The role of guanosine 5'-triphosphate in the initiation of peptide synthesis. 3. Binding of formylmethionyl-tRNA to ribosomes

Identification of Small Molecule Enhancers of Immunotherapy for Melanoma

Small molecule based targeted therapies for the treatment of metastatic melanoma hold promise but responses are often not durable, and tumors frequently relapse. Response to adoptive cell transfer (ACT)-based immunotherapy in melanoma patients are durable but patients develop resistance primarily due to loss of antigen expression. The combination of small molecules that sustain T cell effector function with ACT could lead to long lasting responses. Here, we have developed a novel co-culture cell-based high throughput assay system to identify compounds that could potentially synergize or enhance ACT-based immunotherapy of melanoma. A BRAF^V600E mutant melanoma cell line, SB-3123_p which is resistant to Pmel-1-directed ACT due to low gp100 expression levels was used to develop a homogenous time resolve fluorescence (HTRF), screening assay. This high throughput screening assay quantitates IFNγ released upon recognition of the SB-3123_p melanoma cells by Pmel-1 CD8⁺ T-cells. A focused collection of approximately 500 small molecules targeting a broad range of cellular mechanisms was screened, and four active compounds that increased melanoma antigen expression leading to enhanced IFNγ production were identified and their in vitro activity was validated. These four compounds may provide a basis for enhanced immune recognition and design of novel therapeutic approaches for patients with BRAF mutant melanoma resistant to ACT due to antigen downregulation.

Translation initiation without IF2-dependent GTP hydrolysis

Translation initiation factor IF2 is a guanine nucleotide-binding protein. The free energy change associated with guanosine triphosphate hydrolase (GTPase) activity of these proteins is believed to be the driving force allowing them to perform their functions as molecular switches. We examined role and relevance of IF2 GTPase and demonstrate that an Escherichia coli IF2 mutant bearing a single amino acid substitution (E571K) in its 30S binding domain (IF2-G3) can perform in vitro all individual translation initiation functions of wild type (wt) IF2 and supports faithful messenger RNA translation, despite having a reduced affinity for the 30S subunit and being completely inactive in GTP hydrolysis. Furthermore, the corresponding GTPase-null mutant of Bacillus stearothermophilus (E424K) can replace in vivo wt IF2 allowing an E. coli infB null mutant to grow with almost wt duplication times. Following the E571K (and E424K) mutation, which likely disrupts hydrogen bonding between subdomains G2 and G3, IF2 acquires a guanosine diphosphate (GDP)-like conformation, no longer responsive to GTP binding thereby highlighting the importance of interdomain communication in IF2. Our data underlie the importance of GTP as an IF2 ligand in the early initiation steps and the dispensability of the free energy generated by the IF2 GTPase in the late events of the translation initiation pathway.

Translation Initiation

Selection of correct start codons on messenger RNAs is a key step required for faithful translation of the genetic message. Such a selection occurs in a complex process, during which a translation-competent ribosome assembles, eventually having in its P site a specialized methionyl-tRNAMet base-paired with the start codon on the mRNA. This chapter summarizes recent advances describing at the molecular level the successive steps involved in the process. Special emphasis is put on the roles of the three initiation factors and of the initiator tRNA, which are crucial for the efficiency and the specificity of the process. In particular, structural analyses concerning complexes containing ribosomal subunits, as well as detailed kinetic studies, have shed new light on the sequence of events leading to faithful initiation of protein synthesis in Bacteria.

Nuclease resistance of an extraordinarily thermostable mini-hairpin DNA fragment, d(GCGAAGC) and its application to in vitro protein synthesis

The nuclease resistance of a short, thermostable mini-hairpin, d(GCGAAGC), and other related hairpins was examined. Hairpins possessing a purine-rich (GAA) or (GAAA) loop appeared to be more resistant against nucleases than those with a pyrimidine-rich loop or single-stranded oligomers. Among 8 kinds of oligodeoxyribonucleotides examined, the fragment most resistant against nucleases was a hairpin with the sequence of d(CGCGAAGCG). This hairpin was then utilized for the stabilization of mRNA in an in vitro translation system; the 3'-terminal region of an mRNA was hybridized with an oligodeoxyribonucleotide including the sequence complementary to the 3'-terminus of the mRNA tagged with the nuclease-resistant d(CGCGAAGCG) hairpin sequence. By using this method, dihydrofolate reductase (DHFR) mRNA was stabilized against nucleases contaminating a cell-free translation system of E.coli, with a consequent increase in protein synthesis efficiency of 200%.

Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: an extraordinarily stable structure resistant to nucleases and heat

The three-dimensional structure of a short DNA fragment, d(GCGAAGC) exhibiting an extraordinarily stable hairpin structure was determined by nuclear magnetic resonance spectroscopy. Two possible models were obtained by molecular modelling using distance and torsion constraints. Only one of these two models is the correct structure, which can clearly explain all the 1H chemical shifts. d(GCGAAGC) is folded back on itself between A4 and A5, and all the sugars in the fragment adopt the C2'-endo conformation. This compact molecule is stabilized by regular extensive base-stacking interaction within each B-form helical strand of G1C2G3A4 and A5G6C7, and by two G-C and one G3-A5 base pairs. The molecule is hard to differentiate into stem and loop regions, so that we classify it as a turn (hairpin-turn) structure experted by a single-stranded DNA. This highly stacked structure shows high thermostability and strong resistance against nucleases contained in E. coli extracts and in human serum.

