Lecture 2: Aspects of the Microbial Genome PDF

**3** **ASPECTS OF THE MICROBIAL GENOME** - **Anatomy of microbial and eukaryotic genomes** Biologists recognize that the living world comprises two types of organism ([Figure 2.1](https://www.ncbi.nlm.nih.gov/books/NBK21120/figure/A5469/?report=objectonly)): 1. As mentioned before, prokaryot...

**3** **ASPECTS OF THE MICROBIAL GENOME** - **Anatomy of microbial and eukaryotic genomes** Biologists recognize that the living world comprises two types of organism ([Figure 2.1](https://www.ncbi.nlm.nih.gov/books/NBK21120/figure/A5469/?report=objectonly)): 1. As mentioned before, prokaryotes have smaller genome compared with that of eukaryotes (Figure 26). Genome size is measured in [nucleotide](https://www.ncbi.nlm.nih.gov/books/n/mboc4/A4754/def-item/A5567/) pairs of [DNA](https://www.ncbi.nlm.nih.gov/books/n/mboc4/A4754/def-item/A5084/) per [haploid](https://www.ncbi.nlm.nih.gov/books/n/mboc4/A4754/def-item/A5264/) [genome](https://www.ncbi.nlm.nih.gov/books/n/mboc4/A4754/def-item/A5222/), that is, per single copy of the genome. (The cells of sexually reproducing organisms such as ourselves are generally [diploid](https://www.ncbi.nlm.nih.gov/books/n/mboc4/A4754/def-item/A5077/): they contain two copies of the genome, one inherited from the mother, the other from the father.) Closely related organisms can vary widely in the quantity of DNA in their genomes, even though they contain similar numbers of functionally distinct genes. **Figure 26: Comparison of the length of genomes from different organisms.** 2. Eucaryotes not only have more genes than procaryotes; they also have vastly more [DNA](https://www.ncbi.nlm.nih.gov/books/n/mboc4/A4754/def-item/A5084/) that does not code for [protein](https://www.ncbi.nlm.nih.gov/books/n/mboc4/A4754/def-item/A5688/) or for any other functional product [molecule](https://www.ncbi.nlm.nih.gov/books/n/mboc4/A4754/def-item/A5486/). The human [genome](https://www.ncbi.nlm.nih.gov/books/n/mboc4/A4754/def-item/A5222/) contains a 1000 times as many [nucleotide](https://www.ncbi.nlm.nih.gov/books/n/mboc4/A4754/def-item/A5567/) pairs as the genome of a typical bacterium, 20 times as many genes, and about 10,000 times as much noncoding DNA (\~98.5% of the genome for a human is noncoding, as opposed to 11% of the genome for the bacterium E. coli). Genome regions could be: - **Untranscribed region**: "non-coding regions" does not transcribed as the regions of promoter and Silencers. Promoters provide binding sites for the protein machinery that carries out transcription. **Promoters** are typically found just ahead of the gene on the DNA strand. **Silencers** provide binding sites for proteins that repress transcription. Like enhancers, silencers can be found before or after the gene they control and can be some distance away on the DNA strand. - **Transcribed non-coding region**: genes do not give proteins. Like rRNA and tRNA genes. - **Protein-coding regions**: Genes give protein. Check figure 27  **Figure 27: Different regions in the genome of different types of organisms.** **Write your observation on this figure (27):** 3. Prokaryotic genomes are very different from eukaryotic ones.\ For example, the *[E](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10200/). coli* K12 genome is just **4639 [kb](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10259/) (Check table 2 to know the units for genome length)**, two-fifths the size of the yeast genome, and has only **4405** genes. The physical organization of the genome is also different in eukaryotes and prokaryotes. The traditional view has been that an entire prokaryotic genome is contained in **a single circular [DNA](https://www.ncbi.nlm.nih.gov/books/n/genomes/A9089/def-item/A9330/) molecule**. As well as this single 'chromosome', prokaryotes may also have additional genes on independent smaller, circular or linear DNA molecules **called [plasmid](https://www.ncbi.nlm.nih.gov/books/n/genomes/A9089/def-item/A9784/)s (Fig. 28)**.\ Genes carried by plasmids are useful, coding for properties such as antibiotic resistance or the ability to utilize complex compounds such as toluene as a carbon source, but plasmids appear to be dispensable - a prokaryote can **exist quite effectively without them**.