The DEAD-box RNA helicase CshA is required for fatty acid homeostasis in Staphylococcus aureus
Autoři:
Vanessa Khemici aff001; Julien Prados aff001; Bianca Petrignani aff001; Benjamin Di Nolfi aff001; Elodie Bergé aff001; Caroline Manzano aff001; Caroline Giraud aff001; Patrick Linder aff001
Působiště autorů:
Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
aff001
Vyšlo v časopise:
The DEAD-box RNA helicase CshA is required for fatty acid homeostasis in Staphylococcus aureus. PLoS Genet 16(7): e32767. doi:10.1371/journal.pgen.1008779
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pgen.1008779
Souhrn
Staphylococcus aureus is an opportunistic pathogen that can grow in a wide array of conditions: on abiotic surfaces, on the skin, in the nose, in planktonic or biofilm forms and can cause many type of infections. Consequently, S. aureus must be able to adapt rapidly to these changing growth conditions, an ability largely driven at the posttranscriptional level. RNA helicases of the DEAD-box family play an important part in this process. In particular, CshA, which is part of the degradosome, is required for the rapid turnover of certain mRNAs and its deletion results in cold-sensitivity. To understand the molecular basis of this phenotype, we conducted a large genetic screen isolating 82 independent suppressors of cold growth. Full genome sequencing revealed the fatty acid synthesis pathway affected in many suppressor strains. Consistent with that result, sublethal doses of triclosan, a FASII inhibitor, can partially restore growth of a cshA mutant in the cold. Overexpression of the genes involved in branched-chain fatty acid synthesis was also able to suppress the cold-sensitivity. Using gas chromatography analysis of fatty acids, we observed an imbalance of straight and branched-chain fatty acids in the cshA mutant, compared to the wild-type. This imbalance is compensated in the suppressor strains. Thus, we reveal for the first time that the cold sensitive growth phenotype of a DEAD-box mutant can be explained, at least partially, by an improper membrane composition. The defect correlates with an accumulation of the pyruvate dehydrogenase complex mRNA, which is inefficiently degraded in absence of CshA. We propose that the resulting accumulation of acetyl-CoA fuels straight-chained fatty acid production at the expense of the branched ones. Strikingly, addition of acetate into the medium mimics the cshA deletion phenotype, resulting in cold sensitivity suppressed by the mutations found in our genetic screen or by sublethal doses of triclosan.
Klíčová slova:
Fatty acids – Genetic screens – Operons – RNA extraction – RNA helicases – Staphylococcus aureus – Suppressor genes – DEAD-box
Zdroje
1. Redder P, Hausmann S, Khemici V, Yasrebi H, Linder P. Bacterial versatility requires DEAD-box RNA helicases. FEMS Microbiol Rev. 2015 May;39(3):392–412. doi: 10.1093/femsre/fuv011 25907111.
2. Sloan KE, Bohnsack MT. Unravelling the Mechanisms of RNA Helicase Regulation. Trends in biochemical sciences. 2018 Apr;43(4):237–50. doi: 10.1016/j.tibs.2018.02.001 29486979.
3. Lehnik-Habrink M, Rempeters L, Kovacs AT, Wrede C, Baierlein C, Krebber H, et al. DEAD-Box RNA helicases in Bacillus subtilis have multiple functions and act independently from each other. Journal of bacteriology. 2013 Feb;195(3):534–44. doi: 10.1128/JB.01475-12 23175651. Pubmed Central PMCID: 3554002.
4. Lehnik-Habrink M, Pfortner H, Rempeters L, Pietack N, Herzberg C, Stulke J. The RNA degradosome in Bacillus subtilis: identification of CshA as the major RNA helicase in the multiprotein complex. Molecular microbiology. 2010 Aug;77(4):958–71. doi: 10.1111/j.1365-2958.2010.07264.x 20572937.
5. Commichau FM, Rothe FM, Herzberg C, Wagner E, Hellwig D, Lehnik-Habrink M, et al. Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing. Molecular & cellular proteomics: MCP. 2009 Jun;8(6):1350–60. doi: 10.1074/mcp.M800546-MCP200 19193632. Pubmed Central PMCID: 2690492.
6. Roux CM, DeMuth JP, Dunman PM. Characterization of components of the Staphylococcus aureus mRNA degradosome holoenzyme-like complex. Journal of bacteriology. 2011 Oct;193(19):5520–6. doi: 10.1128/JB.05485-11 21764917. Pubmed Central PMCID: 3187390.
7. Tu Quoc PH, Genevaux P, Pajunen M, Savilahti H, Georgopoulos C, Schrenzel J, et al. Isolation and characterization of biofilm formation-defective mutants of Staphylococcus aureus. Infection and immunity. 2007 Mar;75(3):1079–88. doi: 10.1128/IAI.01143-06 17158901. Pubmed Central PMCID: 1828571.
