Periodic Reporting for period 1 - METHYVIREVOL (Virocellular hybrids and epigenomic changes as driving factors of infection driven cancers.)
Période du rapport: 2019-03-14 au 2021-03-13
• What is the problem/issue being addressed?
The genetic code is defined by the correspondence between codons (structural units of a gene) and amino acids (elementary building blocks of proteins). It is based on three main foundations: it is universal in all living beings (with a few exceptions), it is univocal, i.e. each codon specifies a single amino acid, and it is degenerated: 18 of the 20 amino acids essential to life are encoded by several codons, called synonymous codons. As an example, the amino acid valine is encoded by 4 synonymous codons: GTA, GTC, GTG and GTT.
Synonymous codons do not appear with equal frequency in the coding sequences of living organisms. Understanding the origin of these unequal frequencies is a classical, unsolved question embracing evolutionary and molecular biology. In unicellular organisms, such as the bacterium Escherichia coli or the yeast Saccharomyces cerevisiae, the most commonly observed codons in highly expressed genes correspond to the most abundant tRNAs in the cell, strongly suggesting that codon usage and tRNA content have coevolved in a manner that optimizes translation. Similarly, evidence of natural selection acting through synonymous codon usage has been reported in many organisms, such as flies, nematodes and the branchiopod Daphnia pulex. Besides translational selection, neutral mutational forces can also influence synonymous codon usage. In several vertebrates, the primary driver of the non-random usage of synonymous codons is a molecular mechanism driving the genomic GC content evolution. The overarching question in the field is to determine in a given organism which fraction of the synonymous mutations is impacted by adaptive or non-adaptive processes.
Viruses provide an original model in the field, as all viruses depend on the host translation machinery, especially viruses that do not code their own tRNAs (as is the case for human viruses). Therefore, given the dependence of viruses on the translation machinery of their host, is there a selection pressure on the use of viral synonymous codons? Here I conducted a large-scale investigation of the genetic code variation of virus, including several coronavirus (SARS-CoV2, MERS, SARS-CoV1, etc…). Contrary to our initial hypothesis, selection pressure was not found as the main mechanism driving the genetic code variation. Instead, the mechanism that best explains such variation is non-adaptive evolutionary processes, such as mutational bias. For example, I show in coronaviruses that a strong mutational bias from C to T and G to A is observed. Together, my results compile the current knowledge on the genetic code variation of virus and how adaptive and non-adaptive evolutionary processes drive such variation.
• Why is it important for society?
Vaccine engineering is one of the most efficient ways of fighting against diseases caused by viruses. One technology used to generate vaccine is to weakened or modified the whole or a part of the virus genome, so that they do not case illness, but still the immune system creates cells that can ‘recognise’, and protect against, the disease-causing forms of the virus if these are encountered later. Such form of vaccine is called live attenuated vaccines. The recoded viruses are antigenically identical to their pathogenic parents. The antigenic identity and replicative potential enable attenuated viruses to induce immune responses that are similar to those of virulent strains. By identifying which synonymous codon will weakened the sequence of a virus, my work is located upstream of the creation of live attenuated vaccines.
• What are the overall objectives?
The ultimate aim of this research is to understand the forces that shape codon usage bias in viruses infecting humans, and to evaluate the importance of the match between the codon usage bias of a virus and that of humans to predict its potential zoonotic risk. To answer such question, I aimed to characterize whether the codon usage bias of DNA human viruses is adapted to the human translation protein synthesize mechanism. Then, I narrowed down my analysis to the coronavirus family and further to the SARS-CoV-2 genome to investigate whether codon usage preferences impact the initial zoonotic spillover from animals towards humans and to eventually govern the risks of stable human-to-human transmission. Our results suggest that viral codon usage preferences are largely shaped by neutral mutation forces, with some directional contribution avoiding specific nucleotide patterns, and that its contribution at shaping the host breadth range of a virus is minor.
The genetic code is defined by the correspondence between codons (structural units of a gene) and amino acids (elementary building blocks of proteins). It is based on three main foundations: it is universal in all living beings (with a few exceptions), it is univocal, i.e. each codon specifies a single amino acid, and it is degenerated: 18 of the 20 amino acids essential to life are encoded by several codons, called synonymous codons. As an example, the amino acid valine is encoded by 4 synonymous codons: GTA, GTC, GTG and GTT.
