Horizontal gene transfer of a syp homolog contributes to the virulence of Burkholderia glumae

Horizontal gene transfer(HGT)has been proved a major driving force in prokaryotic evolution.However,the molecular functions of these transferred genes in pathogenic bacteria especially plant pathogenic bacteria are still not fully investigated.In this study,the whole-genome in silico analysis was performed and found a syringopeptin synthetase(syp)homolog in Burkholderia glumae,which can cause bacterial panicle blight in rice,was predicted to be horizontally transferred from Pseudomonas ancestor with solid confidence by phylogenetic analysis.The comprehensive molecular experiments were performed to study the potential role of this gene in B.glumae.Inoculation of rice panicles with the syp mutant resulted in 60%lower disease index compared with the wild type(WT)parent strain,suggesting the requirement of syp for the full virulence of B.glumae.Chromatography analysis of exudates from B.glumae showed suppression of synthesis of metabolites analogous to syringopeptin in the mutants.All these data raise the possibility of HGT phenomenon in shaping the virulence and adaptation of B.glumae over evolutionary time.

Characterizing proteases in an Antarctic Janthinobacterium sp. isolate: Evidence of a protease horizontal gene transfer event

We report the isolation of a cold-adapted bacterium belonging to the genus Janthinobacterium （named AU 11）, from a water sample collected in Lake Uruguay （King George Island, South Shetlands）. AUI 1 （growth between 4℃ and 30℃） produces a single cold-active extracellular protease （ExPAU11）, differentially expressed at low temperature. ExPAU11 was identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry （MALDI-ToF MS） as an alkaline metallo-protease （70% coverage with an extracellular protease of Janthinobacterium sp. PI12）, and by protease-inhibitor screening identified as a serine-protease. To the best of our knowledge this is the first experimental evidence of a cold-active extracellular protease produced by Janthinobacterium. Furthermore, we identified a serine-protease gene （named JSP8A） showing 60% identity （98% query coverage） to subtilisin peptidases belonging to the $8 family （S8A subfamily） of many cyanobacteria. A phylogenetic analysis of the JSP8A protease, along with related bacterial protein sequences, confirms that JSP8A clusters with S8A subtilisin sequences from different cyanobacteria, and is clearly separated from SSA bacterial sequences of other phyla （including its own）. An analysis of the genomic organization around JSP8A suggests that this protease gene was acquired in an event that duplicated a racemase gene involved in transforming L- to D-amino acids. Our results suggest that AU11 probably acquired this subtilisin-like protease gene by horizontal gene transfer （HGT） from a cyanobacterittrn. We discuss the relevance of a bacterial protease-HGT in the Antarctic environment in light of this hypothesis.

An acyltransferase gene that putatively functions in anthocyanin modification was horizontally transferred from Fabaceae into the genus Cuscuta

Horizontal gene transfer(HGT) refers to the flow of genetic materials to non-offspring,and occasionally HGT in plants can improve the adaptation of organisms in new niches due to expanded metabolic capability.Anthocyanins are an important group of water-soluble red,purple,or blue secondary metabolites,whose diversity results from modification after the main skeleton biosynthesis.Cuscuta is a stem holoparasitic genus,whose members form direct connection with hosts to withdraw water,nutrients,and macromolecules.Such intimate association is thought to increase the frequency of HGT.By transcriptome screening for foreign genes in Cuscuta australis,we discovered that one gene encoding a putative anthocyanin acyltransferase gene of the BAHD family,which is likely to be involved in anthocyanin modification,was acquired by C.australis from Fabaceae through HGT.The anthocyanin acyltransferase-like(AT-like) gene was confirmed to be present in the genome assembly of C.australis and the transcriptomes of Cuscuta pentagona.The higher transcriptional level in old stems is consistent with its putative function in secondary metabolism by stabilizing anthocyanin at neutral pH and thus HGT of this AT-like gene may have improved biotic and abiotic resistance of Cuscuta.

Unexpected complex horizontal gene transfer in teleost fish

Horizontal gene transfer(HGT)is a common occurrence across all domains of life.However,most HGT events were reported between single-celled organisms or parasites and hosts(Van Etten and Bhattacharya 2020).A type II antifreeze protein(AFP)gene was the first and sole evidence of HGT direct vertebrate-to-vertebrate DNA transmission.AFP is only found in 3 widely separated branches of teleost fishes(herring,sea raven,and smelts),sharing amino acid similarity up to 80%(Graham et al.2008).

