Human Fibrinogen Inhibits Amyloid Assembly of Biofilm-Forming CsgA

4 days ago - (4) Curli is known to be involved in different functions, including biofilm formation, cell–cell adhesion, and host cell invasion, and ...
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Human Fibrinogen Inhibits Amyloid Assembly of Biofilm-Forming CsgA Hema M. Swasthi, Karishma Bhasne, Sayanta Mahapatra, and Samrat Mukhopadhyay Biochemistry, Just Accepted Manuscript • DOI: 10.1021/acs.biochem.8b00841 • Publication Date (Web): 19 Oct 2018 Downloaded from http://pubs.acs.org on October 21, 2018

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Biochemistry

Human Fibrinogen Inhibits Amyloid Assembly of Biofilm-Forming CsgA Hema M. Swasthi,†¶* Karishma Bhasne,†‡ Sayanta Mahapatra,†‡ and Samrat Mukhopadhyay†‡¶* †Centre

for Protein Science, Design and Engineering, ‡Department of Biological Sciences, and ¶Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India

ABSTRACT: Curli is a biofilm-forming amyloid that is

expressed on the surface of Gram-negative enteric bacteria such as E.coli and Salmonella spp. Curli is primarily composed of the major structural subunit, CsgA, and interacts with a wide range of human proteins that contribute to the bacterial virulence. The adsorption of curli onto the contact-phase proteins and fibrinogen result in a hypocoagulatory state. Using an array of biochemical and biophysical tools, we elucidated the molecular mechanism of interaction between human fibrinogen and CsgA. Our results revealed that sub-stoichiometric concentration of fibrinogen delays the onset of CsgA aggregation by inhibiting the early events of CsgA assembly. The presence of fibrinogen prevents the maturation of CsgA into fibrils and maintains the soluble state of CsgA. We also demonstrate that fibrinogen interacts more effectively with the disordered conformational state of CsgA than with the ordered β-rich state. Our study suggested that fibrinogen is an anti-curli protein and that the interplay of CsgA and fibrinogen might be a host defense mechanism against curli biogenesis, biofilm formation, bacterial colonization, and infection.

Amyloid fibrils are nanostructured protein aggregates composed of the cross-β structural motif. Amyloid deposition is implicated in a range of deadly neurodegenerative diseases such as Parkinson’s disease, Alzheimer’s disease, prion encephalopathies, and systemic amyloidosis (1-5). A growing body of evidence suggests that the transient oligomeric intermediates formed during amyloidogenesis are more toxic than the mature fibrils (1). Functional amyloids share the biophysical and biochemical properties of disease-associated amyloids. Nevertheless, they are employed by an organism to perform physiological functions (6-8). Functional amyloids are evolved to control the spatiotemporal amyloid assembly and sequester the associated toxicity during their formation (3,6). For instance, curli is a functional amyloid produced in the extracellular matrix of enteric bacteria such as E.coli and Salmonella spp in a highly orchestrated manner (7,10,11). The structural constituent of curli is majorly composed of CsgA and the nucleator protein CsgB (csg: curli specific gene). Curli subunits and the accessory proteins are divergently transcribed by the operon csgBAC and csgDEFG. The accessory proteins assist translocation of curli subunits to the outer membrane and maintain their solubility in the periplasm (7,11,12). CsgA and CsgB are translocated to the

