Rickettsiae and Chlamydiae: evidence of horizontal gene transfer and gene exchange

SUMMARYAlthough horizontal gene transfer is recognized as a major evolutionary process in Bacteria and Archaea, its general patterns remain elusive, due to difficulties tracking genes at relevant resolution and scale within complex microbiomes. To circumvent these challenges, we analyzed a randomized sample of >12,000 genomes of individual cells of Bacteria and Archaea in the tropical and subtropical ocean - a well-mixed, global environment. We found that marine microorganisms form gene exchange networks (GENs) within which transfers of both flexible and core genes are frequent, including the rRNA operon that is commonly used as a conservative taxonomic marker. The data revealed efficient gene exchange among genomes with <28% nucleotide difference, indicating that GENs are much broader lineages than the nominal microbial species, which are currently delineated at 4-6% nucleotide difference. The 42 largest GENs accounted for 90% of cells in the tropical ocean microbiome. Frequent gene exchange within GENs helps explain how marine microorganisms maintain millions of rare genes and adapt to a dynamic environment despite extreme genome streamlining of their individual cells. Our study suggests that sharing of pangenomes through horizontal gene transfer is a defining feature of fundamental evolutionary units in marine planktonic microorganisms and, potentially, other microbiomes.

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Plasmid Characteristics Modulate the Propensity of Gene Exchange in Bacterial Vesicles

Journal of Bacteriology ◽

10.1128/jb.00430-18 ◽

2019 ◽

Vol 201 (7) ◽

Cited By ~ 4

Author(s):

Frances Tran ◽

James Q. Boedicker

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Extracellular Vesicles ◽

Copy Number ◽

Genetic Material ◽

Plasmid Copy Number ◽

Gene Exchange ◽

Origin Of Replication ◽

Plasmid Copy ◽

The Impact

ABSTRACTHorizontal gene transfer is responsible for the exchange of many types of genetic elements, including plasmids. Properties of the exchanged genetic element are known to influence the efficiency of transfer via the mechanisms of conjugation, transduction, and transformation. Recently, an alternative general pathway of horizontal gene transfer has been identified, namely, gene exchange by extracellular vesicles. Although extracellular vesicles have been shown to facilitate the exchange of several types of plasmids, the influence of plasmid characteristics on genetic exchange within vesicles is unclear. Here, a set of different plasmids was constructed to systematically test the impact of plasmid properties, specifically, plasmid copy number, size, and origin of replication, on gene transfer in vesicles. The influence of each property on the production, packaging, and uptake of vesicles containing bacterial plasmids was quantified, revealing how plasmid properties modulate vesicle-mediated horizontal gene transfer. The loading of plasmids into vesicles correlates with the plasmid copy number and is influenced by characteristics that help set the number of plasmids within a cell, including size and origin of replication. Plasmid origin also has a separate impact on both vesicle loading and uptake, demonstrating that the origin of replication is a major determinant of the propensity of specific plasmids to transfer within extracellular vesicles.IMPORTANCEExtracellular vesicle formation and exchange are common within bacterial populations. Vesicles package multiple types of biomolecules, including genetic material. The exchange of extracellular vesicles containing genetic material facilitates interspecies DNA transfer and may be a promiscuous mechanism of horizontal gene transfer. Unlike other mechanisms of horizontal gene transfer, it is unclear whether characteristics of the exchanged DNA impact the likelihood of transfer in vesicles. Here, we systematically examine the influence of plasmid copy number, size, and origin of replication on the loading of DNA into vesicles and the uptake of DNA containing vesicles by recipient cells. These results reveal how each plasmid characteristic impacts gene transfer in vesicles and contribute to a greater understanding of the importance of vesicle-mediated gene exchange in the landscape of horizontal gene transfer.

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Horizontal gene transfer in 44 early diverging fungi favors short, metabolic, extracellular proteins from associated bacteria

10.1101/2021.12.02.471044 ◽

2021 ◽

Author(s):

Michał Ciach ◽

Julia Pawłowska ◽

Anna Muszewska

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Phylogenetic Trees ◽

Large Scale ◽

Genetic Material ◽

Small Sample ◽

Extracellular Proteins ◽

Gene Exchange ◽

Statistical Sample

AbstractNumerous studies have been devoted to individual cases of horizontally acquired genes in fungi. It has been shown that such genes expand their metabolic capabilities and contribute to their adaptations as parasites or symbionts. Some studies have provided a more extensive characterization of the horizontal gene transfer (HGT) in Dikarya. However, in the early diverging fungi (EDF), the overall influence of HGT on the ecological adaptation and evolution is largely unknown. In order to fill this gap, we have designed a computational pipeline to obtain a sample of over 600 phylogenetic trees with evidence for recent to moderately old HGT across multiple EDF genomes ranging from Chytridiomycota and Blastocladiomycota to Mucoromycota. Our pipeline is designed to obtain a small sample of reliable HGT events with a possibly minimal number of false detections that distort the overall statistical patterns. We show that transfer rates differ greatly between closely related species and strains, but the ancestrally aquatic fungi are generally more likely to acquire foreign genetic material than terrestrial ones. A close ecological relationship with another organism is a predisposing condition, but does not always result in an extensive gene exchange, with some fungal lineages showing a preference for HGT from loosely associated soil bacteria.ImportanceAlthough it is now recognized that horizontal gene exchange is a factor influencing the adaptation and evolution of eukaryotic organisms, the so far described cases in early diverging fungi (EDF) are fragmentary, and a large-scale comprehensive study is lacking. We have designed a methodology to obtain a reliable, statistical sample of inter-kingdom xenologs across the tree of life of EDF to give a preliminary characterization of their general properties and patterns. We study how different fungal lineages vary in terms of the number of xenologs, what are their ecological associations, and the molecular properties of proteins encoded by the acquired genes. Our results help to better understand to what extent and in what way the incorporation of foreign genetic material shaped the present biodiversity of fungi.

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