Keeping a Genome Clear of Clutter

The adage "use it or lose it" is commonly regarded as true for skills including foreign language or athletic ability, but it also applies to genetic information.  The parts of plant cells responsible for turning sunlight into forms of energy useful to cells, chloroplasts, contain their own genomes separate from the rest of the genetic information of the cell.  These separate genomes, plastomes, are the remnants of when chloroplasts were independent organisms long ago in evolutionary time.  A contributing factor to the apparent organizational prowess of plastomes is that parts of their genomes were transferred to the cells they exist within.  Over time, plastomes shrank so much that the smallest known plastome contains only twenty genes.  The human genome contains over 20,000 genes.  Humans are pathological hoarders in comparison to the tidy plastomes.

Plants that spend their entire lives underground still contain chloroplasts and plastomes, which is counter-intuitive to the "use it or lose it" model since life underground should make information related to turning sunlight into useful forms of energy unimportant.  A research team interested in what causes some information to be transferred to the cell and other information to stay within the plastome examined an Australian underground plant that is now critically endangered.

Photo of Rhizanthella gardneri from 1986.  Image curtsey of jeans_Photos.

The plant, a species of orchid called Rhizanthella gardneri, lives as a parasite on fungus.  The areas of its plastome responsible for making those 20 proteins are identical to parts of the plastome of an above-ground orchid, Phalaenopsis aphrodite.  Comparison of R. gardneri's 20 gene plastome to P. aphrodite's 110 gene plastome revealed 70% of the original genes in R. gardneri were either lost entirely or transferred to the cell.  Some of the 20 genes that remain are responsible for encoding the proteins involved in making more protein from DNA, including the pieces directly responsible for determining what protein building-blocks to put in the correct order, the tRNAs.  However, not enough of the genes which encode those tRNAs remain in the plastome to include all of the necessary building-blocks.  Thus, the chloroplast must be importing those tRNAs from the cell.  This type of import has never yet been seen in plants, making it an interesting opportunity for future investigations.

The similarity of the plastome of R.gardneri to that of P. aphrodite, as well as the plastomes of 172 other species, indicates some evolutionary pressure has kept those genes within the plastome.  Further characterization of those genes will be useful to investigate what makes plastomes so tidy and why plastomes persist when so much other information has been transferred to the cell.

R. gardneri is a plant that lives off of fungus, properly known as a myco-heterotroph.  For a discussion of fungi that live off of plants and other fungal topics, visit this recent post on The Factual Enquirer.