The list also included phage integrase PF, PF, and PF and recombinase PF proteins also indicating the existence of phage-mediated genetic exchange i.
DNA recombination, transposition, and integration and terms involved in metabolic and biosynthetic processes Table 4 , Supplementary Table S9 for complete list. Earlier we suggested that one-to-one gene transfers were more likely to have occurred relatively recently in evolution. These transfers could yield insights into the nature of modern-day genetic exchange mediated by microorganisms associated with the human body.
Notably, the list included several proteins of unknown functions indicating either poor annotation of HMP-genomes or an abundance of novel protein families for which little is currently known , and viral proteins and transposases, in addition to proteins involved in transcription regulation Supplementary Table S For this protein, 5 out of 6 detected HGTs were one-to-one.
The enriched GO terms included several biological processes related to biosynthesis and metabolism, transport, and regulation, consistent with the modern understanding of human microbiota roles in metabolism and food digestion 44 Supplementary Table S We also identified genes tentatively termed HGT-free genes filtered from a total of 26, genes using a criterion of presence in at least 10 genomes since they produced no detectable conflict evidence of HGT during reconciliation with corresponding 16S rRNA species trees.
Supplementary Table S The list included the DNA methylase protein 69 genomes in 5 genera that plays important roles in cellular defense against exogenous DNA, cell replication, sequence mismatch correction, and gene expression regulation This result is consistent with a previous study revealing that phylogenetic trees built from concatenation of 14 core sets of flagellar genes were highly consistent with corresponding species trees Therefore, one utility of HGT-free genes could be in the reconstruction of phylogenetic trees describing the history of prokaryotic life since identification of vertically inherited marker genes is vital to producing error-free phylogenies.
The 6-way Venn diagram illustrates the number of widespread genes that were either unique to each body site or were shared by them Fig. There were no widespread genes unique to either oral cavity or the UG tract likely because both body sites are highly diverse in their composition of genera and species Fig. For example, the microbial genomes in the oral cavity belong to 64 different genera the second largest after the gut microbial community, Table 2.
Similarly, the microbial genomes in the UG tract belong to a total of 41 distinct genera, the next largest among body sites Table 2 , Fig. Therefore, the oral cavity and the UG tract appeared highly heterogeneous in the composition of human microbiota genera. In turn, only 6 and 8 genes were uniquely widespread in the airways and the GI tract, respectively Fig. The gut microbiota is the largest genomes and the most diverse 99 genera and species ecosystem in the human body Table 2 , Fig.
Thus, it is unsurprising that very few genes were uniquely widespread among members of the gut microbial community consistent with its diverse metabolic and physiological roles in the human body Surprisingly, however, blood and skin microbiota encoded and widespread genes, despite harboring only 45 and genomes, respectively Fig.
Indeed, the two body sites were also relatively less diverse 8 and 16 distinct genera, Table 2 , Fig. A mapping of core genes to detailed COG categories confirmed that Widespread and core genes in human microbiota. A Venn diagram highlights the distribution of widespread genes in each body site. B Bar plots illustrate the proportion of COG functional categories mapped to total widespread genes in each body site.
C Pie chart indicate the enrichment of COG functional categories in core genes that by definition were widespread in all six body sites. HGT-index is the number of HGT events detected on a gene tree divided by the total number of taxa in that gene tree. One utility of core genes can be in large-scale phylogenies where universal genes are often concatenated in attempts to resolve the history of life.
These concatenations often involve ribosomal proteins 48 , 49 and are now generally preferred over single-gene phylogenetic analyses due to increased resolution despite concerns that concatenated proteins may have independent evolutionary histories 50 , 51 , 52 , Therefore, an HGT analysis of core genes questions the reliability of utilizing ribosomal proteins in concatenated phylogenetic analyses aimed towards uncovering the origin of life, a central question in evolutionary biology research, and demand caution and detailed evaluation 53 , These genes could become reliable candidates for concatenation and reconstruction of more reliable phylogenies that are less sensitive to non-vertical evolution and could provide more resolution than the 16S rRNA tree read below.
