Transponable elements: the jumping genes of our genome

In the same way that grasshoppers are jumping and moving through the field, there is a type of genes that jump through our genome and change its position. Our genome is not static, so read on to know everything about these kinds of genes.

THE DISCOVERY OF TRANSPONABLE ELEMENTS

Barbara McClintock discovered transposable elements, or also called mobile genetic elements because of their ability to move around the genome. The “jumping genes,” as this American geneticist christened them, changed the knowledge about genetics so far, since at first the scientific community did not believe in the idea that a DNA sequence could move on its own.

She had a special relationship with corn, a plant domesticated by man for 10,000 years and has become one of the three most cultivated cereals in the world. In addition, it is one of the most important staple foods since from it many derived products are made, such as flours and oils. Its great industrial value has made it have been studied in depth and its genome has been sequenced.

McClintock began studying the DNA of corn and observed that there were a number of genetic sequences that, without knowing how, changed position within the genome. Somehow, these sequences turned on or off the expression of other corn genes and this was observed with the naked eye; the grains of a corn cob could be of different colours (Figure 1), even within the same grain there were areas of various colours. Then McClintock sought the answer of how this was possible if the genes responsible for colour were inherited from the parents. The result was the discovery of the transposable elements, which led her to win the Nobel Prize in Medicine in 1983.

Figure 1. (A) P gene gives a purple grain. (B) A transponable element is inserted in the middle of the P gen and the grain has no pigmentation. (C) Corn cob wit some grains with P gene intact and others with P gene interrupted by a mobile genetic element. (Source: Porque biotecnología, adaptation)

EFFECTS OF THE CHANGE OF POSITION

When the transposable elements jump and change position they produce a loss of bases when leaving the place where they rested. This loss of some bases does not have “much” importance. But if the transposable element is inserted into a gene, there is an addition of a large number of bases that will cause the loose of gene’s function. For this reason, mobile genetic elements produce mutations because by jumping and changing their location, they alter the DNA sequence and prevent genes from encoding proteins through the genetic code. However, when they jump again, the gene regains its functionality and expresses itself as if nothing had happened.

Often, these jumping genes are considered parasites, because the cell cannot get rid of them. Although they can also bring benefits to the cell, such as transporting advantageous genes. The best known example is not found in humans, but in bacteria and their resistance to antibiotics such as penicillin, discovered by Alexander Fleming. The spread of antibiotic resistance is due to genes that encode enzymes that inactivate them, and that are located in mobile genetic elements. It is usually related to the horizontal transfer of genes, in which they can move from one cell to another as if they were bees that go from flower to flower. When this happens, the transposable element is introduced into a new cell and inserted into the genome of this new cell. That is when it will be faithfully transmitted to its progeny through the normal process of DNA replication and cell division.

TYPES OF TRANSPONABLE ELEMENTS

It is estimated that in the human genome there are 44% transposable elements, which can amount to 66% taking into account repeated fragments and short sequences derived from them. The consequence is that we have more than 1000 genes regulated, directly or indirectly, by sequences from transposable elements.

So far, two types of transposable elements are known: class I transposable elements or retrotransposons and class II transposable elements or DNA transposons. They are classified according to whether they require reverse transcription to jump and transpose or not.

Reverse transcription is similar to the transcription process, but with the difference that it occurs in reverse. That is, if in the classical transcription process a single strand of RNA is obtained from a double strand of DNA, in reverse transcription of an RNA molecule a DNA molecule is obtained. This is common in viruses such as HIV virus (AIDS) or hepatitis virus, but also in some class I transposable elements. These are very abundant and represent 90% of the transposable elements of our genome.

Instead, the others are class II transposable elements or DNA transposons. These are the elements that McClintock discovered in corn, with a 10% representation in our genome and responsible for the spread of antibiotic resistance in bacterial strains.

It should be noted that DNA transposons never use intermediaries, but are autonomous. They jump from one place of the genome to another by themselves, without any help. The mechanism they use is called “cut and paste” and is similar to the cut and paste we use on the computer. The DNA transposon cuts the DNA sequence that has end and look for another place to settle. Then there it also cuts the DNA sequence and is “hooked” (Figure 2).

Figure 2. Mechanism of cutting and pasting (Source: SITN: science in the news)

It is currently known that the activity of transposable elements is a source of evolutionary innovation due to the generation of mutations, which could have been key both in the development of organisms and in different evolutionary phenomena such as speciation; the process by which a population of a given species gives rise to another or other species.

