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Chapter 13 - Energy, environment and microbial survival

Published online by Cambridge University Press:  04 May 2019

Byung Hong Kim
Korea Institute of Science and Technology, Seoul
Geoffrey Michael Gadd
University of Dundee
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Publisher: Cambridge University Press
Print publication year: 2019

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Primary Sources

Aertsen, A. & Michiels, C. (2004). Stress and how bacteria cope with death and survival. Critical Reviews in Microbiology 30, 263273.
Errington, J., Daniel, R. A. & Scheffers, D. J. (2003). Cytokinesis in bacteria. Microbiology and Molecular Biology Reviews 67, 5265.
Ferenci, T. (2001). Hungry bacteria: definition and properties of a nutritional state. Environmental Microbiology 3, 605611.
Kempes, C. P., van Bodegom, P. M., Wolpert, D., Libby, E., Amend, J. & Hoehler, T. (2017). Drivers of bacterial maintenance and minimal energy requirements. Frontiers in Microbiology 8, 31.
Lever, M. A., Rogers, K. L., Lloyd, K. G., Overmann, J., Schink, B., Thauer, R. K., Hoehler, T. M. & Jørgensen, B. B. (2015). Life under extreme energy limitation: a synthesis of laboratory- and field-based investigations. FEMS Microbiology Reviews 39, 688728.
Matic, I., Taddei, F. & Radman, M. (2004). Survival versus maintenance of genetic stability: a conflict of priorities during stress. Research in Microbiology 155, 337341.
Mukamolova, G. V., Kaprelyants, A. S., Kell, D. B. & Young, M. (2003). Adoption of the transiently non-culturable state – a bacterial survival strategy?Advances in Microbial Physiology 47, 65129.
Nystrom, T. (2004). Growth versus maintenance: a trade-off dictated by RNA polymerase availability and sigma factor competition? Molecular Microbiology 54, 855862.
Peterson, C. N., Mandel, M. J. & Silhavy, T. J. (2005). Escherichia coli starvation diets: essential nutrients weigh in distinctly. Journal of Bacteriology 187, 75497553.

