Abstract
Ribosomal RNAs are generally stable in growing Escherichia coli cells. However, their degradation increases dramatically under conditions that lead to slow cell growth. In addition, incomplete RNA molecules and molecules with defects in processing, folding, or assembly are also eliminated in growing cells in a process termed quality control. Here, we show that there are significant differences between the pathways of ribosomal RNA degradation during glucose starvation and quality control during steady-state growth. In both processes, endonucleolytic cleavage of rRNA in ribosome subunits is an early step, resulting in accumulation of large rRNA fragments when the processive exoribonucleases, RNase II, RNase R, and PNPase are absent. For 23S rRNA, cleavage is in the region of helix 71, but the exact position can differ in the two degradative processes. For 16S rRNA, degradation during starvation begins with shortening of its 3′ end in a reaction catalyzed by RNase PH. In the absence of this RNase, there is no 3′ end trimming of 16S rRNA and no accumulation of rRNA fragments, and total RNA degradation is greatly reduced. In contrast, the degradation pattern in quality control remains unchanged when RNase PH is absent. During starvation, the exoribonucleases RNase II and RNase R are important for fragment removal, whereas for quality control, RNase R and PNPase are more important. These data highlight the similarities and differences between rRNA degradation during starvation and quality control during steady-state growth and describe a role for RNase PH in the starvation degradative pathway. Published by Cold Spring Harbor Laboratory Press.
| Original language | English |
|---|---|
| Pages (from-to) | 338-345 |
| Number of pages | 8 |
| Journal | RNA |
| Volume | 17 |
| Issue number | 2 |
| DOIs | |
| State | Published - Feb 1 2011 |
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Keywords
- Escherichia coli
- Ribonuclease
- Ribosome
ASJC Scopus subject areas
- Molecular Biology
Cite this
Degradation of ribosomal RNA during starvation : Comparison to quality control during steady-state growth and a role for RNase PH. / Basturea, Georgeta N.; Zundel, Michael A.; Deutscher, Murray P.
In: RNA, Vol. 17, No. 2, 01.02.2011, p. 338-345.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Degradation of ribosomal RNA during starvation
T2 - Comparison to quality control during steady-state growth and a role for RNase PH
AU - Basturea, Georgeta N.
AU - Zundel, Michael A.
AU - Deutscher, Murray P
PY - 2011/2/1
Y1 - 2011/2/1
N2 - Ribosomal RNAs are generally stable in growing Escherichia coli cells. However, their degradation increases dramatically under conditions that lead to slow cell growth. In addition, incomplete RNA molecules and molecules with defects in processing, folding, or assembly are also eliminated in growing cells in a process termed quality control. Here, we show that there are significant differences between the pathways of ribosomal RNA degradation during glucose starvation and quality control during steady-state growth. In both processes, endonucleolytic cleavage of rRNA in ribosome subunits is an early step, resulting in accumulation of large rRNA fragments when the processive exoribonucleases, RNase II, RNase R, and PNPase are absent. For 23S rRNA, cleavage is in the region of helix 71, but the exact position can differ in the two degradative processes. For 16S rRNA, degradation during starvation begins with shortening of its 3′ end in a reaction catalyzed by RNase PH. In the absence of this RNase, there is no 3′ end trimming of 16S rRNA and no accumulation of rRNA fragments, and total RNA degradation is greatly reduced. In contrast, the degradation pattern in quality control remains unchanged when RNase PH is absent. During starvation, the exoribonucleases RNase II and RNase R are important for fragment removal, whereas for quality control, RNase R and PNPase are more important. These data highlight the similarities and differences between rRNA degradation during starvation and quality control during steady-state growth and describe a role for RNase PH in the starvation degradative pathway. Published by Cold Spring Harbor Laboratory Press.
AB - Ribosomal RNAs are generally stable in growing Escherichia coli cells. However, their degradation increases dramatically under conditions that lead to slow cell growth. In addition, incomplete RNA molecules and molecules with defects in processing, folding, or assembly are also eliminated in growing cells in a process termed quality control. Here, we show that there are significant differences between the pathways of ribosomal RNA degradation during glucose starvation and quality control during steady-state growth. In both processes, endonucleolytic cleavage of rRNA in ribosome subunits is an early step, resulting in accumulation of large rRNA fragments when the processive exoribonucleases, RNase II, RNase R, and PNPase are absent. For 23S rRNA, cleavage is in the region of helix 71, but the exact position can differ in the two degradative processes. For 16S rRNA, degradation during starvation begins with shortening of its 3′ end in a reaction catalyzed by RNase PH. In the absence of this RNase, there is no 3′ end trimming of 16S rRNA and no accumulation of rRNA fragments, and total RNA degradation is greatly reduced. In contrast, the degradation pattern in quality control remains unchanged when RNase PH is absent. During starvation, the exoribonucleases RNase II and RNase R are important for fragment removal, whereas for quality control, RNase R and PNPase are more important. These data highlight the similarities and differences between rRNA degradation during starvation and quality control during steady-state growth and describe a role for RNase PH in the starvation degradative pathway. Published by Cold Spring Harbor Laboratory Press.
KW - Escherichia coli
KW - Ribonuclease
KW - Ribosome
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U2 - 10.1261/rna.2448911
DO - 10.1261/rna.2448911
M3 - Article
VL - 17
SP - 338
EP - 345
JO - RNA
JF - RNA
SN - 1355-8382
IS - 2
ER -