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. 2020 Mar 1;12(3):160-173.
doi: 10.1093/gbe/evaa038.

The Evolution History of Fe-S Cluster A-Type Assembly Protein Reveals Multiple Gene Duplication Events and Essential Protein Motifs

Hui-Meng Lu  1 , Jing-Di Li  1 , Yu-Dan Zhang  1 , Xiao-Li Lu  1 , Chang Xu  2 , Yuan Huang  2 , Michael Gribskov  3   4
Affiliations

The Evolution History of Fe-S Cluster A-Type Assembly Protein Reveals Multiple Gene Duplication Events and Essential Protein Motifs

Hui-Meng Lu et al. Genome Biol Evol. .

Abstract

Iron-sulfur (Fe-S) clusters play important roles in electron transfer, metabolic and biosynthetic reactions, and the regulation of gene expression. Understanding the biogenesis of Fe-S clusters is therefore relevant to many fields. In the complex process of Fe-S protein formation, the A-type assembly protein (ATAP) family, which consists of several subfamilies, plays an essential role in Fe-S cluster formation and transfer and is highly conserved across the tree of life. However, the taxonomic distribution, motif compositions, and the evolutionary history of the ATAP subfamilies are not well understood. To address these problems, our study investigated the taxonomic distribution of 321 species from a broad cross-section of taxa. Then, we identified common and specific motifs in multiple ATAP subfamilies to explain the functional conservation and nonredundancy of the ATAPs, and a novel, essential motif was found in Eumetazoa IscA1, which has a newly found magnetic function. Finally, we used phylogenetic analytical methods to reconstruct the evolution history of this family. Our results show that two types of ErpA proteins (nonproteobacteria-type ErpA1 and proteobacteria-type ErpA2) exist in bacteria. The ATAP family, consisting of seven subfamilies, can be further classified into two types of ATAPs. Type-I ATAPs include IscA, SufA, HesB, ErpA1, and IscA1, with an ErpA1-like gene as their last common ancestor, whereas type-II ATAPs consist of ErpA2 and IscA2, duplicated from an ErpA2-like gene. During the mitochondrial endosymbiosis, IscA became IscA1 in eukaryotes and ErpA2 became IscA2 in eukaryotes, respectively.

Keywords: Fe–S cluster A-type assembly protein; gene duplication; protein family evolution; protein motif.

