Superoxide Dismutase Is a Really Fast Enzyme

PhilipJ has posted the latest "Molecule of the Month" on Biocurious [Molecule of the Month: Superoxide Dismutase]. The molecule is superoxide dismutase from cow (Bos taurus) drawn by David Goodsell from the 2SOD (formerly 1SOD) structure in the Protein Data Bank. This structure is from 1980.

The formal name of this enzyme is copper-zinc superoxide dismutase in order to distinguish it from other, unrelated, superoxide dismutases. As noted on the Biocurious website, the main reason for having this enzyme is to get rid of dangerous free radical forms of oxygen that are produced in a number of cellular reactions; notably, membrane-associated electron transport and photosynthesis. (Superoxide dismutase is found in all species.)

The reaction involves a copper ion (Cu²⁺) at the active site of the enzyme (E). A free radical, such as the toxic superoxide radical anion, binds to the coper ion and an electron is transferred from the superoxide radical to the copper ion. This leads to the reduction of the copper ion from the +2 form to the +1 form as it picks up a single negative charge from the electron. In the second step, this electron is passed from the copper ion back to another superoxide anion which then combines with two protons to make hydrogen peroxide (H₂O₂). Hydrogen peroxide can be easily converted to water + molecular oxygen by ubiquitous catalase enzymes.


Superoxide dismutase is an important enzyme and it's role in scavenging free radicals would be more than enough to justify its inclusion in biochemistry textbooks. But there's another reason why this enzyme is discussed. It's one of the fastest enzymes known to biochemists as shown in the table below.



I suspect that most of you aren't familiar with the Michaelis-Menten constants k_cat and K_M but that doesn't matter. Trust me, these are very fast enzymes.

In fact, superoxide dismutase is faster than it has any right to be. The maximum rate of an enzymatic reaction was thought to be limited to the rate of diffusion inside the cell. This makes sense since the substrate (superoxide anion) has to collide with the active site copper ion before a reaction can occur. But measurements of the actual enzymatic rate gave a result that was faster than theoretically possible given the diffusion rates inside the cell.

It wasn't until the structure of the enzyme was solved that this mystery was cleared up. Look at the structure shown above. This is the human version of copper-zinc superoxide dismutase from 2003 [1HL5]. The structure is drawn in a way that highlights the charges on the surface of the enzyme. Red side chains are negatively charged and blue side chains are positively charged. The entry channel to the copper ion (green) at the active site is lined with positively charged amino acid residues. These suck in the negatively charged oxygen radicals like a vacuum cleaner and feed them to the active site. That's how the enzyme can operate so fast.

Do You Think Iran Will Get the Messsage?

 
Here's a scary report from the New York Daily News [ Bush eyes 'surgical' strikes vs. Iran, sez mag]. The Daily News article is based on an analysis by Seymour M. Hersh in the New Yorker magazine [Shifting Targets]. Hersh describes the increasing rhetoric about Iran's involvement in Iraq and the intelligence evidence that links Iran to the killing of American soldiers. This ties in with the growing realization that Iran is not about to develop nuclear weapons anytime soon. With that excuse gone, America needs another reason to justify the war against Iran. Here's how Hersh describes the situation ...

This summer, the White House, pushed by the office of Vice-President Dick Cheney, requested that the Joint Chiefs of Staff redraw long-standing plans for a possible attack on Iran, according to former officials and government consultants. The focus of the plans had been a broad bombing attack, with targets including Iran’s known and suspected nuclear facilities and other military and infrastructure sites. Now the emphasis is on “surgical” strikes on Revolutionary Guard Corps facilities in Tehran and elsewhere, which, the Administration claims, have been the source of attacks on Americans in Iraq. What had been presented primarily as a counter-proliferation mission has been reconceived as counterterrorism.

The shift in targeting reflects three developments. First, the President and his senior advisers have concluded that their campaign to convince the American public that Iran poses an imminent nuclear threat has failed (unlike a similar campaign before the Iraq war), and that as a result there is not enough popular support for a major bombing campaign. The second development is that the White House has come to terms, in private, with the general consensus of the American intelligence community that Iran is at least five years away from obtaining a bomb. And, finally, there has been a growing recognition in Washington and throughout the Middle East that Iran is emerging as the geopolitical winner of the war in Iraq.

