scholarly journals Engineering of temperature- and light-switchable Cas9 variants

2013 ◽  
Vol 44 (20) ◽  
Author(s):  
Florian Richter ◽  
Ines Fonfara ◽  
Boris Bouazza ◽  
Charlotte Helene Schumacher ◽  
Majda Bratovič ◽  
...  
Keyword(s):  
Dna Cleavage ◽  
Transcriptional Repression ◽  
Transcriptional Control ◽  
Light Exposure ◽  
Light Sensitivity ◽  
Effector Proteins ◽  
Temperature Sensitive ◽  
Temperature Dependent ◽  
Lov Domain ◽  
Sensory Photoreceptors

Abstract Sensory photoreceptors have enabled non-invasive and spatiotemporal control of numerous biological processes. Photoreceptor engineering has expanded the repertoire beyond natural receptors, but to date no generally applicable strategy exists towards constructing light-regulated protein actuators of arbitrary function. We hence explored whether the homodimeric Rhodobacter sphaeroides light-oxygen-voltage (LOV) domain (RsLOV) that dissociates upon blue-light exposure can confer light sensitivity onto effector proteins, via a mechanism of light-induced functional site release. We chose the RNA-guided programmable DNA endonuclease Cas9 as proof-of-principle effector, and constructed a comprehensive library of RsLOV inserted throughout the Cas9 protein. Screening with a high-throughput assay based on transcriptional repression in Escherichia coli yielded paRC9, a moderately light-activatable variant. As domain insertion can lead to protein destabilization, we also screened the library for temperature-sensitive variants and isolated tsRC9, a variant with robust activity at 29°C but negligible activity at 37°C. Biochemical assays confirmed temperature-dependent DNA cleavage and binding for tsRC9, but indicated that the light sensitivity of paRC9 is specific to the cellular setting. Using tsRC9, the first temperature-sensitive Cas9 variant, we demonstrate temperature-dependent transcriptional control over ectopic and endogenous genetic loci. Taken together, RsLOV can confer light sensitivity onto an unrelated effector; unexpectedly, the same LOV domain can also impart strong temperature sensitivity.

scholarly journals Transcriptional Control of Clostridium autoethanogenum using CRISPRi

2021 ◽  
Author(s):  
Nick Fackler ◽  
James Heffernan ◽  
Alex Juminaga ◽  
Damien Doser ◽  
Shilpa Nagaraju ◽  
...  
Keyword(s):  
Transcriptional Repression ◽  
Transcriptional Control ◽  
Genome Engineering ◽  
Low Cost ◽  
Pathway Engineering ◽  
Industrial Emissions ◽  
Gas Fermentation ◽  
Control Gene Expression ◽  
Clostridium Autoethanogenum ◽  
Commercial Process

Abstract Gas fermentation by Clostridium autoethanogenum is a commercial process for the sustainable biomanufacturing of fuels and valuable chemicals using abundant, low cost C1 feedstocks (CO and CO2) from sources such as inedible biomass, unsorted and non-recyclable municipal solid waste, and industrial emissions. Efforts towards pathway engineering and elucidation of gene function in this microbe have been limited by a lack of genetic tools to control gene expression and arduous genome engineering methods. To increase the pace of progress, here we developed an inducible CRISPR interference (CRISPRi) system for C. autoethanogenum and applied that system towards transcriptional repression of genes with ostensibly crucial functions in metabolism.

scholarly journals Dispersed Mutations in Histone H3 That Affect Transcriptional Repression and Chromatin Structure of the CHA1 Promoter in Saccharomyces cerevisiae

2008 ◽  
Vol 7 (10) ◽  
pp. 1649-1660 ◽  
Author(s):  
Qiye He ◽  
Cailin Yu ◽  
Randall H. Morse
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Chromatin Structure ◽  
Transcriptional Repression ◽  
Histone H3 ◽  
Temperature Sensitive ◽  
Active Chromatin ◽  
Temperature Sensitive Mutants ◽  
Nucleosome Structure ◽  
Lysine Residues ◽  
Chromatin Configuration

