Biology subjects

Darbani, B.

Publications and source records attributed to Darbani, B..

6 recordsLinked to original sources

bioRxiv2026

Phytoplasma mediated transcriptional changes in poinsettia buds suggest MAF3 and bZIP67 transcription factors as potential suppressors of shoot branching

O_LIShoot branching is critical not only in breeding for yield but also for ornamentals architecture. In the ornamental plant poinsettia (Euphorbia pulcherrima), shoot branching has traditionally been induced by phytoplasma (Candidatus Phytoplasma pruni) inoculation. This study aimed to identify regulatory genes that could be leveraged in future breeding-by-genetic engineering efforts to develop phytoplasma-free, branching poinsettia plants. C_LIO_LITo elucidate mechanisms of phytoplasma-induced shoot branching, we performed RNA-sequencing and assembled an axillary bud-specific transcriptome for expression analyses in phytoplasma-infected and -free poinsettia. Phenotyping and RNA-sequencing were also conducted on Arabidopsis mutants and wild-type lines to investigate the transcriptional regulatory effects of candidate genes. C_LIO_LIThe transcription factors EpMAF3 and EpbZIP67 were highly de-regulated in phytoplasma-infected poinsettia. We also found a two-fold increase in primary-stem branching levels of the Arabidopsis maf3 and bzip67 mutants, suggesting the two transcription factors as potential shoot branching suppressors. AtTcp1, a CYC-clade TCP transcription factor, was up-regulated (78x) in leaves of the maf3 mutants. Analyzing previously reported protein-level interactions for the differentially expressed genes (e.g., AtClamt, AtGh3.9/3.15, AtSaur32/36, AtAbi3, AtGamt2, AtTcp3, and AtDwf4) in bzip67 mutants shed light on other shoot branching regulators such as TCPs, PINs, ABIs, DWARF14, and BES1, highlighting two regulatory sub-networks including membrane transport and hormonal signaling. C_LIO_LIThe results open the way to rational engineering of shoot branching in poinsettia by targeted mutagenesis of MAF3 and bZIP67. In that way, the tedious and viral-infection prone process of phytoplasma inoculation can be avoided and poinsettia plants would have more homogenous branching. C_LI One-sentence summaryPhytoplasma infection in poinsettia induces bud-specific repression of the transcription factors EpMaf3 and EpbZip67, consistent with the enhanced stem branching observed in Arabidopsis maf3 and bzip67 mutant lines.

Plant Biology↗

bioRxiv2025

Refining bias correction in genome-wide association analyses of case-control studies

Genome-wide association studies are vulnerable to confounding factors. This study provides evidence-based guidance for minimizing bias associated with genetic relatedness, SNP-specific non-additive allelic interactions, predisposed genotypes among controls, and multi-allelic polymorphism in case-control studies. The analyses demonstrated that genetic similarity within case or control groups introduces experimental bias, whereas genetic relatedness across case-control samples reduces this bias. These findings establish a general framework that can filter genetically related sub-communities or paired samples, whilst preserving maximal statistical power with minimal false-positive rates. Moreover, the skewed odds ratios resulting from predisposed genotypes among controls underscored the importance of age-related filtering to minimize this confounding effect. To ensure accurate genetic estimates, such as polygenic risk scores, the identification of SNP-specific allelic interaction models was also emphasized in case-control studies, contingent on normalization for within-population differences in genotype frequencies. Here, we introduce the Allelic-effect aware Case-Control GWAS (AlleliC-GWAS) tool for identifying SNP-specific allelic effects on binary traits. Finally, we recommend a strategy to accurately capture genetic effects at multi-allelic genomic positions.

bioinformatics↗

bioRxiv2023

SNP Allocation For Estimating Heritability (SAFE-h2): A tool to explore genomic origins of phenotypes for estimation of SNP heritability using additive-only allelic effects or additive and non-additive allelic effects

