Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes

Unusual prophages in Mycobacterium abscessus genomes and strain variations in phage susceptibilities

Mycobacterium abscessus infections are relatively common in patients with cystic fibrosis and are clinically challenging, with frequent intrinsic resistance to antibiotics. Therapeutic treatment with bacteriophages offers some promise but faces many challenges including substantial variation in phage susceptibilities among clinical isolates, and the need to personalize therapies for individual patients. Many strains are not susceptible to any phages or are not efficiently killed by lytic phages, including all smooth colony morphotype strains tested to-date. Here, we analyze a set of new M. abscessus isolates for the genomic relationships, prophage content, spontaneous phage release, and phage susceptibilities. We find that prophages are common in these M. abscessus genomes, but some have unusual arrangements, including tandemly integrated prophages, internal duplications, and they participate in active exchange of polymorphic toxin-immunity cassettes secreted by ESX systems. Relatively few strains are efficiently infected by any mycobacteriophages, and the infection patterns do not reflect the overall phylogenetic relationships of the strains. Characterization of these strains and their phage susceptibility profiles will help to advance the broader application of phage therapies for NTM infections.

Isolation, characterization, and genomic analysis of vB_PaeS_TUMS_P81, a lytic bacteriophage against Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic human pathogen that can lead to nosocomial infections which are in turn life threatening. The increase in antibiotic resistance, at an alarming rate, has resulted in a pressing need for alternative therapeutic approaches such as phage therapy, which hold promise according to several studies. This study featured the isolation and characterization of vB_PaeS_TUMS_P81, a new lytic Pseudomonas phage. The whole-genome sequencing indicated that it has a genome of 73,167 bp containing 93 predicted coding sequences. Genes involved in virulence or lysogeny pathway were nowhere to be found in the genome, so it is potentially safe when it comes to therapeutic applications. Genomic and phylogenetic analysis indicated that vB_PaeS_TUMS_P81 is a member of the genus Litunavirus, belonging to Schitoviridae family. The present study lays the groundwork for further research on treatment of P. aeruginosa infections.

Complete Genome Sequences of Cluster F1 Mycobacteriophages Akhila and MilanaBonita

Akhila and MilanaBonita are mycobacteriophages that were isolated from soil in New York using Mycobacterium smegmatis. Both phages have genomes that are 56,251 bp long and contain 99 genes; the genomes differ by only 1 nucleotide. Based on gene content similarity to phages in the Actinobacteriophage Database, both phages are assigned to cluster F1.

Genome Sequence of Gordonia rubripertincta Phage Survivors, a Cluster CT Siphovirus

Bacteriophage Survivors is a siphovirus isolated from Gordonia rubripertincta NRRL B-16540. Survivors has a 45,436-bp genome encoding 69 predicted protein-coding genes, of which 32 have assigned functions. Based on gene content similarity to sequenced actinobacteriophages, Survivors is assigned to phage cluster CT.

Complete Genome Sequences of Cluster S Mycobacteriophages Beelzebub, Raela, and RedRaider77

We isolated three mycobacteriophages that belong to cluster S, namely, Beelzebub, Raela, and RedRaider77. Annotation revealed a genome structure typical of cluster S phages, including an atypical location of two minor tail protein genes in the right arm of these viral genomes.

Genome Sequence of Subcluster L3 Mycobacterium smegmatis mc(2)155 Phage DuncansLeg

Bacteriophage DuncansLeg is a siphovirius isolated in 2021 from soil on the Coastal Carolina University campus in Conway, South Carolina, using the host Mycobacterium smegmatis mc²155. DuncansLeg has a 75,593-bp circular genome that contains 126 predicted protein-coding genes and 10 tRNA genes. DuncansLeg is assigned to actinobacteriophage cluster L3.

