Snyder and Champness Molecular Genetics of Bacteria. Tina M. Henkin
the DNAs through supercoiling by DNA gyrase and by condensins that hold the DNA in large supercoiled loops.
12 The FtsZ protein forms a ring at the midpoint of the cell, attracting other proteins, which form the division septum.
13 The Min proteins prevent the formation of FtsZ rings anywhere in the cell other than in the middle. Nucleoid occlusion proteins prevent the formation of FtsZ rings over nucleoids.
14 Initiation of a round of chromosome replication occurs once every time the cell divides. Initiation occurs when the ratio of active DnaA protein to origins of replication reaches a critical number. After replication initiates, its ATPase is upregulated by interaction with the β clamp and Hda, converting it to the inactive ADP-bound state to prevent reinitiation. In some bacteria, including E. coli and related enteric bacteria, new initiations are prevented by hemimethylation of the newly replicated DNA at the origin and by sequestration until the replication fork has left the origin.
15 The chromosomal DNA of bacteria is usually one long, continuous circular molecule about 1,000 times as long as the cell itself. This long DNA is condensed in a small part of the cell called the nucleoid. In this structure, the DNA loops out of a central condensed core region. Some of these loops of DNA are negatively supercoiled. In E. coli, most DNAs have one supercoil about every 300 bases.
16 The enzymes that modulate DNA supercoiling in the cell are called topoisomerases. There are two types of topoisomerases in cells. Type I topoisomerases can remove supercoils one at a time by breaking only one strand and passing the other strand through the break. Type II topoisomerases remove or add supercoils two at a time by breaking both strands and passing another region of the DNA through the break. The enzyme responsible for adding the negative supercoils to DNA in bacteria is a type II topoisomerase called gyrase. Topo IV decatenates daughter DNAs after replication.
QUESTIONS FOR THOUGHT
1 1. Some viruses, such as adenovirus, avoid the problem of lagging-strand synthesis by replicating the individual strands of the DNA in the leading-strand direction simultaneously from both ends so that eventually the entire molecule is replicated. Why do bacterial chromosomes not replicate in this way?
2 2. Why are DNA molecules so long? Would it not be easier to have many shorter pieces of DNA? What are the advantages and disadvantages of a single long DNA molecule?
3 3. Why do cells have DNA as their hereditary material instead of RNA, like some viruses?
4 4. What effect would shifting a temperature-sensitive mutant with a mutation in the dnaA gene for initiator protein DnaA have on the rate of DNA synthesis? Would the rate drop linearly or exponentially? Would the slope of the curve be affected by the growth rate of the cells at the time of the shift? Explain.
5 5. The gyrase inhibitor novobiocin inhibits the growth of almost all types of bacteria. What would you predict about the gyrase of the bacterium Streptomyces sphaeroides, which makes this antibiotic? How would you test your hypothesis?
6 6. How do you think chromosome replication and cell division are coordinated in bacteria like E. coli? How would you go about testing your hypothesis?
7 7. Why is termination of chromosome replication so sloppy that the ter region is nonessential for growth and there has to be more than one ter site in each direction to completely stop the replication fork? What are the advantages of not having a definite site on the chromosome at which replication always terminates?
SUGGESTED READING
1 Aussel L, Barre F-X, Aroyo M, Stasiak A, Stasiak AZ, Sherratt D. 2002. FtsK is a DNA motor protein that activates chromosome dimer resolution by switching the catalytic state of the XerC and XerD recombinases. Cell 108:195–205.
2 Bernhardt TG, de Boer PAJ. 2005. SlmA, a nucleoid-associated, FtsZ binding protein required for blocking septal ring assembly over chromosomes in E. coli. Mol Cell 18:555–564.
3 Brézellec P, Hoebeke M, Hiet MS, Pasek S, Ferat JL. 2006. DomainSieve: a protein domain-based screen that led to the identification of dam-associated genes with potential link to DNA maintenance. Bioinformatics 22:1935–1941.
4 Biller SJ, Burkholder WF. 2009. The Bacillus subtilis SftA (YtpS) and SpoIIIE DNA translo cases play distinct roles in growing cells to ensure faithful chromosome partitioning. Mol Microbiol 74:790–809.
