Shannon M. Soucy

Horizontal gene transfer: building the web of life

Horizontal gene transfer (HGT) is the sharing of genetic material between organisms that are not in a parent–offspring relationship. HGT is a widely recognized mechanism for adaptation in bacteria and archaea. Microbial antibiotic resistance and pathogenicity are often associated with HGT, but the scope of HGT extends far beyond disease-causing organisms. In this Review, we describe how HGT has shaped the web of life using examples of HGT among prokaryotes, between prokaryotes and eukaryotes, and even between multicellular eukaryotes. We discuss replacement and additive HGT, the proposed mechanisms of HGT, selective forces that influence HGT, and the evolutionary impact of HGT on ancestral populations and existing populations such as the human microbiome.

Population and genomic analysis of the genus Halorubrum.

The Halobacteria are known to engage in frequent gene transfer and homologous recombination. For stably diverged lineages to persist some checks on the rate of between lineage recombination must exist. We surveyed a group of isolates from the Aran-Bidgol endorheic lake in Iran and sequenced a selection of them. Multilocus Sequence Analysis (MLSA) and Average Nucleotide Identity (ANI) revealed multiple clusters (phylogroups) of organisms present in the lake. Patterns of intein and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) presence/absence and their sequence similarity, GC usage along with the ANI and the identities of the genes used in the MLSA revealed that two of these clusters share an exchange bias toward others in their phylogroup while showing reduced rates of exchange with other organisms in the environment. However, a third cluster, composed in part of named species from other areas of central Asia, displayed many indications of variability in exchange partners, from within the lake as well as outside the lake. We conclude that barriers to gene exchange exist between the two purely Aran-Bidgol phylogroups, and that the third cluster with members from other regions is not a single population and likely reflects an amalgamation of several populations.

The pan-genome as a shared genomic resource: mutual cheating, cooperation and the black queen hypothesis

Cells have long been recognized as life’s building blocks (e.g., Virchow’s dictum “omnis cellula e cellula,” Virchow, 1860). Specifically, a cell’s genome is considered the repository of genetic information that pairs with the cellular machinery to determine the organism’s phenotype. Except for rare circumstances, themajority of a genome is passed on from ancestor to descendant, although the acquisition of genes from organisms that are not direct ancestors is recognized to play an important role in evolution (Swithers et al., 2012). Jeffrey Lawrence, in discussing minimal genome size proposed a meta-cell model (Lawrence, 1999), in which many micelles (small vesicles containing resources, products, and genes) exchange genes frequently. Genes temporarily reside in a micelle and direct the synthesis of compounds important for replication. A micelle only can replicate when all compounds necessary for division have been generated. However, at each point in time only a fraction of the necessary genes are present in an individual micelle. This model relies on gene transfer being so frequent that each of the genes that encode necessary functions visits the individual micelles often enough to allow for sufficient synthesis of the necessary gene products for future micelle divisions. The meta-cell can be considered an organism, whose genome is divided into a network of micelles. Lawrence’s metacell model is reminiscent of Woese’s progenote (Woese, 1998) and Kandler’s pre-cell populations (Kandler, 1994) that were postulated to have existed early in evolution before genes coalesced into genomes.

