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 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 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 Sequence of the Genome of the Temperate, Serotype-Converting,Pseudomonas aeruginosa Bacteriophage D3

2000 ◽  
Vol 182 (21) ◽  
pp. 6066-6074 ◽  
Author(s):  
Andrew M. Kropinski
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Sequence Similarity ◽  
Complete Sequence ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
Virus Family ◽  
Double Stranded Dna ◽  
High Degree ◽  
Phage Proteins ◽  
Reading Frames

ABSTRACT Temperate bacteriophage D3, a member of the virus familySiphoviridae, is responsible for serotype conversion in its host, Pseudomonas aeruginosa. The complete sequence of the double-stranded DNA genome has been determined. The 56,426 bp contains 90 putative open reading frames (ORFs) and four genes specifying tRNAs. The latter are specific for methionine (AUG), glycine (GGA), asparagine (AAC), and threonine (ACA). The tRNAs may function in the translation of certain highly expressed proteins from this relatively AT-rich genome. D3 proteins which exhibited a high degree of sequence similarity to previously characterized phage proteins included the portal, major head, tail, and tail tape measure proteins, endolysin, integrase, helicase, and NinG. The layout of genes was reminiscent of lambdoid phages, with the exception of the placement of the endolysin gene, which parenthetically also lacked a cognate holin. The greatest sequence similarity was found in the morphogenesis genes to coliphages HK022 and HK97. Among the ORFs was discovered the gene encoding the fucosamine O-acetylase, which is in part responsible for the serotype conversion events.

scholarly journals Complete Genome Sequence of Acinetobacter baumannii Phage BS46

2020 ◽  
Vol 9 (22) ◽  
Author(s):  
Anastasia V. Popova ◽  
Mikhail M. Shneider ◽  
Yulia V. Mikhailova ◽  
Andrey A. Shelenkov ◽  
Dmitry A. Shagin ◽  
...  
Keyword(s):  
Complete Genome Sequence ◽  
Complete Genome ◽  
Open Reading Frames ◽  
Capsular Polysaccharides ◽  
Bacterial Host ◽  
Gene Encoding ◽  
Content Type ◽  
Double Stranded Dna ◽  
A Genome ◽  
Reading Frames

ABSTRACT Acinetobacter myovirus BS46 was isolated from sewage by J. S. Soothill in 1991. We have sequenced the genome of BS46 and found it to be almost unique. BS46 contains double-stranded DNA with a genome size of 94,068 bp and 176 predicted open reading frames. The gene encoding the tailspike that presumably possesses depolymerase activity toward the capsular polysaccharides of the bacterial host was identified.

scholarly journals EVOLUTION AND VARIATION OF RENIN GENES IN MICE

Genetics ◽  
1984 ◽  
Vol 108 (3) ◽  
pp. 651-667
Author(s):  
Douglas P Dickinson ◽  
Kenneth W Gross ◽  
Nina Piccini ◽  
Carol M Wilson
Keyword(s):  
Gene Expression ◽  
Submandibular Gland ◽  
Regulation Of Gene Expression ◽  
Inbred Strains ◽  
Duplication Event ◽  
Comparative Sequence Analysis ◽  
Chromosome 1 ◽  
Gene Encoding ◽  
Prior Estimate ◽  
Low Levels

ABSTRACT Inbred strains of mice carry Ren-1, a gene encoding the thermostable Renin-1 isozyme. Ren-1 is expressed at relatively low levels in mouse submandibular gland and kidney. Some strains also carry Ren-2, a gene encoding the thermolabile Renin-2 isozyme. Ren-2 is expressed at high levels in the mouse submandibular gland and at very low levels, if at all, in the kidney. Ren-1 and Ren-2 are closely linked on mouse chromosome 1, show extensive homology in coding and noncoding regions and provide a model for studying the regulation of gene expression. An investigation of renin genes and enzymatic activity in wild-derived mice identified several restriction site polymorphisms as well as putative variants in renin gene expression and protein structure. The number of renin genes carried by different subpopulations of wild-derived mice is consistent with the occurrence of a gene duplication event prior to the divergence of M. spretus (2.75-5.5 million yr ago). This conclusion is in agreement with a prior estimate based upon comparative sequence analysis of Ren-1 and Ren-2 from inbred laboratory mice.

