From passengers to drivers: Impact of bacterial transposable elements on evolvability

Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space

Environmental virus metagenomes, commonly referred to as "viromes", are typically generated by physically separating virus-like particles (VLPs) from the microbial fraction based on their size and mass. However, most methods used to purify VLPs, enrich extracellular vesicles (EVs) and gene transfer agents (GTAs) simultaneously. Consequently, the sequence space traditionally referred to as a "virome" contains host-associated sequences, transported via EVs or GTAs. We therefore propose to call the genetic material isolated from size-fractionated (0.22 µm) and DNase-treated samples protected environmental DNA (peDNA). This sequence space contains viral genomes, DNA transduced by viruses and DNA transported in EVs and GTAs. Since there is no genetic signature for peDNA transported in EVs, GTAs and virus particles, we rely on the successful removal of contaminating remaining cellular and free DNA when analyzing peDNA. Using marine samples collected from the North Sea, we generated a thoroughly purified peDNA dataset and developed a bioinformatic pipeline to determine the potential origin of the purified DNA. This pipeline was applied to our dataset as well as existing global marine "viromes". Through this pipeline, we identified known GTA and EV producers, as well as organisms with actively transducing proviruses as the source of the peDNA, thus confirming the reliability of our approach. Additionally, we identified novel and widespread EV producers, and found quantitative evidence suggesting that EV-mediated gene transfer plays a significant role in driving horizontal gene transfer (HGT) in the world's oceans.

Gene Expression Order Attributed to Genome Reduction and the Steady Cellular State in Escherichia coli

Transcriptomes not only reflect the growth status but also link to the genome in bacteria. To investigate if and how genome or cellular state changes contribute to the gene expression order, the growth profile-associated transcriptomes of an assortment of genetically differentiated Escherichia coli either exponentially growing under varied conditions or in response to environmental disturbance were analyzed. A total of 168 microarray data sets representing 56 transcriptome variations, were categorized by genome size (full length or reduced) and cellular state (steady or unsteady). At the genome-wide level, the power-law distribution of gene expression was found to be significantly disturbed by the genome size but not the cellular state. At the regulatory network level, more networks with improved coordination of growth rates were observed in genome reduction than at the steady state. At the single-gene level, both genome reduction and steady state increased the correlation of gene expression to growth rate, but the enriched gene categories with improved correlations were different. These findings not only illustrate the order of gene expression attributed to genome reduction and steady cellular state but also indicate that the accessory sequences acquired during genome evolution largely participated in the coordination of transcriptomes to growth fitness.

Virus world as an evolutionary network of viruses and capsidless selfish elements

Viruses were defined as one of the two principal types of organisms in the biosphere, namely, as capsid-encoding organisms in contrast to ribosome-encoding organisms, i.e., all cellular life forms. Structurally similar, apparently homologous capsids are present in a huge variety of icosahedral viruses that infect bacteria, archaea, and eukaryotes. These findings prompted the concept of the capsid as the virus "self" that defines the identity of deep, ancient viral lineages. However, several other widespread viral "hallmark genes" encode key components of the viral replication apparatus (such as polymerases and helicases) and combine with different capsid proteins, given the inherently modular character of viral evolution. Furthermore, diverse, widespread, capsidless selfish genetic elements, such as plasmids and various types of transposons, share hallmark genes with viruses. Viruses appear to have evolved from capsidless selfish elements, and vice versa, on multiple occasions during evolution. At the earliest, precellular stage of life's evolution, capsidless genetic parasites most likely emerged first and subsequently gave rise to different classes of viruses. In this review, we develop the concept of a greater virus world which forms an evolutionary network that is held together by shared conserved genes and includes both bona fide capsid-encoding viruses and different classes of capsidless replicons. Theoretical studies indicate that selfish replicons (genetic parasites) inevitably emerge in any sufficiently complex evolving ensemble of replicators. Therefore, the key signature of the greater virus world is not the presence of a capsid but rather genetic, informational parasitism itself, i.e., various degrees of reliance on the information processing systems of the host.

The structural code of cyanobacterial genomes

A periodic bias in nucleotide frequency with a period of about 11 bp is characteristic for bacterial genomes. This signal is commonly interpreted to relate to the helical pitch of negatively supercoiled DNA. Functions in supercoiling-dependent RNA transcription or as a 'structural code' for DNA packaging have been suggested. Cyanobacterial genomes showed especially strong periodic signals and, on the other hand, DNA supercoiling and supercoiling-dependent transcription are highly dynamic and underlie circadian rhythms of these phototrophic bacteria. Focusing on this phylum and dinucleotides, we find that a minimal motif of AT-tracts (AT2) yields the strongest signal. Strong genome-wide periodicity is ancestral to a clade of unicellular and polyploid species but lost upon morphological transitions into two baeocyte-forming and a symbiotic species. The signal is intermediate in heterocystous species and weak in monoploid picocyanobacteria. A pronounced 'structural code' may support efficient nucleoid condensation and segregation in polyploid cells. The major source of the AT2 signal are protein-coding regions, where it is encoded preferentially in the first and third codon positions. The signal shows only few relations to supercoiling-dependent and diurnal RNA transcription in Synechocystis sp. PCC 6803. Strong and specific signals in two distinct transposons suggest roles in transposase transcription and transpososome formation.

Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes

Insertion sequences (IS) are the simplest and most abundant form of transposable DNA found in bacterial genomes. When present in multiple copies, it is thought that they can promote genomic plasticity and genetic exchange, thus being a major force of evolutionary change. The main processes that determine IS content in genomes are, though, a matter of debate. In this work, we take advantage of the large amount of genomic data currently available and study the abundance distributions of 33 IS families in 1811 bacterial chromosomes. This allows us to test simple models of IS dynamics and estimate their key parameters by means of a maximum likelihood approach. We evaluate the roles played by duplication, lateral gene transfer, deletion and purifying selection. We find that the observed IS abundances are compatible with a neutral scenario where IS proliferation is controlled by deletions instead of purifying selection. Even if there may be some cases driven by selection, neutral behavior dominates over large evolutionary scales. According to this view, IS and hosts tend to coexist in a dynamic equilibrium state for most of the time. Our approach also allows for a detection of recent IS expansions, and supports the hypothesis that rapid expansions constitute transient events—punctuations—during which the state of coexistence of IS and host becomes perturbated.

Insertion sequences (IS) are mobile genetic elements found in most prokaryotic genomes. They are able to autonomously change position and proliferate in chromosomes. The nature of the coevolutionary dynamics of IS with the genome that hosts them is a matter of debate: Do IS proliferate to the point of causing the extinction of the host? Is it possible that IS and hosts stably coexist? Can environmental perturbations cause IS expansions? What is the role of selection in controlling IS copy number? In this study, we have analysed abundance patterns of IS families to test two different evolutionary hypotheses: in the first one IS evolve neutrally, while in the second case they are affected by selection. Our results indicate that, most of the time, IS and their hosts coexist stably in a neutral scenario where the proliferation of IS through duplications and lateral gene transfer is balanced by regular deletions. Occasionally, though, this balance may be disrupted, causing temporary explosions of IS abundance.