Inteins as indicators of gene flow in the halobacteria

This research uses inteins, a type of mobile genetic element, to infer patterns of gene transfer within the Halobacteria. We surveyed 118 genomes representing 26 genera of Halobacteria for intein sequences. We then used the presence-absence profile, sequence similarity and phylogenies from the inteins recovered to explore how intein distribution can provide insight on the dynamics of gene flow between closely related and divergent organisms. We identified 24 proteins in the Halobacteria that have been invaded by inteins at some point in their evolutionary history, including two proteins not previously reported to contain an intein. Furthermore, the size of an intein is used as a heuristic for the phase of the inteins life cycle. Larger size inteins are assumed to be the canonical two domain inteins, consisting of self-splicing and homing endonuclease domains (HEN); smaller sizes are assumed to have lost the HEN domain. For many halobacterial groups the consensus phylogenetic signal derived from intein sequences is compatible with vertical inheritance or with a strong gene transfer bias creating these clusters. Regardless, the coexistence of intein-free and intein-containing alleles reveal ongoing transfer and loss of inteins within these groups. Inteins were frequently shared with other Euryarchaeota and among the Bacteria, with members of the Cyanobacteria (Cyanothece, Anabaena), Bacteriodetes (Salinibacter), Betaproteobacteria (Delftia, Acidovorax), Firmicutes (Halanaerobium), Actinobacteria (Longispora), and Deinococcus-Thermus-group.

The Role of Reticulate Evolution in Creating Innovation and Complexity

Reticulate evolution encompasses processes that conflict with traditional Tree of Life efforts. These processes, horizontal gene transfer (HGT), gene and whole-genome duplications through allopolyploidization, are some of the main driving forces for generating innovation and complexity. HGT has a profound impact on prokaryotic and eukaryotic evolution. HGTs can lead to the invention of new metabolic pathways and the expansion and enhancement of previously existing pathways. It allows for organismal adaptation into new ecological niches and new host ranges. Although many HGTs appear to be selected for because they provide some benefit to their recipient lineage, other HGTs may be maintained by chance through random genetic drift. Moreover, some HGTs that may initially seem parasitic in nature can cause complexity to arise through pathways of neutral evolution. Another mechanism for generating innovation and complexity, occurring more frequently in eukaryotes than in prokaryotes, is gene and genome duplications, which often occur through allopolyploidizations. We discuss how these different evolutionary processes contribute to generating innovation and complexity.

Impact of a homing intein on recombination frequency and organismal fitness

Significance Parasitic interactions can result in changes to the host’s behavior in a way that promotes the distribution or life cycle of the parasite. Inteins are molecular parasites found in all three domains of life. Here we look at the influence of an intein in the DNA polymerase on a population of halophilic archaea in simulations, in experiments, and in the wild. This intein has a fitness cost that is higher than expected for a self-splicing genetic element. In these populations, where mating is independent of host replication, the intein increases the recombination rate between cells with and without inteins. This modification may contribute to the long-term persistence of these genetic parasites, despite the fitness burden they impart on their host. Inteins are parasitic genetic elements that excise themselves at the protein level by self-splicing, allowing the formation of functional, nondisrupted proteins. Many inteins contain a homing endonuclease (HEN) domain and rely on its activity for horizontal propagation. However, successful invasion of an entire population will make this activity redundant, and the HEN domain is expected to degenerate quickly under these conditions. Several theories have been proposed for the continued existence of the both active HEN and noninvaded alleles within a population. However, to date, these models were not directly tested experimentally. Using the natural cell fusion ability of the halophilic archaeon Haloferax volcanii we were able to examine this question in vivo, by mating polB intein-positive [insertion site c in the gene encoding DNA polymerase B (polB-c)] and intein-negative cells and examining the dispersal efficiency of this intein in a natural, polyploid population. Through competition between otherwise isogenic intein-positive and intein-negative strains we determined a surprisingly high fitness cost of over 7% for the polB-c intein. Our laboratory culture experiments and samples taken from Israel’s Mediterranean coastline show that the polB-c inteins do not efficiently take over an inteinless population through mating, even under ideal conditions. The presence of the HEN/intein promoted recombination when intein-positive and intein-negative cells were mated. Increased recombination due to HEN activity contributes not only to intein dissemination but also to variation at the population level because recombination tracts during repair extend substantially from the homing site.

