Strain specific proteome discovery in limnospira indica

Motivation:
Limnospira indica has long been a model organism in space biology research at SCK CEN, particularly for its role in closed-loop life support systems. While previous studies have focused on strain P3, recent findings suggest that strain P1 may exhibit distinct proteomic signatures under space-relevant conditions such as radiation and microgravity. Understanding the molecular differences between these strains is crucial for optimizing their use in biotechnological applications. However, conventional annotation pipelines often miss novel or strain-specific proteins, limiting our ability to interpret functional differences.

Objective:
The objective of this project is to perform a comparative proteomics analysis of Limnospira strains P1 and P3 using de novo peptide sequencing tools to identify novel proteins and characterize their functional roles. This will help uncover strain-specific adaptations and improve our understanding of their biological responses.

Approach:

• Perform high-resolution mass spectrometry on both P1 and P3 strains.
• Use de novo sequencing tools to identify novel peptides and proteins not present in current databases.
• Conduct functional enrichment and pathway analysis to interpret biological differences.
• Integrate findings with previous structural predictions to validate and expand protein function annotations.

References:

• https://www.nature.com/articles/s41467-021-23303-9#author-information
• https://www.nature.com/articles/s41467-024-50955-0?fromPaywallRec=false#Abs1
• https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01916-8