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Wang X, Hao X, Yang Y, Jia S, Chen Y, Yang W, Luo Y, Xie Z, Gu Y, Wu Y, Zhang F, Li M, Wang Y, Shen X, Xu L. A phosphodiesterase CpdB in Yersinia pseudotuberculosis degrades CDNs to inhibit innate immune response. Vet Microbiol 2024; 297:110194. [PMID: 39084162 DOI: 10.1016/j.vetmic.2024.110194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 07/08/2024] [Accepted: 07/21/2024] [Indexed: 08/02/2024]
Abstract
Yersinia pseudotuberculosis (Yptb) is a pathogenic gram-negative bacterium that can colonize the intestines of different animals. Its infection leads to the activation of the host's innate immunity. Both host and bacterial-derived cyclic dinucleotides (CDNs) could activate the innate immune response of host cells. In bacteria, CDNs like c-di-AMP, c-di-GMP, or 3'3'-cGAMP can be hydrolyzed by different hydrolases. Recent studies showed that the degradation of those second messengers helps the pathogen evade immune detection. In this study, we identified a hydrolase, YPK_3776, namely CpdB in Yptb. CpdB is predicted to bind bacterial-derived c-di-AMP, c-di-GMP, 3'3'-cGAMP and host-derived 2'3'-cGAMP. Surprisingly, by using high-performance liquid chromatography (HPLC), we found that CpdB could only degrade bacterial-derived CDNs but not host-derived 2'3'-cGAMP. In addition, CpdB has 2'3'-cNMP activity. Consistently, the Yptb mutant lacking the cpdB gene exhibited a higher level of intracellular c-di-GMP. Furthermore, the ∆cpdB mutant elicited stronger innate immune responses during Yptb infection in macrophages, suggesting CpdB enables Yptb to evade host immune surveillance. Furthermore, CpdB inhibited the Yptb-induced innate immune response in a STING-dependent manner. Finally, we showed the ∆cpdB infection in mice model exhibited in lower bacterial burden, as compared to wild-type strain infection, indicating CpdB is important for bacterial survival in the host. Together, we identified a cyclic dinucleotide hydrolase CpdB in Yptb that could degrade bacterial-derived CDNs which help the pathogen to evade immune detection via the STING pathway.
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Affiliation(s)
- Xiao Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinwei Hao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuqing Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Siyu Jia
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yating Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wenguang Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yi Luo
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhen Xie
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanchao Gu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuxuan Wu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fuhua Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mengyuan Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yao Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xihui Shen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Lei Xu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Jana B, Liu X, Dénéréaz J, Park H, Leshchiner D, Liu B, Gallay C, Zhu J, Veening JW, van Opijnen T. CRISPRi-TnSeq maps genome-wide interactions between essential and non-essential genes in bacteria. Nat Microbiol 2024; 9:2395-2409. [PMID: 39030344 PMCID: PMC11371651 DOI: 10.1038/s41564-024-01759-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 06/12/2024] [Indexed: 07/21/2024]
Abstract
Genetic interactions identify functional connections between genes and pathways, establishing gene functions or druggable targets. Here we use CRISPRi-TnSeq, CRISPRi-mediated knockdown of essential genes alongside TnSeq-mediated knockout of non-essential genes, to map genome-wide interactions between essential and non-essential genes in Streptococcus pneumoniae. Transposon-mutant libraries constructed in 13 CRISPRi strains enabled screening of ~24,000 gene pairs. This identified 1,334 genetic interactions, including 754 negative and 580 positive interactions. Network analyses show that 17 non-essential genes pleiotropically interact with more than half the essential genes tested. Validation experiments confirmed that a 7-gene subset protects against perturbations. Furthermore, we reveal hidden redundancies that compensate for essential gene loss, relationships between cell wall synthesis, integrity and cell division, and show that CRISPRi-TnSeq identifies synthetic and suppressor-type relationships between both functionally linked and disparate genes and pathways. Importantly, in species where CRISPRi and Tn-Seq are established, CRISPRi-TnSeq should be straightforward to implement.
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Affiliation(s)
- Bimal Jana
- Department of Biology, Boston College, Chestnut Hill, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Xue Liu
- Department of Pathogen Biology, Base for International Science and Technology Cooperation: Carson Cancer Stem Cell Vaccines R&D Center, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, China
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Julien Dénéréaz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Hongshik Park
- Department of Biology, Boston College, Chestnut Hill, MA, USA
| | | | - Bruce Liu
- Department of Biology, Boston College, Chestnut Hill, MA, USA
| | - Clément Gallay
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Junhao Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| | - Tim van Opijnen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Boston Children's Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, MA, USA.
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Wang Y, Hao W, Guo Z, Sun Y, Wu Y, Sun Y, Gao T, Luo Y, Jin L, Yang J, Cheng K. Structural and functional investigation of the DHH/DHHA1 family proteins in Deinococcus radiodurans. Nucleic Acids Res 2024; 52:7142-7157. [PMID: 38804263 PMCID: PMC11229311 DOI: 10.1093/nar/gkae451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 04/24/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024] Open
Abstract
DHH/DHHA1 family proteins have been proposed to play critical roles in bacterial resistance to environmental stresses. Members of the most radioresistant bacteria genus, Deinococcus, possess two DHH/DHHA1 family proteins, RecJ and RecJ-like. While the functions of Deinococcus radiodurans RecJ (DrRecJ) in DNA damage resistance have been well characterized, the role and biochemical activities of D. radiodurans RecJ-like (DrRecJ-like) remain unclear. Phenotypic and transcriptomic analyses suggest that, beyond DNA repair, DrRecJ is implicated in cell growth and division. Additionally, DrRecJ-like not only affects stress response, cell growth, and division but also correlates with the folding/stability of intracellular proteins, as well as the formation and stability of cell membranes/walls. DrRecJ-like exhibits a preferred catalytic activity towards short single-stranded RNA/DNA oligos and c-di-AMP. In contrast, DrRecJ shows no activity against RNA and c-di-AMP. Moreover, a crystal structure of DrRecJ-like, with Mg2+ bound in an open conformation at a resolution of 1.97 Å, has been resolved. Subsequent mutational analysis was conducted to pinpoint the crucial residues essential for metal cation and substrate binding, along with the dimerization state, necessary for DrRecJ-like's function. This finding could potentially extend to all NrnA-like proteins, considering their conserved amino acid sequence and comparable dimerization forms.
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Affiliation(s)
- Ying Wang
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Wanshan Hao
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Ziming Guo
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Yiyang Sun
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Yu Wu
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Yukang Sun
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Tianwen Gao
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Yun Luo
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Lizan Jin
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Jieyu Yang
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Kaiying Cheng
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
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Liang X, Cui R, Li X, Ning H, Kang J, Lu Y, Zhou S, Huang X, Peng Y, Zhang J, Li S, Ma Y, Bai Y. Ag85B with c-di-AMP as mucosal adjuvant showed immunotherapeutic effects on persistent Mycobacterium tuberculosis infection in mice. Braz J Med Biol Res 2024; 57:e13409. [PMID: 38958367 PMCID: PMC11221865 DOI: 10.1590/1414-431x2024e13409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/22/2024] [Indexed: 07/04/2024] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains the leading cause of mortality by a single infectious agent in the world. M. tuberculosis infection could also result in clinical chronic infection, known as latent TB infection (LTBI). Compared to the current limited treatment, several subunit vaccines showed immunotherapeutic effects and were included in clinical trials. In this study, a subunit vaccine of Ag85B with a novel mucosal adjuvant c-di-AMP (Ag85B:c-di-AMP) was delivered intranasally to a persistent M. tuberculosis H37Ra infection mouse model, which also presented the asymptomatic characteristics of LTBI. Compared with Ag85B immunization, Ag85B:c-di-AMP vaccination induced stronger humoral immune responses, significantly higher CD4+ T cells recruitment, enhanced Th1/Th2/Th17 profile response in the lung, decreased pathological lesions of the lung, and reduced M. tuberculosis load in mice. Taken together, Ag85B:c-di-AMP mucosal route immunization provided an immunotherapeutic effect on persistent M. tuberculosis H37Ra infection, and c-di-AMP, as a promising potential mucosal adjuvant, could be further used in therapeutic or prophylactic vaccine strategies for persistent M. tuberculosis infection as well as LTBI.
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Affiliation(s)
- Xuan Liang
- College of Life Sciences, Northwest University, Xi'an, China
- Department of Microbiology and Pathogen Biology, Air Force Medical University, Xi'an, China
| | - Ruonan Cui
- College of Life Sciences, Northwest University, Xi'an, China
- Department of Microbiology and Pathogen Biology, Air Force Medical University, Xi'an, China
| | - Xue Li
- College of Life Sciences, Northwest University, Xi'an, China
- Department of Microbiology and Pathogen Biology, Air Force Medical University, Xi'an, China
| | - Huanhuan Ning
- Department of Microbiology and Pathogen Biology, Air Force Medical University, Xi'an, China
- Military Medical Innovation Center, Air Force Medical University, Xi'an, China
| | - Jian Kang
- Department of Microbiology and Pathogen Biology, Air Force Medical University, Xi'an, China
| | - Yanzhi Lu
- Department of Microbiology and Pathogen Biology, Air Force Medical University, Xi'an, China
| | - Shan Zhou
- Department of Clinical Laboratory, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Xinying Huang
- Student Brigade, Basic Medical School, Air Force Medical University, Xi'an, China
| | - Yujun Peng
- Student Brigade, Basic Medical School, Air Force Medical University, Xi'an, China
| | - Jingyao Zhang
- Student Brigade, Basic Medical School, Air Force Medical University, Xi'an, China
| | - Shiyun Li
- Student Brigade, Basic Medical School, Air Force Medical University, Xi'an, China
| | - Yanling Ma
- College of Life Sciences, Northwest University, Xi'an, China
| | - Yinlan Bai
- Department of Microbiology and Pathogen Biology, Air Force Medical University, Xi'an, China
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Maccaro JJ, Figueroa LL, McFrederick QS. From pollen to putrid: Comparative metagenomics reveals how microbiomes support dietary specialization in vulture bees. Mol Ecol 2024; 33:e17421. [PMID: 38828760 DOI: 10.1111/mec.17421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 05/12/2024] [Accepted: 05/20/2024] [Indexed: 06/05/2024]
Abstract
For most animals, the microbiome is key for nutrition and pathogen defence, and is often shaped by diet. Corbiculate bees, including honey bees, bumble bees, and stingless bees, share a core microbiome that has been shaped, at least in part, by the challenges associated with pollen digestion. However, three species of stingless bees deviate from the general rule of bees obtaining their protein exclusively from pollen (obligate pollinivores) and instead consume carrion as their sole protein source (obligate necrophages) or consume both pollen and carrion (facultative necrophages). These three life histories can provide missing insights into microbiome evolution associated with extreme dietary transitions. Here, we investigate, via shotgun metagenomics, the functionality of the microbiome across three bee diet types: obligate pollinivory, obligate necrophagy, and facultative necrophagy. We find distinct differences in microbiome composition and gene functional profiles between the diet types. Obligate necrophages and pollinivores have more specialized microbes, whereas facultative necrophages have a diversity of environmental microbes associated with several dietary niches. Our study suggests that necrophagous bee microbiomes may have evolved to overcome cellular stress and microbial competition associated with carrion. We hypothesize that the microbiome evolved social phenotypes, such as biofilms, that protect the bees from opportunistic pathogens present on carcasses, allowing them to overcome novel nutritional challenges. Whether specific microbes enabled diet shifts or diet shifts occurred first and microbial evolution followed requires further research to disentangle. Nonetheless, we find that necrophagous microbiomes, vertebrate and invertebrate alike, have functional commonalities regardless of their taxonomy.
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Affiliation(s)
- Jessica J Maccaro
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Laura L Figueroa
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Quinn S McFrederick
- Department of Entomology, University of California Riverside, Riverside, California, USA
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Foster AJ, van den Noort M, Poolman B. Bacterial cell volume regulation and the importance of cyclic di-AMP. Microbiol Mol Biol Rev 2024; 88:e0018123. [PMID: 38856222 PMCID: PMC11332354 DOI: 10.1128/mmbr.00181-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024] Open
Abstract
SUMMARYNucleotide-derived second messengers are present in all domains of life. In prokaryotes, most of their functionality is associated with general lifestyle and metabolic adaptations, often in response to environmental fluctuations of physical parameters. In the last two decades, cyclic di-AMP has emerged as an important signaling nucleotide in many prokaryotic lineages, including Firmicutes, Actinobacteria, and Cyanobacteria. Its importance is highlighted by the fact that both the lack and overproduction of cyclic di-AMP affect viability of prokaryotes that utilize cyclic di-AMP, and that it generates a strong innate immune response in eukaryotes. In bacteria that produce the second messenger, most molecular targets of cyclic di-AMP are associated with cell volume control. Besides, other evidence links the second messenger to cell wall remodeling, DNA damage repair, sporulation, central metabolism, and the regulation of glycogen turnover. In this review, we take a biochemical, quantitative approach to address the main cellular processes that are directly regulated by cyclic di-AMP and show that these processes are very connected and require regulation of a similar set of proteins to which cyclic di-AMP binds. Altogether, we argue that cyclic di-AMP is a master regulator of cell volume and that other cellular processes can be connected with cyclic di-AMP through this core function. We further highlight important directions in which the cyclic di-AMP field has to develop to gain a full understanding of the cyclic di-AMP signaling network and why some processes are regulated, while others are not.
