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 ? resolution using crystallographic ab initio approaches. The structure shows an intimate dimer of two ?-?-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.     

Tree Climbing Strategies for Primate Ecological Studies

Primate ecological studies can benefit from accessing the canopy to estimate intra-tree and inter-tree variation in food availability and nutrient value, patch and subpatch depletion, foraging efficiency, as well as nest structure and nesting behaviors, parasitic transmission and predator detectability. We compare several ways to access the canopy and examine their suitability for studies of primates. Two of them—the Single Rope Technique and the Climbing Spur Method—allow people to safely access almost all kinds of trees, regardless of their size, height or shape. Modern climbing gear and contemporaneous safety protocols, derived from rock climbers, speleologists, and industrial arborists, are reliable and appropriate for primate ecological studies. Climbing gear is specialized and still expensive for students, but tree climbing can be dangerous during specific maneuvres. Consequently, formal training and preliminary experience are essential before attempting to collect data. We discuss the physics of falling, risk assessment associated with a fall, knots, gear and safety precautions. Finally, we propose a Tree Climbing Safety Protocol adapted for 2 climbing methods and primate field ecology. Researchers should be aware that climbing safety depends on their own judgment, which must be based on competent instruction, experience, and a realistic assessment of climbing ability. Therefore, the information we provide should be used only to supplement competent personal instruction and training in situ. Although most primate observations have been and will mostly be done from the ground in the future, canopy information complements the observations. Canopy data will add a significant new dimension to our knowledge of primates by providing strategic information otherwise unavailable.     

Stereotypic behavior in Asiatic black and Malayan sun bears

The stereotypies of individually caged Asiatic black bears (Ursus thibetanus) and Malayan sun bears (Helarctos malayanus) were studied in detail. Stereotypies were performed by 27 of the 29 subjects, were primarily locomotory in form (e.g., pacing), and occupied on average 18% (standard error of the mean (SEM)=2.5) of daylight hours. Stereotypy levels during the night were almost negligible and were highly correlated with daytime levels. Total stereotypies peaked prior to food arrival, although oral stereotypies were most frequent after feeding. In general, stereotypies were performed in locations from which food arrival could be viewed, although Asiatic black bears were equally likely to exhibit stereotypy near a neighboring bear. Across individuals, stereotypy frequency was inversely correlated with inactivity and increased with age. Older bears also showed less normal activity and a reduced diversity of normal behavior. Stereotypy levels were unrelated to levels of “compulsive” behavior (e.g., hair plucking) or repetitive self‐sucking–a potential deprivation stereotypy. More frequent stereotypies were performed more invariantly (i.e., were more predictable from one repetition to the next) and in more diverse contexts, namely 1) outside the pre‐feeding period, and 2) during the night. Contrary to observations reported elsewhere, higher frequencies of stereotypy were not associated with reduced behavioral diversity, or with a more elaborate repertoire of stereotypy forms and sequences. Although the two species did not differ in overall frequency, the stereotypies of sun bears appeared to be more food‐motivated than those of Asiatic black bears: the sun bears displayed a higher frequency and diversity of oral stereotypies, and higher levels of pre‐feeding stereotypy, and performed significantly more of their total stereotypies in locations from which they could view food arrival. This study demonstrates how analyzing stereotypies in detail can help identify the motivations that underlie these behaviors, and potentially reveal their degree of establishment–both of which are important factors in stereotypy treatment. Zoo Biol 23:409–430, 2004. © 2004 Wiley‐Liss, Inc.     

