scholarly journals Pantoea agglomerans-Infecting Bacteriophage vB_PagS_AAS21: A Cold-Adapted Virus Representing a Novel Genus within the Family Siphoviridae

Viruses ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 479
Author(s):  
Monika Šimoliūnienė ◽  
Lidija Truncaitė ◽  
Emilija Petrauskaitė ◽  
Aurelija Zajančkauskaitė ◽  
Rolandas Meškys ◽  
...  
Keyword(s):  
Comparative Sequence Analysis ◽  
Pantoea Agglomerans ◽  
Open Reading Frames ◽  
Cold Adapted ◽  
Host Interactions ◽  
A Genome ◽  
Protein Encoding ◽  
The Family ◽  
Phage Propagation ◽  
Encoding Genes

A novel cold-adapted siphovirus, vB_PagS_AAS21 (AAS21), was isolated in Lithuania using Pantoea agglomerans as the host for phage propagation. AAS21 has an isometric head (~85 nm in diameter) and a non-contractile flexible tail (~174 × 10 nm). With a genome size of 116,649 bp, bacteriophage AAS21 is the largest Pantoea-infecting siphovirus sequenced to date. The genome of AAS21 has a G+C content of 39.0% and contains 213 putative protein-encoding genes and 29 genes for tRNAs. A comparative sequence analysis revealed that 89 AAS21 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. In total, 63 AAS21 ORFs were functionally annotated, including those coding for the proteins responsible for virion morphogenesis, phage-host interactions, and DNA metabolism. Proteomic analysis led to the experimental identification of 19 virion proteins, including 11 that were predicted by bioinformatics approaches. Based on comparative phylogenetic analysis, AAS21 cannot be assigned to any genus currently recognized by ICTV and may represents a new branch of viruses within the family Siphoviridae.

scholarly journals Pantoea Bacteriophage vB_PagS_AAS23: A Singleton of the Genus Sauletekiovirus

2021 ◽  
Vol 9 (3) ◽  
pp. 668
Author(s):  
Emilija Žukauskienė ◽  
Monika Šimoliūnienė ◽  
Lidija Truncaitė ◽  
Martynas Skapas ◽  
Algirdas Kaupinis ◽  
...  
Keyword(s):  
Single Species ◽  
Comparative Sequence Analysis ◽  
Open Reading Frames ◽  
Cold Adapted ◽  
Double Stranded Dna ◽  
Protein Encoding ◽  
The Family ◽  
Close Relationship ◽  
Phage Propagation ◽  
Encoding Genes

A cold-adapted siphovirus, vB_PagS_AAS23 (AAS23) was isolated in Lithuania using the Pantoea agglomerans strain AUR for the phage propagation. The double-stranded DNA genome of AAS23 (51,170 bp) contains 92 probable protein encoding genes, and no genes for tRNA. A comparative sequence analysis revealed that 25 of all AAS23 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. Based on the phylogenetic analysis, AAS23 has no close relationship to other viruses publicly available to date and represents a single species of the genus Sauletekiovirus within the family Drexlerviridae. The phage is able to form plaques in bacterial lawns even at 4 °C and demonstrates a depolymerase activity. Thus, the data presented in this study not only provides the information on Pantoea-infecting bacteriophages, but also offers novel insights into the diversity of cold-adapted viruses and their potential to be used as biocontrol agents.

scholarly journals Pantoea Bacteriophage vB_PagS_Vid5: A Low-Temperature Siphovirus That Harbors a Cluster of Genes Involved in the Biosynthesis of Archaeosine

Viruses ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 583 ◽  
Author(s):  
Eugenijus Šimoliūnas ◽  
Monika Šimoliūnienė ◽  
Laura Kaliniene ◽  
Aurelija Zajančkauskaitė ◽  
Martynas Skapas ◽  
...  
Keyword(s):  
Low Temperature ◽  
Comparative Sequence Analysis ◽  
Open Reading Frames ◽  
Host Interactions ◽  
Protein Encoding ◽  
The Family ◽  
Virion Morphogenesis ◽  
Phage Propagation ◽  
Encoding Genes ◽  
Reading Frames

