P03743

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research report: Functional annotation of Enterobacteria phage T4 gene 36 (gp36; UniProt P03743)

0) Target verification (mandatory)

The target protein is Enterobacteria phage T4 long-tail fiber protein gp36, encoded by gene 36, UniProt P03743. Multiple authoritative T4 morphogenesis and structural reviews explicitly identify gp36 as a trimeric structural component of the T4 long tail fiber (LTF), positioned in the distal/hinge region and present at 3 copies per fiber (6 fibers per virion). This matches the UniProt identity and rules out unrelated “gene 36” symbols from other organisms. (leiman2003structureandmorphogenesis pages 11-13, leiman2010morphogenesisofthe pages 2-5)

1) Key concepts, definitions, and current understanding

1.1 Long tail fibers (LTFs) as adsorption/sensing devices

In myophages like T4, long tail fibers are elongated viral adhesins that mediate initial, reversible host recognition, act as environmental sensors, and transmit information to the baseplate to trigger downstream infection steps (e.g., baseplate rearrangements and tail sheath contraction). Structurally, the T4 LTF is a ~1440–1450 Å long, hinged fiber with proximal and distal segments. (leiman2003structureandmorphogenesis pages 8-11, leiman2010morphogenesisofthe pages 21-22)

1.2 Where gp36 fits into the LTF architecture

The T4 LTF is assembled from four principal structural proteins: gp34 (proximal rod; trimer), gp35 (kneecap/hinge; monomer), gp36 (distal rod “upper shin”; trimer), and gp37 (distal receptor-binding tip module; trimer). In this framework, gp36 is primarily a structural/assembly adaptor in the distal rod/hinge-proximal region and is not described as the major receptor-binding component (that role is concentrated in gp37). (hyman2018bacteriophaget4long pages 1-2, leiman2010morphogenesisofthe pages 21-22)

2) Molecular function of gp36 (what it does)

2.1 Primary function: structural connector enabling distal half-fiber formation

The strongest evidence-supported functional assignment for gp36 (gene product 36) is as a trimeric structural element of the distal half-fiber that:
1) binds the N-terminal region of gp37 to create a gp36–gp37 assembly, and then
2) accepts binding of gp35 to complete the distal half-fiber before joining the gp34-containing proximal half-fiber. (leiman2010morphogenesisofthe pages 21-22, hyman2018bacteriophaget4long pages 2-4)

This positions gp36 as a key morphogenetic intermediate necessary to create a correctly assembled distal LTF module and to connect the receptor-binding tip region (gp37) to the rest of the LTF. (leiman2010morphogenesisofthe pages 21-22, leiman2003structureandmorphogenesis pages 8-11)

2.2 Role in the hinge/junction between proximal and distal segments

Architectural descriptions of T4 LTFs place gp36 in the distal part/hinge connection, and the hinge is described as involving gp35 and termini of gp34 and gp36. Thus, gp36 likely contributes mechanically to the hinged geometry that allows LTFs to fold against the virion and to adopt different angles during receptor searching on the bacterial surface. (leiman2003structureandmorphogenesis pages 8-11, hyman2018bacteriophaget4long pages 1-2)

3) Biological process context: adsorption-to-infection pathway

3.1 Cooperative use of multiple fibers

T4 virions can deploy up to six LTFs, and infection requires cooperative interactions. A quantitative constraint summarized in the T4 morphogenesis literature is that at least three LTFs are required for infectivity, consistent with a model where multiple fibers increase the probability of productive receptor engagement and correct baseplate activation. (leiman2010morphogenesisofthe pages 21-22)

3.2 Receptor recognition is primarily gp37; gp36 supports the infection-initiating machine

While gp36 is integral to the distal fiber architecture, receptor recognition is emphasized as a function of the gp37 distal tip, which recognizes outer surface features (e.g., LPS and OmpC are commonly cited receptors for T4 LTFs in the broader literature). gp36 is therefore best annotated as a structural component that positions and stabilizes the receptor-binding machinery, enabling signal transmission to the baseplate rather than providing specificity itself. (hyman2018bacteriophaget4long pages 1-2, leiman2003structureandmorphogenesis pages 11-13)

