A generalized computational framework to streamline thermodynamics and kinetics analysis of metabolic pathways

Metabolic engineering is a critical biotechnological approach in addressing global energy and environment challenges. Most engineering efforts, however, consist of laborious and inefficient trial-and-error of target pathways, due in part to the lack of methodologies that can comprehensively assess pathway properties in thermodynamics and kinetics. Metabolic engineering can benefit from computational tools that evaluate feasibility, expense and stability of non-natural metabolic pathways. Such tools can also help us understand natural pathways and their regulation at systems level. Here we introduce a computational toolbox, PathParser, which, for the first time, integrates multiple important functions for pathway analysis including thermodynamics analysis, kinetics-based protein cost optimization and robustness analysis. Specifically, PathParser enables optimization of the driving force of a pathway by minimizing the Gibbs free energy of least thermodynamically favorable reaction. In addition, based on reaction thermodynamics and enzyme kinetics, it can compute the minimal enzyme protein cost that supports metabolic flux, and evaluate pathway stability and flux in response to enzyme concentration perturbations. In a demo analysis of the Calvin–Benson–Bassham cycle and photorespiration pathway in the model cyanobacterium Synechocystis PCC 6803, the computation results are corroborated by experimental proteomics data as well as metabolic engineering outcomes. This toolbox may have broad application in metabolic engineering and systems biology in other microbial systems.     

Controlling bacterial physiology for optimal expression of gene reporter constructs

Bacterial biosensors for the detection of pollutants are based on the regulatory elements that control the corresponding degradation pathways. An increasing number of catabolic pathways under the control of specific regulators are now known to be influenced by the presence of alternative carbon sources, which to different extents repress expression of the pathway despite the presence of the inducer. The molecular basis underlying the control of each catabolic pathway is different, although all sense a high energy state of the cell resulting from the presence of more favourable carbon sources. Biosensor tests mimicking field conditions point to global regulation being relevant for biosensor performance; thus, this global regulation must be taken into account when designing whole-cell biosensors.     

合成生物学在微生物细胞工厂构建中的应用

通过微生物发酵的方法生产大宗化学品和天然产物能够部分替代石油化工炼制和植物提取。合成生物学技术的发展极大地提高了构建微生物细胞工厂生产大宗化学品和天然产物的能力。一方面综述了合成生物学在构建细胞工厂时的关键技术,包括最优合成途径的设计、合成途径的创建与优化、细胞性能的优化;另一方面,介绍了应用这些技术构建细胞工厂生产燃料化学品、大宗化学品和天然产物的典型案例。     

The role of apoptosis in the pathogenesis of malignant melanoma

Malignant melanoma genesis is a very complex process that involves a sequence of pathogenetic cellular events. Mutation of various genes and numerous other cellular mechanisms play an important role in the course of malignant melanocyte alteration and their malignant transformation from naevi into melanoma. Apoptosis is an active, genetically controlled process of programmed cell death, which leads to cell destruction and cell death without involvement of surrounding cells or inflammatory response. In this process, disrupted mechanisms of cell regulation and apoptosis take place in malignant melanoma cells, thus leading to their uncontrolled proliferation and melanocyte growth. Apoptosis is a process that involves two major pathways, the intrinsic and extrinsic apoptotic pathway, which interlace at certain points and ultimately result in apoptosis. It can be said that molecular events regulating cell survival, normal growth arrest, apoptosis and cell differentiation, contribute to the overall pathogenesis of malignant cell growth. It is presumed that in the future, understanding of molecular aberrations and cellular processes, such as cell signaling, cell cycle regulation and cell apoptosis, will be essential for better patient monitoring and rational design of effective treatment.     