Evidence of a Set of Core-Function Genes in 16 Bacillus Podoviral Genomes with Considerable Genomic Diversity

Bacteriophage genomes represent an enormous level of genetic diversity and provide considerable potential to acquire new insights about viral genome evolution. In this study, the genome sequences of sixteen Bacillus-infecting bacteriophages were explored through comparative genomics approaches to reveal shared and unique characteristics. These bacteriophages are in the Salasmaviridae family with small (18,548-27,206 bp) double-stranded DNA genomes encoding 25-46 predicted open reading frames. We observe extensive nucleotide and amino acid sequence divergence among a set of core-function genes that present clear synteny. We identify two examples of sequence directed recombination within essential genes, as well as explore the expansion of gene content in these genomes through the introduction of novel open reading frames. Together, these findings highlight the complex evolutionary relationships of phage genomes that include old, common origins as well as new components introduced through mosaicism.

Isolation, characterization, and genomic analysis of vB_PaeP_TUMS_P121, a new lytic bacteriophage infecting Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic human pathogen that can cause life-threatening nosocomial infections. The alarming increase in antibiotic resistance has led to an urgent need for alternative therapeutic approaches, such as phage therapy, which has shown promising results in many studies. In this study, P121, a new lytic Pseudomonas phage, was isolated and characterized. Whole-genome sequencing showed that it has a genome of 73,001 bp that contains 91 predicted coding sequences. No genes involved in virulence or lysogeny were found in the genome, thus making it potentially safe for therapeutic applications. Genomic and phylogenetic analysis indicated that P121 is a member of the genus Litunavirus, family Schitoviridae. The present study provides some basic information for further research on treatment of P. aeruginosa infections.

Complete Genome Sequences of Genamy16 and NovaSharks, Two Gordonia rubripertincta Bacteriophages Isolated from Soil in Southeastern Florida

We report on two actinobacteriophages, Genamy16 and NovaSharks, that were isolated from soil in Florida using Gordonia rubripertincta NRRL B-16540. The genomes of both phages are ~65,000 bp, with similar GC contents, and, based on gene content similarity to phages in the Actinobacteriophage Database, were assigned to phage cluster DV.

Complete Genome Sequence of Arthrobacter Phage ScienceWizSam

Phage ScienceWizSam was isolated from soil using Arthrobacter sp. strain ATCC 21022. The phage genome is 58,217 bp with 96 open reading frames (ORFs). All of the ORFs are transcribed rightwards. Based on gene content similarity, ScienceWizSam is assigned to phage subcluster AU1.

Mycobacteriophage Tarkin: a Cluster E Phage

Mycobacteriophage Tarkin is a newly isolated phage that infects Mycobacterium smegmatis mc2155. Tarkin was discovered in Providence, RI, and has a 75,998-bp genome sequence. Tarkin is predicted to have 142 protein coding genes and 2 tRNA genes. Based on gene content similarity, Tarkin is grouped with mycobacteriophages in cluster E.

Tracking the phage trends: A comprehensive review of applications in therapy and food production

In the present scenario, the challenge of emerging antimicrobial resistance is affecting human health globally. The increasing incidences of multidrug-resistant infections have become harder to treat, causing high morbidity, and mortality, and are posing extensive financial loss. Limited discovery of new antibiotic molecules has further complicated the situation and has forced researchers to think and explore alternatives to antibiotics. This has led to the resurgence of the bacteriophages as an effective alternative as they have a proven history in the Eastern world where lytic bacteriophages have been used since their first implementation over a century ago. To help researchers and clinicians towards strengthening bacteriophages as a more effective, safe, and economical therapeutic alternative, the present review provides an elaborate narrative about the important aspects of bacteriophages. It abridges the prerequisite essential requirements of phage therapy, the role of phage biobank, and the details of immune responses reported while using bacteriophages in the clinical trials/compassionate grounds by examining the up-to-date case reports and their effects on the human gut microbiome. This review also discusses the potential of bacteriophages as a biocontrol agent against food-borne diseases in the food industry and aquaculture, in addition to clinical therapy. It finishes with a discussion of the major challenges, as well as phage therapy and phage-mediated biocontrols future prospects.

Complete Genome Sequence and Characteristics of Mycobacteriophage IkeLoa

Mycobacteriophage IkeLoa is a lytic myovirus. It has a circularly permuted 155,280-bp genome containing 233 putative protein-coding genes, 32 tRNA genes, one tmRNA gene, and 64.7% G+C content. The RNA genes are distributed in five clusters across the genome. Only 28% of IkeLoa's protein-coding genes can be assigned functions.