We performed an in-depth analysis of HGT activity and sensitivity in the genomes of human-associated microorganisms. We utilized an explicit evolutionary method of HGT detection based on phylogenetic tree reconstructions and reconciliations to detect HGT Tree conflicts arising due to HGT evaluated under a parsimony framework 20 were analyzed against a control dataset of prokaryotic genomes sequenced from diverse environments including human microbiota Overall, we observed significantly higher HGT activity occurring in the human-associated microorganisms relative to the control group both in terms of the number of HGT genes and the number of HGT events per gene, which is confirmatory of previous findings 2.
Observed gene transfers were classified into intra- and inter-niche gene transfers occurring among microorganisms sharing the same body site and dispersed across body sites, respectively.
In general, microorganisms sharing the same niche are united by ecology, spatial proximity, and also phylogenetic similarity since closely-related microorganisms are expected to colonize and adapt to similar habitats. All of these factors can increase HGT activity among microorganisms sharing the same niche.
In turn, inter-niche gene transfers that occur among microorganisms occupying distant and different body sites pose questions regarding their mechanics and timings. We present two explanations for the quantitatively greater number of inter-niche HGTs.
First, such transfers could predate human colonization of microbial organisms. If true, such transfers should be more widespread in nature since they had more time to accumulate among genomes and involve distantly related and many prokaryotic species. Indeed, HGT-ratios of many-to-many and one-to-many gene transfers were highest for phylogenetically diverse microorganisms occupying diverse habitats Figs.
In turn, HGT-ratios for one-to-one transfers were highest for phylogenetically similar microorganisms occupying similar or different habitats Fig. Median protein sequence identity for one-to-many and many-to-many events was also lower compared to one-to-one events Fig. A second intriguing possibility could be the direct movement of bacterial DNA or bacteria from the gut to other body sites via the bloodstream to transform bacterial cells residing in other body sites.
However, the mechanisms responsible for such transfers are presently poorly understood and demand further exploration. We are confident that inter-niche HGTs are not heavily biased by species or strain multi-residence across human body sites.
None of the analyzed genomes were duplicated across body sites at strain level and very few species 6. Notably, the multi-residence ANI matches corresponded to important bacteria that are known to transcend from their primary body site gut and oral cavity and reach other body sites e. UG tract perhaps via the bloodstream Fig. It can also be argued that some hitherto not-sequenced genomes from bacterial species may be discovered later from multiple body sites and bias our inter-niche HGT estimates.
However, this issue applies to all genomic datasets publicly available from NCBI and other common platforms since spatial coverage for the majority of microorganisms on Earth effectively remains unknown.
Continuous sequencing efforts will no doubt help bridge the gap but this limitation is often beyond the control of bioinformaticians and data scientists who rest their conclusions on presently available data. We used the HGT-index as proxy to describe the tendency of genomes and individual genes to participate in HGT see refs. The meaning of the HGT-index in genomes is straightforward - it is the fraction of total genes that participate in HGT.
The HGT-index for genomes can thus be influenced by the inclusion of low-quality or poorly-annotated genomes for which many ORFan genes will miss inclusion in the putatively orthologous gene sets.
In turn, the HGT-index for genes reports the number of detected HGT events on that gene tree divided by the total number of genome taxa members of that gene tree.
Gene trees could be highly heterogeneous in taxa composition as some genes could have broad distribution across many genera and phyla while others would be narrowly distributed. Even in the highly heterogeneous gene trees, HGT events could still be restricted to only a particular small group of microorganisms. Accounting for these factors in HGT-index calculations is a work in progress In the present study we normalized HGT events by total taxa since the true potential of HGT participation of any gene should take into account both genomes that do and do not exchange that gene horizontally see Discussion in ref.
These limitations of the HGT-index should be considered when evaluating our results. Both datasets were generated in a similar manner except for two notable differences. The two orthology detection software however identified proportionally the same number of orthologous gene sets e. However, large gene sets only constituted 0. Just like the HMP dataset, the HGTree dataset also likely includes genomes occupying multiple residences, which are not completely known.
