Synthesis Of Cell Wall Components Research Articles

Melatonin extends shelf life in postharvest okra via delaying fruit softening and reducing weight loss.

Melatonin, a hormone present in animals and some plants, has garnered attention for its potential in preserving harvested produce. Softening due to changes in cell wall composition and wilting caused by weight loss are the major reasons for the loss of commercial value in postharvest okra. This study aimed to evaluate the impact of melatonin on the softening and weight loss of postharvest okra. The results revealed that the application of melatonin had a significant influence on the maintenance of fruit firmness by inhibiting the breakdown and dissolution of cell wall polysaccharides by suppressing the expression of specific genes responsible for cell wall degradation in okra. Conversely, melatonin treatment positively influenced the expression of genes involved in the synthesis of cell wall components. Furthermore, the treatment exhibited notable benefits in reducing weight loss in okra, which was accomplished by promoting the closure of stomata - the tiny pores on the surface of the fruit. Melatonin could serve as a novel approach to reduce water loss, delay fruit softening and extend the shelf life of okra. © 2024 Society of Chemical Industry.

Targeted metabolome and transcriptome analyses reveal changes in gibberellin and related cell wall-acting enzyme-encoding genes during stipe elongation in Flammulina filiformis.

Flammulina filiformis, a typical agaric fungus, is a widely cultivated and consumed edible mushroom. Elongation of its stipe (as the main edible part) is closely related to its yield and commercial traits; however, the endogenous hormones during stipe elongation and their regulatory mechanisms are not well understood. Gibberellin (GA) plays an important role in the regulation of plant growth, but little has been reported in macro fungi. In this study, we first treated F. filiformis stipes in the young stage with PBZ (an inhibitor of GA) and found that PBZ significantly inhibited elongation of the stipe. Then, we performed GA-targeted metabolome and transcriptome analyses of the stipe at both the young and elongation stages. A total of 13 types of GAs were detected in F. filiformis; the contents of ten of them, namely, GA3, GA4, GA8, GA14, GA19, GA20, GA24, GA34, GA44, and GA53, were significantly decreased, and the contents of three (GA5, GA9, and GA29) were significantly increased during stipe elongation. Transcriptome analysis showed that the genes in the terpenoid backbone biosynthesis pathway showed varying expression patterns: HMGS, HMGR, GPS, and FPPS were significantly upregulated, while CPS/KS had no significant difference in transcript level during stipe elongation. In total, 37 P450 genes were annotated to be involved in GA biosynthesis; eight of them were upregulated, twelve were downregulated, and the rest were not differentially expressed. In addition, four types of differentially expressed genes involved in stipe elongation were identified, including six signal transduction genes, five cell cycle-controlling genes, twelve cell wall-related enzymes and six transcription factors. The results identified the types and content of GAs and the expression patterns of their synthesis pathways during elongation in F. filiformis and revealed the molecular mechanisms by which GAs may affect the synthesis of cell wall components and the cell cycle of the stipe through the downstream action of cell wall-related enzymes, transcription factors, signal transduction and cell cycle control, thus regulating stipe elongation. This study is helpful for understanding the roles of GAs in stipe development in mushrooms and lays the foundation for the rational regulation of stipe length in agaric mushrooms during production.

Molecular hydrogen-based irrigation extends strawberry shelf life by improving the synthesis of cell wall components in fruit