The vast majority of these mutations are deleterious to organisms, but some of them will lead to adaptive improvement and tend to spread throughout the population. We could put our hand in the fire and we probably wouldn’t burn to ensure that much of the variability that life shows around us originally comes from the displacement of mobile genetic elements or transposable elements.

(Main picture: ABC Canada)

The reality of mutations

Do you remember the ninja turtles? Leonardo, Raphael, Michelangelo and Donatello were four turtles that suffered a mutation when they were bathed with a radioactive liquid. Fortunately or unfortunately, a mutation cannot turn us into ninja turtles, but it can have other effects. Next, I tell you what mutations are.

WHAT ARE MUTATIONS?

Our body is like a great factory in which our cells are the workers. These, thanks to their internal machinery, make the factory stay afloat with the least possible problems. The constant operation of our cells (24/7), sometimes causes errors in their machinery. This generates imperfections in the genetic code, which generally go unnoticed. It is true that cells do everything possible to fix the failures produced, but sometimes they are inevitable and lead to the generation of diseases or even to the death of the cell.

Mutations are these small errors, it means, mutations are stable and inheritable changes that alter the DNA sequence. This fact introduces new genetic variants in the population, generating genetic diversity.

Generally, mutations tend to be eliminated, but occasionally some can succeed and escape the DNA repair mechanisms of our cells. However, they only remain stable and inheritable in the DNA if they affect a cell type, the germ cells.

The organisms that reproduce sexually have two types of cells: germinal and somatic. While the former transmit genetic information from parents to children, somatic cells form the body of the organism. Because the information of germ cells, which are what will give rise to gametes (sperm and oocytes) passed from generation to generation, they must be protected against different genetic changes to safeguard each individual.

Most mutations are harmful, species cannot allow the accumulation of large number of mutations in their germ cells. For this reason not all mutations are fixed in the population, and many of these variants are usually eliminated. Occasionally some may be incorporated into all individuals of the species.

The mutation rate is the frequency at which new mutations occur in a gene. Each specie has a mutation rate of its own, modulated by natural selection. This implies that each species can be confronted differently from the changes produced by the environment.

Spontaneous mutation rates are very low, in the order of 10^-5-10-⁶ per gene and generation. In this way, mutations do not produce rapid changes in the population.

THE ROLE OF NATURAL SELECTION

Changes of nucleotides in somatic cells can give rise to variant or mutant cells, some of which, through natural selection, get more advantageous with respect to their partners and proliferate very fast, giving us as a result, in the extreme case, cancer, that is, uncontrolled cell proliferation. Some of the cells in the body begin to divide without stopping and spread to surrounding tissues, a process known as metastasis

But the best way to understand the role of natural selection of which the naturist Charles Darwin spoke is with the example of spotted moths (Biston betularia). In England there are two types of moths, those of white colour and those of black colour (Figure 1). The former used to be the most common, but between 1848 and 1898 black moths were imposed.

Figure 1. Biston betularia, white and black moths (Source: TorruBlog)

This change occurred at the same time that cities became more industrial, in which coal became the main fuel for power plants. The soot of this rock dyed the sky, the soil and the buildings of the cities black. Tree trunks were also affected, where the moths were camouflaged.

The consequence of this fact was that white moths could not hide from their predators, whereas those that were black found a successful exit camouflaging well on the tinted trunks. With the change of colour of their hiding place they had more opportunities to survive and reproduce (Video 1).

Video 1. Industrial melanism, white and black moth (Source: YouTube)

This is a clear example of how changes in the environment influence the variability of gene frequencies, which vary in response to new factors in the environment.

TYPES OF MUTATIONS

There is no single type of mutation, but there are several types of mutation that can affect the DNA sequence and, rebound, the genetic code. However, not all mutations have the same effect.

There are many and different types of mutations, which are classified by mutational levels. These levels are based on the amount of hereditary material affected by the mutation and go up in rank according to the number of genes involved. If the mutation affects only one gene we speak of gene mutation, whereas if it affects a chromosomal segment that includes several genes we refer to chromosomal mutation. When the mutation affects the genome, affecting whole chromosomes by excess or by defect, we speak of genomic mutation.

An example of a point mutation is found in cystic fibrosis, a hereditary genetic disease that produces an alteration in the secretion of mucus, affecting the respiratory and digestive systems. A point mutation affects the gene that codes for the CFTR protein. The affected people receive from both parents the defective gene, which, having no copy of the good gene, the protein will not be functional. The result is that the secretions produced by the human body are thicker than usual, producing an accumulation in the respiratory tract.

