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Identification of a broadly conserved family of enzymes that hydrolyze (p)ppApp
Bacteria produce a variety of nucleotide second messengers to adapt to their surroundings. Although chemically similar, the nucleotides guanosine penta- and tetraphosphate [(p)ppGpp] and adenosine penta- and tetraphosphate [(p)ppApp] have distinct functions in bacteria. (p)ppGpp mediates survival un...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
National Academy of Sciences
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10083569/ https://www.ncbi.nlm.nih.gov/pubmed/36989297 http://dx.doi.org/10.1073/pnas.2213771120 |
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author | Ahmad, Shehryar Gordon, Isis J. Tsang, Kara K. Alexei, Andrea G. Sychantha, David Colautti, Jake Trilesky, Sarah L. Kim, Youngchang Wang, Boyuan Whitney, John C. |
author_facet | Ahmad, Shehryar Gordon, Isis J. Tsang, Kara K. Alexei, Andrea G. Sychantha, David Colautti, Jake Trilesky, Sarah L. Kim, Youngchang Wang, Boyuan Whitney, John C. |
author_sort | Ahmad, Shehryar |
collection | PubMed |
description | Bacteria produce a variety of nucleotide second messengers to adapt to their surroundings. Although chemically similar, the nucleotides guanosine penta- and tetraphosphate [(p)ppGpp] and adenosine penta- and tetraphosphate [(p)ppApp] have distinct functions in bacteria. (p)ppGpp mediates survival under nutrient-limiting conditions and its intracellular levels are regulated by synthetases and hydrolases belonging to the RelA-SpoT homolog (RSH) family of enzymes. By contrast, (p)ppApp is not known to be involved in nutrient stress responses and is synthesized by RSH-resembling toxins that inhibit the growth of bacterial cells. However, it remains unclear whether there exists a family of hydrolases that specifically act on (p)ppApp to reverse its toxic effects. Here, we present the structure and biochemical characterization of adenosine 3′-pyrophosphohydrolase 1 (Aph1), the founding member of a monofunctional (p)ppApp hydrolase family of enzymes. Our work reveals that Aph1 adopts a histidine-aspartate (HD)-domain fold characteristic of phosphohydrolase metalloenzymes and its activity mitigates the growth inhibitory effects of (p)ppApp-synthesizing toxins. Using an informatic approach, we identify over 2,000 putative (p)ppApp hydrolases that are widely distributed across bacterial phyla and found in diverse genomic contexts, and we demonstrate that 12 representative members hydrolyze ppApp. In addition, our in silico analyses reveal a unique molecular signature that is specific to (p)ppApp hydrolases, and we show that mutation of two residues within this signature broadens the specificity of Aph1 to promiscuously hydrolyze (p)ppGpp in vitro. Overall, our findings indicate that like (p)ppGpp hydrolases, (p)ppApp hydrolases are widespread in bacteria and may play important and underappreciated role(s) in bacterial physiology. |
format | Online Article Text |
id | pubmed-10083569 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | National Academy of Sciences |
record_format | MEDLINE/PubMed |
spelling | pubmed-100835692023-09-29 Identification of a broadly conserved family of enzymes that hydrolyze (p)ppApp Ahmad, Shehryar Gordon, Isis J. Tsang, Kara K. Alexei, Andrea G. Sychantha, David Colautti, Jake Trilesky, Sarah L. Kim, Youngchang Wang, Boyuan Whitney, John C. Proc Natl Acad Sci U S A Biological Sciences Bacteria produce a variety of nucleotide second messengers to adapt to their surroundings. Although chemically similar, the nucleotides guanosine penta- and tetraphosphate [(p)ppGpp] and adenosine penta- and tetraphosphate [(p)ppApp] have distinct functions in bacteria. (p)ppGpp mediates survival under nutrient-limiting conditions and its intracellular levels are regulated by synthetases and hydrolases belonging to the RelA-SpoT homolog (RSH) family of enzymes. By contrast, (p)ppApp is not known to be involved in nutrient stress responses and is synthesized by RSH-resembling toxins that inhibit the growth of bacterial cells. However, it remains unclear whether there exists a family of hydrolases that specifically act on (p)ppApp to reverse its toxic effects. Here, we present the structure and biochemical characterization of adenosine 3′-pyrophosphohydrolase 1 (Aph1), the founding member of a monofunctional (p)ppApp hydrolase family of enzymes. Our work reveals that Aph1 adopts a histidine-aspartate (HD)-domain fold characteristic of phosphohydrolase metalloenzymes and its activity mitigates the growth inhibitory effects of (p)ppApp-synthesizing toxins. Using an informatic approach, we identify over 2,000 putative (p)ppApp hydrolases that are widely distributed across bacterial phyla and found in diverse genomic contexts, and we demonstrate that 12 representative members hydrolyze ppApp. In addition, our in silico analyses reveal a unique molecular signature that is specific to (p)ppApp hydrolases, and we show that mutation of two residues within this signature broadens the specificity of Aph1 to promiscuously hydrolyze (p)ppGpp in vitro. Overall, our findings indicate that like (p)ppGpp hydrolases, (p)ppApp hydrolases are widespread in bacteria and may play important and underappreciated role(s) in bacterial physiology. National Academy of Sciences 2023-03-29 2023-04-04 /pmc/articles/PMC10083569/ /pubmed/36989297 http://dx.doi.org/10.1073/pnas.2213771120 Text en Copyright © 2023 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by-nc-nd/4.0/This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND) (https://creativecommons.org/licenses/by-nc-nd/4.0/) . |
spellingShingle | Biological Sciences Ahmad, Shehryar Gordon, Isis J. Tsang, Kara K. Alexei, Andrea G. Sychantha, David Colautti, Jake Trilesky, Sarah L. Kim, Youngchang Wang, Boyuan Whitney, John C. Identification of a broadly conserved family of enzymes that hydrolyze (p)ppApp |
title | Identification of a broadly conserved family of enzymes that hydrolyze (p)ppApp |
title_full | Identification of a broadly conserved family of enzymes that hydrolyze (p)ppApp |
title_fullStr | Identification of a broadly conserved family of enzymes that hydrolyze (p)ppApp |
title_full_unstemmed | Identification of a broadly conserved family of enzymes that hydrolyze (p)ppApp |
title_short | Identification of a broadly conserved family of enzymes that hydrolyze (p)ppApp |
title_sort | identification of a broadly conserved family of enzymes that hydrolyze (p)ppapp |
topic | Biological Sciences |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10083569/ https://www.ncbi.nlm.nih.gov/pubmed/36989297 http://dx.doi.org/10.1073/pnas.2213771120 |
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