RESUMO
We investigated SNPs in alternative oxidase (AOX) genes and their connection to ecotype origins (climate, altitude, and rainfall) by using genomic data sets of Arabidopsis and rice populations from 1190 and 90 ecotypes, respectively. Parameters were defined to detect non-synonymous SNPs in the AOX ORF, which revealed amino acid (AA) changes in AOX1c, AOX1d, and AOX2 from Arabidopsis and AOX1c from rice in comparison to AOX references from Columbia-0 and Japonica ecotypes, respectively. Among these AA changes, Arabidopsis AOX1c_A161E&G165R and AOX1c_R242S revealed a link to high rainfall and high altitude, respectively, while all other changes in Arabidopsis and rice AOX was connected to high altitude and rainfall. Comparative 3D modeling showed that all mutant AOX presented structural differences in relation to the respective references. Molecular docking analysis uncovered lower binding affinity values between AOX and the substrate ubiquinol for most of the identified structures compared to their reference, indicating better enzyme-substrate binding affinities. Thus, our in silico data suggest that the majority of the AA changes found in the available ecotypes will confer better enzyme-subtract interactions and thus indicate environment-related, more efficient AOX activity.
Assuntos
Arabidopsis , Oryza , Arabidopsis/metabolismo , Oryza/metabolismo , Ecótipo , Altitude , Simulação de Acoplamento Molecular , Proteínas de Plantas/metabolismo , Proteínas Mitocondriais/metabolismoRESUMO
Babaco is a fast-growing herbaceous shrub with great commercial potential because of the organoleptic properties of its fruit. Babaco mosaic virus (BabMV) is a potexvirus in the family Alphaflexiviridae affecting babaco in all the provinces that produce this crop in Ecuador. BabMV was recently described but it has been affecting babaco for decades and, since many potexviruses are serologically indistinguishable, it may have been previously misidentified as papaya mosaic virus. Based on the coat protein (CP) gene, we aimed to study the distribution and epidemiological patterns of BabMV in babaco and chamburo over the years and to model its three-dimensional structure. Sequences of the CP were obtained from thirty-six isolates from plants collected in the main babaco-producing provinces of Ecuador between 2016 and 2021. The evolution rate of BabMV was estimated at 1.21 × 10-3 nucleotide substitutions site-1 year-1 and a time of origin of the most recent common ancestor around 1958.80. From molecular dynamics simulations, compared to other proteins of BabMV-RDRP, TGB1, and Alkb domain-the CP exhibited a higher flexibility with the C and N terminals as the most flexible regions. The reconstructed viral distribution provides dispersion patterns which have implications for control approaches of BabMV.
RESUMO
BACKGROUND: Early metabolic reorganization was only recently recognized as an essentially integrated part of immunology. In this context, unbalanced ROS/RNS levels connected to increased aerobic fermentation, which is linked to alpha-tubulin-based cell restructuring and control of cell cycle progression, were identified as a major complex trait for early de novo programming ('CoV-MAC-TED') during SARS-CoV-2 infection. This trait was highlighted as a critical target for developing early anti-viral/anti-SARS-CoV-2 strategies. To obtain this result, analyses had been performed on transcriptome data from diverse experimental cell systems. A call was released for wide data collection of the defined set of genes for transcriptome analyses, named 'ReprogVirus', which should be based on strictly standardized protocols and data entry from diverse virus types and variants into the 'ReprogVirus Platform'. This platform is currently under development. However, so far, an in vitro cell system from primary target cells for virus attacks that could ideally serve for standardizing the data collection of early SARS-CoV-2 infection responses has not been defined. RESULTS: Here, we demonstrate transcriptome-level profiles of the most critical 'ReprogVirus' gene sets for identifying 'CoV-MAC-TED' in cultured human nasal epithelial cells infected by two SARS-CoV-2 variants differing in disease severity. Our results (a) validate 'Cov-MAC-TED' as a crucial trait for early SARS-CoV-2 reprogramming for the tested virus variants and (b) demonstrate its relevance in cultured human nasal epithelial cells. CONCLUSION: In vitro-cultured human nasal epithelial cells proved to be appropriate for standardized transcriptome data collection in the 'ReprogVirus Platform'. Thus, this cell system is highly promising to advance integrative data analyses with the help of artificial intelligence methodologies for designing anti-SARS-CoV-2 strategies.
RESUMO
In a perspective entitled 'From plant survival under severe stress to anti-viral human defense' we raised and justified the hypothesis that transcript level profiles of justified target genes established from in vitro somatic embryogenesis (SE) induction in plants as a reference compared to virus-induced profiles can identify differential virus signatures that link to harmful reprogramming. A standard profile of selected genes named 'ReprogVirus' was proposed for in vitro-scanning of early virus-induced reprogramming in critical primary infected cells/tissues as target trait. For data collection, the 'ReprogVirus platform' was initiated. This initiative aims to identify in a common effort across scientific boundaries critical virus footprints from diverse virus origins and variants as a basis for anti-viral strategy design. This approach is open for validation and extension. In the present study, we initiated validation by experimental transcriptome data available in public domain combined with advancing plant wet lab research. We compared plant-adapted transcriptomes according to 'RegroVirus' complemented by alternative oxidase (AOX) genes during de novo programming under SE-inducing conditions with in vitro corona virus-induced transcriptome profiles. This approach enabled identifying a major complex trait for early de novo programming during SARS-CoV-2 infection, called 'CoV-MAC-TED'. It consists of unbalanced ROS/RNS levels, which are connected to increased aerobic fermentation that links to alpha-tubulin-based cell restructuration and progression of cell cycle. We conclude that anti-viral/anti-SARS-CoV-2 strategies need to rigorously target 'CoV-MAC-TED' in primary infected nose and mouth cells through prophylactic and very early therapeutic strategies. We also discuss potential strategies in the view of the beneficial role of AOX for resilient behavior in plants. Furthermore, following the general observation that ROS/RNS equilibration/redox homeostasis is of utmost importance at the very beginning of viral infection, we highlight that 'de-stressing' disease and social handling should be seen as essential part of anti-viral/anti-SARS-CoV-2 strategies.