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Chapter 4 : Molecular Genetics of Bacteria

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Molecular Genetics of Bacteria, Page 1 of 2

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Abstract:

This chapter provides an outline of molecular bacterial genetics as an aid to understanding the origins and nature of bacterial resistance to antibacterial agents through mutation, bacterial recombination, and transfer of bacterial plasmids and transposable elements. Also, the three types of bacterial gene transfer (transformation, transduction, and conjugation) are discussed. Gene expression is accomplished through a sequence of events in which the information contained in the base sequence of DNA is first transcribed into an RNA molecule, which is used to determine the amino acid sequence of a protein molecule. An example of an alkylating mutagen is 1-methyl-3-nitro-1-nitrosoguanidine, which adds a methyl group to the oxygen atom at position 6 of the guanine molecule causing it to mispair with thymine. The chapter provides a general overview of bacterial recombination and on the introduction of both bacterial plasmids and transposable elements. Transduction may be the most common mechanism for gene exchange and recombination in bacteria. The spread of bacteria with resistance to diverse antibacterial agents is one of the most serious threats to the successful treatment of bacterial infections.

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4
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Figures

Image of Figure 4.1
Figure 4.1

Genomic elements of bacteria. The main genomic element of bacteria is a single large circular DNA molecule called the chromosome. It contains the genes for all the “essential” functions and structures of the bacterial cell. Most bacteria carry additional DNA elements. These smaller circular DNA molecules are called plasmids. Topo I, topoisomerase I. The illustrations of the chromosome and the plasmid are not to scale.

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4
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Image of Figure 4.2
Figure 4.2

Transfer of information from DNA to protein. The nucleotide sequence in DNA specifies the sequence of amino acids in a polypeptide. Bacterial DNA usually exists as a circular two-chain structure. The information contained in the nucleotide sequence of only one of the DNA chains (coding strand) is used to specify the nucleotide sequences of the mRNA molecules. This sequence information is used in polypeptide synthesis. A 3-nucleotide sequence in the mRNA molecule codes for a specific amino acid in the polypeptide chain.

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4
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Image of Figure 4.3
Figure 4.3

The genetic code. The code is presented in the RNA form. Reprinted from L. M. Prescott, J. P. Harley, and D. A. Klein, Microbiology, 4th ed. (McGraw-Hill, Boston, Mass., 1999), with permission from the publisher.

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4
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Image of Figure 4.4
Figure 4.4

Codons arising by single-base substitutions from UUA. Reprinted from J. W. Dale, Molecular Genetics of Bacteria, 3rd ed. (John Wiley & Sons, Ltd., Chichester, United Kingdom, 1998), with permission from the publisher.

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4
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Image of Figure 4.5
Figure 4.5

Shifts in the reading frame as a result of deletion or insertion mutations.

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4
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Image of Figure 4.6
Figure 4.6

Figure 4.6 Normally, A-T and C-G pairs are formed when keto groups participate in hydrogen bonds. In contrast, enol tautomers produce A-C and G-T base pairs. A-T pairs are formed when the amino group participates in hydrogen bonding. In contrast, imino tautomers produce A-C.

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4
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Image of Figure 4.7
Figure 4.7

Mutation as a consequence of tautomerization during DNA replication. The temporary enolization of guanine leads to the formation of an A-T base pair in the mutant, and a G-C to A-T transition mutation occurs. The process requires two replication cycles. The mutation occurs only if the abnormal first-generation G-T base pair is missed by repair mechanisms. Reprinted from L. M. Prescott, J. P. Harley, and D. A. Klein, Microbiology, 4th ed. (McGraw-Hill, Boston, Mass., 1999), with permission from the publisher.

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4
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Image of Figure 4.8
Figure 4.8

Mutagenesis by the base analog 5-bromouracil (5-BU). Base pairing of the normal keto form of 5-BU is shown at the top. The enol form of 5-BU (bottom) base-pairs with guanine rather than with adenine as might be expected for a thymine analog. If the keto form of 5-BU is incorporated in place of thymine, its occasional tautomerization to the enol form produces an A-T →G-C transition mutation.

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4
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Image of Figure 4.9
Figure 4.9

1-Methyl-3-nitro-1-nitrosoguanidine mutagenesis. Mutagenesis occurs because of the methylation of guanine.

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4
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Image of Figure 4.10
Figure 4.10

Thymine dimers. (a) UV light cross-links the two thymidine bases on the top strand. This distorts the DNA so that these two bases no longer pair with their adenine partners. (b) The two bonds joining the two thymine residues form a cyclobutane ring.