Stabilization of mRNA in an Escherichia coli cell-free translation system

It became clear that mRNA can be stabilized in a cell-free translation system of Escherichia coli by hybridization with a small DNA fragment at its 3' terminus. The stability increased when a small DNA fragment containing a stable hairpin structure with a GAAA loop was used. The enhancement of stabilization was brought about because the hairpin structure is resistant towards the nucleases contained in the translation system. The hairpin structure is effective by stabilizing the added DNA fragment itself towards the nucleases.

Stimulation by ATP of protein initiation in a prokaryotic organism, B. stearothermophilus

In contrast to E. coli ribosomes, with B. stearothermophilus ribosomes initiation complex formation is stimulated by ATP as well as GTP, but maximum stimulation occurs when both the nucleotides are present; and their terminal phosphate must be hydrolysable. In the presence of ATP and GTP, B. stearothermophilus ribosomes synthesize a highly phosphorylated guanine derivative, ppGpp, and the role of ATP in initiation might be related to this synthesis. We discarded the role of ATP as being trivial and corresponding solely to the well-known effect on eukaryotic systems.

Influence of guanine nucleotides and elongation factors on interaction of release factors with the ribosome

Release of formylmethionine from the reticulocyte ribosomal substrate, f[(3)H]Met-tRNA.ribosome, is promoted by reticulocyte release factor (RF). The initial rate of this reaction is stimulated by GTP but inhibited by GDPCP. Formation of an RF.UA[(3)H]A(2).ribosome complex is a measure of the binding of reticulocyte RF to the ribosome, and the recovery of this complex is increased by GDPCP and, to a lesser extent, GTP. These studies suggest that GTP is involved in the initial association of RF with the ribosome and that hydrolysis of the gamma-phosphate of the guanine nucleotide is required at a subsequent rate-limiting step. The ribosomal-dependent fMet-tRNA hydrolysis and GTPase activities of reticulocyte RF are inhibited when elongation factor (EF)-2 is bound to the respective ribosomal substrate in the presence of fusidic acid and GDP. When EF-G is bound to the f[(3)H]Met-tRNA.AUG.ribosome substrate with fusidic acid and GDP, the fMet-tRNA hydrolysis activity of Escherichia coli RF-1 and RF-2 is also inhibited. The binding of reticulocyte RF and E. coli RF-1 or RF-2 to their respective ribosomes is prevented when fusidic acid.EF-2/EF-G.GDP.ribosome complexes are used.

Translocation of messenger RNA and "accommodation" of fMet-tRNA

Messenger RNA is moved a distance of approximately three nucleotides in the 5' direction relative to the ribosome during the translocation of peptidyl-tRNA from the A to the P site. This movement is catalyzed by G factor and is dependent on the hydrolysis of GTP. In contrast, mRNA is not moved during the f(2)-catalyzed hydrolysis of GTP that is involved in the activation of ribosome-bound fMet-tRNA. This second type of GTP-dependent reaction has been named "Accommodation".

Mammalian peptide chain termination. II. Codon specificity and GTPase activity of release factor

In vitro peptide chain termination with release factor preparations from rabbit reticulocytes, guinea pig liver, or Chinese hamster liver is directed with UAAA, UAGA, or UGAA, suggesting that UAA, UAG, and UGA are terminator condons for mammalian cells. Purified release factor from rabbit reticulocytes has ribosomaldependent GTPase activity, which is stimulated by UAAA. GTP hydrolysis appears requisite for in vitro peptide chain termination in mammals.

Breakdown by streptomycin of initiation complexes formed on ribosomes of Escherichia coli

Streptomycin induces breakdown of the completed 70S initiation complex on ribosomes of Escherichia coli, but it does not interfere with any step in the formation of the complex. Moreover, it does not appear to interact with the ribosome in any special way during initiation, since the kinetics of breakdown are the same whether streptomycin is added before formation of the initiation complex, or after its completion, or (as previously observed) after formation of a polypeptide. fMet-tRNA is released as such, without chain elongation; it is released from a puromycin-reactive ("P") site. Streptomycin thus appears to distort not only the A site of the ribosome (as suggested earlier) but also the P site.

A new protein synthesis factor from Escherichia coli

A new factor that effects protein synthesis by Escherichia coli extracts was partially purified from the 1 M NH(4)Cl wash of E. coli ribosomes. This factor stimulates the binding of aminoacyl-tRNA to 30S ribosomes, and it increases the rate of synthesis of polyphenylalanine in the presence of 30S and 50S subunits.

Evidence for a proposed initiation complex for protein synthesis in reticulocyte polyribosome profiles

Polysomes consisting of 40S ribosomal subunits attached to monosomes, disomes, trisomes, and tetrasomes have been isolated for the first time by the use of isokinetic sucrose density gradients. They are formed upon incubation of rabbit reticulocyte lysate in the presence of 10 mM NaF. It is proposed that these structures represent transient initiation complexes for protein synthesis.