Archive for the ‘endosymbiosis’ Category
more on photosynthesis: stuff about rubisco, or not
don’t ask
So in my wild wanderings on this topic I’ve been informed by a close friend that rubisco is key, and research is ongoing. So, starting off with my key text, Oliver Morton’s Eating the Sun, and a video on rubisco that’s been drawn to my attention, I’ll keep making attempts to educate myself.
So, nitrogen is essential to all living organisms, and our atmosphere is mostly nitrogen – just over 78%. It’s essential to proteins and DNA, but apparently it isn’t something we can directly access. There’s an enzyme complex called nitrogenase, which some bacteria and archaea can produce, which is able to convert inert nitrogen gas into ammonia (NH3). However, nitrogenase falls apart in the presence of oxygen, so atmospheric nitrogen can’t be used by virtually all living organisms. Only anoxic organisms – generally very basic microbes (spoiler alert – nitroplasts) – can make use of it. So, it has generally been a rule of biology that no complex organisms can utilise nitrogen, but a new bacterium was discovered quite recently, or rather its DNA. That’s to say, samples of seawater were examined for the presence of nitrogen-fixing bacteria. What was initially found, in the 1990s, in a search for a key nitrogen-fixing gene, was genetic material, without the organism it belonged to. The searcher, or researcher, felt that he had a good idea what the missing organism would look like. A hunt was on to find this organism, which left its ‘fingerprints’ everywhere, but it took years to find it, all they could find was DNA with a missing owner (I’m relying heavily on a video referenced below for all this). What they did find was quite strange – its DNA didn’t seem to contain the genes for photosynthesis. And this DNA turned up all over the place, ‘complete’ with missing genes – a lot of them, some 80% of its entire genome – which seemed to make its very survival questionable. But then it was worked out that the DNA was inside a species of algae which was hosting it. This algae, Braarudosphaera Bigelowii (Bigelowii for short), was being investigated in Japan by a female scientist, partly because of the symmetrical beauty of its shape at a particular developmental stage. She eventually managed to culture the algae (the video tells the story beautifully and movingly), and found something odd amongst the expected parts, almost like a separated container.
The Japanese researcher came across work from the team who had discovered the DNA with the missing host. It was generally a shock to both sides, but they were able to work together and discover what was effectively a symbiotic process, though the video on this suggests that the process goes beyond symbiosis, and is more like ‘two organisms fusing into one’, as with mitochondria and chloroplasts and their hosts. Bigelowii had become an organelle, dividing and growing at the same rate as its host. It was an important discovery, not only to add to the small family of organelles (it has been called a nitroplast), but to find an organism that effectively fed on nitrogen. Could this be used to produce nitrogen – which is currently produced in expensive and inefficient ways – out of the air?
So, this stuff about nitroplasts is quite recent, so it doesn’t get into Morton’s book to complexify it even further. And it’s the most complex book I’ve read – and I’ve read an awful lot of the bloody things. I can but give an example: this, about chloroplasts:
As they have spread out with and through their wormhole world, its chloroplast inhabitants have changed according to the requirements of the time-tunnels that they find themselves in; evolution applies in there just as it does out here. In some tunnels the chloroplasts are squadrons of small green capsules that still have the look of bacteria. In others they have evolved into swirling spirals pressed tight against the outer membrane like rifling in the barrel of a gun. Some are red five-pointed stars, one to a cell. But they are all descended from the same original ancestor.
There are many dead ends in the network – hundreds of thousands in every leaf that falls – billions of times as many in every fossil species bereft of descendants today. But the threads as yet unbroken are all but uncountable, and multiply still. All around us, moment by moment, the skein of wormholes pushes itself further into the future.
Oliver Morton, Eating the Sun, pp 209-10
Rifling in the barrel of a gun? I’ve managed to avoid going near such an item in the 70 years of my life. And I might know something about the look of love (or not), but the look of bacteria is well beyond me. Never owned a microscope, sadly. As for the rest, lovely writing but I can’t quite get a picture…. But, I will soldier on…
References
Oliver Morton, Eating the Sun, 2007
understanding genomics 1 – mitochondrial DNA
Canto: So maybe if we got humans to mate with bonobos we’d get a more promising hybrid offspring?
