Physiological functions of Atg6/Beclin 1： a unique autophagy-related protein

The most striking morphological feature of eukaryotic cells is the presence of various membrane-enclosed compartments. These compartments, including organelles and transient transport intermediates, are not static. Rather, dynamic exchange of proteins and membrane is needed to maintain cellular homeostasis. One of the most dramatic examples of membrane mobilization is seen during the process ofmacroautophagy. Macroautophagy is the primary cellular pathway for degradation of long-lived proteins and organelles. In response to environmental cues, such as starvation or other types of stress, the cell produces a unique membrane structure, the phagophore. The phagophore sequesters cytoplasm as it forms a double-membrane cytosolic vesicle, an autophagosome. Upon completion, the autophagosome fuses with a lysosome or a vacuole in yeast, which delivers hydrolases that break down the inner autophagosome membrane along with its cargo, and the resulting macromolecules are released back into the cytosol for reuse. Autophagy is therefore a recycling process, allowing cells to survive periods of nutrient limitation; however, it has a wider physiological role, participating in development and aging, and also in protection against pathogen invasion, cancer and certain neurodegenerative diseases. In many cases, the role ofautophagy is identified through studies of an autophagy-related protein, Atg6/Beclin 1. This protein is part of a lipid kinase complex, and recent studies suggest that it plays a central role in coordinating the cytoprotective function ofautophagy and in opposing the cellular death process of apoptosis. Here, we summarize our current knowledge ofAtg6/Beclin 1 in different model organisms and its unique function in the cell.

A multiscale study of the penetrationenhancing mechanism of menthol

Objective:Transdermal drug delivery systems represent a critical focus in the pharmaceutics field;however,their use is limited by the fact that many drugs usually pass through the skin with low permeability.Menthol is a common penetration enhancer because of its high penetration-enhancing efficiency and safety.Our research aimed to reveal the penetrationenhancing mechanisms of menthol via a multiscale study.Methods:First,the interaction of menthol with the stratum corneum was studied using vertical Franz diffusion cells obtained from the abdominal skin of rats as a model.Then,the skin samples were observed via transmission electron microscopy.Finally,the interaction of different concentrations of menthol with a mixed lipid model of the stratum corneum was investigated via molecular dynamics simulation using the GROMOS 54A7 force field on a microcosmic level.Results:At concentrations of 3.5%or lower,menthol changed the original structure of the stratum corneum to varying degrees,which increased its fluidity and facilitated the permeation and storage of menthol.Menthol increased the fluidity of the stratum corneum mainly via two mechanisms.First,menthol had strong hydrogen-bonding capability,and it could compete for the lipidelipid hydrogen bonding sites,thereby weakening the stability of the hydrogenbonding network connecting the skin lipids.In addition,menthol had strong affinity for cholesterol,probably due to their similar molecular structures,suggesting that the incorporation of menthol would increase the fluidity of the lipid membrane similarly to cholesterol.Conclusion:The penetration-enhancing mechanism of menthol was explained using in vitro and molecular dynamics simulation methods.These findings may advance the basic research of transdermal drug delivery systems and facilitate the discoveries of novel penetration enhancers.

斑马鱼类胰岛素生长因子信号途径及作用机制研究进展

斑马鱼是研究早期发育中类胰岛素生长因子(insulin-like growth factors,IGF)信号途径的模式生物,斑马鱼IGF信号系统主要包括IGF配体、受体、结合蛋白(IGFBPs)。IGF配体包括IGF-1,IGF-2。受体为IGF-1R,该受体有两种全长结构(igf-1ra和igf-1rb)。结合蛋白包括IGFBP-1,IGFBP-2,IGFBP-3,IGFBP-5和IGFBP-6,它们的结构特征已经阐明,从斑马鱼模式动物中获得的信息不仅可以为斑马鱼胚胎发育生物学提供新的观点,还可以进一步加深我们对一般意义上的脊椎动物的生长和发育的理解。本文就近年来斑马鱼IGF系统的进展作一综述。

A truth serum for cancer -- microRNAs have major potential as cancer biomarkers

Identification of biological markers of cancer is a major area of research. Biomarkers could identify the presence of a tumor before it could otherwise be easily detected, and the ability to detect cancers at early stages is a key factor in increasing survivability. For example, the American Cancer Society finds that a reason breast cancer survival rates are so high is that there are good methods for early detection of tumors. However, this is not the case for most cancers. For lung cancer, the five-year survival is 15%, but for the 16% of lung cancer cases diagnosed at early stages,

