Molecular and Cellular Biochemistry

, Volume 461, Issue 1–2, pp 23–36 | Cite as

Enforced lysosomal biogenesis rescues erythromycin- and clindamycin-induced mitochondria-mediated cell death in human cells

  • Paresh Prajapati
  • Pooja Dalwadi
  • Dhruv Gohel
  • Kritarth Singh
  • Lakshmi Sripada
  • Khyati Bhatelia
  • Bhavana Joshi
  • Milton Roy
  • Wang-Xia Wang
  • Joe E. Springer
  • Rochika SinghEmail author
  • Rajesh SinghEmail author


Antibiotics are the front-line treatment against many bacterial infectious diseases in human. The excessive and long-term use of antibiotics in human cause several side effects. It is important to understand the underlying molecular mechanisms of action of antibiotics in the host cell to avoid the side effects due to the prevalent uses. In the current study, we investigated the crosstalk between mitochondria and lysosomes in the presence of widely used antibiotics: erythromycin (ERM) and clindamycin (CLDM), which target the 50S subunit of bacterial ribosomes. We report here that both ERM and CLDM induced caspase activation and cell death in several different human cell lines. The activity of the mitochondrial respiratory chain was compromised in the presence of ERM and CLDM leading to bioenergetic crisis and generation of reactive oxygen species. Antibiotics treatment impaired autophagy flux and lysosome numbers, resulting in decreased removal of damaged mitochondria through mitophagy, hence accumulation of defective mitochondria. We further show that over-expression of transcription factor EB (TFEB) increased the lysosome number, restored mitochondrial function and rescued ERM- and CLDM-induced cell death. These studies indicate that antibiotics alter mitochondria and lysosome interactions leading to apoptotsis and may develop a novel approach for targeting inter-organelle crosstalk to limit deleterious antibiotic-induced side effects.


Antibiotics Side effects Mitochondria Lysosome Autophagy 



This work was supported by Department of Science and Technology, Govt. of India, Grant Number—SB/FT/LS-285/2012 to Rochika Singh. Authors acknowledge the instrumentation facility sponsored by Department of Biotechnology, Govt. of India under program support to Indian Institute of Advanced Research (IIAR) and instrumentation facility by DBT MSUB ILSPARE at The M. S. University of Baroda, Vadodara. Lakshmi Sripada and Kritarth Singh received Senior Research fellowship from University Grants Commission (UGC), Govt. of India. Khyati Bhatelia received their Senior Research fellowship from Council of Scientific and Industrial Research (CSIR), Govt. of India.

Supplementary material

11010_2019_3585_MOESM1_ESM.jpg (5.1 mb)
Supplementary material 1 (JPEG 5248 kb)
11010_2019_3585_MOESM2_ESM.jpg (1.7 mb)
Supplementary material 2 (JPEG 1743 kb)
11010_2019_3585_MOESM3_ESM.jpg (2.2 mb)
Supplementary material 3 (JPEG 2264 kb)
11010_2019_3585_MOESM4_ESM.jpg (8.8 mb)
Supplementary material 4 (JPEG 9054 kb)
11010_2019_3585_MOESM5_ESM.jpg (5.2 mb)
Supplementary material 5 (JPEG 5303 kb)
11010_2019_3585_MOESM6_ESM.jpg (4.3 mb)
Supplementary material 6 (JPEG 4433 kb)
11010_2019_3585_MOESM7_ESM.doc (45 kb)
Supplementary material 7 (DOC 45 kb)


