20.109(F12): Journal Club I

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20.109(F12): Laboratory Fundamentals of Biological Engineering

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Contents

Focus: Two Component Signaling

Paper Options

The list of papers below is provided as a guideline for the types of papers that might be relevant for your presentation. You are not limited to the primary research articles on this list. The list is provided simply to give you an idea of the kinds of subjects that could make suitable presentations for the class. Search pubmed yourself to find articles of interest to you.

Note: If you have trouble accessing your article directly, go to http://libraries.mit.edu/vera, which is MIT's collection of journals online. Try selecting "exact title" from the search pulldown menu if the name of your journal is a common word such as Science. For older articles, you need to choose the JSTOR rather than Highwire interface.

Logistics of Paper Selection

  • Once you have decided on a paper for your presentation, please email it to skalford or astachow AT mit DOT edu (according to your lab section), and also "reserve" it by putting your (initials/lab section/team color) next to the listing here.
  • For visibility, please use the following format to sign up if possible, substituting in your own initials and team color: [ANS/WF/Purple]. Thanks!
  • A paper may be presented only once for each lab section.

As you prepare your talk be sure to follow the specific guidelines for oral presentations in this class.

  • Please email your finished journal club presentation to the Stellar site associated with our subject no later than 11 AM on the day of your presentation. The order in which your presentations are uploaded to Stellar will determine the order of speakers.
  • Presentations will take place in room 16-336.

