Gene Transfer - DNA in the Soil
Kaare M. Nielsen, Ph.D., Hartl Lab., Dept. of Evolutionary and Organismic Biology, Harvard University, 16 Divinity Ave., Cambridge, MA 02138
I would like to post the following response to the Dr. Innes question: Horizontal gene transfer happens all the time?
--Recently (May 14) Dr. Innes raises the question; I am confused in that if this (horizontal gene transfer, my addition) happens all the time anyway, what is so unnatural about transgenics? The argument appears inconsistent.
I have not seen the Greenpeace website referred to, so I address the above question only. having followed the field of horizontal gene transfer (HGT) for the last 10 years, I have noticed a remarkable shift has occurred in the argument for why HGT is of no concern for transgenes. Earlier, it was argued from data (or lack thereof) that HGT occurs so rarely, if at all, that it would be insignificant for the spread of transgenes. Today, it is argued (from accumulating data) that HGT occurs all the time so why worry about possible HGT of transgenes?
Whereas the previous argument had some scientific basis, the latter is questionable. The process of horizontal gene transfer (like mutations) can occur frequently without leaving traces in a given bacterial population. This is because purifying selection will remove those individuals (either carrying mutations or horizontally acquired genes) from the populations since the genetic changes introduced do not provide a benefit to the carrier. Such (trans) genes will not reach fixation in the bacterial population. Secondly, horizontally acquired (native) genes from distantly related species are less likely to be retained and function in the recipient bacterium due to differences between the donor organism and the recipient i= n nucleotide sequence, gene expression, codon usage, and possibly posttranslational modification and protein interactions.
Thus, assuming transgenes are equal to any other naturally occurring gene, it is reasonably to assume that transgenes will behave no differently than genes that are transferred from native donors.
However, transgenes do often differ in several ways from native genes. This poses problems.
- Transgenes often contain DNA sequence homology to prokaryotes thereby increasing their likelihood of integration in bacteria significantly. Many studies have shown that DNA homology is the main barrier to HGT of chromosomal DNA (such as transgenes) in bacteria.
- Transgenes are often modified to allow broad expression in a variety of hosts; they often lack introns, contain promoters active across a broad range of hosts (e.g. viral or bacterial of origin), and seldom require extensive interactions with other proteins in the host cytoplasm for functionality. Thus, transgenes may have an increased likelihood of expression if horizontally transferred.
- The transgenes may represent novel genetic variability due to the use of synthetic genes with new protein domains or encoding novel biochemical pathways that have not been subject to natural selection in their new host environment. Therefore, they may or may not provide a selective advantage i= n the new host. Most likely they will not, but this cannot be assumed in all instances. Mechanisms providing genetic variability in bacteria do not combine DNA sequences from several organisms into a compact functional unit within the time scale done by genetic engineering. Thus, the argument that this is naturally occurring, cannot be used when th= e genetic novelty the transgenes extends beyond simple modifications.
Thus, when compared to any native gene of a divergent organism, transgenes may differ both with respect to their likelihood of HGT, expression in the new host, and selection. The current debate on the likelihood of HGT has been much focused on the likelihood of transfer, whereas, as argued above, transfer does not generate an environmental impact. Selection would, if positive.
I enclose some relevant references which also refers to an earlier request in the Agbioview list on fate of DNA in soil.
- J. Maynard Smith et al., Population structure and evolutionary dynamics of pathogenic bacteria, Bioessays 22 (2000) 1115-1122.
- J. P. Claverys et al., Adaptation to the environment: Streptococcus pneumoniae, a paradigm for recombination-mediated genetic plasticity, Molecular Microbiology 35 (2000) 251-259.
- H. Ochman et al., Lateral gene transfer and the nature of bacterial innovation, Nature 405 (2000) 299-304.
- K. M. Nielsen et al., Horizontal gene transfer from transgenic plants t o terrestrial bacteria - a rare event? FEMS Microbiology Reviews 22 (1998) 79-103.
- G-H. Lee and G. Stotzky, Transformation and survival of donor, recipient, transformants of Bacillus subtilis in vitro and in soil, Soil Biology & Biochemistry 31 (1999) 1499-1508.
- K. M. Nielsen et al., Natural transformation of Acinetobacter sp. strai n BD413 with cell lysates of Acinetobacter sp., Pseudomonas fluorescens and Burkholderia cepacia in soil microcosms, Applied and Environmental Microbiology 66 (2000) 206-212.
- M. DrF6ge et al., Horizontal gene transfer among bacteria in terrestrial and aquatic habitats as assessed by microcosms and field studies, Biology and Fertility of Soils 29 (1999) 221-245.
