Bacterial Diversity (AP Bio Interactive Tutorial)

1. Shouldn’t all the bacteria of the same species be clones?

Meet E. coli.

E. coli (Credit: National Institute of Allergies and Infectious Medicine)

E. coli is a bacterial species that lives in the colons of humans and all endothermic (“warm blooded”) vertebrates (specifically: mammals and birds). They’re about 2 micrometers long, and from 0.25 to one micrometer across (Wikipedia). E. coli are a normal and healthy part of what’s called our intestinal flora: you have about as many E. coli cells inside of you at any one moment as you have cells that are you (though that number of E. coli cells, 30 trillion, drops every time you have a bowel movement). Nat. Geo.

All bacteria, including E. coli, reproduce asexually through a process called binary fission, which you can follow through the diagram at right.

In “A,” you see a single bacterial cell with a cell wall (“1”), a membrane (“2”), cytoplasm (“3”), and a single circular chromosome (“4”). Bacteria also have additional pieces of DNA called “plasmids,” which are not shown at right (but which you’ll meet below).

When bacteria divide, they start by elongating, and by replicating their DNA, as shown in “B.” In “C,” you can see that the cell now has two chromosomes, and that a new cell wall is beginning to form (at “5”).

By step “D” the cell wall (now “6”) has divided the parent cell into two daughter cells, which split apart into the two daughter cells (shown at “E”).

This process clones the parent into two identical daughter cells. Yet, bacterial populations are genetically diverse. For example, E. coli consists of several strains, most of which are harmless. but some of which can cause bacterial irritation and diarrhea, which can lead to dehydration that can be fatal (especially in toddlers or people with compromised immunity). Where does this bacterial diversity come from? If bacteria multiply through cloning, why aren’t they all the same? Before reading further, think about what you know biology, and see if you can come up with (at least part of) the answer.

2. Five Causes of Bacterial Genetic Diversity

Bacteria genetically differ from one another for five reasons.

a. Mutation

Source: National Library of Medicine through Wikipedia

Bacterial genes are made of DNA. Despite DNA’s stability, mutations in DNA’s base sequence occasionally occur. And because bacteria reproduce so quickly (E. coli can double itself in as little as 20 minutes), even the smallest mutation rate will lead to large numbers of mutants within any E. coli population.

Note that in the example to the left, a single substitution of cytosine for adenine results in the amino acid proline replacing histidine (which could alter the tertiary interactions that give rise to the protein’s three dimensional conformation, potential changing the protein’s function as well).

b. Transformation

Bacterial transformation is a process that we’ve discussed before, because it played a major role in the identification of DNA as the genetic material in the 1930s and 40s, leading to the elucidation of DNA’s structure by Watson, Crick, Franklin, and Wilkins.

[qwiz]

[q] See if you can explain what’s happening in the diagram below. 

[c*] Show me the answer

[f] Diagrams “1” and “2” show the two strains of pneumonia-causing bacteria that were the subject of Frederick Griffith’s experiment demonstrating bacterial transformation. Strain “1” (called “smooth”) possesses a capsule, and kills mice upon injection, while strain “2” is capsule-free and harmless.
Diagram “3” shows what happens when the deadly smooth strain bacteria are heated. They die, and can be injected without harm. However, when heat-killed smooth-strain bacteria are mixed with living, rough strain bacteria (as shown in “4”) then something in the dead heat-killed bacteria is able to transform the harmless rough strain bacteria into deadly smooth strain bacteria (which are shown in the mice’s blood in step “5.”).

[/qwiz]

Transformation can happen in two ways, each of which is shown below.

[qwiz]

[q] See if you can explain to yourself (or your partner, if you’re working with one) what’s happening in each diagram. Then click the button to confirm your answer.

[c*] Show me the answer

[f]In both diagrams, “b” represents the bacterial chromosome.