Secondary Sources

Chandra, G., Chater, K. F. & Bornemann, S. (2011). Unexpected and widespread connections between bacterial glycogen and trehalose metabolism. Microbiology 157, 15651572.
Elbein, A. D., Pastuszak, I., Tackett, A. J., Wilson, T. & Pan, Y. T. (2010). Last step in the conversion of trehalose to glycogen: a mycobacterial enzyme that transfers maltose from maltose-1-phosphate to glycogen. Journal of Biological Chemistry 285, 98039812.
Wilson, W. A., Roach, P. J., Montero, M., Baroja-Fernández, E., Muñoz, F. J., Eydallin, G., Viale, A. M. & Pozueta-Romero, J. (2010). Regulation of glycogen metabolism in yeast and bacteria. FEMS Microbiology Reviews 34, 952985.
Alvarez, H. M. & Steinbuchel, A. (2002). Triacylglycerols in prokaryotic microorganisms. Applied Microbiology and Biotechnology 60, 367376.
Herman, N. A. & Zhang, W. (2016). Enzymes for fatty acid-based hydrocarbon biosynthesis. Current Opinion in Chemical Biology 35, 2228.
Jendrossek, D. & Pfeiffer, D. (2014). New insights in the formation of polyhydroxyalkanoate granules (carbonosomes) and novel functions of poly(3-hydroxybutyrate). Environmental Microbiology 16, 23572373.
Jiménez-Díaz, L., Caballero, A., Pérez-Hernández, N. & Segura, A. (2017). Microbial alkane production for jet fuel industry: motivation, state of the art and perspectives. Microbial Biotechnology 10, 103124.
Low, K. L., Shui, G., Natter, K., Yeo, W. K., Kohlwein, S. D., Dick, T., Rao, S. P. S. & Wenk, M. R. (2010). Lipid droplet-associated proteins are involved in the biosynthesis and hydrolysis of triacylglycerol in Mycobacterium bovis Bacillus Calmette-Guérin. Journal of Biological Chemistry 285, 2166221670.
Maestro, B. & Sanz, J. M. (2017). Polyhydroxyalkanoate-associated phasins as phylogenetically heterogeneous, multipurpose proteins. Microbial Biotechnology 10, 13231337.
Stubbe, J., Tian, J., He, A., Sinskey, A. J., Lawrence, A. G. & Liu, P. (2005). Nontemplate-dependent polymerization processes: polyhydroxyalkanoate synthases as a paradigm. Annual Review of Biochemistry 74, 433480.
Waltermann, M. & Steinbuchel, A. (2005). Neutral lipid bodies in prokaryotes: recent insights into structure, formation, and relationship to eukaryotic lipid depots. Journal of Bacteriology 187, 36073619.
Baykov, A. A., Malinen, A. M., Luoto, H. H. & Lahti, R. (2013). Pyrophosphate-fueled Na+ and H+ transport in prokaryotes. Microbiology and Molecular Biology Reviews 77, 267276.
Brown, M. R. & Kornberg, A. (2004). Inorganic polyphosphate in the origin and survival of species. Proceedings of the National Academy of Sciences of the USA 101, 1608516087.
Garcia-Contreras, R., Celis, H. & Romero, I. (2004). Importance of Rhodospirillum rubrum H+-pyrophosphatase under low-energy conditions. Journal of Bacteriology 186, 66516655.
Gray, M. J. & Jakob, U. (2015). Oxidative stress protection by polyphosphate – new roles for an old player. Current Opinion in Microbiology 24, 16.
Kellosalo, J., Kajander, T., Kogan, K., Pokharel, K. & Goldman, A. (2012). The structure and catalytic cycle of a sodium-pumping pyrophosphatase. Science 337, 473476.
Kulaev, I. & Kulakovskaya, T. (2000). Polyphosphate and phosphate pump. Annual Review of Microbiology 54, 709734.
Toso, D. B., Henstra, A. M., Gunsalus, R. P. & Zhou, Z. H. (2011). Structural, mass and elemental analyses of storage granules in methanogenic archaeal cells. Environmental Microbiology 13, 25872599.
Heinrich, K., Leslie, D. J. & Jonas, K. (2015). Modulation of bacterial proliferation as a survival strategy. Advances in Applied Microbiology. 92, 127171.
Kaprelyants, A. S., Gottschal, J. C. & Kell, D. B. (1993). Dormancy in nonsporulating bacteria. FEMS Microbiology Reviews 10, 271286.
Al-Hinai, M. A., Jones, S. W. & Papoutsakis, E. T. (2015). The Clostridium sporulation programs: diversity and preservation of endospore differentiation. Microbiology and Molecular Biology Reviews 79, 1937.
Errington, J. (2001). Septation and chromosome segregation during sporulation in Bacillus subtilis. Current Opinion in Microbiology 4, 660666.
Fimlaid, K. A. & Shen, A. (2015). Diverse mechanisms regulate sporulation sigma factor activity in the Firmicutes. Current Opinion in Microbiology 24, 8895.
González-Pastor, J. E. (2011). Cannibalism: a social behavior in sporulating Bacillus subtilis. FEMS Microbiology Reviews 35, 415424.
