by Mechas
When it comes to generating variability in genes and functions, microbes are at the top of the list. Much of their genome plasticity and capacity to adapt to changing environments is driven by horizontal gene transfer (HGT), the acquisition of genetic information from other cells rather than from vertical inheritance upon division. Horizontal transfer of genes is not exclusive to bacteria, but it is certainly a potent evolutionary force and one that oftentimes blurs distinctions among species. Most bacterial genomes bear signatures of mobile elements involved in transfer as well as of genes that have been selected based on their beneficial impact on the host cell. Given the importance of HGT in the microbial world, it is not surprising that diverse mobile genetic elements are involved in this process. The most abundant and well-known of these are phages and plasmids. This is why the discovery of novel elements involved in DNA transfer, often present in less-well-studied microbial systems and environmental microbes, is a welcome surprise.
Fig. 1. Transmission electron microscope (TEM) image of Prochlorococcus marinus with overlay green coloring. Source
The marine bacterium Prochlorococcus is the smallest (0.5 to 0.7 µm in diameter) yet most abundant photosynthetic microbe in the ocean, with an estimated 100,000 cells per milliliter of surface seawater (Fig. 1). These primary producers dominate nutrient-poor waters and produce a large fraction of the oxygen gas in the atmosphere. Despite their small size, Prochlorococcus have a great genomic variability that has puzzled researchers for many years. For one, the collection of all available strain genomes together constitutes a very large gene pool, also known as the pangenome. Prochlorococcus also possess genomic islands, large clusters of genes apparently acquired from other bacteria. These islands are variable in gene content and are important for adaptation to changing environmental conditions and defense against predation by phages. How these genomic islands are acquired in these marine bacteria has thus far remained a mystery.
To address this gap, Thomas Hackl and colleagues from several institutions and led by Penny Chisolm at MIT decided to explore the genomes of cultured and wild Prochlorococcus. As often occurs in research, answers were not immediately evident and on initial inspection they failed to find mobile genetic elements. However, they latched on to a small region conserved in two distant genomes that carried a gene for an integrase. These are enzymes that catalyze DNA strand exchange and whose genes are commonly found in mobile elements. By carefully analyzing genes in the vicinity of this integrase gene, they uncovered features indicative of a putative mobile element and a set of hallmark proteins. They then probed the Prochlorococcus genomes with this set of proteins and identified 937 potential integrase-carrying mobile elements! A great accomplishment that resulted in the characterization of a novel class of mobile element they named tycheposons, after the Greek goddess Tyche, involved in fortune and prosperity.
Fig. 2. Top: Schematic of a tycheposon. Bottom: Examples of tycheposons illustrating their modular structure: cargo-carrying tycheposons with clear ecological relevance in ocean ecosystems. Cargo modules were annotated with roles in nitrate assimilation, phosphate assimilation, zinc homeostasis. Gene labels: Ptgg, tRNA-proline TGG; YR, tyrosine recombinase; xis, excisionase; hel, helicase. Source
Tycheposons turn out to be unique gene transfer elements. They have a site-specific integrase, usually a tyrosine recombinase, that targets tRNA genes, thus leaving tRNA repeats flanking the tycheposon (Fig. 2). Like many other mobile elements, they have genes involved in DNA replication. They also contain a broad array of genes involved in functions important for adaptation to the environment. These include, for example, genes for acquisition of nutrients that are limiting in the ocean ecosystems, like nitrogen, phosphorus, and iron. In other cases, tycheposons carry genes that promote the introduction of DNA into newly formed phage capsids.
However, tycheposons lack genes found in other elements whose products are necessary for actual transfer of genes between cells, such as genes for formation of phage capsids or for conjugation, the process of transferring DNA through direct cell contact. How then do these elements move between cells and generate genomic diversity? Again, the authors look for clues in sequence data. They found tycheposon DNA in viral metagenomic libraries, which indicated that it is encapsulated in phage capsids. Perhaps more striking, they found tycheposon DNA within vesicles obtained from marine water. Many bacteria release small membrane vesicles that contain molecules involved in a range of biological processes such as virulence, detoxification and cell communication. And it just so happens that extracellular vesicles are abundant in oceans. Thus, tycheposons can move from cell to cell using phage capsids and in vesicles.
Fig. 3. A model for genomic island formation promoted by mobile element activity. Mobile elements integrate and excise at the tRNA gene at the proximal end of the island. Genetic material brought in but not excised later, such as flanking DNA from other hosts and degenerated elements, accumulates next to the tRNA leading to gene gain and island growth. Gene gain is countered by gene loss and selection, preserving only beneficial acquisitions which may, in turn, become fixed in descending lineages. Due to the directionality of the process, the observed intrastrain heterogeneity is highest at the proximal end of the island right next to the tRNA and decreases toward the distal end of the island. Source
While tycheposons helped explain gene mobility in Prochlorococcus, some of the variability observed in these genomes was still puzzling. Many of the genomic islands were bounded by hallmark insertion sites (tRNA repeats) but they lacked tycheposon elements themselves. How then can the variability in these islands be explained? The authors hypothesize that tycheposons can capture flanking DNA material as they excise from a previous genomic location in a process comparable to specialized transduction in lysogenic phages. These elements then function as transient vehicles of genomic variability. After integrating into a recipient genome, a subsequent excision leaves behind the flanking DNA as part of the island in the new host (Figure 3). This process results in the gradual accumulation of transferred material and formation of islands that become reservoirs of variability in the Prochlorococcus population. By participating in the formation and remodeling of Prochlorococcus genomic islands, tycheposons also promote diversity of the population in the wild.
Importantly, tycheposons are not restricted to Prochlorococcus cells. They are involved in the diversification of pigments in marine Synechococcus cyanobacteria, and are present in the genomes of marine taxa from the alpha-, gamma- and delta-proteobacteria. Future work will no doubt bring new surprises regarding the mechanisms and roles of these elements both in gene transfer and in the generation of diversity across broader phylogenetic microbial ocean populations. I find it both baffling and fascinating that these tiny elements, be they inside phage capsids or membrane vesicles, exist in the enormity of the Earth's oceans. Microbes never fail to surprise!
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