Structural biology of host-microbe interactions in health and disease, bacterial pili and biofilm

Microbial attachment to host surfaces is a first and critical step in colonization regardless of whether it benefits or harms the host. The subsequent events in the pathogenesis or probiosis are highly dependent on this initial interaction or adherence. Interfering with the host-microbial interface is considered as one of the attractive and efficient approaches in improving health and combating infections.This approach do not directly kill bacteria rather prevent interaction or attachment. Hence, it is also recognized as a promising alternate to antibiotics which often results in development of resistance. Such an approach requires detailed knowledge of how microbes attach to host, and how the adhesive strategies differ among microbes.Towards providing the essential foundations for this approach, we aim to generate structural knowledge by studying key molecules that establish the initial contacts between the host and microbes (both beneficial and pathogenic).

Our major interest lies in visualizing host-microbial interface through structural biology tools at the atomic level towards understanding the mechanism by which microbes adhere to and interact with the host surface for colonization. We currently focus on hair-like surface organelles called pili or fimbriae that enable bacteria to establish the initial contacts with the host surfaces for colonization and biofilm formation.The ongoing structural investigation programme covers beneficial strains from gut microbiota and pathogens for getting insights into tissue tropism and microbial interaction strategies in health and diseases.

• Smita Yadav
  Senior Research Fellow
  smita@rcb.res.in
• Amar Prajapati
  Senior Research Fellow
  amarprajapati@rcb.res.in
• Vinay Sharma
  Senior Research Fellow
  