Evolution of Xanthomonas Gene Content:Gene Gain/Loss History and Species Divergence

Horizontal gene transfer （HGT） plays key roles in the evolution of pathogenetic bacteria, especially in pathogenetic associated genes. In this study, the evolutionary dynamics of Xanthomonas at species level were determined by the comparative analysis of the complete genomes of 15 Xanthomonas strains. A concatenated multiprotein phyletic pattern and a dataset with Xanthomonas clusters of orthologous genes were constructed. Mathematical extrapolation estimates that the core genome will reach a minimum of about 1 547 genes while the pan-genome will increase up to 22 624 genes when sequencing 1 000 genomes. The HGT extent in this genus was assessed by using a Markov-based probabilistic method. The reconstructed gene gain/loss history, which contained several features consistent with biological observations, showed that nearly 60% of the Xanthomonas genes were acquired by HGT. A large fraction of variability was in the clade ancestor nodes and ＂leaves of the tree＂. Coexpression analysis suggested that the pathogenic and metabolic variation between Xanthomonas oryzae pv. oryzicola and Xanthomonas oryzae pv. oryzae might due to recently-transferred genes. Our results strongly supported that the gene gain/loss may play an important role in divergence and pathogenicity variation of Xanthomonas species.

Extracellular Micro-RNAs in Health and Disease: Basic Science, Biogenesis and Release

Small non-protein coding micro-RNAs are regularly exported out of cells, both in health and disease. More than ninety percent of extracellular miRNAs are associated with lower-molecular-mass complexes bound to Argonaute 2 (Ago2), nucleophosmin-1 (NPM1) and high density lipoproteins (HDL), whereas the rest (~10%) are membrane-vesicle-encapsulated within exosomes, shedding microvesicles and apoptotic bodies. Regardless of the debate of the nature of circulating miRNA as byproducts of routine cell activities or mediators of cell-cell communication, proper understanding of the molecular behaviors of miRNA in health and disease, is expected to open a new gate for the discovery of new diagnostic tools and possibly therapeutic implementation in the near future.

VERTICAL HEREDITY VS. HORIZONTAL GENE TRANSFER: A CHALLENGE TO BACTERIAL CLASSIFICATION

The diversity and classification of microbes has been a long-standing issue.Molecular phylogeny of the prokaryotes based on comparison of the 16S rRNA sequences of the small ribosomal subunit has led to a reasonable tree of life in the late 1970s. How-ever, the availability of more and more complete bacterial genomes has brought about complications instead of refinement of the tree. In particular, it turns out that different choice of genes may tell different history. This might be caused by possible horizontal gene transfer (HGT) among species. There is an urgent need to develop phylogenetic methods that make use of whole genome data. We describe a new approach in molecular phylogeny,namely, tree construction based on K-tuple frequency analysis of the genomic sequences.Putting aside the technicalities, we emphasize the transition from randomness to determin-ism when the string length K increases and try to comment on the challenge mentioned in the title.

Horizontal and vertical gene transfer drive sediment antibiotic resistome in an urban lagoon system

Rapid urbanization has resulted in pervasive occurrence of antibiotic resistance genes(ARGs)in urban aquatic ecosystems.However,limited information is available concerning the ARG profiles and the forces responsible for their assembly in urban landscape lagoon systems.Here,we employed high-throughput quantitative PCR(HT-q PCR)to characterize the spatial variations of ARGs in surface and core sediments of Yundang Lagoon,China.The results indicated that the average richness and absolute abundance of ARGs were 11 and 53 times higher in the lagoon sediments as compared to pristine reference Tibetan lake sediments,highlighting the role of anthropogenic activities in ARG pollution.Co-occurrence network analysis indicated that various anaerobic prokaryotic genera belonging to Alpha-,Deltaproteobacteria,Bacteroidetes,Euryarchaeota,Firmicutes and Synergistetes were the potential hosts of ARGs.The partial least squares-path modeling(PLS-PM)analysis revealed positive and negative indirect effects of physicochemical factors and heavy metals on the lagoon ARG profiles,via biotic factors,respectively.The horizontal(mediated by mobile genetic elements)and vertical(mediated by prokaryotic communities)gene transfer may directly contribute the most to drive the abundance and composition of ARGs,respectively.Furthermore,the neutral community model demonstrated that the assembly of sediment ARG communities was jointly governed by deterministic and stochastic processes.Overall,this study provides novel insights into the diversity and distribution of ARGs in the benthic habitat of urban lagoon systems and underlying mechanisms for the spread and proliferation of ARGs.