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4
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Image of Figure 4.11
Figure 4.11

A simplified diagram of homologous recombination. –, mutation; +, wild type. Reprinted from L. Snyder and W. Champness, Molecular Genetics of Bacteria, 2nd ed. (ASM Press, Washington, D.C., 2003), with permission from the American Society for Microbiology.

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4
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Image of Figure 4.12
Figure 4.12

Genetic map of the F (fertility) factor of E. coli. The numbers on the interior show the size of the plasmid in kilobase pairs. The approximate locations of several insertion sequences are shown. The tra (transfer function) genes code for proteins needed in pilus synthesis and conjugation. The rep (replication) genes code for proteins involved in DNA replication. oriV, also called oriS (origin of replication), is the initiation for circular DNA replication, and oriT (origin of transfer), is the site for initiation of rolling-circle replication and gene transfer during conjugation. Reprinted from L. M. Prescott, J. P. Harley, and D. A. Klein, Microbiology, 4th ed. (McGraw-Hill, Boston, Mass., 1999), with permission from the publisher.

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4
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Image of Figure 4.13
Figure 4.13

F factor integration. The reversible integration of an F factor into a host bacterial chromosome is shown. The process begins with the association between plasmid and bacterial insertion sequences. The arrowhead labeled O indicates the site at which the oriented transfer of chromosome to the recipient cell begins. A, B, 1, and 2 represent genetic markers. Reprinted from L. M. Prescott, J. P. Harley, and D. A. Klein, Microbiology, 4th ed. (McGraw-Hill, Boston, Mass., 1999), with permission from the publisher.

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4
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Image of Figure 4.14
Figure 4.14

Insertion sequences and transposons. The structures of insertion sequences (a), composite transposons (b), and target sites (c), are shown. IR, inverted repeat. In panel c, the highlighted 5-base target site is duplicated during Tn3 transposition to form flanking direct repeats. The remainder of Tn3 lies between the inverted repeats. Reprinted from L. M. Prescott, J. P. Harley, and D. A. Klein, Microbiology, 4th ed. (McGraw-Hill, Boston, Mass., 1999), with permission from the publisher.

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4
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Image of Figure 4.15
Figure 4.15

Structures of R factors and transposons. The R plasmid carries resistance genes for five antibacterial agents: chloramphenicol (Cm), streptomycin (Sm), sulfonamide (Su), ampicillin (Ap), and kanamycin (Km). These are contained in the Tn3 and Tn4 transposons. The resistance transfer factor (RTF) codes for the proteins necessary for plasmid replication and transfer. The structure of Tn3 is shown in more detail. The arrows indicate the direction of gene transcription. Reprinted from L. M. Prescott, J. P. Harley, and D. A. Klein, Microbiology, 4th ed. (McGraw-Hill, Boston, Mass., 1999), with permission from the publisher.

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4
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Image of Figure 4.16
Figure 4.16

Mechanism of DNA transfer during conjugation, showing mating-pair formation (Mpf functions). The donor cell produces a pilus, which forms on the cell surface and which may contact a potential recipient cell and bring it into close contact or may help hold the cells in close proximity after contact has been made, depending on the type of pilus. A pore then forms in the adjoining cell membrane. On receiving a signal from the coupling protein that contact with a recipient has been made, the relaxase protein makes a single-stranded cut at the oriT site in the plasmid. A plasmidencoded helicase then separates the strands of the plasmid DNA. The relaxase protein, which has remained attached to the 5' end of the single-stranded DNA, is then transported out of the donor cell through the channel directly into the recipient cell, dragging the single-stranded attached DNA along with it. Once in the recipient, the relaxase protein helps recyclize the single-stranded DNA. A primase, either that of the host or plasmid encoded and injected with the DNA, then primes replication of the complementary strand to make the double-stranded circular plasmid DNA in the recipient. The 3' end at the nick made by the relaxase in the donor can also serve as a primer, making a complementary copy of the single-stranded plasmid DNA remaining in the donor. Therefore, after transfer, both the donor and the recipient bacteria end up with a double-stranded circular copy of the plasmid. Reprinted from L. Snyder and W. Champness, Molecular Genetics of Bacteria, 2nd ed. (ASM Press, Washington, D.C., 2003), with permission from the American Society for Microbiology.

