8 Bacterial Genetics

Natural Selection

Principle that states those with greater fitness (desirable qualities for survival) have higher chance of living and passing them on

Phenotype changes as result

→ influenced by environmental conditions

→ influenced by genotypes that are selectively passed on due to said conditions

Horizontal gene transfer

½ ways genetic change can occur in bacteria.

[__]: acquisition of DNA from other cells and their environment

transformation

1/3 mechanisms on how genes undergo horizontal gene transfer

[__]: acquisition of naked DNA from the surrounding; uptake by bacteria

Frederick Griffith

Discovered mechanism of transformation while working with Streptococcus pneumoniae, which existed in (2) forms

• smooth in appearance (encapsulated) » virulent form

• rough in appearance (nonencapsulated) » avirulent form

Injected varying combinations of the two into mice; found the dead virulent form affected the living avirulent form

living avirulent form —(transformation) → living virulent form

wherein the avirulent form took up the genes of the dead virulent form in their surroundings to learn how to become virulent themselves

transduction

2/3 mechanisms on how genes undergo horizontal gene transfer

[__]: bacterial DNA transfer from donor to recipient via a bacterial virus (bacteriophage)

→ bacteriophage may contain bacterial DNA from its original host cell it was duplicated from by the DNA accidentally entering the phage

→ transfers DNA (and doesn’t infect as it contains only bacterial cell DNA) this way

bacteriophage

Virus that infects bacteria.

Infects host cell to break down its genetic material, and utilize the rest of its cellular components to duplicate their viral DNA instead (not the bacteria’s) » mass production of [__]

• transduction is able to happen when bacterial DNA mistakenly packages the original bacteria’s DNA (from the surroundings) into the [__]

conjugation

3/3 mechanisms on how genes undergo horizontal gene transfer

[__]: DNA transfer between cells via cell-to-cell contact via sex pillus

• mediated by a conjugative plasmid F factor: fertility factor

  • determines if the cell has a sex pillus

  • makes them “F+”

• cells must be of opposite mating types

  • F+ cells » donor cell

  • F- cells » recipient cell (does not have F+ plasmid)

mobile gene pool

All the extrachromosomal DNA not part of chromosome

• plasmids, transposons, genomic islands, phage DNA

• very common

  • found even in our DNAcontributed to the idea that we’re genetically advance due to larger DNA, but in actuality, don’t code for anything

• confers some advantage to bacterium to survive in certain environments

plasmid

Self replicating extrachromosomal DNA (possible due to origin of replication on its DNA)

→ many are R [__]: “resistance” [__] » confer a lot of resistance to antimicrobial medication and heavy metals like mercury and arsenic

→ other [__] can provide beneficial characteristics such as

• nitrogen fixation (Rhizobium sp.)

• oil degradation (Pseudomonas sp.)

Mutation

2/2 ways genetic change can occur in bacteria.

[__]: Changes in base sequence of DNA

Spontaneous mutation

Mutation that occurs randomly in the absence of a mutagen

Mutation rate: 10^-4 and 10^-12 for a given gene

→ DNA polymerase does its job of synthesizing and going back to double-check it, so mutation is very rare

For Bacteria, all and any mutations are passed unto offspring

For Eukaryotes, only mutations in the germ cells are passed on to offspring

amino acid

Note: everything here on forth for mutations are referred in terms of the proteins/[__] that the DNA produces

recall: DNA — mRNA → Protein

when the mRNA has a mutation from any of the following reasons

• incorrect (nitrogenous) base substitution

• nucleotide deletion/addition

• jumping genes

we reference the impact on the [__] synthesized from these mRNA mutations

point mutation

Most common cause of mutation wherein there is a “base substitution” » incorrect nucleotide incorporated during DNA replication

[__]: single base pair is involved in mutation → substituted, inserted, deleted (for insertions/deletions, if it “moves” reading frame, it’s a reading frame mutation!)

• silent mutation: same amino acid, no observable change in protein

  • due to the redudancy of the amino acids

• missense mutation: different amino acid, resulting in partially functional (leaky) protein

• nonsense mutation: stop codon produced. yields a shorter protein

frameshift mutation

Most detrimental form of mutation where there is a “deletion or addition of nucleotides”

[__]: mutation that shifts the translational reading frame

• affects all amino acids downstream

• produces totally different protein or generate stop codons

transposon

Jumping genes. Lead to knock out mutations as the DNA pieces transposition » move spontaneously from one location to another

→ combining DNA this way is called nonhomologous-recombination

→ usually inactivates the gene it hops into

• insertion sequence: simplest type of [__]; contains one gene. has inverted repeats on both ends

  • transposase enzyme → cuts out the IS and inserts it into another gene. recognizes IS by its inversion sequences

• composite [__]: include one or more genes; can confer antimicrobial resistance. has IS on ends

Induced mutations

Mutations that result from outside influence

• done through mutagens: agent that induces DNA change

  • chemical

  • radiation

Nitrous acid

Chemical mutagen.

Changes cytosine to uracil

» base-pairs with adenine instead of guanine

Intercalating agents

Chemical mutagen that works by inserting themselves between adjacent bases

• creates space between bases

• → potentially adds an extra base (can cause frame-shift mutation)

  • ethidium bromide

  • acridine

  • chloroquine

  • (potential pathogen and carcinogen as they can potentially cause this mutation)

Ultraviolet irradiation

Radiation mutagen. Causes thymine dimers: a pair of adjacent thymine bases bonded together, upon exposure

• DNA and RNA polymerase can’t read these during replication and transcription, respectively

• stalls processes till something happens

  • might read thymine dimer as a single base and place a random base → deletion mutation (read 2 bases instead of 1)

X rays

Radiation mutagen. Causes breakages and alterations in DNA that are more detrimental

→ double-strand breaks (lethal)

mismatch repair

Repairing of base substitution during DNA replication

• DNA polymerase proofreads synthesized DNA

• cuts out incorrect base substitution and resynthesizes correct DNA

• fixed DNA gets sealed by DNA ligase

Photoreactivation

Repairing of UV light damage

Light repair

• photolyase: enzyme that utilizes energy from light to break covalent bond of thymine dimer

• restores thymine to their original form!

• only found in bacteria

Excision repair

Repairing of UV light damage

Dark repair

• enzyme recognizes thymine dimer protrusion from DNA

• enzymes remove affected area

• DNA polymerase and DNA ligase fill in and repair gap

Xeroderma pigmentosum

Genetic disorder where there are defects in the genes that produce enzymes for excision repair

→ inability to repair DNA damage caused by UV light

→ exposure to sunlight is limited or forbidden

» very vulnerable to skin carcinoma (skin cancer)