bims-lymeca 2022-03-13 papers

Issue of 2022–03–13
seven papers selected by
Harilaos Filippakis, Harvard University

Cells. 2022 Mar 04. pii: 887. [Epub ahead of print]11(5):

Lysosomal ATP Transporter SLC17A9 Controls Cell Viability via Regulating Cathepsin D.

Peng Huang, Qi Cao, Mengnan Xu, Xian-Ping Dong.

SLC17A9 (solute carrier family 17 member 9) functions as an ATP transporter in lysosomes as well as other secretory vesicles. SLC17A9 inhibition or silence leads to cell death. However, the molecular mechanisms causing cell death are unclear. In this study, we report that cell death induced by SLC17A9 deficiency is rescued by the transcription factor EB (TFEB), a master gene for lysosomal protein expression, suggesting that SLC17A9 deficiency may be the main cause of lysosome dysfunction, subsequently leading to cell death. Interestingly, Cathepsin D, a lysosomal aspartic protease, is inhibited by SLC17A9 deficiency. Heterologous expression of Cathepsin D successfully rescues lysosomal dysfunction and cell death induced by SLC17A9 deficiency. On the other hand, the activity of Cathepsin B, a lysosomal cysteine protease, is not altered by SLC17A9 deficiency, and Cathepsin B overexpression does not rescue lysosomal dysfunction and cell death induced by SLC17A9 deficiency. Our data suggest that lysosomal ATP and SLC17A9 play critical roles in lysosomal function and cell viability by regulating Cathepsin D activity.

Keywords: ATP transporter; lysosome; solute carrier family 17 member 9 (SLC17A9); vesicular nucleotide transporter (VNUT)

DOI: https://doi.org/10.3390/cells11050887

Autophagy. 2022 Mar 10. 1-16

Lamp1 mediates lipid transport, but is dispensable for autophagy in Drosophila.

Norin Chaudhry, Margaux Sica, Satya Surabhi, David Sanchez Hernandez, Ana Mesquita, Adem Selimovic, Ayesha Riaz, Laury Lescat, Hua Bai, Gustavo C Macintosh, Andreas Jenny.

The endolysosomal system not only is an integral part of the cellular catabolic machinery that processes and recycles nutrients for synthesis of biomaterials, but also acts as signaling hub to sense and coordinate the energy state of cells with growth and differentiation. Lysosomal dysfunction adversely influences vesicular transport-dependent macromolecular degradation and thus causes serious problems for human health. In mammalian cells, loss of the lysosome associated membrane proteins LAMP1 and LAMP2 strongly affects autophagy and cholesterol trafficking. Here we show that the previously uncharacterized Drosophila Lamp1 is a bona fide ortholog of vertebrate LAMP1 and LAMP2. Surprisingly and in contrast to lamp1 lamp2 double-mutant mice, Drosophila Lamp1 is not required for viability or autophagy, suggesting that fly and vertebrate LAMP proteins acquired distinct functions, or that autophagy defects in lamp1 lamp2 mutants may have indirect causes. However, Lamp1 deficiency results in an increase in the number of acidic organelles in flies. Furthermore, we find that Lamp1 mutant larvae have defects in lipid metabolism as they show elevated levels of sterols and diacylglycerols (DAGs). Because DAGs are the main lipid species used for transport through the hemolymph (blood) in insects, our results indicate broader functions of Lamp1 in lipid transport. Our findings make Drosophila an ideal model to study the role of LAMP proteins in lipid assimilation without the confounding effects of their storage and without interfering with autophagic processes.Abbreviations: aa: amino acid; AL: autolysosome; AP: autophagosome; APGL: autophagolysosome; AV: autophagic vacuole (i.e. AP and APGL/AL); AVi: early/initial autophagic vacuoles; AVd: late/degradative autophagic vacuoles; Atg: autophagy-related; CMA: chaperone-mediated autophagy; Cnx99A: Calnexin 99A; DAG: diacylglycerol; eMI: endosomal microautophagy; ESCRT: endosomal sorting complexes required for transport; FB: fat body; HDL: high-density lipoprotein; Hrs: Hepatocyte growth factor regulated tyrosine kinase substrate; LAMP: lysosomal associated membrane protein; LD: lipid droplet; LDL: low-density lipoprotein; Lpp: lipophorin; LTP: Lipid transfer particle; LTR: LysoTracker Red; MA: macroautophagy; MCC: Manders colocalization coefficient; MEF: mouse embryonic fibroblast MTORC: mechanistic target of rapamycin kinase complex; PV: parasitophorous vacuole; SNARE: soluble N-ethylmaleimide sensitive factor attachment protein receptor; Snap: Synaptosomal-associated protein; st: starved; TAG: triacylglycerol; TEM: transmission electron microscopy; TFEB/Mitf: transcription factor EB; TM: transmembrane domain; tub: tubulin; UTR: untranslated region.

