Mitochondrial nucleoid interacting proteins support mitochondrial protein synthesis.

Mitochondrial ribosomes and translation factors co-purify with mitochondrial nucleoids of human cells, based on affinity protein purification of tagged mitochondrial DNA binding proteins. Among the most frequently identified proteins were ATAD3 and prohibitin, which have been identified previously as nucleoid components, using a variety of methods. Both proteins are demonstrated to be required for mitochondrial protein synthesis in human cultured cells, and the major binding partner of ATAD3 is the mitochondrial ribosome. Altered ATAD3 expression also perturbs mtDNA maintenance and replication. These findings suggest an intimate association between nucleoids and the machinery of protein synthesis in mitochondria. ATAD3 and prohibitin are tightly associated with the mitochondrial membranes and so we propose that they support nucleic acid complexes at the inner membrane of the mitochondrion.

Mechanisms of chiral discrimination by topoisomerase IV.

Topoisomerase IV (Topo IV), an essential ATP-dependent bacterial type II topoisomerase, transports one segment of DNA through a transient double-strand break in a second segment of DNA. In vivo, Topo IV unlinks catenated chromosomes before cell division and relaxes positive supercoils generated during DNA replication. In vitro, Topo IV relaxes positive supercoils at least 20-fold faster than negative supercoils. The mechanisms underlying this chiral discrimination by Topo IV and other type II topoisomerases remain speculative. We used magnetic tweezers to measure the relaxation rates of single and multiple DNA crossings by Topo IV. These measurements allowed us to determine unambiguously the relative importance of DNA crossing geometry and enzymatic processivity in chiral discrimination by Topo IV. Our results indicate that Topo IV binds and passes DNA strands juxtaposed in a nearly perpendicular orientation and that relaxation of negative supercoiled DNA is perfectly distributive. Together, these results suggest that chiral discrimination arises primarily from dramatic differences in the processivity of relaxing positive and negative supercoiled DNA: Topo IV is highly processive on positively supercoiled DNA, whereas it is perfectly distributive on negatively supercoiled DNA. These results provide fresh insight into topoisomerase mechanisms and lead to a model that reconciles contradictory aspects of previous findings while providing a framework to interpret future results.

Statistical determination of the step size of molecular motors.

Molecular motors are enzymatic proteins that couple the consumption of chemical energy to mechanical displacement. In order to elucidate the translocation mechanisms of these enzymes, it is of fundamental importance to measure the physical step size. The step size can, in certain instances, be directly measured with single-molecule techniques; however, in the majority of cases individual steps are masked by noise. The step size can nevertheless be obtained from noisy single-molecule records through statistical methods. This analysis is analogous to determining the charge of the electron from current shot noise. We review methods for obtaining the step size based on analysing, in both the time and frequency domains, the variance in position from noisy single-molecule records of motor displacement. Additionally, we demonstrate how similar methods may be applied to measure the step size in bulk kinetic experiments.

Characterization of photodamage to Escherichia coli in optical traps.

Optical tweezers (infrared laser-based optical traps) have emerged as a powerful tool in molecular and cell biology. However, their usefulness has been limited, particularly in vivo, by the potential for damage to specimens resulting from the trapping laser. Relatively little is known about the origin of this phenomenon. Here we employed a wavelength-tunable optical trap in which the microscope objective transmission was fully characterized throughout the near infrared, in conjunction with a sensitive, rotating bacterial cell assay. Single cells of Escherichia coli were tethered to a glass coverslip by means of a single flagellum: such cells rotate at rates proportional to their transmembrane proton potential (Manson et al.,1980. J. Mol. Biol. 138:541-561). Monitoring the rotation rates of cells subjected to laser illumination permits a rapid and quantitative measure of their metabolic state. Employing this assay, we characterized photodamage throughout the near-infrared region favored for optical trapping (790-1064 nm). The action spectrum for photodamage exhibits minima at 830 and 970 nm, and maxima at 870 and 930 nm. Damage was reduced to background levels under anaerobic conditions, implicating oxygen in the photodamage pathway. The intensity dependence for photodamage was linear, supporting a single-photon process. These findings may help guide the selection of lasers and experimental protocols best suited for optical trapping work.

Nonlamellar phases induced by the interaction of gramicidin S with lipid bilayers. A possible relationship to membrane-disrupting activity.

The interactions of the cyclic peptide gramicidin S (GS) with a variety of single-component lipid bilayers, and with membrane polar lipid extracts of Acholeplasma laidlawii B and Escherichia coli, were examined by differential scanning calorimetry (DSC), 31P-nuclear magnetic resonance (NMR) spectroscopy, and X-ray diffraction. The DSC data indicate that the effects of GS on the thermotropic phase behavior of phosphatidylcholine and phosphatidylethanolamine dispersions are compatible with those expected of peptides interacting primarily with the polar headgroup and/or the polar/apolar interfaces of lipid bilayers. These DSC studies also suggest that GS exhibits stronger interactions with the more fluid bilayers. For mixtures of GS with lipids such as phosphatidylcholine, phosphatidylserine, cardiolipin, and sphingomyelin, axially symmetric 31P-NMR powder patterns are observed throughout the entire temperature range examined (0-90 degrees C), and there is little evidence for significant destabilization of the lipid bilayer with respect to nonlamellar phases. With mixtures of GS with either phosphatidylethanolamine, phosphatidylglycerol, or a nonlamellar phase-forming phosphatidylcholine, axially symmetric 31P-NMR powder patterns are also observed at low temperatures. However, at high temperatures, an isotropic component is observed in their 31P-NMR spectra, and the relative intensity of this component increases significantly with temperature and with GS concentration. Once formed at high temperatures, this isotropic component exhibits a marked cooling hysteresis and in most cases disappears only when the sample is recooled to temperatures well below the lipid hydrocarbon chain-melting phase transition temperature. We also show that GS induces the formation of isotropic components in the 31P-NMR spectra of heterogeneous lipid mixtures such as occur in A. laidlawii B and E. coli membranes. These observations suggest that GS induces the formation of cubic or other three dimensionally ordered inverted nonlamellar phases when it interacts with some types of lipid bilayers, a suggestion strongly supported by our X-ray diffraction studies. Our results also suggest that the capacity of GS to induce the formation of such phases increases with the intrinsic nonlamellar phase-preferring tendencies of the lipids with which it interacts probably by producing localized increases in membrane monolayer curvature stress. The latter effect could be part of the mechanism through which this peptide exhibits its antimicrobial and hemolytic activities.

Role of lipid polymorphism in pulmonary surfactant.

The development of artificial surfactants for the treatment of respiratory distress syndrome (RDS) requires lipid systems that can spread rapidly from solution to the air-water interface. Because hydration-repulsion forces stabilize liposomal bilayers and oppose spreading, liposome systems that undergo geometric rearrangement from the bilayer (lamellar) phase to the hexagonal II (HII) phase could hasten lipid transfer to the air-water interface through unstable transition intermediates. A liposome system containing dipalmitoylphosphatidylcholine was designed; the system is stable at 23 degrees C but undergoes transformation to the HII phase as the temperature increases to 37 degrees C. The spreading of lipid from this system to the air-water interface was rapid at 37 degrees C but slow at 23 degrees C. When tested in vivo in a neonatal rabbit model, such systems elicited an onset of action equal to that of native human surfactant. These findings suggest that lipid polymorphic phase behavior may have a crucial role in the effective functioning of pulmonary surfactant.