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Affiliation(s)
- Alexander J. Foster
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Marco van den Noort
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
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Rojas EM, Zhang H, Velu SE, Wu H. Tetracyclic homoisoflavanoid (+)-brazilin: a natural product inhibits c-di-AMP-producing enzyme and Streptococcus mutans biofilms. Microbiol Spectr 2024; 12:e0241823. [PMID: 38591917 PMCID: PMC11064632 DOI: 10.1128/spectrum.02418-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 03/02/2024] [Indexed: 04/10/2024] Open
Abstract
The tenacious biofilms formed by Streptococcus mutans are resistant to conventional antibiotics and current treatments. There is a growing need for novel therapeutics that selectively inhibit S. mutans biofilms while preserving the normal oral microenvironment. Previous studies have shown that increased levels of cyclic di-AMP, an important secondary messenger synthesized by diadenylate cyclase (DAC), favored biofilm formation in S. mutans. Thus, targeting S. mutans DAC is a novel strategy to inhibit S. mutans biofilms. We screened a small NCI library of natural products using a fluorescence detection assay. (+)-Brazilin, a tetracyclic homoisoflavanoid found in the heartwood of Caesalpinia sappan, was identified as one of the 11 "hits," with the greatest reduction (>99%) in fluorescence at 100 µM. The smDAC inhibitory profiles of the 11 "hits" established by a quantitative high-performance liquid chromatography assay revealed that (+)-brazilin had the most enzymatic inhibitory activity (87% at 100 µM) and was further studied to determine its half maximal inhibitory concentration (IC50 = 25.1 ± 0.98 µM). (+)-Brazilin non-competitively inhibits smDAC's enzymatic activity (Ki = 140.0 ± 27.13 µM), as determined by a steady-state Michaelis-Menten kinetics assay. In addition, (+)-brazilin's binding profile with smDAC (Kd = 11.87 µM) was illustrated by a tyrosine intrinsic fluorescence quenching assay. Furthermore, at low micromolar concentrations, (+)-brazilin selectively inhibited the biofilm of S. mutans (IC50 = 21.0 ± 0.60 µM) and other oral bacteria. S. mutans biofilms were inhibited by a factor of 105 in colony-forming units when treated with 50 µM (+)-brazilin. In addition, a significant dose-dependent reduction in extracellular DNA and glucan levels was evident by fluorescence microscopy imaging of S. mutans biofilms exposed to different concentrations of (+)-brazilin. Furthermore, colonization of S. mutans on a representative model of enamel using suspended hydroxyapatite discs showed a >90% reduction with 50 µM (+)-brazilin. In summary, we have identified a drug-like natural product inhibitor of S. mutans biofilm that not only binds to smDAC but can also inhibit the function of smDAC. (+)-Brazilin could be a good candidate for further development as a potent therapeutic for the prevention and treatment of dental caries.IMPORTANCEThis study represents a significant advancement in our understanding of potential therapeutic options for combating cariogenic biofilms produced by Streptococcus mutans. The research delves into the use of (+)-brazilin, a natural product, as a potent inhibitor of Streptococcus mutans' diadenylate cyclase (smDAC), an enzyme crucial in the formation of biofilms. The study establishes (+)-brazilin as a non-competitive inhibitor of smDAC while providing initial insights into its binding mechanism. What makes this finding even more promising is that (+)-brazilin does not limit its inhibitory effects to S. mutans alone. Instead, it demonstrates efficacy in hindering biofilms in other oral bacteria as well. The broader spectrum of anti-biofilm activity suggests that (+)-brazilin could potentially serve as a versatile tool in a natural product-based treatment for combating a range of conditions caused by resilient biofilms.
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Affiliation(s)
- Edwin M. Rojas
- School of Dentistry, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Hua Zhang
- Division of Biomaterial & Biomedical Sciences, School of Dentistry, Oregon Health & Science University, Portland, Oregon, USA
| | - Sadanandan E. Velu
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Hui Wu
- Division of Biomaterial & Biomedical Sciences, School of Dentistry, Oregon Health & Science University, Portland, Oregon, USA
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Dengler Haunreiter V, Tarnutzer A, Bär J, von Matt M, Hertegonne S, Andreoni F, Vulin C, Künzi L, Menzi C, Kiefer P, Christen P, Vorholt JA, Zinkernagel AS. C-di-AMP levels modulate Staphylococcus aureus cell wall thickness, response to oxidative stress, and antibiotic resistance and tolerance. Microbiol Spectr 2023; 11:e0278823. [PMID: 37948390 PMCID: PMC10715141 DOI: 10.1128/spectrum.02788-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023] Open
Abstract
IMPORTANCE Antibiotic resistance and tolerance are substantial healthcare-related problems, hampering effective treatment of bacterial infections. Mutations in the phosphodiesterase GdpP, which degrades cyclic di-3', 5'-adenosine monophosphate (c-di-AMP), have recently been associated with resistance to beta-lactam antibiotics in clinical Staphylococcus aureus isolates. In this study, we show that high c-di-AMP levels decreased the cell size and increased the cell wall thickness in S. aureus mutant strains. As a consequence, an increase in resistance to cell wall targeting antibiotics, such as oxacillin and fosfomycin as well as in tolerance to ceftaroline, a cephalosporine used to treat methicillin-resistant S. aureus infections, was observed. These findings underline the importance of investigating the role of c-di-AMP in the development of tolerance and resistance to antibiotics in order to optimize treatment in the clinical setting.
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Affiliation(s)
- Vanina Dengler Haunreiter
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Andrea Tarnutzer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Julian Bär
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Manuela von Matt
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sanne Hertegonne
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Federica Andreoni
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Clément Vulin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Lisa Künzi
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Carmen Menzi
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Patrick Kiefer
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Philipp Christen
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Julia A. Vorholt
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Annelies S. Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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Wright MJ, Bai G. Bacterial second messenger cyclic di-AMP in streptococci. Mol Microbiol 2023; 120:791-804. [PMID: 37898560 DOI: 10.1111/mmi.15187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/10/2023] [Accepted: 10/15/2023] [Indexed: 10/30/2023]
Abstract
Cyclic dimeric adenosine monophosphate (c-di-AMP) has been well studied in bacteria, including those of the genus Streptococcus, since the first recognition of this dinucleotide in 2008. Streptococci possess a sole diadenylate cyclase, CdaA, and distinct c-di-AMP phosphodiesterases. Interestingly, cdaA is required for viability of some streptococcal species but not all when streptococci are grown in standard laboratory media. Bacteria of this genus also have distinct c-di-AMP effector proteins, diverse c-di-AMP-signaling pathways, and subsequent biological outcomes. In streptococci, c-di-AMP may influence bacterial growth, morphology, biofilm formation, competence program, drug resistance, and bacterial pathogenesis. c-di-AMP secreted by streptococci has also been shown to interact with the mammalian host and induces immune responses including type I interferon production. In this review, we summarize the reported c-di-AMP networks in seven species of the genus Streptococcus, which cause diverse clinical manifestations, and propose future perspectives to investigate the signaling molecule in these streptococcal pathogens.
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Affiliation(s)
- Michael J Wright
- Department of Internal Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Guangchun Bai
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, New York, USA
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10
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Jin Z, Song D, Wang W, Feng L, Li Z, Chen H, Xiao X, Liu X. Synthesis and degradation of the cyclic dinucleotide messenger c-di-AMP in the hyperthermophilic archaeon Pyrococcus yayanosii. Protein Sci 2023; 32:e4829. [PMID: 37921047 PMCID: PMC10680344 DOI: 10.1002/pro.4829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/04/2023]
Abstract
Cyclic di-adenosine monophosphate (c-di-AMP) is a newly identified prokaryotic cyclic dinucleotide second messenger well elucidated in bacteria, while less studied in archaea. Here, we describe the enzymes involved in c-di-AMP metabolism in the hyperthermophilic archaeon Pyrococcus yayanosii. Our results demonstrate that c-di-AMP is synthesized from two molecules of ATP by diadenylate cyclase (DAC) and degraded into pApA and then to AMP by a DHH family phosphodiesterase (PDE). DAC can be activated by a wider variety of ions, using two conserved residues, D188 and E244, to coordinate divalent metal ions, which is different from bacterial CdaA and DisA. PDE possesses a broad substrate spectrum like bacterial DHH family PDEs but shows a stricter base selection between A and G in cyclic dinucleotides hydrolysis. PDE shows differences in substrate binding patches from bacterial counterparts. C-di-AMP was confirmed to exist in Thermococcus kodakarensis cells, and the deletion of the dac or pde gene supports that the synthesis and degradation of c-di-AMP are catalyzed by DAC and PDE, respectively. Our results provide a further understanding of the metabolism of c-di-AMP in archaea.
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Affiliation(s)
- Zheng Jin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- Instrumental analysis centerShanghai Jiao Tong UniversityShanghaiChina
| | - Dong Song
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Wei‐Wei Wang
- Shanghai Institute of Applied PhysicsChinese Academy of SciencesShanghaiChina
| | - Lei Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zheng‐Xin Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Hai‐Feng Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- Joint International Research Laboratory of Metabolic & Developmental Sciences (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiChina
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil EngineeringShanghai Jiao Tong UniversityShanghaiChina
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)ZhuhaiGuangdongChina
| | - Xi‐Peng Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
- Joint International Research Laboratory of Metabolic & Developmental Sciences (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiChina
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11
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Zhu X, Baranowski E, Hao Z, Li X, Zhao G, Dong Y, Chen Y, Hu C, Chen H, Citti C, Wang A, Guo A. An atypical GdpP enzyme linking cyclic nucleotide metabolism to osmotic tolerance and gene regulation in Mycoplasma bovis. Front Microbiol 2023; 14:1250368. [PMID: 38098652 PMCID: PMC10720645 DOI: 10.3389/fmicb.2023.1250368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/10/2023] [Indexed: 12/17/2023] Open
Abstract
Nucleotide second messengers play an important role in bacterial adaptation to environmental changes. Recent evidence suggests that some of these regulatory molecular pathways were conserved upon the degenerative evolution of the wall-less mycoplasmas. We have recently reported the occurrence of a phosphodiesterase (PDE) in the ruminant pathogen Mycoplasma bovis, which was involved in c-di-AMP metabolism. In the present study, we demonstrate that the genome of this mycoplasma species encodes a PDE of the GdpP family with atypical DHH domains. Characterization of M. bovis GdpP (MbovGdpP) revealed a multifunctional PDE with unusual nanoRNase and single-stranded DNase activities. The alarmone ppGpp was found unable to inhibit c-di-NMP degradation by MbovGdpP but efficiently blocked its nanoRNase activity. Remarkably, MbovGdpP was found critical for the osmotic tolerance of M. bovis under K+ and Na+ conditions. Transcriptomic analyses further revealed the biological importance of MbovGdpP in tRNA biosynthesis, pyruvate metabolism, and several steps in genetic information processing. This study is an important step in understanding the role of PDE and nucleotide second messengers in the biology of a minimal bacterial pathogen.
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Affiliation(s)
- Xifang Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
- Longhu Laboratory of Advanced Immunology, Zhengzhou, China
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | | | - Zhiyu Hao
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xixi Li
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Gang Zhao
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yaqi Dong
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yingyu Chen
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Changmin Hu
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Huanchun Chen
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People’s Republic of China, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan, China
| | | | - Aiping Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
- Longhu Laboratory of Advanced Immunology, Zhengzhou, China
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People’s Republic of China, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease, Ministry of Science and Technology of the People’s Republic of China, Wuhan, China
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12
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Hou Y, Wang Z, Liu P, Wei X, Zhang Z, Fan S, Zhang L, Han F, Song Y, Chu L, Zhang C. SMPDL3A is a cGAMP-degrading enzyme induced by LXR-mediated lipid metabolism to restrict cGAS-STING DNA sensing. Immunity 2023; 56:2492-2507.e10. [PMID: 37890481 DOI: 10.1016/j.immuni.2023.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/19/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023]
Abstract
Lipid metabolism has been associated with the cyclic guanosine monophosphate (GMP)-AMP synthase (cGAS) stimulator of interferon genes (STING) DNA-sensing pathway, but our understanding of how these signals are integrated into a cohesive immunometabolic program is lacking. Here, we have identified liver X receptor (LXR) agonists as potent inhibitors of STING signaling. We show that stimulation of lipid metabolism by LXR agonists specifically suppressed cyclic GMP-AMP (cGAMP)-STING signaling. Moreover, we developed cyclic dinucleotide-conjugated beads to biochemically isolate host effectors for cGAMP inhibition, and we found that LXR ligands stimulated the expression of sphingomyelin phosphodiesterase acid-like 3A (SMPDL3A), which is a 2'3'-cGAMP-degrading enzyme. Results of crystal structures suggest that cGAMP analog induces dimerization of SMPDL3A, and the dimerization is critical for cGAMP degradation. Additionally, we have provided evidence that SMPDL3A cleaves cGAMP to restrict STING signaling in cell culture and mouse models. Our results reveal SMPDL3A as a cGAMP-specific nuclease and demonstrate a mechanism for how LXR-associated lipid metabolism modulates STING-mediated innate immunity.
