FIGURES
Figure 1. Loops connect domains into modules and modules into PKSs. a) A model assembly line colored by domain types. Acyltransferases (ATs, orange) add extender units to acyl carrier proteins (ACPs, salmon), which collect the growing acyl chain from ketosynthases (KSs, red) through carbon-carbon bond formation. Ketoreductases (KRs, blue), dehydratases (DHs, yellow), and enoylreductases (ERs, green) are often present to modify the α- and β-positions of the extended polyketide chain. A stereodiagram shows how these domains may be relatively oriented within an assembly line. b) The model assembly line colored by type. While α-modules do not contain processing enzymes, β-modules contain a KR, γ-modules contain both a KR and DH, and δ-modules contain a KR, DH, and an ER. The updated definition of the module places KS at the most downstream position. Docking domains (DDs) are present between the ACP and KS domains in 41% of the 949 modules studied here.
Figure 2. Examples of repetitive sequences. a) The MlsA1 polypeptides from the mycolactone PKSs of mycobacteria are 99% identical yet show variation in the number of GSDPAV repeats in the loops between modules. The DNA sequence encoding these repeats is the highly conserved 18-mer, 5’-GGTTCTGATCCCGCAGTG-3’. ml,Mycobacterium liflandii ; ms, Mycobacterium ulcerans subsp.shinshuense ; mu, Mycobacterium ulcerans Agy99. b) Two repetitive sequences are present in the loop between the second and third modules of the nannocystin PKS (encoded by a 46-mer repeated 3.5 times and a 36-mer repeated 4.9 times). Between the KR structural and catalytic subdomains (KRs and KRc) of the same module a 48-mer repeated 9.7 times encodes a 152-residue insertion. Only the inserted regions of the alignment of module NcyB_1c with the reference γ-module (Cmod) are shown. Genetic events such as slipped-strand mispairing may give rise to these seemingly innocuous repetitive sequences.
Figure 3. Repetitive sequences between domains and modules. a) A heat map shows how tolerant or intolerant interdomain loops are to the insertion of repetitive sequences. The most tolerant loops are between modules, while the least tolerant are at the AT-DH, DH-KRs, and ER-KRc junctions in γ- and δ-modules. A bar graph compares the frequencies of loop insertion. b) A stereodiagram of the model assembly line shows the location of interdomain loops, colored red.
Figure 4. Repetitive sequences in the loops of domains. The locations of loops that have been significantly altered compositionally or lengthwise are indicated in red. Frequencies of insertion are reported in the accompanying bar graphs.