The diagram to the left shows uptake of “naked” DNA. Cells absorb fragments of DNA (“a”) in their environment, and this DNA incorporates itself into the host cell chromosome (“c”).  The diagram to the right showns uptake of plasmid DNA. Plasmids (“a”) are small circles of DNA that are not a part of the main bacterial chromosome. Bacteria can exchange plasmids through a process called conjugation (discussed below) or plasmids can enter a bacterial cell. Once inside the cell, the plasmid DNA can be replicated and/or expressed.  

[/qwiz]

c. Bacterial Conjugation

Like one of the forms of transformation that we saw above, bacterial conjugation involves an exchange of plasmids. However, while bacterial transformation involves the accidental acquisition of foreign genetic material, conjugation is much more directed. Here’s how it works.

In step “1” we see two bacteria of the same species. Bacteria “I” has a plasmid, and this plasmid has genes for production of a structure called a pilus (at “c”). The second bacterium, at II, lacks both the plasmid (and the pilus).

Functionally, the pilus is like a retractable hook. When the pilus contacts the surface of another bacterium (as it does in step “2”), it grabs on. As it grabs on, the pilus retracts, pulling the two cells together.

In step 3, the enzyme DNA polymerase (at “e”) replicates the plasmid, Other enzymes (not shown) create a cytoplasmic bridge between the two cells. Through this bridge, a copy of the plasmid enters into cell II.

In step 4, you can see the result. Because cell II now has the plasmid, it expresses genes for the pilus.

Note that the plasmids behind the conjugation process can have a variety of genes. It’s thought that conjugation, in addition to mutation, is a key mechanism by which antibiotic resistance genes spread through bacterial population.

d. Transduction

In the previous module, we looked at transduction, the process by which accidents in viral replication result in moving DNA fragments from one bacterium to another. If you need to review, click here, then come on back to this module.

e. Transposition

Transposons, or transposable genetic elements, are DNA sequences that can move from one location in an organism’s genome to another. They were discovered by the Nobel-Prize winning geneticist Barbara McClintock (who had to wait about 40 years before her work was widely recognized and deemed Nobel Prize worthy).

Transposons occur in all living things, and as we’ll see later in our course, they make up 44% of the human genome Wikipedia (as well as the genomes of of most other mammals).

There are two ways to think about how transposons work.

The first is to imagine them working the way you work when you cut and paste text in a word processor. The transposon (1), which codes for enzymes called transposases (not shown), cuts itself out of its current location within a chromosome (2 and 3), and inserts itself back in somewhere else (4 and 5). This changes the sequence of genes on a chromosome, but it doesn’t increase the size of the genome: the number of nucleotides stays the same.

But transposons can also replicate themselves through a copy and paste mechanism. When you’re typing, and you copy and paste, you increase the number of characters in the document that you’re creating. The transposons that work through copy and paste are retrotransposons, and they work as follows.

“1” shows a retrotransposon. In step 2, this transposon’s DNA is transcribed into RNA, which is shown in red. Next, reverse transcriptase (“3”) creates DNA from the RNA (steps “4” and “5.”)

Notice that the DNA of the original retrotransposon is still in its original location, which means that the DNA at “5” is a clone of “1.” In step 6, the new DNA is inserted somewhere else in the genome (“7”). The transposon, in this case, has both changed this organism’s genetic sequence, and increased its genome size.

Checking Understanding

That explains what you need to know about how genetic diversity is generated in bacteria. Take the quiz below to see how well you’ve mastered what you’ve read.

 

[qwiz]

[q] The process shown below represents [hangman]

[c] transformation

[f] Good!

[q] The process shown below represents transformation with  [hangman] DNA.

[c] naked

[f] Good!

[q] The process shown below represents transformation with a  [hangman].

[c] plasmid

[f] Good!

[q] The process shown below represents  [hangman].

[c] conjugation

[f] Excellent!

[q] The structure shown at “c” is a  [hangman].