ABSTRACT The histone H3 amino terminus, but not that of H4, is required to prevent the constitutively bound activator Cha4 from remodeling chromatin and activating transcription at the CHA1 gene in Saccharomyces cerevisiae. Here we show that neither the modifiable lysine residues nor any specific region of the H3 tail is required for repression of CHA1. We then screened for histone H3 mutations that cause derepression of the uninduced CHA1 promoter and identified six mutants, three of which are also temperature-sensitive mutants and four of which exhibit a sin − phenotype. Histone mutant levels were similar to that of wild-type H3, and the mutations did not cause gross alterations in nucleosome structure. One specific and strongly derepressing mutation, H3 A111G, was examined in depth and found to cause a constitutively active chromatin configuration at the uninduced CHA1 promoter as well as at the ADH2 promoter. Transcriptional derepression and altered chromatin structure of the CHA1 promoter depend on the activator Cha4. These results indicate that modest perturbations in distinct regions of the nucleosome can substantially affect the repressive function of chromatin, allowing activation in the absence of a normal inducing signal (at CHA1) or of Swi/Snf (resulting in a sin − phenotype).

scholarly journals Mutations affecting the tRNA-splicing endonuclease activity of Saccharomyces cerevisiae.

Genetics ◽  
1988 ◽  
Vol 118 (4) ◽  
pp. 609-617
Author(s):  
M Winey ◽  
M R Culbertson
Keyword(s):  
Growth Defect ◽  
Temperature Sensitive ◽  
Gene Products ◽  
Endonuclease Activity ◽  
Temperature Dependent ◽  
Direct Role ◽  
Trna Splicing

Abstract Two unlinked mutations that alter the enzyme activity of tRNA-splicing endonuclease have been identified in yeast. The sen1-1 mutation, which maps on chromosome 12, causes temperature-sensitive growth, reduced in vitro endonuclease activity, and in vivo accumulation of unspliced pre-tRNAs. The sen2-1 mutation does not confer a detectable growth defect, but causes a temperature-dependent reduction of in vitro endonuclease activity. Pre-tRNAs do not accumulate in sen2-1 strains. The in vitro enzyme activities of sen1-1 and sen2-1 complement in extracts from a heterozygous diploid, but fail to complement in mixed extracts from separate sen1-1 and sen2-1 haploid strains. These results suggest a direct role for SEN gene products in the enzymatic removal of introns from tRNA that is distinct from the role of other products known to affect tRNA splicing.

scholarly journals Lactococcal Plasmid pNP40 Encodes a Novel, Temperature-Sensitive Restriction-Modification System

2004 ◽  
Vol 70 (9) ◽  
pp. 5546-5556 ◽  
Author(s):  
Jonathan O'Driscoll ◽  
Frances Glynn ◽  
Oonagh Cahalane ◽  
Mary O'Connell-Motherway ◽  
Gerald F. Fitzgerald ◽  
...  
Keyword(s):  
Restriction Enzymes ◽  
Temperature Sensitive ◽  
Temperature Dependent ◽  
Modification System ◽  
Restriction Modification System ◽  
Naturally Occurring ◽  
Low Copy Number ◽  
Encoding Genes ◽  
Restriction Modification ◽  
Specific Mrna

ABSTRACT A novel restriction-modification system, designated LlaJI, was identified on pNP40, a naturally occurring 65-kb plasmid from Lactococcus lactis. The system comprises four adjacent similarly oriented genes that are predicted to encode two m5C methylases and two restriction endonucleases. The LlaJI system, when cloned into a low-copy-number vector, was shown to confer resistance against representatives of the three most common lactococcal phage species. This phage resistance phenotype was found to be strongly temperature dependent, being most effective at 19°C. A functional analysis confirmed that the predicted methylase-encoding genes, llaJIM1 and llaJIM2, were both required to mediate complete methylation, while the assumed restriction enzymes, specified by llaJIR1 and llaJIR2, were both necessary for the complete restriction phenotype. A Northern blot analysis revealed that the four LlaJI genes are part of a 6-kb operon and that the relative abundance of the LlaJI-specific mRNA in the cells does not appear to contribute to the observed temperature-sensitive profile. This was substantiated by use of a LlaJI promoter-lacZ fusion, which further revealed that the LlaJI operon appears to be subject to transcriptional regulation by an as yet unidentified element(s) encoded by pNP40.

