scholarly journals NAC covers ribosome-associated nascent chains thereby forming a protective environment for regions of nascent chains just emerging from the peptidyl transferase center.

1995 ◽  
Vol 130 (3) ◽  
pp. 519-528 ◽  
Author(s):  
S Wang ◽  
H Sakai ◽  
M Wiedmann
Keyword(s):  
Amino Acids ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Peptidyl Transferase ◽  
Nascent Polypeptide ◽  
Peptidyl Transferase Center ◽  
Protease Resistance ◽  
Protective Environment ◽  
Cytosolic Factors

We demonstrate that nascent polypeptide-associated complex (NAC) is one of the first cytosolic factors that newly synthesized nascent chains encounter. When NAC is present, nascent chains are segregated from the cytosol until approximately 30 amino acids in length, a finding consistent with the well-documented protease resistance of short ribosome-associated nascent chains. When NAC is removed, the normally protected nascent chains are susceptible to proteolysis. Therefore NAC, by covering COOH-terminal segments of nascent chains on the ribosome, perhaps together with ribosomal proteins, forms a protective environment for regions of nascent chains just emerging from the peptidyl transferase center. Since NAC is not a core ribosomal protein, the emergence of nascent chains from the ribosome may be more dynamic than previously thought.

Rapid evolution in sequence and length of the nuclear-located gene for mitochondrial L2 ribosomal protein in cereals

Genome ◽  
2006 ◽  
Vol 49 (3) ◽  
pp. 275-281 ◽  
Author(s):  
Selvi Subramanian ◽  
Linda Bonen
Keyword(s):  
Amino Acids ◽  
Ribosomal Protein ◽  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Rna Binding ◽  
Large Subunit ◽  
Rapid Evolution ◽  
Comparative Sequence Analysis ◽  
Marchantia Polymorpha ◽  
Peptidyl Transferase

The L2 ribosomal protein is typically one of the most conserved proteins in the ribosome and is universally present in bacterial, archaeal, and eukaryotic cytosolic and organellar ribosomes. It is usually 260–270 amino acids long and its binding to the large-subunit ribosomal RNA near the peptidyl transferase center is mediated by a β-barrel RNA-binding domain with 10 β strands. In the diverse land plants Marchantia polymorpha (liverwort) and Oryza sativa (rice), the mitochondrial-encoded L2 ribosomal protein is about 500 amino acids long owing to a centrally located expansion containing the β3–β4 strand region. We have determined that, in wheat, the functional rpl2 gene has been trans ferred to the nucleus and much of the plant-specific internal insert has been deleted. Its mRNA is only 1.2 kb, and two expressed copies in wheat encode proteins of 318 and 319 amino acids, so they are considerably shorter than the maize nuclear-located rpl2 gene of 448 codons. Comparative sequence analysis of cereal mitochondrial L2 ribosomal proteins indicates that the mid region has undergone unexpectedly rapid evolution during the last 60 million years.Key words: mitochondria, ribosomal protein, plants, evolutionary gene transfer.

scholarly journals The GTPase Nog1 co-ordinates the assembly, maturation and quality control of distant ribosomal functional centers

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Purnima Klingauf-Nerurkar ◽  
Ludovic C Gillet ◽  
Daniela Portugal-Calisto ◽  
Michaela Oborská-Oplová ◽  
Martin Jäger ◽  
...  
Keyword(s):  
Quality Control ◽  
Protein Folding ◽  
Atpase Activity ◽  
Ribosomal Protein ◽  
Peptidyl Transferase ◽  
Peptidyl Transferase Center ◽  
Eukaryotic Ribosome ◽  
Ribosomal Stalk ◽  
Exit Tunnel ◽  
Ribosome Formation

Eukaryotic ribosome precursors acquire translation competence in the cytoplasm through stepwise release of bound assembly factors, and proofreading of their functional centers. In case of the pre-60S, these steps include removal of placeholders Rlp24, Arx1 and Mrt4 that prevent premature loading of the ribosomal protein eL24, the protein-folding machinery at the polypeptide exit tunnel (PET), and the ribosomal stalk, respectively. Here, we reveal that sequential ATPase and GTPase activities license release factors Rei1 and Yvh1 to trigger Arx1 and Mrt4 removal. Drg1-ATPase activity removes Rlp24 from the GTPase Nog1 on the pre-60S; consequently, the C-terminal tail of Nog1 is extracted from the PET. These events enable Rei1 to probe PET integrity and catalyze Arx1 release. Concomitantly, Nog1 eviction from the pre-60S permits peptidyl transferase center maturation, and allows Yvh1 to mediate Mrt4 release for stalk assembly. Thus, Nog1 co-ordinates the assembly, maturation and quality control of distant functional centers during ribosome formation.

