The Structure of the Oligomerization Domain of Lsr2 from Mycobacterium tuberculosis Reveals a Mechanism for Chromosome Organization and Protection

Abstract

Lsr2 is a small DNA-binding protein present in mycobacteria and related actinobacteria that regulates gene expression and influences the organization of bacterial chromatin. Lsr2 is a dimer that binds to AT-rich regions of chromosomal DNA and physically protects DNA from damage by reactive oxygen intermediates (ROI). A recent structure of the C-terminal DNA-binding domain of Lsr2 provides a rationale for its interaction with the minor groove of DNA, its preference for AT-rich tracts, and its similarity to other bacterial nucleoid-associated DNA-binding domains. In contrast, the details of Lsr2 dimerization (and oligomerization) via its N-terminal domain, and the mechanism of Lsr2-mediated chromosomal cross-linking and protection is unknown. We have solved the structure of the N-terminal domain of Lsr2 (N-Lsr2) at 1.73 Å resolution using crystallographic ab initio approaches. The structure shows an intimate dimer of two ß–ß–a motifs with no close homologues in the structural databases. The organization of individual N-Lsr2 dimers in the crystal also reveals a mechanism for oligomerization. Proteolytic removal of three N-terminal residues from Lsr2 results in the formation of an anti-parallel β-sheet between neighboring molecules and the formation of linear chains of N-Lsr2. Oligomerization can be artificially induced using low concentrations of trypsin and the arrangement of N-Lsr2 into long chains is observed in both monoclinic and hexagonal crystallographic space groups. In solution, oligomerization of N-Lsr2 is also observed following treatment with trypsin. A change in chromosomal topology after the addition of trypsin to full-length Lsr2-DNA complexes and protection of DNA towards DNAse digestion can be observed using electron microscopy and electrophoresis. These results suggest a mechanism for oligomerization of Lsr2 via protease-activation leading to chromosome compaction and protection, and concomitant down-regulation of large numbers of genes. This mechanism is likely to be relevant under conditions of stress where cellular proteases are known to be upregulated.

Cell cycle progression in Caulobacter requires a nucleoid-associated protein with high AT sequence recognition

“…This clustering suggests that distant genomic loci are colocalized in 3D space, as has been observed for H-NS-bound loci in E. coli (37). In addition to H-NS, multiple NAPs are known to promote long-range intrachromosomal interactions through DNA bending, looping, compaction, and the stabilization of discrete subdomains (4,(55)(56)(57)(58)(59)(60)(61)(62)(63). It may be that the self-association of GapR molecules links together noncontiguous loci that contain AT-rich sequences.…”

Mechanism of DNA organization by Mycobacterium tuberculosis protein Lsr2

“…A relaxed DNA conformation at low DNA tension may then allow dominant binding by another Lsr2 species that causes DNA folding. This scenario is possible given the solution oligomeric nature of Lsr2 (30,48) and can also explain the observation of tension-regulated DNA stiffening and folding by Lsr2.…”

The Normalcy of Dormancy: Common Themes in Microbial Quiescence

“…M. tuberculosis might use a similar mechanism to protect its chromosome. A mycobacterial histone-like protein, Lsr2, mediates chromosome compaction and protection from reactive oxygen and nitrogen species (Summers et al, 2012). The mechanisms underlying this protective ability are unclear, but could be related to the reported association between Lsr2 and FAD-binding flavoprotein that mediates general oxidative stress resistance (Du et al, 2012).…”