DNA Donation Research Articles

The PulE ATPase is required for twitching motility and DNA donation during Thermus thermophilus transjugation.

Thermus thermophilus can acquire DNA through natural competence and through transjugation, a mechanism that involves a two-step process of DNA secretion (push) and DNA internalization (pull) between mating cells of related species. The natural competence apparatus (NCA) is required in the recipient mate for the pull step. However, how the DNA exits of the donor cell is only partially known. The putative DNA translocase TdtA, encoded in mobile genetic element ICETh1 of T. thermophilus HB27, was shown to be required for DNA donation as reported by (Blesa et al.2017a). This ring-shaped hexameric ATPase binds to the membrane and likely interacts with yet unknown secretory components that allow the extrusion of DNA through the membrane; thus, a genetic screening to identify additional putative secretory components was performed. Here, we describe that mutants in gene TT_C1844, which encodes a putative AAA-ATPase named PulE, do not synthesize the recently described "narrow" type 4 pili required for twitching motility and made up of the major PilA5 pilin. Concomitantly, pulE mutants also exhibited DNA donation defects during transjugation, suggesting a role of narrow pili in the donation process. However, single pilA5 null mutants still function as DNA donors in transjugation experiments, so we conclude that the need for PulE in transjugation is independent of its role in narrow pili synthesis and twitching motility.

Spitting on my sources: Depression, DNA, and the ambivalent historian.

While writing a book on the history of postpartum depression in the United States, I became interested in an ongoing study about possible genetic markers of postpartum mental illness. I participated in the first step, an online survey. When I qualified for the next step, saliva collection, I was torn over whether or not to continue. Making this decision required reflecting on some overlapping issues: gender, medicalization, genetic research, and the political functions of DNA donation. In this perspectives essay, I explore tensions around situating myself in my historical research project.

“Donating with eyes shut”: attitudes regarding DNA donation to a large-scale biobank in Israel

DNA collection raises ethical, legal, and social issues around privacy, consent, participatory science, benefits and risks, biodata governance, and, ultimately, trust. While there is a consensus that DNA biobanks’ success depends on public trust, more evidence is needed regarding the determinants, production, and preservation of such trust. We draw on 14 semi-structured interviews with participants – seven people who donated DNA to an Israeli biobank, and seven who refused to donate; as well as on two focus groups with members of the general public. Our findings call into question the relationship between trust/trustworthiness and donation, suggesting moral strategies termed by respondents as “donating with eyes shut.” We conclude by discussing how DNA donation is built on a mixture of attitudes combining criticism, optimism, resistance, and avoiding responsibility as a pragmatic solution to the unresolved conflicts in sharing one’s DNA.

ICETh1 and ICETh2, two interdependent mobile genetic elements in Thermus thermophilus transjugation.

Cell to cell DNA transfer between Thermus thermophilus, or transjugation, requires the natural competence apparatus (NCA) of the recipient cell and a DNA donation machinery in the donor. In T. thermophilus HB27, two mobile genetic elements with functional similarities to Integrative and Conjugative Elements (ICEs) coexist, ICETh1 encoding the DNA transfer apparatus and ICETh2, encoding a putative replication module. Here, we demonstrate that excision and integration of both elements depend on a single tyrosine recombinase encoded by ICETh2, and that excision is not required but improves the transfer of these elements to a recipient cell. These findings along with previous results suggest that ICETh1 and ICETh2 depend on each other for spreading among T. thermophilus by transjugation.

Factors associated with participation by African Americans in a study of the genetics of glaucoma

ABSTRACTObjective: African Americans have been historically underrepresented in research studies. Our aim was to evaluate factors influencing enrollment in the Primary Open-Angle African American Glaucoma Genetics (POAAGG) study.Design: Patients approached to enroll in the POAAGG study were asked to complete a 15-item survey addressing demographic characteristics, knowledge of genetics and glaucoma, and opinions on human research. Survey responses were compared between subjects who enrolled (Enrollers) and did not enroll (Decliners) in the POAAGG study.Results: Enrollers (N = 190) were 3.7 years younger (P = 0.007) and had similar gender, education, and income level to Decliners (N = 117). Knowledge about genetics and glaucoma was similar between groups. Enrollers were more comfortable providing DNA for research studies (93.1% vs 54.1%; P < 0.001) and more likely to have participated in prior studies (P = 0.003) and consider participating in future studies (P < 0.001). Among Decliners, lack of time was the primary reason given for not enrolling.Conclusion: To increase participation of African Americans in genetic research studies, efforts should be made to raise comfort with DNA donation.

Role of Archaeal HerA Protein in the Biology of the Bacterium Thermus thermophilus.

