Biology subjects

Freise, A. C.

Publications and source records attributed to Freise, A. C..

8 recordsLinked to original sources

bioRxiv2025

Comparative genomic analysis of Cluster AZ Arthrobacter phages

Bacteria in the Arthrobacter genus belong to the phylum Actinobacteria and are primarily soil-dwelling. Over 600 bacteriophages infecting Arthrobacter hosts have been isolated and sequenced, and genomic analyses show these phages to be highly diverse with mosaic genome architectures. We describe here a group of 32 Arthrobacter phages grouped in Cluster AZ, isolated on four different Arthrobacter strains all with siphoviral morphologies. The Cluster AZ phages exhibit a spectrum of diversity and can be subdivided into four subclusters. The diversity in minor tail protein and endolysin genes correlates partly with isolation host strain and may be predictive of the host range of these phages. Most of the Cluster AZ phages are temperate, form stable lysogens, and encode an integrase; however, an immunity repressor gene has not been identified. The intracluster diversity was analyzed in-depth at the whole genome level and through individual genes. As more Arthrobacter phages are isolated and analyzed they continue to provide new insights into phage evolution.

genomics↗

bioRxiv2022

Characterization of Genomic Diversity In Bacteriophages Infecting Rhodococcus

Bacteriophages are globally ubiquitous viruses that infect bacteria. With nearly 4,000 sequenced genomes of phages infecting the phylum Actinobacteria available, genomic analyses of these actinobacteriophage genomes has been instrumental in uncovering a diverse genomic landscape often characterized by genome mosaicism. Here, we describe the genomic characterization of 57 sequenced phages capable of infecting the genus Rhodococcus. These phages were previously isolated at multiple institutions by students in the SEA-PHAGES program using four different species of Rhodococcus. Most Rhodococcus phages have been grouped into 4 clusters based on their genomic similarities; 13 phages are singletons too genetically distinct for clustering. These clusters and singletons contain Siphoviridae and Myoviridae phages, and most contain integrase and repressor genes indicative of a potential lysogenic life cycle. The genome size of these phages varies from 14,270 bp to 142,586 bp and their G+C% content ranges from 41.2-68.4%, while that of their Rhodococcus hosts typically exceeds 60%. Through comparative genomic analyses, it was revealed that these Rhodococcus phages display high intracluster similarity but low intercluster similarity, despite their shared ability to infect the same host genus. Additionally, these Rhodococcus phages share similarities with phages that infect other Actinobacterial hosts such as Gordonia, Streptomyces and Arthrobacter.

microbiology↗

bioRxiv2022

Exploring Genomic Conservation in Actinobacteriophages with Small Genomes

Actinobacteriophages of a wide range of genome sizes continue to be isolated and characterized, but only a handful of these have atypically small genomes, defined in this work as genome sizes under 20,000 bp. These "small phages" are relatively rare and have received minimal study thus far. Of the actinobacteriophages published in PhagesDB.org, small phages have been isolated on Arthrobacter, Gordonia, Rhodococcus, and Microbacterium hosts. A previous study by Pope et al. showed that Gordonia small phages have similar gene products and amino acid sequences. Here, we set out to further examine relationships between small Gordonia phages as well as small phages that infect other hosts. Of the 3222 sequenced phages listed on PhagesDB, we identified 109 distinctly small phages with genome sizes under 20,000 bp. The majority of the small phages were isolated on Arthrobacter or Microbacterium hosts. Using comparative genomics, we searched for patterns of similarity among 34 cluster-representative small phages. Dot plot comparisons showed that there was more amino acid conservation than nucleotide identity amongst small phages. Gene content similarity (GCS) analysis revealed that the temperate Gordonia phages in Cluster CW share significant GCS values (over 35%) with the lytic Arthrobacter phages in Cluster AN, suggesting that some small phages have a considerable degree of genomic similarity with each other. SplitsTree analyses of shared phams (genes with substantial amino acid identity) supported the complexity of clustering criteria in small phages, given shuffling of genes across phages of different clusters and close relationships despite varied cluster membership. We observed this continuum of phage diversity through Rhodococcus phage RRH1s closer similarity to phages in Gordonia subcluster CW1 than CW1 is to Gordonia subcluster CW3. Finally, we were able to confirm the presence of conserved phams across not only small Gordonia phages but also within small phages from different clusters and hosts. Studying these genomic trends hidden in small phages allows us to better understand and appreciate the overall diversity of phages.

microbiology↗

bioRxiv2020

Complete Genome Sequences of Nine Cluster A Mycobacteriophages: AgentM, Ajay, Aragog, Archetta, ForGetIt, Koko, Ph8s, Phlorence, and Wilkins

BackgroundBacteriophages are ubiquitous, highly diverse, and relatively understudied. Growing interest in phage therapy has underscored the importance of isolating and characterizing novel bacteriophages. The Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program aims to address this need by involving undergraduates around the world in authentic research. Materials and MethodsNine novel mycobacteriophages - AgentM, Ajay, Aragog, Archetta, ForGetIt, Koko, Ph8s, Phlorence, and Wilkins - were isolated from soil samples in southern California using host Mycobacterium smegmatis mc2155. Each purified phage was characterized using transmission electron microscopy and genome sequencing and annotation. ResultsAll nine bacteriophages were placed into mycobacteriophage Cluster A based on nucleotide similarity with other phages. The average genome length of all nine phages was 50,706 bp. On average, each phage had 87 total coding genes and GC content between 60-63%, consistent with that of other Cluster A phages. Transmission electron microscopy of phage particles revealed they had icosahedral heads and long, flexible tails, consistent with that of the Siphoviridae family. Plaque morphology and genome analysis confirms the nine novel phages are temperate as expected of Cluster A phages. ConclusionsAgentM, Ajay, Aragog, Archetta, ForGetIt, Koko, Ph8s, Phlorence, and Wilkins are all mycobacteriophages that belong to the Siphoviridae family. Comparative genomic analyses revealed genetic mosaicism and diversity among these Cluster A phages. The discovery of these novel phages expands on the existing library of mycobacteriophage genomes.

