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| Open AccessEvolution of lasR mutants in polymorphic Pseudomonas aeruginosa populations facilitates chronic infection of the lung
Chronic infection with the bacterium Pseudomonas aeruginosa often leads to coexistence of heterogeneous bacterial populations carrying diverse mutations. Here, Zhao et al. use genetic and multi-omics functional analyses to shed light on the multistage evolution of bacterial populations in the lungs of chronically infected patients.
- Kelei Zhao
- , Xiting Yang
- & Xikun Zhou
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Article
| Open AccessA de novo evolved gene contributes to rice grain shape difference between indica and japonica
Genetic bases of grain shape differentiation between the two subspecies of Asian cultivated rice have not been fully elucidated. Here, the authors report GSE9, a de novo gene evolved from a non-coding region of wild rice through acquisition of start codon, contributes to the grain shape difference between the two subspecies.
- Rujia Chen
- , Ning Xiao
- & Zefeng Yang
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Article
| Open AccessA single-cell atlas of West African lungfish respiratory system reveals evolutionary adaptations to terrestrialization
The water-to-land transition of vertebrates is a landmark event in evolutionary history. This work utilizes single-cell RNA sequencing to explore the adaptations in African lungfish lungs and gills to terrestrialization.
- Ruihua Zhang
- , Qun Liu
- & Guangyi Fan
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Article
| Open AccessEvolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies
The diverse Heliconius butterflies have evolved key innovations, including pollen feeding, and are a quintessential example of adaptive radiation. Using comparative genomics, Cicconardi et al. identify targets of selection at coding and non-coding loci during major ecological transitions in Heliconius.
- Francesco Cicconardi
- , Edoardo Milanetti
- & Stephen H. Montgomery
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Article
| Open AccessAccelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer
White-tailed deer are an important reservoir of SARS-CoV-2 in the USA and continued monitoring of the virus in deer populations is needed. In this genomic epidemiology study from Ohio, the authors show that the virus has been introduced multiple times to deer from humans, and that it has evolved faster in deer.
- Dillon S. McBride
- , Sofya K. Garushyants
- & Andrew S. Bowman
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Article
| Open AccessSurface frustration re-patterning underlies the structural landscape and evolvability of fungal orphan candidate effectors
Pathogens secrete effectors that evade host immunity and promote disease. The authors identify effectors conserved across fungi in which low structure divergence associates with surface energetics variation, conferring robustness and evolvability.
- Mark C. Derbyshire
- & Sylvain Raffaele
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Article
| Open AccessGenome mining shows that retroviruses are pervasively invading vertebrate genomes
Ongoing retroviral invasion into vertebrates has been rarely documented. Here the authors have identified 412 endogenous retroviruses that are invading the genomes of over a hundred vertebrate species. This may be relevant to conservation of threatened species, zoonoses in the wild, and emerging infectious diseases in humans.
- Jianhua Wang
- & Guan-Zhu Han
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Article
| Open AccessDomain loss enabled evolution of novel functions in the snake three-finger toxin gene superfamily
3-finger toxins are unique to the venoms of caenophidian snakes. This study traces the evolution of these toxins in snakes, highlighting a key shift from membrane-bound to secretory proteins. This transformation, involving the loss of a membrane-anchoring domain and changes in gene expression, paved the way for their venomous function.
- Ivan Koludarov
- , Tobias Senoner
- & Burkhard Rost
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Article
| Open AccessTransmission of SARS-CoV-2 in free-ranging white-tailed deer in the United States
The SARS-CoV-2 virus has been documented to transmit between humans and animals, providing opportunities for viral reservoirs. Here, the authors show SARS-CoV-2 lineages in free-ranging white-tailed deer across the United States, long after the lineages had declined in human populations.
- Aijing Feng
- , Sarah Bevins
- & Xiu-Feng Wan
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Article
| Open AccessParallel and convergent genomic changes underlie independent subterranean colonization across beetles
The genomic underpinnings of cave-related phenotypes are underexplored. Here, the authors investigate adaptation to underground life in cave beetle lineages using transcriptomic and genomic data, finding both parallel and convergent changes in six independent episodes of subterranean colonization.