\ We now know that this traditional view of the prokaryotic genome has been biased by the extensive research on *E. coli*, which has been accompanied by the mistaken assumption that *E. coli* is a typical prokaryote. In fact, prokaryotes display a considerable diversity in genome organization, some having a **unipartite genome**, like *E. coli,* but others being more complex. *Borrelia burgdorferi* B31, for example, has a linear chromosome of 911 kb, carrying 853 genes, accompanied by 17 or 18 linear and circular molecules, which together contribute another 533 kb and at least 430 genes. **Multipartite genomes** are now known in many other bacteria and archaea. **Table 2: Units to express DNA length** Biomedical Data **Which unit is suitable for human genome and a gene??**  **Figure 28: Nucleoids and plasmids of Bacteria.** 4. Prokaryotic genomes are even **more compact** than those of yeast and other lower eukaryotes. We can see this fact illustrated in Figure 29, which shows a 50-[kb](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10259/) segment of the *E. coli* K12 genome **[compared to other organisms same fragment]**. It is immediately obvious that there are more genes and less space between them, with 43 genes taking up 85.9% of the segment. Some genes have virtually no space between them: *thrA* and *thrB*, for example, are separated by a single nucleotide, and *thrC* begins at the nucleotide immediately following the last nucleotide of *thrB*. These three genes are an example of an [operon](https://www.ncbi.nlm.nih.gov/books/n/genomes/A9089/def-item/A9735/), a group of genes involved in a single biochemical pathway (in this case, synthesis of the amino acid threonine) and expressed in conjunction with one another. Operons have been used as model systems for understanding how gene expression is regulated. Check figure 30 to know the genes organization in both prokaryotes and eukaryotes. Figure 2.2. Comparison of the genomes of humans, yeast, fruit flies, maize and Escherichia coli. ### **Figure 29: Comparison of the genomes of humans, yeast, fruit flies, maize and *Escherichia coli.* ([A](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10140/)) is the 50-[kb](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10259/) segment of the human β [T](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10347/)-cell receptor locus shown. This is compared with 50-kb segments from the genomes of (B) *Saccharomyces* *cerevisiae* (chromosome III; redrawn; ([C](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10162/)) *Drosophila melanogaster* ; ([D](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10178/)) maize and ([E](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10200/)) *E. coli* K12. See the text for more details.**  **Figure 30: Operon organization in prokaryotes** 5. In general, **prokaryotic genes are shorter than their eukaryotic counterparts**, the average length of a bacterial gene being about **two-thirds** that of a eukaryotic gene, even after the introns have been removed from the latter. Bacterial genes appear to be slightly longer than archaeal ones. 6. There are **no introns (Figure 31)** in the genes present in this segment of the *[E](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10200/). coli* genome. In fact, *E. coli* has no discontinuous genes at all, and it is generally believed that this type of gene structure is virtually **absent in prokaryotes**, the few exceptions occurring mainly among the archaea. Contrasting the Regulation of Gene Expression in Prokaryotic & Eukaryotic Organisms Practice \| Biology Practice Problems \| Study.com **Figure 31: eukaryotic and prokaryotic genes and operon structure in prokaryotes** 7. The second feature is the **infrequency of repetitive sequences**. Most prokaryotic genomes do not have anything equivalent to the high-copy-number genome-wide repeat families found in eukaryotic genomes. They do, however, possess certain sequences that might be repeated elsewhere in the genome, examples being the [insertion sequences](https://www.ncbi.nlm.nih.gov/books/n/genomes/A9089/def-item/A9558/) IS1 and IS186 that can be seen in the 50-[kb](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10259/) segment shown in Figure 27. 