scholarly journals Kluyveromyces lactis LAC4 Promoter Variants That Lack Function in Bacteria but Retain Full Function in K. lactis

2005 ◽  
Vol 71 (11) ◽  
pp. 7092-7098 ◽  
Author(s):  
Paul A. Colussi ◽  
Christopher H. Taron
Keyword(s):  
Dna Sequences ◽  
Transcription Initiation ◽  
Fluorescent Protein ◽  
Kluyveromyces Lactis ◽  
Targeted Mutagenesis ◽  
Yeast Cells ◽  
Heterologous Proteins ◽  
Gfp Expression ◽  
E Coli ◽  
Cloned Gene

ABSTRACT The strong LAC4 promoter (PLAC4) from Kluyveromyces lactis has been extensively used to drive expression of heterologous proteins in this industrially important yeast. A drawback of this expression method is the serendipitous ability of PLAC4 to promote gene expression in Escherichia coli. This can interfere with the process of assembling expression constructs in E. coli cells prior to their introduction into yeast cells, especially if the cloned gene encodes a protein that is detrimental to bacteria. In this study, we created a series of PLAC4 variants by targeted mutagenesis of three DNA sequences (PBI, PBII, and PBIII) that resemble the E. coli Pribnow box element of bacterial promoters and that reside immediately upstream of two E. coli transcription initiation sites associated with PLAC4. Mutation of PBI reduced the bacterial expression of a reporter protein (green fluorescent protein [GFP]) by ∼87%, whereas mutation of PBII and PBIII had little effect on GFP expression. Deletion of all three sequences completely eliminated GFP expression. Additionally, each promoter variant expressed human serum albumin in K. lactis cells to levels comparable to wild-type PLAC4. We created a novel integrative expression vector (pKLAC1) containing the PLAC4 variant lacking PBI and used it to successfully clone and express the catalytic subunit of bovine enterokinase, a protease that has historically been problematic in E. coli cells. The pKLAC1 vector should aid in the cloning of other potentially toxic genes in E. coli prior to their expression in K. lactis.

6 Invitro validation of gene edited phenotypes using CRISPR-dCas9 transcriptional activators

2020 ◽  
Vol 32 (2) ◽  
pp. 127
Author(s):  
K. M. Polkoff ◽  
N. K. Gupta ◽  
J. A. Piedrahita
Keyword(s):  
Dna Sequences ◽  
Fluorescent Protein ◽  
Transcriptional Start Site ◽  
Fluorescent Microscopy ◽  
Large Animal ◽  
Transcriptional Activators ◽  
Gfp Expression ◽  
Time Investment ◽  
Donor Cells ◽  
Fetal Fibroblasts

Despite the extensive advantages of gene-edited large animals for agriculture and biomedical purposes, they represent a large monetary and time investment due to high husbandry costs, long gestation lengths, and few offspring; that is, 9 months for one calf and almost 4 months for pigs. Even with known DNA sequences before somatic cell nuclear transfer (SCNT), inserted transgenes are often not expressed as expected. Therefore, there is a need to phenotypically validate the gene modifications invitro before investing time and resources in the creation of a gene-edited large animal; however, many gene targets are tissue specific and not expressed in SCNT donor cells. In this work, we show that CRISPR-dCas9 transcriptional activators (TAs) can be used to validate functional transgene insertion in nonexpressing SCNT donor cells, in our case fetal fibroblasts. To demonstrate this concept, we first generated a DNA knockin of the H2B-GFP sequence into the porcine LGR5 locus. CRISPR/Cas9 nuclease was used to create a double-stranded break in the genomic DNA downstream of the LGR5 promoter. A homology-directed repair template plasmid containing H2B-GFP flanked by 1000bp homology arms flanking the cut site was co-transfected with the Cas9 and gRNA, and cells were seeded at low density for colony outgrowth. Colonies were genotyped by PCR and sequencing to verify successful targeted transgene integration. To test whether TAs allow for invitro validation of transgene expression, 5×105 wildtype or gene-edited fibroblasts were nucleofected (Lonza) with 500ng total of four gRNA plasmids (Addgene #43860) designed to target the 1-kb region upstream of the LGR5 transcriptional start site in combination with 500ng VP64-dCas9 (Addgene #47107). Detection of green fluorescent protein (GFP) was analysed by fluorescent microscopy followed by flow cytometry; at least 30 000 events were recorded for each treatment (Cytoflex). Our results show that GFP was detected in on average 28.6% of the gene-edited cells transfected with LGR5 TAs but not detected in gene-edited cells that were not transfected with LGR5 TAs (0%) or in wild-type cells transfected with the LGR5 TAs (0%). The experiment was repeated three times. Next, to prove that our invitro validation replicates the invivo phenotype, the gene-edited colonies heterozygous for the insertion were used for SCNT to generate piglets. Epidermal cells, which contain a population of LGR5+ stem cells, were isolated from the skin and sorted for GFP expression. The RT-qPCR results from GFP+ or GFP− cells showed the presence of LGR5 transcripts in the GFP+ cells but not GFP− cells. In conclusion, TAs were necessary and sufficient to detect LGR5-promoter driven H2B-GFP expression in gene-edited fibroblasts invitro, which faithfully recapitulates the invivo phenotype of the gene-edited animal. Further preliminary data from our laboratory suggest that our novel method can be used to detect successful gene knockouts in addition to transgene knockins and can be used to validate phenotypic outcomes of DNA modifications before the generation of gene-edited animals.