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Affiliation(s)
- Yanfei Hou
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Zhimeng Wang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Peiyuan Liu
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Xubiao Wei
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhengyin Zhang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Shilong Fan
- Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Lulu Zhang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Fangping Han
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yikang Song
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Ling Chu
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Conggang Zhang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
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13
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Kobras CM, Monteith W, Somerville S, Delaney JM, Khan I, Brimble C, Corrigan RM, Sheppard SK, Fenton AK. Loss of Pde1 function acts as an evolutionary gateway to penicillin resistance in Streptococcus pneumoniae. Proc Natl Acad Sci U S A 2023; 120:e2308029120. [PMID: 37796984 PMCID: PMC10576035 DOI: 10.1073/pnas.2308029120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 09/05/2023] [Indexed: 10/07/2023] Open
Abstract
Streptococcus pneumoniae is a major human pathogen and rising resistance to β-lactam antibiotics, such as penicillin, is a significant threat to global public health. Mutations occurring in the penicillin-binding proteins (PBPs) can confer high-level penicillin resistance but other poorly understood genetic factors are also important. Here, we combined strictly controlled laboratory experiments and population analyses to identify a new penicillin resistance pathway that is independent of PBP modification. Initial laboratory selection experiments identified high-frequency pde1 mutations conferring S. pneumoniae penicillin resistance. The importance of variation at the pde1 locus was confirmed in natural and clinical populations in an analysis of >7,200 S. pneumoniae genomes. The pde1 mutations identified by these approaches reduce the hydrolytic activity of the Pde1 enzyme in bacterial cells and thereby elevate levels of cyclic-di-adenosine monophosphate and penicillin resistance. Our results reveal rapid de novo loss of function mutations in pde1 as an evolutionary gateway conferring low-level penicillin resistance. This relatively simple genomic change allows cells to persist in populations on an adaptive evolutionary pathway to acquire further genetic changes and high-level penicillin resistance.
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Affiliation(s)
- Carolin M. Kobras
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - William Monteith
- Department of Biology, Ineos Oxford Institute for Antimicrobial Research, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Sophie Somerville
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - James M. Delaney
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Imran Khan
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Camilla Brimble
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Rebecca M. Corrigan
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - Samuel K. Sheppard
- Department of Biology, Ineos Oxford Institute for Antimicrobial Research, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Andrew K. Fenton
- School for Biosciences, Florey Institute for Host-Pathogen Interactions, University of Sheffield, SheffieldS10 2TN, United Kingdom
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14
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Neumann P, Kloskowski P, Ficner R. Computer-aided design of a cyclic di-AMP synthesizing enzyme CdaA inhibitor. MICROLIFE 2023; 4:uqad021. [PMID: 37223749 PMCID: PMC10167629 DOI: 10.1093/femsml/uqad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/24/2023] [Accepted: 04/13/2023] [Indexed: 05/25/2023]
Abstract
Cyclic di-AMP (c-di-AMP) is an essential secondary messenger regulating cell wall homeostasis and myriads of physiological processes in several Gram-positive and mycobacteria, including human pathogens. Hence, c-di-AMP synthesizing enzymes (DACs) have become a promising antibacterial drug target. To overcome a scarcity of small molecule inhibitors of c-di-AMP synthesizing enzyme CdaA, a computer-aided design of a new compound that should block the enzyme has been performed. This has led to the identification of a molecule comprising two thiazole rings and showing inhibitory potential based on ITC measurements. Thiazole scaffold is a good pharmacophore nucleus known due to its various pharmaceutical applications. It is contained in more than 18 FDA-approved drugs as well as in dozens of experimental drugs. Hence, the designed inhibitor can serve as a potent lead compound for further development of inhibitor against CdaA.
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Affiliation(s)
- Piotr Neumann
- Corresponding author. Department of Molecular Structural Biology, Georg-August-University Goettingen, Institute of Microbiology and Genetics, GZMB, Justus-von-Liebig Weg 11, 37077 Goettingen, Germany. Tel: +495513928624; Fax: +495513928629; E-mail:
| | - Patrick Kloskowski
- Department of Molecular Structural Biology, Georg-August-University Goettingen, Institute of Microbiology and Genetics, GZMB, Justus-von-Liebig Weg 11, 37077 Goettingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Georg-August-University Goettingen, Institute of Microbiology and Genetics, GZMB, Justus-von-Liebig Weg 11, 37077 Goettingen, Germany
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15
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Du Y, Hu Z, Luo Y, Wang HY, Yu X, Wang RF. Function and regulation of cGAS-STING signaling in infectious diseases. Front Immunol 2023; 14:1130423. [PMID: 36825026 PMCID: PMC9941744 DOI: 10.3389/fimmu.2023.1130423] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/24/2023] [Indexed: 02/10/2023] Open
Abstract
The efficacious detection of pathogens and prompt induction of innate immune signaling serve as a crucial component of immune defense against infectious pathogens. Over the past decade, DNA-sensing receptor cyclic GMP-AMP synthase (cGAS) and its downstream signaling adaptor stimulator of interferon genes (STING) have emerged as key mediators of type I interferon (IFN) and nuclear factor-κB (NF-κB) responses in health and infection diseases. Moreover, both cGAS-STING pathway and pathogens have developed delicate strategies to resist each other for their survival. The mechanistic and functional comprehension of the interplay between cGAS-STING pathway and pathogens is opening the way for the development and application of pharmacological agonists and antagonists in the treatment of infectious diseases. Here, we briefly review the current knowledge of DNA sensing through the cGAS-STING pathway, and emphatically highlight the potent undertaking of cGAS-STING signaling pathway in the host against infectious pathogenic organisms.
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Affiliation(s)
- Yang Du
- Department of Medicine, and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Research Center of Medical Sciences, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Zhiqiang Hu
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Yien Luo
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Helen Y. Wang
- Department of Medicine, and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Pediatrics, Children’s Hospital, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Xiao Yu
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Single Cell Technology and Application, Southern Medical University, Guangzhou, Guangdong, China
| | - Rong-Fu Wang
- Department of Medicine, and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Pediatrics, Children’s Hospital, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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16
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Reich SJ, Goldbeck O, Lkhaasuren T, Weixler D, Weiß T, Eikmanns BJ. C-di-AMP Is a Second Messenger in Corynebacterium glutamicum That Regulates Expression of a Cell Wall-Related Peptidase via a Riboswitch. Microorganisms 2023; 11:296. [PMID: 36838266 PMCID: PMC9960051 DOI: 10.3390/microorganisms11020296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
Cyclic di-adenosine monophosphate (c-di-AMP) is a bacterial second messenger discovered in Bacillus subtilis and involved in potassium homeostasis, cell wall maintenance and/or DNA stress response. As the role of c-di-AMP has been mostly studied in Firmicutes, we sought to increase the understanding of its role in Actinobacteria, namely in Corynebacterium glutamicum. This organism is a well-known industrial production host and a model organism for pathogens, such as C. diphtheriae or Mycobacterium tuberculosis. Here, we identify and analyze the minimal set of two C. glutamicum enzymes, the diadenylate cyclase DisA and the phosphodiesterase PdeA, responsible for c-di-AMP metabolism. DisA synthesizes c-di-AMP from two molecules of ATP, whereas PdeA degrades c-di-AMP, as well as the linear degradation intermediate phosphoadenylyl-(3'→5')-adenosine (pApA) to two molecules of AMP. Here, we show that a ydaO/kimA-type c-di-AMP-dependent riboswitch controls the expression of the strictly regulated cell wall peptidase gene nlpC in C. glutamicum. In contrast to previously described members of the ydaO/kimA-type riboswitches, our results suggest that the C. glutamicum nlpC riboswitch likely affects the translation instead of the transcription of its downstream gene. Although strongly regulated by different mechanisms, we show that the absence of nlpC, the first known regulatory target of c-di-AMP in C. glutamicum, is not detrimental for this organism under the tested conditions.
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Affiliation(s)
- Sebastian J. Reich
- Institute of Microbiology and Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Oliver Goldbeck
- Institute of Microbiology and Biotechnology, Ulm University, 89081 Ulm, Germany
- Institute of Biochemistry, Department of Chemistry, University of Cologne, 50674 Cologne, Germany
| | | | - Dominik Weixler
- Institute of Microbiology and Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Tamara Weiß
- Institute of Microbiology and Biotechnology, Ulm University, 89081 Ulm, Germany
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Wu X, Qi M, Liu C, Yang Q, Li S, Shi F, Sun X, Wang L, Li C, Dong B. Near-infrared light-triggered nitric oxide nanocomposites for photodynamic/photothermal complementary therapy against periodontal biofilm in an animal model. Theranostics 2023; 13:2350-2367. [PMID: 37153739 PMCID: PMC10157734 DOI: 10.7150/thno.83745] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/12/2023] [Indexed: 05/10/2023] Open
Abstract
Background: Periodontal disease, an oral disease that initiates with plaque biofilm infection, affects 10% of the global population. Due to the complexity of tooth root anatomy, biofilm resistance and antibiotic resistance, traditional mechanical debridement and antibiotic removal of biofilms are not ideal. Nitric oxide (NO) gas therapy and its multifunctional therapy are effective methods to clear biofilms. However, large and controlled delivery of NO gas molecules is currently a great challenge. Methods: The core-shell structure of Ag2S@ZIF-90/Arg/ICG was developed and characterized in detail. The ability of Ag2S@ZIF-90/Arg/ICG to produce heat, ROS and NO under 808 nm NIR excitation was detected by an infrared thermal camera, probes and Griess assay. In vitro anti-biofilm effects were evaluated by CFU, Dead/Live staining and MTT assays. Hematoxylin-eosin staining, Masson staining and immunofluorescence staining were used to analyze the therapeutic effects in vivo. Results: Antibacterial photothermal therapy (aPTT) and antibacterial photodynamic therapy (aPDT) could be excited by 808 nm NIR light, and the produced heat and ROS further triggered the release of NO gas molecules simultaneously. The antibiofilm effect had a 4-log reduction in vitro. The produced NO caused biofilm dispersion through the degradation of the c-di-AMP pathway and improved biofilm eradication performance. In addition, Ag2S@ZIF-90/Arg/ICG had the best therapeutic effect on periodontitis and NIR II imaging ability in vivo. Conclusions: We successfully prepared a novel nanocomposite with NO synergistic aPTT and aPDT. It had an outstanding therapeutic effect in treating deep tissue biofilm infection. This study not only enriches the research on compound therapy with NO gas therapy but also provides a new solution for other biofilm infection diseases.
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Affiliation(s)
- Xiangrong Wu
- Department of Prosthodontics, Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, School and Hospital of Stomatology, Jilin University, Changchun, 130021, P. R. China
| | - Manlin Qi
- Department of Prosthodontics, Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, School and Hospital of Stomatology, Jilin University, Changchun, 130021, P. R. China
| | - Chengyu Liu
- Department of Prosthodontics, Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, School and Hospital of Stomatology, Jilin University, Changchun, 130021, P. R. China
| | - Qijing Yang
- Department of Prosthodontics, Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, School and Hospital of Stomatology, Jilin University, Changchun, 130021, P. R. China
| | - Sijia Li
- Department of Prosthodontics, Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, School and Hospital of Stomatology, Jilin University, Changchun, 130021, P. R. China
| | - Fangyu Shi
- Department of Prosthodontics, Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, School and Hospital of Stomatology, Jilin University, Changchun, 130021, P. R. China
| | - Xiaolin Sun
- Department of Prosthodontics, Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, School and Hospital of Stomatology, Jilin University, Changchun, 130021, P. R. China
| | - Lin Wang
- Department of Prosthodontics, Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, School and Hospital of Stomatology, Jilin University, Changchun, 130021, P. R. China
- ✉ Corresponding authors: Prof. Chunyan Li, ; Prof. Biao Dong, ; Prof. Lin Wang,
| | - Chunyan Li
- Department of Prosthodontics, Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, School and Hospital of Stomatology, Jilin University, Changchun, 130021, P. R. China
- ✉ Corresponding authors: Prof. Chunyan Li, ; Prof. Biao Dong, ; Prof. Lin Wang,
| | - Biao Dong
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, 130012, P. R. China
- ✉ Corresponding authors: Prof. Chunyan Li, ; Prof. Biao Dong, ; Prof. Lin Wang,
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18
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Weiss CA, Myers TM, Wu CH, Jenkins C, Sondermann H, Lee V, Winkler WC. NrnA is a 5'-3' exonuclease that processes short RNA substrates in vivo and in vitro. Nucleic Acids Res 2022; 50:12369-12388. [PMID: 36478094 PMCID: PMC9757072 DOI: 10.1093/nar/gkac1091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 10/25/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Bacterial RNases process RNAs until only short oligomers (2-5 nucleotides) remain, which are then processed by one or more specialized enzymes until only nucleoside monophosphates remain. Oligoribonuclease (Orn) is an essential enzyme that acts in this capacity. However, many bacteria do not encode for Orn and instead encode for NanoRNase A (NrnA). Yet, the catalytic mechanism, cellular roles and physiologically relevant substrates have not been fully resolved for NrnA proteins. We herein utilized a common set of reaction assays to directly compare substrate preferences exhibited by NrnA-like proteins from Bacillus subtilis, Enterococcus faecalis, Streptococcus pyogenes and Mycobacterium tuberculosis. While the M. tuberculosis protein specifically cleaved cyclic di-adenosine monophosphate, the B. subtilis, E. faecalis and S. pyogenes NrnA-like proteins uniformly exhibited striking preference for short RNAs between 2-4 nucleotides in length, all of which were processed from their 5' terminus. Correspondingly, deletion of B. subtilis nrnA led to accumulation of RNAs between 2 and 4 nucleotides in length in cellular extracts. Together, these data suggest that many Firmicutes NrnA-like proteins are likely to resemble B. subtilis NrnA to act as a housekeeping enzyme for processing of RNAs between 2 and 4 nucleotides in length.