8. **Insertion sequence** [A](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10140/) short transposable element found in bacteria as indicated in figure 32.  **Figure 32: The insertion sequence (transposons) of bacteria** - #### **Complications on the E. coli theme** 1. In recent years it has become clear that the straightforward view of prokaryotic genome anatomy developed from studies of *[E](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10200/). coli* is an over-simplification. Although the majority of bacterial and archaeal chromosomes are indeed circular, an increasing number of linear ones are being found. The first of these was found in for *Borrelia burgdorferi* and  *Streptomyces*. 2. [A](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10140/) second complication concerns the precise status of plasmids with regard to the prokaryotic genome. A plasmid is a small piece of [DNA](https://www.ncbi.nlm.nih.gov/books/n/genomes/A9089/def-item/A9330/), often, but not always circular, that coexists with the main chromosome in a bacterial cell. Some types of plasmid are able to integrate into the main genome, but others are thought to be permanently independent. Plasmids carry genes that are not usually present in the main chromosome, but in many cases these genes are non-essential to the bacterium, coding for characteristics such as antibiotic resistance, which the bacterium does not need if the environmental conditions are amenable Table 3. As well as this apparent dispensability, many plasmids are able to transfer from one cell to another, and the same plasmids are sometimes found in bacteria that belong to different species. These various features of plasmids suggest that they are independent entities and that in most cases the plasmid content of a prokaryotic cell should not be included in the definition of its genome. ### **Table 3: features of typical plasmids** **Type of plasmid** **[Gene](https://www.ncbi.nlm.nih.gov/books/n/genomes/A9089/def-item/A9448/) functions** **Examples** --------------------- ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Resistance Antibiotic resistance Rbk of *Escherichia coli* and other bacteria Fertility [Conjugation](https://www.ncbi.nlm.nih.gov/books/n/genomes/A9089/def-item/A9260/) and [DNA](https://www.ncbi.nlm.nih.gov/books/n/genomes/A9089/def-item/A9330/) transfer between bacteria [F](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10213/) of *[E](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10200/). coli* Killer Synthesis of toxins that kill other bacteria [Col](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10170/) of *[E](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10200/). coli*, for colicin production Degradative Enzymes for metabolism of unusual molecules [TOL](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10359/) of *Pseudomonas putida*, for toluene metabilism Virulence Pathogenicity [Ti](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10353/) of *Agrobacterium tumefaciens*, conferring the ability to cause crown gall disease on dicotyledonous plants With a bacterium such as *[E](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10200/). coli* K12, which has a 4.6-[Mb](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10271/) chromosome and can harbor various combinations of plasmids, none of which is more than a few [kb](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10259/) in size and all of which are dispensable, it is acceptable to define the main chromosome as the 'genome'. With other prokaryotes it is not so easy Table 4. *Vibrio cholerae*, the pathogenic bacterium that causes cholera, has two circular [DNA](https://www.ncbi.nlm.nih.gov/books/n/genomes/A9089/def-item/A9330/) molecules, one of 2.96 Mb and the other of 1.07 Mb, with 71% of the organism\'s 3885 genes on the larger of these ([Heidelberg *et al.