1887

Microbiology Society logo

Volume 161, Issue 4

Degradation of SsrA-tagged proteins in streptococci Free

Abstract

In prokaryotes, a conserved small RNA molecule, called tmRNA, rescues ribosomes from proteins that are abnormally truncated due to the presence of rare codons or degraded mRNA. During the rescue process, a peptide tag (SsrA) encoded by tmRNA is cotranslationally added to the truncated polypeptides, thereby targeting these proteins for proteolytic degradation. In , ClpXP and ClpAP proteases primarily degrade SsrA-tagged proteins. Other proteases such as Lon and FtsH also participate in the degradation in . However, in , ClpXP is the major protease that degrades the SsrA-tagged proteins. Degradation of SsrA-tagged protein in streptococci is not well understood except that ClpXP is responsible for the majority of the degradation. Here we show that in , in addition to ClpXP, two other Clp complexes, ClpCP and ClpEP, are also involved in the degradation. We also found that ClpCP- and ClpEP-mediated proteolysis of SsrA-tagged substrates is induced by heat stress. As ClpCP and ClpEP proteins are highly conserved in streptococci, we predicted that ClpEP- and ClpCP-mediated degradation of SsrA-tagged proteins might be operational in other streptococci.

  • Received:
  • Accepted:
  • Published Online:
© 2015 The Authors
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.000048
2015-04-01
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/micro/161/4/884.html?itemId=/content/journal/micro/10.1099/mic.0.000048&mimeType=html&fmt=ahah

