CRP-Like Transcriptional Regulator MrpC Curbs c-di-GMP and 3′,3′-cGAMP Nucleotide Levels during Development in Myxococcus xanthus
ABSTRACT Myxococcus xanthus has a nutrient-regulated biphasic life cycle forming predatory swarms in the presence of nutrients and spore-filled fruiting bodies in the absence of nutrients. The second messenger 3′-5′, 3′-5 cyclic di-GMP (c-di-GMP) is essential during both stages of the life cycle; ho...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
American Society for Microbiology
2022-02-01
|
| Series: | mBio |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/mbio.00044-22 |
| _version_ | 1818872272711057408 |
|---|---|
| author | Sofya Kuzmich Patrick Blumenkamp Doreen Meier Dobromir Szadkowski Alexander Goesmann Anke Becker Lotte Søgaard-Andersen |
| author_facet | Sofya Kuzmich Patrick Blumenkamp Doreen Meier Dobromir Szadkowski Alexander Goesmann Anke Becker Lotte Søgaard-Andersen |
| author_sort | Sofya Kuzmich |
| collection | DOAJ |
| description | ABSTRACT Myxococcus xanthus has a nutrient-regulated biphasic life cycle forming predatory swarms in the presence of nutrients and spore-filled fruiting bodies in the absence of nutrients. The second messenger 3′-5′, 3′-5 cyclic di-GMP (c-di-GMP) is essential during both stages of the life cycle; however, different enzymes involved in c-di-GMP synthesis and degradation as well as several c-di-GMP receptors are important during distinct life cycle stages. To address this stage specificity, we determined transcript levels using transcriptome sequencing (RNA-seq) and transcription start sites using Cappable sequencing (Cappable-seq) during growth and development genome wide. All 70 genes encoding c-di-GMP-associated proteins were expressed, with 28 upregulated and 10 downregulated during development. Specifically, the three genes encoding enzymatically active proteins with a stage-specific function were expressed stage specifically. By combining operon mapping with published chromatin immunoprecipitation sequencing (ChIP-seq) data for MrpC (M. Robinson, B. Son, D. Kroos, L. Kroos, BMC Genomics 15:1123, 2014, http://dx.doi.org/10.1186/1471-2164-15-1123), the cAMP receptor protein (CRP)-like master regulator of development, we identified nine developmentally regulated genes as regulated by MrpC. In particular, MrpC directly represses the expression of dmxB, which encodes the diguanylate cyclase DmxB that is essential for development and responsible for the c-di-GMP increase during development. Moreover, MrpC directly activates the transcription of pmxA, which encodes a bifunctional phosphodiesterase that degrades c-di-GMP and 3′,3′-cGAMP in vitro and is essential for development. Thereby, MrpC regulates and curbs the cellular pools of c-di-GMP and 3′,3′-cGAMP during development. We conclude that temporal regulation of the synthesis of proteins involved in c-di-GMP metabolism contributes to c-di-GMP signaling specificity. MrpC is important for this regulation, thereby being a key regulator of developmental cyclic di-nucleotide metabolism in M. xanthus. IMPORTANCE The second messenger c-di-GMP is important during both stages of the nutrient-regulated biphasic life cycle of Myxococcus xanthus with the formation of predatory swarms in the presence of nutrients and spore-filled fruiting bodies in the absence of nutrients. However, different enzymes involved in c-di-GMP synthesis and degradation are important during distinct life cycle stages. Here, we show that the three genes encoding enzymatically active proteins with a stage-specific function are expressed stage specifically. Moreover, we find that the master transcriptional regulator of development MrpC directly regulates the expression of dmxB, which encodes the diguanylate cyclase DmxB that is essential for development, and of pmxA, which encodes a bifunctional phosphodiesterase that degrades c-di-GMP and 3′,3′-cGAMP in vitro and is essential for development. We conclude that temporal regulation of the synthesis of proteins involved in c-di-GMP metabolism contributes to c-di-GMP signaling specificity and that MrpC plays an important role in this regulation. |
| first_indexed | 2024-12-19T12:36:11Z |
| format | Article |
| id | doaj.art-90b0b2f2196d48d7ab11362806c86c81 |
| institution | Directory Open Access Journal |
| issn | 2150-7511 |
| language | English |
| last_indexed | 2024-12-19T12:36:11Z |
| publishDate | 2022-02-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mBio |
| spelling | doaj.art-90b0b2f2196d48d7ab11362806c86c812022-12-21T20:21:09ZengAmerican Society for MicrobiologymBio2150-75112022-02-0113110.1128/mbio.00044-22CRP-Like Transcriptional Regulator MrpC Curbs c-di-GMP and 3′,3′-cGAMP Nucleotide Levels during Development in Myxococcus xanthusSofya Kuzmich0Patrick Blumenkamp1Doreen Meier2Dobromir Szadkowski3Alexander Goesmann4Anke Becker5Lotte Søgaard-Andersen6Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, GermanySystems Biology and Bioinformatics, Justus Liebig University Giessen, Gissen, GermanyCenter for Synthetic Microbiology (SYNMIKRO), Philipps Universität Marburg, Marburg, GermanyDepartment of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, GermanySystems Biology and Bioinformatics, Justus Liebig University Giessen, Gissen, GermanyCenter for Synthetic Microbiology (SYNMIKRO), Philipps Universität Marburg, Marburg, GermanyDepartment of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, GermanyABSTRACT Myxococcus xanthus has a nutrient-regulated