- J. Davison, Genetic exchange between bacteria in the environment, Plasmid 42 (1999) 73-91.
- F. Widmer et al., Sensitive detection of transgenic plant marker gene persistence in soil microcosms, Molecular Ecology 5 (1996) 603-13.
- F. Widmer et al., Quantification of transgenic marker gene persistence in the field, Molecular Ecology 6 (1997) 1-7.
- E. Paget et al., The fate of recombinant plant DNA in soil, European Journal of Soil Biology 34 (1998) 81-88.
- F. Gebhard and K. Smalla, Monitoring field releases of genetically modified sugar beets for persistence of transgenic plant DNA and Horizontal gene transfer, FEMS Microbiology Ecology 28 (1999) 261-272.
- G. Ro manowski et al., Use of polymerase chain reaction and electroporation of Escherichia coli to monitor the persistence of extracellular plasmid DNA introduced into natural soils, Applied and Environmental Microbiology 59 (1993) 3438-3446.
- G. Recorbet et al., Kinetics of persistence of chromosomal DNA from genetically engineered Escherichia coli introduced to soil, Applied and Environmental Microbiology 59 (1993) 4289-4294.
- K. M. Nielsen et al., Natural transformation and availability of transforming DNA to Acinetobacter calcoaceticus in soil microcosms, Applied and Environmental Microbiology 63 (1997) 1945-1952.
- K. M. Nielsen et al., Induced natural transformation of Acinetobacter calcoaceticus in soil microcosms. Applied and Environmental Microbiology 63 (1997) 3972-3977.
- K. M. Nielsen et al., Transformation of Acinetobacter sp. BD413(pFG490nptII) with transgenic plant DNA in soil microcosms and effects of kanamycin on selection of transformants, Applied and Environmental Microbiology 66, (2000) 1237-42.
- S. A. E. Blum et al., Mechanisms of retarded DNA degradation and prokaryotic origin of DNases in non-sterile soil, Systematic and Applied Microbiology 20 (1997) 513-521.
- G. Romanowski et al., Adsorption of plasmid DNA to mineral surfaces an d protection against DNase I, Applied and Environmental Microbiology 57 (1991 ) 1057-1061.
- A. Ogram et al., Effects of DNA polymer length on its absorption to soils, Applied and Environmental Microbiology 60 (1994) 393-396.
- M. Khanna and G. Stotzky, Transformation of Bacillus subtilis by DNA bound on montmorillonite and effect of DNase on the availability of bound DNA, Applied and Environmental Microbiology 58 (1992) 1930-1939.
- E. Paget and P. Simonet, On the track of natural transformation in soil, FEMS Microbiology Ecology 15 (1994) 109-118.
- E . Gallori et al., Transformation of Bacillus subtilis by DNA bound on clay in non-sterile soil, FEMS Microbiology Ecology 15 (1994) 119-126.
- M. G. Lorenz and W. Wackernagel, Bacterial gene transfer by natural genetic transformation in the environment, Microbiology Reviews 58 (1994) 563-602.
- M. Vulic et al., Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria, Proceedings of the National Academy of Sciences USA 94 (1997) 9763-9767.
- J. Majewski et al., Barriers to genetic exchange between bacterial species: Streptococcus pneumonia transformation, Journal of Bacteriology 18 2 (2000) 1016-1023.
- K. M. Nielsen et al., Dynamics, horizontal transfer and selection of novel DNA in bacterial populations in the phytosphere of transgenic plants, Annals of Microbiology 51 (2001) (June issue, in press)  P. Shen and H. V. Huang, Homologous recombination in Escherichia coli: dependence on substrate length and homology, Genetics 112 (1986) 441-457
- J. Majewski and F. M. Cohan, DNA sequence similarity requirements for interspecific recombination in Bacillus, Genetics 153 (1999) 1525-1533.
- P. Zawadzki et al., The log-linear relationship between sexual isolation and sequence divergence in Bacillus transformation is robust, Genetics 140 (1995) 917-932.
- F. Gebhard, and K. Smalla. Transformation of Acinetobacter sp. Strain BD413 by transgenic sugar beet DNA, Applied and Environmental Microbiology 64 (1998) 1550-1554.
- J. De Vries, and W. Wackernagel, Detection of npt-II (kanamycin resistance) genes in genomes of transgene by marker-rescue transformation, Molecular and General Genetics 257 (1998) 606-613.
- J. De Vries et al., The natural transformation of the soil bacteria Pseudomonas stutzeri and Acinetobacter sp. by transgenic plant DNA depends strictly on homologous sequences in the recipient cells, FEMS Microbiology Letters 195 (2001) 211-215.
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