outer membrane via CsgG-CsgE complex (13). On the cell surface, membrane-anchored CsgB nucleates the polymerization of CsgA (10,14,15). The matured CsgA is comprised of two distinct domains, the N22 domain and five imperfect repeats (Figure 1a) (4). Curli is known to be involved in different functions which include biofilm formation, cell-cell adhesion, host cell invasion, and can induce an inflammatory response in the host cell (7,16). Biofilm is associated with the pathogenesis of numerous bacterial infections and these microbial cells encased within biofilms are less susceptible to antibiotic treatment. Clinical isolates of E.coli has been demonstrated to produce curli. An immunoblotting assay performed on the blood samples isolated from the sepsis patients has shown binding to the CsgA-specific antibody (17). The ability of curli to interact with a wide range of human proteins contributes to bacterial virulence (18,19). The binding of curli to factor XII and fibrinogen can result in a hypocoagulatory state in the blood plasma. Studies have shown that curliated bacteria exhibit high binding to fibrinogen (18-20). The interaction between curli expressing bacteria and blood plasma can induce fibrin formation around the the bacterial surface and can result in the release of fibrinopeptides (20). Studies using peptides of CsgA have demonstrated that the N-terminal and C-terminal residues of CsgA exhibit high binding to fibrinogen (18 20). However, the aggregation behavior of CsgA in the presence of fibrinogen remains elusive. Fibrinogen is a 340-kDa glycoprotein present in the blood. It is a homodimer which is composed of three distinct polypeptide chains Aα, Bβ, and γ. An elongated structure of these polypeptide chains interacts with another identical molecule via a disulfide bond to form a functional unit (Figure S1a) (21). The concentration of fibrinogen in blood plasma is 2-4 mg/mL (21). Fibrinogen forms one of the key substrates of the blood clot and plays an important role in maintaining hemostasis. A blood clot is composed of long polymerized fibrils of fibrinogen (fibrin) (21). In this work, using an array of biophysical techniques, we show that the presence of sub-stoichiometric amounts of human fibrinogen inhibits CsgA amyloid formation and this property of fibrinogen might be critical for the inhibition of curli biogenesis. In order to investigate whether human fibrinogen modulates CsgA polymerization, we set out to perform aggregation studies using thioflavin T (ThT), which is a wellknown amyloid marker. CsgA aggregation displayed a nucleation-dependent sigmoidal kinetics with an initial lag

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Biochemistry

We postulated that if fibrinogen inhibits the early events of CsgA assembly, there should be soluble CsgA in the fibrinogen-containing reaction mixture. In order to verify the existence of early low molecular weight species, the reaction mixture was passed through a 30 kDa filter during the course of aggregation. His-tagged CsgA is a ~14 kDa protein and under non-reducing condition, fibrinogen has an averaged molecular weight of ~340 kDa. Monomer/dimer species of CsgA are expected to pass-through and come in the filtrate of 30 kDa filter. Whereas, the higher order species are supposed to be in the retentate. We performed a dot blot assay and probed against His-tag of CsgA to confirm its presence. As expected at 0h, CsgA reaction showed the existence of CsgA in the filtrate whereas, after 3h there was no detectable CsgA in the filtrate indicating the formation of higher order species of CsgA (Figure 1d). On the contrary, in the presence of fibrinogen, CsgA was present in the filtrate even after 12h. Fibrinogen failed to pass-through 30 kDa filter and the retentate showed very weak binding to an anti-His antibody. Taken together, these results suggest that fibrinogen inhibits the early CsgA assembly and keeps CsgA in its soluble form. (a)

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phase followed by a growth phase (Figure 1b). Next, we carried out CsgA aggregation in the presence of different stoichiometric ratios of human fibrinogen (Fi) (Figure 1b). Fibrinogen induced delay in the onset of CsgA aggregation in a concentration-dependent manner. The half-times (t1/2) recovered from these reactions further indicate the delay in CsgA amyloid formation upon addition of fibrinogen (Figure 1c). The saturated reactions did not exhibit significant differences in the final ThT intensity. Interestingly, upon increasing the molar ratio of fibrinogen to CsgA (1:5) there was no substantial increase in the ThT intensity which is indicative of the inhibition of CsgA amyloid assembly by fibrinogen. Even in the presence of bovine fibrinogen, CsgA exhibited a similar change in the aggregation process (Figure S1b). In order to verify whether the interaction between human fibrinogen and CsgA is specific, we carried out the aggregation of CsgB (without R5 repeat), the minor subunit of curli, in the presence of human fibrinogen. The presence of a high molar ratio of fibrinogen delays the onset of CsgB aggregation, however, the delay is not as profound as CsgAfibrinogen (Figure S1c). Additionally, we performed aggregation of a similar functional amyloid forming intrinsically disordered yeast prion protein Sup35NM in the presence of human fibrinogen. The overall net charge of Sup35NM and CsgA at pH 7 is -4.8 and -5.4, respectively. Sup35NM aggregates at a low concentration and exhibits a lag time (~30 min) that is similar to CsgA. It is interesting to note that even in the presence of fibrinogen at a high molar ratio did not significantly alter the aggregation kinetics of Sup35NM (Figure S1d). These results suggested that the interaction of CsgA with fibrinogen is specific and affects the nucleation phase of CsgA aggregation. Next, we asked whether the pronounced elongation of the lag phase of CsgA aggregation in the presence of fibrinogen is due to the inhibition of early events of amyloid aggregation.