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Affiliation(s)
| | | | - Chih Hao Wu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Conor Jenkins
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Holger Sondermann
- CSSB – Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany,Christian-Albrechts-Universität, 24118 Kiel, Germany
| | - Vincent T Lee
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Wade C Winkler
- To whom correspondence should be addressed. Tel: +1 301 405 7780;
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吴 沁, 彭 显, 周 学. [Advances in Research on the Role of Bacterial c-di-AMP in Host Immunity]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2022; 53:1098-1103. [PMID: 36443059 PMCID: PMC10408971 DOI: 10.12182/20220860102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Indexed: 06/16/2023]
Abstract
Cyclic dimeric adenosine 3',5'-monophosphate (c-di-AMP) is a newly-discovered second messenger in bacteria and archaea. By directly binding to or affecting the expression of target proteins, c-di-AMP regulates the physiological functions of bacteria, including maintaining osmotic pressure, balancing central metabolism, monitoring DNA damage, and controlling biofilm and spore formation. As a new pathogen-associated molecular pattern (PAMP), it binds to the host pattern recognition receptor (PRR), induces cyclic GMP-AMP synthase (cGAS)-STING signal axis to produce type Ⅰ interferon by activating the stimulator of interferon genes (STING), and promotes the secretion of inflammatory factors through nuclear factor κB (NF-κB) signaling pathway, thereby playing an important role in host immunity to bacterial infection and tumorigenesis. Due to its immunogenicity, c-di-AMP could be used as an immune adjuvant to provide new targets for the development of vaccines. However, the specific mechanism of action of c-di-AMP in host immunity awaits further exploration. Herein, we presented the structure and biological characteristics of c-di-AMP, and summarized the possible mechanism of c-di-AMP's regulation of host immune response. In addition, we also reported the latest findings on using c-di-AMP as an immune adjuvant in clinical treatment. Research on the function of c-di-AMP and its mechanism of action on host immune response provides new ideas for finding clinical solutions to bacterial resistance, infection control, tumor prevention, and vaccine development in the future.
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Affiliation(s)
- 沁蕊 吴
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 牙体牙髓病科 (成都 610041)State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Dental and Endodontic Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - 显 彭
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 牙体牙髓病科 (成都 610041)State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Dental and Endodontic Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - 学东 周
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 牙体牙髓病科 (成都 610041)State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Dental and Endodontic Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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20
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Hou X, Rong C, Zhang Q, Song S, Cong Y, Zhang HT. Cyclic Nucleotide Phosphodiesterases in Alcohol Use Disorders: Involving Gut Microbiota. Int J Neuropsychopharmacol 2022; 26:70-79. [PMID: 36087271 PMCID: PMC9850663 DOI: 10.1093/ijnp/pyac060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 08/18/2022] [Accepted: 09/09/2022] [Indexed: 01/22/2023] Open
Abstract
Alcohol abuse is 1 of the most significant public health problems in the world. Chronic, excessive alcohol consumption not only causes alcohol use disorder (AUD) but also changes the gut and lung microbiota, including bacterial and nonbacterial types. Both types of microbiota can release toxins, further damaging the gastrointestinal and respiratory tracts; causing inflammation; and impairing the functions of the liver, lung, and brain, which in turn deteriorate AUD. Phosphodiesterases (PDEs) are critical in the control of intracellular cyclic nucleotides, including cyclic adenosine monophosphate and cyclic guanosine monophosphate. Inhibition of certain host PDEs reduces alcohol consumption and attenuates alcohol-related impairment. These PDEs are also expressed in the microbiota and may play a role in controlling microbiota-associated inflammation. Here, we summarize the influences of alcohol on gut/lung bacterial and nonbacterial microbiota as well as on the gut-liver/brain/lung axis. We then discuss the relationship between gut and lung microbiota-mediated PDE signaling and AUD consequences in addition to highlighting PDEs as potential targets for treatment of AUD.
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Affiliation(s)
- Xueqin Hou
- Correspondence: Xueqin Hou, PhD, Institute of Pharmacology, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, Shandong 271016, P.R. China ()
| | | | - Qiwei Zhang
- Institute of Pharmacology, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, Shandong 271016, P.R. China
| | - Shuangshuang Song
- Institute of Pharmacology, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, Shandong 271016, P.R. China
| | - Yifan Cong
- Institute of Pharmacology, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, Shandong 271016, P.R. China
| | - Han-Ting Zhang
- Han-Ting Zhang, MD, PhD, Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao, Shandong 266073, P.R. China ()
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21
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Oberkampf M, Hamiot A, Altamirano-Silva P, Bellés-Sancho P, Tremblay YDN, DiBenedetto N, Seifert R, Soutourina O, Bry L, Dupuy B, Peltier J. c-di-AMP signaling is required for bile salt resistance, osmotolerance, and long-term host colonization by Clostridioides difficile. Sci Signal 2022; 15:eabn8171. [PMID: 36067333 PMCID: PMC9831359 DOI: 10.1126/scisignal.abn8171] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
To colonize the host and cause disease, the human enteropathogen Clostridioides difficile must sense, respond, and adapt to the harsh environment of the gastrointestinal tract. We showed that the production and degradation of cyclic diadenosine monophosphate (c-di-AMP) were necessary during different phases of C. difficile growth, environmental adaptation, and infection. The production of this nucleotide second messenger was essential for growth because it controlled the uptake of potassium and also contributed to biofilm formation and cell wall homeostasis, whereas its degradation was required for osmotolerance and resistance to detergents and bile salts. The c-di-AMP binding transcription factor BusR repressed the expression of genes encoding the compatible solute transporter BusAA-AB. Compared with the parental strain, a mutant lacking BusR was more resistant to hyperosmotic and bile salt stresses, whereas a mutant lacking BusAA was more susceptible. A short exposure of C. difficile cells to bile salts decreased intracellular c-di-AMP concentrations, suggesting that changes in membrane properties induce alterations in the intracellular c-di-AMP concentration. A C. difficile strain that could not degrade c-di-AMP failed to persist in a mouse gut colonization model as long as the wild-type strain did. Thus, the production and degradation of c-di-AMP in C. difficile have pleiotropic effects, including the control of osmolyte uptake to confer osmotolerance and bile salt resistance, and its degradation is important for host colonization.
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Affiliation(s)
- Marine Oberkampf
- Institut Pasteur, Université Paris Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France
| | - Audrey Hamiot
- Institut Pasteur, Université Paris Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France
| | - Pamela Altamirano-Silva
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Paula Bellés-Sancho
- Institut Pasteur, Université Paris Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France
| | - Yannick D. N. Tremblay
- Institut Pasteur, Université Paris Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France
| | - Nicholas DiBenedetto
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Roland Seifert
- Institute of Pharmacology and Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Olga Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Clinical Microbiology Laboratory, Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Bruno Dupuy
- Institut Pasteur, Université Paris Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France
| | - Johann Peltier
- Institut Pasteur, Université Paris Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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22
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Cheng X, Ning J, Xu X, Zhou X. The role of bacterial cyclic di-adenosine monophosphate in the host immune response. Front Microbiol 2022; 13:958133. [PMID: 36106081 PMCID: PMC9465037 DOI: 10.3389/fmicb.2022.958133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
Cyclic di-adenosine monophosphate (c-di-AMP) is a second messenger which is widely used in signal transduction in bacteria and archaea. c-di-AMP plays an important role in the regulation of bacterial physiological activities, such as the cell cycle, cell wall stability, environmental stress response, and biofilm formation. Moreover, c-di-AMP produced by pathogens can be recognized by host cells for the activation of innate immune responses. It can induce type I interferon (IFN) response in a stimulator of interferon genes (STING)-dependent manner, activate the nuclear factor kappa B (NF-κB) pathway, inflammasome, and host autophagy, and promote the production and secretion of cytokines. In addition, c-di-AMP is capable of triggering a host mucosal immune response as a mucosal adjuvant. Therefore, c-di-AMP is now considered to be a new pathogen-associated molecular pattern in host immunity and has become a promising target in bacterial/viral vaccine and drug research. In this review, we discussed the crosstalk between bacteria and host immunity mediated by c-di-AMP and addressed the role of c-di-AMP as a mucosal adjuvant in boosting evoked immune responses of subunit vaccines. The potential application of c-di-AMP in immunomodulation and immunotherapy was also discussed in this review.
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Affiliation(s)
- Xingqun Cheng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jia Ning
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin, China
| | - Xin Xu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Xuedong Zhou,
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23
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Lee VT, Sondermann H, Winkler WC. Nano-RNases: oligo- or dinucleases? FEMS Microbiol Rev 2022; 46:6677394. [PMID: 36026528 PMCID: PMC9779919 DOI: 10.1093/femsre/fuac038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 07/28/2022] [Accepted: 08/24/2022] [Indexed: 01/07/2023] Open
Abstract
Diribonucleotides arise from two sources: turnover of RNA transcripts (rRNA, tRNA, mRNA, and others) and linearization of cyclic-di-nucleotide signaling molecules. In both cases, there appears to be a requirement for a dedicated set of enzymes that will cleave these diribonucleotides into mononucleotides. The first enzyme discovered to mediate this activity is oligoribonuclease (Orn) from Escherichia coli. In addition to being the enzyme that cleaves dinucleotides and potentially other short oligoribonucleotides, Orn is also the only known exoribonuclease enzyme that is essential for E. coli, suggesting that removal of the shortest RNAs is an essential cellular function. Organisms naturally lacking the orn gene encode other nanoRNases (nrn) that can complement the conditional E. coli orn mutant. This review covers the history and recent advances in our understanding of these enzymes and their substrates. In particular, we focus on (i) the sources of diribonucleotides; (ii) the discovery of exoribonucleases; (iii) the structural features of Orn, NrnA/NrnB, and NrnC; (iv) the enzymatic activity of these enzymes against diribonucleotides versus other substrates; (v) the known physiological consequences of accumulation of linear dinucleotides; and (vi) outstanding biological questions for diribonucleotides and diribonucleases.
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24
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Ning H, Kang J, Lu Y, Liang X, Zhou J, Ren R, Zhou S, Zhao Y, Xie Y, Bai L, Zhang L, Kang Y, Gao X, Xu M, Ma Y, Zhang F, Bai Y. Cyclic di-AMP as endogenous adjuvant enhanced BCG-induced trained immunity and protection against Mycobacterium tuberculosis in mice. Front Immunol 2022; 13:943667. [PMID: 36081510 PMCID: PMC9445367 DOI: 10.3389/fimmu.2022.943667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Bacillus Calmette-Guérin (BCG) is a licensed prophylactic vaccine against tuberculosis (TB). Current TB vaccine efforts focus on improving BCG effects through recombination or genetic attenuation and/or boost with different vaccines. Recent years, it was revealed that BCG could elicit non-specific heterogeneous protection against other pathogens such as viruses through a process termed trained immunity. Previously, we constructed a recombinant BCG (rBCG-DisA) with elevated c-di-AMP as endogenous adjuvant by overexpressing di-adenylate cyclase of Mycobacterium tuberculosis DisA, and found that rBCG-DisA induced enhanced immune responses by subcutaneous route in mice after M. tuberculosis infection. In this study, splenocytes from rBCG-DisA immunized mice by intravenous route (i.v) elicited greater proinflammatory cytokine responses to homologous and heterologous re-stimulations than BCG. After M. tuberculosis infection, rBCG-DisA immunized mice showed hallmark responses of trained immunity including potent proinflammatory cytokine responses, enhanced epigenetic changes, altered lncRNA expressions and metabolic rewiring in bone marrow cells and other tissues. Moreover, rBCG-DisA immunization induced higher levels of antibodies and T cells responses in the lung and spleen of mice after M. tuberculosis infection. It was found that rBCG-DisA resided longer than BCG in the lung of M. tuberculosis infected mice implying prolonged duration of vaccine efficacy. Then, we found that rBCG-DisA boosting could prolong survival of BCG-primed mice over 90 weeks against M. tuberculosis infection. Our findings provided in vivo experimental evidence that rBCG-DisA with c-di-AMP as endogenous adjuvant induced enhanced trained immunity and adaptive immunity. What’s more, rBCG-DisA showed promising potential in prime-boost strategy against M. tuberculosis infection in adults.
