Evolution and potential function of fibrinogen-like domains across twelve Drosophila species

Abstract

Background: The fibrinogen-like (FBG) domain consists of approximately 200 amino acid residues, which has high sequence similarity to the C-terminal halves of fibrinogen beta and gamma chains. Fibrinogen-related proteins (FREPs) containing one or more FBG domains are found universally in vertebrates and invertebrates. In invertebrates, FREPs are involved in immune responses and other aspects of physiology. To understand the complexity of this gene family in Drosophila, we analyzed FREPs in twelve Drosophila species.

Results: Using the genome data from 12 Drosophila species, we identified FBG domains in each species. The results show that the gene numbers in each species vary from 14 genes up to 43 genes. Using sequence profile analysis, we found that FBG domains have high sequence similarity and are highly conserved throughout. By comparison of structure and sequence conservation, some of the FBG domains in Drosophila melanogaster are predicted to function in recognition of carbohydrates and their derivatives on the surface of microorganisms in innate immunity.

Conclusion: Sequence and structural analyses show that FREP family across 12 Drosophila species contains conserved FBG domains. Expansion of the FREP families in Drosophila is mainly accounted by a major expansion of FBG domains.

Figure 1

Selected clusters of phylogenetic tree of the FBG domains in the 12 Drosophila species. The seed sequence used for constructing the tree was the multiple sequence alignment of FBG domains that excluded truncated FBG domains. Bootstrap was applied to the data. Protein distance was calculated using the Jones-Taylor-Thornton model of change between amino acids and a Hidden Markov Model (HMM) method of inferring different rates of evolution at different amino acid positions. Neighbor-joining was applied to produce the tree. The FBG domains of each FREP are denoted by their gene name or GLEANR gene ID. A. A cluster composed of FBG domains from multiple species (Group D in supplement fig. 2). B. A cluster composed of FBG domains from a single species (D. grmshawii, Group K in supplement fig. 2). C. Majority of FBG domains from D. virilis, D. mojavensis and D. grimshawi are clustered together (Group G in supplement fig. 2).

Figure 2

Scaffold location of selected FREPs in the Drosophila species. Gene locations for the FREP family were retrieved from the AAA database. Scaffold was named using single letter from genus plus the first three letters from subgenus to differentiate species. The scaffold is represented with a green line, which is not scaled. The relative location for each gene was shown on the scaffold using their GLEANR gene ID.

Figure 3

Multiple sequence alignment of a representative set of the FBG domains in D. melanoganster. Multiple sequence alignment was constructed using T-Coffee program. The 100% consensus sequence was boxed with black in the alignment. The PHD secondary structure is shown above the alignment with H representing an α-helix and E representing a β-strand. The sequences are denoted by their gene names in GenBank. The domain P is indicated between two arrows. The amino acids involved in forming binding pocket were shown in star.