- Pau Balart-García
- , Leandro Aristide
- & Rosa Fernández
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Article
| Open AccessEvolvability-enhancing mutations in the fitness landscapes of an RNA and a protein
Whether evolvability itself can be a product of adaptive Darwinian evolution is a debated question. This study proposes that adaptive landscapes harbor mutations that enhance the evolvability of evolving molecules and help populations of these molecules to evolve high fitness.
- Andreas Wagner
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Article
| Open AccessBacteria evolve macroscopic multicellularity by the genetic assimilation of phenotypically plastic cell clustering
Diverse bacteria exhibit phenotypically plastic multicellular clustering. Here the authors show that a single mutation can genetically assimilate ancestrally inducible multicellularity by modulating plasticity at multiple levels of organization to make E. coli grow constitutively as macroscopic multicellular clusters.
- Yashraj Chavhan
- , Sutirth Dey
- & Peter A. Lind
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Article
| Open AccessRapid evolution of A(H5N1) influenza viruses after intercontinental spread to North America
Highly pathogenic avian influenza A(H5N1) viruses of clade 2.3.4.4b underwent an explosive geographic expansion in 2021 among wild birds and domestic poultry. Here, Kandeil et al. show that the Western movement of this clade was followed by reassortment with viruses circulating in wild birds in North America which resulted in different genotypes exhibiting a wide range of disease severity in mammal models (mice, ferrets, chicken) ranging from asymptomatic disease to severe neurological pathology.
- Ahmed Kandeil
- , Christopher Patton
- & Richard J. Webby
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Article
| Open AccessHybrids of RNA viruses and viroid-like elements replicate in fungi
RNA viruses are defined by linear RNA genomes encoding an RNA-dependent RNA polymerase, while viroid-like elements consist of small, single-stranded, circular RNA genomes that, in some cases, encode self-cleaving catalytic RNAs. Here, the authors identify over 20,000 candidate viroid-like elements, and show that infectious agents of fungi display hybrid features of viroid-like RNAs and RNA viruses.
- Marco Forgia
- , Beatriz Navarro
- & Marcos de la Peña
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Article
| Open AccessSelection-driven trait loss in independently evolved cavefish populations
Repeated evolution provides valuable insight into adaptation. In this study, the authors found that repeated evolution of cave-adapted phenotypes of a fish (Astyanax mexicanus) was driven by selection on standing genetic variation and novel mutations and genes repeatedly under selection are longer compared to the rest of the genome.
- Rachel L. Moran
- , Emilie J. Richards
- & Suzanne E. McGaugh
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Article
| Open AccessCharacterization of a fold in TANGO1 evolved from SH3 domains for the export of bulky cargos
The authors characterized a fold in the TANGO1 protein which evolved from SH3 domains for the export of bulky cargos such as collagen. They denote this fold as MOTH (MIA, Otoraplin, TALI/TANGO1 homology) domain.
- Oliver Arnolds
- & Raphael Stoll
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Article
| Open AccessChance promoter activities illuminate the origins of eukaryotic intergenic transcriptions
It is debated whether the pervasive intergenic transcription from eukaryotic genomes has functional significance. Here, Xu et al. find that only 1–5% of yeast intergenic transcription is unattributable to chance promoter activity or neighboring gene expression.
- Haiqing Xu
- , Chuan Li
- & Jianzhi Zhang
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Article
| Open AccessFunctional comparison of metabolic networks across species
Disentangling how evolutionary history and environmental adaptation shape metabolic phenotypes is an open problem, especially for microbes whose phenotypes cannot be determined directly and are inferred from genomic information. Here, Ramon & Stelling propose sensitivity correlations to quantify similarity of predicted metabolic network responses to perturbations, and link genotype and environment to phenotype for 245 bacterial species.
- Charlotte Ramon
- & Jörg Stelling
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Article
| Open AccessEvolutionary conservation of the fidelity of transcription
The molecular mechanisms that ensure faithful transcription of genetic information are still unclear. Chung et al. identify various genes, alleles and processes that affect the fidelity of transcription multiple organisms, suggesting evolutionary conservation of fidelity factors, and compare the error rate of transcription among these species.
