Biology subjects

Currin, A.

Publications and source records attributed to Currin, A..

3 recordsLinked to original sources

bioRxiv2023

High quality de novo genome assembly of non-conventional yeast Kazachstania bulderi a new potential low pH production host for biorefineries.

Kazachstania bulderi is a yeast species belonging to a ubiquitous group of non-conventional yeasts which has the ability to grow efficiently on glucose and {delta}-gluconolactone at low pH. This unique trait makes K. bulderi an ideal candidate as a new host for low pH fermentation processes for sustainable production of green chemicals such as organic acids. To accelerate strain development with this species, detailed information of its genetics is needed. Here, by employing high accuracy long read sequencing we report a high-quality phased genome assembly for three strains belonging to K. bulderi species, including the type strain. The sequences were assembled into 12 chromosomes with a total length of 14Mb, and the genome was fully annotated at structural and functional levels, including allelic and structural variants, ribosomal array, centromeres and mating type locus. This high-quality reference genome provides an essential resource to advance our fundamental knowledge of biotechno-logically relevant non-conventional yeasts and to support the development of genetic tools for manipulating such strains towards their use as production hosts biotechnological processes.

genomics↗

bioRxiv2022

Telomere to telomere sequence of model Aspergillus fumigatus genomes

The pathogenic fungus Aspergillus fumigatus is a major etiological agent of fungal invasive and chronic diseases affecting tens of millions of individuals worldwide. A high-quality reference genome is a fundamental resource to study its biology, pathogenicity and virulence as well as to discover better and more effective treatments against diseases caused by this fungus. Here, we used PacBio Single Molecule Real-Time (SMRT) and Oxford Nanopore sequencing for de novo genome assembly of two laboratory reference strains of A. fumigatus,CEA10 and A1160. We generated full length chromosome assemblies and a comprehensive telomere to telomere coverage for these two strains including ribosomal repeats and the sequences of centromeres, which we discovered to be composed of long transposon elements.

genomics↗

bioRxiv2019

Directed evolution of the PcaV allosteric transcription factor to generate a biosensor for aromatic aldehydes

BackgroundGenetically encoded biosensors are useful tools for the detection of metabolites and industrially valuable molecules, and present many potential applications in biotechnology and biomedicine. However, the most common approach to develop biosensors relies on employing a limited set of naturally occurring allosteric transcript factors (aTFs). Therefore, altering the substrate specificity of aTFs towards the detection of new effectors is an important goal.\n\nResultsHere, the PcaV repressor, a member of the MarR aTF family, was used to develop a biosensor for the detection of hydroxyl-substituted benzoic acids, including protocatechuic acid (PCA). The PCA biosensor was further subjected to directed evolution to alter its substrate specificity towards vanillin and other closely related aromatic aldehydes, to generate the Van2 biosensor. Substrate recognition of Van2 was explored in vitro using a range of biochemical and biophysical analyses, and extensive in vivo genetic-phenotypic analysis was performed to determine the role of each amino acid change upon biosensor performance.\n\nConclusionsThis is the first study to report directed evolution of a member of the MarR aTF family, and demonstrates the plasticity of the PCA biosensor by altering its substrate specificity to generate a biosensor for aromatic aldehydes.

bioengineering↗