Synthetic Scaffold Systems for Increasing the Efficiency of Metabolic Pathways in Microorganisms.

Microbes have been the preferred hosts for producing high-value chemicals from cheap raw materials. However, metabolic flux imbalance, the presence of competing pathways, and toxic intermediates often lead to low production efficiency. The spatial organization of the substrates, intermediates, and enzymes is critical to ensuring efficient metabolic activity by microorganisms. One of the most common approaches for bringing the key components of biosynthetic pathways together is through molecular scaffolds, which involves the clustering of pathway enzymes on engineered molecules via different interacting mechanisms. In particular, synthetic scaffold systems have been applied to improve the efficiency of various heterologous and synthetic pathways in Escherichia coli and Saccharomyces cerevisiae, with varying degrees of success. Herein, we review the recent developments and applications of protein-based and nucleic acid-based scaffold systems and discuss current challenges and future directions in the use of such approaches.

Data on banana transcriptome in response to blood disease infection.

Blood disease of Banana (BDB) is one of the prevalent disease caused by Ralstonia syzygii subsp. celebesensis (Rsc) which cause substantial loss on banana production in Indonesia. To date, the genetic basis of plant defense mechanism caused by blood disease in banana is not available. As a matter of fact, the knowledge of global gene expression will provide important information on plant response to the pathogen infection. Data from transcriptomic analysis in response to blood disease infection from Musa acuminata cv. Mas Kirana (AA group), representing the A genome, and Musa balbisiana cv. Klutuk (BB group), representing the B genome, were firstly reported. The transcriptome data discussed in this publication are accessible through NCBI's Gene Expression Omnibus with GEO Series accession number GSE138749. These data provide the basis for further investigation on the global gene expression which is pivotal to understand the mechanism of disease resistance from two banana genomes in response to blood disease infection.

Crystal structure of the Melampsora lini effector AvrP reveals insights into a possible nuclear function and recognition by the flax disease resistance protein P.

The effector protein AvrP is secreted by the flax rust fungal pathogen (Melampsora lini) and recognized specifically by the flax (Linum usitatissimum) P disease resistance protein, leading to effector-triggered immunity. To investigate the biological function of this effector and the mechanisms of specific recognition by the P resistance protein, we determined the crystal structure of AvrP. The structure reveals an elongated zinc-finger-like structure with a novel interleaved zinc-binding topology. The residues responsible for zinc binding are conserved in AvrP effector variants and mutations of these motifs result in a loss of P-mediated recognition. The first zinc-coordinating region of the structure displays a positively charged surface and shows some limited similarities to nucleic acid-binding and chromatin-associated proteins. We show that the majority of the AvrP protein accumulates in the plant nucleus when transiently expressed in Nicotiana benthamiana cells, suggesting a nuclear pathogenic function. Polymorphic residues in AvrP and its allelic variants map to the protein surface and could be associated with differences in recognition specificity. Several point mutations of residues on the non-conserved surface patch result in a loss of recognition by P, suggesting that these residues are required for recognition.

Low cost HIV-1 quantitative RT-PCR assay in resource-limited settings: improvement and implementation.

Monitoring of HIV viral load in low and middle income settings is limited by high cost of the commercial assays. Therefore, we developed a novel RT-PCR quantitative assay was developed. This assay targets the HIV-1 pol integrase gene (INT). Subsequently, the performance of the INT assay, described previously as a Long Terminal Repeat (LTR) assay and a combined INT/LTR dual target RT-PCR assay was compared. The LTR-assay was found to be sensitive and cost-effective (50-70% cheaper than commercial assays) with the lowest coefficient of variation (%CV). Introduction of an internal standard further improved assay reliability. Therefore, this LTR assay was implemented in West Java, Indonesia. Linearity and precision of the LTR assay were good: %CV ranged from 1.0% to 10.4%. The limit of quantitation was 616 copies/ml. Performance was comparable with the commercial assay (Abbott assay) (r(2)=0.01), although on average the viral loads were 0.39 log(10)copies/ml lower. In clinical practice, it had excellent capability for monitoring treatment failure, the positive predictive value was 99% and the negative predictive value was 93%. In conclusion, the implementation of the improved HIV-1 viral load LTR-assay for routine diagnosis in resource poor settings can be a good alternative when commercial assays are unaffordable.