Evolution of substrate specificity in a retained enzyme driven by gene loss
- Evolution of Metabolic Diversity Laboratory, Mexico
- Argonne National Laboratory, United States
- University of Texas Health Science Cent, United States
- Weizmann Institute of Science, Israel
- University of California, Berkeley, United States
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico
- Centro de Investigación en Matemáticas, Mexico
- University of Texas Health Science Center, United States
Abstract
The connection between gene loss and the functional adaptation of retained proteins is still poorly understood. We apply phylogenomics and metabolic modeling to detect bacterial species that are evolving by gene loss, with the finding that Actinomycetaceae genomes from human cavities are undergoing sizable reductions, including loss of L-histidine and L-tryptophan biosynthesis. We observe that the dual-substrate phosphoribosyl isomerase A or priA gene, at which these pathways converge, appears to coevolve with the occurrence of trp and his genes. Characterization of a dozen PriA homologs shows that these enzymes adapt from bifunctionality in the largest genomes, to a monofunctional, yet not necessarily specialized, inefficient form in genomes undergoing reduction. These functional changes are accomplished via mutations, which result from relaxation of purifying selection, in residues structurally mapped after sequence and X-ray structural analyses. Our results show how gene loss can drive the evolution of substrate specificity from retained enzymes.
Data availability
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The Whole Genome Shotgun (WGS) A. oris MG-1 projectPublicly available at the NCBI Nucleotide (accession no: MAUB00000000).
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Actinomyces oris strain:MG-1 Genome sequencing and assemblyPublicly available at the NCBI BioProject (accession no: PRJNA327886.
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Actinomycetaceae Phylogenomics: Comparative Analysis of ModelsPublicly available, subject to registering an account, at KBase (accession no: ws.17193.obj.1).
Article and author information
Author details
Francisco Barona-Gómez
Funding
Consejo Nacional de Ciencia y Tecnología (132376,179290)
- Ana Lilia Juárez-Vázquez
- Ernesto A Verduzco-Castro
- Julián Santoyo-Flores
- Mauricio Carrillo-Tripp
National Institutes of Health (GM094585)
- Karolina Michalska
- Gyorgy Babnigg
- Michael Endres
- Andrzej Joachimiak
US Department of Energy (DE-AC02-06CH11357)
- Andrzej Joachimiak
- Christopher S Henry
National Science Foundation (1611952)
- Janaka E Edirisinghe
- Christopher S Henry
National Institute of Dental and Craniofacial Research (DE017382)
- Chenggang Wu
- Hung Ton-That
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
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Further reading
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- Biochemistry and Chemical Biology
- Microbiology and Infectious Disease
Glutamine synthetases (GS) are central enzymes essential for the nitrogen metabolism across all domains of life. Consequently, they have been extensively studied for more than half a century. Based on the ATP-dependent ammonium assimilation generating glutamine, GS expression and activity are strictly regulated in all organisms. In the methanogenic archaeon Methanosarcina mazei, it has been shown that the metabolite 2-oxoglutarate (2-OG) directly induces the GS activity. Besides, modulation of the activity by interaction with small proteins (GlnK1 and sP26) has been reported. Here, we show that the strong activation of M. mazei GS (GlnA1) by 2-OG is based on the 2-OG dependent dodecamer assembly of GlnA1 by using mass photometry (MP) and single particle cryo-electron microscopy (cryo-EM) analysis of purified strep-tagged GlnA1. The dodecamer assembly from dimers occurred without any detectable intermediate oligomeric state and was not affected in the presence of GlnK1. The 2.39 Å cryo-EM structure of the dodecameric complex in the presence of 12.5 mM 2-OG demonstrated that 2-OG is binding between two monomers. Thereby, 2-OG appears to induce the dodecameric assembly in a cooperative way. Furthermore, the active site is primed by an allosteric interaction cascade caused by 2-OG-binding towards an adaption of an open active state conformation. In the presence of additional glutamine, strong feedback inhibition of GS activity was observed. Since glutamine dependent disassembly of the dodecamer was excluded by MP, feedback inhibition most likely relies on the binding of glutamine to the catalytic site. Based on our findings, we propose that under nitrogen limitation the induction of M. mazei GS into a catalytically active dodecamer is not affected by GlnK1 and crucially depends on the presence of 2-OG.
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- Biochemistry and Chemical Biology
N 6,2’-O-dimethyladenosine (m6Am) is a modified nucleotide located at the first transcribed position in mRNA and snRNA that is essential for diverse physiological processes. m6Am mapping methods assume each gene uses a single start nucleotide. However, gene transcription usually involves multiple start sites, generating numerous 5’ isoforms. Thus, gene-level annotations cannot capture the diversity of m6Am modification in the transcriptome. Here, we describe CROWN-seq, which simultaneously identifies transcription-start nucleotides and quantifies m6Am stoichiometry for each 5’ isoform that initiates with adenosine. Using CROWN-seq, we map the m6Am landscape in nine human cell lines. Our findings reveal that m6Am is nearly always a high stoichiometry modification, with only a small subset of cellular mRNAs showing lower m6Am stoichiometry. We find that m6Am is associated with increased transcript expression and provide evidence that m6Am may be linked to transcription initiation associated with specific promoter sequences and initiation mechanisms. These data suggest a potential new function for m6Am in influencing transcription.
