20.109(F14): Journal Club I

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20.109(F14): Laboratory Fundamentals of Biological Engineering

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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 MIT's E-journals site, called Vera, which offers online access to MIT's collection of journals. 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 1PM 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. Butanol tolerance regulated by a two-component response regulator Slr1037 in photosynthetic Synechocystis sp. PCC 6803. Chen L, Wu L, Wang J, Zhang W. Biotechnol Biofuels. 2014 Jun 11;7:89. PMID: 24932218
  2. The ColRS signal transduction system responds to the excess of external zinc, iron, manganese, and cadmium. Ainsaar K, Mumm K, Ilves H, Hõrak R. BMC Microbiol. 2014 Jun 20;14:162. PMID: 24946800
  3. Hierarchical management of carbon sources is regulated similarly by the CbrA/B system in Pseudomonas aeruginosa and Pseudomonas putida. Valentini M, Garcia-Mauriño SM, Pérez-Martinez I, Santero E, Canosa I, Lapouge K. Microbiology. 2014 Jul 16. pii: mic.0.078873-0. PMID: 25031426
  4. Modulation of cell wall synthesis and susceptibility to vancomycin by the two-component system AirSR in Staphylococcus aureus NCTC8325. Sun H, Yang Y, Xue T, Sun B. BMC Microbiol.' 2013 Dec 10;13:286. PMID: 24320748 [AL/TR/Tiger]
  5. 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
  6. 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
  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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  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 [JS/TR/Pink]
  19. 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
  20. 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 [MC/TR/Yellow]
  21. EnvZ-OmpR interaction and osmoregulation in Escherichia coli. Cai SJ, Inouye M. J Biol Chem. 2002 Jul 5;277(27):24155-61. PMID: 11973328
  22. 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

Interesting Ways to Study Two Component Regulatory Systems

  1. New insight into transmembrane topology of Staphylococcus aureus histidine kinase AgrC. Wang L, Quan C, Xiong W, Qu X, Fan S, Hu W. Biochim Biophys Acta. 2014 Mar;1838(3):988-93. PMID: 24361366
  2. Mutational analysis of dimeric linkers in peri- and cytoplasmic domains of histidine kinase DctB reveals their functional roles in signal transduction. Liu J, Yang J, Wen J, Yang Y, Wei X, Zhang X, Wang YP. Open Biol. 2014 Jun;4(6):140023. PMID: 24898140
  3. Stochastic simulation of prokaryotic two-component signalling indicates stochasticity-induced active-state locking and growth-rate dependent bistability. Wei K, Moinat M, Maarleveld TR, Bruggeman FJ. Mol Biosyst. 2014 Jul 29;10(9):2338-46. PMID: 24955938
  4. Cys-Scanning Disulfide Crosslinking and Bayesian Modeling Probe the Transmembrane Signaling Mechanism of the Histidine Kinase, PhoQ. Molnar KS, Bonomi M, Pellarin R, Clinthorne GD, Gonzalez G, Goldberg SD, Goulian M, Sali A, DeGrado WF. Structure. 2014 Jul 30. pii: S0969-2126(14)00204-4. PMID: 25087511
  5. Integrated proteomic and metabolomic characterization of a novel two-component response regulator Slr1909 involved in acid tolerance in Synechocystis sp. PCC 6803.Ren Q, Shi M, Chen L, Wang J, Zhang W. J Proteomics. 2014 Jul 3;109C:76-89. PMID: 24998436
  6. Spatial tethering of kinases to their substrates relaxes evolutionary constraints on specificity. Capra EJ, Perchuk BS, Ashenberg O, Seid CA, Snow HR, Skerker JM, Laub MT. Mol Microbiol. 2012 Dec;86(6):1393-403. PMID: 23078131 [KB/TR/Blue]
  7. 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
  8. 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
  9. 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
  10. (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
  11. 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
  12. 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 [KY/TR/Tiger]
  13. 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
  14. 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
  15. 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
  16. 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
  17. Genetic analysis of activation of the Vibrio cholerae Cpx pathway. Slamti L, Waldor MK. J Bacteriol. 2009 Aug;191(16):5044-56. PMID: 19542291
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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[AP/TR/Cherries]

Day Sign-up

Please put your name under the day you wish to present. There are up to 16 (TR) and 8 (WF) slots on each day. Slot location does not determine speaker order.

Slot Day 4 (T/R) Day 8 (T/R) Day 4 (W/F) Day 8 (W/F)
1 Jessica Deniz Laila
2 Michael Laura Gianmarco
3 Kyle Rebecca Camilo
4 Alyssa Victoria Bria
5 Jordan Katharina Ashley
6 Kathryn Melodi Taibo
7 Rafa
8 Xander Justin NA NA

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