Project Status: Finished / October 2020 - April 2023

This project will use systems biology research methodologies to investigate the molecular mechanisms that underly the remarkable growth phenotype of the bacterium Vibrio natriegens, which with a doubling time of 9.8 minutes is the fastest growing organism we know.

In addition, the insights attained from this analysis will be leveraged to develop a synthetic biology based systematic design process for the engineering of Escherichia coli strains with tunable growth rate phenotypes for their use as efficient “chassis” in microbial cell factory applications.

Project Page

SpeedyMicrobesSYNBIO

Project Members & Funding

Research Team

Dr. Nicolas Kylilis

PhD in Synthetic Biology and Molecular Biology

Research Fellow

University of Cyprus

Roles: Project Co-ordinator, Project Manager, Researcher

Dr. Vasilis Promponas

Associate Professor in Bioinformatics

Head, Bioinformatics Research Laboratory

University of Cyprus

Roles: Project Manager, Quality Assurance

Advisory Committee

Prof. Guy-Bart Stan
Professor of BioSystems Engineering & Control

Department of Bioengineering

Imperial College London

Prof. Christos Ouzounis

Professor in Bioinformatics

Aristotle University of Thessaloniki

Funders

Cyprus National Research & Innovation Foundation (RIF)

Funding Programme:

“HORIZON 2020 – 2nd OPPORTUNITY”

European Regional Development Fund (EDRF)

Project Implementation

Work Package 1 - Project Management

The objective of this Work Package (WP) is the co-ordination and oversight of the project implementation to ensure delivery of the stated objectives. The project management will ensure the completion of project objectives in a timely manner according to stated timeframes, ensure results are of the highest quality, optimum allocation of financial/material/human resources, transfer of knowledge between the project participants and proper documentation of results and progress achieved.

Work Package 2 - Dissemination Activities

The objective of this WP is the communication of research outcomes to various target audiences (eg. scientific community, general public) and the exploitation of the research results for further research funding and/or establishment of IPRs

Work Package 3 -Research into the Systems Biology of fast growing bacteria

The bacterium Vibrio natriegens is the fastest growing organism known with 9.8 minutes doubling time. To understand how it is able to efficiently allocate cellular resources to achieve such a remarkable growth rate this work package will use a combination of genomics, phenomenological assays of bacterial growth and mathematical modelling to gain a qualitative and quantitative understanding of the systems biology of Vibrio natriegens.

Work Package 4 - Research into Synthetic Biology/systematic design for fast growth

Microbial cell factory applications typically use domesticated bacteria as chassis that include genes necessary for the successful colonization of natural habitats, but which are not relevant for the nutrient-rich, stable conditions of the modern industrial bioreactor. Previous effort for streamlining chassis relied on high-throughput genome minimization methodologies in the absence of a considerate approach to cellular resource rebalancing to materialize gains in growth rate.

Instead, the objective of this WP includes the application of the insights from the V. natriegens studies (WP3) to systematically and rationally design synthetic E. coli strains that actively allocate cellular resources optimally for increased bioproduction capacities and faster growth phenotypes.

Work Package 5 - Transfer of knowledge

The objectives of this WP include:

Transfer of knowledge from the HO to the ER: Enrich skillset, secure further funding for research and expand network of ER towards a career as an independent researcher in academia
Transfer of knowledge from the ER to the HO that aims to enhance the R&D capabilities of the HO in Synthetic Biology research.

Project Outcomes

Research into the Systems Biology of fast growing bacteria

The pangenome of the Vibrio species was analysed
The genomic features (presence of genes, their numbers and organisation on the chromosome) was compared against the genomes of ~300 other bacteria
Vibrio natriegens cell growth rate was measured when grown in different growth media
Vibrio natriegens transcriptome was quantified by the use of RNA-seq technology when grown in different growth media, and analysed for differentially expressed genes and metabolic pathways
Vibrio natriegens proteome was quantified by the use of shotgun proteomics technology when grown in different growth media and analysed for differentially expressed genes and metabolic pathways
Escherichia coli transcriptome was quantified by the use of RNA-seq technology when grown in different concentrations of the antibiotic chloramphenicol, and analysed for differentially expressed genes and metabolic pathways

Research into the Synthetic Biology/systematic design for fast growth

A new mathematical model was developed that describes the bacterial cell growth at the biomolecular level and implemented in Python
A virtual Escherichia coli cell was created by parametrising the bacterial cell growth model using experimental data, bioinformatics analysis & optimisation algorithms
The virtual Escherichia coli cell was integrated with synthetic biology CAD tools for predictive in-silico designs of synthetic genetic circuits/systems
Genetically engineered Escherichia coli strains were developed with altered biomolecular resource allocations using plasmid vectors & chromosomal integration vectors

Dissemination

Follow the project profile @MicrobesSpeedy on Twitter for project news and related news on synthetic biology, molecular biotechnology, microbiology, and microbial bioinformatics & systems biology
Join us for an introductory presentation to the technological & research fields of Synthetic Biology to the “Postgraduate Seminar Series” of the Department of Biological Sciences of the University of Cyprus. The presentation will be deliver (hybrid or online) by the Project Coordinator Nicolas Kylilis, PhD in Synthetic Biology & Molecular Biology on October 7, 2020, at 17:00 in Panepistimioupoli campus of the University of Cyprus, in Aglatzia, Nicosia.
The Project Coordinator Dr.Nicolas Kylilis will be presenting on Synthetic Biology and the SpeedyMicrobes SYNBIO project at the 1st βιος-SBSCy National Conference on Molecular Life Sciences, to be held in Nicosia on 22-23 October 2022 at the University of Cyprus new campus.
The Project Coordinator Dr.Nicolas Kylilis will be presenting on Synthetic Biology and the SpeedyMicrobes SYNBIO project at 2022 Bioinformatics and Computational Biology Conference on December 13-15, 2022