Browsing by Subject "RECOMBINATION"

Sort by: Order: Results:

Now showing items 21-30 of 30
  • Rasila, Tiina S; Pulkkinen, Elsi; Kiljunen, Saija; Haapa-Paananen, Saija; Pajunen, Maria I; Salminen, Anu; Paulin, Lars; Vihinen, Mauno; Rice, Phoebe A; Savilahti, Harri (2018)
    The phage Mu DNA transposition system provides a versatile species non-specific tool for molecular biology, genetic engineering and genome modification applications. Mu transposition is catalyzed by MuA transposase, with DNA cleavage and integration reactions ultimately attaching the transposon DNA to target DNA. To improve the activity of the Mu DNA transposition machinery, we mutagenized MuA protein and screened for hyperactivity-causing substitutions using an in vivo assay. The individual activity-enhancing substitutions were mapped onto the MuA–DNA complex structure, containing a tetramer of MuA transposase, two Mu end segments and a target DNA. This analysis, combined with the varying effect of the mutations in different assays, implied that the mutations exert their effects in several ways, including optimizing protein–protein and protein–DNA contacts. Based on these insights, we engineered highly hyperactive versions of MuA, by combining several synergistically acting substitutions located in different subdomains of the protein. Purified hyperactive MuA variants are now ready for use as second-generation tools in a variety of Mu-based DNA transposition applications. These variants will also widen the scope of Mu-based gene transfer technologies toward medical applications such as human gene therapy. Moreover, the work provides a platform for further design of custom transposases.
  • Awad, Shady Adnan; Kankainen, Matti; Ojala, Teija; Koskenvesa, Perttu; Eldfors, Samuli; Ghimire, Bishwa; Kumar, Ashwini; Kytölä, Soili; Kamel, Mahmoud M.; Heckman, Caroline A.; Porkka, Kimmo; Mustjoki, Satu (2020)
    Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm accounting for similar to 15% of all leukemia. Progress of the disease from an indolent chronic phase to the more aggressive accelerated phase or blast phase (BP) occurs in a minority of cases and is associated with an accumulation of somatic mutations. We performed genetic profiling of 85 samples and transcriptome profiling of 12 samples from 59 CML patients. We identified recurrent somatic mutations in ABL1 (37%), ASXL1 (26%), RUNX1 (16%), and BCOR (16%) in the BP and observed that mutation signatures in the BP resembled those of acute myeloid leukemia (AML). We found that mutation load differed between the indolent and aggressive phases and that nonoptimal responders had more nonsilent mutations than did optimal responders at the time of diagnosis, as well as in follow-up. Using RNA sequencing, we identified other than BCR-ABL1 cancer-associated hybrid genes in 6 of the 7 BP samples. Uncovered expression alterations were in turn associated with mechanisms and pathways that could be targeted in CML management and by which somatic alterations may emerge in CML. Last, we showed the value of genetic data in CML management in a personalized medicine setting.
  • Harrow, Gabrielle L.; Lees, John A.; Hanage, William P.; Lipsitch, Marc; Corander, Jukka; Colijn, Caroline; Croucher, Nicholas J. (2021)
    Streptococcus pneumoniae can be divided into many strains, each a distinct set of isolates sharing similar core and accessory genomes, which co-circulate within the same hosts. Previous analyses suggested the short-term vaccine-associated dynamics of S. pneumoniae strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), which maintains accessory loci at equilibrium frequencies. Long-term simulations demonstrated NFDS stabilised clonally-evolving multi-strain populations through preventing the loss of variation through drift, based on polymorphism frequencies, pairwise genetic distances and phylogenies. However, allowing symmetrical recombination between isolates evolving under multi-locus NFDS generated unstructured populations of diverse genotypes. Replication of the observed data improved when multi-locus NFDS was combined with recombination that was instead asymmetrical, favouring deletion of accessory loci over insertion. This combination separated populations into strains through outbreeding depression, resulting from recombinants with reduced accessory genomes having lower fitness than their parental genotypes. Although simplistic modelling of recombination likely limited these simulations' ability to maintain some properties of genomic data as accurately as those lacking recombination, the combination of asymmetrical recombination and multi-locus NFDS could restore multi-strain population structures from randomised initial populations. As many bacteria inhibit insertions into their chromosomes, this combination may commonly underlie the co-existence of strains within a niche.