Jacinta: Haha well it’s not that simple, and I don’t mean just physiologically…
Canto: Okay those species wouldn’t be much attracted to each other – though I’ve heard that New Zealanders are very much attracted to sheep, but that just might be fantasy. But seriously, if two species – like bonobos and chimps, can interbreed, why can’t bonobos and humans? And they’d don’t have to canoodle, you can do it like in vitro fertilisation, right?
Jacinto: Well, bonobos and chimps are much more closely related to each other than they are to humans. And if you think bonobo-human hybridisation will somehow create a female-dominant libertarian society, well – it surely ain’t that simple. What we see in bonobo society is a kind of social evolution, not merely a matter of genetics. But having said that, I’m certainly into exploring genetics and genomics more than I’ve done so far.
Canto: Yes, I’ve been trying to educate myself on alleles, haplotypes, autosomal and mitochondrial DNA, homozygotism and heterozygotism (if there are such words), single nucleotide polymorphisms and…. I’m confused.
Jacinta: Well, let’s see if we can make more sense of the science, starting with, or continuing with Who we are and how we got here, which is mostly about ancient DNA but also tells us much about the past by looking at genetic variation within modern populations. Let me quote at length from Reich’s book, a passage about mitochondrial DNA – the DNA in our mitochondria which is somehow passed down only along female lines. I’ve no idea how that happens, but…
The first startling application of genetics to the study of the past involved mitochondrial DNA. This is a tiny proportion of the genome – only approximately 1/200,000th of it – which is passed down from mother to daughter to granddaughter. In 1987, Allan Wilson and his colleagues sequenced a few hundred letters of mitochondrial DNA from diverse people around the world. By comparing the mutations that were different among these sequences, he and his colleagues were able to construct a family tree of maternal relationships. What they found is that the deepest branch of the tree – the branch that left the main trunk earliest – is found today only in people of sub-Saharan African ancestry, suggesting that the ancestors of modern humans lived in Africa. In contrast, all non-Africans today descend from a later branch of the tree.
Canto: Yes, I can well understand the implications of that analysis, but it skates fairly lightly over the science, understandably for a book aimed at the general public. To be clear, they looked at the same stretches of mitochondrial DNA in diverse people, comparing differences – mutations – among them. And in some there were many mutations, suggesting time differences, due to that molecular clock thing. And I suppose those that differed most – from who? – had sub-Saharan ancestry.
Jacinta: Dating back about 160,000 years, according to best current estimates.
Canto: The science still eludes me. First, how does mitochondrial DNA pass only through the female line? We all have mitochondria, after all.
Jacinta: Okay, I’ve suddenly made made myself an expert. It all has to do with the sperm and the egg. One’s much bigger than the other, as you know, because the egg carries nutrients, including mitochondria, the only organelle in your cytoplasm that has its own DNA. Your own little spermatozoa are basically just packages of nuclear DNA, with a tail. Our mitochondrial DNA appears to have evolved separately from our nuclear DNA because mitochondria, or their ancestors, had a separate existence before being engulfed by the ancestors of our somatic or eukaryotic cells, in a theory that’s generally accepted if difficult to prove. It’s called the endosymbiosis theory.
Canto: So mitochondria probably had a separate, prokaryotic existence?
Jacinta: Most likely, which could take us to the development, the ‘leap’ if you like, of prokaryotic life into the eukaryotic, but we won’t go there. Interestingly, they’ve found that some species have mitochondrion-related organelles with no genome, and our own and other mammalian mitochondria are full of proteins – some 1500 different types – that are coded for by nuclear rather than mitochondrial DNA. Our mitochondrial DNA only codes for 13 different types of protein. It may be that there’s an evolutionary process going on that’s transferring all of our mitochondrial DNA to the nucleus, or there might be an evolutionary reason for why we’re retaining a tiny proportion of coding DNA in the mitochondria.
Canto: So – we’ve explained why mitochondrial DNA follows the female line, next I’d like to know how we trace it back 160,000 years, and can place the soi-disant mitochondrial Eve in sub-Saharan Africa.
