Intrinsically Disordered Proteins have no evolution over billions of years

-


The article "Genes encoding intrinsic disorder in Eukaryota have high GC content," Zhenling Peng and colleagues investigate the correlation between the GC content of genes and the level of intrinsic disorder in their corresponding proteins in eukaryotes. 

This is caused by GC bias. GC bias is a non-Darwinian mechanism of change. It is a process by which the proportion of guanine and cytosine (GC) nucleotides in DNA can change over time without being driven by natural selection. It involves biased DNA repair during recombination.


The authors found that genes encoding intrinsically disordered proteins (IDPs) have a higher GC content than genes encoding ordered proteins. This correlation is present across proteins and species characterized by varying amounts of disorder, and is due to the higher rate of amino acids coded by GC-rich codons in the disordered regions. 

Intrinsically disordered proteins (IDPs) are a class of proteins that do not fold into a unique three-dimensional structure. Instead, they exist as a dynamic ensemble of conformations. IDPs are involved in a wide range of cellular processes, including signaling, regulation, and transport. 

Intrinsically Disordered Proteins make up the majority of proteins in organisms.


GC content is the percentage of guanine and cytosine nucleotides in a DNA sequence. GC content varies widely across species and between different genomic regions. For example, GC content is generally higher in coding regions than in non-coding regions.

It has been previously observed that IDPs tend to be encoded by genes with a higher GC content. 

Peng and colleagues analyzed the GC content of genes and the disorder levels of their corresponding proteins in 12 eukaryotic species. They used a variety of computational methods to predict protein disorder, including IUPred, VSL2, and PONDR-VLXT.

The authors found that genes encoding IDPs had a higher GC content than genes encoding ordered proteins. This correlation was present across all 12 species analyzed. The authors also found that the correlation between GC content and disorder level was stronger for proteins with high levels of disorder.

To investigate the reason for the correlation between GC content and disorder, the authors analyzed the amino acid composition of disordered and ordered regions. They found that disordered regions were enriched in GC-rich codons. For example, the amino acids arginine (R), lysine (K), and proline (P) are all encoded by GC-rich codons, and these amino acids are all associated with disorder.

The authors also investigated the relationship between GC content, disorder, and protein development. They found that the amino acids that are most associated with disorder are also the oldest amino acids. This suggests that disorder may have played a role in the early development of proteins.

Peng and colleagues conclude that the GC content of genes is enriched in intrinsically disordered regions, irrespective of the overall amount of disorder in a given organism. They propose that this correlation may be due to the higher rate of amino acids coded by GC-rich codons in the disordered regions.

The findings of this study have a number of implications for our understanding of IDPs and their development. For example, the correlation between GC content and disorder suggests that GC content may be a useful predictor of protein disorder. Additionally, the finding that the oldest amino acids are also the most associated with disorder suggests that disorder may have played a role in the early development of proteins.

The study by Peng and colleagues is a significant contribution to our understanding of IDPs and their development. The authors provide strong evidence that the GC content of genes is correlated with the level of intrinsic disorder in their corresponding proteins. This correlation is likely due to the higher rate of amino acids coded by GC-rich codons in the disordered regions. The authors also propose that disorder may have played a role in the early development of proteins.

The findings of this study have a number of implications for our understanding of IDPs and their development. For example, the correlation between GC content and disorder suggests that GC content may be a useful predictor of protein disorder. Additionally, the finding that the oldest amino acids are also the most associated with disorder suggests that disorder may have played a role in the early development of proteins.

The implications of the article challenges Neo Darwinism in the following ways:

  • It concludes that there are non-adaptive forces driving protein evolution. Neo Darwinism is based on the idea that natural selection is the primary driver of evolution. However, the findings of this article suggest that GC content, which is a non-adaptive factor, plays a significant role in the development of intrinsically disordered proteins (IDPs). 

  • It indicates that the evolution of protein function is more complex than Neo Darwinism can explain. Neo Darwinism views protein function as being determined by proteins (rigid) structure. 


However, the findings of this article suggest that GC content may also play a role in determining protein function. This is because GC-rich codons are more likely to code for amino acids that are found in IDPs. IDPs are often involved in binding to other molecules, and their flexibility is thought to be important for this function.