Strawberries (Fragaria × ananassa Duch.) are highly perishable due to their soft texture, and easily decay during transportation and storage. Our previous report showed that molecular hydrogen-based irrigation in the form of hydrogen nanobubble water (HNW) could obviously improve flavor and consumer preferences of strawberry fruit at the harvesting stage. This study further investigated whether this approach could influence the shelf life of strawberry. During storage for 15 d at 4 ℃, HNW delayed the degradation in the quality of strawberry fruit, evaluated by alteration in sensory attributes (including aroma, luster, color, shape, and general evaluation), weight loss, contents of vitamin C, soluble sugar, and titratable acidity, and sugar/acid ratio. The higher levels of lignin, cellulose, and hemicellulose were observed. Compared to conventional surface water (control) irrigation, the firmness of fruit was increased by HNW irrigation at the harvest stage, and progressively maintained during the storage period. Molecular evidence revealed that before the harvesting period, the transcripts of cinnamyl CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD), as well as cellulose synthase 1/4/6 (CesF1/4/6), the representative genes for the synthesis of lignin, cellulose, and hemicellulose, were induced by HNW irrigation. These changes were positively matched with the increased lignin, cellulose, and hemicellulose contents at the harvesting period. Overall, the extended shelf life of strawberries achieved by molecular hydrogen-based irrigation might be due to the improvement in lignin, cellulose, and hemicellulose accumulation. Therefore, this study demonstrated the effectiveness of HNW irrigation for retarding the decay of harvested strawberries.

Gene expression of a canopy‐forming kelp, Eisenia bicyclis ( Laminariales, Phaeophyceae ), under high temperature stress

Gene expression of a canopy‐forming kelp, <scp> <i>Eisenia bicyclis</i> </scp> ( <scp>Laminariales, Phaeophyceae</scp> ), under high temperature stress

Anatomical Characteristics and Variation Mechanisms on the Thick-Walled and Dwarfed Culm of Shidu Bamboo (Phyllostachys nidularia f. farcta)

Stable culm variants are valuable and important material for the study of culm development in bamboo plants. However, to date, there are few reports on the mechanism of variation of these bamboo variants. Phyllostachys nidularia f. farcta (Shidu bamboo) is a bamboo variant with stable phenotypes such as a dwarf culm with a thickened wall. In this study, we systematically investigated the cytological characteristics and underlying mechanism of morphological variation in culms of this variant using anatomical, mathematical statistical, physiological, and genomic methods. The anatomical observation and statistical results showed that the lateral increase of ground tissue in the inner layer of culm wall and the enlargement of vascular bundles are the anatomical essence of the wall thickening of Shidu bamboo; the limited elongation of fiber cells and the decrease in the number of parenchyma cells longitudinally are probably the main causes of the shortening of its internodes. A number of genes involved in the gibberellin synthesis pathway and in the synthesis of cell wall components are differentially expressed between the variant and its prototype, Ph. nidularia, and may play an important role in determining the phenotype of internode shortening in Shidu bamboo. The decrease in gibberellin content and the content of the major chemical components of the cell wall of Shidu bamboo confirmed the results of the above transcriptome. In addition, the variation in culm morphology in Shidu bamboo had little effect on the volume of the culm wall of individual internodes, suggesting that the decrease in the total number of internodes and the decrease in dry matter content (lignin, cellulose, etc.) may be the main factor for the sharp decline in culm biomass of Shidu bamboo.

Challenges of Biomass Utilization for Bioenergy in a Climate Change Scenario.

Simple SummaryThe most recent intergovernmental panel on climate change (IPCC 2021) has shown that the human influence on climate change has been unprecedented, predicting a global temperature increase of 1.5 °C in the earlies 2030s. The burning of fossil fuels has increased the emissions of nitrous oxide (N2O), methane (CH4), and carbon dioxide (CO2) to the atmosphere, amplifying the greenhouse effect in the last decades. In this scenario, the use of biorefineries, a renewable analog to petroleum refineries, has attracted a lot of attention since they use renewable sources as lignocellulosic feedstocks. However, climate change alters the temperature, rainfall patterns, drought, CO2 levels, and air moisture impacting biomass growth, productivity, chemical composition, and soil microbial community. Here, we discuss strategies to produce fuels and value-added products from biomass in a climate change scenario, potential feedstocks for bioenergy purposes, the chemical composition of lignocellulosic biomass, enzymes involved in biomass deconstruction, and other processes related to biomass production, processing, and conversion. Understanding these integrated factors involved in bioenergy production with plant responses to climate change shows that climate-smart agriculture is the only way to lower the negative impact of climate changes on crop adaptation and its use for bioenergy.The climate changes expected for the next decades will expose plants to increasing occurrences of combined abiotic stresses, including drought, higher temperatures, and elevated CO2 atmospheric concentrations. These abiotic stresses have significant consequences on photosynthesis and other plants’ physiological processes and can lead to tolerance mechanisms that impact metabolism dynamics and limit plant productivity. Furthermore, due to the high carbohydrate content on the cell wall, plants represent a an essential source of lignocellulosic biomass for biofuels production. Thus, it is necessary to estimate their potential as feedstock for renewable energy production in future climate conditions since the synthesis of cell wall components seems to be affected by abiotic stresses. This review provides a brief overview of plant responses and the tolerance mechanisms applied in climate change scenarios that could impact its use as lignocellulosic biomass for bioenergy purposes. Important steps of biofuel production, which might influence the effects of climate change, besides biomass pretreatments and enzymatic biochemical conversions, are also discussed. We believe that this study may improve our understanding of the plant biological adaptations to combined abiotic stress and assist in the decision-making for selecting key agronomic crops that can be efficiently adapted to climate changes and applied in bioenergy production.

