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Review
. 2021 Jul 31;13(8):538.
doi: 10.3390/toxins13080538.

The Natterin Proteins Diversity: A Review on Phylogeny, Structure, and Immune Function

Carla Lima  1 , Geonildo Rodrigo Disner  1 , Maria Alice Pimentel Falcão  1 , Ana Carolina Seni-Silva  1   2 , Adolfo Luis Almeida Maleski  1   2 , Milena Marcolino Souza  1 , Mayara Cristina Reis Tonello  1 , Monica Lopes-Ferreira  1
Affiliations
Review

The Natterin Proteins Diversity: A Review on Phylogeny, Structure, and Immune Function

Carla Lima et al. Toxins (Basel). .

Abstract

Since the first record of the five founder members of the group of Natterin proteins in the venom of the medically significant fish Thalassophryne nattereri, new sequences have been identified in other species. In this work, we performed a detailed screening using available genome databases across a wide range of species to identify sequence members of the Natterin group, sequence similarities, conserved domains, and evolutionary relationships. The high-throughput tools have enabled us to dramatically expand the number of members within this group of proteins, which has a remote origin (around 400 million years ago) and is spread across Eukarya organisms, even in plants and primitive Agnathans jawless fish. Overall, the survey resulted in 331 species presenting Natterin-like proteins, mainly fish, and 859 putative genes. Besides fish, the groups with more species included in our analysis were insects and birds. The number and variety of annotations increased the knowledge of the obtained sequences in detail, such as the conserved motif AGIP in the pore-forming loop involved in the transmembrane barrel insertion, allowing us to classify them as important constituents of the innate immune defense system as effector molecules activating immune cells by interacting with conserved intracellular signaling mechanisms in the hosts.

Keywords: Natterin; Thalassophryne nattereri; aerolysin; bioinformatics; immune function; protein evolution.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Phylogenetic trees generated using the software PhyloT that represent all the species found sharing any Natterin or Natterin-like protein in the tree of life. The circular tree with the corresponding species (top) and the unrooted tree with the main clades (bottom) demonstrate the species’ evolutionary relationship.
Figure 2
Figure 2
Phylogenetic tree generated using the software PhyloT to represent exclusively the fish species included in the group of Natterin-like proteins, 109 representatives. The species that presented the protein sequences with the higher identity percentage with the founder members Natterin-1–4 are highlighted.
Figure 3
Figure 3
The seven fish species presenting the Natterin proteins (the topmost 15 sequences) with a higher percentage of identity (pid) compared with founder members Natterins-1–4 (top); The queried sequences’ average identity percentage comparing to the founder members Natterins-1–4 (bottom).
Figure 4
Figure 4
Multiple alignment and conserved residues found on the 15 topmost similar fish sequences compared with the founder members Natterins-1–4, based on the percentage of identity (pid). The conserved residues “TAGIP” and “AGIP” are highlighted in the pictures, picture (A–D), respectively.
Figure 5
Figure 5
Model built by SWISS-MODEL representing the overall structure of founder Natterins-1–4 from Thalassophryne nattereri. In the top, cartoon representation of Natterin proteins using as template the crystal structure of Dln1 dimer (PDB 5DI0), a Natterin-like protein of Danio rerio (Method: X-Ray diffraction; resolution: 1.70 Å; R-value free: 0.209; R-value work: 0.172; R-value observed: 0.174; deposited by Jia et al. [10]). The Aerolysin module shared by all founder proteins is colored whereas the additional modeled N-terminal portion present only in the founder Natterin-1 and -2 is presented overlapped in gray. The zoomed part within the 3D representation shows the AGIP motif localization, which remains preserved in all Natterin-like proteins. In the bottom, multiple-sequence alignment of an Aerolysin module segment highlighting the conserved motifs shared by the template and the four founder members: AGIP and PP.
Figure 6
Figure 6
The founder members Natterins-1–4 conserved domains followed by the most found conserved domains and their superfamilies in the fish protein sequences in the group of Natterin-like proteins using the NCBI Conserved Domains Tool.
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