Understanding the rapid spread of antimicrobial resistance genes mediated by IS26

Insertion sequences(ISs)promote the transmission of antimicrobial resistance genes(ARGs)across bacterial populations.However,their contributions and dynamics during the transmission of resistance remain unclear.In this study,we selected is26 as a representative transposable element to decipher the relationship between ISs and ARGs and to investigate their transfer features and transmission trends.We retrieved 2656 translocatable IS26-bounded units with ARGs(tiS26-bUs-ARGs)in complete bacterial genomes from the NCBI RefSeq database.In total,124 ARGs spanning 12 classes of antibiotics were detected,and the average contribution rate of IS26 to these genes was 41.2%.We found that IS26-bounded units(IS26-bUs)mediated extensive ARG dissemination within the bacteria of the Gammaproteobacteria class,showing strong transfer po-tential between strains,species,and even phyla.The Is26-bUs expanded in bacterial populations over time,and their temporal expansion trend was significantly correlated with antibiotic usage.This wide dissemination could be due to the nonspecific target site preference of is26.Finally,we experimentally confirmed that the introduction of a single copy of is26 could lead to the formation of a composite transposon mediating the transmission of“passenger”genes.These observations extend our knowledge of the IS26 and provide new insights into the mediating role of ISs in the dissemination of antibiotic resistance.

In silico Analysis of the Potential Infection Mechanisms of Magnaporthe grisea from Horizontal Gene Transfer Hypothesis

Horizontal gene transfer （HGT） has long been considered as a principal force for an organism to gain novel genes in genome evolution. Homology search, phylogenetic analysis and nucleotide composition analysis are three major objective approaches to arguably determine the occurrence and directionality of HGT. Here, 21 genes that possess the potential to horizontal transfer were acquired from the whole genome of Magnaporthe grisea according to annotation, among which three candidate genes （corresponding protein accession numbers are EAA55123, EAA47200 and EAA52136） were selected for further analysis. According to BLAST homology results, we subsequently conducted phylogenetic analysis of the three candidate HGT genes. Moreover, nucleotide composition analysis was conducted to further validate these HGTs. In addition, the functions of the three candidate genes were searched in COG database. Consequently, we conclude that the gene encoding protein EAA55123 is transferred from Clostridium perfringens. Another HGT event is between EAA52136 and a certain metazoan＇s corresponding gene, but the direction remains uncertain. Yet, EAA47200 is not a transferred gene.

Strand-biased Gene Distribution in Bacteria Is Related to both Horizontal Gene Transfer and Strand-biased Nucleotide Composition

Although strand-biased gene distribution （SGD） was described some two decades ago, the underlying molecular mechanisms and their relationship remain elusive. Its facets include, but are not limited to, the degree of biases, the strand-preference of genes, and the influence of background nucleotide composition variations. Using a dataset composed of 364 non-redundant bacterial genomes, we sought to illus- trate our current understanding of SGD. First, when we divided the collection of bacterial genomes into non-polC and polC groups according to their possession of DnaE isoforms that correlate closely with taxonomy, the SGD of the polC group stood out more sig- nificantly than that of the non-polC group. Second, when examining horizontal gene transfer, coupled with gene functional conservation （essentiality） and expressivity （level of expression）, we realized that they all contributed to SGD. Third, we further demonstrated a weaker G-dominance on the leading strand of the non-polC group but strong purine dominance （both G and A） on the leading strand of the polC group. We propose that strand-biased nucleotide composition plays a decisive role for SGD since the polC-bearing genomes are not only AT-rich but also have pronounced purine-rich leading strands, and we believe that a special mutation spectrum that leads to a strong purine asymmetry and a strong strand-biased nucleotide composition coupled with functional selections for genes and their functions are both at work.

Phage-mediated horizontal gene transfer and its implications for the human gut microbiome

Horizontal gene transfer(HGT)in the microbiome has profound consequences for human health and disease.The spread of antibiotic resistance genes,virulence,and pathogenicity determinants predominantly occurs by way of HGT.Evidence exists of extensive horizontal transfer in the human gut microbiome.Phage transduction is a type of HGT event in which a bacteriophage transfers non-viral DNA from one bacterial host cell to another.The abundance of tailed bacteriophages in the human gut suggests that transduction could act as a significant mode of HGT in the gut microbiome.Here we review in detail the known mechanisms of phage-mediated HGT,namely specialized and generalized transduction,lateral transduction,gene-transfer agents,and molecular piracy,as well as methods used to detect phage-mediated HGT,and discuss its potential implications for the human gut microbiome.