4) Subcellular/virion localization

4.1 Location within the mature virion

Stoichiometry and localization compiled for T4 tail fibers indicate:
- 3 gp36 subunits per long tail fiber, with 6 LTFs per virion (implying 18 gp36 copies per virion). (leiman2003structureandmorphogenesis pages 11-13)
- gp36 is located in the distal part at the hinge connection. (leiman2010morphogenesisofthe pages 2-5)

A detailed morphogenesis description localizes gp36 at the proximal end of the distal half-fiber, forming the upper part of the “shin,” consistent with an internal distal-rod role. (leiman2010morphogenesisofthe pages 21-22)

5) Structural features and domains (what is known vs inferred)

5.1 Experimental structural knowledge: gp36 remains structurally under-resolved

Compared with gp34 and gp37, for which partial crystal structures exist in the literature base, gp36 lacks a widely cited high-resolution experimental structure in the sources retrieved here. Consequently, most gp36 structural insight is inferential (sequence/secondary structure prediction and comparative analyses). (hyman2018bacteriophaget4long pages 1-2, hyman2018bacteriophaget4long pages 6-7)

5.2 Bioinformatic inference from authoritative review

A domain-focused review reports that gp36 is:
- a small (221-residue) homo-trimer,
- predominantly β-structured, and
- predicted to lack coiled-coil regions.
Additionally, HHpred detects a short similarity between gp36 residues 35–61 and gp34 residues 1234–1250, interpreted as potential evidence of a shared/analogous interface involved in assembly junctions, including possible gp35-binding architecture at gp34/gp36 ends. (hyman2018bacteriophaget4long pages 6-7)

6) Quantitative “stats & data” relevant to gp36 functional annotation

6.1 Fiber geometry and dimensions

T4 LTF architecture is described quantitatively as:
- total length ~1440–1450 Å;
- proximal half ~700 Å and distal half ~740 Å;
- fiber diameter ~40–50 Å;
- commonly conceptualized as two ~80 nm rods joined at ~160°. (leiman2003structureandmorphogenesis pages 8-11, leiman2010morphogenesisofthe pages 21-22, hyman2018bacteriophaget4long pages 1-2)

6.2 Infectivity constraint

As noted above, ≥3 LTFs are required for infectivity, giving a quantitative systems-level constraint on the LTF module in which gp36 is embedded. (leiman2010morphogenesisofthe pages 21-22)

7) Recent developments (prioritizing 2023–2024)

7.1 2024: Tail fiber structural “atlas” and segmentation-based modeling (RBPseg)

A 2024 preprint introduces RBPseg, a method combining monomeric ESMfold predictions with sigmoid distance pair (sDp) segmentation to divide tail fibers into domains and then model segments using AlphaFold2-multimer (AF2M v2.3.2), improving confidence and feasibility for elongated trimeric RBPs. The authors explicitly use T4 LTF composition (gp34/gp35/gp36/gp37) as a canonical example of multi-protein tail fiber systems. (kleinsousa2024towardsacomplete pages 1-4)

This work also provides quantitative ecosystem-level statistics valuable for annotation and engineering: after filtering UniProtKB, they analyzed 16,345 annotated tail-fiber sequences (from >64,000 initial hits) and report structural-class HMM recovery of 4,417 unique proteins and coverage of ~24% of the known tail-fiber universe (E-value < 10^-10). (kleinsousa2024towardsacomplete pages 21-25)

7.2 2023: Modern cryo-EM + AlphaFold workflows for myophage tail fibers

A 2023 Nature Communications cryo-EM study of a therapeutic-cocktail-relevant myophage (E217) shows the current state of practice: tail fibers were modeled in fragments using AlphaFold2, and tail fiber N-termini were fit into a 3.6 Å focused reconstruction (reported CC = 0.84). The study provides concrete experimental parameters (e.g., 22,015 micrographs, 10,826 final particles) and demonstrates functional host-interaction assays, such as LPS incubation with defined masses (500/50/5 µg) followed by EOP measurement. These methods are directly relevant to resolving proteins like gp36 that remain structurally under-characterized. (li2023highresolutioncryoemstructure pages 12-13)

