Sequencing the
genome of a useful bacteria: Paenarthrobacter
nicotinovorans – next step in extending it’s
biotechnological applications
(PaeNicGenom)
PN-III-P4-ID-PCE-2020-0656, No. PCE 152 / 2021
- Research
project funded by the Ministry of Education and
Scientific Research - Executive Unit for Financing
Higher Education, Research, Development and Innovation
(UEFISCDI), PNCDI III - P4 - Fundamental and frontier
research
- Funding
amount - 1.198.032 lei (approx. 246.000 euro);
- Funding period - 36 months (4.01.2021 - 32.12.2023).
Project summary:
Paenarthrobacter nicotinovorans pAO1 is a nicotine degrading microorganism that shows promising applications in converting nicotine-containing waste into useful green chemicals. Its biotechnological applications are nevertheless hampered by the lack of knowledge and tools to perform genetic and metabolic engineering. After solving the nicotine-induced proteome of this bacteria, the project leader of the current proposal concluded that none of the draft genomes available for this strain are complete. The current application aims to provide the first complete and annotated genome of P. nicotinovorans pAO1, and, as such, the first complete genome of a nicotine degrading microorganism. In order to achieve this, P. nicotinovorans pAO1 gDNA will be isolated and whole-genome sequencing (WGS) will be performed using two platforms: NGS Illumina for reading depth and ONT MinION for scaffolding and assembling the genome. The quality of the assembly and annotation will be addressed using dRNA-seq and the already available raw proteomics data. The project will not only strengthen the much need bioinformatics know-how in the already existing team of the project leader, but also will group allow the group to generate a genome-scale metabolic model of the nicotine metabolism, and, consecutively, to develop high yield bio-technologies for production on nicotine derivatives
Main results and impact:
The most important result of the project is making available to the scientific community a set of reference data-sets:
- the first complete and annotated genome of an nicotine-degrading bacteria Paenarthrobacter nicotinovorans ATCC 49199: GenBank CP089293 and CP089294, as well as the associated raw data: PRJNA693273
- a transcriptomics data-set dealing with the nicotine metabolism in Paenarthrobacter nicotinovorans ATCC 49199: Gene Expression Omnibus GSE240220;
- a complete re-analysis of the proteomics data-set PXD008756 and its integration with the genomics and transcriptomics data-sets to offer a multi-omics analysis if nicotine metabolism.
These public data-sets will allow a better understanding of the nicotine degradation pathway and will allow researchers to manipulate the pathway in order to develop a biotechnology for conversion of nicotine containing waste into green chemicals such as succinic acid, methyl-amine, or nicotine derivatives.
Project members:
| Alexandru Ioan Cuza
University of Iași |
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Project coordinator | More details | |
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Microbiology | U-1700-039M-8493 | |
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Biochemistry and Molecular Biology | More details | |
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| MunteanuIustin Tiberius | |||
| Amada El-Sabeh | |||
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| Honceriu Iasmina |
master student |
General objective - Provide the first complete and annotated genome of P. nicotinovorans pAO1, and, as such, the first complete genome of a nicotine degrading microorganism. In order to achieve this, P. nicotinovorans pAO1 gDNA will be isolated and whole-genome sequencing (WGS) will be performed using two platforms: NGS Illumina for reading depth and ONT MinION for scaffolding and assembling the genome. The quality of the assembly and annotation will be addressed using dRNA-seq and the already available raw proteomics data.
Activities in 2021:
A.1.
gDNA isolation from Paenarthrobacter nicotinovorans;
A.2.WGS (whole geneome sequencing) of isoalated gDNA;
A.3. RNA-seq library prep
A.4. Data analysis and literature survey;
Activities in 2022:
A1.
Assemble the draft genome.
A.2.Prepare RNA-seq libraries from P. nicotinovorans grown
in the presence and absence of nicotine;
A.3. Direct dRNA-seq of P. nicotinovorans transcriptome;
A.4. Data analysis and literature survey;
A.1. Direct dRNA-seq of P. nicotinovorans transcriptome;
A.2. Data analysis and literature survey;
A.2. Dissemination of the results
Contact
Project manager:
Marius Mihășan, PhD
E-mail: marius.mihasan@uaic.ro
Phone: 40(0)232201102 - 1524
Fax: 40(0)232201472
Further details: here