Higgins, D. & Dworkin, J. (2012). Recent progress in Bacillus subtilis sporulation. FEMS Microbiology Reviews 36, 131148.
Hilbert, D. W. & Piggot, P. J. (2004). Compartmentalization of gene expression during Bacillus subtilis spore formation. Microbiology and Molecular Biology Reviews 68, 234262.
McKenney, P. T., Driks, A. & Eichenberger, P. (2013). The Bacillus subtilis endospore: assembly and functions of the multilayered coat. Nature Reviews Microbiology 11, 3344.
Moir, A. (2003). Bacterial spore germination and protein mobility. Trends in Microbiology 11, 452454.
Paredes-Sabja, D., Setlow, P. & Sarker, M. R. (2011). Germination of spores of Bacillales and Clostridiales species: mechanisms and proteins involved. Trends in Microbiology 19, 8594.
Setlow, P. (2014). Germination of spores of Bacillus species: what we know and do not know. Journal of Bacteriology 196, 12971305.
Stephenson, K. & Hoch, J. A. (2002). Evolution of signalling in the sporulation phosphorelay. Molecular Microbiology 46, 297304.
Loiko, N., Kryazhevskikh, N., Suzina, N., Demkina, E., Muratova, A., Turkovskaya, O., Kozlova, A., Galchenko, V. & El’-Registan, G. (2011). Resting forms of Sinorhizobium meliloti. Microbiology-Moscow 80, 472482.
Marden, J. N., Dong, Q., Roychowdhury, S., Berleman, J. E. & Bauer, C. E. (2011). Cyclic GMP controls Rhodospirillum centenum cyst development. Molecular Microbiology 79, 600615.
Bari, S. M. N., Roky, M. K., Mohiuddin, M., Kamruzzaman, M., Mekalanos, J. J. & Faruque, S. M. (2013). Quorum-sensing autoinducers resuscitate dormant Vibrio cholerae in environmental water samples. Proceedings of the National Academy of Sciences of the USA 110, 99269931.
Cohen-Gonsaud, M., Keep, N. H., Davies, A. P., Ward, J., Henderson, B. & Labesse, G. (2004). Resuscitation-promoting factors possess a lysozyme-like domain. Trends in Biochemical Sciences 29, 710.
Epstein, S. S. (2013). The phenomenon of microbial uncultivability. Current Opinion in Microbiology 16, 636642.
Kell, D. B. & Young, M. (2000). Bacterial dormancy and culturability: the role of autocrine growth factors. Current Opinion in Microbiology 3, 238243.
Oliver, J. D. (2005). The viable but nonculturable state in bacteria. Journal of Microbiology-Seoul 43, 93100.
Pinto, D., Santos, M. A. & Chambel, L. (2015). Thirty years of viable but nonculturable state research: unsolved molecular mechanisms. Critical Reviews in Microbiology 41, 6176.
Sexton, D. L., St-Onge, R. J., Haiser, H. J., Yousef, M. R., Brady, L., Gao, C., Leonard, J. & Elliot, M. A. (2015). Resuscitation-promoting factors are cell wall-lytic enzymes with important roles in the germination and growth of Streptomyces coelicolor. Journal of Bacteriology 197, 848860.
Gerdes, K. & Maisonneuve, E. (2012). Bacterial persistence and toxin–antitoxin loci. Annual Review of Microbiology 66, 103123.
Harms, A., Maisonneuve, E. & Gerdes, K. (2016). Mechanisms of bacterial persistence during stress and antibiotic exposure. Science 354, 13901399.
Lewis, K. (2010). Persister cells. Annual Review of Microbiology 64, 357372.
Maisonneuve, E., Castro-Camargo, M. & Gerdes, K. (2013). (p)ppGpp controls bacterial persistence by stochastic induction of toxin–antitoxin activity. Cell 154, 11401150.
Duda, V., Suzina, N., Polivtseva, V. & Boronin, A. (2012). Ultramicrobacteria: formation of the concept and contribution of ultramicrobacteria to biology. Microbiology-Moscow 81, 379390.
Silbaq, F. S. (2009). Viable ultramicrocells in drinking water. Journal of Applied Microbiology 106, 106117.
Vainshtein, M. B. & Kudryashova, E. B. (2000). Nanobacteria. Microbiology-Moscow 69, 129138.
Durand, P. M., Sym, S. & Michod, R. E. (2016). Programmed cell death and complexity in microbial systems. Current Biology 26, R587R593.
Lewis, K. (2000). Programmed death in bacteria. Microbiology and Molecular Biology Reviews 64, 503514.
Prozorov, A. & Danilenko, V. (2011). Allolysis in bacteria. Microbiology-Moscow 80, 19.
Ramisetty, B. C. M., Natarajan, B. & Santhosh, R. S. (2015). mazEF-mediated programmed cell death in bacteria: “What is this?”. Critical Reviews in Microbiology 41, 89100.
Rice, K. C. & Bayles, K. W. (2003). Death’s toolbox: examining the molecular components of bacterial programmed cell death. Molecular Microbiology 50, 729738.