It looks like the American people weren't buying the nuclear bomb spin so something new was needed. Who do you think is behind this new tactic? It's Dick Cheney, of course. Hersh quotes his unnamed source,

The former intelligence official added, “There is a desperate effort by Cheney et al. to bring military action to Iran as soon as possible. Meanwhile, the politicians are saying, ‘You can’t do it, because every Republican is going to be defeated, and we’re only one fact from going over the cliff in Iraq.’ But Cheney doesn’t give a rat’s ass about the Republican worries, and neither does the President.”

Judging from what I saw on television last week, the media is buying into the switch in tactics. Almost everyone who interviewed Ahmadinejad asked about "killing American soldiers in Iraq." Is it really this easy to trick the media? Doesn't anyone have the gumption to stand up to the propaganda machine and ask the hard questions?

Realistically, what do you expect Iran to do? There's a bloody civil war going on just across the river. It involves, among other things, religious groups with which Iran has some sympathy. In addition, Iraq is being occupied by 150,000 troops from a foreign country that labels Iran as a member of the axis of evil. It would be shocking if Iran didn't have people in Iraq with a view to influencing the outcome. I suspect Saudi Arabia and Kuwait are also sending "advisors" and supplies into Iraq.

The logic of the "surgical strike" tactic escapes me. Does the American administration really believe that Iran would roll over and play dead as soon as American bombers attacked supply bases in Iran? Isn't it likely that such an attack would galvanize Iranian public opinion leading to greater involvement in Iraq? Is it possible that some foreign nations like China or Russia would ship anti-aircraft missiles to Iran so it could defend itself? What if Iran retaliated by firing surface-to-sea missiles at the next aircraft carrier to pass through the Strait of Hormuz [Iran tests upgraded surface-to-sea missile]?

“They’re moving everybody to the Iran desk,” one recently retired C.I.A. official said. “They’re dragging in a lot of analysts and ramping up everything. It’s just like the fall of 2002”—the months before the invasion of Iraq, when the Iraqi Operations Group became the most important in the agency. He added, “The guys now running the Iranian program have limited direct experience with Iran. In the event of an attack, how will the Iranians react? They will react, and the Administration has not thought it all the way through.”

That theme was echoed by Zbigniew Brzezinski, the former national-security adviser, who said that he had heard discussions of the White House’s more limited bombing plans for Iran. Brzezinski said that Iran would likely react to an American attack “by intensifying the conflict in Iraq and also in Afghanistan, their neighbors, and that could draw in Pakistan. We will be stuck in a regional war for twenty years.”

Surely those who advise the American President can't be this stupid? You'd think they would have learned a thing or two from their previous mistakes in 2003, wouldn't you? This is a dangerous game. Expanding the war into Iran is not going to make America safer and it's not going to win any friends. America needs people like Zbigniew Brzezinski to speak up now. It's clear that you can't rely on Congress, just like you couldn't rely on it in October 2002 [Iranian Army Is a Terrorist Organization - What's This All About?].

The Price of Atheism

 
From an ABC 20/20 special on atheism in July 2007.

Billy Learns About Transposase

 

Monday's Molecule #45

 
There's no structure today. Instead, I've given you a photograph of a flower. Isn't it pretty?

You have to guess what molecule I'm thinking about, using the peculiar colored flower as a clue. It's the pattern of purple/pink stripes that gives it away. What molecule caused that pattern? There's a direct connection between this molecule and Wednesday's Nobel Laureate(s).

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous free lunch winners are ineligible for one month from the time they first collected the prize. There are three ineligible candidates for this Wednesday's reward. The prize is a free lunch at the Faculty Club.

Send your guess to Sandwalk (sandwalk(at)bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and the Nobel Laureate(s). Correct responses will be posted tomorrow along with the time that the message was received on my server. This way I may select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

The Toronto Star Endorses First-Pass-the-Post

 


Today's editorial in The Toronto Star speaks against the mixed member proportional (MMP) electoral system and in favor of the status quo [Electoral reform a backward step].

The editors note that John Tory, the Progressive Conservative leader, is cool on the idea of MPP. The editors say,

Although the new system promises to deliver a legislature that mirrors the voters' intent, Tory notes it would also create two classes of members of the Legislature. Some would have a direct mandate from the voters; others could simply be appointed by party bosses.