This is a knowledge gap that needs to be filled. Thus, the potential role of microbiota-mediated HGT in human disease is not depicted by our study. These tasks can however be easily accomplished using the online HGTree webserver 16 that provides user-friendly tools for large-scale HGT evaluation of user-provided genomic datasets.
Recall that studied HMP reference genomes were sequenced from different individuals. Therefore, our analysis can miss the very recent HGT events that have occurred during the life course of each individual.
A recent study has expanded the HMP dataset and attempted to provide a baseline microbiome composition across individuals over multiple time points Such efforts will ensure that we have, in the future, sufficient reference genome data from different body sites in the same individuals.
First, it can fail to detect HGT occurring between closely-related strains belonging to the same species as they do not produce species tree conflict note that we excluded gene sets harboring genomes belonging to only one species from the analysis, see Methods. In such cases, composition-based HGT detection methods see Liu et al. However, composition-based methods tend to give contrasting results when the methods are changed see ref.
Hence, there is a definite need to couple multiple approaches of HGT detection for improved global precision in HGT estimation. Second, an important aspect is the reconciliation of gene and species trees. Multiple reconciliations may exist that may be optimal i. Therefore, it is important to traverse through the entire solution search space and to produce quantitative indicators similar to bootstrap support for trees to support selected reconciliations 58 , a task that is computationally intensive.
Bansal et al. Similarly, HGT detection via tree reconciliation can differ according to the different event costs, choice of alternatively rooted gene trees among equally optimal rootings, the existence of multifurcated non-binary branches, and inability to handle species tree with poorly supported nodes.
These limitations that imply incompleteness of the DTL model 20 cannot be overcome since searching for the entire solution space is computationally unfeasible, especially considering the size of our datasets. Third, an important dilemma is whether to build phylogenetic trees using single-gene this study or concatenated genes e.
The latter has become popular because it provides more resolution than single-genes. However, concatenated gene sets pose additional problems because member genes could have independent evolutionary histories 60 , 61 as also demonstrated by the high HGT-indices of ribosomal proteins in Supplementary Table S13 that are popular markers in gene concatenation , in addition to gaps introduced by heterogeneous protein domain make-up among distantly-related taxa Since we rooted prokaryotic trees using the eukaryotic outgroup sequence i.
In practice, the number of universal single-copy genes truly conserved across Bacteria and Eukarya declines sharply with the increase and diversity in genomes being studied Nevertheless, when there is a consistent signal of HGT between donor and recipient species, it will no doubt prove more useful to concatenate those genes into a single alignment to improve resolution. It will therefore be important to identify single-copy genes conserved across a wide range of organisms that are mostly inherited vertically to hopefully improve species tree resolution.
We would like to carefully study this possibility in the future and highlight here that the 16S rRNA tree does not fully resolve the bacterial tree of life but it is the best method given the challenges mentioned above.
In sum, we expect that the phylogeny-based HGT detection method presented in this study will facilitate large-scale simultaneous analysis of meta -genomes routinely produced by sequencing platforms and will aid in our understanding of the many complex interactions of humans with the microbial inhabitants of the planet.
The method may especially be superior for detection of ancient HGT events but poses several technical and conceptual challenges that we have also attempted to address or highlight in this study. The open challenges are to adapt the phylogeny-based HGT detection pipeline to also integrate viral and eukaryotic genomes since viruses are now recognized as major players in gene transfer and innovation 63 , 64 , 65 and eukaryotes are also subjected to gene transfer see refs.
Both genomic datasets however pose unique challenges since viral genes are highly variable and lack a conserved marker like the 16S rRNA gene to produce reliable phylogenies. In this regard, utilizing structure-based approaches may be more fruitful 68 , In turn, eukaryotic genomes are several times larger than prokaryotic genomes and include many non-coding regions that can also be inherited horizontally.
We hope to incorporate these solutions into a future release. These genomes corresponded to the following human body sites: airways no. Heart, liver, and lymph node were subsequently removed from the analysis, as they did not meet the four-taxa minimum requirement needed to reconstruct a phylogenetic tree.
