scholarly journals Characterization and genome analysis of two novel Aeromonas hydrophila phages PZL-Ah1and PZL-Ah8

2021 ◽  
Author(s):  
Huabo Yu ◽  
Chao Feng ◽  
Liang Zhang ◽  
Teng Chi ◽  
Yanling Qi ◽  
...  
Keyword(s):  
Aeromonas Hydrophila ◽  
Bacterial Infections ◽  
Genomic Sequence ◽  
Gene Annotation ◽  
Gc Content ◽  
Opportunistic Pathogen ◽  
Open Reading Frames ◽  
Genome Database ◽  
Narrow Host Range ◽  
Phage T7

Abstract Aeromonas hydrophila (A.hydrophila) is an opportunistic pathogen of fish-human-livestock, which poses a seriously affects to the development of aquaculture. Phage therapy is considered as a process to alternatively control bacterial infections and contaminations. In this study, the genomes of two Aeromonas hydrophila- specific phages PZL-Ah1 and PZL-Ah8 were isolated, characterized and genomic sequence analyzed. Transmission electron microscopy showed that the two phages had been classified as the member of the Podoviridae family. Both the two phages in this study had relatively narrow host range with lytic activity against Aeromonas spp. strains. However, they could lyse 3 common A.hydrophila strain. As revealed from the whole genomic sequence analysis, PZL-Ah1 and PZL-Ah8 coverd the double-stranded genome of 38,641 bp and 40,855 bp in length, with the GC content of 53.68% and 51.89%, respectively. Through gene comparison in NCBI database revealed that PZL-Ah1 and PZL-Ah8 were 97.67% − 95.51% identical to Stenotrophomonas phage IME15 and Aeromonas Phage T7-Ah. Phylogenetic analysis showed that PZL-Ah8, PZL-Ah1 and other two phages belonged to the same genus. A total of 44 and 52 open reading frames (ORFs) were predicted in the PZL-Ah1 and PZL-Ah8 genome, respectively. In the process of gene annotation, 28 (63.6%) ORFs in PZL-Ah1 and 29 (55.8%) ORFs in PZL-Ah8 were known to functional proteins in NCBI database, while the remaining ORFs were classified as “hypothetical proteins”, whose functions were yet unknown. By comparing, ORF 02, ORF 29 and ORF 04 in PZL-Ah1, ORF24 in PZL-Ah8 were responsible for the host cell lysis. In conclusion, genomic studies of these two novel phages would lay the foundation for expanding the phage genome database and providing good candidates for phage typing applications.

scholarly journals M1CR0B1AL1Z3R—a user-friendly web server for the analysis of large-scale microbial genomics data

2019 ◽  
Vol 47 (W1) ◽  
pp. W88-W92 ◽  
Author(s):  
Oren Avram ◽  
Dana Rapoport ◽  
Shir Portugez ◽  
Tal Pupko
Keyword(s):  
Large Scale ◽  
Ad Hoc ◽  
Evolutionary Dynamics ◽  
Gene Annotation ◽  
Gc Content ◽  
Web Server ◽  
Disease Outbreaks ◽  
Open Reading Frames ◽  
Microbial Genomics ◽  
Bacterial Strains

Abstract Large-scale mining and analysis of bacterial datasets contribute to the comprehensive characterization of complex microbial dynamics within a microbiome and among different bacterial strains, e.g., during disease outbreaks. The study of large-scale bacterial evolutionary dynamics poses many challenges. These include data-mining steps, such as gene annotation, ortholog detection, sequence alignment and phylogeny reconstruction. These steps require the use of multiple bioinformatics tools and ad-hoc programming scripts, making the entire process cumbersome, tedious and error-prone due to manual handling. This motivated us to develop the M1CR0B1AL1Z3R web server, a ‘one-stop shop’ for conducting microbial genomics data analyses via a simple graphical user interface. Some of the features implemented in M1CR0B1AL1Z3R are: (i) extracting putative open reading frames and comparative genomics analysis of gene content; (ii) extracting orthologous sets and analyzing their size distribution; (iii) analyzing gene presence–absence patterns; (iv) reconstructing a phylogenetic tree based on the extracted orthologous set; (v) inferring GC-content variation among lineages. M1CR0B1AL1Z3R facilitates the mining and analysis of dozens of bacterial genomes using advanced techniques, with the click of a button. M1CR0B1AL1Z3R is freely available at https://microbializer.tau.ac.il/.