If that is a democratic gain, it is hard to see.

Under the current system, nominees are appointed by a tiny number of dedicated people in each riding. Sometimes there are nomination meetings attended by a sizable crowd but those meetings are prone to stacking and all kinds of other abuses. The point is not that this is evil, the point is that the current system isn't as pristine as the first-past-the-post advocates claim.

The selection of party lists can be done in many different ways. It could be by party bosses in some dark room or it could be a much more open process. We don't know how it will work out under the new mixed member proportional system. I tend to think that a more open process will prevail since all of Ontario will be watching to see who's at the top of the list. In the case of the Green Party, for example, it will be interesting to see who the four new members will be if they pull 3% of the votes. It will certainly influence whether I cast a vote in their direction.

The same thing applies to all other parties. I won't be inclined to vote for a list of stooges, and you can be sure the other parties will be certain to point out the defects in party lists.

I think this argument against MMP is almost completely bogus. It's scaremongering and nothing more. One of the advantages of the MMP system, in my opinion, is the opportunity to get people into the legislature who might otherwise have little chance of getting elected. People who aren't wealthy enough to personally finance a campaign or a contested nomination, for example, or people who aren't good door-to-door campaigners but who would be an asset to Parliament. (Scientists, who aren't good at spinning framing sticking to the party line?)

The other argument used by the editors is more of the same whining we've heard dozens of times before.

Jurisdictions that have adopted some form or other of proportional representation – think of Italy, Israel, Germany, Belgium – have become notorious for chaotic politics and legislative gridlock.

While the occasional minority or coalition government beats the odds and performs well, far more commonly they are bitterly divisive, short-lived and paralyzed by conflict. Routinely, whoever heads the leading party is forced to cater to the demands of small, sometimes radical special-interest parties that enjoy no wide support, just to stay in power. That in itself is a distortion of the voters' will.

Let's get one thing straight, an inconvenient truth that's often ignored by all those who oppose MMP; as noted in the editorial, the last time a government of Ontario was elected by a clear majority was 70 yeas ago. Ever since then it's been the will of the people to cast their votes for a number of different parties such that no one party gets 50% of the votes. In other words, the people don't want majority governments. Nevertheless, majority governments are what the first-past-the-post system delivered in almost all elections. The Toronto Star editors are arguing that the real will of the people should be ignored in the interests of "stability." It's an argument that's often used against democracy.

No one suggests that first-past-the post is perfect. But Ontario's current system is democratic and robust, delivering strong, stable government that works. Why strain to "fix" what isn't broken?

If you're going to use this argument then please grant us the courtesy of explaining why you think "stability" should trump the clear preferences of the electorate and tell us just how far you're prepared to go in that direction.

There's no point in creating worse case scenarios in order to frighten people. I could just as easily bring up cases under first-past-the-post where a majority government, elected by less than 50% of the votes, thwarted the expressed will of the majority. "Stability" isn't always desirable at the expense of true democracy.

Yes, there are examples in foreign countries of legislatures that are gridlocked because the people want it that way. This happens under all kinds of electoral systems but it is more likely under true proportional systems and less likely under the mixed proportional system that we are considering. Will it happen in Ontario? I don't know, and neither do the editors. Personally, I think it's very unlikely given our history. It seems to me that there's very little chance that the government of Ontario would end up becoming beholding to a small party of four or five members.

Incidentally, all four of the countries mentioned (Italy, Belgium, Germany, Israel) are modern progressive countries with histories of social reforms that Canadians have emulated, or envied. The idea that nothing gets done in the legislatures of these countries does not stand up to close scrutiny.

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[Photo Credit:Top: Police demonstrating how to maintain stability during the Queen's Park anti-poverty protest on June 15, 2000. Bottom: An example of the results produced by a first-past-the-post electoral system. "Thousands of teachers rallying at Queen's Park in the fall of 1997 were dismayed by government's lack of respect for the teaching profession." (Catholic Teachers Association) In 1995 Mike Harris' conservative government got 45% of the popular vote and 64% of the seats. In the 1999 election Mike Harris got 45% of the vote and 57% of the seats.]

