Recently, new serine integrases have been identified, increasing the possibility of scaling up genomic modulation tools. Here, we describe the use of unidirectional genetic switches to evaluate the functionality of six serine integrases in different eukaryotic systems: the HEK 293T cell lineage, bovine fibroblasts and plant protoplasts. Moreover, integrase activity was also tested in human cell types of therapeutic interest: peripheral blood mononuclear cells (PBMCs), neural stem cells (NSCs) and undifferentiated embryonic stem (ES) cells. The switches were composed of plasmids designed to flip two different genetic parts driven by serine integrases. Cell-based assays were evaluated by measurement of EGFP fluorescence and by molecular analysis of attL/attR sites formation after integrase functionality. Our results demonstrate that all the integrases were capable of inverting the targeted DNA sequences, exhibiting distinct performances based on the cell type or the switchable genetic sequence. These results should support the development of tunable genetic circuits to regulate eukaryotic gene expression.

The genome of a novel group II alphabaculovirus, Perigonia lusca single nucleopolyhedrovirus (PeluSNPV), was sequenced and shown to contain 132,831 bp with 145 putative ORFs (open reading frames) of at least 50 amino acids. An interesting feature of this novel genome was the presence of a putative nucleotide metabolism enzyme-encoding gene (pelu112). The pelu112 gene was predicted to encode a fusion of thymidylate kinase (tmk) and dUTP diphosphatase (dut). Phylogenetic analysis indicated that baculoviruses have independently acquired tmk and dut several times during their evolution. Two homologs of the tmk-dut fusion gene were separately introduced into the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) genome, which lacks tmk and dut. The recombinant baculoviruses produced viral DNA, virus progeny, and some viral proteins earlier during in vitro infection and the yields of viral occlusion bodies were increased 2.5-fold when compared to the parental virus. Interestingly, both enzymes appear to retain their active sites, based on separate modeling using previously solved crystal structures. We suggest that the retention of these tmk-dut fusion genes by certain baculoviruses could be related to accelerating virus replication and to protecting the virus genome from deleterious mutation.

BackgroundTospovirus is a plant-infecting genus within the family Bunyaviridae, which also includes four animal-infecting genera: Hantavirus, Nairovirus, Phlebovirus and Orthobunyavirus. Compared to these members, the structures of Tospovirus proteins still are poorly understood. Despite multiple studies have attempted to identify candidate N protein regions involved in RNA binding and protein multimerization for tospovirus using yeast two-hybrid systems (Y2HS) and site-directed mutagenesis, the tospovirus ribonucleocapsids (RNPs) remains largely uncharacterized at the molecular level and the lack of structural information prevents detailed insight into these interactions.ResultsHere we used the nucleoprotein structure of LACV (La Crosse virus-Orthobunyavirus) and molecular dynamics simulations to access the structure and dynamics of the nucleoprotein from tospovirus GRSV (Groundnut ringspot virus). The resulting model is a monomer composed by a flexible N-terminal and C-terminal arms and a globular domain with a positively charged groove in which RNA is deeply encompassed. This model allowed identifying the candidate amino acids residues involved in RNA interaction and N-N multimerization. Moreover, most residues predicted to be involved in these interactions are highly conserved among tospoviruses.ConclusionsCrucially, the interaction model proposed here for GRSV N is further corroborated by the all available mutational studies on TSWV (Tomato spotted wilt virus) N, so far. Our data will help designing further and more accurate mutational and functional studies of tospovirus N proteins. In addition, the proposed model may shed light on the mechanisms of RNP shaping and could allow the identification of essential amino acid residues as potential targets for tospovirus control strategies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1339-4) contains supplementary material, which is available to authorized users.

