Fall, 2009

Selected references for lectures not covered in the text. 

Lecture 11: Horizontal transfer of metabolic genes

Lawrence, J., and H. Hendrickson.  2003.  Lateral gene transfer: when will adolescence end?  Mol. Microbiol. 50:739-749.

Friedrich, M.W.  2002.  Phylogenetic analysis reveals multiple lateral transfers of adenosine-5 '-phosphosulfate reductase genes among sulfate-reducing microorganisms.  J. Bacteriol. 184: 278-289.

Springael, D. et al.  2002.  Community shifts in a seeded 3-chlorobenzoate degrading membrane biofilm reactor: indications for involvement of in situ horizontal transfer of the clc-element from inoculum to contaminant bacteria.  Environ. Microbiol. 4:70-80.

Boucher, Y., H. Huber, S. L'Haridon, K.O. Stetter, and W.F. Doolittle.  2001.  Bacterial origin for the isoprenoid biosynthesis enzyme HMG-CoA reductase of the archaeal orders Thermoplasmatales and Archaeoglobales.  Molec. Biol. Evol. 18: 1378-1388.

Ramírez-Arcos, S., L.A. Fernández-Herrero, I. Marín, and J. Berenguer.  1998.  Anaerobic growth, a property horizontally transferred by an Hfr-like mechanism among extreme thermophiles.  J. Bacteriol. 180:3137-3143.

Lecture 18:  Suicide phage

Westers, H., R. Dorenbos, J.M. van Dijl, J. Kabel, T. Flanagan, K.M. Devine, F. Jude, S.J. Séror, A.C. Beekman, E. Darmon, C. Eschevins, A. de Jong, S. Bron, O.P. Kuipers, A.M. Albertini, H. Antelmann, M. Hecker, N. Zamboni, U. Sauer, C. Bruand, D.S. Ehrlich, J.C. Alonso, M. Salas, and W.J. Quax.  2003.  Genome engineering reveals large dispensable regions in Bacillus subtilis.  Mol. Biol. Evol. 20:2076-2090.

Krogh, S., S.T. Jorgensen, and K.M. Devine.  1998. Lysis genes of the Bacillus subtilis defective prophage PBSX.  J. Bacteriol. 180:2110-2117.

Krogh, S., M. O'Reilly, N. Nolan, and K.M. Devine.  1996.  The phage-like element PBSX and part of the skin element, which are resident at different locations on the Bacillus subtilis chromosome, are highly homologous.  Microbiology 142:2031-2040.

McKonnell, G.E., H. Wood, K.M. Devine, and D.J. McConnell. 1994. Genetic control of bacterial suicide: regulation of the induction of PBSX in Bacillus subtilis. J. Bacteriol. 176:5820-5830.

Anderson, L.M., and K.F. Bott.  1985.  DNA packaging by the Bacillus subtilis defective bacteriophage PBSX.  J. Virol. 54:773-780.

Lecture 19:  Phage-encoded bacterial toxins

Davis, B.M., M.K. Waldor. 2003. Filamentous phages linked to virulence of Vibrio cholerae. Curr. Opin. Microbiol. 6:35-42.

Wagner, P.L., J. Livny, M.N. Neely, D.W.K. Acheson, D.I. Friedman, and M.K. Waldor.  2002.  Bacteriophage control of Shiga toxin 1 production and release by Escherichia coli.  Mol. Microbiol. 44:957-970.

Lecture 22:  Integrons, Mobile Gene Cassettes, Pathogenicity Islands

Fluit, A.C., and F.-J. Schmitz.  2004.  Resistance integrons and super-integrons.  Clin. Microbiol. Infect. 10:272-288.

Rowe-Magnus, D.A., A.-M. Guerout, and D. Mazel.  2002  Bacterial resistance evolution by recruitment of super-integron gene cassettes.  Molec. Microbiol. 43:1657-1669.

Vaisvila, R., R.D. Morgan, J. Posfai, and E.A. Raleigh.  2001.  Discovery and distribution of super-integrons among Pseudomonads.  Molec. Microbiol. 42:587-601.

Hall, R.M., and C.M. Collis. 1995. Mobile gene cassettes and integrons: capture and spread of genes by site-specific recombination. Mol. Microbiol. 15:593-600.

Schmidt, H., and M. Hensel.  2004.  Pathogenicity islands in bacterial pathogenesis.  Clin. Microbiol. Rev. 17:14-56.

Tauschek, M., R.A. Strugnell, and R.M. Robins-Browne.  2002.  Characterization and evidence of mobilization of the LEE pathogenicity island of rabbit-specific strains of enteropathogenic Escherichia coli.  Molec. Microbiol. 44:1533-1550.

