Punctuated and continuous structural diversity of S-layers across the prokaryotic tree of life
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Abstract
Surface layers (S-layers) are two-dimensional (2D) crystalline lattices that frequently coat prokaryotic cells, playing a crucial role in protection, maintaining cellular integrity, and mediating environmental interactions. However, the molecular landscape of these abundant proteins has remained underexplored due to a lack of structural data. By employing AlphaFold2multimer together with planar symmetry constraints in a workflow validated by electron cryomicroscopy structure determination, we have elucidated the lattice structures of over 150 S-layers from diverse archaea and bacteria. Our findings unveil a multifaceted evolutionary landscape for S-layer proteins, highlighting key differences in the evolution of bacterial and archaeal S-layers. Our study allows us to discover underlying patterns in S-layer structure, organisa-tion, and cell anchoring mechanisms across the prokaryotic tree of life, deepening our understanding of the intricately complex microbial cell surfaces, which appear to have evolved proteinaceous S-layers independently on multiple occasions. This work will open avenues for rational manipulation of prokaryotic cellular interactions in multicellular microbiomes, as well as for innovative 2D biomaterial design.
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Thank for your paper on S-layer structures across the bacterial and archaeal domains! I think this is a great use case for AlphaFold-multimer. Your work should help us understand much more about S-layer biology in the coming years. In my postdoc, I studied the interactions between a Type VI secretion system effector (Tae1) and the bacterial peptidoglycan (PG) layer. Scientists have made some progress on understanding how proteins interact with the heterogeneous megadalton mesh that is the PG layer but there are still many interesting questions that remain. For example, how does a protein find its binding site, or cut site, in 3D space? Besides the active site, what are the protein surfaces that interact with the PG layer? And how are these interactions different as the PG layer changes throughout the lifetime of a bacterial cell? …
Thank for your paper on S-layer structures across the bacterial and archaeal domains! I think this is a great use case for AlphaFold-multimer. Your work should help us understand much more about S-layer biology in the coming years. In my postdoc, I studied the interactions between a Type VI secretion system effector (Tae1) and the bacterial peptidoglycan (PG) layer. Scientists have made some progress on understanding how proteins interact with the heterogeneous megadalton mesh that is the PG layer but there are still many interesting questions that remain. For example, how does a protein find its binding site, or cut site, in 3D space? Besides the active site, what are the protein surfaces that interact with the PG layer? And how are these interactions different as the PG layer changes throughout the lifetime of a bacterial cell? Although there are significant differences, there are also multiple similarities between the S-layer and the PG layer. I think these questions about protein and PG layer interactions could also be asked about the protein interactions with the S-layer. I was wondering if your modeling approach and your S-layer structures could help us understand how proteins interact with the massive 2D crystalline structure of the S-layer rather than with individual S-layer proteins? Thank you for your time! And thanks again for all of your hard work that went into producing this publication!
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