Cellular Demand Research Articles

Nuclear transport of nicotinamide phosphoribosyltransferase is cell cycle–dependent in mammalian cells, and its inhibition slows cell growth

Nicotinamide phosphoribosyltransferase (NAMPT) is located in both the nucleus and cytoplasm and has multiple biological functions including catalyzing the rate-limiting step in NAD synthesis. Moreover, up-regulated NAMPT expression has been observed in many cancers. However, the determinants and regulation of NAMPT's nuclear transport are not known. Here, we constructed a GFP-NAMPT fusion protein to study NAMPT's subcellular trafficking. We observed that in unsynchronized 3T3-L1 preadipocytes, 25% of cells had higher GFP-NAMPT fluorescence in the cytoplasm, and 62% had higher GFP-NAMPT fluorescence in the nucleus. In HepG2 hepatocytes, 6% of cells had higher GFP-NAMPT fluorescence in the cytoplasm, and 84% had higher GFP-NAMPT fluorescence in the nucleus. In both 3T3-L1 and HepG2 cells, GFP-NAMPT was excluded from the nucleus immediately after mitosis and migrated back into it as the cell cycle progressed. In HepG2 cells, endogenous, untagged NAMPT displayed similar changes with the cell cycle, and in nonmitotic cells, GFP-NAMPT accumulated in the nucleus. Similarly, genotoxic, oxidative, or dicarbonyl stress also caused nuclear NAMPT localization. These interventions also increased poly(ADP-ribosyl) polymerase and sirtuin activity, suggesting an increased cellular demand for NAD. We identified a nuclear localization signal in NAMPT and amino acid substitution in this sequence (424RSKK to ASGA), which did not affect its enzymatic activity, blocked nuclear NAMPT transport, slowed cell growth, and increased histone H3 acetylation. These results suggest that NAMPT is transported into the nucleus where it presumably increases NAD synthesis required for cell proliferation. We conclude that specific inhibition of NAMPT transport into the nucleus might be a potential avenue for managing cancer.

The mitochondrial metabolic function of DJ-1 is modulated by 14-3-3β.

Mitochondrial metabolic plasticity is a key adaptive mechanism in response to changes in cellular metabolic demand. Changes in mitochondrial metabolic efficiency have been linked to pathophysiological conditions, including cancer, neurodegeneration, and obesity. The ubiquitously expressed DJ-1 (Parkinsonism-associated deglycase) is known as a Parkinson's disease gene and an oncogene. The pleiotropic functions of DJ-1 include reactive oxygen species scavenging, RNA binding, chaperone activity, endocytosis, and modulation of major signaling pathways involved in cell survival and metabolism. Nevertheless, how these functions are linked to the role of DJ-1 in mitochondrial plasticity is not fully understood. In this study, we describe an interaction between DJ-1 and 14-3-3β that regulates the localization of DJ-1, in a hypoxia-dependent manner, either to the cytosol or to mitochondria. This interaction acts as a modulator of mitochondrial metabolic efficiency and a switch between glycolysis and oxidative phosphorylation. Modulation of this novel molecular mechanism of mitochondrial metabolic efficiency is potentially involved in the neuroprotective function of DJ-1 as well as its role in proliferation of cancer cells.-Weinert, M., Millet, A., Jonas, E. A., Alavian, K. N. The mitochondrial metabolic function of DJ-1 is modulated by 14-3-3β.

Mitochondrial ultrastructure, function, and calcium buffering by massive calcium loading observed using advanced cryo‐electron microscopy, high‐resolution respirometry and spectrofluorimetry

Excessive calcium accumulation is the main cause of cardiac tissue and cell death after a myocardial infarction. As a result of calcium overload, mitochondria become dysfunctional, produce excessive reactive oxygen species (ROS), cannot support the cellular energetic demand, and activate the cyclosporine A‐sensitive mitochondrial permeability transition pore. To discern the molecular, bioenergetic, and structural events associated with this phenomenon, we collected and analyzed a time‐course series of images obtained by utilizing recent advances in electron cryo‐microscopy methods. Energized mitochondria exposed to high calcium boluses, sufficient to elicit mitochondrial permeability transition, resulted in the formation of calcium phosphate granules. Under high calcium loading, the size of the calcium‐phosphate granules ranged from 50–120 nm causing OMM/IMM rupture. CsA treatment resulted in mitochondria with aberrant morphologies, increased cristae density and number, and with larger calcium‐phosphate granules ranging from 40–200 nm. The OMM was partially or completely lost; however, the mitochondria were fully functional and capable of synthesizing ATP. Our tomographic reconstruction placed these granules in close vicinity to the IMM and cristae. In addition, CsA treatment increases the calcium buffering power at greater calcium concentrations, whereas untreated mitochondria had much lower calcium buffering. Our results demonstrate that these granules form an intricate part of the mitochondrial calcium sequestration system. Overall, these results suggest CsA may interact with IMM components to: 1) modulate calcium buffering by facilitating more abundant and larger calcium phosphate granules and 2) preserve the cristae shape and number which avoids cytochrome c loss and mitochondrial permeability transition. Our data reveal that drugs capable of modulating cristae shape and number may be an effective strategy to prevent mitochondrial dysfunction stemming from calcium overload.Support or Funding InformationThis work was supported by NIH grant R00‐HL121160.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