8) Current applications and real-world implementations (2024 emphasis)

8.1 Phage therapy development and host-range engineering targets implicating tail-fiber genes

A 2024 experimental study characterized 16 bacteriophages infecting multidrug-resistant uropathogenic E. coli (UPEC). Quantitative outcomes include:
- Individual phages infected 2–44 strains out of 77 (reported as 3–57% breadth depending on phage);
- A six-phage cocktail productively infected 52 strains (67%);
- Adsorption rates 72–98% in 5 min, latent periods 7.5–15 min, burst sizes 38–211;
- In liquid culture, the cocktail produced complete suppression in the first 5–22 h, and at 24 h reduced growth to 43–92% of control (also 53–79% in artificial urine). (markuskova2024characterizationofbacteriophages pages 1-2, markuskova2024characterizationofbacteriophages pages 3-5, markuskova2024characterizationofbacteriophages pages 5-7, markuskova2024characterizationofbacteriophages pages 7-11)

Crucially for gp36-related functional annotation and engineering rationale, the study’s genome analysis highlights variability in receptor-recognition genes and notes differences involving long tail fiber proteins gp36/gp37/gp38 as determinants of host specificity—supporting the expert view that tail fiber gene modules are primary levers for altering host range in T4-like phages. (markuskova2024characterizationofbacteriophages pages 3-5, markuskova2024characterizationofbacteriophages pages 5-7)

9) Expert synthesis and analysis (authoritative interpretations)

9.1 Consensus view: gp36 is an internal structural adaptor in the distal half-fiber

Across independent expert reviews spanning 2003–2018, gp36 is consistently described as:
- a small, trimeric structural protein;
- positioned at the proximal end of the distal half-fiber (the “upper shin”);
- functioning in assembly and mechanical linkage between the gp35 hinge and the gp37 receptor-binding module, and between distal and proximal LTF segments. (leiman2010morphogenesisofthe pages 21-22, hyman2018bacteriophaget4long pages 1-2)

9.2 Knowledge gaps

Despite detailed architectural placement, a key remaining gap is the lack (in the retrieved evidence set) of a high-resolution experimental structure of gp36 and of direct biochemical binding constants for gp36 interactions (e.g., gp36–gp37 affinity). The field is moving toward resolving such gaps using integrated cryo-EM and deep-learning modeling workflows. (hyman2018bacteriophaget4long pages 6-7, li2023highresolutioncryoemstructure pages 12-13)

10) Summary of evidence map

Table: This table summarizes verified evidence about Enterobacteria phage T4 gp36, including its identity, structural role in the long tail fiber, assembly partners, and recent methodological advances relevant to studying gp36-like proteins.

Key references (with dates and URLs)

• Leiman PG et al. 2003-11. Structure and morphogenesis of bacteriophage T4. Cellular and Molecular Life Sciences. https://doi.org/10.1007/s00018-003-3072-1 (leiman2003structureandmorphogenesis pages 8-11, leiman2003structureandmorphogenesis pages 11-13)
• Leiman PG et al. 2010-12. Morphogenesis of the T4 tail and tail fibers. Virology Journal. https://doi.org/10.1186/1743-422x-7-355 (leiman2010morphogenesisofthe pages 21-22, leiman2010morphogenesisofthe pages 2-5, leiman2010morphogenesisofthe media 0ee2a966, leiman2010morphogenesisofthe media 683f1989)
• Hyman P, van Raaij MJ. 2018-12. Bacteriophage T4 long tail fiber domains. Biophysical Reviews. https://doi.org/10.1007/s12551-017-0348-5 (hyman2018bacteriophaget4long pages 6-7, hyman2018bacteriophaget4long pages 2-4, hyman2018bacteriophaget4long pages 1-2)
• Li F et al. 2023-07. High-resolution cryo-EM structure of the Pseudomonas bacteriophage E217. Nature Communications. https://doi.org/10.1038/s41467-023-39756-z (li2023highresolutioncryoemstructure pages 12-13)
• Klein-Sousa V et al. 2024-10. Towards a complete phage tail fiber structure atlas. bioRxiv. https://doi.org/10.1101/2024.10.28.620165 (kleinsousa2024towardsacomplete pages 7-11, kleinsousa2024towardsacomplete pages 21-25, kleinsousa2024towardsacomplete pages 1-4, kleinsousa2024towardsacomplete pages 29-32)
• Markusková B et al. 2024-06. Characterization of bacteriophages infecting multidrug-resistant uropathogenic Escherichia coli strains. Archives of Virology. https://doi.org/10.1007/s00705-024-06063-x (markuskova2024characterizationofbacteriophages pages 1-2, markuskova2024characterizationofbacteriophages pages 3-5, markuskova2024characterizationofbacteriophages pages 5-7, markuskova2024characterizationofbacteriophages pages 7-11, markuskova2024characterizationofbacteriophages pages 2-3)

