{
"@id": "./",
"filename": "isa.investigation.xlsx",
"identifier": "2024_GrowthCoupledHemeSensor",
"title": "Biosensor-based growth-coupling as an evolutionary strategy towards elevated hrtB expression in Corynebacterium glutamicum",
"description": "The iron-containing porphyrin heme is of high interest for the food industry for the production of artificial meat as well as for medical applications, e.g. for anemia treatment. Recently, the biotechnological platform strain Corynebacterium glutamicum has emerged as a promising host for animal-free heme production. Beyond engineering of complex heme biosynthetic pathways, improving heme export offers significant yet untapped potential for enhancing production strains. In this study, a growth-coupled biosensor was designed to impose a selection pressure on the increased expression of the hrtBA operon encoding an ABC-type heme exporter in C. glutamicum. For this purpose, the promoter region PhrtB was replaced with that of the growth-regulating genes pfkA (phosphofructokinase) and aceE (pyruvate dehydrogenase), creating biosensor strains with a selection pressure for hrtBA activation. Resulting sensor strains were used for plate-based selections and for a repetitive batch f(luorescent)ALE using a robotics platform. Genome sequencing of isolated clones featuring increased hrtBA expression revealed three distinct mutational hotspots: (i) chrS, (ii) chrA, and (iii) cydD. Mutations in the genes of the ChrSA two-component system, which regulates hrtBA in response to heme levels, were identified as a promising target to enhance export activity. Furthermore, causal mutations within cydD, encoding an ABC-transporter essential for cytochrome bd oxidase assembly, were confirmed by the construction of a deletion mutant, which showed strongly increased hrtBA expression as well as increased cellular heme levels. These results further support the proposed role of CydDC as a heme transporter. Mutations identified in this study therefore underline the potential of biosensor-based growth coupling and provide promising engineering targets to improve microbial heme production.",
"publications": [
{
"pubMedID": "39402655",
"doi": "10.1186/s12934-024-02556-1",
"authorList": "Aileen Kr\u00fcger, Janik G\u00f6ddecke, Michael Osthege, Luis Navratil, Ulrike Weber, Marco Oldiges, Julia Frunzke",
"title": "Biosensor-based growth-coupling as an evolutionary strategy to improve heme export in Corynebacterium glutamicum",
"status": {
"annotationValue": "published",
"termSource": "EFO",
"termAccession": "https://bioregistry.io/EFO:0001796"
}
}
],
"people": [
{
"@id": "0000-0001-7060-4879",
"firstName": "Aileen",
"lastName": "Kr\u00fcger",
"email": "ai.krueger@fz-juelich.de",
"address": "Wilhelm-Johnen-Stra\u00dfe, 52428 J\u00fclich",
"affiliation": "Forschungszentrum J\u00fclich GmbH, IBG-1: Institute for Bio- and Geosciences",
"comments": [
{
"name": "ORCID",
"value": "0000-0001-7060-4879"
}
]
},
{
"@id": "janik.goeddecke@web.de",
"firstName": "Janik",
"lastName": "G\u00f6ddecke",
"email": "janik.goeddecke@web.de",
"address": "Wilhelm-Johnen-Stra\u00dfe, 52428 J\u00fclich",
"affiliation": "Forschungszentrum J\u00fclich GmbH, IBG-1: Institute for Bio- and Geosciences"
},
{
"@id": "https://orcid.org/0000-0002-2734-7624",
"firstName": "Michael",
"lastName": "Osthege",
"email": "m.osthege@fz-juelich.de",
"address": "Wilhelm-Johnen-Stra\u00dfe, 52428 J\u00fclich",
"affiliation": "Forschungszentrum J\u00fclich GmbH, IBG-1: Institute for Bio- and Geosciences",
"comments": [
{
"name": "ORCID",
"value": "https://orcid.org/0000-0002-2734-7624"
}
]
},
{
"@id": "Luis.Navratil@hhu.de",
"firstName": "Luis",
"lastName": "Navratil",
"email": "Luis.Navratil@hhu.de",
"address": "Wilhelm-Johnen-Stra\u00dfe, 52428 J\u00fclich",
"affiliation": "Forschungszentrum J\u00fclich GmbH, IBG-1: Institute for Bio- and Geosciences"
},
{
"@id": "ul.weber@fz-juelich.de",
"firstName": "Ulrike",
"lastName": "Weber",
"email": "ul.weber@fz-juelich.de",
"address": "Wilhelm-Johnen-Stra\u00dfe, 52428 J\u00fclich",
"affiliation": "Forschungszentrum J\u00fclich GmbH, IBG-1: Institute for Bio- and Geosciences"
},
{
"@id": "0000-0003-0704-5597",
"firstName": "Marco",
"lastName": "Oldiges",
"email": "m.oldiges@fz-juelich.de",
"address": "Wilhelm-Johnen-Stra\u00dfe, 52428 J\u00fclich",
"affiliation": "Forschungszentrum J\u00fclich GmbH, IBG-1: Institute for Bio- and Geosciences",
"comments": [
{
"name": "ORCID",
"value": "0000-0003-0704-5597"
}
]
},
{
"@id": "0000-0001-6209-7950",
"firstName": "Julia",
"lastName": "Frunzke",
"email": "j.frunzke@fz-juelich.de",
"address": "Wilhelm-Johnen-Stra\u00dfe, 52428 J\u00fclich",
"affiliation": "Forschungszentrum J\u00fclich GmbH, IBG-1: Institute for Bio- and Geosciences",
"comments": [
{
