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Cyclic diguanylate monophosphate directly binds to human siderocalin and inhibits its antibacterial activity.

Li W, Cui T, Hu L, Wang Z, Li Z, He ZG - Nat Commun (2015)

Bottom Line: We demonstrate that c-di-GMP specifically binds to LCN2.In addition, c-di-GMP can compete with bacterial ferric siderophores to bind LCN2.Furthermore, c-di-GMP can significantly reduce LCN2-mediated inhibition on the in vitro growth of Escherichia coli.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.

ABSTRACT
Cyclic diguanylate monophosphate (c-di-GMP) is a well-conserved second messenger in bacteria. During infection, the innate immune system can also sense c-di-GMP; however, whether bacterial pathogens utilize c-di-GMP as a weapon to fight against host defense for survival and possible mechanisms underlying this process remain poorly understood. Siderocalin (LCN2) is a key antibacterial component of the innate immune system and sequesters bacterial siderophores to prevent acquisition of iron. Here we show that c-di-GMP can directly target the human LCN2 protein to inhibit its antibacterial activity. We demonstrate that c-di-GMP specifically binds to LCN2. In addition, c-di-GMP can compete with bacterial ferric siderophores to bind LCN2. Furthermore, c-di-GMP can significantly reduce LCN2-mediated inhibition on the in vitro growth of Escherichia coli. Thus, LCN2 acts as a c-di-GMP receptor. Our findings provide insight into the mechanism by which bacteria utilize c-di-GMP to interfere with the innate immune system for survival.

No MeSH data available.


Related in: MedlinePlus

Inverse docking screen for c-di-GMP receptor from human immune proteins.(a) Flow diagram of c-di-GMP receptor screen from human immune proteins using the inverse docking approach. (b) 3D structure of the cis (or closed) c-di-GMP conformation. (c) Three proteins with the highest scores in the inverse docking screen. The predicted binding score of the closed c-di-GMP conformation with LCN2 is comparable to those of two known c-di-GMP receptor proteins, STING and VCA0042. (d) Surface representation of the siderophore-binding pockets of LCN2 in complex with c-di-GMP (green).
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f1: Inverse docking screen for c-di-GMP receptor from human immune proteins.(a) Flow diagram of c-di-GMP receptor screen from human immune proteins using the inverse docking approach. (b) 3D structure of the cis (or closed) c-di-GMP conformation. (c) Three proteins with the highest scores in the inverse docking screen. The predicted binding score of the closed c-di-GMP conformation with LCN2 is comparable to those of two known c-di-GMP receptor proteins, STING and VCA0042. (d) Surface representation of the siderophore-binding pockets of LCN2 in complex with c-di-GMP (green).

Mentions: We first utilized an inverse docking strategy to screen candidate c-di-GMP receptors against human immune proteins, in which 1448 3D structures are currently available in the Protein Data Bank (PDB) database (Supplementary Data 1). Defining the 6.0 Å space around each ligand of protein surface, we constructed a ready-for-dock protein pocket library (Fig. 1a), then calculated and ranked the scores of the binding energy of c-di-GMP molecules (Fig. 1b, Supplementary Data 2) in each of these pockets. The 3D structure of c-di-GMP was extracted from the crystal structure of the cyclic di-GMP-VCA0042 complex, which represents a typical interaction between the c-di-GMP molecule and a receptor protein10. The cis (or closed) c-di-GMP conformation was further used for docking experiments and for calculating the binding energy of c-di-GMP with each protein pocket. As a characterized c-di-GMP receptor among innate immune proteins whose 3D structure has been solved11121314, STING was ranked as a potential candidate in the library and placed immediately behind VCA0042 (Fig. 1c), a reference protein used for screening and the most early characterized c-di-GMP receptor10. This indicates that the currently programmed inverse docking screen works well. Interestingly, LCN2 yielded a similar score as two positive proteins, namely, STING and VCA0042 (Fig. 1c). This observation suggests that siderocalin is a potential c-di-GMP receptor. Thus, our bioinformatics screen showed that LCN2 likely acts as a receptor of c-di-GMP (Fig. 1d) in addition to its function as a hunter of the ferric siderophore complex.


