Pilin

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Pilin refers to a class of fibrous proteins that are found in pilus structures in bacteria. These structures can be used for the exchange of genetic material, or as a cell adhesion mechanism. Although not all bacteria have pili or fimbriae, bacterial pathogens often use their fimbriae to attach to host cells. In Gram-negative bacteria, where pili are more common, individual pilin molecules are linked by noncovalent protein-protein interactions, while Gram-positive bacteria often have polymerized LPXTG pilin.{{cite journal |vauthors=Telford JL, Barocchi MA, Margarit I, Rappuoli R, Grandi G |title=Pili in gram-positive pathogens |journal=Nat. Rev. Microbiol. |volume=4 |issue=7 |pages=509–19 |year=2006 |pmid=16778837 |doi=10.1038/nrmicro1443 |s2cid=6369483 |doi-access=free }}

Type IV pilin

{{Pfam_box

| Symbol = Pili

| Name = Pilin in Type IV pili

| image = Pilin-2pil.png

| width = 200 px

| caption = Pilin protein from Neisseria gonorrhoeae, a parasitic bacterium that requires functional pili for pathogenesis.

| Pfam= PF00114

| InterPro= IPR001082

| SMART=

| Prosite = PDOC00342

| SCOP = 1paj

| TCDB =

| OPM family= 68

| OPM protein= 2hil

| PDB=

}}

Type IV pilin proteins are α+β proteins characterized by a very long N-terminal alpha helix. The assembly of these pili relies on interactions between the N-terminal helices of the individual monomers. The pilus structure sequesters the helices in the center of the fiber lining a central pore, while antiparallel beta sheets occupy the exterior of the fiber.{{cite journal |vauthors=Forest KT, Tainer JA |title=Type-4 pilus-structure: outside to inside and top to bottom--a minireview |journal=Gene |volume=192 |issue=1 |pages=165–9 |year=1997 |pmid=9224887 |doi= 10.1016/s0378-1119(97)00008-5}}

= Role of ComP pilin in bacterial transformation =

Genetic transformation is the process by which a recipient bacterial cell takes up DNA from a neighboring cell and integrates this DNA into the recipient’s genome by homologous recombination. In Neisseria meningitidis, DNA transformation requires the presence of short DNA uptake sequences (DUSs) which are 9-10mers residing in coding regions of the donor DNA. Specific recognition of DUSs is mediated by a type IV pilin, ComP.{{cite journal |vauthors=Berry JL, Cehovin A, McDowell MA, Lea SM, Pelicic V |title=Functional analysis of the interdependence between DNA uptake sequence and its cognate ComP receptor during natural transformation in Neisseria species |journal=PLOS Genet. |volume=9 |issue=12 |pages=e1004014 |year=2013 |pmid=24385921 |pmc=3868556 |doi=10.1371/journal.pgen.1004014 |doi-access=free }}{{cite journal |vauthors=Cehovin A, Simpson PJ, McDowell MA, Brown DR, Noschese R, Pallett M, Brady J, Baldwin GS, Lea SM, Matthews SJ, Pelicic V |title=Specific DNA recognition mediated by a type IV pilin |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=110 |issue=8 |pages=3065–70 |year=2013 |pmid=23386723 |pmc=3581936 |doi=10.1073/pnas.1218832110 |bibcode=2013PNAS..110.3065C |doi-access=free }} Menningococcal type IV pili bind DNA through the minor pilin ComP via an electropositive stripe that is predicted to be exposed on the filament's surface. ComP displays an exquisite binding preference for selective DUSs. The distribution of DUSs within the N. meningitidis genome favors certain genes, suggesting that there is a bias for genes involved in genomic maintenance and repair.{{cite journal |vauthors=Davidsen T, Rødland EA, Lagesen K, Seeberg E, Rognes T, Tønjum T |title=Biased distribution of DNA uptake sequences towards genome maintenance genes |journal=Nucleic Acids Res. |volume=32 |issue=3 |pages=1050–8 |year=2004 |pmid=14960717 |pmc=373393 |doi=10.1093/nar/gkh255 }}{{cite journal |vauthors=Caugant DA, Maiden MC |title=Meningococcal carriage and disease--population biology and evolution |journal=Vaccine |volume=27 |pages=B64–70 |year=2009 |issue=Suppl 2 |pmid=19464092 |pmc=2719693 |doi=10.1016/j.vaccine.2009.04.061 }}

Chaperone-usher pilin

The Cup family is known for its use of a chaperone and at least an usher. They exhibit an Ig fold.{{cite journal |vauthors=Verger D, etal | title=Crystal structure of the P-pilus rob subunit PapA | journal=PLOS ONE | year=2007 | doi=10.1371/journal.ppat.0030073 | volume=3 | issue=5 | pages=e73| pmc=1868955 | pmid=17511517 | doi-access=free }}

