Cfp Gene Research Articles

Peeling back the many layers of competitive exclusion.

Baby chicks administered a fecal transplant from adult chickens are resistant to Salmonella colonization by competitive exclusion. A two-pronged approach was used to investigate the mechanism of this process. First, Salmonella response to an exclusive (Salmonella competitive exclusion product, Aviguard®) or permissive microbial community (chicken cecal contents from colonized birds containing 7.85 Log10Salmonella genomes/gram) was assessed ex vivo using a S. typhimurium reporter strain with fluorescent YFP and CFP gene fusions to rrn and hilA operon, respectively. Second, cecal transcriptome analysis was used to assess the cecal communities' response to Salmonella in chickens with low (≤5.85 Log10 genomes/g) or high (≥6.00 Log10 genomes/g) Salmonella colonization. The ex vivo experiment revealed a reduction in Salmonella growth and hilA expression following co-culture with the exclusive community. The exclusive community also repressed Salmonella's SPI-1 virulence genes and LPS modification, while the anti-virulence/inflammatory gene avrA was upregulated. Salmonella transcriptome analysis revealed significant metabolic disparities in Salmonella grown with the two different communities. Propanediol utilization and vitamin B12 synthesis were central to Salmonella metabolism co-cultured with either community, and mutations in propanediol and vitamin B12 metabolism altered Salmonella growth in the exclusive community. There were significant differences in the cecal community's stress response to Salmonella colonization. Cecal community transcripts indicated that antimicrobials were central to the type of stress response detected in the low Salmonella abundance community, suggesting antagonism involved in Salmonella exclusion. This study indicates complex community interactions that modulate Salmonella metabolism and pathogenic behavior and reduce growth through antagonism may be key to exclusion.

Peripheral signature of altered synaptic integrity in young onset cannabis use disorder: A proteomic study of circulating extracellular vesicles

Background Rates of Cannabis Use Disorder (CUD) are highest amongst young adults. Paucity of brain tissue samples limits the ability to examine the molecular basis of cannabis related neuropathology. Proteomic studies of neuron-derived extracellular vesicles (NDEs) isolated from the biofluids may reveal markers of neuropathology in CUD. Methods NDEs were extracted using ExoSORT, an immunoaffinity method to enrich NDEs from plasma samples from patients with young onset CUD and matched controls. Differential proteomic profiles were explored with Label Free Quantification (LFQ) mass spectrometry. Selected proteins were validated using orthogonal methods. Results A total of 231 (±10) proteins were identified in NDE preparations from CUD and controls of which 28 were differentially abundant between groups. The difference in abundance of properdin (CFP gene) was statistically significant. SHANK1 (SHANK1 gene), an adapter protein at the post-synaptic density, was nominally depleted in the CUD NDE preparations. Conclusion In this pilot study, we noted a decrease in SHANK1 protein, involved in the structural and functional integrity of glutamatergic post-synapse, a potential peripheral signature of CUD neuropathology. The study shows that LFQ mass spectrometry proteomic analysis of NDEs derived from plasma may yield important insights into the synaptic pathology associated with CUD.

Nitrogen starvation-inducible promoter of microalga Neochloris oleoabundans lipogenic gene encoding diacylglycerol acyltransferase 2

Microalgal lipid triacylglycerol (TAG) is a promising source for sustainable production of biofuels and edible oils. TAG biosynthesis in microalgae can be induced by nitrogen starvation (−N); however, regulation of the genes involved in this process is poorly known. To explore the regulation of gene encoding diacylglycerol acyltransferase 2 of oleaginous microalga Neochloris oleoabundans (NeoDGAT2) responsible for TAG biosynthesis, regulatory sequence of NeoDGAT2 gene (RDG) was cloned, and its functional regions were mapped by deletion analysis using the modified cyan fluorescent protein gene (CFP) as a reporter. The efficiency of CFP gene mTurquoise2 (Tq) without any intron, Tq1 and Tq2 with one and two copies of Chlamydomonas reinhardtii rbcS2 intron 1, respectively, was evaluated; Tq2 exhibited the highest CFP fluorescence activity in N. oleoabundans was therefore used as reporter for RDG deletion analysis. Deletion analysis of RDG revealed that the −N inducible region contained the predicted binding site of MYB transcription factor (MYB-bs). Specific binding between MYB-bs of RDG and the DNA-binding domain of MYB-related transcription factor ROC40 from C. reinhardtii was observed using electrophoretic mobility shift assay. Therefore, the corresponding MYB transcription factor in N. oleoabundans is probably the transcription factor regulating NeoDGAT2. The interaction between MYB transcription factor and the MYB-bs may play a role in regulating −N induced expression of NeoDGAT2, affecting TAG accumulation. MYB transcription factors can be the potential targets for engineering to increase TAG content. Increasing TAG content is essential for products derived from microalgal TAG to achieve economic viability.