Keywords: Autophagy; Drosophila; LAMP proteins; lipid transport; lysosome

DOI: https://doi.org/10.1080/15548627.2022.2038999

Cancer Sci. 2022 Mar 10.

The metabolomic landscape plays a critical role in glioma oncogenesis.

Kenta Masui, Webster K Cavenee, Paul S Mischel, Noriyuki Shibata.

Cancer cells depend on metabolic reprogramming for survival, undergoing profound shifts in nutrient-sensing, nutrient uptake and flux through anabolic pathways, in order to drive nucleotide, lipid, and protein synthesis and provide key intermediates needed for those pathways. Although metabolic enzymes themselves can be mutated, including to generate oncometabolites, this is a relatively rare event in cancer. Usually, gene amplification, overexpression, and/or downstream signal transduction upregulate rate-limiting metabolic enzymes and limit feedback loops, to drive persistent tumor growth. Recent molecular genetic advances revealed discrete links between oncogenotypes and the resultant metabolic phenotypes. However, more comprehensive approaches are needed to unravel the dynamic spatio-temporal regulatory map of enzymes and metabolites that enable cancer cells to adapt to their microenvironment to maximize tumor growth. Proteomic and metabolomic analyses are powerful tools for analyzing a repertoire of metabolic enzymes as well as intermediary metabolites, and in conjunction with other omic approaches could provide critical information in this regard. Here, we provide an overview of cancer metabolism, especially from an "omics" perspective and with a particular focus on the genomically well-characterized malignant tumor, glioblastoma. We further discuss how metabolomics could be leveraged to improve the management of patients, by linking cancer cell genotype, epigenotype and phenotype through metabolic reprogramming.

Keywords: OMICS; epigenetics; glioblastoma; mTOR complex; metabolome

DOI: https://doi.org/10.1111/cas.15325

Biochim Biophys Acta Rev Cancer. 2022 Mar 08. pii: S0304-419X(22)00030-0. [Epub ahead of print] 188705

Metabolic tricks of cancer cells.

Katerina Hönigova, Jiri Navratil, Barbora Peltanova, Hana Holcova Polanska, Martina Raudenska, Michal Masarik.

One of the characteristics of cancer cells important for tumorigenesis is their metabolic plasticity. Indeed, in various stress conditions, cancer cells can reshape their metabolic pathways to support the increased energy request due to continuous growth and rapid proliferation. Moreover, selective pressures in the tumor microenvironment, such as hypoxia, acidosis, and competition for resources, force cancer cells to adapt by complete reorganization of their metabolism. In this review, we highlight the characteristics of cancer metabolism and discuss its clinical significance, since overcoming metabolic plasticity of cancer cells is a key objective of modern cancer therapeutics and a better understanding of metabolic reprogramming may lead to the identification of possible targets for cancer therapy.