Protein Secretion and Vesicle Traffic by Randy Schekman

 
Randy Schekman is a Professor at the University of California, Berkeley. He is one of the world's leading experts on sorting and secretion. The recent postings on The Signal Hypothesis and Signal Recognition particle focus on part of the sorting and secretion pathway. Schekman delivers three lectures on another part of this process, namely the formation of secretion vesicle in the cell and how they travel to the cell surface where they deliver their contents. The lectures are part of the iBioSeminars sponsored by The American Society for Cell Biology [Protein Secretion and Vesicle Traffic].

I think these lectures are examples of high quality science education unencumbered by any overt attempt to persuade the audience to adopt a particular social or political point of view.

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[Hat Tip: Bertalan Meskó at ScienceRoll (iBioSeminars: Bringing the best in biological research to the world]

Big Ideas: Saturday September 29, 2007

 
Every weekend TV Ontario broadcasts talks given by prominent thinkers at lectures given in Toronto. The broadcasts are at 4pm Saturday, repeated at 4pm on Sunday. You can also watch them on the Big Ideas website. The host, Andrew Moodie (photo below), often has insightful comments so it's better to watch the actual TV broadcast than the website video presentations. While Moodie is good, he's not as good as the previous host, Irshad Manji, in my opinion.

Today's lecturers will be of interest to Sandwalk readers. University of Toronto students will be familiar with Sue Varmuza.

Mark Abrahams
Marc Abrahams, editor of The Annals of Improbable Research and one of the organizers of the annual Ig-Nobel Prize ceremonies at Harvard University, discusses the work of scientists and academics that, "first makes you laugh, and then makes you think". Highlights of the lecture include discussions of a study that proves that Kansas is flatter than a pancake and a paper investigating The Forces Required to Drag Sheep Over Various Surfaces.

Sue Varmuza
The second lecture in this episode of Big Ideas is by University of Toronto Zoology researcher Susannah Varmuza who discusses the evolving field of Epigenetics and what research into such things as mouse coat colour is telling scientists about the age-old "nature versus nurture" debate.

Here's the link: Susannah Varmusa.

MMP & Party Lists

 


I suppose it's to be expected. People who are opposed to the Mixed Member Proportional system are making up stories in order to make it seem as bad as possible.

There seems to be a lot of confusion about the party lists. Here's a brief summary from the Vote for MMP website.

Elections Ontario will publish the selection of candidates that each party has democratically elected before the election.

This information will be widely available in advance, as required by law:

• you'll know who party members selected before you vote for that party
• you'll know whether a party valued having a good balance of women and men
• you'll know whether a party valued having candidates from across the province, from rural and urban regions
• you'll know whether a party valued having candidates who reflected Ontario's diverse population
• you'll be able to decide before you vote whether a party created its list in a fair and democratic way

The important point here is that you will know who's on the list before you vote. You don't have to vote for the party if you don't like the list. Some people seem to think that a defeated candidate can be moved to the list after the votes have been counted and get elected by the back door.

Most people are worried about the party lists. They seem to think that the people on the list will be worthless party hacks. I don't think this is a major concern for two reasons.

1. Local ridings are already nominating worthless party hacks so the situation could hardly get any worse.
2. You won't vote for a party if their list is full of people who shouldn't be in the legislature.

Transcription of the 7SL Gene

Theme:
Transcription
There are five different kinds of RNA polymerase in eukaryotes. Each of them is responsible for transcription of a different class of gene [Eukaryotic RNA Polymerases]. RNA polymerase III transcribes a heterogeneous class of genes that give rise to small RNAs.


The class III genes can be subdivided into four types depending on the location of the promoter regions. Type 1 genes possess an internal control region (ICR) that functions as the promoter. What this means is that the site of binding of the pol III transcription complex is within the gene. 5S RNA genes are the only kind of type 1 gene.

A cartoon drawing of the pol III transcription complex on a 5S RNA gene is shown above (Moran, Scrimgeour et al. 1994). The transcription factor TFIIIA binds to the internal control region (ICR). Another transcription factor, TFIIIC, binds TFIIIA and it, in turn, interacts with TFIIIB and RNA polymerase III. Transcription is initiated at a site (+1) upstream from the internal control region. Note that when the 5S RNA is produced it will contain the binding sites for TFIIIA. The significance of this fact will become clear in a few minutes.

