New nucleoside hydrolase with transribosylation activity from Agromyces sp. MM-1 and its application for enzymatic synthesis of 2′-O-methylribonucleosides

Mitsukawa, Yuuki; Hibi, Makoto; Matsutani, Narihiro; Horinouchi, Nobuyuki; Takahashi, Satoshi; Ogawa, Jun

doi:10.1016/j.jbiosc.2017.07.016

“…It was reported recently that a newly discovered bi-functional nucleoside hydrolase from Agromyces sp. MM-1 that catalyzes both hydrolysis of 2′- O -methylribonucleosides and transribosylation between 2′- O -methyluridine and various nucleobases, had 97% homology with a putative nucleoside hydrolase of Microbacterium resistens , which formed a gene cluster together with nucleoside-metabolizing enzymes such as 2-deoxyribose-5-phosphate aldolase, formamidopyrimidine-DNA glycosylase and ribokinase [ 29 ]. It is worth mentioning that a ribokinase gene is also present upstream of the aldolase coding gene in the genome of Intrasporangium chromatireducens .…”

Section: Discussionmentioning

confidence: 99%

“…Hence, nucleic acid drugs comprising modified DNA or RNA oligomers are the next-generation medicine with various applications such as antisense drugs, ribozymes, small interfering RNA drugs and aptamers [ 45 ]. Enzymatic synthesis of methylated nucleosides has only recently been achieved [ 28 , 29 ], which means that the RK9NH enzyme is the gateway to a new and promising field of biocatalysis. In addition, since 5-fluoro-2′- O -methyluridine is a good substrate of RK9NH hydrolase, a novel prodrug/enzyme combination might be considered as an addition to the existing systems generating 5-fluorouracil, a well-known anticancer compound [ 46 , 47 , 48 ].…”

Section: Discussionmentioning

confidence: 99%

“…The ribose 2′- O -methylation increases the hydrophobicity of nucleotides and protects them against the action of nucleases [ 25 , 26 ], which is a desired trait, especially for, e.g., DNA aptamers [ 24 ]. Despite the countless possibilities of practical use for the metabolic enzymes associated with methylated nucleosides, there are very few reports regarding enzymes involved in the metabolism of 2′- O -alkyl nucleosides [ 27 , 28 , 29 ]. The presented work focuses on the cellular degradation of 2′- O -methyluridine that is found naturally in rRNA, snRNA, snoRNA and tRNA of Archaea , Eubacteria , and Eukaryota [ 1 ].…”

Section: Introductionmentioning

confidence: 99%

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Identification of a 2′-O-Methyluridine Nucleoside Hydrolase Using the Metagenomic Libraries

Aučynaitė

¹

,

Rutkienė

²

,

Tauraitė

³

et al. 2018

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Ribose methylation is among the most ubiquitous modifications found in RNA. 2′-O-methyluridine is found in rRNA, snRNA, snoRNA and tRNA of Archaea, Bacteria, and Eukaryota. Moreover, 2′-O-methylribonucleosides are promising starting materials for the production of nucleic acid-based drugs. Despite the countless possibilities of practical use for the metabolic enzymes associated with methylated nucleosides, there are very few reports regarding the metabolic fate and enzymes involved in the metabolism of 2′-O-alkyl nucleosides. The presented work focuses on the cellular degradation of 2′-O-methyluridine. A novel enzyme was found using a screening strategy that employs Escherichia coli uracil auxotroph and the metagenomic libraries. A 2′-O-methyluridine hydrolase (RK9NH) has been identified together with an aldolase (RK9DPA)—forming a part of a probable gene cluster that is involved in the degradation of 2′-O-methylated nucleosides. The RK9NH is functional in E. coli uracil auxotroph and in vitro. The RK9NH nucleoside hydrolase could be engineered to enzymatically produce 2′-O-methylated nucleosides that are of great demand as raw materials for production of nucleic acid-based drugs. Moreover, RK9NH nucleoside hydrolase converts 5-fluorouridine, 5-fluoro-2′-deoxyuridine and 5-fluoro-2′-O-methyluridine into 5-fluorouracil, which suggests it could be employed in cancer therapy.

