An explosive episode of biological diversification occurred near the beginning of the Cambrian period. Evolutionary rates in the Cambrian have been difficult to quantify accurately because of a lack of high-precision ages. Currently, uranium-lead zircon geochronology is the most powerful method for dating rocks of Cambrian age. Uranium-lead zircon data from lower Cambrian rocks located in northeast Siberia indicate that the Cambrian period began at approximately 544 million years ago and that its oldest (Manykaian) stage lasted no less than 10 million years. Other data indicate that the Tommotian and Atdabanian stages together lasted only 5 to 10 million years. The resulting compression of Early Cambrian time accentuates the rapidity of both the faunal diversification and subsequent Cambrian turnover.
In eukaryotic ribosome, the N domain of polypeptide release factor eRF1 is involved in decoding stop signals in mRNAs. However, structure of the decoding site remains obscure. Here, we specifically altered the stop codon recognition pattern of human eRF1 by point mutagenesis of the invariant Glu55 and Tyr125 residues in the N domain. The 3D structure of generated eRF1 mutants was not destabilized as demonstrated by calorimetric measurements and calculated free energy perturbations. In mutants, the UAG response was most profoundly and selectively affected. Surprisingly, Glu55Arg mutant completely retained its release activity. Substitution of the aromatic ring in position 125 reduced response toward all stop codons. This result demonstrates the critical importance of Tyr125 for maintenance of the intact structure of the eRF1 decoding site. The results also suggest that Tyr125 is implicated in recognition of the 3d stop codon position and probably forms an H-bond with Glu55. The data point to a pivotal role played by the YxCxxxF motif (positions 125–131) in purine discrimination of the stop codons. We speculate that eRF1 decoding site is formed by a 3D network of amino acids side chains.
To study positioning of the polypeptide release factor eRF1 toward a stop signal in the ribosomal decoding site, we applied photoactivatable mRNA analogs, derivatives of oligoribonucleotides. The human eRF1 peptides cross-linked to these short mRNAs were identified. Cross-linkers on the guanines at the second, third, and fourth stop signal positions modified fragment 31-33, and to lesser extent amino acids within region 121-131 (the ''YxCxxxF loop'') in the N domain. Hence, both regions are involved in the recognition of the purines. A cross-linker at the first uridine of the stop codon modifies Val66 near the NIKS loop (positions 61-64), and this region is important for recognition of the first uridine of stop codons. Since the N domain distinct regions of eRF1 are involved in a stop-codon decoding, the eRF1 decoding site is discontinuous and is not of ''protein anticodon'' type. By molecular modeling, the eRF1 molecule can be fitted to the A site proximal to the P-site-bound tRNA and to a stop codon in mRNA via a large conformational change to one of its three domains. In the simulated eRF1 conformation, the YxCxxxF motif and positions 31-33 are very close to a stop codon, which becomes also proximal to several parts of the C domain. Thus, in the A-site-bound state, the eRF1 conformation significantly differs from those in crystals and solution. The model suggested for eRF1 conformation in the ribosomal A site and cross-linking data are compatible.
