||The specific chaperone requirements for the folding of each protein were compiled for other bacteria (see sources below), and mapped to M. genitalium by homology.
Tig – may interact with all nascent peptides at the ribosome polypeptide exit site (L23) [PUB_0005, PUB_0009, PUB_0014, PUB_0388, PUB_0644] and assist in early folding. Highly epxressed protein. Binds vacant ribosomes with half-life of 11 s [PUB_0005]; binds ribosome-peptide complexes with half-life of 15-50 s [PUB_0005]; remains associated with the peptide for a up to 35 more seconds after peptide release from the ribosome [PUB_0005]. Trigger factor-50S ribosome affinity: KD=1 µM [PUB_0005] and kon=200 × 103 M-1s-1. We model trigger as required for the proper folding of all proteins.
DnaK – Deuerling et al performed a proteome-scale search for DnaK substrates in E. coli [PUB_0388]. Functions as a monomer and binds short, linear, unfolded peptide segments [PUB_0014, PUB_0644]. Interacts with peptide backbone [PUB_0014, PUB_0644]. Regulated by co-chaperones (eg DnaJ) [PUB_0014, PUB_0644]. GrpE co-chaperone catalyzes ATP hydrolysis and peptide release [PUB_0014, PUB_0644]. DnaK folds 5-18% of proteins. DnaK substrates are generally > 30 kDa in size. DnaK binds proteins with half life < 2 min.
DnaJ - Co-chaperone for DnaK and a chaperone itself [PUB_0014, PUB_0644]. Recognizes hydrophobic and aromatic residues and interacts with peptide side chains [PUB_0014, PUB_0644].
GroEL – Kerner et al performed a proteome-scale search for GroEL substrates in E. coli [PUB_0389] and Endo and Kurusu performed a proteome-scale search for GroEL substrates in B. subtilis [PUB_0391]. Kener et al found that 250 of 2400 cytosolic proteins interact with GroEL and that 85 of these require GroEL for folding. GroEL Functions as two heptameric rings [PUB_0014, PUB_0644]. GroEL folds 10-15% of proteins. GroEL substrates are 20-60 kDa in size. GroEL binds proteins with half life 30 s - 10 min.
FtsH – may act as molecule chaperone for membrane proteins [PUB_0014]. Several other functions have also been associated with FtsH. To date no proteome-scale studies of FtsH activity has been performed, and FtsH's chaperone substrates are not well characterized. Conequently we chose not to model FtsH as a molecular chaperone, but rather a protease.
Substrates of SecB, a molecular chaperone not present in M. genitalium, have also been identified on proteome-scale in E. coli [PUB_0390].
Eds Lund P. Molecular Chaperones in the Cell. Oxford University Press, New York (2001). WholeCell: PUB_0014, ISBN: 9780199638673
Eds Pain R. Mechanisms of protein folding. Oxford University Press: USA (2000). WholeCell: PUB_0644, ISBN: 9780199637881
Baars L, Ytterberg AJ, Drew D, Wagner S, Thilo C, van Wijk KJ, de Gier JW. Defining the role of the Escherichia coli chaperone SecB using comparative proteomics. J Biol Chem 281, 10024-34 (2006). WholeCell: PUB_0390, PubMed: 16352602
Deuerling E, Patzelt H, Vorderwülbecke S, Rauch T, Kramer G, Schaffitzel E, Mogk A, Schulze-Specking A, Langen H, Bukau B. Trigger Factor and DnaK possess overlapping substrate pools and binding specificities. Mol Microbiol 47, 1317-28 (2003). WholeCell: PUB_0388, PubMed: 12603737
Endo A, Kurusu Y. Identification of in vivo substrates of the chaperonin GroEL from Bacillus subtilis. Biosci Biotechnol Biochem 71, 1073-7 (2007). WholeCell: PUB_0391, PubMed: 17420574
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