  1. 1.
    Pacheu-Grau D, Gomez-Duran A, Lopez-Gallardo E, Pinos T, Andreu AL, Lopez-Perez MJ, Montoya J, Ruiz-Pesini E (2011) ‘Progress’ renders detrimental an ancient mitochondrial DNA genetic variant. Hum Mol Genet 20:4224–4231. CrossRefPubMedGoogle Scholar
  2. 2.
    Brummett RE, Fox KE (1989) Aminoglycoside-induced hearing loss in humans. Antimicrob Agents Chemother 33:797–800CrossRefGoogle Scholar
  3. 3.
    Mingeot-Leclercq MP, Tulkens PM (1999) Aminoglycosides: nephrotoxicity. Antimicrob Agents Chemother 43:1003–1012CrossRefGoogle Scholar
  4. 4.
    Khaliq Y, Zhanel GG (2003) Fluoroquinolone-associated tendinopathy: a critical review of the literature. Clin Infect Dis 36:1404–1410. CrossRefPubMedGoogle Scholar
  5. 5.
    Gray MW, Burger G, Lang BF (2001) The origin and early evolution of mitochondria. Genome Biol 2:REVIEWS1018CrossRefGoogle Scholar
  6. 6.
    Koc EC, Burkhart W, Blackburn K, Moyer MB, Schlatzer DM, Moseley A, Spremulli LL (2001) The large subunit of the mammalian mitochondrial ribosome. Analysis of the complement of ribosomal proteins present. J Biol Chem 276:43958–43969. CrossRefPubMedGoogle Scholar
  7. 7.
    Susin SA, Zamzami N, Kroemer G (1998) Mitochondria as regulators of apoptosis: doubt no more. Biochim Biophys Acta 1366:151–165CrossRefGoogle Scholar
  8. 8.
    Lartigue L, Faustin B (2013) Mitochondria: metabolic regulators of innate immune responses to pathogens and cell stress. Int J Biochem Cell Biol 45:2052–2056. CrossRefPubMedGoogle Scholar
  9. 9.
    Detmer SA, Chan DC (2007) Functions and dysfunctions of mitochondrial dynamics. Nat Rev Mol Cell Biol 8:870–879. CrossRefPubMedGoogle Scholar
  10. 10.
    Palikaras K, Lionaki E, Tavernarakis N (2015) Balancing mitochondrial biogenesis and mitophagy to maintain energy metabolism homeostasis. Cell Death Differ 22:1399–1401. CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Fernandez-Marcos PJ, Auwerx J (2011) Regulation of PGC-1alpha, a nodal regulator of mitochondrial biogenesis. Am J Clin Nutr 93:884S-90. CrossRefPubMedGoogle Scholar
  12. 12.
    Kim I, Rodriguez-Enriquez S, Lemasters JJ (2007) Selective degradation of mitochondria by mitophagy. Arch Biochem Biophys 462:245–253. CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Heo JM, Ordureau A, Paulo JA, Rinehart J, Harper JW (2015) The PINK1-PARKIN mitochondrial ubiquitylation pathway drives a program of OPTN/NDP52 recruitment and TBK1 activation to promote mitophagy. Mol Cell 60:7–20. CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Baixauli F, Acin-Perez R, Villarroya-Beltri C, Mazzeo C, Nunez-Andrade N, Gabande-Rodriguez E, Ledesma MD, Blazquez A, Martin MA, Falcon-Perez JM, Redondo JM, Enriquez JA, Mittelbrunn M (2015) Mitochondrial respiration controls lysosomal function during inflammatory T cell responses. Cell Metab 22:485–498. CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Settembre C, Zoncu R, Medina DL, Vetrini F, Erdin S, Erdin S, Huynh T, Ferron M, Karsenty G, Vellard MC, Facchinetti V, Sabatini DM, Ballabio A (2012) A lysosome-to-nucleus signalling mechanism senses and regulates the lysosome via mTOR and TFEB. EMBO J 31:1095–1108. CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Kabeya Y, Mizushima N, Ueno T, Yamamoto A, Kirisako T, Noda T, Kominami E, Ohsumi Y, Yoshimori T (2000) LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing. EMBO J 19:5720–5728. CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Pankiv S, Clausen TH, Lamark T, Brech A, Bruun JA, Outzen H, Overvatn A, Bjorkoy G, Johansen T (2007) p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy. J Biol Chem 282:24131–24145. CrossRefPubMedGoogle Scholar
  18. 18.
    Prajapati P, Sripada L, Singh K, Bhatelia K, Singh R, Singh R (2015) TNF-alpha regulates miRNA targeting mitochondrial complex-I and induces cell death in dopaminergic cells. Biochim Biophys Acta 1852:451–461. CrossRefPubMedGoogle Scholar
  19. 19.
    Singh K, Poteryakhina A, Zheltukhin A, Bhatelia K, Prajapati P, Sripada L, Tomar D, Singh R, Singh AK, Chumakov PM, Singh R (2015) NLRX1 acts as tumor suppressor by regulating TNF-alpha induced apoptosis and metabolism in cancer cells. Biochim Biophys Acta 1853:1073–1086. CrossRefPubMedGoogle Scholar