Keywords: Cancer metabolism; Cell death; Glutaminolysis; Metabolic symbiosis; Mitochondrial bioenergetics; Warburg effect

DOI: https://doi.org/10.1016/j.bbcan.2022.188705

Autophagy. 2022 Mar 08. 1-2

The V-ATPase complex regulates non-canonical Atg8-family protein lipidation through ATG16L1 recruitment.

Lewis Timimi, Carmen Figueras-Novoa, Elena Marcassa, Oliver Florey, J Kenneth Baillie, Rupert Beale, Rachel Ulferts.

Conjugation of the Atg8 (autophagy related 8) family of ubiquitin-like proteins to phospholipids of the phagophore is a hallmark of macroautophagy/autophagy. Consequently, Atg8 family members, especially LC3B, are commonly used as a marker of autophagosomes. However, the Atg8 family of proteins are not found solely attached to double-membrane autophagosomes. In non-canonical Atg8-family protein lipidation they become conjugated to single membranes. We have shown that this process is triggered by recruitment of ATG16L1 by the vacuolar-type H+-translocating ATPase (V-ATPase) proton pump, suggesting a role for pH sensing in recruitment of Atg8-family proteins to single membranes.

Keywords: ATG16L1; Atg4; Atg8; CASM; SopF; V-ATPase; influenza; lipidation; non-canonical autophagy

DOI: https://doi.org/10.1080/15548627.2022.2029233

J Cell Sci. 2022 Mar 01. pii: jcs259357. [Epub ahead of print]135(5):

A possible role for VPS13-family proteins in bulk lipid transfer, membrane expansion and organelle biogenesis.

Thomas J Melia, Karin M Reinisch.

At organelle-organelle contact sites, proteins have long been known to facilitate the rapid movement of lipids. Classically, this lipid transport involves the extraction of single lipids into a hydrophobic pocket on a lipid transport protein. Recently, a new class of lipid transporter has been described with physical characteristics that suggest these proteins are likely to function differently. They possess long hydrophobic tracts that can bind many lipids at once and physically span the entire gulf between membranes at contact sites, suggesting that they may act as bridges to facilitate bulk lipid flow. Here, we review what has been learned regarding the structure and function of this class of lipid transporters, whose best characterized members are VPS13 and ATG2 proteins, and their apparent coordination with other lipid-mobilizing proteins on organelle membranes. We also discuss the prevailing hypothesis in the field, that this type of lipid transport may facilitate membrane expansion through the bulk delivery of lipids, as well as other emerging hypotheses and questions surrounding these novel lipid transport proteins.

Keywords: Membrane contact sites; Membrane homeostasis; Protein-mediated lipid transport

DOI: https://doi.org/10.1242/jcs.259357

Front Mol Biosci. 2022 ;9 825028

Intracellular pH Control by Membrane Transport in Mammalian Cells. Insights Into the Selective Advantages of Functional Redundancy.

Denis Doyen, Mallorie Poët, Gisèle Jarretou, Didier F Pisani, Michel Tauc, Marc Cougnon, Mederic Argentina, Yann Bouret, Laurent Counillon.

Intracellular pH is a vital parameter that is maintained close to neutrality in all mammalian cells and tissues and acidic in most intracellular compartments. After presenting the main techniques used for intracellular an vesicular pH measurements we will briefly recall the main molecular mechanisms that affect and regulate intracellular pH. Following this we will discuss the large functional redundancy found in the transporters of H+ or acid-base equivalents. For this purpose, we will use mathematical modeling to simulate cellular response to persistent and/or transient acidification, in the presence of different transporters, single or in combination. We will also test the presence or absence of intracellular buffering. This latter section will highlight how modeling can yield fundamental insight into deep biological questions such as the utility of functional redundancy in natural selection.

Keywords: functional redundancy; mathematical modelling; natural selection; pH measurements; pH regulation; transmembrane transport

DOI: https://doi.org/10.3389/fmolb.2022.825028