8.10

Pan genome

The sum total of genes encoded by the various strains of a given species. Has 3 sets of genes. Core genome, accessory genome and unique genome

Core genome

Common to all strains of the species

Accessory genome

Present in more than one but not all strains of the same species

Unique genome

Food in only one strain of the species. 

Mobile genetic elements

segments of DNA that are significant contributors to genome variation which can move from one DNA molecule to another. Some are plasmids, transposons, genomic islands and phage DNA

Mobilome

Total set of MBEs in a genome

Plasmids

Common in the microbial world and are found in many bacteria and archaea and in some eukaryotic like yeasts. Most are circular double stranded DNA molecules. They has an origin. of replication so they can be replicated in a cell and passed to progeny cells. They don’t encode information essential to life so cells can survive if they're lost. Theyre important bc they provide cells w the ability to survive in a particular environment. Some are small and carry only a few genes while others are large and carry many

Low copy number plasmids

occur in only 1 or a few copies per cell

High copy number plasmids

Present in many copies, even 500. 

Narrow host range

Most plasmids have a narrow host range meaning they can replicate in only 1 species.

Broad host range

plasmids that can replicate in many different species including gram positive and negative species 

How are bacterial plasmids transferred

By conjugation. Conjugative classmates are self transmissible so they carry out all the genetic information needed for transfer, including origin of transfer

Mobilizable plasmids

they encode an origin of transfer, but lack other genetic information required for transfer. But what when a self transmissible plasma is in the same cell as a mobilizable plasmid either possibly can be transferred. some plasmids can be transferred to unrelated species. Jeans carried on one type of bacterial plasmid can be transferred to plant cells by processes similar to conjugation.

resistance or R plasmids

Important medically because they encode resistance to antimicrobial chemicals like antibiotics. Many of these plasmids are conjugative carrying genes encoding resistance, and also genes for pilus synthesis and other properties required for conjugation. because most of them have a broad host range and carrying multiple resistance genes, they can allow a wide variety of organisms to become resistant to many different anti-microbials. Members of the normal microbiota that carry R plasmids can potentially transfer them to pathogens.

Transposons

in addition to causing mutations, transponsons provide a mechanism for transferring genes. They can move into other replicons in the same cell without any specificity to where they insert.

Insertion sequence

The simplest type of transposons. Encodes only transposase (the enzyme responsible for transposition) On each side of the genes are inverted repeats, sequences that are identical when read in the 5-3 direction.

Composite transponsons

Type of transposon that consists of one or more genes flaked by IS. they can move into other the same replacing or from one replicon to another in the cell. The movement is easily followed if they encode a recognizable gene product like antibiotic resistance. They integrate into their new location through non-homologous recombination

Non-homologous recombination

Process that doesn’t require a similar nucleotide sequence in the region of recombination. The transposon inserts into a stretch of DNA but does not replace the existing sequence. If a transposon inserts into a combative plasmid, it can be transferred into other cells. Any gene or group of genes flanked by ISs can move to another site but transposons that carry genes for antibiotic resistance are important metabolically.

Genomic islands

Large DNA segments in a cells genome that originated in other species. Came to this conclusion bc their nucleotide comosition is different from the rest of the cells genome. Each bacterial species has a characteristic proportion of GC base pairs, so large segments of DNA that has a very different GC ratio, suggests that the segment originated from a foreign source and was transferred to the cell through horizontal gene transfer.

characteristics encoded by genomic islands

the use of specific energy sources, acid tolerance, the development of symbiosis, and the ability to cause disease diseases

pathogenicity Islands

genomic islands that encode the latter

what can certain phages do?

certain types of phages can insert their DNA into the host cells, chromosome causing the phage DNA to become a part of the host cells genome which will be replicated in past to offspring.

prophage

when inserted into the host sells DNA that phage DNA is called a prophage