MRNA expression disturbance of complement system related genes in acute arterial thrombotic and paroxysmal atrial fibrillation patients.

This study aimed to compare the characteristics of mRNA expression of genes in complement system between acute arterial thrombotic patients and paroxysmal atrial fibrillation (PAF) patients. Twenty acute myocardial infarction (AMI) patients and 20 PAF patients were assigned into the experiment groups, and 20 stable angina pectoris (SAP) patients were enrolled in the control group. When compared with the control group, mRNA expression of C1QA, C1QB, C1QC, C1R, CFP, C5, CR1, ITGAM, ITGAX, ITGB2, C5AR1, CD46, CD55 and CD59 genes was significantly upregulated, and CR2 gene significantly downregulated in the AMI group (P<0.05); while mRNA expression of CFD, MBL2, MASP2, C5, C6, C8B, C9, C5AR1, CR2, CFI, CFHR1, CD46, CD55, VTN and CD59 genes was significantly downregulated in PAF patients (P<0.05). Results of the comparison between the AMI and PAF group showed that mRNA expression of C1QA, C1QB, C1QC, C1R, CFB, CFD, CFP, MBL2, MASP2, C5, C6, C8B, C9, CR1, ITGAM, ITGAX, ITGB2, C5AR1, CFI, CFHR1, CD46, CD55, CLU, VTN and CD59 genes was significantly upregulated in the AMI group (P<0.05). Taken SAP patients as controls, the complement system is in a high-intensive disturbance with simultaneous activation and inhibition in AMI patients, indicating that the cascade response of complement system is disturbed, and then the membrane attack complex (MAC) cannot form finally. The mRNA expression of related genes in the complement system is under a status of downregulation in PAF patients, indicating that the functions of cascade response in the complement system decreased significantly in PAF patients, leading to significantly decreased MAC functions.

Two dominant selectable markers for genetic manipulation in Neurospora crassa.

Neurospora crassa is an excellent model fungus for studies on molecular genetics, biochemistry, physiology, and molecular cell biology. Along with the rapid progress of Neurospora research, new tools facilitating more efficient and accurate genetic analysis are in high demand. Here, we tested whether the dominant selective makers widely used in yeasts are applicable in N. crassa. Among them, we found that the strains of N. crassa are sensitive to the aminoglycoside antibiotics, G418 and nourseothricin. 1000μg/mL of G418 or 50μg/mL of nourseothricin is sufficient to inhibit Neurospora growth completely. When the neomycin phosphotransferase gene (neo) used in mammalian cells is expressed, N. crassa shows potent resistance to G418. This establishes G418-resistant marker as a dominant selectable marker to use in N. crassa. Similarly, when the nourseothricin acetyltransferase gene (nat) from Streptomyces noursei is induced by qa-2 promoter in the presence of quinic acid (QA), N. crassa shows potent resistance to nourseothricin. When nat is constitutively expressed by full-length or truncated versions of the promoter from the N. crassa cfp gene (NCU02193), or by the trpC promoter of Aspergillus nidulans, the growth of N. crassa in the presence of nourseothricin is proportional to the expression levels of Nat. Finally, these two markers are used to knock-out wc-2 or al-1 gene from the N. crassa genome. The successful development of these two markers in this study expands the toolbox for N. crassa and very likely for other filamentous fungi as well.