Organisms with unknown body affiliations were also excluded. This reduced the dataset to a total of 1, non-redundant prokaryotic genomes including 1, bacteria and 2 archaea both in the GI tract corresponding to six major body sites airways, blood, GI tract, oral, skin, and UG tract and comprising of 7 bacterial Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria, Spirochaetes, and Synergistetes and 1 archaeal phyla Euryarchaeota , genera and distinct species Supplementary Table S2 and Fig.
The possibility that any HMP-genome resides in two or more human body sites was examined at both strain and species levels. For this, we utilized average nucleotide identity ANI that is the standard measure to demark microorganisms using genomic sequences Since we were interested in the multi-residence of a genome, genome pairs derived from the same body sites were excluded in this analysis and pairs of genomes that belonged to different genera were also not compared since they cannot be grouped together into species.
Exceptionally, self-to-self comparisons of each of the 1, HMP-genomes was conducted as a positive control to check the reliability of the ANI value calculation. After calculating the ANI values of all possible genome pairs, thresholds In addition, the possibility that some of the 1, HMP-genomes were derived from non-human sources was also evaluated due to possibility of contamination arising during DNA extraction and sequencing library preparation.
Salter et al. Thus, scientific names of HMP-genomes were compared with contaminant genera names to identify suspected contaminants. The HGT detection strategy largely followed the methods described in ref. Orthologous genes for each species were mapped to corresponding 16S rRNA genes.
Gene sets where all pair-wise neighbor-joining NJ distances were close to zero were filtered to improve resolution during downstream steps of tree reconciliation. FastTree ver. Specifically, the program embeds each gene tree onto its corresponding species tree by mapping each node of the gene tree onto a unique node of the species tree and assigning one of the four possible evolutionary events i. Total cost of embedding reconciliation is calculated in terms of assigned values of DTL parameters.
Multiple embeddings are possible for each gene tree inside the species tree and the embedding where total cost is the minimum is considered the most optimal reconciliation Multiple optimal solutions may exist, however, event assignments tend to generally remain conserved for the most part For nodes representing transfers, the program also identifies the edge on the species tree that constitutes the edges of the gene tree node to label the recipient species of transfers Because gene trees were unrooted and species trees were rooted, reconciliation was done by considering all possible rootings for gene trees followed by random selection of a root amongst rootings that yielded the most parsimonious reconciliation.
For each gene and corresponding species tree, local support values based on SH test 74 were calculated along with direction of gene transfer i. HGT-participating genes hereafter HGT-genes were assigned to microbial genomes residing in six body sites. PfamScan ver. To test the reliability of this approach, we scanned all proteins in randomly selected gene sets against the Pfam library. We discovered that our approach i. GO enrichment using hypergeometric test was conducted using an open-source R package of the domain-centric gene ontology dcGO resource ver.
An HGT-index was defined for each genome and every gene set. For genomes, the index represents the total number of genes that participate in HGT divided by the total number of genes in that genome For genes, the index represents the total number of HGT events detected in that gene tree when reconciled with the corresponding reference species tree divided by the total number of genomes taxa member of that gene tree Both indices are given on a scale from 0 to 1 with higher values representing higher tendencies to participate in HGT.
Widespread genes present in all six body sites were termed core genes. Sequence similarity between genomes derived from different body sites was calculated using the ANI method 24 as mentioned above. Users can reuse data for academic use with an acknowledgement and citation to the present study. Soucy, S. Horizontal gene transfer: building the web of life. Smillie, C. Ecology drives a global network of gene exchange connecting the human microbiome.
Nature , — Liu, L. The human microbiome: a hot spot of microbial horizontal gene transfer. Genomics , —70 Huddleston, J. Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes. Drug Resist. Madsen, J. The interconnection between biofilm formation and horizontal gene transfer. FEMS Immunol. Mazodier, P. Philippe, H. Horizontal gene transfer and phylogenetics.
Ravenhall, M. Inferring horizontal gene transfer. Plos Comput. Daubin, V. The source of laterally transferred genes in bacterial genomes. Genome Biol. Apoptotic bodies: particular extracellular vesicles involved in intercellular communication. Biology 9:E Bergsmedh, A. Horizontal transfer of oncogenes by uptake of apoptotic bodies. Berridge, M. Bliven, K. Evolution of bacterial pathogens within the human host. Boothby, T. Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade.