• Shivangi Tyagi
  Junior Research Fellow
  
• Sanjoy Das
  Junior Research Fellow
  
• Lisha
  Junior Research Fellow
  
• Shivam Tiwari
  Junior Research Fellow
  

1. Deb A, Nagpal S, Yadav RK, Thakur H, Nair D, Krishnan V, Vrati S.Japanese encephalitis virus NS5 protein interacts with nucleolin to enhance the virus replication.J Virol. 2024 Jul 30:e0085824. doi: 10.1128/jvi.00858-24. Online ahead of print. PMID: 39078257
2. Prajapati A, Palva A, von Ossowski I, Krishnan V. The crystal structure of the N-terminal domain of the backbone pilin LrpA reveals a new closure-and-twist motion for assembling dynamic pili in Ligilactobacillus ruminis.Acta Crystallogr D Struct Biol. 2024 Jul 1. doi: 10.1107/S2059798324005114. Online ahead of print. PMID: 38935340
3. Kaushik JK, Krishnan V, von Ossowski I.Editorial: Functional insights into the probiotic mechanisms of surface protein action.Front Microbiol. 2024 Jan 5;14:1355529. doi: 10.3389/fmicb.2023.1355529. eCollection 2023. PMID: 38249455 Free PMC article.
4. Tyagi N, Roy S, Vengadesan K, Gupta D. Multi-omics approach for identifying CNV-associated lncRNA signatures with prognostic value in prostate cancer.RNA Res. 2023 Oct 10;9(1):66-75. doi: 10.1016/j.ncrna.2023.10.001. eCollection 2024 Mar.
5. Tyagi S, Yadav RK, Krishnan V.Determination of the Crystal Structure of the Cell Wall-Anchored Proteins and Pilins.Methods Mol Biol. 2024;2727:159-191. doi: 10.1007/978-1-0716-3491-2_14.PMID: 37812996
6. Yadav S, Parijat P, Krishnan V.Crystal structure of the pilus-specific sortase from early colonizing oral Streptococcus sanguinis captures an active open-lid conformation.Int J Biol Macromol. 2023 Jul 15;243:125183. doi: 10.1016/j.ijbiomac.2023.125183. Epub 2023 Jun 3.PMID: 37276901
7. Kumar V, Murmu S, Krishnan V. (2022) Deciphering the substrate specificity of housekeeping sortase A and pilus-specific sortase C of probiotic bacterium Lactococcus lactis. Biochimie, 200:140
8. Yadav RK, Krishnan V. (2022) New structural insights into the PI-2 pilus from Streptococcus oralis, an early dental plaque colonizer. FEBS J, 289:6342
9. Prajapati A, Palva A, von Ossowski I, Krishnan V. (2021) LrpCBA pilus proteins of gut-dwelling Ligilactobacillus ruminis: crystallization and X-ray diffraction analysis. Acta Crystallogr F Struct Biol Commun, 77:238
10. Sharma V, von Ossowski I, Krishnan V. (2021) Exploiting pilus-mediated bacteria-host interactions for health benefits. Mol Aspects Med, 81:1000998
11. Banerjee S, Katiyar P, Kumar V, Waghmode B, Nathani S, Krishnan V, Sircar D, Roy P. (2021) Wheatgrass inhibits the lipopolysaccharide-stimulated inflammatory effect in RAW 264.7 macrophages. Curr Res Toxicol. 2:116
12. Banerjee S, Katiyar P, Kumar V, Saini SS, Varshney R, Krishnan V, Sircar D, Roy P. (2021) Black pepper and piperine induce anticancer effects on leukemia cell line. Toxicology Research, 10:169
13. Banerjee S, Katiyar P, Kumar L, Kumar V, Saini SS, Krishnan V, Sircar D, Roy P. (2021) Black pepper prevents anemia of inflammation by inhibiting hepcidin over-expression through BMP6-SMAD1/ IL6-STAT3 signaling pathway. Free Radic Biol Med, 168:189
14. Kumar Megta A, Pratap S, Kant A, Palva A, von Ossowski I, Krishnan V. (2020) Crystal structure of the atypically adhesive SpaB basal pilus subunit: Mechanistic insights about its incorporation in lactobacillar SpaCBA pili. Curr Res Struct Biol. 2:229
15. Kant A, Palva A, von Ossowski I, Krishnan V. (2020) Crystal structure of lactobacillar SpaC reveals an atypical five-domain pilus tip adhesin: Exposing its substrate-binding and assembly in SpaCBA pili. J Struct Biol, 211:107571
16. Yadav R.K. and Krishnan V. (2020) The adhesive PitA pilus protein from the early dental plaque colonizer Streptococcus oralis: expression, purification, crystallization and X-ray diffraction analysis. Acta Cryst. F76:8