Inhibition of protein expression by the interaction of G-Quadruplex and RHAU peptide in E. coli

Introduction: G-quadurplex (G4) formation plays a role in many biological processes such as replication, transcription, translation and telomeric maintenance. Stabilization of G4 structure by peptide has recently emerged as a potential approach in the regulation of protein expression. In this study, we reported on regulation of cyan fluorescent protein (CFP) expression by the interaction of G4 and RNA helicase associated with AU-rich elements (RHAU) peptide in E. coli.&#x0D; Methods: A sequence of TTGGGTGGGTGGGTGGGT (formed into G4 structure) was genetically applied to cfp gene as a reporter gene (g4-cfp). Both g4-cfp and DHX36 (or ΔDHX36) genes were cloned to pET-Duet1 vector that allowed to simultaneously express both G4-CFP protein and RHAU (or ΔRHAU) protein under IPTG inducer.&#x0D; Results: The level of G4-CFP expression in the presence of RHAU (pD64) was around 2-fold and 3-fold lower than that of G4-CFP expression in the presence of ΔRHAU (pD65) and G4-CFP expression alone (pD21), respectively.&#x0D; Conclusion: RHAU might selectively bind G4 structure of mRNA of G4-CFP, resulting in inhibition of G4-CFP expression in E. coli. The G4 and RHAU peptide interaction would provide a promising approach for inhibition of gene expression in many biomedical applications.&#x0D;

Gene expression in E. coli influences the position and motion of the lac operon and vicinal loci

Transcription and translation of active genes play an important role in determining the global organization of the chromosome. To further elucidate this phenomenon, we examined how the expression of either the lacY or the cfp gene in the native lac operon influences adjacent chromosomal segments by fluorescently labeling loci upstream and downstream of the expressed gene. Based on the positions and motile behaviors of these loci, our results reveal that the local organization of the vicinal chromosomal segments and its position in the nucleoid are both influenced by gene expression. Furthermore, we found that the effects on local organization depend on whether the expressed gene encodes a membrane protein or a cytoplasmic protein. Our measurements showing the movement of loci toward the membrane and the correlation between the motions of the upstream and downstream loci support the conclusion that the expression of genes encoding membrane proteins greatly influences chromosome dynamics.

Rapid and efficient genetic transformation of the green microalga Chlorella vulgaris

Chlorella is a green unicellular alga that has a wide range of future biotechnical applications such as production of pharmaceuticals and biodiesel. Efficient genetic transformation of Chlorella vulgaris has been difficult due to technical limitations. In this study, an efficient and reliable transformation system of electroporation was established using two different reporter genes. First, C. vulgaris cell wall was digested with enzyme mixture for preparing protoplasts. The optimal transformation efficiency was 1.67 × 104 ± 0.083 cfu μg−1 plasmid under the following conditions: 2 × 106 cells mL−1 of growing culture; 655 V pulse voltage with 3.4 ms pulse width. After transformation, green and cyan fluorescence were observed from transgenic C. vulgaris harboring gfp (green fluorescent protein) gene of pCAMBIA1302 and cfp (cyan fluorescent protein) gene of pSK397, respectively, using laser confocal microscope. RT-PCR analysis as well as Southern blot confirmed the integration of reporter gene at the molecular level. This efficient transformation system of C. vulgaris would be valuable for the production of recombinant proteins in the future.

Polymorphisms in genes related to the complement system and antibody-mediated cardiac allograft rejection

Heart transplantation (HT) is a life-saving treatment for patients with end-stage heart failure. One of the main problems after HT is the humoral response termed antibody-mediated rejection (AMR). Complement activation plays a key role in AMR contributing to graft damage. The aim of this study was to analyze genetic variants in genes related to the complement pathways that could be associated with the development of AMR. Analysis of 51 genes related to the complement pathway was performed by next-generation sequencing in 46 HT recipients, 23 with and 23 without AMR. Statistical analysis was performed with SNPstats and R. We identified 2 single nucleotide polymorphisms, 1 in the mannose-binding lectin 2 gene (p.Gly54Asp-MBL2) and 1 in the complement factor properdin gene (p.Asn428(p=)-CFP), that showed significant association with the absence and development of AMR, respectively. Moreover, the presence of the rare allele in p.Gly54Asp-MBL2 control patients correlated with an immunodeficiency of mannose-binding lectin (6.24 ng/ml vs 207.50 ng/ml, p < 0.01), whereas the presence of the rare allele p.Asn428(p=)-CFP in patients with AMR correlated with higher levels of properdin protein (14.65 μg/ml vs 10.77 μg/ml, p < 0.05). AMR is a complex phenotype affected by many recipient factors. Variants in p.Gly54Asp-MBL2 and p.Asn428(p=)-CFP genes, encoding mannose-binding lectin 2 and properdin, may influence the risk of AMR.

