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README.md

A systematic overexpression approach reveals native targets to increase squalene production in Synechocystis sp. PCC 6803

Original publication

Germann AT, Nakielski A, Dietsch M, Petzel T, Moser D, Triesch S, Westhoff P and Axmann IM (2023) A systematic overexpression approach reveals native targets to increase squalene production in Synechocystis sp. PCC 6803. Front. Plant Sci. 14:1024981. doi: 10.3389/fpls.2023.1024981

Copyright

Copyright © 2023 Germann, Nakielski, Dietsch, Petzel, Moser, Triesch, Westhoff and Axmann. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

ARC structure

green indicates a study; yellow indicates an assay

flowchart LR
p(publication)-->s1(Englund-2014) & s5(KnoopAndSteuer-2015)
s1-->s2
s3-->s2
s5--->a5
p-->s2(Synechocystis) -->a1(AbsorptionSpectraAndODMeasurements) & a2(DCWMeasurement) & a3(PigmentQuantification) & a4(qPCR) 
p-->s3(PlasmidAndStrainConstruction)--->a5(MetabolicModeling) & a7(cPCR)
p-->s4(MeasurementsOfSqualeneProduction)--->a6(GS-MSMeasurementsForTheQuantificationOfSqualene)

%%Define styles
    classDef study fill:#58D68D,stroke:#010802,color:#010802;
    classDef publication fill:#E9544A,stroke:#010802,color:#010802;
    classDef assay fill:#F4D03F,stroke:#010802,color:#010802;
%%Assign styles
class s1,s2,s3,s4,s5 study;
class p publication;
class a1,a2,a3,a4,a5,a6,a7 assay;    

flowchart LR
subgraph studies\PlasmidAndStrainConstruction
direction LR
pl1(pEERM4_Cm_001)-->|PlasmidConstruction.md|pl10(pEERM4_Prha_dxs)-->m
pl2(pEERM4_Cm_002)-->|PlasmidConstruction.md|pl20(pEERM4_Prha_ispD)-->m
pl3(pEERM4_Cm_003)-->|PlasmidConstruction.md|pl30(pEERM4_Prha_ispE)-->m
pl4(pEERM4_Cm_004)-->|PlasmidConstruction.md|pl40(pEERM4_Prha_ispF)-->m
pl5(pEERM4_Cm_005)-->|PlasmidConstruction.md|pl50(pEERM4_Prha_ispG)-->m
pl6(pEERM4_Cm_006)-->|PlasmidConstruction.md|pl60(pEERM4_Prha_ispH)-->m
pl7(pEERM4_Cm_007)-->|PlasmidConstruction.md|pl70(pEERM4_Prha_idi)-->m
pl8(pEERM4_Cm_008)-->|PlasmidConstruction.md|pl80(pEERM4_Prha_sqs)-->m
pl9(pEERM4_Cm_009)-->|PlasmidConstruction.md|pl90(pEERM4_Prha_crtE)-->m
pl010(pEERM4_Cm_010)-->|PlasmidConstruction.md|pl0100(pEERM4_Prha_gap2)-->m
pl11(pEERM4_Cm_011)-->|PlasmidConstruction.md|pl110(pEERM4_Prha_pyrK)-->m
pl12(pEERM4_Cm_012)-->|PlasmidConstruction.md|pl120(pEERM4_Prha_tpi)-->m
pr(pSHDY)-->|PromoterInduction.md|pr01(pSHDY_J23119_rhaS)-->m
m-->|StrainConstruction.md|str1(dxs_strain) & str2(ispD_strain) & str3(ispE_strain) & str4(ispF_strain) & str5(ispG_strain) & str6(ispH_strain) & str7(Idi_strain) & str8(sqs_strain) & str9(crtE_strain) & str10(gap2_strain) & str11(pyrK_strain) & str12(tpi_strain) & str13(Δshc_strain) & str14(WT_strain)
end

subgraph studies\KnoopAndSteuer-2015
direction LR
ks(KnoopAndSteuer-2015)
end
studies\KnoopAndSteuer-2015-->assays\MetabolicModeling

subgraph studies\MeasurementsOfSqualene
direction LR
mos(QuantificationOfSqualeneProduction.md)
end