Two Component Regulatory Systems

Interesting Examples of Two Component Regulatory Systems

  1. The QseC sensor kinase: a bacterial adrenergic receptorClarke MB, Hughes DT, Zhu C, Boedeker EC, Sperandio V. PNAS2006 Jul 5;103(27):10420-5. PMID: 16803956
  2. The auxiliary protein complex SaePQ activates the phosphatase activity of sensor kinase SaeS in the SaeRS two-component system of Staphylococcus aureusJeong DW, Cho H, Jones MB, Shatzkes K, Sun F, Ji Q, Liu Q, Peterson SN, He C, Bae T.Mol Microbiol2012 Aug 9. doi: 10.1111/j.1365-2958.2012.08198.x.PMID:22882143
  3. Two-Component Systems Are Involved in the Regulation of Botulinum Neurotoxin Synthesis in Clostridium botulinum Type A Strain HallConnan C, Brueggemann H, Mazuet C, Raffestin S, Cayet N, Popoff MR. PLoS One2012;7(7):e41848.PMID: 22848632
  4. Control of CydB and GltA1 expression by the SenX3 RegX3 two component regulatory system of Mycobacterium tuberculosis. Roberts G, Vadrevu IS, Madiraju MV, Parish T. PLoS One. 2011;6(6):e21090. PMID: 21698211
  5. The novel two-component regulatory system BfiSR regulates biofilm development directly through CafA by its control over the small RNA rsmZ.Petrova OE, Sauer K. J Bacteriol. 2010 Jul 23. PMID: 20656909 [CL/TR/Blue]
  6. CrdS and CrdA Comprise a Two-Component System That Is Cooperatively Regulated by the Che3 Chemosensory System in Myxococcus xanthus.Willett JW, Kirby JR.MBio. 2011 Aug 2;2(4). pii: e00110-11.PMID: 21810965
  7. The Two-Component Signal Transduction System CopRS of Corynebacterium glutamicum Is Required for Adaptation to Copper-Excess Stress.Schelder S, Zaade D, Litsanov B, Bott M, Brocker M.PLoS One. 2011;6(7):e22143.PMID: 21799779 [MT/WF/GREEN]
  8. The GacS/GacA signal transduction system of Pseudomonas aeruginosa acts exclusively through its control over the transcription of the RsmY and RsmZ regulatory small RNAs. Brencic A, McFarland KA, McManus HR, Castang S, Mogno I, Dove SL, Lory S. Mol Microbiol. 2009 Aug;73(3):434-45. PMID: 19602144
  9. OmpA influences Escherichia coli biofilm formation by repressing cellulose production through the CpxRA two-component system. Ma Q, Wood TK. Environ Microbiol. 2009 Jul 6. PMID: 19601955
  10. Kinetic buffering of cross talk between bacterial two-component sensors. Groban ES, Clarke EJ, Salis HM, Miller SM, Voigt CA. J Mol Biol. 2009 Jul 17;390(3):380-93. PMID: 19445950
  11. Mutations that alter the kinase and phosphatase activities of the two-component sensor EnvZ. Hsing W, Russo FD, Bernd KK, Silhavy TJ. J Bacteriol. 1998 Sep;180(17):4538-46. PMID: 9721293 [AN/TR/PURPLE]
  12. Cross-talk suppression between the CpxA-CpxR and EnvZ-OmpR two-component systems in E. coli. Siryaporn A, Goulian M. Mol Microbiol. 2008 Oct;70(2):494-506. PMID: 18761686
  13. Design and signaling mechanism of light-regulated histidine kinases. Möglich A, Ayers RA, Moffat K. J Mol Biol. 2009 Feb 6;385(5):1433-44. PMID: 19109976
  14. EnvZ-OmpR interaction and osmoregulation in Escherichia coli. Cai SJ, Inouye M. J Biol Chem. 2002 Jul 5;277(27):24155-61. PMID: 11973328 [SC/TR/RED]
  15. Cross-talk between an orphan response regulator and a noncognate histidine kinase in Streptomyces coelicolor. Wang W, Shu D, Chen L, Jiang W, Lu Y. FEMS Microbiol Lett. 2009 May;294(2):150-6. PMID: 19341396
  16. Histidine kinase and response regulator genes as they relate to salinity tolerance in rice. Karan R, Singla-Pareek SL, Pareek A. Funct Integr Genomics. 2009 Aug;9(3):411-7. PMID: 19277738
  17. Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm. Kyriakidis DA, Tiligada E. Amino Acids. 2009 Feb 8. PMID: 19198978
  18. A bifunctional kinase-phosphatase in bacterial chemotaxis. Porter SL, Roberts MA, Manning CS, Armitage JP. Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18531-6. PMID: 19020080
  19. Global transcriptional response of Lactobacillus reuteri to the sourdough environment.Hüfner E, Britton RA, Roos S, Jonsson H, Hertel C. Syst Appl Microbiol. 2008 Oct;31(5):323-38. PMID: 18762399
  20. Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA. Mandin P, Gottesman S. EMBO J. 2010 Aug 3. PMID: 20683441
  21. Characterization of a functional C-terminus of the Mycobacterium tuberculosis MtrA responsible for both DNA binding and interaction with its two-component partner protein, MtrB.Li Y, Zeng J, He ZG. J Biochem. 2010 Jul 29. PMID: 20671191