biphasic life cycle forming predatory swarms in the presence of nutrients and spore-filled fruiting bodies in the absence of nutrients. The second messenger 3′-5′, 3′-5 cyclic di-GMP (c-di-GMP) is essential during both stages of the life cycle; however, different enzymes involved in c-di-GMP synthesis and degradation as well as several c-di-GMP receptors are important during distinct life cycle stages. To address this stage specificity, we determined transcript levels using transcriptome sequencing (RNA-seq) and transcription start sites using Cappable sequencing (Cappable-seq) during growth and development genome wide. All 70 genes encoding c-di-GMP-associated proteins were expressed, with 28 upregulated and 10 downregulated during development. Specifically, the three genes encoding enzymatically active proteins with a stage-specific function were expressed stage specifically. By combining operon mapping with published chromatin immunoprecipitation sequencing (ChIP-seq) data for MrpC (M. Robinson, B. Son, D. Kroos, L. Kroos, BMC Genomics 15:1123, 2014, http://dx.doi.org/10.1186/1471-2164-15-1123), the cAMP receptor protein (CRP)-like master regulator of development, we identified nine developmentally regulated genes as regulated by MrpC. In particular, MrpC directly represses the expression of dmxB, which encodes the diguanylate cyclase DmxB that is essential for development and responsible for the c-di-GMP increase during development. Moreover, MrpC directly activates the transcription of pmxA, which encodes a bifunctional phosphodiesterase that degrades c-di-GMP and 3′,3′-cGAMP in vitro and is essential for development. Thereby, MrpC regulates and curbs the cellular pools of c-di-GMP and 3′,3′-cGAMP during development. We conclude that temporal regulation of the synthesis of proteins involved in c-di-GMP metabolism contributes to c-di-GMP signaling specificity. MrpC is important for this regulation, thereby being a key regulator of developmental cyclic di-nucleotide metabolism in M. xanthus. IMPORTANCE The second messenger c-di-GMP is important during both stages of the nutrient-regulated biphasic life cycle of Myxococcus xanthus with the formation of predatory swarms in the presence of nutrients and spore-filled fruiting bodies in the absence of nutrients. However, different enzymes involved in c-di-GMP synthesis and degradation are important during distinct life cycle stages. Here, we show that the three genes encoding enzymatically active proteins with a stage-specific function are expressed stage specifically. Moreover, we find that the master transcriptional regulator of development MrpC directly regulates the expression of dmxB, which encodes the diguanylate cyclase DmxB that is essential for development, and of pmxA, which encodes a bifunctional phosphodiesterase that degrades c-di-GMP and 3′,3′-cGAMP in vitro and is essential for development. We conclude that temporal regulation of the synthesis of proteins involved in c-di-GMP metabolism contributes to c-di-GMP signaling specificity and that MrpC plays an important role in this regulation.https://journals.asm.org/doi/10.1128/mbio.00044-22c-di-GMPcGAMPCRPCappable-seqsporulationfruiting body formation |
| spellingShingle | Sofya Kuzmich Patrick Blumenkamp Doreen Meier Dobromir Szadkowski Alexander Goesmann Anke Becker Lotte Søgaard-Andersen CRP-Like Transcriptional Regulator MrpC Curbs c-di-GMP and 3′,3′-cGAMP Nucleotide Levels during Development in Myxococcus xanthus mBio c-di-GMP cGAMP CRP Cappable-seq sporulation fruiting body formation |
| title | CRP-Like Transcriptional Regulator MrpC Curbs c-di-GMP and 3′,3′-cGAMP Nucleotide Levels during Development in Myxococcus xanthus |
| title_full | CRP-Like Transcriptional Regulator MrpC Curbs c-di-GMP and 3′,3′-cGAMP Nucleotide Levels during Development in Myxococcus xanthus |
| title_fullStr | CRP-Like Transcriptional Regulator MrpC Curbs c-di-GMP and 3′,3′-cGAMP Nucleotide Levels during Development in Myxococcus xanthus |
| title_full_unstemmed | CRP-Like Transcriptional Regulator MrpC Curbs c-di-GMP and 3′,3′-cGAMP Nucleotide Levels during Development in Myxococcus xanthus |
| title_short | CRP-Like Transcriptional Regulator MrpC Curbs c-di-GMP and 3′,3′-cGAMP Nucleotide Levels during Development in Myxococcus xanthus |
| title_sort | crp like transcriptional regulator mrpc curbs c di gmp and 3 3 cgamp nucleotide levels during development in myxococcus xanthus |
| topic | c-di-GMP cGAMP CRP Cappable-seq sporulation fruiting body formation |
| url | https://journals.asm.org/doi/10.1128/mbio.00044-22 |
| work_keys_str_mv | AT sofyakuzmich crpliketranscriptionalregulatormrpccurbscdigmpand33cgampnucleotidelevelsduringdevelopmentinmyxococcusxanthus AT patrickblumenkamp crpliketranscriptionalregulatormrpccurbscdigmpand33cgampnucleotidelevelsduringdevelopmentinmyxococcusxanthus AT doreenmeier crpliketranscriptionalregulatormrpccurbscdigmpand33cgampnucleotidelevelsduringdevelopmentinmyxococcusxanthus AT dobromirszadkowski crpliketranscriptionalregulatormrpccurbscdigmpand33cgampnucleotidelevelsduringdevelopmentinmyxococcusxanthus AT alexandergoesmann crpliketranscriptionalregulatormrpccurbscdigmpand33cgampnucleotidelevelsduringdevelopmentinmyxococcusxanthus AT ankebecker crpliketranscriptionalregulatormrpccurbscdigmpand33cgampnucleotidelevelsduringdevelopmentinmyxococcusxanthus AT lottesøgaardandersen crpliketranscriptionalregulatormrpccurbscdigmpand33cgampnucleotidelevelsduringdevelopmentinmyxococcusxanthus |