De novo genome assembly and pan-genome analysis of the fast-growing Indian isolates of Synechococcus elongatus: Potential chassis for bioproduction

• Published in: The Microbe Vol. 2; no. C; p. 100048
• Main Authors: Jain, Virmal S., Schubert, Max G., Sarnaik, Aditya P., Pritam, Prem, Jaiswal, Damini, Church, George M., Wangikar, Pramod P.
• Format: Journal Article
• Language: English
• Published: Elsevier Ltd 01.03.2024; Elsevier
• Subjects: Bio-production; Comparative genomics; Cyanobacteria; Episomes; Promoter portability; Synthetic biology; Comparative genomics; Episomes; Promoter portability; Synthetic biology; Bio-production; Cyanobacteria
• ISSN: 2950-1946
• DOI: 10.1016/j.microb.2024.100048

Cyanobacteria are explored as phototrophic cell factories for the conversion of CO2 to chemicals. Although several cyanobacterial platforms have been established, discovering novel cyanobacterial strains with different growth and metabolic traits would be advantageous. Here, we describe de novo genome assembly and pan-genome analysis of eight fast-growing Indian isolates of Synechococcus elongatus, displaying an average doubling time of 3–4 h. The draft genome sequences of S. elongatus PCC 11801 and PCC 11802 were earlier reported by our group. However, here we present circular un-gapped genome sequences of all the eight strains. Their pan-genome analysis showed that these strains form a distinct sub-clade within the S. elongatus clade, and are closely related to a widely used cyanobacterium S. elongatus PCC 7942. Pan-genome and extra-chromosomal DNA sequence analyses further revealed intriguing features, including CRISPR-associated protein genes, circular episomal elements, and other essential genes which were previously not reported for this clade. Further, from bio-engineering perspective, we optimized their transformation using neutral site integrative plasmids. The heterologous protein expression was confirmed using eYFP reporter system, and validated by engineering a mannitol biosynthesis pathway in these strains. Although the strains exhibited comparable eYFP fluorescence, the mannitol production varied significantly, indicating physiological differences among the strains. The maximum mannitol was obtained from S. elongatus IITB6 strain. Overall, this work encompasses comparative growth analysis of the eight Indian isolates of S. elongatus, their genome sequences and pan-genome analysis. We demonstrated their potential as phototrophic cell factories, providing cyanobacterial bio-chassis options. [Display omitted] •Complete genome sequence and features of eight fast-growing cyanobacterial isolates from India.•Discovery of intriguing genetic elements like episomes, novel genes, and indels.•Cloning using optimized transformation protocol and heterologous protein expression analysis.•Demonstrating the strain-specific potential of CO2 to chemical-producing cell factories.