Central Role of Sibling Small RNAs NgncR_162 and NgncR_163 in Main Metabolic Pathways of Neisseria gonorrhoeae
ABSTRACT Small bacterial regulatory RNAs (sRNAs) have been implicated in the regulation of numerous metabolic pathways. In most of these studies, sRNA-dependent regulation of mRNAs or proteins of enzymes in metabolic pathways has been predicted to affect the metabolism of these bacteria. However, on...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2023-02-01
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| Series: | mBio |
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| Online Access: | https://journals.asm.org/doi/10.1128/mbio.03093-22 |
| _version_ | 1811163389344350208 |
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| author | Thomas Steiner Marie Zachary Susanne Bauer Martin J. Müller Markus Krischke Sandra Radziej Maximilian Klepsch Bruno Huettel Wolfgang Eisenreich Thomas Rudel Dagmar Beier |
| author_facet | Thomas Steiner Marie Zachary Susanne Bauer Martin J. Müller Markus Krischke Sandra Radziej Maximilian Klepsch Bruno Huettel Wolfgang Eisenreich Thomas Rudel Dagmar Beier |
| author_sort | Thomas Steiner |
| collection | DOAJ |
| description | ABSTRACT Small bacterial regulatory RNAs (sRNAs) have been implicated in the regulation of numerous metabolic pathways. In most of these studies, sRNA-dependent regulation of mRNAs or proteins of enzymes in metabolic pathways has been predicted to affect the metabolism of these bacteria. However, only in a very few cases has the role in metabolism been demonstrated. Here, we performed a combined transcriptome and metabolome analysis to define the regulon of the sibling sRNAs NgncR_162 and NgncR_163 (NgncR_162/163) and their impact on the metabolism of Neisseria gonorrhoeae. These sRNAs have been reported to control genes of the citric acid and methylcitric acid cycles by posttranscriptional negative regulation. By transcriptome analysis, we now expand the NgncR_162/163 regulon by several new members and provide evidence that the sibling sRNAs act as both negative and positive regulators of target gene expression. Newly identified NgncR_162/163 targets are mostly involved in transport processes, especially in the uptake of glycine, phenylalanine, and branched-chain amino acids. NgncR_162/163 also play key roles in the control of serine-glycine metabolism and, hence, probably affect biosyntheses of nucleotides, vitamins, and other amino acids via the supply of one-carbon (C1) units. Indeed, these roles were confirmed by metabolomics and metabolic flux analysis, which revealed a bipartite metabolic network with glucose degradation for the supply of anabolic pathways and the usage of amino acids via the citric acid cycle for energy metabolism. Thus, by combined deep RNA sequencing (RNA-seq) and metabolomics, we significantly extended the regulon of NgncR_162/163 and demonstrated the role of NgncR_162/163 in the regulation of central metabolic pathways of the gonococcus. IMPORTANCE Neisseria gonorrhoeae is a major human pathogen which infects more than 100 million people every year. An alarming development is the emergence of gonococcal strains that are resistant against virtually all antibiotics used for their treatment. Despite the medical importance and the vanishing treatment options of gonococcal infections, the bacterial metabolism and its regulation have been only weakly defined until today. Using RNA-seq, metabolomics, and 13C-guided metabolic flux analysis, we here investigated the gonococcal metabolism and its regulation by the previously studied sibling sRNAs NgncR_162/163. The results demonstrate the regulation of transport processes and metabolic pathways involved in the biosynthesis of nucleotides, vitamins, and amino acids by NgncR_162/163. In particular, the combination of transcriptome and metabolic flux analyses provides a heretofore unreached depth of understanding the core metabolic pathways and their regulation by the neisserial sibling sRNAs. This integrative approach may therefore also be suitable for the functional analysis of a growing number of other bacterial metabolic sRNA regulators. |
| first_indexed | 2024-04-10T06:44:22Z |
| format | Article |
| id | doaj.art-c44d9e06a3d543ac83889cfa6b873f02 |
| institution | Directory Open Access Journal |
| issn | 2150-7511 |
| language | English |
| last_indexed | 2024-04-10T06:44:22Z |
| publishDate | 2023-02-01 |
| publisher | American Society for Microbiology |
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| series | mBio |
