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Chapter 25 : Genetics and Regulation of Base Modification in the tRNA and rRNA of Prokaryotes and Eukaryotes

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Abstract:

This chapter describes some of the better-understood systems, primarily in bacteria and yeast, that exhibit regulation of modification enzyme activity or gene expression. It attempts to bring out the common themes about regulation that are emerging from ongoing studies of the modification process. The efficiency of nonsense codon suppression has been exploited to analyze the effects of tRNA modification on decoding and codon context in bacteria and eukaryotes. New genetic approaches combined with high-pressure liquid chromatography (HPLC) screening and reverse genetics will likely lead to the identification of the remaining tRNA and rRNA modification genes in bacteria and yeast. A recent determination by quantitative Western immunoblotting showed that the MiaA (iA37) prenyltransferase is also a moderately abundant enzyme at about 650 monomers per cell (≈ 1 μM) in bacteria growing exponentially in enriched minimal-glucose medium. MiaA may need to be present in comparatively high cellular amounts, because its activity is strongly competitively inhibited for its prenyl substrate, dimethylallyl diphosphate (alternatively called Δ-isopentenyl pyrophosphate), by nucleotide di- and triphosphates. The genes whose expression is affected by these undermodifications need to be identified by two-dimensional gel analyses or genetic methods using random fusions. After these targets are identified, it will be possible to access whether the magnitude of the effects of undermodification on gene expression is sufficiently large to readily indicate physiological significance.

Citation: Winkler M. 1998. Genetics and Regulation of Base Modification in the tRNA and rRNA of Prokaryotes and Eukaryotes, p 441-469. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch25

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Figures

Image of Figure 1
Figure 1

Structures of the modified bases in tRNA and rRNA discussed in this chapter. Abbreviations for the modified bases and the enzymes that catalyze the modifications, which are enclosed in dotted lines, are indicated. Structures were redrawn or modified from . Positions refer to eubacterial or eukaryotic tRNA unless rRNA is indicated. (A) iA37, -Isopentenyladenosine; (B) msiA37, 2-methylthio- -isopentenyladenosine; (C) Ψ (various positions), pseudouridine; (D)m A2058 (in 23S rRNA) or 1518 and 1519 in 16S rRNA, , -dimethyladenosine; (E) sU8, 4-thiouridine; (F) mcmsU34, 5-methoxycarbonylmethyl-2-thiouridine; (G) m G26 , , -dimethylguanosine; (H) msU54, ribosylthymine; (I) msioA37, 2-methylthio- -(-hydroxyisopentenyl)adenosine; ( J) mtA37, -methyl- -threonylcarbamoyladenosine; (K) mA37, 2-methyladenosine; (L) sC32, 2-thiocytidine; (M) mG37, 1-methylguanosine; (N) D, 5,6-dihydrouridine (various positions); (O) mG46, 7-methylguanosine; (P) Q34, queuosine; (Q) preQ,34, 7-aminomethyl-7-deazaguanosine; (R) tA37, -threonylcarbamoyladenosine; (S) Ar(p)64, 2′--ribosyladenosine (phosphate); (T) mC34, 48, 49, 5-methylcytidine; (U) mА14, 58, 1-methyladenosine; (V) mnmsU34, 5-methylaminomethyl-2-thiouridine.

Citation: Winkler M. 1998. Genetics and Regulation of Base Modification in the tRNA and rRNA of Prokaryotes and Eukaryotes, p 441-469. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch25
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Image of Figure 2
Figure 2

Structure of the monocistronic operon (mU54 methyltransferase; Fig. 1H ) in (89.65 min) and . The locations of the FIS protein binding site and stringent discriminator in the P promoter and the bifunctional transcription terminator structure at the ends of and ( ) are indicated. The divergently transcribed gene encodes an outer membrane protein involved in vitamin B uptake. See text for additional details. Adapted from .

Citation: Winkler M. 1998. Genetics and Regulation of Base Modification in the tRNA and rRNA of Prokaryotes and Eukaryotes, p 441-469. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch25
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Image of Figure 3
Figure 3

Structure of the (9.17 min) and locus, which catalyzes Q34 biosynthesis ( Fig. IP ). encodes the preQ,34 transglycosylase that inserts preQ, into tRNA ( Fig. 1Q ), and encodes epoxy-queuosine synthase, which catalyzes a step in the conversion of the inserted preQ,34 to Q34 (see ). The locations of promoters and terminators are indicated along with transcripts detected on Northern blots ( ). The relationship between the and the downstream , and genes is discussed in the text. Adapted from , based on data from Poghano and Beckwith (1994)V and .

Citation: Winkler M. 1998. Genetics and Regulation of Base Modification in the tRNA and rRNA of Prokaryotes and Eukaryotes, p 441-469. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch25
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Image of Figure 4
Figure 4

Structure of the multifunctional operon (mG37 methyltransferase; Fig. 1M ) of (59.10 min) and . The four genes of the operon (ribosomal protein S16), (function unknown), , and (ribosomal protein L19) are transcribed into the single long mRNA indicated. The locations of the promoter (P), Rho-factor independent attenuator before the first () gene, and terminator (T) at the end of the operon are indicated along with folded secondary structures in the mRNA that are thought to inhibit translation of the 21K and TrmD proteins. Control of the adjacent (protein component of signal recognition protein) and () (nonessential protein) genes is separate from that of the operon. See text for additional details. Adapted from .