REFERENCES

• Ramos, M. et al. El código genético, el secreto de la vida (2017) RBA Libros
• Alberts, B. et al. Biología molecular de la célula (2010). Editorial Omega, 5a edición
• Cooper, G.M., Hausman R.E. La Célula (2009). Editorial Marbán, 5a edición
• Bioinformática UAB
• Webs UCM
• Main picture: Cine Premiere

Abrahim’ story: the child with 3 people’s DNA

On last 27^th September media echoed with the news of the first birth of a child with DNA from three people, through the experimental technique, called spindle nuclear transfer. What is this technique? Is it possible to have DNA from other people besides our parents? Then, I will explain the news in detail.

THE FAMILY

We need to know well his parents. They are a couple from Jordan, whose wife is a 36-year-old woman with a gene mutation in her mitochondrial DNA. It is right: mitochondrial DNA. A part of the nuclear DNA, where is found in our cell’s core and we currently mean, there is also DNA in our mitochondria. Mitochondria are double membrane-bound organelles found in all eukaryotic organisms and play a crucial role in energy production. They are necessary for our cells breathe and produce energy.

Like nuclear DNA, mitochondrial DNA can suffer mutations caused inherited diseases. For example Leber’s hereditary optic neuropathy (LHON), a rare inherited disease that causes blindness due to degeneration of the optic nerve.

Well, the mutation suffered by the protagonist of the story in their mitochondrial DNA cause Leigh syndrome. It is an early-onset progressive neurodegenerative disorder with a characteristic neuropathology consisting of focal, bilateral lesions in one or more areas of the central nervous system, including the brainstem, thalamus, basal ganglia, cerebellum, and spinal cord. Clinical symptoms depend on which areas of the central nervous system are involved.

Mitochondria are inherited only from mothers, a pattern known as maternal inheritance. This is the reason that they need to find a solution and avoid to transmit mitochondrial DNA (with mutations) to offspring. Previously, she had 4 pregnancy losses and 2 deceased children at age 8 months and 6 years from Leigh syndrome. The percentage of mutant DNA in mother’s mitochondria is enough for her to have no symptoms of the disease and only be a carrier. However, the probability of transmitting the mutation to offspring is very high.

THE TECHNIQUE: SPINDLE NUCLEAR TRANSFER

The couple sought out the help of John Zhang and his team at the New Hope Fertility Center in New York City. They work researching techniques to prevent diseases caused by mutations in mitochondrial DNA.

Currently, there are two methods for mitochondrial replacement: pronuclear transfer or transfer of the mitotic spindle. In both cases a donor is needed, who has not any mitochondrial DNA mutation.

The first technique is called pronuclear transfer (Figure 1) and involves fertilising both the mother’s egg and a donor egg with the father’s sperm. Before the fertilised eggs start dividing into early-stage embryos, each nucleus is removed. The nucleus from the donor’s fertilised egg is discarded and replaced by that from the mother’s fertilised egg.

But this technique wasn’t appropriate for the couple for religious reasons (they are Muslims). And this method involves the destruction of two embryos.

Figure 1. Pronuclear transfer. An egg from the mother (yellow) and an egg from the donor (purple) are fertilized with sperm from the father (yellow). When the pronucleus is formed in each egg, its is eliminated from the donor and the mother’s pronucleus is inserted in the donor’s egg (Source: A Scientist’s Guide to Making Babies…)

So Zhang’s team took a different approach, called spindle nuclear transfer (Figure 2). They removed the nucleus from one of the mother’s eggs and inserted it into a donor egg that had had its own nucleus removed. The resulting egg (with nuclear DNA from the mother and mitochondrial DNA from a donor) was then fertilised with the father’s sperm.

Figure 2. Spindle muclear transfer. The red egg corresponds to the mother, and her mitotic spindle is removed and inserted into the donor’s egg (orange), which previously has been extracted her mitotic spindle. Later, the egg is fertilized with sperm from the father (blue) (Source: Revista Genética Médica, modification)

In either methods the new egg is 100% free of maternal mitochondrial DNA (mitochondrial DNA with mutations) because it is estimated that about 1% of the mitochondrial DNA can be entrained with the nuclear genetic material. However, it is considered that the levels are low enough to cause Leigh syndrome.