Genome Sequences of Gordonia rubripertincta Phages LilyPad and PokyPuppy

Two lytic phages infecting Gordonia rubripertincta were isolated from irrigated desert soil. Phage LilyPad and PokyPuppy have 64,158-bp and 77,065-bp genomes, respectively. Based on gene content similarity to phages in the Actinobacteriophage database, LilyPad is assigned to phage subcluster DG1 and PokyPuppy to subcluster CS2.

Complete Genome Sequences of Microbacterium paraoxydans Phages Cassita and Fransoyer

Phages Cassita and Fransoyer were isolated from soil in northwestern Wisconsin using Microbacterium paraoxydans as the host. The genomes of Cassita and Fransoyer are 61,868 bp and 62,277 bp, respectively, with direct terminal repeats. Both phages exhibit siphoviral morphology and are predicted to have lytic life cycles.

Genome Sequences of Three Actinobacteriophage from Cluster FH Isolated Using Arthrobacter globiformis

We report the discovery and genome sequences of three FH cluster actinophage infecting Arthrobacter globiformis B2979. Lilmac1015 and Klevey were isolated from riverbank soil and Prairie from soil collected below a tree. Their respective genome lengths are 49,978, 50,075, and 49,392 bp, with 80, 81, and 78 predicted protein-coding genes.

Genome Sequences of Two Gordonia rubripertincta Cluster DJ Bacteriophages, Pherobrine and Burley

Pherobrine and Burley are siphoviruses infecting Gordonia rubripertincta . Pherobrine has a 60,305-bp genome with 89 predicted protein-coding genes, and Burley has a 60,111-bp genome with 90 predicted protein-coding genes. Both phages are assigned to cluster DJ, where they share 78% gene content similarity with each other.

Genome Sequences of Gordonia Phages GrootJr and NovumRegina

Two Gordonia bacteriophages, GrootJr and NovumRegina, were discovered, sequenced, and annotated. These phages were isolated from distinct soil and water samples, respectively, on Gordonia terrae 3612. These phages belong to the CR2 subcluster and are similar in genome size and gene content.

Expansion of Known Rhodobacter capsulatus Bacteriophage Diversity with 24 Additional Genomes

We report the genome sequences of 24 newly discovered bacteriophages that infect Rhodobacter capsulatus , a model for photosynthesis and horizontal gene transfer studies. All have substantial relatedness to previously reported siphovirus bacteriophages. Most are categorized in known clusters (RcB, RcC, RcD, and RcF), with one forming a new cluster, RcG.

Genome Sequence of Cluster BI1 Streptomyces griseus Phage TaidaOne

Bacteriophage TaidaOne was isolated from soil collected in Taipei, Taiwan, using the host Streptomyces griseus . It is a siphovirus with a 56,183-bp genome that contains 86 protein-coding genes. Based on gene content similarity, it was assigned to actinobacteriophage subcluster BI1, within which only TaidaOne and GirlPower genomes contain an acetyltransferase homolog gene.

Complete Genome Sequences of Actinobacteriophages Anaysia and Caviar

Anaysia and Caviar are temperate siphoviruses isolated from soil using Gordonia terrae 3612 and Mycobacterium smegmatis mc 2 155, respectively. Anaysia’s 52,861-bp genome carries 102 genes, while Caviar’s 47,074-bp genome carries 79 genes. Based on gene content similarity, Anaysia and Caviar are assigned to phage clusters A15 and A3, respectively.

Genome Characteristics of Vardy, a Cluster DJ Actinobacteriophage Isolated on Gordonia rubripertincta in Western North Carolina

Phage Vardy is a lytic siphovirus isolated from creek soil in Cullowhee, NC, using Gordonia rubripertincta NRRL B-16540. Vardy’s 60,144-bp genome contains 90 predicted genes and five copies of a 50-bp motif that may regulate gene expression. Based on gene content similarity, Vardy is assigned to cluster DJ.

