The essential gene set of a photosynthetic organism.
Synechococcus elongatus PCC 7942 is a model organism used for studying photosynthesis and the circadian clock, and it is being developed for the production of fuel, industrial chemicals, and pharmaceuticals. To identify a comprehensive set of genes and intergenic regions that impacts fitness in S. elongatus, we created a pooled library of ∼ 250,000 transposon mutants and used sequencing to identify the insertion locations. By analyzing the distribution and survival of these mutants, we identified 718 of the organism's 2,723 genes as essential for survival under laboratory conditions. The validity of the essential gene set is supported by its tight overlap with well-conserved genes and its enrichment for core biological processes. The differences noted between our dataset and these predictors of essentiality, however, have led to surprising biological insights. One such finding is that genes in a large portion of the TCA cycle are dispensable, suggesting that S. elongatus does not require a cyclic TCA process. Furthermore, the density of the transposon mutant library enabled individual and global statements about the essentiality of noncoding RNAs, regulatory elements, and other intergenic regions. In this way, a group I intron located in tRNA(Leu), which has been used extensively for phylogenetic studies, was shown here to be essential for the survival of S. elongatus. Our survey of essentiality for every locus in the S. elongatus genome serves as a powerful resource for understanding the organism's physiology and defines the essential gene set required for the growth of a photosynthetic organism.
Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093;
Benjamin E
BE
Rubin
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
Kelly M
KM
Wetmore
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
Morgan N
MN
Price
Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093;
Spencer
S
Diamond
Kavli Institute for Brain and Mind, University of California, San Diego, La Jolla, CA 92093;
Ryan K
RK
Shultzaberger
Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093;
Laura C
LC
Lowe
Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093;
Genevieve
G
Curtin
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; Department of Bioengineering, University of California, Berkeley, CA 94720.
Adam P
AP
Arkin
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
Adam
A
Deutschbauer
Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093; sgolden@ucsd.edu.
Susan S
SS
Golden
D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D002244:Carbon / Q000737:chemistry; D004251:DNA Transposable Elements; D018076:DNA, Complementary / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D015723:Gene Library; D020043:Genes, Essential; D016680:Genome, Bacterial; D005838:Genotype; D007438:Introns; D008969:Molecular Sequence Data; D009154:Mutation; D010788:Photosynthesis / Q000235:genetics*; D010802:Phylogeny; D012356:RNA, Transfer, Leu / Q000378:metabolism; D022661:RNA, Untranslated / Q000378:metabolism; D046940:Synechococcus / Q000235:genetics*
D001426:Bacterial Proteins; D004251:DNA Transposable Elements; D018076:DNA, Complementary; D012356:RNA, Transfer, Leu; D022661:RNA, Untranslated; D002244:Carbon
RB-TnSeq; Tn-seq; cyanobacteria; photosynthesis; transposon mutagenesis