My favorite bacterium has two alleles of the same gene, lets say, the yfgA gene, located at different loci on the same chromosome.
How should I refer to these two alleles? A good guess would be as yfgA1 and yfgA2, however, Journal of Bacteriology is clear that yfgA1 and yfgA2 are used to refer to mutant alleles. My alleles are both wild type, and in fact, confer enzyme activity to an E. coli strain lacking a copy of the yfgAgene.
Any help from some genetics experts?
If they are present at different loci, they are different genes. They could be nearly identical, representing a recent gene-duplication events. You will need to follow the convention for your species for naming these two highly similar, but different genes.
Nick, I would guess that they are most likely the result of a recent duplication, but I don't think that they are "different genes". They are definitely different alleles of the SAME gene. It's a well characterized gene at that, and they reside in well characterized operons. The strain is effectively merodiploid with two distinct wild type alleles.
The two alleles have 83% identity at both the protein and nucleotide level. We've cloned both operons, and the operons confer the expected phenotype when introduced into E. coli. I can't think of any reason NOT to give them the same gene name.
Hi Heather,
If they are present at different loci then they are not alleles. You are not describing natural variants of the same gene, present at the same locus in different accession of the species you are working on. I’m quite sure that for something to be considered allelic, they must be present at the same locus.
That doesn't mean that these genes don't encode identical proteins, or have nearly identical nucleotide sequence, or retain similar expression patterns. Or share a common evolutionary history. If you give them the same name, you are saying they are present at the same locus - and they are not. Perhaps look at how genes belonging to multigene families are named in your species. It would make sense to give them a similar name, if you have confirmed they have identical function and share high sequence identity.
If these genes are at different loci, they are evolving independently (although epistasis can occur). You said there is 83% identity between the two genes - this is moderately high, but does suggest that the genes are evolving independently from each other. This doesn't mean that they don't still encode proteins with the same activity, or express from their operon in the same manner.
I've worked on genes that comprise a complex locus - ~5kb was duplicated and are located in tandem. This occurred very recently, and there is >95% nucleotide identity. They are both present within the same complex locus, but they are two separate genes – these genes have identical activity. In this case, they genes have been called "GeneX-1" and "GeneX-2" - and then alleles of each gene can be annotated GeneX-1a, GeneX1b etc. This is highly dependent upon the nomenclature for your species, and potentially, for the type of genes you are working on. I should also say, that we had initially identified ‘alleles’ for these genes, before realising they existed within a complex locus – it isn’t always easy to know if you have alleles or not. In hindsight here were telltale signs these were not alleles – the two genes had numerous small indels (in frame) and too many SNPs.
I do hope this is helpful. Nomenclature can be really frustrating!
Best wishes,
Nick
Hi Heather I agree with Nick. You can call these genes reitarations, most probably they are paralogues but I would not call the strain merodiploid just based on the fact that you observed reitarated functions. Merodiploid strains (in bacteria) as far as I know were originally described as genetic backgrounds containing an ectopic copy or variant of a chromosomal gene.
Take Rhizobia for example, these organisms encode several reitarations of symbiotic or nitrogen fixation genes. Most of these reitarations are annotated as you propose for your gene, for example fixK1 and fixK2 (doi: 10.1128/JB.00748-08. Epub 2008 Aug 8.). Apprerently in these cases you can put the number as a subindex to avoid confusion with the nomenclature for mutations.
In the case of Rhizobium etli we have named such reitarations by adding an identifier of the replicon. For example fixKf would be present in the f plasmid while fixKd would be in the plasmid d or symbiotic plasmid. Of course this will only work if the copies are in different replicons.
I hope this is helpful, let me know if I made any erroneous statements I am always willing to learn.
All the best,
David
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