Gene Expression Analysis of Non-Clinical Strain of Aspergillus fumigatus (LMB-35Aa): Does Biofilm Affect Virulence?

Aspergillus fumigatus LMB-35Aa, a saprophytic fungus, was used for cellulase production through biofilms cultures. Since biofilms usually favor virulence in clinical strains, the expression of the related genes of the LMB 35-Aa strain was analyzed by qPCR from the biomass of planktonic cultures and biofilms developed on polyester cloth and polystyrene microplates. For this, virulence-related genes reported for the clinical strain Af293 were searched in A. fumigatus LMB 35-Aa genome, and 15 genes were identified including those for the synthesis of cell wall components, hydrophobins, invasins, efflux transporters, mycotoxins and regulators. When compared with planktonic cultures at 37 °C, invasin gene calA was upregulated in both types of biofilm and efflux transporter genes mdr4 and atrF were predominantly upregulated in biofilms on polystyrene, while aspHs and ftmA were upregulated only in biofilms formed on polyester. Regarding the transcription regulators, laeA was downregulated in biofilms, and medA did not show a significant change. The effect of temperature was also evaluated by comparing the biofilms grown on polyester at 37 vs. 28 °C. Non-significant changes at the expression level were found for most genes evaluated, except for atrF, gliZ and medA, which were significantly downregulated at 37 °C. According to these results, virulence appears to depend on the interaction of several factors in addition to biofilms and growth temperature.

Mechanism of S. aureus ATCC 25923 in response to heat stress under different water activity and heating rates

Water activity (aw) and heating rates are two major factors altering heat resistance of food-borne pathogens. The specific mechanism of heat resistance triggered by these two factors is still unclear. In this study, S. aureus ATCC 25923 was inoculated in walnut shells with two aw values (0.965, HC samples; 0.586, LC samples), and heated to 60 °C with two heating rates of 5 °C/min (HT and LT samples, respectively) and 0.5 °C/min (LST samples) by a heating block system (HBS). The transcriptional response of S. aureus ATCC 25923 to aw and heating rate was characterized by using RNA-Seq. The results showed that the cell integrity of S. aureus ATCC 25923 was damaged under all heat treatment conditions. Genes involved in the pathway of ribosome were all up-regulated in HT samples while down-regulated in LST samples. Some genes (lysC, vraS, vraR, sgt and etc) involved in cell-wall synthesis were down-regulated more than 2-fold in HT samples. Genes involved in the pathways of energy metabolism were also down-regulated in LST samples. The cells in LT samples prevented external damage by stimulating the synthesis of cell wall components and inhibiting membrane function related metabolisms as compared to those in HT samples. The suppression of energy metabolism in LST samples indicated that cells under this condition needed to reduce metabolic activity to survive. These results provide valuable insights into survival strategies of S. aureus ATCC 25923 under different thermal treatment conditions and clarify the mechanism of heat resistance altered by aw and heating rate for S. aureus ATCC 25923.

