Bacterial Genomes: Trees and Networks
- Aswin Sai Narain Seshasayee(author)
Title | Bacterial Genomes |
---|---|
Subtitle | Trees and Networks |
Contributor | Aswin Sai Narain Seshasayee(author) |
DOI | https://doi.org/10.11647/OBP.0446 |
Landing page | https://www.openbookpublishers.com/books/10.11647/OBP.0446 |
License | https://creativecommons.org/licenses/by-nc/4.0/ |
Copyright | Aswin Sai Narain Seshasayee; |
Publisher | Open Book Publishers |
Publication place | Cambridge, UK |
Published on | 2025-02-28 |
ISBN | 978-1-80511-495-6 (Paperback) |
978-1-80511-496-3 (Hardback) | |
978-1-80511-497-0 (PDF) | |
978-1-80511-499-4 (HTML) | |
978-1-80511-498-7 (EPUB) | |
Short abstract | In Bacterial Genomes, the evolutionary and regulatory processes that shape bacterial life are brought to life. This textbook offers a conceptual exploration of how bacterial genomes are organized, how they evolve, and how their genetic information is interpreted through intricate molecular networks. Drawing on both cutting-edge research and the historical milestones that shaped microbiology, it illuminates how bacteria navigate the intersection of genetic adaptation and ecological resilience. |
Long abstract | Microbes form the “unseen majority” of life on Earth, with bacteria at the forefront as both the architects of life’s chemical foundations and agents of disease. But their story is far more complex. Bacteria thrive in diverse and extreme environments, driven by the dynamic evolution of their genomes. These tiny organisms wield an extraordinary ability to adapt, balancing genetic changes across generations with rapid physiological responses to environmental shifts. In Bacterial Genomes, the evolutionary and regulatory processes that shape bacterial life are brought to life. This textbook offers a conceptual exploration of how bacterial genomes are organized, how they evolve, and how their genetic information is interpreted through intricate molecular networks. Drawing on both cutting-edge research and the historical milestones that shaped microbiology, it illuminates how bacteria navigate the intersection of genetic adaptation and ecological resilience. Designed for college students, interdisciplinary researchers, and even the determined amateur, Aswin Seshasayee moves beyond technical jargon to provide a thought-provoking synthesis of bacterial evolution and adaptation. Unlike traditional genomics texts, this book blends historical insights with contemporary discoveries, offering a fresh perspective on the role of bacteria in shaping the living world. |
