Phylogenetic trees of Eukaryotic dCache_1AA proteins
Structures, models, and molecular docking
- Modeled structures of prokaryotic dCache_1AA domain protein sensors
- Structures of eukaryotic dCache_1AA proteins docked with ligands
We have discovered a universal amino acid binding motif (AA_motif) present in dCache_1 domain (http://pfam.xfam.org/family/PF02743) containing proteins throughout the Tree of Life (link to the paper: https://www.pnas.org/doi/10.1073/pnas.2110415119). The motif in its canonical form has the following definition:
Y....R.WY{n1}Y{n2}D.
Studying variability of the motif positions in experimentally studied organisms that still permits amino acid binding we deduced the following generalized motif definition:
[YFWL]....[RK].W[WYF]{n1}[YF]{n2}[D].
In these expressions any amino acid inside the given brackets can be present in the corresponding position, n1 - a varying distance of approximately 13-17 amino acid residues, n2 - a varying distance of approximately 27-34 residues.
As we have established, two dCache_1 domains are present in eukaryotic proteins that have the motif. In alpha2/delta-1 subunits of Voltage gated calcium channels and in their homologs the motif is present in the dCache_1 domain with the VWA insertion that splits the motif in two parts, and, correspondingly, n1 in the above expression is a varying distance of approximately 215-245 amino acid residues. In CACHD1 proteins and in their homologs the motif is present in the second dCache_1 domain that does not have the VWA insertion and, correspondengly, the distance is within the regular range of 27-34 residues.
Using the generalized universal amino acid binding motif (AA_motif) definition we scanned three protein sequence databases: GTDB (representative dataset; https://gtdb.ecogenomic.org/), NCBI RefSeq (https://www.ncbi.nlm.nih.gov/refseq/), and Uniprot (https://www.uniprot.org/). The details of this procedure can be found in Materials and Methods section of the paper describing the discovery of the motif throughout the Tree of Life.
Extracting regions corresponding to the dCache_1 domains in the identified protein sequences containing the AA_motif we constructed multiple sequence alignments (MSAs).
The RefSeq alignment is in RefSeq folder. There are 32395 dCache_1 domain containing proteins in the RefSeq database that have the amino acid binding motif.
Positions corresponding to the motif in this MSA:
Y(2091)....R(2302).W(2385)Y(2414){n1}Y(2727){n2}D(3326)
The Uniprot alignment is in Uniprot folder. There are 11330 dCache_1 domain containing proteins in the Uniprot database that have the amino acid binding motif.
Positions corresponding to the motif in this MSA:
Y(308)....R(313).W(315)Y(316){n1}Y(345){n2}D(420)
The GTDB alignment is in GTDB_Representative_Set folder. There are 10700 bacterial and 114 archaeal dCache_1 domain containing proteins in the GTDB database that have the universal amino acid binding motif.
Positions corresponding to the motif in the bacterial proteins MSA:
Y(1160)....R(1278).W(1290)Y(1291){n1}Y(1431){n2}D(1647)
Positions corresponding to the motif in the archaeal proteins MSA:
Y(163)....R(168).W(170)Y(171){n1}Y(189){n2}D(219)
Multiple sequence alignments of eukaryotic protein sequences of dCache_1 domains with the AA_motif is in Eukaryotes folder.
As eukaryotic alpha-2/delta-1 and CACHD1 proteins comprised of two dCache_1 domains, one of which has the VWA insertion (see the paper describing the universal AA_motif for details), and the number of sequenced eukaryotic genomes is limited, several databases (NCBI RefSeq, NCBI NR, Uniprot, 1KP, and EukProt) have been scanned to identify and extract homologous proteins. We have verified the presence of the motif constructing MSAs including in the alignment already identified motif-containing eukaryotic and bacterial sequences.
MSA of double dCache_1AA proten sequences from the representative set of eukaryotic organisms (file Eukaryotes_double_dCache_1_aln.fa). Positions corresponding to the motif in the first dCache_1 domain (in those proteins, in which the motif is preserved):
Y(295)....R(300).W(302)Y(303){n1}Y(648){n2}D(715)
Positions corresponding to the motif in the second dCache_1 domain (in those proteins, in which the motif is preserved):
Y(1231)....R(1236).W(1242)Y(1243){n1}Y(1265){n2}D(1363)
MSA of all dCache_1AA proten sequences from the complete set of eukaryotic organisms (zip archive Eukaryotic_proteins_Complete_set_aln.fa.zip): Positions corresponding to the motif in the first dCache_1 domain (in those proteins, in which the motif is preserved):
Y(8986)....R(8999).W(9001)Y(9002){n1}Y(11639){n2}D(12545)
Positions corresponding to the motif in the second dCache_1 domain (in those proteins, in which the motif is preserved):
Y(16149)....R(16226).W(16228)Y(16229){n1}Y(16362){n2}D(17717)
The trees are located in Eukaryotes folder. There are two trees in the folder: (i) inferred using maximum likelihood estimation implemented in RaXML in Newick format (file Eukaryotes_double_dCache_1_RaXML_tree.newick) and (ii) inferred using Bayesian inference implemented in MrBayes in Nexus format (file Eukaryotes_double_dcache_1_MrBayes_tree.tre).