Cyclic diguanylate monophosphate directly binds to human siderocalin and inhibits its antibacterial activity.

Li W, Cui T, Hu L, Wang Z, Li Z, He ZG - Nat Commun (2015)

Inverse docking screen for c-di-GMP receptor from human immune proteins.(a) Flow diagram of c-di-GMP receptor screen from human immune proteins using the inverse docking approach. (b) 3D structure of the cis (or closed) c-di-GMP conformation. (c) Three proteins with the highest scores in the inverse docking screen. The predicted binding score of the closed c-di-GMP conformation with LCN2 is comparable to those of two known c-di-GMP receptor proteins, STING and VCA0042. (d) Surface representation of the siderophore-binding pockets of LCN2 in complex with c-di-GMP (green).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4595737&req=5

f1: Inverse docking screen for c-di-GMP receptor from human immune proteins.(a) Flow diagram of c-di-GMP receptor screen from human immune proteins using the inverse docking approach. (b) 3D structure of the cis (or closed) c-di-GMP conformation. (c) Three proteins with the highest scores in the inverse docking screen. The predicted binding score of the closed c-di-GMP conformation with LCN2 is comparable to those of two known c-di-GMP receptor proteins, STING and VCA0042. (d) Surface representation of the siderophore-binding pockets of LCN2 in complex with c-di-GMP (green).
Mentions: We first utilized an inverse docking strategy to screen candidate c-di-GMP receptors against human immune proteins, in which 1448 3D structures are currently available in the Protein Data Bank (PDB) database (Supplementary Data 1). Defining the 6.0 Å space around each ligand of protein surface, we constructed a ready-for-dock protein pocket library (Fig. 1a), then calculated and ranked the scores of the binding energy of c-di-GMP molecules (Fig. 1b, Supplementary Data 2) in each of these pockets. The 3D structure of c-di-GMP was extracted from the crystal structure of the cyclic di-GMP-VCA0042 complex, which represents a typical interaction between the c-di-GMP molecule and a receptor protein10. The cis (or closed) c-di-GMP conformation was further used for docking experiments and for calculating the binding energy of c-di-GMP with each protein pocket. As a characterized c-di-GMP receptor among innate immune proteins whose 3D structure has been solved11121314, STING was ranked as a potential candidate in the library and placed immediately behind VCA0042 (Fig. 1c), a reference protein used for screening and the most early characterized c-di-GMP receptor10. This indicates that the currently programmed inverse docking screen works well. Interestingly, LCN2 yielded a similar score as two positive proteins, namely, STING and VCA0042 (Fig. 1c). This observation suggests that siderocalin is a potential c-di-GMP receptor. Thus, our bioinformatics screen showed that LCN2 likely acts as a receptor of c-di-GMP (Fig. 1d) in addition to its function as a hunter of the ferric siderophore complex.

Bottom Line: We demonstrate that c-di-GMP specifically binds to LCN2.In addition, c-di-GMP can compete with bacterial ferric siderophores to bind LCN2.Furthermore, c-di-GMP can significantly reduce LCN2-mediated inhibition on the in vitro growth of Escherichia coli.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.

ABSTRACT
Cyclic diguanylate monophosphate (c-di-GMP) is a well-conserved second messenger in bacteria. During infection, the innate immune system can also sense c-di-GMP; however, whether bacterial pathogens utilize c-di-GMP as a weapon to fight against host defense for survival and possible mechanisms underlying this process remain poorly understood. Siderocalin (LCN2) is a key antibacterial component of the innate immune system and sequesters bacterial siderophores to prevent acquisition of iron. Here we show that c-di-GMP can directly target the human LCN2 protein to inhibit its antibacterial activity. We demonstrate that c-di-GMP specifically binds to LCN2. In addition, c-di-GMP can compete with bacterial ferric siderophores to bind LCN2. Furthermore, c-di-GMP can significantly reduce LCN2-mediated inhibition on the in vitro growth of Escherichia coli. Thus, LCN2 acts as a c-di-GMP receptor. Our findings provide insight into the mechanism by which bacteria utilize c-di-GMP to interfere with the innate immune system for survival.

No MeSH data available.


Related in: MedlinePlus