Fluorescence-based sensors to monitor localization and functions of linear and k63-linked ubiquitin chains in cells

Ubiquitin chains modify a major subset of the proteome, but detection of ubiquitin signaling dynamics and localization is limited due to a lack of appropriate tools. Here, we employ ubiquitin-binding domain (UBD)-based fluorescent sensors to monitor linear and K63-linked chains in?vitro and in?vivo. We utilize the UBD in NEMO and ABIN (UBAN) for detection of linear chains, and RAP80 ubiquitin-interacting motif (UIM) and TAB2 Npl4 zinc finger (NZF) domains to detect K63 chains. Linear and K63 sensors decorated the ubiquitin coat surrounding cytosolic Salmonella during bacterial autophagy, whereas K63 sensors selectively monitored Parkin-induced mitophagy and DNA damage responses in fixed and living cells. In addition, linear and K63 sensors could be used to monitor endogenous signaling pathways, as demonstrated by their ability to differentially interfere with TNF- and IL-1-induced NF-κB pathway. We propose that UBD-based biosensors could serve as prototypes to track and trace other chain types and ubiquitin-like signals in?vivo.     

Transcript profiling of terpenoid indole alkaloid pathway genes and regulators reveals strong expression of repressors in <Emphasis Type="Italic">Catharanthus roseus</Emphasis> cell cultures

The understanding of the complexities and molecular events regulating genes and the activators involved in terpenoid indole alkaloid (TIA) metabolism is known to a certain extent in cell cultures of an important TIA yielding plant, Catharanthus roseus, though it is not yet complete. Recently, the repressors of early TIA pathway genes have also been identified. However, their roles in the regulation of TIA pathway in C. roseus cell cultures remains yet unknown. We have made a comparative profiling of genes catalyzing the important steps of 2-C methyl-D-erythritol-4-phosphate (MEP), shikimate and TIA biosynthetic pathways, their activator and repressors using macroarray, semiquantitative RT-PCR and northern analyses in a rotation culture system of C. roseus comprising differentiated and proliferated cells. Our results demonstrate that TIA biosynthetic pathway genes and their activators show variable expression pattern, which was correlated with the changes in the cellular conditions in these systems. Under similar conditions, TIA pathway repressors show strong and consistent expression. The role of repressors in the complex regulation of the TIA pathway in C. roseus cell cultures is discussed. The results were supported by HPLC data, which demonstrated that the molecular program of cellular differentiation is intimately linked with TIA pathway gene expression and TIA production in C. roseus cell cultures.     

3D-biohybrid systems: applications in drug screening

Biotechnology demands powerful methods for the functional characterisation and monitoring of molecular alterations in tissues in response to various stimuli. Currently, cellular biosensors provide information about cell and tissue internal transduction pathways. In this article, recent biosensor systems are briefly described and the use of 3D tissue aggregates as recognition elements is discussed. An example of an innovative approach for drug testing using 3D heart muscle aggregates, as well as tumor models, positioned in capillary systems for electrical potential recording and impedance measurement is described. The effectiveness of drugs and therapies can be tested and monitored in a short time using such biohybrid sensors.     

Conserved mechanisms regulate outgrowth in zebrafish fins

Regulation of size is one of the fundamental problems in biology. One general strategy has been to identify molecules required for cell growth and cell proliferation within an organ. This has been particularly revealing, identifying cell-autonomous pathways involved in cell growth, survival and proliferation. In order to identify pathways regulating overall limb growth and morphology, experiments have evaluated gene expression, transplanted and removed tissues, and knocked out genes. This work has provided a vast amount of information identifying molecular mechanisms regulating limb axis formation, outgrowth, and pattern formation. Using the zebrafish fin, genetic, cellular and molecular strategies have also been employed to follow both normal patterns of fin growth and growth in fin mutants. This review will focus on cellular and molecular regulation of the outgrowth and patterning of the zebrafish caudal fin during regeneration, and will emphasize similarities to other systems. Future perspectives describe opportunities using the zebrafish fin to reveal mechanisms underlying the regulation of final size.     

