The unique N‐terminal zinc finger of synaptotagmin‐like protein 4 reveals FYVE structure

Synaptotagmin‐like protein 4 (Slp4), expressed in human platelets, is associated with dense granule release. Slp4 is comprised of the N‐terminal zinc finger, Slp homology domain, and C2 domains. We synthesized a compact construct (the Slp4N peptide) corresponding to the Slp4 N‐terminal zinc finger. Herein, we have determined the solution structure of the Slp4N peptide by nuclear magnetic resonance (NMR). Furthermore, experimental, chemical modification of Cys residues revealed that the Slp4N peptide binds two zinc atoms to mediate proper folding. NMR data showed that eight Cys residues coordinate zinc atoms in a cross‐brace fashion. The Simple Modular Architecture Research Tool database predicted the structure of Slp4N as a RING finger. However, the actual structure of the Slp4N peptide adopts a unique C₄C₄‐type FYVE fold and is distinct from a RING fold. To create an artificial RING finger (ARF) with specific ubiquitin‐conjugating enzyme (E2)‐binding capability, cross‐brace structures with eight zinc‐ligating residues are needed as the scaffold. The cross‐brace structure of the Slp4N peptide could be utilized as the scaffold for the design of ARFs.     

Increased Arf/p53 activity in stem cells,aging and cancer

Arf/p53 pathway protects the cells against DNA damage induced by acute stress. This characteristic is the responsible for its tumor suppressor activity. Moreover, it regulates the chronic type of stress associated with aging. This is the basis of its anti‐aging activity. Indeed, increased gene dosage of Arf/p53 displays elongated longevity and delayed aging. At a cellular level, it has been recently shown that increased dosage of Arf/p53 delays age‐associated stem cell exhaustion and the subsequent decline in tissue homeostasis and regeneration. However, p53 can also promote aging if constitutively activated. In this context, p53 reduces tissue regeneration, which correlates with premature exhaustion of stem cells. We discuss here the current evidence linking the Arf/p53 pathway to the processes of aging and cancer through stem cell regulation.     

Suppression of Rotylenchulus reniformis on Cotton by the Nematophagous Fungus ARF

The reniform nematode, Rotylenchulus reniformis Linford &Oliveira, has become a serious threat to cotton (Gossypium hirsutum L.) production in the United States during the past decade. The objective of this study is to isolate fungi from eggs of R. reniformis and select potential biological control agents for R. reniformis on cotton. Soil samples were collected from cotton fields located in Jefferson County, Arkansas. Eight genera of fungi were included in the 128 fungal isolates obtained, and among them were five strains of the nematophagous fungus ARF. The mtDNA RFLP pattern, colony growth characteristics, and pathogenicity indicate the five ARF isolates represent one described strain and one new strain. Light and electron microscopic observations suggest ARF is an active parasite of R. reniformis, with parasitism ranging from 48% to 79% in in vitro tests. Three greenhouse experiments demonstrated ARF successfully suppressed the number of reniform nematodes during the first and second generation of the nematode. Reductions in numbers of R. reniformis on the roots for the seven application rates of 0.01%, 0.05%, 0.1%, 0.2%, 0.3%, 0.4%, and 0.5% ARF were 87%, 92%, 94%, 96%, 97%, 98%, and and 98%, respectively.     

