Abstract
We have identified a variety of proteins in species of the Legionella, Aeromonas, Pseudomonas, Vibrio, Nitrosomonas, Nitrosospira, Variovorax, Halomonas, and Rhizobia genera, which feature repetitive modules of different length and composition, invariably ending at the COOH side with Asp–Asp–x–Pro (DDxP) motifs. DDxP proteins range in size from 900 to 6200 aa (amino acids), and contain 1 to 5 different module types, present in one or multiple copies. We hypothesize that DDxP proteins were modeled by the action of specific endonucleases inserting DNA segments into genes encoding DDxP motifs. Target site duplications (TSDs) formed upon repair of staggered ends generated by endonuclease cleavage would explain the DDxP motifs at repeat ends. TSDs acted eventually as targets for the insertion of more modules of the same or different types. Repeat clusters plausibly resulted from amplification of both repeat and flanking TSDs. The proposed growth shown by the insertion model is supported by the identification of homologous proteins lacking repeats in Pseudomonas and Rhizobium. The 85 DDxP repeats identified in this work vary in length, and can be sorted into short (136–215 aa) and long (243–304 aa) types. Conserved Asp–Gly–Asp–Gly–Asp motifs are located 11–19 aa from the terminal DDxP motifs in all repeats, and far upstream in most long repeats.
Highlights
In most Gram-negative bacteria, large modular proteins, featuring sequence repeats ranging in size from 20 to 200 amino acids, are translocated outside the cell via the action of different secretion systems [1,2]
We have identified a variety of proteins in species of the Legionella, Aeromonas, Pseudomonas, Vibrio, Nitrosomonas, Nitrosospira, Variovorax, Halomonas, and Rhizobia genera, which feature repetitive modules of different length and composition, invariably ending at the COOH side with Asp–Asp–x–Pro (DDxP) motifs
RTX proteins are brought outside the cell by type 1 secretion systems (T1SSs), tripartite protein complexes in which an inner membrane (HlyB), a fusion membrane (HlyD), and an outer membrane (TolC) protein interact to form a channel through which proteins are transferred from the cytoplasm to the extracellular environment
Summary
In most Gram-negative bacteria, large modular proteins, featuring sequence repeats ranging in size from 20 to 200 amino acids, are translocated outside the cell via the action of different secretion systems [1,2]. These proteins vary significantly in size (1000 to 6000 aa) and exert a variety of functions.
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