The type 2 genes have an intragenic promoter with two binding sites, A and B. TFIIIC binds directly to this promoter causing the assembly of a transcription complex upstream in the same manner as the type 1 genes. Most of the transfer RNA (tRNA) genes are type 2 genes.

Type 3 genes have an upstream promoter and no internal promoter. In this sense they resemble the typical class II genes (transcribed by RNA polymerase II), such as those that encode protein. The U6 snRNA gene, a component of the spliceosome [RNA Splicing: Introns and Exons] is the prototype gene of this category.

Finally, type 4 genes have both an internal region where the regular class III transcription factors bind and a promoter at the 5′ end of the gene where regulatory transcription factors bind to control transcription. The 7SL RNA gene is a type 4 gene.

Recall that 7SL RNA is the major component of Signal Recognition Particle (SRP). There are three genes for this RNA located on human chromosome 14 [Human Genes Involved in the Signal Hypothesis Pathway]. Since 7SL RNA is one of the small RNAs present in most cells it should not come as a surprise that its gene is transcribed by RNA polymerase III.


The RN7SL promoter has been characterized by Englert et al. (2004). The main features are shown in the diagram above. The solid blue box represents the gene—the DNA sequence corresponding to the 7SL RNA. There's a start site for transcription (+1) that's determined by the positioning of RNA polymerase III upstream. The transcription complex is assembled when TFIIIC binds to an internal control region specified by box A and box B. These are short DNA sequences (10 bp) that resemble the binding sites in tRNA genes. The upstream promoter region consists of a TATA box where RNA polymerase III binds and a regulatory site where unknown transcription factors (TF) bind.

Transcription terminates at a short stretch of thymidylate residues (T) at the 3′ end of the gene.

All four regulatory sites have to be present for maximum rates of transcription but—and this is important—there will still be low levels of transcription if only the A box and the B box are present.


From time to time cellular RNAs are copied by an enzyme called reverse transcriptase to create a DNA:RNA double-stranded molecule. On occasion this hybrid molecule will become integrated into the genome through a nonhomologous recombination event. (Sometimes the RNA strand will be replaced by DNA synthesis to create double-stranded DNA corresponding to the 7SL sequence.) This creates something called a processed pseudogene. Most genomes have hundreds of these pseudogenes derived from hundreds of different genes. They have arisen from accidental events over the course of millions of year of evolution and since there's no pressure to eliminate them, they are retained in the genome as junk.

Theme:
Junk DNA
If the processed pseudogene is derived from a class III gene there's a good chance that it will retain prompter activity because a good part of the promoter sequence was present in the RNA molecule. This is the case with 7SL pseudogenes and tRNA pseudogenes. They are often transcribed at low levels. The production of additional RNAs from the processed pseudogenes increases the probability that more pseudogenes will be created. More significantly, if the processed 7SL or tRNA pseudogenes happen to integrate near certain mobilization sequences they will be converted to retrotransposons because they can direct transcription of themselves—a necessary step in transposition. When this happens the pseudogenes will spread rapidly throughout the genome. We call this selfish DNA.

More than 10% of your genome consists of degenerate 7SL genes. That's where some of the junk DNA in your genome comes from.

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Englert, M., Felis, M., Junker, V. and Beier, H. (2004) Novel upstream and intragenic control elements for the RNA polymerase III-dependent transcription of human 7SL RNA genes. Biochimie. 86:867-74. [PubMed]

DNA Tatoo

 
Carl Zimmer has been collecting biological tattoos. The latest is a DNA tattoo [Science Tattoo Friday: A Textbook On Your Back]. Here's what the victim fan has to say ...

"My tattoo is from an Irving Geis illustration of DNA. I was attracted to his attention to the molecular detail while also drawing in a representational spiral that doesn't ignore the basic beauty of the double helix. This particular sequence (I've BLASTED) is too short to be specific to only one gene, but one human gene it's found it is the 5' UTR of one of our tight junctions."-Matthew MacDougall, 4th year medical student

The figure is, indeed, a drawing by Irving Geis. It's based on a structure of the dodecamer CGCGAATTCGCG solved by Drew et al. (1981). You can download the PDB file yourself at 1BNA and look at it in your favorite structure viewer. Mine is RasMol. The DNA is in the typical B-DNA form first predicted by Watson & Crick.