The role of ADP-ribosylation factor and SAR1 in vesicular trafficking in plants

Ras-like small GTP binding proteins regulate a wide variety of intracellular signalling and vesicular trafficking pathways in eukaryotic cells including plant cells. They share a common structure that operates as a molecular switch by cycling between active GTP-bound and inactive GDP-bound conformational states. The active GTP-bound state is regulated by guanine nucleotide exchange factors (GEF), which promote the exchange of GDP for GTP. The inactive GDP-bound state is promoted by GTPase-activating proteins (GAPs) which accelerate GTP hydrolysis by orders of magnitude. Two types of small GTP-binding proteins, ADP-ribosylation factor (Arf) and secretion-associated and Ras-related (Sar), are major regulators of vesicle biogenesis in intracellular traffic and are founding members of a growing family that also includes Arf-related proteins (Arp) and Arf-like (Arl) proteins. The most widely involved small GTPase in vesicular trafficking is probably Arf1, which not only controls assembly of COPI- and AP1, AP3, and AP4/clathrin-coated vesicles but also recruits other proteins to membranes, including some that may be components of further coats. Recent molecular, structural and biochemical studies have provided a wealth of detail of the interactions between Arf and the proteins that regulate its activity as well as providing clues for the types of effector molecules which are controlled by Arf. Sar1 functions as a molecular switch to control the assembly of protein coats (COPII) that direct vesicle budding from ER. The crystallographic analysis of Sar1 reveals a number of structurally unique features that dictate its function in COPII vesicle formation. In this review, I will summarize the current knowledge of Arf and Sar regulation in vesicular trafficking in mammalian and yeast cells and will highlight recent advances in identifying the elements involved in vesicle formation in plant cells. Additionally, I will briefly discuss the similarities and dissimilarities of vesicle traffic in plant, mammalian and yeast cells.     

Research progresses on <Emphasis Type="Italic">GH3s</Emphasis>, one family of primary auxin-responsive genes

Auxin plays a very important role in plant growth and development. Those genes that are specifically induced by auxin within minutes of exposure to the hormone are referred to as early/primary auxin-responsive genes, mainly including the auxin/indole-3-acetic acid (Aux/IAA), the small auxin-up RNA (SAUR), and the GH3 gene families. So far, GH3 genes have been identified in various plant species including soybean, Arabidopsis, rice, tobacco, pungent pepper, sweet orange, pine, and moss. Twenty members of GH3 family were identified in Arabidopsis and these genes were classified into three groups (Group I–III) based on their sequence similarities and substrate specificities. GH3s belong to acyl adenylate-forming firefly luciferase superfamily and can catalyze adenylation of specific substrates. Group I adenylates jasmonic acid (JA), and Group II adenylates indole-3-acetic acid (IAA) and salicylic acid (SA), respectively. Because of the presence of Auxin-Responsive Elements (AuxRE) in the GH3s’ promoter regions, Auxin Response Factors (ARFs) are able to bind to the AuxRE and regulate expression of some GH3s, which in turn modulate the auxin homeostasis. Identification of GH3 mutants in Arabidopsis reveals the function of GH3s in hypocotyl elongation under different light conditions, root growth, stress adaptation, sensitivity to MeJA, or susceptibility to P. syringae. Taken together, GH3s may be linkers among auxin, JA, SA and light signal transduction pathways.     

Elimination of p19ARF‐expressing cells protects against pulmonary emphysema in mice

Senescent cells accumulate in tissues during aging and are considered to underlie several aging‐associated phenotypes and diseases. We recently reported that the elimination of p19^ARF‐expressing senescent cells from lung tissue restored tissue function and gene expression in middle‐aged (12‐month‐old) mice. The aging of lung tissue increases the risk of pulmonary diseases such as emphysema, and cellular senescence is accelerated in emphysema patients. However, there is currently no direct evidence to show that cellular senescence promotes the pathology of emphysema, and the involvement of senescence in the development of this disease has yet to be clarified. We herein demonstrated that p19^ARF facilitated the development of pulmonary emphysema in mice. The elimination of p19^ARF‐expressing cells prevented lung tissue from elastase‐induced lung dysfunction. These effects appeared to depend on reduced pulmonary inflammation, which is enhanced after elastase stimulation. Furthermore, the administration of a senolytic drug that selectively kills senescent cells attenuated emphysema‐associated pathologies. These results strongly suggest the potential of senescent cells as therapeutic/preventive targets for pulmonary emphysema.     

