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Prokaryotic Genome The term Genome was created in 1920 by Hans Winkler,[2] professor of botany at the University of Hamburg, Germany. The Oxford English Dictionary suggests the name to be a blend of the words gene and chromosome. In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of viruses, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA.[1] Genome size Genome size is the total number of DNA base pairs in one copy of a haploid genome. The genome size is positively correlated with the morphological complexity among prokaryotes and lower eukaryotes; however, after mollusks and all the other higher eukaryotes above, this correlation is no longer effective.[13][15] The genome size is positively correlated with the morphological complexity among prokaryotes Table 8.3 Genomes 3 (© Garland Science 2007) Genome Size and Gene Numbers in Various Organisms The number of genes in bacterial and archael genomes is proportional to the genome size 7 Comparative Genome Sizes Relationship of Gene Number and Genome Size While the number of genes in prokaryotes correlates well with the sizes of their genome, the number of genes in eukaryotes does not correct well with their genome sizes Size range BACTERIA E. coli: Example species Ex. Size 1-10 Mb 4.639 Mb FUNGI 10-40 Mb S. cerevisiae 13 Mb INSECTS 100-5000 Mb D. melanogaster 165 Mb BIRDS 1000-1500 Mb Chicken 1300 Mb PLANTS FLOWERING 100 to 100,000 Mb Corn 2500 Mb MAMMALS 3000-4000 Mb Human 3000 Mb 1 Mb = 1 million base pairs. (Probably the number of essential genes does not differ greatly among various multicellular organisms. Most estimates are that humans have about 40,000 genes.) Prokaryotic and Eukaryotic Chromosomes Not only the genomes of eukaryotes are more complex than prokaryotes, but the DNA of eukaryotic cell is also organized differently from that of prokaryotic cells. The genomes of prokaryotes are contained in single chromosomes, which are usually circular DNA molecules. In contrast, the genomes of eukaryotes are composed of multiple chromosomes, each containing a linear molecular of DNA. In prokaryotes, most of the genome (85-90%) is non-repetitive DNA, which means coding DNA mainly forms it, while noncoding regions only take a small part.[12] On the contrary, eukaryotes have the feature of exon-intron organization of protein coding genes; the variation of repetitive DNA content in eukaryotes is also extremely high. When refer to mammalians and plants, the major part of genome is composed by repetitive DNA.[1 The DNA of eukaryotic cell is tightly bound to small basic proteins (histones) that package the DNA in an orderly way in the cell nucleus. For e.g., the total extended length of DNA in a human cell is nearly 2 m, but this must be fit into a nucleus with a diameter of only 5 to 10µm. Although DNA packaging is also a problem in bacteria, the mechanism by which prokaryotic DNA are packaged in the cell appears distinct from that eukaryotes and is not well understood. When talking about genome composition, one should distinguish between prokaryotes and eukaryotes as the big differences on contents structure they have. Prokaryotes Most genome is coding Small amount of non-coding is regulatory sequences Eukaryotes Most genome is non-coding (95%) ▪ Regulatory sequences ▪ Introns ▪ Repetitive DNA • Haploid circular genomes (0.5-10 MB, 500-10000 genes) The prokaryotes usually have only one chromosome, and it bears little morphological resemblance to eukaryotic chromosomes. The typical prokaryotic genome is a ring of DNA that is not surrounded by a membrane and that is located in a nucleoid region Some species of bacteria also have smaller rings of DNA called plasmids Among prokaryotes there is considerable variation in genome length bearing genes. The genome length is smallest in RNA viruses In this case, the organism is provided with only a few genes in its chromosome. The number of gene may be as high as 150 in some larger bacteriophage genome. Table 8.2 part 1 of 2 Genomes 3 (© Garland Science 2007) Package of DNA in Microorganisms • • In viruses, genomic DNA molecule is associated with protein molecules and packaged inside the viral capsids. In bacteria and fungi, the genomic DNA is associated with proteins and is packaged as a compact mass inside the center of the cell. It is called as “nucleoid” E.coli, about 3000 to 4000 genes are organized into its one circular chromosome. The chromosome exists as a highly folded and coiled structure dispersed throughout the cell. The folded nature of chromosome is due to the incorporation of RNA with DNA. During replication of DNA, the coiling must be relaxed. DNA gyrase is necessary for the unwinding the coils. There are about 50 loops in the chromosome of E.coli. These loops are highly twisted or supercoiled structure with about four million nucleotide pairs. Its molecular weight is about 2.8 X109 Single, circular DNA molecule located in the nucleoid region of cell Most common type of supercoiling Helix twists on itself in the opposite direction; twists to the left Model for genome organization Figure 8.3 Genomes 3 (© Garland Science 2007) Mechanism of folding of a bacterial chromosome There are many supercoiled loops (~100 in E. coli) attached to a central core. Each loop can be independently relaxed or condensed. Topoisomerase enzyme – (Type I and II) that introduce or remove supercoiling. Gene organization in prokaryotic genomes • Bacterial genes are organized in by gene systems known as Operons: polycistronic transcription units • Transcription and translation take place in the same compartment Example: E. coli 89% coding 4,285 genes 122 structural RNA genes • Environment-specific genes on plasmids and other types of mobile genetic elements EPFL Bioinformatics