Protein Folding by Domain V of Escherichia coli 23S rRNA: Specificity of RNA-Protein Interactions

ABSTRACT The peptidyl transferase center, present in domain V of 23S rRNA of eubacteria and large rRNA of plants and animals, can act as a general protein folding modulator. Here we show that a few specific nucleotides in Escherichia coli domain V RNA bind to unfolded proteins and, as shown previously, bring the trapped proteins to a folding-competent state before releasing them. These nucleotides are the same for the proteins studied so far: bovine carbonic anhydrase, lactate dehydrogenase, malate dehydrogenase, and chicken egg white lysozyme. The amino acids that interact with these nucleotides are also found to be specific in the two cases tested: bovine carbonic anhydrase and lysozyme. They are either neutral or positively charged and are present in random coils on the surface of the crystal structure of both the proteins. In fact, two of these amino acid-nucleotide pairs are identical in the two cases. How these features might help the process of protein folding is discussed.

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A comparison of the unfolding and dissociation of the large ribosome subunits from Rhodopseudomonas·spheroides N.C.I.B. 8253 and Escherichia coli M.R.E. 600

Biochemical Journal ◽

10.1042/bj1330739 ◽

1973 ◽

Vol 133 (4) ◽

pp. 739-747 ◽

Cited By ~ 2

Author(s):

A. Robinson ◽

J. Sykes

Keyword(s):

Escherichia Coli ◽

Protein Interactions ◽

Ribosomal Proteins ◽

Ribosomal Subunit ◽

23S Rrna ◽

Core Particle ◽

Protein Loss ◽

E Coli ◽

Rrna Species ◽

Rhodopseudomonas Spheroides

1. The behaviour of the large ribosomal subunit from Rhodopseudomonas spheroides (45S) has been compared with the 50S ribosome from Escherichia coli M.R.E. 600 (and E. coli M.R.E. 162) during unfolding by removal of Mg2+ and detachment of ribosomal proteins by high univalent cation concentrations. The extent to which these processes are reversible with these ribosomes has also been examined. 2. The R. spheroides 45S ribosome unfolds relatively slowly but then gives rise directly to two ribonucleoprotein particles (16.6S and 13.7S); the former contains the intact primary structure of the 16.25S rRNA species and the latter the 15.00S rRNA species of the original ribosome. No detectable protein loss occurs during unfolding. The E. coli ribosome unfolds via a series of discrete intermediates to a single, unfolded ribonucleoprotein unit (19.1S) containing the 23S rRNA and all the protein of the original ribosome. 3. The two unfolded R. spheroides ribonucleoproteins did not recombine when the original conditions were restored but each simply assumed a more compact configuration. Similar treatments reversed the unfolding of the E. coli 50S ribosomes; replacement of Mg2+ caused the refolding of the initial products of unfolding and in the presence of Ni2+ the completely unfolded species (19.1S) again sedimented at the same rate as the original ribosomes (44S). 4. Ribosomal proteins (25%) were dissociated from R. spheroides 45S ribosomes by dialysis against a solution with a Na+/Mg2+ ratio of 250:1. During this process two core particles were formed (21.2S and 14.2S) and the primary structures of the two original rRNA species were conserved. This dissociation was not reversed. With E. coli 50S approximately 15% of the original ribosomal protein was dissociated, a single 37.6S core particle was formed, the 23S rRNA remained intact and the ribosomal proteins would reassociate with the core particle to give a 50S ribosome. 5. The ribonuclease activities in R. spheroides 45S and E. coli M.R.E. 600 and E. coli M.R.E. 162 50S ribosomes are compared. 6. The observations concerning unfolding and dissociation are consistent with previous reports showing the unusual rRNA complement of the mature R. spheroides 45S ribosome and show the dependence of these events upon the rRNA and the importance of protein–protein interactions in the structure of the R. spheroides ribosome.

