The sea urchin kinome: a first look

This paper reports a preliminary in silico analysis of the sea urchin kinome. The predicted protein kinases in the sea urchin genome were identified, annotated and classified, according to both function and kinase domain taxonomy. The results show that the sea urchin kinome, consisting of 353 protein kinases, is closer to the Drosophila kinome (239) than the human kinome (518) with respect to total kinase number. However, the diversity of sea urchin kinases is surprisingly similar to humans, since the urchin kinome is missing only 4 of 186 human subfamilies, while Drosophila lacks 24. Thus, the sea urchin kinome combines the simplicity of a non-duplicated genome with the diversity of function and signaling previously considered to be vertebrate-specific. More than half of the sea urchin kinases are involved with signal transduction, and approximately 88% of the signaling kinases are expressed in the developing embryo. These results support the strength of this nonchordate deuterostome as a pivotal developmental and evolutionary model organism.     

The generality of kinase-catalyzed biotinylation

Kinase-catalyzed protein phosphorylation is involved in a wide variety of cellular events. Development of methods to monitor phosphoproteins in normal and diseased states is critical to fully characterize cell signaling. Towards phosphoprotein analysis tools, our lab reported kinase-catalyzed labeling where γ-phosphate modified ATP analogs are utilized by kinases to label peptides or protein substrates with a functional tag. In particular, the ATP-biotin analog was developed for kinase-catalyzed biotinylation. However, kinase-catalyzed labeling has been tested rigorously with only a few kinases, preventing use of ATP-biotin as a general tool. Here, biotinylation experiments, gel or HPLC-based quantification, and kinetic measurements indicated that twenty-five kinases throughout the kinome tree accepted ATP-biotin as a cosubstrate. With this rigorous characterization of ATP-biotin compatibility, kinase-catalyzed labeling is now immediately useful for studying phosphoproteins and characterizing the role of phosphorylation in various biological events.     

两种基因编码的探针特异性检测小鼠脑5-HT信号的比较

摘要 目的：五羟色胺（5-HT）对中枢神经系统发挥着重要的调控作用,其功能失调与许多精神类疾病密切相关,因此开发能实时灵敏检测5-HT的工具对研究此类疾病及研发靶向药物至关重要。最近新开发的iSeroSnFR和GRAB_5-HT1.0两类5-HT荧光探针,具有细胞特异性、反应灵敏以及高时空分辨率等显著优势,已经成为深入探究5-HT作用机制的有力工具。本研究旨在探究荧光探针iSeroSnFR和GRAB_5-HT1.0哪种能更有效地检测5-HT递质释放及动态变化,从而为后续优化5-HT荧光探针和利用这一有力工具解析神经疾病中的递质异常提供新思路。方法：将iSeroSnFR或GRAB_5-HT1.0探针的基因序列插入到Sindbis病毒表达载体,然后把病毒分别转染到培养的小鼠离体脑片的海马CA1区,比较两种探针在神经元中的表达差异;并检测其对外源性5-HT药物诱导产生的荧光反应。另外,将上述病毒转染到急性小鼠脑片中缝核（DRN）区,给与电刺激检测两种探针响应内源5-HT释放的荧光信号差异。结果：在转染iSeroSnFR的海马CA1区神经元中均有荧光表达,但细胞边界不清晰;而转染了GRAB_5-HT1.0的神经元细胞膜上表达有强烈的绿色荧光信号。用1 μM 5-HT处理培养的小鼠脑片海马CA1神经元时,iSeroSnFR探针没有明显的荧光强度变化;而GRAB_5-HT1.0探针产生的荧光强度显著增强;用1 mM 5-HT处理时,iSeroSnFR探针产生一定强度的荧光反应,但响应幅度弱于GRAB_5-HT1.0探针。另外,利用上述病毒转染急性小鼠脑片DRN区,通过电刺激诱导内源性5-HT释放,发现仅在表达GRAB_5-HT1.0探针的DRN神经元中观察到显著增强的荧光反应;而iSeroSnFR探针几乎未产生明显荧光变化。结论：在小鼠脑中,GRAB_5-HT1.0荧光探针对外源性及内源性的5-HT的亲和力更高、灵敏度更强。     

Utilizing Natural and Engineered Peroxiredoxins As Intracellular Peroxide Reporters

It is increasingly apparent that nature evolved peroxiredoxins not only as H₂O₂ scavengers but also as highly sensitive H₂O₂ sensors and signal transducers. Here we ask whether the H₂O₂ sensing role of Prx can be exploited to develop probes that allow to monitor intracellular H₂O₂ levels with unprecedented sensitivity. Indeed, simple gel shift assays visualizing the oxidation of endogenous 2-Cys peroxiredoxins have already been used to detect subtle changes in intracellular H₂O₂ concentration. The challenge however is to create a genetically encoded probe that offers real-time measurements of H₂O₂ levels in intact cells via the Prx oxidation state. We discuss potential design strategies for Prx-based probes based on either the redox-sensitive fluorophore roGFP or the conformation-sensitive fluorophore cpYFP. Furthermore, we outline the structural and chemical complexities which need to be addressed when using Prx as a sensing moiety for H₂O₂ probes. We suggest experimental strategies to investigate the influence of these complexities on probe behavior. In doing so, we hope to stimulate the development of Prx-based probes which may spearhead the further study of cellular H₂O₂ homeostasis and Prx signaling.     