Jacinta: Well the term’s a bit Judeo-Christian (there’s also a Y-chromosomal Adam), but she’s the matrilineal most recent common ancestor (mt-MRCA, and ‘Adam’ is designated Y-MRCA).
Canto: But both of these characters had parents and grandparents – who would be somehow just as common in their ancestry but less recent? I want to know more.
Jacinta: To quote Wikipedia…
… she is defined as the most recent woman from whom all living humans descend in an unbroken line purely through their mothers and through the mothers of those mothers, back until all lines converge on one woman.
… but I’m not sure if I understand that convergence. It clearly doesn’t refer to the first female H sapiens, it refers to cell lines, haplogroups and convergence in Africa. One of the cell lines used to pinpoint this convergence was HeLa, the very first and most commonly used cell line for a multiplicity of purposes…
Canto: That’s the Henrietta Lacks cell line! We read The Immortal Life of Henrietta Lacks! What a story!
Jacinta: Indeed. She would be proud, if she only knew… So, after obtaining data from HeLa and another cell line, that of an !Kung woman from Southern Africa, as well as from 145 women from a variety of populations:
The published conclusion was that all current human mtDNA originated from a single population from Africa, at the time dated to between 140,000 and 200,000 years ago.
Canto: So mt-MRCA is really a single population rather than a single person?
Jacinta: Yeah, maybe sorta, but don’t quote me. The Wikipedia article on this gives the impression that it’s been sheeted home to a single person, but it’s vague on the details. Given the way creationists leap on these things, I wish it was made more clear. Anyway the original analysis from the 1980s seems to be still robust as to the time-frame. The key is to work out when all female lineages converge, given varied mutation rates. So, I’m going to quote at length from the Wikipedia article on mt-MRCA, and try to translate it into Jacinta-speak.
Branches are identified by one or more unique markers which give a mitochondrial “DNA signature” or “haplotype” (e.g. the CRS [Cambridge Reference Sequence] is a haplotype). Each marker is a DNA base-pair that has resulted from an SNP [single nucleotide polymorphism] mutation. Scientists sort mitochondrial DNA results into more or less related groups, with more or less recent common ancestors. This leads to the construction of a DNA family tree where the branches are in biological terms clades, and the common ancestors such as Mitochondrial Eve sit at branching points in this tree. Major branches are said to define a haplogroup (e.g. CRS belongs to haplogroup H), and large branches containing several haplogroups are called “macro-haplogroups”.
So let’s explain some terms. A genetic marker is simply a DNA sequence with a known location on a chromosome. A haplotype or haploid genotype is, as the haploid term suggests, inherited from one rather than both parents – in this case a set of alleles inherited together. SNPs or ‘snips’ are differences of a single nucleotide – e.g the exchange of a cytosine (C) with a thymine (T). As to the rest of the above paragraph, I’m not so sure. As to haplogroups, another lengthy quote makes it fairly clear:
A haplogroup is…. a group of similar haplotypes that share a common ancestor with a single-nucleotide polymorphism mutation.More specifically, a haplogroup is a combination of alleles at different chromosomal regions that are closely linked and that tend to be inherited together. As a haplogroup consists of similar haplotypes, it is usually possible to predict a haplogroup from haplotypes. Haplogroups pertain to a single line of descent. As such, membership of a haplogroup, by any individual, relies on a relatively small proportion of the genetic material possessed by that individual.
Canto: Anyway, getting back to mt-MRCA, obviously not as memorable a term as mitochondrial Eve, it seems to be more a concept than a person, if only we could get people to understand that. If you want to go back to the first individual, it would be the first mitochondrion that managed to synthesise with a eukaryotic cell, or vice versa. From the human perspective, mt-MRCA can be best conceptualised as the peak of a pyramid from which all… but then she still had parents, and presumably aunts and uncles…. It just does my head in.
References
https://www.genome.gov/genetics-glossary/Mitochondrial-DNA
https://en.wikipedia.org/wiki/Mitochondrial_Eve
https://en.wikipedia.org/wiki/Haplogroup