I – 09 Jan 2006 Figure 8.8a Genomes 3 (© Garland Science 2007) Figure 8.8b Genomes 3 (© Garland Science 2007) Its an easy place to start history we know more about it ▪ systems better understood simpler genome good model for control of genes ▪ build concepts from there to eukaryotes bacterial genetic systems are exploited in biotechnology Single circular chromosome haploid naked DNA ▪ no histone proteins ~4 million base pairs ▪ ~4300 genes ▪ 1/1000 DNA in eukaryote No nuclear membrane chromosome in cytoplasm transcription & translation are coupled together ▪ no processing of mRNA no introns but Central Dogma still applies ▪ use same genetic code 2005-2006 Replication of bacterial chromosome Asexual reproduction offspring genetically identical to parent 2005-2006 Without meiosis prokaryotes loos an important source of genetic variation. Rapid reproduction and horizontal gene transfer facilitate the evolution of prokaryotes in changing environments Sources of variation spontaneous mutation Transformation transduction conjugation transposons bacteria shedding DNA ▪ ▪ Spontaneous mutation is a significant source of variation in rapidly reproducing species Example: E. coli, human colon (large intestines) 2 x 1010 (billion) new E. coli each day! spontaneous mutations ▪ for 1 gene, only ~1 mutation in 10 million replications ▪ each day, ~2,000 bacteria develop mutation in that gene but consider all 4300 genes, then: 4300 x 2000 = 9 million mutations per day per human host! There are have three different mechanisms of genetic recombination: - transformation – genes are taken from the surrounding environment; - conjugation – direct gene transfer from one prokaryote to another; - transduction – the gene transfer by viruses. . 5/12/2017 Plasmids Plasmids, small rings of DNA consist of only a few genes, present in some prokaryotes ▪ 5000 - 20,000 base pairs ▪ self-replicating carry extra genes ▪ 2-30 genes ▪ rapid evolution can be exchanged between bacteria ▪ bacterial sex!! ( sexual reproduction) 2005-2006 Plasmids Plasmid genes provide:a- resistance to antibiotics b- direct metabolism of unusual nutrients c- other special functions Plasmids replicate, a- independently of the chromosome b- can be transferred between partners during conjugation Table 8.1 Genomes 3 (© Garland Science 2007) Bacterial Conjugation is genetic recombination in which there is a transfer of DNA from a living donor bacterium to a recipient bacterium. Often involves a sex pilus. The 3 conjugative processes + I. F conjugation II. Hfr conjugation III. Resistance plasmid conjugation Direct transfer of DNA between 2 bacterial cells that are temporarily joined results from presence of F plasmid with F factor ▪ F for “fertility” DNA 2005-2006 I) F+ Conjugation Process F+ ConjugationGenetic recombination in which there is a transfer of an F+ plasmid (coding only for a sex pilus) from a male donor bacterium to a female recipient bacterium. Other plasmids present in the cytoplasm of the bacterium, such as those coding for antibiotic resistance, may also be transferred during this process. 1. The F+ male has an F+ plasmid coding for a sex pilus and can serve as a genetic donor 2. The sex pilus adheres to an F- female (recipient). One strand of the F+ plasmid breaks 3. The sex pilus retracts and a bridge is created between the two bacteria. One strand of the F+ plasmid enters the recipient bacterium 4. Both bacteria make a complementary strand of the F+ plasmid and both are now F+ males capable of producing a sex pilus. Note: There was no transfer of donor chromosomal DNA although other plasmids the donor bacterium carries may also be transferred during F+ conjugation. http://www.cat.cc.md.us/courses/bio141/lecguide/unit4/genetics/recombination/conjugation/f.htm l Genetic recombination in which fragments of chromosomal DNA from a male donor bacterium are transferred to a female recipient bacterium, following insertion of an F+ plasmid into the nucleoid of the donor bacterium. Involves a sex (conjugation)pilus. 1. An F+ plasmid inserts into the donor bacterium's nucleoid to form an Hfr male. 2. The sex pilus adheres to an F- female (recipient). One donor DNA strand breaks in the middle of the inserted F+ plasmid. 3. The sex pilus retracts and a bridge forms between the two bacteria. One donor DNA strand begins to enter the recipient bacterium. a portion of the donor's DNA strand is usually transferred to the recipient bacterium. 4. The donor bacterium makes a complementary copy of the remaining DNA strand and remains an Hfr The recipient bacterium complementary strand transferred donor DNA. makes a of the male. 5. Since there was transfer of some donor chromosomal DNA but usually not a complete F+ plasmid, the recipient bacterium usually remains Fhttp://www.cat.cc.md.us/courses/bio141/lecguide/unit4/genetics/recombination/conjugation/hfr.htm l Genetic recombination in which there is a transfer of an R plasmid (a plasmid coding for multiple antibiotic resistance and often a sex pilus) from a male donor bacterium to a female recipient bacterium. Involves a sex (conjugation) pilus 4 steped Resistant Plasmid Conjugation 1. The bacterium with an Rplasmid is multiple antibiotic resistant and can produce a sex pilus (serve as a genetic donor). 2. The sex pilus adheres to an F- female (recipient). One strand of the R-plasmid breaks. 4 stepped Resistant Plasmid Conjugation (cont’d) 3. The sex pilus retracts and a bridge is created between the two bacteria. One strand of the Rplasmid enters the recipient bacterium. 4. Both bacteria make a complementary strand of the Rplasmid and both are now multiple antibiotic resistant and capable of producing a sex pilus. http://www.cat.cc.md.us/courses/bio141/lecguide/unit4/genetics/recombination/conjugation/r.html That is the end