Diversification of plasmids in a genus of pathogenic and nitrogen-fixing bacteria

Trehalose synthases from the subfamily GH13_16 involved in α-glucan biosynthesis - a focus on their maltokinase domain

The subfamily GH13_16 trehalose synthase (TreS) converts maltose to trehalose and vice versa. Typically, it consists of three domains, but it may contain a C-terminal extension exhibiting clear sequence features of a maltokinase (MaK). The present in silico study was focused on collection of naturally fused TreS-MaKs and their subsequent detailed bioinformatics analysis. Hence a set of total 3354 unique sequences was compared consisting of 1900 single TreSs, 1426 fused TreS-MaKs and 28 single MaKs. Fused TreS-MaKs were divided into five groups, namely with a standard MaK, with mutations in the maltose-binding site, of the catalytic nucleophile, of the general acid/base and of both catalytic residues. Sequence logos bearing the best conserved sequence regions were prepared for both TreSs and MaKs in an effort to find unique sequence features. In addition, linkers connecting the TreS and MaK parts in the fused enzymes were analysed. This analysis revealed that MaKs in fused enzymes have an extended N-terminal regions compared to single MaKs. Finally, the evolutionary relationships were demonstrated by phylogenetic trees of TreS parts from single TreSs and fused TreS-MaKs from the same organism as well as of single TreSs existing in multiple isoforms in the same organism.

Mobile Genetic Element Flexibility as an Underlying Principle to Bacterial Evolution

Mobile genetic elements are key to the evolution of bacteria and traits that affect host and ecosystem health. Here, we use a framework of a hierarchical and modular system that scales from genes to populations to synthesize recent findings on mobile genetic elements (MGEs) of bacteria. Doing so highlights the role that emergent properties of flexibility, robustness, and genetic capacitance of MGEs have on the evolution of bacteria. Some of their traits can be stored, shared, and diversified across different MGEs, taxa of bacteria, and time. Collectively, these properties contribute to maintaining functionality against perturbations while allowing changes to accumulate in order to diversify and give rise to new traits. These properties of MGEs have long challenged our abilities to study them. Implementation of new technologies and strategies allows for MGEs to be analyzed in new and powerful ways.

Virulence and Ecology of Agrobacteria in the Context of Evolutionary Genomics

Among plant-associated bacteria, agrobacteria occupy a special place. These bacteria are feared in the field as agricultural pathogens. They cause abnormal growth deformations and significant economic damage to a broad range of plant species. However, these bacteria are revered in the laboratory as models and tools. They are studied to discover and understand basic biological phenomena and used in fundamental plant research and biotechnology. Agrobacterial pathogenicity and capability for transformation are one and the same and rely on functions encoded largely on their oncogenic plasmids. Here, we synthesize a substantial body of elegant work that elucidated agrobacterial virulence mechanisms and described their ecology. We review findings in the context of the natural diversity that has been recently unveiled for agrobacteria and emphasize their genomics and plasmids. We also identify areas of research that can capitalize on recent findings to further transform our understanding of agrobacterial virulence and ecology.

Diversity and Evolutionary History of Ti Plasmids of "tumorigenes" Clade of Rhizobium spp. and Their Differentiation from Other Ti and Ri Plasmids