Proteomic Analysis of Paracoccidioides brasiliensis During Infection of Alveolar Macrophages Primed or Not by Interferon-Gamma.

Although members of the Paracoccidioides complex are not obligate intracellular pathogens, they present the ability to survive and multiply inside epithelial cells and phagocytes of mammals, which may favor the spread of the fungus in host tissues. Macrophages resident in the lung are the first line of defense against paracoccidioidomycosis (PCM), presenting mechanisms to control the pathogen dissemination through the granuloma formation or eliminating the fungus through phagocytosis. Phagocytosis triggers an oxidative burst, in which there is an increase in the production of toxic elements, derived from oxygen and nitrogen. The interior of the phagolysosome is a harsh environment to the internalized pathogens, since in addition to the oxygen and nitrogen reactive species, microorganisms face nutrient shortages and proteases activity. Through the NanoUPLC-MSE technology, we analyzed the proteomic response of Paracoccidioides brasiliensis during the infection of alveolar macrophages primed or not by interferon gamma (IFN-γ). At 6 hs post-infection, only (IFN-γ)-primed macrophages were able to kill the fungus. We observed the regulation of amino acids degradation, tricarboxylic acid cycle, respiratory chain, ATP synthesis, glyoxylate cycle, as well as an increase in the expression of defense proteins related to oxidative stress, heat shock, and virulence factors under both conditions analyzed. However, some pathways described as essential for the survival of pathogens inside macrophages were observed only or with higher intensity in yeast cells recovered from non-primed macrophages, as phosphate pentoses pathway, methylcitrate cycle, synthesis of cell wall components, and mitochondrial activity. The data indicate that the intracellular environment of non-primed macrophages could be more permissive to the survival and multiplication of P. brasiliensis. The identification of key molecules for the establishment of infection can help the understanding of the nature of the parasite–host relationship and pathogenesis of PCM.

Echinocandin Resistance in Aspergillus fumigatus Has Broad Implications for Membrane Lipid Perturbations That Influence Drug-Target Interactions.

Echinocandin drugs target the fungal enzyme β-(1,3)-glucan synthase (GS), which is required for the synthesis of cell wall component β-(1,3)-d-glucan. They are first-line therapy for Candida infections but are increasingly used as second-line therapy for Aspergillus infections. Resistance to echinocandins has been mainly studied in Candida and occurs due to mutations in FKS genes encoding GS. In our recent report, we identified a novel mechanism of echinocandin resistance in Aspergillus fumigatus. We showed that caspofungin exposure modifies GS, rendering it insensitive to echinocandins. This mechanism of resistance involved alteration of the GS lipid microenvironment and was mediated via an off-target effect on mitochondria leading to increased reactive oxygen species (ROS). We hypothesized that caspofungin-induced ROS alters the lipid composition around GS, changing its conformation and making it insensitive to echinocandins. In this commentary, we review both fks1-dependent and fks1-independent mechanisms of echinocandin resistance in A fumigatus. We believe this new resistance mechanism is also conserved among Candida spp. with implications for drug tolerance and/or resistance. Furthermore, we propose that ROS acts as a signaling molecule regulating lipid biogenesis, which impacts the structure-function of membrane proteins with implications for other types of drug-target interactions.

RNA-Seq analysis of global transcriptomic changes suggests a roles for the MAPK pathway and carbon metabolism in cell wall maintenance in a Saccharomyces cerevisiae FKS1 mutant

FKS1 encodes a β-1,3-glucan synthase, which is a key player in cell wall assembly in Saccharomyces cerevisiae. Here we analyzed the global transcriptomic changes in the FKS1 mutant to establish a correlation between the changes in the cell wall of the FKS1 mutant and the molecular mechanism of cell wall maintenance. These transcriptomic profiles showed that there are 1151 differentially expressed genes (DEGs) in the FKS1 mutant. Through KEGG pathway analysis of the DEGs, the MAPK pathway and seven pathways involved in carbon metabolism were significantly enriched. We found that the MAPK pathway is activated for FKS1 mutant survival and the synthesis of cell wall components are reinforced in the FKS1 mutant. Our results confirm that the FKS1 mutant has a β-1,3-glucan defect that affects the cell wall and partly elucidate the molecular mechanism responsible for cell wall synthesis. Our greater understanding of these mechanisms helps to explain how the FKS1 mutant survives, has useful implications for the study of similar pathways in other fungi, and increases the theoretical foundation for the regulation of the cell wall in S. cerevisiae.