  • Uusitalo, Elina; Hammais, Anna; Palonen, Elina; Brandt, Annika; Makela, Ville-Veikko; Kallionpaa, Roope; Jouhilahti, Eeva-Mari; Poyhonen, Minna; Soini, Juhani; Peltonen, Juha; Peltonen, Sirkku (2014)
  • Fang, Bohao; Kemppainen, Petri; Momigliano, Paolo; Feng, Xueyun; Merilä, Juha (2020)
    The three-spined stickleback (Gasterosteus aculeatus) is an important model system for the study of parallel evolution in the wild, having repeatedly colonized and adapted to freshwater from the sea throughout the northern hemisphere. Previous studies identified numerous genomic regions showing consistent genetic differentiation between freshwater and marine ecotypes but these had typically limited geographic sampling and mostly focused on the Eastern Pacific region. We analysed population genomic data from global samples of the three-spined stickleback marine and freshwater ecotypes to detect loci involved in parallel evolution at different geographic scales. Most signatures of parallel evolution were unique to the Eastern Pacific and trans-oceanic marine-freshwater differentiation was restricted to a limited number of shared genomic regions, including three chromosomal inversions. On the basis of simulations and empirical data, we demonstrate that this could result from the stochastic loss of freshwater-adapted alleles during the invasion of the Atlantic basin and selection against freshwater-adapted variants in the sea, both of which can reduce standing genetic variation available for freshwater adaptation outside the Eastern Pacific region. Moreover, the elevated linkage disequilibrium associated with marine-freshwater differentiation in the Eastern Pacific is consistent with secondary contact between marine and freshwater populations that evolved in isolation from each other during past glacial periods. Thus, contrary to what earlier studies from the Eastern Pacific region have led us to believe, parallel marine-freshwater differentiation in sticklebacks is far less prevalent and pronounced in all other parts of the species global distribution range. Population genomic data from a global dataset of three-spined sticklebacks show that parallel signatures of marine to freshwater differentiation are less common than previously thought.
  • Torregrosa-Munumer, Ruben; Hangas, Anu; Goffart, Steffi; Blei, Daniel; Zsurka, Gabor; Griffith, Jack; Kunz, Wolfram S.; Pohjoismäki, Jaakko L. O. (2019)
    Replication stalling has been associated with the formation of pathological mitochondrial DNA (mtDNA) rearrangements. Yet, almost nothing is known about the fate of stalled replication intermediates in mitochondria. We show here that replication stalling in mitochondria leads to replication fork regression and mtDNA double-strand breaks. The resulting mtDNA fragments are normally degraded by a mechanism involving the mitochondrial exonuclease MGME1, and the loss of this enzyme results in accumulation of linear and recombining mtDNA species. Additionally, replication stress promotes the initiation of alternative replication origins as an apparent means of rescue by fork convergence. Besides demonstrating an interplay between two major mechanisms rescuing stalled replication forks - mtDNA degradation and homology-dependent repair - our data provide evidence that mitochondria employ similar mechanisms to cope with replication stress as known from other genetic systems.
  • Natri, Heini M.; Merilä, Juha; Shikano, Takahito (2019)
    Sex determination is a fundamentally important and highly diversified biological process, yet the mechanisms behind the origin of this diversity are mostly unknown. Here we suggest that the evolution of sex determination systems can be driven by a chromosomal inversion. We show that an XY system evolved recently in particular nine-spined stickleback (Pungitius pungitius) populations, which arose from ancient hybridization between two divergent lineages. Our phylogenetic and genetic mapping analyses indicate that the XY system is formed in a large inversion that is associated with hybrid sterility between the divergent lineages. We suggest that a new male-determining gene evolved in the inversion in response to selection against impaired male fertility in a hybridized population. Given that inversions are often associated with hybrid incompatibility in animals and plants, they might frequently contribute to the diversification of sex determination systems.
  • Yan, Chao; Dada, Lubna; Rose, Clémence; Jokinen, Tuija; Nie, Wei; Schobesberger, Siegfried; Junninen, Heikki; Lehtipalo, Katrianne; Sarnela, Nina; Makkonen, Ulla; Garmash, Olga; Wang, Yonghong; Zha, Qiaozhi; Paasonen, Pauli; Bianchi, Federico; Sipilä, Mikko; Ehn, Mikael; Petäjä, Tuukka; Kerminen, Veli-Matti; Worsnop, Douglas R.; Kulmala, Markku (2018)
    New particle formation (NPF) provides a large source of atmospheric aerosols, which affect the climate and human health. In recent chamber studies, ion-induced nucleation (IIN) has been discovered as an important pathway of forming particles; however, atmospheric investigation remains incomplete. For this study, we investigated the air anion compositions in the boreal forest in southern Finland for three consecutive springs, with a special focus on H2SO4-NH3 anion clusters. We found that the ratio between the concentrations of highly oxygenated organic molecules (HOMs) and H2SO4 controlled the appearance of H2SO4-NH3 clusters (3 <no.S <13): all such clusters were observed when [HOM] / [H2SO4] was smaller than 30. The number of H2SO4 molecules in the largest observable cluster correlated with the probability of ion-induced nucleation (IIN) occurrence, which reached almost 100 % when the largest observable cluster contained six or more H2SO4 molecules. During selected cases when the time evolution of H2SO4-NH3 clusters could be tracked, the calculated ion growth rates exhibited good agreement across measurement methods and cluster (particle) sizes. In these cases, H2SO4-NH3 clusters alone could explain ion growth up to 3 nm (mobility diameter). IIN events also occurred in the absence of H2SO4-NH3, implying that other NPF mechanisms also prevail at this site, most likely involving HOMs. It seems that H2SO4 and HOMs both affect the occurrence of an IIN event, but their ratio ([HOMs] / [H2SO4]) defines the primary mechanism of the event. Since that ratio is strongly influenced by solar radiation and temperature, the IIN mechanism ought to vary depending on conditions and seasons.
