bims-mecosi 2023-10-29 papers

Issue of 2023–10–29
six papers selected by
Verena Kohler, Umeå University

Biochem Biophys Res Commun. 2023 Oct 15. pii: S0006-291X(23)01200-7. [Epub ahead of print]683 149116

CCDC127 regulates lipid droplet homeostasis by enhancing mitochondria-ER contacts.

Yuchen Xia, Yue Zhang, Yuwei Sun, Li He.

Lipid droplets (LDs) are both energy storage and signaling organelles playing important roles in various physiological and pathological conditions. The mitochondria-ER contacts have been implicated in regulating the homeostasis of lipid droplets. However, our knowledge about the molecular mechanism behind this regulation is still limited. In this study, we identified CCDC127, a previously uncharacterized protein, as a new regulator of LDs by enhancing the mitochondria-ER contact sites (MERCS). Knockdown and overexpression of CCDC127 in HeLa cells significantly change the LDs abundance in opposite directions, suggesting that CCDC127 positively regulates the LDs. Additional analysis showed that CCDC127 localizes on the outer membrane of mitochondria through its N-terminus and promotes mitochondria fragmentation. Importantly, knockdown or overexpression of CCDC127 significantly down- or up-regulates, respectively, the formation of MERCS. Further experiments showed that CCDC127 is required to stabilize the MERCS tether protein VAPA. And overexpression or knockdown of VAPA reversed the effects of CCDC127 reduction or overexpression on LDs. Finally, we demonstrated that knocking down CCDC127 in the mesenchymal stem cells reduced their differentiation towards adipocytes. These findings provide a new molecular connection between LD homeostasis and MERCS regulation.

Keywords: CCDC127; Lipid droplet; Mitochondria-ER contact

DOI: https://doi.org/10.1016/j.bbrc.2023.10.048

Proc Natl Acad Sci U S A. 2023 Oct 31. 120(44): e2313010120

Misregulation of mitochondria-lysosome contact dynamics in Charcot-Marie-Tooth Type 2B disease Rab7 mutant sensory peripheral neurons.

Yvette C Wong, Nirupa D Jayaraj, Tayler B Belton, George C Shum, Hannah E Ball, Dongjun Ren, Abigail L D Tadenev, Dimitri Krainc, Robert W Burgess, Daniela M Menichella.

Inter-organelle contact sites between mitochondria and lysosomes mediate the crosstalk and bidirectional regulation of their dynamics in health and disease. However, mitochondria-lysosome contact sites and their misregulation have not been investigated in peripheral sensory neurons. Charcot-Marie-Tooth type 2B disease is an autosomal dominant axonal neuropathy affecting peripheral sensory neurons caused by mutations in the GTPase Rab7. Using live super-resolution and confocal time-lapse microscopy, we showed that mitochondria-lysosome contact sites dynamically form in the soma and axons of peripheral sensory neurons. Interestingly, Charcot-Marie-Tooth type 2B mutant Rab7 led to prolonged mitochondria-lysosome contact site tethering preferentially in the axons of peripheral sensory neurons, due to impaired Rab7 GTP hydrolysis-mediated contact site untethering. We further generated a Charcot-Marie-Tooth type 2B mutant Rab7 knock-in mouse model which exhibited prolonged axonal mitochondria-lysosome contact site tethering and defective downstream axonal mitochondrial dynamics due to impaired Rab7 GTP hydrolysis as well as fragmented mitochondria in the axon of the sciatic nerve. Importantly, mutant Rab7 mice further demonstrated preferential sensory behavioral abnormalities and neuropathy, highlighting an important role for mutant Rab7 in driving degeneration of peripheral sensory neurons. Together, this study identifies an important role for mitochondria-lysosome contact sites in the pathogenesis of peripheral neuropathy.

Keywords: Charcot–Marie–Tooth disease; inter-organelle contact site; lysosome; mitochondria; peripheral neuropathy

DOI: https://doi.org/10.1073/pnas.2313010120

J Biol Chem. 2023 Oct 20. pii: S0021-9258(23)02406-7. [Epub ahead of print] 105378

Progesterone receptor membrane component 1 facilitates Ca2+ signal amplification between endosomes and the endoplasmic reticulum.