scholarly journals Mutation in the ntrR Gene, a Member of the vap Gene Family, Increases the Symbiotic Efficiency of Sinorhizobium meliloti

2001 ◽  
Vol 14 (7) ◽  
pp. 887-894 ◽  
Author(s):  
Boglárka Oláh ◽  
Erno Kiss ◽  
Zoltán Györgypál ◽  
Judit Borzi ◽  
Gyöngyi Cinege ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Pathogenic Bacteria ◽  
Sinorhizobium Meliloti ◽  
Root Nodules ◽  
Nifh Gene ◽  
Dry Weight ◽  
Nodule Occupancy ◽  
Gene Encoding ◽  
Symbiotic Efficiency ◽  
Host Interactions

In specific plant organs, namely the root nodules of alfalfa, fixed nitrogen (ammonia) produced by the symbiotic partner Sinorhizobium meliloti supports the growth of the host plant in nitrogen-depleted environment. Here, we report that a derivative of S. meliloti carrying a mutation in the chromosomal ntrR gene induced nodules with enhanced nitrogen fixation capacity, resulting in an increased dry weight and nitrogen content of alfalfa. The efficient nitrogen fixation is a result of the higher expression level of the nifH gene, encoding one of the subunits of the nitrogenase enzyme, and nifA, the transcriptional regulator of the nif operon. The ntrR gene, controlled negatively by its own product and positively by the symbiotic regulator syrM, is expressed in the same zone of nodules as the nif genes. As a result of the nitrogen-tolerant phenotype of the strain, the beneficial effect of the mutation on efficiency is not abolished in the presence of the exogenous nitrogen source. The ntrR mutant is highly competitive in nodule occupancy compared with the wild-type strain. Sequence analysis of the mutant region revealed a new cluster of genes, termed the “ntrPR operon,” which is highly homologous to a group of vap-related genes of various pathogenic bacteria that are presumably implicated in bacterium-host interactions. On the basis of its favorable properties, the strain is a good candidate for future agricultural utilization.

scholarly journals Characterization of a Novel Thermobifida fusca Bacteriophage P318

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1042
Author(s):  
Cheepudom ◽  
Lin ◽  
Lee ◽  
Meng
Keyword(s):  
Plant Cell Wall ◽  
Hydrolytic Enzymes ◽  
Thermobifida Fusca ◽  
Genome Replication ◽  
Putative Orfs ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Virion Morphogenesis ◽  
Genome Information

Thermobifida fusca is of biotechnological interest due to its ability to produce an array of plant cell wall hydrolytic enzymes. Nonetheless, only one T. fusca bacteriophage with genome information has been reported to date. This study was aimed at discovering more relevant bacteriophages to expand the existing knowledge of phage diversity for this host species. With this end in view, a thermostable T. fusca bacteriophage P318, which belongs to the Siphoviridae family, was isolated and characterized. P318 has a double-stranded DNA genome of 48,045 base pairs with 3′-extended COS ends, on which 52 putative ORFs are organized into clusters responsible for the order of genome replication, virion morphogenesis, and the regulation of the lytic/lysogenic cycle. In comparison with T. fusca and the previously discovered bacteriophage P1312, P318 has a much lower G+C content in its genome except at the region encompassing ORF42, which produced a protein with unknown function. P1312 and P318 share very few similarities in their genomes except for the regions encompassing ORF42 of P318 and ORF51 of P1312 that are homologous. Thus, acquisition of ORF42 by lateral gene transfer might be an important step in the evolution of P318.

