RNA processing in prokaryotic cells

Apirion, David; Miczák, András

doi:10.1002/bies.950150207

Cited by 99 publications

(78 citation statements)

References 52 publications

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“…Mature rRNA species are produced from pre-rRNA by the action of a number of different RNases (for review see Apirion & Miczak, 1993). Early cleavages produce precursors of the mature species : namely, pre-16s rRNA pre-23s rRNA and pre-5S rRNA (see Fig.…”

Section: Processing Pre-rrnamentioning

confidence: 99%

Nucleotide sequences of the spacer-1, spacer-2 and trailer regions of the rrn operons and secondary structures of precursor 23S rRNAs and precursor 5S rRNAs of slow-growing mycobacteria

Kempsell

Colston

et al. 1994

Microbiology

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Nucleotide sequences of the spacer-1, spacer-2 and trailer regions of the rrn operons and secondary structures of precursor 23s rRNAs and precursor 5s rRNAs of slow-growing rnyco bacter ia Yuan- The single ribosomal RNA (rrn) operons of slow-growing mycobacteria comprise the genes for 165, 235 and 55 rRNA, in that order. PCR methodology was used to amplify parts of the rrn operons, namely the spacer-1 region separating the 165 rRNA and 235 rRNA genes and the spacer-2 region separating the 235 rRNA and 55 rRNA genes of Mycobacterium avium, Mycobacterium intracellulare, 'Mycobacterium lufu ' and Mycobacterium simiae. The amplified DNA was sequenced. The spacer-2 region, the 55 rRNA gene, the trailer region and the downstream region of the rrn operon of Mycobacterium tuberculosis were cloned and sequenced. These data, together with those obtained previously for Mycobacterium leprae, were used to identify putative antitermination signals and RNase 111 processing sites within the spacer4 region. Notable features include two adjacent potential Box B elements and a Box A element. The latter is located within a sequence of 46 nucleotides which is very highly conserved among the slow-growers which were examined. The conserved sequence has the capacity to interact through base-pairing with part of the spacer-2 region. Secondary structures for mycobacterial precursor 235 rRNA and for precursor 55 rRNA were devised, based on sequence homologies and homologous nucleotide substitutions. All the slow-growers, including M. leprae, conform to the same scheme of secondary structure. A putative motif for the intrinsic termination of transcription was identified approximately 33 bp downstream from the 3'-end of the 55 rRNA gene. The spacer-1 and spacer-2 sequences may prove a useful supplement to 165 rRNA sequences in establishing phylogenetic relationships between very closely related species. The EMBL accession numbers for the nucleotide sequence data reported in this paper are X74056X74063 and X75599-X75602. (Shepard, 1960; K'inder & Rooney, 1970). Although ribosome biosynthesis is essential to cell proliferation, the strategy (or strategies) used by slow-growing mycobacteria to control the production of new ribosomes is not known. One facet of this strategy is the regulation of the biosynthesis of rRNA. The slow-growing mycobacteria have a single rRNA (rm) operon (Bercovier et a/., 1986) comprising genes for the rRNA family in the order 16s rRNA, 23s rRNA and 5s rRNA (see Fig. 1). The operon is transcribed as a single unit (precursor rRNA or prerRNA) which is cleaved by RNases to precursors of 16s rRNA (pre-16s rRNA), 23s rRNA (pre-23s rRNA) and Keywords

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Section: Processing Pre-rrnamentioning

confidence: 99%

Nucleotide sequences of the spacer-1, spacer-2 and trailer regions of the rrn operons and secondary structures of precursor 23S rRNAs and precursor 5S rRNAs of slow-growing mycobacteria

Kempsell

Colston

et al. 1994

Microbiology

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“…RNase P is the ubiquitous endonuclease found in prokaryotes, eukaryotes, and archaebacteria responsible for catalyzing the hydrolysis of a specific phosphodiester bond in pre-tRNA, yielding a mature tRNA with a 5Ј phosphate group (Apirion and Miczak 1993). In all organisms, RNase P is a ribonucleoprotein complex (having both RNA and protein components; Xiao et al 2002).…”

Section: Introductionmentioning

confidence: 99%

Ionic interactions between PRNA and P protein in Bacillus subtilis RNase P characterized using a magnetocapture-based assay

