Recent advances in systems metabolic engineering tools and strategies

Chae, Tong Un,Choi, So Young,Kim, Je Woong,Ko, Yoo-Sung,Lee, Sang Yup Current Biology 2017 Current opinion in biotechnology Vol.47 No.-

<P>Metabolic engineering has been playing increasingly important roles in developing microbial cell factories for the production of various chemicals and materials to achieve sustainable chemical industry. Nowadays, many tools and strategies are available for performing systems metabolic engineering that allows systems-level metabolic engineering in more sophisticated and diverse ways by adopting rapidly advancing methodologies and tools of systems biology, synthetic biology and evolutionary engineering. As an outcome, development of more efficient microbial cell factories has become possible. Here, we review recent advances in systems metabolic engineering tools and strategies together with accompanying application examples. In addition, we describe how these tools and strategies work together in simultaneous and synergistic ways to develop novel microbial cell factories.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Microbial cell factories are becoming important in sustainable chemical production. </LI> <LI> Systems metabolic engineering allows efficient microbial cell factory development. </LI> <LI> Tools and strategies of systems metabolic engineering work synergistically. </LI> <LI> Systems metabolic engineering for production of chemicals are showcased. </LI> <LI> Strains for poly(lactate-<I>co</I>-glycolate) and opioids production are showcased. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>

Journal of Cell Science

Current Biology Ltd ; Elsevier Science Ltd 1996 Current biology Vol.6 No.10

Combining Suppression of Stemness with Lineage-Specific Induction Leads to Conversion of Pluripotent Cells into Functional Neurons

Halder, D.,Chang, G.E.,De, D.,Cheong, E.,Kim, K.,Shin, I. Current Biology Ltd ; Elsevier Science Ltd 2015 Chemistry & biology Vol.22 No.11

Sox2 is a key player in the maintenance of pluripotency and stemness, and thus inhibition of its function would abrogate the stemness of pluripotent cells and induce differentiation into several types of cells. Herein we describe a strategy that relies on a combination of Sox2 inhibition with lineage-specific induction to promote efficient and selective differentiation of pluripotent P19 cells into neurons. When P19 cells transduced with Skp protein, an inhibitor of Sox2, are incubated with a neurogenesis inducer, the cells are selectively converted into neurons that generate depolarization-induced sodium currents and action potentials. This finding indicates that the differentiated neurons are electrophysiologically active. Signaling pathway studies lead us to conclude that a combination of Skp with the neurogenesis inducer enhances neurogenesis in P19 cells by activating Wnt and Notch pathways. The present differentiation protocol could be valuable to selectively generate functionally active neurons from pluripotent cells.

Emergence of plant vascular system: roles of hormonal and non-hormonal regulatory networks

Cho, H.,Dang, T.V.T.,Hwang, I. Current Biology, Ltd ; Elsevier Science Ltd 2017 Current opinion in plant biology Vol.35 No.-

<P>The divergence of land plants followed by vascular plants has entirely changed the terrestrial ecology. The vascular system is a prerequisite for this evolutionary event, providing upright stature and communication for sink demand-source capacity and facilitating the development of plants and colonization over a wide range of environmental habitats. Various hormonal and non-hormonal regulatory networks have been identified and reviewed as key processes for vascular formation; however, how these factors have evolutionarily emerged and interconnected to trigger the emergence of the vascular system still remains elusive. Here, to understand the intricacy of cross talks among these factors, we highlight how core hormonal signaling and transcriptional networks are coalesced into the appearance of vascular plants during evolution.</P>

Monocular Perceptual Deprivation from Interocular Suppression Temporarily Imbalances Ocular Dominance

Kim, H.W.,Kim, C.Y.,Blake, R. Current Biology Ltd ; Elsevier Science Ltd 2017 Current Biology Vol.27 No.6

<P>Early visual experience sculpts neural mechanisms that regulate the balance of influence exerted by the two eyes on cortical mechanisms underlying binocular vision [1, 2], and experience's impact on this neural balancing act continues into adulthood [3-5]. One recently described, compelling example of adult neural plasticity is the effect of patching one eye for a relatively short period of time: contrary to intuition, monocular visual deprivation actually improves the deprived eye's competitive advantage during a subsequent period of binocular rivalry [6-8], the robust form of visual competition prompted by dissimilar stimulation of the two eyes [9, 10]. Neural concomitants of this improvement in monocular dominance are reflected in measurements of brain responsiveness following eye patching [11, 12]. Here we report that patching an eye is unnecessary for producing this paradoxical deprivation effect: interocular suppression of an ordinarily visible stimulus being viewed by one eye is sufficient to produce shifts in subsequent predominance of that eye to an extent comparable to that produced by patching the eye. Moreover, this imbalance in eye dominance can also be induced by prior, extended viewing of two monocular images differing only in contrast. Regardless of how shifts in eye dominance are induced, the effect decays once the two eyes view stimuli equal in strength. These novel findings implicate the operation of interocular neural gain control that dynamically adjusts the relative balance of activity between the two eyes [13, 14].</P>