Borgeaud, S. The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer. Science , 63— Boschetti, C. Biochemical diversification through foreign gene expression in bdelloid rotifers. PLoS Genet. Bragg, D. Briggs, E. Long interspersed nuclear element-1 expression and retrotransposition in prostate cancer cells. Brimacombe, C. Homologues of genetic transformation DNA import genes are required for Rhodobacter capsulatus gene transfer agent recipient capability regulated by the response regulator CtrA.
Bronkhorst, A. The emerging role of cell-free DNA as a molecular marker for cancer management. Brown, B. Genomic erosion and extensive horizontal gene transfer in gut-associated Acetobacteraceae.
BMC Genomics Cai, J. Extracellular vesicle-mediated transfer of donor genomic DNA to recipient cells is a novel mechanism for genetic influence between cells. Cell Biol. PLoS One 9:e Cajuso, T. Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival. Campos, M. Simulating multilevel dynamics of antimicrobial resistance in a membrane computing model.
Caruso, S. Apoptotic cell-derived extracellular vesicles: more than just debris. Castellano-Castillo, D. Altered adipose tissue DNA methylation status in metabolic syndrome: relationships between global DNA methylation and specific methylation at adipogenic, lipid metabolism and inflammatory candidate genes and metabolic variables.
Chang, J. Mitochondrial transplantation regulates antitumour activity, chemoresistance and mitochondrial dynamics in breast cancer. Chen, J. Fibros 7, 37— Chen, S.
Recurrent horizontal transfer of arsenite methyltransferase genes facilitated adaptation of life to arsenic. Chung, N. Transcriptome analyses of tumor-adjacent somatic tissues reveal genes co-expressed with transposable elements. Chuong, E. Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Cooper, R. Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance. Cordaux, R.
Estimating the retrotransposition rate of human Alu elements. Gene , — Costello, K. Chromatin modifications in metabolic disease: potential mediators of long-term disease risk. Wiley interdisciplinary reviews. Crisp, A. Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes. Genome Biol. Crofts, T. Next-generation approaches to understand and combat the antibiotic resistome.
Croucher, N. Horizontal DNA transfer mechanisms of bacteria as weapons of intragenomic conflict. PLoS Biol. Cusimano, N. Reevaluation of the cox1 group I intron in Araceae and angiosperms indicates a history dominated by loss rather than horizontal transfer. Dauros Singorenko, P. Isolation of membrane vesicles from prokaryotes: a technical and biological comparison reveals heterogeneity.
Vesicles M-Trap: exosome-based capture of tumor cells as a new technology in peritoneal metastasis. Cancer Inst. Apoptotic conversion: evidence for exchange of genetic information between prostate cancer cells mediated by apoptosis. PubMed Abstract Google Scholar. Regulation of transposable elements by DNA modifications. Dianat-Moghadam, H. Cancer stem cells-emanated therapy resistance: implications for liposomal drug delivery systems. Control Release , 62— Domingues, S.
Membrane vesicles and horizontal gene transfer in prokaryotes. Dong, L. Horizontal transfer of whole mitochondria restores tumorigenic potential in mitochondrial DNA-deficient cancer cells. Dong, Q. Cancer cells arise from bacteria. Cancer Cell Int. Dubey, G. Intercellular nanotubes mediate bacterial communication. Cell , — El Baidouri, M. Widespread and frequent horizontal transfers of transposable elements in plants.
Genome Res. The evolutionary dynamics of integrons in changing environments. ISME J. Ewing, A. High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Eyres, I. Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats. BMC Biol. Ficht, T. Bacterial exchange via nanotubes: lessons learned from the history of molecular biology.
Fischer, F. Characterization in Helicobacter pylori of a nickel transporter essential for colonization that was acquired during evolution by gastric Helicobacter species. PLoS Pathog. Fischer, S. Indication of horizontal DNA gene transfer by extracellular vesicles. PLoS One e Flot, J. Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga.
