Survey and Validation of TRNA Modifications and Their Corresponding Genes in Sp Subtilis Strain 168

Overview

Journal Biomolecules

Publisher MDPI

Specialties Biochemistry
Molecular Biology

Date 2020 Jul 8

PMID 32629984

Citations 18

Authors

Valerie de Crecy-Lagard

Robert L Ross

Marshall Jaroch

Virginie Marchand

Christina Eisenhart

Damien Bregeon

Yuri Motorin

Patrick A Limbach

Affiliations

Soon will be listed here.

Abstract

Extensive knowledge of both the nature and position of tRNA modifications in all cellular tRNAs has been limited to two bacteria, and . sp subtilis strain 168 is the model Gram-positive bacteria and the list of the genes involved in tRNA modifications in this organism is far from complete. Mass spectrometry analysis of bulk tRNA extracted from , combined with next generation sequencing technologies and comparative genomic analyses, led to the identification of 41 tRNA modification genes with associated confidence scores. Many differences were found in this model Gram-positive bacteria when compared to . In general, tRNAs are less modified than those in , even if some modifications, such as mA22 or mstA, are only found in the model Gram-positive bacteria. Many examples of non-orthologous displacements and of variations in the most complex pathways are described. Paralog issues make uncertain direct annotation transfer from to based on homology only without further experimental validation. This difficulty was shown with the identification of the enzyme that introduces ψ at positions 31/32 of the tRNAs. This work presents the most up to date list of tRNA modification genes in , identifies the gaps in knowledge, and lays the foundation for further work to decipher the physiological role of tRNA modifications in this important model organism and other bacteria.

Citing Articles

Combined Prokaryotic Transcriptomics and Proteomics Analysis of Clinical Isolates with Distinctive Cytotoxicity.

Liu N, Li Q, Shan Q Int J Mol Sci. 2025; 26(4).

PMID: 40003955 PMC: 11854922. DOI: 10.3390/ijms26041490.

A sweeping view of avian mycoplasmas biology drawn from comparative genomic analyses.

Yacoub E, Baby V, Sirand-Pugnet P, Arfi Y, Mardassi H, Blanchard A BMC Genomics. 2025; 26(1):24.

PMID: 39789465 PMC: 11720521. DOI: 10.1186/s12864-024-11201-5.

The binding of RbgA to a critical 50S assembly intermediate facilitates YphC function in bacterial ribosomal assembly.

Arpin D, Palacios A, Basu K, Ortega J Nucleic Acids Res. 2024; 53(2.

PMID: 39658043 PMC: 11754645. DOI: 10.1093/nar/gkae1197.

Stress-induced modification of tRNA generates 5-methylcytidine in the variable loop.

Valesyan S, Jora M, Addepalli B, Limbach P Proc Natl Acad Sci U S A. 2024; 121(46):e2317857121.

PMID: 39495928 PMC: 11572931. DOI: 10.1073/pnas.2317857121.

Temperature-Dependent tRNA Modifications in Bacillales.

Hoffmann A, Lorenz C, Fallmann J, Wolff P, Lechner A, Betat H Int J Mol Sci. 2024; 25(16).

PMID: 39201508 PMC: 11354880. DOI: 10.3390/ijms25168823.

References

Deutsch C, El Yacoubi B, de Crecy-Lagard V, Iwata-Reuyl D . Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. J Biol Chem. 2012; 287(17):13666-73. PMC: 3340167. DOI: 10.1074/jbc.M112.344028. View

Guy M, Podyma B, Preston M, Shaheen H, Krivos K, Limbach P . Yeast Trm7 interacts with distinct proteins for critical modifications of the tRNAPhe anticodon loop. RNA. 2012; 18(10):1921-33. PMC: 3446714. DOI: 10.1261/rna.035287.112. View

Juhling F, Morl M, Hartmann R, Sprinzl M, Stadler P, Putz J . tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res. 2008; 37(Database issue):D159-62. PMC: 2686557. DOI: 10.1093/nar/gkn772. View

Ross R, Cao X, Yu N, Limbach P . Sequence mapping of transfer RNA chemical modifications by liquid chromatography tandem mass spectrometry. Methods. 2016; 107:73-8. PMC: 5014671. DOI: 10.1016/j.ymeth.2016.03.016. View

