Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: The essential gene set of a photosynthetic organism

doi: 10.1073/pnas.1519220112

Figure Lengend Snippet: Gene essentiality in central metabolism. (A) The number of genes that are conserved and nonredundant members of the Calvin–Benson cycle (CBC), the TCA cycle, glycolysis (Gly), and the pentose phosphate pathway (PPP). In the disagreements column, conserved nonredundant members of these pathways that are not essential are shown. (B) Genotypic characterization of the recreated fumC mutant. Lane 1, standard 1-kb ladder (New England BioLabs); lane 2, amplification of WT DNA with primers surrounding the fumC gene; lane 3, amplification of fumC mutant (8S42-O6), in which a 1.3-kb insertion is present, with the same primers. Each band is representative of three colonies tested. (C) Growth curves of the WT and fumC mutant strain. The error bars indicate the SDs for three independent replicates. (D) Essentiality in the TCA cycle. For enzymes that are present in S. elongatus, their names are shown: acnB (SynPCC7942_0903), icd (SynPCC7942_1719), sdhB (SynPCC7942_1533), fumC (SynPCC7942_1007), gltA (SynPCC7942_0612), maeA (SynPCC7942_1297), and ppc (SynPCC7942_2252). Abbreviations for enzymes that are missing are shown in white boxes: MDH, malate dehydrogenase; MQO, malate:quinone oxidoreductase; 2-OGDH, 2-oxoglutarate dehydrogenase; STK, succinate thiokinase.

Article Snippet: Lane 1, standard 1-kb ladder (New England BioLabs); lane 2, amplification of WT DNA with primers surrounding ncRNA136 and both flanking genes; lane 3, amplification with the same primers of the region, in which the gene that flanks the ncRNA136 on the left, SynPCC7942_0413 (2E11-E-C4), carries a 1.3-kb insertion; lane 4, amplification with the same primers of a putative transformant, in which interruption of ncRNA136 (2E11-E-N7) was attempted, but the 1.3-kb insertion is absent; lane 5, amplification with the same primers of the region, in which the gene that flanks the ncRNA136 on the right, SynPCC7942_0414 (2E11-E-N11), carries a 1.3-kb insertion.

Techniques: Mutagenesis, Amplification

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: The essential gene set of a photosynthetic organism

doi: 10.1073/pnas.1519220112

Figure Lengend Snippet: Genotypic characterization of the recreated tal mutant. Lane 1, standard 1-kb ladder (New England BioLabs); lane 2, amplification of WT DNA with primers surrounding the tal gene; lane 3, amplification of tal mutant (UGS-3-C-11), which carries a 1.3-kb insertion, with the same primers. Each band is representative of three colonies tested.

Article Snippet: Lane 1, standard 1-kb ladder (New England BioLabs); lane 2, amplification of WT DNA with primers surrounding ncRNA136 and both flanking genes; lane 3, amplification with the same primers of the region, in which the gene that flanks the ncRNA136 on the left, SynPCC7942_0413 (2E11-E-C4), carries a 1.3-kb insertion; lane 4, amplification with the same primers of a putative transformant, in which interruption of ncRNA136 (2E11-E-N7) was attempted, but the 1.3-kb insertion is absent; lane 5, amplification with the same primers of the region, in which the gene that flanks the ncRNA136 on the right, SynPCC7942_0414 (2E11-E-N11), carries a 1.3-kb insertion.

Techniques: Mutagenesis, Amplification

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: The essential gene set of a photosynthetic organism

doi: 10.1073/pnas.1519220112

Figure Lengend Snippet: Essentiality of ncRNAs. (A) The distribution of insertion indexes for the recently discovered ncRNAs (45). Axes are the same as in Fig. 2A. (B) The insertion distribution in and around the group I intron: ncRNA136. Lengths of black vertical bars represent numbers of sequence reads, and green bars indicate positions of insertions. The nonessential genes surrounding the essential ncRNA136 (red arrow) are shown as blue arrows. Black triangles indicate the locations of insertion mutations used to support the essentiality of ncRNA136. (C) Genotypic characterization of the failure to create a mutant of ncRNA136. Lane 1, standard 1-kb ladder (New England BioLabs); lane 2, amplification of WT DNA with primers surrounding ncRNA136 and both flanking genes; lane 3, amplification with the same primers of the region, in which the gene that flanks the ncRNA136 on the left, SynPCC7942_0413 (2E11-E-C4), carries a 1.3-kb insertion; lane 4, amplification with the same primers of a putative transformant, in which interruption of ncRNA136 (2E11-E-N7) was attempted, but the 1.3-kb insertion is absent; lane 5, amplification with the same primers of the region, in which the gene that flanks the ncRNA136 on the right, SynPCC7942_0414 (2E11-E-N11), carries a 1.3-kb insertion. Each band is representative of genotyping of three colonies.

Article Snippet: Lane 1, standard 1-kb ladder (New England BioLabs); lane 2, amplification of WT DNA with primers surrounding ncRNA136 and both flanking genes; lane 3, amplification with the same primers of the region, in which the gene that flanks the ncRNA136 on the left, SynPCC7942_0413 (2E11-E-C4), carries a 1.3-kb insertion; lane 4, amplification with the same primers of a putative transformant, in which interruption of ncRNA136 (2E11-E-N7) was attempted, but the 1.3-kb insertion is absent; lane 5, amplification with the same primers of the region, in which the gene that flanks the ncRNA136 on the right, SynPCC7942_0414 (2E11-E-N11), carries a 1.3-kb insertion.

Techniques: Sequencing, Mutagenesis, Amplification