Download Course Outline - Molecular Genetics

MGY 434H1S
Lecture Topics
1. The Effect Second Generation Nucleotide Sequencing on Bacteriology Jan. 5, 2017
Review: van Dijk, E. L., Auger, H., Jaszczyszyn, Y., and Thermes, C. (2014) Ten years of next
generation sequencing. Trends in Genetics 30, 418-26.
Paper: Schlebusch, S. et al. (2016) - MALDI TOF MS meets WGS in a VRE outbreak
investigation Eur. J. Clin. Microbiol. Infect. Dis. DOI 10.1007/s10096-016-2824-4.
2. Bacterial Genomes and Metagenomes
Jan. 10, 2017
Review: Wang J, Jia H. (2016) Metagenome-wide association studies: fine-mining the
microbiome. Nat Rev Microbiol.14:508-22.
Paper: Ridaura, V. K. et al. (2013) Gut microbiota from twins discordant for obesity modulate
metabolism in mice. Science 341, 1241214.
3. CRISPR: Mechanism and Applications in Gene Editing
Jan. 12, 2017
Review: Peters JM, Silvis MR, Zhao D, Hawkins JS, Gross CA, Qi LS. (2015) Bacterial
CRISPR: accomplishments and prospects. Curr Opin Microbiol. 2015 Oct;27:121-6. doi:
10.1016/j.mib.2015.08.007.
Paper: Jinek, M., Chylinski, K., Fonfara, I., Hauer, M. Doudna, J.A., and Charpentier, E. (2012)
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
Science 337:816-21.
4. Microbiomes Jan. 17, 2017
Reviews: Interactions between the microbiota and pathogenic bacteria in the gut.
Bäumler AJ, Sperandio V. Nature. 2016 Jul 6;535(7610):85-93. doi: 10.1038/nature18849. Review.
PMID: 27383983
Science Special Issue June 8 2012
Paper: Thompson, J. A., Oliveira, R. A., Djukovic, A., Ubeda, C. & Xavier, K. B. (2015)
Manipulation of the quorum sensing signal AI-2 affects the antibiotic-treated gut microbiota.
Cell Rep. 10: 1861–1871.
5. Metabolomics Jan. 19, 2017
Review: Nicholson, J.K. et al. (2012) Host-Gut Microbiota Metabolic Interactions Science 336: 1262-7.
Paper: Vogt, S. L., Pena-Diaz, J. & Finlay, B. B. (2015) Chemical communication in the gut:
effects of microbiota-generated metabolites on gastrointestinal bacterial pathogens. Anaerobe 34:
106–115.
How Bacteria Sense their Environment and Respond to it
6. Two Component Systems
Jan. 24, 2017
Reviews: Zschiedrich, C.P., Keidel, V.and Szurmant, H. (2016) Molecular Mechanisms of Two
Component Signal Transduction J. Mol. Biol. (2016),
http://dx.doi.org/10.1016/j.jmb.2016.08.003.
Stock AM, Robinson VL, Goudreau PN. (2000). Two-component signal transduction. Annu. Rev.
Biochem. 69:183–215.
Paper: Tao, J., Li, C., Luo, C., and He, C. (2014) RavA/RavR two-component system regulates
Xanthomonas campestris pathogenesis and c-di-GMP turnover. FEMS Microbiol. Lett.
358(1):81-90.
7. Quorum Sensing
Jan. 26, 2017
Review: Papenfort, K., and Bassler, B.L. (2016) Quorum sensing signal-response systems in
Gram-negative bacteria. Nat Rev Microbiol. 14(9):576-88.
Paper: Kim, M., Ingremeau, F., Zhao, A., Bassler, B. L.& Stone, H. A. (2016) Local and global
consequences of flow on bacterial quorum sensing. Nat. Microbiol. 1, 15005.
8. sRNA’s
Jan. 31, 2017
Reviews: Michaux, C., Verneuil, N., Hartke, A., and Giard, J.C. (2014) Physiological roles of small RNA
molecules. Microbiology 160:1007-19.
Barquist,L. and Vogel, J. (2015) Accelerating Discovery and Functional Analysis of Small
RNAs with New Technologies Annu. Rev. Genet. 49: 367–94.
Paper: Papenfort, K., Forstner, K. U., Cong, J. P., Sharma, C. M. & Bassler, B. L. (2015)
Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of
biofilm formation. Proc. Natl Acad. Sci. USA 112: E766–E775.
Global Regulatory Pathways and Stress Responses
9. The SOS Response Feb 2, 2017
Review: Baharoglu1, Z. & Mazel, D. (2014) SOS, the formidable strategy of bacteria against
1
aggressions
FEMS Microbiol Rev. 2014 Nov;38(6):1126-45. doi:
10.1111/1574-6976.12077. Epub 2014 Jun 30.
Paper: Baharoglu Z, Krin E & Mazel D (2012) Transformation-induced SOS regulation and
carbon catabolite control of the V. cholerae integron integrase: connecting environment and
genome plasticity. J Bacteriol 194: 1659–1667
Midterm Test
10. Heat Shock
Feb 7 2017
Feb. 9, 2017
Review: Guo, M.S. and Gross, C.A. (2014) Stress-Induced Remodeling of the Bacterial Proteome
Current Biology 24: R424-34.