THE CRITICS

The procedure is not legal in the United States, so it was done in Mexico, where rules around human embryo manipulation are more lax than in the United States, which has declined to greenlight the experimental procedure.

The technique has gained notoriety because it leaves the baby with three genetic parents. But there is a part of the scientific community that is not quite agree because he fears are not complied with all ethical codes. The limited information in the abstract left many wanting more.

Zhang’s team created 5 embryos and only one had a normal karyotype (46,XY). It was implanted into the mother and 9 months later Abrahim was born (Figure 3). He is a boy and there is no risk to transmit his mitochondria (donor’s mitochondria) to his offspring.

Now, this Jordanian family enjoys their healthy baby at home, and for the moment the mutation was detected in less than 1% of mitochondria

Figure 3. Fertility specialist John Zhang with the newborn baby Abrahim (Source: Science)

REFERENCES

• Revista Genética Médica
• New Scientist
• OMIM
• Science
• J. Zhang et al. First live birth using human oocytes reconstituted by spindle nuclear transfer for mitochondrial DNA mutation causing Leigh syndrome. Fertility and Sterility. 2016
• Cooper, G.M., Hausman R.E. La Célula. Editorial Marbán, 5a edició
• Main picture: MaxiSciences

Evolution for beginners

Biological evolution is still not well understood by general public, and when we speak of it in our language abound expressions that confuse even more how mechanisms that lead to species diversity work. Through questions you may have ever asked yourself, in this article we will have a first look at the basic principles of evolution and debunk misconceptions about it.

IS EVOLUTION REAL? IT IS NOT JUST A THEORY OR AN IDEA WITHOUT EVIDENCES?

Outside the scientific field, the word “theory” is used to refer to events that have not been tested or assumptions. But a scientific theory is the explanation of a phenomenon supported by evidence resulting from the application of the scientific method.

The scientific method. Image by Margreet de Heer.

Theories can be modified, improved or revised if new data don’t continue to support the theory, but they are always based on some data, repeatable and verifiable experiments by any researcher to be considered valid.

So few people (sic) doubts about the heliocentric theory (the Earth rotates around the Sun), or the gravitational theory of Newton, but in the popular imagination some people believe that the theory of evolution made by Charles Darwin (and Alfred Russell Wallace) is simply a hypothesis and has no evidence to support it. With new scientific advances, his theory has been improved and detailed, but more than 150 years later, nobody has been able to prove it wrong, just the contrary.

WHAT EVIDENCE WE HAVE THAT EVOLUTION IS TRUE?

We have many evidences and in this post we will not delve into them. Some of the evidence available to us are:

• Paleontological record: the study of fossils tell us about the similarities and differences of existing species with others thousands or millions old, and to establish relationships respect each other.
• Comparative anatomy: comparison of certain structures that are very similar between different organisms, can establish whether they have a common ancestor (homologous structures, for example, five fingers in some vertebrates) if they have developed similar adaptations (analogous structures, for example, the wings of birds and insects), or if they have lost their function (vestigial organs, such as the appendix).

Homologous organs in humans, cats, whales and bats

• Embryology: the study of embryos of related groups shows a strong resemblance in the earliest stages of development.
• Biogeography: The study of the geographical distribution of living beings reveals that species generally inhabit the same regions as their ancestors, although there are other regions with similar climates.
• Biochemistry and genetics: chemical similarities and differences allow to establish relationships among different species. For example, species closely related to each other have a structure of their DNA more similar than others more distant. All living beings share a portion of DNA that is part of your “instructions”, so there are also found in a fly, a plant or a bacterium, proof that all living things have a common ancestor.

IS IT TRUE THAT ORGANISMS ADAPT TO THE ENVIRONMENT AND ARE DESIGNED FOR LIVING IN THEIR HABITAT?

Both expressions, frequently used, mean that living beings have an active role to adapt to the environment or “someone” has designed them to live exactly where they are. It is a typical example of Lamarck and giraffes: as a result of stretching the neck to reach the higher leaves of the trees,  currently giraffes have this neck for giving it this use. They have a necessity, they change their bodies to success. It is precisely upside down: it is the habitat that selects the fittest, nature “selects” those that are most effective to survive, and therefore reproduce. It is what is known as natural selection, one of the main mechanisms of evolution. It needs three requirements to act:

• Phenotypic variability: there must be differences between individuals. Some giraffes necks were slightly longer than others, just as there are taller people than others, with blue or brown eyes.
• Biological fitness: this difference has to suppose an advantage. For example, giraffes with a slightly longer neck could survive and reproduce, while the others don’t.
  