- Claire Chung
- , Bert M. Verheijen
- & Marc Vermulst
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Article
| Open AccessEvolution of enzyme functionality in the flavin-containing monooxygenases
Detoxification enzymes are crucial for the survival of animals in new environments. Here, the authors study the molecular mechanism behind the catalytic diversification of a major family of tetrapod detoxification enzymes—the FMOs—during evolution.
- Gautier Bailleul
- , Guang Yang
- & Maria Laura Mascotti
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Article
| Open AccessA bivalent remipede toxin promotes calcium release via ryanodine receptor activation
Insect toxins with tandem repeats of neurotoxin domains have been found with enhanced receptor avidity. Here, the authors describe a bivalent toxin from remipede venom that targets ryanodine receptors, a rare target for animal venoms.
- Michael J. Maxwell
- , Chris Thekkedam
- & Mehdi Mobli
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Article
| Open AccessA molecular atlas reveals the tri-sectional spinning mechanism of spider dragline silk
The genetic basis of spider major ampullate (Ma) gland silk production remains unknown. Hu et al. unveil a molecular atlas of this gland for the golden orb-weaving spider combining genome assembly and multiomics, revealing the single-cell spatial architecture of silk production in the Ma gland.
- Wenbo Hu
- , Anqiang Jia
- & Yi Wang
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Article
| Open AccessTranscription factor binding sites are frequently under accelerated evolution in primates
Characterizing genomic elements under accelerated evolution is crucial for understanding the genomic basis of human evolution and disease. Here, Zhang et al. introduce GroupAcc, a collection of two pooling-based phylogenetic methods with enhanced sensitivity to examine accelerated evolution in transcription factor binding sites.
- Xinru Zhang
- , Bohao Fang
- & Yi-Fei Huang
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Article
| Open AccessEvolution of protease activation and specificity via alpha-2-macroglobulin-mediated covalent capture
Custom proteases find applications as therapeutics, in research and in biotechnological applications. Here, the authors establish a protease selection system based on bacterial alpha-2-macroglobulin protease inhibitors and evolve staphylococcal proteases for increased activity and altered specificity.
- Philipp Knyphausen
- , Mariana Rangel Pereira
- & Florian Hollfelder
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Matters Arising
| Open AccessReply to: Available data do not rule out Ctenophora as the sister group to all other Metazoa
- Anthony K. Redmond
- & Aoife McLysaght
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Matters Arising
| Open AccessAvailable data do not rule out Ctenophora as the sister group to all other Metazoa
- Nathan V. Whelan
- & Kenneth M. Halanych
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Article
| Open AccessArchaeal DNA-import apparatus is homologous to bacterial conjugation machinery
Bacteria can exchange DNA through extracellular appendages (‘mating pili’) in a process known as conjugation. Here, Beltran et al. determine atomic structures by cryo-electron microscopy of a bacterial conjugative pilus and two archaeal pili, showing that the archaeal pili are homologous to bacterial mating pili.
- Leticia C. Beltran
- , Virginija Cvirkaite-Krupovic
- & Mart Krupovic
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Article
| Open AccessA paralog of Pcc1 is the fifth core subunit of the KEOPS tRNA-modifying complex in Archaea
Many eukaryotic and archaeal tRNAs carry a modified adenosine (t6A) that is synthesized by the KEOPS complex, which is composed of four subunits. A fifth subunit (Gon7) is found only in fungi and metazoa. Here the authors show that archaea also possess a fifth subunit, which is structurally and functionally similar to eukaryotic Gon7.
- Marie-Claire Daugeron
- , Sophia Missoury
- & Tamara Basta
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Article
| Open AccessThe function and evolution of a genetic switch controlling sexually dimorphic eye differentiation in honeybees
Sexual dimorphism results in widely diverse animal forms, but sexual determination is generally attributed to a single gene in animal models. Here they find that the glu gene regulates sexual dimorphism of honeybee eyes, demonstrating diversification of genetic programs for dimorphism.
- Oksana Netschitailo
- , Yidong Wang
- & Martin Beye
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Article
| Open AccessDesign and characterization of a protein fold switching network
In this work the authors investigate the structure-sequence dependance. The ability to design and characterize proteins at interfaces between three common folds suggests that fold switching is an intrinsic feature of protein folding language and likely important in the evolution of protein structure and function.
