Genetics - A. V. Sivolob 2008

Genetics of Bacteria, Viruses, and Unicellular Eukaryotes
Bacteriophages

Bacteriophages (bacterial Viruses) are divided into two types: virulent phages, which penetrate the host Cell, replicate, and cause cell lysis (the lytic pathway); and temperate phages, which can follow either the lytic pathway or the lysogenic pathway, where the phage DNA is integrated into the bacterial genome via Site-Specific Recombination (see the next subsection), transforming the phage into a prophage. In the latter case, under conditions unfavorable to the bacterium, bacteriophage induction can occur, leading to a transition to the lytic pathway.

The process of transferring genetic material between bacterial Cells mediated by bacteriophage activity is called Transduction. This is typically carried out by temperate phages: following a virtually unlimited period of phage DNA persistence within the bacterial genome, induction occasionally leads to the excision of the phage DNA along with adjacent bacterial sequences. This is followed by METABOLISM/36.html">DNA Replication, the synthesis of phage capsid Proteins (encoded within the phage DNA genes), and the assembly of phage particles. These phage particles then infect other cells and, if the lysogenic pathway is adopted, integrate into the host cell's genome along with the previously captured bacterial genes. Examples of temperate phages include phages P1, P22, and λ (see the Overview of the λ phage life cycle below). The DNA of temperate phages can be viewed as a component of the bacterial genome that occasionally escapes regulation: bacteriophage genes are indistinguishable from bacterial genes, meaning they operate under the control of promoters recognized by the host cell's bacterial RNA polymerase.

Group T bacteriophages are strictly lytic. Like temperate phages, their genome consists of a single linear double-stranded DNA molecule. The DNA of T-even phages (T2, T4, T6) contains approximately 200 kb of Base Pairs, encoding replication system proteins (including their own DNA polymerase), capsid proteins, and specific regulatory proteins that hijack cellular machinery to favor the bacteriophage. Upon DNA entry into The Cell, Transcription of a group of phage genes is initiated by bacterial RNA polymerase, followed by phage DNA replication, synthesis of phage proteins, assembly of bacteriophage particles, and cell lysis.

T-odd phages (T1, T3, T5, T7) follow a similar lytic pathway, with a slightly smaller genome (~40 kb). Immediately after the DNA enters the host cell, the Gene encoding a monomeric phage RNA polymerase is expressed, which then efficiently transcribes the remaining bacteriophage genes.

Bacterial cells possess their own defense systems against bacteriophage DNA. The foundation of this unique "immune system" is restriction Enzymes (Restriction Endonucleases), a large group of specific Nucleases that cleave only specific short Structure/155.html">Sequence Motifs (usually four or six NUCLEOTIDES). The activity of restriction enzymes depends on the methylation of particular nitrogenous bases within specific restriction sites: sites within the bacterial DNA are methylated and thus protected from the restriction enzyme, whereas unmethylated bacteriophage DNA sites remain vulnerable.

Besides phages containing double-stranded DNA as their genetic material, There are two other groups of phages whose genomes deviate from this "canon." The first group comprises bacteriophages with single-stranded circular DNA (φX174, M13). This DNA is relatively small, with phage genes encoding only 10–12 proteins. For instance, The Genome of φX174 (read as "phi-ten"), which was the first genome ever sequenced, is structured with remarkable economy: ten genes (one of which, gene A, produces two different RNA transcripts) span virtually the entire circular bacteriophage DNA (Fig. 5.4). Furthermore, several genes overlap due to The Use of different reading frames: genes A and C, as well as C and D, overlap at their ends, while genes B, K, and E are entirely nested within other genes; three genes—A, C, and K—utilize all three possible reading frames within the same DNA region (naturally, all three frames are open in this case). The phenomenon of gene overlap via alternative reading frames is also observed in several other bacteriophages and occurs in eukaryotes as well.

Inside the bacterial cell, the phage DNA, designated as the (+)-strand, serves as a template for the Synthesis of the (-)-strand. This results in The formation of double-stranded circular DNA, which serves as a template for gene transcription (with the (-)-strand acting as the template) and, following a single-strand nick in the (+)-strand, drives rolling-circle replication (see Fig. 5.2): numerous copies of the (+)-strand are synthesized on the circular (-)-strand, and these fragments are cleaved, circularized, and packaged into the phage capsid.

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Fig. 5.4. Genome of bacteriophage φX174.

The start and end of each gene are indicated; total DNA length is 5386 base pairs.

The final group of bacteriophages (R17, F2, MS2) contains an RNA molecule as its genetic material, comprising only four genes (the phage RNA simultaneously Functions as mRNA) that encode: an RNA-dependent RNA polymerase responsible for copying the phage RNA; two coat proteins; and a lysis protein. Thus, these smallest of all known viruses execute the simplest pathway of hereditary information transfer—exclusively from RNA to RNA and to protein.