THEME

Deoxyribonucleic Acid (DNA)I've prepared two views of this structure (below) so you see how it compares to the Geis drawing. The drawing is in some textbooks, notably Voet & Voet Biochemistry 3rd ed. (p.1108). If you look closely, you will notice that Geis has taken a few "liberties" with his drawing. It's not quite the same as the actual molecular model but it's pretty close. I don't think our 4th year medical student has to worry about anyone noticing the difference, except for curmudgeonly biochemistry Professors!

Inflating a Little Man

 
TIME magazine gets it (mostly) right in a column by Joe Klein [Inflating a Little Man].

Well, at the top of the list are our old friends the neoconservatives, the folks who provided the intellectual rationale for Bush's war in Iraq, many of whom are now itching for a war with Iran. Norman Podhoretz, the neocon paterfamilias, has written a trifle called World War IV: The Long Struggle Against Islamofascism and loves to posit Ahmadinejad and Osama bin Laden—a far more dangerous character—as the heirs to Hitler and Stalin. "They follow the path of fascism, Nazism and totalitarianism," he writes. This is incendiary foolishness. Terrorists have the ability to wreak terrible damage intermittently, but they don't represent an existential threat to the U.S. Ahmadinejad commands no legions—not even the Hizballah forces in Lebanon that attacked Israel in the summer of 2006—and if Podhoretz doesn't know that, he should. Taking Ahmadinejad literally, as the neoconservatives do, is being disingenuous with lethal intent. It gives license to a conga line of politicians—especially Republicans running for �President—to strut their stuff by jumping on Ahmadinejad and Columbia University and liberals in general. Mitt Romney runs an ad in which he brags that he denied the milquetoast reformer Khatami a police escort to Harvard University in 2006. Now there's a man! The New York Daily News, owned by neoconservative Mort Zuckerman, runs the headline the evil has landed. The cable news networks hyperventilate. Even the president of Columbia University, Lee Bollinger, feels the need to demolish Ahmadinejad — elegantly, I must say — before the speech. A giant toxic bubble overwhelms the public square.

And then, there he is — and laughter is freedom's only appropriate reaction. The bubble bursts. He denies not only the Holocaust but also homosexuality? Suddenly, it all becomes obvious: We are being played by extremists on both sides. To be sure, Iran does arm Hizballah, and it does have an active nuclear program that may or may not be proved to have hostile intent, and it is making trouble for the U.S. in Iraq, supplying weapons to our enemies. These are all problems to be addressed soberly and perhaps even, eventually, with multilateral force. But the neoconservative campaign to transform Ahmadinejad into Hitler or Stalin, to pretend that he has the ability to destroy the world, to make a hoo-ha over letting the little man speak, is a cynical attempt to plump for war. Ahmadinejad may be ridiculous, but Podhoretz—who recently spent 45 minutes with Bush arguing for more war—isn't very funny at all. 

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[Hat Tip: John Wilkins at Evolving Thoughts (How to fix Iraq, and not invade Iran)]

US High School Dropout Rate

 
According to the University of Minnesota, the high school dropout rate in the USA is close to 25% [U of Minnesota study finds that US high school dropout rate higher than thought].

University of Minnesota sociologists have found that the U.S. high school dropout rate is considerably higher than most people think -- with one in four students not graduating -- and has not improved appreciably in recent decades. Their findings point to discrepancies in the two major data sources on which most governmental and non-governmental agencies base their findings.

The U.S. Census Bureau’s Current Population Survey (CPS) is widely used by governmental and non-governmental sources -- from the Annie E. Casey Foundation to the White House -- to report high school dropout rates. The CPS paints a rosy picture, showing dropout rates at about 10 percent in recent years and declining some 40 percent over the past generation. On the other hand, measures of high school completion based on the National Center for Education Statistics’ Common Core of Data survey (CCD) paint a darker picture, with high school completion rates holding steady at about 75 percent in recent decades.

Here's the important question that everyone seems to ignore: What is the optimal high school dropout rate? Surely it shouldn't be zero because that would be setting the bar too low. It probably shouldn't be 50% because that sets the bar too high. What should it be, assuming that lack of ability to complete high school was the only reason for dropping out?

If we're interested in keeping students in high school by addressing those other reasons for dropping out, then how will we know if we're succeeding unless we establish the minimum dropout rate? Is 25% good?

