Distinctive Types of ATP-dependent Clp Proteases in Cyanobacteria

Abstract

Cyanobacteria are the only prokaryotes that perform oxygenic photosynthesis and are thought to be ancestors to plant chloroplasts. Like chloroplasts, cyanobacteria possess a diverse array of proteolytic enzymes, with one of the most prominent being the ATP-dependent Ser-type Clp protease. The model Clp protease in Escherichia coli consists of a single ClpP proteolytic core flanked on one or both ends by a HSP100 chaperone partner. In comparison, cyanobacteria have multiple ClpP paralogs plus a ClpP variant (ClpR), which lacks the catalytic triad typical of Ser-type proteases. In this study, we reveal that two distinct soluble Clp proteases exist in the unicellular cyanobacterium Synechococcus elongatus. Each protease consists of a unique proteolytic core comprised of two separate Clp subunits, one with ClpP1 and ClpP2, the other with ClpP3 and ClpR. Each core also associates with a particular HSP100 chaperone partner, ClpC in the case of the ClpP3/R core, and ClpX for the ClpP1/P2 core. The two adaptor proteins, ClpS1 and ClpS2 also interact with the ClpC chaperone protein, likely increasing the range of protein substrates targeted by the Clp protease in cyanobacteria. We also reveal the possible existence of a third Clp protease in Synechococcus, one which associates with the internal membrane network. Altogether, we show that presence of several distinctive Clp proteases in cyanobacteria, a feature which contrasts from that in most other organisms.

NblA, a Key Protein of Phycobilisome Degradation, Interacts with ClpC, a HSP100 Chaperone Partner of a Cyanobacterial Clp Protease

“…4), indicating that NblA binding to phycobiliproteins mediates its recognition by ClpC. Thus, a ternary complex between NblA, the phycobiliproteins, and ClpC appears to be necessary for PBS degradation, probably by a thylakoid-associated ClpP complex like the one tentatively identified by Stanne et al (41). However, because ClpC itself can function as a molecular chaperone even in the absence of a Clp protease (72), we cannot exclude the possibility that it helps unfold phycobiliproteins, which are then degraded by other proteases.…”

“…In bacteria and cyanobacteria, several adaptor proteins of Clp proteases have already been characterized. Examples are ClpS (40, 52, 53), RssB (54, 55), and SspB (56 -58) in E. coli, MecA (59 -61) and YpbH (62,63) in B. subtilis, as well as ClpS1 and ClpS2 in Synechococcus 7942 (41). Adaptor proteins are not restricted to bacteria but also occur in yeasts and other eukaryotes (64 -66).…”

“…This residual GST-ClpC Alr2999 apparently bound to Glutathione-Sepharose in the pull-down experiments. The observed binding of non-tagged ClpC Alr2999 could be explained by formation of oligomeric complexes between tagged and non-tagged versions of ClpC Alr2999 , a phenomenon that is well known for other members of the Clp family (41)(42)(43)(44).…”

Structural and functional insights into caseinolytic proteases reveal an unprecedented regulation principle of their catalytic triad

“…Although most organisms possess a single ClpP protein with a conserved fold (6, 11, 13-16, 18, 20), the genomes of some organisms encode two or more ClpP isoforms (21)(22)(23)(24). For a cyanobacterial system, heptameric rings of mixed composition have been reported that interact with different chaperones (22).…”

Acyl depsipeptide (ADEP) resistance in Streptomyces

“…ClpP4 also lacks a canonical catalytic triad. Non-functional ClpP proteins have been described in cyanobacteria and are predicted to have regulatory roles (Stanne et al, 2007). In view of these observations, we focused on clpP1clpP2 and clpP3clpP4 rather than clpP5.…”