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Mutation in 23S rRNA Responsible for Resistance to 16-Membered Macrolides and Streptogramins in Streptococcus pneumoniae

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.45.1.319-323.2001 ◽

2001 ◽

Vol 45 (1) ◽

pp. 319-323 ◽

Cited By ~ 90

Author(s):

Florence Depardieu ◽

Patrice Courvalin

Keyword(s):

Escherichia Coli ◽

Streptococcus Pneumoniae ◽

Clinical Isolate ◽

23S Rrna ◽

Resistance Phenotype ◽

Domain V

ABSTRACT Streptococcus pneumoniae clinical isolate BM4455 was resistant to 16-membered macrolides and to streptogramins. This unusual resistance phenotype was due to an A2062C (Escherichia coli numbering) mutation in domain V of the four copies of 23S rRNA.

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Complementation of an Escherichia coli DnaK Defect by Hsc70-DnaK Chimeric Proteins

Journal of Bacteriology ◽

10.1128/jb.186.18.6248-6253.2004 ◽

2004 ◽

Vol 186 (18) ◽

pp. 6248-6253 ◽

Cited By ~ 9

Author(s):

Jean-Philippe Suppini ◽

Mouna Amor ◽

Jean-Hervé Alix ◽

Moncef M. Ladjimi

Keyword(s):

Escherichia Coli ◽

High Temperatures ◽

Protein Interactions ◽

Peptide Binding ◽

Binding Domain ◽

Protein Protein Interactions ◽

Unfolded Proteins ◽

E Coli ◽

Hsp70 Family ◽

Phage Propagation

ABSTRACT Escherichia coli DnaK and rat Hsc70 are members of the highly conserved 70-kDa heat shock protein (Hsp70) family that show strong sequence and structure similarities and comparable functional properties in terms of interactions with peptides and unfolded proteins and cooperation with cochaperones. We show here that, while the DnaK protein is, as expected, able to complement an E. coli dnaK mutant strain for growth at high temperatures and λ phage propagation, Hsc70 protein is not. However, an Hsc70 in which the peptide-binding domain has been replaced by that of DnaK is able to complement this strain for both phenotypes, suggesting that the peptide-binding domain of DnaK is essential to fulfill the specific functions of this protein necessary for growth at high temperatures and for λ phage replication. The implications of these findings on the functional specificities of the Hsp70s and the role of protein-protein interactions in the DnaK chaperone system are discussed.

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In vitro Protein Folding by Ribosomes from Escherichia coli, Wheat Germ and Rat Liver. The Role of the 50S Particle and its 23S rRNA

European Journal of Biochemistry ◽

10.1111/j.1432-1033.1996.00613.x ◽

1996 ◽

Vol 235 (3) ◽

pp. 613-621 ◽

Cited By ~ 66

Author(s):

Biswadip Das ◽

Subrata Chattopadhyay ◽

Aloke Kumar Bera ◽

Chanchal DasGupta

Keyword(s):

Escherichia Coli ◽

Protein Folding ◽

Rat Liver ◽

Wheat Germ ◽

23S Rrna ◽

Vitro Protein

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Mutations in 23S rRNA are associated with clarithromycin resistance in Helicobacter pylori.

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.40.2.477 ◽

1996 ◽

Vol 40 (2) ◽

pp. 477-480 ◽

Cited By ~ 274

Author(s):

J Versalovic ◽

D Shortridge ◽

K Kibler ◽

M V Griffy ◽

J Beyer ◽

...

Keyword(s):

Escherichia Coli ◽

Helicobacter Pylori ◽

Peptic Ulcer ◽

23S Rrna ◽

Treatment Regimens ◽

Clarithromycin Resistance ◽

Transition Mutation ◽

H Pylori ◽

Domain V ◽

Ulcer Treatment

Twelve clarithromycin-resistant Helicobacter pylori isolates (100% of resistant isolates examined) from seven different patients each contained an A-->G transition mutation within a conserved loop of 23S rRNA. A-->G transition mutations at positions cognate with Escherichia coli 23S rRNA positions 2058 and 2059 were identified. Clarithromycin-susceptible H. pylori isolates from 14 different patients displayed no polymorphisms in a conserved loop within domain V of 23S rRNA. The study is the first to report mutations in H. pylori associated with resistance to an antimicrobial agent used in established peptic ulcer treatment regimens.

