Wednesday, October 21, 2009

Microbes continue: endosymbiosis

Here's a recap on previous papers in the ARJ microbe series:

Francis & Purdom: "More abundant than stars: an introductory overview of creaation microbiology"
HTML - PDF - My comments

Liu & Soper: "The natural history of retroviruses: exogenization vs endogenization"
HTML - PDF - My comments

The third paper in this series is Dan Criswell's "A Review of Mitoribosome Structure and Function Does not Support the Serial Endosymbiotic Theory." What does that mean? Well, there are two basic kinds of cell architecture, prokarytic and eukaryotic. Prokaryotes are basically like a sac of jelly (OK, they're a LOT more complicated than that, but I'm mostly interested in the architecture). Eukaryotes are also sacs of jelly but inside those sacs they have smaller sacs called organelles. These smaller sacs do stuff like our organs do stuff for us. There's an organelle that digests food (like our stomach), and there's an organelle for energy production (like our liver). The energy organelle is called a mitochondrion (plural mitochondria), and it has some interesting characteristics. Mitochondria are surrounded by two membranes, and they have their own circular chromosomes. Back in the 1970s, Lynn Margulis proposed that mitochondria were derived from bacteria. Her theory is called the Serial Endosymbiosis Theory (SET) ("serial" refers to additional bacteria that supposedly became other organelles like chloroplasts in plants). Research in the 1980s on mitochondrial and bacterial genes showed that the bacteria most similar to mitochondria were from a group called alpha proteobacteria. Today, the evolutionary origin of mitochondria is believed to have happened about two billion years ago at the origin of the eukaryotic cell. That first eukaryotic cell became the ancestor of plants, animals, fungi, and a bunch of one-celled organisms.

So Criswell's paper is a little controversial just with its title. I think the paper can be summed up in this snippet from the abstract:
According to the theory of serial endosymbiosis, the ribosomes present in mammalian mitochondria were expected to resemble the prokaryote 70S ribosome. However, the structure of mammalian mitochondrial ribosomes and their RNA and amino acid sequences indicate that mammalian mitochondrial ribosomes are completely different from prokaryotic ribosomes.

The paper discusses interesting information about mammalian mitochondrial ribosomes, which are the molecules that make proteins. Criswell's approach follows this strategy:
However, for SET to be plausible there must be observable evidence connecting the descendents (mitochondria) to an ancestor (prokaryote) and a feasible mechanism to convert the existing structures from the ancestral state.
He denies that there is any such evidence connecting mammalian mitochondrial ribosomes to bacterial ribosomes, and he rejects the idea of variation and natural selection as the source of the differences between mammalian mitochondrial ribosomes and bacterial ribosomes.

How does his argument hold up? Not so well. As I read his paper, I was really surprised by some of his claims. For example, he wrote,
Sequence comparisons between prokaryote and mitoribosome RNA genes (rDNA) or the rRNA sequences in the small or large subunits are difficult due to a lack of sequence homology. The sequence differences are so significant, that alignment programs available at the National Center for Biotechnology Information (NCBI) will not align these sequences partly due to the difference in length (for example, prokaryote E.coli ssu RNA is 1540 nucleotides; human mitoribosome ssu RNA is 954 nucleotides) and partly due to the different frequencies of rRNA nucleotides. An alignment can be forced manually using a program like ClustalX, but these alignments, which are highly subjective, show less than 40% homology between the two types of small subunit RNA with long stretches of gaps resulting in insignificant alignment scores.
If that's true, it's a staggering discovery. How could anyone have missed that over all these years? Since it was easily checked, I went to GenBank and looked up the sequence of the large subunit of the mitochondrial ribosome from humans. Then I did a BLASTN search against just bacterial sequences, and here's what I found:

The top hits all have excellent expectation values (E values) and the percent identities go as high as 75%. So the human mitochondrial and bacterial ribosomes are definitely homologous, and they can be aligned. What's curious is that the alignment only covers about 16% of the sequence length of the human sequence. So what happens if we do the reciprocal search using a bacterial sequence to find eukaryotic sequences?

