1. Genetics of Bacteria Ⅰ Genetic Materials Ⅱ Mechanisms of variation
ⅠⅡⅢ
Ⅰ Genetic Materials
Ⅱ Mechanisms of variation
DR.Ahmed MD

2. Ⅰ. Genetic materials

3. Plasmid Chromosome DNA of bacteriophage Transposable element
(transposon)

4. Virulence changing: pathogenicity island
1.Chromosome
Virulence changing: pathogenicity island
(PAI), encoding drug resistance
All of the essential genes and many nonessential genes of the bacterium are generally carried on a single, long piece of circular double-stranded DNA. This molecular structure is called the “chromosome” by analogy with the heredity-carriers of eukaryotic cells.
Most bacteria have chromosomes that contain 2,000 to 4,000
genes.

5. Pathogenicity islands
Pathogenicity islands are discrete genetic elements that encode virulence factors, such as toxins, adhesins, secretion systems, and iron transport proteins. These islands, which range in size from 10 to 200 kB, can be horizontally transferred between bacteria, resulting in enhanced virulence and fitness in the recipient.
Horizontal gene transfer is any process (such as transformation, transduction, or bacterial conjugation) in which an organism incorporates genetic material from another organism without being the progeny of that organism.
By contrast, vertical transfer occurs when an organism receives genetic material from its ancestor, for example, a species from which it has evolved.
Pathogenicity islands differ from the rest of the chromosome in G+C content and are usually flanked in the recipient's chromosome by repeated sequence elements or genes that encode tRNAs.

6. 2.Plasmids
definition: Extrachromosomal genetic elements that are capable of autonomous replication (replicon) episome - a plasmid that can integrate into the chromosome

8. plasmid Self-replicating circular pieces of DNA
1-5% the size of bacterial chromosome
“mini-chromosome”
Bacteria can store up many different plasmids for their use & can transfer these to other bacteria.
They can contain any gene that the bacteria don’t require but are useful to the survival of the bacteria. For example antibiotic resistance genes, toxin production, etc.

9. Plasmids can carry genes that encode toxins or proteins that promote the transfer of the plasmid to other cells but usually do not include genes that are essential for cell growth or replication.
Many plasmids contain mobile DNA sequences (transposons) that can move between plasmids and between plasmids and the chromosome .
Transposons, the repository for many antibiotic resistance genes, are responsible for the ability of some plasmids to integrate into the chromosome.

10. Types of Plasmids Transfer properties Phenotypic effects Conjugative
Nonconjugative
Phenotypic effects
Fertility (F plasmid)
Virulence plasmid (Vi plasmid)
Colicinogenic plasmid ( Col plasmid)
Resistance plasmid (R plasmid)
Throughout

11. Antibiotic Resistance (R) Plasmids
Some plasmids can carry many antibiotic resistance genes.
When bacteria collect many plasmids and these plasmids have many antibiotic resistance genes, a “superbug” may originate.

12. 3.Transportable Elements
Definition: Segments of DNA that are able to move from one location to another (IS+Tn)
Properties
“Random” movement
Not capable of self replication
Transposition mediated by site-specific recombination
Transposase
Transposition may be accompanied by duplication

13. Transposons (Tn)
Definition: Elements that carry other genes except those involved in transposition
Nomenclature - Tn10
Structure
Composite Tns IS
Resistance Gene(s)
Importance
Antibiotic resistance

14. Transposons Transposons-
Small segments of DNA that can move (be transposed) from one region of a DNA molecule to another.
“jumping genes”
Involved in
Changes in traits such as colony morphology, pigmentation, and antigenic characteristics
Replacement of damaged DNA
Intermicrobial transfer of drug resistance (in bacteria)

15. A replicative transposon can move from place to place in the chromosome, leaving a copy of itself behind at the previous site.