The fitness cost and benefit of phase‐separated protein deposits

Phase separation of soluble proteins into insoluble deposits is associated with numerous diseases. However, protein deposits can also function as membrane‐less compartments for many cellular processes. What are the fitness costs and benefits of forming such deposits in different conditions? Using a model protein that phase‐separates into deposits, we distinguish and quantify the fitness contribution due to the loss or gain of protein function and deposit formation in yeast. The environmental condition and the cellular demand for the protein function emerge as key determinants of fitness. Protein deposit formation can influence cell‐to‐cell variation in free protein abundance between individuals of a cell population (i.e., gene expression noise). This results in variable manifestation of protein function and a continuous range of phenotypes in a cell population, favoring survival of some individuals in certain environments. Thus, protein deposit formation by phase separation might be a mechanism to sense protein concentration in cells and to generate phenotypic variability. The selectable phenotypic variability, previously described for prions, could be a general property of proteins that can form phase‐separated assemblies and may influence cell fitness.

Mitochondrial Biogenesis and Mitochondrial Reactive Oxygen Species (ROS): A Complex Relationship Regulated by the cAMP/PKA Signaling Pathway.

Mitochondrial biogenesis is a complex process. It requires the contribution of both the nuclear and the mitochondrial genomes and therefore cross talk between the nucleus and mitochondria. Cellular energy demand can vary by great length and it is now well known that one way to adjust adenosine triphosphate (ATP) synthesis to energy demand is through modulation of mitochondrial content in eukaryotes. The knowledge of actors and signals regulating mitochondrial biogenesis is thus of high importance. Here, we review the regulation of mitochondrial biogenesis both in yeast and in mammalian cells through mitochondrial reactive oxygen species.

Heterologous phosphoketolase expression redirects flux towards acetate, perturbs sugar phosphate pools and increases respiratory demand in Saccharomyces cerevisiae

IntroductionPhosphoketolases (Xfpk) are a non-native group of enzymes in yeast, which can be expressed in combination with other metabolic enzymes to positively influence the yield of acetyl-CoA derived products by reducing carbon losses in the form of CO2. In this study, a yeast strain expressing Xfpk from Bifidobacterium breve, which was previously found to have a growth defect and to increase acetate production, was characterized.ResultsXfpk-expression was found to increase respiration and reduce biomass yield during glucose consumption in batch and chemostat cultivations. By cultivating yeast with or without Xfpk in bioreactors at different pHs, we show that certain aspects of the negative growth effects coupled with Xfpk-expression are likely to be explained by proton decoupling. At low pH, this manifests as a reduction in biomass yield and growth rate in the ethanol phase. Secondly, we show that intracellular sugar phosphate pools are significantly altered in the Xfpk-expressing strain. In particular a decrease of the substrates xylulose-5-phosphate and fructose-6-phosphate was detected (26% and 74% of control levels) together with an increase of the products glyceraldehyde-3-phosphate and erythrose-4-phosphate (208% and 542% of control levels), clearly verifying in vivo Xfpk enzymatic activity. Lastly, RNAseq analysis shows that Xfpk expression increases transcription of genes related to the glyoxylate cycle, the TCA cycle and respiration, while expression of genes related to ethanol and acetate formation is reduced. The physiological and transcriptional changes clearly demonstrate that a heterologous phosphoketolase flux in combination with endogenous hydrolysis of acetyl-phosphate to acetate increases the cellular demand for acetate assimilation and respiratory ATP-generation, leading to carbon losses.ConclusionOur study shows that expression of Xfpk in yeast diverts a relatively small part of its glycolytic flux towards acetate formation, which has a significant impact on intracellular sugar phosphate levels and on cell energetics. The elevated acetate flux increases the ATP-requirement for ion homeostasis and need for respiratory assimilation, which leads to an increased production of CO2. A majority of the negative growth effects coupled to Xfpk expression could likely be counteracted by preventing acetate accumulation via direct channeling of acetyl-phosphate towards acetyl-CoA.