To find out, I used BLASTN to search for eukaryotic homologues of the large ribosomal subunit of the Rickettsia prowazekii (an alpha proteobacterium) in the refseq_genomic database. Here are my results:

Notice that the top hits are all mitochondrial ribosomes, with alignments that cover almost the entire length of the Rickettsia sequence and similarities as high as 91%! None of them are animals, however. Reclinomonas and Malawimonas are both one-celled critters. Phytophthora is kind of like a fungus. Marchantia, Megaceros, Physcomitrella, and Cycas are all plants. Beginning to see the problem? By focusing exclusively on the similarity between bacterial and mammalian mitochondrial ribosomes, you completely miss the staggering similarity between bacterial and mitochondrial ribosomes in general.

Next, I got really creative. I took the mitochondrial large ribosomal subunit sequence from Reclinomonas (AKA the top hit from the Rickettsia search), and I searched again with BLASTN looking for just animal homologues in the refseq_genomic database. I was most interested in the alignment lengths. Why do the mitochondrial ribosomes of plants and one-celled eukaryotes align nearly the whole length of the bacterial sequence while the human mitochondrial ribosome aligns only 16% of the sequence? Maybe there's an intermediate... Here's what I found:

Notice among the top hits there are sequences that align to well over a third of the Reclinomonas sequence! See the ones that align to more than 40% of the sequence? Geodia, Topsentia, Iotrochota, and Negombata align nearly half of their length to the Reclinomonas sequence, and they're all sponges! Not only do we have nice intermediate alignments between Reclinomonas and vertebrates, but the intermediates happen to come from what are considered to be the most primitive animals!

Given these few BLAST searches, it seems to me that a strong case can be made for the affinity of mitochondria and bacteria, much stronger than Criswell implies in his article. Broadly speaking, mitochondrial ribosomes are very similar to bacterial ribosomes, and it is misleading to focus exclusively on the least similar ribosomes. Now, I'm sure this was an honest mistake that could have been fixed at some stage of writing or editing, but it is difficult to read articles critically when you agree with the basic premise. Don't think I'm making excuses, though. Regardless of how it happened, the article is erroneous and misleading.

By now my creationist readers are probably beside themselves with exasperation. Surely a creationist cannot endorse the evolutionary origin of mitochondria? That's totally incompatible with young-age creation doctrine! True enough, and I do not endorse the serial endosymbiosis theory. I also do not endorse misrepresenting the evidence for that theory. This is exactly the kind of thing I was talking about in the truth about evolution. We cannot keep pretending that there is no evidence for evolution. We reject serial endosymbiosis not because it's scientifically inadequate (as you've seen here, it's quite compelling) but because it is inconsistent with the biblical record of creation. According to the Bible, we know creation is true by faith (Heb. 11:3).

How do I explain these undeniable similarities between bacteria and mitochondria? I think Joe Francis is on the right track with his interest in symbiosis, from which he formulated the idea of a biomatrix, a living network connected by microbes that makes macrobial (i.e. visible) life possible. In a recent article in Answers Magazine, he put it this way:
All creatures on earth live in symbiotic partnerships, including lowly single-celled pond-dwelling organisms. It appears that the Creator wants us to "clearly see" in these pervasive symbiotic relationships how much we depend on others - and ultimately Him - for life. From the very beginning of time, all the different creatures on earth had to be alive and working together, and we continue to depend on them (and God) for a healthy life.

Exactly! So let's apply that to mitochondria: What if mitochondria really are bacteria? Not evolved bacteria, but bacteria so interconnected with our bodies that we depend on them for life itself, just as they depend on us. An inescapable symbiosis in every cell in our bodies. A picture of our dependence on God. What if we're looking at bacteria incorrectly as well? What if bacteria should really be thought of as external organelles? That seems far more satisfying to me than just trying to discredit a theory for which the evidence is surprisingly strong.

Criswell. 2009. A review of mitoribosome structure and function does not support the serial endosymbiotic theory. ARJ 2:107-115.

Francis. 2008. The matrix: life's support system. Answers 3(3):42-54.