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Figure 2: Human fibrinogen prevents CsgA fibrillation. AFM images of CsgA in the absence (a) 0h, (b) 6h, and in the presence of fibrinogen (c) 0h, (d,e) 24h. The height profiles are shown below the respective images. (f) Fluorescence anisotropy of FITC-labeled CsgA in the absence (black) and presence of fibrinogen (red).

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CsgA CsgA:Fi (5:1) Fi Figure 1: Inhibition of CsgA aggregation by human fibrinogen (Fi). (a) Amino acid sequence of CsgA (lysines are shown in red). (b) Aggregation kinetics of CsgA in the presence of fibrinogen. (c) Halftimes were recovered from three independent experiments. (d) Time-dependent dot blots of filtrate (Fil) and retentate (Ret). For

Next, we utilized atomic force microscopy (AFM) which is a widely used technique to visualize the nanoscale morphology of the protein aggregates. Immediately after purification, CsgA exhibited as spherical oligomers of ~10 nm and as time progressed they formed long and straight fibrils (Figure 2a and 2b). AFM image of CsgA-fibrinogen sample at 0h revealed the formation of oligomers of 35-45 nm in size (Figure 2c) and even the fibrinogen sample displayed oligomers of similar size (Figure S2a and S2b). This could be possibly due to the aggregation of fibrinogen on the mica surface. It is interesting to note, even after 6h (Figure S2c) or 24h (Figure 2d), CsgA-fibrinogen sample did not show any

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fibrils. However, after 24h, along with oligomers of 35-45 nm (Figure 2d), oligomers of ~20 nm were also present (Figure 2e). AFM imaging revealed that in the presence of fibrinogen, CsgA fails to form typical long and straight fibrils. In order to further establish that the CsgA aggregates formed in the presence and absence of fibrinogen are different, we monitored fluorescence anisotropy which provides information about the rotational mobility of the fluorophore. To perform fluorescence anisotropy measurements, we utilized two lysine residues located in the R3 and R4 repeats of CsgA (Figure 1a) and these residues were labeled with amine-active fluorescein isothiocyanate (FITC). The initial low anisotropy of ~ 0.07 exhibited by CsgA with and without fibrinogen suggested that the fluorophore is in a highly flexible environment (Figure 2f). In the absence of fibrinogen, within 2h, FITC-labeled CsgA showed a high anisotropy of ~0.28 which is indicative of the rotational constraint experienced by this region of the protein upon fibril formation. On the contrary, in the presence of fibrinogen for ~ 8h CsgA showed a low anisotropy of ~0.07 that increased to ~0.2. Half-times recovered from anisotropy measurements without and with fibrinogen are ~40 min and ~12h, respectively. The difference in the anisotropy value of CsgA in the absence and presence of fibrinogen at the saturated phase is suggestive of the structural difference in the CsgA aggregates formed. The formation of the small oligomers (Figure 2e) accounts for the gradual increase in the anisotropy of CsgA in the presence of fibrinogen. AFM imaging, ThT-kinetics, and dot-blot assays suggest that fibrinogen prevents CsgA fibrillization.

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phase of CsgA aggregation has no significant effect on the rate of elongation (Figure 3b). Addition of fibrinogen in the saturation-phase did not substantially change the ThT intensity (Figure S3a). Next, in order to discern the secondary structure of CsgA during the addition of fibrinogen, we performed far-UV circular dichroism (CD) spectroscopy. Just after purification, CsgA exhibits a randomcoil conformation and even during the addition of fibrinogen in the lag phase (20 min), CsgA possess a disordered structure (Figure 3c). In the growth phase (50 min), there is an increase in the β-sheet content at the expense of randomcoil and as the time progresses CsgA adopts a complete βsheet secondary structure. AFM imaging of the 20-min CsgA sample revealed the formation of spherical oligomers of ~ 10 nm that are comparable to the 0-min CsgA (Figure S3b and 2a). Interestingly, the 50-min CsgA sample showed the existence of both fibrils and oligomers (Figure S3c). The spherical oligomers formed at 0 min and 20 min exhibit disordered conformational state, whereas, fibrils are rich in β-sheet content. CD data together with AFM imaging and aggregation kinetics suggest that fibrinogen interacts efficiently with the early unstructured intermediates of CsgA. Next, we carried out CsgA aggregation in the presence of CsgA seeds and fibrinogen. Seeds of CsgA accelerate CsgA aggregation by shortening the lag phase (Figure 3d). At a higher molar ratio of fibrinogen, there was no significant increase in the ThT intensity which is possibly due to the interaction of fibrinogen with CsgA monomers preventing the recruitment of monomer to the growing fibril ends (seeds). The secondary structure of CsgA monitored immediately upon addition of CsgA seeds suggested that the protein is in the random-coil conformation (Figure S3d). Therefore, these results suggest that fibrinogen can interact efficiently with disordered conformational states of CsgA and inhibits CsgA aggregation.