[c] pilus

[f] Nice Job!

[q] The enzyme shown at “e” is DNA [hangman].

[c] polymerase

[f] Nice Job!

[q] The process shown below is [hangman].

[c] transposition

[f] Awesome!

[q] The DNA elements shown at 1, 3, and 5 are [hangman].

[c] transposons

[f] Awesome!

[q] The DNA elements shown at 1, 5, and 7 are [hangman].

[c] retrotransposons

[q] The enzyme shown at 3 is reverse  [hangman].

[c] transcriptase

[f] Awesome!

[q] The process shown below is  [hangman].

[c] transduction

[q] The result of the process below is two daughter cells that are genetic [hangman] of the parent cell.

[c] clones

[f] Awesome!

[q] The process below is called  [hangman].

[c] mutation

[f] Awesome!

[q]Mutation, transduction, transformation, conjugation, and transposition are all processes that increase genetic [hangman] in bacterial populations.

[c] diversity

[f] Awesome!

[q multiple_choice=”true”] The process below shows

[c] mutation

[f] No. Mutation involves a random change in nucleotide sequence

[c] transposition

[f] No. Transposition involves transposons moving from one location in the genome to another location.

[c*] transformation

[f] Excellent. This diagram shows how DNA from heat killed virulent bacteria was able to transform harmless bacteria into deadly bacteria.

[c] conjugation

[f] No. Conjugation involves transfer of a plasmid  by means of a pilus.

[c] transduction

[f] No. Transduction involves transfer of bacterial DNA  that comes about through accidents in the viral replication process.

[q multiple_choice=”true”] The process below shows

[c*] mutation

[f] Yes. Mutation involves a random change in nucleotide sequence, which is exactly what you see here.

[c] transposition

[f] No. Transposition involves transposons moving from one location in the genome to another location.

[c] transformation

[f] No. This diagram shows how DNA from heat killed virulent bacteria was able to transform harmless bacteria into deadly bacteria.

[c] conjugation

[f] No. Conjugation involves transfer of a plasmid  by means of a pilus.

[c] transduction

[f] No. Transduction involves transfer of bacterial DNA  that comes about through accidents in the viral replication process.

[q multiple_choice=”true”] The process below shows

[c] mutation

[f] No. Mutation involves a random change in nucleotide sequence,

[c*] transposition

[f] Yes. Transposition involves transposons moving from one location in the genome to another location.

[c] transformation

[f] No. This diagram shows how DNA from heat killed virulent bacteria was able to transform harmless bacteria into deadly bacteria.

[c] conjugation

[f] No. Conjugation involves transfer of a plasmid  by means of a pilus.

[c] transduction

[f] No. Transduction involves transfer of bacterial DNA  that comes about through accidents in the viral replication process.

[q multiple_choice=”true”] The process below shows

[c] mutation

[f] No. Mutation involves a random change in nucleotide sequence,

[c] transposition

[f] No. Transposition involves transposons moving from one location in the genome to another location.

[c] transformation

[f] No. This diagram shows how DNA from heat killed virulent bacteria was able to transform harmless bacteria into deadly bacteria.

[c*] conjugation

[f] Yes. Conjugation involves transfer of a plasmid  by means of a pilus.

[c] transduction

[f] No. Transduction involves transfer of bacterial DNA  that comes about through accidents in the viral replication process.

[q multiple_choice=”true”] The process below shows

[c] mutation

[f] No. Mutation involves a random change in nucleotide sequence,

[c] transposition

[f] No. Transposition involves transposons moving from one location in the genome to another location.

[c] transformation

[f] No. This diagram shows how DNA from heat killed virulent bacteria was able to transform harmless bacteria into deadly bacteria.

[c] conjugation

[f] Yes. Conjugation involves transfer of a plasmid  by means of a pilus.

[c*] transduction

[f] Yes. Transduction involves transfer of bacterial DNA  that comes about through accidents in the viral replication process.