Day-Storms¹,

Niranjanakumari²,

Fierke³

2004

RNA

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Ribonuclease P (RNase P) is a ribonucleoprotein complex that catalyzes the cleavage of the 5 end of precursor tRNA. To characterize the interface between the Bacillus subtilis RNA (PRNA) and protein (P protein) components, the intraholoenzyme K D is determined as a function of ionic strength using a magnetocapture-based assay. Three distinct phases are evident. At low ionic strength, the affinity of PRNA for P protein is enhanced as the ionic strength increases mainly due to stabilization of the PRNA structure by cations. Lithium substitution in lieu of potassium enhances the affinity at low ionic strength, whereas the addition of ATP, known to stabilize the structure of P protein, does not affect the affinity. At high ionic strength, the observed affinity decreases as the ionic strength increases, consistent with disruption of ionic interactions. These data indicate that three to four ions are released on formation of holoenzyme, reflecting the number of ion pairs that occur between the P protein and PRNA. At moderate ionic strength, the two effects balance so that the apparent K D is not dependent on the ionic strength. The K D between the catalytic domain (C domain) and P protein has a similar triphasic dependence on ionic strength. Furthermore, the intraholoenzyme K D is identical to or tighter than that of full-length PRNA, demonstrating that the P protein binds solely to the C domain. Finally, pre-tRNA asp (but not tRNA asp ) stabilizes the PRNA·P protein complex, as predicted by the direct interaction between the P protein and pre-tRNA leader.

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“…The question is whether the polymorphism observed for the six operons of E. hirae (Sechi & Daneo-Moore, 1993) is a general feature of enterococci. Based on detailed studies made on the rRNA maturation process of Escherichia coli (review by Apirion & Miczak, 1993), both spacer region 1 and the 23s-5s rRNA spacer region (spacer region 2), play a crucial role in pre-rRNA maturation. Studies on Esch.…”

Section: Introductionmentioning

confidence: 99%

“…Indeed, RNase E, which is involved in 5 s rRNA maturation in Esch. coli, has a recognition site within spacer region 2 (5'-ACAGAAUUUG-3') (reviewed by Apirion & Miczak, 1993). X81782 X87183 X87177 X87178 X87179 X87180 X87181 X87190 X87191 X87184 X87185 X87187 X87188 X87189 1, tRNAA'" 1 2 1, tRNAAla 1 2 1 2 1 2 1 2 1, tRNAAla 1 2 328 226 96 330 277 92 344 94 344 94 232 94 33 1 230 89 '' 1, 16s-23s rRNA spacer DNA; 2,23S-SS rRNA spacer DNA.…”

Section: Introductionmentioning

confidence: 99%

Primary and secondary structures of rRNA spacer regions in enterococci

Naimi¹,

Beck²,

Branlant³

1997

Microbiology

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The 165-235 and 235-55 rRNA spacer DNA regions (spacer regions 1 and 2, respectively) from Enterococcus faecalis, Enterococcus faecium, Enterncoccus hirae, Enterococcus durans and Enterncoccus mundtii were amplified by PCR. Their nucleotide sequences were established and a secondary structure model showing the interaction between the two spacer regions was built. Whereas lactococci and Streptococcus sensu stricto are characterized by a single type of spacer region 1 , the enterococci show a high degree of variability in this region; thus the spacer regions 1 with and without tRNAAia were characterized. However, as shown for lactococci and Streptococcus sensu stricto, the tRNAAia gene does not encode the 3'4erminal CCA trinucleotide. A putative antitermination signal is found downstream from the tRNAAia gene. Based on comparison with Lactococcus lactis and Streptococcus thermophilus, a doublestranded processing stem is proposed. In €. hirae, one of the three different types of spacer region 1 contains no tRNAAia, but displays a 107 nt insertion that forms a long stem-loop structure. A similar insertion (1 15 nt in length) was found in E. faecium and base compensatory mutations preserve the ability to form the long stem-loop structure. Such insertions may correspond to mobile intervening sequences, as found in the 235 rRNA coding sequences of some Gram-negative bacteria. The spacer regions 1 and 2 from the three subgroups of streptococci were compared, and except for the tRNAAia gene and the double-stranded processing sites, little similarity was found, which opens large possibilities for future development of DNA-based typing methods.

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RNA processing in prokaryotic cells

Cited by 99 publications

References 52 publications

Nucleotide sequences of the spacer-1, spacer-2 and trailer regions of the rrn operons and secondary structures of precursor 23S rRNAs and precursor 5S rRNAs of slow-growing mycobacteria

Nucleotide sequences of the spacer-1, spacer-2 and trailer regions of the rrn operons and secondary structures of precursor 23S rRNAs and precursor 5S rRNAs of slow-growing mycobacteria

Ionic interactions between PRNA and P protein in Bacillus subtilis RNase P characterized using a magnetocapture-based assay

Primary and secondary structures of rRNA spacer regions in enterococci

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