KEX2 mutations suppress RNA polymerase II mutants and alter the temperature range of yeast cell growth

1989 ◽  
Vol 9 (6) ◽  
pp. 2341-2349
Author(s):  
C Martin ◽  
R A Young
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Single Gene ◽  
Yeast Cells ◽  
Temperature Sensitive ◽  
Temperature Dependent ◽  
Growth Properties ◽  
Cold Sensitive ◽  
Dependent Growth ◽  
Kex2 Protease

Suppressors of a temperature-sensitive RNA polymerase II mutation were isolated to identify proteins that interact with RNA polymerase II in yeast cells. Ten independently isolated extragenic mutations that suppressed the temperature-sensitive mutation rpb1-1 and produced a cold-sensitive phenotype were all found to be alleles of a single gene, SRB1. An SRB1 partial deletion mutant was further investigated and found to exhibit several pleiotropic phenotypes. These included suppression of numerous temperature-sensitive RNA polymerase II mutations, alteration of the temperature growth range of cells containing wild-type RNA polymerase, and sterility of cells of alpha mating type. The ability of SRB1 mutations to suppress the temperature-sensitive phenotype of RNA polymerase II mutants did not extend to other temperature-sensitive mutants investigated. Isolation of the SRB1 gene revealed that SRB1 is KEX2. These results indicate that the KEX2 protease, whose only known substrates are hormone precursors, can have an important influence on RNA polymerase II and the temperature-dependent growth properties of yeast cells.

scholarly journals Molecular Cloning of Apicoplast-Targeted Plasmodium falciparum DNA Gyrase Genes: Unique Intrinsic ATPase Activity and ATP-Independent Dimerization of PfGyrB Subunit

2007 ◽  
Vol 6 (3) ◽  
pp. 398-412 ◽  
Author(s):  
Mohd Ashraf Dar ◽  
Atul Sharma ◽  
Neelima Mondal ◽  
Suman Kumar Dhar
Keyword(s):  
Plasmodium Falciparum ◽  
Atpase Activity ◽  
Dna Cleavage ◽  
Functional Characterization ◽  
Dna Gyrase ◽  
Heptad Repeat ◽  
Malarial Parasite ◽  
Temperature Sensitive ◽  
Linear Pattern ◽  
Gyrase A

ABSTRACT DNA gyrase, a typical type II topoisomerase that can introduce negative supercoils in DNA, is essential for replication and transcription in prokaryotes. The apicomplexan parasite Plasmodium falciparum contains the genes for both gyrase A and gyrase B in its genome. Due to the large sizes of both proteins and the unusual codon usage of the highly AT-rich P. falciparum gyrA (PfgyrA) and PfgyrB genes, it has so far been impossible to characterize these proteins, which could be excellent drug targets. Here, we report the cloning, expression, and functional characterization of full-length PfGyrB and functional domains of PfGyrA. Unlike Escherichia coli GyrB, PfGyrB shows strong intrinsic ATPase activity and follows a linear pattern of ATP hydrolysis characteristic of dimer formation in the absence of ATP analogues. These unique features have not been reported for any known gyrase so far. The PfgyrB gene complemented the E. coli gyrase temperature-sensitive strain, and, together with the N-terminal domain of PfGyrA, it showed typical DNA cleavage activity. Furthermore, PfGyrA contains a unique leucine heptad repeat that might be responsible for dimerization. These results confirm the presence of DNA gyrase in eukaryotes and confer great potential for drug development and organelle DNA replication in the deadliest human malarial parasite, P. falciparum.

scholarly journals Loss of DIAPH3, a Formin Family Protein, Leads to Cytokinetic Failure Only under High Temperature Conditions in Mouse FM3A Cells

2020 ◽  
Vol 21 (22) ◽  
pp. 8493
Author(s):  
Hiroki Kazama ◽  
Shu-ichiro Kashiwaba ◽  
Sayaka Ishii ◽  
Keiko Yoshida ◽  
Yuta Yatsuo ◽  
...  
Keyword(s):  
Cell Division ◽  
High Temperature ◽  
Temperature Sensitive ◽  
Dependent Manner ◽  
Temperature Dependent ◽  
Over Expression ◽  
Temperature Conditions ◽  
Family Protein ◽  
Temperature Environment ◽  
Ts Mutant

