scholarly journals Identification of the conjugative and mobilizable plasmid fragments in the plasmidome using sequence signatures

2020 ◽  
Vol 6 (11) ◽  
Author(s):  
Zhencheng Fang ◽  
Hongwei Zhou
Keyword(s):  
Microbial Community ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Dna Sequences ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Dna Fragments ◽  
Transmissible Plasmid ◽  
The Difference ◽  
Sequence Signatures

Plasmids are the key element in horizontal gene transfer in the microbial community. Recently, a large number of experimental and computational methods have been developed to obtain the plasmidomes of microbial communities. Distinguishing transmissible plasmid sequences, which are derived from conjugative or at least mobilizable plasmids, from non-transmissible plasmid sequences in the plasmidome is essential for understanding the diversity of plasmids and how they regulate the microbial community. Unfortunately, due to the highly fragmented characteristics of DNA sequences in the plasmidome, effective identification methods are lacking. In this work, we used information entropy from information theory to assess the randomness of synonymous codon usage over 4424 plasmid genomes. The results showed that for all amino acids, the choice of a synonymous codon in conjugative and mobilizable plasmids is more random than that in non-transmissible plasmids, indicating that transmissible plasmids have different sequence signatures from non-transmissible plasmids. Inspired by this phenomenon, we further developed a novel algorithm named PlasTrans. PlasTrans takes the triplet code sequences and base sequences of plasmid DNA fragments as input and uses the convolutional neural network of the deep learning technique to further extract the more complex signatures of the plasmid sequences and identify the conjugative and mobilizable DNA fragments. Tests showed that PlasTrans could achieve an AUC of as high as 84–91%, even though the fragments only contained hundreds of base pairs. To the best of our knowledge, this is the first quantitative analysis of the difference in sequence signatures between transmissible and non-transmissible plasmids, and we developed the first tool to perform transferability annotation for DNA fragments in the plasmidome. We expect that PlasTrans will be a useful tool for researchers who analyse the properties of novel plasmids in the microbial community and horizontal gene transfer, especially the spread of resistance genes and virulence factors associated with plasmids. PlasTrans is freely available via https://github.com/zhenchengfang/PlasTrans

scholarly journals Organization of lin Genes and IS6100 among Different Strains of Hexachlorocyclohexane-Degrading Sphingomonas paucimobilis: Evidence for Horizontal Gene Transfer

2004 ◽  
Vol 186 (8) ◽  
pp. 2225-2235 ◽  
Author(s):  
Charu Dogra ◽  
Vishakha Raina ◽  
Rinku Pal ◽  
Mrutyunjay Suar ◽  
Sukanya Lal ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Dna Sequences ◽  
Dna Hybridization ◽  
Gene Organization ◽  
Mycobacterium Fortuitum ◽  
Sphingomonas Paucimobilis ◽  
Hybridization Data ◽  
Different Strains ◽  
Geographical Locations

ABSTRACT The organization of lin genes and IS6100 was studied in three strains of Sphingomonas paucimobilis (B90A, Sp+, and UT26) which degraded hexachlorocyclohexane (HCH) isomers but which had been isolated at different geographical locations. DNA-DNA hybridization data revealed that most of the lin genes in these strains were associated with IS6100, an insertion sequence classified in the IS6 family and initially found in Mycobacterium fortuitum. Eleven, six, and five copies of IS6100 were detected in B90A, Sp+, and UT26, respectively. IS6100 elements in B90A were sequenced from five, one, and one regions of the genomes of B90A, Sp+, and UT26, respectively, and were found to be identical. DNA-DNA hybridization and DNA sequencing of cosmid clones also revealed that S. paucimobilis B90A contains three and two copies of linX and linA, respectively, compared to only one copy of these genes in strains Sp+ and UT26. Although the copy number and the sequence of the remaining genes of the HCH degradative pathway (linB, linC, linD, and linE) were nearly the same in all strains, there were striking differences in the organization of the linA genes as a result of replacement of portions of DNA sequences by IS6100, which gave them a strange mosaic configuration. Spontaneous deletion of linD and linE from B90A and of linA from Sp+ occurred and was associated either with deletion of a copy of IS6100 or changes in IS6100 profiles. The evidence gathered in this study, coupled with the observation that the G+C contents of the linA genes are lower than that of the remaining DNA sequence of S. paucimobilis, strongly suggests that all these strains acquired the linA gene through horizontal gene transfer mediated by IS6100. The association of IS6100 with the rest of the lin genes further suggests that IS6100 played a role in shaping the current lin gene organization.

Underrepresentation of short palindromes in Selenomonas ruminantium DNA: evidence for horizontal gene transfer of restriction and modification systems?

2005 ◽  
Vol 51 (4) ◽  
pp. 315-318 ◽  
Author(s):  
Peter Pristas ◽  
Maria Piknova
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Dna Sequences ◽  
Human Adenovirus ◽  
Restriction Endonucleases ◽  
Rumen Bacterium ◽  
Control Analysis ◽  
Dna Evidence ◽  
Selenomonas Ruminantium ◽  
Specific Restriction

Molecular analysis of isolates of the rumen bacterium Selenomonas ruminantium revealed a high variety and frequency of site-specific (restriction) endonucleases. While all known S. ruminantium restriction and modification systems recognize hexanucleotide sequences only, consistently low counts of both 6-bp and 4-bp palindromes were found in DNA sequences of S. ruminantium. Statistical analysis indicated that there is some correlation between the degree of underrepresentation of tetranucleotide words and the number of known restriction endonucleases for a given sequence. Control analysis showed the same correlation in lambda DNA but not in human adenovirus DNA. Based on the data presented, it could be proposed that there is a much higher historical occurrence of restriction and modification systems in S. ruminantium and (or) frequent horizontal gene transfer of restriction and modification gene complexes.Key words: Selenomonas, palindromes, restriction-modification.