scholarly journals A temperate phage 5W infecting multidrug-resistant Acinetobacter baumannii

2021 ◽  
Author(s):  
Wenyi Peng ◽  
Fei Zeng ◽  
Zeyuan Jin ◽  
Wanxia Li ◽  
Mingzhuo Zhu ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Gc Content ◽  
Pond Water ◽  
Multidrug Resistant ◽  
Temperate Phage ◽  
Open Reading Frames ◽  
Narrow Host Range ◽  
C Terminus ◽  
Complete Lysis ◽  
The One

Abstract We isolated 5W, a temperate phage that infects multidrug-resistant Acinetobacter baumannii from pond water, using an enrichment method that involves the addition of host bacteria. 5W is a long-tailed phage with a narrow host range lysed four of 19 A. baumannii clinical isolates tested, and complete lysis was observed for A. baumannii clinical isolate Ab1. 5W adsorbed rapidly to its Ab1 host and > 80% adsorption was observed after 2 min of mixing. The one-step growth curve showed that 5W has a 20 min latent period and a ~ 100 min rise period, with a burse size of ~ 180 PFU/cell. 5W contains a dsDNA genome 43,032 bp in length, with 61 open reading frames and a GC content of 39.85%. The genome lacks any known virulence and drug resistance genes, but encodes an N-acetyl-β-D-muramidase with numerous positively charged amino acids at its C-terminus that belongs to the GH_108 family. The M/S subunits of the restriction endonuclease are inserted in the lysogenic gene cluster. The first and second halves of the 5W genome are highly homologous with prophages phiABCR01-03 and phiABCR01-02 in the A. baumannii ABCR01 genome, respectively, which suggests that 5W may be a product of recombination between the two prophages.

scholarly journals M1CR0B1AL1Z3R—a user-friendly web server for the analysis of large-scale microbial genomics data

2020 ◽  
Vol 2 (7A) ◽  
Author(s):  
Oren Avram ◽  
Dana Rapoport ◽  
Shir Portugez ◽  
Tal Pupko
Keyword(s):  
Large Scale ◽  
Ad Hoc ◽  
Evolutionary Dynamics ◽  
Gene Annotation ◽  
Gc Content ◽  
Web Server ◽  
Disease Outbreaks ◽  
Open Reading Frames ◽  
Microbial Genomics ◽  
Bacterial Strains

Large-scale mining and analysis of bacterial datasets contribute to the comprehensive characterization of complex microbial dynamics within a microbiome and among different bacterial strains, e.g., during disease outbreaks. The study of large-scale bacterial evolutionary dynamics poses many challenges. These include data-mining steps, such as gene annotation, ortholog detection, sequence alignment, and phylogeny reconstruction. These steps require the use of multiple bioinformatics tools and ad-hoc programming scripts, making the entire process cumbersome, tedious and error-prone due to manual handling. This motivated us to develop the M1CR0B1AL1Z3R web server, a ‘one-stop shop’ for conducting microbial genomics data analyses via a simple graphical user interface (Avram, et al., Nucleic Acids Res., 2019). Some of the features implemented in M1CR0B1AL1Z3R are: (i) extracting putative open reading frames and comparative genomics analysis of gene content; (ii) extracting orthologous sets and analyzing their size distribution; (iii) analyzing gene presence-absence patterns; (iv) reconstructing a phylogenetic tree based on the extracted orthologous set; (v) inferring GC-content variation among lineages. M1CR0B1AL1Z3R facilitates the mining and analysis of dozens of bacterial genomes using advanced techniques, with the click of a button. M1CR0B1AL1Z3R is freely available at https://microbializer.tau.ac.il/ [https://microbializer.tau.ac.il/].