Agrobacteria are important plant pathogens responsible for crown/cane gall and hairy root diseases. Crown/cane gall disease is associated with strains carrying tumor-inducing (Ti) plasmids, while hairy root disease is caused by strains harboring root-inducing (Ri) plasmids. In this study, we analyzed the sequences of Ti plasmids of the novel "tumorigenes" clade of the family Rhizobiaceae ("tumorigenes" Ti plasmids), which includes two species, Rhizobium tumorigenes and Rhizobium rhododendri. The sequences of reference Ti/Ri plasmids were also included, which was followed by a comparative analysis of their backbone and accessory regions. The "tumorigenes" Ti plasmids have novel opine signatures compared with other Ti/Ri plasmids characterized so far. The first group exemplified by pTi1078 is associated with production of agrocinopine, nopaline, and ridéopine in plant tumors, while the second group comprising pTi6.2 is responsible for synthesis of leucinopine. Bioinformatic and chemical analyses, including opine utilization assays, indicated that leucinopine associated with pTi6.2 most likely has D,L stereochemistry, unlike the L,L-leucinopine produced in tumors induced by reference strains Chry5 and Bo542. Most of the "tumorigenes" Ti plasmids have conjugative transfer system genes that are unusual for Ti plasmids, composed of avhD4/avhB and traA/mobC/parA regions. Next, our results suggested that "tumorigenes" Ti plasmids have a common origin, but they diverged through large-scale recombination events, through recombination with single or multiple distinct Ti/Ri plasmids. Lastly, we showed that Ti/Ri plasmids could be differentiated based on pairwise Mash or average amino-acid identity distance clustering, and we supply a script to facilitate application of the former approach by other researchers.

Agrobacterium tumefaciens: a Transformative Agent for Fundamental Insights into Host-Microbe Interactions, Genome Biology, Chemical Signaling, and Cell Biology

Agrobacterium tumefaciens incites the formation of readily visible macroscopic structures known as crown galls on plant tissues that it infects. Records from biologists as early as the 17th century noted these unusual plant growths and began examining the basis for their formation. These studies eventually led to isolation of the infectious agent, A. tumefaciens, and decades of study revealed the remarkable mechanisms by which A. tumefaciens causes crown gall through stable horizontal genetic transfer to plants. This fundamental discovery generated a barrage of applications in the genetic manipulation of plants that is still under way. As a consequence of the intense study of A. tumefaciens and its role in plant disease, this pathogen was developed as a model for the study of critical processes that are shared by many bacteria, including host perception during pathogenesis, DNA transfer and toxin secretion, bacterial cell-cell communication, plasmid biology, and more recently, asymmetric cell biology and composite genome coordination and evolution. As such, studies of A. tumefaciens have had an outsized impact on diverse areas within microbiology and plant biology that extend far beyond its remarkable agricultural applications. In this review, we attempt to highlight the colorful history of A. tumefaciens as a study system, as well as current areas that are actively demonstrating its value and utility as a model microorganism.

The Ti Plasmid, Driver of Agrobacterium Pathogenesis

The phytopathogenic bacterium Agrobacterium tumefaciens causes crown gall disease in plants, characterized by the formation of tumor-like galls where wounds were present. Nowadays, however, the bacterium and its Ti (tumor-inducing) plasmid is better known as an effective vector for the genetic manipulation of plants and fungi. In this review, I will briefly summarize some of the major discoveries that have led to this bacterium now playing such a prominent role worldwide in plant and fungal research at universities and research institutes and in agricultural biotechnology for the production of genetically modified crops. I will then delve a little deeper into some aspects of Agrobacterium biology and discuss the diversity among agrobacteria and the taxonomic position of these bacteria, the diversity in Ti plasmids, the molecular mechanism used by the bacteria to transform plants, and the discovery of protein translocation from the bacteria to host cells as an essential feature of Agrobacterium-mediated transformation.

Genomics of the “tumorigenes” clade of the family Rhizobiaceae and description of Rhizobium rhododendri sp. nov

