Genetic Responses of Metabolically Active Limnospira indica Strain PCC 8005 Exposed to γ-Radiation during Its Lifecycle

Anu Yadav; Laurens Maertens; Tim Meese; Filip Van Nieuwerburgh; Mohamed Mysara; Natalie Leys; Ann Cuypers; Paul Jaak Janssen

doi:10.3390/microorganisms9081626

Genetic Responses of Metabolically Active Limnospira indica Strain PCC 8005 Exposed to γ-Radiation during Its Lifecycle

Microorganisms. 2021 Jul 30;9(8):1626. doi: 10.3390/microorganisms9081626.

Authors

Anu Yadav^{1

2}, Laurens Maertens^{1

3}, Tim Meese⁴, Filip Van Nieuwerburgh⁴, Mohamed Mysara¹, Natalie Leys¹, Ann Cuypers², Paul Jaak Janssen¹

Affiliations

¹ Interdisciplinary Biosciences, Microbiology Unit, Belgian Nuclear Research Centre (SCKCEN), 2400 Mol, Belgium.
² Environmental Biology, Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium.
³ Research Unit in Biology of Microorganisms (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium.
⁴ Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium.

Abstract

Two morphotypes of the cyanobacterial Limnospira indica (formerly Arthrospira sp.) strain PCC 8005, denoted as P2 (straight trichomes) and P6 (helical trichomes), were subjected to chronic gamma radiation from spent nuclear fuel (SNF) rods at a dose rate of ca. 80 Gy·h^-1 for one mass doubling period (approximately 3 days) under continuous light with photoautotrophic metabolism fully active. Samples were taken for post-irradiation growth recovery and RNA-Seq transcriptional analysis at time intervals of 15, 40, and 71.5 h corresponding to cumulative doses of ca. 1450, 3200, and 5700 Gy, respectively. Both morphotypes, which were previously reported by us to display different antioxidant capacities and differ at the genomic level in 168 SNPs, 48 indels and 4 large insertions, recovered equally well from 1450 and 3200 Gy. However, while the P2 straight type recovered from 5700 Gy by regaining normal growth within 6 days, the P6 helical type took about 13 days to recover from this dose, indicating differences in their radiation tolerance and response. To investigate these differences, P2 and P6 cells exposed to the intermediate dose of gamma radiation (3200 Gy) were analyzed for differential gene expression by RNA-Seq analysis. Prior to batch normalization, a total of 1553 genes (887 and 666 of P2 and P6, respectively, with 352 genes in common) were selected based on a two-fold change in expression and a false discovery rate FDR smaller or equal to 0.05. About 85% of these 1553 genes encoded products of yet unknown function. Of the 229 remaining genes, 171 had a defined function while 58 genes were transcribed into non-coding RNA including 21 tRNAs (all downregulated). Batch normalization resulted in 660 differentially expressed genes with 98 having a function and 32 encoding RNA. From PCC 8005-P2 and PCC 8005-P6 expression patterns, it emerges that although the cellular routes used by the two substrains to cope with ionizing radiation do overlap to a large extent, both strains displayed a distinct preference of priorities.

Keywords: Arthrospira; Limnospira; RNA-Seq; expression analysis; gamma radiation; genetic response; genomics; morphology; radiation resistance.