Nature , — Frezza, C. Mitochondria in cancer: not just innocent bystanders. Cancer Biol. Fronzes, R. The structural biology of type IV secretion systems. Gao, L. Tumor-derived exosomes antagonize innate antiviral immunity. Cell-free nucleic acids circulating in the plasma of colorectal cancer patients induce the oncogenic transformation of susceptible cultured cells.
Garcia-Solache, M. The enterococcus: a model of adaptability to its environment. Horizontal gene transfer in bacterial and archaeal complete genomes. Gillings, M. Integrons: past, present, and future. Goldberg, Y. Gomari, H. Targeted cancer therapy using engineered exosome as a natural drug delivery vehicle. Onco Targets Ther. Griessinger, E. Mitochondrial transfer in the leukemia microenvironment.
Trends Cancer 3, — Guo, Y. Effects of exosomes on pre-metastatic niche formation in tumors. Cancer Hall, J. Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria.
B Biol. Hancks, D. Roles for retrotransposon insertions in human disease. Active human retrotransposons: variation and disease. Hashimoto, T. Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein.
Holmgren, L. Horizontal transfer of DNA by the uptake of apoptotic bodies. Blood 93, — Hong, J. Analysis of the Escherichia coli extracellular vesicle proteome identifies markers of purity and culture conditions. Hoshino, A. Tumour exosome integrins determine organotropic metastasis.
Husnik, F. Repeated replacement of an intrabacterial symbiont in the tripartite nested mealybug symbiosis. Functional horizontal gene transfer from bacteria to eukaryotes.
Horizontal gene transfer from diverse bacteria to an insect genome enables a tripartite nested mealybug symbiosis. Ivancevic, A. Horizontal transfer of BovB and L1 retrotransposons in eukaryotes.
Jachowicz, J. LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo. Jacques, P. The majority of primate-specific regulatory sequences are derived from transposable elements. Jahr, S. DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells. Jang, H. Transposable elements drive widespread expression of oncogenes in human cancers. Jiang, L.
Determining the contents and cell origins of apoptotic bodies by flow cytometry. Jose, C. Acta , — Karnkowska, A. A eukaryote without a mitochondrial organelle. Kawamura, Y. Extracellular vesicles mediate the horizontal transfer of an active LINE-1 retrotransposon. Kazazian, H. Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man.
Keeling, P. Horizontal gene transfer in eukaryotic evolution. Kirkup, B. Horizontal gene transfer: learning from losers. Klieve, A. Naturally occurring DNA transfer system associated with membrane vesicles in cellulolytic Ruminococcus spp. Evolution of antibiotic resistance without antibiotic exposure. Agents Chemother. Kumar, P. Molecular insights into antimicrobial resistance traits of multidrug resistant enteric pathogens isolated from India.
Kunarso, G. Transposable elements have rewired the core regulatory network of human embryonic stem cells. Kuroda, M. Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet , — Lacroix, B. Transfer of DNA from bacteria to eukaryotes. Lang, A. Gene transfer agents: phage-like elements of genetic exchange. Leclerc, Q. Mathematical modelling to study the horizontal transfer of antimicrobial resistance genes in bacteria: current state of the field and recommendations.
Interface Lepuschitz, S. Limoni, S. Liu, Y. Focused ultrasound-augmented targeting delivery of nanosonosensitizers from homogenous exosomes for enhanced sonodynamic cancer therapy. Theranostics 9, — Gram-positive bacterial extracellular vesicles and their impact on health and disease. Lu, X. Ma, Q. Mature osteoclast-derived apoptotic bodies promote osteogenic differentiation via RANKL-mediated reverse signaling.
The genome directs the bacterium's metabolic machinery to manufacture bacteriophage components and enzymes. Bacteriophage-coded enzymes will also breakup the bacterial chromosome. Step 3: Occasionally, a bacteriophage capsid mistakenly assembles around either a fragment of the donor bacterium's chromosome or around a plasmid instead of around a phage genome.
Step 4 : The bacteriophages are released as the bacterium is lysed. Note that one bacteriophage is carrying a fragment of the donor bacterium's DNA rather than a bacteriophage genome.