8. Oun S, Redder P, Didier JP, Francois P, Corvaglia AR, Buttazzoni E, et al. The CshA DEAD-box RNA helicase is important for quorum sensing control in Staphylococcus aureus. RNA Biol. 2013 Jan;10(1):157–65. doi: 10.4161/rna.22899 23229022. Pubmed Central PMCID: 3590232.
9. Giraud C, Hausmann S, Lemeille S, Prados J, Redder P, Linder P. The C-terminal region of the RNA helicase CshA is required for the interaction with the degradosome and turnover of bulk RNA in the opportunistic pathogen Staphylococcus aureus. RNA Biol. 2015;12(6):658–74. doi: 10.1080/15476286.2015.1035505 25997461. Pubmed Central PMCID: 4615653.
10. Kim S, Corvaglia AR, Leo S, Cheung A, Francois P. Characterization of RNA Helicase CshA and Its Role in Protecting mRNAs and Small RNAs of Staphylococcus aureus Strain Newman. Infection and immunity. 2016 Jan 11;84(3):833–44. doi: 10.1128/IAI.01042-15 26755161. Pubmed Central PMCID: 4771345.
11. Armitano J, Redder P, Guimaraes VA, Linder P. An Essential Factor for High Mg2+ Tolerance of Staphylococcus aureus. Frontiers in microbiology. 2016;7:1888. doi: 10.3389/fmicb.2016.01888 27933050. Pubmed Central PMCID: 5122736.
12. Charollais J, Dreyfus M, Iost I. CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the biogenesis of 50S ribosomal subunit. Nucleic acids research. 2004;32(9):2751–9. doi: 10.1093/nar/gkh603 15148362. Pubmed Central PMCID: 419605.
13. Proux F, Dreyfus M, Iost I. Identification of the sites of action of SrmB, a DEAD-box RNA helicase involved in Escherichia coli ribosome assembly. Molecular microbiology. 2011 Oct;82(2):300–11. doi: 10.1111/j.1365-2958.2011.07779.x 21859437.
14. Kaneda T. Iso- and anteiso-fatty acids in bacteria: biosynthesis, function, and taxonomic significance. Microbiological reviews. 1991 Jun;55(2):288–302. 1886522. Pubmed Central PMCID: 372815.
15. Zhang YM, Rock CO. Membrane lipid homeostasis in bacteria. Nature reviews Microbiology. 2008 Mar;6(3):222–33. doi: 10.1038/nrmicro1839 18264115.
16. Chattopadhyay MK, Jagannadham MV. A branched chain fatty acid promotes cold adaptation in bacteria. Journal of biosciences. 2003 Jun;28(4):363–4. doi: 10.1007/BF02705110 12799482.
17. Patel MS, Nemeria NS, Furey W, Jordan F. The pyruvate dehydrogenase complexes: structure-based function and regulation. The Journal of biological chemistry. 2014 Jun 13;289(24):16615–23. doi: 10.1074/jbc.R114.563148 24798336. Pubmed Central PMCID: 4059105.
18. Parsons JB, Broussard TC, Bose JL, Rosch JW, Jackson P, Subramanian C, et al. Identification of a two-component fatty acid kinase responsible for host fatty acid incorporation by Staphylococcus aureus. Proc Natl Acad Sci U S A. 2014 Jul 22;111(29):10532–7. doi: 10.1073/pnas.1408797111 25002480. Pubmed Central PMCID: 4115530.
19. Oku H, Kaneda T. Biosynthesis of branched-chain fatty acids in Bacillus subtilis. A decarboxylase is essential for branched-chain fatty acid synthetase. The Journal of biological chemistry. 1988 Dec 5;263(34):18386–96. 3142877.
20. Singh VK, Hattangady DS, Giotis ES, Singh AK, Chamberlain NR, Stuart MK, et al. Insertional inactivation of branched-chain alpha-keto acid dehydrogenase in Staphylococcus aureus leads to decreased branched-chain membrane fatty acid content and increased susceptibility to certain stresses. Applied and environmental microbiology. 2008 Oct;74(19):5882–90. doi: 10.1128/AEM.00882-08 18689519. Pubmed Central PMCID: 2565972.
21. Albanesi D, de Mendoza D. FapR: From Control of Membrane Lipid Homeostasis to a Biotechnological Tool. Frontiers in molecular biosciences. 2016;3:64. doi: 10.3389/fmolb.2016.00064 27766255. Pubmed Central PMCID: 5052256.
22. Albanesi D, Reh G, Guerin ME, Schaeffer F, Debarbouille M, Buschiazzo A, et al. Structural basis for feed-forward transcriptional regulation of membrane lipid homeostasis in Staphylococcus aureus. PLoS pathogens. 2013 Jan;9(1):e1003108. doi: 10.1371/journal.ppat.1003108 23300457. Pubmed Central PMCID: 3536700.