The YDA-MKK4/MKK5-MPK3/MPK6 Cascade Functions Downstream of the RGF1-RGI Ligand-Receptor Pair in Regulating Mitotic Activity in Root Apical Meristem

The mitotic activity of root apical meristem(RAM)is critical to primary root growth and development.Previous studies have identified the roles of ROOT GROWTH FACTOR 1(RGF1),a peptide ligand,and its receptors,RGF1 INSENSITIVEs(RGIs),a clade of five leucine-rich-repeat receptor-like kinases,in promoting cell division in the RAM,which determines the primary root length.However,the downstream signaling components remain elusive.In this study,we identify a complete mitogen-activated protein kinase(MAPK or MPK)cascade,composed of YDA,MKK4/MKK5,and MPK3/MPK6,that functions downstream of the RGF1-RGI ligand-receptor pair.Similar to the rgi1/2/3/4/5 quintuple mutant,loss-of-function mutants of MPK3 and MPK6,MKK4 and MKK5,or YDA show a short-root phenotype,which is associated with reduced mitotic activity and lower expression of PLETHORA 1(PLT1)/PLT2 in the RAM.Furthermore,MPK3/MPK6 activation in response to exogenous RGF1 treatment is impaired in the rgi1/2/3/4/5 quintuple,yda single,and mkk4 m kk5 double mutants.Epistatic analyses demonstrated that the expression of constitutively active MKK4,MKK5,or YDA driven by the RGI2 promoter can rescue the short-root phenotype of the rgi1/2/3/4/5 mutant.Taken together,these results suggest that the YDA-MKK4/MKK5-MPK3/MPK6 cascade functions downstream of the RGF1-RGI ligand-receptor pair and upstream of PLT1/PLT2 to modulate the stem cell population and primary root growth in Arabidopsis.

Plasma Membrane Localization and Potential Endocytosis of Constitutively Expressed XA21 Proteins in Transgenic Rice

The rice pattern recognition receptor （PRR） XA21 confers race-specific resistance in leaf infection by bacterial blight Xathornonas oryzae pv. oryzae （Xoo）, and was shown to be primarily localized to the endoplasmic reticulum （ER） when expressed with its native promoter or overexpressed in the protoplast. However, whether the protein is still ER- localization in the intact cell when overexpressed remains to be identified. Here, we showed that XA21, its kinase-dead mutant XA21PK736EP and the triple autophosphorylation mutant XA21PS686AJT688AJS699A GFP fusions were primarily localized to the plasma membrane （PM） when overexpressed in the intact transgenic rice cell, and also localized to the ER in the transgenic protoplast. The transgenic plants constitutively expressing the wild-type XA21 or its GFP fusion displayed racespecific resistance to Xoo at the adult and seedling stages. XA21 and XA21PK736EP could be internalized probably via the SCAMP-positive early endosomal compartment in the protoplast, suggesting that XA21 might be endocytosed to initiate resistance responses during pathogen infection. We also established a root infection system and demonstrated that XA21 also mediated race-specific resistance responses to Xoo in the root. Our current study provides an insight into the nature of the XA21-mediated resistance and a practical approach using the root cell system to further dissect the cellular signaling of the PRR during the rice-Xoo interaction.

Genomic Features and Regulatory Roles of Intermediate-Sized Non-Coding RNAs in Arabidopsis

ABSTRACT Recent advances in genome-wide techniques allowed the identification of thousands of non-coding RNAs with various sizes in eukaryotes, some of which have further been shown to serve important functions in many biologi- cal processes. However, in model plant Arabidopsis, novel intermediate-sized ncRNAs （im-ncRNAs） （50-300 nt） have very limited information. By using a modified isolation strategy combined with deep-sequencing technology, we identified 838 im-ncRNAs in Arabidopsis globally. More than half （58%） are new ncRNA species, mostly evolutionary divergent. Interestingly, annotated protein-coding genes with 5＇-UTR-derived novel im-ncRNAs tend to be highly expressed. For intergenic im-ncRNAs, their average abundances were comparable to mRNAs in seedlings, but subsets exhibited signifi- cantly lower expression in senescing leaves. Further, intergenic im-ncRNAs were regulated by similar genetic and epige- netic mechanisms to those of protein-coding genes, and some showed developmentally regulated expression patterns. Large-scale reverse genetic screening showed that the down-regulation of a number of im-ncRNAs resulted in either obvious molecular changes or abnormal developmental phenotypes in vivo, indicating the functional importance of im-ncRNAs in plant growth and development. Together, our results demonstrate that novel Arabidopsis im-ncRNAs are developmentally regulated and functional components discovered in the transcriptome.