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Biochemistry

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Figure 3: Interaction of human fibrinogen (Fi) at various aggregation phase of CsgA. Fibrinogen was added at (a) 20 min and (b) 50 min after the commencement of aggregation. (c) CD spectra of CsgA at the time of fibrinogen addition. (d) Interaction of fibrinogen with CsgA (5 µM) in seeded (10%) aggregation.

In order to study the interaction of fibrinogen with the different conformational states of CsgA, we added fibrinogen at varying time-points during CsgA aggregation. When fibrinogen was added at 20 min after the commencement of CsgA aggregation, there was a delay in the onset of CsgA aggregation and in its mid-point of transition (Figure 3a). Interestingly, the addition of fibrinogen in the exponential

Figure 4: A proposed model for the inhibition of CsgA aggregation by human fibrinogen.

Based on all of our results described here, we propose a model for the inhibition of CsgA aggregation by fibrinogen (Figure 4). The presence of fibrinogen either in the beginning or in the lag phase of CsgA aggregation inhibits CsgA amyloid fibril formation. The interaction of fibrinogen with the disordered conformational state of CsgA displays a better inhibitory property. Production of biofilm by bacteria is a strategy for their survival, which also provides tolerance and resistance to the cells against antibiotics (22). A recent study has shown that the curli protects E.coli from complementmediated killing (23). Helicobacter pylori, Salmonella enteritidis, Yersinia pestis, Staphylococcus aureus, and so forth target fibrinogen for their propagation and survival (2427). A body of evidence suggests that fibrinogen acts as an early line of host defense by preventing bacterial growth,

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suppressing the spread of microbes to distant sites, and activating the host immune system (24,28). The curli accessory protein CsgC and human transthyretin that shares structural similarity with CsgC have also been shown to prevent CsgA fibrillation (12,29,30). In summary, our results demonstrate that the heterotypic interaction between human fibrinogen and CsgA could be a host defense mechanism against curli biogenesis that might have implications in combating bacterial colonization and infection.

(11) Van Gerven, N., Klein, R. D., Hultgren, S. J., and Remaut, H. (2015) Trends Microbiol. 23, 693-706.

ASSOCIATED CONTENT

(15) Swasthi, H. M., and Mukhopadhyay, S. (2017) J. Biol. Chem. 292, 19861-19872.

Supporting Information

(12) Evans, M. L., Chorell, E., Taylor, J. D., Åden, J., Götheson, A., Li, F., Koch, M., Sefer, L., Matthews, S. J., Wittung-Stafshede, P., Almqvist, F., and Chapman M. R. (2015) Mol. Cell 57, 445-455. (13) Goyal, P., Krasteva, P. V., Van Gerven, N., Gubellini, F., Van den Broeck, I., Troupiotis-Tsaïlaki, A., Jonckheere, W., Péhau-Arnaudet, G., Pinkner, J. S., Chapman, M. R. Hultgren, S. J., Howorka, S., Fronzes, R., and Remaut, H. (2014) Nature 516, 250. (14) Hammar, M., Bian, Z., and Normark, S. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 6562-6566.

The supporting information contains detailed experimental procedure and supporting figures S1-S3. (PDF)

(16) Tükel, Ç., Nishimori, J. H., Wilson, R. P., Winter, M. G., Keestra, A. M., Van Putten, J. P., and Bäumler, A. J. (2010) Cell Microbiol. 12, 1495-1505.

AUTHOR INFORMATION

(17) Bian, Z.; Brauner, A.; Li, Y.; Normark, S. (2000) J. Infect. Dis. 181, 602-12.