"name": "ORCID",
"value": "0000-0001-6209-7950"
}
]
}
],
"studies": [
{
"@id": "studies/ALECloneScreening/",
"filename": "studies/ALECloneScreening/isa.study.xlsx",
"identifier": "ALECloneScreening",
"title": "ALECloneScreening",
"description": "After a solid ALE on plates and a liquid automated ALE (fALE), the selected clones were screened for hrtB expression. Consequently, a set of different hrtB expressing strains were selected for whole genome sequencing, based on differing hrtB expressions.",
"people": [
{
"@id": "#Ulrike_Weber",
"firstName": "Ulrike",
"lastName": "Weber",
"affiliation": "Forschungszentrum J\u00fclich GmbH, IBG-1: Institute for Bio- and Geosciences",
"comments": [
{
"name": "performer (ARC:00000168) WholeGenomeSequencing",
"value": "WholeGenomeSequencing"
}
]
}
],
"materials": {
"samples": [
{
"@id": "#Sample_::PhrtB-pfkA",
"name": "::PhrtB-pfkA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=C. glutamicum ATCC13032 ::PhrtB-pfkA",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032_::PhrtB-pfkA",
"annotationValue": "C. glutamicum ATCC13032 ::PhrtB-pfkA"
}
},
{
"@id": "#MaterialAttributeValue/plasmid=pJC1-PhrtB-eyfp",
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"@id": "#MaterialAttribute/OBI:0000430",
"characteristicType": {
"@id": "OBI:0000430",
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"@id": "#UserTerm_pJC1-PhrtB-eyfp",
"annotationValue": "pJC1-PhrtB-eyfp"
}
}
]
},
{
"@id": "#Sample_::PhrtB-aceE",
"name": "::PhrtB-aceE",
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{
"@id": "#MaterialAttributeValue/organism=C. glutamicum ATCC13032 ::PhrtB-aceE",
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"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
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}
},
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"@id": "#UserTerm_C._glutamicum_ATCC13032_::PhrtB-aceE",
"annotationValue": "C. glutamicum ATCC13032 ::PhrtB-aceE"
}
},
{
"@id": "#MaterialAttributeValue/plasmid=pJC1-PhrtB-eyfp",
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"characteristicType": {
"@id": "OBI:0000430",
"annotationValue": "plasmid",
"termSource": "OBI",
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}
},
"value": {
"@id": "#UserTerm_pJC1-PhrtB-eyfp",
"annotationValue": "pJC1-PhrtB-eyfp"
}
}
]
},
{
"@id": "#Sample_pfkA1",
"name": "pfkA1"
},
{
"@id": "#Sample_pfkA2",
"name": "pfkA2"
},
{
"@id": "#Sample_pfkA3",
"name": "pfkA3"
},
{
"@id": "#Sample_pfkA4",
"name": "pfkA4"
},
{
"@id": "#Sample_pfkA5",
"name": "pfkA5"
},
{
"@id": "#Sample_aceE1",
"name": "aceE1"
},
{
"@id": "#Sample_aceE2",
"name": "aceE2"
},
{
"@id": "#Sample_aceE3",
"name": "aceE3"
},
{
"@id": "#Sample_aceE4",
"name": "aceE4"
},
{
"@id": "#Sample_aceE5",
"name": "aceE5"
},
{
"@id": "#Sample_pfkA6",
"name": "pfkA6"
},
{
"@id": "#Sample_pfkA7",
"name": "pfkA7"
},
{
"@id": "#Sample_pfkA8",
"name": "pfkA8"
},
{
"@id": "#Sample_pfkA_control",
"name": "pfkA_control"
},
{
"@id": "#Sample_aceE_control",
"name": "aceE_control"
}
]
},
"processSequence": [
{
"@id": "#Process_Adaptive_laboratory_evolution_0",
"name": "Adaptive laboratory evolution_0",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Pre-culture_conditions",
"parameterName": {
"@id": "#UserTerm_Pre-culture_conditions",
"annotationValue": "Pre-culture conditions"
}
},
"value": {
"@id": "#UserTerm_5_ml_BHI_+_Kan25_in_tubes,_30\u00b0C,_120_rpm,_~16_h",
"annotationValue": "5 ml BHI + Kan25 in tubes, 30\u00b0C, 120 rpm, ~16 h"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_ALE_type",
"parameterName": {
"@id": "#UserTerm_ALE_type",
"annotationValue": "ALE type"
}
},
"value": {
"@id": "#UserTerm_on_plates",
"annotationValue": "on plates"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_ALE_conditions",
"parameterName": {
"@id": "#UserTerm_ALE_conditions",
"annotationValue": "ALE conditions"
}
},
"value": {
"@id": "#UserTerm_Streaking_on_CGXII_+_2%_glucose_+_iron_excess_(100_\u00b5M_FeSO4)_+_Kan25_agar_plates,_10^0-10-^-7",
"annotationValue": "Streaking on CGXII + 2% glucose + iron excess (100 \u00b5M FeSO4) + Kan25 agar plates, 10^0-10-^-7"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000185",
"parameterName": {
"@id": "DPBO:1000185",
"annotationValue": "incubation time",
"termSource": "DPBO",
"termAccession": "DPBO:1000185"
}
},
"value": {
"@id": "#UserTerm_72_h,_30\u00b0C",
"annotationValue": "72 h, 30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Clone_selection",
"parameterName": {
"@id": "#UserTerm_Clone_selection",
"annotationValue": "Clone selection"
}
},
"value": {
"@id": "#UserTerm_Based_on_stereomicroscopy",
"annotationValue": "Based on stereomicroscopy"
}
}
],
"inputs": [
{
"@id": "#Sample_::PhrtB-pfkA",