Step 5: The bacteriophage carrying the donor bacterium's DNA adsorbs to a recipient bacterium. Step 6: The bacteriophage inserts the donor bacterium's DNA it is carrying into the recipient bacterium. Step 1: A temperate bacteriophage adsorbs to a susceptible bacterium and injects its genome. Step 2: The bacteriophage inserts its genome into the bacterium's chromosome to become a prophage.
Step 3: Occasionally during spontaneous induction, the DNA is excised incorrectly and a small piece of the donor bacterium's DNA is picked up as part of the bacteriophage's genome in place of some of the bacteriophage DNA that remains in the bacterium's chromosome.
Step 4: As the bacteriophage replicates, the segment of bacterial DNA replicates as part of the bacteriophage's genome. Every bacteriophage now carries that segment of bacterial DNA. Step 5: The bacteriophage adsorbs to a recipient bacterium and injects its genome.
Step 6: The bacteriophage genome carrying the donor bacterial DNA inserts into the recipient bacterium's chromosome. Conjugation Genetic recombination in which there is a transfer of DNA from a living donor bacterium to a living recipient bacterium by cell-to-cell contact. Mobilizable plasmids, that lack the tra genes for self-transmissibility but possess the oriT sequences for initiation of DNA transfer, may also be transferred by conjugation if the bacterium containing them also possesses a conjugative plasmid.
The tra genes of the conjugative plasmid enable a mating pair to form while the oriT quences of the mobilizable plasmid enables the DNA to move through the conjugative bridge.
General mechanism of transfer of conjugative plasmids by conjugation in Gram-negative bacteria In Gram-negative bacteria, the first step in conjugation involves a conjugation pilus sex pilus or F pilus on the donor bacterium binding to a recipient bacterium lacking a conjugation pilus.
Step 1: In Gram-negative bacteria, the first step in conjugation involves a conjugation pilus sex pilus or F pilus on the donor bacterium binding to a recipient bacterium lacking a conjugation pilus. Step 2: Typically the conjugation pilus retracts or depolymerizes pulling the two bacteria together.
Step 3: Using the rolling circle model of DNA replication, a nuclease breaks one strand of the plasmid DNA at the origin of transfer site oriT of the plasmid. The nuclease also has helicase activity and unwinds the strand that is going to be transferred. Step 4: The nicked plasmid strand enters the recipient bacterium. Step 5: Both the donor and the recipient plasmid strands then make a complementary copy of themselves.
Step 6: Both bacteria now possess the conjugative plasmid and can make a conjugation pilus. Exercise: Think-Pair-Share Questions A strain of living Streptococcus pneumoniae that cannot make a capsule is injected into mice and has no adverse effect.
This strain is then mixed with a culture of heat-killed Streptococcus pneumoniae that when alive was able to make a capsule and kill mice. After a period of time, this mixture is injected into mice and kills them. In terms of horizontal gene transfer, describe what might account for this.
A gram-negative bacterium that was susceptible to most common antibiotics suddenly becomes resistant to several of them. It also appears to be spreading this resistance to others of its kind. Describe the mechanism that most likely accounts for this. Summary Mutation is a modification of gene function within a bacterium and while it enables bacteria to adapt to new environments, it occurs relatively slowly. Horizontal gene transfer enables bacteria to respond and adapt to their environment much more rapidly by acquiring large DNA sequences from another bacterium in a single transfer.
Horizontal gene transfer is a process in which an organism transfers genetic material to another organism that is not its offspring. Mechanisms of bacterial horizontal gene transfer include transformation, transduction, and conjugation.
During transformation, a DNA fragment from a dead, degraded bacterium enters a competent recipient bacterium and is exchanged for a piece of DNA of the recipient. Transduction involves the transfer of either a chromosomal DNA fragment or a plasmid from one bacterium to another by a bacteriophage. Conjugation is a transfer of DNA from a living donor bacterium to a living recipient bacterium by cell-to-cell contact.
In Gram-negative bacteria it involves a conjugation pilus. A conjugative plasmid is self-transmissible, that is, it possesses conjugation genes known as tra genes enable the bacterium to form a mating pair with another organism, and oriT origin of transfer sequences that determine where on the plasmid DNA transfer is initiated.
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