  • It indicates that there are limits to the power of natural selection. Neo Darwinism is often seen as explaining all aspects of evolution. However, the findings of this article suggest that there are factors, such as GC content, that are not subject to natural selection. This is because GC content is influenced by a variety of factors, including natural DNA repair mechanisms and recombination (GC bias). Overall, the findings of this article challenge Neo Darwinism by suggesting that non-adaptive forces drive protein evolution, that the evolution of protein function is more complex than Neo Darwinism can explain, and that there are limits to the power of natural selection.

They do raise some important questions that need to be addressed by evolutionary biologists.

Here are some specific examples of how the findings of this article challenge Neo Darwinism:

  • Neo Darwinism views proteins as evolving to adopt a specific three-dimensional structure in order to perform a specific function. 

However, IDPs do not have a fixed three-dimensional structure. 

Instead, they exist as a dynamic ensemble of different structures. This suggests that protein function is not determined by protein structure.

  • Neo Darwinism views natural selection as being the primary driver of protein evolution. However, the findings of this article shows that GC content, which is a non-adaptive factor, plays a significant role in the evolution of IDPs. This indicates that non-adaptive forces plays a more important role in protein evolution than previously thought.

  • Neo Darwinism views protein evolution as being a gradual process. However, the findings of this article suggest that the development of IDPs are more rapid than previously thought. This is due to the speed of GC bias which causes codon bias. 


These GC-rich codons are more likely to code for amino acids that are found in IDPs. And, GC-rich codons are also less likely to be mutated. This is due to the fact GC pairs have three hydrogen bonds and are more stable. This indicates that the development of IDPs are driven by GC bias rather than natural selection.

Overall, the findings of this article challenge Neo Darwinism by suggesting that protein development is a more complex process than previously thought. They suggest that non-adaptive forces play a more important role in protein development  than previously thought, and that the development  of IDPs are more resistant to change over billions of years.

Comments

Post a Comment

Popular posts from this blog

No, the EES is not just a add on to Neo-Darwinism aka the Modern Synthesis

-
Image
" The summary of the state of affairs on the 150th anniversary of the Origin is somewhat shocking: in the post-genomic era, all major tenets of the Modern Synthesis fthe theory of evolution) are, if not outright overturned replaced by a new and incomparably more complex vision of the key aspects of evolution (EES). So, not to mince words , the Modern Synthesis is gone" -Eugene Koonin, an evolutionary biologist (Cited by over 270,000 evolutionary scientists.) The Extended Evolutionary Synthesis (EES) represents a significant departure from the traditional neo-Darwinian framework, also known as the Modern Synthesis . While both theories aim to explain evolutionary change, they differ fundamentally in their underlying mechanisms and the roles they assign to various biological processes. A crucial point of divergence lies in the interpretation and application of the term " evolutionary ," particularly concerning the incorporation of epigenetic mechanisms....
Read more

Is the random mutational model of evolution on its way out?

-
Image
While the random mutational model of evolution has long been a cornerstone of evolutionary biology, the Extended Evolutionary Synthesis (EES) and the study of epigenetics are challenging its core assumptions. The Random Mutational Model and Its Limitations The traditional view of evolution, often called the Modern Synthesis or neo-Darwinism , emphasizes random genetic mutations as the primary source of variation. Natural selection then acts upon this variation, favoring individuals with advantageous traits. This model has been successful in explaining some evolutionary phenomena, but it also has limitations: It struggles to explain complex adaptations: The idea that complex features like the eye or the immune system arose solely through random mutations seems statistically improbable. It overlooks the role of the environment: The traditional model treats the environment as a selective force, but it doesn't fully consider how organisms can actively respond to and s...
Read more

ERVs and Common Descent: A Reassessment in Light of Recent Findings

-
Image
Endogenous retroviruses (ERVs) have long been considered strong evidence for the common descent of humans and chimpanzees. These remnants of ancient viral infections, embedded in the genomes of both species, were once thought to be non-functional "junk DNA." The premise was that the shared presence of these seemingly random insertions in corresponding genomic locations could best be explained by a shared evolutionary history. However, recent research, such as the "Switching Sides" article published in May 2021, has challenged this assumption by demonstrating that ERVs play a functional role in the development of the human embryo and immune system. This discovery raises questions about the validity of using ERVs as primary evidence for common descent. The Traditional Argument for Common Descent The traditional argument for common descent based on ERVs rests on the following points: Random Insertion: Retroviral insertions are thought to occur randomly in...
Read more