Explosive Expansion of βγ-Crystallin Genes in the Ancestral Vertebrate

Abstract

In jawed vertebrates, βγ-crystallins are restricted to the eye lens and thus excellent markers of lens evolution. These βγ-crystallins are four Greek key motifs/two domain proteins, whereas the urochordate βγ-crystallin has a single domain. To trace the origin of the vertebrate βγ-crystallin genes, we searched for homologues in the genomes of a jawless vertebrate (lamprey) and of a cephalochordate (lancelet). The lamprey genome contains orthologs of the gnathostome βB1-, βA2- and γN-crystallin genes and a single domain γN-crystallin-like gene. It contains at least two γ-crystallin genes, but lacks the gnathostome γS-crystallin gene. The genome also encodes a non-lenticular protein containing βγ-crystallin motifs, AIM1, also found in gnathostomes but not detectable in the uro- or cephalochordate genome. The four cephalochordate βγ-crystallin genes found encode two-domain proteins. Unlike the vertebrate βγ-crystallins but like the urochordate βγ-crystallin, three of the predicted proteins contain calcium-binding sites. In the cephalochordate βγ-crystallin genes, the introns are located within motif-encoding region, while in the urochordate and in the vertebrate βγ-crystallin genes the introns are between motif- and/or domain encoding regions. Coincident with the evolution of the vertebrate lens an ancestral urochordate type βγ-crystallin gene rapidly expanded and diverged in the ancestral vertebrate before the cyclostomes/gnathostomes split. The β- and γN-crystallin genes were maintained in subsequent evolution, and, given the selection pressure imposed by accurate vision, must be essential for lens function. The γ-crystallin genes show lineage specific expansion and contraction, presumably in adaptation to the demands on vision resulting from (changes in) lifestyle.Electronic supplementary materialThe online version of this article (doi:10.1007/s00239-010-9379-2) contains supplementary material, which is available to authorized users.

Ca2+-binding Motif of βγ-Crystallins

“…An analysis demonstrates that it exists in several hundred species (source: Pfam database, accession number PF00030). Three out of four protein sequences of ␤␥-crystallins from an invertebrate species Branchiostoma floridae (amphioxus) also possess Ca 2ϩ binding fingerprints probably similar to that seen in Ci-␤␥-crystallin from Ciona intestinalis (21). In a limited analysis of sequences, it was observed that the domain is recruited in serine proteases (Sorangium cellulosum), aspartate metalloproteases (Saccharophagus degradans), carbohydratebinding glycosyl hydrolases (Flavobacterium johnsoniae and other bacterial species), and cell adhesion molecules (Dictyostelium discoideum).…”

“…The ␤␥-crystallin domain is an ancient protein fold, and several proteins across different domains of life are found to have this fold, a majority of them being expressed in bacterial species (15,17,21). Many ␤␥-crystallin domains have been studied in the recent past, and insights obtained from ion binding in these ␤␥-crystallins have led to the proposition that proteins of this superfamily possess a universal Ca 2ϩ -binding motif (22,23).…”

Functions of crystallins in and out of lens: Roles in elongated and post-mitotic cells

“…The binding sites can be detected in the sequences by the presence of the fingerprint D/N -X-X- S on each Greek key motif of a βγ-domain, with each calcium site requiring one conserved side chain from two motifs. Confidence in assigning one or two calcium binding sites in cephalochordate (amphioxus) βγ-domain sequences (Kappe et al, 2010) is bolstered by the single calcium binding site observed in the crystal structure of a βγ-domain protein from the sponge Geodia cydonium (pdb 4iau, (Vergara et al, 2013)). The recent genomic sequence determination for the Ctenophore (comb jelly) Mnemiopsis leidyi, a representative of another nonbilaterian metazoan lineage (Ryan et al, 2013), predicts the presence of several βγ-domain proteins, apparently from intron-less genes, some of which also contain the calcium binding site fingerprint.…”

“…Recent genome sequence for the phylum Ctenophora (comb jellies, whose few species, characterized by their glass-clear transparency, are common ocean surface swimmers around the world) (Ryan et al, 2013) also predicts the presence of proteins with βγ-crystallin domains. The tunicate and ctenophoran proteins and several microbial βγ-crystallin superfamily members have conserved calcium-binding sites that are lost in the lens crystallins (Kappe et al, 2010; Shimeld et al, 2005). Some of these proteins are involved in specialized calcium-dependent cellular roles associated with formation or maintenance of cellular structures such as spore coats or cysts (Wistow, 1990; Wistow et al, 1985).…”

Decoding the Molecular Design Principles Underlying Ca2+ Binding to βγ-Crystallin Motifs

“…1). Members of this expanding structural superfamily containing diverse members from various organisms have structural features similar to those of lens β-and γ-crystallins [10][11][12] and exhibit moderate to low affinity toward Ca 2+ . Apart from lens βγ-crystallins, some earlier studied members are protein S from Myxococcus xanthus, 8,9,13 spherulin 3a from Physarum polycephalum, 2,14-16 Yersinia crystallin from Yersinia pestis, 17 geodin from the sponge Geodia cydonium, 18 Ci-βγ-crystallin from the urochordate Ciona intestinalis, 3 absent in melanoma (AIM1), [19][20][21] nitrollin from Nitrosospira multiformis, 22 M-crystallin from an archaea Methanosarcina acetivorans 23 and so on.…”