Genome Sequence of Arthrobacter Phage NathanVaag

We report the genome sequence of bacteriophage NathanVaag, an actinobacteriophage isolated from soil in El Paso, Texas, that infects Arthrobacter sp. strain ATCC 21022. The 49,645-bp genome contains 73 predicted protein-coding genes. Based on gene content similarity to phages in the Actinobacteriophage Database, NathanVaag is assigned to phage cluster AO1.

Genome Sequences of Microbacterium foliorum Phages Anseraureola, Pondwater, and Yasuo

Anseraureola, Pondwater, and Yasuo are bacteriophages with siphovirus morphology that infect Microbacterium foliorum NRRL B-24224. They were isolated from soil collected in Amherst, Massachusetts, and have genome lengths between 17,362 bp and 17,453 bp. These phages each contain 25 predicted protein-coding genes and are assigned to phage cluster EE.

Complete Genome Sequences of Microbacterium Phages Clayda5 and Gshelby23 and Gordonia Phages Wrigley and Santhid

Bacteriophages Clayda5, Gshelby23, Wrigley, and Santhid were isolated from soil samples collected in Iowa, with genomes typical of actinobacteriophages from clusters EB, EM, CY, and DY, respectively. Wrigley and Santhid were isolated on Gordonia terrae and are likely to be temperate. Clayda5 and Gshelby23 were isolated on Microbacterium foliorum .

Genome Sequence and Characteristics of the Microbacterium foliorum Cluster EE Bacteriophage Burgy

Burgy is a siphovirus that was isolated from compost soil near Fremont Township, Iowa, using Microbacterium foliorum NRRL B-24224. The genome has a length of 17,453 bp and contains 25 total protein-coding genes, 20 of which were assigned functions. Based on gene content, Burgy was assigned to actinobacteriophage cluster EE.

Genome Characterization of Gordonia Phage Amore2

Novel Gordonia phage Amore2 was isolated from Pittsburgh, Pennsylvania and infects Gordonia terrae 3612. Amore2 was placed into Actinobacteria cluster CS1. Its genome is 73,842 bp with 105 predicted open reading frames and 56.6% GC content. The closest similarity of Amore2 is Gordonia phage Austin, with a 98% nucleotide identity.

Complete Genome Sequence of Bacteriophage Eula, Isolated on Microbacterium foliorum

Eula is a lytic microbacteriophage extracted from a soil sample collected in Statesville, NC, and isolated on Microbacterium foliorum NRRL B-24224. The Eula double-stranded DNA genome is 41,379 bp, with 69 predicted protein-coding genes and 1 tRNA. Based on gene content similarity, Eula was assigned to bacteriophage cluster EB.

Forty Years without Family: Three Novel Bacteriophages with High Similarity to SPP1 Reveal Decades of Evolutionary Stasis since the Isolation of Their Famous Relative

SPP1, an extensively studied bacteriophage of the Gram-positive Bacillus subtilis, is a model system for the study of phage-host interactions. Despite progress in the isolation and characterization of Bacillus phages, no previously fully sequenced phages have shared more than passing genetic similarity to SPP1. Here, we describe three virulent phages very similar to SPP1; SPP1 has greater than 80% nucleotide sequence identity and shares more that 85% of its protein coding genes with these phages. This is remarkable, given more than 40 years between the isolation of SPP1 and these phages. All three phages have somewhat larger genomes and more genes than SPP1. We identified a new putative gene in SPP1 based on a conserved sequence found in all phages. Gene conservation connotes purifying selection and is observed in structural genes and genes involved in DNA metabolism, but also in genes of unknown function, suggesting an important role in phage survival independent of the environment. Patterns of divergence point to genes or gene domains likely involved in adaptation to diverse hosts or different environments. Ultimately, comparative genomics of related phages provides insight into the long-term selective pressures that affect phage-bacteria interactions and alter phage genome content.

