scholarly journals Role of ribosome assembly in Escherichia coli ribosomal RNA degradation

2018 ◽  
Author(s):  
Chaitanya Jain
Keyword(s):  
Escherichia Coli ◽  
Ribosomal Rna ◽  
Rna Degradation ◽  
Ribosome Assembly

scholarly journals The modifying enzyme Tsr3 establishes the hierarchy of Rio kinase activity in 40S ribosome assembly

2021 ◽  
Author(s):  
Haina Huang ◽  
Melissa Parker ◽  
Katrin Karbstein
Keyword(s):  
Quality Control ◽  
Binding Site ◽  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Kinase Activity ◽  
Ribosomal Subunit ◽  
Ribosome Assembly ◽  
Small Ribosomal Subunit ◽  
Yeast Strains

AbstractRibosome assembly is an intricate process, which in eukaryotes is promoted by a large machinery comprised of over 200 assembly factors (AF) that enable the modification, folding, and processing of the ribosomal RNA (rRNA) and the binding of the 79 ribosomal proteins. While some early assembly steps occur via parallel pathways, the process overall is highly hierarchical, which allows for the integration of maturation steps with quality control processes that ensure only fully and correctly assembled subunits are released into the translating pool. How exactly this hierarchy is established, in particular given that there are many instances of RNA substrate “handover” from one highly related AF to another remains to be determined. Here we have investigated the role of Tsr3, which installs a universally conserved modification in the P-site of the small ribosomal subunit late in assembly. Our data demonstrate that Tsr3 separates the activities of the Rio kinases, Rio2 and Rio1, with whom it shares a binding site. By binding after Rio2 dissociation, Tsr3 prevents rebinding of Rio2, promoting forward assembly. After rRNA modification is complete, Tsr3 dissociates, thereby allowing for recruitment of Rio1. Inactive Tsr3 blocks Rio1, which can be rescued using mutants that bypass the requirement for Rio1 activity. Finally, yeast strains lacking Tsr3 randomize the binding of the two kinases, leading to the release of immature ribosomes into the translating pool. These data demonstrate a role for Tsr3 and its modification activity in establishing a hierarchy for the function of the Rio kinases.

Ribosomal RNA Degradation and the Degradation Products in Starved Escherichia coli

1970 ◽  
Vol 67 (4) ◽  
pp. 559-565 ◽  
Author(s):  
HIROMI MARUYAMA ◽  
MITSUKO ONO-ONITSUKA ◽  
DEN'ICHI MIZUNO
Keyword(s):  
Escherichia Coli ◽  
Ribosomal Rna ◽  
Degradation Products ◽  
Rna Degradation

scholarly journals The modifying enzyme Tsr3 establishes the hierarchy of Rio kinase activity in 40S ribosome assembly

RNA ◽  
2022 ◽  
pp. rna.078994.121
Author(s):  
Haina Huang ◽  
Melissa D Parker ◽  
Katrin Karbstein
Keyword(s):  
Quality Control ◽  
Binding Site ◽  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Kinase Activity ◽  
Ribosomal Subunit ◽  
Ribosome Assembly ◽  
Small Ribosomal Subunit ◽  
Yeast Strains

Ribosome assembly is an intricate process, which in eukaryotes is promoted by a large machinery comprised of over 200 assembly factors (AF) that enable the modification, folding, and processing of the ribosomal RNA (rRNA) and the binding of the 79 ribosomal proteins. While some early assembly steps occur via parallel pathways, the process overall is highly hierarchical, which allows for the integration of maturation steps with quality control processes that ensure only fully and correctly assembled subunits are released into the translating pool. How exactly this hierarchy is established, in particular given that there are many instances of RNA substrate “handover” from one highly related AF to another remains to be determined. Here we have investigated the role of Tsr3, which installs a universally conserved modification in the P-site of the small ribosomal subunit late in assembly. Our data demonstrate that Tsr3 separates the activities of the Rio kinases, Rio2 and Rio1, with whom it shares a binding site. By binding after Rio2 dissociation, Tsr3 prevents rebinding of Rio2, promoting forward assembly. After rRNA modification is complete, Tsr3 dissociates, thereby allowing for recruitment of Rio1. Inactive Tsr3 blocks Rio1, which can be rescued using mutants that bypass the requirement for Rio1 activity. Finally, yeast strains lacking Tsr3 randomize the binding of the two kinases, leading to the release of immature ribosomes into the translating pool. These data demonstrate a role for Tsr3 and its modification activity in establishing a hierarchy for the function of the Rio kinases.