"name": "::PhrtB-pfkA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=C. glutamicum ATCC13032 ::PhrtB-pfkA",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032_::PhrtB-pfkA",
"annotationValue": "C. glutamicum ATCC13032 ::PhrtB-pfkA"
}
},
{
"@id": "#MaterialAttributeValue/plasmid=pJC1-PhrtB-eyfp",
"category": {
"@id": "#MaterialAttribute/OBI:0000430",
"characteristicType": {
"@id": "OBI:0000430",
"annotationValue": "plasmid",
"termSource": "OBI",
"termAccession": "OBI:0000430"
}
},
"value": {
"@id": "#UserTerm_pJC1-PhrtB-eyfp",
"annotationValue": "pJC1-PhrtB-eyfp"
}
}
]
},
{
"@id": "#Sample_::PhrtB-pfkA",
"name": "::PhrtB-pfkA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=C. glutamicum ATCC13032 ::PhrtB-pfkA",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032_::PhrtB-pfkA",
"annotationValue": "C. glutamicum ATCC13032 ::PhrtB-pfkA"
}
},
{
"@id": "#MaterialAttributeValue/plasmid=pJC1-PhrtB-eyfp",
"category": {
"@id": "#MaterialAttribute/OBI:0000430",
"characteristicType": {
"@id": "OBI:0000430",
"annotationValue": "plasmid",
"termSource": "OBI",
"termAccession": "OBI:0000430"
}
},
"value": {
"@id": "#UserTerm_pJC1-PhrtB-eyfp",
"annotationValue": "pJC1-PhrtB-eyfp"
}
}
]
},
{
"@id": "#Sample_::PhrtB-pfkA",
"name": "::PhrtB-pfkA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=C. glutamicum ATCC13032 ::PhrtB-pfkA",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032_::PhrtB-pfkA",
"annotationValue": "C. glutamicum ATCC13032 ::PhrtB-pfkA"
}
},
{
"@id": "#MaterialAttributeValue/plasmid=pJC1-PhrtB-eyfp",
"category": {
"@id": "#MaterialAttribute/OBI:0000430",
"characteristicType": {
"@id": "OBI:0000430",
"annotationValue": "plasmid",
"termSource": "OBI",
"termAccession": "OBI:0000430"
}
},
"value": {
"@id": "#UserTerm_pJC1-PhrtB-eyfp",
"annotationValue": "pJC1-PhrtB-eyfp"
}
}
]
},
{
"@id": "#Sample_::PhrtB-pfkA",
"name": "::PhrtB-pfkA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=C. glutamicum ATCC13032 ::PhrtB-pfkA",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032_::PhrtB-pfkA",
"annotationValue": "C. glutamicum ATCC13032 ::PhrtB-pfkA"
}
},
{
"@id": "#MaterialAttributeValue/plasmid=pJC1-PhrtB-eyfp",
"category": {
"@id": "#MaterialAttribute/OBI:0000430",
"characteristicType": {
"@id": "OBI:0000430",
"annotationValue": "plasmid",
"termSource": "OBI",
"termAccession": "OBI:0000430"
}
},
"value": {
"@id": "#UserTerm_pJC1-PhrtB-eyfp",
"annotationValue": "pJC1-PhrtB-eyfp"
}
}
]
},
{
"@id": "#Sample_::PhrtB-pfkA",
"name": "::PhrtB-pfkA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=C. glutamicum ATCC13032 ::PhrtB-pfkA",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032_::PhrtB-pfkA",
"annotationValue": "C. glutamicum ATCC13032 ::PhrtB-pfkA"
}
},
{
"@id": "#MaterialAttributeValue/plasmid=pJC1-PhrtB-eyfp",
"category": {
"@id": "#MaterialAttribute/OBI:0000430",
"characteristicType": {
"@id": "OBI:0000430",
"annotationValue": "plasmid",
"termSource": "OBI",
"termAccession": "OBI:0000430"
}
},
"value": {
"@id": "#UserTerm_pJC1-PhrtB-eyfp",
"annotationValue": "pJC1-PhrtB-eyfp"
}
}
]
},
{
"@id": "#Sample_::PhrtB-aceE",
"name": "::PhrtB-aceE",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=C. glutamicum ATCC13032 ::PhrtB-aceE",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032_::PhrtB-aceE",
"annotationValue": "C. glutamicum ATCC13032 ::PhrtB-aceE"
}
},
{
"@id": "#MaterialAttributeValue/plasmid=pJC1-PhrtB-eyfp",
"category": {
"@id": "#MaterialAttribute/OBI:0000430",
"characteristicType": {
"@id": "OBI:0000430",
"annotationValue": "plasmid",
"termSource": "OBI",
"termAccession": "OBI:0000430"
}
},
"value": {
"@id": "#UserTerm_pJC1-PhrtB-eyfp",
"annotationValue": "pJC1-PhrtB-eyfp"
}
}
]
},
{
"@id": "#Sample_::PhrtB-aceE",
"name": "::PhrtB-aceE",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=C. glutamicum ATCC13032 ::PhrtB-aceE",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032_::PhrtB-aceE",
"annotationValue": "C. glutamicum ATCC13032 ::PhrtB-aceE"
}
},
{
"@id": "#MaterialAttributeValue/plasmid=pJC1-PhrtB-eyfp",
"category": {
"@id": "#MaterialAttribute/OBI:0000430",
"characteristicType": {
"@id": "OBI:0000430",
"annotationValue": "plasmid",
"termSource": "OBI",
"termAccession": "OBI:0000430"
}
},
"value": {
"@id": "#UserTerm_pJC1-PhrtB-eyfp",
"annotationValue": "pJC1-PhrtB-eyfp"
}
}
]
},
{
"@id": "#Sample_::PhrtB-aceE",
"name": "::PhrtB-aceE",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=C. glutamicum ATCC13032 ::PhrtB-aceE",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
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"termSource": "OBI",
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032_::PhrtB-aceE",
"annotationValue": "C. glutamicum ATCC13032 ::PhrtB-aceE"
}
},
{
"@id": "#MaterialAttributeValue/plasmid=pJC1-PhrtB-eyfp",
"category": {
"@id": "#MaterialAttribute/OBI:0000430",