Genome Sequences and Characteristics of Six Cluster B1 Mycobacteriophages Discovered at Saint Joseph’s University

We report on six new siphoviruses infecting Mycobacterium smegmatis that were isolated from soil samples collected on the campus of Saint Joseph’s University, on the western edge of Philadelphia, Pennsylvania. All phages have circularly permuted genomes that are 68,721 to 68,929 bp long, with an average G+C content of 66.4%.

Complete Genome Sequence of Microbacterium foliorum Bacteriophage Librie

Bacteriophage Librie was isolated from a soil sample from Clarksville, TN, using the bacterium Microbacterium foliorum. Librie has a 39,941 bp genome with 62 predicted protein-coding genes and 1 predicted gene for tRNA. Based on its gene content similarity to actinobacteriophages, Librie is grouped with phages in cluster EA5.

Annotation of the Complete Genome Sequences of Bacteriophages Sara and Birdfeeder

Sara is a siphovirus with a linear 17,362bp genome containing 25 genes. Birdfeeder is a podovirus with a circularly permuted 53,897bp genome containing 52 genes. Sara and Birdfeeder were isolated from environmental samples in Plattsburgh, NY, USA and Forest Hill, MD, USA, respectively, using Microbacterium foliorum NRRL B-24224.

Genome Sequence and Annotation of Bacteriophage Tokki Isolated on Arthrobacter globiformis B-2979

Arthrobacter phage Tokki is a siphovirus isolated from soil in River Falls, Wisconsin. The genome contains 57,652-bp encoding 98 proteins, of which 23 were assigned a function. Tokki’s genome structure and content is typical of other AU2 subcluster phages, except for the lack of an identifiable acetyltransferase.

Complete Genome Sequences of Two Bacteroides uniformis Bacteriophages

Here, we describe the isolation and genomic annotation of two novel siphovirus species of bacteriophages that infect Bacteroides uniformis : Bacteroides phage EMB1 and Bacteroides phage EMB2. EMB1 has a 34,204-bp genome with 48 coding sequences, and EMB2 has a 34,008-bp genome with 47 coding sequences.

Genome Annotation for Pinkcreek, a C1 Subcluster Mycobacteriophage from New Orleans, Louisiana

The mycobacteriophage Pinkcreek (C1 subcluster) was extracted from soil collected on the Dr. Norman C. Francis Parkway Bike Trail in New Orleans, Louisiana. It is a member of the family Myoviridae and infects Mycobacterium smegmatis mc 2 155. The Pinkcreek genome is 153,184 bp and contains 216 predicted protein-coding genes, 29 tRNAs, and 1 transfer-messenger RNA.

Complete Genome Sequences of Two Temperate Bacillus subtilis Phages Isolated at Tumamoc Hill Desert Laboratory

Bacteriophages are important in structuring bacterial communities, including desert soils dominated by Bacillus species. Here, we describe two genetically similar temperate phages isolated on a Bacillus subtilis strain from soil in Tucson, Arizona. Their double-stranded DNA (dsDNA) genomes contain 98 and 102 genes, with a set of 4 genes being found in only one phage.

Complete Genome Sequence of the Cluster P Mycobacteriophage Phegasus

We characterized the complete genome of the cluster P mycobacteriophage Phegasus. Its 47.5-kb genome contains 81 protein-coding genes, 36 of which could be assigned a putative function. Phegasus is most closely related to two subcluster P1 bacteriophages, Mangethe and Majeke, with an average nucleotide identity of 99.63% each.

Genome Sequences of Elezi, Asa16, and Niobe, Three Cluster AZ Phages Isolated Using Arthrobacter globiformis B-2979

The Actinobacteriophages Elezi, Asa16, and Niobe infect Arthrobacter globiformisB-2979 and are closely related to Eraser and London in Cluster AZ. They have flexible noncontractile tails, are predicted to be temperate phages, and their genome sizes range between 43,471 bp and 43,602 bp.

Complete Genome Sequence of Finnry, a Subcluster L3 Mycobacteriophage from Charleston, South Carolina

Subcluster L3 bacteriophage Finnry was isolated from soil collected in Charleston, South Carolina, using Mycobacterium smegmatis mc 2 155 as a host. The genome of this temperate siphovirus is 75,632 bp long (130 predicted protein-coding genes, 9 tRNAs, and no transfer-messenger RNAs), and BLASTn alignment revealed 99.86% identity with the genome of L3 mycobacteriophage Samty.