References

  1. Ahlawat S., Morrison D. A.(2009). ClpXP degrades SsrA-tagged proteins in Streptococcus pneumoniae. J Bacteriol 191, 2894–2898. [View Article][PubMed] [Google Scholar]
  2. Ajdić D., McShan W. M., McLaughlin R. E., Savić G., Chang J., Carson M. B., Primeaux C., Tian R., Kenton S. et al.(2002). Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen. Proc Natl Acad Sci U S A 99, 14434–14439. [View Article][PubMed] [Google Scholar]
  3. Andersson F. I., Blakytny R., Kirstein J., Turgay K., Bukau B., Mogk A., Clarke A. K.(2006). Cyanobacterial ClpC/HSP100 protein displays intrinsic chaperone activity. J Biol Chem 281, 5468–5475. [View Article][PubMed] [Google Scholar]
  4. Baba T., Ara T., Hasegawa M., Takai Y., Okumura Y., Baba M., Datsenko K. A., Tomita M., Wanner B. L., Mori H.(2006). Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2, 0008. [View Article][PubMed] [Google Scholar]
  5. Banerjee A., Biswas I.(2008). Markerless multiple-gene-deletion system for Streptococcus mutans. Appl Environ Microbiol 74, 2037–2042. [View Article][PubMed] [Google Scholar]
  6. Bewley M. C., Graziano V., Griffin K., Flanagan J. M.(2009). Turned on for degradation: ATPase-independent degradation by ClpP. J Struct Biol 165, 118–125. [View Article][PubMed] [Google Scholar]
  7. Biswas S., Biswas I.(2006). Regulation of the glucosyltransferase (gtfBC) operon by CovR in Streptococcus mutans. J Bacteriol 188, 988–998. [View Article][PubMed] [Google Scholar]
  8. Biswas I., Drake L., Johnson S., Thielen D.(2007). Unmarked gene modification in Streptococcus mutans by a cotransformation strategy with a thermosensitive plasmid. Biotechniques 42, 487–490. [View Article][PubMed] [Google Scholar]
  9. Biswas I., Jha J. K., Fromm N.(2008). Shuttle expression plasmids for genetic studies in Streptococcus mutans. Microbiology 154, 2275–2282. [View Article][PubMed] [Google Scholar]
  10. Boutry C., Wahl A., Delplace B., Clippe A., Fontaine L., Hols P.(2012). Adaptor protein MecA is a negative regulator of the expression of late competence genes in Streptococcus thermophilus. J Bacteriol 194, 1777–1788. [View Article][PubMed] [Google Scholar]
  11. Chatterjee I., Becker P., Grundmeier M., Bischoff M., Somerville G. A., Peters G., Sinha B., Harraghy N., Proctor R. A., Herrmann M.(2005). Staphylococcus aureus ClpC is required for stress resistance, aconitase activity, growth recovery, and death. J Bacteriol 187, 4488–4496. [View Article][PubMed] [Google Scholar]
  12. Chatterjee I., Schmitt S., Batzilla C. F., Engelmann S., Keller A., Ring M. W., Kautenburger R., Ziebuhr W., Hecker M. et al.(2009). Staphylococcus aureus ClpC ATPase is a late growth phase effector of metabolism and persistence. Proteomics 9, 1152–1176. [View Article][PubMed] [Google Scholar]
  13. Chatterjee I., Neumayer D., Herrmann M.(2010). Senescence of staphylococci: using functional genomics to unravel the roles of ClpC ATPase during late stationary phase. Int J Med Microbiol 300, 130–136. [View Article][PubMed] [Google Scholar]
  14. Choy J. S., Aung L. L., Karzai A. W.(2007). Lon protease degrades transfer-messenger RNA-tagged proteins. J Bacteriol 189, 6564–6571. [View Article][PubMed] [Google Scholar]
  15. Donegan N. P., Marvin J. S., Cheung A. L.(2014). Role of adaptor TrfA and ClpPC in controlling levels of SsrA-tagged proteins and antitoxins in Staphylococcus aureus. J Bacteriol 196, 4140–4151. [View Article][PubMed] [Google Scholar]
  16. Dunn A. K., Handelsman J.(1999). A vector for promoter trapping in Bacillus cereus. Gene 226, 297–305. [View Article][PubMed] [Google Scholar]
  17. Farrell C. M., Grossman A. D., Sauer R. T.(2005). Cytoplasmic degradation of ssrA-tagged proteins. Mol Microbiol 57, 1750–1761. [View Article][PubMed] [Google Scholar]
  18. Flynn J. M., Levchenko I., Seidel M., Wickner S. H., Sauer R. T., Baker T. A.(2001). Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis. Proc Natl Acad Sci U S A 98, 10584–10589. [View Article][PubMed] [Google Scholar]
  19. Frees D., Savijoki K., Varmanen P., Ingmer H.(2007). Clp ATPases and ClpP proteolytic complexes regulate vital biological processes in low GC, Gram-positive bacteria. Mol Microbiol 63, 1285–1295. [View Article][PubMed] [Google Scholar]
  20. Ge Z., Karzai A. W.(2009). Co-evolution of multipartite interactions between an extended tmRNA tag and a robust Lon protease in Mycoplasma. Mol Microbiol 74, 1083–1099. [View Article][PubMed] [Google Scholar]
