Hydrolytic editing activities are present in aminoacyl-tRNA synthetases possessing reduced amino acid discrimination in the synthetic reactions. Post-transfer hydrolysis of misacylated tRNA in class I editing enzymes occurs in a spatially separate domain inserted into the catalytic Rossmann fold, but the location and mechanisms of pre-transfer hydrolysis of misactivated amino acids have been uncertain. Here, we use novel kinetic approaches to distinguish among three models for pre-transfer editing by Escherichia coli isoleucyl-tRNA synthetase (IleRS). We demonstrate that tRNA-dependent hydrolysis of noncognate valyl-adenylate by IleRS is largely insensitive to mutations in the editing domain of the enzyme and that noncatalytic hydrolysis after release is too slow to account for the observed rate of clearing. Measurements of the microscopic rate constants for amino acid transfer to tRNA in IleRS and the related valyl-tRNA synthetase (ValRS) further suggest that pre-transfer editing in IleRS is an enzyme-catalyzed activity residing in the synthetic active site. In this model, the balance between pretransfer and post-transfer editing pathways is controlled by kinetic partitioning of the noncognate aminoacyl-adenylate. Rate constants for hydrolysis and transfer of a noncognate intermediate are roughly equal in IleRS, whereas in ValRS transfer to tRNA is 200-fold faster than hydrolysis. In consequence, editing by ValRS occurs nearly exclusively by post-transfer hydrolysis in the editing domain, whereas in IleRS both pre-and post-transfer editing are important. In both enzymes, the rates of amino acid transfer to tRNA are similar for cognate and noncognate aminoacyl-adenylates, providing a significant contrast with editing DNA polymerases.

No abstract

Background: Error-prone aminoacyl-tRNA synthetases clear noncognate aminoacyl-adenylates and misacylated tRNAs within synthetic and editing sites, respectively. Results: Product release limits the rate of post-transfer editing by leucyl-tRNA synthetase. Conclusion: Kinetic partitioning of misacylated tRNA determines the relative contribution of cis and trans editing. Significance: In contrast to DNA polymerases, error correction in class I tRNA synthetases relies on substrate selection by the editing site.

No abstract

The fidelity of protein synthesis depends on the capacity of aminoacyl-tRNA synthetases (AARSs) to couple only cognate amino acidtRNA pairs. If amino acid selectivity is compromised, fidelity can be ensured by an inherent AARS editing activity that hydrolyses mischarged tRNAs. Here, we show that the editing activity of Escherichia coli leucyl-tRNA synthetase (EcLeuRS) is not required to prevent incorrect isoleucine incorporation. Rather, as shown by kinetic, structural and in vivo approaches, the prime biological function of LeuRS editing is to prevent mis-incorporation of the non-standard amino acid norvaline. This conclusion follows from a reassessment of the discriminatory power of LeuRS against isoleucine and the demonstration that a LeuRS editing-deficient E. coli strain grows normally in high concentrations of isoleucine but not under oxygen deprivation conditions when norvaline accumulates to substantial levels. Thus, AARS-based translational quality control is a key feature for bacterial adaptive response to oxygen deprivation. The non-essential role for editing under normal bacterial growth has important implications for the development of resistance to antimicrobial agents targeting the LeuRS editing site.

Animal genomes vary in size by orders of magnitude 1 . While genome size expansion relates to transposable element mobilisation 2-5 and polyploidisation 6-9 , the causes and consequences of genome reduction are unclear 1 . This is because our understanding of genome compaction relies on animals with extreme lifestyles, such as parasites 10,11 , and free-living animals with exceptionally high rates of evolution 12-15 . Here, we decode the extremely compact genome of the annelid Dimorphilus gyrociliatus, a morphologically miniature meiobenthic segmented worm 16 . With a ~68 Mb size, Dimorphilus genome is the second smallest ever decoded for a free-living animal. Yet, it retains many traits classically associated with larger and slower-evolving genomes, such as an ordered, intact Hox cluster, a generally conserved developmental toolkit, and traces of ancestral 3 bilaterian linkage. Unlike animals with small genomes, the analysis of Dimorphilus epigenome revealed canonical features of genome regulation, excluding the presence of operons and trans-splicing. Instead, the gene dense Dimorphilus genome presents divergent kynurenine and Myc pathways, key physiological regulators of growth, proliferation and genome stability in animal cells that can cause small body size when impaired 17-21 . Altogether, our results uncover a novel, conservative route to extreme genome compaction, suggesting a mechanistic relationship between genome size reduction and morphological miniaturisation in animals.Animals, and eukaryotes generally, exhibit a striking range of genome sizes across species 1 , seemingly uncorrelated with morphological complexity and gene content, which has been deemed the "C-value enigma" 22 . Animal genomes often increase in size mobilising their transposable element (TE) repertoire (e.g. in rotifers 2 , chordates 3,4 and insects 5 ) and through chromosome rearrangements and polyploidisation (e.g. in vertebrates and teleosts 6-8 , and insects 9 ), which is usually counterbalanced through TE removal 23 , DNA deletions 24,25 and rediploidisation 26 . Although the adaptive impact of these changes is complex and probably often influenced by neutral nonadaptive population dynamics 27 , genome expansions might also increase the evolvability of a lineage by providing new genetic material that can stimulate species radiation 6 and the evolution of new genome regulatory contexts 28 and gene architectures 29 . By contrast, the adaptive value of genome compaction is more debated and hypotheses are often based on correlative associations 1 , e.g. with changes in metabolic 30 and developmental rates 31 , cell sizes 1,32 , and the evolution of radically new lifestyles (e.g. powered flight in birds and bats 25,33 , and parasitism in nematodes 11 and orthonectids 10 ).Besides, extreme genomic compaction leading to minimal genome sizes, as in some freeliving species of nematodes 34 , tardigrades 35 and appendicularians 4,36 , co-occurs with 4 prominent changes in gene repertoire 37,38 , genome architecture (e.g. loss of macrosynt...

No abstract

The causes and consequences of genome reduction in animals are unclear because our understanding of this process mostly relies on lineages with often exceptionally high rates of evolution. Here, we decode the compact 73.8-megabase genome of Dimorphilus gyrociliatus, a meiobenthic segmented worm. The D. gyrociliatus genome retains traits classically associated with larger and slower-evolving genomes, such as an ordered, intact Hox cluster, a generally conserved developmental toolkit and traces of ancestral bilaterian linkage. Unlike some other animals with small genomes, the analysis of the D. gyrociliatus epigenome revealed canonical features of genome regulation, excluding the presence of operons and trans-splicing. Instead, the gene-dense D. gyrociliatus genome presents a divergent Myc pathway, a key physiological regulator of growth, proliferation and genome stability in animals. Altogether, our results uncover a conservative route to genome compaction in annelids, reminiscent of that observed in the vertebrate Takifugu rubripes.