Intense gene flux between prokaryotes result in high percentage of archaeal genes in the genome of the thermophilic bacteria Thermus spp. Among these archaeal genes a homolog to the Sulfolobus spp. HerA protein appears in all of the Thermus spp. strains so far sequenced (HepA). The role of HepA in Thermus thermophilus HB27 has been analyzed using deletion mutants, and its structure resolved at low resolution by electron microscopy. Recombinant HepA shows DNA-dependent ATPase activity and its structure revealed a double ring, conically-shaped hexamer with an upper diameter of 150 Å and a bottom module of 95 Å. A central pore was detected in the structure that ranges from 13 Å at one extreme, to 30 Å at the other. Mutants lacking HepA show defective natural competence and DNA donation capability in a conjugation-like process termed “transjugation”, and also high sensitivity to UV and dramatic sensitivity to high temperatures. These data support that acquisition of an ancestral archaeal HerA has been fundamental for the adaptation of Thermus spp. to high temperatures.

The transjugation machinery of Thermus thermophilus: Identification of TdtA, an ATPase involved in DNA donation.

In addition to natural competence, some Thermus thermophilus strains show a high rate of DNA transfer via direct cell-to-cell contact. The process is bidirectional and follows a two-step model where the donor cell actively pushes out DNA and the recipient cell employs the natural competence system to take up the DNA, in a hybrid transformation-dependent conjugation process (transjugation). While the DNA uptake machinery is well known as in other bacterial species that undergo transformation, the pushing step of transjugation remains to be characterized. Here we have searched for hypothetical DNA translocases putatively involved in the pushing step of transjugation. Among candidates encoded by T. thermophilus HB27, the TdtA protein was found to be required for DNA pushing but not for DNA pulling during transjugation, without affecting other cellular processes. Purified TdtA shows ATPase activity and oligomerizes as hexamers with a central opening that can accommodate double-stranded DNA. The tdtA gene was found to belong to a mobile 14 kbp-long DNA element inserted within the 3′ end of a tRNA gene, flanked by 47 bp direct repeats. The insertion also encoded a homolog of bacteriophage site-specific recombinases and actively self-excised from the chromosome at high frequency to form an apparently non-replicative circular form. The insertion also encoded a type II restriction endonuclease and a NurA-like nuclease, whose activities were required for efficient transjugation. All these data support that TdtA belongs to a new type of Integrative and Conjugative Element which promotes the generalized and efficient transfer of genetic traits that could facilitate its co-selection among bacterial populations.

Naming the dead: DNA-based identification of historical remains as an act of care

Empirical knowledge of how DNA matching for identifications following mass fatality events is used, and how it interacts with existing social practices and values, is important not only to enlarge our understanding of the technology but also to inform normative thinking about its use. This paper draws on preliminary empirical material from a study of World War I dead at Fromelles to consider DNA matching as an act of care. Family members' involvement in the process of identifying historical human remains may be a way to demonstrate care toward a vulnerable subject, or toward the past and present family, as much as it is a way to confirm an individual's death. Framing DNA donation as an act of care enables it to be analyzed from the perspective of the ethics of care, thereby highlighting ethical issues of relationality, power, and obligation, which have relevance to the normative evaluation of the technology.

Personal DNA Donation to Energize Genomic Medicine

Immense strides toward improved human genomic sequencing have been made over the past decade, but significant obstacles to clinical research and translation are now evident. Novel approaches able to traverse financial, regulatory, and ethical obstacles on behalf of patients and the public health are needed. We propose a novel approach to the collection and annotation of personal genomic data using an organized donation program analogous to the national organ-procurement system.

Mating Pair Formation Homologue TraG Is a Variable Membrane Protein Essential for Contact-Independent Type IV Secretion of Chromosomal DNA by Neisseria gonorrhoeae

Neisseria gonorrhoeae uses a type IV secretion system (T4SS) to secrete chromosomal DNA into the surrounding milieu. The DNA is effective in transforming gonococci in the population, and this mechanism of DNA donation may contribute to the high degree of genetic diversity in this species. Similar to other F-like T4SSs, the gonococcal T4SS requires a putative membrane protein, TraG, for DNA transfer. In F-plasmid and related systems, the homologous protein acts in pilus production, mating pair stabilization, and entry exclusion. We characterized the localization, membrane topology, and variation of TraG in N. gonorrhoeae. TraG was found to be an inner-membrane protein with one large periplasmic region and one large cytoplasmic region. Each gonococcal strain carried one of three different alleles of traG. Strains that carried the smallest allele of traG were found to lack the peptidoglycanase gene atlA but carried a peptidoglycan endopeptidase gene in place of atlA. The purified endopeptidase degraded gonococcal peptidoglycan in vitro, cutting the peptide cross-links. Although the other two traG alleles functioned for DNA secretion in strain MS11, the smallest traG did not support DNA secretion. Despite the requirement for a mating pair stabilization homologue, static coculture transformation experiments demonstrated that DNA transfer was nuclease sensitive and required active uptake by the recipient, thus demonstrating that transfer occurred by transformation and not conjugation. Together, these results demonstrate the TraG acts in a process of DNA export not specific to conjugation and that different forms of TraG affect what substrates can be transported.