Brantl, S. & Jahn, N. (2015). sRNAs in bacterial type I and type III toxin–antitoxin systems. FEMS Microbiology Reviews 39, 413427.
Chan, W. T., Moreno-Córdoba, I., Yeo, C. C. & Espinosa, M. (2012). Toxin–antitoxin genes of the Gram-positive pathogen Streptococcus pneumoniae: So few and yet so many. Microbiology and Molecular Biology Reviews 76, 773791.
Lobato-Márquez, D., Díaz-Orejas, R. & García-del Portillo, F. (2016). Toxin–antitoxins and bacterial virulence. FEMS Microbiology Reviews 40, 592609.
Yamaguchi, Y., Park, J.-H. & Inouye, M. (2011). Toxin–antitoxin systems in bacteria and archaea. Annual Review of Genetics 45, 6179.
Barrangou, R. & Doudna, J. A. (2016). Applications of CRISPR technologies in research and beyond. Nature Biotechnology 34, 933941.
Bondy-Denomy, J. and Davidson, A.R. (2015). To acquire or resist: the complex biological effects of CRISPR–Cas systems. Trends in Microbiology 22, 218225.
Bondy-Denomy, J., Pawluk, A., Maxwell, K. L. & Davidson, A. R. (2013). Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature 493, 429432.
Dedrick, R. M., Jacobs-Sera, D., et al. (2017). Prophage-mediated defence against viral attack and viral counter-defence. Nature Microbiology 2, 16251.
Doerflinger, M., Forsyth, W., Ebert, G., Pellegrini, M. & Herold, M. J. (2017). CRISPR/Cas9 – the ultimate weapon to battle infectious diseases? Cellular Microbiology 19, e12693.
Doudna, J. A. & Charpentier, E. (2014). The new frontier of genome engineering with CRISPR-Cas9. Science 346, 1258096.
Garneau, J. E., Dupuis, M.-E., Villion, M., Romero, D. A., Barrangou, R., Boyaval, P., Fremaux, C., Horvath, P., Magadan, A. H. & Moineau, S. (2010). The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 6771.
Heussler, G. E. & O’Toole, G. A. (2016). Friendly fire: Biological functions and consequences of chromosomal targeting by CRISPR–Cas systems. Journal of Bacteriology 198, 14811486.
Jackson, S. A., McKenzie, R. E., Fagerlund, R. D., Kieper, S. N., Fineran, P. C. & Brouns, S. J. J. (2017). CRISPR–Cas: adapting to change. Science 356, eaal5056.
Louwen, R., Staals, R. H. J., Endtz, H. P., van Baarlen, P. & van der Oost, J. (2014). The role of CRISPR–Cas systems in virulence of pathogenic bacteria. Microbiology and Molecular Biology Reviews 78, 7488.
Makarova, K. S., Wolf, Y. I., Alkhnbashi, O. S., Costa, F., Shah, S. A., Saunders, S. J., Barrangou, R., Brouns, S. J. J., Charpentier, E., Haft, D. H., Horvath, P., Moineau, S., Mojica, F. J. M., Terns, R. M., Terns, M. P., White, M., Yakunin, F. A. F., Garrett, R. A., van der Oost, J., Backofen, R. & Koonin, E. V. (2015). An updated evolutionary classification of CRISPR–Cas systems. Nature Reviews Microbiology 13, 722736.
Marraffini, L. A. (2015). CRISPR–Cas immunity in prokaryotes. Nature 526, 5561.
Mojica, F. J. M. & Rodriguez-Valera, F. (2016). The discovery of CRISPR in archaea and bacteria. FEBS Journal 283, 31623169.
Peters, J. M., Silvis, M. R., Zhao, D., Hawkins, J. S., Gross, C. A. & Qi, L. S. (2015). Bacterial CRISPR: accomplishments and prospects. Current Opinion in Microbiology 27, 121126.
Selle, K. & Barrangou, R. (2015). Harnessing CRISPR–Cas systems for bacterial genome editing. Trends in Microbiology 23, 225232.
Sorek, R., Lawrence, C. M. & Wiedenheft, B. (2013). CRISPR-mediated adaptive immune systems in bacteria and archaea. Annual Review of Biochemistry 82, 237266.
van Houte, S., Buckling, A. & Westra, E. R. (2016). Evolutionary ecology of prokaryotic immune mechanisms. Microbiology and Molecular Biology Reviews 80, 745763.
Claverys, J. P., Prudhomme, M. & Martin, B. (2006). Induction of competence regulons as a general response to stress in Gram-positive bacteria. Annual Review of Microbiology 60, 451475.
Krüger, N.-J. & Stingl, K. (2011). Two steps away from novelty – principles of bacterial DNA uptake. Molecular Microbiology 80, 860867.
Martin, B., Quentin, Y., Fichant, G. & Claverys, J. P. (2006). Independent evolution of competence regulatory cascades in streptococci? Trends in Microbiology 14, 339345.
Mell, J. C. & Redfield, R. J. (2014). Natural competence and the evolution of DNA uptake specificity. Journal of Bacteriology 196, 14711483.

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