References

1. (leiman2003structureandmorphogenesis pages 11-13): P. G. Leiman, S. Kanamaru, V. V. Mesyanzhinov, F. Arisaka, and M. G. Rossmann. Structure and morphogenesis of bacteriophage t4. Cellular and Molecular Life Sciences CMLS, 60:2356-2370, Nov 2003. URL: https://doi.org/10.1007/s00018-003-3072-1, doi:10.1007/s00018-003-3072-1. This article has 359 citations.

2. (leiman2010morphogenesisofthe pages 2-5): Petr G Leiman, Fumio Arisaka, Mark J van Raaij, Victor A Kostyuchenko, Anastasia A Aksyuk, Shuji Kanamaru, and Michael G Rossmann. Morphogenesis of the t4 tail and tail fibers. Virology Journal, 7:355-355, Dec 2010. URL: https://doi.org/10.1186/1743-422x-7-355, doi:10.1186/1743-422x-7-355. This article has 319 citations and is from a peer-reviewed journal.

3. (leiman2003structureandmorphogenesis pages 8-11): P. G. Leiman, S. Kanamaru, V. V. Mesyanzhinov, F. Arisaka, and M. G. Rossmann. Structure and morphogenesis of bacteriophage t4. Cellular and Molecular Life Sciences CMLS, 60:2356-2370, Nov 2003. URL: https://doi.org/10.1007/s00018-003-3072-1, doi:10.1007/s00018-003-3072-1. This article has 359 citations.

4. (leiman2010morphogenesisofthe pages 21-22): Petr G Leiman, Fumio Arisaka, Mark J van Raaij, Victor A Kostyuchenko, Anastasia A Aksyuk, Shuji Kanamaru, and Michael G Rossmann. Morphogenesis of the t4 tail and tail fibers. Virology Journal, 7:355-355, Dec 2010. URL: https://doi.org/10.1186/1743-422x-7-355, doi:10.1186/1743-422x-7-355. This article has 319 citations and is from a peer-reviewed journal.

5. (hyman2018bacteriophaget4long pages 1-2): Paul Hyman and Mark van Raaij. Bacteriophage t4 long tail fiber domains. Biophysical Reviews, 10:463-471, Dec 2018. URL: https://doi.org/10.1007/s12551-017-0348-5, doi:10.1007/s12551-017-0348-5. This article has 64 citations and is from a peer-reviewed journal.

6. (hyman2018bacteriophaget4long pages 2-4): Paul Hyman and Mark van Raaij. Bacteriophage t4 long tail fiber domains. Biophysical Reviews, 10:463-471, Dec 2018. URL: https://doi.org/10.1007/s12551-017-0348-5, doi:10.1007/s12551-017-0348-5. This article has 64 citations and is from a peer-reviewed journal.

7. (hyman2018bacteriophaget4long pages 6-7): Paul Hyman and Mark van Raaij. Bacteriophage t4 long tail fiber domains. Biophysical Reviews, 10:463-471, Dec 2018. URL: https://doi.org/10.1007/s12551-017-0348-5, doi:10.1007/s12551-017-0348-5. This article has 64 citations and is from a peer-reviewed journal.

