Carbon catabolite repression (CCR) is a key regulatory system found in most microorganisms that ensures preferential utilization of energy-efficient carbon sources. CCR helps microorganisms obtain a proper balance between their metabolic capacity and the maximum sugar uptake capability. It also constrains the deregulated utilization of a preferred cognate substrate, enabling microorganisms to survive and dominate in natural environments. On the other side of the same coin lies the tenacious bottleneck in microbial production of bioproducts that employs a combination of carbon sources in varied proportion, such as lignocellulose-derived sugar mixtures. Preferential sugar uptake combined with the transcriptional and/or enzymatic exclusion of less preferred sugars turns out one of the major barriers in increasing the yield and productivity of fermentation process. Accumulation of the unused substrate also complicates the downstream processes used to extract the desired product. To overcome this difficulty and to develop tailor-made strains for specific metabolic engineering goals, quantitative and systemic understanding of the molecular interaction map behind CCR is a prerequisite. Here we comparatively review the universal and strain-specific features of CCR circuitry and discuss the recent efforts in developing synthetic cell factories devoid of CCR particularly for lignocellulose-based biorefinery. [BMB reports 2012; 45(2): 59-70]

A mutator is an allele that increases the mutation rate throughout the genome by disrupting some aspect of DNA replication or repair. Mutators that increase the mutation rate by the order of 100-fold have been observed to spontaneously emerge and achieve high frequencies in natural populations and in longterm laboratory evolution experiments with Escherichia coli. In principle, the fixation of mutator alleles is limited by (i) competition with mutations in wild-type backgrounds, (ii) additional deleterious mutational load, and (iii) random genetic drift. Using a multiple-locus model and employing both simulation and analytic methods, we investigate the effects of these three factors on the fixation probability P fix of an initially rare mutator as a function of population size N, beneficial and deleterious mutation rates, and the strength of mutations s. Our diffusion-based approximation for P fix successfully captures effects ii and iii when selection is fast compared to mutation (m=s > 1). This enables us to predict the conditions under which mutators will be evolutionarily favored. Surprisingly, our simulations show that effect i is typically small for strong-effect mutators. Our results agree semiquantitatively with existing laboratory evolution experiments and suggest future experimental directions.

Why metalloenzymes often show dramatic changes in their catalytic activity when subjected to chemically similar but non-native metal substitutions is a long-standing puzzle. Here, we report on the catalytic roles of metal ions in a model metalloenzyme system, human carbonic anhydrase II (CA II). Through a comparative study on the intermediate states of the zinc-bound native CA II and non-native metal-substituted CA IIs, we demonstrate that the characteristic metal ion coordination geometries (tetrahedral for Zn2+, tetrahedral to octahedral conversion for Co2+, octahedral for Ni2+, and trigonal bipyramidal for Cu2+) directly modulate the catalytic efficacy. In addition, we reveal that the metal ions have a long-range (~10 Å) electrostatic effect on restructuring water network in the active site. Our study provides evidence that the metal ions in metalloenzymes have a crucial impact on the catalytic mechanism beyond their primary chemical properties.

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Recent genomic analyses on the cellular metabolic network show that reaction flux across enzymes are diverse and exhibit power-law behavior in its distribution. While intuition might suggest that the reactions with larger fluxes are more likely to be lethal under the blockade of its catalysing gene products or gene knockouts, we find, by in silico flux analysis, that the lethality rarely has correlations with the flux level owing to the widespread backup pathways innate in the genome-wide metabolism of Escherichia coli. Lethal reactions, of which the deletion generates cascading failure of following reactions up to the biomass reaction, are identified in terms of the Boolean network scheme as well as the flux balance analysis. The avalanche size of a reaction, defined as the number of subsequently blocked reactions after its removal, turns out to be a useful measure of lethality. As a means to elucidate phenotypic robustness to a single deletion, we investigate synthetic lethality in reaction level, where simultaneous deletion of a pair of nonlethal reactions leads to the failure of the biomass reaction. Synthetic lethals identified via flux balance and Boolean scheme are consistently shown to act in parallel pathways, working in such a way that the backup machinery is compromised.