scholarly journals Genomic Sequence and Transcriptional Analysis of a 23-Kilobase Mycobacterial Linear Plasmid: Evidence for Horizontal Transfer and Identification of Plasmid Maintenance Systems

2001 ◽  
Vol 183 (7) ◽  
pp. 2157-2164 ◽  
Author(s):  
Corinne Le Dantec ◽  
Nathalie Winter ◽  
Brigitte Gicquel ◽  
Véronique Vincent ◽  
Mathieu Picardeau
Keyword(s):  
Horizontal Transfer ◽  
Genomic Sequence ◽  
Opportunistic Pathogen ◽  
Open Reading Frames ◽  
Transcriptional Analysis ◽  
Linear Plasmid ◽  
Rt Pcr ◽  
Maintenance Systems ◽  
Function Sequence ◽  
Reading Frames

ABSTRACT Linear plasmids were unknown in mycobacteria until recently. Here, we report the complete nucleotide sequence of 23-kb linear plasmid pCLP from Mycobacterium celatum, an opportunistic pathogen. The sequence of pCLP revealed at least 19 putative open reading frames (ORFs). Expression of pCLP genes in exponential-phase cultures was determined by reverse transcriptase PCR (RT-PCR). Twelve ORFs were expressed, whereas no transcription of the 7 other ORFs of pCLP was detected. Five of the 12 transcribed ORFs detected by RT-PCR are of unknown function. Sequence analysis revealed similar loci in bothM. celatum pCLP and the Mycobacterium tuberculosis chromosome, including transposase-related sequences. This result suggests horizontal transfer between these two organisms. pCLP also contains ORFs that are similar to genes of bacterial circular plasmids involved in partition (par operon) and postsegregational (pem operon) mechanisms. Functional analysis of these ORFs suggests that they probably carry out similar maintenance roles in pCLP.

scholarly journals Molecular Characterization of Ahp2, a Lytic Bacteriophage of Aeromonas hydrophila

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 477
Author(s):  
Jian-Bin Wang ◽  
Mei-Shiuan Yu ◽  
Tsai-Tien Tseng ◽  
Ling-Chun Lin
Keyword(s):  
Aeromonas Hydrophila ◽  
Burst Size ◽  
Polyacrylamide Gel Electrophoresis ◽  
Gc Content ◽  
Opportunistic Pathogen ◽  
Aeromonas Salmonicida ◽  
Lytic Bacteriophage ◽  
Protein Sequence Analysis ◽  
Double Stranded Dna ◽  
A Genome

Aeromonas hydrophila is an opportunistic pathogen that infects fish, amphibians, mammals, and humans. This study isolated a myophage, vB_AhyM_Ahp2 (Ahp2), that lytically infects A. hydrophila. We observed that 96% of the Ahp2 particles adsorbed to A. hydrophila within 18 min. Ahp2 also showed a latent period of 15 min with a burst size of 142 PFU/cell. This phage has a linear double-stranded DNA genome of 47,331 bp with a GC content of 57%. At least 20 Ahp2 proteins were detected by SDS-polyacrylamide gel electrophoresis; among them, a 40-kDa protein was predicted as the major capsid protein. Sequence analysis showed that Ahp2 has a genome organization closely related to a group of Aeromonas phages (13AhydR10RR, 14AhydR10RR, 85AhydR10RR, phage 3, 32 Asp37, 59.1), which infect Aeromonas hydrophila and Aeromonas salmonicida. The tail module encompassing ORF27-29 in the Ahp2 genome was present in all Aeromonas phages analyzed in this study and likely determines the host range of the virus. This study found that Ahp2 completely lyses A. hydrophila AH300206 in 3.5 h at a MOI of 0.0001 and does not lysogenize its host. Altogether, these findings show that Ahp2 is a lytic Aeromonas phage and could be a candidate for therapeutic phage cocktails.