A novel low-temperature siphovirus, vB_PagS_Vid5 (Vid5), was isolated in Lithuania using Pantoea agglomerans isolate for the phage propagation. The 61,437 bp genome of Vid5 has a G–C content of 48.8% and contains 99 probable protein encoding genes and one gene for tRNASer. A comparative sequence analysis revealed that 46 out of 99 Vid5 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. In total, 33 Vid5 ORFs were given a putative functional annotation, including those coding for the proteins responsible for virion morphogenesis, phage-host interactions, and DNA metabolism. In addition, a cluster of genes possibly involved in the biosynthesis of 7-deazaguanine derivatives was identified. Notably, one of these genes encodes a putative preQ0/preQ1 transporter, which has never been detected in bacteriophages to date. A proteomic analysis led to the experimental identification of 11 virion proteins, including nine that were predicted by bioinformatics approaches. Based on the phylogenetic analysis, Vid5 cannot be assigned to any genus currently recognized by ICTV, and may represent a new one within the family of Siphoviridae.

scholarly journals Pantoea Bacteriophage vB_PagS_MED16—A Siphovirus Containing a 2′-deoxy-7-amido-7-deazaguanosine-Modified DNA

2021 ◽  
Vol 22 (14) ◽  
pp. 7333
Author(s):  
Monika Šimoliūnienė ◽  
Emilija Žukauskienė ◽  
Lidija Truncaitė ◽  
Liang Cui ◽  
Geoffrey Hutinet ◽  
...  
Keyword(s):  
Comparative Sequence Analysis ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
Host Interactions ◽  
Double Stranded Dna ◽  
New Information ◽  
Modified Dna ◽  
Phage Dna ◽  
Virion Morphogenesis ◽  
Phage Propagation

A novel siphovirus, vB_PagS_MED16 (MED16) was isolated in Lithuania using Pantoea agglomerans strain BSL for the phage propagation. The double-stranded DNA genome of MED16 (46,103 bp) contains 73 predicted open reading frames (ORFs) encoding proteins, but no tRNA. Our comparative sequence analysis revealed that 26 of these ORFs code for unique proteins that have no reliable identity when compared to database entries. Based on phylogenetic analysis, MED16 represents a new genus with siphovirus morphology. In total, 35 MED16 ORFs were given a putative functional annotation, including those coding for the proteins responsible for virion morphogenesis, phage–host interactions, and DNA metabolism. In addition, a gene encoding a preQ0 DNA deoxyribosyltransferase (DpdA) is present in the genome of MED16 and the LC–MS/MS analysis indicates 2′-deoxy-7-amido-7-deazaguanosine (dADG)-modified phage DNA, which, to our knowledge, has never been experimentally validated in genomes of Pantoea phages. Thus, the data presented in this study provide new information on Pantoea-infecting viruses and offer novel insights into the diversity of DNA modifications in bacteriophages.

scholarly journals Genome-Wide Effects of Selenium and Translational Uncoupling on Transcription in the Termite Gut Symbiont Treponema primitia

mBio ◽  
2013 ◽  
Vol 4 (6) ◽  
Author(s):  
Eric G. Matson ◽  
Adam Z. Rosenthal ◽  
Xinning Zhang ◽  
Jared R. Leadbetter
Keyword(s):  
Protein Synthesis ◽  
Large Body ◽  
Transcriptional Responses ◽  
Translational Coupling ◽  
Genome Wide ◽  
A Genome ◽  
Protein Encoding ◽  
Termite Gut ◽  
Inhibiting Protein ◽  
Encoding Genes