Metabolic signatures of cancer cells and stem cells.

In contrast to terminally differentiated cells, cancer cells and stem cells retain the ability to re-enter the cell cycle and proliferate. In order to proliferate, cells must increase the uptake and catabolism of nutrients to support anabolic cell growth. Intermediates of central metabolic pathways have emerged as key players that can influence cell differentiation 'decisions', processes relevant for both oncogenesis and normal development. Consequently, how cells rewire metabolic pathways to support proliferation may have profound consequences for cellular identity. Here, we discuss the metabolic programs that support proliferation and explore how metabolic states are intimately entwined with the cell fate decisions that characterize stem cells and cancer cells. By comparing the metabolism of pluripotent stem cells and cancer cells, we hope to illuminate common metabolic strategies as well as distinct metabolic features that may represent specialized adaptations to unique cellular demands.

Rodent Skeletal Muscle Metabolomic Changes Associated With Static Cold Storage

ObjectiveThe aim of this study was to evaluate the impact of static cold storage preservation on skeletal muscle metabolism using a rodent model. MethodsSixteen male Lewis rats (250 ± 25 g) were distributed into 4 groups, including naive control, warm ischemia for 2 hours, static warm storage for 6 hours, and static cold storage for 6 hours. Energy status, metabolomics profiling, and histopathology of the muscle were analyzed. ResultsIn the warm ischemia and static warm storage groups, glycolytic pathway metabolites decreased, but the Krebs cycle metabolite of succinate and the purine degradation product of hypoxanthine accumulated. Increased succinate and hypoxanthine levels were associated with increased injury severity scores. During static cold storage, the glycolytic pathway activity and the energy status were preserved. Succinate and hypoxanthine levels showed no significant difference from the naive group. ConclusionWarm ischemia results in reduced glycolysis and Krebs cycle metabolites. Static cold storage preserves the glycolytic pathway and represents a favorable contribution to cellular energy demand. Succinate and hypoxanthine might be used as novel potential biomarkers for the assessment of viability and injury severity.

Intricate Crosstalk Between Lipopolysaccharide, Phospholipid and Fatty Acid Metabolism in Escherichia coli Modulates Proteolysis of LpxC.

Lipopolysaccharides (LPS) in the outer membrane of Gram-negative bacteria provide the first line of defense against antibiotics and other harmful compounds. LPS biosynthesis critically depends on LpxC catalyzing the first committed enzyme in this process. In Escherichia coli, the cellular concentration of LpxC is adjusted in a growth rate-dependent manner by the FtsH protease making sure that LPS biosynthesis is coordinated with the cellular demand. As a result, LpxC is stable in fast-growing cells and prone to degradation in slow-growing cells. One of the factors involved in this process is the alarmone guanosine tetraphosphate (ppGpp) but previous studies suggested the involvement of yet unknown factors in LpxC degradation. We established a quantitative proteomics approach aiming at the identification of proteins that are associated with LpxC and/or FtsH at high or low growth rates. The identification of known LpxC and FtsH interactors validated our approach. A number of proteins involved in fatty acid biosynthesis and degradation, including the central regulator FadR, were found in the LpxC and/or FtsH interactomes. Another protein associated with LpxC and FtsH was WaaH, a LPS-modifying enzyme. When overproduced, several members of the LpxC/FtsH interactomes were able to modulate LpxC proteolysis. Our results go beyond the previously established link between LPS and phospholipid biosynthesis and uncover a far-reaching network that controls LPS production by involving multiple enzymes in fatty acid metabolism, phospholipid biosynthesis and LPS modification.