8. (kleinsousa2024towardsacomplete pages 1-4): Victor Klein-Sousa, Aritz Roa-Eguiara, Claudia S. Kielkopf, Nicholas Sofos, and Nicholas M. I. Taylor. Towards a complete phage tail fiber structure atlas. bioRxiv, Oct 2024. URL: https://doi.org/10.1101/2024.10.28.620165, doi:10.1101/2024.10.28.620165. This article has 2 citations.

9. (kleinsousa2024towardsacomplete pages 21-25): Victor Klein-Sousa, Aritz Roa-Eguiara, Claudia S. Kielkopf, Nicholas Sofos, and Nicholas M. I. Taylor. Towards a complete phage tail fiber structure atlas. bioRxiv, Oct 2024. URL: https://doi.org/10.1101/2024.10.28.620165, doi:10.1101/2024.10.28.620165. This article has 2 citations.

10. (li2023highresolutioncryoemstructure pages 12-13): Fenglin Li, Chun-Feng David Hou, Ravi K. Lokareddy, Ruoyu Yang, Francesca Forti, Federica Briani, and Gino Cingolani. High-resolution cryo-em structure of the pseudomonas bacteriophage e217. Nature Communications, Jul 2023. URL: https://doi.org/10.1038/s41467-023-39756-z, doi:10.1038/s41467-023-39756-z. This article has 56 citations and is from a highest quality peer-reviewed journal.

11. (markuskova2024characterizationofbacteriophages pages 1-2): Barbora Markusková, Sulafa Elnwrani, Michal Andrezál, Tatiana Sedláčková, Tomáš Szemes, Lívia Slobodníková, Michal Kajsik, and Hana Drahovská. Characterization of bacteriophages infecting multidrug-resistant uropathogenic escherichia coli strains. Archives of Virology, Jun 2024. URL: https://doi.org/10.1007/s00705-024-06063-x, doi:10.1007/s00705-024-06063-x. This article has 20 citations and is from a peer-reviewed journal.

12. (markuskova2024characterizationofbacteriophages pages 3-5): Barbora Markusková, Sulafa Elnwrani, Michal Andrezál, Tatiana Sedláčková, Tomáš Szemes, Lívia Slobodníková, Michal Kajsik, and Hana Drahovská. Characterization of bacteriophages infecting multidrug-resistant uropathogenic escherichia coli strains. Archives of Virology, Jun 2024. URL: https://doi.org/10.1007/s00705-024-06063-x, doi:10.1007/s00705-024-06063-x. This article has 20 citations and is from a peer-reviewed journal.

13. (markuskova2024characterizationofbacteriophages pages 5-7): Barbora Markusková, Sulafa Elnwrani, Michal Andrezál, Tatiana Sedláčková, Tomáš Szemes, Lívia Slobodníková, Michal Kajsik, and Hana Drahovská. Characterization of bacteriophages infecting multidrug-resistant uropathogenic escherichia coli strains. Archives of Virology, Jun 2024. URL: https://doi.org/10.1007/s00705-024-06063-x, doi:10.1007/s00705-024-06063-x. This article has 20 citations and is from a peer-reviewed journal.

14. (markuskova2024characterizationofbacteriophages pages 7-11): Barbora Markusková, Sulafa Elnwrani, Michal Andrezál, Tatiana Sedláčková, Tomáš Szemes, Lívia Slobodníková, Michal Kajsik, and Hana Drahovská. Characterization of bacteriophages infecting multidrug-resistant uropathogenic escherichia coli strains. Archives of Virology, Jun 2024. URL: https://doi.org/10.1007/s00705-024-06063-x, doi:10.1007/s00705-024-06063-x. This article has 20 citations and is from a peer-reviewed journal.

