A gene is a specific sequence of DNA that holds the instructions for building a functional product, such as a protein or an RNA molecule, which perform a vast array of tasks inside a cell. A “novel gene” is one that appears in a particular evolutionary lineage but lacks a recognizable, related version (a homolog) in closely related species. These genetic newcomers provide fresh material for natural selection, enabling organisms to develop new traits, adapt to their environments, and drive evolutionary change.
Origins of New Genetic Material
New genes can arise through several distinct molecular events.
De Novo Origination
A gene can emerge from previously non-coding DNA through a process called de novo origination. This occurs when random mutations create a start signal, or open reading frame (ORF), allowing a cell’s machinery to produce a molecule from that DNA. If this new molecule is not harmful, it may persist and eventually acquire a function, becoming a new gene.
Gene Duplication and Divergence
Gene duplication occurs when an existing gene is accidentally copied. One version continues its original function, while the second is free to accumulate mutations over generations. These changes can alter the new copy so much that it performs a different task, becoming a novel gene. This mechanism allows for innovation without losing an existing function.
Horizontal Gene Transfer
Genes can be acquired from other species through horizontal gene transfer (HGT), a process most common in bacteria but also seen in complex life. A gene from one organism is transferred into the genome of another, where it can be integrated permanently. This allows for the rapid acquisition of new capabilities, such as antibiotic resistance or the ability to digest new food sources.
Genetic Rearrangements
Complex rearrangements can also forge new genes. Exon shuffling combines coding segments (exons) from different pre-existing genes to create a hybrid with a new combination of functions. Retrotransposition creates a new gene when an RNA copy of a gene is reverse-transcribed back into DNA and inserted elsewhere in the genome. This “retrogene” may evolve a new function if inserted near a region that promotes its activation.
Methods for Discovering Novel Genes
Scientists use several high-tech approaches to identify novel genes within an organism’s genome. Comparative genomics involves lining up the genomes of closely related species to find genes present in one lineage but absent in its relatives. The discovery of such lineage-specific genes points to a recent, novel origin, as they are missing from the common ancestor.
Transcriptomics focuses on the RNA molecules being produced in a cell. Using methods like RNA-Seq, researchers can see which genes are active, or transcribed. This can reveal transcription from DNA regions previously thought to be non-coding, suggesting the presence of a previously unknown de novo gene.
Computational bioinformatics uses algorithms to scan genomes for signs of a gene, such as open reading frames (ORFs) and other sequence patterns. By cross-referencing these findings with databases of known genes, bioinformaticians can identify potential novel genes that lack homologs in other species.
A challenge in this field is distinguishing a truly novel gene from a known gene that has evolved so rapidly it is hard to recognize. Scientists must carefully analyze evidence from multiple methods to confirm a candidate gene is a new invention and not just a highly divergent version of an ancestral one.
The Role of Novel Genes in Biological Systems
Once fixed in a population, a novel gene provides the raw material for new traits that allow an organism to adapt or exploit new environments. For example, a new gene might produce a protein enabling an insect to digest a previously toxic plant, opening up a new food source. The cumulative impact of such genes can lead to major evolutionary transitions.
Novel genes are often responsible for the unique, species-specific characteristics that distinguish organisms. While core biological processes are controlled by ancient, shared genes, newer genes often fine-tune an organism’s development, physiology, or behavior. They contribute to distinct features, from the shape of a flower to the complexity of a primate’s brain.
The integration of a new gene can create new biological pathways. Its product might interact with existing proteins, modifying their function or creating an entirely new network of molecular interactions. This can result in new metabolic capabilities, developmental processes, or signaling pathways by rewiring a part of the cell’s operations.
Illustrative Examples of Novel Genes
An example is the antifreeze glycoprotein (AFGP) gene in Antarctic notothenioid fish, which live in waters that would freeze the blood of most vertebrates. The AFGP gene arose from a non-coding DNA segment and part of an existing gene. It produces a protein that binds to ice crystals in the blood, preventing them from growing and allowing the fish to thrive in an extreme environment.
Another case is the evolution of nylon-degrading enzymes in Arthrobacter bacteria, found in the wastewater of a nylon factory. This environment did not exist before the 1930s. A novel gene, nylB, emerged from a mutation in a pre-existing gene, altering its function to allow the bacteria to digest byproducts of nylon manufacturing.
Researchers have also identified novel genes specific to primates that influenced brain development. One such gene, FLJ33706, arose de novo in the common ancestor of humans and chimpanzees. Studies suggest this gene is highly expressed in the human brain and may play a role in its development, highlighting how new genes can contribute to complex, lineage-specific traits.