Complete Genome Sequences of the Novel Cluster BP Phages Infecting Streptomyces sanglieri, AxeJC, Cumberbatch, Eastland, Eklok, HFrancette, Ignacio, Piccadilly, and Vondra

The Streptomyces sanglieri bacteriophages AxeJC, Cumberbatch, Eastland, Eklok, HFrancette, Ignacio, Piccadilly, and Vondra form a novel actinobacteriophage cluster, BP. These siphoviruses have circularly permuted genomes with an average size of 37,700 bp and a GC content of 71%. Each genome contains approximately 58 protein-coding genes, with no tRNAs.

Characterization and Genome Sequence of Arthrobacter Phage Iter

Arthrobacter phage Iter was isolated in North Georgia. Its genome is 43,963 bp with 70 open reading frames (ORFs) and a GC content of 67.4%. It shares 89.11% nucleotide identity with Arthrobacter phage Phives. Actinobacteriophages that share over 50% nucleotide identity are sorted into clusters, with Iter in cluster AZ.

Complete Genome Sequence of Bacteriophage Loca, Isolated on a Microbacterium foliorum Culture

Microbacteriophage Loca was extracted from a shopping cart handle swab sample in Stephenville, TX, and isolated on a Microbacterium foliorum NRRL-24224 culture. The 17,475-bp double-stranded DNA genome contains 25 predicted protein-coding genes and has >96% nucleotide identity to bacteriophages Quaker and Livingwater.

Genomic characterization of a novel bacteriophage STP55 revealed its prominent capacity in disrupting the dual-species biofilm formed by Salmonella Typhimurium and Escherichia coli O157: H7 strains

Salmonella and Escherichia coli are important foodborne pathogens, forming bacterial biofilms that contribute to their virulence, antimicrobial resistance, and survival on surfaces. Broad lytic phages are promising alternatives to conventional technologies for pathogen biocontrol and reducing biofilms. Herein, we isolated and characterized a novel polyvalent phage STP55 that not only lyse some serotypes of Salmonella, but also some E. coli strains. It had a wide range of pH (4-12) and thermal (30-60 °C) tolerances. The latent time was determined to be 10 min in the one-step growth experiment. Morphological observations by transmission electron microscopy and phylogenetic analysis using terminase gene classified STP55 to family Ackermannviridae in the order Caudovirales, with a complex tail structure. The genome was found to comprise 157,708 bp double-stranded DNA, with 44.57% GC content, 207 predicted ORFs and with no genes associated with antibiotic resistance, toxins, lysogeny, and virulence factors. Particularly, phage STP55 was able to inhibit single- and dual-species biofilms formation by S. Typhimurium ATCC 14028 and E. coli O157: H7, with a reduction percentage of 51.0%, 47.8% and 52.8%, respectively. Moreover, more than 65.0%, 72.9% and 46.2% of an established, single- and dual-species biofilms by S. Typhimurium ATCC 14028 and E. coli O157: H7 were removed after 8 h exposure to the phage STP55, respectively. The elimination effect of STP55 on dual-species biofilm formed on lettuce was further observed by SEM. Overall, our results demonstrated that STP55 is a promising antimicrobial against Salmonella and E. coli.

Comparative Genomics of Six Lytic Bacillus subtilis Phages from the Southwest United States

Background

Despite their importance to microbial dynamics involving Bacillus subtilis, we have a limited understanding of the diversity of phages that can lyse this model organism.

Materials and Methods

Phages were isolated from soil samples collected from various sites in the southwest U.S. deserts on a wild B. subtilis strain. Their genomes were assembled, characterized, and bioinformatically compared.

Results

Six Siphoviruses with high nucleotide and amino acid similarity to each other (>80%) but very limited similarity to phages currently in GenBank were isolated. These phages have double-stranded DNA genomes (55,312 to 56,127 bp) with 86-91 putative protein coding genes, and a low GC content. Comparative genomics reveal differences in loci encoding proteins that are putatively involved in bacterial adsorption with evidence for genomic mosaicism and a possible role for small genes.