scholarly journals Cloning, Expression, Characterization, and Biocatalytic Investigation of the 4-Hydroxyacetophenone Monooxygenase from Pseudomonas putida JD1

2009 ◽  
Vol 75 (10) ◽  
pp. 3106-3114 ◽  
Author(s):  
Jessica Rehdorf ◽  
Christian L. Zimmer ◽  
Uwe T. Bornscheuer
Keyword(s):  
Pseudomonas Putida ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
Open Chain ◽  
Aromatic Ketones ◽  
Heteroaromatic Compounds ◽  
Aliphatic Ketones ◽  
Expression Characterization ◽  
Reading Frames ◽  
Villiger Oxidation

ABSTRACT While the number of available recombinant Baeyer-Villiger monooxygenases (BVMOs) has grown significantly over the last few years, there is still the demand for other BVMOs to expand the biocatalytic diversity. Most BVMOs that have been described are dedicated to convert efficiently cyclohexanone and related cyclic aliphatic ketones. To cover a broader range of substrate types and enantio- and/or regioselectivities, new BVMOs have to be discovered. The gene encoding a BVMO identified in Pseudomonas putida JD1 converting aromatic ketones (HAPMO; 4-hydroxyacetophenone monooxygenase) was amplified from genomic DNA using SiteFinding-PCR, cloned, and functionally expressed in Escherichia coli. Furthermore, four other open reading frames could be identified clustered around this HAPMO. It has been suggested that these proteins, including the HAPMO, might be involved in the degradation of 4-hydroxyacetophenone. Substrate specificity studies revealed that a large variety of other arylaliphatic ketones are also converted via Baeyer-Villiger oxidation into the corresponding esters, with preferences for para-substitutions at the aromatic ring. In addition, oxidation of aldehydes and some heteroaromatic compounds was observed. Cycloketones and open-chain ketones were not or poorly accepted, respectively. It was also found that this enzyme oxidizes aromatic ketones such as 3-phenyl-2-butanone with excellent enantioselectivity (E ≫100).

scholarly journals The Nucleotide Sequence of Shiga Toxin (Stx) 2e-Encoding Phage φP27 Is Not Related to Other Stx Phage Genomes, but the Modular Genetic Structure Is Conserved

2002 ◽  
Vol 70 (4) ◽  
pp. 1896-1908 ◽  
Author(s):  
Jürgen Recktenwald ◽  
Herbert Schmidt
Keyword(s):  
Nucleotide Sequence ◽  
Shiga Toxin ◽  
Phage Genome ◽  
Genetic Recombination ◽  
Genome Structure ◽  
Open Reading Frames ◽  
Functional Modules ◽  
Phage Propagation ◽  
Reading Frames ◽  
Lambdoid Phages

ABSTRACT In this study we determined the complete nucleotide sequence of Shiga toxin 2e-encoding bacteriophage φP27, isolated from the Shiga toxin-producing Escherichia coli patient isolate 2771/97. φP27 is integrated as a prophage in the chromosomal yecE gene. This integration generates identity segments of attL and attR sites with lengths of 11 nucleotides. The integrated prophage genome has a size of 42,575 bp. We identified 58 open reading frames (ORFs), each with a length of >150 nucleotides. The deduced proteins of 44 ORFs showed significant homologies to other proteins present in sequence databases, whereas 14 putative proteins did not. For 29 proteins, we could deduce a putative function. Most of these are related to the basic phage propagation cycle. The φP27 genome represents a mosaic composed of genetic elements which are obviously derived from related and unrelated phages. We identified five short linker sequences of 22 to 151 bp in the φP27 sequence which have also been detected in a couple of other lambdoid phages. These linkers are located between functional modules in the phage genome and are thought to play a role in genetic recombination. Although the overall DNA sequence of φP27 is not highly related to other known phages, the data obtained demonstrate a typical lambdoid genome structure.

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