Solution structure of the iron-sulfur cluster cochaperone HscB and its binding surface for the iron-sulfur assembly scaffold protein IscU

The interaction between IscU and HscB is critical for successful assembly of iron-sulfur clusters. NMR experiments were performed on HscB to investigate which of its residues might be part of the IscU binding surface. Residual dipolar couplings ( (1) D HN and (1) D CalphaHalpha) indicated that the crystal structure of HscB [Cupp-Vickery, J. R., and Vickery, L. E. (2000) Crystal structure of Hsc20, a J-type cochaperone from Escherichia coli, J. Mol. Biol. 304, 835-845] faithfully represents its solution state. NMR relaxation rates ( (15)N R 1, R 2) and (1)H- (15)N heteronuclear NOE values indicated that HscB is rigid along its entire backbone except for three short regions which exhibit flexibility on a fast time scale. Changes in the NMR spectrum of HscB upon addition of IscU mapped to the J-domain/C-domain interface, the interdomain linker, and the C-domain. Sequence conservation is low in the interface and in the linker, and NMR changes observed for these residues likely result from indirect effects of IscU binding. NMR changes observed in the conserved patch of residues in the C-domain (L92, M93, L96, E97, E100, E104, and F153) were suggestive of a direct interaction with IscU. To test this, we replaced several of these residues with alanine and assayed for the ability of HscB to interact with IscU and to stimulate HscA ATPase activity. HscB(L92A,M93A,F153A) and HscB(E97A,E100A,E104A) both showed decreased binding affinity for IscU; the (L92A,M93A,F153A) substitution also strongly perturbed the allosteric interaction within the HscA.IscU.HscB ternary complex. We propose that the conserved patch in the C-domain of HscB is the principal binding site for IscU.     

L-phenylisopropyladenosine (L-PIA) diminishes halothane anesthetic requirements and decreases noradrenergic neurotransmission in rats

The effect of L-phenylisopropyladenosine (L-PIA), the A1 adenosine agonist, on the depth of anesthesia was investigated in halothane-anesthetized rats. L-PIA treatment reduced the minimum anesthetic concentration (MAC) of halothane that prevented 50% of animals from moving in response to a painful stimulus by 49%. MAC experiments performed with L-PIA given in conjunction with A1 adenosine receptor antagonists which either permeate the blood-brain barrier (8-phenyltheophylline [8-PT] or do not (8-sulphophenyltheophylline [8-So-PT]) indicate that central mechanisms are involved. Noradrenergic neurotransmission was diminished following L-PIA administration in halothane-anesthetized rats in all brain regions. These data suggest that acute L-PIA treatment decreases central noradrenergic neurotransmission and may represent the mechanism for the decrease in halothane dose to achieve an anesthetic endpoint anesthetic response to halothane.     

Inhibition of aromatase cytochrome P-450 by 10-oxirane and 10-thiirane substituted androgens. Implications for the structure of the active site

The mechanism of inhibition of estrogen synthetase (P-450arom) by 19R- and 19S-isomers of 10-oxiranyl-and 10-thiiranyl-4-estrene-3,17-dione was investigated using human placental microsomes and purified enzyme preparations. The 19R-isomers were potent inhibitors and exhibited affinities 36-fold (10-oxirane) and 80-fold (10-thiirane) greater than the respective 19S-isomers. Kinetic experiments showed that inhibition by the 19R-isomers is competitive with respect to substrate; inhibition constants for the (19R)-10-oxirane (Ki = 10 nM) and the 19R-10-thiirane (Ki = 2 nM) indicate that each binds with greater affinity than the androgen substrates androstenedione and testosterone. Inhibition time courses and kinetic data were consistent with high affinity, reversible binding. Spectral titrations of microsomal preparations and purified P-450arom showed that binding of the 19R-isomers shifts the Soret maximum of the ferric enzyme to 411 nm (10-oxirane) or 425 nm (10-thiirane); addition of excess androstenedione reversed the spectral changes, producing the high spin form of the enzyme with a Soret peak at 393 nm. These spectral shifts suggest that the oxygen atom of the 10-oxirane and the sulfur atom of the 10-thiirane are bound to the heme iron in the inhibitor complexes. These results suggest that the high affinities of the inhibitors arise from their dual interaction with the androgen binding site and with the heme. Coordination of the C19 heteroatom to the heme indicates that C19 of androgen substrates may be positioned sufficiently close to the heme to allow direct attack by an iron-bound oxidant. Stereoselective binding of the 19R-isomers by P-450arom further suggests that the heme is likely to be positioned above C1 and C2 of the A ring.