In universal-code eukaryotes, a single-translation termination factor, eukaryote class-1 polypeptide release factor (eRF1), decodes the three stop codons: UAA, UAG, and UGA. In some ciliates, like Stylonychia and Paramecium, eRF1s exhibit UGA-only decoding specificity, whereas UAG and UAA are reassigned as sense codons. Because variant-code ciliates may have evolved from universalcode ancestor(s), structural features should exist in ciliate eRF1s that restrict their stop codon recognition. In omnipotent eRF1s, stop codon recognition is associated with the N-terminal domain of the protein. Using both in vitro and in vivo assays, we show here that chimeric molecules composed of the N-terminal domain of Stylonychia eRF1 fused to the core domain (MC domain) of human eRF1 retained specificity toward UGA; this unambiguously associates eRF1 stop codon specificity to the nature of its N-terminal domain. Functional analysis of eRF1 chimeras constructed by swapping ciliate N-terminal domain sequences with the matching ones from the human protein highlighted the crucial role of the tripeptide QFM in restricting Stylonychia eRF1 specificity toward UGA. Using the site-directed mutagenesis, we show that Paramecium eRF1 specificity toward UGA resides within the NIKS (amino acids 61-64) and YxCxxxF (amino acids 124 -131) motifs. Thus, we establish that eRF1 from two different ciliates relies on different molecular mechanisms to achieve specificity toward the UGA stop codon. This finding suggests that eRF1 restriction of specificity to only UGA might have been an early event occurring in independent instances in ciliate evolutionary history, possibly facilitating the reassignment of UAG and UAA to sense codons. ciliated protozoa ͉ dual gene reporter system ͉ eukaryote class-1 polypeptide release factors ͉ interdomain and intradomain protein chimeras ͉ stop codon decoding I n the universal genetic code, three stop codons (UAA, UAG, and UGA) located at the termini of mRNA sequences are decoded at the termination step of translation by class-1 polypeptide release factors (RF) (reviewed in refs. 1-3). However, in organisms with variations in the genetic code, like ciliates, class-1 factors are able to decode only one or two stop codons with the remaining stop codon(s) reassigned to encode certain amino acids (for review, see refs. 4 and 5). The molecular mechanisms that restrict stop codon recognition are entirely unknown and represent major unresolved problems in molecular biology and genetics. In eukaryotes with the standard code, a single class-1 RF, designated eukaryote class-1 polypeptide release factor (eRF1), decodes all three stop codons. Stop codon decoding results in signal transduction from the small to the large ribosomal subunit leading to cleavage of peptidyl-tRNA at the peptidyl transferase center of the ribosome.The eRF1 protein family is highly conserved and similar to archaeal class-1 RFs but differs profoundly from bacterial class-1 RFs (6-8). The only known structural element common to all class-1 RFs is a univer...
Background: Isolated Eph transmembrane domains (TMD) dimerize in membrane mimetics, but the functional significance of these interactions is unclear. Results: Mutations introduced into the alternative dimerization motifs of the EphA2 TMD induced an opposite effect on receptor activity. Conclusion: Alternative TMD interactions promote either the active or inactive EphA2 conformation. Significance: The involvement of TMD interactions in Eph receptor activity is discovered.The EphA2 receptor tyrosine kinase plays a central role in the regulation of cell adhesion and guidance in many human tissues. The activation of EphA2 occurs after proper dimerization/ oligomerization in the plasma membrane, which occurs with the participation of extracellular and cytoplasmic domains. Our study revealed that the isolated transmembrane domain (TMD) of EphA2 embedded into the lipid bicelle dimerized via the heptad repeat motif L 535 X 3 G 539 X 2 A 542 X 3 V 546 X 2 L 549 rather than through the alternative glycine zipper motif A 536 X 3 G 540 X 3 G 544(typical for TMD dimerization in many proteins). To evaluate the significance of TMD interactions for full-length EphA2, we substituted key residues in the heptad repeat motif (HR variant: G539I, A542I, G553I) or in the glycine zipper motif (GZ variant: G540I, G544I) and expressed YFP-tagged EphA2 (WT, HR, and GZ variants) in HEK293T cells. Confocal microscopy revealed a similar distribution of all EphA2-YFP variants in cells. The expression of EphA2-YFP variants and their kinase activity (phosphorylation of Tyr 588 and/or Tyr 594) and ephrin-A3 binding were analyzed with flow cytometry on a single cell basis. Activation of any EphA2 variant is found to occur even without ephrin stimulation when the EphA2 content in cells is sufficiently high. Ephrin-A3 binding is not affected in mutant variants. Mutations in the TMD have a significant effect on EphA2 activity. Both ligand-dependent and ligand-independent activities are enhanced for the HR variant and reduced for the GZ variant compared with the WT. These findings allow us to suggest TMD dimerization switching between the heptad repeat and glycine zipper motifs, corresponding to inactive and active receptor states, respectively, as a mechanism underlying EphA2 signal transduction.Receptor tyrosine kinases of the Eph family and their ephrin ligands are key regulators of cell-cell and cell-matrix adhesion, coordinating cell migration and positioning in various adult and embryonic tissues of human organisms (1, 2). The EphA2 receptor, a representative of the human 14-member Eph family, controls such diverse processes as capillary stabilization by pericytes (3), keratinocyte movement out of the basal layer (2), blastocyst entry into the endometrial layer (4), and cardiac stem cell mobilization from the niche (5). Activation of EphA2 leads to cell detachment (mobilization), loss of intercellular contacts (an increase in cell layer permeability), or cell repulsion (guidance).A classical model of EphA2 activation assumes the binding of a li...
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