Matsumoto T, Ohta T, Kumagai I, Oshima T, Murao K, Hasegawa T . A thermostable Gm-methylase recognizes the tertiary structure of tRNA. J Biochem. 1987; 101(5):1191-8. DOI: 10.1093/oxfordjournals.jbchem.a121983. View

OFENGAND J, Bakin A . Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts. J Mol Biol. 1997; 266(2):246-68. DOI: 10.1006/jmbi.1996.0737. View

Grosjean H, Edqvist J, Straby K, Giege R . Enzymatic formation of modified nucleosides in tRNA: dependence on tRNA architecture. J Mol Biol. 1996; 255(1):67-85. DOI: 10.1006/jmbi.1996.0007. View

Wattam A, Davis J, Assaf R, Boisvert S, Brettin T, Bun C . Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res. 2016; 45(D1):D535-D542. PMC: 5210524. DOI: 10.1093/nar/gkw1017. View

Motorin Y, Marchand V . Detection and Analysis of RNA Ribose 2'-O-Methylations: Challenges and Solutions. Genes (Basel). 2018; 9(12). PMC: 6316082. DOI: 10.3390/genes9120642. View

10.

Poldermans B, Bakker H, Van Knippenberg P . Studies on the function of two adjacent N6,N6-dimethyladenosines near the 3' end of 16S ribosomal RNA of Escherichia coli. IV. The effect of the methylgroups on ribosomal subunit interaction. Nucleic Acids Res. 1980; 8(1):143-51. PMC: 327248. DOI: 10.1093/nar/8.1.143. View

11.

Ryu H, Grove T, Almo S, Kim J . Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine. Nucleic Acids Res. 2018; 46(17):9160-9169. PMC: 6158493. DOI: 10.1093/nar/gky592. View

12.

Pallan P, Kreutz C, Bosio S, Micura R, Egli M . Effects of N2,N2-dimethylguanosine on RNA structure and stability: crystal structure of an RNA duplex with tandem m2 2G:A pairs. RNA. 2008; 14(10):2125-35. PMC: 2553729. DOI: 10.1261/rna.1078508. View

13.

Ikeuchi Y, Kitahara K, Suzuki T . The RNA acetyltransferase driven by ATP hydrolysis synthesizes N4-acetylcytidine of tRNA anticodon. EMBO J. 2008; 27(16):2194-203. PMC: 2500205. DOI: 10.1038/emboj.2008.154. View

14.

Sakai Y, Miyauchi K, Kimura S, Suzuki T . Biogenesis and growth phase-dependent alteration of 5-methoxycarbonylmethoxyuridine in tRNA anticodons. Nucleic Acids Res. 2015; 44(2):509-23. PMC: 4737166. DOI: 10.1093/nar/gkv1470. View

15.

Cao X, Limbach P . Enhanced detection of post-transcriptional modifications using a mass-exclusion list strategy for RNA modification mapping by LC-MS/MS. Anal Chem. 2015; 87(16):8433-40. PMC: 4542202. DOI: 10.1021/acs.analchem.5b01826. View

16.

Lorenz C, Lunse C, Morl M . tRNA Modifications: Impact on Structure and Thermal Adaptation. Biomolecules. 2017; 7(2). PMC: 5485724. DOI: 10.3390/biom7020035. View

17.

Miyauchi K, Kimura S, Suzuki T . A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification. Nat Chem Biol. 2012; 9(2):105-11. DOI: 10.1038/nchembio.1137. View

18.

El Yacoubi B, Lyons B, Cruz Y, Reddy R, Nordin B, Agnelli F . The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA. Nucleic Acids Res. 2009; 37(9):2894-909. PMC: 2685093. DOI: 10.1093/nar/gkp152. View

19.

Sayer C, Barat B, Popham D . Identification of L-Valine-initiated-germination-active genes in Bacillus subtilis using Tn-seq. PLoS One. 2019; 14(6):e0218220. PMC: 6568419. DOI: 10.1371/journal.pone.0218220. View

20.

Taniguchi T, Miyauchi K, Sakaguchi Y, Yamashita S, Soma A, Tomita K . Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis. Nat Chem Biol. 2018; 14(11):1010-1020. DOI: 10.1038/s41589-018-0119-z. View