Print length | 254 pages (xvi+238) |
Language | English (Original) |
Dimensions | 178 x 21 x 254 mm | 7.01" x 0.83" x 10" (Paperback) |
178 x 38 x 254 mm | 7.01" x 1.5" x 10" (Hardback) | |
Weight | 605g | 21.34oz (Paperback) |
820g | 28.92oz (Hardback) | |
Media | 38 illustrations |
OCLC Number | 1503962568 |
THEMA |
|
BISAC |
|
Keywords |
|
Preface
(pp. 1–4)- Aswin Sai Narain Seshasayee
1. All creatures great and small
(pp. 5–32)- Aswin Sai Narain Seshasayee
2. The molecules of bacteria and of life
(pp. 33–64)- Aswin Sai Narain Seshasayee
3. The genome: how much DNA?
(pp. 65–106)- Aswin Sai Narain Seshasayee
4. The ebb and flow of bacterial genomes
(pp. 107–160)- Aswin Sai Narain Seshasayee
5. Reading and organising the genome
(pp. 161–218)- Aswin Sai Narain Seshasayee
Aswin Sai Narain Seshasayee
(author)Aswin Sai Narain Seshasayee is a researcher and Associate Professor at the National Centre for Biological Sciences (NCBS), a centre of Tata Institute of Fundamental Research (TIFR) in Bangalore, India. His lab is interested in fundamental aspects of the function and evolution of bacterial genomes and gene regulatory networks. His career in the sciences started off with a Bachelors of Technology at Anna University, Chennai, India, during which a lot of time left alone to explore and break things in the bioinformatics laboratory of Professor Gautam Pennathur and in the experimental microbiology and protein engineering laboratory of Professor Sankaran encouraged him to take up research for a career. He then pursued research as an intern, a PhD student and then briefly a postdoc with Nicholas Luscombe at EMBL-European Bioinformatics Institute, Hinxton, Cambridge, UK (and St John’s College and Girton College, University of Cambridge). He has been with NCBS since December 2010, his research here funded over the years by the Department of Atomic Energy (Govt of India) core support to TIFR and NCBS, Department of Biotechnology, Department of Science and Technology and Science and Engineering Research Board (all Govt of India), CEFIPRA and DBT-Wellcome Trust India Alliance. Beyond science, he enjoys making music, painting watercolour landscapes and reading classic crime and fantasy fiction and popular history.
- Fleming, A., Nobel Lecture (1945). https://www.nobelprize.org/uploads/2018/06/fleming-lecture.pdf
- Cobb, M., ‘Who discovered messenger RNA?’, Current Biology 25 (2015), R525–R532. https://doi.org/10.1016/j.cub.2015.05.032
- Doolittle, W.F., ‘Is junk DNA bunk? A critique of ENCODE’, Proceedings of the National Academy of Sciences USA 110 (2013), 5294–5300. https://doi.org/10.1073/pnas.1221376110
- Doolittle, W.F., ‘Phylogenetic classification and the universal tree’, Science 284 (1999), 2124–2129. https://doi.org/10.1126/science.284.5423.2124
- Browning, D.F., and S.J.W. Busby, ‘The regulation of bacterial transcription initiation’, Nature Reviews Microbiology 2 (2004), 57–65. https://doi.org/10.1038/nrmicro787
- Kolter, R., ‘The History of Microbiology—A Personal Interpretation’, Annual Review of Microbiology 75 (2021), 1–17. https://doi.org/10.1146/annurev-micro-033020-020648
- Lane, N., ‘The unseen world: reflections on Leeuwenhoek (1677) “Concerning little animals”’, Phil Trans Royal Soc. B. 370 (2015), 20140344. https://doi.org/10.1098/rstb.2014.0344
- Moberg, C.L., ‘René Dubos, a harbinger of microbial resistance to antibiotics’, Perspectives in Biology and Medicine 42 (1999), 559–580. https://doi.org/10.1089/mdr.1996.2.287
- Salyers, A.A., and D.D. Whitt, Revenge of the Microbes: How Bacterial Resistance is Undermining the Antibiotic Miracle (Washington, DC: ASM Press, 2005). https://doi.org/10.1128/9781555817602
- Whitman, W.B., D.C. Coleman, and W.J. Wiebe, ‘Prokaryotes: the unseen majority’, Proc. Natl. Acad. Sci. USA 95 (1998), 6578–6583. https://doi.org/10.1073/pnas.95.12.6578
- Dubos, R., ‘Oswald Theodore Avery, 1877–1955’, Biographical Memoirs of the Fellows of the Royal Society 2 (1956), 35–48. https://doi.org/10.1098/rsbm.1956.0003
- Duckworth, D., ‘Who discovered bacteriophage?’, Bacteriological Reviews 40 (1976), 793–802. https://doi.org/10.1128/mmbr.40.4.793-802.1976
- Hayes, W., ‘Genetic transformation: a retrospective appreciation’, Journal of General Microbiology 45 (1966), 385–397. https://doi.org/10.1099/00221287-45-3-385
- Hershey, A.D., ‘The injection of DNA into cells by phage’, Phage and the Origins of Molecular Biology (Plainview, NY: Cold Spring Harbor Laboratory Press, 1966).