Adaptive immunity at the crossroads of autophagy and metabolism

The function of lymphocytes is dependent on their plasticity,particularly their adaptation to energy availability and environmental stress,and their protein synthesis machinery.Lymphocytes are constantly under metabolic stress,and macroautophagy/autophagy is the primary metabolic pathway that helps cells overcome stressors.The intrinsic role of autophagy in regulating the metabolism of adaptive immune cells has recently gained increasing attention.In this review,we summarize and discuss the versatile roles of autophagy in regulating cellular metabolism and the implications of autophagy for immune cell function and fate,especially for T and B lymphocytes.

CSN1 inhibits c-Jun phosphorylation and down-regulates ectopic expression of JNK1

CSN1 is a component of the COP9 signalosome(CSN),a conserved protein complex with pleiotropic functions in many organs and cell types.CSN regulates ubiquitinproteasome dependent protein degradation via the deneddylation and the associated deubiquitination activities.In addition,CSN associates with protein kinases and modulates cell signaling,particularly the activator protein 1(AP-1)pathway.We have shown previously that CSN1 suppresses AP-1 transcription activity and inhibits ultraviolet(UV)and serum activation of c-fos expression.Here we show that CSN1 can inhibit phosphorylation of proto-oncogene c-Jun product and repress c-Jun dependent transcription.Further,CSN1 dramatically downregulates ectopic expression of c-Jun N-terminal kinase 1(JNK1)in cultured cells.The decline in JNK1 is not caused by excessive proteolysis or by 3′UTR-dependent mRNA instability,but by CSN1-dependent repression of one or multiple steps in transcriptional and posttranscriptional mechanisms.Thus,in contrast to CSN5/Jab1,which promotes AP-1 activity,CSN1 displays a negative effect on the AP-1 pathway.Finally,we discuss about the dynamic equilibrium of the CSN complexes in regulation of the AP-1 pathway.

Mitochondrial abnormalities drive cell death in Wolfram syndrome 2

Wolfram syndrome （WFS; MIM 222300） is an autosomal recessive disorder with highly variable clinical manifestations. It is characterized by diabetes insipidus, diabetes mellitus, optic atrophy, and deafness （thus, known as DIDMOAD syndrome） [ 1 ]. Other neurological and endocrine manifestations include dementia, psychiatric illnesses, renal-tract abnormalities, and bladder atony [2]. Gene linkage and positional cloning analysis reveal that a subset of Wolfram syndrome patients belonging to the WFS 1 group （MIM 606201） carry a loss-of-function mutation in the WFS1 gene, which encodes a transmembrane protein, Wolframin, localizing in the endoplasmic reticulm （ER） [3, 4]. Wolframin is thought to be involved in the regulation of ER stress and calcium ho- meostasis, and Wolframin deficiency in mice leads to progressive loss of β cells and impaired glucose tolerance, which is presumably caused by increased ER stress and apoptosis in the β cells.

A Genome-Wide Transcription Analysis Reveals a Close Correlation of Promoter INDEL Polymorphism and Heterotic Gene Expression in Rice Hybrids

Heterosis, or hybrid vigor, refers to the phenomenon in which hybrid progeny of two inbred varieties exhibits enhanced growth or agronomic performance. Although a century-long history of research has generated several hypotheses regarding the genetic basis of heterosis, the molecular mechanisms underlying heterosis and heterotic gene expression remain elusive. Here, we report a genome-wide gene expression analysis of two heterotic crosses in rice, taking advantage of its fully sequenced genomes. Approximately 7-9% of the genes were differentially expressed in the seedling shoots from two sets of heterotic crosses, including many transcription factor genes, and exhibited multiple modes of gene action. Comparison of the putative promoter regions of the ortholog genes between inbred parents revealed extensive sequence variation, particularly small insertions/deletions （INDELs）, many of which result in the formation/disruption of putative cis-regulatory elements. Together, these results suggest that a combinatorial interplay between expression of transcription factors and polymorphic promoter cis-regulatory elements in the hybrids is one plausible molecular mechanism underlying heterotic gene action and thus heterosis in rice.