17. Pratap S, Megta A.K, Krishnan V. (2019) Sortases from a Probiotic Lactobacillus rhamnosus GG: Cloning, Expression, Purification, Crystallization and Preliminary X-Ray Diffraction Study. Crystallography Reports. 64:1117
18. Kumar Megta A, Palva A, von Ossowski I, Krishnan V. (2019) SpaB, an atypically adhesive basal pilin from the lactobacillar SpaCBA pilus: crystallization and X-ray diffraction analysis. Acta Crystallogr F Struct Biol Commun. | F75:731
19. Megta AK, Mishra AK, Palva A, von Ossowski I, Krishnan V (2019) Crystal structure of basal pilin SpaE reveals the molecular basis of its incorporation in the lactobacillar SpaFED pilus. J Struct Biol | 207:74
20. Mohapatra G, Gaur P, Prabhakar M, Singh M, Rana S, Singh S, Kaur N, Verma S, Krishna V, Singh N, Srikanth CV (2019) A SUMOylation-dependent switch of RAB7 governs intracellular life and pathogenesis of Salmonella Typhimurium. J Cell Sci 32: jcs.222612
21. Chaurasia P, Pratap S, , Palva A, von Ossowski I, Krishnan V. (2018) Bent conformation of a backbone pilin N-terminal domain supports a three-stage pilus assembly mechanism. Commun Biol 1:94
22. Mishra AK, Megta AK, Palva A, von Ossowski I, Krishnan V. (2017) Crystallization and X-ray diffraction analysis of SpaE, a basal pilus protein from the gut-adapted Lactobacillus rhamnosus GG. Acta Crystallogr F Struct Biol Commun 73:321
23. Krishnan V, Kant A, Chaurasia P (2016) Pili in Probiotic Bacteria in “Prebiotics and Probiotics in Human Nutrition and Health", ISBN 978-953-51-4715-2, InTech:115
24. Chaurasia P, Pratap S, von Ossowski I, Palva A, Krishnan V, (2016) New insights about pilus formation in gut-adapted Lactobacillus rhamnosus GG from the crystal structure of the SpaA backbone-pilin subunit. Sci Rep. 6:28664
25. Kant A, von Ossowski I, Palva A, Krishnan V (2016)  Crystallization and X-ray Crystallographic Analysis of the Adhesive SpaC Pilin Subunit in the SpaCBA Pilus of Gut-adapted Lactobacillus rhamnosus GG. Protein & Peptide Letters 23:365
26. Chaurasia P, von Ossowski I, Palva A, Krishnan V. (2015) X-ray diffraction analysis of two crystals forms of backbone pilin SpaA fragment from Lactobacillus rhamnosus GG. Journal of proteins and proteomics 6:30
27. Krishnan V (2015)  Pilins in gram-positive bacteria: A structural perspective. IUBMB Life 67:533
28. Chaurasia P, von Ossowski I, Palva A, Krishnan V, (2015) Purification, crystallization and preliminary X-ray diffraction analysis of SpaD, a backbone-pilin subunit encoded by the fimbrial spaFED operon in Lactobacillus rhamnosus GG. Acta Crystallogr F71:103.
29. Chen C, Vengadesan K, Macon K, Manne K, Narayana SV, Schneewind O. (2013) Secreted Proteases Control Autolysin-mediated Biofilm Growth of Staphylococcus aureus. Journal of Biological Chemistry 288:29440.
30. Singh D, von Ossowski I, Palva A, Vengadesan k.(2013) Purification, crystallization and preliminary crystallographic analysis of the SpaA backbone-pilin subunit from probiotic Lactobacillus rhamnosus GG. Acta Crystallogr Sect F Struct Biol Cryst Commun 69:1182.
31. Vengadesan K, Dwivedi P, Kim BJ, Samal A, Macon K, Ma X, Mishra A, Doran KS, Ton-That H, Narayana SV.(2013) Structure of Streptococcus agalactiae tip pilin GBS104: a model for GBS pili assembly and host interactions. Acta Crystallographica Section D: Biological Crystallography 69:1073.
32. Vengadesan K, Macon K, Sugumoto S, Mizunoe Y, Iwase T, Narayana SV.(2013) Purification, crystallization and preliminary X-ray diffraction analysis of the Staphylococcus epidermidis extracellular serine protease Esp. Acta Crystallogr Sect F Struct Biol Cryst Commun 69(Pt1):49.
33. Vengadesan, K. and S. V. L. Narayana. (2011) Structural biology of gram-positive bacterial adhesins. Protein Science 20(5):759.
34. Vengadesan K, Ma X, Dwivedi P, Ton-That H, Narayana SV. (2011) A Model for Group B Streptococcus Pilus Type 1: The Structure of a 35-kDa C-Terminal Fragment of the Major Pilin GBS80. Journal of molecular biology 407(5):731.