"characteristicType": {
"@id": "OBI:0000430",
"annotationValue": "plasmid",
"termSource": "OBI",
"termAccession": "OBI:0000430"
}
},
"value": {
"@id": "#UserTerm_pJC1-PhrtB-eyfp",
"annotationValue": "pJC1-PhrtB-eyfp"
}
}
]
},
{
"@id": "#Sample_::PhrtB-aceE",
"name": "::PhrtB-aceE",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=C. glutamicum ATCC13032 ::PhrtB-aceE",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032_::PhrtB-aceE",
"annotationValue": "C. glutamicum ATCC13032 ::PhrtB-aceE"
}
},
{
"@id": "#MaterialAttributeValue/plasmid=pJC1-PhrtB-eyfp",
"category": {
"@id": "#MaterialAttribute/OBI:0000430",
"characteristicType": {
"@id": "OBI:0000430",
"annotationValue": "plasmid",
"termSource": "OBI",
"termAccession": "OBI:0000430"
}
},
"value": {
"@id": "#UserTerm_pJC1-PhrtB-eyfp",
"annotationValue": "pJC1-PhrtB-eyfp"
}
}
]
},
{
"@id": "#Sample_::PhrtB-aceE",
"name": "::PhrtB-aceE",
"characteristics": [
{
"@id": "#MaterialAttributeValue/organism=C. glutamicum ATCC13032 ::PhrtB-aceE",
"category": {
"@id": "#MaterialAttribute/OBI:0100026",
"characteristicType": {
"@id": "OBI:0100026",
"annotationValue": "organism",
"termSource": "OBI",
"termAccession": "OBI:0100026"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032_::PhrtB-aceE",
"annotationValue": "C. glutamicum ATCC13032 ::PhrtB-aceE"
}
},
{
"@id": "#MaterialAttributeValue/plasmid=pJC1-PhrtB-eyfp",
"category": {
"@id": "#MaterialAttribute/OBI:0000430",
"characteristicType": {
"@id": "OBI:0000430",
"annotationValue": "plasmid",
"termSource": "OBI",
"termAccession": "OBI:0000430"
}
},
"value": {
"@id": "#UserTerm_pJC1-PhrtB-eyfp",
"annotationValue": "pJC1-PhrtB-eyfp"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_pfkA1",
"name": "pfkA1"
},
{
"@id": "#Sample_pfkA2",
"name": "pfkA2"
},
{
"@id": "#Sample_pfkA3",
"name": "pfkA3"
},
{
"@id": "#Sample_pfkA4",
"name": "pfkA4"
},
{
"@id": "#Sample_pfkA5",
"name": "pfkA5"
},
{
"@id": "#Sample_aceE1",
"name": "aceE1"
},
{
"@id": "#Sample_aceE2",
"name": "aceE2"
},
{
"@id": "#Sample_aceE3",
"name": "aceE3"
},
{
"@id": "#Sample_aceE4",
"name": "aceE4"
},
{
"@id": "#Sample_aceE5",
"name": "aceE5"
}
]
},
{
"@id": "#Process_Adaptive_laboratory_evolution_1",
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"@id": "#UserTerm_Pre-culture_conditions",
"annotationValue": "Pre-culture conditions"
}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
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}
},
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}
},
{
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_random_picking_after_restreak",
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}
}
],
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{
"@id": "#Sample_::PhrtB-pfkA",
"name": "::PhrtB-pfkA",
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{
"@id": "#MaterialAttributeValue/organism=C. glutamicum ATCC13032 ::PhrtB-pfkA",
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}
},
"value": {
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}
},
{
"@id": "#MaterialAttributeValue/plasmid=pJC1-PhrtB-eyfp",
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}
},
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}
]
},
{
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{
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}
},
"value": {
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}
},
{
"@id": "#MaterialAttributeValue/plasmid=pJC1-PhrtB-eyfp",
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}
},
"value": {
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}
}
]
},
{
"@id": "#Sample_::PhrtB-pfkA",
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{
"@id": "#MaterialAttributeValue/organism=C. glutamicum ATCC13032 ::PhrtB-pfkA",
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}
},
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}
},
{
"@id": "#MaterialAttributeValue/plasmid=pJC1-PhrtB-eyfp",
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"characteristicType": {
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}
},
"value": {
"@id": "#UserTerm_pJC1-PhrtB-eyfp",
"annotationValue": "pJC1-PhrtB-eyfp"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_pfkA6",
"name": "pfkA6"
},
{
"@id": "#Sample_pfkA7",
"name": "pfkA7"
},
{
"@id": "#Sample_pfkA8",
"name": "pfkA8"
}
]
},
{
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}
},
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}
},
{
"category": {
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}
},
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}
},
{
"category": {
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}
},
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}
},
{
"category": {
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"termAccession": "DPBO:1000185"