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Affiliation(s)
- Huanhuan Ning
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
| | - Jian Kang
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
| | - Yanzhi Lu
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
| | - Xuan Liang
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
- College of Life Sciences, Northwest University, Xi’an, China
| | - Jie Zhou
- Department of Endocrinology, Xijing Hospital, Air Force Medical University, Xi’an, China
| | - Rui Ren
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
| | - Shan Zhou
- Department of Clinical Laboratory, Xijing Hospital, Air Force Medical University, Xi’an, China
| | - Yong Zhao
- Laboratory Animal Center, Air Force Medical University, Xi’an, China
| | - Yanling Xie
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
- School of Life Sciences, Yan’an University, Yan’an, China
| | - Lu Bai
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
- School of Life Sciences, Yan’an University, Yan’an, China
| | - Linna Zhang
- Department of Physiology, Basic Medical School, Ningxia Medical University, Yinchuan, China
| | - Yali Kang
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
- Department of Physiology, Basic Medical School, Ningxia Medical University, Yinchuan, China
| | - Xiaojing Gao
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
- Department of Physiology, Basic Medical School, Ningxia Medical University, Yinchuan, China
| | - Mingze Xu
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
| | - Yanling Ma
- College of Life Sciences, Northwest University, Xi’an, China
| | - Fanglin Zhang
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
- *Correspondence: Yinlan Bai, ; Fanglin Zhang,
| | - Yinlan Bai
- Department of Microbiology and Pathogen Biology, School of Preclinical Medicine, Air Force Medical University, Xi’an, China
- *Correspondence: Yinlan Bai, ; Fanglin Zhang,
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25
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Lu Y, Ning H, Kang J, Bai G, Zhou L, Kang Y, Wu Z, Tian M, Zhao J, Ma Y, Bai Y. Cyclic-di-AMP Phosphodiesterase Elicits Protective Immune Responses Against Mycobacterium tuberculosis H37Ra Infection in Mice. Front Cell Infect Microbiol 2022; 12:871135. [PMID: 35811674 PMCID: PMC9256937 DOI: 10.3389/fcimb.2022.871135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Many antigens from Mycobacterium tuberculosis (M. tuberculosis) have been demonstrated as strong immunogens and proved to have application potential as vaccine candidate antigens. Cyclic di-AMP (c-di-AMP) as a bacterial second messenger regulates various bacterial processes as well as the host immune responses. Rv2837c, the c-di-AMP phosphodiesterase (CnpB), was found to be relative to virulence of M. tuberculosis and interference with host innate immune response. In this study, recombinant CnpB was administered subcutaneously to mice. We found that CnpB had strong immunogenicity and induced high levels of humoral response and lung mucosal immunity after M. tuberculosis intranasally infection. CnpB immunization stimulated splenocyte proliferation and the increasing number of activated NK cells but had little effects on Th1/Th2 cellular immune responses in spleens. However, CnpB induced significant Th1/Th2 cellular immune responses with a decreased number of T and B cells in the lungs, and significantly recruits of CD4+ and CD8+ T cells after M. tuberculosis attenuated strain H37Ra infection. Besides, we first reported that CnpB could stimulate IFN-β expression transitorily and inhibit the autophagy of macrophages in vitro. In mice intranasally infection model, CnpB immunization alleviated pathological changes and reduced M. tuberculosis H37Ra loads in the lungs. Thus, our results suggested that CnpB interferes with host innate and adaptive immune responses and confers protection against M. tuberculosis respiratory infection, which should be considered in vaccine development as well as a drug target.
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Affiliation(s)
- Yanzhi Lu
- Department of Microbiology and Pathogen Biology, Basic Medical School, Air Force Medical University, Xi’an, China
| | - Huanhuan Ning
- Department of Microbiology and Pathogen Biology, Basic Medical School, Air Force Medical University, Xi’an, China
| | - Jian Kang
- Department of Microbiology and Pathogen Biology, Basic Medical School, Air Force Medical University, Xi’an, China
| | - Guangchun Bai
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, United States
| | - Lei Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital, Air Force Medical University, Xi’an, China
| | - Yali Kang
- Department of Physiology, Basic Medical School, Ningxia Medical University, Yinchuan, China
| | - Zhengfeng Wu
- Student Brigade, Basic Medical School, Air Force Medical University, Xi’an, China
| | - Maolin Tian
- Student Brigade, Basic Medical School, Air Force Medical University, Xi’an, China
| | - Junhao Zhao
- Student Brigade, Basic Medical School, Air Force Medical University, Xi’an, China
| | - Yueyun Ma
- Department of Clinical Laboratory, The First Affiliated Hospital, Air Force Medical University, Xi’an, China
- Department of Clinical Laboratory, Air Force Medical Center, Air Force Medical University, Beijing, China
- *Correspondence: Yinlan Bai, ; Yueyun Ma,
| | - Yinlan Bai
- Department of Microbiology and Pathogen Biology, Basic Medical School, Air Force Medical University, Xi’an, China
- *Correspondence: Yinlan Bai, ; Yueyun Ma,
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26
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Wang M, Wamp S, Gibhardt J, Holland G, Schwedt I, Schmidtke KU, Scheibner K, Halbedel S, Commichau FM. Adaptation of Listeria monocytogenes to perturbation of c-di-AMP metabolism underpins its role in osmoadaptation and identifies a fosfomycin uptake system. Environ Microbiol 2022; 24:4466-4488. [PMID: 35688634 DOI: 10.1111/1462-2920.16084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/25/2022] [Indexed: 11/29/2022]
Abstract
The human pathogen Listeria monocytogenes synthesizes and degrades c-di-AMP using the diadenylate cyclase CdaA and the phosphodiesterases PdeA and PgpH respectively. c-di-AMP is essential because it prevents the uncontrolled uptake of osmolytes. Here, we studied the phenotypes of cdaA, pdeA, pgpH and pdeA pgpH mutants with defects in c-di-AMP metabolism and characterized suppressor mutants restoring their growth defects. The characterization of the pdeA pgpH mutant revealed that the bacteria show growth defects in defined medium, a phenotype that is invariably suppressed by mutations in cdaA. The previously reported growth defect of the cdaA mutant in rich medium is suppressed by mutations that osmotically stabilize the c-di-AMP-free strain. We also found that the cdaA mutant has an increased sensitivity against isoleucine. The isoleucine-dependent growth inhibition of the cdaA mutant is suppressed by codY mutations that likely reduce the DNA-binding activity of encoded CodY variants. Moreover, the characterization of the cdaA suppressor mutants revealed that the Opp oligopeptide transport system is involved in the uptake of the antibiotic fosfomycin. In conclusion, the suppressor analysis corroborates a key function of c-di-AMP in controlling osmolyte homeostasis in L. monocytogenes.
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Affiliation(s)
- Mengyi Wang
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany.,Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany.,FG Molecular Microbiology, Institute of Biology, University of Hohenheim, 70599, Stuttgart, Germany
| | - Sabrina Wamp
- Division of Enteropathogenic Bacteria and Legionella, Robert-Koch-Institute, 38855, Wernigerode, Germany
| | - Johannes Gibhardt
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany.,Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany.,Research Complex NanoBio, Peter the Great Saint Petersburg Polytechnic University, Politekhnicheskaya ulitsa 29A, Saint Petersburg, 195251, Russia
| | - Gudrun Holland
- ZBS4 - Advanced Light and Electron Microscopy, Robert-Koch-Institute, Seestraße 10, 13353, Berlin, Germany
| | - Inge Schwedt
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany.,FG Molecular Microbiology, Institute of Biology, University of Hohenheim, 70599, Stuttgart, Germany
| | - Kai-Uwe Schmidtke
- FG Enzyme Technology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany
| | - Katrin Scheibner
- FG Enzyme Technology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany
| | - Sven Halbedel
- Division of Enteropathogenic Bacteria and Legionella, Robert-Koch-Institute, 38855, Wernigerode, Germany
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany.,FG Molecular Microbiology, Institute of Biology, University of Hohenheim, 70599, Stuttgart, Germany
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Zhang Y, Xu Z, Luo H, Hao X, Li M. 细菌c-di-AMP特异性磷酸二酯酶的研究进展. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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New Mechanistic Insights into Purine Biosynthesis with Second Messenger c-di-AMP in Relation to Biofilm-Related Persistent Methicillin-Resistant Staphylococcus aureus Infections. mBio 2021; 12:e0208121. [PMID: 34724823 PMCID: PMC8561390 DOI: 10.1128/mbio.02081-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Persistent methicillin-resistant Staphylococcus aureus (MRSA) endovascular infections represent a significant clinically challenging subset of invasive, life-threatening S. aureus infections. We have recently demonstrated that purine biosynthesis plays an important role in such persistent infections. Cyclic di-AMP (c-di-AMP) is an essential and ubiquitous second messenger that regulates many cellular pathways in bacteria. However, whether there is a regulatory connection between the purine biosynthesis pathway and c-di-AMP impacting persistent outcomes was not known. Here, we demonstrated that the purine biosynthesis mutant MRSA strain, the ΔpurF strain (compared to its isogenic parental strain), exhibited the following significant differences in vitro: (i) lower ADP, ATP, and c-di-AMP levels; (ii) less biofilm formation with decreased extracellular DNA (eDNA) levels and Triton X-100-induced autolysis paralleling enhanced expressions of the biofilm formation-related two-component regulatory system lytSR and its downstream gene lrgB; (iii) increased vancomycin (VAN)-binding and VAN-induced lysis; and (iv) decreased wall teichoic acid (WTA) levels and expression of the WTA biosynthesis-related gene, tarH. Substantiating these data, the dacA (encoding diadenylate cyclase enzyme required for c-di-AMP synthesis) mutant strain (dacAG206S strain versus its isogenic wild-type MRSA and dacA-complemented strains) showed significantly decreased c-di-AMP levels, similar in vitro effects as seen above for the purF mutant and hypersusceptible to VAN treatment in an experimental biofilm-related MRSA endovascular infection model. These results reveal an important intersection between purine biosynthesis and c-di-AMP that contributes to biofilm-associated persistence in MRSA endovascular infections. This signaling pathway represents a logical therapeutic target against persistent MRSA infections.
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Mudgal S, Manikandan K, Mukherjee A, Krishnan A, Sinha KM. Cyclic di-AMP: Small molecule with big roles in bacteria. Microb Pathog 2021; 161:105264. [PMID: 34715302 DOI: 10.1016/j.micpath.2021.105264] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/20/2021] [Accepted: 10/21/2021] [Indexed: 01/15/2023]
Abstract
Cyclic dinucleotides are second messengers that are present in all the three domains of life, bacteria, archaea, and eukaryotes. These dinucleotides have important physiological and pathophysiological roles in bacteria. Cyclic di-AMP (cdA) is one of the recently discovered cyclic dinucleotides present predominantly in gram-positive bacteria. cdA is synthesized through diadenylate cyclase (DAC) activity from ATP in a two-step process and hydrolyzed to linear dinucleotide pApA (and to 5' AMP in certain cases) by specific phosphodiesterases. cdA regulates various physiological processes like K+ transport and osmotic balance, DNA repair, cell wall homeostasis, drug resistance, central metabolism either by binding directly to the target protein or regulating its expression. It also participates in host-pathogen interaction by binding to host immune receptors ERAdP, RECON, and STING.
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Affiliation(s)
- Sudhanshu Mudgal
- Amity Institute of Biotechnology, Amity University Haryana, Haryana, India
| | - Kasi Manikandan
- Amity Institute of Biotechnology, Amity University Haryana, Haryana, India
| | - Ahana Mukherjee
- Amity Institute of Biotechnology, Amity University Haryana, Haryana, India
| | - Anuja Krishnan
- Department of Molecular Medicine, Jamia Hamdard, New Delhi, India.
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Kundra S, Lam LN, Kajfasz JK, Casella LG, Andersen MJ, Abranches J, Flores-Mireles AL, Lemos JA. c-di-AMP Is Essential for the Virulence of Enterococcus faecalis. Infect Immun 2021; 89:e0036521. [PMID: 34424750 PMCID: PMC8519298 DOI: 10.1128/iai.00365-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/11/2021] [Indexed: 12/12/2022] Open
Abstract
Second messenger nucleotides are produced by bacteria in response to environmental stimuli and play a major role in the regulation of processes associated with bacterial fitness, including but not limited to osmoregulation, envelope homeostasis, central metabolism, and biofilm formation. In this study, we uncovered the biological significance of c-di-AMP in the opportunistic pathogen Enterococcus faecalis by isolating and characterizing strains lacking genes responsible for c-di-AMP synthesis (cdaA) and degradation (dhhP and gdpP). Using complementary approaches, we demonstrated that either complete loss of c-di-AMP (ΔcdaA strain) or c-di-AMP accumulation (ΔdhhP, ΔgdpP, and ΔdhhP ΔgdpP strains) drastically impaired general cell fitness and virulence of E. faecalis. In particular, the ΔcdaA strain was highly sensitive to envelope-targeting antibiotics, was unable to multiply and quickly lost viability in human serum or urine ex vivo, and was virtually avirulent in an invertebrate (Galleria mellonella) and in two catheter-associated mouse infection models that recapitulate key aspects of enterococcal infections in humans. In addition to evidence linking these phenotypes to altered activity of metabolite and peptide transporters and inability to maintain osmobalance, we found that the attenuated virulence of the ΔcdaA strain also could be attributed to a defect in Ebp pilus production and activity that severely impaired biofilm formation under both in vitro and in vivo conditions. Collectively, these results demonstrate that c-di-AMP signaling is essential for E. faecalis pathogenesis and a desirable target for drug development.