Interesting Ways to Study Two Component Regulatory Systems

  1. Adaptive Mutations that Prevent Crosstalk Enable the Expansion of Paralogous Signaling Protein FamiliesCapra EJ, Perchuk BS, Skerker JM, Laub MT.Cell2012 Jul 6;150(1):222-32.PMID: 22770222
  2. Two component systems: physiological effect of a third component Salvado B, Vilaprinyo E, Karathia H, Sorribas A, Alves R. PLoS One 2012;7(2):e31095 PMID: 22363555
  3. Intrinsic negative feedback governs activation surge in two-component regulatory systems Yeo WS, Zwir I, Huang HV, Shin D, Kato A, Groisman EA.Molecular Cell 2012 Feb 10;45(3):409-21.PMID: 22325356[AL/TR/YELLOW]
  4. (1)H, (13)C and (15)N resonance assignments of the C-terminal DNA-binding domain of RstA protein from Klebsiella pneumoniaeChen SC, Chang CF, Fan PJ, Cheng YH, Yu T, Huang TH.BioMol NMR Assign.2012 Apr 6 PMID: 22481468
  5. The transcriptional regulatory network of Corynebacterium jeikeium K411 and its interaction with metabolic routes contributing to human body odor formationBarzantny H, Schröder J, Strotmeier J, Fredrich E, Brune I, Tauch A. J Biotechnol2012 Jun 15;159(3):235-48 PMID: 22342369
  6. Investigation of the Staphylococcus aureus GraSR Regulon Reveals Novel Links to Virulence, Stress Response and Cell Wall Signal Transduction Pathways.Falord M, Mäder U, Hiron A, Débarbouillé M, Msadek T.PLoS One. 2011;6(7):e21323. PMID: 21765893
  7. Comparative Genomic and Phylogenetic Analyses Reveal the Evolution of the Core Two-Component Signal Transduction Systems in Enterobacteria.Qi M, Sun FJ, Caetano-Anollés G, Zhao Y.J Mol Evol. 2010 Jan 5.PMID: 20049425
  8. Expression, purification, crystallization and preliminary X-ray analysis of the DNA-binding domain of a Chlamydia trachomatis OmpR/PhoB-subfamily response regulator homolog, ChxR. Hickey JM, Hefty PS, Lamb AL. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Aug 1;65(Pt 8):791-4. PMID: 19652341
  9. Global Transcriptional Analysis of Acid-Inducible Genes in Streptococcus mutans: Multiple Two-Component Systems Involved in Acid Adaptation. Gong Y, Tian XL, Sutherland T, Sisson G, Mai J, Ling J, Li YH. Microbiology. 2009 Jul 16. PMID: 19608608
  10. Discovery of novel inhibitors of Streptococcus pneumoniae based on the virtual screening with the homology-modeled structure of histidine kinase (VicK). Li N, Wang F, Niu S, Cao J, Wu K, Li Y, Yin N, Zhang X, Zhu W, Yin Y. BMC Microbiol. 2009 Jun 27;9:129. PMID: 19558698
  11. Genetic analysis of activation of the Vibrio cholerae Cpx pathway. Slamti L, Waldor MK. J Bacteriol. 2009 Aug;191(16):5044-56. PMID: 19542291
  12. SpaK/SpaR two-component system characterized by a structure-driven domain-fusion method and in vitro phosphorylation studies. Chakicherla A, Ecale Zhou CL, Dang ML, Rodriguez V, Hansen JN, Zemla A. PLoS Comput Biol. 2009 Jun;5(6):e1000401. PMID: 19503843
  13. The GacS-GacA two-component regulatory system of Pseudomonas fluorescens: a bacterial two-hybrid analysis.Workentine ML, Chang L, Ceri H, Turner RJ. FEMS Microbiol Lett. 2009 Mar;292(1):50-6. PMID: 19191877
  14. Identification of direct residue contacts in protein-protein interaction by message passing.Weigt M, White RA, Szurmant H, Hoch JA, Hwa T. Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):67-72. PMID: 19116270 [CO/TR/GREEN]
  15. High stimulus unmasks positive feedback in an autoregulated bacterial signaling circuit.Miyashiro T, Goulian M. Proc Natl Acad Sci U S A. 2008 Nov 11;105(45):17457-62. PMID: 18987315 [MD/TR/Purple] [KK/WF/Blue]
  16. System-level mapping of Escherichia coli response regulator dimerization with FRET hybrids. Gao R, Tao Y, Stock AM. Mol Microbiol. 2008 Sep;69(6):1358-72. PMID: 18631241 [IS/WF/Blue]
  17. Information processing and signal integration in bacterial quorum sensingPankaj Mehta, Sidhartha Goyal, Tao Long, Bonnie L Bassler & Ned S WingreenMolecular Systems Biology2009 5:325.doi:10.1038/msb.2009.79
  18. Engineering key components in a synthetic eukaryotic signal transduction pathway Antunes MS, Morey KJ, Tewari-Singh N, Bowen TA, Smith JJ, Webb CT, Hellinga HW, Medford JI.Mol Syst Biol 2009;5:270. PMID: 19455134 [JY/TR/GREEN]
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