Syntenin and syndecan in the biogenesis of exosomes

Cells communicate with their environment in various ways, including by secreting vesicles. Secreted vesicles are loaded with proteins, lipids and RNAs that compose ‘a signature’ of the cell of origin and potentially can reprogram recipient cells. Secreted vesicles recently gained in interest for medicine. They represent potential sources of biomarkers that can be collected from body fluids and, by disseminating pathogenic proteins, might also participate in systemic diseases like cancer, atherosclerosis and neurodegeneration. The mechanisms controlling the biogenesis and the uptake of secreted vesicles are poorly understood. Some of these vesicles originate from endosomes and are called ‘exosomes’. In this review, we recapitulate recent insight on the role of the syndecan (SDC) heparan sulphate proteoglycans, the small intracellular adaptor syntenin and associated regulators in the biogenesis and loading of exosomes with cargo. SDC–syntenin‐associated regulators include the endosomal sorting complex required for transport accessory component ALG‐2‐interacting protein X, the small GTPase adenosine 5′‐diphosphate‐ribosylation factor 6, the lipid‐modifying enzyme phospholipase D2 and the endoglycosidase heparanase. All these molecules appear to support the budding of SDC–syntenin and associated cargo into the lumen of endosomes. This highlights a major mechanism for the formation of intraluminal vesicles that will be released as exosomes.     

ARF——一种新的抑癌因子的研究进展

INK4a/ARF基因位于人染色体9p21,是人类肿瘤中最常见的基因失活位点之一.INK4a/ARF基因有两套各自独立的启动子,通过可变阅读框,能够编码两种蛋白质：p16^INK4a和p14^ARF（ARF在鼠细胞中为p19^ARF）.p16作为CDK4/6的抑制因子,能够阻断pRb磷酸化,将细胞周期阻断在G1期;而ARF可结合原癌蛋白MDM2,稳定p53,将细胞周期阻断在G1期和G2/M转换期,或诱导细胞凋亡.因此ARF蛋白和p16一样也是一种肿瘤抑制因子.     

细胞内物质转运调节分子ARFGAP3的克隆表达及生化活性

ADP核糖基化因子-GTP酶活化蛋白(ARF GAP)是重要的细胞内物质转运调节分子.在22周孕龄人胎肝cDNA文库中发现一种新基因,其编码的氨基酸序列与大鼠ARF1 GAP有32%同源性.将这种新基因命名为“ARFGAP3”,对其进行功能研究,利用逆转录-聚合酶链式反应(RT-PCR),从人胎盘总RNA中扩增ARFGAP3全长cDNA序列,并将其亚克隆到pGEM-T载体;采用RNA印迹法和斑点杂交法,检测其组织表达谱,发现在多种腺体和睾丸中有很高水平ARFGAP3基因转录,并且只有一种约2.7 kb的转录本.利用基因重组技术,构建表达质粒pBAD/Thio-ARFGAP3,在大肠杆菌中表达,采用亲和层析法纯化表达产物,利用肠激酶切除重组融合蛋白N端引导序列.检测重组ARFGAP3的生化活性,证实ARFGAP3对ARF1具有GAP活性,促进ARF1结合的GTP水解为GDP,磷脂酰肌醇二磷酸(PIP2)增强其GAP活性,而磷脂酰胆碱(PC)抑制其GAP活性.     

Light Promotes Protein Stability of Auxin Response Factor 7

Light is an environmental signaling, whereas Aux/IAA proteins and Auxin Response Factors (ARFs) are regulators of auxin signalling. Aux/IAA proteins are unstable, and their degradation dependents on 26S ubiquitin-proteasome and is promoted by Auxin. Auxin binds directly to a SCF-type ubiquitin-protein ligase, TIR1, facilitates the interaction between Aux/IAA proteins and TIR1, and then the degradation of Aux/IAA proteins. A few studies have reported that some ARFs are also unstable proteins, and their degradation is also mediated by 26S proteasome. In this study, by using of antibodies recognizing endogenous ARF7 proteins, we found that protein stability of ARF7 was affected by light. By expressing MYC tagged ARF activators in protoplasts, we found that degradation of ARF7 was inhibited by 26 proteasome inhibitors. In addition, at least ARF5 and ARF19 were also unstable proteins, and degradation of ARF5 via 26S proteasome was further confirmed by using stable transformed plants overexpressing ARF5 with a GUS tag.