YeasTSS: An Integrative Web Database of Yeast Transcription Start Sites

McMillan, Jonathan; Lü, Zheng; Rodríguez, Juan Luis Rodríguez; Ahn, Tae-Hyuk; Lin, Zhenguo

doi:10.1101/511477

Cited by 5 publications

(6 citation statements)

References 64 publications

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“…Next, we analyzed the Gcn4 binding signals around the transcription and translation start site of the genes found within 750bp around the identified peaks. Transcription start site data available for cells in log phase grown in YPD (rich, complex medium with glucose) -- the nearest possible condition to that used in this study -- was obtained from the YeasTSS database (McMillan et al, 2019). The TSS identified using the CAGE method reported in this database was used for our analysis.…”

Section: Gcn4 Strongly Binds To Its Target Promoters In the Presence mentioning

confidence: 99%

Genome-scale reconstruction of Gcn4/ATF4 networks driving a growth program

Srinivasan

Walvekar

Seshasayee

et al. 2020

Preprint

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How cells manage biomolecule supply to enable constructive metabolism for growth is a fundamental question. Methionine directly activates genomic programs where translation and metabolism are induced. In otherwise amino acid limitations, methionine induced ribosomal biogenesis, carbon metabolism, amino acid and nucleotide biosynthesis. Here, we find that the methionine--induced anabolic program is carbon--source independent, and requires the 'starvation-responsive' transcription factor Gcn4/ATF4. Integrating transcriptome and ChIP--Seq analysis, we decipher direct and indirect, methionine--dependent roles for Gcn4. Methionine--induced genes enabling metabolic precursor biosynthesis critically require Gcn4; contrastingly ribosomal genes are partly repressed by Gcn4. Gcn4 binds promoter--regions and transcribes a subset of metabolic genes, driving amino acid (particularly lysine and arginine) biosynthesis. This sustained lys/arg supply maintains high translation capacity, by allowing the translation of lys/arg enriched transcripts, notably the translation machinery itself. Thus, we discover how Gcn4 enabled metabolic--precursor supply bolsters protein synthesis demand, and drive a methionine--mediated anabolic program.

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Section: Gcn4 Strongly Binds To Its Target Promoters In the Presence mentioning

confidence: 99%

Genome-scale reconstruction of Gcn4/ATF4 networks driving a growth program

Srinivasan

Walvekar

Seshasayee

et al. 2020

Preprint

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“…We, therefore, focused our attention on promoter sequences downstream of TATA box upto the initiation codon (ATG). In yeast promoters, transcription start site (TSS) is located 40-120 bp downstream of TATA box and it corresponds to the first base of mRNA (McMillan et al, 2019). The region between the TSS and the ATG in the promoter corresponds to the 5’ untranslated region (5’ UTR) of mRNA which often contains cis-acting elements referred to as riboswitches that bind to small molecules and regulate translation of downstream open reading frames (Garst et al, 2011).…”

Section: Resultsmentioning

confidence: 99%

Post-transcriptional regulation of glutamate metabolism ofPichia pastorisand development of a glutamate-inducible yeast expression system

Rangarajan

2021

Preprint

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Pichia pastoris harbours a unique glutamate utilization pathway in which glutamate dehydrogenase 2 (GDH2), aspartate aminotransferase 2 (AAT2) and phosphoenolpyruvate carboxykinase (PEPCK) catalyze the conversion of glutamate to α-ketoglutarate, oxaloacetate, and phosphoenolpyruvate respectively in the cytosol. GDH2 and PEPCK are glutamate-inducible enzymes and their synthesis is regulated post-transcriptionally by Rtg1p, a cytosolic basic helix-loop-helix protein via Rtg1p response elements located downstream of TATA box of GDH2 and PEPCK promoters. Glutamate-inducible synthesis of PEPCK is abrogated in Δgdh2 and Δaat2. α-ketoglutarate induces PEPCK synthesis in Δgdh2 but not Δaat2. We propose that oxaloacetate derived from glutamate is the inducer of PEPCK synthesis. Enzymes of glutamate utilization pathway are synthesized during carbon starvation and they enable P. pastoris to overcome nutritional stress. Finally, green fluorescent protein can be synthesized efficiently from GDH2 and PEPCK promoters using food-grade monosodium glutamate as inducer indicating that the post-transcriptional regulatory circuit described here can be exploited for the development of glutamate-inducible P. pastoris expression system.

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“…Increased gene dosage could lead to a quantitative increase in gene expression and production of protein. To determine the impact of gene duplication on the production of RP transcripts, we calculated the total transcription abundance of all RP genes using our transcriptomic data generated by Cap Analysis of Gene Expression (CAGE) (McMillan, et al 2019). The CAGE technique captures and sequences the first 75 bp of transcripts, which quantifies the transcription abundance based on numbers of mapped reads (Murata, et al 2014).…”

Section: Resultsmentioning

confidence: 99%

“…The transcriptomic data of nine budding yeasts and two fission yeasts examined were obtained from (McMillan, et al 2019) based on CAGE. The expression abundance of an RP gene was defined as the sum of transcripts initiated from all core promoters within 500 base pairs upstream of its annotated start codon, which were normalized as TPM (tags per million mapped reads, and each tag represent one sequenced transcript).…”

Section: Methodsmentioning

confidence: 99%

Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance

Mullis¹,

Lü²,

Ye³

et al. 2019

Preprint

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9Ribosomal proteins (RPs) genes encode structure components of ribosomes, the cellular 2 0 machinery for protein synthesis. A single functional copy has been maintained in most of 78-80 2 1 RP families in animals due to evolutionary constraints imposed by gene dosage balance. Some 2 2 fungal species have maintained duplicate copies in most RP families. How the RP genes were 2 3 duplicated and maintained in these fungal species, and their functional significance remains 2 4 unresolved. To address these questions, we identified all RP genes from 295 fungi and inferred 2 5 the timing and nature of gene duplication for all RP families. We found that massive duplications 2 6 of RP genes have independently occurred by different mechanisms in three distantly related 2 7 lineages. The RP duplicates in two of them, budding yeast and Mucoromycota, were mainly 2 8 created by whole genome duplication (WGD) events. However, in fission yeasts, duplicate RP 2 9 genes were likely generated by retroposition, which is unexpected considering their dosage 3 0 sensitivity. The sequences of most RP paralogs in each species have been homogenized by 3 1 repeated gene conversion, demonstrating parallel concerted evolution, which might have 3 2 facilitated the retention of their duplicates. Transcriptomic data suggest that the duplication and 3 3 retention of RP genes increased RP transcription abundance. Physiological data indicate that 3 4increased ribosome biogenesis allowed these organisms to rapidly consuming sugars through 3 5 fermentation while maintaining high growth rates, providing selective advantages to these 3 6 species in sugar-rich environments.

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YeasTSS: An Integrative Web Database of Yeast Transcription Start Sites

Cited by 5 publications

References 64 publications

Genome-scale reconstruction of Gcn4/ATF4 networks driving a growth program

Genome-scale reconstruction of Gcn4/ATF4 networks driving a growth program

Post-transcriptional regulation of glutamate metabolism ofPichia pastorisand development of a glutamate-inducible yeast expression system

Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance

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