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“…Certain species of the genus Agromyces produce catabolic or lytic enzymes that can degrade environmental pollutants such as halo-organic compounds [9] and nylon-oligomer materials [10]. Other species can grow in the presence of heavy metals [11] and other strains have been found to carry interesting transribosylation reactions [12]. As member of the Actinobacteria, species of the genus Agromyces are expected to produce bioactive metabolites.…”

Section: Full-textmentioning

confidence: 99%

Agromyces archimandritae sp. nov., isolated from the cockroach Archimandrita tessellata

Guzman

¹

,

Ortúzar

²

,

Daniel

³

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-positive bacterial strain, designated G127ATT, was isolated as soft small white colonies from the hindgut of the cockroach Archimandrita tesselata. Examination of the complete 16S rRNA sequence mapped the strain to the genus Agromyces . The type strain with the highest pairwise similarity was Agromyces marinus H23-8T (97.3%). The genome of G127ATT was sequenced by a combination of Illumina and Nanopore methods and consisted of a single circular DNA molecule with a size of 3.45 Mb. The DNA G+C content was 71.3 mol%. A phylogenomic tree based on conserved single copy housekeeping genes, placed G127ATT among the ancestral species of the genus Agromyces , and only Agromyces atrinae P27T was found to diverge earlier than G127ATT. Genome distance metrics average nucleotide identity (ANI) (76–78 %) and digital DNA–DNA hybridization (dDDH) (20.2–21.5 %) of the isolate against available genomes of several type strains of species of the genus Agromyces indicated that G127ATT represented a previously undescribed species of the genus Agromyces . Morphological, physiological and biochemical characteristics, including lipid profile, cellular fatty acids and peptidoglycan type were in accordance with usual attributes of members of the genus Agromyces . The novel isolate could be differentiated from the most closely related species by extracellular expression of acid and alkaline phosphatases, trypsin and α-chymotrypsin, and utilization of l-arabinose and salicin as sole carbon sources. On the basis of the combined genomic and phenotypic features, isolate G127ATT (=DSM 111850T=LMG 32099T) is considered to represent a novel species of the genus Agromyces , for which we propose the name Agromyces archimandritae sp. nov.

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“…However, there are a lot of unknowns about this genus that remain to be investigated. Interestingly, some of the products or metabolic capability of the genus Agromyces have huge industrial and ecological potential, either by producing enzymes of higher quantity/ quality (Yasuhira et al, 2007;Mitsukawa et al, 2018) or by providing the bioremediation of contaminated soil (Corretto et al, 2016;Zhao et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Agromyces laixinhei sp. nov. isolated from bat feces in China

Cheng

¹

,

Bai

²

,

Huang

³

et al. 2021

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Three rod-shaped, Gram-stain-positive, and catalase-positive, phenotypically closely related isolates (HY052 T , HY050, and HY045) were obtained from fecal samples collected from bats in Guangxi province and Chongqing city of China. Circular, smooth, light-yellow colonies appeared on brain heart infusion plate after 24–48 h incubation at 28°C. The optimal pH for growth was between 6.0 and 7.5. Based on 16S rRNA, the three isolates were phylogenetically related to Agromyces terreus DS-10 T , Agromyces aureus AR33 T , Agromyces salentinus 20-5 T , Agromyces allii UMS-62 T , Agromyces lapidis CD55 T , and Agromyces italicus CD1 T . Moreover, based on 296 core genes, the phylogenomic tree indicated that the three isolates clustered together, closest to Agromyces cerinus VKM Ac-1340 T and Agromyces fucosus VKM Ac-1345 T but separated distantly from other Agromyces species. The average nucleotide identity values between strain HY052 T and other Agromyces species ranged from 79.3% to 87.9%, lower than the 95–96% threshold. Furthermore, the genome of strain HY052 T contains a circular chromosome of 3,437,203 bp with G + C content of 69.0 mol%. Main fatty acids were anteiso -C 15:0 and anteiso -C 17:0 . The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, and unidentified glycolipids. Rhamnose, ribose, and glucose were the primary cell wall sugars. The major peptidoglycan amino acids included alanine, glutamic acid, glycine, and 2,4-diaminobutyric acid. An additional remarkable difference from other Agromyces species is that MK-12 was the sole menaquinone in strain HY052 T . Based on results from the polyphasic characterizations performed in this study, our isolates are proposed to be members of a novel species in genus Agromyces , named Agromyces laixinhei. The type strain is HY052 T (= CGMCC 1.17175 T = JCM 33695 T ). Electronic Supplementary Material Supplementary material is available in the online version of this article at 10.1007/s12275-021-0546-5.

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New nucleoside hydrolase with transribosylation activity from Agromyces sp. MM-1 and its application for enzymatic synthesis of 2′-O-methylribonucleosides

Cited by 6 publications

References 41 publications

Identification of a 2′-O-Methyluridine Nucleoside Hydrolase Using the Metagenomic Libraries

Identification of a 2′-O-Methyluridine Nucleoside Hydrolase Using the Metagenomic Libraries

Agromyces archimandritae sp. nov., isolated from the cockroach Archimandrita tessellata

Agromyces laixinhei sp. nov. isolated from bat feces in China

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