  20. 20.
    Khvorostov I, Zhang J, Teitell M (2008) Probing for mitochondrial complex activity in human embryonic stem cells. J Vis Exp. CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Yuki K, Miyauchi T, Kakinuma Y, Murakoshi N, Suzuki T, Hayashi J, Goto K, Yamaguchi I (2000) Mitochondrial dysfunction increases expression of endothelin-1 and induces apoptosis through caspase-3 activation in rat cardiomyocytes in vitro. J Cardiovasc Pharmacol 36:S205–S208CrossRefGoogle Scholar
  22. 22.
    Wojtala A, Bonora M, Malinska D, Pinton P, Duszynski J, Wieckowski MR (2014) Methods to monitor ROS production by fluorescence microscopy and fluorometry. Methods Enzymol 542:243–262. CrossRefPubMedGoogle Scholar
  23. 23.
    Wurstle ML, Laussmann MA, Rehm M (2012) The central role of initiator caspase-9 in apoptosis signal transduction and the regulation of its activation and activity on the apoptosome. Exp Cell Res 318:1213–1220. CrossRefPubMedGoogle Scholar
  24. 24.
    Parone PA, Da Cruz S, Tondera D, Mattenberger Y, James DI, Maechler P, Barja F, Martinou JC (2008) Preventing mitochondrial fission impairs mitochondrial function and leads to loss of mitochondrial DNA. PLoS ONE 3:e3257. CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Stowe DF, Camara AK (2009) Mitochondrial reactive oxygen species production in excitable cells: modulators of mitochondrial and cell function. Antioxid Redox Signal 11:1373–1414. CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Lenaz G, Fato R, Genova ML, Bergamini C, Bianchi C, Biondi A (2006) Mitochondrial complex I: structural and functional aspects. Biochim Biophys Acta 1757:1406–1420. CrossRefPubMedGoogle Scholar
  27. 27.
    Bleier L, Drose S (2013) Superoxide generation by complex III: from mechanistic rationales to functional consequences. Biochim Biophys Acta 1827:1320–1331. CrossRefPubMedGoogle Scholar
  28. 28.
    Laker RC, Xu P, Ryall KA, Sujkowski A, Kenwood BM, Chain KH, Zhang M, Royal MA, Hoehn KL, Driscoll M, Adler PN, Wessells RJ, Saucerman JJ, Yan Z (2014) A novel MitoTimer reporter gene for mitochondrial content, structure, stress, and damage in vivo. J Biol Chem 289:12005–12015. CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Hernandez G, Thornton C, Stotland A, Lui D, Sin J, Ramil J, Magee N, Andres A, Quarato G, Carreira RS, Sayen MR, Wolkowicz R, Gottlieb RA (2013) MitoTimer: a novel tool for monitoring mitochondrial turnover. Autophagy 9:1852–1861. CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Ashrafi G, Schwarz TL (2013) The pathways of mitophagy for quality control and clearance of mitochondria. Cell Death Differ 20:31–42. CrossRefPubMedGoogle Scholar
  31. 31.
    Tanida I, Ueno T, Kominami E (2008) LC3 and autophagy. Methods Mol Biol 445:77–88. CrossRefPubMedGoogle Scholar
  32. 32.
    Crider BP, Xie XS, Stone DK (1994) Bafilomycin inhibits proton flow through the H + channel of vacuolar proton pumps. J Biol Chem 269:17379–17381PubMedGoogle Scholar
  33. 33.
    Tomar D, Singh R, Singh AK, Pandya CD, Singh R (2012) TRIM13 regulates ER stress induced autophagy and clonogenic ability of the cells. Biochim Biophys Acta 1823:316–326. CrossRefPubMedGoogle Scholar
  34. 34.
    Zhou J, Tan SH, Nicolas V, Bauvy C, Yang ND, Zhang J, Xue Y, Codogno P, Shen HM (2013) Activation of lysosomal function in the course of autophagy via mTORC1 suppression and autophagosome-lysosome fusion. Cell Res 23:508–523. CrossRefPubMedPubMedCentralGoogle Scholar
  35. 35.
    Mizushima N, Yoshimori T, Levine B (2010) Methods in mammalian autophagy research. Cell 140:313–326. CrossRefPubMedPubMedCentralGoogle Scholar
  36. 36.
    Katsuragi Y, Ichimura Y, Komatsu M (2015) p62/SQSTM1 functions as a signaling hub and an autophagy adaptor. FEBS J 282:4672–4678. CrossRefPubMedGoogle Scholar
  37. 37.
    Johansen T, Lamark T (2011) Selective autophagy mediated by autophagic adapter proteins. Autophagy 7:279–296CrossRefGoogle Scholar
  38. 38.