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[Photo Credit: "Joining nationwide demonstrations, high-school students in Valparaíso [Chile] take to the streets on May 30 [2006] to protest proposed changes in Chile's public education system." Eliseo Fernandez—Reuters /Landov (Encyclopedia Britanica Online)]

The Giardia lamblia Genome

 
The sequence of the Giardia lamblia genome has just been published in this month's issue of Science [Morrison et al., 2007].

Giardia lamblia is a single-celled eukaryote with two nuclei and prominent flagella (undulipodia, cilia) [Giardia lamblia, Wikipedia]. In most classification schemes it is placed in the Diplomonadida group, which may or may not be accorded the rank of phylum [Giardia lamblia NCBI Taxonomy]. Giardia is an intestinal parasite that colonizes the small intestine causing diarrhea and sometimes pain and nausea.

Many of the press releases focus on the medical relevance of the work on Giardia but the direct quotations from the scientists involved in the project reveal the real purpose behind this genome sequencing project. For example, Mitchell Sogin is quoted in the Marine Biogical Laboratory press release [Giardia Genome Unlocked].

“We embarked upon this genome project because of its importance to human health and suggestions from earlier molecular analyses that Giardia represents a very early-diverging lineage in the evolutionary history of eukaryotes,” Sogin says. “Giardia’s genome content and architecture support these theories about the parasite’s ancestral character.”

Sogin has a long standing interest in the evolution of eukaryotes and I think it's fair to say that Giardiasis is not the main focus of his research at the Marine Biological Laboratory in Woods Hole, Maine Massachusetts (USA) .

The Giardia lamblia genome is ~11.7 Mb in size (11,700,00 base pairs). This makes it about the same size as the yeast genome and the largest bacterial genomes. Mammalian genomes are about 200-300 times larger.

Preliminary results indicate 6470 genes distributed on five chromosomes. Most of the genes do not have introns and the average distance between genes is a few hundred nucleotides. What this means is that the genome is very compact with hardly any junk DNA (77% of the genome corresponds to coding regions as opposed to less than 2% in humans).

The number of genes is similar to the number found in yeast [Saccharomyces Genome Database (SGD)]. Multicellular species have 15-25,000 genes.

The introduction to the Morrison et al. (2007) paper has a nice summary of the main problems with relating Giardia to other eukaryotes.

Unusual features of this enigmatic protist include the presence of two similar, transcriptionally active diploid nuclei and the absence of mitochondria and peroxisomes. Giardia is a member of the Diplomonadida, which includes both free-living (e.g., Trepomonas) and parasitic species. The phylogenetic position of diplomonads and related excavate taxa is perplexing. Ribosomal RNA (rRNA), vacuolar ATPase (adenosine triphosphatase), and elongation factor phylogenies identify Giardia as a basal eukaryote (2–4). Other gene trees position diplomonads as one of many eukaryotic lineages that diverged nearly simultaneously with the opisthokonts and plants. Discoveries of a mitochondrial-like cpn60 gene and a mitosome imply that the absence of respiring mitochondria in Giardia may reflect adaptation to a microaerophilic life-style rather than divergence before the endosymbiosis of the mitochondrial ancestor.

Originally, it was thought that Giardia must be part of a group that diverged very early on in eukaryotic evolution, before other lineages acquired mitochondria. However, in the past ten years or so these amitochondrial species have been shown to contain genes that are clearly derived from mitiochondria (e.g., cpn60, dnaK). Thus, it now appears that these species have lost their original mitochondria, calling into question their position at the root of the eukaryotic tree.

One of the main surprises is the confirmation of what had long been suspected: Giardia is missing some common eukaryotic genes. The title of the paper highlights this finding: "Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia."

In many cases the protein machines in Giardia are simpler than those in other eukaryotes and some key metabolic enzymes are not present. Is this a derived phenomenon resulting from a parasitic lifestyle or is it indicative of a primitive state in eukaryotic evolution?

Morrison et al. (2007) indicate their preference ...