*, 2000](https://www.ncbi.nlm.nih.gov/books/NBK21120/)). It would appear obvious that these two DNA molecules together constitute the *Vibrio* genome, but closer examination reveals that most of the genes for the central cellular activities such as genome expression and energy generation, as well as the genes that confer pathogenicity, are located on the larger molecule. The smaller molecule contains many essential genes but also has certain features that are considered characteristic of plasmids, notably an [integron](https://www.ncbi.nlm.nih.gov/books/n/genomes/A9089/def-item/A9565/), a set of genes and other DNA sequences that enable plasmids to capture genes from bacteriophages and other plasmids. It therefore appears possible that the smaller genome is a 'megaplasmid' that was acquired by the ancestor to *Vibrio* at some period in the bacterium\'s evolutionary past. *Deinococcus radiodurans* R1, whose genome is of particular interest because it contains many genes that help this bacterium resist the harmful effects of radiation, is constructed on similar lines, with essential genes distributed among two circular chromosomes and two plasmids ([White *et al.*, 1999](https://www.ncbi.nlm.nih.gov/books/NBK21120/)). However, the *Vibrio* and *Deinococcus* genomes are relatively non-complex compared with *Borrelia burgdorferi* B31, whose linear chromosome of 911 kb, carrying 853 genes, is accompanied by 17 or 18 linear and circular plasmids which together contribute another 533 kb and at least 430 genes ([Fraser *et al.*, 1997](https://www.ncbi.nlm.nih.gov/books/NBK21120/)). ### **Table 4: Examples of genome organization in prokaryotes** **[Genome](https://www.ncbi.nlm.nih.gov/books/n/genomes/A9089/def-item/A9469/) organization** ------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------- --------------------- **Species** **[DNA](https://www.ncbi.nlm.nih.gov/books/n/genomes/A9089/def-item/A9330/) molecules** **Size ([Mb](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10271/))** **Number of genes** *Escherichia coli* [K](https://www.ncbi.nlm.nih.gov/books/n/genomes/A10138/def-item/A10258/)-12 One circular molecule 4.639 4397 *Vibrio cholerae* El Tor N16961 **Two circular molecules**  Main chromosome 2.961 2770  Megaplasmid 1.073 1115 *Deinococcus radiodurans* R1 **Four circular molecules**  [Chromosome](https://www.ncbi.nlm.nih.gov/books/n/genomes/A9089/def-item/A9225/) 1 2.649 2633  [Chromosome](https://www.ncbi.nlm.nih.gov/books/n/genomes/A9089/def-item/A9225/) 2 0.412 369  Megaplasmid 0.177 145  [Plasmid](https://www.ncbi.nlm.nih.gov/books/n/genomes/A9089/def-item/A9784/) 0.046 40 *Borrelia burgdorferi* B31 **Three circular molecules, 11 linear molecules**  Linear chromosome 0.911 853  Circular plasmid cp9 0.009 12  Circular plasmid cp26 0.026 29  Circular plasmid cp32\* 0.032 Not known  Linear plasmid lp17 0.017 25  Linear plasmid lp25 0.024 32  Linear plasmid lp28-1 0.027 32  Linear plasmid lp28-2 0.030 34  Linear plasmid lp28-3 0.029 41  Linear plasmid lp28-4 0.027 43  Linear plasmid lp36 0.037 54  Linear plasmid lp38 0.039 52  Linear plasmid lp54 0.054 76  Linear plasmid lp56 0.056 Not known Although the functions of most of these genes are unknown, those that have been identified include several that would not normally be considered dispensable, such as genes for membrane proteins and purine biosynthesis. The implication is that at least some of the *Borrelia* plasmids are essential components of the genome, leading to the possibility that some prokaryotes have highly multipartite genomes, comprising a number of separate DNA molecules, more akin to what we see in the eukaryotic nucleus rather than the 'typical' prokaryotic arrangement. This interpretation of the *Borrelia* genome is still controversial, and is complicated by the fact that the related bacterium *Treponema pallidum*, whose genome is a single circular DNA molecule of 1138 kb containing 1041 genes ([Fraser *et al.*, 1998](https://www.ncbi.nlm.nih.gov/books/NBK21120/)), does not contain any of the genes present on the *Borrelia* plasmids. 3. The final complication regarding the physical structures of prokaryotic genomes concerns differences between the packaging systems for bacterial and archaeal [DNA](https://www.ncbi.nlm.nih.gov/books/n/genomes/A9089/def-item/A9330/) molecules. One reason why the archaea are looked upon as a distinct group of organisms, different from the bacteria, is that archaea do not possess packaging proteins such as HU but instead have proteins that are much more similar to histones. Currently we have no information on the structure of the archaeal nucleoid, but the assumption is that these histone-like proteins play a central role in DNA packaging. **Compare between pro and eu-karyotic genomes** *li*.