15. (leiman2010morphogenesisofthe media 0ee2a966): Petr G Leiman, Fumio Arisaka, Mark J van Raaij, Victor A Kostyuchenko, Anastasia A Aksyuk, Shuji Kanamaru, and Michael G Rossmann. Morphogenesis of the t4 tail and tail fibers. Virology Journal, 7:355-355, Dec 2010. URL: https://doi.org/10.1186/1743-422x-7-355, doi:10.1186/1743-422x-7-355. This article has 319 citations and is from a peer-reviewed journal.

16. (kleinsousa2024towardsacomplete pages 29-32): Victor Klein-Sousa, Aritz Roa-Eguiara, Claudia S. Kielkopf, Nicholas Sofos, and Nicholas M. I. Taylor. Towards a complete phage tail fiber structure atlas. bioRxiv, Oct 2024. URL: https://doi.org/10.1101/2024.10.28.620165, doi:10.1101/2024.10.28.620165. This article has 2 citations.

17. (leiman2010morphogenesisofthe media 683f1989): Petr G Leiman, Fumio Arisaka, Mark J van Raaij, Victor A Kostyuchenko, Anastasia A Aksyuk, Shuji Kanamaru, and Michael G Rossmann. Morphogenesis of the t4 tail and tail fibers. Virology Journal, 7:355-355, Dec 2010. URL: https://doi.org/10.1186/1743-422x-7-355, doi:10.1186/1743-422x-7-355. This article has 319 citations and is from a peer-reviewed journal.

18. (kleinsousa2024towardsacomplete pages 7-11): Victor Klein-Sousa, Aritz Roa-Eguiara, Claudia S. Kielkopf, Nicholas Sofos, and Nicholas M. I. Taylor. Towards a complete phage tail fiber structure atlas. bioRxiv, Oct 2024. URL: https://doi.org/10.1101/2024.10.28.620165, doi:10.1101/2024.10.28.620165. This article has 2 citations.

19. (markuskova2024characterizationofbacteriophages pages 2-3): Barbora Markusková, Sulafa Elnwrani, Michal Andrezál, Tatiana Sedláčková, Tomáš Szemes, Lívia Slobodníková, Michal Kajsik, and Hana Drahovská. Characterization of bacteriophages infecting multidrug-resistant uropathogenic escherichia coli strains. Archives of Virology, Jun 2024. URL: https://doi.org/10.1007/s00705-024-06063-x, doi:10.1007/s00705-024-06063-x. This article has 20 citations and is from a peer-reviewed journal.

Artifacts

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Citations

1. leiman2010morphogenesisofthe pages 21-22
2. leiman2003structureandmorphogenesis pages 11-13
3. leiman2010morphogenesisofthe pages 2-5
4. kleinsousa2024towardsacomplete pages 1-4
5. kleinsousa2024towardsacomplete pages 21-25
6. li2023highresolutioncryoemstructure pages 12-13
7. leiman2003structureandmorphogenesis pages 8-11
8. markuskova2024characterizationofbacteriophages pages 1-2
9. markuskova2024characterizationofbacteriophages pages 3-5
10. markuskova2024characterizationofbacteriophages pages 5-7
11. markuskova2024characterizationofbacteriophages pages 7-11
12. kleinsousa2024towardsacomplete pages 29-32
13. kleinsousa2024towardsacomplete pages 7-11
14. markuskova2024characterizationofbacteriophages pages 2-3
15. https://doi.org/10.1007/s00018-003-3072-1
16. https://doi.org/10.1186/1743-422x-7-355
17. https://doi.org/10.1007/s12551-017-0348-5
18. https://doi.org/10.1038/s41467-023-39756-z
19. https://doi.org/10.1101/2024.10.28.620165
20. https://doi.org/10.1007/s00705-024-06063-x
21. https://doi.org/10.1007/s00018-003-3072-1,
22. https://doi.org/10.1186/1743-422x-7-355,
23. https://doi.org/10.1007/s12551-017-0348-5,
24. https://doi.org/10.1101/2024.10.28.620165,
25. https://doi.org/10.1038/s41467-023-39756-z,
26. https://doi.org/10.1007/s00705-024-06063-x,