Design,synthesis, and evaluation of a selective chemosensor for leucine-rich repeat kinase 2

We describe the design, synthesis, and evaluation of a selective activity probe for leucine-rich repeat kinase 2 (LRRK2), a possible molecular target for the treatment of Parkinson’s disease. Our optimal chemosensor design, termed Nictide-S2, incorporates a phosphorylation-sensitive sulfonamido-oxine fluorophore at an engineered cysteine within the substrate sequence. This design allows for the direct, real-time analysis of LRRK2 kinase activity with a detection limit of 2.5 nM. Under optimized conditions, we measured a Z′ factor of 0.7 demonstrating the potential utility of this assay for inhibitor screening. Off-target kinases capable of phosphorylating Nictide-S2 are identified and an optimized inhibitor cocktail for suppressing background signal is provided. The resulting chemosensor could be utilized to identify LRRK2 inhibitors as well as selectively report on LRRK2 activity in the presence of off-target kinases.     

Flavoprotein miniSOG as a genetically encoded photosensitizer for cancer cells

Background

Genetically encoded photosensitizers are a promising optogenetic instrument for light-induced production of reactive oxygen species in desired locations within cells in vitro or whole body in vivo. Only two such photosensitizers are currently known, GFP-like protein KillerRed and FMN-binding protein miniSOG. In this work we studied phototoxic effects of miniSOG in cancer cells.

Methods

HeLa Kyoto cell lines stably expressing miniSOG in different localizations, namely, plasma membrane, mitochondria or chromatin (fused with histone H2B) were created. Phototoxicity of miniSOG was tested on the cells in vitro and tumor xenografts in vivo.

Results

Blue light induced pronounced cell death in all three cell lines in a dose-dependent manner. Caspase 3 activation was characteristic of illuminated cells with mitochondria- and chromatin-localized miniSOG, but not with miniSOG in the plasma membrane. In addition, H2B-miniSOG-expressing cells demonstrated light-induced activation of DNA repair machinery, which indicates massive damage of genomic DNA. In contrast to these in vitro data, no detectable phototoxicity was observed on tumor xenografts with HeLa Kyoto cell lines expressing mitochondria- or chromatin-localized miniSOG.

Conclusions

miniSOG is an excellent genetically encoded photosensitizer for mammalian cells in vitro, but it is inferior to KillerRed in the HeLa tumor.

General significance

This is the first study to assess phototoxicity of miniSOG in cancer cells. The results suggest an effective ontogenetic tool and may be of interest for molecular and cell biology and biomedical applications.     

New red-fluorescent calcium indicators for optogenetics,photoactivation and multi-color imaging

Most chemical and, with only a few exceptions, all genetically encoded fluorimetric calcium (Ca²⁺) indicators (GECIs) emit green fluorescence. Many of these probes are compatible with red-emitting cell- or organelle markers. But the bulk of available fluorescent-protein constructs and transgenic animals incorporate green or yellow fluorescent protein (GFP and YFP respectively). This is, in part, not only heritage from the tendency to aggregate of early-generation red-emitting FPs, and due to their complicated photochemistry, but also resulting from the compatibility of green-fluorescent probes with standard instrumentation readily available in most laboratories and core imaging facilities. Photochemical constraints like limited water solubility and low quantum yield have contributed to the relative paucity of red-emitting Ca²⁺ probes compared to their green counterparts, too. The increasing use of GFP and GFP-based functional reporters, together with recent developments in optogenetics, photostimulation and super-resolution microscopies, has intensified the quest for red-emitting Ca²⁺ probes. In response to this demand more red-emitting chemical and FP-based Ca²⁺-sensitive indicators have been developed since 2009 than in the thirty years before.     

微生物——几种溶栓药物的重要来源

综述了几种来源于微生物的重要溶栓剂的性质及研究状况。微生物是溶栓剂的重要来源 ,从微生物中寻找溶栓药物是一种理想有效的途径。     

Calcium signalling in Drosophila photoreceptors measured with GCaMP6f

Drosophila phototransduction is mediated by phospholipase C leading to activation of cation channels (TRP and TRPL) in the 30000 microvilli forming the light-absorbing rhabdomere. The channels mediate massive Ca²⁺ influx in response to light, but whether Ca²⁺ is released from internal stores remains controversial. We generated flies expressing GCaMP6f in their photoreceptors and measured Ca²⁺ signals from dissociated cells, as well as in vivo by imaging rhabdomeres in intact flies. In response to brief flashes, GCaMP6f signals had latencies of 10–25 ms, reached 50% F_max with ∼1200 effectively absorbed photons and saturated (ΔF/F₀ ∼ 10–20) with 10000–30000 photons. In Ca²⁺ free bath, smaller (ΔF/F₀ ∼4), long latency (∼200 ms) light-induced Ca²⁺ rises were still detectable. These were unaffected in InsP₃ receptor mutants, but virtually eliminated when Na⁺ was also omitted from the bath, or in trpl;trp mutants lacking light-sensitive channels. Ca²⁺ free rises were also eliminated in Na⁺/Ca²⁺ exchanger mutants, but greatly accelerated in flies over-expressing the exchanger. These results show that Ca²⁺ free rises are strictly dependent on Na⁺ influx and activity of the exchanger, suggesting they reflect re-equilibration of Na⁺/Ca²⁺ exchange across plasma or intracellular membranes following massive Na⁺ influx. Any tiny Ca²⁺ free rise remaining without exchanger activity was equivalent to <10 nM (ΔF/F₀ ∼0.1), and unlikely to play any role in phototransduction.