of the entire genome of Mycoplasma mycoides was synthesized from scratch, assembled by recombination, and used to replace the DNA in a related species (see Gibson et al., Suggested Reading). In one of the first demonstrations of the utility of this technique, in 2016, a minimal bacterial genome encoding only 473 genes was designed and synthesized, placing it as the smallest known genome in an autonomously replicating organism (see Hutchison et al., Suggested Reading). Amazingly and humbling, 149 of the 473 genes found necessary to support the growth of this organism are of unknown biological function, indicating that we still have much to learn about the molecular genetics of bacteria. While the ability to design bacteria de novo will likely have to include certain safeguards and greater public understanding, these types of experiments hold great promise for industrial use, as tools in medicine, and for addressing basic scientific questions, such as what is the minimum genetic requirement for life as a free-living organism.
These examples illustrate that bacteria and their phages have been central to the development of molecular genetics and recombinant DNA technology. Contrast the timing of these developments with the timing of comparable major developments in physics (early 1900s) and chemistry (1920s and 1930s), and you can see that molecular genetics is arguably the most recent major conceptual breakthrough in the history of science.
What Is Ahead
This textbook emphasizes how classical and molecular genetic approaches can be used to solve biological problems. As an educational experience, understanding the methods used and the interpretation of experiments is at least as important as the conclusions drawn. Therefore, whenever possible, the experiments that led to the conclusions are presented. The first two chapters, of necessity, review the concepts of macromolecular synthesis that are essential to understanding bacterial molecular genetics. However, they also introduce more current material, including interesting recent advances in bacterial cell biology. Chapter 1, besides reviewing the basics of DNA replication and the techniques of molecular biology, presents some recent advances in our understanding of how replication is coordinated with other cellular processes. Chapter 2, in addition to reviewing the basics of protein synthesis, presents current developments concerning protein folding, transport, and degradation. Chapter 3, similarly, reviews basic genetic principles, but with a special emphasis on bacterial genetics. Students are not likely to get some of this material in more general genetics courses, at least not in the same depth. This chapter also includes more current applications, such as gene knockouts, reverse genetics, and saturation genetics. Chapters 4 through 12 deal with more specific topics and the techniques that can be used to study them, with particular emphasis on recent evidence concerning the relatedness of seemingly disparate topics. The last chapter, chapter 13, focuses on how the genome is structured, the tools we use to analyze the genome, and even how to construct “new” genomes. We hope that this textbook will help put modern molecular genetics into a historical perspective, bring the reader up to date on current advances in bacterial molecular genetics, and position the reader to understand future developments in this exciting and rapidly progressing field of science.
SUGGESTED READING
1 Angert ER. 2012. DNA replication and genomic architecture of very large bacteria. Annu Rev Microbiol 66:197–212.
2 Avery OT, Macleod CM, McCarty M. 1944. Studies on the chemical nature of the substance inducing transformation of pneumococcal types. I. Induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. J Exp Med 79:137–158.
3 Brenner S, Jacob F, Meselson M. 1961. An unstable intermediate carrying information from genes to ribosomes for protein synthesis. Nature 190:576–581.
4 Cairns J, Stent GS, Watson JD. 1966. Phage and the Origins of Molecular Biology. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
5 Cohen SN, Chang ACY, Boyer HW, Helling RB. 1973. Construction of biologically functional bacterial plasmids in vitro. Proc Natl Acad Sci USA 70:3240–3244.
6 Crick FHC, Barnett L, Brenner S, Watts-Tobin RJ. 1961. General nature of the genetic code for proteins. Nature 192:1227–1232.
7 Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang R-Y, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi Z-Q, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA III, Smith HO, Venter JC. 2010. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329:52–56.
8 Hershey AD, Chase M. 1952. Independent functions of viral protein and nucleic acid in growth of bacteriophage. J Gen Physiol 36: 39–56.
9 Hug LA, et al. 2016. A new view of the tree of life. Nature Microbiol 1:16048. (Letter.) http://doi.org/10.1038/nmicrobiol.2016.48
10 Hutchison CA III, Chuang R-Y, Noskov VN, Assad-Garcia N, Deerinck TJ, Ellisman MH, Gill J, Kannan K, Karas BJ, Ma L, Pelletier JF, Qi Z-Q, Richter RA, Strychalski EA, Sun L, Suzuki Y, Tsvetanova B, Wise KS, Smith HO, Glass JI, Merryman C, Gibs on DG, Venter JC. 2016. Design and synthesis of a minimal bacterial genome. Science 351: aad6253.
11 Imachi H, et al. 2020. Isolation of an archaeon at the prokaryote-eukaryote interface. Nature 577: 519–525.
12 Jacob F, Monod J. 1961. Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3:318–356.
13 Koonin EVE. 2015. Archaeal ancestors of eukaryotes: not so elusive any more. BMC Biol 13:84.
14 Lederberg J, Tatum EL. 1946. Gene recombination in Escherichia coli. Nature 158:558.
15 Leipe DD, Aravind L, Koonin EV. 1999. Did DNA replication evolve twice independently? Nucleic Acids Res 27:3389–3401.
16 Linn S, Arber W. 1968. Host specificity of DNA produced by Escherichia coli. X. In vitro restriction of phage fd replicative form. Proc Natl Acad Sci USA 59:1300–1306.
17 Luria SE, Delbrück M. 1943. Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28:491–511.
18 Meselson M, Stahl FW. 1958. The replication of DNA in Escherichia coli. Proc Natl Acad Sci USA 44:671–682.
19 Nirenberg MW, Matthaei JH. 1961. The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides. Proc Natl Acad Sci USA 47: 1588–1602.
20 Olby R. 1974. The Path to the Double Helix. Macmillan Press, London, United Kingdom.
21 Olsen GJ, Woese CR, Overbeek R. 1994. The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol 176:1–6.
22 Pace NR. 2009. Mapping the tree of life: progress and prospects. Microbiol Mol Biol Rev 73:565–576.
23 Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJG. 2015. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521:173–179.
24 Schrodinger E. 1944. What Is Life? The Physical Aspect of the Living Cell. Cambridge University Press, Cambridge, United Kingdom.
25 Watson JD. 1968. The Double Helix. Atheneum, New York, NY.
26 Woese CR, Fox GE. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088–5090.
27 Yang D, Oyaizu Y, Oyaizu H, Olsen GJ, Woese CR. 1985. Mitochondrial origins. Proc Natl Acad Sci USA 82:4443–4447.
28 Zinder ND, Lederberg J. 1952. Genetic exchange in Salmonella. J Bacteriol 64:679–699.