ABSTRACTWhen prokaryotic cells acquire mutations, encounter translation-inhibiting substances, or experience adverse environmental conditions that limit their ability to synthesize proteins, transcription can become uncoupled from translation. Such uncoupling is known to suppress transcription of protein-encoding genes in bacteria. Here we show that the trace element selenium controls transcription of the gene for the selenocysteine-utilizing enzyme formate dehydrogenase (fdhFSec) through a translation-coupled mechanism in the termite gut symbiontTreponema primitia, a member of the bacterial phylumSpirochaetes. We also evaluated changes in genome-wide transcriptional patterns caused by selenium limitation and by generally uncoupling translation from transcription via antibiotic-mediated inhibition of protein synthesis. We observed that inhibiting protein synthesis inT. primitiainfluences transcriptional patterns in unexpected ways. In addition to suppressing transcription of certain genes, the expected consequence of inhibiting protein synthesis, we found numerous examples in which transcription of genes and operons is truncated far downstream from putative promoters, is unchanged, or is even stimulated overall. These results indicate that gene regulation in bacteria allows for specific post-initiation transcriptional responses during periods of limited protein synthesis, which may depend both on translational coupling and on unclassified intrinsic elements of protein-encoding genes.IMPORTANCEA large body of literature demonstrates that the coupling of transcription and translation is a general and essential method by which bacteria regulate gene expression levels. However, the potential role of noncanonical amino acids in regulating transcriptional output via translational control remains, for the most part, undefined. Furthermore, the genome-wide transcriptional state in response to translational decoupling is not well quantified. The results presented here suggest that the noncanonical amino acid selenocysteine is able to tune transcription of an important metabolic gene via translational coupling. Furthermore, a genome-wide analysis reveals that transcriptional decoupling produces a wide-ranging effect and that this effect is not uniform. These results exemplify how growth conditions that impact translational processivity can rapidly feed back on transcriptional productivity of prespecified groups of genes, providing bacteria with an efficient response to environmental changes.

scholarly journals Contribution of Penicillin-Binding Protein Homologs to Antibiotic Resistance, Cell Morphology, and Virulence of Listeria monocytogenes EGDe

2006 ◽  
Vol 50 (8) ◽  
pp. 2824-2828 ◽  
Author(s):  
Caitriona M. Guinane ◽  
Paul D. Cotter ◽  
R. Paul Ross ◽  
Colin Hill
Keyword(s):  
Listeria Monocytogenes ◽  
Cell Morphology ◽  
Insertional Mutagenesis ◽  
Binding Protein ◽  
Open Reading Frames ◽  
Penicillin Binding Protein ◽  
Virulence Potential ◽  
Protein Encoding ◽  
Encoding Genes ◽  
Reading Frames

ABSTRACT Seven open reading frames, annotated as potential penicillin-binding-protein-encoding genes (lmo0441, lmo0540, lmo1438, lmo1892, lmo2039, lmo2229, and lmo2754), were targeted for insertional mutagenesis in Listeria monocytogenes EGDe. These genes were found to contribute in various degrees to β-lactam resistance, cell morphology, or the virulence potential of this organism.

scholarly journals A genome-wide resource of cell cycle and cell shape genes of fission yeast

Open Biology ◽  
2013 ◽  
Vol 3 (5) ◽  
pp. 130053 ◽  
Author(s):  
Jacqueline Hayles ◽  
Valerie Wood ◽  
Linda Jeffery ◽  
Kwang-Lae Hoe ◽  
Dong-Uk Kim ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Fission Yeast ◽  
Cell Shape ◽  
Cell Cycle Progression ◽  
Cycle Progression ◽  
Gene Deletions ◽  
Genome Wide ◽  
A Genome ◽  
Protein Encoding ◽  
Encoding Genes

To identify near complete sets of genes required for the cell cycle and cell shape, we have visually screened a genome-wide gene deletion library of 4843 fission yeast deletion mutants (95.7% of total protein encoding genes) for their effects on these processes. A total of 513 genes have been identified as being required for cell cycle progression, 276 of which have not been previously described as cell cycle genes. Deletions of a further 333 genes lead to specific alterations in cell shape and another 524 genes result in generally misshapen cells. Here, we provide the first eukaryotic resource of gene deletions, which describes a near genome-wide set of genes required for the cell cycle and cell shape.

scholarly journals Characterization of the first Pseudomonas grimontii bacteriophage, PMBT3

2021 ◽  
Author(s):  
Sabrina Sprotte ◽  
Erik Brinks ◽  
Natalia Wagner ◽  
Andrew M. Kropinski ◽  
Horst Neve ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Phage Genome ◽  
Genome Sequences ◽  
Significant Similarity ◽  
Protein Encoding ◽  
The Family ◽  
Encoding Genes