Citation: Winkler M. 1998. Genetics and Regulation of Base Modification in the tRNA and rRNA of Prokaryotes and Eukaryotes, p 441-469. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch25
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Image of Figure 5
Figure 5

Structure of the multifunctional operon (iA37 prenyltransferase; Fig. 1A ) in K-12 (94.75 min). The figure is drawn to scale. Besides , the multifunctional operon, which has no intercistronic spaces between , and , includes (cell wall amidase), (DNA mismatch repair), (RNA chaperon global regulator), and the region (protease). The locations of multiple standard Eσ-specific promoters (P), heat shock Eσ-specific promoters (P-HS), transcript processing sites (PT), transcriptional attenuators (Atn), and the transcription terminator at the end of the operon (TERM) are indicated. The Hfq chaperone is thought to act as a negative regulator of MiaA expression by destabilizing the transcript. See text for additional details. Adapted from .

Citation: Winkler M. 1998. Genetics and Regulation of Base Modification in the tRNA and rRNA of Prokaryotes and Eukaryotes, p 441-469. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch25
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Image of Figure 6
Figure 6

Structure of the multifunctional operon (m A1518 and 1519 dimethyltransferase; Fig. ID ) of (1.11 min). Besides , the operon consists of (peptidyl-prolyl isomerase), (pyridoxine 5′-phosphate ring closure), (unknown function), and (diadenosine [AppppA] tetraphosphatase). The positions of the mapped P and P promoters are indicated. The locations of the P and P promoters are approximate. About 50% of transcription originates from promoters upstream from Р. See text for other details. Adapted from , based on and .

Citation: Winkler M. 1998. Genetics and Regulation of Base Modification in the tRNA and rRNA of Prokaryotes and Eukaryotes, p 441-469. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch25
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Image of Figure 7
Figure 7

Structure and transcriptional control of the rRNA operon of (89.74 min). The upper figure shows the structure of the entire operon, which extends from the PI and P2 promoters to the T1 and T2 transcription terminators and includes genes for 16S rRNA, tRNA , 23S rRNA, and 5S rRNA. The lower figure shows the FIS binding sites and Up elements that contribute to expression from the P1 and P2 promoters and the box A element that functions in transcription antitermination of the nontranslated operon. See text and for additional details. Adapted from .

Citation: Winkler M. 1998. Genetics and Regulation of Base Modification in the tRNA and rRNA of Prokaryotes and Eukaryotes, p 441-469. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch25
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Figure 8

Antiattenuation model for induction of operon (m62A2058 dimethyltransferase; Fig. 1D ) expression by the antibiotic erythromycin in and other gram-positive bacteria. The top two alternative mRNA secondary structures, which sequester the ribosome binding site (RBS), form when the leader transcript is translated in the absence of erythromycin. The bottom structure, which allows translation, forms when ribosomes stall during translation of the leader peptide in the presence of erythromycin. See text for additional details. Adapted from . Start leader, translation start codon of leader peptide; stop leader, translation stop codon of leader peptide; SD, Shine-Dalgarno sequence preceding start, translation start codon.

Citation: Winkler M. 1998. Genetics and Regulation of Base Modification in the tRNA and rRNA of Prokaryotes and Eukaryotes, p 441-469. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch25
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Image of Figure 9
Figure 9

Model for regulation of Tgt (Q34) transglycosylase activity by phosphorylation by protein kinase С (PKC) in mammalian cells. The unphosphorylated form of the Tgt enzyme (top) exists as a heterodimer containing a catalytic and a regulatory subunit. Phosphorylation of the regulatory subunit by PKC (bottom) causes the subunits to dissociate releasing the active catalytic subunit. Based on .

Citation: Winkler M. 1998. Genetics and Regulation of Base Modification in the tRNA and rRNA of Prokaryotes and Eukaryotes, p 441-469. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch25
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Image of Figure 10
Figure 10

Differential expression of yeast (m G26 dimethyltransferase; Fig. 1G ) and (iA37 prenyltransferase; Fig. 1A ) that leads to isozyme sorting in yeast. (A) Transcription and translation start points in and . is transcribed from two different promoters. The larger isozyme (Trm1p-I) is translated from ATG1 in the longer transcript, and the smaller isozyme (Trm1p-II) is translated from ATG17, which is the first start codon in the shorter transcript. is also transcribed from two promoters, but both transcripts contain the ATG1 and ATG12 translation start codons. The larger (Mod5p-I) and smaller (Mod5p-II) isozymes are translated from ATG1 and ATG12, respectively, in the larger bifunc-tional transcript. See text and for additional details. (B) Signals for targeting and isozyme distribution of the and gene products in yeast. The amino acid sequences of the isozymes are indicated by the lines. Open boxes, regions sufficient for efficient targeting to mitochondria; shaped box in Trm1p-I, region that improves import into mitochondria; hatched boxes, nuclear targeting or localization signals. + and –, present and absent, respectively, in the indicated subcellular compartments. See text and for additional details. Adapted from .

Citation: Winkler M. 1998. Genetics and Regulation of Base Modification in the tRNA and rRNA of Prokaryotes and Eukaryotes, p 441-469. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch25
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Tables

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Table 1

Summary of known modes of regulation of tRNA and rRNA modification genes in prokaryotes and eukaryotes

Citation: Winkler M. 1998. Genetics and Regulation of Base Modification in the tRNA and rRNA of Prokaryotes and Eukaryotes, p 441-469. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch25

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