As discussed earlier, Giardia consistently shows a pattern of simplified molecular machinery, cytoskeletal structure, and metabolic pathways compared to later diverging lineages such as fungi and even Trichomonas or Entamoeba (Supporting Online Material; table S7 and fig. S5). A parsimonious explanation of this pattern is that Giardia never had many components of what may be considered "eukaryotic machinery," not that it had and lost them through genome reduction as is evident for Encephalitozoon. Taking a whole-evidence approach, one sees that these data reflect early divergence, not a derived genome.

They attempt to construct phylogenetic trees based on a number of newly sequenced genes but immediately encountered problems.

Phylogenetic inference alone cannot resolve Giardia's evolutionary history. Because so many of Giardia's genes may have been derived from horizontal transfer or be subject to accelerated evolution, only a subset can be used to infer phylogeny. Of the ~1500 genes for which there are known homologs, only a handful included diverse eukaryotic taxa and generated robust trees, largely because the sequences could not be unambiguously aligned. We generated and examined trees for many conserved proteins, and selected ribosomal proteins for a multigene data set because they are an ancient family, whose nature—interaction with rRNAs and with all cellular proteins during their synthesis—constrains their divergence.

Their data suggests that Giardia and its close relatives form a lineage that branches deeply in the eukaryotic tree suggesting that they diverged very early on in eukaryotic evolution (above, from the supplemental data). (Probably close to two billion years ago.)

In an article accompanying the original paper, Keeling (2007) discusses the implications. He includes the phylogenetic tree shown here [Deep Questions in the Tree of Life].

Eukaryotic evolution. The hypothetical evolutionary tree consists of five "supergroups" based on several kinds of evidence (15). The branching order of supergroups is unresolved, implying that the relationships are unknown rather than a simultaneous radiation. CM indicates the presence of cryptic mitochondria (hydrogenosomes or mitosomes). A question mark indicates that no organelle has yet been found.

This is not a consensus tree by any stretch. The existence of the five groups is hotly contested and it remains to be seen whether these groupings will gain widespread support. Notice that Keeling does not commit to a branching order for the five groups in spite of the conclusions of Morrison et al. (2007) in the paper he is reviewing.

What is clear is that the old trees based on ribosomal RNA genes are not reliable and other genes will have to be examined in future work. That's the real significance of the Giardia lamblia genome sequence and the sequences of the genomes of other simple eukaryotes. Given that Giardia is missing some important genes—posibly because of its parasitic lifestyle—this may not be an easy task. Keeling (2007) sums it up like this ....

The outcome of this debate affects not only our understanding of early eukaryotic evolution, but also our view of Giardia biology. Simple characteristics could be primitive or derived via reduction, alternatives with very different meanings. The simplicity of Giardia's molecular systems differs from that of known derived parasites (1, 13). However, different lineages can follow different reductive paths (14), so determining Giardia's origins independently of its simplicity is essential. Given the depth of these questions, the new life that Morrison et al. have breathed into the debates is welcome, and will ensure continued attention on both a fascinating cell and the origin of eukaryotes.

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[Photo Credits: The life cycle diagram is from the National Institutes of Health (USA) (Wikimedia Commons). The scanning electron micrograph of Giardia is from the Centers for Disease Control and Prevention (USA) (Wikimedia Commons)]

Morrison, H.G., McArthur, A.G., Gillin, F.D., Aley, S.B., et al. (2007) Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia. Science 317:1921 - 1926. [Science]

Keeling, P.J. (2007) Deep Questions in the Tree of Life. Science 317:1875-1876. [Science]

I Wish I Could Be There to See the Flaming Framing

 
SPECIAL EVENT:
Speaking Science 2.0: New Directions in Science Communications
Friday, September 28, 2007
7:30 p.m.
Bell Museum Auditorium
$5 Suggested Donation

Seed magazine writers and influential science bloggers gather to discuss new directions in science communication. This lively panel discussion will cover a range of topics, including science and culture, public engagement with science, the role of scientists in the public discussion of science, and communication via the Internet, film, museums and other media. Author and journalist Chris Mooney, American University communications professor Matthew Nisbet, and University of Minnesota anthropologist Greg Laden will join moderator Jessica Marshall, a U of M science journalism professor. A reception in Dinkytown will follow the event. Co-sponsored by the Bell Museum of Natural History; Seed Magazine/ScienceBlogs; The Humphrey Institute's Center for Science, Technology and Public Policy; and the Minnesota Journalism Center.

Will PZ Myers be there?