  21. Gottesman S., Roche E., Zhou Y., Sauer R. T.(1998). The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system. Genes Dev 12, 1338–1347. [View Article][PubMed] [Google Scholar]
  22. Graham J. W., Lei M. G., Lee C. Y.(2013). Trapping and identification of cellular substrates of the Staphylococcus aureus ClpC chaperone. J Bacteriol 195, 4506–4516. [View Article][PubMed] [Google Scholar]
  23. Gribun A., Kimber M. S., Ching R., Sprangers R., Fiebig K. M., Houry W. A.(2005). The ClpP double ring tetradecameric protease exhibits plastic ring–ring interactions, and the N termini of its subunits form flexible loops that are essential for ClpXP and ClpAP complex formation. J Biol Chem 280, 16185–16196. [View Article][PubMed] [Google Scholar]
  24. Griffith K. L., Grossman A. D.(2008). Inducible protein degradation in Bacillus subtilis using heterologous peptide tags and adaptor proteins to target substrates to the protease ClpXP. Mol Microbiol 70, 1012–1025.[PubMed] [Google Scholar]
  25. Gur E., Sauer R. T.(2008). Evolution of the ssrA degradation tag in Mycoplasma: specificity switch to a different protease. Proc Natl Acad Sci U S A 105, 16113–16118. [View Article][PubMed] [Google Scholar]
  26. Herman C., Thévenet D., Bouloc P., Walker G. C., D’Ari R.(1998). Degradation of carboxy-terminal-tagged cytoplasmic proteins by the Escherichia coli protease HflB (FtsH). Genes Dev 12, 1348–1355. [View Article][PubMed] [Google Scholar]
  27. Hersch G. L., Baker T. A., Sauer R. T.(2004). SspB delivery of substrates for ClpXP proteolysis probed by the design of improved degradation tags. Proc Natl Acad Sci U S A 101, 12136–12141. [View Article][PubMed] [Google Scholar]
  28. Jennings L. D., Bohon J., Chance M. R., Licht S.(2008a). The ClpP N-terminus coordinates substrate access with protease active site reactivity. Biochemistry 47, 11031–11040. [View Article][PubMed] [Google Scholar]
  29. Jennings L. D., Lun D. S., Médard M., Licht S.(2008b). ClpP hydrolyzes a protein substrate processively in the absence of the ClpA ATPase: mechanistic studies of ATP-independent proteolysis. Biochemistry 47, 11536–11546. [View Article][PubMed] [Google Scholar]
  30. Karradt A., Sobanski J., Mattow J., Lockau W., Baier K.(2008). NblA, a key protein of phycobilisome degradation, interacts with ClpC, a HSP100 chaperone partner of a cyanobacterial Clp protease. J Biol Chem 283, 32394–32403. [View Article][PubMed] [Google Scholar]
  31. Keiler K. C., Waller P. R., Sauer R. T.(1996). Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science 271, 990–993. [View Article][PubMed] [Google Scholar]
  32. Kim Y. I., Burton R. E., Burton B. M., Sauer R. T., Baker T. A.(2000). Dynamics of substrate denaturation and translocation by the ClpXP degradation machine. Mol Cell 5, 639–648. [View Article][PubMed] [Google Scholar]
  33. Kim Y. I., Levchenko I., Fraczkowska K., Woodruff R. V., Sauer R. T., Baker T. A.(2001). Molecular determinants of complex formation between Clp/Hsp100 ATPases and the ClpP peptidase. Nat Struct Biol 8, 230–233. [View Article][PubMed] [Google Scholar]
  34. Kirstein J., Dougan D. A., Gerth U., Hecker M., Turgay K.(2007). The tyrosine kinase McsB is a regulated adaptor protein for ClpCP. EMBO J 26, 2061–2070. [View Article][PubMed] [Google Scholar]
  35. Kirstein J., Molière N., Dougan D. A., Turgay K.(2009). Adapting the machine: adaptor proteins for Hsp100/Clp and AAA+ proteases. Nat Rev Microbiol 7, 589–599. [View Article][PubMed] [Google Scholar]
  36. Levchenko I., Seidel M., Sauer R. T., Baker T. A.(2000). A specificity-enhancing factor for the ClpXP degradation machine. Science 289, 2354–2356. [View Article][PubMed] [Google Scholar]
  37. Lies M., Maurizi M. R.(2008). Turnover of endogenous SsrA-tagged proteins mediated by ATP-dependent proteases in Escherichia coli. J Biol Chem 283, 22918–22929. [View Article][PubMed] [Google Scholar]
  38. Maguin E., Prévost H., Ehrlich S. D., Gruss A.(1996). Efficient insertional mutagenesis in lactococci and other gram-positive bacteria. J Bacteriol 178, 931–935.[PubMed] [Google Scholar]
  39. Martin A., Baker T. A., Sauer R. T.(2007). Distinct static and dynamic interactions control ATPase-peptidase communication in a AAA+ protease. Mol Cell 27, 41–52. [View Article][PubMed] [Google Scholar]