| spelling | doaj.art-c44d9e06a3d543ac83889cfa6b873f022023-02-28T14:06:24ZengAmerican Society for MicrobiologymBio2150-75112023-02-0114110.1128/mbio.03093-22Central Role of Sibling Small RNAs NgncR_162 and NgncR_163 in Main Metabolic Pathways of Neisseria gonorrhoeaeThomas Steiner0Marie Zachary1Susanne Bauer2Martin J. Müller3Markus Krischke4Sandra Radziej5Maximilian Klepsch6Bruno Huettel7Wolfgang Eisenreich8Thomas Rudel9Dagmar Beier10Bavarian NMR Center–Structural Membrane Biochemistry, Department of Chemistry, Technical University of Munich, Garching, GermanyChair of Microbiology, Theodor-Boveri-Institute, University of Würzburg, Würzburg, GermanyChair of Microbiology, Theodor-Boveri-Institute, University of Würzburg, Würzburg, GermanyDepartment of Pharmaceutical Biology, Julius von Sachs Institute, University of Würzburg, Würzburg, GermanyDepartment of Pharmaceutical Biology, Julius von Sachs Institute, University of Würzburg, Würzburg, GermanyBavarian NMR Center–Structural Membrane Biochemistry, Department of Chemistry, Technical University of Munich, Garching, GermanyChair of Microbiology, Theodor-Boveri-Institute, University of Würzburg, Würzburg, GermanyMax Planck Genome Centre, Cologne, GermanyBavarian NMR Center–Structural Membrane Biochemistry, Department of Chemistry, Technical University of Munich, Garching, GermanyChair of Microbiology, Theodor-Boveri-Institute, University of Würzburg, Würzburg, GermanyChair of Microbiology, Theodor-Boveri-Institute, University of Würzburg, Würzburg, GermanyABSTRACT Small bacterial regulatory RNAs (sRNAs) have been implicated in the regulation of numerous metabolic pathways. In most of these studies, sRNA-dependent regulation of mRNAs or proteins of enzymes in metabolic pathways has been predicted to affect the metabolism of these bacteria. However, only in a very few cases has the role in metabolism been demonstrated. Here, we performed a combined transcriptome and metabolome analysis to define the regulon of the sibling sRNAs NgncR_162 and NgncR_163 (NgncR_162/163) and their impact on the metabolism of Neisseria gonorrhoeae. These sRNAs have been reported to control genes of the citric acid and methylcitric acid cycles by posttranscriptional negative regulation. By transcriptome analysis, we now expand the NgncR_162/163 regulon by several new members and provide evidence that the sibling sRNAs act as both negative and positive regulators of target gene expression. Newly identified NgncR_162/163 targets are mostly involved in transport processes, especially in the uptake of glycine, phenylalanine, and branched-chain amino acids. NgncR_162/163 also play key roles in the control of serine-glycine metabolism and, hence, probably affect biosyntheses of nucleotides, vitamins, and other amino acids via the supply of one-carbon (C1) units. Indeed, these roles were confirmed by metabolomics and metabolic flux analysis, which revealed a bipartite metabolic network with glucose degradation for the supply of anabolic pathways and the usage of amino acids via the citric acid cycle for energy metabolism. Thus, by combined deep RNA sequencing (RNA-seq) and metabolomics, we significantly extended the regulon of NgncR_162/163 and demonstrated the role of NgncR_162/163 in the regulation of central metabolic pathways of the gonococcus. IMPORTANCE Neisseria gonorrhoeae is a major human pathogen which infects more than 100 million people every year. An alarming development is the emergence of gonococcal strains that are resistant against virtually all antibiotics used for their treatment. Despite the medical importance and the vanishing treatment options of gonococcal infections, the bacterial metabolism and its regulation have been only weakly defined until today. Using RNA-seq, metabolomics, and 13C-guided metabolic flux analysis, we here investigated the gonococcal metabolism and its regulation by the previously studied sibling sRNAs NgncR_162/163. The results demonstrate the regulation of transport processes and metabolic pathways involved in the biosynthesis of nucleotides, vitamins, and amino acids by NgncR_162/163. In particular, the combination of transcriptome and metabolic flux analyses provides a heretofore unreached depth of understanding the core metabolic pathways and their regulation by the neisserial sibling sRNAs. This integrative approach may therefore also be suitable for the functional analysis of a growing number of other bacterial metabolic sRNA regulators.https://journals.asm.org/doi/10.1128/mbio.03093-22sRNANeisseria gonorrhoeaeposttranscriptional regulationamino acid transporterbipartite metabolism |
| spellingShingle | Thomas Steiner Marie Zachary Susanne Bauer Martin J. Müller Markus Krischke Sandra Radziej Maximilian Klepsch Bruno Huettel Wolfgang Eisenreich Thomas Rudel Dagmar Beier Central Role of Sibling Small RNAs NgncR_162 and NgncR_163 in Main Metabolic Pathways of Neisseria gonorrhoeae mBio sRNA Neisseria gonorrhoeae posttranscriptional regulation amino acid transporter bipartite metabolism |
| title | Central Role of Sibling Small RNAs NgncR_162 and NgncR_163 in Main Metabolic Pathways of Neisseria gonorrhoeae |
| title_full | Central Role of Sibling Small RNAs NgncR_162 and NgncR_163 in Main Metabolic Pathways of Neisseria gonorrhoeae |
| title_fullStr | Central Role of Sibling Small RNAs NgncR_162 and NgncR_163 in Main Metabolic Pathways of Neisseria gonorrhoeae |
| title_full_unstemmed | Central Role of Sibling Small RNAs NgncR_162 and NgncR_163 in Main Metabolic Pathways of Neisseria gonorrhoeae |
| title_short | Central Role of Sibling Small RNAs NgncR_162 and NgncR_163 in Main Metabolic Pathways of Neisseria gonorrhoeae |
| title_sort | central role of sibling small rnas ngncr 162 and ngncr 163 in main metabolic pathways of neisseria gonorrhoeae |
| topic | sRNA Neisseria gonorrhoeae posttranscriptional regulation amino acid transporter bipartite metabolism |
| url | https://journals.asm.org/doi/10.1128/mbio.03093-22 |
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