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: Community composition and distribution of macroinvertebrates on natural and artificial substrates in North Island lakes and ponds

authors: Taitibe, Heather

subjects: Community composition

abstract: Artificial structures in freshwater ecosystems are becoming increasingly common. The introduction of these structures in marine systems lead to changes in the physical structure and the biotic assemblages. Even though artificial structures provide hard substrates for species to colonize and settle on, they are commonly shown to support a smaller number of taxa than natural substrates and are also known to facilitate the settlement of disproportionate numbers of non-native species. Nevertheless, little is known of their effects in freshwaters. 
In the second chapter of my thesis, I compare macroinvertebrate communities on three substrate types, macrophytes, sediments and artificial structures, among twenty-two ponds, to identify differences in community composition and distribution of macroinvertebrates between natural and artificial substrates. In addition, I investigated whether non-native macroinvertebrates prefer artificial substrates more than natural substrates. The similarities between artificial substrates and macrophytes can be attributed to the habitat structure, i.e., hard surfaces and the provision of refugia for macroinvertebrates from their predators. The differences between sediments and macrophytes, and artificial substrates were attributed to the difference in habitat structure and the fauna they supported (i.e., sediments contained large proportions of infauna). Non-native species that were collected in my study did not show preference for any of the habitats that were sampled.  
In the third chapter of my thesis, I identified important environmental factors that affect the distribution of macroinvertebrates communities across the twenty-two ponds sampled. The most important factor identified was temperature, nutrient gradients, pH and dissolved oxygen levels.  
Both chapters of my thesis offer an understanding of how existing artificial substrates and environmental variables in lakes and ponds on the North Island, New Zealand, affect macroinvertebrate community composition and distribution in relation to natural substrates.

text: Community composition and distribution of macroinvertebrates on natural and artificial substrates in North Island lakes and ponds Artificial structures in freshwater ecosystems are becoming increasingly common. The introduction of these structures in marine systems lead to changes in the physical structure and the biotic assemblages. Even though artificial structures provide hard substrates for species to colonize and settle on, they are commonly shown to support a smaller number of taxa than natural substrates and are also known to facilitate the settlement of disproportionate numbers of non-native species. Nevertheless, little is known of their effects in freshwaters. 
In the second chapter of my thesis, I compare macroinvertebrate communities on three substrate types, macrophytes, sediments and artificial structures, among twenty-two ponds, to identify differences in community composition and distribution of macroinvertebrates between natural and artificial substrates. In addition, I investigated whether non-native macroinvertebrates prefer artificial substrates more than natural substrates. The similarities between artificial substrates and macrophytes can be attributed to the habitat structure, i.e., hard surfaces and the provision of refugia for macroinvertebrates from their predators. The differences between sediments and macrophytes, and artificial substrates were attributed to the difference in habitat structure and the fauna they supported (i.e., sediments contained large proportions of infauna). Non-native species that were collected in my study did not show preference for any of the habitats that were sampled.  
In the third chapter of my thesis, I identified important environmental factors that affect the distribution of macroinvertebrates communities across the twenty-two ponds sampled. The most important factor identified was temperature, nutrient gradients, pH and dissolved oxygen levels.  
Both chapters of my thesis offer an understanding of how existing artificial substrates and environmental variables in lakes and ponds on the North Island, New Zealand, affect macroinvertebrate community composition and distribution in relation to natural substrates.

year: 2019

title: To act or not to act? That is the question!

authors: Bruce Ferguson, Pip

abstract: The year was 2003. I was a new Research Manager working in a Māori tertiary institution that had a history of inequitable treatment by government, through not receiving establishment funding that had gone unproblematically to non-Māori institutions. Repeating a common pattern in New Zealand, our government had decided to implement a research funding scheme, to be measured at the level of the individual academic. My institution’s decision to participate in the PBRF was not without its difficulties, and it is here that the ethics of participation become problematic. This chapter is about our ability to articulate our values, to show how we work these out in our practice, and how we are accountable to ourselves and others for that practice. Would I, with the benefit of hindsight, have encouraged my institution to enter the PBRF again?

text: To act or not to act? That is the question! The year was 2003. I was a new Research Manager working in a Māori tertiary institution that had a history of inequitable treatment by government, through not receiving establishment funding that had gone unproblematically to non-Māori institutions. Repeating a common pattern in New Zealand, our government had decided to implement a research funding scheme, to be measured at the level of the individual academic. My institution’s decision to participate in the PBRF was not without its difficulties, and it is here that the ethics of participation become problematic. This chapter is about our ability to articulate our values, to show how we work these out in our practice, and how we are accountable to ourselves and others for that practice. Would I, with the benefit of hindsight, have encouraged my institution to enter the PBRF again?

year: 2013