scholarly journals Complete Genome Sequence of a Novel Umbra-like Mycovirus From the Plant Pathogenic Fungus Phoma Matteucciicola

2021 ◽  
Author(s):  
Jia Zhou ◽  
Daipeng Chen ◽  
Xiaofei Liang ◽  
Siyu Zhou ◽  
Zhensheng Kang ◽  
...  
Keyword(s):  
Metal Binding ◽  
Genomic Sequence ◽  
Rna Virus ◽  
Pathogenic Fungus ◽  
Gc Content ◽  
Hypothetical Protein ◽  
Macrophomina Phaseolina ◽  
Open Reading Frames ◽  
Erysiphe Necator ◽  
Gdd Motif

Abstract Here, a novel umbra-like mycovirus, ‘Phoma matteucciicola RNA virus 2’ (PmRV2), isolated from Phoma matteucciicola strain HNQH1 in Hainan province of China, was sequenced and analyzed. The complete genomic sequence of PmRV2 is 3,460 nucleotides (nts) with a GC content of 56.71%. Sequence analysis of PmRV2 indicated that the presence of two noncontiguous open reading frames (ORFs) encoding a hypothetical protein and a RNA-dependent RNA polymerase (RdRp), respectively. PmRV2 contains a metal-binding ‘GDN’ triad in Motif C of RdRp while most + ssRNA mycoviruses contained a ‘GDD’ motif in the same region. Additionally, a BLASTp search showed that the RdRp amino acid sequence of PmRV2 was most closely related to the RdRp of Macrophomina phaseolina umbra-like virus 1 (50.72% identity) and Erysiphe necator umbra-like virus 2 (44.84% identity). Phylogenetic analysis indicated that PmRV2 grouped together with Erysiphe necator umbra-like virus 2 (EnUlV2) within the recently proposed family of ‘Mycotombusviridae’.

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 Characterization of Cestrum yellow leaf curling virus: a new member of the family Caulimoviridae

2003 ◽  
Vol 84 (12) ◽  
pp. 3459-3464 ◽  
Author(s):  
Livia Stavolone ◽  
Antonio Ragozzino ◽  
Thomas Hohn
Keyword(s):  
Genomic Sequence ◽  
Infected Plant ◽  
Virus Genome ◽  
Mosaic Disease ◽  
Open Reading Frames ◽  
Primer Binding Site ◽  
Yellow Leaf ◽  
Leaf Curling ◽  
Chlorotic Mottle Virus ◽  
Chlorotic Mottle

Cestrum yellow leaf curling virus (CmYLCV) has been characterized as the aetiological agent of the Cestrum parqui mosaic disease. The virus genome was cloned and the clone was proven to be infectious to C. parqui. The presence of typical viroplasms in virus-infected plant tissue and the information obtained from the complete genomic sequence confirmed CmYLCV as a member of the Caulimoviridae family. All characteristic domains conserved in plant pararetroviruses were found in CmYLCV. Its genome is 8253 bp long and contains seven open reading frames (ORFs). Phylogenetic analysis of the relationships with other members of the Caulimoviridae revealed that CmYLCV is closely related to the Soybean chlorotic mottle virus (SbCMV)-like genus and particularly to SbCMV. However, in contrast to the other members of this genus, the primer-binding site is located in the intercistronic region following ORF Ib rather than within this ORF, and an ORF corresponding to ORF VII is missing.