The Development of Protein Microarrays and Their Applications in DNA-Protein and Protein-Protein Interaction Analyses of Arabidopsis Transcription Factors

We used our collection of Arabidopsis transcription factor （TF） ORFeome clones to construct protein microarrays containing as many as 802 TF proteins. These protein microarrays were used for both protein-DNA and proteinprotein interaction analyses. For protein-DNA interaction studies, we examined AP2/ERF family TFs and their cognate cis-elements. By careful comparison of the DNA-binding specificity of 13 TFs on the protein microarray with previous non-microarray data, we showed that protein microarrays provide an efficient and high throughput tool for genome-wide analysis of TF-DNA interactions. This microarray protein-DNA interaction analysis allowed us to derive a comprehensive view of DNA-binding profiles of AP2/ERF family proteins in Arabidopsis. It also revealed four TFs that bound the EE （evening element） and had the expected phased gene expression under clock-regulation, thus providing a basis for further functional analysis of their roles in clock regulation of gene expression. We also developed procedures for detecting protein interactions using this TF protein microarray and discovered four novel partners that interact with HY5, which can be validated by yeast two-hybrid assays. Thus, plant TF protein microarrays offer an attractive high-throughput alternative to traditional techniques for TF functional characterization on a global scale.

Expression Analysis of miRNAs and Highly-expressed Small RNAs in Two Rice Subspecies and their Reciprocal Hybrids

Heterosis,or hybrid vigor,is the phenomenon whereby progeny of two inbred lines exhibit superior agronomic performance compared with either parent.We analyzed the expression of miRNAs and highly expressed small RNAs （defined according to Solexa sequencing results） in two rice （Oryza sativa） subspecies （japonica cv.Nipponbare and indica cv.93-11） and their reciprocal hybrids using microarrays.We found that of all the 1141 small RNAs tested,140 （12%,140 of 1141） and 157 （13%,157 of 1141） were identified being significantly differentially expressed in two reciprocal hybrids,respectively.All possible modes of action,including additive,high-and low-parent,above high-and below low-parent modes were exhibited.Both F1 hybrids showed non-additive expression patterns,with downregulation predominating.Interestingly,15 miRNAs displayed stark opposite expression trends relative to midparent in reciprocal hybrids.Computational prediction of targets of differentially expressed miRNAs showed that they participated in multifaceted developmental pathways,and were not distinguishable from the targets of non-differentially expressed miRNAs.Together,our findings reveal that small RNAs play roles in heterosis and add a new layer in the understanding and exploitation of molecular mechanisms of heterosis.

Expanding roles for pectins in plant development

Pectins are complex cell wall polysaccharides important for many aspects of plant development. Recent studies have discovered extensive physical interactions between pectins and other cell wall components,implicating pectins in new molecular functions. Pectins are often localized in spatially-restricted patterns, and some of these non-uniform pectin distributions contribute to multiple aspects of plant development, including the morphogenesis of cells and organs. Furthermore, a growing number of mutants affecting cell wall composi- tion have begun to reveal the distinct contributions of different pectins to plant development. This review discusses the interactions of pectins with other cell wall components, the functions of pectins in controlling cellular morphology, and how non-uniform pectin composition can be an important determinant of developmental processes.

ETV2 expression increases the efficiency of primitive endothelial cell derivation from human embryonic stem cells

Background:Endothelial cells line the luminal surface of blood vessels and form a barrier between the blood and other tissues of the body.Ets variant 2(ETV2)is transiently expressed in both zebrafish and mice and is necessary and sufficient for vascular endothelial cell specification.Overexpression of this gene in early zebrafish and mouse embryos results in ectopic appearance of endothelial cells.Ectopic expression of ETV2 in later development results in only a subset of cells responding to the signal.Findings:We have examined the expression pattern of ETV2 in differentiating human embryonic stem cells(ESCs)to determine when the peak of ETV2 expression occurs.We show that overexpression of ETV2 in differentiating human ESC is able to increase the number of endothelial cells generated when administered during or after the endogenous peak of gene expression.Conclusions:Addition of exogenous ETV2 to human ESCs significantly increased the number of cells expressing angioblast genes without arterial or venous specification.This may be a viable solution to generate in vitro endothelial cells for use in research and in the clinic.