scholarly journals An improved molecular tool for screening bacterial colonies using GFP expression enhanced by a Dictyostelium sequence

BioTechniques ◽  
2020 ◽  
Vol 68 (2) ◽  
pp. 91-95 ◽  
Author(s):  
Tomo Kondo ◽  
Shigehiko Yumura
Keyword(s):  
Escherichia Coli ◽  
Gene Sequence ◽  
Fluorescent Protein ◽  
Gfp Expression ◽  
Magnetospirillum Gryphiswaldense ◽  
E Coli ◽  
Molecular Tool ◽  
Visual Confirmation ◽  
Green Fluorescent ◽  
User Friendly

During molecular cloning, screening bacterial transformants is a time-consuming and labor-intensive process; however, tractable tools that can be applied to various vectors for visual confirmation of desired colonies are limited. Recently, we reported that translational enhancement by a Dictyostelium gene sequence (TED) boosted protein expression even without an expression inducer in Escherichia coli. Here, we demonstrate a generally applicable molecular tool using the expression of green fluorescent protein enhanced by TED. By inserting a module related to TED into the cloning site in advance, we effectively screened E. coli colonies harboring the desired plasmid functions in a prokaryote ( Magnetospirillum gryphiswaldense) or eukaryote ( Dictyostelium discoideum). Thus, our system represents a user-friendly technique for cloning.

scholarly journals Transcribing paramyxovirus RNA polymerase engages the template at its 3′ extremity

2006 ◽  
Vol 87 (3) ◽  
pp. 665-672 ◽  
Author(s):  
Samuel Cordey ◽  
Laurent Roux
Keyword(s):  
Rna Polymerase ◽  
Transcription Initiation ◽  
Fluorescent Protein ◽  
Sendai Virus ◽  
Rna Viruses ◽  
Mrna Transcription ◽  
Gfp Expression ◽  
Rnase Protection ◽  
Virus Rna ◽  
Green Fluorescent

For the non-segmented, negative-stranded RNA viruses, the mechanism controlling transcription or replication is still a matter of debate. To gain information about this mechanism and about the nature of the RNA polymerase involved, the length of an intervening sequence separating the 3′ end of Sendai virus minigenomes and a downstream transcription-initiation signal was increased progressively. It was found that transcription, as measured by green fluorescent protein (GFP) expression, decreased progressively in proportion to the increase in length of the intervening sequence. GFP expression correlated well with the levels of GFP mRNA in the cells, as measured by quantitative primer extension and by RNase protection. Thus, mRNA transcription was inversely proportional to the length of the inserted sequence. These data are evidence that the RNA polymerase initiating transcription at the downstream transcription signal somehow sees the distance separating this signal and the template 3′ extremity. Implication of this observation for the nature of the Sendai virus RNA polymerase and for the mechanism by which it synthesizes mRNAs or replication products is presented.

scholarly journals Cryptococcus neoformans Differential Gene Expression Detected In Vitro and In Vivo with Green Fluorescent Protein