Gihan S Gunaratne, Sushil Kumar, Yaping Lin-Moshier, James T Slama, Eugen Brailiou, Sandip Patel, Timothy F Walseth, Jonathan S Marchant.

Membrane contact sites (MCSs) between endosomes and the endoplasmic reticulum (ER) are thought to act as specialized trigger zones for Ca2+ signaling, where local Ca2+ released via endolysosomal ion channels is amplified by ER Ca2+-sensitive Ca2+ channels into global Ca2+ signals. Such amplification is integral to the action of the second messenger, nicotinic acid adenine dinucleotide phosphate (NAADP). However, functional regulators of inter-organellar Ca2+ crosstalk between endosomes and the ER remain poorly defined. Here, we identify progesterone receptor membrane component 1 (PGRMC1), an ER transmembrane protein that undergoes a unique heme-dependent dimerization, as an interactor of the endosomal two pore channel, TPC1. NAADP-dependent Ca2+ signals were potentiated by PGRMC1 overexpression through enhanced functional coupling between endosomal and ER Ca2+ stores and inhibited upon PGRMC1 knockdown. Point mutants in PGMRC1 or pharmacological manipulations that reduced its interaction with TPC1 were without effect. PGRMC1 therefore serves as a TPC1 interactor that regulates ER-endosomal coupling with functional implications for cellular Ca2+ dynamics and potentially the distribution of heme.

Keywords: NAADP; calcium signaling; endosomes; heme; lysosomes

DOI: https://doi.org/10.1016/j.jbc.2023.105378

Nat Commun. 2023 Oct 23. 14(1): 6729

Lipocalin 2 regulates mitochondrial phospholipidome remodeling, dynamics, and function in brown adipose tissue in male mice.

Hongming Su, Hong Guo, Xiaoxue Qiu, Te-Yueh Lin, Chao Qin, Gail Celio, Peter Yong, Mark Senders, Xianlin Han, David A Bernlohr, Xiaoli Chen.

Mitochondrial function is vital for energy metabolism in thermogenic adipocytes. Impaired mitochondrial bioenergetics in brown adipocytes are linked to disrupted thermogenesis and energy balance in obesity and aging. Phospholipid cardiolipin (CL) and phosphatidic acid (PA) jointly regulate mitochondrial membrane architecture and dynamics, with mitochondria-associated endoplasmic reticulum membranes (MAMs) serving as the platform for phospholipid biosynthesis and metabolism. However, little is known about the regulators of MAM phospholipid metabolism and their connection to mitochondrial function. We discover that LCN2 is a PA binding protein recruited to the MAM during inflammation and metabolic stimulation. Lcn2 deficiency disrupts mitochondrial fusion-fission balance and alters the acyl-chain composition of mitochondrial phospholipids in brown adipose tissue (BAT) of male mice. Lcn2 KO male mice exhibit an increase in the levels of CLs containing long-chain polyunsaturated fatty acids (LC-PUFA), a decrease in CLs containing monounsaturated fatty acids, resulting in mitochondrial dysfunction. This dysfunction triggers compensatory activation of peroxisomal function and the biosynthesis of LC-PUFA-containing plasmalogens in BAT. Additionally, Lcn2 deficiency alters PA production, correlating with changes in PA-regulated phospholipid-metabolizing enzymes and the mTOR signaling pathway. In conclusion, LCN2 plays a critical role in the acyl-chain remodeling of phospholipids and mitochondrial bioenergetics by regulating PA production and its function in activating signaling pathways.

DOI: https://doi.org/10.1038/s41467-023-42473-2

Eur J Cell Biol. 2023 Oct 16. pii: S0171-9335(23)00080-8. [Epub ahead of print]102(4): 151365

Call to action to properly utilize electron microscopy to measure organelles to monitor disease.

