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

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.

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

Canadian Journal of Microbiology ◽

10.1139/w05-004 ◽

2005 ◽

Vol 51 (4) ◽

pp. 315-318 ◽

Cited By ~ 1

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.

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Horizontal Transfer and the Evolution of Host-Pathogen Interactions

International Journal of Evolutionary Biology ◽

10.1155/2012/679045 ◽

2012 ◽

Vol 2012 ◽

pp. 1-9 ◽

Cited By ~ 10

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.

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

10.1101/596379 ◽

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.

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Exploring tRNA gene cluster in archaea

10.1101/370668 ◽

2018 ◽

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Gene Cluster ◽

Trna Gene ◽

Gene Clusters ◽

Gene Organization ◽

Trna Genes ◽

Genomic Analyses ◽

Living Organisms

AbstractShared traits between prokaryotes and eukaryotes are helpful in the understanding of the tree of life evolution. In bacteria and eukaryotes, it has been shown a particular organization of tRNA genes as clusters, but this trait has not been explored in archaea domain. Here, based on analyses of complete and draft archaeal genomes, we demonstrated the prevalence of tRNA gene clusters in archaea. tRNA gene cluster was identified at least in three Archaea class, Halobacteria, Methanobacteria and Methanomicrobia from Euryarchaeota supergroup. Genomic analyses also revealed evidence of tRNA gene cluster associated with mobile genetic elements and horizontal gene transfer inter/intra-domain. The presence of tRNA gene clusters in the three domain of life suggests a role of this type of tRNA gene organization in the biology of the living organisms.

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Recombinant DNA Plasmid Transmission to Indigenous Organisms during Waste Treatment

Water Science & Technology ◽

10.2166/wst.1988.0282 ◽

1988 ◽

Vol 20 (11-12) ◽

pp. 179-184 ◽

Cited By ~ 5

Author(s):

M. A. Gealt

Keyword(s):

Gene Transfer ◽

Dna Sequences ◽

Dna Hybridization ◽

Waste Treatment ◽

Recombinant Dna ◽

Genetically Engineered ◽

Environmental Damage ◽

Bacterial Conjugation ◽

Genetically Engineered Microorganisms ◽

Dna Plasmid

The release of genetically engineered microorganisms into the environment will occur because of its importance to industrial and agricultural progress. Since organisms designed for release can be modified to survive only the time necessary for their function, the greatest potential for environmental damage depends upon the capability for mobilization of the genetically engineered DNA sequences (GEDS). Mobilization of GEDS to indigenous wastewater organisms by the process of bacterial conjugation has been demonstrated. This gene transfer, which will occur in a laboratory-scale waste treatment facility (~20 L capacity), depends on the presence of bacteria containing conjugative plasmids, many of which are indigenous to waste water. Sensitive detection of GEDS transfer requires the use of DNA-DNA hybridization. Environmental conditions do affect the frequency of conjugal gene transfer.

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

Microbial Genomics ◽

10.1099/mgen.0.000459 ◽

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

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