AbstractThe complete genome sequence of the virulent bacteriophage PMBT3, isolated on the proteolytic Pseudomonas grimontii strain MBTL2-21, showed no significant similarity to other known phage genome sequences, making this phage the first reported to infect a strain of P. grimontii. Electron microscopy revealed PMBT3 to be a member of the family Siphoviridae, with notably long and flexible whiskers. The linear, double-stranded genome of 87,196 bp has a mol% G+C content of 60.4 and contains 116 predicted protein-encoding genes. A putative tellurite resistance (terB) gene, originally reported to occur in the genome of a bacterium, was detected in the genome of phage PMBT3.

scholarly journals The Zymoseptoria tritici ORFeome: a functional genomics community resource

2019 ◽  
Author(s):  
Yogesh Chaudhari ◽  
Timothy C. Cairns ◽  
Yaadwinder Sidhu ◽  
Victoria Attah ◽  
Graham Thomas ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Open Reading Frames ◽  
Zymoseptoria Tritici ◽  
Entry Vector ◽  
Plant Infection ◽  
Plasmid Library ◽  
A Genome ◽  
Protein Encoding ◽  
Genomic Characterization ◽  
Serious Disease

AbstractLibraries of protein-encoding sequences can be generated by identification of open reading frames (ORFs) from a genome of choice that are then assembled into collections of plasmids termed ORFeome libraries. These represent powerful resources to facilitate functional genomic characterization of genes and their encoded products. Here, we report the generation of an ORFeome for Zymoseptoria tritici, which causes the most serious disease of wheat in temperate regions of the world. We screened the genome of strain IP0323 for high confidence gene models, identifying 4075 candidates from 10,933 predicted genes. These were amplified from genomic DNA, cloned into the Gateway® Entry Vector pDONR207, and sequenced, providing a total of 3022 quality-controlled plasmids. The ORFeome includes genes predicted to encode effectors (n = 410) and secondary metabolite biosynthetic proteins (n = 171), in addition to genes residing at dispensable chromosomes (n= 122), or those that are preferentially expressed during plant infection (n = 527). The ORFeome plasmid library is compatible with our previously developed suite of Gateway® Destination vectors, which have various combinations of promoters, selection markers, and epitope tags. The Z. tritici ORFeome constitutes a powerful resource for functional genomics, and offers unparalleled opportunities to understand the biology of Z. tritici.

scholarly journals Grimontia sedimenti sp. nov., isolated from benthic sediments near coral reefs south of Kuwait

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Huda Mahmoud ◽  
Liny Jose ◽  
Susan Eapen
Keyword(s):  
Coral Reefs ◽  
Type Species ◽  
Phenotypic Analysis ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
A Genome ◽  
Protein Encoding ◽  
Benthic Sediments ◽  
Encoding Genes

A Gram-stain-negative, rod and rod-curved shaped motile bacterium designated strain S25T was obtained from benthic sediment collected near the Kubbar Island coral reefs south of Kuwait. Phenotypic analysis revealed that strain S25T was slightly halophilic, mesophilic and facultative anaerobic, fermenting d-glucose, d-ribose, d-mannose, d-mannitol, maltose, fructose, gentiobiose, cellobiose, melibiose, trehalose and sucrose. It was positive for oxidase and indole production and negative for arginine dihydrolase and lysine and ornithine decarboxylases. It contained C16 : 1  ω7c/C16 : 1  ω6c (summed feature 3), C18 : 1 ω7c (summed feature 8) and C16 : 0 as the major fatty acids. Strain S25T grew optimally at 30 °C and pH 8 in the presence of 3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA sequences revealed that strain S25T is related to species of the genus Grimontia , having 99.15 % similarity to ‘Grimontia indica’ AK16T, 99.08 % to Grimontia celer 96-237T and 98.66 % to Grimontia marina IMCC 5001T. The DNA G+C content was 48.8 mol% and the full genome analysis for the strain S25T showed that the bacterium has a genome size of 5 158 621 bp and contains 4730 predicted protein-encoding genes. The average nucleotide identity values between the S25T genome and the genomes of its nearest matches ranged between 81.39 and 94.16 %. The strain was distinguishable from the phylogenetically related genera through differences in several phenotypic properties. On the basis of the phenotypic, phylogenetic and genetic data, strain S25T represents a novel species in the genus Grimontia , for which the name Grimontia sedimenti sp. nov. is proposed. The type strain of Grimontia sedimenti is S25T (=DSM 28878T=LMG 28315T).

Sign in / Sign up

Export Citation Format

Share Document