Conclusions

A comparative approach provides insights into phage evolution, including the role of indels in protein folding.

Complete Genome Sequences of Mycobacteriophages SynergyX, Abinghost, Bananafish, and Delton

Four lytic mycobacteriophages, namely, SynergyX, Abinghost, Bananafish, and Delton, were isolated from soil in Washington, DC, using the bacterial host Mycobacterium smegmatis mc²155. Analysis of the genomes revealed that they belong to two subclusters of actinobacteriophage cluster B (subclusters B2 and B3) and subcluster D1 of cluster D.

Genome Sequence of Arthrobacter globiformis Phage KeAlii from Hawaiʻi

Here, we report the genome sequence of bacteriophage KeAlii, a Siphoviridae that infects Arthrobacter globiformis strain B-2979, from Honolulu, Hawaiʻi. The 41,850-bp genome contains 66 predicted protein-coding genes and 1 gene that encodes a tRNA for tryptophan. Genome comparisons suggest KeAlii is closely related to actinobacteriophage Adolin.

Genome Sequence of CaiB, a DR Cluster Actinobacteriophage That Infects Gordonia rubripertincta

CaiB is a DR cluster actinobacteriophage that was isolated from soil in Florida using Gordonia rubripertincta NRRL B-16540 as the host. The genome is 61,620 bp, has a GC content of 68.6%, and contains 85 predicted protein coding genes. CaiB has several putative operons and has repeated intergenic regions that may be involved in gene regulation.

A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence

Regulation of bacteriophage gene expression involves repressor proteins that bind and downregulate early lytic promoters. A large group of mycobacteriophages code for repressors that are unusual in also terminating transcription elongation at numerous binding sites (stoperators) distributed across the phage genome. Here we provide the X-ray crystal structure of a mycobacteriophage immunity repressor bound to DNA, which reveals the binding of a monomer to an asymmetric DNA sequence using two independent DNA binding domains. The structure is supported by small-angle X-ray scattering, DNA binding, molecular dynamics, and in vivo immunity assays. We propose a model for how dual DNA binding domains facilitate regulation of both transcription initiation and elongation, while enabling evolution of other superinfection immune specificities.

Bacteriophage repressor proteins downregulate viral lytic gene expression. Herein, the authors present the X-ray crystal structure of a monomeric repressor that binds an asymmetric DNA sequence using two independent domains.

Mycobacteriophages: From Petri dish to patient

Mycobacteriophages-bacteriophages infecting Mycobacterium hosts-contribute substantially to our understanding of viral diversity and evolution, provide resources for advancing Mycobacterium genetics, are the basis of high-impact science education programs, and show considerable therapeutic potential. Over 10,000 individual mycobacteriophages have been isolated by high school and undergraduate students using the model organism Mycobacterium smegmatis mc2155 and 2,100 have been completely sequenced, giving a high-resolution view of the phages that infect a single common host strain. The phage genomes are revealed to be highly diverse and architecturally mosaic and are replete with genes of unknown function. Mycobacteriophages have provided many widely used tools for Mycobacterium genetics including integration-proficient vectors and recombineering systems, as well as systems for efficient delivery of reporter genes, transposons, and allelic exchange substrates. The genomic insights and engineering tools have facilitated exploration of phages for treatment of Mycobacterium infections, although their full therapeutic potential has yet to be realized.

Isolation and Annotation of the Genome Sequences of Bacteriophages InvictusManeo (Subcluster K5) and Netyap (Subcluster L2)

The mycobacteriophages InvictusManeo (K5 subcluster) and Netyap (L2 subcluster) were isolated from soils in Cullowhee Creek, Cullowhee, North Carolina. Both exhibit Siphoviridae morphology and infect Mycobacterium smegmatis mc2155. The InvictusManeo genome is 61,147 bp and contains 96 predicted protein-coding genes, whereas the Netyap genome is 76,366 bp with 131 predicted protein-coding genes.