The Role of Retroviruses in Primate Evolution
Examining how retroviruses influence primate genetics and evolutionary processes.
― 5 min read
Table of Contents
- Types of Retroviruses
- Understanding the Genes
- Analyzing ERVs in Primate Genomes
- Steps in Researching Retroviruses
- Phylogenetic Analysis
- Recombination Events
- Results from Primate Genomes
- Presence of Endogenous Retroviruses
- Functional Roles of ERVs
- Importance of Studying ERVs
- Conclusion
- Original Source
- Reference Links
Retroviruses are a type of virus that were discovered over a hundred years ago. They can be found in many animals and share a similar way of replicating themselves. When a retrovirus infects a cell, it first converts its RNA into DNA. This DNA then becomes part of the host cell’s DNA and can remain there over time. When this DNA is integrated into the host’s genetic material, it is called a provirus. Proviruses have specific regions that allow them to make new virus particles and proteins needed for their life cycle.
Types of Retroviruses
Retroviruses can be classified mainly into two types: exogenous and endogenous retroviruses. Exogenous retroviruses are the ones that infect and spread between individuals, while endogenous retroviruses, or ERVs, are those that have integrated into the host genome and are inherited across generations.
Over millions of years, many copies of ERVs have built up in the DNA of vertebrates. Some of these copies are complete, while others are broken fragments. Exogenous retroviruses have a set of key genes which help them to function. These genes include gag, pro, pol, and Env, which are important for making new virus particles.
Understanding the Genes
The env gene is particularly interesting as it determines how the virus infects specific types of cells. The env gene produces proteins that allow the virus to enter host cells. These proteins have a unique structure and are under constant change due to pressure from the host immune system. This variation is crucial for the virus to adapt and survive.
The other three genes - gag, pro, and pol - have roles in forming the virus and assisting with its replication. They are generally conserved, meaning they remain similar across different retrovirus types, while the env gene is more diverse.
Analyzing ERVs in Primate Genomes
Researchers have studied the presence of these retroviral genes, particularly in primates, to understand their evolution and interaction with host genomes. By examining the genomes of various primate species, scientists can identify ERVs and their environments. The study of ERVs can reveal how these ancient viruses have shaped and influenced the evolution of their hosts.
In this research, scientists looked at the env genes across 43 species of primates, including both Old World monkeys and New World monkeys. They focused on three classes of ERVs: Class I, Class II, and Class III.
Steps in Researching Retroviruses
To understand the distribution of these retroviruses, the researchers collected existing data and sequences of env genes from various databases. Then, they used specific computer programs to align these sequences and identify similarities, which helped them trace back the evolutionary history of these genes.
The research involved:
- Collecting env sequences.
- Performing alignments to see how similar the sequences are.
- Analyzing the relationships between different species and the presence of specific ERVs.
Phylogenetic Analysis
After gathering the data, researchers built trees to visualize the relationships among different sequences. This method helps understand how ERVs have evolved over time and how they relate to each other. The trees indicated how certain ERVs clustered together and the lineage of each virus type.
Recombination Events
One of the key aspects of the study was looking for recombination events. Recombination occurs when two viruses exchange genetic material during replication, which can lead to new variants. This can happen when two different retroviruses infect the same cell and their genetic material mixes.
The researchers used specific software to find potential recombination events in the ERV sequences. They found several instances where recombination had occurred, which contributed to the diversity of the viruses.
Results from Primate Genomes
The researchers found that many gamma-like ERVs were present in the primate genomes they analyzed. These gamma-type ERVs are believed to have integrated into primate ancestors around 30 to 45 million years ago. They observed that these ERVs are spread widely across many primate species, particularly in the lineages of Old World monkeys and great apes.
In contrast, the study found fewer examples of spuma-like ERVs, suggesting they may integrate less frequently or persist for shorter periods.
Presence of Endogenous Retroviruses
In addition to identifying the presence of ERVs, the study reported that several ERVs had not been documented previously in certain primate species. This points to the evolutionary history of these viruses being more complex than initially understood.