Kit Neikirk, Edgar-Garza Lopez, Andrea G Marshall, Ahmad Alghanem, Evan Krystofiak, Bartosz Kula, Nathan Smith, Jianqiang Shao, Prasanna Katti, Antentor Hinton.

This review provides an overview of the current methods for quantifying mitochondrial ultrastructure, including cristae morphology, mitochondrial contact sites, and recycling machinery and a guide to utilizing electron microscopy to effectively measure these organelles. Quantitative analysis of mitochondrial ultrastructure is essential for understanding mitochondrial biology and developing therapeutic strategies for mitochondrial-related diseases. Techniques such as transmission electron microscopy (TEM) and serial block face-scanning electron microscopy, as well as how they can be combined with other techniques including confocal microscopy, super-resolution microscopy, and correlative light and electron microscopy are discussed. Beyond their limitations and challenges, we also offer specific magnifications that may be best suited for TEM analysis of mitochondrial, endoplasmic reticulum, and recycling machinery. Finally, perspectives on future quantification methods are offered.

Keywords: 3D EM; MERCs; Mitochondria; Quantification; TEM

DOI: https://doi.org/10.1016/j.ejcb.2023.151365

bioRxiv. 2023 Oct 14. pii: 2023.10.13.562302. [Epub ahead of print]

The fatty liver disease-causing protein PNPLA3-I148M alters lipid droplet-Golgi dynamics.

David J Sherman, Lei Liu, Jennifer L Mamrosh, Jiansong Xie, John Ferbas, Brett Lomenick, Mark S Ladinsky, Rati Verma, Ingrid C Rulifson, Raymond J Deshaies.

Non-alcoholic fatty liver disease (NAFLD), recently renamed metabolic dysfunction-associated steatotic liver disease (MASLD), is a progressive metabolic disorder that begins with aberrant triglyceride accumulation in the liver and can lead to cirrhosis and cancer. A common variant in the gene PNPLA3 , encoding the protein PNPLA3-I148M, is the strongest known genetic risk factor for MASLD to date. Despite its discovery twenty years ago, the function of PNPLA3, and now the role of PNPLA3-I148M, remain unclear. In this study, we sought to dissect the biogenesis of PNPLA3 and PNPLA3-I148M and characterize changes induced by endogenous expression of the disease-causing variant. Contrary to bioinformatic predictions and prior studies with overexpressed proteins, we demonstrate here that PNPLA3 and PNPLA3-I148M are not endoplasmic reticulum-resident transmembrane proteins. To identify their intracellular associations, we generated a paired set of isogenic human hepatoma cells expressing PNPLA3 and PNPLA3-I148M at endogenous levels. Both proteins were enriched in lipid droplet, Golgi, and endosomal fractions. Purified PNPLA3 and PNPLA3-I148M proteins associated with phosphoinositides commonly found in these compartments. Despite a similar fractionation pattern as the wild-type variant, PNPLA3-I148M induced morphological changes in the Golgi apparatus, including increased lipid droplet-Golgi contact sites, which were also observed in I148M-expressing primary human patient hepatocytes. In addition to lipid droplet accumulation, PNPLA3-I148M expression caused significant proteomic and transcriptomic changes that resembled all stages of liver disease. Cumulatively, we validate an endogenous human cellular system for investigating PNPLA3-I148M biology and identify the Golgi apparatus as a central hub of PNPLA3-I148M-driven cellular change.
Significance Statement: Fatty liver disease affects nearly a quarter of the world's population and has both environmental and genetic risk factors. A mutation in the gene PNPLA3 that converts Ile 148 to Met is the strongest known genetic risk factor for developing fatty liver disease. Using a series of techniques to track endogenous PNPLA3 and PNPLA3-I148M biogenesis and localization, we reveal new insights into how the mutation changes cellular dynamics. Although previous reports focus on its role on lipid droplets, we reveal that PNPLA3-I148M also functions at the Golgi apparatus, an organelle critical for protein transport into and out of the cell and lipid signaling. PNPLA3-I148M causes altered Golgi morphology and drives changes reminiscent of liver disease.

DOI: https://doi.org/10.1101/2023.10.13.562302