Kinesin-12 Kif15 Targets Kinetochore Fibers through an Intrinsic Two-Step Mechanism

Sturgill, Emma G.,Das, D.,Takizawa, Y.,Shin, Y.,Collier, Scott E.,Ohi, Melanie D.,Hwang, W.,Lang, Matthew J.,Ohi, R. Current Biology Ltd ; Elsevier Science Ltd 2014 Current biology Vol.24 No.19

Proteins that recognize and act on specific subsets of microtubules (MTs) enable the varied functions of the MT cytoskeleton. We recently discovered that Kif15 localizes exclusively to kinetochore fibers (K-fibers) [1, 2] or bundles of kinetochore-MTs within the mitotic spindle. It is currently speculated that the MT-associated protein TPX2 loads Kif15 onto spindle MTs [3-5], but this model has not been rigorously tested. Here, we show that Kif15 accumulates on MT bundles as a consequence of two inherent biochemical properties. First, Kif15 is self-repressed by its C terminus. Second, Kif15 harbors a nonmotor MT-binding site, enabling dimeric Kif15 to crosslink and slide MTs. Two-MT binding activates Kif15, resulting in its accumulation on and motility within MT bundles but not on individual MTs. We propose that Kif15 targets K-fibers via an intrinsic two-step mechanism involving molecular unfolding and two-MT binding. This work challenges the current model of Kif15 regulation and provides the first account of a kinesin that specifically recognizes a higher-order MT array.

Adaptation through horizontal gene transfer in the cryptoendolithic red alga Galdieria phlegrea

Qiu, H.,Price, D.C.,Weber, A.P.M.,Reeb, V.,Chan Yang, E.,Lee, J.M.,Kim, S.Y.,Yoon, H.S.,Bhattacharya, D. Current Biology Ltd ; Elsevier Science Ltd 2013 Current biology Vol.23 No.19

Thriving in the hot, acidic, and metal-rich environments associated with geothermal areas is possible for only a few eukaryotes, with the Cyanidiophytina red algae (Cyanidium, Galdieria, and Cyanidioschyzon) being a famous example. These unicellular taxa can live in pH 0-4 and temperatures reaching up to 56<SUP>o</SUP>C [1,2]. Because Cyanidiophytina is sister to a vast array of mesophilic red algae (the Rhodophytina), such as the unicellular Porphyridium and the seaweed Chondrus[3], the genetic basis of their adaptation to extreme environments is of great interest from both the perspective of biotechnology and of evolution. The recently completed 13.7 Mbp genome sequence from the hot-spring dwelling Galdieria sulphuraria demonstrated that horizontal gene transfer (HGT) from prokaryotic sources provided this taxon with remarkable metabolic versatility (e.g., glycerol metabolism) and the ability to survive in its hostile environment (e.g., genes to detoxify mercury and arsenic) [4]. To explore the role of HGT in other members of this genus, we generated an 11.4 Mbp draft genome assembly from the sister taxon G. phlegrea DBV 009 [5]. In contrast to G. sulphuraria, this species is adapted to dry habitats near fumaroles such as fissures between rocks or cryptoendolithic environments [5,6]. Here, we provide evidence for extensive gene loss in the common ancestor of Cyanidiophytina that includes the eukaryote-derived loci required for urea utilization. Surprisingly, we find that G. phlegrea has regained the complete set of genes required for urea hydrolysis through HGT from eubacteria. The unlinked nature of these genes is likely explained by multiple gene transfers that resulted in assembly of the pathway in G. phlegrea. Our study demonstrates that genome reduction, a common outcome in eukaryotes for adaptation to a specialized niche, can be ameliorated by the gain of once lost, or novel functions through HGT.