}
},
"value": {
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Clone_selection",
"parameterName": {
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"annotationValue": "Clone selection"
}
},
"value": {
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}
}
],
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{
"@id": "#Sample_::PhrtB-pfkA",
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{
"@id": "#MaterialAttributeValue/organism=C. glutamicum ATCC13032 ::PhrtB-pfkA",
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"termSource": "OBI",
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}
},
"value": {
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"annotationValue": "C. glutamicum ATCC13032 ::PhrtB-pfkA"
}
},
{
"@id": "#MaterialAttributeValue/plasmid=pJC1-PhrtB-eyfp",
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},
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"@id": "#UserTerm_pJC1-PhrtB-eyfp",
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}
}
]
},
{
"@id": "#Sample_::PhrtB-aceE",
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{
"@id": "#MaterialAttributeValue/organism=C. glutamicum ATCC13032 ::PhrtB-aceE",
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"termSource": "OBI",
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}
},
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}
},
{
"@id": "#MaterialAttributeValue/plasmid=pJC1-PhrtB-eyfp",
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}
},
"value": {
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}
}
]
}
],
"outputs": [
{
"@id": "#Sample_pfkA_control",
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},
{
"@id": "#Sample_aceE_control",
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}
]
}
],
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{
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},
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{
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},
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},
{
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{
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{
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{
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},
{
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},
{
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},
{
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},
{
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},
{
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},
{
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},
{
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},
{
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{
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{
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{
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},
{
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},
{
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},
{
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},
{
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},
{
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},
{
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{
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}
],
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},
{
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}
},
{
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}
}
],
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{
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},
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},
{
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},
{
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},
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}
],
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}
}
]
},
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},
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}
},
{
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}
},
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}
},
{
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}
},
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},
{
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},
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}
}
],
"inputs": [
{
"@id": "#Source_pfkA1",
"name": "pfkA1",
"characteristics": [
{
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}
},
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}
},
{
"@id": "#MaterialAttributeValue/Treatment=Adaptive laboratory evolution on plates",
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}
},
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},
{
