Photolysis of caged phosphatidic acid induces flagellar excision in Chlamydomonas

Chemical Approaches for Measuring and Manipulating Lipids at the Organelle Level

As the products of complex and often redundant metabolic pathways, lipids are challenging to measure and perturb using genetic tools. Yet by virtue of being the major constituents of cellular membranes, lipids are highly regulated in space and time. Chemists have stepped into this methodological void, developing an array of techniques for the precise quantification and manipulation of lipids at the subcellular, organelle level. Here, we survey the landscape of these methods. For measuring lipids, we summarize the use of metabolic labeling and click chemistry tagging, photoaffinity labeling, isotopic tagging for Raman microscopy, and chemoenzymatic labeling for tracking lipid production and interorganelle transport. For perturbing lipids, we describe synthetic photocaged lipids and membrane editing approaches using optogenetic enzymes for precise manipulation of lipid signaling. Collectively, these chemical and biochemical tools are revealing phenomena and mechanisms underlying lipid functions at the subcellular level.

Caged lipid probes for controlling lipid levels on subcellular scales

Lipids exert their cellular functions in individual organelles, in some cases on the scale of even smaller, specialized membrane domains. Thus, the experimental capacity to precisely manipulate lipid levels at the subcellular level is crucial for studying lipid-related processes in cell biology. Photo-caged lipid probes which partition into specific cellular membranes prior to photoactivation have emerged as key tools for localized and selective perturbation of lipid concentration in living cells. In this review, we provide an overview of the recent advances in the area and outline which developments are still required for the methodology to be more widely implemented in the wider membrane biology community.

A WDR35-dependent coat protein complex transports ciliary membrane cargo vesicles to cilia

Intraflagellar transport (IFT) is a highly conserved mechanism for motor-driven transport of cargo within cilia, but how this cargo is selectively transported to cilia is unclear. WDR35/IFT121 is a component of the IFT-A complex best known for its role in ciliary retrograde transport. In the absence of WDR35, small mutant cilia form but fail to enrich in diverse classes of ciliary membrane proteins. In Wdr35 mouse mutants, the non-core IFT-A components are degraded and core components accumulate at the ciliary base. We reveal deep sequence homology of WDR35 and other IFT-A subunits to α and ß' COPI coatomer subunits and demonstrate an accumulation of 'coat-less' vesicles that fail to fuse with Wdr35 mutant cilia. We determine that recombinant non-core IFT-As can bind directly to lipids and provide the first in situ evidence of a novel coat function for WDR35, likely with other IFT-A proteins, in delivering ciliary membrane cargo necessary for cilia elongation.

Optical Control of Phosphatidic Acid Signaling

Phosphatidic acids (PAs) are glycerophospholipids that regulate key cell signaling pathways governing cell growth and proliferation, including the mTOR and Hippo pathways. Their acyl chains vary in tail length and degree of saturation, leading to marked differences in the signaling functions of different PA species. For example, in mTOR signaling, saturated forms of PA are inhibitory, whereas unsaturated forms are activating. To enable rapid control over PA signaling, we describe here the development of photoswitchable analogues of PA, termed AzoPA and dAzoPA, that contain azobenzene groups in one or both lipid tails, respectively. These photolipids enable optical control of their tail structure and can be reversibly switched between a straight trans form and a relatively bent cis form. We found that cis-dAzoPA selectively activates mTOR signaling, mimicking the bioactivity of unsaturated forms of PA. Further, in the context of Hippo signaling, whose growth-suppressing activity is blocked by PA, we found that the cis forms of both AzoPA and dAzoPA selectively inhibit this pathway. Collectively, these photoswitchable PA analogues enable optical control of mTOR and Hippo signaling, and we envision future applications of these probes to dissect the pleiotropic effects of physiological and pathological PA signaling.

Light-triggered release of photocaged therapeutics - Where are we now?

The current available therapeutics face several challenges such as the development of ideal drug delivery systems towards the goal of personalized treatments for patients benefit. The application of light as an exogenous activation mechanism has shown promising outcomes, owning to the spatiotemporal confinement of the treatment in the vicinity of the diseased tissue, which offers many intriguing possibilities. Engineering therapeutics with light responsive moieties have been explored to enhance the bioavailability, and drug efficacy either in vitro or in vivo. The tailor-made character turns the so-called photocaged compounds highly desirable to reduce the side effects of drugs and, therefore, have received wide research attention. Herein, we seek to highlight the potential of photocaged compounds to obtain a clear understanding of the mechanisms behind its use in therapeutic delivery. A deep overview on the progress achieved in the design, fabrication as well as current and possible future applications in therapeutics of photocaged compounds is provided, so that novel formulations for biomedical field can be designed.