Hentschel, U., and J. Hacker.  2001.  Pathogenicity islands: the tip of the iceberg.  Microbes Infect. 3:545-548.

Franken, C., G. Haase, C. Brandt, J. Weber-Heynemann, S. Martin, C. Lammler, A. Podbielski, R. Lutticken, and B. Spellerberg.  2001.  Horizontal gene transfer and host specificity of beta-haemolytic streptococci: the role of a putative composite transposon containing scpB and lmb.  Molec. Microbiol. 41:925-935.

Brown, J.S., S.M. Gilliland, and D.W. Holden.  2001.  A Streptococcus pneumoniae pathogenicity island encoding an ABC transporter involved in iron uptake and virulence.  Molec. Microbiol. 40:572-585.

Lecture 27:  Quroum Sensing: Bacterial luminescence

Xavier, K.B., and B.L. Bassler.  2003.  LuxS quorum sensing: more than just a numbers game.  Curr. Opin. Microbiol. 6:191-197.

Czyz, A., K. Plata, and G. Wegrzyn.  2003.  Stimulation of DNA repair as an evolutionary drive for bacterial luminescence.  Luminescence 18:140-144.

Choi, S.H., and M.B. Gu.  2002.  A portable toxicity biosensor using freeze-dried recombinant bioluminescent bacteria.  Biosens. Bioelectron. 17: 433-440.

Coulthurst, S.J., N.A. Whitehead, M. Welch, and G.P.C. Salmond.  2002.  Can boron get bacteria talking?  Trends Biochem. Sci. 27: 217-219.

Visick, K.L., J. Foster, J. Doino, M. McFall-Ngai, and E.G. Ruby.  2000.  Vibrio fischeri lux genes play an important role in colonization and development of the host light organ.  J. Bacteriol. 182:4578-4586.

Sitnikov, D.M., J.B. Schineller, and T.O. Baldwin. 1995. Transcriptional regulation of bioluminescence genes from Vibrio fischeri. Mol. Microbiol. 17:801-812.

Lecture 31-33:  Small RNA

Gottesman. 2004. Annu. Rev. Microbiol. 58:303-328.
Storz et al. 2004. Curr. Opin. Microbiol. 7:140-144.
Winkler and Breaker. 2005. Annu. Rev. Microbiol. 59:487-517.

Lecture 34: Plasmid addiction

Deane, S.M., and D.E. Rawlings.  2004.  Plasmid evolution and interaction between the plasmid addiction stability systems of two related broad-host-range IncQ-like plasmids.  J. Bacteriol. 186:2123-2133.

Cooper T.F., and J.A. Heinemann.  2000.  Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids.  Proc. Natl. Acad. Sci. USA 97: 12643-12648.

Smith, A.S.G., and D.E. Rawlings.  1997.  The poison-antidote stability system of the broad-host-range Thiobacillus ferrooxidans plasmid pTF-FC2.  Molec. Microbiol. 26:961-970.

Magnuson, R., H. Lehnherr, G. Mukhopadhyay, and M.B. Yarmolinsky. 1996. Autoregulation of the plasmid addiction operon of bacteriophage P1. J. Biol. Chem. 271:18705-18710.

Lecture 35:  Programmed Cell Death in Bacteria

Rice, K.C., and K.W. Bayles.  2003.  Death's toolbox: examining the molecular components of bacterial programmed cell death.  Mol. Microbiol. 50:729-738.

Sat, B., R. Hazan, T. Fisher, H. Khaner, G. Glaser, and H. Engelberg-Kulka.  2001.  Programmed cell death in Escherichia coli: Some antibiotics can trigger mazEF lethality.  J. Bacteriol. 183: 2041-2045.

Lewis, K. 2000. Programmed death in bacteria. Microbiol. Mol. Biol. Rev. 64:503-514.

Engelberg-Kulka, H., and G. Glaser.  1999.  Addiction modules and programmed cell death and antideath in bacterial cultures.  Ann. Rev. Microbiol. 53: 43-70.

Aizenman, E., H. Engelberg-Kulka, and G. Glaser.  1996.  An Escherichia coli chromosomal "addiction module" regulated by 3',5'-bispyrophosphate: A model for programmed bacterial cell death.  Proc. Natl. Acad. Sci. USA 93:6059-6063.

Lecture 36:  Antibiotic Resistance: The new apocalypse?

Hall, B.G.  2004.  Predicting the evolution of antibiotic resistance genes.  Nature Rev. Microbiol. 2:430-435.