scholarly journals Resistance to the Peptidyl Transferase Inhibitor Tiamulin Caused by Mutation of Ribosomal Protein L3

2003 ◽  
Vol 47 (9) ◽  
pp. 2892-2896 ◽  
Author(s):  
Jacob Bøsling ◽  
Susan M. Poulsen ◽  
Birte Vester ◽  
Katherine S. Long
Keyword(s):  
Ribosomal Protein ◽  
Drug Binding ◽  
Mechanisms Of Resistance ◽  
Peptidyl Transferase ◽  
Peptidyl Transferase Center ◽  
Resistance Determinants ◽  
Drug Binding Site ◽  
Gene Coding ◽  
Bacterial Ribosome ◽  
Ribosomal Protein L3

ABSTRACT The antibiotic tiamulin targets the 50S subunit of the bacterial ribosome and interacts at the peptidyl transferase center. Tiamulin-resistant Escherichia coli mutants were isolated in order to elucidate mechanisms of resistance to the drug. No mutations in the rRNA were selected as resistance determinants using a strain expressing only a plasmid-encoded rRNA operon. Selection in a strain with all seven chromosomal rRNA operons yielded a mutant with an A445G mutation in the gene coding for ribosomal protein L3, resulting in an Asn149Asp alteration. Complementation experiments and sequencing of transductants demonstrate that the mutation is responsible for the resistance phenotype. Chemical footprinting experiments show a reduced binding of tiamulin to mutant ribosomes. It is inferred that the L3 mutation, which points into the peptidyl transferase cleft, causes tiamulin resistance by alteration of the drug-binding site. This is the first report of a mechanism of resistance to tiamulin unveiled in molecular detail.

scholarly journals Association of snR190 snoRNA chaperone with early pre-60S particles is regulated by the RNA helicase Dbp7 in yeast

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Mariam Jaafar ◽  
Julia Contreras ◽  
Carine Dominique ◽  
Sara Martín-Villanueva ◽  
Régine Capeyrou ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Ribosomal Subunit ◽  
Rna Helicase ◽  
Genetic Interactions ◽  
Large Ribosomal Subunit ◽  
Base Pairing ◽  
Peptidyl Transferase ◽  
Peptidyl Transferase Center

AbstractSynthesis of eukaryotic ribosomes involves the assembly and maturation of precursor particles (pre-ribosomal particles) containing ribosomal RNA (rRNA) precursors, ribosomal proteins (RPs) and a plethora of assembly factors (AFs). Formation of the earliest precursors of the 60S ribosomal subunit (pre-60S r-particle) is among the least understood stages of ribosome biogenesis. It involves the Npa1 complex, a protein module suggested to play a key role in the early structuring of the pre-rRNA. Npa1 displays genetic interactions with the DExD-box protein Dbp7 and interacts physically with the snR190 box C/D snoRNA. We show here that snR190 functions as a snoRNA chaperone, which likely cooperates with the Npa1 complex to initiate compaction of the pre-rRNA in early pre-60S r-particles. We further show that Dbp7 regulates the dynamic base-pairing between snR190 and the pre-rRNA within the earliest pre-60S r-particles, thereby participating in structuring the peptidyl transferase center (PTC) of the large ribosomal subunit.

scholarly journals The ribosome can discriminate the chirality of amino acids within its peptidyl-transferase center

2015 ◽  
Vol 112 (19) ◽  
pp. 6038-6043 ◽  
Author(s):  
Michael T. Englander ◽  
Joshua L. Avins ◽  
Rachel C. Fleisher ◽  
Bo Liu ◽  
Philip R. Effraim ◽  
...  
Keyword(s):  
Amino Acids ◽  
Physiological Role ◽  
Peptidyl Transferase ◽  
Translational Machinery ◽  
Peptidyl Transferase Center ◽  
Peptidyl Transfer ◽  
Site Use ◽  
Dynamics Simulations ◽  
A Site ◽  
Trna Binding