1999 ◽  
Vol 67 (4) ◽  
pp. 1812-1820 ◽  
Author(s):  
Maurizio del Poeta ◽  
Dena L. Toffaletti ◽  
Thomas H. Rude ◽  
Sara D. Sparks ◽  
Joseph Heitman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fluorescent Protein ◽  
Yeast Cells ◽  
Cns Infection ◽  
Gfp Expression ◽  
Gfp Reporter ◽  
Gfp Reporter Gene ◽  
Differential Gene ◽  
Green Fluorescent

ABSTRACT Synthetic green fluorescent protein (GFP) was used as a reporter to detect differential gene expression in the pathogenic fungusCryptococcus neoformans. Promoters from the C. neoformans actin, GAL7, or mating-type alpha pheromone (MFα1) genes were fused to GFP, and the resulting reporter genes were used to assess gene expression in serotype A C. neoformans. Yeast cells containing an integrated pACT::GFP construct demonstrated that the actin promoter was expressed during vegetative growth on yeast extract-peptone-dextrose medium. In contrast, yeast cells containing the inducible GAL7::GFP or MFα1::GFP reporter genes expressed significant GFP activity only during growth on galactose medium or V-8 agar, respectively. These findings demonstrated that the GAL7 and MFα1 promoters from a serotype D C. neoformans strain function when introduced into a serotype A strain. Because the MFα1 promoter is induced by nutrient deprivation and the MATα locus containing the MFα1 gene has been linked with virulence, yeast cells containing the pMFα1::GFP reporter gene were analyzed for GFP expression in the central nervous system (CNS) of immunosuppressed rabbits. In fact, significant GFP expression from the MFα1::GFP reporter gene was detected after the first week of a CNS infection. These findings suggest that there are temporal, host-specific cues that regulate gene expression during infection and that the MFα1 gene is induced during the proliferative stage of a CNS infection. In conclusion, GFP can be used as an effective and sensitive reporter to monitor specific C. neoformans gene expression in vitro, and GFP reporter constructs can be used as an approach to identify a novel gene(s) or to characterize known genes whose expression is regulated during infection.

scholarly journals High-Salinity Growth Conditions Promote Tat-Independent Secretion of Tat Substrates in Bacillus subtilis

2012 ◽  
Vol 78 (21) ◽  
pp. 7733-7744 ◽  
Author(s):  
René van der Ploeg ◽  
Carmine G. Monteferrante ◽  
Sjouke Piersma ◽  
James P. Barnett ◽  
Thijs R. H. M. Kouwen ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Fusion Proteins ◽  
Fluorescent Protein ◽  
High Salinity ◽  
Growth Conditions ◽  
Signal Peptides ◽  
Control Mechanisms ◽  
Heterologous Proteins ◽  
Content Type ◽  
E Coli

ABSTRACTThe Gram-positive bacteriumBacillus subtiliscontains two Tat translocases, which can facilitate transport of folded proteins across the plasma membrane. Previous research has shown that Tat-dependent protein secretion inB. subtilisis a highly selective process and that heterologous proteins, such as the green fluorescent protein (GFP), are poor Tat substrates in this organism. Nevertheless, when expressed inEscherichia coli, bothB. subtilisTat translocases facilitated exclusively Tat-dependent export of folded GFP when the twin-arginine (RR) signal peptides of theE. coliAmiA, DmsA, or MdoD proteins were attached. Therefore, the present studies were aimed at determining whether the same RR signal peptide-GFP precursors would also be exported Tat dependently inB. subtilis. In addition, we investigated the secretion of GFP fused to the full-length YwbN protein, a strict Tat substrate inB. subtilis. Several investigated GFP fusion proteins were indeed secreted inB. subtilis, but this secretion was shown to be completely Tat independent. At high-salinity growth conditions, the Tat-independent secretion of GFP as directed by the RR signal peptides from theE. coliAmiA, DmsA, or MdoD proteins was significantly enhanced, and this effect was strongest in strains lacking the TatAy-TatCy translocase. This implies that high environmental salinity has a negative influence on the avoidance of Tat-independent secretion of AmiA-GFP, DmsA-GFP, and MdoD-GFP. We conclude that as-yet-unidentified control mechanisms reject the investigated GFP fusion proteins for translocation by theB. subtilisTat machinery and, at the same time, set limits to their Tat-independent secretion, presumably via the Sec pathway.