Cell division is essential for the maintenance of life and involves chromosome segregation and subsequent cytokinesis. The processes are tightly regulated at both the spatial and temporal level by various genes, and failures in this regulation are associated with oncogenesis. Here, we investigated the gene responsible for defects in cell division by using murine temperature-sensitive (ts) mutant strains, tsFT101 and tsFT50 cells. The ts mutants normally grow in a low temperature environment (32 °C) but fail to divide in a high temperature environment (39 °C). Exome sequencing and over-expression analyses identified Diaph3, a member of the formin family, as the cause of the temperature sensitivity observed in tsFT101 and tsFT50 cells. Interestingly, Diaph3 knockout cells showed abnormality in cytokinesis at 39 °C, and the phenotype was rescued by re-expression of Diaph3 WT, but not Diaph1 and Diaph2, other members of the formin family. Furthermore, Diaph3 knockout cells cultured at 39 °C showed a significant increase in the level of acetylated α-tubulin, an index of stabilized microtubules, and the level was reduced by Diaph3 expression. These results suggest that Diaph3 is required for cytokinesis only under high temperature conditions. Therefore, our study provides a new insight into the mechanisms by which regulatory factors of cell division function in a temperature-dependent manner.

scholarly journals Combining Transcriptomics and Proteomics Reveals Potential Post-transcriptional Control of Gene Expression After Light Exposure in Metarhizium acridum

2019 ◽  
Vol 9 (9) ◽  
pp. 2951-2961 ◽  
Author(s):  
Guilherme T. P. Brancini ◽  
Márcia E. S. Ferreira ◽  
Drauzio E. N. Rangel ◽  
Gilberto Ú. L. Braga
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Light Exposure ◽  
Control Of Gene Expression ◽  
Metarhizium Acridum

Cyclic AMP has no effect on the generation, recovery, or background adaptation of light responses in functionally intact rod outer segments: With implications about the function of phosducin

2000 ◽  
Vol 17 (6) ◽  
pp. 887-892 ◽  
Author(s):  
HANA JINDROVA ◽  
PETER B. DETWILER
Keyword(s):  
Outer Segment ◽  
Light Exposure ◽  
Cell Voltage ◽  
Light Sensitivity ◽  
Rod Outer Segments ◽  
Light Responses ◽  
Outer Segments ◽  
Sequence Of Events ◽  
Background Adaptation ◽  
Dependent Processes

In retinal rods, light exposure decreases the total outer segment content of both cGMP and cAMP by about 50%. The functional role of the light-evoked change in cAMP is not known. It is postulated to trigger changes in the phosphorylation state of phosducin, a phosphoprotein that is phosphorylated in the dark by cAMP-dependent protein kinase (PKA) and dephosphorylated by basal phosphatase activity when PKA is inhibited by the light-evoked drop in cAMP. In biochemical studies, dephosphorylated phosducin binds to free βγ dimer of transducin (Tβγ) and prevents the regeneration of heterotrimeric transducin by blocking the re-association of the βγ and α subunits. Phosducin's interaction with Tβγ is blocked when it is phosphorylated on a single residue by PKA. To evaluate the effect of the light-evoked fall in cAMP, functionally intact isolated lizard rod outer segments were dialyzed in whole-cell voltage clamp with a standard internal solution and electrical light responses were recorded with and without adding cAMP to the dialysis solution. Since the total outer segment content of cAMP in darkness is ∼5 μM, internal dialysis with solution containing a much higher concentration (100 μM) of cAMP (or 8-bromo-cAMP) will overcome the effects of a light-evoked decrease in its concentration by keeping cAMP-dependent processes fully activated. Neither cyclic nucleotide had any influence on the generation, light sensitivity, recovery, or background adaptation of the flash response. These results also argue against the participation of phosducin in the sequence of events that are responsible for these aspects of rod function. This does not exclude the possibility of phosducin being involved in adaptation caused by higher light levels than used in the present study, that is, bleaching adaptation, or in light-dependent processes other than phototransduction.

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