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Affiliation(s)
- Shivani Kundra
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Ling Ning Lam
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Jessica K. Kajfasz
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Leila G. Casella
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Marissa J. Andersen
- Department of Biological Sciences, University of Norte Dame, Notre Dame, Indiana, USA
| | - Jacqueline Abranches
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Ana L. Flores-Mireles
- Department of Biological Sciences, University of Norte Dame, Notre Dame, Indiana, USA
| | - José A. Lemos
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
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31
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Bandera AM, Bartho J, Lammens K, Drexler DJ, Kleinschwärzer J, Hopfner KP, Witte G. BusR senses bipartite DNA binding motifs by a unique molecular ruler architecture. Nucleic Acids Res 2021; 49:10166-10177. [PMID: 34432045 PMCID: PMC8517857 DOI: 10.1093/nar/gkab736] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/27/2021] [Accepted: 08/12/2021] [Indexed: 12/18/2022] Open
Abstract
The cyclic dinucleotide second messenger c-di-AMP is a major player in regulation of potassium homeostasis and osmolyte transport in a variety of bacteria. Along with various direct interactions with proteins such as potassium channels, the second messenger also specifically binds to transcription factors, thereby altering the processes in the cell on the transcriptional level. We here describe the structural and biochemical characterization of BusR from the human pathogen Streptococcus agalactiae. BusR is a member of a yet structurally uncharacterized subfamily of the GntR family of transcription factors that downregulates transcription of the genes for the BusA (OpuA) glycine-betaine transporter upon c-di-AMP binding. We report crystal structures of full-length BusR, its apo and c-di-AMP bound effector domain, as well as cryo-EM structures of BusR bound to its operator DNA. Our structural data, supported by biochemical and biophysical data, reveal that BusR utilizes a unique domain assembly with a tetrameric coiled-coil in between the binding platforms, serving as a molecular ruler to specifically recognize a 22 bp separated bipartite binding motif. Binding of c-di-AMP to BusR induces a shift in equilibrium from an inactivated towards an activated state that allows BusR to bind the target DNA, leading to transcriptional repression.
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Affiliation(s)
- Adrian M Bandera
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Joseph Bartho
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Katja Lammens
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - David Jan Drexler
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Jasmin Kleinschwärzer
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Karl-Peter Hopfner
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Gregor Witte
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, D-81377 München, Germany
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32
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Rørvik GH, Naemi A, Edvardsen PKT, Simm R. The c-di-AMP signaling system influences stress tolerance and biofilm formation of Streptococcus mitis. Microbiologyopen 2021; 10:e1203. [PMID: 34459556 PMCID: PMC8289670 DOI: 10.1002/mbo3.1203] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/07/2021] [Accepted: 05/14/2021] [Indexed: 11/16/2022] Open
Abstract
Streptococcus mitis is a commensal bacterial species of the oral cavity, with the potential for opportunistic pathogenesis. For successful colonization, S. mitis must be able to adhere to surfaces of the oral cavity and survive and adapt to frequently changing environmental conditions. Cyclic-di-AMP (c-di-AMP) is a nucleotide second messenger, involved in the regulation of stress responses and biofilm formation in several bacterial species. Cyclic-di-AMP is produced by diadenylate cyclases and degraded by phosphodiesterases. We have previously shown that in S. mitis, one diadenylate cyclase (CdaA) and at least two phosphodiesterases (Pde1 and Pde2) regulate the intracellular concentration of c-di-AMP. In this study, we utilized S. mitis deletion mutants of cdaA, pde1, and pde2 to analyze the role of c-di-AMP signaling in various stress responses, biofilm formation, and adhesion to eukaryotic cells. Here, we demonstrate that the Δpde1 mutant displayed a tendency toward increased susceptibility to acetic acid at pH 4.0. Deletion of cdaA increases auto-aggregation of S. mitis but reduces biofilm formation on an abiotic surface. These phenotypes are more pronounced under acidic extracellular conditions. Inactivation of pde1 or pde2 reduced the tolerance to ciprofloxacin, and UV radiation and the Δpde1 mutant was more susceptible to Triton X-100, indicating a role for c-di-AMP signaling in responses to DNA damage and cell membrane perturbation. Finally, the Δpde2 mutant displayed a tendency toward a reduced ability to adhere to oral keratinocytes. Taken together, our results indicate an important role for c-di-AMP signaling in cellular processes important for colonization of the mouth.
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Affiliation(s)
| | | | - Per Kristian Thorén Edvardsen
- Institute of Oral BiologyUniversity of OsloOsloNorway
- Present address:
Faculty of Chemistry, Biotechnology and Food ScienceNorwegian University of Life SciencesÅsNorway
| | - Roger Simm
- Institute of Oral BiologyUniversity of OsloOsloNorway
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33
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A rationally designed c-di-AMP FRET biosensor to monitor nucleotide dynamics. J Bacteriol 2021; 203:e0008021. [PMID: 34309402 DOI: 10.1128/jb.00080-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3'3'-cyclic di-adenosine monophosphate (c-di-AMP) is an important nucleotide second messenger found throughout the bacterial domain of life. C-di-AMP is essential in many bacteria and regulates a diverse array of effector proteins controlling pathogenesis, cell wall homeostasis, osmoregulation, and central metabolism. Despite the ubiquity and importance of c-di-AMP, methods to detect this signaling molecule are limited, particularly at single cell resolution. In this work, crystallization of the Listeria monocytogenes c-di-AMP effector protein Lmo0553 enabled structure guided design of a Förster resonance energy transfer (FRET) based biosensor, which we have named CDA5. CDA5 is a fully genetically encodable, specific, and reversible biosensor which allows for the detection of c-di-AMP dynamics both in vitro and within live cells in a nondestructive manner. Our initial studies identify a distribution of c-di-AMP in Bacillus subtilis populations first grown in Luria Broth and then resuspended in diluted Luria Broth compatible with florescence analysis. Furthermore, we find that B. subtilis mutants lacking either a c-di-AMP phosphodiesterase or cyclase have respectively higher and lower FRET responses. These findings provide novel insight into the c-di-AMP distribution within bacterial populations and establish CDA5 as a powerful platform for characterizing new aspects of c-di-AMP regulation. Importance C-di-AMP is an important nucleotide second messenger for which detection methods are severely limited. In this work we engineer and implement a c-di-AMP specific FRET biosensor to remedy this dearth. We present this biosensor, CDA5, as a versatile tool to investigate previously intractable facets of c-di-AMP biology.
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Abstract
Potassium is an essential mineral nutrient required by all living cells for normal physiological function. Therefore, maintaining intracellular potassium homeostasis during bacterial infection is a requirement for the survival of both host and pathogen. However, pathogenic bacteria require potassium transport to fulfill nutritional and chemiosmotic requirements, and potassium has been shown to directly modulate virulence gene expression, antimicrobial resistance, and biofilm formation. Host cells also require potassium to maintain fundamental biological processes, such as renal function, muscle contraction, and neuronal transmission; however, potassium flux also contributes to critical immunological and antimicrobial processes, such as cytokine production and inflammasome activation. Here, we review the role and regulation of potassium transport and signaling during infection in both mammalian and bacterial cells and highlight the importance of potassium to the success and survival of each organism.
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35
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Bosma EF, Rau MH, van Gijtenbeek LA, Siedler S. Regulation and distinct physiological roles of manganese in bacteria. FEMS Microbiol Rev 2021; 45:6284802. [PMID: 34037759 PMCID: PMC8632737 DOI: 10.1093/femsre/fuab028] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
Manganese (Mn2+) is an essential trace element within organisms spanning the entire tree of life. In this review, we provide an overview of Mn2+ transport and the regulation of its homeostasis in bacteria, with a focus on its functions beyond being a cofactor for enzymes. Crucial differences in Mn2+ homeostasis exist between bacterial species that can be characterized to have an iron- or manganese-centric metabolism. Highly iron-centric species require minimal Mn2+ and mostly use it as a mechanism to cope with oxidative stress. As a consequence, tight regulation of Mn2+ uptake is required, while organisms that use both Fe2+ and Mn2+ need other layers of regulation for maintaining homeostasis. We will focus in detail on manganese-centric bacterial species, in particular lactobacilli, that require little to no Fe2+ and use Mn2+ for a wider variety of functions. These organisms can accumulate extraordinarily high amounts of Mn2+ intracellularly, enabling the nonenzymatic use of Mn2+ for decomposition of reactive oxygen species while simultaneously functioning as a mechanism of competitive exclusion. We further discuss how Mn2+ accumulation can provide both beneficial and pathogenic bacteria with advantages in thriving in their niches.
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Affiliation(s)
- Elleke F Bosma
- Chr. Hansen A/S, Discovery, R&D, 2970 Hoersholm, Denmark
| | - Martin H Rau
- Chr. Hansen A/S, Discovery, R&D, 2970 Hoersholm, Denmark
| | | | - Solvej Siedler
- Corresponding author: Boege Allé 10-12, 2970 Hoersholm, Denmark. Tel: +45 52 18 08 25; E-mail:
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36
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The Diadenylate Cyclase CdaA Is Critical for Borrelia turicatae Virulence and Physiology. Infect Immun 2021; 89:IAI.00787-20. [PMID: 33846120 PMCID: PMC8316131 DOI: 10.1128/iai.00787-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/22/2021] [Indexed: 12/16/2022] Open
Abstract
Relapsing fever (RF), caused by spirochetes of the genus Borrelia, is a globally distributed, vector-borne disease with high prevalence in developing countries. To date, signaling pathways required for infection and virulence of RF Borrelia spirochetes are unknown. Cyclic di-AMP (c-di-AMP), synthesized by diadenylate cyclases (DACs), is a second messenger predominantly found in Gram-positive organisms that is linked to virulence and essential physiological processes. Although Borrelia is Gram-negative, it encodes one DAC (CdaA), and its importance remains undefined. To investigate the contribution of c-di-AMP signaling in the RF bacterium Borrelia turicatae, a cdaA mutant was generated. The mutant was significantly attenuated during murine infection, and genetic complementation reversed this phenotype. Because c-di-AMP is essential for viability in many bacteria, whole-genome sequencing was performed on cdaA mutants, and single-nucleotide polymorphisms identified potential suppressor mutations. Additionally, conditional mutation of cdaA confirmed that CdaA is important for normal growth and physiology. Interestingly, mutation of cdaA did not affect expression of homologs of virulence regulators whose levels are impacted by c-di-AMP signaling in the Lyme disease bacterium Borrelia burgdorferi Finally, the cdaA mutant had a significant growth defect when grown with salts, at decreased osmolarity, and without pyruvate. While the salt treatment phenotype was not reversed by genetic complementation, possibly due to suppressor mutations, growth defects at decreased osmolarity and in media lacking pyruvate could be attributed directly to cdaA inactivation. Overall, these results indicate CdaA is critical for B. turicatae pathogenesis and link c-di-AMP to osmoregulation and central metabolism in RF spirochetes.
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37
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Yin W, Cai X, Ma H, Zhu L, Zhang Y, Chou SH, Galperin MY, He J. A decade of research on the second messenger c-di-AMP. FEMS Microbiol Rev 2021; 44:701-724. [PMID: 32472931 DOI: 10.1093/femsre/fuaa019] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/28/2020] [Indexed: 02/07/2023] Open
Abstract
Cyclic dimeric adenosine 3',5'-monophosphate (c-di-AMP) is an emerging second messenger in bacteria and archaea that is synthesized from two molecules of ATP by diadenylate cyclases and degraded to pApA or two AMP molecules by c-di-AMP-specific phosphodiesterases. Through binding to specific protein- and riboswitch-type receptors, c-di-AMP regulates a wide variety of prokaryotic physiological functions, including maintaining the osmotic pressure, balancing central metabolism, monitoring DNA damage and controlling biofilm formation and sporulation. It mediates bacterial adaptation to a variety of environmental parameters and can also induce an immune response in host animal cells. In this review, we discuss the phylogenetic distribution of c-di-AMP-related enzymes and receptors and provide some insights into the various aspects of c-di-AMP signaling pathways based on more than a decade of research. We emphasize the key role of c-di-AMP in maintaining bacterial osmotic balance, especially in Gram-positive bacteria. In addition, we discuss the future direction and trends of c-di-AMP regulatory network, such as the likely existence of potential c-di-AMP transporter(s), the possibility of crosstalk between c-di-AMP signaling with other regulatory systems, and the effects of c-di-AMP compartmentalization. This review aims to cover the broad spectrum of research on the regulatory functions of c-di-AMP and c-di-AMP signaling pathways.