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Figures

<sc>Fig</sc>. 1.
Fig. 1.
—(a) The main steps in the Fe–S cluster biogenesis process in eukaryotes mitochondria. Briefly, [2Fe–2S] proteins biosynthesis includes three steps: first, the [2Fe–2S] cluster assembles on the U-type protein; second, the assembled [2Fe–2S] cluster on IscU is transferred to the monothiol glutaredoxin with Hsp70 as chaperon and finally transfers to apoproteins. Further steps are needed for [4Fe–4S] proteins: two [2Fe–2S] clusters transferred by Grx5 form [4Fe–4S] cluster on the IscA1, IscA2, and Iba57 complex, which transfers the [4Fe–4S] cluster to apoproteins. (b) The biosynthesis of Fe–S proteins in prokaryotes by ISC pathway. First, [2Fe–2S] cluster assembles on IscU dimer with IscA as the Fe donor, then the assembled [2Fe–2S] cluster is transferred to IscA dimer and can be transferred to apoprotein to form [2Fe–2S] proteins; or [4Fe–4S] cluster can be assembled on the IscA and then be transferred to be [4Fe–4S] proteins.
<sc>Fig</sc>. 2.
Fig. 2.
—(a) The seven unique motifs generated by MEME algorithm, the first four motifs were core motifs 1–4, which were present in almost all ATAPs. Motifs 5–7 were lineage-specific motifs. Motif 5 is an IscA2-specific motif, which is present widely in eukaryotes. Motif 6 is an IscA1-specific N-terminal motif and is present widely in the Eumetazoa. Motif 7 is a HesB C-terminal hallmark motif. (b) The length and signature characteristics of each motif, the right side of each motif presented the functional site found using PROSITE. Motif 1, hypothetical hesB/yadR/yfhF family signature; motif 2, N-myristoylation site; motif 3, casein kinase II phosphorylation site; motif 4, casein kinase II phosphorylation site; motif 5, protein kinase C phosphorylation site, casein kinase II phosphorylation site; motif 6, protein kinase C phosphorylation site.
<sc>Fig</sc>. 3.
Fig. 3.
—Motif characterization and sequence length among the seven ATAP subfamilies. Motifs 1–4 are present in all the ATAPs with similar arrangements, motif 6 is widely present in Eumetazoa IscA1 and located in the N-terminal of the sequence, motif 5 is an IscA2-specific motif, and motif 7 is a HesB-specific motif.
<sc>Fig</sc>. 4.
Fig. 4.
—(a) The structure of IscA1-composed magnetic polymer without the Cry. Two IscA1 first form dimers via intermolecular interactions, then, two IscA1 dimers form a functional tetramer with Fe located in the active center of the tetramer. Then, the tetramers form a long chain of protein complex by intermolecular interactions. The two joining IscA1 monomers between neighboring tetramers were labeled by oval-shaped red line. (b) The enlarged description of the two joining IscA1 monomers labeled by the red oval in (a). The IscA1-specific motif 6 (colored in red) were shown to be located in the junction surface between the two neighboring IscA1 tetramers. (c) The 3D structure of the two joining bacterial IscA monomers (PDB: 1R95) without motif 6 showed that the two monomers did not link with each other. (d) The result of sMD simulation using the SMD-CV protocol on the structure in (b). The left-side plot showed the fluctuation of the pulling force during the sMD, in which the maximum pulling force increased up to 871 pN. The 3D structures retrieved at several checkpoints (labeled by the yellow arrows) were shown on the right side which showed that the two IscA1 monomers were separated after pulling for about 90 ns (labeled by the red arrow in the left-side plot). (e) The result of the sMD simulation using the SMD-CV protocol on the combined structure of the two bacterial IscA monomers in (c). The left-side plot showed the fluctuation of the pulling force during the sMD, in which the maximum pulling force increased up to 684 pN. The 3D structures retrieved at several checkpoints (labeled by the yellow arrows) were shown on the right side which showed that the two IscA monomers were separated after pulling for about 35 ns (labeled by the red arrow in the left-side plot).
<sc>Fig</sc>. 5.
Fig. 5.
—The annotated collapsed phylogeny of the ATAP family and an outgroup (NfuA). Different ATAP subfamilies have been indicated by the triangles filled with different color and the bootstrap value for each clade was labeled. There were mainly two clades found, indicating the type-I ATAP family and the type-II ATAP family, respectively. In the type-I ATAP family, nonproteobacteria ErpA1 clustered with the other five ATAP subfamilies (eukaryotic IscA1, HesB, SufA, prokaryotic IscA, and cpIscA). In the type-II ATAP family, proteobacteria ErpA2 formed a separate clade with eukaryotic IscA2. There was also a branch of archaea-type ErpA3 located distantly from the two major types of ATAPs.
<sc>Fig</sc>. 6.
Fig. 6.
—Evolutionary history inferred for the ATAP family. The LCA of the entire ATAP family was likely an ErpA-like gene. In the first round of gene duplication event, the ancestor ErpA-like gene duplicated into an ErpA1-like gene, an ErpA2-like gene and presumably an ErpA3-like gene which can only be found in archaea now and is waiting to be explored. After the divergence of the major bacterial groups, both the proteobacteria and nonproteobacteria contain both the ErpA1-like and ErpA2-like genes. Then, the ErpA1-like gene duplicated into ErpA1, IscA, SufA, and HesB in the second round of gene duplication event. Before the endosymbiosis, several gene loss events happened in prokaryotes through which proteobacteria lost the ErpA1 and nonproteobacteria lost ErpA2, this explains why nowadays we can only detect one type of ErpA in these two major prokaryotic groups. Then, the ATAPs were transferred from proteobacteria and cyanobacteria through endosymbiosis of mitochondria and chloroplast, after which the IscA1 (from prokaryotic IscA) and IscA2 (from prokaryotic ErpA2) were harbored by eukaryotic mitochondria and cpIscA (from prokaryotic SufA) was harbored by the plant plastids. How the archaea-type ErpA3 evolved during the time is waiting to be explored.
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