Modelling overflow metabolism in Escherichia coli with flux balance analysis incorporating differential proteomic efficiencies of energy pathways

BackgroundThe formation of acetate by fast-growing Escherichia coli (E. coli) is a commonly observed phenomenon, often referred to as overflow metabolism. Among various studies that have been carried over decades, a recent work (Basan, M. et al. Nature528, 99–104, 2015) suggested and validated that it is the differential proteomic efficiencies in energy biogenesis between fermentation and respiration that lead to the production of acetate at rapid growth conditions, as the consequence of optimally allocating the limited proteomic resource. In the current work, we attempt to incorporate this newly developed proteome allocation theory into flux balance analysis (FBA) to capture quantitatively the extent of overflow metabolism in different E. coli strains.ResultsA concise constraint was introduced into a FBA-based model with three proteomic cost parameters to represent constrained allocation of proteome over two energy (respiration and fermentation) pathways and biomass synthesis. Linear relationships were shown to exist between the three proteomic cost parameters. Tests with three different strains revealed that the proteomic cost of fermentation was consistently lower than that of respiration. A slow-growing strain appeared to have a higher proteomic cost for biomass synthesis than fast-growing strains. Different assumed levels of carbon flowing into pentose phosphate pathway affected the absolute value of model parameters, but had no qualitative impact on the comparative proteomic costs. For the prediction of biomass yield, significant errors that occurred for one of the tested strains (ML308) were rectified by adjusting the cellular energy demand according to literature data.ConclusionsWith the aid of a concise proteome allocation constraint, our FBA-based model is able to quantitatively predict the onset and extent of the overflow metabolism in various E. coli strains. Such prediction is enabled by three linearly-correlated (as opposed to uniquely determinable) proteomic cost parameters. The linear relationships between these parameters, when determined using data from cell culturing experiments, render biologically meaningful comparative proteomic costs between fermentation and respiration pathways and between the biomass synthesis sectors of slow- and fast-growing species. Simultaneous prediction of acetate production and biomass yield in the overflow region requires the use of reliable cellular energy demand data.

Ribosomal DNA instability and genome adaptability.

Ribosomes are large, multi-subunit ribonucleoprotein complexes, essential for protein synthesis. To meet the high cellular demand for ribosomes, all eukaryotes have numerous copies of ribosomal DNA (rDNA) genes that encode ribosomal RNA (rRNA), usually far in excess of the requirement for ribosome biogenesis. In all eukaryotes studied, rDNA genes are arranged in one or more clusters of tandem repeats localized to nucleoli. The tandem arrangement of repeats, combined with the high rates of transcription at the rDNA loci, and the difficulty of replicating repetitive sequences make the rDNA inherently unstable and particularly susceptible to large variations in repeat copy number. Despite mounting evidence suggesting extra-ribosomal functions of the rDNA, its repetitive nature has excluded it from traditional sequencing-based studies. However, more recently, several studies have revealed the unique potential of the rDNA to act as a "canary in the coalmine," being particularly sensitive to genomic stresses and acting as a source of adaptive response. Here, we review evidence uncovering mechanisms of regulation of instability and copy number variation at the rDNA and their role in adaptation to the environment, which could serve to understand the basic principles governing the behavior of other tandem repeats and their role in shaping the genome.

Mitochondrial Heterogeneity in Stem Cells.

Mitochondria are customarily acknowledged as the powerhouse of the cell by virtue of their indispensable role in cellular energy production. In addition, it plays an important role in pluripotency, differentiation, and reprogramming. This review describes variation in the stem cells and their mitochondrial heterogeneity. The mitochondrial variation can be described in terms of structure, function, and subcellular distribution. The mitochondria cristae development status and their localization patterns determine the oxygen consumption rate and ATP production which is a central controller of stem cell maintenance and differentiation. Generally, stem cells show spherical, immature mitochondria with perinuclear distribution. Such mitochondria are metabolically less energetic and low polarized. Moreover, mostly glycolytic energy production is found in pluripotent stem cells with a variation in naïve stem cells which perform oxidative phosphorylation (OXPHOS). This article also describes the structural and functional journey of mitochondria during development. Future insight into underlying mechanisms associated with such alternation in mitochondria of stem cells during embryonic stages could uncover mitochondrial adaptability on cellular demands. Moreover, investigating the importance of mitochondria in pluripotency maintenance might unravel the cause of mitochondrial diseases, aging, and regenerative therapies.