Drusano, G.L.  2004.  Antimicrobial pharmacodynamics: critical interactions of 'bug and drug.'  Nature Rev. Microbiol. 2:289-300.

Wegener, H.C.  2003.  Antibiotics in animal feed and their role in resistance development.  Curr. Opin. Microbiol. 6:439-445.

Séveno, N.A., D. Kallifidas, K. Smalla, J.D. van Elsas, J.-M. Collard, A.D. Karagouni, and E.M. Wellington.  2002.  Occurrence and reservoirs of antibiotic resistance genes in the environment. Rev. Med. Microbiol. 13:15-27.

Kariuki, S., and C.A. Hart.  2001.  Global aspects of antimicrobial-resistant enteric bacteria.  Curr. Opin. Infect. Dis. 14:579-586.

Putman, M., H.W. van Veen, and W.N. Konings. 2000. Molecular properties of bacterial multidrug transporters.  Microbiol. Mol. Biol. Rev. 64:672-693.

Ash, C.  1996.  Antibiotic resistance: the new apocalypse?  Trends Microbiol. 4:371-372.

Lecture 37:  Reading the 'Text' of a Bacterial Genome:  Annotation and computer access

Daubin, V., and H. Ochman.  2004.  Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. Genome Res. 14:1036-1042.

Ochman, H., and S.R. Santos.  2003.  Eyeing bacterial genomes.  Curr. Opin. Microbiol. 6:109-113.

Enault, F., K. Suhre, C. Abergel, O. Poirot, and J.M. Claverie.  2003.  Annotation of bacterial genomes using improved phylogenomic profiles.  Bioinformatics 19 Suppl 1:105-107.

Ermolaeva, M.D., O. White, and S.L. Salzberg.  2001.  Prediction of operons in microbial genomes. Nucl. Acids Res. 29:1216-1221.

Delcher, A.L. , D. Harmon, S. Kasif, O. White, and S.L. Salzberg.  1999.  Improved microbial gene identification with GLIMMER.  Nucl. Acids Res. 27:4636-4641.

Lecture 38:  Microarrays:  Tracking the metabolic ringleaders

Hinton, J.C.D., I. Hautefort, S. Eriksson, A. Thompson, and M. Rhen.  2004.  Benefits and pitfalls of using microarrays to monitor bacterial gene expression during infection.  Curr. Opin. Microbiol. 7:277-282.

Rhodius, V.A., and R.A. LaRossa.  2003.  Uses and pitfalls of microarrays for studying transcriptional regulation.  Curr. Opin. Microbiol. 6:114-119.

Conway, T., and G.K. Schoolnik.  2003.  Microarray expression profiling: capturing a genome-wide portrait of the transcriptome.  Mol. Microbiol. 47:879-889.

Zhou, J.  2003.  Microarrays for bacterial detection and microbial community analysis.  Curr. Opin. Microbiol. 6:288-294.

Hatfield, G.W., S. Hung, and P. Baldi.  2003.  Differential analysis of DNA microarray gene expression data.  Mol. Microbiol. 47:871-877.

Wu, L.Y., D.K. Thompson, G.S. Li, R.A. Hurt, J.M. Tiedje, and J.Z. Zhou.  2001.  Development and evaluation of functional gene arrays for detection of selected genes in the environment.  Appl. Environ. Microbiol. 67: 5780-5790.

Ye, R.W., T. Wang, L. Bedzyk, and K.M. Croker.  2001.  Applications of DNA microarrays in microbial systems.  J. Microbiol. Meth. 47: 257-272.

 Extra Topics

Sequences Without Organisms: Microbial diversity

Schleifer, K.-H.  2004.  Microbial diversity: facts, problems and prospects.  System. Appl. Microbiol. 27:3-9.

Tyson, G.W., J. Chapman, P. Hugenholtz, E.E. Allen, R.J. Ram, P.M. Richardson, V.V. Solovyev, E.M. Rubin, D.S. Rokhsar, and J.F. Banfield. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment.  Nature 428:25-26.

Leadbetter, J.R.  2003.  Cultivation of recalcitrant microbes: cells are alive, well and revealing their secrets in the 21st century laboratory.  Curr. Opin. Microbiol. 6:274-281.

Newman, D.K., and J.F. Banfield.  2002.  Geomicrobiology: How molecular-scale interactions underpin biogeochemical systems.  Science 296: 1071-1077.

DeLong, E.F.  2001.  Microbial seascapes revisited.  Curr. Opin. Microbiol. 4: 290-295.

Barns, S.M., R.E. Fundyga, M.W. Jeffries, and N.R. Pace. 1994. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl. Acad. Sci. USA 91:1609-1613.

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