  • Chaguza, Chrispin; Cornick, Jennifer E.; Harris, Simon R.; Andam, Cheryl P.; Bricio-Moreno, Laura; Yang, Marie; Yalcin, Feyruz; Ousmane, Sani; Govindpersad, Shanil; Senghore, Madikay; Ebruke, Chinelo; Du Plessis, Mignon; Kiran, Anmol M.; Pluschke, Gerd; Sigauque, Betuel; McGee, Lesley; Klugman, Keith P.; Turner, Paul; Corander, Jukka; Parkhill, Julian; Collard, Jean-Marc; Antonio, Martin; von Gottberg, Anne; Heyderman, Robert S.; French, Neil; Kadioglu, Aras; Hanage, William P.; Everett, Dean B.; Bentley, Stephen D.; PAGe Consortium (2016)
    Background: Pneumococcus kills over one million children annually and over 90 % of these deaths occur in low-income countries especially in Sub-Saharan Africa (SSA) where HIV exacerbates the disease burden. In SSA, serotype 1 pneumococci particularly the endemic ST217 clone, causes majority of the pneumococcal disease burden. To understand the evolution of the virulent ST217 clone, we analysed ST217 whole genomes from isolates sampled from African and Asian countries. Methods: We analysed 226 whole genome sequences from the ST217 lineage sampled from 9 African and 4 Asian countries. We constructed a whole genome alignment and used it for phylogenetic and coalescent analyses. We also screened the genomes to determine presence of antibiotic resistance conferring genes. Results: Population structure analysis grouped the ST217 isolates into five sequence clusters (SCs), which were highly associated with different geographical regions and showed limited intracontinental and intercontinental spread. The SCs showed lower than expected genomic sequence, which suggested strong purifying selection and small population sizes caused by bottlenecks. Recombination rates varied between the SCs but were lower than in other successful clones such as PMEN1. African isolates showed higher prevalence of antibiotic resistance genes than Asian isolates. Interestingly, certain West African isolates harbored a defective chloramphenicol and tetracycline resistance-conferring element (Tn5253) with a deletion in the loci encoding the chloramphenicol resistance gene (cat(pC194)), which caused lower chloramphenicol than tetracycline resistance. Furthermore, certain genes that promote colonisation were absent in the isolates, which may contribute to serotype 1's rarity in carriage and consequently its lower recombination rates. Conclusions: The high phylogeographic diversity of the ST217 clone shows that this clone has been in circulation globally for a long time, which allowed its diversification and adaptation in different geographical regions. Such geographic adaptation reflects local variations in selection pressures in different locales. Further studies will be required to fully understand the biological mechanisms which makes the ST217 clone highly invasive but unable to successfully colonise the human nasopharynx for long durations which results in lower recombination rates.
  • Laine, Anna-Liisa; Barres, Benoit; Numminen, Elina; Siren, Jukka P. (2019)
    Many pathogens possess the capacity for sex through outcrossing, despite being able to reproduce also asexually and/or via selfing. Given that sex is assumed to come at a cost, these mixed reproductive strategies typical of pathogens have remained puzzling. While the ecological and evolutionary benefits of outcrossing are theoretically well-supported, support for such benefits in pathogen populations are still scarce. Here, we analyze the epidemiology and genetic structure of natural populations of an obligate fungal pathogen, Podosphaera plantaginis. We find that the opportunities for outcrossing vary spatially. Populations supporting high levels of coinfection -a prerequisite of sex - result in hotspots of novel genetic diversity. Pathogen populations supporting coinfection also have a higher probability of surviving winter. Jointly our results show that outcrossing has direct epidemiological consequences as well as a major impact on pathogen population genetic diversity, thereby providing evidence of ecological and evolutionary benefits of outcrossing in pathogens.