A Comparative Study of Host Response against Macrophomina phaseolina Infection in Sensitive and Resistant Jute (Corchorus sp) Species Unravels a Possible Defense Mechanism

Plants are inherently able to save themselves from any unfavorable conditions. However, they fail to exert ample response when encountered with pathogens like Macrophomina phaseolina which infects more than 500 crops. Wild plant species empowered by superlative mechanisms can conquest deadly pathogens, an example of which is C. trilocularis, a jute plant, resistant to this necrotrophic fungal pathogen. This study tried to ascertain the underlying resistance mechanism regarding the systemic acquired resistance (SAR) and cell wall fortification. Identification and characterization of genes involved in the systemic acquired resistant pathway implicated an activity of these genes with a basal expression in resistant species but irregular in the sensitive one (C. olitorius). Real-time expression analysis of genes involved in the synthesis of cell wall components like cellulose, hemicellulose, and lignin along with chemical and microscopic examinations signified preeminent lignification in C. trilocularis. However, this vital plant cell wall component was found to decrease in C. olitorius. The present investigation provided a deep insight into the defense strategy employed by the two species of jute at the molecular level. This study is expected to help in improving the fungal resistance of susceptible but farmer popular jute species. The same should be applicable to other vulnerable crops as well. Understanding how the pathogen is recognized, and an effective defensive response mounted, could ultimately lead to the development of novel strategies for providing durable plant resistance.

Cell Wall Associated Factors of Mycobacterium tuberculosis as Major Virulence Determinants: Current Perspectives in Drugs Discovery and Design.

Mycobacteria genus is responsible for deadly diseases like tuberculosis and leprosy. Cell wall of bacteria belonging to this genus is unique in many ways. It plays a major role in the pathogenesis and intracellular survival inside the host. In intracellular pathogens, their cell wall acts as molecular shield and interacts with host cell milieu to modulate host defense responses. In this review, we summarize the factors that participate in the biosynthesis of unique mycobacterial cell wall, understand their potential as drug targets and the recent developments where they have been evaluated as possible drug targets. Several cell wall associated factors that play crucial roles in the synthesis of cell wall components like Antigen 85 complex, Glycosyltransferases (GTs), LM (lipomannan) and LAM (lipoarabinomannan), mAGP Complex, lipolytic enzyme have been categorically documented. Most of the presently used anti TB regimens interrupted cell wall synthesis, but the emergence of drug resistant strains made it mandatory to identify new drug targets. Novel drug candidates which could inhibit the synthesis of cell wall components have been thoroughly studied worldwide. Studies demonstrated that the cell wall components are unique in terms of their contribution in mycobacterium pathogenesis. Targeting these can hamper the growth of M. tuberculosis. In this study, we scrutinize the drugs under trials and the potential candidates screened through in silico findings.

Microbial P450 Enzymes in Bioremediation and Drug Discovery: Emerging Potentials and Challenges.