Paper: Guo, MS, Updegrove, TB, Gogol, EB, Shabalina, SA, Gross, CA, Storz , G. (2014) MicL, a new sE-
dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer
membrane lipoprotein Genes Dev. 28:1620-34. doi: 10.1101/gad.243485.114.
11. Responses to Reactive Oxygen Species
Feb. 14, 2017
Review: Dubbs, J.M., and Mongkolsuk, S. (2012) Peroxide-sensing Transcriptional Regulators in
Bacteria. J. Bacteriol., 194: 5495. DOI: 10.1128/JB.00304-12.
Paper: Diaz-Ochoa VE, Lam D, Lee CS, Klaus S, Behnsen J, Liu JZ, Chim N, Nuccio SP, Rathi SG,
Mastroianni JR, Edwards RA, Jacobo CM, Cerasi M, Battistoni A, Ouellette AJ, Goulding CW, Chazin
WJ, Skaar EP, Raffatellu M. Salmonella Mitigates Oxidative Stress and Thrives in the Inflamed Gut by
Evading Calprotectin-Mediated Manganese Sequestration. Cell Host Microbe. 2016 Jun 8;19(6):814-25.
doi: 10.1016/j.chom.2016.05.005. PMID: 27281571
12. cAMP and Catabolite Repression
Feb. 16, 2017
Review: Rabinowitz, J.D. and Silhavy, T.J. (2013) Metabolite turns master regulator. Nature
500: 283-4.
Paper: You, C. et al. (2013) Coordination of bacterial proteome with metabolism by cyclic AMP
signalling. Nature 500: 301-6.
Reading Week
Feb. 21-24, 2017
13. ppGpp and the Stringent Response
Feb. 28, 2017
Review: Hauriliuk, V. et al. (2015) Recent functional insights into the role of (p)ppGpp in
bacterial physiology. Nature Rev.|Microbiol. 13: 298-309.
14. SigmaS and the General Stress Response
March 2, 2017
Review: Schellhorn, H.E. (2014) Elucidating the function of the RpoS regulon.
Future Microbiol. 9: 497–507.
Paper: Baharoglu Z, Krin E & Mazel D (2013) RpoS plays a central role in the SOS induction
by sub-lethal aminoglycoside concentrations in Vibrio cholerae. PLoS Genet 9: e1003421.
Bacterial Lifestyles
15. Motility and Chemotaxis
March 7, 2017
Review: Islam, S. T. and Mignot, T. (2015) The mysterious nature of bacterial surface
(gliding) motility: A focal adhesion-based mechanism in Myxococcus xanthus Seminars
in Cell & Developmental Biology 46:143–154
Paper: Xu, L. et al. (2016) A cyclic di-GMP–binding adaptor protein interacts with a
chemotaxis methyltransferase to control flagellar motor switching Science Signaling 18 Oct
2016: Vol. 9, Issue 450, pp. ra102 DOI: 10.1126/scisignal.aaf7584
16. Type 3 Secretion Systems: The Weaponization of Motility
March 9, 2017
Review: How bacterial pathogens use type III and type IV secretion systems to facilitate their
transmission. Byndloss MX, Rivera-Chávez F, Tsolis RM, Bäumler AJ. Curr Opin Microbiol.
2016 Sep 9;35:1-7. doi: 10.1016/j.mib.2016.08.007. [Epub ahead of print] Review. PMID:
27621139
Paper: Shigella flexneri suppresses NF-κB activation by inhibiting linear ubiquitin chain
ligation. de Jong MF, Liu Z, Chen D, Alto NM. Nat Microbiol. 2016 May 27;1(7):16084. doi:
10.1038/nmicrobiol.2016.84. PMID: 27572974
17. Biofilms
March 14, 2017
Review: Flemming, H.-C., Wingender, J., Szewzyk, U., Steinberg, P., Rice, S. A. and
Kjelleberg, S. (2016) Biofilms, an Emergent Form of Bacterial Life. Nature Rev. Microbiol. 14:
563–575.
Paper: Desai, SK, Winardhi, RS, Periasamy, S, Dykas, MM, Jie, Y, Kenney, LJ. (2016)
The horizontally acquired response regulator SSrB drives the Salmonella lifestyle switch by
relieving biofilm silencing Elife Feb 2 e10747
18. c-di-GMP and Regulating the Motile vs Biofilm Lifestyle
March 16,2017
Review: Schirmer, T. and Jenal, U. (2009) Structural and mechanistic determinants of c-di-GMP
signaling. Nature Rev. Microbiol. 7: 724-35.
Paper: Roleofs, K. G. et al. (2015) Systematic Identification of Cyclic-di-GMP Binding Proteins
in Vibrio cholerae Reveals a Novel Class of Cyclic-di-GMP-Binding ATPases Associated with
Type II Secretion Systems. PLoS Pathog. 2015 Oct 27;11(10):e1005232. doi:
10.1371/journal.ppat.1005232. eCollection 2015.
Student Presentations
March 21, 23, 28, 30, April 5