Polygenicity requires the inclusion of all SNPs to ensure accurate estimation of SNP heritability. However, SNPs with large association p-values should be excluded, as they impose biologically meaningless negative contributions, i.e., downward bias, to heritability estimates. This is demonstrated with simulated data and validated using real-world datasets. We introduce SAFE-h2 as a solution to this dilemma. SAFE-h2 performs heritability profiling and establishes a p-value threshold to filter out SNPs with negative contributions. By examining 74 phenotypes across eight species, SAFE-h2 revealed an average negative contribution of 30 units, imposed by SNPs from the upper-bounds of p-value thresholds. SAFE-h2 also provides a safe p-value interval to minimize false-positive SNP hits and facilitates capturing intra-locus (Ref -alleleSNPi x Ref -alleleSNPi, Ref - alleleSNPi x Alt -alleleSNPi, and Alt -alleleSNPi x Alt -alleleSNPi) additive and non-additive effects within the framework of linear models. The allelic adjustment algorithm of SAFE-h2 revealed considerable uncaptured phenotypic variance when relying on additive effects and improved the SNP heritability estimations by up to 56 units across 50 phenotypes in six species through the combined capture of both additive and non-additive allelic effects.

bioinformatics↗

bioRxiv2020

A Novel Efficient L-Lysine Exporter Identified by Functional Metagenomics

Lack of active export system often limits the industrial bio-based production processes accumulating the intracellular product and hence complexing the purification steps. L-lysine, an essential amino acid, is produced biologically in quantities exceeding two million tons per year; yet, L-lysine production is challenged by efficient export system at high titres during fermentation. To address this issue, new exporter candidates for efficient efflux of L-lysine are needed. Using metagenomic functional selection, we identified 58 genes encoded on 28 unique metagenomic fragments from cow gut microbiome library that improved L-lysine tolerance. These genes include a novel putative L-lysine transporter, belonging to a previously uncharacterized EamA superfamily. Characterization using Xenopus oocyte expression system as well as an Escherichia coli host demonstrates activity as a L-lysine transporter. This novel exporter improved L-lysine tolerance in E. coli by 40% and enhanced the specific productivity of L-lysine in an industrial Corynebacterium glutamicum strain by 12%. Our approach allows the sequence-independent discovery of novel exporters and can be deployed to increase titres and productivity of toxicity-limited bioprocesses.

molecular biology↗

bioRxiv2019

Engineering the yeast Saccharomyces cerevisiae for the production of L-(+)-ergothioneine

L-(+)-Ergothioneine is an unusual, naturally occurring antioxidant nutraceutical that has been shown to help reduce cellular oxidative damage. Humans do not biosynthesise it, so can acquire it only from their diet; it exploits a specific transporter (SLC22A4) for its uptake. ERG is considered to be a nutraceutical and possible vitamin that is involved in the maintenance of health, and seems to be at too low a concentration in several diseases in vivo. Ergothioneine is thus a potentially useful dietary supplement. Present methods of commercial production rely on extraction from natural sources or on chemical synthesis. Here we describe the engineering of the bakers yeast Saccharomyces cerevisiae to produce ergothioneine by fermentation in defined media. After integrating combinations of ERG biosynthetic pathways from different organisms, we screened yeast strains for their production of ERG. The highest-producing strain was also engineered with known ergothioneine transporters. The effect of amino acid supplementation of the medium was investigated and the nitrogen metabolism of S. cerevisiae was altered by knock-out of TOR1 or YIH1. We also optimized the media composition using fractional factorial methods. Our optimal strategy led to a titer of 598 {+/-} 18 mg/L ergothioneine in fed-batch culture in bioreactors. Because S. cerevisiae is a GRAS ( generally recognised as safe) organism that is widely used for nutraceutical production, this work provides a promising process for the biosynthetic production of ERG.

bioengineering↗

bioRxiv2017

Energetic Evolution of Cellular Transportomes

Transporter proteins mediate the translocation of substances across the membranes of living cells. We performed a genome-wide analysis of the compositional reshaping of cellular transporters (the transportome) across the kingdoms of bacteria, archaea, and eukarya. We show that the transportomes of eukaryotes evolved strongly towards a higher energetic efficiency, as ATP-dependent transporters diminished and secondary transporters and ion channels proliferated. This change has likely been important in the development of tissues performing energetically costly cellular functions. The transportome analysis also indicated seven bacterial species, including Neorickettsia risticii and Neorickettsia sennetsu, as likely origins of the mitochondrion in eukaryotes, due to the restricted presence therein of clear homologues of modern mitochondrial solute carriers.

evolutionary biology↗