scholarly journals Horizontal Transfer and the Evolution of Host-Pathogen Interactions

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Elena de la Casa-Esperón
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Dna Sequences ◽  
Horizontal Transfer ◽  
Close Contact ◽  
Dna Transfer ◽  
Host Pathogen Interactions ◽  
Important Impact ◽  
Host Pathogen

Horizontal gene transfer has been long known in viruses and prokaryotes, but its importance in eukaryotes has been only acknowledged recently. Close contact between organisms, as it occurs between pathogens and their hosts, facilitates the occurrence of DNA transfer events. Once inserted in a foreign genome, DNA sequences have sometimes been coopted by pathogens to improve their survival or infectivity, or by hosts to protect themselves against the harm of pathogens. Hence, horizontal transfer constitutes a source of novel sequences that can be adopted to change the host-pathogen interactions. Therefore, horizontal transfer can have an important impact on the coevolution of pathogens and their hosts.

scholarly journals Horizontal gene transfer in an acid mine drainage microbial community

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Jiangtao Guo ◽  
Qi Wang ◽  
Xiaoqi Wang ◽  
Fumeng Wang ◽  
Jinxian Yao ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Acid Mine Drainage ◽  
Mine Drainage ◽  
Acid Mine

scholarly journals Horizontal gene transfer by natural transformation promotes both genetic and epigenetic inheritance of traits

2019 ◽  
Author(s):  
Ankur B. Dalia ◽  
Triana N. Dalia
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Dna Sequences ◽  
Natural Transformation ◽  
Temporal Dynamics ◽  
Epigenetic Inheritance ◽  
Major Mechanism ◽  
A Cell ◽  
Dna 2

AbstractNatural transformation (NT) is a major mechanism of horizontal gene transfer in microbial species that promotes the spread of antibiotic resistance determinants and virulence factors. Here, we develop a cell biological approach to characterize the spatial and temporal dynamics of homologous recombination during NT inVibrio cholerae. Our results directly demonstrate (1) that transforming DNA efficiently integrates into the genome as single-stranded DNA, (2) that the resulting heteroduplexes are resolved by chromosome replication and segregation, and (3) that integrated DNA is rapidly expressed prior to cell division. We show that the combination of these properties results in the epigenetic transfer of gene products within transformed populations, which can support the transgenerational epigenetic inheritance of antibiotic resistance in bothV. choleraeandStreptococcus pneumoniae. Thus, beyond the genetic acquisition of novel DNA sequences, NT can also promote the epigenetic inheritance of traits during this conserved mechanism of horizontal gene transfer.

Microbial communities and their interactions in biofilm systems: an overview

2004 ◽  
Vol 49 (11-12) ◽  
pp. 327-336 ◽  
Author(s):  
S. Wuertz ◽  
S. Okabe ◽  
M. Hausner
Keyword(s):  
Microbial Community ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Microbial Communities ◽  
Enrichment Culture ◽  
Community Analysis ◽  
Microbial Populations ◽  
Community Members ◽  
Biofilm Architecture

Several important advances have been made in the study of biofilm microbial populations relating to their spatial structure (or architecture), their community structure, and their dependence on physicochemical parameters. With the knowledge that hydrodynamic forces influence biofilm architecture came the realization that metabolic processes may be enhanced if certain spatial structures can be forced. An example is the extent of plasmid-mediated horizontal gene transfer in biofilms. Recent in situ work in defined model systems has shown that the biofilm architecture plays a role for genetic transfer by bacterial conjugation in determining how far the donor cells can penetrate the biofilm. Open channels and pores allow for more efficient donor transport and hence more frequent cell collisions leading to rapid spread of the genes by horizontal gene transfer. Such insight into the physical environment of biofilms can be utilized for bioenhancement of catabolic processes by introduction of mobile genetic elements into an existing microbial community. If the donor organisms themselves persist, bioaugmentation can lead to successful establishment of newly introduced species and may be a more successful strategy than biostimulation (the addition of nutrients or specific carbon sources to stimulate the authochthonous population) as shown for an enrichment culture of nitrifying bacteria added to rotating disk biofilm reactors using fluorescent in situ hybridization (FISH) and microelectrode measurements of NH4+, NO2-, NO3-, and O2. However, few studies have been carried out on full-scale systems. Bioaugmentation and bioenhancement are most successful if a constant selective pressure can be maintained favoring the promulgation of the added enrichment culture. Overall, knowledge gain about microbial community interactions in biofilms continues to be driven by the availability of methods for the rapid analysis of microbial communities and their activities. Molecular tools can be grouped into those suitable for ex situ and in situ community analysis. Non-spatial community analysis, in the sense of assessing changes in microbial populations as a function of time or environmental conditions, relies on general fingerprinting methods, like DGGE and T-RFLP, performed on nucleic acids extracted from biofilm. These approaches have been most useful when combined with gene amplification, cloning and sequencing to assemble a phylogenetic inventory of microbial species. It is expected that the use of oligonucleotide microarrays will greatly facilitate the analysis of microbial communities and their activities in biofilms. Structure-activity relationships can be explored using incorporation of 13C-labeled substrates into microbial DNA and RNA to identify metabolically active community members. Finally, based on the DNA sequences in a biofilm, FISH probes can be designed to verify the abundance and spatial location of microbial community members. This in turn allows for in situ structure/function analysis when FISH is combined with microsensors, microautoradiography, and confocal laser scanning microscopy with advanced image analysis.

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