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Affiliation(s)
- Wen Yin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xia Cai
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Hongdan Ma
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Li Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Yuling Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Shan-Ho Chou
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
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Latoscha A, Drexler DJ, Witte G, Tschowri N. Assessment of Diadenylate Cyclase and c-di-AMP-phosphodiesterase Activities Using Thin-layer and Ion Exchange Chromatography. Bio Protoc 2021; 11:e3870. [PMID: 33732760 DOI: 10.21769/bioprotoc.3870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 11/02/2022] Open
Abstract
All living cells use cyclic nucleotides as second messengers for signal sensing and transduction. Cyclic di-3',5'-adenosine monophosphate (c-di-AMP) is primarily involved in the control of bacterial and euryarcheal osmoadaptation and is produced by diadenylate cyclases from two molecules of ATP. Specific phosphodiesterases hydrolyze c-di-AMP to the linear phosphoadenylate adenosine 5'-pApA or to AMP. Different methods including high-performance liquid chromatography (HPLC), thin-layer chromatography (TLC) and ion exchange chromatography (IEX) can be used to determine activities of c-di-AMP-synthesizing and degrading enzymes. Here, we describe in detail the TLC and IEX methods adapted for characterization of the diadenylate cyclase DisA and the phosphodiesterase AtaC from Streptomyces venezuelae. TLC allows quick and easy separation of radioactive-labeled substrates and products, while IEX avoids utilization of potentially hazardous radioactive substrates and can be used as a good substitute if an HPLC system is not available. Unlike in TLC assays, samples cannot be analyzed in parallel by using the IEX assay, thus it is more time consuming.
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Affiliation(s)
- Andreas Latoscha
- Department of Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - David Jan Drexler
- Gene Center, Ludwig-Maximilians-Universität München, 81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Gregor Witte
- Gene Center, Ludwig-Maximilians-Universität München, 81377 München, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Natalia Tschowri
- Department of Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
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Dutta A, Batish M, Parashar V. Structural basis of KdpD histidine kinase binding to the second messenger c-di-AMP. J Biol Chem 2021; 296:100771. [PMID: 33989637 PMCID: PMC8214093 DOI: 10.1016/j.jbc.2021.100771] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/03/2021] [Accepted: 05/07/2021] [Indexed: 11/17/2022] Open
Abstract
The KdpDE two-component system regulates potassium homeostasis and virulence in various bacterial species. The KdpD histidine kinases (HK) of this system contain a universal stress protein (USP) domain which binds to the second messenger cyclic-di-adenosine monophosphate (c-di-AMP) for regulating transcriptional output from this two-component system in Firmicutes such as Staphylococcus aureus. However, the structural basis of c-di-AMP specificity within the KdpD-USP domain is not well understood. Here, we resolved a 2.3 Å crystal structure of the S. aureus KdpD-USP domain (USPSa) complexed with c-di-AMP. Binding affinity analyses of USPSa mutants targeting the observed USPSa:c-di-AMP structural interface enabled the identification of the sequence residues that are required for c-di-AMP specificity. Based on the conservation of these residues in other Firmicutes, we identified the binding motif, (A/G/C)XSXSX2N(Y/F), which allowed us to predict c-di-AMP binding in other KdpD HKs. Furthermore, we found that the USPSa domain contains structural features distinct from the canonical standalone USPs that bind ATP as a preferred ligand. These features include inward-facing conformations of its β1-α1 and β4-α4 loops, a short α2 helix, the absence of a triphosphate-binding Walker A motif, and a unique dual phospho-ligand binding mode. It is therefore likely that USPSa-like domains in KdpD HKs represent a novel subfamily of the USPs.
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Affiliation(s)
- Anirudha Dutta
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Mona Batish
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Vijay Parashar
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA.
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40
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The Many Roles of the Bacterial Second Messenger Cyclic di-AMP in Adapting to Stress Cues. J Bacteriol 2020; 203:JB.00348-20. [PMID: 32839175 DOI: 10.1128/jb.00348-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bacteria respond to changes in environmental conditions through adaptation to external cues. Frequently, bacteria employ nucleotide signaling molecules to mediate a specific, rapid response. Cyclic di-AMP (c-di-AMP) was recently discovered to be a bacterial second messenger that is essential for viability in many species. In this review, we highlight recent work that has described the roles of c-di-AMP in bacterial responses to various stress conditions. These studies show that depending on the lifestyle and environmental niche of the bacterial species, the c-di-AMP signaling network results in diverse outcomes, such as regulating osmolyte transport, controlling plant attachment, or providing a checkpoint for spore formation. c-di-AMP achieves this signaling specificity through expression of different classes of synthesis and catabolic enzymes as well as receptor proteins and RNAs, which will be summarized.
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c-di-AMP Accumulation Impairs Muropeptide Synthesis in Listeria monocytogenes. J Bacteriol 2020; 202:JB.00307-20. [PMID: 33020220 DOI: 10.1128/jb.00307-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/17/2020] [Indexed: 12/14/2022] Open
Abstract
Cyclic di-AMP (c-di-AMP) is an essential and ubiquitous second messenger among bacteria. c-di-AMP regulates many cellular pathways through direct binding to several molecular targets in bacterial cells. c-di-AMP depletion is well known to destabilize the bacterial cell wall, resulting in increased bacteriolysis and enhanced susceptibility to cell wall targeting antibiotics. Using the human pathogen Listeria monocytogenes as a model, we found that c-di-AMP accumulation also impaired cell envelope integrity. An L. monocytogenes mutant deleted for c-di-AMP phosphodiesterases (pdeA pgpH mutant) exhibited a 4-fold increase in c-di-AMP levels and several cell wall defects. For instance, the pdeA pgpH mutant was defective for the synthesis of peptidoglycan muropeptides and was susceptible to cell wall-targeting antimicrobials. Among different muropeptide precursors, we found that the pdeA pgpH strain was particularly impaired in the synthesis of d-Ala-d-Ala, which is required to complete the pentapeptide stem associated with UDP-N-acetylmuramic acid (MurNAc). This was consistent with an increased sensitivity to d-cycloserine, which inhibits the d-alanine branch of peptidoglycan synthesis. Finally, upon examining d-Ala:d-Ala ligase (Ddl), which catalyzes the conversion of d-Ala to d-Ala-d-Ala, we found that its activity was activated by K+ Based on previous reports that c-di-AMP inhibits K+ uptake, we propose that c-di-AMP accumulation impairs peptidoglycan synthesis, partially through the deprivation of cytoplasmic K+ levels, which are required for cell wall-synthetic enzymes.IMPORTANCE The bacterial second messenger c-di-AMP is produced by a large number of bacteria and conditionally essential to many species. Conversely, c-di-AMP accumulation is also toxic to bacterial physiology and pathogenesis, but its mechanisms are largely undefined. We found that in Listeria monocytogenes, elevated c-di-AMP levels diminished muropeptide synthesis and increased susceptibility to cell wall-targeting antimicrobials. Cell wall defects might be an important mechanism for attenuated virulence in bacteria with high c-di-AMP levels.
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Xiong ZQ, Fan YZ, Song X, Liu XX, Xia YJ, Ai LZ. The second messenger c-di-AMP mediates bacterial exopolysaccharide biosynthesis: a review. Mol Biol Rep 2020; 47:9149-9157. [PMID: 33128205 DOI: 10.1007/s11033-020-05930-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/17/2020] [Indexed: 12/13/2022]
Abstract
Cyclic dimeric adenosine 3'-5'-monophosphate (c-di-AMP) is a recently discovered nucleotide messenger in bacteria. It plays an important role in signaling, transcription, and cell physiology, such as in bacterial growth, potassium transport, fatty acid synthesis, the metabolic balance of cell wall components, and biofilm formation. Exopolysaccharides (EPSs) have distinct physico-chemical properties and diverse bioactivities including antibacterial, hypolipidemic, and antioxidative activities, and they are widely used in the food, pharmaceutical, and cosmetic industries. Although c-di-AMP has been demonstrated to regulate the biosynthesis of bacterial EPSs, only a single c-di-AMP receptor, CabpA, has been identified in EPS synthesis. With the aim of describing current understanding of the regulation of microbial EPSs, this review summarizes c-di-AMP biosynthesis and degradation as well as the mechanism through which c-di-AMP regulates bacterial EPSs.
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Affiliation(s)
- Zhi-Qiang Xiong
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Yi-Zhou Fan
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Xin Song
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Xin-Xin Liu
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Yong-Jun Xia
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Lian-Zhong Ai
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.
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Rørvik GH, Liskiewicz KA, Kryuchkov F, Naemi AO, Aasheim HC, Petersen FC, Küntziger TM, Simm R. Cyclic Di-adenosine Monophosphate Regulates Metabolism and Growth in the Oral Commensal Streptococcus mitis. Microorganisms 2020; 8:microorganisms8091269. [PMID: 32825526 PMCID: PMC7570391 DOI: 10.3390/microorganisms8091269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/14/2020] [Accepted: 08/18/2020] [Indexed: 01/15/2023] Open
Abstract
Cyclic di-adenosine monophosphate (c-di-AMP) has emerged as an important bacterial signaling molecule that functions both as an intracellular second messenger in bacterial cells and an extracellular ligand involved in bacteria-host cross-talk. In this study, we identify and characterize proteins involved in controlling the c-di-AMP concentration in the oral commensal and opportunistic pathogen Streptococcusmitis (S. mitis). We identified three known types of c-di-AMP turnover proteins in the genome of S. mitis CCUG31611: a CdaA-type diadenylate cyclase as well as GdpP-, and DhhP-type phosphodiesterases. Biochemical analyses of purified proteins demonstrated that CdaA synthesizes c-di-AMP from ATP whereas both phosphodiesterases can utilize c-di-AMP as well as the intermediary metabolite of c-di-AMP hydrolysis 5'-phosphadenylyl-adenosine (pApA) as substrate to generate AMP, albeit at different catalytic efficiency. Using deletion mutants of each of the genes encoding c-di-AMP turnover proteins, we show by high resolution MS/MS that the intracellular concentration of c-di-AMP is increased in deletion mutants of the phosphodiesterases and non-detectable in the cdaA-mutant. We also detected pApA in mutants of the DhhP-type phosphodiesterase. Low and high levels of c-di-AMP were associated with longer and shorter chains of S. mitis, respectively indicating a role in regulation of cell division. The deletion mutant of the DhhP-type phosphodiesterase displayed slow growth and reduced rate of glucose metabolism.
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Affiliation(s)
- Gro Herredsvela Rørvik
- Institute of Oral Biology, University of Oslo, 0316 Oslo, Norway; (G.H.R.); (K.A.L.); (A.-O.N.); (H.-C.A.); (F.C.P.); (T.M.K.)
| | - Krystyna Anna Liskiewicz
- Institute of Oral Biology, University of Oslo, 0316 Oslo, Norway; (G.H.R.); (K.A.L.); (A.-O.N.); (H.-C.A.); (F.C.P.); (T.M.K.)
| | - Fedor Kryuchkov
- Norwegian Veterinary Institute, Pb 750 Sentrum, 0106 Oslo, Norway;
| | - Ali-Oddin Naemi
- Institute of Oral Biology, University of Oslo, 0316 Oslo, Norway; (G.H.R.); (K.A.L.); (A.-O.N.); (H.-C.A.); (F.C.P.); (T.M.K.)
| | - Hans-Christian Aasheim
- Institute of Oral Biology, University of Oslo, 0316 Oslo, Norway; (G.H.R.); (K.A.L.); (A.-O.N.); (H.-C.A.); (F.C.P.); (T.M.K.)
| | - Fernanda C. Petersen
- Institute of Oral Biology, University of Oslo, 0316 Oslo, Norway; (G.H.R.); (K.A.L.); (A.-O.N.); (H.-C.A.); (F.C.P.); (T.M.K.)
| | - Thomas M. Küntziger
- Institute of Oral Biology, University of Oslo, 0316 Oslo, Norway; (G.H.R.); (K.A.L.); (A.-O.N.); (H.-C.A.); (F.C.P.); (T.M.K.)
| | - Roger Simm
- Institute of Oral Biology, University of Oslo, 0316 Oslo, Norway; (G.H.R.); (K.A.L.); (A.-O.N.); (H.-C.A.); (F.C.P.); (T.M.K.)
- Correspondence:
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Abstract
The second messenger molecule cyclic di-AMP (c-di-AMP) is formed by many bacteria and archaea. In many species that produce c-di-AMP, this second messenger is essential for viability on rich medium. Recent research has demonstrated that c-di-AMP binds to a large number of proteins and riboswitches, which are often involved in potassium and osmotic homeostasis. c-di-AMP becomes dispensable if the bacteria are cultivated on minimal media with low concentrations of osmotically active compounds. Thus, the essentiality of c-di-AMP does not result from an interaction with a single essential target but rather from the multilevel control of complex homeostatic processes. This review summarizes current knowledge on the homeostasis of c-di-AMP and its function(s) in the control of cellular processes.
