Genomic Considerations for the Modification of Saccharomyces cerevisiae for Biofuel and Metabolite Biosynthesis
Abstract
1. Background and Introduction
2. Heterochromatic Genomic Regions Silence Transcriptional Activity
2.1. Telomeric Heterochromatin
2.2. Ribosomal DNA and the Silent Mating Loci
3. Global Position Effects Result in Large Differences in Reporter and Transgene Expression
3.1. The Neighboring Gene Effect
3.2. Global Position Effect Variance
4. Adjacent Gene Co-Regulation and Functional Clustering
4.1. Adjacent Gene Co-Regulation
4.2. Functional Clustering
5. Lessons and Conclusions
Funding
Acknowledgments
Conflicts of Interest
References
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Construct/Analysis | Position Effect Observed | Ref. |
---|---|---|
pTEF1-LacZ and pACT1-LacZ | 8-fold difference in expression across 20 integration sites. | [63] |
pPRS3-LacZ | 14-fold difference in expression across 18 integration sites. | [64] |
pTEF-KANR | 4-fold variation in expression across chromosome I. | [62] |
pTEF-KANR in yeast knock out collect | Characterized the ‘Neighboring Gene Effect’. Transcription disruption by the KANR cassette resulted in missannotation of gene function in genetic screens (parenthesis represents frequence of missannotation): telomere length mutant screen (24.1%), resoponse to rapamycin screen (21.5%), topoisomerase mutant sensitivity (15.7%), and 5-fluorouracil sensitivity (7.2%). | [58] |
Double deletion mutant screen | ‘Neighboring Gene Effect’ resulted in 18% global missannotation of a systematic synthetic double deletion screen. | [59] |
pRPL5-GFP | Characterized effects from 63 loci on chromosome I and 482 total sites globally. 22.6% of integration sites exhibited significant expressional differences, 36.5% demonstrated significant transcriptional noise, and there was 15-fold deviation in overal expression levels. | [60] |
pTEF1-RFP and pURA3-RFP | 13-fold difference in expression across 1044 integration sites. Different promoters resulted in different overall levels of expression; however, position affected both constructs to the same degree. | [61] |
Chromosome | Arm | Coordinates | SCC (10kB Window) * | SCC (10 Gene Window) ** |
---|---|---|---|---|
II | R | 415,500 | 0.0340 | 0.0130 |
IV | R | 1301,500 | −0.0500 | −0.0280 |
IV | R | 1451,200 | −0.0160 | −0.0112 |
IV | L | 130,100 | −0.0170 | 0.0030 |
IV | L | 117,200 | −0.0140 | −0.0220 |
IV | L | 217,200 | 0.0100 | 0.0330 |
IV | L | 308,200 | 0.0240 | 0.0350 |
V | L | 53,400 | −0.0404 | −0.0250 |
VII | L | 254,000 | −0.1820 | −0.0750 |
VII | L | 366,200 | −0.0720 | −0.0200 |
VII | R | 649,200 | −0.0390 | −0.0220 |
VII | L | 310,400 | −0.0320 | −0.0330 |
VII | R | 270,600 | 0.0330 | −0.0083 |
VIII | L | 36,200 | 0.0690 | 0.0480 |
IX | L | 316,400 | −0.3000 | 0.0850 |
IX | L | 99,600 | 0.0600 | −0.0043 |
X | L | 75,600 | 0.0644 | 0.1030 |
XI | L | 431,500 | 0.0011 | −0.0080 |
XII | R | 932,000 | −0.0500 | 0.0120 |
XII | R | 805,500 | −0.0190 | 0.0100 |
XII | R | 282,600 | 0.0380 | 0.0620 |
XII | R | 522,600 | 0.0720 | −0.0280 |
XII | R | 1028,500 | 0.3100 | 0.2470 |
XIII | R | 754,500 | 0.0900 | 0.0300 |
XIV | L | 330,800 | −0.0470 | −0.0680 |
XIV | L | 65,200 | −0.0190 | −0.0300 |
XV | R | 444,200 | −0.0038 | 0.0211 |
XV | L | 80,000 | 0.0053 | −0.0610 |
XVI | L | 173,000 | 0.0180 | 0.0290 |
XVI | L | 135,600 | 0.1040 | 0.1170 |
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Arnone, J.T. Genomic Considerations for the Modification of Saccharomyces cerevisiae for Biofuel and Metabolite Biosynthesis. Microorganisms 2020, 8, 321. https://doi.org/10.3390/microorganisms8030321
Arnone JT. Genomic Considerations for the Modification of Saccharomyces cerevisiae for Biofuel and Metabolite Biosynthesis. Microorganisms. 2020; 8(3):321. https://doi.org/10.3390/microorganisms8030321
Chicago/Turabian StyleArnone, James T. 2020. "Genomic Considerations for the Modification of Saccharomyces cerevisiae for Biofuel and Metabolite Biosynthesis" Microorganisms 8, no. 3: 321. https://doi.org/10.3390/microorganisms8030321
APA StyleArnone, J. T. (2020). Genomic Considerations for the Modification of Saccharomyces cerevisiae for Biofuel and Metabolite Biosynthesis. Microorganisms, 8(3), 321. https://doi.org/10.3390/microorganisms8030321