Mechanistic dissection of premature translation termination induced by acidic residues-enriched nascent peptide

Promoting ribosomal incorporation of backbone-modifying nonproteinogenic amino acids into nascent peptides by ATP-binding cassette family-F proteins and EF-P

In the past two decades, tremendous efforts for increasing the efficiency of ribosomal incorporation of backbone-modifying nonproteinogenic amino acids (npAAs) have been made and given significant successes. For instance, the use of an engineered body sequence of transfer RNA (tRNA), known as tRNAPro1E2, that efficiently recruits EF-Tu and EF-P significantly improves consecutive incorporation of npAAs, giving a notion that certain protein factors paired with right tRNAs can enhance their incorporation efficiency. However, the consecutive incorporation of certain npAAs, e.g.N-methyl-l-leucine, remains more challenging. Here we have explored Escherichia coli ATP-binding cassette family-F proteins (EttA, Uup, YbiT, and YhsS) and RbbA for a possibility of enhancing the translation efficiency for such npAAs since these proteins are known to alleviate nascent peptide-dependent translation arrest. Indeed, among them the presence of Uup increases the translation level of model peptides bearing two consecutive npAAs by an average of 1.7-fold for 12 kinds of npAAs and that of a macrocyclic peptide bearing d-α-amino, N-methyl-l-α-amino, and β-amino acids by 1.8-fold. Moreover, the combination of EF-P and Uup further enhances the incorporation of npAAs charged on tRNAPro1E2, demonstrating a four-fold enhancement for two consecutive incorporations of N-methyl-l-leucine.

Three Stages of Nascent Protein Translocation Through the Ribosome Exit Tunnel

All proteins in living organisms are produced in ribosomes that facilitate the translation of genetic information into a sequence of amino acid residues. During translation, the ribosome undergoes initiation, elongation, termination, and recycling. In fact, peptide bonds are formed only during the elongation phase, which comprises periodic association of transfer RNAs and multiple auxiliary proteins with the ribosome and the addition of an amino acid to the nascent polypeptide one at a time. The protein spends a considerable amount of time attached to the ribosome. Here, we conceptually divide this portion of the protein lifetime into three stages. We define each stage on the basis of the position of the N-terminus of the nascent polypeptide within the ribosome exit tunnel and the context of the catalytic center. We argue that nascent polypeptides experience a variety of forces that determine how they translocate through the tunnel and interact with the tunnel walls. We review current knowledge about nascent polypeptide translocation and identify several white spots in our understanding of the birth of proteins.

The ABCF proteins in Escherichia coli individually cope with 'hard-to-translate' nascent peptide sequences

Organisms possess a wide variety of proteins with diverse amino acid sequences, and their synthesis relies on the ribosome. Empirical observations have led to the misconception that ribosomes are robust protein factories, but in reality, they have several weaknesses. For instance, ribosomes stall during the translation of the proline-rich sequences, but the elongation factor EF-P assists in synthesizing proteins containing the poly-proline sequences. Thus, living organisms have evolved to expand the translation capability of ribosomes through the acquisition of translation elongation factors. In this study, we have revealed that Escherichia coli ATP-Binding Cassette family-F (ABCF) proteins, YheS, YbiT, EttA and Uup, individually cope with various problematic nascent peptide sequences within the exit tunnel. The correspondence between noncanonical translations and ABCFs was YheS for the translational arrest by nascent SecM, YbiT for poly-basic sequence-dependent stalling and poly-acidic sequence-dependent intrinsic ribosome destabilization (IRD), EttA for IRD at the early stage of elongation, and Uup for poly-proline-dependent stalling. Our results suggest that ATP hydrolysis-coupled structural rearrangement and the interdomain linker sequence are pivotal for handling 'hard-to-translate' nascent peptides. Our study highlights a new aspect of ABCF proteins to reduce the potential risks that are encoded within the nascent peptide sequences.

N-Terminal Amino Acid Affects the Translation Efficiency at Lower Temperatures in a Reconstituted Protein Synthesis System

The Escherichia coli (E. coli)-based protein synthesis using recombinant elements (PURE) system is a cell-free protein synthesis system reconstituted from purified factors essential for E. coli translation. The PURE system is widely used for basic and synthetic biology applications. One of the major challenges associated with the PURE system is that the protein yield of the system varies depending on the protein. Studies have reported that the efficiency of translation is significantly affected by nucleotide and amino acid sequences, especially in the N-terminal region. Here, we investigated the inherent effect of various N-terminal sequences on protein synthesis using the PURE system. We found that a single amino acid substitution in the N-terminal region significantly altered translation efficiency in the PURE system, especially at low temperatures. This result gives us useful suggestions for the expression of the protein of interest in vitro and in vivo.