The DNA Binding Protein Lsr2 from Mycobacterium tuberculosis

Lsr2 is a small, basic DNA binding protein that is highly conserved in mycobacteria and related actinomycetes. Lsr2 is essential for growth in Mycobacterium tuberculosis and previous studies have shown that Lsr2 is involved in down-regulating a wide range of genes involved in cell wall synthesis and metabolic functions. This regulatory function is likely to influence bacterial growth and survival. This research investigated the biochemistry and 3D structure of Lsr2 from M. tuberculosis. Transmission electron microscopy (TEM) analysis of Lsr2 in complex with DNA revealed a regular fibril-like arrangement of protein coating double-stranded DNA. In addition, it was shown that Lsr2 physically protected DNA from DNase activity. The structure of the C-terminal DNA binding domain of Lsr2, determined by others part way through this research, prompted site directed mutagenesis of residues proposed to interact with DNA. Modification of arginine residues significantly reduced the binding of Lsr2 to DNA and fibril-like structures were not observed using TEM, for arginine mutants. The first crystal structure of the N-terminal domain of Lsr2 is reported here. Two high resolution structures in monoclinic and hexagonal space groups were solved using X-ray crystallography and ab initio phasing. Proteolytic processing of the N-terminus of Lsr2 was revealed by the structure in P2₁ and this process was recreated using the protease trypsin which resulted in crystal formation in a P3₁21 space group. Both structures show linear chains of dimeric N-terminal Lsr2, as shown by crystallographic symmetry, linked by overlapping anti-parallel β-sheets, revealing a mechanism of protein oligomerisation. Oligomerisation only occurs after the removal of the first three residues M1, A2 and K3. In solution, protein oligomerisation was recreated with trypsin, resulting in the formation of large protein complexes. A change in DNA topology after the addition of trypsin to full-length Lsr2/DNA complexes was observed using TEM. This mechanism is likely to be important to M. tuberculosis under “stress” conditions where proteases are known to be upregulated and where cross-linking and condensation of DNA is critical

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

The structure of a glycoside hydrolase 29 family member from a rumen bacterium reveals unique, dual carbohydrate-binding domains

Glycoside hydrolase (GH) family 29 consists solely of α-l-fucosidases. These enzymes catalyse the hydrolysis of glycosidic bonds. Here, the structure of GH29-0940, a protein cloned from metagenomic DNA from the rumen of a cow, has been solved, which reveals a multi-domain arrangement that has only recently been identified in bacterial GH29 enzymes. The microbial species that provided the source of this enzyme is unknown. This enzyme contains a second carbohydrate-binding domain at its C-terminal end in addition to the typical N-terminal catalytic domain and carbohydrate-binding domain arrangement of GH29-family proteins. GH29-0940 is a monomer and its overall structure consists of an N-terminal TIM-barrel-like domain, a central β-sandwich domain and a C-terminal β-sandwich domain. The TIM-barrel-like catalytic domain exhibits a (β/α)8/7 arrangement in the core instead of the typical (β/α)8 topology, with the 'missing' α-helix replaced by a long meandering loop that 'closes' the barrel structure and suggests a high degree of structural flexibility in the catalytic core. This feature was also noted in all six other structures of GH29 enzymes that have been deposited in the PDB. Based on sequence and structural similarity, the residues Asp162 and Glu220 are proposed to serve as the catalytic nucleophile and the proton donor, respectively. Like other GH29 enzymes, the GH29-0940 structure shows five strictly conserved residues in the catalytic pocket. The structure shows two glycerol molecules in the active site, which have also been observed in other GH29 structures, suggesting that the enzyme catalyses the hydrolysis of small carbohydrates. The two binding domains are classed as family 32 carbohydrate-binding modules (CBM32). These domains have residues involved in ligand binding in the loop regions at the edge of the β-sandwich. The predicted substrate-binding residues differ between the modules, suggesting that different modules bind to different groups on the substrate(s). Enzymes that possess multiple copies of CBMs are thought to have a complex mechanism of ligand recognition. Defined electron density identifying a long 20-amino-acid hydrophilic loop separating the two CBMs was observed. This suggests that the additional C-terminal domain may have a dynamic range of movement enabled by the loop, allowing a unique mode of action for a GH29 enzyme that has not been identified previously.A high-resolution crystal structure of an unknown glycoside hydrolase enzyme from the rumen of B. taurus is presented. Unique dual carbohydrate-binding domains are revealed