scholarly journals An improved molecular tool for screening bacterial colonies using GFP expression enhanced by a Dictyostelium sequence

2019 ◽  
Author(s):  
Tomo Kondo ◽  
Shigehiko Yumura
Keyword(s):  
Escherichia Coli ◽  
Gene Sequence ◽  
Fluorescent Protein ◽  
Gfp Expression ◽  
Magnetospirillum Gryphiswaldense ◽  
E Coli ◽  
Molecular Tool ◽  
Visual Confirmation ◽  
Green Fluorescent ◽  
User Friendly

AbstractDuring molecular cloning, screening of bacterial transformants is a time-consuming and labor-intensive process. However, tractable tools that can be applied to various vectors for visual confirmation of desired colonies are limited. Recently, we reported that TED (translational enhancement by a Dictyostelium gene sequence) boosted protein expression even without an expression inducer in Escherichia coli. Here, we demonstrate a generally applicable molecular tool using the expression of green fluorescent protein (GFP) enhanced by TED. By inserting a module related to TED into the cloning site in advance, we effectively screened E. coli colonies harboring the desired plasmid functions in a prokaryote (Magnetospirillum gryphiswaldense) or eukaryote (Dictyostelium discoideum). Thus, our system represents a user-friendly technique for cloning.

scholarly journals Customized yeast cell factories for biopharmaceuticals: from cell engineering to process scale up

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Aravind Madhavan ◽  
K. B. Arun ◽  
Raveendran Sindhu ◽  
Jayaram Krishnamoorthy ◽  
R. Reshmy ◽  
...  
Keyword(s):  
Secretory Pathway ◽  
Kluyveromyces Lactis ◽  
Hansenula Polymorpha ◽  
Scale Up ◽  
Yeast Cells ◽  
Pathway Engineering ◽  
Heterologous Proteins ◽  
Pharmaceutical Protein ◽  
Cell Factories ◽  
Industrial Manufacture

AbstractThe manufacture of recombinant therapeutics is a fastest-developing section of therapeutic pharmaceuticals and presently plays a significant role in disease management. Yeasts are established eukaryotic host for heterologous protein production and offer distinctive benefits in synthesising pharmaceutical recombinants. Yeasts are proficient of vigorous growth on inexpensive media, easy for gene manipulations, and are capable of adding post translational changes of eukaryotes. Saccharomyces cerevisiae is model yeast that has been applied as a main host for the manufacture of pharmaceuticals and is the major tool box for genetic studies; nevertheless, numerous other yeasts comprising Pichia pastoris, Kluyveromyces lactis, Hansenula polymorpha, and Yarrowia lipolytica have attained huge attention as non-conventional partners intended for the industrial manufacture of heterologous proteins. Here we review the advances in yeast gene manipulation tools and techniques for heterologous pharmaceutical protein synthesis. Application of secretory pathway engineering, glycosylation engineering strategies and fermentation scale-up strategies in customizing yeast cells for the synthesis of therapeutic proteins has been meticulously described.

scholarly journals Identification of a Novel Prophage-Like Gene Cluster Actively Expressed in Both Virulent and Avirulent Strains of Leptospira interrogans Serovar Lai

2008 ◽  
Vol 76 (6) ◽  
pp. 2411-2419 ◽  
Author(s):  
Jin-Hong Qin ◽  
Qing Zhang ◽  
Zhi-Ming Zhang ◽  
Yi Zhong ◽  
Yang Yang ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Dna Sequences ◽  
Transcription Initiation ◽  
Gene Annotation ◽  
Specific Binding ◽  
Expression Profiles ◽  
Regulatory Sequences ◽  
Leptospira Interrogans ◽  
E Coli