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Affiliation(s)
- Jörg Stülke
- Department of General Microbiology, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077 Göttingen, Germany;
| | - Larissa Krüger
- Department of General Microbiology, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077 Göttingen, Germany;
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45
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Zhu X, Baranowski E, Dong Y, Li X, Hao Z, Zhao G, Zhang H, Lu D, A. Rasheed M, Chen Y, Hu C, Chen H, Sagné E, Citti C, Guo A. An emerging role for cyclic dinucleotide phosphodiesterase and nanoRNase activities in Mycoplasma bovis: Securing survival in cell culture. PLoS Pathog 2020; 16:e1008661. [PMID: 32598377 PMCID: PMC7373297 DOI: 10.1371/journal.ppat.1008661] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/21/2020] [Accepted: 05/27/2020] [Indexed: 12/26/2022] Open
Abstract
Mycoplasmas are host-restricted prokaryotes with a nearly minimal genome. To overcome their metabolic limitations, these wall-less bacteria establish intimate interactions with epithelial cells at mucosal surfaces. The alarming rate of antimicrobial resistance among pathogenic species is of particular concern in the medical and veterinary fields. Taking advantage of the reduced mycoplasma genome, random transposon mutagenesis was combined with high-throughput screening in order to identify key determinants of mycoplasma survival in the host-cell environment and potential targets for drug development. With the use of the ruminant pathogen Mycoplasma bovis as a model, three phosphodiesterases of the DHH superfamily were identified as essential for the proliferation of this species under cell culture conditions, while dispensable for axenic growth. Despite a similar domain architecture, recombinant Mbov_0327 and Mbov_0328 products displayed different substrate specificities. While rMbovP328 protein exhibited activity towards cyclic dinucleotides and nanoRNAs, rMbovP327 protein was only able to degrade nanoRNAs. The Mbov_0276 product was identified as a member of the membrane-associated GdpP family of phosphodiesterases that was found to participate in cyclic dinucleotide and nanoRNA degradation, an activity which might therefore be redundant in the genome-reduced M. bovis. Remarkably, all these enzymes were able to convert their substrates into mononucleotides, and medium supplementation with nucleoside monophosphates or nucleosides fully restored the capacity of a Mbov_0328/0327 knock-out mutant to grow under cell culture conditions. Since mycoplasmas are unable to synthesize DNA/RNA precursors de novo, cyclic dinucleotide and nanoRNA degradation are likely contributing to the survival of M. bovis by securing the recycling of purines and pyrimidines. These results point toward proteins of the DHH superfamily as promising targets for the development of new antimicrobials against multidrug-resistant pathogenic mycoplasma species.
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Affiliation(s)
- Xifang Zhu
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease of Ministry of Science and Technology of China, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Key Laboratory of Ruminant Bio-products, Ministry of Agriculture and Rural Affairs of China, Wuhan, China
| | | | - Yaqi Dong
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xixi Li
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhiyu Hao
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Gang Zhao
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Hui Zhang
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Doukun Lu
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Muhammad A. Rasheed
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yingyu Chen
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Changmin Hu
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Huanchun Chen
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease of Ministry of Science and Technology of China, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Key Laboratory of Ruminant Bio-products, Ministry of Agriculture and Rural Affairs of China, Wuhan, China
| | - Eveline Sagné
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | | | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, International Research Center for Animal Disease of Ministry of Science and Technology of China, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Key Laboratory of Ruminant Bio-products, Ministry of Agriculture and Rural Affairs of China, Wuhan, China
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46
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He J, Yin W, Galperin MY, Chou SH. Cyclic di-AMP, a second messenger of primary importance: tertiary structures and binding mechanisms. Nucleic Acids Res 2020; 48:2807-2829. [PMID: 32095817 DOI: 10.1093/nar/gkaa112] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/09/2020] [Accepted: 02/21/2020] [Indexed: 12/12/2022] Open
Abstract
Cyclic diadenylate (c-di-AMP) is a widespread second messenger in bacteria and archaea that is involved in the maintenance of osmotic pressure, response to DNA damage, and control of central metabolism, biofilm formation, acid stress resistance, and other functions. The primary importance of c-di AMP stems from its essentiality for many bacteria under standard growth conditions and the ability of several eukaryotic proteins to sense its presence in the cell cytoplasm and trigger an immune response by the host cells. We review here the tertiary structures of the domains that regulate c-di-AMP synthesis and signaling, and the mechanisms of c-di-AMP binding, including the principal conformations of c-di-AMP, observed in various crystal structures. We discuss how these c-di-AMP molecules are bound to the protein and riboswitch receptors and what kinds of interactions account for the specific high-affinity binding of the c-di-AMP ligand. We describe seven kinds of non-covalent-π interactions between c-di-AMP and its receptor proteins, including π-π, C-H-π, cation-π, polar-π, hydrophobic-π, anion-π and the lone pair-π interactions. We also compare the mechanisms of c-di-AMP and c-di-GMP binding by the respective receptors that allow these two cyclic dinucleotides to control very different biological functions.
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Affiliation(s)
- Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China
| | - Wen Yin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Shan-Ho Chou
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China.,Institute of Biochemistry and Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan, Republic of China
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47
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Gibhardt J, Heidemann JL, Bremenkamp R, Rosenberg J, Seifert R, Kaever V, Ficner R, Commichau FM. An extracytoplasmic protein and a moonlighting enzyme modulate synthesis of c-di-AMP in Listeria monocytogenes. Environ Microbiol 2020; 22:2771-2791. [PMID: 32250026 DOI: 10.1111/1462-2920.15008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/17/2020] [Accepted: 03/31/2020] [Indexed: 01/06/2023]
Abstract
The second messenger cyclic di-AMP (c-di-AMP) is essential for growth of many bacteria because it controls osmolyte homeostasis. c-di-AMP can regulate the synthesis of potassium uptake systems in some bacteria and it also directly inhibits and activates potassium import and export systems, respectively. Therefore, c-di-AMP production and degradation have to be tightly regulated depending on the environmental osmolarity. The Gram-positive pathogen Listeria monocytogenes relies on the membrane-bound diadenylate cyclase CdaA for c-di-AMP production and degrades the nucleotide with two phosphodiesterases. While the enzymes producing and degrading the dinucleotide have been reasonably well examined, the regulation of c-di-AMP production is not well understood yet. Here we demonstrate that the extracytoplasmic regulator CdaR interacts with CdaA via its transmembrane helix to modulate c-di-AMP production. Moreover, we show that the phosphoglucosamine mutase GlmM forms a complex with CdaA and inhibits the diadenylate cyclase activity in vitro. We also found that GlmM inhibits c-di-AMP production in L. monocytogenes when the bacteria encounter osmotic stress. Thus, GlmM is the major factor controlling the activity of CdaA in vivo. GlmM can be assigned to the class of moonlighting proteins because it is active in metabolism and adjusts the cellular turgor depending on environmental osmolarity.
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Affiliation(s)
- Johannes Gibhardt
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany.,FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany
| | - Jana L Heidemann
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, University of Goettingen, 37077, Göttingen, Germany
| | - Rica Bremenkamp
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Jonathan Rosenberg
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Roland Seifert
- Institute of Pharmacology & Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Volkhard Kaever
- Institute of Pharmacology & Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, University of Goettingen, 37077, Göttingen, Germany
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany
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48
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Increased Excess Intracellular Cyclic di-AMP Levels Impair Growth and Virulence of Bacillus anthracis. J Bacteriol 2020; 202:JB.00653-19. [PMID: 32071095 DOI: 10.1128/jb.00653-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 02/09/2020] [Indexed: 12/23/2022] Open
Abstract
Cyclic di-AMP (c-di-AMP) is a recently identified bacterial second messenger that regulates biological processes. In this study, we found that inactivation of two c-di-AMP phosphodiesterases (PDEs), GdpP and PgpH, resulted in accumulation of 3.8-fold higher c-di-AMP levels than in the parental strain Sterne in Bacillus anthracis and inhibited bacterial growth. Moreover, excess c-di-AMP accumulation decreased bacterial toxin expression, increased sensitivity to osmotic stress and detergent, and attenuated virulence in both C57BL/6J and A/J mice. Complementation of the PDE mutant with a plasmid carrying gdpP or pgpH in trans from a Pspac promoter restored bacterial growth, virulence factor expression, and resistance to detergent. Our results indicate that c-di-AMP is a pleiotropic signaling molecule in B. anthracis that is important for host-pathogen interaction.IMPORTANCE Anthrax is an ancient and deadly disease caused by the spore-forming bacterial pathogen Bacillus anthracis Vegetative cells of this species produce anthrax toxin proteins and S-layer components during infection of mammalian hosts. So far, how the expression of these virulence factors is regulated remains largely unknown. Our results suggest that excess elevated c-di-AMP levels inhibit bacterial growth and reduce expression of S-layer components and anthracis toxins as well as reduce virulence in a mouse model of disease. These results indicate that c-di-AMP signaling plays crucial roles in B. anthracis biology and disease.
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49
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He J, Yin W, Galperin MY, Chou SH. Cyclic di-AMP, a second messenger of primary importance: tertiary structures and binding mechanisms. Nucleic Acids Res 2020. [PMID: 32095817 DOI: 10.1093/nar/gkaa112"] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cyclic diadenylate (c-di-AMP) is a widespread second messenger in bacteria and archaea that is involved in the maintenance of osmotic pressure, response to DNA damage, and control of central metabolism, biofilm formation, acid stress resistance, and other functions. The primary importance of c-di AMP stems from its essentiality for many bacteria under standard growth conditions and the ability of several eukaryotic proteins to sense its presence in the cell cytoplasm and trigger an immune response by the host cells. We review here the tertiary structures of the domains that regulate c-di-AMP synthesis and signaling, and the mechanisms of c-di-AMP binding, including the principal conformations of c-di-AMP, observed in various crystal structures. We discuss how these c-di-AMP molecules are bound to the protein and riboswitch receptors and what kinds of interactions account for the specific high-affinity binding of the c-di-AMP ligand. We describe seven kinds of non-covalent-π interactions between c-di-AMP and its receptor proteins, including π-π, C-H-π, cation-π, polar-π, hydrophobic-π, anion-π and the lone pair-π interactions. We also compare the mechanisms of c-di-AMP and c-di-GMP binding by the respective receptors that allow these two cyclic dinucleotides to control very different biological functions.
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Affiliation(s)
- Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China
| | - Wen Yin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Shan-Ho Chou
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China.,Institute of Biochemistry and Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan, Republic of China
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50
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Wooten AK, Shenoy AT, Arafa EI, Akiyama H, Martin IMC, Jones MR, Quinton LJ, Gummuluru S, Bai G, Mizgerd JP. Unique Roles for Streptococcus pneumoniae Phosphodiesterase 2 in Cyclic di-AMP Catabolism and Macrophage Responses. Front Immunol 2020; 11:554. [PMID: 32300347 PMCID: PMC7145409 DOI: 10.3389/fimmu.2020.00554] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/11/2020] [Indexed: 11/13/2022] Open
Abstract
Cyclic di-AMP (c-di-AMP) is an important signaling molecule for pneumococci, and as a uniquely prokaryotic product it can be recognized by mammalian cells as a danger signal that triggers innate immunity. Roles of c-di-AMP in directing host responses during pneumococcal infection are only beginning to be defined. We hypothesized that pneumococci with defective c-di-AMP catabolism due to phosphodiesterase deletions could illuminate roles of c-di-AMP in mediating host responses to pneumococcal infection. Pneumococci deficient in phosphodiesterase 2 (Pde2) stimulated a rapid induction of interferon β (IFNβ) expression that was exaggerated in comparison to that induced by wild type (WT) bacteria or bacteria deficient in phosphodiesterase 1. This IFNβ burst was elicited in mouse and human macrophage-like cell lines as well as in primary alveolar macrophages collected from mice with pneumococcal pneumonia. Macrophage hyperactivation by Pde2-deficient pneumococci led to rapid cell death. STING and cGAS were essential for the excessive IFNβ induction, which also required phagocytosis of bacteria and triggered the phosphorylation of IRF3 and IRF7 transcription factors. The select effects of Pde2 deletion were products of a unique role of this enzyme in c-di-AMP catabolism when pneumococci were grown on solid substrate conditions designed to enhance virulence. Because pneumococci with elevated c-di-AMP drive aberrant innate immune responses from macrophages involving hyperactivation of STING, excessive IFNβ expression, and rapid cytotoxicity, we surmise that c-di-AMP is pivotal for directing innate immunity and host-pathogen interactions during pneumococcal pneumonia.
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Affiliation(s)
- Alicia K Wooten
- Pulmonary Center, Boston University School of Medicine, Boston, MA, United States.,Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Anukul T Shenoy
- Pulmonary Center, Boston University School of Medicine, Boston, MA, United States
| | - Emad I Arafa
- Pulmonary Center, Boston University School of Medicine, Boston, MA, United States.,Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Hisashi Akiyama
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States
| | - Ian M C Martin
- Pulmonary Center, Boston University School of Medicine, Boston, MA, United States
| | - Matthew R Jones
- Pulmonary Center, Boston University School of Medicine, Boston, MA, United States.,Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Lee J Quinton
- Pulmonary Center, Boston University School of Medicine, Boston, MA, United States.,Department of Medicine, Boston University School of Medicine, Boston, MA, United States.,Department of Microbiology, Boston University School of Medicine, Boston, MA, United States.,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Suryaram Gummuluru
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States
| | - Guangchun Bai
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, United States
| | - Joseph P Mizgerd
- Pulmonary Center, Boston University School of Medicine, Boston, MA, United States.,Department of Medicine, Boston University School of Medicine, Boston, MA, United States.,Department of Microbiology, Boston University School of Medicine, Boston, MA, United States.,Department of Biochemistry, Boston University School of Medicine, Boston, MA, United States
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