Nurses\u27 Alumnae Association Bulletin, June 1965

President\u27s Page Officers and Committee Chairmen Financial Report Hospital and School of Nursing Report Student Activities Annual Report Students Activities Annual Report Student Activities Annual Report Jefferson Expansion Program Psychiatric Unit Progress of the Alumnae Association Nightingale Pledge Resume of Alumnae Meetings Nursing Service Staff Association Scholarship Program Sick and Welfare Social Committee Report Bulletin Membership- WHY JOIN? Private Duty Report Annual Giving Report - 1964 PIT Alumnae Day Notes Building Fund Report - 1965 Vital Statistics IN MEMORIAM Class News Affiliated Institutions Notice

Nurses\u27 Alumnae Association Bulletin, June 1964

President\u27s Message Officers and Committee Chairmen Financial Report Hospital and School of Nursing Report Student Activities Jefferson Expansion Program Resume of Alumnae Meetings Staff Nurses Private Duty Social Committee Reports Program Scholarship Bulletin Committee Report Annual Luncheon Notes Membership and Dues Units in Jefferson Expansion Program Center Annual Giving Drive 1963 Report of Ways and Means Committee Jefferson Building Fund Contributions Annual Giving Contributions 1964 Jefferson Building Fund Report Help the Building Fund Committee! Vital Statistics Class News Notice

Exploring rumen microbe-derived fibre-degrading activities for improving feed digestibility

Ruminal fibre degradation is mediated by a complex community of rumen microbes, and its efficiency is crucial for optimal dairy productivity. Enzymes produced by rumen microbes are primarily responsible for degrading the complex structural polysaccharides that comprise fibre in the plant cell walls of feed materials. Because rumen microbes have evolved with their ruminant hosts over millions of years to perform this task, their enzymes are hypothesised to be optimally suited for activity at the temperature, pH range, and anaerobic environment of the rumen. However, fibre-rich diets are not fully digested, which represents a loss in potential animal productivity. Thus, there is opportunity to improve fibre utilisation through treating feeds with rumen microbe-derived fibrolytic enzymes and associated activities that enhance fibre degradation. This research aims to gain a better understanding of the key rumen microbes involved in fibre degradation and the mechanisms they employ to degrade fibre, by applying cultivation-based and culture-independent genomics approaches to rumen microbial communities of New Zealand dairy cattle. Using this knowledge, we aim to identify new opportunities for improving fibre degradation to enhance dairy productivity. Rumen content samples were taken over the course of a year from a Waikato dairy production herd. Over 1,000 rumen bacterial cultures were obtained from the plant-adherent fraction of the rumen contents. Among these cultures, two, 59 and 103 potentially new families, genera and species of rumen bacteria were identified, respectively. Many of the novel strains are being genome sequenced within the Hungate 1000 rumen microbial reference genome programme, which is providing deeper insights into the range of mechanisms used by the individual strains for fibre degradation. This information has been used to guide the selection of rumen bacterial strains with considerable potential as fibrolytic enzyme producers in vitro, with the intent of developing the strains so that their enzymes may be used as feed pre-treatments for use on farm. Culture-independent metagenomic approaches were also used to explore the activities involved in fibre degradation from the rumen microbial communities. Functional screening has revealed a range of novel enzymes and a novel fibre disrupting activity. Enrichment for the cell-secreted proteins from the community revealed evidence of a diverse range of cellulosomes, which are cell-surface associated multi-enzyme complexes that efficiently degrade plant cell wall polysaccharides. Biochemical and structural characterisation of these proteins has been conducted. In conclusion, cultivation and culture-independent genomic approaches have been applied to New Zealand bovine rumen microbial communities, and have provided considerable new insights into ruminal fibre degradation processes. Novel activities and bacterial species that display desirable activities on fibrous substrates in vitro are now being explored for their potential to improve ruminal fibre degradation, to allow the development of new technologies that will enhance dairy productivity