23. Schujman GE, Paoletti L, Grossman AD, de Mendoza D. FapR, a bacterial transcription factor involved in global regulation of membrane lipid biosynthesis. Developmental cell. 2003 May;4(5):663–72. doi: 10.1016/s1534-5807(03)00123-0 12737802.
24. Satiaputra J, Shearwin KE, Booker GW, Polyak SW. Mechanisms of biotin-regulated gene expression in microbes. Synthetic and systems biotechnology. 2016 Mar;1(1):17–24. doi: 10.1016/j.synbio.2016.01.005 29062923. Pubmed Central PMCID: 5640590.
25. Larsen R, Buist G, Kuipers OP, Kok J. ArgR and AhrC are both required for regulation of arginine metabolism in Lactococcus lactis. Journal of bacteriology. 2004 Feb;186(4):1147–57. doi: 10.1128/jb.186.4.1147-1157.2004 14762010. Pubmed Central PMCID: 344216.
26. Sen S, Sirobhushanam S, Johnson SR, Song Y, Tefft R, Gatto C, et al. Growth-Environment Dependent Modulation of Staphylococcus aureus Branched-Chain to Straight-Chain Fatty Acid Ratio and Incorporation of Unsaturated Fatty Acids. PloS one. 2016;11(10):e0165300. doi: 10.1371/journal.pone.0165300 27788193. Pubmed Central PMCID: 5082858.
27. Parsons JB, Yao J, Jackson P, Frank M, Rock CO. Phosphatidylglycerol homeostasis in glycerol-phosphate auxotrophs of Staphylococcus aureus. BMC microbiology. 2013 Nov 16;13:260. doi: 10.1186/1471-2180-13-260 24238430. Pubmed Central PMCID: 3840577.
28. Qiu X, Choudhry AE, Janson CA, Grooms M, Daines RA, Lonsdale JT, et al. Crystal structure and substrate specificity of the beta-ketoacyl-acyl carrier protein synthase III (FabH) from Staphylococcus aureus. Protein science: a publication of the Protein Society. 2005 Aug;14(8):2087–94. doi: 10.1110/ps.051501605 15987898. Pubmed Central PMCID: 2279320.
29. Singh VK, Sirobhushanam S, Ring RP, Singh S, Gatto C, Wilkinson BJ. Roles of pyruvate dehydrogenase and branched-chain alpha-keto acid dehydrogenase in branched-chain membrane fatty acid levels and associated functions in Staphylococcus aureus. Journal of medical microbiology. 2018 Apr;67(4):570–8. doi: 10.1099/jmm.0.000707 29498620. Pubmed Central PMCID: 5982145.
30. Khemici V, Prados J, Linder P, Redder P. Decay-Initiating Endoribonucleolytic Cleavage by RNase Y Is Kept under Tight Control via Sequence Preference and Sub-cellular Localisation. PLoS Genet. 2015 Oct;11(10):e1005577. doi: 10.1371/journal.pgen.1005577 26473962. Pubmed Central PMCID: 4608709.
31. Tiwari KB, Gatto C, Wilkinson BJ. Interrelationships between Fatty Acid Composition, Staphyloxanthin Content, Fluidity, and Carbon Flow in the Staphylococcus aureus Membrane. Molecules. 2018 May 17;23(5). doi: 10.3390/molecules23051201 29772798. Pubmed Central PMCID: 6099573.
32. Braungardt H, Singh VK. Impact of Deficiencies in Branched-Chain Fatty Acids and Staphyloxanthin in Staphylococcus aureus. BioMed research international. 2019;2019:2603435. doi: 10.1155/2019/2603435 30805362. Pubmed Central PMCID: 6362504.
33. Weiss A, Ibarra JA, Paoletti J, Carroll RK, Shaw LN. The delta subunit of RNA polymerase guides promoter selectivity and virulence in Staphylococcus aureus. Infection and immunity. 2014 Apr;82(4):1424–35. doi: 10.1128/IAI.01508-14 24491578. Pubmed Central PMCID: 3993407.
34. Ericson ME, Subramanian C, Frank MW, Rock CO. Role of Fatty Acid Kinase in Cellular Lipid Homeostasis and SaeRS-Dependent Virulence Factor Expression in Staphylococcus aureus. mBio. 2017 Aug 1;8(4). doi: 10.1128/mBio.00988-17 28765222. Pubmed Central PMCID: 5539427.
35. DeMars Z, Bose JL. Redirection of Metabolism in Response to Fatty Acid Kinase in Staphylococcus aureus. Journal of bacteriology. 2018 Oct 1;200(19). doi: 10.1128/JB.00345-18 30012726. Pubmed Central PMCID: 6148474.