=Saf, N-terminal extension=

{{Infobox protein family

| Symbol = Saf-Nte_pilin

| Name = Saf-Nte_pilin

| image = PDB 2co1 EBI.jpg

| width =

| caption = Salmonella enterica SafA pilin in complex with a 19-residue SafA Nte peptide (f17a mutant)

| Pfam = PF09460

| Pfam_clan =

| InterPro = IPR018569

| SMART =

| PROSITE =

| MEROPS =

| SCOP =

| TCDB =

| OPM family =

| OPM protein =

| CAZy =

| CDD =

}}

The Saf pilin N-terminal extension protein domain helps the pili to form, via a complex mechanism named the chaperone/usher pathway. It is found in all c-u pilins.{{cite journal |last1=Waksman |first1=G |last2=Hultgren |first2=SJ |title=Structural biology of the chaperone-usher pathway of pilus biogenesis. |journal=Nature Reviews. Microbiology |date=November 2009 |volume=7 |issue=11 |pages=765–74 |doi=10.1038/nrmicro2220 |pmid=19820722 |pmc=3790644 |doi-access=free}}

This protein domain is very important for such bacteria, as without pili formation, they could not infect the host. Saf is a Salmonella operon containing a c-u pilus system.

=Function=

This protein domain, has an important function in forming pili. These are virulence factors crucial for cell adhesion to the host and biofilm formation with successful infection.{{cite journal | vauthors = Salih O, Remaut H, Waksman G, Orlova EV | title = Structural analysis of the Saf pilus by electron microscopy and image processing | journal = Journal of Molecular Biology | volume = 379 | issue = 1 | pages = 174–87 | date = May 2008 | pmid = 18448124 | doi = 10.1016/j.jmb.2008.03.056 | url = https://pubmed.ncbi.nlm.nih.gov/18448124 }}

= Structure =

This protein domain consists of the adjacent Saf-Nte and Saf-pilin chains of the pilus-forming complex. They are Chaperone/usher (CU) pili, and have an N-terminal extension (Nte) of around 10-20 amino acids. Salmonella Saf pili, which are assembled by FGl chaperones. The structure has been well conserved, as they contain a set of alternating hydrophobic residues that form an essential part of the subunit–subunit interaction.{{cite journal | vauthors = Waksman G, Hultgren SJ | title = Structural biology of the chaperone-usher pathway of pilus biogenesis | journal = Nature Reviews. Microbiology | volume = 7 | issue = 11 | pages = 765–74 | date = November 2009 | pmid = 19820722 | pmc = 3790644| doi = 10.1038/nrmicro2220 }}

=Mechanism=

The mechanism for the assembly reaction is termed donor strand exchange DSE which

Pilus assembly in Gram-negative bacteria involves a Donor-strand exchange mechanism between the C- and the N-termini of this domain. The C-terminal subunit forms an incomplete Ig-fold which is then complemented by the 10-18 residue N terminus of another.

The N terminus sequences contain a motif of alternating hydrophobic residues that occupy the P2 to P5 binding pockets in the groove of the first pilus subunit.{{cite journal | vauthors = Remaut H, Rose RJ, Hannan TJ, Hultgren SJ, Radford SE, Ashcroft AE, Waksman G | title = Donor-strand exchange in chaperone-assisted pilus assembly proceeds through a concerted beta strand displacement mechanism | journal = Molecular Cell | volume = 22 | issue = 6 | pages = 831–42 | date = June 2006 | pmid = 16793551 | doi = 10.1016/j.molcel.2006.05.033 | doi-access = free }}

LPXTG pilin

LPXTG pilin is common in gram-positive cocci. They are named for a C-terminal motif used by the sortase. There is also a LPXTGase.

= Development of molecular tools =

LPXTG Pili in Gram-positive bacteria contain spontaneously formed isopeptide bonds. These bonds provide enhanced mechanical{{cite journal |vauthors=Alegre-Cebollada J, Badilla CL, Fernández JM |title=Isopeptide bonds block the mechanical extension of pili in pathogenic Streptococcus pyogenes |journal=J. Biol. Chem. |volume=285 |issue=15 |pages=11235–11242 |year=2010 |pmid=20139067 |doi=10.1074/jbc.M110.102962 |pmc=2857001|doi-access=free }} and proteolytic{{cite journal | vauthors = Kang HJ, Coulibaly F, Clow F, Proft T, Baker EN | year = 2007 | title = Stabilizing isopeptide bonds revealed in gram-positive bacterial pilus structure | journal = Science | volume = 318 | issue = 5856| pages = 1625–1628 | doi=10.1126/science.1145806 | pmid=18063798| bibcode = 2007Sci...318.1625K | s2cid = 5627277 }} stability to the pilin protein. Recently, the pilin protein from Streptococcus pyogenes has been split into two fragments to develop a new molecular tool called the isopeptag.{{cite journal |vauthors=Zakeri B, Howarth M |title=Spontaneous intermolecular amide bond formation between side chains for irreversible peptide targeting |journal=J. Am. Chem. Soc. |volume=132 |issue=13 |pages=4526–7 |year=2010 |pmid=20235501 |doi=10.1021/ja910795a |bibcode=2010JAChS.132.4526Z |citeseerx=10.1.1.706.4839 }} The isopeptag is a short peptide that can be attached to a protein of interest and can bind its binding partner through a spontaneously formed isopeptide bond. This new peptide tag can allow scientists to target and isolate their proteins of interest through a permanent covalent bond.