Otto Berg

Horizontal gene transfer: A critical view

It has been suggested that horizontal gene transfer (HGT) is the “essence of phylogeny.” In contrast, much data suggest that this is an exaggeration resulting in part from a reliance on inadequate methods to identify HGT events. In addition, the assumption that HGT is a ubiquitous influence throughout evolution is questionable. Instead, rampant global HGT is likely to have been relevant only to primitive genomes. In modern organisms we suggest that both the range and frequencies of HGT are constrained most often by selective barriers. As a consequence those HGT events that do occur most often have little influence on genome phylogeny. Although HGT does occur with important evolutionary consequences, classical Darwinian lineages seem to be the dominant mode of evolution for modern organisms.

Mutation frequency and biological cost of antibiotic resistance in Helicobacter pylori

Among the several factors that affect the appearance and spread of acquired antibiotic resistance, the mutation frequency and the biological cost of resistance are of special importance. Measurements of the mutation frequency to rifampicin resistance in Helicobacter pylori strains isolated from dyspeptic patients showed that ≈1/4 of the isolates had higher mutation frequencies than Enterobacteriaceae mismatch-repair defective mutants. This high mutation frequency could explain why resistance is so frequently acquired during antibiotic treatment of H. pylori infections. Inactivation of the mutS gene had no substantial effect on the mutation frequency, suggesting that MutS-dependent mismatch repair is absent in this bacterium. Furthermore, clarithromycin resistance conferred a biological cost, as measured by a decreased competitive ability of the resistant mutants in mice. In clinical isolates this cost could be reduced, indicating that compensation is a clinically relevant phenomenon that could act to stabilize resistant bacteria in a population.

Biological Costs and Mechanisms of Fosfomycin Resistance in Escherichia coli

ABSTRACT Fosfomycin is a cell wall inhibitor used mainly for the treatment of uncomplicated lower urinary tract infections. As shown here, resistance to fosfomycin develops rapidly in Escherichia coli under experimental conditions, but in spite of the relatively high mutation rate in vitro, resistance in clinical isolates is rare. To examine this apparent contradiction, we mathematically modeled the probability of resistance development in the bladder during treatment. The modeling showed that during a typical episode of urinary tract infection, the probability of resistance development was high (>10−2). However, if resistance was associated with a reduction in growth rate, the probability of resistance development rapidly decreased. To examine if fosfomycin resistance causes a reduced growth rate, we isolated in vitro and in vivo a set of resistant strains. We determined their resistance mechanisms and examined the effect of the different resistance mutations on bacterial growth in the absence and presence of fosfomycin. The types of mutations found in vitro and in vivo were partly different. Resistance in the mutants isolated in vitro was caused by ptsI, cyaA, glpT, uhpA/T, and unknown mutations, whereas no cyaA or ptsI mutants could be found in vivo. All mutations caused a decreased growth rate both in laboratory medium and in urine, irrespective of the absence or presence of fosfomycin. According to the mathematical model, the reduced growth rate of the resistant strains will prevent them from establishing in the bladder, which could explain why fosfomycin resistance remains rare in clinical isolates.

Near-Critical Phenomena in Intracellular Metabolite Pools

The supply and consumption of metabolites in living cells are catalyzed by enzymes. Here we consider two of the simplest schemes where one substrate is eliminated through Michaelis-Menten kinetics, and where two types of substrates are joined together by an enzyme. It is demonstrated how steady-state substrate concentrations can change ultrasensitively in response to changes in their supply rates and how this is coupled to slow relaxation back to steady state after a perturbation. In the one-substrate system, such near-critical behavior occurs when the supply rate approaches the maximal elimination rate, and in the two-substrate system it occurs when the rates of substrate supply are almost balanced. As systems that operate near criticality tend to display large random fluctuations, we also carried out a stochastic analysis using analytical approximations of master equations and compared the results with molecular-level Monte Carlo simulations. It was found that the significance of random fluctuations was directly coupled to the steady-state sensitivity and that the two substrates can fluctuate greatly because they are anticorrelated in such a way that the product formation rate displays only small variation. Basic relations are highlighted and biological implications are discussed.