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},
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}
]
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],
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{
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]
},
{
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},
{
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},
{
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{
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},
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"annotationValue": "30 ng/\u00b5l"
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},
{
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{
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},
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{
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{
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]
},
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{
"@id": "#Source_aceE1",
"name": "aceE1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC13032 ::PhrtB-aceE",
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},
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},
{
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},
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},
{
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"annotationValue": "single-end library",
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}
]
}
],
"outputs": [
{
"@id": "assays/WholeGenomeSequencing/dataset/Raw_reads/aceE1.7z",
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]
},
{
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{
"@id": "#ProtocolParameter/#UserTerm_Harvest_of_material",
"parameterName": {
"@id": "#UserTerm_Harvest_of_material",
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},
{
"@id": "#ProtocolParameter/NCIT:C41185",
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},
{
"@id": "#ProtocolParameter/GENEPIO:0000085",
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}
},
{
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}
],
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{
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}
]
},
"parameterValues": [
{
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},
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"annotationValue": "120 ng/\u00b5l"
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},
{
"category": {
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{
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],
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{
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"name": "aceE2",
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{
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{
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},
{
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},
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"annotationValue": "single-end library",
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}
]
}
],
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{
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"type": "Raw Data File"
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]
},
{
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{
"@id": "#ProtocolParameter/#UserTerm_Harvest_of_material",
"parameterName": {
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},
{
"@id": "#ProtocolParameter/NCIT:C41185",
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},
{
"@id": "#ProtocolParameter/GENEPIO:0000085",
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},
{
"@id": "#ProtocolParameter/DPBO:0000040",
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}
]
},
"parameterValues": [
{
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},
{
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},
"value": {
"@id": "#UserTerm_158_ng/\u00b5l",
"annotationValue": "158 ng/\u00b5l"
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},
{
"category": {
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"@id": "#Source_aceE3",
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{
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}
}
]
}
],
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{
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"type": "Raw Data File"
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]
},
{
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{
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{
"@id": "#ProtocolParameter/GENEPIO:0000085",
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},
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}
]
}
],
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]
},
{
