Systems biology of lactic acid bacteria: a critical review

Understanding the properties of a system as emerging from the interaction of well described parts is the most important goal of Systems Biology. Although in the practice of Lactic Acid Bacteria (LAB) physiology we most often think of the parts as the proteins and metabolites, a wider interpretation of what a part is can be useful. For example, different strains or species can be the parts of a community, or we could study only the chemical reactions as the parts of metabolism (and forgetting about the enzymes that catalyze them), as is done in flux balance analysis. As long as we have some understanding of the properties of these parts, we can investigate whether their interaction leads to novel or unanticipated behaviour of the system that they constitute

A systematic assessment of current genome-scale metabolic reconstruction tools

Background: Several genome-scale metabolic reconstruction software platforms have been developed and are being continuously updated. These tools have been widely applied to reconstruct metabolic models for hundreds of microorganisms ranging from important human pathogens to species of industrial relevance. However, these platforms, as yet, have not been systematically evaluated with respect to software quality, best potential uses and intrinsic capacity to generate high-quality, genome-scale metabolic models. It is therefore unclear for potential users which tool best fits the purpose of their research. Results: In this work, we perform a systematic assessment of current genome-scale reconstruction software platforms. To meet our goal, we first define a list of features for assessing software quality related to genome-scale reconstruction. Subsequently, we use the feature list to evaluate the performance of each tool. To assess the similarity of the draft reconstructions to high-quality models, we compare each tool’s output networks with that of the high-quality, manually curated, models of Lactobacillus plantarum and Bordetella pertussis, representatives of gram-positive and gram-negative bacteria, respectively. We additionally compare draft reconstructions with a model of Pseudomonas putida to further confirm our findings. We show that none of the tools outperforms the others in all the defined features. Conclusions: Model builders should carefully choose a tool (or combinations of tools) depending on the intended use of the metabolic model. They can use this benchmark study as a guide to select the best tool for their research. Finally, developers can also benefit from this evaluation by getting feedback to improve their software

Functional identification in Lactobacillus reuteri of a PocR-like transcription factor regulating glycerol utilization and vitamin B12 synthesis

<p>Abstract</p> <p>Background</p> <p><it>Lactobacillus reuteri </it>harbors the genes responsible for glycerol utilization and vitamin B₁₂synthesis within a genetic island phylogenetically related to gamma-Proteobacteria. Within this island, resides a gene (<it>lreu_1750</it>) that based on its genomic context has been suggested to encode the regulatory protein PocR and presumably control the expression of the neighboring loci. However, this functional assignment is not fully supported by sequence homology, and hitherto, completely lacks experimental confirmation.</p> <p>Results</p> <p>In this contribution, we have overexpressed and inactivated the gene encoding the putative PocR in <it>L. reuteri</it>. The comparison of these strains provided metabolic and transcriptional evidence that this regulatory protein controls the expression of the operons encoding glycerol utilization and vitamin B₁₂synthesis.</p> <p>Conclusions</p> <p>We provide clear experimental evidence for assigning Lreu_1750 as PocR in <it>Lactobacillus reuteri</it>. Our genome-wide transcriptional analysis further identifies the loci contained in the PocR regulon. The findings reported here could be used to improve the production-yield of vitamin B₁₂, 1,3-propanediol and reuterin, all industrially relevant compounds.</p

Microtubule nucleation complex behavior is critical for cortical array homogeneity and xylem wall patterning

Plant cell walls are versatile materials that can adopt a wide range of mechanical properties through controlled deposition of cellulose fibrils. Wall integrity requires a sufficiently homogeneous fibril distribution to cope effectively with wall stresses. Additionally, specific conditions, such as the negative pressure in water transporting xylem vessels, may require more complex wall patterns, e.g., bands in protoxylem. The orientation and patterning of cellulose fibrils are guided by dynamic cortical microtubules. New microtubules are predominantly nucleated from parent microtubules causing positive feedback on local microtubule density with the potential to yield highly inhomogeneous patterns. Inhomogeneity indeed appears in all current cortical array simulations that include microtubule-based nucleation, suggesting that plant cells must possess an as-yet unknown balancing mechanism to prevent it. Here, in a combined simulation and experimental approach, we show that a limited local recruitment of nucleation complexes to microtubules can counter the positive feedback, whereas local tubulin depletion cannot. We observe that nucleation complexes preferentially appear at the plasma membrane near microtubules. By incorporating our experimental findings in stochastic simulations, we find that the spatial behavior of nucleation complexes delicately balances the positive feedback, such that differences in local microtubule dynamics—as in developing protoxylem—can quickly turn a homogeneous array into a banded one. Our results provide insight into how the plant cytoskeleton has evolved to meet diverse mechanical requirements and greatly increase the predictive power of computational cell biology studies

Shifts in growth strategies reflect tradeoffs in cellular economics

The growth rate-dependent regulation of cell size, ribosomal content, and metabolic efficiency follows a common pattern in unicellular organisms: with increasing growth rates, cell size and ribosomal content increase and a shift to energetically inefficient metabolism takes place. The latter two phenomena are also observed in fast growing tumour cells and cell lines. These patterns suggest a fundamental principle of design. In biology such designs can often be understood as the result of the optimization of fitness. Here we show that in basic models of self-replicating systems these patterns are the consequence of maximizing the growth rate. Whereas most models of cellular growth consider a part of physiology, for instance only metabolism, the approach presented here integrates several subsystems to a complete self-replicating system. Such models can yield fundamentally different optimal strategies. In particular, it is shown how the shift in metabolic efficiency originates from a tradeoff between investments in enzyme synthesis and metabolic yields for alternative catabolic pathways. The models elucidate how the optimization of growth by natural selection shapes growth strategies