Time-series lipidomic analysis of the oleaginous green microalga species Ettlia oleoabundans under nutrient stress

BACKGROUND

Microalgae are uniquely advantageous organisms cultured and harvested for several value-added biochemicals. A majority of these compounds are lipid-based, such as triacylglycerols (TAGs), which can be used for biofuel production, and their accumulation is most affected under nutrient stress conditions. As such, the balance between cellular homeostasis and lipid metabolism becomes more intricate to achieve efficiency in bioproduct synthesis. Lipidomics studies in microalgae are of great importance as biochemical diversity also plays a major role in lipid regulation among oleaginous species.

METHODS

The aim of this study was to analyze time-series changes in lipid families produced by microalga under different nutrient conditions and growth phases to gain comprehensive information at the cellular level. For this purpose, we worked with a highly adaptable, oleaginous, non-model green microalga species, Ettlia oleoabundans (a.k.a. Neochloris oleoabundans). Using a mass spectrometry-based untargeted and targeted metabolomics' approach, we analyzed the changes in major lipid families under both replete and deplete nitrogen and phosphorus conditions at four different time points covering exponential and stationary growth phases.

RESULTS

Comprehensive analysis of the lipid metabolism highlighted the accumulation of TAGs, which can be utilized for the production of biodiesel via transesterification, and depletion of chlorophylls and certain structural lipids required for photosynthesis, under nutrient deprived conditions. We also found a correlation between the depletion of digalactosyldiacylglycerols (DGDGs) and sulfoquinovosyldiacylglycerols (SQDGs) under nutrient deprivation.

CONCLUSIONS

High accumulation of TAGs under nutrient limitation as well as a depletion of other lipids of interest such as phosphatidylglycerols (PGs), DGDGs, SQDGs, and chlorophylls seem to be interconnected and related to the microalgal photosynthetic efficiency. Overall, our results provided key biochemical information on the lipid regulation and physiology of a non-model green microalga, along with optimization potential for biodiesel and other value-added product synthesis.

Regulation of Chlamydomonas flagella and ependymal cell motile cilia by ceramide-mediated translocation of GSK3

Cilia are important organelles formed by cell membrane protrusions; however, little is known about their regulation by membrane lipids. A novel, evolutionarily conserved activation mechanism for GSK3 by the sphingolipid (phyto)ceramide is characterized that is critical for ciliogenesis in Chlamydomonas and murine ependymal cells.

Cilia are important organelles formed by cell membrane protrusions; however, little is known about their regulation by membrane lipids. We characterize a novel activation mechanism for glycogen synthase kinase-3 (GSK3) by the sphingolipids phytoceramide and ceramide that is critical for ciliogenesis in Chlamydomonas and murine ependymal cells, respectively. We show for the first time that Chlamydomonas expresses serine palmitoyl transferase (SPT), the first enzyme in (phyto)ceramide biosynthesis. Inhibition of SPT in Chlamydomonas by myriocin led to loss of flagella and reduced tubulin acetylation, which was prevented by supplementation with the precursor dihydrosphingosine. Immunocytochemistry showed that (phyto)ceramide was colocalized with phospho–Tyr-216-GSK3 (pYGSK3) at the base and tip of Chlamydomonas flagella and motile cilia in ependymal cells. The (phyto)ceramide distribution was consistent with that of a bifunctional ceramide analogue UV cross-linked and visualized by click-chemistry–mediated fluorescent labeling. Ceramide depletion, by myriocin or neutral sphingomyelinase deficiency (fro/fro mouse), led to GSK3 dephosphorylation and defective flagella and cilia. Motile cilia were rescued and pYGSK3 localization restored by incubation of fro/fro ependymal cells with exogenous C24:1 ceramide, which directly bound to pYGSK3. Our findings suggest that (phyto)ceramide-mediated translocation of pYGSK into flagella and cilia is an evolutionarily conserved mechanism fundamental to the regulation of ciliogenesis.