Structures of dCache_1AA domain protein sensors from various phyla of Archaea and Bacteria were modeled by Phyre2 and are located in RefSeq folder (zip archive Structures_modeled_by_Phyre2.zip).
Structures of alpha2/delta-1 and CACHD1 are located in Eukaryotes/Structures_Autodock folder.
The list of files in the folder:
- File 1. Rabbit_alpha2delta1_docked_with_ligands.pdb
A cryo-EM structure was used for docking experiments.
- File 2. Fly_alpha2delta1_docked_with_ligands.pdb
An AlphaFold model was used for docking experiments.
- File 3. Human_CACHD1_docked_with_ligands.pdb
An AlphaFold model was used for docking experiments.
- File 4. Fly_CACHD1_docked_with_ligands.pdb
An AlphaFold model was used for docking experiments.
In 2019 I was investigating the mechanism of amino acid binding by three paralogous chemoreceptors encoded in the genome of the pathogenic bacterium Pseudomonas aeruginosa PAO1. While analyzing crystal structures of their sensor dCache_1 domains I have noticed that among the residues making hydrogen bonds with amino acid ligands five were common for all three paralogs. Exploring protein sequences of dCache_1 domain from all Proteobacteria I have established that positions corresponding to these five residues and one more are conserved throughout Proteobacteria. This was the first sign that I found an important and probably widely distributed motif. In the next step I have scanned all available bacterial and archaeal proteins for the presence of the motif and found it essentially in all bacterial and archaeal phyla that had available sequenced genomes.
While analyzing proteins in the UniProt database, to my surprise, I found the motif in some ancient eukaryotes. The next step was a leap of faith: I have immediately decided to look at the proteoms of vertebrate. I was doing my search using the string corresponding to the motif completely ignoring whether I am looking at dCache_1 domain or any other domain. To my great surprise I found the motif in the proteome of bull. This was truly amazing! What I found next was puzzling at first. In some eukaryotic proteins only the first part of the motif was present, while in others the entire motif was found. Investigating multiple sequence alignments I have later established that in those proteins that had just the first part of the motif, the second part was located more than 200 amino acids C-terminally and that there is an insertion between the two parts that split the motif. In eukaryotes the proteins I found the motif in were alpha2/delta and CACHD1 modulatory subunits of Voltage Gated Calcium channels. In CACHD1 homologs the motif was intact – no insertion splitting it, wheres in alpha2/delta the motif was split in two parts. At this point I did not have a complete understanding what these proteins were from the structural point of view.
In the same 2019 the rabbit alpha2/delta-1 protein Cryo-EM was published and the authors of the work claimed that the protein includes four Cache domains and VWA domain. I have depicted my findings on the board in the lab and these domains and a wild guess hit me: these are not four Cache domains, but 2 dCache_1 domains and the motif is located in the distal pocket of the N-terminal dCache_1 in alpha2/delta protein and of the C-terminal in CACHD1. Next, I have decided to do something unimaginable in the opinion of some of my colleagues – superimpose structurally the bacterial dCache_1 domain with the alpha2/delta-1 protein. And - success! The bacterial dCache_1 domain could be strcuturally aligned with too parts of the protein and those parts looked like the bacterial domain. Next, I found that the two parts of the motif, that are split by the VWA domain insertion, come together spatially forming the same interaface as in the bacterial proteins!
Another realization was that the C-terminal dCache_1 is inserted into the N-terminal one. Thus, two insertions occurred that gave rise to eukaryotic proteins! And as my molecular docking experiments and the experiments from the collaborating labs showed the functionality of the motif was not affected neither in CACHD1 nor in alpha2/delta-1 proteins.
Evolutionary analysis gave incredible results – in many proteins from pre-vertebrate eukaryotes the motif was preserved in both dCache_1 domains and over the course of evolution it was differentially lost in different groups of eukaryotes.