Slow-growing cells within isogenic populations have increased RNA polymerase error rates and DNA damage.
Isogenic cells show a large degree of variability in growth rate, even when cultured in the same environment. Such cell-to-cell variability in growth can alter sensitivity to antibiotics, chemotherapy and environmental stress. To characterize transcriptional differences associated with this variability, we have developed a method--FitFlow--that enables the sorting of subpopulations by growth rate. The slow-growing subpopulation shows a transcriptional stress response, but, more surprisingly, these cells have reduced RNA polymerase fidelity and exhibit a DNA damage response. As DNA damage is often caused by oxidative stress, we test the addition of an antioxidant, and find that it reduces the size of the slow-growing population. More generally, we find a significantly altered transcriptome in the slow-growing subpopulation that only partially resembles that of cells growing slowly due to environmental and culture conditions. Slow-growing cells upregulate transposons and express more chromosomal, viral and plasmid-borne transcripts, and thus explore a larger genotypic--and so phenotypic--space.
1] Department of Biological Sciences, Columbia University, New York, New York 10027, USA [2] Department of Systems Biology, Columbia University, New York, New York 10027, USA [3] Department of Applied Mathematics, Weizmann Institute of Science, Rehovot, 7610001, Israel [4] Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel.
David
D
van Dijk
1] EMBL-CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain.
Riddhiman
0000000346420492
R
Dhar
Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona Spain.
Alsu M
AM
Missarova
Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona Spain.
Lorena
L
Espinar
1] Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain [2] Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain.
William R
WR
Blevins
1] EMBL-CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain [2] Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain [3] Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, 08010 Barcelona, Spain.
Ben
B
Lehner
Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona Spain.
Lucas B
0000000272456379
LB
Carey
D049109:Cell Proliferation / Q000502:physiology*; D004249:DNA Damage; D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000378:metabolism*; D005434:Flow Cytometry / Q000379:methods; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism*; D015966:Gene Expression Regulation, Fungal / Q000502:physiology; D012331:RNA, Fungal / Q000235:genetics / Q000378:metabolism; D015003:Yeasts / Q000235:genetics* / Q000378:metabolism*
D005656:Fungal Proteins; D012331:RNA, Fungal; D012321:DNA-Directed RNA Polymerases