The statistical power of k-mer based aggregative statistics for alignment-free detection of horizontal gene transfer

Alignment-based database search and sequence comparison are commonly used to detect horizontal gene transfer(HGT).However,with the rapid increase of sequencing depth,hundreds of thousands of contigs are routinely assembled from metagenomics studies,which challenges alignment-based HGT analysis by overwhelming the known reference sequences.Detecting HGT by k-mer statistics thus becomes an attractive alternative.These alignment-free statistics have been demonstrated in high performance and efficiency in wholegenome and transcriptome comparisons.To adapt k-mer statistics for HGT detection,we developed two aggregative statistics T^(S)_(sum ) and T^(*)_(sum),which subsample metagenome contigs by their representative regions,and summarize the regional D^(S) _(2) and D^(*)_(2)metrics by their upper bounds.We systematically studied the aggregative statistics’power at different k-mer size using simulations.Our analysis showed that,in general,the power of T^(S)_(sum) and T^(*)_(sum) increases with sequencing coverage,and reaches a maximum power>80%at k=6,with 5%Type-I error and the coverage ratio>0.2x.The statistical power ofT^(S)_(sum) and T^(*)_(sum) was evaluated with realistic simulations of HGT mechanism,sequencing depth,read length,and base error.We expect these statistics to be useful distance metrics for identifying HGT in metagenomic studies.

The Influence of Bt-Transgenic Maize Pollen on the Bacterial Diversity in the Midgut of Chinese Honeybees, Apis cerana cerana

Using culture-independent technique polymerase chain reaction-denaturing gradient gel electrophoresis （PCR-DGGE） and conventional culture techniques, ecological risk of transgenic maize pollen on gut bacteria of the Chinese honeybee, Apis cerana cerana, was assessed. Honeybees were fed with Bt-transgenic maize pollen, non-transgenic near isoline pollen, linear crylAh gene （800 ng mL^-1） and supercoiled plasmid DNA （800 ng mL^-1） under laboratory conditions. The DGGE profile showed that the number of DGGE bands varied from 10.7 to 14.7 per sample, and the Shannon＇s index ranged from 0.85 to 1.00. The similarity calculated by PAST was mostly above 92%, indicating no obvious changes among treatments or within replicates. 14 bacterial strains affiliated with Alphaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria were isolated and characterized on media under aerobic and anaerobic conditions. These results demonstrated that transgenic crylAh maize pollen did not induce significant changes of the honeybee gut bacterial community composition under laboratory conditions.

Herbicide promotes the conjugative transfer of multi-resistance genes by facilitating cellular contact and plasmid transfer

The global dissemination of antibiotic resistance genes(ARGs),especially via plasmid-mediated horizontal transfer,is becoming a pervasive health threat.While our previous study found that herbicides can accelerate the horizontal gene transfer(HGT)of ARGs in soil bacteria,the underlying mechanisms by which herbicides promote the HGT of ARGs across and within bacterial genera are still unclear.Here,the underlying mechanism associ-ated with herbicide-promoted HGT was analyzed by detecting intracellular reactive oxygen species(ROS)production,extracellular polymeric substance composition,cell membrane integrity and proton motive force combined with genome-wide RNA sequencing.Exposure to herbicides induced a series of the above bacterial responses to promote HGT except for the ROS response,including compact cell-to-cell contact by enhancing pilus-encoded gene expression and decreasing cell surface charge,increasing cell membrane permeability,and enhancing the proton motive force,providing additional power for DNA uptake.This study provides a mechanistic understanding of the risk of bacterial resistance spread promoted by herbicides,which elucidates a new perspective on nonantibiotic agrochemical acceleration of the HGT of ARGs.

Towards a better understanding of antimicrobial resistance dissemination:what can be learnt from studying model conjugative plasmids?

Bacteria can evolve rapidly by acquiring new traits such as virulence,metabolic properties,and most importantly,antimicrobial resistance,through horizontal gene transfer(HGT).Multidrug resistance in bacteria,especially in Gram-negative organisms,has become a global public health threat often through the spread of mobile genetic elements.Conjugation represents a major form of HGT and involves the transfer of DNA from a donor bacterium to a recipient by direct contact.Conjugative plasmids,a major vehicle for the dissemination of antimicrobial resistance,are selfish elements capable of mediating their own transmission through conjugation.To spread to and survive in a new bacterial host,conjugative plasmids have evolved mechanisms to circumvent both host defense systems and compete with co-resident plasmids.Such mechanisms have mostly been studied in model plasmids such as the F plasmid,rather than in conjugative plasmids that confer antimicrobial resistance(AMR)in important human pathogens.A better understanding of these mechanisms is crucial for predicting the flow of antimicrobial resistance-conferring conjugative plasmids among bacterial populations and guiding the rational design of strategies to halt the spread of antimicrobial resistance.Here,we review mechanisms employed by conjugative plasmids that promote their transmission and establishment in Gram-negative bacteria,by following the life cycle of conjugative plasmids.

