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Data from: Tek/Tie2 is not required for cardiovascular development in zebrafish

Citation

Jiang, Zhen et al. (2020), Data from: Tek/Tie2 is not required for cardiovascular development in zebrafish, Dryad, Dataset, https://doi.org/10.5061/dryad.np5hqbzr0

Abstract

Angiopoietin/TIE signalling plays a major role in blood and lymphatic vessel development.  In mouse, Tek/Tie2 mutants die prenatally due to a severely underdeveloped cardiovascular system.  In contrast, in zebrafish, previous studies have reported that while embryos injected with tek morpholinos (MOs) exhibit severe vascular defects, tek mutants display no obvious vascular malformations.  To further investigate the function of zebrafish Tek, we generated a panel of loss-of-function tek mutants, including RNA-less alleles, an allele lacking the MO-binding site, an in-frame deletion allele, and a premature termination codon-containing allele.  Our data show that all these mutants survive to adulthood with no obvious cardiovascular defects.  MO injections into tek mutants lacking the MO-binding site or the entire tek locus cause similar vascular defects as those observed in MO-injected +/+ siblings, indicating off-target effects of the MOs.  Surprisingly, comprehensive phylogenetic profiling and synteny analyses reveal that Tek was lost in the largest teleost clade, suggesting a lineage-specific shift in the function of TEK during vertebrate evolution.  Altogether, these data show that Tek is dispensable for zebrafish development, and probably dispensable in most teleost species.

Methods

Evolutionary analysis of TEK, TIE1 and Angiopoietins

We used HaMStR-OneSeq v1.8.0 (Ebersberger et al., 2014) (https://github.com/BIONF/HaMStR) to determine the presence-absence pattern of orthologs to human TEK (UniprotID: Q02763), TIE1 (UniprotID: P35590), Angiopoietin-1 (UniprotID: Q15389) and Angiopoietin-2 (UniprotID: O15123) across 255 species represented in the RefSeq partition of non-mammalian vertebrate genomes available at NCBI Genome (Februrary 2020) (https://ftp.ncbi.nlm.nih.gov/genomes/refseq/), complemented with the Quest For Orthologs reference proteomes (https://www.ebi.ac.uk/reference_proteomes/), and with the sea urchin (Strongylocentrotus purpuratus) proteome from NCBI Genome.  The full list of taxa is provided in Table S3Pairwise protein feature architecture similarities (Koestler et al., 2010) between the human seed proteins and their respective orthologs were assessed and scored with feature architecture similarity (https://github.com/BIONF/FAS).  Phylogenetic profiles together with the protein feature architecture were visualized and analysed with PhyloProfile (Tran et al., 2018).  Representative orthologs from 5 Sarcopterygians, 76 Actinopterygians, 5 Chondrichthyans, and additionally from 2 chordate outgroup species were aligned with Muscle v3.8.31 (Edgar, 2004), and alignment columns with more than 50% gaps were excluded prior to phylogeny reconstruction using a custom Perl script.  The processed alignment served as an input for a maximum likelihood tree reconstruction with RAxML v.8.2.11 (Stamatakis, 2014) choosing the option to automatically select the optimal model of sequence evolution (option PROTGAMMAAUTO).  Branch support was assessed with 100 non-parametric bootstrap replicates using the rapid bootstrapping algorithm implemented into RAxML (Stamatakis et al., 2008).  Tree display and editing were performed with iTOL (Letunic and Bork, 2019).

Usage Notes

The files in this folder provide the necessary information to visualise and analyse the phylogenetic profiles of human Tek (Q02763), Tie1 (P35590), ANGP1 (Q15389), and ANGP2 (O15123) that were created with fDOG (https://github.com/BIONF/fDOG). The information can be viewed in any text editor, however, we suggest to use PhyloProfile (https://github.com/BIONF/PhyloProfile) for this purpose.

Please find below a brief description of the files and their content.

 

tektie_angp.phyloprofile: This file contains the presence-absence pattern of orthologs to the four seed proteins across a selection of animal species focussing on vertebrates. The file format is a tab-delimited text with the following information:

  • geneID - the name of the human seed protein
  • ncbiID - is the NCBI taxonomy id of the species/strain the ortholog was identified in 
  • orthoID - a compound identifier of the orthologous protein. The individual fields are separated by a ‘|’ (Examle: TIE1|DICTD@515635@3|B8E0P1|1)
  • TIE1 - Seed name
  • DICTD@515635@3 - Identifier of the species the ortholog was found in. Here, Dictiostelium discoideum (Ncbi Tax Id 515635) internal version 3
  • B8E0P1 - Sequence id of the ortholog (here Uniprot)
  • 1 - flag indicating that the protein is the representative ortholog (either the only one found, or in the case that more than one co-ortholog was found, the one that is most similar to the seed protein. If the sequence is not the representative ortholog, the flag will be ‘0'
  • FAS_F - The feature architecture similarity score between the seed protein and its ortholog (seed is reference). For details see (https://github.com/BIONF/FAS)
  • FAS_B - The feature architecture similarity score between the ortholog and its seed protein (ortholog is reference). For details see (https://github.com/BIONF/fDOG)

                       

tektie_angp.extended.fa: This file holds the sequence information of the seed proteins and their orthologs in a multi-sequence FASTA format. There is a 1:1 relation between the entires in the tektie_angp.phyloprofile file and the sequences in the FASTA file, and the information in the ‘orthoID’ field is used as sequence identifier in the FASTA file

 

tektie_angp_forward.domains - This file holds the information from the feature architecture similarity analysis in a tab delimited text format. The human seed sequence serves as reference.

Example: TEK#DICTD@515635@3|B8E0P1|1     HUMAN@9606@3|Q02763     1124    pfam_Ig_Tie2_1  24      118     0.2161  Y

  • TEK#DICTD@515635@3|B8E0P1|1 - Seed name (TEK) and id of the ortholog
  • HUMAN@9606@3|Q02763 - seed species and id information
  • 1124 - length of the protein
  • pfam_Ig_Tie2_1 - Feature name
  • 24 - feature start in sequence
  • 118 - feature end in sequence
  • 0.2161 - Weight of the feature during similarity scoring (see https://github.com/BIONF/FAS)
  • Y - Feature was used in the architecture comparison between the seed and the ortholog. ’N’ otherwise

 

tektie_angp_reverse.domains - Same as *_forward.domains but using the orthologous sequence serves as reference

Funding

Max Plack Society

European Research Council, Award: AdG project: ZMOD 694455

Deutsche Forschungsgemeinschaft