Genome Sequence of Rhodococcus erythropolis Type Strain JCM 3201

Yoshida, Kiyomi; Kitagawa, Wataru; Ishiya, Koji; Mitani, Yasuo; Nakashima, Naotoshi; Aburatani, Sachiyo; Tamura, Tomohide

doi:10.1128/mra.01730-18

Cited by 2 publications

(4 citation statements)

References 19 publications

(17 reference statements)

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“…The genome lengths of E3 and Finch are similar to one another (142,536 bp and 138,896 bp, respectively) with their differences attributable to discrepancies in their number of ORFs (209 and 228, respectively) (Supplemental Table 1). There is some discrepancy between the G+C% content of E3 and Finch (67.5% and 63.1%); however, these values are similar to that of their respective host’s genomes (Delegan et al, 2019; Khairy et al, 2016; Song et al, 2022; Strnad et al, 2014; Yoshida et al, 2019).…”

Section: Resultsmentioning

confidence: 88%

“…For 3 of the 4 Rhodococcus clusters, their average G+C% content values are considerably lower than those reported for their respective host types. Clusters CB (41.3%) and CE (44.8%) both contain phages that infect R. erythropolis whose average G+C% content has been reported as usually exceeding 60% (Delegan et al, 2019; Khairy et al, 2016; Strnad et al, 2014; Yoshida et al, 2019). A similar finding exists between Cluster CC phages (53.4%) and their respective host type of R. equi whose average G+C% content values hover around 68.72% (Song et al, 2022).…”

Section: Resultsmentioning

confidence: 99%

“…Jace was isolated on Rhodococcus erythropolis RIA 643 and has a genome length of 53,912 bp (Supplemental Table 1). Jace's genome has a G+C% content of 67%, which aligns closely with that of its host type (Delegan et al, 2019;Khairy et al, 2016;Strnad et al, 2014;Yoshida et al, 2019). Approximately 50% of Jace's genes belong to orphams.…”

Section: Singletons E3 and Finchmentioning

confidence: 94%

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Characterization of Genomic Diversity In Bacteriophages InfectingRhodococcus

Garza

Blasi

Bruns

et al. 2022

Preprint

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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 genusRhodococcus.These phages were previously isolated at multiple institutions by students in the SEA-PHAGES program using four different species ofRhodococcus.MostRhodococcusphages have been grouped into 4 clusters based on their genomic similarities; 13 phages are singletons too genetically distinct for clustering. These clusters and singletons containSiphoviridaeandMyoviridaephages, 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 theirRhodococcushosts typically exceeds 60%. Through comparative genomic analyses, it was revealed that theseRhodococcusphages display high intracluster similarity but low intercluster similarity, despite their shared ability to infect the same host genus. Additionally, theseRhodococcusphages share similarities with phages that infect other Actinobacterial hosts such asGordonia, StreptomycesandArthrobacter.

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Section: Resultsmentioning

confidence: 88%

Section: Resultsmentioning

confidence: 99%

Section: Singletons E3 and Finchmentioning

confidence: 94%

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Characterization of Genomic Diversity In Bacteriophages InfectingRhodococcus

Garza

Blasi

Bruns

et al. 2022

Preprint

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“…Isolate PFA D8–1 was obtained by repetition of such streaking and testing and showed fast and robust ZEN conversion activity. Initial 16S rDNA sequencing identified it as Rhodococcus erythropolis , and subsequent whole genome sequencing confirmed that PFA D8–1 and the R. erythropolis type strain DSM 43066 T shared identical genes for 16S rRNA. For stability testing, daughter colonies were generated by plating cell suspension on LB agar plates.…”

Section: Resultsmentioning

confidence: 99%

Bacterial Lactonases ZenA with Noncanonical Structural Features Hydrolyze the Mycotoxin Zearalenone

Fruhauf,

Pühringer,

Thamhesl

et al. 2024

ACS Catal.

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Zearalenone (ZEN) is a mycoestrogenic polyketide produced by Fusarium graminearum and other phytopathogenic members of the genus Fusarium. Contamination of cereals with ZEN is frequent, and hydrolytic detoxification with fungal lactonases has been explored. Here, we report the isolation of a bacterial strain, Rhodococcus erythropolis PFA D8−1, with ZEN hydrolyzing activity, cloning of the gene encoding α/β hydrolase ZenA encoded on the linear megaplasmid pSFRL1, and biochemical characterization of nine homologues. Furthermore, we report sitedirected mutagenesis as well as structural analysis of the dimeric ZenA Re of R. erythropolis and the more thermostable, tetrameric ZenA Scfl of Streptomyces coelicoflavus with and without bound ligands. The X-ray crystal structures not only revealed canonical features of α/β hydrolases with a cap domain including a Ser-His-Asp catalytic triad but also unusual features including an uncommon oxyanion hole motif and a peripheral, short antiparallel β-sheet involved in tetramer interactions. Presteady-state kinetic analyses for ZenA Re and ZenA Scfl identified balanced rate-limiting steps of the reaction cycle, which can change depending on temperature. Some new bacterial ZEN lactonases have lower K M and higher k cat than the known fungal ZEN lactonases and may lend themselves to enzyme technology development for the degradation of ZEN in feed or food.

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Genome Sequence of Rhodococcus erythropolis Type Strain JCM 3201

Abstract: Rhodococcus erythropolis JCM 3201 can express several recombinant proteins that are difficult to express in Escherichia coli. It is used as one of the hosts for protein expression and bioconversion.

Cited by 2 publications

References 19 publications

Characterization of Genomic Diversity In Bacteriophages InfectingRhodococcus

Characterization of Genomic Diversity In Bacteriophages InfectingRhodococcus

Bacterial Lactonases ZenA with Noncanonical Structural Features Hydrolyze the Mycotoxin Zearalenone

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