Worms are a lot more similar to people than you may think!

Believe it or not, nematodes (and most other animals for that matter) have many of the same kinds of body tissues, such as nerves and muscles, that humans have. In fact, if you looked at a micrograph of a C. elegans nerve or muscle next to pictures of those from humans, you probably couldn't tell which tissue came from which organism.

But worms and humans are similar at an even more basic level than their body tissues. The deeper molecular biologists peer into the cells and genes of organisms, the clearer it becomes that all the creatures on earth share many of the same cellular and biochemical strategies for living. The very genetic code that spells out the language of life is essentially identical in every life form from viruses to humans. Many of the genes found in nematodes, fruitflies, yeast, and other model organisms have counterparts in humans that are so closely similar that they are functionally interchangeable.

Still don't believe it? See for yourself!
(Skepticism is a healthy trait for a scientist)

Let's do an experiment.

We'll look at actin, a very important molecule in humans. Actin is the protein that, together with another protein, myosin, is responsible for moving our muscles. Actin also forms the main scaffolding structure, or cytoskeleton, that gives cells their shape. Like all proteins, actin as composed of chemical building blocks called amino acids strung together in a long chain. There are 20 amino acids that form the protein "alphabet", and the order in which the amino acids are strung together is what imparts the protein with its characteristic structure and function. Below is a diagram of a single molecule of actin. The string of amino acids is folded upon itself like a ball of yarn, but the pattern of folding is very precise and always forms the shape that you see here. The physical and chemical properties of the actin molecule, in turn, are governed by this shape. This is how all proteins get their structure and function. In the case of actin, the particular shape and chemical properties allow individual molecules to attach to one another to form long cables, which are attracted to myosin and other proteins.

Here's the amino acid sequence for human actin. Each letter stands for a particular amino acid.:

>gi|2116655|gnl|PID|d1021082 (human beta-actin)
MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKD
SYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHP
VLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVM
DSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTA
EREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERF
RCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMY
PGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWI
SKQEYDESGPSIVHRKCF

We're ready for the experiment. Let's see if we can find protein molecules from other organisms that look something like human actin. The web is a great tool for doing this sort of experiment. Over the past few decades, molecular biologists have been determining the sequences of many proteins and genes from a multitude of plants and animals and depositing the sequences in databases on the web. There are computer programs that can very quickly search through all these sequences and compare them to a particular sequence. We'll compare the human actin sequence to all the protein sequences in the databases, and see if we can pick out any similar sequences. The experiment should take under a minute (or maybe a bit longer, depending on web traffic).

Experimental Procedure:

 1. Using your browser, select and copy all the text containing the actin sequence (including the name in the top line) in the box above.
 2. Follow this link to the database searching program. Your browser should open a new window so that you can continue to follow the procedure in this window.
 3 In the new window, make sure the first pulldown menu, between the "Program" and Database" test links, is set to blastp. This tells the searching program that you want to search protein sequences with another protein sequence.
 4 In the pulldown menu directly beneath the one you just set, select nr. This tells the program to search all of the various databases on the web that have protein sequences in them.
 5 In the next pulldown menu, after the line "Enter here your input data as", select Sequence in FASTA format. This is simply the text format that you copied from above. Paste the copied actin sequence into the box.
 6 Don't change any other settings or make any other text entries
 7 Click the Submit Query button at the bottom of the page to start your search

 

Results:

Now let's see what you found in your search. At the top of the page you'll probably see a diagram that looks something like this:

(Hint: If instead, you get a message that says "...Searchingdone No hit found...," go back and make sure you selected blastp for the program, not blastn or one of the others.)

 

The Color Key at the top of the figure shows the colors that represent how similar the "Query" sequence (the actin sequence) is to the various sequences from the database that are shown below the figure. Red means the most similar. The thick red line under the color key represents the actin sequence; the numbers represent the amino acid positions along the sequence. The thinner red lines each represent proteins in the database that have sequence similarity to actin. The fact that the lines are all red all the way from the the beginning to end indicates that all these proteins are highly similar to actin along their entire lengths. If you hold your mouse curser on top of one of the lines you'll see the words change in the text box above the figure. The text box shows the name of the sequence (along with some ID numbers and possibly some descriptive text) of the sequence you are pointing at. Now, drag your mouse down slowly to see what sequences each red line represents. They are all actin! But if you look carefully at the descriptions you'll see that they are not all human actin. Look for words like "bovine" (cow), Mus musculus (mouse), Drosophila melanogaster (fruitfly), and other words indicating that these actin sequences are from other species. Move your mouse over each of the red lines until you see Caenorhabditis elegans (the nematode!) in the text box. Now, click on that line. Your browser window now shows the two sequences (the human actin query sequence on top and the C. elegans sequence on the bottom) aligned to show how well they match up. The sequence in the middle shows all the amino acids that match and a + sign between two amino acids that don't match. There aren't very many + signs! (and if you can read the amino acid code and know about the chemistry of the amino acids, you'll see that where there are amino acid changes, usually they are subtle ones.). Scroll down the alignments of other proteins that you found with your search. You can see at a quick glance how strikingly similar they all are to the human actin sequence you searched the database with. The few differences between the various actin "relatives" illustrates that proteins do evolve--but in the case of actin, this evolution is very slow indeed.

http://www.mcb.arizona.edu/wardlab/transformation.html
All Contents Copyright © 2001. All rights reserved.
Last Modified: March 24, 2001
Paul Muhlrad pmuhlrad@u.arizona.edu