Bacterial Diversification in the Light of the Interactions with Phages: The Genetic Symbionts and Their Role in Ecological Speciation

Phages have a major impact on microbial populations. In this work, we discuss how predation, transduction, lysogeny, and phage domestication lead to symbio-centric genomic interactions between bacteria and phage, ranging from antagonistic to mutualistic. Furthermore, these interactions influence bacterial diversification and ecotype formation. We then propose an additional consideration in the form of symbio-centric ecological speciation framework for bacteria. Our framework builds upon classical morphological and molecular taxonomy by also considering bacteria and their phages as a unit of evolutionary selection. This framework acknowledges the considerable effect that phage interaction has on bacterial genomic content, regulation, and evolution, and will advance our understanding of bacterial evolution.

Insights into origin and evolution of α-proteobacterial gene transfer agents

Abstract Several bacterial and archaeal lineages produce nanostructures that morphologically resemble small tailed viruses, but, unlike most viruses, contain apparently random pieces of the host genome. Since these elements can deliver the packaged DNA to other cells, they were dubbed gene transfer agents (GTAs). Because many genes involved in GTA production have viral homologs, it has been hypothesized that the GTA ancestor was a virus. Whether GTAs represent an atypical virus, a defective virus, or a virus co-opted by the prokaryotes for some function, remains to be elucidated. To evaluate these possibilities, we examined the distribution and evolutionary histories of genes that encode a GTA in the α-proteobacterium Rhodobacter capsulatus (RcGTA). We report that although homologs of many individual RcGTA genes are abundant across bacteria and their viruses, RcGTA-like genomes are mainly found in one subclade of α-proteobacteria. When compared with the viral homologs, genes of the RcGTA-like genomes evolve significantly slower, and do not have higher %A+T nucleotides than their host chromosomes. Moreover, they appear to reside in stable regions of the bacterial chromosomes that are generally conserved across taxonomic orders. These findings argue against RcGTA being an atypical or a defective virus. Our phylogenetic analyses suggest that RcGTA ancestor likely originated in the lineage that gave rise to contemporary α-proteobacterial orders Rhizobiales, Rhodobacterales, Caulobacterales, Parvularculales, and Sphingomonadales, and since that time the RcGTA-like element has co-evolved with its host chromosomes. Such evolutionary history is compatible with maintenance of these elements by bacteria due to some selective advantage. As for many other prokaryotic traits, horizontal gene transfer played a substantial role in the evolution of RcGTA-like elements, not only in shaping its genome components within the orders, but also in occasional dissemination of RcGTA-like regions across the orders and even to different bacterial phyla.

Comparative Analysis of Surface Layer Glycoproteins and Genes Involved in Protein Glycosylation in the Genus Haloferax

Within the Haloferax genus, both the surface (S)-layer protein, and the glycans that can decorate it, vary between species, which can potentially result in many different surface types, analogous to bacterial serotypes. This variation may mediate phenotypes, such as sensitivity to different viruses and mating preferences. Here, we describe S-layer glycoproteins found in multiple Haloferax strains and perform comparative genomics analyses of major and alternative glycosylation clusters of isolates from two coastal sites. We analyze the phylogeny of individual glycosylation genes and demonstrate that while the major glycosylation cluster tends to be conserved among closely related strains, the alternative cluster is highly variable. Thus, geographically- and genetically-related strains may exhibit diverse surface structures to such an extent that no two isolates present an identical surface profile.

Inteins as Indicators of Bio-Communication

Genetic information is stored in DNA molecules, horizontal gene transfer shares this information between organisms. The transfer of genetic information thus is an important method of bio-communication. Communities of organisms made up of either the same species, or different species can transfer genetic material between community members. In Bacteria and Archaea these transfers are unidirectional, except for mating described for Haloarchaea (Naor et al. 2012) and possibly also occurring in other archaea. Inteins are selfish genetic elements found in all domains of life. As is the case for most mobile selfish genetic elements, horizontal gene transfer is an important part of the intein’s life cycle. Several unique properties of inteins make them particularly well suited as markers of horizontal gene transfer pathways. In this chapter, we explore these properties, and provide examples of their uses to reveal patterns of horizontal gene transfer.