Combinatorial metabolic pathway assembly approaches and toolkits for modular assembly

Synthetic Biology is a rapidly growing interdisciplinary field that is primarily built upon foundational advances in molecular biology combined with engineering design principles such as modularity and interoperability. The field considers living systems as programmable at the genetic level and has been defined by the development of new platform technologies and methodological advances. A key concept driving the field is the Design-Build-Test-Learn cycle which provides a systematic framework for building new biological systems. One major application area for synthetic biology is biosynthetic pathway engineering that requires the modular assembly of different genetic regulatory elements and biosynthetic enzymes. In this review we provide an overview of modular DNA assembly and describe and compare the plethora of in vitro and in vivo assembly methods for combinatorial pathway engineering. Considerations for part design and methods for enzyme balancing are also presented, and we briefly discuss alternatives to intracellular pathway assembly including microbial consortia and cell-free systems for biosynthesis. Finally, we describe computational tools and automation for pathway design and assembly and argue that a deeper understanding of the many different variables of genetic design, pathway regulation and cellular metabolism will allow more predictive pathway design and engineering.     

A Hippo in the ointment: MST signalling beyond the fly

The regulation of cell cycle and apoptosis is fundamental to the control of cell growth and organism homeostasis. Failure to efficiently regulate these processes often results in the increased cell growth observed in tumours. Accumulation of genetic lesions frequently eliminates these regulatory steps so it is imperative that multiple signalling pathways are employed to ensure that efficient control is maintained. Over the last few years a novel signalling pathway entered the limelight that prevents inappropriate activation of the cell cycle and can elicit apoptosis to limit cell numbers. Denoted the MST/hippo pathway, it is involved in regulating cell number in organism development and tumour progression. Here we aim to review the evidence for a conserved pathway from flies to mammals, and of equal importance to initiate the discussion on the additional cellular and signalling processes that have been adopted by this pathway to achieve further regulation and diversified cellular outcomes in mammals.     

Parallel tracking of cAMP and PKA signaling dynamics in living cells with FRET-based fluorescent biosensors

Proper regulation of cellular functions relies upon a network of intricately interwoven signaling cascades in which multiple components must be tightly coordinated both spatially and temporally. To better understand how this network operates within the cellular environment, it is important to define the parameters of various signaling activities and to reveal the characteristic activity structure of the signaling cascades. This task calls for molecular tools capable of parallelly tracking multiple activities in cellular time and space with high sensitivity and specificity. Here, we present new biosensors developed based on two conveniently co-imageable FRET pairs consisting of CFP-RFP and YFP-RFP, specifically Cerulean-mCherry and mVenus-mCherry, for parallel monitoring of PKA activity and cAMP dynamics in living cells. These biosensors provide orthogonal readouts in co-imaging experiments and display a comparable dynamic range to their cyan-yellow counterparts. Characterization of signaling responses induced by a panel of pathway activators using this co-imaging approach reveals distinct activity and kinetic patterns of cAMP and PKA dynamics arising from differential signal activation and processing. This technique is therefore useful for parallel monitoring of multiple signaling dynamics in single living cells and represents a promising approach towards a more precise characterization of the activity structure of the dynamic cellular signaling network.     

Protein kinase sensors: an overview of new designs for visualizing kinase dynamics in single plant cells

Protein kinase dynamics play key roles in regulation of cell differentiation, growth, development and in diverse cell signaling networks. Protein kinase sensors enable visualization of protein kinase activity in living cells and tissues in time and space. These sensors have therefore become important and powerful molecular tools for investigation of diverse kinase activities and can resolve long-standing and challenging biological questions. In the present Update, we review new advanced approaches for genetically encoded protein kinase biosensor designs developed in animal systems together with the basis of each biosensor’s working principle and components. In addition, we review recent first examples of real time plant protein kinase activity biosensor development and application. We discuss how these sensors have helped to resolve how stomatal signal transduction in response to elevated CO₂ merges with abscisic acid signaling downstream of a resolved basal SnRK2 kinase activity in guard cells. Furthermore, recent advances, combined with the new strategies described in this Update, can help deepen the understanding of how signaling networks regulate unique functions and responses in distinct plant cell types and tissues and how different stimuli and signaling pathways can interact.