16. Insertion sequences (IS)
Definition: Elements that carry no other genes except those involved in transposition
Transposase
ABCDEFG
GFEDCBA
Importance
Mutation
Plasmid insertion
Inversive repeat sequence

17. 4. Bacteriophage (Phage)
Definition - Obligate intracellular parasites that multiply inside bacteria
by making use of some or all of the host biosynthetic machinery.
Utilize

18. Bacteriophage replication. Clock
indicates total elapsed time starting with attachment at t = 0.

19. Bacteriophage

20. Composition and Structure
Nucleic acid
Genome
Modified bases
Protein
Protection
Infection
Head/Capsid
Contractile Sheath
Tail
shell
Structure (T4)
Head or capsid
Tail
Tail Fibers
Base Plate

21. Infection of Host Cells
Adsorption
LPS for T4
Irreversible attachment
Penetration
Sheath Contraction
Nucleic acid injection

22. Types of Bacteriophage
Virulent pgage
Lysogenic or temperate phage
1.Lytic or virulent phage:
Phage that can only multiply within bacteria and kill the cell by lysis. (e.g., T4)

23. Virulent phage
Infection of a bacterium with a virulent phage inevitably results in the death of the cell by lysis, with release of newly replicated phage particles. Under optimal conditions, a bacterial cell infected with only one phage particle can produce hundreds of progeny in 20 minutes.
[Note: Generally, phage that attack one bacterial species do not attack other bacterial species.]

24. Bacteriophage lytic life cycle

25. 2.Lysogenic or temperate phage:
Phage that can either multiply via the lytic cycle or enter a quiescent state in the bacterial cell. (e.g., )
Expression of most phage genes repressed
Prophage
Lysogen

26. A bacterium infected with a temperate phage can have the same fate as a bacterium infected with a virulent phage (lysis rapidly following infection).
However, an alternative outcome is also possible: Namely, after entering the cell, the phage DNA, rather than replicating autonomously, can integrate into the chromosome of the host cell. In this state (prophage), the expression of phage genes is repressed indefinitely by a regulatory protein encoded within the phage genome. No new phage particles are produced, the host cell survives, and the phage DNA replicates as part of the host‘ chromosome.

28. Significance of Lysogeny
Lysogenic or phage conversion
Definition: A change in the phenotype of a bacterial cell as a consequence of lysogeny
Modification of Salmonella O antigen
Toxin production by Corynebacterium diphtheriae
Epitope, phenotype

29. Bacteriophage Significance
Gene transfer in bacteria or in mechanisms of bacterial variation
Medical applications
Identification of bacteria - phage typing
Treatment and prophylaxis
Understanding variation of bacteria in virulence and drug resistance

30. Mechanism of lysogeny
Lysogenic bacteria carry a prophage. This phenomenon is termed “lysogeny,” and the bacterial cell is said to be “lysogenized.” Nonlysogenic bacteria can be made lysogenic by infection with a temperate phage. The association of prophage and bacterial cell is highly stable but can be destabilized by various treatments, such as exposure to ultraviolet light, that damage the host DNA. When DNA damage occurs, repression of phage genes is lifted, and the prophage excises from the host chromosome, replicates autonomously, and produces progeny phag particles. The host cell is lysed just as with a virulent phage. The emergence of the virus from its latent prophage state is called induction. The acquisition by bacteria of properties due to the presence of a prophage is called lysogenic conversion.

31. Ⅱ. Mechanisms of Variation
Gene mutation
Gene transfer and recombination

32. Mechanisms of genetic variation of bacteria
1. Gene Mutation

33. Some mutations are unstable (that is, they frequentl revert back to their original state), and others do not noticeabl affect the organism. Mutations that come under study are usually those that are stable and that cause some change in the characteristics of the organism. Mutations can be classified according to the kind of chemical change that occurs in the DNA or, when the mutation affects a protein-coding gene, by the effect the mutation has on the translation of the message.

34. Mutations arise in bacterial populations
Mutations in Bacteria
Mutations arise in bacterial populations
Induced
Spontaneous
Gene transfer occurs in bacteria
Phenotypic variation
rug-resistant mutants

35. Experiment of Replica culture
Confirmed selection of drug resistance

36. 2. Gene transfer and recombination
Mechanisms of genetic variation of bacteria
2. Gene transfer and
recombination

37. Transformation
Definition: Gene transfer resulting from the uptake of DNA from a donor.
Factors affecting transformation
DNA size and state 10~20 genes
Sensitive to nucleases
Competence of the recipient (Bacillus, Haemophilus, Neisseria, Streptococcus)
Competence factor
Induced competence