Influence of Glucose Concentrations on Biofilm Formation, Motility, Exoprotease Production, and Quorum Sensing in Aeromonas hydrophila

2013 ◽  
Vol 76 (2) ◽  
pp. 239-247 ◽  
Author(s):  
IQBAL KABIR JAHID ◽  
NA-YOUNG LEE ◽  
ANNA KIM ◽  
SANG-DO HA
Keyword(s):  
Quorum Sensing ◽  
Aeromonas Hydrophila ◽  
Biofilm Formation ◽  
Opportunistic Pathogen ◽  
Homoserine Lactone ◽  
Protease Production ◽  
Acyl Homoserine Lactone ◽  
Human Pathogen ◽  
Initial Biofilm ◽  
Motility Inhibition

Aeromonas hydrophila recently has received increased attention because it is opportunistic and a primary human pathogen. A. hydrophila biofilm formation and its control are a major concern for food safety because biofilms are related to virulence. Therefore, we investigated biofilm formation, motility inhibition, quorum sensing, and exoprotease production of this opportunistic pathogen in response to various glucose concentrations from 0.05 to 2.5% (wt/vol). More than 0.05% glucose significantly impaired (P < 0.05) quorum sensing, biofilm formation, protease production, and swarming and swimming motility, whereas bacteria treated with 0.05% glucose had activity similar to that of the control (0% glucose). A stage shift biofilm assay revealed that the addition of glucose (2.5%) inhibited initial biofilm formation but not later stages. However, addition of quorum sensing molecules N-3-butanoyl-DL-homoserine lactone and N-3-hexanoyl homoserine lactone partially restored protease production, indicating that quorum sensing is controlled by glucose concentrations. Thus, glucose present in food or added as a preservative could regulate acyl-homoserine lactone quorum sensing molecules, which mediate biofilm formation and virulence in A. hydrophila.

scholarly journals Genome of Deerpox Virus

2005 ◽  
Vol 79 (2) ◽  
pp. 966-977 ◽  
Author(s):  
C. L. Afonso ◽  
G. Delhon ◽  
E. R. Tulman ◽  
Z. Lu ◽  
A. Zsak ◽  
...  
Keyword(s):  
Host Range ◽  
Chemokine Receptors ◽  
Transforming Growth Factor ◽  
Genomic Sequence ◽  
Core Protein ◽  
Interleukin 1 ◽  
Transforming Growth Factor Β1 ◽  
Open Reading Frames ◽  
Host Responses ◽  
Tgf Β1

ABSTRACT Deerpox virus (DPV), an uncharacterized and unclassified member of the Poxviridae, has been isolated from North American free-ranging mule deer (Odocoileus hemionus) exhibiting mucocutaneous disease. Here we report the genomic sequence and comparative analysis of two pathogenic DPV isolates, W-848-83 (W83) and W-1170-84 (W84). The W83 and W84 genomes are 166 and 170 kbp, containing 169 and 170 putative genes, respectively. Nucleotide identity between DPVs is 95% over the central 157 kbp. W83 and W84 share similar gene orders and code for similar replicative, structural, virulence, and host range functions. DPV open reading frames (ORFs) with putative virulence and host range functions include those similar to cytokine receptors (R), including gamma interferon receptor (IFN-γR), interleukin 1 receptor (IL-1R), and type 8 CC-chemokine receptors; cytokine binding proteins (BP), including IL-18BP, IFN-α/βBP, and tumor necrosis factor binding protein (TNFBP); serpins; and homologues of vaccinia virus (VACV) E3L, K3L, and A52R proteins. DPVs also encode distinct forms of major histocompatibility complex class I, C-type lectin-like protein, and transforming growth factor β1 (TGF-β1), a protein not previously described in a mammalian chordopoxvirus. Notably, DPV encodes homologues of cellular endothelin 2 and IL-1R antagonist, novel poxviral genes also likely involved in the manipulation of host responses. W83 and W84 differ from each other by the presence or absence of five ORFs. Specifically, homologues of a CD30 TNFR family protein, swinepox virus SPV019, and VACV E11L core protein are absent in W83, and homologues of TGF-β1 and lumpy skin disease virus LSDV023 are absent in W84. Phylogenetic analysis indicates that DPVs are genetically distinct from viruses of other characterized poxviral genera and that they likely comprise a new genus within the subfamily Chordopoxvirinae.

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