- Hesse, S., and S. Adhya, ‘Phage Therapy in the Twenty-First Century: Facing the Decline of the Antibiotic Era; Is It Finally Time for the Age of the Phage?’, Annual Review of Microbiology 73 (2019), 155–174. https://doi.org/10.1146/annurev-micro-090817-062535
- Stanier, R., and C.B. van Niel, ‘The concept of a bacterium’, Archiv für Mikrobiologie 42 (1962), 17–35. https://doi.org/10.1007/bf00425185
- Woese, C.R., ‘Bacterial evolution’, Microbiology and Molecular Biology Reviews 51 (1987), 221. https://doi.org/10.1128/mmbr.51.2.221-271.1987
- Doolittle, W.F., and C. Sapienza, ‘Selfish genes, the phenotype paradigm and genome evolution’, Nature 284 (1980), 601–603. https://doi.org/10.1038/284601a0
- Gil, R., F.J. Silva, J. Pereto, and A. Moya, ‘Determination of the core of a minimal bacterial gene set’, Microbiology and Molecular Biology Reviews 68 (2004), 518–537. https://doi.org/10.1128/mmbr.68.3.518-537.2004
- Koonin, E.V., and Y.I. Wolf, ‘Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world’, Nucleic Acids Research 36 (2008), 6688–6719. https://doi.org/10.1093/nar/gkn668
- Lynch, M., and G. Marinov, ‘The bioenergetic costs of a gene’, Proceedings of the National Academy of Sciences USA 112 (2015), 15690–15695. https://doi.org/10.1073/pnas.1514974112
- Romero, M.L.R., A. Rabin, and D. Tawfik, ‘Functional Proteins from Short Peptides: Dayhoff’s Hypothesis Turns 50’, Angewandte Chemie International Edition 55 (2016), 15966–15971. https://doi.org/10.1002/anie.201609977
- Thomas, C.A. Jr, ‘The genetic organization of chromosomes’, Annual Review of Genetics 5 (1971), 237–256. https://doi.org/10.1146/annurev.ge.05.120171.001321
- Wu, D., S.C. Daugherty, S.E. Van Aken, G.H. Pai, K.L. Watkins, H. Khouri, L.J. Tallon, J.M. Zaborsky, H.E. Dunbar, P.L. Tran, N.A. Moran, and J.A. Eisen, ‘Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters’, PLoS Biology 4 (2006), e188. https://doi.org/10.1371/journal.pbio.0040188
- Gómez-Valero, L., E.P.C. Rocha, A. Latorre, and F.J. Silva, ‘Reconstructing the ancestor of Mycobacterium leprae: The dynamics of gene loss and genome reduction’, Genome Research 17 (2007), 1178–1185. https://doi.org/10.1101/gr.6360207
- Hood, D., and R. Moxon, ‘Gene variation and gene regulation in bacterial pathogenesis’, in D.A. Hodgson and C.M. Thomas (ed.) Signals, Switches, Regulons and Cascades (Cambridge: Cambridge University Press, 2002).
