The Neurospora crassa Inducible Q System Enables Simultaneous Optogenetic Amplification and Inversion in Saccharomyces cerevisiae for Bidirectional Control of Gene Expression

2021 ◽  
Author(s):  
Makoto A. Lalwani ◽  
Evan M. Zhao ◽  
Scott A. Wegner ◽  
José L. Avalos
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Neurospora Crassa ◽  
Control Of Gene Expression ◽  
And Inversion ◽  
Q System

Neurospora crassa clock-controlled genes are regulated at the level of transcription

1991 ◽  
Vol 11 (1) ◽  
pp. 558-563
Author(s):  
J J Loros ◽  
J C Dunlap
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Circadian Rhythm ◽  
Neurospora Crassa ◽  
Regulatory Networks ◽  
Biological Clock ◽  
Transcriptional Analysis ◽  
Biological Processes ◽  
Control Of Gene Expression ◽  
A Cell

Although an extensive number of biological processes are under the daily control of the circadian biological clock, little is known about how the clock maintains its regulatory networks within a cell. An important aspect of this temporal control is the daily control of gene expression. Previously we identified two morning-specific genes that are regulated by the clock through daily control of gene expression (J. Loros, S. Denome, and J.C. Dunlap, Science 243:385-388, 1989). We have now introduced a method for transcriptional analysis in Neurospora crassa and used this nuclear run-on procedure to show that regulation of mRNA abundance for these two morning-specific genes occurs at the level of transcription. This transcriptional regulation by the circadian clock provides a basis for isolating circadian rhythm mutants.

scholarly journals Control of Gene Expression from the SUC2 Promoter of Saccharomyces cerevisiae using Two Carbon Sources.

1992 ◽  
Vol 18 (5) ◽  
pp. 693-700 ◽  
Author(s):  
Takayuki Ohshima ◽  
Xiao-Li Zhang ◽  
Shinji Iijima ◽  
Takeshi Kobayashi ◽  
Fumio Hishinuma
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Carbon Sources ◽  
Control Of Gene Expression ◽  
Suc2 Promoter

scholarly journals Translation Initiation from Conserved Non-AUG Codons Provides Additional Layers of Regulation and Coding Capacity

mBio ◽  
2017 ◽  
Vol 8 (3) ◽  
Author(s):  
Ivaylo P. Ivanov ◽  
Jiajie Wei ◽  
Stephen Z. Caster ◽  
Kristina M. Smith ◽  
Audrey M. Michel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Neurospora Crassa ◽  
Open Reading Frames ◽  
Reading Frame ◽  
Coding Sequence ◽  
Cell Extracts ◽  
Upstream Open Reading Frames ◽  
Reading Frames

ABSTRACT Neurospora crassa cpc-1 and Saccharomyces cerevisiae GCN4 are homologs specifying transcription activators that drive the transcriptional response to amino acid limitation. The cpc-1 mRNA contains two upstream open reading frames (uORFs) in its >700-nucleotide (nt) 5′ leader, and its expression is controlled at the level of translation in response to amino acid starvation. We used N. crassa cell extracts and obtained data indicating that cpc-1 uORF1 and uORF2 are functionally analogous to GCN4 uORF1 and uORF4, respectively, in controlling translation. We also found that the 5′ region upstream of the main coding sequence of the cpc-1 mRNA extends for more than 700 nucleotides without any in-frame stop codon. For 100 cpc-1 homologs from Pezizomycotina and from selected Basidiomycota, 5′ conserved extensions of the CPC1 reading frame are also observed. Multiple non-AUG near-cognate codons (NCCs) in the CPC1 reading frame upstream of uORF2, some deeply conserved, could potentially initiate translation. At least four NCCs initiated translation in vitro . In vivo data were consistent with initiation at NCCs to produce N-terminally extended N. crassa CPC1 isoforms. The pivotal role played by CPC1, combined with its translational regulation by uORFs and NCC utilization, underscores the emerging significance of noncanonical initiation events in controlling gene expression. IMPORTANCE There is a deepening and widening appreciation of the diverse roles of translation in controlling gene expression. A central fungal transcription factor, the best-studied example of which is Saccharomyces cerevisiae GCN4, is crucial for the response to amino acid limitation. Two upstream open reading frames (uORFs) in the GCN4 mRNA are critical for controlling GCN4 synthesis. We observed that two uORFs in the corresponding Neurospora crassa cpc-1 mRNA appear functionally analogous to the GCN4 uORFs. We also discovered that, surprisingly, unlike GCN4, the CPC1 coding sequence extends far upstream from the presumed AUG start codon with no other in-frame AUG codons. Similar extensions were seen in homologs from many filamentous fungi. We observed that multiple non-AUG near-cognate codons (NCCs) in this extended reading frame, some conserved, initiated translation to produce longer forms of CPC1, underscoring the significance of noncanonical initiation in controlling gene expression.

scholarly journals Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae

PLoS ONE ◽  
2016 ◽  
Vol 11 (2) ◽  
pp. e0148320 ◽  
Author(s):  
Anssi Rantasalo ◽  
Elena Czeizler ◽  
Riitta Virtanen ◽  
Juho Rousu ◽  
Harri Lähdesmäki ◽  
...  
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Control Of Gene Expression

Control of gene expression by artificial introns in Saccharomyces cerevisiae

Science ◽  
1989 ◽  
Vol 244 (4910) ◽  
pp. 1346-1348 ◽  
Author(s):  
T Yoshimatsu ◽  
F Nagawa
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Control Of Gene Expression

Dynamic control of gene expression in Saccharomyces cerevisiae engineered for the production of plant sesquitepene α-santalene in a fed-batch mode

2012 ◽  
Vol 14 (2) ◽  
pp. 91-103 ◽  
Author(s):  
Gionata Scalcinati ◽  
Christoph Knuf ◽  
Siavash Partow ◽  
Yun Chen ◽  
Jérôme Maury ◽  
...  
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Dynamic Control ◽  
Fed Batch ◽  
Batch Mode ◽  
Control Of Gene Expression

scholarly journals Neurospora crassa clock-controlled genes are regulated at the level of transcription.

1991 ◽  
Vol 11 (1) ◽  
pp. 558-563 ◽  
Author(s):  
J J Loros ◽  
J C Dunlap
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Circadian Rhythm ◽  
Neurospora Crassa ◽  
Regulatory Networks ◽  
Biological Clock ◽  
Transcriptional Analysis ◽  
Biological Processes ◽  
Control Of Gene Expression ◽  
A Cell

Although an extensive number of biological processes are under the daily control of the circadian biological clock, little is known about how the clock maintains its regulatory networks within a cell. An important aspect of this temporal control is the daily control of gene expression. Previously we identified two morning-specific genes that are regulated by the clock through daily control of gene expression (J. Loros, S. Denome, and J.C. Dunlap, Science 243:385-388, 1989). We have now introduced a method for transcriptional analysis in Neurospora crassa and used this nuclear run-on procedure to show that regulation of mRNA abundance for these two morning-specific genes occurs at the level of transcription. This transcriptional regulation by the circadian clock provides a basis for isolating circadian rhythm mutants.

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