<p>UCYN-A is actively undergoing genome reduction as part of its evolution towards an organelle: the reason it cannot live independently is that essential proteins for its survival are no longer present in its genome, but are now encoded in B. bigelowii’s and then imported into UCYN-A.
Using recently released proteomics data on B. bigelowii and UCYN-A, along with older genomics and transcriptomics data, we have identified a putative list of proteins that are imported into the organelle. This data provides a solid foundation for further research into which proteins are essential, as we suspect many are redundant. Identifying a list of essential host-encoded proteins is crucial to successfully transplanting UCYN-A into a new host.
</p><p>We have also created a new transcriptome assembly of B. bigelowii based on raw data from previous studies, using improved algorithms. This allowed us to create a new predicted proteome.
We are making all of our omics data available for future iGEM teams along with documentation. </p>
<p>Read more on our <ahref="https://2024.igem.wiki/tu-delft/results">Results</a> page
<p>You can read more <ahref="https://2024.igem.wiki/tu-delft/results">here</a>
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<divclass="h1">UCYN-A transit peptide</div>
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<p>Based on previous studies and the proteomics data on B. bigelowii we identified a strongly preserved motif on the C-terminal end of B. bigelowii proteins that are imported to UCYN-A. This sequence was hypothesized to correspond to a transit peptide (UCYN-A transit peptide or uTP), responsible for localizing proteins to the organelle.</p>
<p>The characterization of the transit peptide is a crucial step in understanding the nitroplast protein import pathway in B. bigelowii. The part allows future teams to run experiments aiming to deliver proteins to UCYN-A, whether in its native host to investigate its behavior or within a different recipient cell, to create an environment where the nitroplast could survive if transplanted. This all has implications on advancing research toward engineering new nitroplast-containing, nitrogen-fixing eukaryote strains.</p>
<p>You can read more <ahref="https://2024.igem.wiki/tu-delft/results">here</a></p>
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<divclass="h1">Peptide binding model</div>
<p>Based on the previously identified transit peptide and the predicted B. bigelowii proteome, we attempted to find any proteins which interact with uTP and thus might play a role in the UCYN-A protein import system. To achieve this, we began developing a proteome-scale peptide-binding prediction tool, which, to our knowledge, does not yet exist.</p>
<p>Unfortunately, due to the strict time constraints in iGEM, we were not able to finish work on this tool, but we are making our existing code and data available to aid any future teams.</p>
<p>Read more on our Materials and Methods page</p>
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<divclass="h1">UCYN-A isolation</div>
<p>To facilitate the study of UCYN-A, a protocol to isolate the organelle from B. bigelowii is required. This has been done before, relying on a Percoll gradient. We attempted to develop an alternative protocol for future research via cell sorting which should prove quicker and less laborious, for future teams to be able to use.</p>
<p>Read more on our <ahref="https://2024.igem.wiki/tu-delft/results">Results</a> page </p>
<p>You can read more <ahref="https://2024.igem.wiki/tu-delft/results">here</p>
