TABLE 1

Genes of JCVI-syn2.0 that show a skew in the orientation of transposon insertionsa

BegEndDirectionPreferred insertion orientationRGD fragmentLength (aa)Locus tagGene HSW 150126P1FP1RP1F:RP2FP2RP2F:RP6FP6RP6F:RLikely reasonFlanking gene affectedNew context in syn2.0?Current annotationFunctional classificationSystem
26753217ff1180_0003i501630.33100.99Upstream train wreck avoided(_0002) DNA Pol III beta subunitNoRNase MSEquivalogRibosome biogenesis
5590956499rr1196_0046n01213130.62041Downstream read-through needed(_0045) thymidylate kinaseNoRecombination proteinEquivalogDNA repair
6372764701ff1324_0063n2270.5253120.632220.83Downstream read-through needed(_0064) lysyl tRNA synthetaseNoUncharacterized tRNA dihydrouridine synthaseGenerictRNA modification
7469775536rr1279_0077n190.83270.8041Downstream read-through needed(_0076) asparaginal tRNA synthetaseNoLow-specificity hydrolasePutativeUnclear
7775277973rr173_0080n0612100.67021??NoUncharacterized proteinUnknownUnclear
8770888820rr2370_0108i3150.672120.71021Downstream read-through needed(_0107) nusB transcription antiterminationNoLipoprotein, putativeGenericLipoprotein
91384192304rf2306_0114i410.6620.5000Downstream train wreck avoided(_0113) glycosyl transferase, group 2NoGlycosyltransferase, group 2 family proteinPutativeLipid salvage and biogenesis
101419102480fr2353_0132i031071000Downstream read-through lethal(_0133) toxin-peptidase, S8/S53 familyNoToxin-antitoxin AAA ATPaseProbableToxin-antitoxin
125069125563rr2164_0164i061140.6000Downstream read-through needed(_0163) alanyl tRNA synthetaseNoHypothetical proteinUnknownUnclear
204874205368rr3164_0301i260.5010.99000Downstream read-through needed(_0300) nusA transcription termination/antiterminationNorimPPutativeRibosome biogenesis
294566297532rr4988_0415i160.71130.5000??NoChromosome segregation protein SMCEquivalogChromosome segregation
468223469179rr7318_0697n4110.47350.25081Downstream read-through needed(_0696) RDD family proteinYes (upstream)Glycosyltransferase, group 2 family proteinGenericUnclear
477490478326ff7278_0728i1550.5610.71000Downstream read-through needed(_0729) phosphoglycerate mutaseNoHAD hydrolase, family IIBGenericUnclear
483396484049ff7217_0747i910.8021000??Yes (up- and downstream)punAProbableNucleotide salvage
506742507185rr8147_0800i190.8100.99000Downstream read-through needed(_0799) glyA, serine hydroxymethyltransferaseYes (upstream)rpiB: ribose 5-phosphate isomerase BEquivalogMetabolic process
514997516172rr8391_0805i2180.8061021Downstream read-through needed(_0804) RNA Pol, beta subunitNoTranscription factorGenericRegulation
  • a Data correspond to the indicated 16 genes that show a skew in the orientation of viable Tn5-Puror insertions. The coordinates of each gene on the JCVI-syn2.0 genome (GenBank accession no. CP014992.1) are listed in the “Beg” (beginning) and “End” columns. Columns P1F, P2F, and P6F list the numbers of different insertion sites for Tn5-Puror in a particular gene in the “forward orientation” observed for passages 1, 2, and 6. The analogous numbers of insertion sites in the “reverse orientation” are shown in columns P1R, P2R, and P6R. Skew values were calculated for each gene at generations 1, 2, and 6 as described in the text, and data are listed as PnF:R (where “n” represents the passage number). For example, the skew value for gene _0046 in passage 2 is P2F:R = ABS (3 − 14)/16 = 0.62. A likely reason for the observed skew is listed where the data suggest one (see column “Likely reason”). The flanking gene whose functionality likely depends on the orientation of the Tn5-Puror insertion is indicated in the “Flanking gene affected” column. If the context of the gene in JCVI-syn2.0 is different from that in JCVI-syn1.0, due to removal of flanking genes, then this is indicated. Information concerning the annotation for each listed gene is shown in the last three columns, “Current annotation,” “Functional classification,” and “System” (updated from a previously described annotation [2]). aa, amino acids; Equivalog, gene (or corresponding encoded protein) that is known to have been conserved in function since the last common ancestral sequence; Pol III, polymerase III; RGD, Arg-Gly-Asp.