subgraph studies\Englund-2014
direction LR
wt(WT001)-->|knockdown|m(Δshc1)
end

subgraph studies\Synechocystis
direction LR
str1-->|CultureConditions.md|clt1(dxs_culture)
str2-->|CultureConditions.md|clt2(ispD_culture)
str3-->|CultureConditions.md|clt3(ispE_culture)
str4-->|CultureConditions.md|clt4(ispF_culture)
str5-->|CultureConditions.md|clt5(ispG_culture)
str6-->|CultureConditions.md|clt6(ispH_culture)
str7-->|CultureConditions.md|clt7(Idi_culture)
str8-->|CultureConditions.md|clt8(sqs_culture)
str9-->|CultureConditions.md|clt9(crtE_culture)
str10-->|CultureConditions.md|clt10(gap2_culture)
str11-->|CultureConditions.md|clt11(pyrK_culture)
str12-->|CultureConditions.md|clt12(tpi_culture)
str13-->|CultureConditions.md|clt13(Δshc_culture)
str14-->|CultureConditions.md|clt14(WT_culture)
end

subgraph assays\AbsorptionSpectraAndODMeasurements
direction LR
clt1-->|AbsorptionSpectraAndODMeasurements.md|od1(dxs_absorption_OD_sample)
clt2-->|AbsorptionSpectraAndODMeasurements.md|od2(ispD_absorption_OD_sample)
clt3-->|AbsorptionSpectraAndODMeasurements.md|od3(ispE_absorption_OD_sample)
clt4-->|AbsorptionSpectraAndODMeasurements.md|od4(ispF_absorption_OD_sample)
clt5-->|AbsorptionSpectraAndODMeasurements.md|od5(ispG_absorption_OD_sample)
clt6-->|AbsorptionSpectraAndODMeasurements.md|od6(ispH_absorption_OD_sample)
clt7-->|AbsorptionSpectraAndODMeasurements.md|od7(Idi_absorption_OD_sample)
clt8-->|AbsorptionSpectraAndODMeasurements.md|od8(sqs_absorption_OD_sample)
clt9-->|AbsorptionSpectraAndODMeasurements.md|od9(crtE_absorption_OD_sample)
clt10-->|AbsorptionSpectraAndODMeasurements.md|od10(gap2_absorption_OD_sample)
clt11-->|AbsorptionSpectraAndODMeasurements.md|od11(pyrK_absorption_OD_sample)
clt12-->|AbsorptionSpectraAndODMeasurements.md|od12(tpi_absorption_OD_sample)
clt13-->|AbsorptionSpectraAndODMeasurements.md|od13(Δshc_absorption_OD_sample)
clt14-->|AbsorptionSpectraAndODMeasurements.md|od14(WT_absorption_OD_sample)
end

subgraph assays\DCWMeasuremnet
direction LR
clt1-->|DCWMeasurement.md|dcw1(dxs_DCW)
clt2-->|DCWMeasurement.md|dcw2(ispD_DCW)
clt3-->|DCWMeasurement.md|dcw3(ispE_DCW)
clt4-->|DCWMeasurement.md|dcw4(ispF_DCW)
clt5-->|DCWMeasurement.md|dcw5(ispG_DCW)
clt6-->|DCWMeasurement.md|dcw6(ispH_DCW)
clt7-->|DCWMeasurement.md|dcw7(Idi_DCW)
clt8-->|DCWMeasurement.md|dcw8(sqs_DCW)
clt9-->|DCWMeasurement.md|dcw9(crtE_DCW)
clt10-->|DCWMeasurement.md|dcw10(gap2_DCW)
clt11-->|DCWMeasurement.md|dcw11(pyrK_DCW)
clt12-->|DCWMeasurement.md|dcw12(tpi_DCW)
clt13-->|DCWMeasurement.md|dcw13(Δshc_DCW)
clt14-->|DCWMeasurement.md|dcw14(WT_DCW)
end

subgraph assays\GC-MSMeasurementsForTheQuantificationOfSqualene
direction LR
clt1-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms1(dxs_GC-MS)
clt2-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms2(ispD_GC-MS)
clt3-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms3(ispE_GC-MS)
clt4-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms4(ispF_GC-MS)
clt5-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms5(ispG_GC-MS)
clt6-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms6(ispH_GC-MS)
clt7-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms7(Idi_GC-MS)
clt8-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms8(sqs_GC-MS)
clt9-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms9(crtE_GC-MS)
clt10-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms10(gap2_GC-MS)
clt11-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms11(pyrK_GC-MS)
clt12-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms12(tpi_GC-MS)
clt13-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms13(Δshc_GC-MS)
clt14-->|GC-MSMeasurementsForTheQuantificationOfSqualene.md|gc-ms14(WT_GC-MS)
end

subgraph assays\MetabolicModeling
model(MetabolicModeling.md)
end
studies\PlasmidAndStrainConstruction-->model