Title

Evolutionary analyses of Vertebrate Nucleoporin 214 (Nup214): Insights into a Fundamental Component of the Nuclear Pore Complex

Results

Figure 1. Phylogenetic Tree

Figure 2. Purifying and Positive selection in vertebrate Nup214

You can view the interactive results here:
http://vision.hyphy.org/FEL?resultsUrl=https://raw.githubusercontent.com/aglucaci/AOC-Nup214/main/results/Craniata/nup214_processed_distributed_recombinationfree.fas.FEL.json

We find a high degree of purifying selection (2266/5716) ~40% (All sites). We find a high degree of purifying selection (2266/3594) ~63% (Non-invariant sites). We find 2122 invariant sites out of 5716 sites, ~37%. Positive selection (re: adaptation) in 46/3594 = 1.3% of sites. Note: These need to be mapped to the Human reference

Figure 3. Integrated results

Figure 4. PDB structure

Figure 5. AMES Analysis

Figure 6. Network analysis

Figure 7. AlphaMissense analysis

Figure 8. Coevolution analysis

Figure 9. MEME Results

Figure 10. BUSTED model testing results

Figure 11. Ancestral resurrection analysis

Supplementary Figure 1. Genetic distance histogram

Methods

Data Retrieval (NCBI)

We queried the NCBI database for the Nup214 gene using the following URL, https://www.ncbi.nlm.nih.gov/gene/8021/ortholog/?scope=89593&term=NUP214 (last accessed June 2023).

This query returned 517 full gene sets which transcript and protein sequences, with one sequence per species.

We downloaded all available files: Reference sequence (RefSeq) protein sequences, RefSeq transcript sequences, and Tabular data (CSV) which contains sequence metadata.

Selection analyses (preliminary)

FEL (Detects positive and negative selection)

Recombination detection (validation)

Using RDP v4.101

RDP Settings v4.101

Rejected all events which raised a warning upon reexamination

Found 3 events in:

XM_015567742_1_PREDICTED_Myotis_davidii_nucleopori_15586-16528

XM_023536519_1_PREDICTED_Pteropus_vampyrus_nucleop_15928-17148

XM_017849892_1_PREDICTED_Rhinopithecus_bieti_nucle_8449-8796

Additional analyses (Left to do)

UTR analyses

Are there any correlations we can draw from untranslated regions to substitutions in coding regions?

AMES

Ancestral sequence reconstruction (SLAC), and protein structural prediction (Alphafold2)

Network analysis (using StringDB)

This is a new analysis, look at protein interaction networks for Nup214 across the species in our analysis, is there any conservation of protein-protein interactions we can examine?

Genetic distances (TN93)

Phylogenetic Tree (full tree)

Discussion

The study of nucleoporin 214 (NUP214) is of significant interest in the field of cell biology due to its crucial role in nucleocytoplasmic transport. This protein, a key component of the nuclear pore complex (NPC), has been conserved across eukaryotic lineages, underscoring its fundamental importance in cellular processes. In this discussion, we delve into the evolutionary history of NUP214, examining its conservation, diversification, and potential functional adaptations over time.

Conservation and Ancient Origins

The analysis of NUP214 orthologs across diverse eukaryotic taxa reveals a remarkable degree of sequence conservation, indicating its ancient origins. From unicellular organisms to multicellular eukaryotes, NUP214 homologs can be identified, suggesting an early establishment of its fundamental role in cellular function. This conservation underscores the essential nature of NUP214 in cellular physiology and its potential involvement in critical biological processes predating the emergence of complex organisms.

Diversification and Domain Architecture

While NUP214's overall sequence is conserved, its domain architecture displays intriguing diversification across different lineages. Evolutionary pressures and selective forces have led to the emergence of distinct domain compositions, potentially contributing to the protein's functional versatility. For example, certain species exhibit variations in FG-repeat motifs within NUP214, indicating potential adaptations in nucleocytoplasmic transport mechanisms in response to specific environmental or physiological demands.

Phylogenetic Analyses and Functional Significance

Phylogenetic reconstructions of NUP214 homologs offer insights into the evolutionary relationships between different taxa and shed light on potential functional implications. Clustering patterns suggest that certain groups of organisms may have undergone unique evolutionary trajectories, potentially leading to specialized roles for NUP214 in specific cellular contexts. Comparative studies of NUP214's functional properties in these divergent lineages could provide valuable insights into the protein's adaptive significance.

Co-evolutionary Relationships with Interacting Proteins

NUP214 does not function in isolation but is part of a complex network of proteins within the NPC. Investigating the co-evolutionary relationships between NUP214 and its interacting partners provides further clues about its functional constraints and adaptations. Co-evolutionary analyses can reveal conserved residues and structural features that are critical for protein-protein interactions, offering a deeper understanding of how NUP214 contributes to the overall architecture and function of the NPC.

Functional Implications and Future Directions

The evolutionary history of NUP214 offers a foundation for exploring its functional significance in various biological contexts. Understanding how this protein has evolved can guide experimental studies aimed at unraveling its specific roles in nucleocytoplasmic transport, cellular signaling, and potential contributions to disease states. Future research should focus on targeted investigations into NUP214's interactions, post-translational modifications, and subcellular localization in diverse organisms to elucidate its multifaceted functions.

Summary

The evolutionary history of NUP214 provides a valuable framework for exploring its functional diversity and adaptability across eukaryotic lineages. By combining phylogenetic analyses, comparative genomics, and experimental approaches, we can gain a comprehensive understanding of how NUP214 has shaped cellular processes throughout evolutionary history and its potential implications for modern cell biology and medicine.

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