35. Mishra A, Devarajan B, Reardon ME, Dwivedi P, Krishnan V, Cisar JO, Das A, Narayana SV, Ton-That H.(2011) Two autonomous structural modules in the fimbrial shaft adhesin FimA mediate Actinomyces interactions with streptococci and host cells during oral biofilm development. Molecular microbiology 81(5):1205.
36. Vengadesan K, Macon K, Sugumoto S, Mizunoe Y, Iwase T, Narayana SV.(2011) Crystallography of gram-positive bacterial adhesins. Adv Exp Med Biol 715: 175.
37. Khare B, Vengadesan K, Rajashankar KR, I-Hsiu H, Xin M, Ton-That H, Narayana SV. (2011) Structural Differences between the Streptococcus agalactiae Housekeeping and Pilus-Specific Sortases: SrtA and SrtC1. PLoS One 6(8):e22995.
38. Vengadesan K, Ma X, Dwivedi P, Ton-That H, Narayana SV. (2010) Purification, crystallization and halide phasing of a Streptococcus agalactiae backbone pilin GBS80 fragment. Acta Crystallographica Section F: Structural Biology and Crystallization Communications 66(12):1666.
39. Khare B, Samal A, Vengadesan K, Rajashankar KR, Ma X, Huang IH, Ton-That H, Narayana SV. (2010) Preliminary crystallographic study of the Streptococcus agalactiae sortases, sortase A and sortase C1. Acta Crystallographica Section F: Structural Biology and Crystallization Communications 66(9):1096.
40. Vengadesan K, Xu Y, Macon K, Volanakis JE, Narayana SV. (2009) The structure of C2b, a fragment of complement component C2 produced during C3 convertase formation. Acta Crystallographica Section D: Biological Crystallography 65(3):266.
41. Vengadesan K, Ponnuraj K, Xu Y, Macon K, Volanakis JE, Narayana SV.(2009) The crystal structure of cobra venom factor, a cofactor for C3-and C5-convertase CVFBb. Structure 17(4):611.
42. Vengadesan K, Macon K, Narayana SV. (2008) The crystal structure of cobra venom factor, a complement-activating protein from Naje Naja Kouthia. Molecular Immunology 45(16):4120.
43. Vengadesan K, XU Y, Macon K, Volanakis JE, Narayana SV. (2007) The Crystal Structure of C2a, the Catalytic Fragment of Classical Pathway C3-and C5-convertase of Human Complement. Journal of molecular biology 367(1):224.
44. Vengadesan K, XU Y,Macon K, Narayana SV. (2007) Crystal structure of C2a, the catalytic subunit of classical pathway C3-convertase. Molecular Immunology 44(1):199.
45. Vengadesan K, Gaspar AH, Ye N, Mandlik A, Ton-That H, Narayana SV. (2007) An IgG-like Domain in the Minor Pilin GBS52 of Streptococcus agalactiae Mediates Lung Epithelial Cell Adhesion. Structure 15(8):893.
46. Gautham N, Vengadesan K. (2003) METHOD AND SYSTEM TO BUILD OPTIMAL MODELS OF 3-DIMENSIONAL MOLECULAR STRUCTURES, US Patent.
47. Vengadesan K, Gautham N. (2005) A new conformational search technique and its applications. Curr Sci 88:1759.
48. Prasad PA, Vengadesan K, Gautham N. (2005) MOLS-A program to explore the potential energy surface of a peptide and locate its low energy conformations. In silico biology 5(4):401.
49. Vengadesan K, Gautham N. (2004) Conformational studies on enkephalins using the MOLS technique. Biopolymers 74(6):476.
50. Vengadesan K, Gautham N. (2004) Energy landscape of Met-enkephalin and Leu-enkephalin drawn using mutually orthogonal Latin squares sampling. The Journal of Physical Chemistry B 108(30):11196.
51. Vengadesan K, Anbupalam T, Gautham N. (2004) An application of experimental design using mutually orthogonal Latin squares in conformational studies of peptides. Biochem Biophys Res Commun 316(3):731.
52. Vengadesan K, Gautham N. (2003) Enhanced sampling of the molecular potential energy surface using mutually orthogonal Latin squares: Application to peptide structures. Biophysical journal 84(5):2897.
53. Gautham N, Vengadesan K. (2003) METHOD AND SYSTEM TO BUILD OPTIMAL MODELS OF 3-DIMENSIONAL MOLECULAR STRUCTURES, WO Patent 081:510.
54. Thirumurugan R, Vengadesan K, Raj SS, Shanmugam G, Fun HK. (2000) Crystal Structure of N, N'-Bis (3-(o-dimethylaminoimino-ethyl)-2-hydroxy-5-methyl)-benzylpiperazine. Crystal Research and Technology 35(8):987.