The cellular translational machinery (TM) synthesizes proteins using exclusively L- or achiral aminoacyl-tRNAs (aa-tRNAs), despite the presence of D-amino acids in nature and their ability to be aminoacylated onto tRNAs by aa-tRNA synthetases. The ubiquity of L-amino acids in proteins has led to the hypothesis that D-amino acids are not substrates for the TM. Supporting this view, protein engineering efforts to incorporate D-amino acids into proteins using the TM have thus far been unsuccessful. Nonetheless, a mechanistic understanding of why D-aa-tRNAs are poor substrates for the TM is lacking. To address this deficiency, we have systematically tested the translation activity of D-aa-tRNAs using a series of biochemical assays. We find that the TM can effectively, albeit slowly, accept D-aa-tRNAs into the ribosomal aa-tRNA binding (A) site, use the A-site D-aa-tRNA as a peptidyl-transfer acceptor, and translocate the resulting peptidyl-D-aa-tRNA into the ribosomal peptidyl-tRNA binding (P) site. During the next round of continuous translation, however, we find that ribosomes carrying a P-site peptidyl-D-aa-tRNA partition into subpopulations that are either translationally arrested or that can continue translating. Consistent with its ability to arrest translation, chemical protection experiments and molecular dynamics simulations show that P site-bound peptidyl-D-aa-tRNA can trap the ribosomal peptidyl-transferase center in a conformation in which peptidyl transfer is impaired. Our results reveal a novel mechanism through which D-aa-tRNAs interfere with translation, provide insight into how the TM might be engineered to use D-aa-tRNAs, and increase our understanding of the physiological role of a widely distributed enzyme that clears D-aa-tRNAs from cells.

The Conservation of Amino Acids in the N-Terminal Position of Ribosomal and Cytosol Proteins from Escherichia coli, Bacillus stearothermophilus, and Halobacterium cutirubrum

1975 ◽  
Vol 53 (12) ◽  
pp. 1323-1327 ◽  
Author(s):  
Alastair T. Matheson ◽  
Makoto Yaguchi ◽  
Louis P. Visentin
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Bacillus Stearothermophilus ◽  
Protein Fractions ◽  
Extreme Halophile ◽  
Terminal Position ◽  
E Coli ◽  
Terminal Residue

Alanine, methionine, and serine are the predominant N-terminal residues in the cytosol and ribosomal protein fractions from the thermophile Bacillus stearothermophilus and the extreme halophile Halobacterium cutirubrum, a similar situation to that previously found in Escherichia coli. In all three bacteria the N-terminal residues of the 30S ribosomal proteins are mainly alanine [Formula: see text] methionine > serine whereas in the 50S ribosomal proteins from E. coli and B. stearothermophilus the predominant residues are methionine > alanine > serine suggesting conservation of specific N-terminal residues in these ribosomal proteins. However, the 50S ribosomal proteins from H. cutirubrum showed serine as the major N-terminal residue.

scholarly journals Mutations in Ribosomal Protein L3 Are Associated with Oxazolidinone Resistance in Staphylococci of Clinical Origin

2009 ◽  
Vol 53 (12) ◽  
pp. 5275-5278 ◽  
Author(s):  
Jeffrey B. Locke ◽  
Mark Hilgers ◽  
Karen Joy Shaw
Keyword(s):  
Staphylococcus Aureus ◽  
Sequence Analysis ◽  
Ribosomal Protein ◽  
Binding Site ◽  
Staphylococcus Epidermidis ◽  
Peptidyl Transferase ◽  
Peptidyl Transferase Center ◽  
Ribosomal Protein L3

ABSTRACT Following recent reports of ribosomal protein L3 mutations in laboratory-derived linezolid-resistant (LZDr) Staphylococcus aureus, we investigated whether similar mutations were present in LZDr staphylococci of clinical origin. Sequence analysis of a variety of LZDr isolates revealed two L3 mutations, ΔSer145 (S. aureus NRS127) and Ala157Arg (Staphylococcus epidermidis 1653059), both occurring proximal to the oxazolidinone binding site in the peptidyl transferase center. The oxazolidinone torezolid maintained a ≥8-fold potency advantage over linezolid for both strains.

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