microbiology↗

bioRxiv2020

Novel Cluster AZ Arthrobacter phages Powerpuff, Lego, and YesChef exhibit close functional relationships with Microbacterium phages

Bacteriophages exhibit a vast spectrum of relatedness and there is increasing evidence of close genomic relationships independent of host genus. The variability in phage similarity at the nucleotide, amino acid, and gene content levels confounds attempts at quantifying phage relatedness, especially as more novel phages are isolated. This study describes three highly similar novel Arthrobacter globiformis phages-Powerpuff, Lego, and YesChef-which were assigned to Cluster AZ using a nucleotide-based clustering parameter. Phages in Cluster AZ and Microbacterium Cluster EH, as well as the former Microbacterium singleton Zeta1847, exhibited low nucleotide similarity but gene content similarity in excess of the recently adopted Microbacterium clustering parameter, which resulted in the reassignment of Zeta1847 to Cluster EH. Additionally, Clusters AZ and EH phages encode a shared integrase indicative of a lysogenic life cycle; in the first experimental verification of a Cluster AZ phages life cycle, we show that phage Powerpuff is a true temperate phage and forms stable lysogens that exhibit immunity to superinfection by related phages, despite lacking identifiable repressors typically required for lysogenic maintenance and superinfection immunity. The ability of phage Powerpuff to undergo and maintain lysogeny suggests that other closely related phages encoding an integrase but lacking an identified repressor may be temperate as well. Our findings further highlight the importance of using multiple metrics to capture phage relatedness, provide additional evidence of significant shared phage genomic content spanning multiple actinobacterial host genera, and demonstrate the continued need for verification and characterization of life cycles in newly isolated phages.

microbiology↗

bioRxiv2020

Singleton phage BlueFeather reveals novel relationships in the Arthrobacter phage population

Bacteriophages (phages) exhibit high genetic diversity, and the mosaic nature of the shared genetic pool makes quantifying phage relatedness a shifting target. Early parameters for clustering of related Mycobacteria and Arthrobacter phage genomes relied on nucleotide identity thresholds but, more recently, clustering of Gordonia and Microbacterium phages has been performed according to shared gene content. Singleton phages lack the nucleotide identity and/or shared gene content required for clustering newly sequenced genomes with known phages. Whole genome metrics of novel Arthrobacter phage BlueFeather, originally designated a putative singleton, showed low nucleotide identity but high amino acid and gene content similarity with Arthrobacter phages originally assigned to Clusters FE and FI. Gene content similarity revealed that BlueFeather shared genes with these phages in excess of the parameter for clustering Gordonia and Microbacterium phages. Single gene analyses revealed evidence of horizontal gene transfer between BlueFeather and phages in unique clusters that infect a variety of bacterial hosts. Our findings highlight the advantage of using shared gene content to study seemingly genetically isolated phages and have resulted in the reclustering of BlueFeather, a putative singleton, as well as former Cluster FI phages, into a newly expanded Cluster FE.

microbiology↗

bioRxiv2020

Nine Novel Cluster E Mycobacteriophages Isolated from Soil

Novel mycobacteriophages FireRed, MISSy, MPhalcon, Murica, Sassay, Terminus, Willez, YassJohnny, and Youngblood were isolated from soil samples on the host Mycobacterium smegmatis. Transmission electron microscopy revealed phage structures suggestive of the Siphoviridae family of phages. Phage genomes were sequenced and annotated, revealing that they belong to actinobacteriophage Cluster E. Here, we describe the features of these phage genomes and discuss their similarity to previously discovered cluster E phages.

microbiology↗

bioRxiv2020

Characterization of novel Actinobacteriophage Giantsbane reveals potential genomic recombination hotspot and unexpected intra-cluster similarities

Bacteriophages that infect Arthrobacter, a genus of bacteria which play key ecological roles in soil, warrant further study. Giantsbane, a novel Actinobacteriophage, was isolated using Arthrobacter globiformis as a host. Transmission electron microscopy and whole-genome sequencing revealed a Siphoviridae morphology and a genome length of 56,734 bp. Genome annotation identified 94 putative genes, such as a duplicated major tail protein and a major capsid and protease fusion protein. No genes were associated with lysogeny, indicating a lytic phage. Giantsbane was assigned to the phage cluster AU. Batch average nucleotide identity analysis and phylogenetic networks constructed from shared genes revealed unexpected nucleotide and gene content similarities within cluster AU. These findings have resulted in the creation of two new AU subclusters and the resubclustering of three AU bacteriophages. Analysis using Phamerator and MEME identified repeated motifs and a gene cassette present in all evaluated cluster AU phages which may promote recombination. These findings offer the first intra-cluster analysis of cluster AU phages and further our understanding of the relationships between closely related bacteriophages.

genomics↗