 

[q] In the diagram below, which letter or number indicates fragments of DNA that are floating in the environment?

[textentry single_char=”true”]

[c*] a

[f] Excellent! Letter “a” represents DNA fragments that are floating in the environment.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No, Just look for something outside of the cell.

 

[q] In the diagram below, which letter or number indicates the pre-transformation bacterial chromosome?

[textentry single_char=”true”]

[c*] b

[f] Excellent! Letter “b” represents the bacterial chromosome before transformation.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No, but here’s a hint: Bacteria have a single circular chromosome.

[q] In the diagram below, which letter indicates the a transformed chromosome (one that has taken up foreign DNA)?

[textentry single_char=”true”]

[c*] c;3

[f] Excellent! Letter “c” represents a bacterial chromosome that has taken up foreign DNA, and has been transformed.

[c] Enter word

[f] No.

[c] *

[f] No, but here’s a hint: find a chromosome that consists of both the original DNA and the foreign DNA that entered the cell.

[q] In the diagram below, which letter or number indicates a plasmid?

[textentry single_char=”true”]

[c*] a

[f] Nice! Letter “a” represents a plasmid.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No, but here’s a hint: A plasmid is a circle of extra-chromosomal DNA found outside the main bacterial chromosome.

[q] In the diagram below, which letter or number indicates a plasmid?

[textentry single_char=”true”]

[c*] b

[f] Nice! Letter “b” represents a plasmid.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No, but here’s a hint: A plasmid is a circle of extra-chromosomal DNA found outside the main bacterial chromosome.

[q] In the diagram below, which letter or number indicates the main bacterial chromosome?

[textentry single_char=”true”]

[c*] a

[f] Nice! Letter “a” represents the main bacterial chromosome.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No, The bacterial chromosome is a long loop of DNA, much bigger than the plasmid (which is show at “b”)

[q] In the diagram below, which letter or number indicates a pilus?

[textentry single_char=”true”]

[c*] c

[f] Nice! Letter “c” represents a pilus.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No, The pilus is an extension from the cell that grabs onto other cells.

[q] In the diagram below, which letter or number indicates DNA polymerase?

[textentry single_char=”true”]

[c*] e

[f] Nice! Letter “e” represents DNA polymerase.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No, Try to find something the could represent an enzyme that is replicating the plasmid.

[q] In the diagram below, which number represents a transposon that has moved to a new position in the genome?

[textentry single_char=”true”]

[c*] 5

[f] Nice! Letter “5” represents a transposon that has moved to a new position in the genome.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. If “1” is the original transposon, what’s the only thing that could represent this transposon in a new position in the genome?

[q] In the diagram below, which number represents the process of transposon insertion?

[textentry single_char=”true”]

[c*] 4

[f] Nice! Letter “4” represents the process of transposon insertion.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. If “3” is the transposon away from its original position, and “5” represents the transposon in its new position, what’s the only thing that could represent the process of insertion?

[q] In the diagram below, which number represents reverse transcriptase?

[textentry single_char=”true”]

[c*] 3

[f] Nice! Letter “3” represents reverse transcriptase.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. An RNA transcript of the retrotransposon DNA is shown in red, right below number “2.” Which number on the diagram represents an enzyme that is converting this transposon RNA into transposon DNA?

[q] In the diagram below, which letter represents a phage that has picked up bacterial DNA, instead of viral DNA?

[textentry single_char=”true”]

[c*] f

[f] Nice! Letter “f” represents a phage that has picked up DNA from the bacterium it just attacked, instead of viral DNA.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. Start by noting the colors of the viral DNA and bacterial DNA in figure 1. Then carefully examine figures 2 and 3, and identify the virus that has picked up the wrong DNA.

[/qwiz]

Links

  1. Continue to Operons (the next tutorial in this series)
  2. Return to the Module 16 (Bacterial Genetics /Operons) Menu