12. Bacteria

Question 1

Deifinition

What is OTU (Optional Taxonomic Units)?

Answer 1

Practical Grouping units used classify microorganisms -especially bacteria- Based on similarity of their DNA seq. (mostly 16S rRNA seq)

Variation of 16-18S rRNA shows the relationship of different organisms (phylogenic tree)
Therefore, all living creatures classified as
* Eukaryotes
* Bacteria
* Archaea

e.g.)
- Endosymbiosis
Mitochondria: shows relation to purple bacteria
Chloroplast close to cyanobacteria

Question 2

How prokaryotes recombine genes? (How genetic variations of bacteria formed?)

Answer 2

1. Conjugation
2. Transformation
3. Transduction
4. Plasmids
5. Transporsable Elements

Question 3

What are the differences between auxotrophic and prototrophic?

Answer 3

Note 参照

Question 4

Write the steps of Conjugation between bacteria

Answer 4

ノート参照

Question 5

Is F+ factor replication happens dependent on chromosomal replication?

Answer 5

No. F+ factor replication happens independent on chromosomal replication.

⇒ allow large copy number

Question 6

How high frequency conjugation happen? Name the substance which responsible for it and it definition.

Answer 6

> A bacterial strain in which the F factor is integrated into the chromosomal DNA.During conjugation, the Hfr cell transfers chromosomal genes to an F⁻ recipient at a very high frequency.Because the entire F factor is rarely transferred, the recipient usually remains F⁻ but becomes recombined.

Key points to include in a definition:

• F factor integrated into chromosome
• Transfers chromosomal genes at high frequency
• Recipient typically remains F⁻
• Results in high recombination rates

Question 7

What are the differences between F+ plasmid and Hfr strain?

Answer 7

F+ plasmid
* location: plasmid
* recipient get: F plasmid

Hfr strain
* location: in chromosome
* recipient get: whole chromosomal genes

Question 8

What is the plasmids, and list some types of plasmid

Answer 8

Plasmid = 染色体外に存在する 小型の環状DNA (細菌の生存や競争力を高める遺伝子を運んでいる)

1. R plasmids (Resistance plasmids)

Plasmids that carry genes providing resistance to antibiotics, toxic compounds, or heavy metals, enabling bacteria to survive antimicrobial treatment.

2. Virulence plasmids

Plasmids encoding virulence factors such as toxins or adhesion molecules, allowing bacteria to cause disease in the host.

3. Killer plasmids (K plasmids / Col plasmids)

Plasmids that code for bacteriocins, proteins that kill or inhibit other bacteria, giving the host cell a competitive advantage.

4. Degradative plasmids

Plasmids that contain genes for enzymes capable of degrading unusual or complex organic substances, such as crude oil, keratin, or plastics.

5. Biosynthetic plasmids

Plasmids coding for enzymes of biosynthetic pathways that allow the production of antibiotics or other structurally complex molecules.

Question 9

What are the differences between general transduction and specialized transduction?

Answer 9

General Transduction

• Any random piece of bacterial DNA can be transferred by a lytic phage.
• Occurs due to accidental packaging of host DNA into a phage particle.

Specialized Transduction

• Only specific genes adjacent to the prophage insertion site are transferred.
• Occurs with temperate phages (e.g., λ phage) during incorrect excision from the chromosome.

Question 10

Write the mechanism of transduction and specialized transduction

Answer 10

General Transduction

1. Phage infects the bacterium.
2. Bacterial DNA is fragmented.
3. A fragment of bacterial DNA is mistakenly packaged into a phage head.
4. This transducing phage injects the bacterial DNA into another cell.

Specialized Transduction

1. Temperate phage integrates into the chromosome (lysogeny).
2. When excising, the phage accidentally cuts bacterial genes adjacent to the prophage.
3. Phage particles carry a mixture of phage DNA + specific bacterial genes.
4. This DNA is transferred to the next host.

Question 11

Write the two main pathway of bacteriophage cycles.

Answer 11

lysogenic & Lytic cycle

Question 12

What is pathogenic island? List one example

Answer 12

Bacterial fenome (chromosome), plasmid, bacteriophage に存在する、pathogen に関わるgeneがまとまって配置された大きなDNA region

contains both: virulence + antibiotic registanse gene ⇒ 同じDNA unitで移動

→ Pathogenicity ↑, antibiotic registanse ↑

E.g. ) pB10: tetracyclin resistacse gene + mercury resistance + streptomyocin resistance gene

Question 13

What is virulence gene?

Answer 13

Gene encodes factors enabling microorganism to colonize host, evade or suppress the immune system, cellular damage or obtain essential nutrients

⇒ increase organisms pathogenicity

Question 14

How virulence genes and multiple antibiotic resistance transmitted ？

Answer 14

by conjugation

Question 15

What would happen to the virulence gene if patient infected by multiple infection by ,multiple infections? E.g. インフルエンザ + Haemophilus influenzae

Answer 15

virulence factors of the pathogens add ups

• simultaneous infections are more severe
• infection by one pathogen helps other pathogens (or opportunists) to infect

Question 16

What would happen if the virulence gene’s Virulence factor is weak or less effective?

Answer 16

opportunists (日和見感染)

Less effective virulent factor (weak)

普段は無害 ↔ 病気発生 when Immune system decreases, wound, and burn

e.g. HIV感染

Question 17

What is selective marker? Describe how it is used and an example.

Answer 17

a gene that allows the identification of cells that have successfully taken up a plasmid or genetic element by providing survival under specific selective conditions, such as antibiotic resistance.

Question 18

What is Visible Marker?

Answer 18

A visible marker is a gene whose expression produces an observable phenotype—such as color change, colony morphology, pigment production, or metabolic activity—allowing the researcher to distinguish different bacterial strains without applying lethal selection.

（高得点ポイント：“observable phenotype” と “without lethal selection” が入っている）

見た目の変化（色・形・代謝・コロニー形態など）で判別できるマーカー。

例：

• lacZ → 青白選択（X-gal を使うと青になる）
• pigment genes（色素遺伝子）→ 赤・黄など色が出る
• motility genes（運動遺伝子）→ 動くかどうかで判別

これは抗生物質のような「生死の選択」ではなく、見た目で識別が可能なマーカー。

ポイント：死なない。見た目で識別する。

Question 19

What is Fertility Marker?

Answer 19

細菌が接合(conjugation)できるかどうかを決める能力（F因子に関係した性決定マーカー）。

ノート参照