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

Amend, Amber M; Bifone, Jacob P; Brewer, Justin C; Denton, Makayla N; Gilbert, Eden B; Grimm, Abigail C; Hogan, Jaden M; Kelley, Reagan M; Kelly-Brooner, Lennon J; Mukerji, Jit A; Osterhoudt, Matthew; Senn, Cody R; Smith, Bethanie R; Stillwell, Olive G; Vo, Jimmy; Watt, Danielle K; Connerly, Pamela L.; Rueschhoff, Elizabeth E.

doi:10.1128/mra.01086-22

Cited by 3 publications

(3 citation statements)

References 14 publications

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“…Soos, a novel bacteriophage that infects Gordonia rubripertincta NRRL B-16540 , was isolated from a soil sample from Jeffersonville, Indiana, USA (Global Positioning System [GPS] coordinates 38.34446 N, 85.81798 W) using standard protocols ( 3 , 4 ). The sample was washed in peptone yeast calcium agar (PYCa) media, which was then filtered through a 0.22 µm filter.…”

Section: Announcementmentioning

confidence: 99%

“…The following programs were employed to annotate the genome as previously described ( 4 ) using default parameters: DNA Master (v5.23.6 Build 2705 24 October 2021) ( https://phagesdb.org/DNAMaster/ ), Glimmer (v3.02b) ( 7 ), GeneMark [v2.5p (09.08.06)] ( 8 ), Starterator (v532; http://phages.wustl.edu/starterator/ ), Phamerator (Actino_Draft v532) ( 9 ), BLASTp (v2.14.0) ( 10 ), HHPred [utilizing databases: PDB_mmCIF70_10_Jan, Pfam-A_v35, UniProt-SwissProt-viral70_3_Nov_2021, and NCBI_Conserved_Domains(CD)_v3.19] ( 11 ), Aragorn (v1.2.41) ( 12 ), tRNAscanSE (v2.0.012) ( 13 ), and DeepTMHMM (version 1.0.24) ( 14 ). All 87 annotated genes were protein-coding genes transcribed in the same direction.…”

Section: Announcementmentioning

confidence: 99%

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Genome sequence of Soos: a siphovirus of the CP cluster infecting Gordonia rubripertincta  

Adams,

Britton,

Bruce

et al. 2024

Microbiol Resour Announc

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Section: Announcementmentioning

confidence: 99%

Section: Announcementmentioning

confidence: 99%

Genome sequence of Soos: a siphovirus of the CP cluster infecting Gordonia rubripertincta  

Adams,

Britton,

Bruce

et al. 2024

Microbiol Resour Announc

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“…Initially regarded as opportunistic pathogens in humans, 10 Gordonia species have attracted considerable interest in recent years owing to their ability to biodegrade environmental pollutants and synthesize organic compounds beneficial for both environmental and industrial applications. 11 Moreover, Gordonia strains have demonstrated proficiency in synthesizing non-toxic pigments, especially carotenoids. 12 Carotenoids rank among the high-value natural pigments due to their diverse biological activities, 13 ranging from antioxidant capacities to serving as precursors to vitamins and exhibiting antitumor and antimicrobial properties.…”

Section: Introductionmentioning

confidence: 99%

Optimized carotenoid production and antioxidant capacity of Gordonia hongkongensis

Rhenals-Montoya,

Villamil,

Sánchez-Suárez

et al. 2024

Science Progress

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The current emphasis within the cosmetic market on sustainable ingredients has heightened the exploration of new sources for natural, active components. Actinomycetota, recognized for producing pigments with bioactive potential, offer promising functional cosmetic ingredients. This study aimed to optimize pigment and antioxidant metabolite production from the Gordonia hongkongensis strain EUFUS-Z928 by implementing the Plackett-Burman experimental design and response surface methodology. Extracts derived from this strain exhibited no cytotoxic activity against human primary dermal fibroblast (HDFa, ATCC® PCS-201-012™, Primary Dermal Fibroblast; Normal, Human, Adult). Eight variables, including inoculum concentration, carbon and nitrogen source concentration, NaCl concentration, pH, incubation time, temperature, and stirring speed, were analyzed using the Plackett-Burman experimental design. Subsequently, factors significantly influencing pigment and antioxidant metabolite production, such as temperature, inoculum concentration, and agitation speed, were further optimized using response surface methodology and Box-Behnken design. The results demonstrated a substantial increase in absorbance (from 0.091 to 0.32), DPPH radical scavenging capacity (from 27.60% to 84.61%), and ABTS radical scavenging capacity (from 17.39% to 79.77%) compared to responses obtained in the isolation medium. The validation of the mathematical model accuracy exceeded 90% for all cases. Furthermore, liquid chromatography coupled with mass spectrometry (LC-MS) facilitated the identification of compounds potentially responsible for enhanced pigment production and antioxidant capacity in extracts derived from G. hongkongensis. Specifically, six carotenoids, red-orange pigments with inherent antioxidant capacity, were identified as the main enhanced compounds. This comprehensive approach effectively optimized the culture conditions and medium of a G. hongkongensis strain, resulting in enhanced carotenoid production and antioxidant capacity. Beyond identifying bioactive compounds and their potential cosmetic applications, this study offers insights into the broader industrial applicability of these extracts. It underscores the potential of G. hongkongensis and hints at the future utilization of other untapped sources of rare actinomycetes within the industry.

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Genomic and proteomic characterization of vB_SauM-UFV_DC4, a novel Staphylococcus jumbo phage

da Silva,

Melo,

Santos

et al. 2023

Appl Microbiol Biotechnol

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Staphylococcusaureus is one of the most relevant mastitis pathogens in dairy cattle, and the acquisition of antimicrobial resistance genes presents a significant health issue in both veterinary and human fields. Among the different strategies to tackle S. aureus infection in livestock, bacteriophages have been thoroughly investigated in the last decades; however, few specimens of the so-called jumbo phages capable of infecting S. aureus have been described. Herein, we report the biological, genomic, and structural proteomic features of the jumbo phage vB_SauM-UFV_DC4 (DC4). DC4 exhibited a remarkable killing activity against S. aureus isolated from the veterinary environment and stability at alkaline conditions (pH 4 to 12). The complete genome of DC4 is 263,185 bp (GC content: 25%), encodes 263 predicted CDSs (80% without an assigned function), 1 tRNA (Phe-tRNA), multisubunit RNA polymerase, and an RNA-dependent DNA polymerase. Moreover, comparative analysis revealed that DC4 can be considered a new viral species belonging to a new genus DC4 and showed a similar set of lytic proteins and depolymerase activity with closely related jumbo phages. The characterization of a new S. aureus jumbo phage increases our understanding of the diversity of this group and provides insights into the biotechnological potential of these viruses. Key points • vB_SauM-UFV_DC4 is a new viral species belonging to a new genus within the class Caudoviricetes. • vB_SauM-UFV_DC4 carries a set of RNA polymerase subunits and an RNA-directed DNA polymerase. • vB_SauM-UFV_DC4 and closely related jumbo phages showed a similar set of lytic proteins.

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

Cited by 3 publications

References 14 publications

Genome sequence of Soos: a siphovirus of the CP cluster infecting Gordonia rubripertincta

Genome sequence of Soos: a siphovirus of the CP cluster infecting Gordonia rubripertincta

Optimized carotenoid production and antioxidant capacity of Gordonia hongkongensis

Genomic and proteomic characterization of vB_SauM-UFV_DC4, a novel Staphylococcus jumbo phage

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