  40. Maurizi M. R., Clark W. P., Kim S. H., Gottesman S.(1990). Clp P represents a unique family of serine proteases. J Biol Chem 265, 12546–12552.[PubMed] [Google Scholar]
  41. McGinness K. E., Baker T. A., Sauer R. T.(2006). Engineering controllable protein degradation. Mol Cell 22, 701–707. [View Article][PubMed] [Google Scholar]
  42. McGinness K. E., Bolon D. N., Kaganovich M., Baker T. A., Sauer R. T.(2007). Altered tethering of the SspB adaptor to the ClpXP protease causes changes in substrate delivery. J Biol Chem 282, 11465–11473. [View Article][PubMed] [Google Scholar]
  43. Mei Z., Wang F., Qi Y., Zhou Z., Hu Q., Li H., Wu J., Shi Y.(2009). Molecular determinants of MecA as a degradation tag for the ClpCP protease. J Biol Chem 284, 34366–34375. [View Article][PubMed] [Google Scholar]
  44. Miethke M., Hecker M., Gerth U.(2006). Involvement of Bacillus subtilis ClpE in CtsR degradation and protein quality control. J Bacteriol 188, 4610–4619. [View Article][PubMed] [Google Scholar]
  45. Nair S., Frehel C., Nguyen L., Escuyer V., Berche P.(1999). ClpE, a novel member of the HSP100 family, is involved in cell division and virulence of Listeria monocytogenes. Mol Microbiol 31, 185–196. [View Article][PubMed] [Google Scholar]
  46. Persuh M., Mandic-Mulec I., Dubnau D.(2002). A MecA paralog, YpbH, binds ClpC, affecting both competence and sporulation. J Bacteriol 184, 2310–2313. [View Article][PubMed] [Google Scholar]
  47. Que Y. A., Haefliger J. A., Francioli P., Moreillon P.(2000). Expression of Staphylococcus aureus clumping factor A in Lactococcus lactis subsp. cremoris using a new shuttle vector. Infect Immun 68, 3516–3522. [View Article][PubMed] [Google Scholar]
  48. Rouquette C., de Chastellier C., Nair S., Berche P.(1998). The ClpC ATPase of Listeria monocytogenes is a general stress protein required for virulence and promoting early bacterial escape from the phagosome of macrophages. Mol Microbiol 27, 1235–1245. [View Article][PubMed] [Google Scholar]
  49. Sauer R. T., Baker T. A.(2011). AAA+ proteases: ATP-fueled machines of protein destruction. Annu Rev Biochem 80, 587–612. [View Article][PubMed] [Google Scholar]
  50. Schlothauer T., Mogk A., Dougan D. A., Bukau B., Turgay K.(2003). MecA, an adaptor protein necessary for ClpC chaperone activity. Proc Natl Acad Sci U S A 100, 2306–2311. [View Article][PubMed] [Google Scholar]
  51. Spiers A., Lamb H. K., Cocklin S., Wheeler K. A., Budworth J., Dodds A. L., Pallen M. J., Maskell D. J., Charles I. G., Hawkins A. R.(2002). PDZ domains facilitate binding of high temperature requirement protease A (HtrA) and tail-specific protease (Tsp) to heterologous substrates through recognition of the small stable RNA A (ssrA)-encoded peptide. J Biol Chem 277, 39443–39449. [View Article][PubMed] [Google Scholar]
  52. Tao L., Chattoraj P., Biswas I.(2012). CtsR regulation in mcsAB-deficient Gram-positive bacteria. J Bacteriol 194, 1361–1368. [View Article][PubMed] [Google Scholar]
  53. Turgay K., Hahn J., Burghoorn J., Dubnau D.(1998). Competence in Bacillus subtilis is controlled by regulated proteolysis of a transcription factor. EMBO J 17, 6730–6738. [View Article][PubMed] [Google Scholar]
  54. Wang F., Mei Z., Qi Y., Yan C., Hu Q., Wang J., Shi Y.(2011). Structure and mechanism of the hexameric MecA–ClpC molecular machine. Nature 471, 331–335. [View Article][PubMed] [Google Scholar]
  55. Wiegert T., Schumann W.(2001). SsrA-mediated tagging in Bacillus subtilis. J Bacteriol 183, 3885–3889. [View Article][PubMed] [Google Scholar]
  56. Zhang J., Banerjee A., Biswas I.(2009a). Transcription of clpP is enhanced by a unique tandem repeat sequence in Streptococcus mutans. J Bacteriol 191, 1056–1065. [View Article][PubMed] [Google Scholar]
  57. Zhang Q., Xu S. X., Wang H., Xu W. C., Zhang X. M., Wu K. F., Liu L., Yin Y. B.(2009b). Contribution of ClpE to virulence of Streptococcus pneumoniae. Can J Microbiol 55, 1187–1194. [View Article][PubMed] [Google Scholar]
  58. Zwieb C., Gorodkin J., Knudsen B., Burks J., Wower J.(2003). tmRDB (tmRNA database). Nucleic Acids Res 31, 446–447. [View Article][PubMed] [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.000048
Loading
Degradation of SsrA-tagged proteins in streptococci
Microbiology 161, 884 (2015); https://doi.org/10.1099/mic.0.000048
/content/journal/micro/10.1099/mic.0.000048
/content/journal/micro/10.1099/mic.0.000048
Loading

Data & Media loading...

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error