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BackgroundZucchini lethal chlorosis virus (ZLCV) causes significant losses in the production of cucurbits in Brazil. This virus belongs to the genus Tospovirus (family Bunyaviridae) and seems to be exclusively transmitted by Frankliniella zucchini (Thysanoptera). Tospoviruses have a tripartite and single-stranded RNA genome classified as S (Small), M (Medium) and L (Large) RNAS. Although ZLCV was identified as a member of the genus Tospovirus in 1999, its complete genome had not been sequenced until now.FindingsWe sequenced the full-length genome of two ZLCV isolates named ZLCV-SP and ZLCV-DF. The phylogenetic analysis showed that ZLCV-SP and ZLCV-DF clustered with the previously reported isolate ZLCV-BR09. Their proteins were closely related, except the non-structural protein (NSm), which was highly divergent (approximately 90 % identity). All viral proteins clustered similarly in our phylogenetic analysis, excluding that these ZLCV isolates have originated from reassortment events of different tospovirus species.ConclusionHere we report for the first time the complete genome of two ZLCV isolates that were found in the field infecting zucchini and cucumber.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-016-0577-4) contains supplementary material, which is available to authorized users.

Background: Meloidogyne incognita is the most frequently reported species from the root-knot nematode (RKN) complex responsible for causing damage in several different crops worldwide. The interaction between M. incognita and host plants involves the secretions of molecular factors from the nematode, which mainly suppress the defense response and promote plant parasitism. On the other hand, several plant elements are associated with the immune defense system that opposes nematode infection.Results: In this study, the interaction of the Mi-EFF1/Minc17998 effector with the soybean GmHub6 (Glyma.17G099100; TCP14) protein was identi ed and characterized in vitro and in vivo. Data showed that the GmHub6 gene is upregulated by M. incognita infection in a nematode-resistant soybean cultivar (PI595099) compared to a susceptible cultivar (BRS133). Accordingly, the Arabidopsis thaliana AtHub6 mutant line (AT3G47620, orthologous gene of GmHub6 displayed normal vegetative development of the plant but was more susceptible to M. incognita. Thus, since the soybean and A. thaliana Hub6 proteins are TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) transcription factors involved in plant development and morphogenesis modulation, owering time regulation, and the activation of the plant immune system, our data suggest that the interaction of Mi-EFF1/Minc17998 and Hub6 proteins is associated with an increase in plant susceptibility to nematode infection during parasitism. It is suggested that this interaction may prevent the nuclear localization or disturb the activity of GmHub6 as a typical transcription factor modulating the cell cycle of the plant, avoid the activation of the host's defense response, and successfully promote parasitism. Conclusion:Our ndings indicate the potential of the Mi-EFF1/Minc17998 effector for the development of biotechnological tools based on the approaches of RNA interference and GmHub6 gene overexpression for RKN control.

Toehold switches are biosensors useful for the detection of endogenous and environmental RNAs. They have been engineered to detect virus RNAs in cell-free gene expression reactions. Their inherent sequence programmability makes engineering a fast and predictable process. Despite improvements in the design, toehold switches suffer from leaky translation in the OFF state, which compromises the fold change and sensitivity of the biosensor. To address this, we constructed and tested signal amplification circuits for three toehold switches triggered by Dengue and Sars-CoV-2 RNAs and an artificial RNA. The serine integrase circuit efficiently contained leakage, boosted the expression fold-change from OFF to ON, and decreased the detection limit of the switches by three to four orders of magnitude. Ultimately, the integrase circuit converted the analog switches signals into digital-like output. The circuit is broadly useful for biosensors and eliminates the hard work of designing and testing multiple switches to find the best possible performer.

Recently, soybean consumption has increased, not only because of its potential for industrial and livestock use but also due to its beneficial effects on human health in the treatment and prevention of various diseases because soy can produce a wide number of functional proteins. Despite the soybean-producing high, elevated, nutritive and functional proteins, it also produces allergenic proteins, harmful secondary metabolites, and carcinogenic elements. So, recombinant protein systems that mimic the structures and functions of the natural proteins supply a single tunable and valuable source of advanced materials. But the availability of the technology to produce synthetic functional proteins is still limited. Therefore, Synthetic Biology is a powerful and promising science field for the development of new devices and systems able to tackle the challenges that exist in conventional studies on the development of functional protein systems. Thus, representing a new disruptive frontier that will allow better use of soybean functional proteins, both for animal and human food and for the pharmaceutical and chemistry industry.