Targets and Mechanisms of Geminivirus Silencing Suppressor Protein AC2

Geminiviruses are plant DNA viruses that infect a wide range of plant species and cause significant losses to economically important food and fiber crops. The single-stranded geminiviral genome encodes a small number of proteins which act in an orchestrated manner to infect the host. The fewer proteins encoded by the virus are multifunctional, a mechanism uniquely evolved by the viruses to balance the genome-constraint. The host-mediated resistance against incoming virus includes post-transcriptional gene silencing, transcriptional gene silencing, and expression of defense responsive genes and other cellular regulatory genes. The pathogenicity property of a geminiviral protein is linked to its ability to suppress the host-mediated defense mechanism. This review discusses what is currently known about the targets and mechanism of the viral suppressor AC2/AL2/transcriptional activator protein (TrAP) and explore the biotechnological applications of AC2.

FIRST REPORT OF Begomovirus INFECTION ON PAPAYA IN BENGKULU, INDONESIA

A field survey was conducted during 2019, we found a severe systemic yellow mosaic, striped green mosaic on leaves petiole, green spots on the fruit of papaya, leaf malformation, and stunting symptoms on three papaya cultivation area in Rejang Lebong, Kepahiang, Bengkulu Tengah, and Seluma, Bengkulu Province, Indonesia. A begomo-like virus was inferred to be the possible cause of the virus-disease-like symptoms. The study aimed to identify the causal of those typical symptoms on papaya. PCR using universal primer for transcriptional activator protein (TrAp) and replication-associated protein (Rep) gene of Begomovirus successfully amplified the DNA fragments of 900 bp in all 10 detected samples, except for samples with leaf malformation and stunting symptoms. It is indicating that those typical symptoms on papaya is associated with Begomovirus infection, while the causal of leaf malformation and stunting is unknown yet. This work is the first report of Begomovirus infected papaya in Indonesia. Severe disease incidence caused by this pathogen was observed on papaya plants in Bengkulu Province that was in the range of 42–100%. This finding is a precious information to be used for identification, and characterization the species of the virus, determining control strategies against the disease.

Classification of genomic components and prediction of genes of Begomovirus based on subsequence natural vector and support vector machine

Background Begomoviruses are widely distributed and causing devastating diseases in many crops. According to the number of genomic components, a begomovirus is known as either monopartite or bipartite begomovirus. Both the monopartite and bipartite begomoviruses have the DNA-A component which encodes all essential proteins for virus functions, while the bipartite begomoviruses still contain the DNA-B component. The satellite molecules, known as betasatellites, alphasatellites or deltasatellites, sometimes exist in the begomoviruses. So, the genomic components of begomoviruses are complex and varied. Different genomic components have different gene structures and functions. Classifying the components of begomoviruses is important for studying the virus origin and pathogenic mechanism. Methods We propose a model combining Subsequence Natural Vector (SNV) method with Support Vector Machine (SVM) algorithm, to classify the genomic components of begomoviruses and predict the genes of begomoviruses. First, the genome sequence is represented as a vector numerically by the SNV method. Then SVM is applied on the datasets to build the classification model. At last, recursive feature elimination (RFE) is used to select essential features of the subsequence natural vectors based on the importance of features. Results In the investigation, DNA-A, DNA-B, and different satellite DNAs are selected to build the model. To evaluate our model, the homology-based method BLAST and two machine learning algorithms Random Forest and Naive Bayes method are used to compare with our model. According to the results, our classification model can classify DNA-A, DNA-B, and different satellites with high accuracy. Especially, we can distinguish whether a DNA-A component is from a monopartite or a bipartite begomovirus. Then, based on the results of classification, we can also predict the genes of different genomic components. According to the selected features, we find that the content of four nucleotides in the second and tenth segments (approximately 150-350 bp and 1,450–1,650 bp) are the most different between DNA-A components of monopartite and bipartite begomoviruses, which may be related to the pre-coat protein (AV2) and the transcriptional activator protein (AC2) genes. Our results advance the understanding of the unique structures of the genomic components of begomoviruses.

Isolation of full-length IgG antibodies from combinatorial libraries expressed in the cytoplasm of Escherichia coli

We describe a facile and robust genetic selection for isolating full-length IgG antibodies from combinatorial libraries expressed in the cytoplasm of the genetically engineered Escherichia coli strain, SHuffle. The method is based on the transport of a bifunctional substrate comprised of an antigen fused to chloramphenicol acetyltransferase, which allows positive selection of bacterial cells co-expressing cytoplasmic IgGs called ‘cyclonals’ that specifically capture the chimeric antigen and sequester the antibiotic resistance marker in the cytoplasm. The selective power of this approach was demonstrated by facile isolation of novel complementarity-determining regions for a cyclonal that specifically recognized the basic-region leucine zipper domain of the yeast transcriptional activator protein Gcn4.

Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening

BackgroundFruit ripening in Prunus persica melting varieties involves several physiological changes that have a direct impact on the fruit organoleptic quality and storage potential. By studying the proteomic differences between the mesocarp of mature and ripe fruit, it would be possible to highlight critical molecular processes involved in the fruit ripening.ResultsTo accomplish this goal, the proteome from mature and ripe fruit was assessed from the variety O’Henry through shotgun proteomics using 1D-gel (PAGE-SDS) as fractionation method followed by LC/MS-MS analysis. Data from the 131,435 spectra could be matched to 2,740 proteins, using the peach genome reference v1. After data pre-treatment, 1,663 proteins could be used for comparison with datasets assessed using transcriptomic approaches and for quantitative protein accumulation analysis. Close to 26% of the genes that code for the proteins assessed displayed higher expression at ripe fruit compared to other fruit developmental stages, based on published transcriptomic data. Differential accumulation analysis between mature and ripe fruit revealed that 15% of the proteins identified were modulated by the ripening process, with glycogen and isocitrate metabolism, and protein localization overrepresented in mature fruit, as well as cell wall modification in ripe fruit. Potential biomarkers for the ripening process, due to their differential accumulation and gene expression pattern, included a pectin methylesterase inhibitor, a gibbellerin 2-beta-dioxygenase, an omega-6 fatty acid desaturase and an ACC oxidase. These genes would be regulated by transcription factors enriched in zinc finger and GAGA-binding transcriptional activator protein domains.ConclusionsShotgun proteomics is an unbiased approach to get deeper into the proteome allowing to detect differences in protein abundance between samples. This technique provided a resolution so that individual gene products could be identified. Many proteins likely involved in cell wall and sugar metabolism, aroma and color, change their abundance during the transition from firm to soft fruit.

Role of microRNA-21 in hypertrophic cardiac remodeling

Hypertension is a major public health problem among with aging population worldwide. It causes cardiac remodeling, including hypertrophy and interstitial fibrosis, which leads to development of hypertensive heart disease (HHD). Although microRNA-21 (miR-21) is associated with fibrogenesis in multiple organs, its impact on hypertrophic cardiac remodeling in hypertension is not known. Circulating miR-21 level was higher in patients with HHD than that in the control subjects. It also positively correlated with serum myocardial fibrotic markers. MiR-21 expression levels were significantly upregulated in the mice hearts after angiotensin II (Ang II) infusion or transverse aortic constriction (TAC) compared with control mice. Expression level of programmed cell death 4 (PDCD4), a main target of miR-21, was significantly decreased in Ang II infused mice and TAC mice compared with control mice. Expression levels of transcriptional activator protein 1 (AP-1) and transforming growth factor-β1 (TGF-β1), which were downstream targets of PDCD4, were increased in Ang II infused mice and TAC mice compared with control mice. In vitro, mirVana-miR-21-specific inhibitor attenuated Ang II-induced PDCD4 downregulation and contributed to subsequent deactivation of AP-1/TGF-β1 signaling pathway in neonatal rat cardiomyocytes. Thus, suppression of miR-21 prevents hypertrophic cardiac remodeling by regulating PDCD4, AP-1, and TGF-β1 signaling pathway.

Kloning Gen Transcriptional Activator Protein dan Replication-Associated Protein dari Squash leaf curl China virus Penyebab Penyakit Daun Kuning pada Tanaman Mentimun

Yellow disease on Cucurbitaceae caused by Squash leaf curl China virus (SLCCNV; Begomovirus) is an important disease in many countries. Typical yellow leaf curl symptoms was found on cucumber in Tabanan, Bali. The objective of this research is to clone Transcriptional Activator Protein (TrAp) and Replication-Associated Protein (Rep) of SLCCNV Indonesian isolate. Universal primer for Begomovirus, i.e. SPG1/SPG2 was used to amplify DNA fragment of Begomovirus which cover the TrAp and Rep gene. The amplicon of ± 912 bp in size was then cloned into pTZ57R/T plasmid vector by TA-cloning method to obtain plasmid recombinant pTZ-SLCCNV. The plasmid recombinant was successfully confirmed by PCR colony and DNA sequencing. The nucleotide sequences analysis of plasmid recombinant showed highest homology (98%) of the corresponding gene to pumpkin isolate of SLCCNV from Malaysia.