I work with a set of 3 conserved proteins that have similar function, very similar structures and about 50% sequence identity. The genes for these proteins are, however, present on different chromosomes. Is this event possible through duplication? Can such proteins/genes be called isoforms?
I am not sure why you specify that the genes not move/duplicate via transposition, but most gene duplications do not happen by being captured in a characterized transposon. Most genes/proteins are duplicates of others. For example the serine/threonine kinase gene family has dozens of different lineages in the eukaryotic genomes. There are also dozens of GTPase regulatory proteins. Homeo box developmental regulation proteins exist in many copies in all animals. There are several copies of the hemoglobin gene in mammals, etc.
At 50% amino acid identity I would not call the different proteins "isoforms" of the same protein, but I suppose that could depend on how "similar" their functions are, and maybe also on how unique that function is. The alpha and beta hemoglobins in vertebrates are for example called isoforms of the same protein. http://scop.berkeley.edu/sunid=46524
Gene duplication likely created many of the families of genes and proteins in vertebrates. In most cases we can trace their origins back to a single ancestral gene, based on sequence conservation. This is very common among gene families such as the developmental regulators (Hox, Pax, Fox, Sox genes). They are not isoforms, rather we refer to them as family members and usually they are numbered (FoxA1, FoxB2..). Duplication must have occurred at some ancestral time point and the genes sequences diverge over time since. I think gene duplication allows for new regulatory information to be linked to the duplicated gene such that it can assume a new expression pattern. Some family members have very similar functions and can substitute for each other (Pax5 and Pax8 for example, but not Pax6). Many signaling ligands are also in large gene families (hedgehog, BMPs, FGFs) but we do not refer to them as isoforms.
Thank you for the answers Brian and Gregory.
My question was not whether genes can duplicate or not, but rather how such duplications can be present on different chromosomes. Are such genes a result of a genome duplication then?
Genes can move around on a chromosome and between chromosomes by a large variety of different mechanisms, but the most common would be crossing over, where the tip (or substantial part) or one chromosome exchanges places with the tip (or larger part) of another chromosome. This be facilitated by homologous (identical or nearly identical sequence due to recent shared ancestry) sequences on both chromosomes, such as several copies of the same endogenous retrovirus, or copies of other types of repetitive DNA present on both chromosomes involved in the event. Gene duplication can also happen by a variety of mechanisms, some of which would be likely to put the newly copied gene onto another chromosome from the beginning.
Complete genome duplication to tetraploidy or higher polyploidy is rather common in many lineages of eukaryotes. http://www.macroevolution.net/prevalence-of-polyploidy.html Determining whether your gene/protein was duplicated during a polyploidy event, or some time earlier or later, may be possible. Are the 3 copies exactly equidistant from each other (same percent amino acid identity/distance)?
For an example of a gene family whose members are found in many different chromosomes and on a discussion of their possible etiology, see one of our papers on the POTE gene: Hahn et al. (2006) Duplication and extensive remodeling shaped POTE family genes encoding proteins containing repeat and coiled coil domains. Gene 366:238-245.
These would be considered paralogs (result from duplication within a genome), generally considered to be part of the same "gene family". Orthologs are the "same" gene in different species (shared ancestral gene, usually retain the same function). Both are types of homologous genes (descended from a common ancestral DNA sequence). The wikipedia definitions are accurate:http://en.wikipedia.org/wiki/Homology_%28biology%29#Sequence_homology
research "double minutes" and "homogeneously staining regions"
You can start here
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2928498/
http://www.the-scientist.com//?articles.view/articleNo/41055/title/The-Rainbow-Connection/ duplication of the opsin genes in primates. Very interesting story.