Structure and reactivity of a siderophore-interacting protein from the marine bacterium Shewanella reveals unanticipated functional versatility

Siderophores make iron accessible under iron-limited conditions and play a crucial role in the survival of microorganisms. Because of their remarkable metal-scavenging properties and ease in crossing cellular envelopes, siderophores hold great potential in biotechnological applications, raising the need for a deeper knowledge of the molecular mechanisms underpinning the siderophore pathway. Here, we report the structural and functional characterization of a siderophore-interacting protein from the marine bacterium Shewanella frigidimarina NCIBM400 (SfSIP). SfSIP is a flavin-containing ferric-siderophore reductase with FAD- and NAD(P)H-binding domains that have high homology with other characterized SIPs. However, we found here that it mechanistically departs from what has been described for this family of proteins. Unlike other FAD-containing SIPs, SfSIP did not discriminate between NADH and NADPH. Furthermore, SfSIP required the presence of the Fe2+-scavenger, ferrozine, to use NAD(P)H to drive the reduction of Shewanella-produced hydroxamate ferric-siderophores. Additionally, this is the first SIP reported that also uses a ferredoxin as electron donor, and in contrast to NAD(P)H, its utilization did not require the mediation of ferrozine, and electron transfer occurred at fast rates. Finally, FAD oxidation was thermodynamically coupled to deprotonation at physiological pH values, enhancing the solubility of ferrous iron. On the basis of these results and the location of the SfSIP gene downstream of a sequence for putative binding of aerobic respiration control protein A (ArcA), we propose that SfSIP contributes an additional layer of regulation that maintains cellular iron homeostasis according to environmental cues of oxygen availability and cellular iron demand.

Mitochondrial Populations Exhibit Differential Dynamic Responses to Increased Energy Demand during Exocytosis In Vivo

SummaryMitochondria are dynamic organelles undergoing fission, fusion, and translocation. These processes have been studied in cultured cells; however, little is known about their regulation in cells within tissues in vivo. We applied four-dimensional intravital microscopy to address this in secretory cells of the salivary gland. We found that mitochondria are organized in two populations: one juxtaposed to the basolateral plasma membrane and the other dispersed in the cytosol. Under basal conditions, central mitochondria exhibit microtubule-dependent motility and low fusion rate, whereas basolateral mitochondria are static and display high fusion rate. Increasing cellular energy demand by β-adrenergic stimulation of regulated exocytosis selectively enhanced motility and fusion of central mitochondria. Inhibition of microtubule polymerization led to inhibition of central mitochondrial motility and fusion and a marked reduction in exocytosis. This study reveals a conserved heterogeneity in mitochondrial positioning and dynamics in exocrine tissues that may have fundamental implications in organ pathophysiology.

Metabolite Transporters—The Gatekeepers for T Cell Metabolism

Abstract Metabolism is the fundamental biological process that drives the survival and death at both organismal and cellular level. It is also intimately involved in all cellular functions, proliferation, differentiation, and response to environmental cues and stress. During infection, successful immune response depends on the proper activation of various cell types. T cells are a key component of adaptive immunity. They remain metabolically quiescent before meeting their cognate antigens, however upon antigen encounter, these activated T cells have increased demands for energy and biological building blocks for differentiation, proliferation, and effector molecules production. These biosynthetic needs are met through metabolic reprogramming. Multilayered metabolite sensing machinery is in place to interact with the environment and coordinates the cellular metabolism with cell signaling and gene expression to meet the cellular demand in a timely manner. As most of the metabolites are cell membrane impermeable and require specialized membrane proteins to facilitate their translocation, metabolite transporters serve as gatekeepers and an important layer of regulation of metabolism in general. In this review, we discuss how key metabolite transporters are involved in T cell metabolism and shape T cell responses.

Glycogen metabolism and glycogen storage disorders.

Glucose is the main energy fuel for the human brain. Maintenance of glucose homeostasis is therefore, crucial to meet cellular energy demands in both - normal physiological states and during stress or increased demands. Glucose is stored as glycogen primarily in the liver and skeletal muscle with a small amount stored in the brain. Liver glycogen primarily maintains blood glucose levels, while skeletal muscle glycogen is utilized during high-intensity exertion, and brain glycogen is an emergency cerebral energy source. Glycogen and glucose transform into one another through glycogen synthesis and degradation pathways. Thus, enzymatic defects along these pathways are associated with altered glucose metabolism and breakdown leading to hypoglycemia ± hepatomegaly and or liver disease in hepatic forms of glycogen storage disorder (GSD) and skeletal ± cardiac myopathy, depending on the site of the enzyme defects. Overall, defects in glycogen metabolism mainly present as GSDs and are a heterogenous group of inborn errors of carbohydrate metabolism. In this article we review the genetics, epidemiology, clinical and metabolic findings of various types of GSD, and glycolysis defects emphasizing current treatment and implications for future directions.