- Biao Ruan
- , Yanan He
- & Philip N. Bryan
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Article
| Open AccessPhylogeography and transmission of Mycobacterium tuberculosis spanning prisons and surrounding communities in Paraguay
To role that carceral institutions play in Mycobacterium tuberculosis transmission remains somewhat unknown. Authors perform a prospective genomic surveillance study, to assess transmission dynamics in prisons and surrounding communities in Paraguay.
- Gladys Estigarribia Sanabria
- , Guillermo Sequera
- & Katharine S. Walter
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Article
| Open AccessMicro and macroevolution of sea anemone venom phenotype
Venom is a complex trait with unresolved underlying toxin expression dynamics. Here, the authors compare expression across sea anemone species, revealing variation in dominant toxin diploid copy number across populations which generates distinct haplotypes.
- Edward G. Smith
- , Joachim M. Surm
- & Yehu Moran
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Article
| Open AccessSARS-CoV-2 escape from cytotoxic T cells during long-term COVID-19
Here, the authors report accelerated intrahost evolution of SARS-CoV-2 in an immunocompromised patient with non-Hodgkin’s lymphoma with 318 days long COVID-19, and show that changes in the viral genome resulted in escape from T cellular immune response.
- Oksana V. Stanevich
- , Evgeniia I. Alekseeva
- & Georgii A. Bazykin
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Article
| Open AccessPrediction of designer-recombinases for DNA editing with generative deep learning
Design of recombinases with new target sites is usually achieved through cycles of directed molecular evolution. Here the authors report Recombinase Generator, RecGen, an algorithm for generation of designer-recombinases; they perform experimental validation to show that this can predict recombinase sequences.
- Lukas Theo Schmitt
- , Maciej Paszkowski-Rogacz
- & Frank Buchholz
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Article
| Open AccessThousands of human non-AUG extended proteoforms lack evidence of evolutionary selection among mammals
Analysis of a large number of Ribo-seq datasets and genomic alignments led to detection of novel non-AUG proteoforms. Unexpectedly the number of non-AUG proteoforms identified with Ribo-seq greatly exceeds those with strong phylogenetic support.
- Alla D. Fedorova
- , Stephen J. Kiniry
- & Pavel V. Baranov
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Article
| Open AccessImmunogenetic losses co-occurred with seahorse male pregnancy and mutation in tlx1 accompanied functional asplenia
Seahorses may have required adaptations to avoid immunological rejection of allogenic embryos by males. The authors show that a single substitution in tlx1 is associated with loss of the spleen in seahorses, and that across the clade, degree of male pregnancy is negatively correlated with immune gene repertoire complexity.
- Yali Liu
- , Meng Qu
- & Qiang Lin
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Article
| Open AccessVarying strength of selection contributes to the intragenomic diversity of rRNA genes
Ribosomal RNA genes are abundant in eukaryotic genomes and code for the universal and essential RNA components of the ribosome. This study uncovers high sequence diversity of the genes within a single species and discusses the contribution of selection in the evolution of ribosomal RNA.
- Daniel Sultanov
- & Andreas Hochwagen
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Article
| Open AccessGenomic signatures of recent convergent transitions to social life in spiders
Sociality has evolved repeatedly in arthropods. Tong et al. compare the genomes of 22 spider species with a range of social complexity and eight independent origins of sociality, and identify specific genetic changes associated with the evolution of sociality in spiders.
- Chao Tong
- , Leticia Avilés
- & Timothy A. Linksvayer
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Article
| Open AccessStructure of the reduced microsporidian proteasome bound by PI31-like peptides in dormant spores
Proteasomes are vital eukaryotic complexes that recycle unneeded proteins. Here, the authors present the structure of a compacted proteasome derived from the dormant stage of parasitic microsporidia and bound by an endogenous inhibitory protein.
- Nathan Jespersen
- , Kai Ehrenbolger
- & Jonas Barandun
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Article
| Open AccessTranslation and natural selection of micropeptides from long non-canonical RNAs
Translation of 100 to 300 micropeptides from small ORFs within lncRNA was detected by Ribosomal Profiling in Drosophila embryos. These translated small ORFs showed natural selection conserving micropeptide sequence and function.