Group level and individual activity of broiler chickens hatched in 3 different systems

Information on the behavior of chickens hatched in different systems is limited and inconsistent across different studies. Changes in broiler activity can be measured automatically and continuously. The aim of this study was to assess the effects of 3 hatching systems on flock activity using a commercial tracking system, and to compare these findings to individual activity measured under experimental conditions. As this experiment was part of a larger study, it was possible to investigate the effects of vaccination on individual activity. In study 1, flock activity was measured in chickens that hatched either conventionally in the hatchery (HH), in a system which provided nutrition in the hatcher (HF), or on-farm (OH). Chickens were reared in 2 batches, in 12 pens/batch (1,155 animals/pen). One camera recorded top-view images of each pen. A daily activity index (moved pixels/total pixels × 100) was calculated by automated image analysis. In study 2, individual activity was measured under experimental conditions using an ultra-wideband (UWB) system. Chickens from the 3 hatching systems were reared in 3 pens (1 pen/treatment, 30 animals/pen). At d14, UWB-tags were attached to 5 chickens/pen, which tracked the distances moved (DM). In study 1, group level activity showed a significant age × hatching system interaction (F 8,752= 5.83, P < 0.001). HH and HF chickens showed higher activity levels than OH chickens in wk 1, 4, and 5. In wk 3, higher activity levels were measured in HH compared to HF, and in HF compared to OH pens. In contrast, HH chickens in small groups in study 2 showed lower DM than HF and OH chickens in wk 3 (P < 0.001). DM did not differ between treatments before vaccination, however, thereafter, HH chickens showed longer DM, whereas HF and OH chickens moved less. The results indicate that hatching system affected broiler activity at specific ages. Effects found at flock level could not be reproduced by individual measurements in study 2, although stocking density was comparable

Effects of hatching system on chick quality, welfare and health of young breeder flock offspring

Alternative hatching systems have been developed for broiler chickens to provide immediately feed and water after hatch and reduce the number or severity of early life stressors. Besides beneficial effects of these alternative hatching systems on chick quality and performance, broiler health and welfare may be positively affected as well. Especially offspring from young broiler breeder flocks may benefit, as they have been shown to be more sensitive to preturbations than offspring from older breeder flocks. This study evaluated effects of hatching systems on chick quality, health and welfare of young breeder flock offspring, using 3 different hatching systems: conventional hatchery-hatched (HH), hatchery-fed (HF), and on-farm hatching (OH). A total of 24 pens were used in a completely randomized block design, with 8 pens per hatching system and 30 chickens per pen. Chick quality at hatch and performance until 35 d of age was improved in the HF and OH compared to HH treatment, but only minor effects were found on the welfare indicators: footpad dermatitis, hock burn, cleanliness, skin lesion and gait score. No effect was observed on the dynamics of a humoral immune response after NCD vaccination, given at d 0 and 14 of age, as no differences between NCD titers were found at d 18. Animals were vaccinated with a live attenuated infectious bronchitis vaccine virus (IBV) at d 28 to address treatment related differences to disease resilience. The expressions of inflammation and epithelial integrity related genes in the trachea and histo-pathological changes in the trachea were examined at 3 d after vaccine administration. No differences between treatment groups were observed. Although beneficial effects of HF and OH systems were found for young breeder flock offspring on chick quality at hatch and body weight posthatch, only one effect of alternative hatching systems on welfare and health indicators were found. No effect of hatching system on humoral immune response or disease resilience was found

Lipidomic profiling of rat hepatic stellate cells during activation reveals a two-stage process accompanied by increased levels of lysosomal lipids

Hepatic stellate cells (HSCs) are liver-resident cells best known for their role in vitamin A storage under physiological conditions. Upon liver injury, HSCs activate into myofibroblast-like cells, a key process in the onset of liver fibrosis. Lipids play an important role during HSC activation. Here, we provide a comprehensive characterization of the lipidomes of primary rat HSCs during 17 days of activation in vitro. For lipidomic data interpretation, we expanded our previously described Lipid Ontology (LION) and associated web application (LION/Web) with the LION-PCA heatmap module, which generates heatmaps of the most typical LION-signatures in lipidomic datasets. Furthermore, we used LION to perform pathway analysis to determine the significant metabolic conversions in lipid pathways. Together, we identify two distinct stages of HSC activation. In the first stage, we observe a decrease of saturated phosphatidylcholine, sphingomyelin, and phosphatidic acid and an increase in phosphatidylserine and polyunsaturated bis(monoacylglycero)phosphate (BMP), a lipid class typically localized at endosomes and lysosomes. In the second activation stage, BMPs, hexosylceramides, and ether-linked phosphatidylcholines are elevated, resembling a lysosomal lipid storage disease profile. The presence of isomeric structures of BMP in HSCs was confirmed ex vivo in MS-imaging datasets of steatosed liver sections. Finally, treatment with pharmaceuticals targeting the lysosomal integrity led to cell death in primary HSCs but not in HeLa cells. In summary, our combined data suggest that lysosomes play a critical role during a two-stage activation process of HSCs