36. Percy MG, Grundling A. Lipoteichoic acid synthesis and function in gram-positive bacteria. Annual review of microbiology. 2014;68:81–100. doi: 10.1146/annurev-micro-091213-112949 24819367.
37. Schmaler M, Jann NJ, Gotz F, Landmann R. Staphylococcal lipoproteins and their role in bacterial survival in mice. International journal of medical microbiology: IJMM. 2010 Feb;300(2–3):155–60. doi: 10.1016/j.ijmm.2009.08.018 19805005.
38. Rosario-Cruz Z, Chahal HK, Mike LA, Skaar EP, Boyd JM. Bacillithiol has a role in Fe-S cluster biogenesis in Staphylococcus aureus. Molecular microbiology. 2015 Oct;98(2):218–42. doi: 10.1111/mmi.13115 26135358. Pubmed Central PMCID: 4705035.
39. Mashruwala AA, Pang YY, Rosario-Cruz Z, Chahal HK, Benson MA, Mike LA, et al. Nfu facilitates the maturation of iron-sulfur proteins and participates in virulence in Staphylococcus aureus. Molecular microbiology. 2015 Feb;95(3):383–409. doi: 10.1111/mmi.12860 25388433. Pubmed Central PMCID: 4428306.
40. Mashruwala AA, Roberts CA, Bhatt S, May KL, Carroll RK, Shaw LN, et al. Staphylococcus aureus SufT: an essential iron-sulphur cluster assembly factor in cells experiencing a high-demand for lipoic acid. Molecular microbiology. 2016 Dec;102(6):1099–119. doi: 10.1111/mmi.13539 27671355. Pubmed Central PMCID: 5161685.
41. Wilkinson KD, Williams CH Jr. NADH inhibition and NAD activation of Escherichia coli lipoamide dehydrogenase catalyzing the NADH-lipoamide reaction. The Journal of biological chemistry. 1981 Mar 10;256(5):2307–14. 7007381.
42. Altabe SG, Aguilar P, Caballero GM, de Mendoza D. The Bacillus subtilis acyl lipid desaturase is a delta5 desaturase. Journal of bacteriology. 2003 May;185(10):3228–31. doi: 10.1128/jb.185.10.3228-3231.2003 12730185. Pubmed Central PMCID: 154086.
43. Mansilla MC, de Mendoza D. The Bacillus subtilis desaturase: a model to understand phospholipid modification and temperature sensing. Archives of microbiology. 2005 May;183(4):229–35. doi: 10.1007/s00203-005-0759-8 15711796.
44. Redder P, Linder P. New range of vectors with a stringent 5-fluoroorotic acid-based counterselection system for generating mutants by allelic replacement in Staphylococcus aureus. Applied and environmental microbiology. 2012 Jun;78(11):3846–54. doi: 10.1128/AEM.00202-12 22447609. Pubmed Central PMCID: 3346405.
45. Simpson JT, Durbin R. Efficient de novo assembly of large genomes using compressed data structures. Genome research. 2012 Mar;22(3):549–56. doi: 10.1101/gr.126953.111 22156294. Pubmed Central PMCID: 3290790.
46. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv e-prints. 2013:arXiv:1303.3997.
47. Stead MB, Agrawal A, Bowden KE, Nasir R, Mohanty BK, Meagher RB, et al. RNAsnap: a rapid, quantitative and inexpensive, method for isolating total RNA from bacteria. Nucleic acids research. 2012 Nov 1;40(20):e156. doi: 10.1093/nar/gks680 22821568. Pubmed Central PMCID: 3488207.
48. Eleaume H, Jabbouri S. Comparison of two standardisation methods in real-time quantitative RT-PCR to follow Staphylococcus aureus genes expression during in vitro growth. Journal of microbiological methods. 2004 Dec;59(3):363–70. doi: 10.1016/j.mimet.2004.07.015 15488279.
Článek vyšel v časopise
PLOS Genetics
2020 Číslo 7
- Antibiotika na nachlazení nezabírají! Jak můžeme zpomalit šíření rezistence?
- FDA varuje před selfmonitoringem cukru pomocí chytrých hodinek. Jak je to v Česku?
- Prof. Jan Škrha: Metformin je bezpečný, ale je třeba jej bezpečně užívat a léčbu kontrolovat
- Ibuprofen jako alternativa antibiotik při léčbě infekcí močových cest
- Jak a kdy u celiakie začíná reakce na lepek? Možnou odpověď poodkryla čerstvá kanadská studie
Nejčtenější v tomto čísle
- Holocentric chromosomes
- Repression of tick microRNA-133 induces organic anion transporting polypeptide expression critical for Anaplasma phagocytophilum survival in the vector and transmission to the vertebrate host
- A FAS solution to a DEAD case
- Brassinosteroids regulate root meristem development by mediating BIN2-UPB1 module in Arabidopsis