ABSTRACT DNA microarray analysis was used to compare the differential gene expression profiles between Leptospira interrogans serovar Lai type strain 56601 and its corresponding attenuated strain IPAV. A 22-kb genomic island covering a cluster of 34 genes (i.e., genes LA0186 to LA0219) was actively expressed in both strains but concomitantly upregulated in strain 56601 in contrast to that of IPAV. Reverse transcription-PCR assays proved that the gene cluster comprised five transcripts. Gene annotation of this cluster revealed characteristics of a putative prophage-like remnant with at least 8 of 34 sequences encoding prophage-like proteins, of which the LA0195 protein is probably a putative prophage CI-like regulator. The transcription initiation activities of putative promoter-regulatory sequences of transcripts I, II, and III, all proximal to the LA0195 gene, were further analyzed in the Escherichia coli promoter probe vector pKK232-8 by assaying the reporter chloramphenicol acetyltransferase (CAT) activities. The strong promoter activities of both transcripts I and II indicated by the E. coli CAT assay were well correlated with the in vitro sequence-specific binding of the recombinant LA0195 protein to the corresponding promoter probes detected by the electrophoresis mobility shift assay. On the other hand, the promoter activity of transcript III was very low in E. coli and failed to show active binding to the LA0195 protein in vitro. These results suggested that the LA0195 protein is likely involved in the transcription of transcripts I and II. However, the identical complete DNA sequences of this prophage remnant from these two strains strongly suggests that possible regulatory factors or signal transduction systems residing outside of this region within the genome may be responsible for the differential expression profiling in these two strains.

scholarly journals Quantifying the regulatory role of individual transcription factors in Escherichia coli

2021 ◽  
Author(s):  
Sunil Guharajan ◽  
Shivani Chhabra ◽  
Vinuselvi Parisutham ◽  
Robert C Brewster
Keyword(s):  
Transcription Factors ◽  
Dna Sequences ◽  
Transcription Initiation ◽  
Target Genes ◽  
Regulatory Role ◽  
E Coli ◽  
Regulatory Dna Sequences ◽  
The Individual ◽  
Regulatory Dna

Transcription factors (TFs) modulate gene expression by binding to regulatory DNA sequences surrounding target genes. To isolate the fundamental regulatory interactions of E. coli TFs, we measure regulation of TFs acting on synthetic target genes that are designed to isolate the individual TF regulatory effect. This data is interpreted through a thermodynamic model that decouples the role of TF copy number and TF binding affinity from the interactions of the TF on RNA polymerase through two distinct mechanisms: (de)stabilization of the polymerase and (de)acceleration of transcription initiation. We find the contribution of each mechanism towards the observed regulation depends on TF identity and binding location; for the set of TFs studied here, regulation immediately downstream of the promoter is not sensitive to TF identity, however these same TFs regulate through distinct mechanisms at an upstream binding site. Furthermore, depending on binding location, these two mechanisms of regulation can act coherently, to reinforce the observed regulatory role (activation or repression), or incoherently, where the TF regulates two distinct steps with opposing effect.

Transcription factor/DNA interactions visualized by electron spectroscopic imaging

1992 ◽  
Vol 50 (1) ◽  
pp. 450-451
Author(s):  
David P. Bazett-Jones ◽  
Mark L. Brown
Keyword(s):  
Transcription Factor ◽  
Dna Sequences ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Phosphorus Content ◽  
Spectroscopic Imaging ◽  
Electron Spectroscopic Imaging ◽  
Dna Backbone ◽  
Two Parameters ◽  
High Level

A multisubunit RNA polymerase enzyme is ultimately responsible for transcription initiation and elongation of RNA, but recognition of the proper start site by the enzyme is regulated by general, temporal and gene-specific trans-factors interacting at promoter and enhancer DNA sequences. To understand the molecular mechanisms which precisely regulate the transcription initiation event, it is crucial to elucidate the structure of the transcription factor/DNA complexes involved. Electron spectroscopic imaging (ESI) provides the opportunity to visualize individual DNA molecules. Enhancement of DNA contrast with ESI is accomplished by imaging with electrons that have interacted with inner shell electrons of phosphorus in the DNA backbone. Phosphorus detection at this intermediately high level of resolution (≈lnm) permits selective imaging of the DNA, to determine whether the protein factors compact, bend or wrap the DNA. Simultaneously, mass analysis and phosphorus content can be measured quantitatively, using adjacent DNA or tobacco mosaic virus (TMV) as mass and phosphorus standards. These two parameters provide stoichiometric information relating the ratios of protein:DNA content.

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