Low Species Barriers in Halophilic Archaea and the Formation of Recombinant Hybrids

Speciation of sexually reproducing organisms requires reproductive barriers. Prokaryotes reproduce asexually butoften exchange DNA by lateral gene transfer mechanisms and recombination [1], yet distinct lineages are still observed. Thus, barriers to gene flow such as geographic isolation, genetic incompatibility or a physiological inability to transfer DNA represent potential underlying mechanisms behind preferred exchange groups observed in prokaryotes [2-6]. In Bacteria, experimental evidence showed that sequence divergence impedes homologous recombination between bacterial species [7-11]. Here we study interspecies gene exchange in halophilic archaea that possess a parasexual mechanism of genetic exchange that is functional between species [12, 13]. In this process, cells fuse forming a diploid state containing the full genetic repertoire of both parental cells, which facilitates genetic exchange and recombination. Later, cells separate, occasionally resulting in hybrids of the parental strains [14]. We show high recombination frequencies between Haloferax volcanii and Haloferax mediterranei, two species that have an average nucleotide sequence identity of 86.6%. Whole genome sequencing of Haloferax interspecies hybrids revealed the exchange of chromosomal fragments ranging from 310Kb to 530Kb. These results show that recombination barriers may be more permissive in halophilic archaea than they are in bacteria.

Interaction between α-Synuclein and Tau Genotypes and the Progression of Parkinson's Disease

To determine whether α-synuclein NACP-Rep1 and tau genotypes can predict the rate of progression of Parkinson's disease. 123 Parkinson's disease cases were recruited for neurological examination and DNA donation. The rate of progression was assessed as the motor Unified Parkinson's disease Rating Score divided by symptom duration at the time of assessment and associations determined with α-synuclein NACP-Rep1 and tau genotypes. There was a significant effect of genotype on the rate of progression of Parkinson's disease. In MAPT H2 haplotype carriers, some NACP-Rep1 genotypes, thought to be associated with increasing α-synuclein expression, were linked with a higher rate of progression. In NACP-Rep1 0/0 genotype carriers, patients without MAPT H2 haplotype had a higher rate of progression of Parkinson's disease. The relative risk to develop a more rapid disease progression in these genotypes reached 5.8. Genetic factors not only influence the risk of Parkinson's disease, but also the progression of Parkinson's disease.

DNA Damage Triggers Genetic Exchange in Helicobacter pylori

Many organisms respond to DNA damage by inducing expression of DNA repair genes. We find that the human stomach pathogen Helicobacter pylori instead induces transcription and translation of natural competence genes, thus increasing transformation frequency. Transcription of a lysozyme-like protein that promotes DNA donation from intact cells is also induced. Exogenous DNA modulates the DNA damage response, as both recA and the ability to take up DNA are required for full induction of the response. This feedback loop is active during stomach colonization, indicating a role in the pathogenesis of the bacterium. As patients can be infected with multiple genetically distinct clones of H. pylori, DNA damage induced genetic exchange may facilitate spread of antibiotic resistance and selection of fitter variants through re-assortment of preexisting alleles in this important human pathogen.

Proband Race/Ethnicity Affects Pedigree Completion Rate in a Genetic Study of Ischemic Stroke

A recent meta-analysis suggested that racial/ethnic status is not a major determinant of willingness to participate in observational studies or treatment trials. However, little is known about the predictors of enrollment in family-based observational genetic studies. We tested the hypothesis that proband race/ethnicity is a significant predictor of enrolling a pedigree. Univariable and multivariable logistic regression modeling was used to determine proband characteristics that predict DNA donation from both members of an affected sibling pair. A total of 619 adult male and female probands with first-time or recurrent ischemic stroke and a positive sibling history of stroke enrolled across 53 hospitals and clinics in the United States and Canada into the Siblings with Ischemic Stroke Study, a family-based prospective genomics study. In univariable analysis, probands with siblings who agreed to a blood draw for DNA analyses were more likely to be male and less likely to be nonwhite. In multivariable analysis, only race/ethnicity was significantly associated with likelihood of a proband's having a sibling who agreed to a blood draw. Contrary to observational studies that are not family based, the willingness of family members to participate in observational genetics studies may be influenced by race/ethnicity. This result reinforces the need for improving methods for recruiting diverse populations into genetic studies of stroke.

A novel relaxase homologue is involved in chromosomal DNA processing for type IV secretion in Neisseria gonorrhoeae.

