The Structure of Escherichia coli TcdA (Also Known As CsdL) Reveals a Novel Topology and Provides Insight into the tRNA Binding Surface Required for N(6)-Threonylcarbamoyladenosine Dehydratase Activity

Structure-function analysis of an ancient TsaD-TsaC-SUA5-TcdA modular enzyme reveals a prototype of tRNA t6A and ct6A synthetases

N 6-threonylcarbamoyladenosine (t6A) is a post-transcriptional modification found uniquely at position 37 of tRNAs that decipher ANN-codons in the three domains of life. tRNA t6A plays a pivotal role in promoting translational fidelity and maintaining protein homeostasis. The biosynthesis of tRNA t6A requires members from two evolutionarily conserved protein families TsaC/Sua5 and TsaD/Kae1/Qri7, and a varying number of auxiliary proteins. Furthermore, tRNA t6A is modified into a cyclic hydantoin form of t6A (ct6A) by TcdA in bacteria. In this work, we have identified a TsaD-TsaC-SUA5-TcdA modular protein (TsaN) from Pandoraviruses and determined a 3.2 Å resolution cryo-EM structure of P. salinus TsaN. The four domains of TsaN share strong structural similarities with TsaD/Kae1/Qri7 proteins, TsaC/Sua5 proteins, and Escherichia coli TcdA. TsaN catalyzes the formation of threonylcarbamoyladenylate (TC-AMP) using L-threonine, HCO3- and ATP, but does not participate further in tRNA t6A biosynthesis. We report for the first time that TsaN catalyzes a tRNA-independent threonylcarbamoyl modification of adenosine phosphates, leading to t6ADP and t6ATP. Moreover, TsaN is also active in catalyzing tRNA-independent conversion of t6A nucleoside to ct6A. Our results imply that TsaN from Pandoraviruses might be a prototype of the tRNA t6A- and ct6A-modifying enzymes in some cellular organisms.

A hydantoin isoform of cyclic N6-threonylcarbamoyladenosine (ct6A) is present in tRNAs

N⁶-Threonylcarbamoyladenosine (t⁶A) and its derivatives are universally conserved modified nucleosides found at position 37, 3΄ adjacent to the anticodon in tRNAs responsible for ANN codons. These modifications have pleiotropic functions of tRNAs in decoding and protein synthesis. In certain species of bacteria, fungi, plants and protists, t⁶A is further modified to the cyclic t⁶A (ct⁶A) via dehydration catalyzed by TcdA. This additional modification is involved in efficient decoding of tRNA^Lys. Previous work indicated that the chemical structure of ct⁶A is a cyclic active ester with an oxazolone ring. In this study, we solved the crystal structure of chemically synthesized ct⁶A nucleoside. Unexpectedly, we found that the ct⁶A adopted a hydantoin isoform rather than an oxazolone isoform, and further showed that the hydantoin isoform of ct⁶A was actually present in Escherichia coli tRNAs. In addition, we observed that hydantoin ct⁶A is susceptible to epimerization under mild alkaline conditions, warning us to avoid conventional deacylation of tRNAs. A hallmark structural feature of this isoform is the twisted arrangement of the hydantoin and adenine rings. Functional roles of ct⁶A37 in tRNAs should be reconsidered.

Bacterial tail anchors can target to the mitochondrial outer membrane

Background

During the generation and evolution of the eukaryotic cell, a proteobacterial endosymbiont was re-fashioned into the mitochondrion, an organelle that appears to have been present in the ancestor of all present-day eukaryotes. Mitochondria harbor proteomes derived from coding information located both inside and outside the organelle, and the rate-limiting step toward the formation of eukaryotic cells may have been development of an import apparatus allowing protein entry to mitochondria. Currently, a widely conserved translocon allows proteins to pass from the cytosol into mitochondria, but how proteins encoded outside of mitochondria were first directed to these organelles at the dawn of eukaryogenesis is not clear. Because several proteins targeted by a carboxyl-terminal tail anchor (TA) appear to have the ability to insert spontaneously into the mitochondrial outer membrane (OM), it is possible that self-inserting, tail-anchored polypeptides obtained from bacteria might have formed the first gate allowing proteins to access mitochondria from the cytosol.

Results

Here, we tested whether bacterial TAs are capable of targeting to mitochondria. In a survey of proteins encoded by the proteobacterium Escherichia coli, predicted TA sequences were directed to specific subcellular locations within the yeast Saccharomyces cerevisiae. Importantly, TAs obtained from DUF883 family members ElaB and YqjD were abundantly localized to and inserted at the mitochondrial OM.

Conclusions

Our results support the notion that eukaryotic cells are able to utilize membrane-targeting signals present in bacterial proteins obtained by lateral gene transfer, and our findings make plausible a model in which mitochondrial protein translocation was first driven by tail-anchored proteins.

Reviewers

This article was reviewed by Michael Ryan and Thomas Simmen.

Electronic supplementary material

The online version of this article (doi:10.1186/s13062-017-0187-0) contains supplementary material, which is available to authorized users.

Diverse Mechanisms of Sulfur Decoration in Bacterial tRNA and Their Cellular Functions

Sulfur-containing transfer ribonucleic acids (tRNAs) are ubiquitous biomolecules found in all organisms that possess a variety of functions. For decades, their roles in processes such as translation, structural stability, and cellular protection have been elucidated and appreciated. These thionucleosides are found in all types of bacteria; however, their biosynthetic pathways are distinct among different groups of bacteria. Considering that many of the thio-tRNA biosynthetic enzymes are absent in Gram-positive bacteria, recent studies have addressed how sulfur trafficking is regulated in these prokaryotic species. Interestingly, a novel proposal has been given for interplay among thionucleosides and the biosynthesis of other thiocofactors, through participation of shared-enzyme intermediates, the functions of which are impacted by the availability of substrate as well as metabolic demand of thiocofactors. This review describes the occurrence of thio-modifications in bacterial tRNA and current methods for detection of these modifications that have enabled studies on the biosynthesis and functions of S-containing tRNA across bacteria. It provides insight into potential modes of regulation and potential evolutionary events responsible for divergence in sulfur metabolism among prokaryotes.

The crystal structure of Escherichia coli CsdE

Sulfur incorporations both in the biosynthesis of sulfur-containing cofactors and in the sulfur-modifications of certain tRNAs are all mediated by the sulfur initially delivered from the cysteine desulfurases. Sulfur generated as persulfide from cysteine is transferred to the sulfur acceptor protein to further allow delivery to the required steps within an enzymatic process. CsdA which is one of the three cysteine desulfurases identified in Escherichia coli transfers sulfur to the non Fe-S sulfur-acceptor CsdE, however, the consequence of CsdE accepted sulfur is mostly unknown. In this study, we report the 2.4Å structure of free CsdE determined using X-ray crystallography, and compare the structure with the CsdE structure determined using NMR and also CsdE within the crystal CsdA-CsdE complex. Further analysis suggests that the positive electrostatic potential surfaces of CsdE may mediate interaction with a yet unidentified protein or possibly tRNA to deliver sulfur.