Transcript quantification based on chemical labeling of RNA associated with fluorescent detection

The impact of measurement errors in the identification of regulatory networks

BACKGROUND

There are several studies in the literature depicting measurement error in gene expression data and also, several others about regulatory network models. However, only a little fraction describes a combination of measurement error in mathematical regulatory networks and shows how to identify these networks under different rates of noise.

RESULTS

This article investigates the effects of measurement error on the estimation of the parameters in regulatory networks. Simulation studies indicate that, in both time series (dependent) and non-time series (independent) data, the measurement error strongly affects the estimated parameters of the regulatory network models, biasing them as predicted by the theory. Moreover, when testing the parameters of the regulatory network models, p-values computed by ignoring the measurement error are not reliable, since the rate of false positives are not controlled under the null hypothesis. In order to overcome these problems, we present an improved version of the Ordinary Least Square estimator in independent (regression models) and dependent (autoregressive models) data when the variables are subject to noises. Moreover, measurement error estimation procedures for microarrays are also described. Simulation results also show that both corrected methods perform better than the standard ones (i.e., ignoring measurement error). The proposed methodologies are illustrated using microarray data from lung cancer patients and mouse liver time series data.

CONCLUSIONS

Measurement error dangerously affects the identification of regulatory network models, thus, they must be reduced or taken into account in order to avoid erroneous conclusions. This could be one of the reasons for high biological false positive rates identified in actual regulatory network models.

Identification and functional characterisation of cellobiose and lactose transport systems in Lactococcus lactis IL1403

Physiological, biochemical and macroarray analyses of Lactococcus lactis IL1403 and its ccpA and bglR single and double mutants engaged in lactose and beta-glucosides catabolism were performed. The kinetic analysis indicated the presence of different transport systems for salicin and cellobiose. The control of salicin catabolism was found to be mediated by the transcriptional regulator BglR and the CcpA protein. The transcriptional analysis by macroarray technology of genes from the PEP:PTS regions showed that several genes, like ybhE, celB, ptcB and ptcA, were expressed at higher levels both in wild type cells exposed to cellobiose and in the ccpA mutant. We also demonstrated that in L. lactis IL1403 cultured on medium with cellobiose and lactose as carbon sources, after the first phase of cellobiose consumption and then co-metabolism of the two sugars, when cellobiose is exhausted the strain uses lactose as the only carbon source. These data could indicate that lactose and cellobiose are transported by a unique system-a PTS carrier induced by the presence of cellobiose, and negatively controlled by the CcpA regulator.

Regulation of sugar catabolism in Lactococcus lactis

The increasing number of genomic and post-genomic studies on Gram-positive organisms and especially on lactic acid bacteria brings a lot of information on sugar catabolism in these bacteria. Like for many other bacteria, glucose is the most preferred source of carbon and energy for Lactococcus lactis. Other carbon sources can induce their own utilization in the absence of well-metabolized sugar. These processes engage numbers of genes and undergo complex mechanisms of regulation. In this review, we discuss various biochemical and genetic control mechanisms involved in sugar catabolism, like regulation by repressors, activators, antiterminators or carbon catabolite repression control.

Degradation of aromatic compounds by Acinetobacter radioresistens S13: growth characteristics on single substrates and mixtures

Acinetobacter radioresistens S13 is able to grow on phenol or benzoate as the sole carbon and energy source: both these compounds are catabolized through the beta-ketoadipate pathway. Genes encoding the catabolic enzymes for degradation of aromatic compounds are localized on A. radioresistens S13 chromosome and organized in, at least, two distinct sets, one for benzoate degradation and another for phenol catabolism. In the present study, the growth and biodegradation kinetics for benzoate and phenol, and an easily metabolized substrate (acetate) were established. Benzoate was degraded slower and supports a less rapid and efficient growth than either acetate or phenol. A combined transcript-proteomic analysis of some of the major catabolic genes and their products nonetheless has shown that benzoate induces the expression of both benzoate and phenol catabolic operons. This result was confirmed by the fact that benzoate-acclimatized bacteria were rapidly able to degrade phenol too. Finally, the growth and biodegradation kinetics for different mixtures of acetate, benzoate and phenol were determined. Results indicate that a hierarchy of substrate utilization, benzoate > acetate > phenol, occurred: benzoate was the preferred substrate, despite its lower growth and biodegradation parameters. Hypotheses explaining these unusual metabolic features of A. radioresistens S13 are discussed.

Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation

The stability of mRNA was investigated for the first time at the genomic scale during carbon starvation adaptation of Lactococcus lactis IL1403. In exponential phase, mRNA half-lives were correlated positively to open reading frame length. A polypurine sequence, AGGAG, was identified as a putative 5'-stabilizer and inverted repeated sequences as a 3'-destabilizer. These original findings suggested that multiple pathways of mRNA degradation should coexist: internal cleavage, endonuclease cleavage initiated at the 5'-end, and exonuclease attack at the 3'-end. During carbon starvation adaptation, mRNA stability globally increased, but specific mechanisms allowing a wide range of stabilization factors between genes and differential kinetic evolution were involved. A formal method allowing the quantification of the relative influences of transcription and degradation on the mRNA pool control was developed and applied in L. lactis. Gene expression was mostly controlled by altered transcription prior to carbon source exhaustion, while the influence of mRNA stability increased during the starvation phase. This study highlighted that stability modulation in response to adverse growth conditions can govern gene regulation to the same extent as transcription in bacteria.

Transcriptional, translational and metabolic regulation of glycolysis in Lactococcus lactis subsp. cremoris MG 1363 grown in continuous acidic cultures

The physiological behaviour of Lactococcus lactis subsp. cremoris MG 1363 was characterized in continuous culture under various acidic conditions (pH 4.7-6.6). Biomass yield was diminished in cultures with low pH and the energy dedicated to maintenance increased due to organic acid inhibition and cytoplasmic acidification. Under such acidic conditions, the specific rate of glucose consumption by the bacterium increased, thereby enhancing energy supply. This acceleration of glycolysis was regulated by both an increase in the concentrations of glycolytic enzymes (hierarchical regulation) and the specific modulation of enzyme activities (metabolic regulation). However, when the inhibitory effect of intracellular pH on enzyme activity was taken into account in the model of regulation, metabolite regulation was shown to be the dominant factor controlling pathway flux. The changes in glycolytic enzyme concentrations were not correlated directly to modifications in transcript concentrations. Analyses of the relative contribution of the phenomena controlling enzyme synthesis indicated that translational regulation had a major influence compared to transcriptional regulation. An increase in the translation efficiency was accompanied by an important decrease of total cellular RNA concentrations, confirming that the translation apparatus of L. lactis was optimized under acid stress conditions.

Development of Sinorhizobium meliloti pilot macroarrays for transcriptome analysis

In order to prepare for whole-genome expression analysis in Sinorhizobium meliloti, pilot DNA macroarrays were designed for 34 genes of known regulation. The experimental parameters assessed were the length of the PCR products, the influence of a tag at the 5' end of the primers, and the method of RNA labeling. Variance and principal-component analysis showed that the most important nonbiological parameter was the labeling method. The sizes of PCR products were also found to be important, whereas the influence of 5' tags was minimal. The variability between replicated spots on a membrane was found to be low. These experimental procedures were validated by analyzing the effects of microaerobic conditions on gene expression.

Dynamic response of catabolic pathways to autoacidification in Lactococcus lactis: transcript profiling and stability in relation to metabolic and energetic constraints

The dynamic response of the central metabolic pathways to autoacidification (accumulation of organic acid fermentation products) in Lactococcus lactis was investigated in a global manner by integrating molecular data (cellular transcript concentrations, mRNA turnover) within physiological investigations of metabolic and energetic parameters. The decrease in pH associated with the accumulation of organic acids modified the physiological state of the cell considerably. Cytoplasmic acidification led to inhibition of enzyme activities and, consequently, to a diminished catabolic flux through glycolysis and a decreased rate of biochemical energy synthesis. This decrease in energy production together with the increased energy expenditure to counter cytoplasmic acidification led to energetic limitations for biomass synthesis. In these conditions, the specific growth rate decreased progressively, and growth ultimately stopped, although a diminished catabolic flux was maintained in the absence of growth. The cellular response to this phenomenon was to maintain significant levels of mRNA of catabolic genes, involving both continued transcription of the genes and also, in certain cases, an increase in transcript stability. Thus, translation was maintained, and intracellular concentration of certain enzymes increased, partially compensating for the inhibition of activity provoked by the diminished pH. When catabolic activity ceased after prolonged exposure to stress-induced stationary phase, endogenous RNA catabolism was observed.