Starting with the first publication of lacZ gene fusion in 1980, reporter genes have just entered their fourth decade. Initial studies relied on the simple fusion of a promoter or gene with a particular reporter gene of interest. Such constructs were then used to determine the promoter activity under specific conditions or within a given cell or organ. Although this protocol was, and still is, very effective, current research shows a paradigm shift has occurred in the use of reporter systems. With the advent of innovative cloning and synthetic biology techniques and microfluidic/nanodroplet systems, reporter genes and their proteins are now finding themselves used in increasingly intricate and novel applications. For example, researchers have used fluorescent proteins to study biofilm formation and discovered that microchannels develop within the biofilm. Furthermore, there has recently been a "fusion" of art and science; through the construction of genetic circuits and regulatory systems, researchers are using bacteria to "paint" pictures based upon external stimuli. As such, this review will discuss the past and current trends in reporter gene applications as well as some exciting potential applications and models that are being developed based upon these remarkable proteins. [BMB reports 2010; 43(7): 451-460]

We investigate the kinetic roughening of Ar + ion-sputtered Pd(001) surface both experimentally and theoretically. In situ real-time x-ray reflectivity and in situ scanning tunneling microscopy show that nanoscale adatom islands form and grow with increasing sputter time t. Surface roughness, W (t), and lateral correlation length, ξ(t), follows the scaling laws, W (t) ∼ t β and ξ(t) ∼ t 1/z with the exponents β ≃ 0.20 and 1/z ≃ 0.20, for ion beam energy ε = 0.5 keV, which is inconsistent with the prediction of the Kuramoto-Sivashinsky (KS) model. We thereby extend the KS model by applying the Sigmund theory of sputter erosion to the higher order, O(∇ 4 , h 2 ), where h is surface height, and derive a new term of the form ∇ 2 (∇h) 2 which plays an indispensable role in describing the observed morphological evolution of the sputtered surface. 64.60.Cn, 79.20.Rf Recently, the observation of ordered nanostructures such as ripples and two-dimensional patterns on ion-sputtered surfaces has attracted much attention due to the demonstration of the possibility of fabrication of ordered nanoscale structures in a relatively easy and affordable way [1,2,3,4,5,6, 7]. Such experimental results have motivated extensive theoretical investigations aiming to understand the mechanism of the morphological evolution of ion-sputtered surfaces. A linear model, proposed by Bradley and Harper (BH) [8], has been successful in predicting the formation of the ripple structure. The wavelength, orientation and amplitude of the ripples can be predicted in terms of experimental parameters such as the incident angle of the ion beam and substrate temperature [9]. The BH theory, however, fails to explain a number of experimental observations such as the saturation of the ripple amplitude [10,11,12], or the appearance of kinetic roughening [13,14]. To remedy such shortcomings, the noisy Kuramoto-Sivashinsky (KS) equation [15,16] was introduced based on the Sigmund theory of sputter erosion [17]. In addition to the linear terms of the BH model, it contains a nonlinear term proportional to (∇h) 2 , known as the Kardar-ParisiZhang (KPZ) term [18], where h is surface height. Due to the nonlinear term, the surface roughness (or the ripple amplitude), which was growing exponentially with increasing sputter time in the linear model, changes to the type following a power law and eventually saturates to a constant value [19]. Although the KS model seems to be successful in offering insights for understanding the nonlinear behavior of sputtereroded surfaces, it has not been convincing yet because the detailed properties of the kinetic roughening predicted by the KS equation have not been fully tested experimentally. Kinetic roughening behavior is described by the scaling theory [20].The surface roughness of the sam-The roughness and growth exponents α and β are related via scaling relations to give the dynamic exponent, z = α/β, which determines the scaling of the saturation time with the system size L. Below, we will deal with the inverse dynamic expon...

We evaluated the bactericidal activity of Bdellovibrio bacteriovorus, strain HD100, within blood sera against bacterial strains commonly associated with bacteremic infections, including E. coli, Klebsiella pneumoniae and Salmonella enterica. Tests show that B. bacteriovorus HD100 is not susceptible to serum complement or its bactericidal activity. After a two hour exposure to human sera, the prey populations decreased 15- to 7,300-fold due to the serum complement activity while, in contrast, the B. bacteriovorus HD100 population showed a loss of only 33%. Dot blot analyses showed that this is not due to the absence of antibodies against this predator. Predation in human serum was inhibited, though, by both the osmolality and serum albumin. The activity of B. bacteriovorus HD100 showed a sharp transition between 200 and 250 mOsm/kg, and was progressively reduced as the osmolality increased. Serum albumin also acted to inhibit predation by binding to and coating the predatory cells. This was confirmed via dot blot analyses and confocal microscopy. The results from both the osmolality and serum albumin tests were incorporated into a numerical model describing bacterial predation of pathogens. In conclusion, both of these factors inhibit predation and, as such, they limit its effectiveness against pathogenic prey located within sera.