Enhancing Cellular Performance Through Device-to-Device Distributed MIMO

The integration of local device-to-device (D2D) communications and cellular connections has been intensively studied to satisfy co-existing D2D and cellular communication demand. In future cellular networks, there will be numerous standby users possessing D2D communication capabilities in close proximity to each other. Considering that these standby users do not necessarily request D2D communications all the time, in this paper we propose a hybrid D2D-cellular scheme to make use of these standby users and to improve the rate performance for cellular users. More specifically, through D2D links, a virtual antenna array can be formed by sharing antennas across different terminals to realize the diversity gain of MIMO channels. This paper considers the use of millimeter wave links to enable high data rate D2D communications. We then design an orthogonal D2D multiple access protocol and formulate the optimization problem of joint cellular and D2D resource allocation for downlink transmissions using the proposed scheme. We obtain a closed-form solution for D2D resource allocation, which reveals useful insights for practical system design. Numerical results from extensive system-level simulations demonstrate that the rate performance of cellular users is significantly improved.

DeepTP: An End-to-End Neural Network for Mobile Cellular Traffic Prediction

The past 10 years have witnessed the rapid growth of global mobile cellular traffic demands due to the popularity of mobile devices. While accurate traffic prediction becomes extremely important for stable and high-quality Internet service, the performance of existing methods is still poor due to three challenges: complicated temporal variations including burstiness and long periods, multi-variant impact factors such as the point of interest and day of the week, and potential spatial dependencies introduced by the movement of population. While existing traditional methods fail in characterizing these features, especially the latter two, deep learning models with powerful representation ability give us a chance to consider these from a new perspective. In this article, we propose Deep Traffic Predictor (DeepTP), a deep-learning-based end-toend model, which forecasts traffic demands from spatial-dependent and long-period cellular traffic. DeepTP consists of two components: a general feature extractor for modeling spatial dependencies and encoding the external information, and a sequential module for modeling complicated temporal variations. In the general feature extractor, we introduce a correlation selection mechanism for a spatial modeling and embedding mechanism to encode external information. Moreover, we apply a seq2seq model with attention mechanism to build the sequential model. Extensive experiments based on large-scale mobile cellular traffic data demonstrate that our model outperforms the state-of-the-art traffic prediction models by more than 12.31 percent.

Genomic Copy-Number Loss Is Rescued by Self-Limiting Production of DNA Circles

Copy-number changes generate phenotypic variability in health and disease. Whether organisms protect against copy-number changes is largely unknown. Here, we show that Saccharomyces cerevisiae monitors the copy number of its ribosomal DNA (rDNA) and rapidly responds to copy-number loss with the clonal amplification of extrachromosomal rDNA circles (ERCs) from chromosomal repeats. ERC formation is replicative, separable from repeat loss, and reaches a dynamic steady state that responds to the addition of exogenous rDNA copies. ERC levels are also modulated by RNAPI activity and diet, suggesting that rDNA copy number is calibrated against the cellular demand for rRNA. Last, we show that ERCs reinsert into the genome in a dosage-dependent manner, indicating that they provide a reservoir for ultimately increasing rDNA array length. Our results reveal a DNA-based mechanism for rapidly restoring copy number in response to catastrophic gene loss that shares fundamental features with unscheduled copy-number amplifications in cancer cells.

Mitophagy-driven metabolic switch reprograms stem cell fate.

"Cellular reprogramming" facilitates the generation of desired cellular phenotype through the cell fate transition by affecting the mitochondrial dynamics and metabolic reshuffle in the embryonic and somatic stem cells. Interestingly, both the processes of differentiation and dedifferentiation witness a drastic and dynamic alteration in the morphology, number, distribution, and respiratory capacity of mitochondria, which are tightly regulated by the fission/fusion cycle, and mitochondrial clearance through autophagy following mitochondrial fission. Intriguingly, mitophagy is said to be essential in the differentiation of stem cells into various lineages such as erythrocytes, eye lenses, neurites, myotubes, and M1 macrophages. Mitophagy is also believed to play a central role in the dedifferentiation of a terminally differentiated cell into an induced pluripotent cell and in the acquisition of 'stemness' in cancer cells. Mitophagy-induced alteration in the mitochondrial dynamics facilitates metabolic shift, either into a glycolytic phenotype or into an OXPHOS phenotype, depending on the cellular demand. Mitophagy-induced rejuvenation of mitochondria regulates the transition of bioenergetics and metabolome, remodeling which facilitates an alteration in their cellular developmental capability. This review describes the detailed mechanism of the process of mitophagy and its association with cellular programming through alteration in the mitochondrial energetics. The metabolic shift post mitophagy is suggested to be a key factor in the cell fate transition during differentiation and dedifferentiation.