    Youle RJ, van der Bliek AM (2012) Mitochondrial fission, fusion, and stress. Science 337:1062–1065. CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Chen H, Chan DC (2009) Mitochondrial dynamics–fusion, fission, movement, and mitophagy–in neurodegenerative diseases. Hum Mol Genet 18:R169–R176. CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Twig G, Shirihai OS (2011) The interplay between mitochondrial dynamics and mitophagy. Antioxid Redox Signal 14:1939–1951. CrossRefPubMedPubMedCentralGoogle Scholar
  41. 41.
    Allen GF, Toth R, James J, Ganley IG (2013) Loss of iron triggers PINK1/Parkin-independent mitophagy. EMBO Rep 14:1127–1135. CrossRefPubMedPubMedCentralGoogle Scholar
  42. 42.
    Settembre C, Di Malta C, Polito VA, Garcia Arencibia M, Vetrini F, Erdin S, Erdin SU, Huynh T, Medina D, Colella P, Sardiello M, Rubinsztein DC, Ballabio A (2011) TFEB links autophagy to lysosomal biogenesis. Science 332:1429–1433. CrossRefPubMedPubMedCentralGoogle Scholar
  43. 43.
    Ilarslan E, AydEn B, Kabatas EU, Beken S, Dilli D, Zenciroglu A, Okumus N (2014) Cataract in a preterm newborn: a possible side effect of linezolid therapy. J Coll Physicians Surg Pak 24(Suppl 3):S281–S283PubMedGoogle Scholar
  44. 44.
    Weintraub AS, Ferrara L, Deluca L, Moshier E, Green RS, Oakman E, Lee MJ, Rand L (2012) Antenatal antibiotic exposure in preterm infants with necrotizing enterocolitis. J Perinatol 32:705–709. CrossRefPubMedGoogle Scholar
  45. 45.
    Chandel NS, Budinger GR (2013) The good and the bad of antibiotics. Sci Transl Med 5:192fs25. CrossRefPubMedPubMedCentralGoogle Scholar
  46. 46.
    Kalghatgi S, Spina CS, Costello JC, Liesa M, Morones-Ramirez JR, Slomovic S, Molina A, Shirihai OS, Collins JJ (2013) Bactericidal antibiotics induce mitochondrial dysfunction and oxidative damage in Mammalian cells. Sci Transl Med 5:192ra85. CrossRefPubMedPubMedCentralGoogle Scholar
  47. 47.
    Lamb R, Ozsvari B, Lisanti CL, Tanowitz HB, Howell A, Martinez-Outschoorn UE, Sotgia F, Lisanti MP (2015) Antibiotics that target mitochondria effectively eradicate cancer stem cells, across multiple tumor types: treating cancer like an infectious disease. Oncotarget 6:4569–4584. CrossRefPubMedPubMedCentralGoogle Scholar
  48. 48.
    Jornayvaz FR, Shulman GI (2010) Regulation of mitochondrial biogenesis. Essays Biochem 47:69–84. CrossRefPubMedGoogle Scholar
  49. 49.
    Schulze H, Kolter T, Sandhoff K (2009) Principles of lysosomal membrane degradation: cellular topology and biochemistry of lysosomal lipid degradation. Biochim Biophys Acta 1793:674–683. CrossRefPubMedGoogle Scholar
  50. 50.
    Wong YC, Kim S, Peng W, Krainc D (2019) Regulation and function of mitochondria-lysosome membrane contact sites in cellular homeostasis. Trends Cell Biol 29:500–513. CrossRefPubMedGoogle Scholar
  51. 51.
    Demers-Lamarche J, Guillebaud G, Tlili M, Todkar K, Belanger N, Grondin M, Nguyen AP, Michel J, Germain M (2016) Loss of mitochondrial function impairs lysosomes. J Biol Chem 1:1. CrossRefGoogle Scholar
  52. 52.
    Sardiello M, Palmieri M, di Ronza A, Medina DL, Valenza M, Gennarino VA, Di Malta C, Donaudy F, Embrione V, Polishchuk RS, Banfi S, Parenti G, Cattaneo E, Ballabio A (2009) A gene network regulating lysosomal biogenesis and function. Science 325:473–477. CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Paresh Prajapati
    • 1
    • 3
    • 6
  • Pooja Dalwadi
    • 1
  • Dhruv Gohel
    • 1
  • Kritarth Singh
    • 1
  • Lakshmi Sripada
    • 1
  • Khyati Bhatelia
    • 1
  • Bhavana Joshi
    • 1
  • Milton Roy
    • 1
  • Wang-Xia Wang
    • 3
    • 4
    • 5
  • Joe E. Springer
    • 3
    • 6
  • Rochika Singh
    • 2
    Email author
  • Rajesh Singh
    • 1
    Email author
  1. 1.Department of Bio-Chemistry, Faculty of ScienceThe Maharaja Sayajirao University of BarodaVadodaraIndia
  2. 2.Department of Cell Biology, School of Biological Sciences and BiotechnologyIndian Institute of Advanced ResearchGandhinagarIndia
  3. 3.Spinal Cord and Brain Injury Research CenterUniversity of KentuckyLexingtonUSA
  4. 4.Sanders Brown Center on Aging CenterUniversity of KentuckyLexingtonUSA
  5. 5.Pathology & Laboratory MedicineUniversity of KentuckyLexingtonUSA
  6. 6.NeuroscienceUniversity of KentuckyLexingtonUSA

Personalised recommendations