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{
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},
{
"@id": "#ProtocolParameter/NCIT:C41185",
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},
{
"@id": "#ProtocolParameter/GENEPIO:0000085",
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{
"@id": "#ProtocolParameter/DPBO:0000040",
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],
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},
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},
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{
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{
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},
{
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}
},
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}
],
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]
},
{
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},
"parameters": [
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"parameterName": {
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"annotationValue": "Harvest of material"
}
},
{
"@id": "#ProtocolParameter/NCIT:C41185",
"parameterName": {
"@id": "NCIT:C41185",
"annotationValue": "Concentration",
"termSource": "NCIT",
"termAccession": "NCIT:C41185"
}
},
{
"@id": "#ProtocolParameter/GENEPIO:0000085",
"parameterName": {
"@id": "GENEPIO:0000085",
"annotationValue": "library preparation kit",
"termSource": "GENEPIO",
"termAccession": "GENEPIO:0000085"
}
},
{
"@id": "#ProtocolParameter/DPBO:0000040",
"parameterName": {
"@id": "DPBO:0000040",
"annotationValue": "next generation sequencing instrument model",
"termSource": "DPBO",
"termAccession": "DPBO:0000040"
}
}
],
"components": [
{
"componentName": "Genomic DNA (NCIT:C95940)",
"componentType": {
"@id": "NCIT:C48187",
"annotationValue": "Material",
"termSource": "NCIT",
"termAccession": "NCIT:C48187"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Harvest_of_material",
"parameterName": {
"@id": "#UserTerm_Harvest_of_material",
"annotationValue": "Harvest of material"
}
},
"value": {
"@id": "#UserTerm_1_ml_BHI_medium_in_Deepwell_Plate,_inoculated_from_a_colony_from_the_agar_plates,_30\u00b0C,_900_rpm,_~_16_h",
"annotationValue": "1 ml BHI medium in Deepwell Plate, inoculated from a colony from the agar plates, 30\u00b0C, 900 rpm, ~ 16 h"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C41185",
"parameterName": {
"@id": "NCIT:C41185",
"annotationValue": "Concentration",
"termSource": "NCIT",
"termAccession": "NCIT:C41185"
}
},
"value": {
"@id": "#UserTerm_80_ng/\u00b5l",
"annotationValue": "80 ng/\u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/GENEPIO:0000085",
"parameterName": {
"@id": "GENEPIO:0000085",
"annotationValue": "library preparation kit",
"termSource": "GENEPIO",
"termAccession": "GENEPIO:0000085"
}
},
"value": {
"@id": "#UserTerm_NEBNext_Ultra_II_DNA_Library_Kit_for_Illumina,_MiSeq_Reagent_Kit_v2",
"annotationValue": "NEBNext Ultra II DNA Library Kit for Illumina, MiSeq Reagent Kit v2"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000040",
"parameterName": {
"@id": "DPBO:0000040",
"annotationValue": "next generation sequencing instrument model",
"termSource": "DPBO",
"termAccession": "DPBO:0000040"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NFDI4PSO_1000050",
"annotationValue": "Illumina MiSeq",
"termSource": "NFDI4PSO",
"termAccession": "http://purl.obolibrary.org/obo/NFDI4PSO_1000050"
}
}
],
"inputs": [
{
"@id": "#Source_aceE_control",
"name": "aceE_control",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC13032 ::PhrtB-aceE",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_Corynebacterium_glutamicum_ATCC13032_::PhrtB-aceE",
"annotationValue": "Corynebacterium glutamicum ATCC13032 ::PhrtB-aceE"
}
},
{
"@id": "#MaterialAttributeValue/Treatment=control, parental strain",
"category": {
"@id": "#MaterialAttribute/NCIT:C15368",
"characteristicType": {
"@id": "NCIT:C15368",
"annotationValue": "Treatment",
"termSource": "NCIT",
"termAccession": "NCIT:C15368"
}
},
"value": {
"@id": "#UserTerm_control,_parental_strain",
"annotationValue": "control, parental strain"
}
},
{
"@id": "#MaterialAttributeValue/output data=single-end library",
"category": {
"@id": "#MaterialAttribute/#UserTerm_output_data",
"characteristicType": {
"@id": "#UserTerm_output_data",
"annotationValue": "output data"
}
},
"value": {
"@id": "https://bioregistry.io/OBI:0002481",
"annotationValue": "single-end library",
"termSource": "OBI",
"termAccession": "https://bioregistry.io/OBI:0002481"
}
}
]
}
],
"outputs": [
{
"@id": "assays/WholeGenomeSequencing/dataset/Raw_reads/aceE_control.7z",
"name": "assays/WholeGenomeSequencing/dataset/Raw reads/aceE_control.7z",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_trimmed_reads",
"name": "trimmed reads",
