Title: Complete genome sequence of the Streptomyces bacteriophage Amabiko
Amabiko is a lytic subcluster BE2 bacteriophage that infects Streptomyces scabiei — a bacterium causing common scab in potatoes. Its 131,414 bp genome has a GC content of 49.5% and contains 245 putative protein-coding genes, 45 tRNAs, and one tmRNA. Amabiko is closely related to Streptomyces bacteriophage MindFlayer (gene content similarity: 86.5%). more »« less
ABSTRACT Here, we report the draft genome sequences of two related Streptomyces sp. strains, JV180 and SP18CM02. Despite their isolation from soils in Connecticut and Missouri (USA), respectively, they are strikingly similar in gene content. Both belong to the Streptomyces griseus clade and harbor several secondary metabolite biosynthetic gene clusters.
Gates, Alexandra D; French, Austin M; Demetros, Alexander A; Kelley, Brittni R; Lebeis, Sarah L
(, Phytobiomes Journal)
Although plant microbiome assembly involves a series of both plant–microbe and microbe–microbe interactions, the latter is less often directly tested. Here, we investigate a role for Streptomyces strains to influence assembly of other bacteria into root microbiomes through the use of two synthetic communities (SynComs): a 21-member community including four Streptomyces strains and a 17-member community lacking those Streptomyces strains. Following inoculation with these SynComs on wild-type Arabidopsis thaliana Col-0, differential abundance modeling on root endosphere 16S ribosomal RNA gene amplicon sequencing data revealed altered abundance of four diverse SynCom members: Arthrobacter sp. 131, Agrobacterium sp. 33, Burkholderia sp. CL11, and Ralstonia sp. CL21. Modeling results were tested by seedling coinoculation experiments with the four Streptomyces strains and differentially abundant members, which confirmed the predicted decreased abundance for Arthrobacter sp. 131, Agrobacterium sp. 33, and Ralstonia sp. CL21 when Streptomyces strains were present. We further characterized how the phytohormone salicylic acid (SA) mediates Streptomyces strains’ influence over Agrobacterium sp. 33 and Burkholderia sp. CL11 seedling colonization. Although decreased colonization of Ralstonia sp. CL21 and Arthrobacter sp. 131 when Streptomyces spp. are present were not influenced by SA, direct antibiosis of Arthrobacter sp. 131 by Streptomyces was observed. These results highlight a role for Streptomyces-mediated microbial interactions during plant root microbiome assembly as well as distinct mechanisms that mediate them. Understanding the role of microbial interactions during microbiome assembly will inform the production of beneficial microbial treatments for use in agricultural fields.
Here, we characterized the complete genome of the Siphoviridae BiggityBass, a lytic subcluster DR bacteriophage infecting Gordonia terrae CAG3. Its 63.2-kb genome contains 84 protein-coding genes, of which 40 could be assigned a putative function. BiggityBass is related most closely to AnClar and Yago84 with 90.61% and 90.52% nucleotide identity, respectively.
Milhaven, Mark; Cai, Lindsey; Cherian, Sanjana; Johnson, Kamalei; Salas Perez, Kevin; Blanco, Madison; Garg, Aman; Lobatos, Jackelyn; Mitra, Corinne; Strasser, Maria; et al
(, Microbiology Resource Announcements)
Roux, Simon
(Ed.)
ABSTRACT We characterized the complete genome sequence of Chako, an obligate lytic bacteriophage with siphovirus morphology from subcluster EA1 that infects Microbacterium foliorum NRRL B-24224. Its 41.6-kb genome contains 62 putative protein-coding genes and is highly similar to that of bacteriophage HanSolo (99.26% nucleotide identity).
Qi, Yunci; Nepal, Keshav K.; Blodgett, Joshua A.
(, Proceedings of the National Academy of Sciences)
Streptomyces genomes harbor numerous, biosynthetic gene clusters (BGCs) encoding for drug-like compounds. While some of these BGCs readily yield expected products, many do not. Biosynthetic crypticity represents a significant hurdle to drug discovery, and the biological mechanisms that underpin it remain poorly understood. Polycyclic tetramate macrolactam (PTM) antibiotic production is widespread within the Streptomyces genus, and examples of active and cryptic PTM BGCs are known. To reveal further insights into the causes of biosynthetic crypticity, we employed a PTM-targeted comparative metabologenomics approach to analyze a panel of S. griseus clade strains that included both poor and robust PTM producers. By comparing the genomes and PTM production profiles of these strains, we systematically mapped the PTM promoter architecture within the group, revealed that these promoters are directly activated via the global regulator AdpA, and discovered that small promoter insertion–deletion lesions (indels) differentiate weaker PTM producers from stronger ones. We also revealed an unexpected link between robust PTM expression and griseorhodin pigment coproduction, with weaker S. griseus –clade PTM producers being unable to produce the latter compound. This study highlights promoter indels and biosynthetic interactions as important, genetically encoded factors that impact BGC outputs, providing mechanistic insights that will undoubtedly extend to other Streptomyces BGCs. We highlight comparative metabologenomics as a powerful approach to expose genomic features that differentiate strong, antibiotic producers from weaker ones. This should prove useful for rational discovery efforts and is orthogonal to current engineering and molecular signaling approaches now standard in the field.
@article{osti_10568258,
place = {Country unknown/Code not available},
title = {Complete genome sequence of the Streptomyces bacteriophage Amabiko},
url = {https://par.nsf.gov/biblio/10568258},
DOI = {10.1128/mra.00182-24},
abstractNote = {Amabiko is a lytic subcluster BE2 bacteriophage that infects Streptomyces scabiei — a bacterium causing common scab in potatoes. Its 131,414 bp genome has a GC content of 49.5% and contains 245 putative protein-coding genes, 45 tRNAs, and one tmRNA. Amabiko is closely related to Streptomyces bacteriophage MindFlayer (gene content similarity: 86.5%).},
journal = {Microbiology Resource Announcements},
volume = {13},
number = {6},
publisher = {ASM Journals},
author = {Milhaven, Mark and Bakry, Heba A and Batra, Anuvi and Bermingham, Amanda M and Grama, Gloria and Kebe, Jacob and Martinez, Shawn S and Mudunuri, Rishika V and Nelson, Megan R and Nguyen, Evie T and Peterson, Mia M and Pruitt, Alexis and Tran, Kristan and Brar, Akarshi and Cerna, Gabriella and Chaffee, Elaine and Caruso, Steven M and Pfeifer, Susanne P},
editor = {Dennehy, John J}
}
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