Tuned SMC Arms Drive Chromosomal Loading of Prokaryotic Condensin

Abstract

SummarySMC proteins support vital cellular processes in all domains of life by organizing chromosomal DNA. They are composed of ATPase “head” and “hinge“ dimerization domains and a connecting coiled-coil “arm.” Binding to a kleisin subunit creates a closed tripartite ring, whose ∼47-nm-long SMC arms act as barrier for DNA entrapment. Here, we uncover another, more active function of the bacterial Smc arm. Using high-throughput genetic engineering, we resized the arm in the range of 6–60 nm and found that it was functional only in specific length regimes following a periodic pattern. Natural SMC sequences reflect these length constraints. Mutants with improper arm length or peptide insertions in the arm efficiently target chromosomal loading sites and hydrolyze ATP but fail to use ATP hydrolysis for relocation onto flanking DNA. We propose that SMC arms implement force transmission upon nucleotide hydrolysis to mediate DNA capture or loop extrusion.

Structure of Full-Length SMC and Rearrangements Required for Chromosome Organization

“…These results demonstrate that head engagement—albeit being essential—is not sufficient for chromosome targeting and that Smc arm integrity is critical in this process. Together, our results support the view that Smc arms mechanically promote chromosome targeting and relocation using distinct mechanisms: chromosome targeting is relatively robust, only being blocked by a double insertion in the Smc arm (Figure 6F), while Smc relocation is sensitive to single peptide insertions as well as to illegitimate Smc arm shortening (Bürmann et al., 2017). …”

“…Loss of arm rigidity may therefore uncouple head engagement from rod dissolution and block targeting of Smc to the chromosome. Consistent with the notion of rigid Smc arms, we recently found, by a random peptide insertion screen, that the arms are particularly sensitive to the insertion of peptide sequences at any position except in parts of the Smc joint domain and at the hinge-proximal end of the coiled coil (Bürmann et al., 2017). Two such insertions (at residue 394 and 479), however, do not interfere with the initial recruitment of Smc to the chromosome but rather block the downstream event of Smc relocation from parS sites (Bürmann et al., 2017).…”

“…Consistent with the notion of rigid Smc arms, we recently found, by a random peptide insertion screen, that the arms are particularly sensitive to the insertion of peptide sequences at any position except in parts of the Smc joint domain and at the hinge-proximal end of the coiled coil (Bürmann et al., 2017). Two such insertions (at residue 394 and 479), however, do not interfere with the initial recruitment of Smc to the chromosome but rather block the downstream event of Smc relocation from parS sites (Bürmann et al., 2017). This suggests that arm rigidity is either dispensable for chromosome targeting or that the two tested peptide insertions do not sufficiently compromise arm rigidity to prevent rod dissolution.…”

Deformation mechanisms in a metastable beta titanium twinning induced plasticity alloy with high yield strength and high strain hardening rate

“…This could conceivably extend to Kite-containing complexes (Palecek and Gruber, 2015). There is a striking similarity between the phenotype caused by smc1DDD and that by alterations in the length of Smc coiled coils in B. subtilis (Bü rmann et al, 2017). Both affect loading and translocation without adversely affecting ATPase activity in vitro or indeed association of E1158Q mutation (EQ) complexes with loading sites.…”

Combing Chromosomal DNA Mediated by the SMC Complex: Structure and Mechanisms

“…Recently, the Gruber's group has tackled this challenging question and succeeded in constructing a structural model of a full‐length SMC protein (Figure A). First, Bürmann et al have clarified that the SMC coiled‐coil length faithfully reflects a helical periodicity between the two juxtaposed arms . Even among prokaryotic SMC proteins, the primary sequence of the coiled‐coil region is not conserved, whereas the length is evolutionarily conserved in several groups, in which contact area between arms appears in multiples of 91 amino acids (Figure A).…”