Tumorigenic members of the family Rhizobiaceae, known as agrobacteria, are responsible for crown and cane gall diseases of various crops worldwide. Tumorigenic agrobacteria are commonly found in the genera Agrobacterium, Allorhizobium, and Rhizobium. In this study, we analyzed a distinct “tumorigenes” clade of the genus Rhizobium, which includes the tumorigenic species Rhizobium tumorigenes, as well as strains causing crown gall disease on rhododendron. Here, high‐quality, closed genomes of representatives of the “tumorigenes” clade were generated, followed by comparative genomic and phylogenomic analyses. Additionally, the phenotypic characteristics of representatives of the “tumorigenes” clade were analyzed. Our results showed that the tumorigenic strains isolated from rhododendron represent a novel species of the genus Rhizobium for which the name Rhizobium rhododendri sp. nov. is proposed. This species also includes additional strains originating from blueberry and Himalayan blackberry in the United States, whose genome sequences were retrieved from GenBank. Both R. tumorigenes and R. rhododendri contain multipartite genomes, including a chromosome, putative chromids, and megaplasmids. Synteny and phylogenetic analyses indicated that a large putative chromid of R. rhododendri resulted from the cointegration of an ancestral megaplasmid and two putative chromids, following its divergence from R. tumorigenes. Moreover, gene clusters specific for both species of the “tumorigenes” clade were identified, and their biological functions and roles in the ecological diversification of R. rhododendri and R. tumorigenes were predicted and discussed.

How do interactions between mobile genetic elements affect horizontal gene transfer?

Horizontal gene transfer is central to bacterial adaptation and is facilitated by mobile genetic elements (MGEs). Increasingly, MGEs are being studied as agents with their own interests and adaptations, and the interactions MGEs have with one another are recognised as having a powerful effect on the flow of traits between microbes. Collaborations and conflicts between MGEs are nuanced and can both promote and inhibit the acquisition of new genetic material, shaping the maintenance of newly acquired genes and the dissemination of important adaptive traits through microbiomes. We review recent studies that shed light on this dynamic and oftentimes interlaced interplay, highlighting the importance of genome defence systems in mediating MGE-MGE conflicts, and outlining the consequences for evolutionary change, that resonate from the molecular to microbiome and ecosystem levels.

Modular evolution of secretion systems and virulence plasmids in a bacterial species complex

BACKGROUND

Many named species as defined in current bacterial taxonomy correspond to species complexes. Uncertainties regarding the organization of their genetic diversity challenge research efforts. We utilized the Agrobacterium tumefaciens species complex (a.k.a. Agrobacterium biovar 1), a taxon known for its phytopathogenicity and applications in transformation, as a study system and devised strategies for investigating genome diversity and evolution of species complexes.

RESULTS

We utilized 35 genome assemblies, including 14 newly generated ones, to achieve a phylogenetically balanced sampling of A. tumefaciens. Our genomic analysis suggested that the 10 genomospecies described previously are distinct biological species and supported a quantitative guideline for species delineation. Furthermore, our inference of gene content and core-genome phylogeny allowed for investigations of genes critical in fitness and ecology. For the type VI secretion system (T6SS) involved in interbacterial competition and thought to be conserved, we detected multiple losses and one horizontal gene transfer. For the tumor-inducing plasmids (pTi) and pTi-encoded type IV secretion system (T4SS) that are essential for agrobacterial phytopathogenicity, we uncovered novel diversity and hypothesized their involvement in shaping this species complex. Intriguingly, for both T6SS and T4SS, genes encoding structural components are highly conserved, whereas extensive diversity exists for genes encoding effectors and other proteins.

CONCLUSIONS

We demonstrate that the combination of a phylogeny-guided sampling scheme and an emphasis on high-quality assemblies provides a cost-effective approach for robust analysis in evolutionary genomics. We show that the T6SS VgrG proteins involved in specific effector binding and delivery can be classified into distinct types based on domain organization. The co-occurrence patterns of VgrG-associated domains and the neighboring genes that encode different chaperones/effectors can be used to infer possible interacting partners. Similarly, the associations between plant host preference and the pTi type among these strains can be used to infer phenotype-genotype correspondence. Our strategies for multi-level investigations at scales that range from whole genomes to intragenic domains and phylogenetic depths from between- to within-species are applicable to other bacteria. Furthermore, modularity observed in the molecular evolution of genes and domains is useful for inferring functional constraints and informing experimental works.