Cytochrome P450 enzymes are a structurally conserved but functionally diverse group of heme-containing mixed function oxidases found across both prokaryotic and eukaryotic forms of the microbial world. Microbial P450s are known to perform diverse functions ranging from the synthesis of cell wall components to xenobiotic/drug metabolism to biodegradation of environmental chemicals. Conventionally, many microbial systems have been reported to mimic mammalian P450-like activation of drugs and were proposed as the in-vitro models of mammalian drug metabolism. Recent reports suggest that native or engineered forms of specific microbial P450s from these and other microbial systems could be employed for desired specific biotransformation reactions toward natural and synthetic (drug) compounds underscoring their emerging potential in drug improvement and discovery. On the other hand, microorganisms particularly fungi and actinomycetes have been shown to possess catabolic P450s with unusual potential to degrade toxic environmental chemicals including persistent organic pollutants (POPs). Wood-rotting basidiomycete fungi in particular have revealed the presence of exceptionally large P450 repertoire (P450ome) in their genomes, majority of which are however orphan (with no known function). Our pre- and post-genomic studies have led to functional characterization of several fungal P450s inducible in response to exposure to several environmental toxicants and demonstration of their potential in bioremediation of these chemicals. This review is an attempt to summarize the postgenomic unveiling of this versatile enzyme superfamily in microbial systems and investigation of their potential to synthesize new drugs and degrade persistent pollutants, among other biotechnological applications.

Osmotic stress adaptation of Paracoccidioides lutzii, Pb01, monitored by proteomics

The ability to respond to stressful conditions is essential for most living organisms. In pathogenic organisms, this response is required for effective transition from a saprophytic lifestyle to the establishment of pathogenic interactions within a susceptible host. Hyperosmotic stress has been used as a model to study signal transduction and seems to cause many cellular adaptations, including the alteration of protein expression and cellular volume as well as size regulation. In this work, we evaluated the proteomic profile of Paracoccidioides lutzii Pb01 yeast cells during osmotic stress induced by potassium chloride. We performed a high accuracy proteomic technique (NanoUPLC-MSE) to identify differentially expressed proteins during osmotic shock. The data describe an osmoadaptative response of this fungus when subjected to this treatment. Proteins involved in the synthesis of cell wall components were modulated, which suggested cell wall remodeling. In addition, alterations in the energy metabolism were observed. Furthermore, proteins involved in amino acid metabolism and hydrogen peroxide detoxification were modulated during osmotic stress. Our study suggests that P. lutzii Pb01. presents a vast osmoadaptative response that is composed of different proteins that act together to minimize the effects caused by osmotic stress.

Invertase activity in trunk tissues of Karelian birch

We investigated two forms of Betula pendula Roth: common silver birch (B. pendula var. pendula) and Karelian birch (B. pendula var. carelica) differing in wood texture. Activity of different forms of invertase in the tissues of birch trunk was determined for the first time. In the period of active operation of cambium, all three forms of invertase (vacuolar, cytoplasmic, and apoplastic) were present in the phloem and xylem of both forms of birch. Phloem and xylem of Karelian birch were notable for a high activity of apoplastic invertase. It was assumed that reprogramming of cell differentiation in cambial zone of Karelian birch causing a more pronounced parenchymatization of conducting tissues is related to an intense hydrolysis of sucrose in the apoplast. The obtained results corroborate the opinion formed in the literature about a possible participation of invertase in the synthesis of cell wall components.

Loss of FERULATE 5-HYDROXYLASE Leads to Mediator-Dependent Inhibition of Soluble Phenylpropanoid Biosynthesis in Arabidopsis.

Phenylpropanoids are phenylalanine-derived specialized metabolites and include important structural components of plant cell walls, such as lignin and hydroxycinnamic acids, as well as ultraviolet and visible light-absorbing pigments, such as hydroxycinnamate esters (HCEs) and anthocyanins. Previous work has revealed a remarkable degree of plasticity in HCE biosynthesis, such that most Arabidopsis (Arabidopsis thaliana) mutants with blockages in the pathway simply redirect carbon flux to atypical HCEs. In contrast, the ferulic acid hydroxylase1 (fah1) mutant accumulates greatly reduced levels of HCEs, suggesting that phenylpropanoid biosynthesis may be repressed in response to the loss of FERULATE 5-HYDROXYLASE (F5H) activity. Here, we show that in fah1 mutant plants, the activity of HCE biosynthetic enzymes is not limiting for HCE accumulation, nor is phenylpropanoid flux diverted to the synthesis of cell wall components or flavonol glycosides. We further show that anthocyanin accumulation is also repressed in fah1 mutants and that this repression is specific to tissues in which F5H is normally expressed. Finally, we show that repression of both HCE and anthocyanin biosynthesis in fah1 mutants is dependent on the MED5a/5b subunits of the transcriptional coregulatory complex Mediator, which are similarly required for the repression of lignin biosynthesis and the stunted growth of the phenylpropanoid pathway mutant reduced epidermal fluorescence8. Taken together, these observations show that the synthesis of HCEs and anthocyanins is actively repressed in a MEDIATOR-dependent manner in Arabidopsis fah1 mutants and support an emerging model in which MED5a/5b act as central players in the homeostatic repression of phenylpropanoid metabolism.

