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Research Paper

Maturation of 23S rRNA includes removal of helix H1 in many bacteria

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Pages 856-865 | Received 19 Aug 2021, Accepted 26 Oct 2021, Published online: 23 Nov 2021

References

  • Shajani Z, Sykes MT, Williamson JR. Assembly of bacterial ribosomes. Annu Rev Biochem. 2011;80(1):501–526.
  • Theissen G, Thelen L, Wagner R. Some base substitutions in the leader of an Escherichia coli ribosomal RNA operon affect the structure and function of ribosomes. Evidence for a transient scaffold function of the rRNA leader. J Mol Biol. 1993;233(2):203–218.
  • Liiv A, Remme J. Base-pairing of 23 S rRNA ends is essential for ribosomal large subunit assembly. J Mol Biol. 1998;276(3):537–545.
  • Mangiarotti G, Turco E, Perlo C, et al. Role of precursor 16S RNA in assembly of E. coli 30S ribosomes. Nature. 1975;253:569–571.
  • Bechhofer DH, Deutscher MP. Bacterial ribonucleases and their roles in RNA metabolism. Crit Rev Biochem Mol Biol. 2019;54(3):242–300.
  • Young RA, Steitz JA. Complementary sequences 1700 nucleotides apart form a ribonuclease III cleavage site in Escherichia coli ribosomal precursor RNA. Proc Natl Acad Sci U S A. 1978;75(8):3593–3597.
  • Saito R, Ozawa Y, Kuzuno N, et al. Computer analysis of potential stem structures of rRNA operons in various procaryote genomes. Gene. 2000;259(1–2):217–222.
  • Condon C. The phylogenetic distribution of bacterial ribonucleases. Nucleic Acids Res. 2002;30(24):5339–5346.
  • Perez Luz S, Rodriguez-Valera F, Lan R, et al. Variation of the ribosomal operon 16S-23S gene spacer region in representatives of salmonella enterica subspecies. J Bacteriol. 1998;180(8):2144–2151.
  • Gurtler V, Stanisich VA. New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology (Reading). 1996;142(Pt 1):3–16.
  • Anton AI, Martinez-Murcia AJ, Rodriguez-Valera F. Sequence diversity in the 16S-23S intergenic spacer region (ISR) of the rRNA operons in representatives of the Escherichia coli ECOR collection. J Mol Evol. 1998;47(1):62–72.
  • Stahl DA, Pace B, Marsh T, et al. The ribonucleoprotein substrate for a ribosomal RNA-processing nuclease. J Biol Chem. 1984;259(18):11448–11453.
  • Redko Y, Bechhofer DH, Condon C. Mini-III, an unusual member of the RNase III family of enzymes, catalyses 23S ribosomal RNA maturation in B. subtilis. Mol Microbiol. 2008;68(5):1096–1106.
  • Jha V, Roy B, Jahagirdar D, et al. Structural basis of sequestration of the anti-shine-dalgarno sequence in the bacteroidetes ribosome. Nucleic Acids Res. 2021;49(1):547–567.
  • Cannone JJ, Subramanian S, Schnare MN, et al. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinf. 2002;3(1):2.
  • Lalanne JB, Taggart JC, and Guo MS, et al. Evolutionary convergence of pathway-specific enzyme expression stoichiometry. Cell. 2018;173:749–761 e38.
  • Zahn K, Inui M, Yukawa H. Characterization of a separate small domain derived from the 5ʹ end of 23S rRNA of an alpha-proteobacterium. Nucleic Acids Res. 1999;27(21):4241–4250.
  • Spahn CM, Grassucci RA, Penczek P, et al. Direct three-dimensional localization and positive identification of RNA helices within the ribosome by means of genetic tagging and cryo-electron microscopy. Structure. 1999;7(12):1567–1573.
  • Youngman EM, Green R. Affinity purification of in vivo-assembled ribosomes for in vitro biochemical analysis. Methods. 2005;36(3):305–312.
  • Flygaard RK, Boegholm N, Yusupov M, et al. Cryo-EM structure of the hibernating Thermus thermophilus 100S ribosome reveals a protein-mediated dimerization mechanism. Nat Commun. 2018;9(1):4179.
  • Halfon Y, Jimenez-Fernandez A, La Rosa R, et al. Structure of Pseudomonas aeruginosa ribosomes from an aminoglycoside-resistant clinical isolate. Proc Natl Acad Sci U S A. 2019;116(44):22275–22281.
  • Hentschel J, Burnside C, Mignot I, et al. The complete structure of the mycobacterium smegmatis 70S ribosome. Cell Rep. 2017;20(1):149–160.
  • Kaminishi T, Schedlbauer A, Fabbretti A, et al. Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A. Nucleic Acids Res. 2015;43(20):10015–10025.
  • Khusainov I, Vicens Q, Bochler A, et al. Structure of the 70S ribosome from human pathogen Staphylococcus aureus. Nucleic Acids Res. 2016;44(21):10491–10504.
  • Morgan CE, Huang W, and Rudin SD, et al. Cryo-electron microscopy structure of the acinetobacter baumannii 70s ribosome and implications for new antibiotic development. mBio. 2020 11(1) ;e03117–19.
  • Murphy EL, Singh KV, Avila B, et al. Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis. Sci Rep. 2020;10(1):16301.
  • Noeske J, Wasserman MR, Terry DS, et al. High-resolution structure of the Escherichia coli ribosome. Nat Struct Mol Biol. 2015;22(4):336–341.