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4
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Image of Figure 4.17
Figure 4.17

Transformation in Haemophilus influenzae. Double-stranded DNA is first taken up in transformasomes. One strand is degraded, and the other strand invades the chromosome, displacing one chromosome strand. Reprinted from L. Snyder and W. Champness, Molecular Genetics of Bacteria, 2nd ed. (ASM Press, Washington, D.C., 2003), with permission from the American Society for Microbiology.

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4
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Image of Figure 4.18
Figure 4.18

An example of generalized transduction. A phage infects a Trp+ bacterium, and in the course of packaging DNA into heads, the phage mistakenly packages some bacterial DNA containing the trp region instead of its own DNA into a head. In the next infection, this transducing phage injects the Trp+ bacterial DNA instead of phage DNA into the Trp bacterium. If the incoming DNA recombines with the chromosome, a Trp+ recombinant transductant may arise. Only one strand of the DNA is shown. Reprinted from L. Snyder and W. Champness, Molecular Genetics of Bacteria, 2nd ed. (ASM Press, Washington, D.C., 2003), with permission from the American Society for Microbiology.

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4
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References

/content/book/10.1128/9781555817794.chap4
1. Dale, J. W.1998. Molecular Genetics of Bacteria, 3rd ed.John Wiley & Sons, Ltd., Chichester, United Kingdom.
2. Klug, W. S.,, and M. R. Cummings.2001. Essentials of Genetics, 4th ed.Prentice-Hall, Upper Saddle River, N.J.
3. Madigan, M. T.,, J. M. Martinko,, and J. Parker.2000. Brock Biology of Microorganisms, 9th ed.Prentice Hall, Upper Saddle River, N.J.
4. Prescott, L. M.,, J. P. Harley,, and D. A. Klein.1999. Microbiology, 4th ed.McGraw-Hill, Boston, Mass.
5. Snyder, L.,, and W. Champness.2003. Molecular Genetics of Bacteria,2nd ed.ASM Press, Washington, D.C.
6. Winter, P. C.,, G. I. Hickey,, and H. L. Fletcher.1998. Genetics.Springer Verlag, New York, N.Y.
7. Drlica, K.,2000. Chromosome, bacterial, p. 808821. In J. Lederberg (ed.), Encyclopedia of Microbiology, 2nd ed., vol. 1.Academic Press, Inc., San Diego, Calif.
8. Khan, S. A.1997. Rolling-circle replication of bacterial plasmids.Microbiol. Mol. Biol. Rev.61:442455.
9. Thomas, C. M.,2000. Plasmids, bacterial, p. 711729. In J. Lederberg (ed.), Encyclopedia of Microbiology, 2nd ed., vol. 3.Academic Press, Inc., San Diego, Calif.
10. De la Cruz, F.,, and J. Davies.2000. Horizontal gene transfer and the origin of species: lessons from bacteria.Trends Microbiol.8:128133.
11. Heinemann, J. A.,2000. Horizontal transfer of genes between microorganisms, p. 698707. In J. Lederberg (ed.), Encyclopedia of Microbiology, 2nd ed., vol. 2.Academic Press, Inc., San Diego, Calif.
12. MaGee, D. J.,, C. Coker,, J. M. Harro,, and H. L. T. Mobley.Bacterial genetic exchange. Accepted for publication in Encyclopedia of Life Sciences.Nature Publishing, London, United Kingdom.
13. Frost, L. S.,2000. Conjugation, bacterial,, p. 847862. In J. Lederberg (ed.), Encyclopedia of Microbiology, 2nd ed., vol. 1.Academic Press, Inc., San Diego, Calif.
14. Wilkins, B. M.,, and P. A. Meacock,, 2000. Transformation, genetic, p. 651665. In J. Lederberg (ed.), Encyclopedia of Microbiology, 2nd ed., vol. 4.Academic Press, Inc., San Diego, Calif.
15. Masters, M.,2000. Transduction: host DNA transfer by bacteriophages, p. 637650. In J. Lederberg (ed.), Encyclopedia of Microbiology, 2nd ed., vol. 4.Academic Press, Inc., San Diego, Calif.
16. Bennett, P. M.,2000. Transposable elements, p. 704724. In J. Lederberg (ed.), Encyclopedia of Microbiology, 2nd ed., vol. 4.Academic Press, Inc., San Diego, Calif.
17. Rice, L. B.1998. Tn916 family conjugative transposons and dissemination of antimicrobial resistance determinants.Antimicrob. Agents Chemother.42:18711877.

Tables

Generic image for table
Table 4.1

Major types of plasmids a

Citation: Mascaretti O. 2003. Molecular Genetics of Bacteria, p 69-86. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch4

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