New genetically encoded biosensor design approaches and visualization of protein kinase activity in living plant cells and tissues in time and space are reviewed.     

p53 Regulation of the IGF-1/AKT/mTOR Pathways and the Endosomal Compartment

In response to various stress signals, which introduce infidelity into the processes of cell growth and division, p53 initiates cell-cycle arrest, apoptosis, or senescence to maintain fidelity throughout the cell cycle. Although these functions are traditionally thought of as the major functions of the p53 protein for tumor suppression, recent studies have revealed some additional novel functions of the p53 pathway. These include the down-regulation of two central cell-growth pathways, the IGF/AKT-1 and mTOR pathways, and the up-regulation of the activities of the endosomal compartment. The IGF-1/AKT and mTOR pathways are two evolutionarily conserved pathways that play critical roles in regulation of cell proliferation, survival, and energy metabolism. In response to stress, p53 transcribes a group of critical negative regulators in these two pathways, including IGF-BP3, PTEN, TSC2, AMPK β1, and Sestrin1/2, which leads to the reduction in the activities of these two pathways. Furthermore, p53 transcribes several critical genes regulating the endosomal compartment, including TSAP6, Chmp4C, Caveolin-1, and DRAM, and increases exosome secretion, the rate of endosomal removal of growth factor receptors (e.g., EGFR) from cell surface, and enhances autophagy. These activities all function to slow down cell growth and division, conserve and recycle cellular resources, communicate with adjacent cells and dendritic cells of the immune system, and inform other tissues of the stress signals. This coordinated regulation of IGF-1/AKT/mTOR pathways and the endosomal compartment by the p53 pathway integrates the molecular, cellular, and systemic levels of activities and prevents the accumulations of errors in response to stress and restores cellular homeostasis after stress.     

Expanding Metabolic Capabilities Using Novel Pathway Designs: Computational Tools and Case Studies

Design and selection of efficient metabolic pathways is critical for the success of metabolic engineering endeavors. Convenient pathways should not only produce the target metabolite in high yields but also are required to be thermodynamically feasible under production conditions, and to prefer efficient enzymes. To support the design and selection of such pathways, different computational approaches have been proposed for exploring the feasible pathway space under many of the above constraints. In this review, an overview of recent constraint‐based optimization frameworks for metabolic pathway prediction, as well as relevant pathway engineering case studies that highlight the importance of rational metabolic designs is presented. Despite the availability and suitability of in silico design tools for metabolic pathway engineering, scarce—although increasing—application of computational outcomes is found. Finally, challenges and limitations hindering the broad adoption and successful application of these tools in metabolic engineering projects are discussed.     

Study of spatiotemporal regulation of kinase signaling using genetically encodable molecular tools

Precise spatiotemporal organization and regulation of signal transduction networks are essential for cellular response to internal and external cues. To understand how this biochemical activity architecture impacts cellular function, many genetically encodable tools which regulate kinase activity at a subcellular level have been developed. In this review, we highlight various types of genetically encodable molecular tools, including tools to regulate endogenous kinase activity and biorthogonal techniques to perturb kinase activity. Finally, we emphasize the use of these tools alongside biosensors for kinase activity to measure and perturb kinase activity in real time for a better understanding of the cellular biochemical activity architecture.     

Rho protein crosstalk: another social network?

Many fundamental processes in cell biology are regulated by Rho GTPases, including cell adhesion, migration and differentiation. While regulating cellular functions, members of the Rho protein family cooperate or antagonize each other. The resulting molecular network exhibits many levels of interaction dynamically regulated in time and space. In the first part of this review we describe the main mechanisms of this crosstalk, which can occur at three different levels of the pathway: (i) through regulation of activity, (ii) through regulation of protein expression and stability, and (iii) through regulation of downstream signaling pathways. In the second part we illustrate the importance of Rho protein crosstalk with two examples: integrin-based adhesion and cell migration.