  • Sohmen D, Chiba S, Shimokawa-Chiba N, et al. Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling. Nat Commun. 2015;6(1):6941.
  • Cole C, Byrne A, Beaudin AE, et al. Tn5Prime, a Tn5 based 5′ capture method for single cell RNA-seq. Nucleic Acids Res. 2018;46(10):e62.
  • Machida RJ, Lin YY, Oudejans C. Four methods of preparing mRNA 5ʹ end libraries using the Illumina sequencing platform. PLoS One. 2014;9:e101812.
  • Leinonen R, Sugawara H, Shumway M. International nucleotide sequence database C. The sequence read archive. Nucleic Acids Res. 2011;39:D19–21.
  • Davis MP, van Dongen S, Abreu-Goodger C, et al. Kraken: a set of tools for quality control and analysis of high-throughput sequence data. Methods. 2013;63(1):41–49.
  • Jiang H, Lei R, Ding SW, et al. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics. 2014;15(1):182.
  • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–359.
  • Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–2079.
  • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–842.
  • Larkin MA, Blackshields G, Brown NP, et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23(21):2947–2948.
  • Salazar G, Paoli L, Alberti A, et al. Gene expression changes and community turnover differentially shape the global ocean metatranscriptome. Cell. 2019;179(5):1068–83 e21.
  • Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 2011; 17(1): 10–12 .
  • Parks DH, Chuvochina M, Chaumeil PA, et al. A complete domain-to-species taxonomy for bacteria and archaea. Nat Biotechnol. 2020;38(9):1079–1086.
  • Hauswedell H, Singer J, Reinert K. Lambda: the local aligner for massive biological data. Bioinformatics. 2014;30(17):i349–55.
  • Letunic I, Bork P. Interactive Tree of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49:W293–W6.
  • Thomason MK, Bischler T, Eisenbart SK, et al. Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli. J Bacteriol. 2015;197(1):18–28.
  • Amman F, D’Halluin A, Antoine R, et al. Primary transcriptome analysis reveals importance of IS elements for the shaping of the transcriptional landscape of Bordetella pertussis. RNA Biol. 2018;15:967–975.
  • Heidrich N, Bauriedl S, Barquist L, et al. The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq. Nucleic Acids Res. 2017;45:6147–6167.
  • Myers KS, Vera JM, and Lemmer KC, et al. Genome-wide identification of transcription start sites in two alphaproteobacteria, rhodobacter sphaeroides 2.4.1 and novosphingobium aromaticivorans DSM 12444. Microbiol Resour Announc. 2020;9(36):e00880–20.
  • Vera JM, Ghosh IN, and Zhang Y, et al. Genome-scale transcription-translation mapping reveals features of zymomonas mobilis transcription units and promoters. mSystems. 2020;5(4) ;e00250–20.
  • Frohlich KS, Forstner KU, Gitai Z. Post-transcriptional gene regulation by an Hfq-independent small RNA in Caulobacter crescentus. Nucleic Acids Res. 2018;46:10969–10982.
  • Kienesberger S, Sprenger H, Wolfgruber S, et al. Comparative genome analysis of Campylobacter fetus subspecies revealed horizontally acquired genetic elements important for virulence and niche specificity. PLoS One. 2014;9(1):e85491.
  • Bischler T, Tan HS, Nieselt K, et al. Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori. Methods. 2015;86:89–101.
  • Hilzinger JM, Raman V, and Shuman KE, et al. Differential RNA sequencing implicates sulfide as the master regulator of S(0) metabolism in chlorobaculum tepidum and other green sulfur bacteria. Appl Environ Microbiol. 2018;84(3) ;e01966–17.
  • Ryan D, Jenniches L, Reichardt S, et al. A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe bacteroides thetaiotaomicron. Nat Commun. 2020;11(1):3557.
  • Tan X, Hou S, Song K, et al. The primary transcriptome of the fast-growing cyanobacterium synechococcus elongatus UTEX 2973. Biotechnol Biofuels. 2018;11(1):218.
  • Koch R, Kupczok A, Stucken K, et al. Plasticity first: molecular signatures of a complex morphological trait in filamentous cyanobacteria. BMC Evol Biol. 2017;17(1):209.
  • Lee Y, Lee N, Jeong Y, et al. The transcription unit architecture of streptomyces lividans TK24. Front Microbiol. 2019;10:2074.
  • Shell SS, Wang J, Lapierre P, et al. Leaderless transcripts and small proteins are common features of the mycobacterial translational landscape. PLoS Genet. 2015;11(11):e1005641.
  • Lecrivain AL, Le Rhun A, Renault TT, et al. In vivo 3′-to-5′ exoribonuclease targetomes of Streptococcus pyogenes. Proc Natl Acad Sci U S A. 2018;115(46):11814–11819.
  • Soutourina O, Dubois T, Monot M, et al. Genome-wide transcription start site mapping and promoter assignments to a sigma factor in the human enteropathogen clostridioides difficile. Front Microbiol. 2020;11:1939.