Two-photon sensitive protecting groups operating via intramolecular electron transfer: uncaging of GABA and tryptophan

Improved photo-labile protecting groups, with high sensitivity to two-photon excitation, are needed for the controlled release of drugs, as tools in neuroscience and physiology. Here we present a new modular approach to the design of caging groups based on photoinduced electron transfer from an electron-rich two-photon dye to an electron acceptor, followed by scission of an ester to release a carboxylic acid. Three different electron acceptors were tested: nitrobenzyl, phenacyl and pyridinium. The nitrobenzyl system was ineffective, giving only photochemical decomposition and no release of the carboxylic acid. The phenacyl system also performed poorly, liberating the carboxylic acid in 20% chemical yield and 0.2% photochemical yield. The pyridinium system was most successful, and was tested for the release of two carboxylic acids: γ-amino butyric acid (GABA) and tryptophan. The caged GABA undergoes photochemical cleavage with a chemical yield of >95% and a photochemical yield of 1%; it exhibits a two-photon absorption cross section of 1100 GM at 700 nm, corresponding to a two-photon uncaging cross section of 10 ± 3 GM.

Enhanced small interfering RNA delivery into cells by exploiting the additive effect between photo-sensitive peptides and targeting ligands

OBJECTIVES

To enhance the targeting delivery efficiency of small interfering RNA (siRNA) to tumour cells, a novel multifunctional liposome (PSP/NGR-L) comodified with photo-sensitive cell-penetrating peptides (PSP) and asparagine-glycine-arginine peptide (NGR) was constructed and investigated.

METHODS

PSP was conjugated to 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-maleimide(polyethylene glycol)-2000 (DSPE-PEG2000 -MAL) to generate DSPE-PEG2000 -PSP and used to form PSP/NGR-L, the features of the liposomes were determined. HT-1080 and MCF-7 cells were used for cellular uptake tests, and the cellular uptake pathways were identified. Intracellular trafficking and endosomal escape were also evaluated. In-vitro siRNA transfection evaluations were carried out in HT-1080 cells.

KEY FINDINGS

The encapsulation efficiencies of liposomes were about 80%, and the mean particle sizes were around 100 nm. The targeting specificity of PSP/NGR-L was significantly enhanced via NGR navigation and ultraviolet (UV) light illumination. The internalization of PSP/NGR-L in HT-1080 cells was mediated by more than one cellular uptake mechanisms. The constructed nanocarrier could escape from the endosome to produce its effects in the cellular cytoplasm with the help of UV illumination. PSP/NGR-L could down-regulate expression of c-myc and augmented cell apoptosis in HT-1080 cells.

CONCLUSIONS

The application of combined PSP and NGR modifications may be a new approach for the selectively targeted delivery of siRNA to cancer cells.

Caged lipids as tools for investigating cellular signaling

Lipid derivatives that can be activated by light, often referred to as 'caged' lipids, are useful tools to manipulate intact cells non-invasively. Here we focus on experimental approaches that have made use of caged lipids. Apart from summarizing the recent advances and available tools in the field, we strive to highlight the experimental challenges that arise from lipid-specific biophysical properties and the abundance of an enormous diversity of distinct molecular lipid species in cells. This article is part of a Special Issue entitled Tools to study lipid functions.

Light induced drug delivery into cancer cells

Cell-penetrating peptides (CPPs) can be used for intracellular delivery of a broad variety of cargoes, including various nanoparticulate pharmaceutical carriers. However, the cationic nature of all CPP sequences, and thus lack of cell specificity, limits their in vivo use for drug delivery applications. Here, we have devised and tested a strategy for site-specific delivery of dyes and drugs into cancer cells by using polymers bearing a light activated caged CPP (cCPP). The positive charge of Lys residues on the minimum sequence of the CPP penetratin ((52)RRMKWKK(58)) was masked with photo-cleavable groups to minimize non-specific adsorption and cellular uptake. Once illuminated by UV light, these protecting groups were cleaved, the positively charged CPP regained its activity and facilitated rapid intracellular delivery of the polymer-dye or polymer-drug conjugates into cancer cells. We have found that a 10-min light illumination time was sufficient to enhance the penetration of the polymer-CPP conjugates bearing the proapoptotic peptide, (D)(KLAKLAK)(2), into 80% of the target cells, and to promote a 'switch' like cytotoxic activity resulting a shift from 100% to 10% in cell viability after 2 h. This report provides an example for tumor targeting by means of light activation of cell-penetrating peptides for intracellular drug delivery.