Corresponding Authors

(18) Olsén, A., Herwald, H., Wikström, M., Persson, K., Mattsson, E., and Björck, L. (2002) J. Biol. Chem. 277, 34568-34572.

*E-mail: [email protected] [email protected]

(19) Herwald, H., Mörgelin, M., Olsén, A., Rhen, M., Dahlbäck, B., Müller-Esterl, W., and Björck, L. (1998) Nat. Med. 4, 298.

Notes

The authors declare no competing financial interests.

(20) Persson, K., Russell, W., Mörgelin, M., and Herwald, H. (2003) J. Biol. Chem. 278, 31884-31890.

ACKNOWLEDGMENT

(21) Davalos, D., and Akassoglou, K. (2012) Semin. Immunol. 43-62.

We thank IISER Mohali, the Department of Science and Technology (INSPIRE fellowship to K.B. & S. Mahapatra and NanoMission grant to S. Mukhopadhyay) and the Ministry of Human Resource Development, Govt. of India (Centre of Excellence grant) for financial support, Prof. M. Chapman (University of Michigan, USA) for the kind gift of plasmids, and the members of the Mukhopadhyay lab for critically reading the manuscript and for making valuable suggestions.

(22) Hall, C. W., and Mah, T.-F. (2017) FEMS Microbiol. Rev. 41, 276301. (23) Biesecker, S. G., Nicastro, L. K., Wilson, R. P., and Tükel, Ç. (2018) Biomolecules 8, 5. (24) Ko, Y.-P., and Flick, M. J. (2016) Semin. Thromb. Hemost, 42 408421. (25) Korhonen, T. (2015) J. Thromb. Haemost. 13 (Suppl 1) S115-S120. (26) Ringnér, M., Valkonen, K. H., and Wadström, T. (1994) FEMS Immunol. Med. Microbiol. 9, 29-34.

ABBREVIATIONS

(27) Hartford, O. M., Wann, E. R., Höök, M., and Foster, T. J. (2001) J. Biol. Chem. 276, 2466-2473.

AFM: atomic force microscopy; CD: circular dichroism; Csg: curli specific gene; Fi: fibrinogen; FITC: fluorescein isothiocyanate; GdnHCl: guanidine hydrochloride; ThT: thioflavin-T

(28) Degen, J., Bugge, T., and Goguen, J. (2007) J. Thromb. Haemost. 5, 24-31.

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(29) Taylor, J., Hawthorne, W. J., Lo, J., Dear, A., Jain, N., Meisl, G., Andreasen, M., Fletcher, C., Koch, M., Darvill, N., Scull, N., EscaleraMaurer, A., Sefer, L., Wenman, R., Lambert, S., Jean, J., Xu, Y., Turner, B., Kazarian, S. G., Chapman, M. R., Bubeck, D., Simone, A., Knowles, T., and Matthews S. J. (2016) Sci. Rep. 6, 24656. (30) Jain, N., Ådén, J., Nagamatsu, K., Evans, M. L., Li, X., McMichael, B., Ivanova, M. I., Almqvist, F., Buxbaum, J. N., and Chapman, M. R. (2017) Proc. Natl. Acad. Sci. U. S. A. 12184-12189.

(3) Hartl, F. U. (2017) Annu. Rev. Biochem. 86, 21-26. (4) Ke, P. C., Sani, M.-A., Ding, F., Kakinen, A., Javed, I., Separovic, F., Davis, T. P., and Mezzenga, R. (2017) Chem. Soc. Rev. 46, 64926531. (5) Gershenson, A., Gierasch, L. M., Pastore, A., and Radford, S. E. (2014) Nat. Chem. Biol. 10, 884-891. (6) Chuang, E., Hori, A. M., Hesketh, C. D., and Shorter, J. (2018) J. Cell Sci. 131, jcs189928. (7) Barnhart, M. M., and Chapman, M. R. (2006) Annu. Rev. Microbiol. 60, 131-147. (8) Fowler, D. M., Koulov, A. V., Balch, W. E., and Kelly, J. W. (2007) Trends Biochem. Sci. 32, 217-224. (9) Otzen, D. (2010) Prion 4, 256-264. (10) Chapman, M. R., Robinson, L. S., Pinkner, J. S., Roth, R., Heuser, J., Hammar, M., Normark, S., and Hultgren, S. J. (2002) Science 295, 851-855.

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