Genomic streamlining is a theory in evolutionary biology and microbial ecology that suggests that there is a reproductive benefit to prokaryotes having a smaller genome size with less non-coding DNA and fewer non-essential genes. There is a lot of variation in prokaryotic genome size, with the smallest free-living cell's genome being roughly ten times smaller than the largest prokaryote. Two of the bacterial taxa with the smallest genomes are Prochlorococcus and Pelagibacter ubique, both highly abundant marine bacteria commonly found in oligotrophic regions. Similar reduced genomes have been found in uncultured marine bacteria, suggesting that genomic streamlining is a common feature of bacterioplankton. This theory is typically used with reference to free-living organisms in oligotrophic environments.
Overview
Genome streamlining theory states that certain prokaryotic genomes tend to be small in size in comparison to other prokaryotes, and all eukaryotes, due to selection against the retention of non-coding DNA. The known advantages of small genome size include faster genome replication for cell division, fewer nutrient requirements, and easier co-regulation of multiple related genes, because gene density typically increases with decreased genome size. This means that an organism with a smaller genome is likely to be more successful, or have higher fitness, than one hindered by excessive amounts of unnecessary DNA, leading to selection for smaller genome sizes.
Some mechanisms that are thought to underlie genome streamlining include deletion bias and purifying selection. Deletion bias is the phenomenon in bacterial genomes where the rate of DNA loss is naturally higher than the rate of DNA acquisition. This is a passive process that simply results from the difference in these two rates. Purifying selection is the process by which extraneous genes are selected against, making organisms lacking this genetic material more successful by effectively reducing their genome size. Genes and non-coding DNA segments that are less crucial for an organism survival will be more likely to be lost over time.
This selective pressure is stronger in large marine prokaryotic populations, because intra-species competition favours fast, efficient and inexpensive replication. This is because large population sizes increase competition among members of the same species, and thus increases selective pressure and causes the reduction in genome size to occur more readily among organisms of large population sizes, like bacteria. This may explain why genome streamlining seems to be particularly prevalent in prokaryotic organisms, as they tend to have larger population sizes than eukaryotes.
It has also been proposed that having a smaller genome can help minimize overall cell size, which increases a prokaryotes surface-area to volume ratio. A higher surface-area to volume ratio allows for more nutrient uptake proportional to their size, which allows them to outcompete other larger organisms for nutrients. This phenomenon has been noted particularly in nutrient depleted waters.
Genomic signatures
Genomic analysis of streamlined organisms have shown that low GC content, low percentage of non-coding DNA, and a low fraction of genes encoding for cytoplasmic membrane proteins, periplasmic proteins, transcriptionally related proteins, and signal transduction pathways are all characteristic of free-living streamlined prokaryotic organisms. Oftentimes, highly streamlined organisms are difficult to isolate by culturing in a laboratory (SAR11 being a central example).
Model organisms
Pelagibacter ubique (SAR11) Pelagibacter ubique are members of the SAR11 clade, a heterotrophic marine group which are found throughout the oceans and are rather common. These microbes have the smallest genome and encode the smallest number of Open Reading Frames of any known non-sessile microorganism. P. ubique has complete biosynthetic pathways and all necessary enzymes for the synthesis of 20 amino acids and only lack a few cofactors despite the genome's small size. The genome size for this microorganism is achieved by lack of, "pseudogenes, introns, transposons, extrachromosomal elements, or inteins". The genome also contains fewer paralogs compared to other members of the same clade and the shortest intergenic spacers for any living cell. In these organisms, unusual nutrient requirements were found due to the streamlining selection and gene loss when selection occurred for more efficient resource utilization in oceans with limited nutrients for uptake. These observations indicate that some microbes may be difficult to grow in a laboratory setting because of unusual nutrient requirements.