The Neisseria gonorrhoeae type IV secretion system secretes chromosomal DNA that acts in natural transformation. To examine the mechanism of DNA processing for secretion, we made mutations in the putative relaxase gene traI and used nucleases to characterize the secreted DNA. The nuclease experiments demonstrated that the secreted DNA is single-stranded and blocked at the 5' end. Mutation of traI identified Tyr93 as required for DNA secretion, while substitution of Tyr201 resulted in intermediate levels of DNA secretion. TraI exhibits features of relaxases, but also has features that are absent in previously characterized relaxases, including an HD phosphohydrolase domain and an N-terminal hydrophobic region. The HD domain residue Asp120 was required for wild-type levels of DNA secretion. Subcellular localization studies demonstrated that the TraI N-terminal region promotes membrane interaction. We propose that Tyr93 initiates DNA processing and Tyr201 is required for termination or acts in DNA binding. Disruption of an inverted-repeat sequence eliminated DNA secretion, suggesting that this sequence may serve as the origin of transfer for chromosomal DNA secretion. The TraI domain architecture, although not previously described, is present in 53 uncharacterized proteins, suggesting that the mechanism of TraI function is a widespread process for DNA donation.

Natural transformation of Neisseria gonorrhoeae: from DNA donation to homologous recombination

Gonococci undergo frequent and efficient natural transformation. Transformation occurs so often that the population structure is panmictic, with only one long-lived clone having been identified. This high degree of genetic exchange is likely necessary to generate antigenic diversity and allow the persistence of gonococcal infection within the human population. In addition to spreading different alleles of genes for surface markers and allowing avoidance of the immune response, transformation facilitates the spread of antibiotic resistance markers, a continuing problem for treatment of gonococcal infections. Transforming DNA is donated by neighbouring gonococci by two different mechanisms: autolysis or type IV secretion. All types of DNA are bound non-specifically to the cell surface. However, for DNA uptake, Neisseria gonorrhoeae recognizes only DNA containing a 10-base sequence (GCCGTCTGAA) present frequently in the chromosome of neisserial species. Type IV pilus components and several pilus-associated proteins are necessary for gonococcal DNA uptake. Incoming DNA is subject to restriction, making establishment of replicating plasmids difficult but not greatly affecting chromosomal transformation. Processing and integration of transforming DNA into the chromosome involves enzymes required for homologous recombination. Recent research on DNA donation mechanisms and extensive work on type IV pilus biogenesis and recombination proteins have greatly improved our understanding of natural transformation in N. gonorrhoeae. The completion of the gonococcal genome sequence has facilitated the identification of additional transformation genes and provides insight into previous investigations of gonococcal transformation. Here we review these recent developments and address the implications of natural transformation in the evolution and pathogenesis N. gonorrhoeae.

Neisseria gonorrhoeae secretes chromosomal DNA via a novel type IV secretion system

The process of DNA donation for natural transformation of bacteria is poorly understood and has been assumed to involve bacterial cell death. Recently in Neisseria gonorrhoeae we found that mutations in three genes in the gonococcal genetic island (GGI) reduced the ability of a strain to act as a donor in transformation and to release DNA into the culture. To better characterize the GGI and the process of DNA donation, the 57 kb genetic island was cloned, sequenced and subjected to insertional mutagenesis. DNA sequencing revealed that the GGI has characteristics of a horizontally acquired genomic island and encodes homologues of type IV secretion system proteins. The GGI was found to be incorporated near the chromosomal replication terminus at the dif site, a sequence targeted by the site-specific recombinase XerCD. Using a plasmid carrying a small region of the GGI and the associated dif site, we demonstrated that this model island could be integrated at the dif site in strains not carrying the GGI and was spontaneously excised from that site. Also, we were able to delete the entire 57 kb region by transformation with DNA from a strain lacking the GGI. Thus the GGI was likely acquired and integrated into the gonococcal chromosome by site-specific recombination and may be lost by site-specific recombination or natural transformation. We made mutations in six putative type IV secretion system genes and assayed these strains for the ability to secrete DNA. Five of the mutations greatly reduced or completely eliminated DNA secretion. Our data indicate that N. gonorrhoeae secretes DNA via a specific process. Donated DNA may be used in natural transformation, contributing to antigenic variation and the spread of antibiotic resistance, and it may modulate the host immune response.

Rights and Responsibilities in the New Genetics Era

This article critically explores the distribution of rights and responsibilities associated with recent developments in genetic testing and DNA donation. The author identifies two key discourses in various accounts of genetics in the clinical and policy domains: patients' rights to informed choice and the public's right to involvement in policy decisions. However, other discourses among professionals, patients and members of the public around responsibilities for supporting genetic research and testing and managing their social implications are also present. The author goes on to argue that these discourses undermine the case for a dramatic difference between past eugenics and present genetics, as the prevention of genetic disease remains of paramount importance. This suggests that `new genetic citizenship' is not so new after all.