- Pedro Patraquim
- , Emile G. Magny
- & Juan Pablo Couso
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Article
| Open AccessPrevalence and mechanisms of evolutionary contingency in human influenza H3N2 neuraminidase
Lei et al. systematically characterized the epistasis among natural mutations in the neuraminidase of human influenza H3N2 virus, which provide insights into the biophysical constraints that shaped its evolution trajectory over the past half-century.
- Ruipeng Lei
- , Timothy J. C. Tan
- & Nicholas C. Wu
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Article
| Open AccessGenomic signatures associated with maintenance of genome stability and venom turnover in two parasitoid wasps
Parasitoid wasps are rapidly developing as a model for evolutionary biology. Here, the authors analyze the genomes of two Anastatus wasps, revealing genomic innovations related to maintenance of genomic stability, and rapid turnover of venom genes.
- Xinhai Ye
- , Yi Yang
- & Gongyin Ye
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Article
| Open AccessSpatiotemporal variations in retrovirus-host interactions among Darwin’s finches
Endogenous retroviruses (ERV) are inherited remains of retroviruses that have colonized host genomes during evolution. Here the authors observe considerable species-specific ERV variation among Darwin’s finches, reflecting historic retrovirus-host interactions.
- Jason Hill
- , Mette Lillie
- & Patric Jern
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Article
| Open AccessAn ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases
Mitochondrial ATP synthase assemble into oligomers. Here, authors resolve the structure of trypanosomal ATP synthase, showing that its dimerization is essential for function and evolutionary conserved.
- Ondřej Gahura
- , Alexander Mühleip
- & Alexey Amunts
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Article
| Open AccessEnergy landscape reshaped by strain-specific mutations underlies epistasis in NS1 evolution of influenza A virus
Influenza A virus (IAV) nonstructural protein 1 (NS1) is a multifunctional virulence factor that interacts with several host factors such as phosphatidylinositol-3-kinase (PI3K). NS1 binds specifically to the p85β regulatory subunit of PI3K and subsequently activates PI3K signaling. Here, Kim et al. show that functionally near-neutral, strain-specific NS1 mutations lead to variations in binding kinetics to p85β exhibit long-range epistatic interactions. Applying NMR they provide evidence that the structural dynamics of the NS1 hydrophobic core have evolved over time and contributed to epistasis.
- Iktae Kim
- , Alyssa Dubrow
- & Jae-Hyun Cho
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Article
| Open AccessTwo modes of evolution shape bacterial strain diversity in the mammalian gut for thousands of generations
Here, the authors show that a colonizing bacterial strain evolves in the gut by either generating ecotypes or continuously fixing beneficial mutations. They associate the first mode to metabolic mutations and the second to domestication of bacteriophages that are incorporated into the bacterial genome.
- N. Frazão
- , A. Konrad
- & I. Gordo
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Article
| Open AccessThe evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases
Barley β-d-glucan glucohydrolase is a glycoside hydrolase family 3 (GH3) enzyme critical for growth and development. Here the authors carryout mutagenesis, structural analyses and multi-scale molecular dynamics to examine the binding and conformational behaviour of several β-d-glucosides during the substrate-product assisted catalysis that operates in GH3 hydrolases.
- Sukanya Luang
- , Xavier Fernández-Luengo
- & Maria Hrmova
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Article
| Open AccessEvolutionary origin of vertebrate OCT4/POU5 functions in supporting pluripotency
By constructing an evolutionary trajectory of the cyclostome-gnathostome Pou5 gene family and comparing the structural and phenotypic protein variations, the authors uncover the origin of functional characteristics for the pluripotency factor Oct4.
- Woranop Sukparangsi
- , Elena Morganti
- & Joshua M. Brickman
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Article
| Open AccessStructural basis for shape-selective recognition and aminoacylation of a D-armless human mitochondrial tRNA
Mitochondrial tRNAs are indispensable and yet underwent an extreme mutational erosion. The authors report the structures of a mitochondrial aaRS-tRNA complex and show how the most degenerated of all human mtRNAs is recognized by its cognate synthetase to maintain mitochondrial gene expression.
- Bernhard Kuhle
- , Marscha Hirschi
- & Paul Schimmel