitivity, effect of temperature and transmission electron microscopy. The size of long noncontractile tail of the phage was 100 nm in length and 10 nm in width with 20 nm diameter of head. The isometric head of the phage predicted to belong to Siphoviridae (dsDNA viruses) family of bacteriophages. These phages may be useful tool in specific and efficient detection and control of Xcc causing black rot disease in cole crops.
... NC_021073.1) were also detected, together with a site-specific recombinase gene (K931_13548) related to that of Bacillus phage W (74) and a terminase gene similar to one found in Xanthomonas phage phiL7 (75). ...
Aeromonas salmonicida subsp. pectinolytica 34mel(T) can be considered an extremophile due to the characteristics of the heavily polluted river from which it was isolated. While four subspecies of A. salmonicida are known fish pathogens, 34mel(T) belongs to the only subspecies isolated solely from the environment. Genome analysis revealed high metabolic versatility, the capability to cope with diverse stress agents, and the lack of several virulence factors found in pathogenic Aeromonas. The most relevant phenotypic characteristics of 34mel(T) are pectin degradation, a distinctive trait of the pectinolytica subspecies, and melanin production. Genes coding for three pectate lyases were detected in a cluster unique for this microorganism, that contains all genes needed for pectin degradation. Melanin synthesis in 34mel(T) is hypothesized to occur through the homogentisate pathway, as no tyrosinases or laccases were detected, and the homogentisate 1,2-dioxygenase gene is inactivated by a transposon insertion, leading to the accumulation of the melanin precursor homogentisate. Comparative genome analysis of other melanogenic Aeromonas revealed that this gene was inactivated by transposon insertions or point mutations, indicating that melanin biosynthesis in Aeromonas occurs through the homogentisate pathway. Horizontal gene transfer could have contributed to the adaptation of 34mel(T) to a highly polluted environment, as thirteen genomic islands were identified in its genome, some of them containing genes coding for fitness related traits. Heavy metal resistance genes, along with others associated to oxidative and nitrosative stress were also found. These characteristics, together with melanin production and the ability to use different substrates, could explain the capability of this microorganism to live in an extremely polluted environment.
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