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Use of affinity capillary electrophoresis to determine kinetic and equilibrium constants for binding of arylsulfonamides to bovine carbonic anhydrase

Journal of Medicinal Chemistry ◽

10.1021/jm00053a016 ◽

1993 ◽

Vol 36 (1) ◽

pp. 126-133 ◽

Cited By ~ 132

Author(s):

Luis Z. Avila ◽

Yen Ho Chu ◽

Erich C. Blossey ◽

George M. Whitesides

Keyword(s):

Capillary Electrophoresis ◽

Carbonic Anhydrase ◽

Equilibrium Constants ◽

Affinity Capillary Electrophoresis ◽

Bovine Carbonic Anhydrase

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Macrolide-Resistant and Macrolide-Sensitive Mycoplasma pneumoniae Pneumonia in Children Treated Using Early Corticosteroids

Journal of Clinical Medicine ◽

10.3390/jcm10061309 ◽

2021 ◽

Vol 10 (6) ◽

pp. 1309

Author(s):

Hye Young Han ◽

Ki Cheol Park ◽

Eun-Ae Yang ◽

Kyung-Yil Lee

Keyword(s):

Mycoplasma Pneumoniae ◽

Serological Test ◽

Corticosteroid Treatment ◽

23S Rrna ◽

Laboratory Parameters ◽

The Mean ◽

Domain V ◽

Positive Results ◽

Mycoplasma Pneumoniae Pneumonia

We have found that early corticosteroid therapy was effective for reducing morbidity during five Korea-wide epidemics. We evaluated the clinical and laboratory parameters of 56 children who received early corticosteroid treatment for pneumonia that was caused by macrolide-resistant Mycoplasma pneumoniae (M. pneumoniae) or macrolide-sensitive M. pneumoniae between July 2019 and February 2020. All subjects had dual positive results from a PCR assay and serological test, and received corticosteroids within 24–36 h after admission. Point mutation of residues 2063, 2064, and 2067 was identified in domain V of 23S rRNA. The mean age was 6.8 years and the male:female ratio was 1.2:1 (31:25 patients). Most of the subjects had macrolide-resistant M. pneumoniae (73%), and all mutated strains had the A2063G transition. No significant differences in clinical and laboratory parameters were observed between macrolide-resistant and macrolide-sensitive M. pneumoniae groups that were treated with early dose-adjusted corticosteroids. Higher-dose steroid treatment may be needed for patients who have fever that persists for >48 h or increased biomarkers such as lactate dehydrogenase concentration at follow-up despite a usual dose of steroid therapy.

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Lipid-protein interactions in membranes: interaction of phospholipids with respiratory enzymes of Escherichia coli membrane.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(17)40370-x ◽

1977 ◽

Vol 252 (10) ◽

pp. 3194-3198

Author(s):

M Esfahani ◽

B B Rudkin ◽

C J Cutler ◽

P E Waldron

Keyword(s):

Escherichia Coli ◽

Protein Interactions ◽

Respiratory Enzymes ◽

Lipid Protein Interactions

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The Protein Interactome of Glycolysis in Escherichia coli

Proteomes ◽

10.3390/proteomes9020016 ◽

2021 ◽

Vol 9 (2) ◽

pp. 16

Author(s):

Shomeek Chowdhury ◽

Stephen Hepper ◽

Mudassir K. Lodi ◽

Milton H. Saier ◽

Peter Uetz

Keyword(s):

Escherichia Coli ◽

Protein Interactions ◽

Allosteric Regulation ◽

Glycolytic Enzymes ◽

Protein Protein Interactions ◽

Post Translational Modification ◽

Interacting Protein ◽

E Coli ◽

Protein Interactome ◽

The Impact

Glycolysis is regulated by numerous mechanisms including allosteric regulation, post-translational modification or protein-protein interactions (PPI). While glycolytic enzymes have been found to interact with hundreds of proteins, the impact of only some of these PPIs on glycolysis is well understood. Here we investigate which of these interactions may affect glycolysis in E. coli and possibly across numerous other bacteria, based on the stoichiometry of interacting protein pairs (from proteomic studies) and their conservation across bacteria. We present a list of 339 protein-protein interactions involving glycolytic enzymes but predict that ~70% of glycolytic interactors are not present in adequate amounts to have a significant impact on glycolysis. Finally, we identify a conserved but uncharacterized subset of interactions that are likely to affect glycolysis and deserve further study.

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