Microbial Genetics ICA

Consider the mode of transfer and the types of bacterial genes that can be transferred via transformation

Mode of Transfer: This process involves the uptake of "naked" extracellular DNA directly from the surrounding environment. For transformation to occur, the recipient bacterium must be in a physiological state called competence, allowing it to transport DNA fragments across its cell wall and membrane. No physical contact between cells or external vectors are required.

Types of Genes Transferred: Typically limited to small, random fragments of chromosomal DNA or small plasmids released into the environment when nearby cells lyse (burst open).

Consider the mode of transfer and the types of bacterial genes that can be transferred via transduction

Mode of Transfer: This process is mediated entirely by bacteriophages (viruses that infect bacteria). When a phage infects a bacterium, it hijacks the cell's machinery to make new viruses. During viral assembly, the phage accidentally packages a piece of the host bacterium's DNA instead of its own viral genome, injecting that bacterial DNA into the next cell it infects.

Types of Genes Transferred:

• Generalized __: Any random fragment of the host's chromosomal DNA can be packaged and transferred. (Result of an error in phage replication –packaging bacterial DNA into a phage head rather than phage DNA, by accident)

• Specialized __: Only specific, restricted sets of host genes—specifically those located right next to where a temperate phage integrates into the chromosome—are transferred. (production of transducing phage from a rare mistake in prophage excision from the chromosome, leads to infection of a recipient cell by a transducing phage)

Consider the mode of transfer and the types of bacterial genes that can be transferred via conjugation

Mode of Transfer: Often referred to as "bacterial sex," conjugation requires direct physical contact between two living cells. A donor cell forms a specialized protein tube called a sex pilus (or mating bridge) to attach to a recipient cell and directly transfer a single strand of DNA.

Types of Genes Transferred: Primarily plasmids (such as resistance plasmids or virulence plasmids). Because plasmids often carry genes that benefit survival under stress, conjugation is a primary driver for spreading multi-drug resistance and pathogenicity across bacterial populations. Sometimes, if a plasmid has integrated into the chromosome (an Hfr strain), large chunks of chromosomal DNA can also be transferred. (In general, a much larger quantity of DNA can be transferred by means of ____ than by transformation or transduction.)

Consider the genes that can be transferred and how the transferred genes can be inherited by progeny cells via F plasmid Conjugation

Standard F Plasmid Conjugation (F+ to F-)

In standard conjugation, the donor cell carries a separate, autonomous F plasmid.

• Genes Transferred: Only the genes encoded on the F plasmid itself (such as genes for the sex pilus, surface exclusion, and plasmid replication). Host chromosomal genes are left behind and not transferred.

• Inheritance by Progeny: The recipient cell receives a complete copy of the F plasmid, turning it into a new donor (F+). Because the F plasmid possesses its own origin of replication, it replicates independently within the cell and is passed down to all daughter cells via standard plasmid segregation during binary fission.

Consider the genes that can be transferred and how the transferred genes can be inherited by progeny cells via Hfr Conjugation

The F plasmid physically integrates directly into the host bacterium's main chromosome, creating an Hfr strain.

• Genes Transferred: During conjugation, the transfer machinery starts inside the integrated F plasmid sequence and begins dragging a long, linear chunk of the host bacterium's chromosomal genes along with it into the recipient cell in a specific direction. (The amount of DNA transferred depends on the amount of time the conjugation lasts.). Because conjugation usually breaks before the entire chromosome can cross, the recipient almost never receives the complete tail-end of the F plasmid, meaning the recipient remains F- (non-donor).

• Inheritance by Progeny: Because the transferred host genes are linear and lack an independent origin of replication, they cannot survive on their own. For progeny cells to inherit them, the linear fragments must undergo homologous recombination with the recipient cell's own chromosome. If recombination occurs, the traits are permanently integrated and passed down vertically through binary fission.

Consider the genes that can be transferred and how the transferred genes can be inherited by progeny cells via F’ Conjugation

An F' plasmid is born from a "mistake." When an integrated F plasmid tries to loop out and exit the chromosome of an Hfr strain, it makes an imprecise excision, accidentally pulling a specific piece of adjacent host chromosomal DNA out with it into a new, circular plasmid–the F’ plasmid, the F plasmid that also carries some chromosomal genes. The genes on the F’ plasmid are transferred to a recipient F- cell during conjugation. 

• Genes Transferred: The modified F' plasmid, which carries both the standard F plasmid genes and specific host chromosomal genes that were trapped during excision.

• When this F' plasmid is transferred to a recipient cell, the recipient becomes an F' donor and is temporarily a partial diploid (having two copies of those specific host genes). Because the F' element is a self-replicating plasmid, it replicates autonomously and is stably passed down to progeny cells during division, though its chromosomal components can also undergo recombination.

Theoretically can any gene be transferred by Hfr conjugation?

Yes. Given sufficient time and an unbroken conjugation bridge, an Hfr strain can theoretically transfer the entire circular bacterial chromosome starting from the origin of transfer within the integrated F plasmid. Additionally, because the F plasmid can integrate at multiple different sites around the chromosome across various strains, any specific gene can theoretically be positioned near the leading edge of transfer.

Theoretically can any gene be transferred by F’ conjugation?

No. An F' plasmid is generated by the imprecise (aberrant) excision of an integrated F plasmid from the chromosome. As a result, it can only carry the plasmid sequences along with a small, specific set of host genes immediately flanking the integration boundaries. It cannot transfer arbitrary genes located elsewhere on the chromosome.

Theoretically can any gene be transferred by generalized transduction?

Yes. Because lytic bacteriophages package random fragments of host chromosomal DNA into capsids by mistake during the packaging stage, any gene has a theoretical chance of being packaged and transferred to a new host.

Theoretically can any gene be transferred by specialized transduction?

No. This mechanism is strictly site-specific and restricted to temperate phages that integrate into a specific attachment site (such as the attB site). Only genes directly adjacent to the prophage insertion site can be aberrantly excised and transferred.

Theoretically can any gene be transferred by transformation?

Yes. Because any portion of the bacterial chromosome can be sheared into naked extracellular DNA and taken up by a competent recipient cell, any gene can theoretically be acquired and integrated via homologous recombination.

Which genes (1, 2, 3, 4, and/or 5) are more likely to be transferred via Hfr conjugation and explain why.

5 is most likely because of directionality of where the integrated F plasmid is going to be dragged
which is → according to picture

Which genes (1, 2, 3, 4, and/or 5) are more likely to be transferred via F’ conjugation and explain why.

1 and 5, because they are the closest to the F plasmid

Which genes (1, 2, 3, 4, and/or 5) are more likely to be transferred via generalized transduction and explain why.

All of them are equally likely, and there is no favoritism because of the randomness in the mistake in phage replication

Which genes (1, 2, 3, 4, and/or 5) are more likely to be transferred via specialized transduction and explain why.

3 and 4, because they are closest to the attb (excision) site

Which genes (1, 2, 3, 4, and/or 5) are more likely to be transferred via transformation and explain why.

All genes are equal, because it’s completely random.