Abstract
BACKGROUND: Soybean (Glycine max) has been bred for thousands of years to produce seeds rich in protein for human and animal consumption, making them an appealing bioreactor for producing valuable recombinant proteins at high levels. However, the effects of expressing recombinant protein at high levels on bean physiology are not well understood. To address this, we investigated whether gene expression within transgenic soybean seed tissue is altered when large amounts of recombinant proteins are being produced and stored exclusively in the seeds. We used RNA-Seq to survey gene expression in three transgenic soybean lines expressing recombinant protein at levels representing up to 1.61 % of total protein in seed tissues. The three lines included: ST77, expressing human thyroglobulin protein (hTG), ST111, expressing human myelin basic protein (hMBP), and 764, expressing a mutant, nontoxic form of a staphylococcal subunit vaccine protein (mSEB). All lines selected for analysis were homozygous and contained a single copy of the transgene. METHODS: Each transgenic soybean seed was screened for transgene presence and recombinant protein expression via PCR and western blotting. Whole seed mRNA was extracted and cDNA libraries constructed for Illumina sequencing. Following alignment to the soybean reference genome, differential gene expression analysis was conducted using edgeR and cufflinks. Functional analysis of differentially expressed genes was carried out using the gene ontology analysis tool AgriGO. RESULTS: The transcriptomes of nine seeds from each transgenic line were sequenced and compared with wild type seeds. Native soybean gene expression was significantly altered in line 764 (mSEB) with more than 3000 genes being upregulated or downregulated. ST77 (hTG) and ST111 (hMBP) had significantly less differences with 52 and 307 differentially expressed genes respectively. Gene ontology enrichment analysis found that the upregulated genes in the 764 line were annotated with functions related to endopeptidase inhibitors and protein synthesis, but suppressed expression of genes annotated to the nuclear pore and to protein transport. No significant gene ontology terms were detected in ST77, and only a few genes involved in photosynthesis and thylakoid functions were downregulated in ST111. Despite these differences, transgenic plants and seeds appeared phenotypically similar to non-transgenic controls. There was no correlation between recombinant protein expression level and the quantity of differentially expressed genes detected. CONCLUSIONS: Measurable unscripted gene expression changes were detected in the seed transcriptomes of all three transgenic soybean lines analyzed, with line 764 being substantially altered. Differences detected at the transcript level may be due to T-DNA insert locations, random mutations following transformation or direct effects of the recombinant protein itself, or a combination of these. The physiological consequences of such changes remain unknown.
Abstract from the paper’s OpenAlex record; open copy licensed cc-by. Read at the source ↗
The text the model read, with the source record’s inline markup (italics, sub- and superscripts) rendered and its character entities decoded; quote offsets refer to the raw text.
Claims 9
Claim · model-written summary
Line 764 (mSEB) significantly altered native soybean gene expression, with more than 3000 genes up- or downregulated relative to wild type seeds.
- Taxon
- soybean
Glycine maxe1 - Material
- 764e1
- Organ / stage
- seedse3
- Treatment
- expressing a mutant, nontoxic form of a staphylococcal subunit vaccine proteine2
- Outcome
- gene expressione1
- Value
- more than 3000 genese1
- Comparator
- wild type seedse3
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Native soybean gene expression was significantly altered in line 764 (mSEB) with more than 3000 genes being upregulated or downregulated”
e2“764, expressing a mutant, nontoxic form of a staphylococcal subunit vaccine protein (mSEB)”
e3“compared with wild type seeds”
Claim · model-written summary
Line ST77 (hTG) showed no significant gene ontology enrichment.
- Taxon
- soybeanGlycine maxt0
- Material
- ST77e1
- Outcome
- gene ontology termse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“transgenic and wild type soybean seeds”
e1“No significant gene ontology terms were detected in ST77”
Claim · model-written summary
Line ST77 (hTG) had significantly fewer differences from wild type, with 52 differentially expressed genes.
- Taxon
- soybeanGlycine maxt0
- Material
- ST77e1
- Outcome
- differentially expressed genese1
- Value
- 52e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“transgenic and wild type soybean seeds”
e1“ST77 (hTG) and ST111 (hMBP) had significantly less differences with 52 and 307 differentially expressed genes respectively”
Claim · model-written summary
Line ST111 (hMBP) had significantly fewer differences from wild type, with 307 differentially expressed genes.
- Taxon
- soybeanGlycine maxt0
- Material
- ST111e1
- Outcome
- differentially expressed genese1
- Value
- 307e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“transgenic and wild type soybean seeds”
e1“ST77 (hTG) and ST111 (hMBP) had significantly less differences with 52 and 307 differentially expressed genes respectively”
Claim · model-written summary
Only a few genes involved in photosynthesis and thylakoid functions were downregulated in line ST111.
- Taxon
- soybeanGlycine maxt0
- Material
- ST111e1
- Outcome
- genes involved in photosynthesis and thylakoid functionse1
- Direction
- downregulatede1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“transgenic and wild type soybean seeds”
e1“only a few genes involved in photosynthesis and thylakoid functions were downregulated in ST111”
Claim · model-written summary
Genes annotated to endopeptidase inhibitors and protein synthesis were upregulated in line 764.
- Taxon
- soybeanGlycine maxt0
- Material
- 764e1
- Outcome
- functions related to endopeptidase inhibitors and protein synthesise1
- Direction
- upregulatede1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“transgenic and wild type soybean seeds”
e1“Gene ontology enrichment analysis found that the upregulated genes in the 764 line were annotated with functions related to endopeptidase inhibitors and protein synthesis, but suppressed expression of genes annotated to the nuclear pore and to protein transport.”
Claim · model-written summary
Genes annotated to the nuclear pore and to protein transport were suppressed in line 764.
- Taxon
- soybeanGlycine maxt0
- Material
- 764e1
- Outcome
- genes annotated to the nuclear pore and to protein transporte1
- Direction
- suppressede1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“transgenic and wild type soybean seeds”
e1“Gene ontology enrichment analysis found that the upregulated genes in the 764 line were annotated with functions related to endopeptidase inhibitors and protein synthesis, but suppressed expression of genes annotated to the nuclear pore and to protein transport.”
Claim · model-written summary
Transgenic soybean plants and seeds appeared phenotypically similar to non-transgenic controls.
- Taxon
- soybeanGlycine maxt0
- Outcome
- phenotypically similare1
- Comparator
- non-transgenic controlse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“transgenic and wild type soybean seeds”
e1“transgenic plants and seeds appeared phenotypically similar to non-transgenic controls”
Claim · model-written summary
No correlation was found between recombinant protein expression level and the quantity of differentially expressed genes.
- Taxon
- soybeanGlycine maxt0
- Treatment
- recombinant protein expression levele1
- Outcome
- quantity of differentially expressed genese1
- Direction
- no_changeinferrede1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“transgenic and wild type soybean seeds”
e1“There was no correlation between recombinant protein expression level and the quantity of differentially expressed genes detected”