5 Blakely G, May G, McCulloch R, Arciszewska LK, Burke M, Lovett ST, Sherratt DJ. 1993. Two related recombinases are required for site-specific recombination at dif and cer in E. coli K12. Cell 75:351–361.
6 Britton RA, Lin DC, Grossman AD. 1998. Characterization of a prokaryotic SMC protein involved in chromosome partitioning. Genes Dev 12:1254–1259.
7 Camara JE, Breier AM, Brendler T, Austin S, Cozzarelli NR, Crooke E. 2005. Hda inactivation of DnaA is the predominant mechanism preventing hyperinitiation of Escherichia coli DNA replication. EMBO Rep 6:736–741.
8 Cortez D, Quevillon-Cheruel S, Gribaldo S, Desnoues N, Sezonov G, Forterre P, Serre M-CM. 2010. Evidence for a Xer/dif system for chromosome resolution in archaea. PLoS Genet 6:e1001166.
9 Dervyn E, Suski C, Daniel R, Bruand C, Chapuis J, Errington J, Jannière L, Ehrlich SD. 2001. Two essential DNA polymerases at the bacterial replication fork. Science 294:1716–1719.
10 Dohrmann PR, Correa R, Frisch RL, Rosenberg SM, McHenry CS. 2016. The DNA polymerase III holoenzyme contains γ and is not a trimeric polymerase. Nucleic Acids Res 44:1285–1297.
11 Fournes F, Val M-E, Skovgaard O, Mazel D. 2018. Replicate once per cell cycle: replication control of secondary chromosomes. Front Microbiol 9:1833.
12 Fricker AD, Peters JE. 2014. Vulnerabilities on the lagging-strand template: opportunities for mobile elements. Annu Rev Genet 48:167–186.
13 Fujimitsu K, Senriuchi T, Katayama T. 2009. Specific genomic sequences of E. coli promote replicational initiation by directly reactivating ADP-DnaA. Genes Dev 23:1221–1233.
14 Gabbai CB, Yeeles JTP, Marians KJ. 2014. Replisome-mediated translesion synthesis and leading strand template lesion skipping are competing bypass mechanisms. J Biol Chem 289:32811–32823.
15 Galli E, Ferat J-L, Desfontaines J-M, Val M-E, Skovgaard O, Barre FX, Possoz C. 2019. Replication termination without a replication fork trap. Sci Rep 9:8315. http://doi.org/10.1038/s41598-019-43795-2
16 Guy CP, Atkinson J, Gupta MK, Mahdi AA, Gwynn EJ, Rudolph CJ, Moon PB, van Knippenberg IC, Cadman CJ, Dillingham MS, Lloyd RG, McGlynn P. 2009. Rep provides a second motor at the replisome to promote duplication of protein-bound DNA. Mol Cell 36:654–666.
17 Hayama R, Marians KJ. 2010. Physical and functional interaction between the condensin MukB and the decatenase topoisomerase IV in Escherichia coli. Proc Natl Acad Sci USA 107:18826–18831.
18 Heller RC, Marians KJ. 2006. Replication fork reactivation downstream of a blocked nascent leading strand. Nature 439:557–562.
19 Helmstetter CE, Cooper S. 1968. DNA synthesis during the division cycle of rapidly growing Escherichia coli B/r. J Mol Biol 31:507–518.
20 Jean NK, Rutherford TJ, Löwe J. 2019. FtsK in motion reveals its mechanism for doublestranded DNA translocation. bioRxiv 1–24.
21 Joshi MC, Magnan D, Montminy TP, Lies M, Stepankiw N, Bates D. 2013. Regulation of sister chromosome cohesion by the replication fork tracking protein SeqA. PLoS Genet 9:e1003673.
22 Kasho K, Katayama T. 2013. DnaA binding locus datA promotes DnaA-ATP hydrolysis to enable cell cycle-coordinated replication initiation. Proc Natl Acad Sci USA 110:936–941.
23 Kohanski MA, Dwyer DJ, Hayete B, Lawrence CA, Collins JJ. 2007. A common mechanism of cellular death induced by bactericidal antibiotics. Cell 130:797–810.
24 Kysela DT, Randich AM, Caccamo PD, Brun YV. 2016. Diversity takes shape: understanding the mechanistic and adaptive basis of bacterial morphology. PLoS Biol 14:e1002565.
25 Le