Stochastic reaction-diffusion kinetics in the microscopic limit

Quantitative analysis of biochemical networks often requires consideration of both spatial and stochastic aspects of chemical processes. Despite significant progress in the field, it is still computationally prohibitive to simulate systems involving many reactants or complex geometries using a microscopic framework that includes the finest length and time scales of diffusion-limited molecular interactions. For this reason, spatially or temporally discretized simulations schemes are commonly used when modeling intracellular reaction networks. The challenge in defining such coarse-grained models is to calculate the correct probabilities of reaction given the microscopic parameters and the uncertainty in the molecular positions introduced by the spatial or temporal discretization. In this paper we have solved this problem for the spatially discretized Reaction-Diffusion Master Equation; this enables a seamless and physically consistent transition from the microscopic to the macroscopic frameworks of reaction-diffusion kinetics. We exemplify the use of the methods by showing that a phosphorylation-dephosphorylation motif, commonly observed in eukaryotic signaling pathways, is predicted to display fluctuations that depend on the geometry of the system.

The determination of monolayer structure by infrared spectroscopy: CO2 on NaCl(100)

Infrared spectra of a 12C16O2 monolayer on NaCl(100) are reported for the first time. The polarization and coverage dependence of spectroscopic signals indicate that there is only one kind of adsorption site, in which the molecular axis is tilted 68° from the surface normal. The adsorbate layer grows in the form of constant-density islands. Plane group symmetry analysis reveals a unique structure: there are two tilted molecules per layer unit cell, arranged in herringbone fashion. This structure is in quantitative agreement with the photometric observations. Splitting of the molecular v3 band is interpreted by a vibration-vibration coupling mechanism.

Surface molecular view of colloidal gelation

We investigate the phase behavior of surface-functionalized silica colloids at both the molecular and macroscopic levels. This investigation allows us to relate collective properties such as aggregation, gelation, and aging directly to molecular interfacial behavior. By using surface-specific vibrational spectroscopy, we reveal dramatic changes in the conformation of alkyl chains terminating submicrometer silica particles. In fluid suspension at high temperatures, the interfacial molecules are in a liquid-like state of conformational disorder. As the temperature is lowered, the onset of gelation is identified by macroscopic phenomena, including changes in turbidity, heat release, and diverging viscosity. At the molecular level, the onset of this transition coincides with straightening of the carbon–carbon backbones of the interfacial molecules. In later stages, their intermolecular crystalline packing improves. It is the increased density of this ordered boundary layer that increases the van der Waals attraction between particles, causing the colloidal gas to aggregate. The approach presented here can provide insights into phase transitions that occur through surface modifications in a variety of colloidal systems.

Lost in presumption: stochastic reactions in spatial models

Physical modeling is increasingly important for generating insights into intracellular processes. We describe situations in which combined spatial and stochastic aspects of chemical reactions are needed to capture the relevant dynamics of biochemical systems.

Optical dephasing in pentacene-doped PMMA under high pressure

Pressure- and temperature-dependent photon echo results are obtained for pentacene doped polymethyl methacrylate (PMMA). A unique pressure effect is observed in which the optical dephasing rate increases as the pressure is increased from ambient pressure to 4 kbar, above which the optical dephasing rate is pressure independent up to 43 kbar. The present results are also compared with pressure- and temperature-dependent photon echo results for rhodamine 101 in PMMA, in which the optical dephasing rate was completely insensitive to pressure over the range 0 to 30 kbar. A negative correlation is also observed between the optical dephasing rate and the spectral hole burning efficiency. Line broadening due to pressure induced spectral diffusion may be responsible for both the increased dephasing rate and the reduced spectral hole-burning at high pressure.

Ligand Responses of Vfr, the Virulence Factor Regulator from Pseudomonas aeruginosa

Vfr, a transcription factor homologous to the Escherichia coli cyclic AMP (cAMP) receptor protein (CRP), regulates many aspects of virulence in Pseudomonas aeruginosa. Vfr, like CRP, binds to cAMP and then recognizes its target DNA and activates transcription. Here we report that Vfr has important functional differences from CRP in terms of ligand sensing and response. First, Vfr has a significantly higher cAMP affinity than does CRP, which might explain the mysteriously unidirectional functional complementation between the two proteins (S. E. H. West et al., J. Bacteriol. 176:7532-7542, 1994). Second, Vfr is activated by both cAMP and cGMP, while CRP is specific to cAMP. Mutagenic analyses show that Thr133 (analogous to Ser128 of CRP) is the key residue for both of these distinct Vfr properties. On the other hand, substitutions that cause cAMP-independent activity in Vfr are similar to those seen in CRP, suggesting that a common cAMP activation mechanism is present. In the course of these analyses, we found a remarkable class of Vfr variants that have completely reversed the regulatory logic of the protein: they are active in DNA binding without cAMP and are strongly inhibited by cAMP. The physiological impact of Vfrs ligand sensing and response is discussed, as is a plausible basis for the fundamental change in protein allostery in the novel group of Vfr variants.