Synonymous codons do not appear with equal frequency in the coding sequences of living organisms. Understanding the origin of these unequal frequencies is a classical, unsolved question embracing evolutionary and molecular biology. In unicellular organisms, such as the bacterium Escherichia coli or the yeast Saccharomyces cerevisiae, the most commonly observed codons in highly expressed genes correspond to the most abundant tRNAs in the cell, strongly suggesting that codon usage and tRNA content have coevolved in a manner that optimizes translation. Similarly, evidence of natural selection acting through synonymous codon usage has been reported in many organisms, such as flies, nematodes and the branchiopod Daphnia pulex. Besides translational selection, neutral mutational forces can also influence synonymous codon usage. In several vertebrates, the primary driver of the non-random usage of synonymous codons is a molecular mechanism driving the genomic GC content evolution. The overarching question in the field is to determine in a given organism which fraction of the synonymous mutations is impacted by adaptive or non-adaptive processes.
Viruses provide an original model in the field, as all viruses depend on the host translation machinery, especially viruses that do not code their own tRNAs (as is the case for human viruses). Therefore, given the dependence of viruses on the translation machinery of their host, is there a selection pressure on the use of viral synonymous codons? Here I conducted a large-scale investigation of the genetic code variation of virus, including several coronavirus (SARS-CoV2, MERS, SARS-CoV1, etc…). Contrary to our initial hypothesis, selection pressure was not found as the main mechanism driving the genetic code variation. Instead, the mechanism that best explains such variation is non-adaptive evolutionary processes, such as mutational bias. For example, I show in coronaviruses that a strong mutational bias from C to T and G to A is observed. Together, my results compile the current knowledge on the genetic code variation of virus and how adaptive and non-adaptive evolutionary processes drive such variation.
• Why is it important for society?
Vaccine engineering is one of the most efficient ways of fighting against diseases caused by viruses. One technology used to generate vaccine is to weakened or modified the whole or a part of the virus genome, so that they do not case illness, but still the immune system creates cells that can ‘recognise’, and protect against, the disease-causing forms of the virus if these are encountered later. Such form of vaccine is called live attenuated vaccines. The recoded viruses are antigenically identical to their pathogenic parents. The antigenic identity and replicative potential enable attenuated viruses to induce immune responses that are similar to those of virulent strains. By identifying which synonymous codon will weakened the sequence of a virus, my work is located upstream of the creation of live attenuated vaccines.
• What are the overall objectives?
The ultimate aim of this research is to understand the forces that shape codon usage bias in viruses infecting humans, and to evaluate the importance of the match between the codon usage bias of a virus and that of humans to predict its potential zoonotic risk. To answer such question, I aimed to characterize whether the codon usage bias of DNA human viruses is adapted to the human translation protein synthesize mechanism. Then, I narrowed down my analysis to the coronavirus family and further to the SARS-CoV-2 genome to investigate whether codon usage preferences impact the initial zoonotic spillover from animals towards humans and to eventually govern the risks of stable human-to-human transmission. Our results suggest that viral codon usage preferences are largely shaped by neutral mutation forces, with some directional contribution avoiding specific nucleotide patterns, and that its contribution at shaping the host breadth range of a virus is minor.
During the course of the project founded by the MSC-fellowship, I conducted on of the largest large-scale study of genetic code usage bias in human-infecting DNA viruses. My work formally demonstrated that translational selection -which is generally so widespread in organisms with large population sizes- does not apply in human DNA viruses. Instead, the large heterogeneity in the frequencies of synonymous codons reported among virus, is primarily impacted by a non-adaptive evolutionary mechanism whose main driver is genetic recombination. In parallel, in SARS-CoV-2 and other coronavirus, I have shown that codon usage bias occur independently of viral taxonomy and of the hosts virus infect (see figure in summary for publication). I interpret that as the role of CUB at modifying the chances of a coronavirus zoonotic spillover to thrive in humans is negligible. Notwithstanding, upon colonization of humans endemic human coronavirus have experienced a compositional drift towards a novel compositional equilibrium in the new hosts, and that this could also be the case for SARS-CoV-2 if the current pandemics transforms into an endemic circulation in humans. Initial critical results have been disseminated through publication in open public repositories. Moreover, the results have been presented to scientist in different areas at national and international conferences and workshops. To communicate to the general public, our main findings were posted on Twitter.
Investigation on the codon usage bias of the genetic code within human infecting viruses is critical as this field of study is directly located upstream of the molecular engineering work aiming at creating live attenuated vaccines used to fight against viral diseases. Classically, viral genomes have been empirically attenuated in cell culture via mutation accumulation. This lengthy and stochastic process produces vaccine strains of attenuated viruses with major impact in human health through vaccination. However, reversion to virulence by reversion of a small number of attenuating mutations is a well-known problem, as in the case of polio virus vaccines. My work relates to one of the strategies being considered to solve the problem via the use of genetic code degeneracy and synonymous codon mutations. These synonymous mutations would have the advantage of using a large number of mutations, each of which would only slightly reduce the replicative ability of the virus but taken together would produce significant attenuation.