"inputs": [
{
"@id": "assays/WholeGenomeSequencing/dataset/Raw_reads/pfkA1.7z",
"name": "assays/WholeGenomeSequencing/dataset/Raw reads/pfkA1.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Raw_reads/pfkA2.7z",
"name": "assays/WholeGenomeSequencing/dataset/Raw reads/pfkA2.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Raw_reads/pfkA3.7z",
"name": "assays/WholeGenomeSequencing/dataset/Raw reads/pfkA3.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Raw_reads/pfkA4.7z",
"name": "assays/WholeGenomeSequencing/dataset/Raw reads/pfkA4.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Raw_reads/pfkA5.7z",
"name": "assays/WholeGenomeSequencing/dataset/Raw reads/pfkA5.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Raw_reads/pfkA6.7z",
"name": "assays/WholeGenomeSequencing/dataset/Raw reads/pfkA6.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Raw_reads/pfkA7.7z",
"name": "assays/WholeGenomeSequencing/dataset/Raw reads/pfkA7.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Raw_reads/pfkA8.7z",
"name": "assays/WholeGenomeSequencing/dataset/Raw reads/pfkA8.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Raw_reads/pfkA_control.7z",
"name": "assays/WholeGenomeSequencing/dataset/Raw reads/pfkA_control.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Raw_reads/aceE1.7z",
"name": "assays/WholeGenomeSequencing/dataset/Raw reads/aceE1.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Raw_reads/aceE2.7z",
"name": "assays/WholeGenomeSequencing/dataset/Raw reads/aceE2.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Raw_reads/aceE3.7z",
"name": "assays/WholeGenomeSequencing/dataset/Raw reads/aceE3.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Raw_reads/aceE4.7z",
"name": "assays/WholeGenomeSequencing/dataset/Raw reads/aceE4.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Raw_reads/aceE5.7z",
"name": "assays/WholeGenomeSequencing/dataset/Raw reads/aceE5.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Raw_reads/aceE_control.7z",
"name": "assays/WholeGenomeSequencing/dataset/Raw reads/aceE_control.7z",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "assays/WholeGenomeSequencing/dataset/Trimmed_reads/pfkA1_trimmed.7z",
"name": "assays/WholeGenomeSequencing/dataset/Trimmed reads/pfkA1_trimmed.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Trimmed_reads/pfkA2_trimmed.7z",
"name": "assays/WholeGenomeSequencing/dataset/Trimmed reads/pfkA2_trimmed.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Trimmed_reads/pfkA3_trimmed.7z",
"name": "assays/WholeGenomeSequencing/dataset/Trimmed reads/pfkA3_trimmed.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Trimmed_reads/pfkA4_trimmed.7z",
"name": "assays/WholeGenomeSequencing/dataset/Trimmed reads/pfkA4_trimmed.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Trimmed_reads/pfkA5_trimmed.7z",
"name": "assays/WholeGenomeSequencing/dataset/Trimmed reads/pfkA5_trimmed.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Trimmed_reads/pfkA6_trimmed.7z",
"name": "assays/WholeGenomeSequencing/dataset/Trimmed reads/pfkA6_trimmed.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Trimmed_reads/pfkA7_trimmed.7z",
"name": "assays/WholeGenomeSequencing/dataset/Trimmed reads/pfkA7_trimmed.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Trimmed_reads/pfkA8_trimmed.7z",
"name": "assays/WholeGenomeSequencing/dataset/Trimmed reads/pfkA8_trimmed.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Trimmed_reads/pfkA_control_trimmed.7z",
"name": "assays/WholeGenomeSequencing/dataset/Trimmed reads/pfkA_control_trimmed.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Trimmed_reads/aceE1_trimmed.7z",
"name": "assays/WholeGenomeSequencing/dataset/Trimmed reads/aceE1_trimmed.7z",
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},
{
"@id": "assays/WholeGenomeSequencing/dataset/Trimmed_reads/aceE2_trimmed.7z",
"name": "assays/WholeGenomeSequencing/dataset/Trimmed reads/aceE2_trimmed.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Trimmed_reads/aceE3_trimmed.7z",
"name": "assays/WholeGenomeSequencing/dataset/Trimmed reads/aceE3_trimmed.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Trimmed_reads/aceE4_trimmed.7z",
"name": "assays/WholeGenomeSequencing/dataset/Trimmed reads/aceE4_trimmed.7z",
"type": "Raw Data File"
},
{
"@id": "assays/WholeGenomeSequencing/dataset/Trimmed_reads/aceE5_trimmed.7z",
"name": "assays/WholeGenomeSequencing/dataset/Trimmed reads/aceE5_trimmed.7z",
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},
{
"@id": "assays/WholeGenomeSequencing/dataset/Trimmed_reads/aceE_control_trimmed.7z",
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}
]
}
]
}
],
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}
},
{
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}
}
]
}
]
}