20.109(F09): Journal Club I: Difference between revisions

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As you prepare your talk be sure to follow the [[20.109(F09):Guidelines for oral presentations| specific guidelines for oral presentations]] in this class.
As you prepare your talk be sure to follow the [[20.109(F09):Guidelines for oral presentations| specific guidelines for oral presentations]] in this class.


*Please email your finished journal club presentation to 20.109.f09.pptsubmit AT gmail DOT com no later than 1 pm on the day of your presentation. The order in which your presentations are received will be the order of speakers.
*Please email your finished journal club presentation to [http://stellar.mit.edu/S/course/20/fa09/20.109/index.html the Stellar site] associated with our subject no later than 1 pm 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.
*Presentations will take place in room 16-336.


==Two Component Regulatory Systems==
==Two Component Regulatory Systems==
===Interesting Examples of Two Component Regulatory Systems===
# ''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]]<font color = blue>'''[AF/WF/Blue]''' </font color>
# ''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]]
# ''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]]
# ''Engineered single- and multi-cell chemotaxis pathways in E. coli.'' Goldberg SD, Derr P, DeGrado WF, Goulian M. '''Mol Syst Biol. 2009''';5:283. [[PMID: 19536206]] <font color = pink>'''[KK/WF/Pink]''' </font color>
#''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]] <font color = green>'''[TT/TR/Green]'''</font color>
#''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]] <font color = blue>'''[WM/TR/Blue]''' </font color>
#''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]]
#''EnvZ-OmpR interaction and osmoregulation in Escherichia coli.'' Cai SJ, Inouye M. '''J Biol Chem.''' 2002 Jul 5;277(27):24155-61. [[PMID: 11973328]]<font color = red>'''[SH/TR/red]''' </font color><font color = purple>'''[OA/WF/purple]''' </font color>
#''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]] <font color = purple>'''[PC/WF/Purple]''' </font color>
#''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]]<font color = blue>'''[KC/TR/Blue]''' </font color>
#''The three-component signalling system HbpS-SenS-SenR as an example of a redox sensing pathway in bacteria.''Ortiz de Orué Lucana D, Groves MR. '''Amino Acids.''' 2009 Mar 4. [[PMID: 19259771]]
#''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]]
#''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]]
#''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]]
# ''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]]
===Interesting Ways to Study Two Component Regulatory Systems===
# ''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]]
# ''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]]
# ''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]] <font color=red> '''[ML/WF/red]''' </font color>
# ''Genetic analysis of activation of the Vibrio cholerae Cpx pathway.'' Slamti L, Waldor MK. '''J Bacteriol.''' 2009 Aug;191(16):5044-56. [[PMID: 19542291]]
# ''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]] <font color = blue>'''[JK/WF/blue]'''</font color>
# ''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]]
#''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]]
#''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]] <font color = red> '''[AR/TR/red]'''</font color>
#''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]]
#''Information processing and signal integration in bacterial quorum sensing''Pankaj Mehta, Sidhartha Goyal, Tao Long, Bonnie L Bassler & Ned S Wingreen'''Molecular Systems Biology'''2009 5:325.[[doi:10.1038/msb.2009.79]]

Latest revision as of 07:38, 3 December 2009


20.109(F09): Laboratory Fundamentals of Biological Engineering

Home        People        Schedule Fall 2009        Assignments        Lab Basics        OWW Basics       
DNA Engineering        System Engineering        Biomaterials Engineering              

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 20.109.f09.talks AT gmail DOT com, 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!
  • The same paper may be presented by a T/R and a W/F student, but may only be presented once per 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 1 pm 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 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[AF/WF/Blue]
  2. 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
  3. 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
  4. Engineered single- and multi-cell chemotaxis pathways in E. coli. Goldberg SD, Derr P, DeGrado WF, Goulian M. Mol Syst Biol. 2009;5:283. PMID: 19536206 [KK/WF/Pink]
  5. 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 [TT/TR/Green]
  6. 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 [WM/TR/Blue]
  7. 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
  8. EnvZ-OmpR interaction and osmoregulation in Escherichia coli. Cai SJ, Inouye M. J Biol Chem. 2002 Jul 5;277(27):24155-61. PMID: 11973328[SH/TR/red] [OA/WF/purple]
  9. 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 [PC/WF/Purple]
  10. 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[KC/TR/Blue]
  11. The three-component signalling system HbpS-SenS-SenR as an example of a redox sensing pathway in bacteria.Ortiz de Orué Lucana D, Groves MR. Amino Acids. 2009 Mar 4. PMID: 19259771
  12. 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
  13. 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
  14. 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
  15. 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

Interesting Ways to Study Two Component Regulatory Systems

  1. 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
  2. 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
  3. 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 [ML/WF/red]
  4. Genetic analysis of activation of the Vibrio cholerae Cpx pathway. Slamti L, Waldor MK. J Bacteriol. 2009 Aug;191(16):5044-56. PMID: 19542291
  5. 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 [JK/WF/blue]
  6. 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
  7. 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
  8. 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 [AR/TR/red]
  9. 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
  10. 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
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