Biology subjects

Borah, M.

Publications and source records attributed to Borah, M..

3 recordsLinked to original sources

bioRxiv2026

FASTOP - Fast editing toolkit for top expression sites in yeast

Budding yeast Saccharomyces cerevisiae is a workhorse chassis for producing added food and agricultural compounds. However, building multi-enzymatic pathways for these chemicals often requires iterative genomic integration, underscoring the need for efficient, rapid genome-editing tools that can reliably target transcriptionally active chromosomal regions. In this study, to accelerate strain construction, we established a genome-editing toolkit to rapidly engineer eight loci, highly expressed hot-spots, but nonessential genomic sites suitable for stable pathway assembly. Our approach integrates three key design features: (i) selectable markers to enable rapid screening of edited cells, (ii) extended homology arms that leverage the yeast homology-directed repair machinery for robust genomic integration, and (iii) co-delivery of Cas9 and guide RNAs to promote efficient double-stranded DNA breaks at specific integration sites. The sequence independence of FASTOP relies on the release of integration cassettes from integrative vectors, mediated by restriction digestion at two flanking multiple-cutting sites in the integration module to minimize the risk of introducing sequence errors during PCR amplification of the integration cassettes. Following the introduction of a fluorescent reporter cassette, we observed high integration efficiencies across the target sites. We then integrated the biosynthetic pathway of plant-derived flavonoid naringenin into the hot-spots of the yeast genome using the FASTOP toolkit. Our results demonstrated that upon expressing the five essential genes in simple shake flask culture, naringenin production reached 505.7 mg/L, representing a significant (69-fold) increase over previously reported titers for comparable minimal heterologous pathways in S. cerevisiae. Together, the FATSOP toolkit provides a user-friendly platform for reliably modifying hot-spot loci to rapidly construct multi-enzymatic metabolic pathways in S. cerevisiae, while achieving high production levels for high-value food-relevant metabolites.

synthetic biology↗

bioRxiv2026

Fine-tuned synthetic transcription factors for production of 3' phosphoadenosine-5'-phosphosulfate in yeast

Technologies developed over the past decade have made Saccharomyces cerevisiae a promising platform for producing various natural products. Balancing multi-enzyme expression, while maintaining robust microbial growth, remains a limiting factor for engineering long biosynthetic pathways in yeast. Here, we improved the transcriptional capacity of our previously developed isopropyl {beta}-D-1-thiogalactopyranoside (IPTG)-inducible synthetic transcription factors (synTFs) derived from the plant JUB1 DNA-binding domain. To this end, at cysteine positions within surface-exposed loop regions of a JUB1-derived DNA-binding scaffold, we introduced a short peptide to enhance loop flexibility while providing local stability and orientation. The generated synTFs, so-called JUB1-X synTFs, varying in strength, have been successfully used to improve the synthesis of 3-phosphoadenosine 5-phosphosulfate (PAPS), a universal sulfate donor necessary for the synthesis of bioactive molecules, including therapeutic glycosaminoglycans and sulfolipids. Using only this engineered yeast strain in simple batch culture, PAPS accumulation of 21.4 {+/-} 5.8 mg g-1 cdw was achieved after only 5 hours of inducing the expression of JUB1-X synTFs. Beyond PAPS production, the design principle demonstrated here provides a generalizable strategy to fine-tune other plant-derived synTFs, expanding the regulatory capabilities of existing synTF collections. Together, this work offers a modular, scalable approach to constructing high-performance gene circuits and supports the development of yeast cell factories for complex metabolic and synthetic biology applications.

synthetic biology↗

bioRxiv2018

Diversity of Culturable Endophytic bacteria from Wild and Cultivated Rice showed potential Plant Growth Promoting activities

In this paper, we report the endophytic microbial diversity of cultivated and wild Oryza sativa plants including their functional traits related to multiple traits that promote plant growth and development. Around 255 bacteria were isolated out of which 70 isolates were selected for further studies based on their morphological differences. The isolates were characterized both at biochemical and at the molecular level by 16s rRNA gene sequencing. Based on 16S rRNA gene sequencing the isolates were categorized into three major phyla, viz, Firmicutes (57.1 %), Actinobacteria (20.0 %) and Proteobacteria (22.8 %). Firmicutes was the dominant group of bacteria of which the most abundant genus was Bacillus. The isolates were further screened in vitro for plant growth promoting activities which revealed a hitherto unreported endophytic bacterial isolate, Microbacteriaceae bacterium RS01 11 as the highest secretor of a phytohormone, IAA (28.39 {+/-} 1.39 g/ml) and GA (67.23 {+/-} 1.83 g/ml). Bacillus subtilis RHS 01 displayed highest phosphate solubilizing activity (81.70 {+/-} 1.98 g/ml) while, Microbacterium testaceum MK LS01, and Microbacterium trichothecenolyticum MI03 L05 exhibited highest potassium solubilizing activity (53.42{+/-}0.75g/ml) and zinc solubilizing efficiency (157.50%) respectively. Bacillus barbaricus LP20 05 produced highest siderophore units (64.8 %). Potential plant growth promoting isolated were tested in vivo in pot culture under greenhouse conditions. A consortium consisting of Microbacteriaceae bacterium RS01 11, Bacillus testaceum MK LS01 and Bacillus subtilis RHS promoted plant growth and increased the yield 3.4 fold in rice when compared to control T0 when tested in pot culture and reduce application rates of chemical fertilizer to half the recommended dose. Our study confirms the potentiality of the rice endophytes isolated as good plant growth promoter and effective biofertilizer.

microbiology↗