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Bi 116 Microbial Genetics

MICROBIAL GENETICS

BI 116

Dianne K. Newman & Sarkis K. Mazmanian

TAs: Ana Moiseyenko & James Ousey

Winter Term 2019/2020

Tu, Th 1pm-2:30pm, 101 Kerckhoff

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Syllabus Final Proposal Details Download Coursereader
Syllabus Final Proposal Details Download Coursereader
Content

Week 1

Background Reading:
Beckwith, J.R., A. Galizzi, and G.R. Smith. 1985. The tools of bacterial genetics. In: Genetics of Bacteria, eds. J. Scaife, D. Leach, and A. Galizzi. Academic Press. Pp. 1-23Shuman, H.A., and T.J. Silhavy. 2003. The art and design of genetic screens: Escherichia coli. Nat. Rev. Genet. 4:419-431.
Papers:
1-1A: F. Jacob and E.L. Wollman, 1958, Genetic and physical determinations of chromosomal segments in Escherichia coli.

1-2A: F.H.C. Crick, L. Barnett, S. Brenner, and R.J. Watts-Tobin, 1961, General nature of the genetic code for proteins.

Week 2

Background Reading:
Luria & Delbrück: Jackpots and Epiphanies
Papers:
2-1A: S. Brenner, L. Barnett, F.H.C. Crick, and A. Orgel, 1961, The theory of mutagenesis.2-1B: J.A. Shapiro, 1969, Mutations caused by the insertion of genetic material into the galactose operon of Escherichia coli.

2-2A: S.E. Luria and M. Delbrück, 1943, Mutations of bacteria from virus sensitivity to virus resistant.2-2B: J. Cairns, J. Overbaugh and S. Miller, 1988, The origin of mutants.

Week 3

Background Reading:
Background: J. Beckwith, 2009, Genetic Suppressors and Recovery of Repressed Biochemical Memory.
Papers:
3-1A: J. Jarvik and D. Botstein, 1975, Conditional-lethal mutations that suppress genetic defects in morphogenesis by altering structural proteins.3-1B: K.L. Bieker and T.J. Silhavy, 1989, PrlA is important for the translocation of exported proteins across the cytoplasmic membrane of Escherichia coli.3-2A: A.B. Pardee, F. Jacob and J. Monod (PaJaMo paper), 1959, The genetic control and cytoplasmic expression of "inducibility" in the synthesis of -galactosidase by E. coli.3-2B: E. Englesberg et al., 1969, An analysis of "revertants" of a deletion mutant in the C gene of the L-arabinose gene complex in Escherichia coli B/r: isolation of initiator constitutive mutants (Ic)

Week 4

Background Reading:
Papers:
4-1A: M. Gottesman and M. Yarmolinksy, 1968, Integration-negative mutants of bacteriophage lambda4-1B: M. Silverman and M. Simon, 1980, Phase variation: genetic analysis of switching mutants4-2A: N. Kleckner, R. Chan, BK Tye, and D. Botstein, 1975, Mutagenesis by insertion of a drug-resistance element carrying an inverted repetition4-2B: V. Freeman, 1951, Studies on the virulence of bacteriophage-infected strains of Corynebacterium diphtheriae

Week 5

Background Reading:
S. Gottesman, 2019, Trouble is coming: Signaling pathways that regulate general stress response in bacteria

S. Finkel, 2006, Long-term survival during stationary phase: evolution and the GASP phenotype
Papers:
5-1A: R. Lange and R. Hengge-Aronis, 1991, Identification of a central regulator of stationary-phase gene expression in Escherichia coli.5-1B: B.M. TJ. Mescas et al., 1993, The activity of an Escherichia coli heat-inducible -factor, is modulated by expression of outer membrane proteins.