- Mira, A., H. Ochman, and N.A. Moran, ‘Deletional bias and the evolution of bacterial genomes’, Trends in Genetics 17 (2001), 589–596. https://doi.org/10.1016/s0168-9525(01)02447-7
- Nilsson, A.I., S. Koskiniemi, S. Eriksson, E. Kugelberg, J.C.D. Hinton, and D.I. Andersson, ‘Bacterial genome size reduction by experimental evolution’, Proceedings of the National Academy of Sciences USA 102 (2005), 12112–12116. https://doi.org/10.1073/pnas.0503654102
- Puigbó, P., A.E. Lobkovsky, D.M. Kristensen, Y.I. Wolf, and E.V. Koonin, ‘Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes’, BMC Biology 12 (2014), 66. https://doi.org/10.1186/s12915-014-0066-4
- Puigbo, P., Y.I. Wolf, and E.V. Koonin, ‘The Tree and Net Components of Prokaryote Evolution’, Genome Biology and Evolution 2 (2010), 745–756. https://doi.org/10.1093/gbe/evq062
- Tenaillon, O., J.E. Barrick, N. Ribeck, D.E. Deatherage, J.L. Blanchard, et al., ‘Tempo and mode of genome evolution in a 50,000-generation experiment’, Nature 536 (2016), 165–170. https://doi.org/10.1038/nature18959
- Treangen, T.J., and E.P.C. Rocha, ‘Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes’, PLoS Genetics 7 (2011), e1001284. https://doi.org/10.1371/journal.pgen.1001284
- Waldor, M.K. and J.J. Mekalanos, ‘Lysogenic conversion by a filamentous phage encoding cholera toxin’, Science 272 (1996), 1910–1914. https://doi.org/10.1126/science.272.5270.1910
- Cohen, Y., and R. Hershberg, ‘Rapid Adaptation Often Occurs through Mutations to the Most Highly Conserved Positions of the RNAP Core Enzyme’, Genome Biology and Evolution 14 (2022), evac105. https://doi.org/10.1093/gbe/evac105
- Dorman, C.J., ‘H-NS, the genome sentinel’, Nature Reviews Microbiology 5 (2007), 157–161. https://doi.org/10.1038/nrmicro1598
- Dorman, C.J., ‘DNA supercoiling and transcription in bacteria: a two-way street’, BMC Molecular and Cell Biology 20 (2019), 26. https://doi.org/10.1186/s12860-019-0211-6
- Ferenci, T., ‘What is driving the acquisition of mutS and rpoS polymorphisms in Escherichia coli?’, Trends in Microbiology 11 (2003), 457–461. https://doi.org/10.1016/j.tim.2003.08.003
- Gruber, T.M., and C.A. Gross, ‘Multiple sigma subunits and the partitioning of bacterial transcription space’, Annual Review of Microbiology 57 (2003), 441–466. https://doi.org/10.1146/annurev.micro.57.030502.090913
- Lucchini, S., G. Rowley, M.D. Goldberg, D. Hurd, M. Harrison, and J.C. Hinton, ‘H-NS Mediates the Silencing of Laterally Acquired Genes in Bacteria’, PLoS Pathogens 2 (2006), e81. https://doi.org/10.1371/journal.ppat.0020081
- Price, M.N., P.S. Dehal, and A.P. Arkin, ‘Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli’, Genome Biology 9 (2008), R4. https://doi.org/10.1186/gb-2008-9-1-r4
- Ptashne, M., A Genetic Switch: Phage Lambda Revisited (Plainview, NY: Cold Spring Harbor Laboratory Press, 2004).
- Rocha, E.P.C., ‘The replication-related organization of bacterial genomes’, Microbiology 150 (2004), 1609–1627. https://doi.org/10.1099/mic.0.26974-0
- Srinivasan, R., V.F. Scolari, M.C. Lagomarsino, and A.S.N. Seshasayee, ‘The genome-scale interplay amongst xenogene silencing, stress response and chromosome architecture in Escherichia coli’, Nucleic Acids Res. 43 (2015), 295–308. https://doi.org/10.1093/nar/gku1229
- Srivatsan, A., A. Tehranchi, D.M. MacAlpine, and J.D. Wang, ‘Co-orientation of replication and transcription preserves genome integrity’, PLoS Genetics 6 (2010), e1000810. https://doi.org/10.1371/journal.pgen.1000810
- van Nimwegen, E., ‘Scaling laws in the functional content of genomes’, Trends in Genetics 19 (2009), 479–484. https://doi.org/10.1007/0-387-33916-7_14
- Visweswaraiah, S., and S.J.W. Busby, ‘Evolution of bacterial transcription factors: how proteins take on new tasks, but do not always stop doing the old ones’, Trends in Microbiology 23 (2015), 463–467. https://doi.org/10.1016/j.tim.2015.04.009