Ecological functions of uncultured microorganisms in the cobaltrich ferromanganese crust of a seamount in the central Pacific are elucidated by fosmid sequencing

Cobalt-rich ferromanganese is an important seafloor mineral and is abundantly present in the seamount crusts. Such crusts form potential hotspots for biogeochemical activity and microbial diversity, yet our understanding of their microbial communities is lacking. In this study, a cultivation-independent approach was used to recover genomic information and derive ecological functions of the microbes in a sediment sample collected from the cobalt-rich ferromanganese crust of a seamount region in the central Pacific. A total of 78 distinct clones were obtained by fosmid library screening with a 16S rRNA based PCR method. Proteobacteria and MGI Thaumarch-aeota dominated the bacterial and archaeal 16S rRNA gene sequence results in the microbial community. Nine fosmid clones were sequenced and annotated. Numerous genes encoding proteins involved in metabolic functions and heavy metal resistance were identified, suggesting alternative metabolic pathways and stress responses that are essential for microbial survival in the cobalt-rich ferromanganese crust. In addition, genes that participate in the synthesis of organic acids and exoploymers were discovered. Reconstruction of the metabolic pathways revealed that the nitrogen cycle is an important biogeochemical process in the cobalt-rich ferromanganese crust. In addition, horizontal gene transfer （HGT） events have been observed, and most of them came from bacteria, with some occurring in archaea and plants. Clone W4-93a, belonging to MGI Thaumarch-aeota, contained a region of gene synteny. Comparative analyses suggested that a high frequency of HGT events as well as genomic divergence play important roles in the microbial adaption to the deep-sea environment.

A Minireview of Marine Algal Virus-Coccolithoviruses

Coccolithophorid is unicellular marine microalgae with a global distribution in temperate and sub-temperate oceanic regions and has the ability to produce ＇the coccoliths＇. It is considered to be the second most productive calcifying organism on earth and becoming an important factor in the global carbonate cycle. Emiliania huxleyi is one of the only two bloom-forming coccolithophores and becomes a species crucial to the study of global biogeochemical cycles and climate modeling. Coccolithoviruse is a recently discovered group of viruses infecting the marine coceolithophorid E. huxleyi. They are a major cause of coceolithophore bloom termination, and DMSP concentration is increasing in the process of viral lysis. Phylogenetic evidences support that some genes are functional both in E. huxleyi and its virus （EhV）. Horizontal gene transfer （HGT） of multiple functionally coupled enzymes occurs in E. huxleyi and its DNA virus EhV has been confirmed, which contributes to the diversification and adaptation of plankton in the oceans and also critically regulates virus-host infection by allowing viruses to control host metabolic pathways for their repli- cation. Therefore, it is of particular interest to understand this host-virus interaction. On this issue, we have made a minireview of coeeolithoviruses focusing on the basic characteristics, phylogenesis, horizontal gene transfer and the interaction between the host and its viruses, as well as its important role in global biogeochemical cycling.

Release the iron: does the infection of magnetotactic bacteria by phages play a role in making iron available in aquatic environments?

Magnetotactic bacteria(MTB)are ubiquitous prokaryotes that orient along magnetic field lines due to magnetosomes’biomineralization within the cell.These structures are ferrimagnetic organelles that impart a magnetic moment to the cell.To succeed in producing magnetosomes,MTB accumulate iron in(i)cytoplasm;(ⅱ)magnetosomes;and(ⅲ)nearby the organelle.It has already been estimated that a single MTB has an iron content of 10 to 100-fold higher than Escherichia coli.Phages are the most abundant entity in oceans and are known for controlling nutrient flow such as carbon and nitrogen by viral shunt and pump.The current work addresses the putative role of phages that infect MTB on the iron biogeochemical cycle.Can phage infection in MTB hosts cause a biogenic iron fertilization-like event in localized microenvironments?Are phages critical players in driving magnetosome biomineralization genes(BGs)horizontal transfer?Further investigation of those events,including frequency of occurrence,is necessary to fully comprehend MTB’s effect on iron cycling in aqueous environments.

A kinetic model for horizontal transfer and bacterial antibiotic resistance

This paper presents a mathematical model for bacterial growth, mutations, horizontal transfer and development of antibiotic resistance. The model is based on the so-called kinetic theory for active particles that is able to capture the main complexity features of the system. Bacterial and immune cells are viewed as active particles whose microscopic state is described by a scalar variable. Particles interact among them and the temporal evolution of the system is described by a generalized distribution function over the microscopic state. The model is derived and tested in a couple of case studies in order to confirm its ability to describe one of the most fundamental problems of modern medicine, namely bacterial resistance to antibiotics.