38. Transformation
Occurs when naked DNA fragments of one bacteria are close to another living cell.
Some bacteria have the ability to pick up naked DNA fragments and recombine the DNA into their own DNA
The new recombinant cell now has some new DNA from the disintegrating cell.
The now transformed bacteria could have just picked up a new virulence factor or antibody resistance

39. Transformation of S.pneumonia

40. Steps Significance Uptake of exogenous DNA Recombination
Recombinant DNA technology

41. Transduction Types of transduction
The transfer of donor gene to recipient is mediated by temperate phage Bacterial DNA is transferred from a donor cell to recipient inside a virus that infects bacteria
Bacteriophage (phage)
Types of transduction
Generalized Transduction in which
potentially any donor bacterial gene can be
transferred.
Specialized Transduction in which only certain donor genes can be transferred

42. Mechanism of Transduction
Virus mediated gene transfer
The virus injects its genetic material into the bacteria
The bacterial DNA is fragmented

43. Mechanism of Transduction
Viral particles are produced by the bacteria
When the cell lyses, the viral particles which have picked up DNA from the original bacterial cell now insert that DNA into a new cell.
The new cell may or may not insert the new DNA sequence into its chromosome.
Transduction can be a problem when the inserted DNA codes for an antibiotic resistance gene.

44. Generalized Transduction
Infection of Donor
Phage replication and degradation of host DNA
Assembly of phages particles
Release of phage
Infection of recipient
Recombination

45. Generalized transduction

46. Specialized Transduction mediated by lysogenic phage
Excision of the prophage
Replication and release of phage
Infection of the recipient
Lysogenization of the recipient
A deviation take place this moment called specialization transduction.

48. Lysogenic conversion
The gene transfer from donor to recipient is mediated by temperate phage
Exotoxin
( virulent protein )
prophage

49. Significance Lysogenic conversion
Corynebacterium diphtheriae producing diphtheria toxin
Clostridium botulinum produceing Botulinum toxin
Stretococcus pyogen producing pyrogenic exotoxin

50. Conjugation
Gene of donor transferred to recipient is mediated by sex pilus , Movement of a plasmid b/w two cells
Plasmid: small, self-replicating, gene-containing circular piece of DNA
Requires direct cell to cell contact
Opposite mating types (donor cell has a plasmid, recipient cells do not)

51. Conjugation
A donor cell contains a F (fertility) plasmid making it F+.
A conjugation pilus (genes for which are on the F+ plasmid) forms and the donor cell transfers a copy of the F plasmid to the recipient.
Now, both cells have a F plasmid F+ plasmids can have other genes on them too, for example antibody resistance containing genes

53. Mating types in bacteria
Donor
Mating types in bacteria
Donor
F factor (Fertility factor)
F (sex) pilus F+
Recipient
Recipient
Lacks an F factor F-

54. Physiological states of F factor
Autonomous (F+)
Characteristics of F+ x F- crosses
F- becomes F+ while F+ remains F+
Low transfer of donor chromosomal genes F+

55. Autonomous with donor genes (F’)
Characteristics of F’ x F- crosses
F- becomes F’ while F’ remains F’
High transfer of donor genes on F’ and low transfer of other donor chromosomal genes
Hfr F’
Automatic autonomous

56. Resistant transfer factor, RTF
R determinant
R plasmid

57. Significance of conjugation
Gram negative bacteria
Antibiotic resistance
Rapid spread
Gram positive bacteria
Production of adhesive factors by donor cells

58. Mechanisms of acquired antibiotic resistance
1. Decreased uptake of antibiotic: Gram-negative organisms can limit the penetration of certain agents, including β-lactam anti - biotics, tetracyclines, and chloramphenicol, as a result of alteration in the number and structure of porins (proteins that form channels) in the outer membrane.
2. Antibiotic efflux: Some gram-negative organisms encode multicomponent membrane-imbedded efflux systems that recognize and pump out diverse, toxic substances, including detergents and antibiotics. Expression of these systems is generally tightly regulated and often induced by the presence of substrates recognized by the pump.

59. 3. Alteration of the target site for antibiotic: Streptococcu pneumoniae resistance to β-lactam antibiotics, for example, involves alterations in one or more of the major bacterial penicillin-binding proteins ,which results in decreased binding of the antibiotic to its target.
4. Acquisition of the ability to destroy or modify the antibiotic: Examples of antibiotic inactivating enzymes include: 1) β-lactamases that hydrolytically inactivate the β-lactam ring of penicillins, cephalosporins, and related drugs; 2) acetyltransferases that transfer an acetyl group to the antibiotic, inactivating chloramphenicol or aminoglycosides; and 3) esterases that hydrolyze the lactone ring of macrolides.