• Heredity: these characters must be transmitted to the next generation, the offspring will be slightly different to that feature, while “short neck” feature transmits less and less.

The variability in the population causes individuals with favorable characteristics to reproduce more and pass on their genes to the next generation, increasing the proportion of those genes. Image taken from Understanding evolution

Over the years these changes are accumulated until the genetic differences are so big that some populations may not mate with others: a new species has appeared.

If you thought that this is similar to artificial selection that we do with the different breeds of dogs, cows who give more milk, trees bearing more fruit and larger, congratulations, you think like Darwin as it was inspired by some of these facts. Therefore, living beings are mere spectators of the evolutionary process, depending of changes in their habitat and their genetic material.

WHY ORGANISMS ARE SO DIVERSE?

Genetic variability allows natural selection act. Changes in the genetic material (usually DNA) are caused by:

• Mutations: changes in the genome that may be adverse or lethal for survival, indifferent or beneficial to survival and reproduction. If they have benefits, they will pass to the next generations.
• Gene flow: is the motion of genes between populations (migration of individuals allows this exchange when mate with others in a different population).
• Sexual reproduction: allows recombination of genetic material of different individuals, giving rise to new combinations of DNA.

Populations that have more genetic variability are more likely to survive if happen any changes in their habitat. Populations with less variability (eg, being geographically isolated) are more sensitive to any changes in their habitat, which may cause their extinction.

Evolution can be observed in beings with a very high reproduction rate, for example bacteria, since mutations accumulate more quickly. Have you ever heard that bacteria become resistant to our antibiotics or some insects to pesticides? They evolve so quickly that within a few years were selected the fittest to survive our antibiotics.

ARE WE THE MOST EVOLVED ANIMALS?

Theory of Evolution has various consequences, such as the existence of a common ancestor and that therefore, that we are animals. Even today, and even among the young ones, there is the idea that we are something different between living beings and we are in a special podium in the collective imagination. This anthropocentric thinking caused Darwin mockery and confrontations over 150 years ago.

Caricature of Darwin as an orangutan. Public domain image first published in 1871

We use our language to be “more evolved” as a synonym for more complex, and we consider ourselves one species that has reached a high level of understanding of their environment, so many people believe that evolution has come to an end with us.

The question has a mistake of formulation: actually evolving pursues no end, it just happens, and the fact that millions of years allows the emergence of complex structures, it does not mean that simpler lifeforms are not perfectly matched in the habitat where they are. Bacteria, algae, sharks, crocodiles, etc., have remained very similar over millions of years. Evolution is a process that started acting when life first appeared and continues to act in all organisms, including us, although we have changed the way in which natural selection works  (medical and technological breakthroughs, etc.).

SO IF WE COME FROM MONKEYS, WHY DO STILL MONKEYS EXIST?

The truth is that we don’t come from monkeys, we are monkeys, or to be more rigorous, apes. We have not evolved from any existing primate. As we saw in a previous post, humans and other primates share a common ancestor and natural selection has been acting differently in each of us. That is, evolution has to be viewed as a tree, and not as a straight line, where each branch would be a species .

First scheme of the evolutionary tree of Darwin in his notebook (1837). Public domain image.

Some branches stop growing (species become extinct), while others continue to diversify. The same applies to other species, in case you have asked yourself, “if amphibians come from fish, why are there still fish?”. Currently, genetic analyzes have contributed so much data that they make so difficult to redesign the classical Dariwn’s tree.

Classification of live organisms based on the three domains Archaea, Bacteria and Eukarya, data of Carl R. Woese (1990). Included in Eukarya there are the Protista, Fungi, Plantae and Animalia kingdoms. Image by Rita Daniela Fernández.

Evolution is a very broad topic that still generates doubts and controversies. In this article we have tried to bring to uninitiated people some basics, where we can delve into the future. Do you have any questions about evolution? Are you interested into a subject that we have not talked about? You can leave your comments below.

REFERENCES

• Darwin’s Tree of Life is a Tangled Bramble Bush
• Algunas reflexiones sobre la clasificación de los seres vivos
• Museos vivos. Evidencias de la evolución
• Las ideas en la ciencia: Teoría, hipótesis y leyes
• Frequently asked questions about evolution
• Brock et. al. 1999. Biología de los microorganismos. Ed. Prentice Hall.
• Massa, Renato. El origen de la vida. La evolución de las especies. Ed. Susaeta.
• Cover image