Rapid expansion of pigmentation genes in penaeid shrimp with absolute preservation of function

Abstract

Crustaceans form their distinct patterns and colours through the interaction of the carotenoid astaxanthin with a protein called crustacyanin (CRCN). Presently, the expression of just two genes is thought to provide the protein subunits that combine to form the crustacyanin complex and associated carotenoid colour change from red to blue. This study aimed to explore the genetic complexity underlying the production of pigmentation and camouflage in penaeid shrimp. We isolated 35 new genes from 12 species, and their sequence analysis indicated that this gene family has undergone significant expansion and diversification in this lineage. Despite this duplication and sequence divergence, the structure of the CRCN proteins and their functional role in shrimp colour production has been strictly conserved. Using isoforms from as an example, we showed that isoforms were differentially expressed, and that subtle phenotypes were produced by the specific downregulation of individual isoforms. These findings demonstrate that our knowledge of the molecular basis of pigmentation in shrimp was overly simplistic, and suggests that multiple copies of the genes within species may be advantageous for colour production. This result is of interest for the origin and evolution of pigmentation in crustaceans, and the mechanisms by which gene function is maintained, diversified or sub-functionalized.

The level of putative carotenoid-binding proteins determines the body color in two species of endemic Lake Baikal amphipods

“…The molecular-level mechanism of color formation is still an open question. Lobster proteins act as octamers of heterodimers (Chayen et al, 2003), and the crustacyanins of penaeid shrimps probably act in a similar way, as they form two clear clusters on the phylogenetic tree (Budd et al, 2017). However, there is no available information on subunit composition except for the two distinct carotenoid-binding proteins forming blue complexes in G. lacustris (Czeczuga & Krywuta, 1981).…”

“…5). The known sequences included crustacyanins A and C from penaeid shrimps (Fenneropenaeus merguiensis, Litopenaeus vannamei and Penaeus monodon) (Budd et al, 2017) and the lobster H. gammarus (Keen et al, 1991a;Keen et al, 1991b). To compare our results with the published phylogeny of crustacyanins (Wade et al, 2009), we included the same sequences from G. pulex, as well as putative carotenoid-binding proteins from blue copepods (Acartia fossae) and appendicularia (Oikopleura dioica) (Mojib et al, 2014), and also searched the GenBank database for other sequences annotated as crustacyanins.…”

“…(A) M. branickii (Dybowsky, 1874); (B) Brandtia latissima latior (Dybowsky, 1874); (C) Micruropus wohlii wohlii (Dybowsky, 1874); (D) Gmelinoides fasciatus (Stebbing, 1899); (E) E. verrucosus (Gerstfeldt, 1858); (F-G) different color morphs of E. cyaneus (Dybowsky, 1874); (H-J) different color morphs of E. vittatus (Dybowsky, 1874); (K) E. maackii (Gerstfeldt, 1858); (L-M) different color morphs of E. messerschmidtii (Bedulina et Takhteev, 2014); (N) E. ussolzewii ussolzewii (Dybowsky, 1874); (O) E. cruentus (Dorogostaisky, 1930); (P) O. albinus (Dybowsky, 1874); (Q) O. flavus (Dybowsky, 1874); (R) O. carneolus melanophthalmus (Bazikalova, 1945) belonging to the lipocalin family and found in decapods and stomatopods, appear to be a strictly crustacean-specific innovation (Wade et al, 2009). Apart from lobster species, they were explored on the sequence level in other decapods, mainly penaeid shrimps (Ertl et al, 2013;Budd et al, 2017). Decapod crustacyanins form two groups, A and C, which (at least in lobster) form heterodimers called β-crustacyanin binding to two astaxanthin molecules each, and eight β-crustacyanin subunits form one α-crustacyanin molecule (Chayen et al, 2003).…”

Peer Review #1 of "The level of putative carotenoid-binding proteins determines the body color in two species of endemic Lake Baikal amphipods (v0.2)"

“…The molecular-level mechanism of color formation is still an open question. Lobster proteins act as octamers of heterodimers (Chayen et al, 2003), and the crustacyanins of penaeid shrimps probably act in a similar way, as they form two clear clusters on the phylogenetic tree (Budd et al, 2017). However, there is no available information on subunit composition except PeerJ reviewing PDF | (2020:01:44934:2:0:NEW 21 May 2020)…”

Peer Review #2 of "The level of putative carotenoid-binding proteins determines the body color in two species of endemic Lake Baikal amphipods (v0.1)"

“…Crustacyanins, belonging to the lipocalin family and found in decapods and stomatopods, appear to be a strictly crustacean-specific innovation (Wade et al, 2009). Apart from lobster species, they were explored on the sequence level in other decapods, mainly penaeid shrimps (Ertl et al, 2013;Budd et al, 2017). Decapod crustacyanins form two groups, A and C, which (at least in lobster) form heterodimers called βcrustacyanin binding to two astaxanthin molecules each, and eight β-crustacyanin subunits form one α-crustacyanin molecule (Chayen et al, 2003).…”