60. 5. Acquisition of a new target: Some Staphylococcus aureus isolates, for example, are vancomycin resistant due to expression of newly acquired genes that modify the D-ala-D-ala (the target of vancomycin) residues on the stem peptide, converting them instead to D-ala-D-lac. Although this new target is effectively polymerized to form a peptidoglycan network with sufficient stability, D-ala-D-lac is not bound by vancomycin, and, therefore, the antimicrobial agent is no longer effective.

61. A. Glycine bridge in the peptidoglycan of Staphylococcus aureus. B
A. Glycine bridge in the peptidoglycan of Staphylococcus aureus. B. Organization of peptidoglycan layer in gram-positive cells.

62. Question 1 A lysogenic bacterium A. carries a prophage.
B. causes lysis of other bacteria on contact.
C. cannot support the replication of a virulent phage.
D. is often a human pathogen.
E. is usually not capable of conjugal genetic transfer.

63. Correct answer = A.
A lysogenic bacterium can generate phage because it carries phage genes in a latent state (prophage).
Lysogeny does not impart any special lytic properties to the bacterium nor, in general, does it affect conjugal transfer or the ability to support the replication of other unrelated phage. The presence of a prophage can convert certain bacteria to human pathogens, but such cases are rare.

64. Question 2
Which one of the following statements concerning plasmids is true?
A. All plasmids can be transfered between bacteria by conjugation.
B. Much of the information coded in the plasmid is essential to the survival of the bacteria cell.
C. Resistance plasmids carry genes for antibiotic resistance.
D. Resistance plasmids cannot be transferred to other bacterial cells.
E. Plasmids lack an origin of replication.

65. Correct answer = C.
Plasmids are small, circular, supercoiled DNA molecules found in some bacteria. They usually do not carry essential genes, but some plasmids, such as R (resistance) plasmids, carry genes coding for antibiotic resistance. All plasmids have their own origin of replication, so that they are replicated along with the host chromosome and passed along to progeny cells. Only some plasmids possess genes that allow for transmittal to other bacteria by the process of conjugation.

66. Question 3
What occurs when a temperate bacteriophage enters a state called “lysogeny”?
A. Most viral genes are expressed.
B. The bacterial cell is lysed.
C. Many new viruses are produced.
D. Most normal bacterial functions are turned off.
E. The virus may become integrated into the host genome.

67. Correct answer = E There are two types of bacteriophages:
1 lytic and 2 temperate.
The distinction is made according to the life cycle of the bacteriophage. On entering a bacterium, lytic phages produce phage nucleic acids and proteins, assemble many new phage particles, lyse the cell, and release the progeny phage. Temperate phages, however, can penetrate the bacterium and enter a dormant state called lysogeny, in which most viral genes are repressed. Bacterial functions remain active and the bacterium is not harmed. Some dormant phages replicate as plasmids; others, such as phage λ (lambda), become integrated into the host genome as prophages. The prophage DNA is replicated along with the host DNA as the bacterium grows and divides.

68. Question 4
A virulence factor can be transferred from one strain of bacteria to another in a genetic process that is independent of cell-to-cell contact between the donor and the recipient. Addition of DNase does not interfere with the transfer of the virulence factor either. From these characteristics, which of the following processes is involved in this genetic transfer?
A. Conjugation
B. Transformation
C. Transduction
D. Transposition
E. Transversion

69. Correct answer = C
Transduction is the process by which genetic material is transferred from donor to recipient within a bacteriophage. This process does not require cell-to-cell contact and is resistant to DNase.
Conjugation requires cellto- cell contact between the donor and receipient cells.
Transformation involves the exchange of naked DNA between donor and recipient in the absence of cell-to cell contact. However, DNA transformation is sensitive to DNase treatment.
Transposition is the process in which a transposon excises from one location and integrates in another location within the same bacterial cell. Thus this process would not explain the transfer of a genetic marker between different bacterial cells.
Transversion is not a means of genetic exchange.