5-2A: M.M. Zambrano et al., 1993, Microbial competition: Escherichia coli mutants that take over stationary phase cultures.5-2B: S. Finkel and R. Kolter, 1999, Evolution of microbial diversity during prolonged starvation5-2C: E.R. Zinser and R. Kolter, 1999, Mutations enhancing amino acid catabolism confer a growth advantage in stationary phase

Week 6

Background Readings:
R. Losick and P. Stragier, 1992, Crisscross regulation of cell-type-specific gene expression during development in B. subtilis (Pdf)
Papers:
6-1A: J. Dworkin and R. Losick, 2005, Developmental commitment in a bacterium.6-1B: C.D. Webb et al., 1997, Bipolar Localization of the Replication Origin Regions of Chromosomes in Vegetative and Sporulating Cells of B. subtilis.6-2A: D. Oliver and J. Beckwith, 1982, Identification of a New Gene (secA) and Gene Product Involved in the Secretion of Envelope Proteins in Escherichia coli.6-2B: S.K. Mazmanian et al., 1999, Staphylococcus aureus Sortase, an Enzyme that Anchors Surface Proteins to the Cell Wall.

Week 7

Background Reading:
M.E. Davey and G.A.O'Toole (2000), Microbial Biofilms: from Ecology to Molecular Genetics, MMBR (Pdf)
Papers:
7-1A: M. Silverman and M. Simon, 1974, Flagellar rotation and the mechanism of bacterial motility.7-1B: J.S. Parkinson and S.R. Parker, 1979, Interaction of the cheC and cheZ gene products is required for chemotactic behavior in Escherichia coli.

7-2A: G.A. O'Toole and R. Kolter, 1998, Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development.7-2B: R.N. Esquivel and M. Pohlschroder, 2014, A conserved type IV pilin signal peptide H-domain is critical for the post-translational regulation of flagella-dependent motility

Week 8

Background Reading:
National Institutes of Health. A Conversation with 2013 Nobel Laureate Randy Schekman (Transcript)A.A. Salyers et al., 2000, Starting a New Genetic System: Lessons from Bacteroides, Methods, 20:35-46.

Papers:
8-1A: P. Novick, C. Field, R. Schekman, 1980, Identification of 23 Complementation Groups Required for Post-translational Events in the Yeast Secretory Pathway.8-1B: R.J. Deshaies and R. Schekman, 1987, A Yeast Mutant Defective at an Early Stage in Import of Secretory Protein Precursors into the Endoplasmic Reticulum.

8-2A: Abdul-Halim et al., 2019. Preprint. Lipid Anchoring of Archaeosort Substrates and Mid-Cell Growth in Haloarchaea.8-2B: W.W. Metcalf et al., 1997, A genetic system for Archaea of the genus Methanosarcina: liposome-mediated transformation and construction of shuttle vectors

Week 9

Background Reading:
D.K. Newman, V.J. Orphan, and A. Reysenbach, 2012. Chapter. Molecular Biology's Contributions to Geobiology. Fundamentals of Geobiology.

D.K. Newman and J.A. Gralnick, 2005. Chapter. What Genetics Offers Geobiology. Molecular Geomicrobiology.

R.E. Ley, D.A. Peterson, J.L. Gordon, 2006, Ecological and Evolutionary Forces Shaping Microbial Diversity in the Human Intestine. Review.
Papers:
9-1A: C.W. Saltikov et al., 2003, The ars detoxification system is advantageous but not required for As(V) respiration by the genetically tractable Shewanella species strain ANA-3.9-1B: C.W. Saltikov and D.K. Newman, 2003, Genetic identification of a respiratory arsenate reductase9-1C: D. Malasarn et al., 2004, arrA is a reliable marker for As(V) respiration.

9-2A: C. Lozupone and R. Knight, 2005, UniFrac: A New Phylogenetic Method for Comparing Microbial Communities.9-2B: Caporaso et al., 2010. QIIME allows analysis of high-throughput community sequencing data.9-2C: J. Qin et al., 2010. A Human Gut Microbial Gene Catalog Established by Metagenomic Sequencing. (Supplement)

Week 10

Background Reading:
M. Knox, 2014. Is the Gene-Editing Revolution Finally Here? Scientific American.
Papers:
10-1A: S.M. Lee et al., 2013, Bacterial Colonization Factors Control Specificity and Stability of the Gut Microbiota.10-1B: A.L. Goodman, 2009. Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat. (Supplement)10-2A: S. Moriano-Gutierrez et al., 2019, Critical Symbiont Signals Drive Both Local and Systemic Changes in Diel and Developmental Host Gene Expression. (Supplement)10-2B: L.A. Marraffini and E.J. Sontheimer, 2010, Self Versus Non-self Discrimination During CRISPR RNA-directed Immunity. (Supplement)