1
|
Shaposhnikov LA, Savin SS, Tishkov VI, Pometun AA. Ribonucleoside Hydrolases-Structure, Functions, Physiological Role and Practical Uses. Biomolecules 2023; 13:1375. [PMID: 37759775 PMCID: PMC10526354 DOI: 10.3390/biom13091375] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/01/2023] [Accepted: 09/03/2023] [Indexed: 09/29/2023] Open
Abstract
Ribonucleoside hydrolases are enzymes that catalyze the cleavage of ribonucleosides to nitrogenous bases and ribose. These enzymes are found in many organisms: bacteria, archaea, protozoa, metazoans, yeasts, fungi and plants. Despite the simple reaction catalyzed by these enzymes, their physiological role in most organisms remains unclear. In this review, we compare the structure, kinetic parameters, physiological role, and potential applications of different types of ribonucleoside hydrolases discovered and isolated from different organisms.
Collapse
Affiliation(s)
- Leonid A. Shaposhnikov
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow 119071, Russia; (S.S.S.); (V.I.T.)
- Department of Chemical Enzymology, Chemistry Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Svyatoslav S. Savin
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow 119071, Russia; (S.S.S.); (V.I.T.)
- Department of Chemical Enzymology, Chemistry Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Vladimir I. Tishkov
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow 119071, Russia; (S.S.S.); (V.I.T.)
- Department of Chemical Enzymology, Chemistry Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Anastasia A. Pometun
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, Moscow 119071, Russia; (S.S.S.); (V.I.T.)
- Department of Chemical Enzymology, Chemistry Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
| |
Collapse
|
3
|
Guzman J, Ortúzar M, Poehlein A, Daniel R, Trujillo ME, Vilcinskas A. Agromyces archimandritae sp. nov., isolated from the cockroach Archimandrita tessellata. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005283] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Juan Guzman
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Maite Ortúzar
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Martha E. Trujillo
- Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| |
Collapse
|
4
|
Cheng Y, Bai Y, Huang Y, Yang J, Lu S, Jin D, Pu J, Zheng H, Li J, Huang Y, Wang S, Xu J. Agromyces laixinhei sp. nov. isolated from bat feces in China. J Microbiol 2021; 59:467-475. [PMID: 33779960 PMCID: PMC8006105 DOI: 10.1007/s12275-021-0546-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/18/2021] [Accepted: 02/09/2021] [Indexed: 11/30/2022]
Abstract
Three rod-shaped, Gram-stain-positive, and catalase-positive, phenotypically closely related isolates (HY052T, 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-10T, Agromyces aureus AR33T, Agromyces salentinus 20-5T, Agromyces allii UMS-62T, Agromyces lapidis CD55T, and Agromyces italicus CD1T. Moreover, based on 296 core genes, the phylogenomic tree indicated that the three isolates clustered together, closest to Agromyces cerinus VKM Ac-1340T and Agromyces fucosus VKM Ac-1345T but separated distantly from other Agromyces species. The average nucleotide identity values between strain HY052T and other Agromyces species ranged from 79.3% to 87.9%, lower than the 95-96% threshold. Furthermore, the genome of strain HY052T contains a circular chromosome of 3,437,203 bp with G + C content of 69.0 mol%. Main fatty acids were anteiso-C15:0 and anteiso-C17:0. 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 HY052T. 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 HY052T (= CGMCC 1.17175T = JCM 33695T).
Collapse
Affiliation(s)
- Yanpeng Cheng
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi, 030001, China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yibo Bai
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi, 030001, China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, 201508, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, 201508, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, 201508, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Han Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Junqin Li
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi, 030001, China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Ying Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Suping Wang
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi, 030001, China
| | - Jianguo Xu
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi, 030001, China.
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, 201508, China.
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| |
Collapse
|
5
|
Aučynaitė A, Rutkienė R, Tauraitė D, Meškys R, Urbonavičius J. Identification of a 2'- O-Methyluridine Nucleoside Hydrolase Using the Metagenomic Libraries. Molecules 2018; 23:molecules23112904. [PMID: 30405065 PMCID: PMC6278475 DOI: 10.3390/molecules23112904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/30/2018] [Accepted: 11/04/2018] [Indexed: 11/16/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Agota Aučynaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania.
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, LT-10223 Vilnius, Lithuania.
| | - Rasa Rutkienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania.
| | - Daiva Tauraitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania.
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, LT-10223 Vilnius, Lithuania.
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania.
| | - Jaunius Urbonavičius
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania.
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, LT-10223 Vilnius, Lithuania.
| |
Collapse
|