Same Concept Different Outcomes:Sugars Determine Circadian Clock Protein Fate in Animals and Plants

Most eukaryotes have a self-sustaining circadian clock that senses environmental cues and the internal metabolic state and then imposes daily temporal organization of the physiology.The clock,by nature,regulates the daily creation and destruction of a large quantity of RNA and proteins,including those at the core of the oscillator itself.Although a transcriptional-translational feedback loop maintains the rhythmicity of the oscillator,various post-translational modifications(PTMs)of clock proteins play fundamental roles in keeping the pace of the circadian clock near 24 h.To maintain circadian clock pacing,PTMs act to ensure the rapid,efficient,and precise activation,inactivation,and finally destruction of core clock proteins(Hirano et al.,2016).

Chemical genetics and drug screening in Drosophila cancer models

Drug candidates often fail in preclinical and clinical testing because of reasons of efficacy and/or safety. It would be time- and cost-efficient to have screening models that reduce the rate of such false positive candidates that appear promising at first but fail later. In this regard, it would be particularly useful to have a rapid and inexpensive whole animal model that can pre-select hits from high-throughput screens but before testing in costly rodent assays. Drosophila melanogaster has emerged as a potential whole animal model for drug screening. Of particular interest have been drugs that must act in the context of multi-cellularity such as those for neurological disorders and cancer. A recent review provides a comprehensive summary of drug screening in Drosophila, but with an emphasis on neurodegenerative disorders. Here, we review Drosophila screens in the literature aimed at cancer therapeutics.

Transcriptional regulators that differentially control dendrite and axon development

Neurons are the basic units of connectivity in the nervous system. As a signature feature, neurons form polarized structures： dendrites and axons, which integrate either sensory stimuli or inputs from upstream neurons and send outputs to target cells, respectively. The separation of dendritic and axonal compartments is achieved in two steps during development： 1） dendrite and axon specification： how neurites are initially specified as dendrites and axons; and 2） dendrite and axon commitment： how dendrites and axons are committed to distinct compartmental fates and architectures. To understand neural circuit assembly and to correct erroneous dendrite or axon growth in a compartment-specific manner, it is essential to understand the regulatory mechanisms underlying dendrite and axon commitment. Compared to extensive studies on dendrite and axon specification, little is known about the molecular mechanisms exclusively dedicated to dendrite or axon commitment. Recent studies have uncovered the requirement of transcriptional regulation in this process. Here, we review the studies on transcriptional regulators： Darl, p300-SnoN, NeuroD, which have been shown to separate dendrite- and axon-specific growth of the same neuron type after compartmental fates are specified.

缺氧诱导因子-1和缺氧诱导因子-2:结构、功能及调节

缺氧诱导因子-1(HIF-1)和缺氧诱导因子-2(HIF-2)是细胞应对缺氧时关键的转录因子,在生物体生理及病理过程中有重要的作用。HIF由一个α亚基和一个β亚基组成二聚体。在蛋白水平上,HIF的稳定性及转录活性受到多种机制的调控,除为人所熟知的O2/PHDs/pVHL降解途径及FIH-1羟基化作用外,分别针对HIF-1α和HIF-2α的特异性调控机制也相继被报道。从HIF-1α和HIF-2α的蛋白结构、稳定性调控、转录激活功能以及两者在细胞代谢、肿瘤发生中的作用等方面对两者的相似性和差异性进行综述。

Cold-Induced CBF–PIF3 Interaction Enhances Freezing Tolerance by Stabilizing the phyB Thermosensor in Arabidopsis

Growth inhibition and cold-acclimation strategies help plants withstand cold stress,which adversely affects growth and survival.PHYTOCHROME B(phyB)regulates plant growth through perceiving both light and ambient temperature signals.However,the mechanism by which phyB mediates the plant response to cold stress remains elusive.Here,we show that the key transcription factors mediating cold acclimation,C-REPEAT BINDING FACTORs(CBFs),interact with PHYTOCHROME-INTERACTING FACTOR 3(PIF3)under cold stress,thus attenuating the mutually assured destruction of PIF3–phyB.Cold-stabilized phyB acts downstream of CBFs to positively regulate freezing tolerance by modulating the expression of stress-responsive and growth-related genes.Consistent with this,phyB mutants exhibited a freezing-sensitive phenotype,whereas phyB-overexpression transgenic plants displayed enhanced freezing tolerance.Further analysis showed that the PIF1,PIF4,and PIF5 proteins,all of which negatively regulate plant freezing tolerance,were destabilized by cold stress in a phytochrome-dependent manner.Collectively,our study reveals that CBFs–PIF3–phyB serves as an important regulatory module for modulating plant response to cold stress.