Phylogeny, Function, and Evolution of the Cupins, a Structurally Conserved, Functionally Diverse Superfamily of Proteins

Abstract

The cupin superfamily is a group of functionally diverse proteins that are found in all three kingdoms of life, Archaea, Eubacteria, and Eukaryota. These proteins have a characteristic signature domain comprising two histidine- containing motifs separated by an intermotif region of variable length. This domain consists of six beta strands within a conserved beta barrel structure. Most cupins, such as microbial phosphomannose isomerases (PMIs), AraC- type transcriptional regulators, and cereal oxalate oxidases (OXOs), contain only a single domain, whereas others, such as seed storage proteins and oxalate decarboxylases (OXDCs), are bi-cupins with two pairs of motifs. Although some cupins have known functions and have been characterized at the biochemical level, the majority are known only from gene cloning or sequencing projects. In this study, phylogenetic analyses were conducted on the conserved domain to investigate the evolution and structure/function relationships of cupins, with an emphasis on single- domain plant germin-like proteins (GLPs). An unrooted phylogeny of cupins from a wide spectrum of evolutionary lineages identified three main clusters, microbial PMIs, OXDCs, and plant GLPs. The sister group to the plant GLPs in the global analysis was then used to root a phylogeny of all available plant GLPs. The resulting phylogeny contained three main clades, classifying the GLPs into distinct subfamilies. It is suggested that these subfamilies correlate with functional categories, one of which contains the bifunctional barley germin that has both OXO and superoxide dismutase (SOD) activity. It is proposed that GLPs function primarily as SODs, enzymes that protect plants from the effects of oxidative stress. Closer inspection of the DNA sequence encoding the intermotif region in plant GLPs showed global conservation of thymine in the second codon position, a character associated with hydrophobic residues. Since many of these proteins are multimeric and enzymatically inactive in their monomeric state, this conservation of hydrophobicity is thought to be associated with the need to maintain the various monomer- monomer interactions. The type of structure-based predictive analysis presented in this paper is an important approach for understanding gene function and evolution in an era when genomes from a wide range of organisms are being sequenced at a rapid rate.

Nitric Oxide Contributes to Cadmium Toxicity in Arabidopsis by Promoting Cadmium Accumulation in Roots and by Up-Regulating Genes Related to Iron Uptake

“…The two genes showing the highest difference of expression, At5g05340 and At5g39190, encode a putative peroxidase and GER2, a germin-like protein, respectively. Several studies proposed that germin-like proteins might function primarily as superoxide dismutases and/or oxalate oxidases and serve to protect plants from the effects of oxidative stress induced by a range of both biotic and abiotic stresses (Khuri et al, 2001). GER2 was found to be resistant to protease degradation but did not display oxalate oxidase activity (Membré et al, 2000).…”

Phaseolin: Structure and Evolution

“…1). More recent studies by Khuri et al [73] trace back the evolution of seed proteins to the cupin superfamily [74], a small group of functionally diverse proteins found in all three kingdoms of life, Archaea, Eubacteria and Eukaryota. The conserved domain seen in these proteins is the characteristic six-stranded -barrel structure, based on which seed storage proteins are termed as bi-cupins (Fig.…”

“…The conserved domain seen in these proteins is the characteristic six-stranded -barrel structure, based on which seed storage proteins are termed as bi-cupins (Fig. 2) because of a two-domain structure [73]. It remains to be seen whether the evolution of phaseolin can be traced back to a prokaryotic ancestor based on the cupin superfamily evolution pathway.…”

“…Fig. (3) illustrates a hypothetical scenario for phaseolin evolution from our present knowledge of seed protein evolution [69][70][71][72][73][74].…”

Estudio transcriptómico de los mecanismos implicados en la tolerancia inducida por el curado al daño de frío y por el etileno al colapso de la corteza en los frutos cítricos.

“…Los miembros de esta última familia se han relacionado con las respuestas de defensa frente a estímulos abióticos como el calor o la deshidratación, y algunos de ellos poseen actividad SOD (Dunwell et al, 2000;Khuri et al, 2001). En los frutos tratados con 1-MCP almacenados 14 días en aire, sin embargo, el análisis FatiGO+ mostró una represión de su biosíntesis en el albedo (Tabla 29B y Tabla 30).…”