The presence of various ERVs across different primate species indicates that these viruses have contributed to genetic diversity and evolution among primates. Their integration into the host genome can lead to changes in gene expression and regulation, affecting the host's development and adaptation.
Functional Roles of ERVs
ERVs are not just remnants of past infections; they can also play essential roles in the host. Some ERV proteins, like syncytins, have been co-opted for crucial functions in human reproduction, especially in the formation of the placenta. These proteins help in the fusion of cells during development.
Moreover, certain ERV proteins can act as restriction factors, preventing new viral infections by competing with exogenous retroviral proteins. This illustrates how ERVs can influence not only their host's genome but also their ability to respond to new viral threats.
Importance of Studying ERVs
Understanding ERVs provides insight into the co-evolution of viruses and their hosts. By studying the patterns of ERV distribution and diversity, researchers can uncover mechanisms that have shaped the evolutionary trajectory of primates. This knowledge can also contribute to our understanding of diseases and potential treatments in the future.
Conclusion
Retroviruses and their integration into host genomes represent a fascinating area of study in evolutionary biology. By analyzing these ancient viruses, researchers gain insights into the complex interplay between viruses and their hosts, revealing stories of adaptation, survival, and evolutionary change over millions of years.
The ongoing research into ERVs highlights their significance not only as remnants of past infections but also as functional elements that may play critical roles in various biological processes. As science progresses, understanding these viruses could lead to advances in medicine, genetics, and our comprehension of life itself.
Title: Screening Envelope Genes Across Primate Genomes Reveals Evolution and Diversity Patterns of Endogenous Retroviruses
Abstract: Endogenous Retroviruses (ERVs) are integrated into the host DNA as result of ancient germ line infections, majorly by extinct exogenous retroviruses. In fact, vertebrates genomes contain thousands of ERV copies, providing "fossil" records for the ancestral retroviral diversity and its evolution within the host. Like exogenous retroviruses, ERV proviral sequence consists of gag, pro, pol, and env genes flanked by long terminal repeats (LTRs). Among them, the characterization of env gene changes over time allows both to understand ERVs evolutionary trajectory and possible physiological and pathological domestication. To this aim, we reconstructed 32 Env sequences representing the prototypes of these ancestral proteins in Class I, Class II, and Class III HERVs. These reconstructed Envs were then employed in diverse methods comprising similarity search, phylogenetic analysis, and examination of recombination events occurred within primates genomes that were applied to 43 primate species across the Catarrhini and Platyrrhini parvorders. Through a comprehensive pipeline we reconstitute a phylogenetic distribution of ERV based specifically on the env genes, showing that the ERVs have been prevalent and widely distributed across the primate lineage. We observed for the first time the presence of the HML groups in the Platyrrhini parvorder, possibly indicating initiation of spread of HML supergroup before the split between New World Monkeys (NWM) and Old World Monkeys (OWM) i.e. even before 40 mya. Importantly, we confirmed notable interclass and intra-class env recombination events showing the phenomenon of "env snatching" among primates ERVs. As a result, we demonstrate that tracing the diversity patterns of ERVs env provides relevant insights into the retroviral evolutionary history of ERVs in Catarrhini and Platyrrhini parvorders. Overall, our findings reveal that env recombination contributes to the diversification of ERVs, thereby broadening our comprehension of retroviral and primate evolution.
Authors: Enzo Tramontano, S. Chabukswar, N. Grandi, E. Soddu, L. T. Lin
Last Update: Oct 28, 2024
Language: English
Source URL: https://www.biorxiv.org/content/10.1101/2024.10.28.620668
Source PDF: https://www.biorxiv.org/content/10.1101/2024.10.28.620668.full.pdf
Licence: https://creativecommons.org/licenses/by/4.0/
Changes: This summary was created with assistance from AI and may have inaccuracies. For accurate information, please refer to the original source documents linked here.
Thank you to biorxiv for use of its open access interoperability.