Early Pheromone Experience Modifies a Synaptic Activity to Influence Adult Pheromone Responses of <i>C. elegans</i>

Hong, Myeongjin,Ryu, Leesun,Ow, Maria C.,Kim, Jinmahn,Je, A Reum,Chinta, Satya,Huh, Yang Hoon,Lee, Kea Joo,Butcher, Rebecca A.,Choi, Hongsoo,Sengupta, Piali,Hall, Sarah E.,Kim, Kyuhyung Current Biology Ltd 2017 Current Biology Vol.27 No.20

<P><B>Summary</B></P> <P>Experiences during early development can influence neuronal functions and modulate adult behaviors []. However, the molecular mechanisms underlying the long-term behavioral effects of these early experiences are not fully understood. The <I>C. elegans</I> ascr#3 (asc-ΔC9; C9) pheromone triggers avoidance behavior in adult hermaphrodites []. Here, we show that hermaphrodites that are briefly exposed to ascr#3 immediately after birth exhibit increased ascr#3-specific avoidance as adults, indicating that ascr#3-experienced animals form a long-lasting memory or imprint of this early ascr#3 exposure []. ascr#3 imprinting is mediated by increased synaptic activity between the ascr#3-sensing ADL neurons and their post-synaptic SMB motor neuron partners via increased expression of the <I>odr-2</I> glycosylated phosphatidylinositol (GPI)-linked signaling gene in the SMB neurons. Our study suggests that the memory for early ascr#3 experience is imprinted via alteration of activity of a single synaptic connection, which in turn shapes experience-dependent plasticity in adult ascr#3 responses.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Early pheromone exposure modulates behavioral responses to the pheromone as adults </LI> <LI> Pheromone experience is imprinted as increased synaptic activity </LI> <LI> The <I>odr-2</I> GPI-linked signaling protein mediates pheromone imprinting </LI> </UL> </P>

TOR Signaling Promotes Accumulation of BZR1 to Balance Growth with Carbon Availability in Arabidopsis

Zhang, Z.,Zhu, J.Y.,Roh, J.,Marchive, C.,Kim, S.K.,Meyer, C.,Sun, Y.,Wang, W.,Wang, Z.Y. Current Biology Ltd ; Elsevier Science Ltd 2016 Current biology Vol.26 No.14

<P>For maintenance of cellular homeostasis, the actions of growth-promoting hormones must be attenuated when nutrient and energy become limiting. The molecular mechanisms that coordinate hormone-dependent growth responses with nutrient availability remain poorly understood in plants [1, 2]. The target of rapamycin (TOR) kinase is an evolutionarily conserved master regulator that integrates nutrient and energy signaling to regulate growth and homeostasis in both animals and plants [3-7]. Here, we show that sugar signaling through TOR controls the accumulation of the brassinosteroid (BR)-signaling transcription factor BZR1, which is essential for growth promotion by multiple hormonal and environmental signals [8-11]. Starvation, caused by shifting of light-grown Arabidopsis seedlings into darkness, as well as inhibition of TOR by inducible RNAi, led to plant growth arrest and reduced expression of BR-responsive genes. The growth arrest caused by TOR inactivation was partially recovered by BR treatment and the gain-of-function mutation bzr1-1D, which causes accumulation of active forms of BZR1 [12]. Exogenous sugar promoted BZR1 accumulation and seedling growth, but such sugar effects were largely abolished by inactivation of TOR, whereas the effect of TOR inactivation on BZR1 degradation is abolished by inhibition of autophagy and by the bzr1-1D mutation. These results indicate that cellular starvation leads sequentially to TOR inactivation, autophagy, and BZR1 degradation. Such regulation of BZR1 accumulation by glucose-TOR signaling allows carbon availability to control the growth promotion hormonal programs, ensuring supply-demand balance in plant growth.</P>

Inhibition of Respiration Extends C. elegans Life Span via Reactive Oxygen Species that Increase HIF-1 Activity

Lee, S.J.,Hwang, A.B.,Kenyon, C. Current Biology Ltd ; Elsevier Science Ltd 2010 Current biology Vol.20 No.23

A mild inhibition of mitochondrial respiration extends the life span of many organisms, including yeast, worms, flies, and mice [1-10], but the underlying mechanism is unknown. One environmental condition that reduces rates of respiration is hypoxia (low oxygen). Thus, it is possible that mechanisms that sense oxygen play a role in the longevity response to reduced respiration. The hypoxia-inducible factor HIF-1 is a highly conserved transcription factor that activates genes that promote survival during hypoxia [11, 12]. In this study, we show that inhibition of respiration in C. elegans can promote longevity by activating HIF-1. Through genome-wide screening, we found that RNA interference (RNAi) knockdown of many genes encoding respiratory-chain components induced hif-1-dependent transcription. Moreover, HIF-1 was required for the extended life spans of clk-1 and isp-1 mutants, which have reduced rates of respiration [1, 4, 13]. Inhibiting respiration appears to activate HIF-1 by elevating the level of reactive oxygen species (ROS). We found that ROS are increased in respiration mutants and that mild increases in ROS can stimulate HIF-1 to activate gene expression and promote longevity. In this way, HIF-1 appears to link respiratory stress in the mitochondria to a nuclear transcriptional response that promotes longevity.