Sequence comparison and phylogenetic analysis by the Maximum Likelihood method of ribosome-inactivating proteins from angiosperms

Abstract

Ribosome-inactivating proteins (RIPs) from angiosperms are rRNA N-glycosidases that have been proposed as defence proteins against virus and fungi. They have been classified as type 1 RIPs, consisting of single-chain proteins, and type 2 RIPs, consisting of an A chain with RIP properties covalently linked to a B chain with lectin properties. In this work we have carried out a broad search of RIP sequence data banks from angiosperms in order to study their main structural characteristics and phylogenetic evolution. The comparison of the sequences revealed the presence, outside of the active site, of a novel structure that might be involved in the internal protein dynamics linked to enzyme catalysis. Also the B-chains presented another conserved structure that might function either supporting the beta-trefoil structure or in the communication between both sugar-binding sites. A systematic phylogenetic analysis of RIP sequences revealed that the most primitive type 1 RIPs were similar to that of the actual monocots (Poaceae and Asparagaceae). The primitive RIPs evolved to the dicot type 1 related RIPs (like those from Caryophyllales, Lamiales and Euphorbiales). The gene of a type 1 RIP related with the actual Euphorbiaceae type 1 RIPs fused with a double beta trefoil lectin gene similar to the actual Cucurbitaceae lectins to generate the type 2 RIPs and finally this gene underwent deletions rendering either type 1 RIPs (like those from Cucurbitaceae, Rosaceae and Iridaceae) or lectins without A chain (like those from Adoxaceae).

Metazoan Ribosome Inactivating Protein encoding genes acquired by Horizontal Gene Transfer

“…The occurrence of RIP genes has been experimentally confirmed in a wide range of plant taxa, as well as in several species of Gram positive and Gram negative bacteria 7–9 . Additionally, the exponential increase of information in databases has suggested the presence of genes coding for RIP–domain containing proteins in lineages of Fungi, Cyanobacteria and Metazoa 10–12 . Although several of these toxins have been extensively studied at the biochemical level, their biological roles remain open to speculation.…”

Structural characterization of dioicin 1 from Phytolacca dioica L. gains novel insights into phylogenetic relationships of Phytolaccaceae type 1 RIPs

“…S1A] as well as additional invariant amino acid residues [i.e. Ser215(227) and Phe181(193)] were found to be conserved in dioicin 1 sequence [11,37]. As evidenced by the identity/similarity matrix (Fig.…”

“…The highest number of RIPs was found in Caryophyllaceae, Sambucaceae, Cucurbitaceae, Euphorbiaceae, and Poaceae [4,11]. In addition, several isoforms of type 1 RIPs were purified from Phytolaccaceae [4,12,13] and in particular from Phytolacca dioica L., a woody plant introduced in Italy from South America.…”

“…Though several aspects of the P. dioica type 1 RIP characterization have been studied [11,12,16], some important questions remain to be answered especially with respect to Phytolaccaceae RIP evolution. One of the major problems encountered in approaching RIPs phylogeny concerns the availability of their sequences, either derived from protein or nucleotide sequencing.…”

Two Saporin-Containing Immunotoxins Specific for CD20 and CD22 Show Different Behavior in Killing Lymphoma Cells

“…RIPs are largely distributed in the plant kingdom [12], and many plants producing RIPs have been used for centuries in traditional medicine [13]. RIPs are mainly divided into type 1, consisting of a single-chain enzymatic protein, and type 2, consisting of an A chain with the same enzymatic activity linked to a B chain with lectin properties [14].…”