Protein folding in Escherichia coli: role of 23S ribosomal RNA

1999 ◽  
Vol 1429 (2) ◽  
pp. 293-298 ◽  
Author(s):  
Subrata Chattopadhyay ◽  
Saumen Pal ◽  
Debashis Pal ◽  
Dibyendu Sarkar ◽  
Suparna Chandra ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protein Folding ◽  
Ribosomal Rna ◽  
23S Ribosomal Rna

scholarly journals Role of 16S ribosomal RNA methylations in translation initiation in Escherichia coli

2008 ◽  
Vol 27 (6) ◽  
pp. 840-851 ◽  
Author(s):  
Gautam Das ◽  
Dinesh Kumar Thotala ◽  
Suman Kapoor ◽  
Sheelarani Karunanithi ◽  
Suman S Thakur ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Ribosomal Rna ◽  
Translation Initiation ◽  
16S Ribosomal Rna

scholarly journals Identification and Characterization of Growth Suppressors of Escherichia coli Strains Lacking Phosphorolytic Ribonucleases

2009 ◽  
Vol 191 (18) ◽  
pp. 5622-5627 ◽  
Author(s):  
Chaitanya Jain
Keyword(s):  
Escherichia Coli ◽  
Rna Degradation ◽  
Cellular Growth ◽  
Ribosome Assembly ◽  
Rnase R ◽  
Growth Defects ◽  
Suppressor Mutations ◽  
Identification And Characterization ◽  
Critical Aspects

ABSTRACT RNases are involved in critical aspects of RNA metabolism in all organisms. Two classes of RNases that digest RNA from an end (exo-RNases) are known: RNases that use water as a nucleophile to catalyze RNA degradation (hydrolytic RNases) and RNases that use inorganic phosphate (phosphorolytic RNases). It has been shown previously that the absence of the two known Escherichia coli phosphorolytic RNases, polynucleotide phosphorylase and RNase PH, leads to marked growth and ribosome assembly defects. To investigate the basis for these defects, a screen for growth suppressors was performed. The majority of suppressor mutations were found to lie within nsrR, which encodes a nitric oxide (NO)-sensitive transcriptional repressor. Further analysis showed that the suppressors function not by inactivating nsrR but by causing overexpression of a downstream gene that encodes a hydrolytic RNase, RNase R. Additional studies revealed that overexpression of another hydrolytic RNase, RNase II, similarly suppressed the growth defects. These results suggest that the requirement for phosphorolytic RNases for robust cellular growth and efficient ribosome assembly can be bypassed by increased expression of hydrolytic RNases.

scholarly journals Three Ribosomal Operons of Escherichia coli Contain Genes Encoding Small RNAs That Interact With Hfq and CsrA in vitro

2021 ◽  
Vol 12 ◽  
Author(s):  
Thomas Søndergaard Stenum ◽  
Mette Kongstad ◽  
Erik Holmqvist ◽  
Birgitte Kallipolitis ◽  
Sine Lo Svenningsen ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Ribosomal Rna ◽  
Small Rnas ◽  
Genes Encoding ◽  
Ribosomal Operons ◽  
Dependent Processes ◽  
Fine Tune

Three out of the seven ribosomal RNA operons in Escherichia coli end in dual terminator structures. Between the two terminators of each operon is a short sequence that we report here to be an sRNA gene, transcribed as part of the ribosomal RNA primary transcript by read-through of the first terminator. The sRNA genes (rrA, rrB and rrF) from the three operons (rrnA, rrnB and rrnD) are more than 98% identical, and pull-down experiments show that their transcripts interact with Hfq and CsrA. Deletion of rrA, B, F, as well as overexpression of rrB, only modestly affect known CsrA-regulated phenotypes like biofilm formation, pgaA translation and glgC translation, and the role of the sRNAs in vivo may not yet be fully understood. Since RrA, B, F are short-lived and transcribed along with the ribosomal RNA components, their concentration reflect growth-rate regulation at the ribosomal RNA promoters and they could function to fine-tune other growth-phase-dependent processes in the cell. The primary and secondary structure of these small RNAs are conserved among species belonging to different genera of Enterobacteriales.

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