Modular synthesis of biologically active phosphatidic acid probes using click chemistry

Phosphatidic acid (PA) is an important signaling lipid that plays roles in a range of biological processes including both physiological and pathophysiological events. PA is one of a number of signaling lipids that can act as site-specific ligands for protein receptors in binding events that enforce membrane association and generally regulate both receptor function and subcellular localization. However, elucidation of the full scope of PA activities has proven problematic, primarily due to the lack of a consensus sequence among PA-binding receptors. Thus, experimental approaches, such as those employing lipid probes, are necessary for characterizing interactions at the molecular level. Herein, we describe an efficient modular approach to the synthesis of a range of PA probes that employs a late stage introduction of reporter groups. This strategy was exploited in the synthesis of PA probes bearing fluorescent and photoaffinity tags as well as a bifunctional probe containing both a photoaffinity moiety and an azide as a secondary handle for purification purposes. To discern the ability of these PA analogs to mimic the natural lipid in protein-binding properties, each compound was incorporated into vesicles for binding studies using a known PA receptor, the C2 domain of PKCalpha. In these studies, each compound exhibited binding properties that were comparable to those of synthetic PA, indicating their viability as probes for effectively studying the activities of PA in cellular processes.

Caged molecules: principles and practical considerations

A caged molecule is an inert but photosensitive molecule that is transformed by photolysis into a biologically active molecule at high speed (typically 1 msec). The process is referred to as photorelease. The spatial resolution of photorelease is limited by the properties of light; submicrometer resolution is potentially achievable. Therefore, focal photorelease of caged molecules enables one to control biological processes with high spatio-temporal precision. The principles underlying caged molecules as well as practical considerations for their use are discussed in this unit.

Rapid spatiotemporal patterning of cytosolic Ca2+ underlies flagellar excision in Chlamydomonas reinhardtii

Ca(2+)-dependent signalling processes are implicated in many aspects of flagella function in the green alga, Chlamydomonas. In this study, we examine the spatiotemporal dynamics of cytosolic Ca2+ ([Ca2+](cyt)) in single Chlamydomonas cells during the process of flagellar excision, using biolistically loaded calcium-responsive dyes. Acid-induced deflagellation occurred in parallel with a single transient elevation in whole-cell [Ca2+](cyt), which was absent in the acid deflagellation-deficient adf1 mutant. Deflagellation could also be induced by elevated external Ca2+ ([Ca2+](ext)), which promoted very rapid spiking of [Ca2+](cyt) across the whole cell and in the flagella. We also detected very rapid apically localised Ca2+ signalling events with an approximate duration of 500 msec. Ninety-seven per cent of deflagellation events coincided with a rapid elevation in [Ca2+](cyt) in the apical region of the cell, either in the form of a whole cell or an apically localised increase, indicating that [Ca2+](cyt) elevations in the apical region play an underlying role in deflagellation. Our data indicate that elevated [Ca2+](ext) acts to disrupt Ca2+ homeostasis which induces deflagellation by both Adf1-dependent and Adf1-independent mechanisms. Elevated [Ca2+](ext) also results in further [Ca2+](cyt) elevations after the main period of whole cell spiking which are very strongly associated with deflagellation, exhibit a high degree of apical localisation and are largely absent in the adf1 mutant. We propose that these later elevations may act as specific signals for deflagellation.

Biologically active molecules with a "light switch"

Biologically active compounds which are light-responsive offer experimental possibilities which are otherwise very difficult to achieve. Since light can be manipulated very precisely, for example, with lasers and microscopes rapid jumps in concentration of the active form of molecules are possible with exact control of the area, time, and dosage. The development of such strategies started in the 1970s. This review summarizes new developments of the last five years and deals with "small molecules", proteins, and nucleic acids which can either be irreversibly activated with light (these compounds are referred to as "caged compounds") or reversibly switched between an active and an inactive state.

Photochemical control of biological processes

Photochemical regulation of biological processes offers a high level of control to study intracellular mechanisms with unprecedented spatial and temporal resolution. This report summarizes the advances made in recent years, focusing predominantly on the in vivo regulation of gene function using irradiation with UV light. The majority of the described applications entail the utilization of photocaging groups installed either on a small molecule modulator of biomolecular function or directly on a biological macromolecule itself.