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

authors: Summers, Emma Louise

subjects: biology

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.

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

year: 2012

title: Facilitating rafting on the Kaituna River: The effect of manipulating Lake Rotoiti outflow on the function of the Ohau diversion wall

authors: Jones, Hannah Frances Emily

abstract: The University of Waikato was requested by Bay of Plenty Regional Council to quantify the effectiveness of the Ohau diversion wall when controlling the Kaituna River outflow during high and low flows. The Ohau diversion wall was constructed to divert nutrient-enriched water from Lake Rotorua away from the main basin of Lake Rotoiti and towards the Kaituna River outflow. Bay of Plenty Regional Council wished to determine whether controlling the Lake Rotoiti outflow to enable rafting on the Kaituna River would impact on the efficacy of the Ohau diversion wall.
The Kaituna River is used for commercial and recreational white-water rafting and kayaking, and is a proposed venue for the 2013 World Rafting Championships. However, control of the Kaituna outflow to regulate the water level in the lake may conflict with the use of the Kaituna River for rafting, which requires discharge to be between minimum and maximum raftable flows (13 m³ s⁻¹ and 26 m³ s⁻¹, respectively). Outflow from the lake may be controlled so that flows in the river are within the raftable range for a number of hours a day, and then adjusted for the remainder of the day to prevent high or low water levels. However, it is possible that this may affect the efficacy of the Ohau diversion wall, leading to concerns that this mode of operation could impact on the water quality in Lake Rotoiti. To address these concerns, three-dimensional hydrodynamic modelling was used to quantify the transfer of water from the Ohau channel to Lake Rotoiti under scenarios that facilitated rafting operations. The model was set up so that a tracer (transported by water flow) would be released in the Ohau inflow for the duration of the simulation. Tracer concentrations were output from the model simulations as depth profiles for five stations in the lake to quantify the transport of water from the Ohau channel into Lake Rotoiti.

text: Facilitating rafting on the Kaituna River: The effect of manipulating Lake Rotoiti outflow on the function of the Ohau diversion wall The University of Waikato was requested by Bay of Plenty Regional Council to quantify the effectiveness of the Ohau diversion wall when controlling the Kaituna River outflow during high and low flows. The Ohau diversion wall was constructed to divert nutrient-enriched water from Lake Rotorua away from the main basin of Lake Rotoiti and towards the Kaituna River outflow. Bay of Plenty Regional Council wished to determine whether controlling the Lake Rotoiti outflow to enable rafting on the Kaituna River would impact on the efficacy of the Ohau diversion wall.
The Kaituna River is used for commercial and recreational white-water rafting and kayaking, and is a proposed venue for the 2013 World Rafting Championships. However, control of the Kaituna outflow to regulate the water level in the lake may conflict with the use of the Kaituna River for rafting, which requires discharge to be between minimum and maximum raftable flows (13 m³ s⁻¹ and 26 m³ s⁻¹, respectively). Outflow from the lake may be controlled so that flows in the river are within the raftable range for a number of hours a day, and then adjusted for the remainder of the day to prevent high or low water levels. However, it is possible that this may affect the efficacy of the Ohau diversion wall, leading to concerns that this mode of operation could impact on the water quality in Lake Rotoiti. To address these concerns, three-dimensional hydrodynamic modelling was used to quantify the transfer of water from the Ohau channel to Lake Rotoiti under scenarios that facilitated rafting operations. The model was set up so that a tracer (transported by water flow) would be released in the Ohau inflow for the duration of the simulation. Tracer concentrations were output from the model simulations as depth profiles for five stations in the lake to quantify the transport of water from the Ohau channel into Lake Rotoiti.

year: 2013

title: Telling “Us” in the “Days Destined to You: Response Life-Telling: Indigenous Oral Autobiography and the Performance of Relation

authors: Mahuika, Nepia

subjects: Arts & Humanities

abstract: This “tau-utuutu” (responsive) protocol feels familiar to me.² My turn to speak, to respond, to share in a conversation with Warren Cariou’s stimulating essay on “Life-Telling,” Indigenous autobiography, and Dovie Thomason. It reminds me of how life-telling, orality, and history, interweave and work in my tribal universe. At home, we take turns speaking. We inherit our words, we respond, carve, and weave new narratives—make them ours. Where I come from, lives are frequently “told,” sung, cried, carved, and performed, through tribal conversations, a chorus of textured tones, sometimes in a grand debate within which our personal and collective pasts, presents, and futures converge and diverge.³ I am glad, then, to be invited, to add my voice to this present discussion. It feels natural . . . normal . . . Native.

text: Telling “Us” in the “Days Destined to You: Response Life-Telling: Indigenous Oral Autobiography and the Performance of Relation This “tau-utuutu” (responsive) protocol feels familiar to me.² My turn to speak, to respond, to share in a conversation with Warren Cariou’s stimulating essay on “Life-Telling,” Indigenous autobiography, and Dovie Thomason. It reminds me of how life-telling, orality, and history, interweave and work in my tribal universe. At home, we take turns speaking. We inherit our words, we respond, carve, and weave new narratives—make them ours. Where I come from, lives are frequently “told,” sung, cried, carved, and performed, through tribal conversations, a chorus of textured tones, sometimes in a grand debate within which our personal and collective pasts, presents, and futures converge and diverge.³ I am glad, then, to be invited, to add my voice to this present discussion. It feels natural . . . normal . . . Native.

year: 2016