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Project Resolution – Pseudogenes in Myobacterium species: Dr. Christine Boinett and Professor Pablo Tsukayama

Project Resolution: Dr. Christine Boinett and Professor Pablo Tsukayama discuss pseudogenes in _Myobacterium_ species
Hello, I’m Pablo Tsukayama, and today, I’m with Christine Boinett to discuss the Activities in Week 3 of this module. Christine. Yeah. We have used Artemis to explore the genomes of two related Mycobacterium pathogens. Indeed, yes, we’re going to be using two genomes, which is Mycobacterium leprae and Mycobacterium tuberculosis. Although these are related organisms, they cause very different infections in humans, and have evolved towards different lifestyles over millions of years. Yeah, indeed tuberculosis. Even though they’re both [the Mycobacterium are] infectious to humans, tuberculosis mainly causes as you’ve seen, its a lung infection, it affects the lungs but can affect other parts of the body.
leprae leprosy for which the causative agent is Mycobacterium leprae causes mainly, sort of, effects mucosal surfaces, so lungs and eyes. But as well causes numbness in the peripheral nervous system. So those are the main affected areas, but obviously, it’s a more outward disease. So you see it [on] lots of limbs, it affects the limbs, so you can see visually the infection sites.Yeah. We have seen in this activity that the genome of Mycobacterium leprae gets streamlined over the years, over millions of years, and can you tell us how these genome reductions takes place? Yeah, sure, of course. What’s interesting to study, in these two organisms, is even though they’re from the same genus, so Mycobacterium.
Both of them [from] the Mycobacterium genus, leprae has about 1,000, just over 1,000 pseudogenes. Whereas when you look at tuberculosis, which is a genome of slightly bigger size, so tuberculosis is 4 megabase, and leprae is about 3.2. And what we see is that with pseudogenes, tuberculosis only has six, and then about over 3,000 functional genes. As opposed to leprae, which has only about 1,000 or 1600 functional genes, and the rest are pseudogenes. So about 1300 are pseudogenes. All right. Yeah. So these pseudogenes, so can you tell us how we can visualise them and identify them in the genomes using Artemis? Yeah, sure. So how we normally do it is using comparative genomics.
And because they are of the same genus, and they’re relatively comparable, we look through the genome using a genome browser such as Artemis. And you go across them, and looking at the open reading frames, you see a shift in GC [guanine-cytosine] content mainly. So, because they have stop codons, this is what we normally define as pseudogenes, but it can also be frame frameshift mutations. But in mainly leprae, you do see a sort of drop in GC content where the pseudogenes are, and lots of stop codons, about five stop codons within each CDS (CoDing Sequence), whereas in TB, you can see the functional protein.
So it’s a nice way to compare them because even though it’s labelled as a them as pseudogene in leprae, it is a functional gene sometimes in tuberculosis. As we have discussed previously, coding sequences must first be transcribed into messenger RNAs so that these can be translated into proteins by the ribosomes. In the case of these pseudogenes, do they get transcribed into messenger RNAs? Yeah, it’s actually really interesting. In leprae, the pseudogenes are transcribed. So it’s very unlike, I think, most other Gram- negatives.
I think in Enterobacteriaceae, which you work on: are they transcribed normally? Like in Salmonella? Yes, sometimes you see signatures of transcription happening, but it’s not always the case. And some people suggest that these may have a function in itself. The transcription of truncated sequences, but we don’t know about that yet. And I think it’s the same also in leprae, so they don’t know why they’ve transcribed these pseudogenes.
But they think as well because of transcription that it has or may have some sort of metabolic impact on the genome but also the bacterium, so they are very, very slow growing, so maybe the energy it takes to transcribe these, what we would say, these nonfunctional genes that maybe cause the slow growing, and so have a negative impact on the growth of the bacterium. Yeah. Yes, and in leprae, it’s notorious for being very difficult to grow and very slow to grow in the laboratory. From these analyses that we’ve run, can you tell us something about the genes that are lost that might be contributing to the slow metabolism? That’s true, yeah. It’s actually interesting.
This is how, thankfully, with genomic sequencing, they found that the pseudogenes were mainly in genes that would be causing it to be able to function or grow in various carbon sources. So it’s sort of lost its ability to grow in various carbon sources, which means in the lab, it’s really hard to grow it in vitro. So, I think, in the paper described by Singh and Cole, which is the paper - that we - the learners will be working on. They’ve sort of postulated that …this would be the reason you can’t grow it in the lab. And actually, armadillos are used to growing it. Armadillos?
Yeah, this is where they got the first DNA, enough just to be able to sequence it. Because of the lower temperatures of the body, yeah, in armadillos, Yeah. And so we’ve seen that there’s more than 1,000 pseudogenes in the genome in leprae. What does this mean in terms of the biology, and the evolution, and the lifestyle of Mycobacterium leprae compared to in tuberculosis? So, I think, it’s what we’d call reductive evolution, and what scientists think is it has evolved and lost its ability to grow in the environment. As opposed to TB, TB can grow pretty much anywhere, But leprae is host restricted, so it has to grow inside your cells.
So having lost the ability by the accumulation of pseudogenes, you can’t grow it in the lab or just in the environment. So it’s very specific, and it’s sort of lost its ability to be ubiquitous in the environment, Yeah. That’s really interesting. Yeah, it’s really cool. It’s really cool. To our learners out there, this case of comparing two Mycobacterium species is a prime example of how we can use genomes and genome annotations to give us clues about the adaptation and evolution of an organism over millions of years. So, I hope that was useful. As always, if you have any questions or feedback, please leave it in the comments section below. Thank you.

In this Project we looked at the reductive evolution shown in Myobacterium leprae which has resulted in specific genomic and subsequently metabolic changes that makes M. lepae dramatically different from Myobacterium tuberculosis, a closely related species of the same genus.

We find that some genes have been replaced by pseudogenes and that these changes have an effect on the metabolism of the organism. As a consequence, the bacterium is able to grow on only a limited number of carbon sources. This has resulted in the shift from M. leprae living free in the environment like most mycobacteria to only living in host cells.

Understanding the nature of M. leprae’s genome, in the comments area, share your thinking on:

  • how this disease spreads?

  • how M. leprae achieves drug resistance?

  • how scientists can track the M. leprae infections using DNA sequencing?

If you know how this or similar bacterial infections are tracked in your country, region, city, or town, share and compare this knowledge with other learners in the comments area.

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Bacterial Genomes II: Accessing and Analysing Microbial Genome Data Using Artemis

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