Populus × canescens grown on Cr-rich tannery waste: Comparison of leaf and root biochemical and proteomic responses

Treatment of tannery effluents generates large amounts of sediments containing concentrated doses of metals (mainly chromium). Such waste is most commonly disposed of by landfilling, which is hazardous to the ecosystem due to Cr leaching. Afforestation of disposal sites with fast growing trees could stabilize contaminants in the soil and prevent them from spreading. The aim of this study was to examine the adaptation of Populus × canescens Sm. to tannery waste using biochemical and proteomic methods. We analyzed changes in the leaves and fine roots of poplar planted in soil or tannery waste. We found no obvious symptoms of metal stress, such as: elevated hydrogen peroxide levels or lipid peroxidation, but we observed activation of many elements of antioxidative system. Comparison of 2-DE protein profiles of leaves and fine roots from poplar grown on soil or tannery waste revealed increased expression of glycolytic enzymes and proteins involved in the synthesis of cell wall components, changes in the levels of proteins associated with photosynthesis, stress-related proteins, proteasome subunits and methionine biosynthesis enzymes. This experiment demonstrated that proteomic analysis has the potential to link the effects of Cr-rich tannery waste with biological consequences.

Fluorescent tags to explore cell wall structure and dynamics

Plant cell walls are highly dynamic and heterogeneous structures, which vary between cell types, growth stages but also between microdomains within a single cell wall. In this review, we summarize the imaging techniques using fluorescent tags that are currently being used and which should in the coming years revolutionize our understanding of the dynamics of cell wall architecture and the cellular processes involved in the synthesis of cell wall components.

Differential Producibility Analysis (DPA) of Transcriptomic Data with Metabolic Networks: Deconstructing the Metabolic Response of M. tuberculosis

A general paucity of knowledge about the metabolic state of Mycobacterium tuberculosis within the host environment is a major factor impeding development of novel drugs against tuberculosis. Current experimental methods do not allow direct determination of the global metabolic state of a bacterial pathogen in vivo, but the transcriptional activity of all encoded genes has been investigated in numerous microarray studies. We describe a novel algorithm, Differential Producibility Analysis (DPA) that uses a metabolic network to extract metabolic signals from transcriptome data. The method utilizes Flux Balance Analysis (FBA) to identify the set of genes that affect the ability to produce each metabolite in the network. Subsequently, Rank Product Analysis is used to identify those metabolites predicted to be most affected by a transcriptional signal. We first apply DPA to investigate the metabolic response of E. coli to both anaerobic growth and inactivation of the FNR global regulator. DPA successfully extracts metabolic signals that correspond to experimental data and provides novel metabolic insights. We next apply DPA to investigate the metabolic response of M. tuberculosis to the macrophage environment, human sputum and a range of in vitro environmental perturbations. The analysis revealed a previously unrecognized feature of the response of M. tuberculosis to the macrophage environment: a down-regulation of genes influencing metabolites in central metabolism and concomitant up-regulation of genes that influence synthesis of cell wall components and virulence factors. DPA suggests that a significant feature of the response of the tubercle bacillus to the intracellular environment is a channeling of resources towards remodeling of its cell envelope, possibly in preparation for attack by host defenses. DPA may be used to unravel the mechanisms of virulence and persistence of M. tuberculosis and other pathogens and may have general application for extracting metabolic signals from other “-omics” data.