Quantitative characterization of gene regulation by Rho dependent transcription termination

Rho factor dependent transcription termination (RTT) is common within the coding sequences of bacterial genes and it acts to couple transcription and translation levels. Despite the importance of RTT for gene regulation, its effects on mRNA and protein concentrations have not been quantitatively characterized. Here we demonstrate that the exogenous cfp gene encoding the cyan fluorescent protein can serve as a model for gene regulation by RTT. This was confirmed by showing that Psu and bicyclomycin decrease RTT and increase full length cfp mRNAs (but remarkably they have little effect on protein production). We then use cfp to characterize the relationship between its protein and full length mRNA concentrations when the translation initiation rate is varied by sequence modifications of the translation initiation region (TIR). These experiments reveal that the fold change in protein concentration (RP) and the fold change in full length mRNA concentration (Rm) have the relationship RP≈Rmb, where b is a constant. The average value of b was determined from three separate data sets to be ~3.6. We demonstrate that the above power law function can predict how altering the translation initiation rate of a gene in an operon will affect the mRNA concentrations of downstream genes and specify a lower bound for the associated changes in protein concentrations. In summary, this study defines a simple phenomenological model to help program expression from single genes and operons that are regulated by RTT, and to guide molecular models of RTT.

584. Improvement of Gene Delivery By Inhibition of Endonucleases

One of the fundamental problems for gene therapy is poor gene transfer/expression efficiency resulting from DNase/endonuclease activity that plays important role of the host cell defense by degrading foreign DNA. The bulk of endonuclease activity in cells and biological fluids is formed by apoptotic endonucleases which depolymerize DNA by hydrolyzing phosphodiester bonds within the polynucleotide chain. Among the identified nine apoptotic endonucleases, deoxyribonuclease 1 (DNase I) and endonuclease G (EndoG) are the most abundant and most active in mammals. However, there is small number of available inhibitors for DNase I and EndoG, and they are mostly non-specific and inapplicable in vivo. Our in vitro experiments comparing blood plasma of DNase I or EndoG knockout mice with wild-type mice showed that DNase I and EndoG are responsible for degradation of DNA in blood plasma. The genetic inactivation of endonucleases resulted in an improvement of CFP gene expression in HCC1954 cell line after exposure with pECFP plasmid DNA with blood plasma. However using chemical inhibitors would be more translation in this regard. To search for endonuclease inhibitors, we have developed a high-throughput DNase assay using fluorophore-labeled oligonucleotide to screen a home-made chemical library and identify two inhibitors: IG-17 (1, 3-phenylene-bis-aminoguanidine hydrochloride) for DNase I and PNR-3-82 (5-((1-(2-naphthoyl)-5-methoxy-1H-indol-3-yl)methylene)-2-thioxodihydropyrimidine-4,6(1H, 5H)-dione) for EndoG. The inhibitors are found to be specific in vitro and non-toxic in cellular assays. They significantly reduced the in vitro and in vivo (total body) endonuclease activity. In addition, we found that CFP gene delivery to various mouse organs measured by real-time RT-PCR was increased if the inhibitors were administered 2 days before intravenously injection of pECFP plasmid DNA compared to the vehicle-injected mice. This finding can be utilized for further improvement of gene delivery-based therapeutic strategies.

Fluorescent Protein Candidate Genes in the Coral Acropora digitifera Genome

The vivid coloration of corals depends on fluorescent proteins that include cyan (CFP), green (GFP) and red (RFP) fluorescent proteins, and a non-fluorescent blue/purple chromoprotein. We examined how many genes encoding fluorescent proteins are present in the recently sequenced genome of the coral Acropora digitifera. Based on molecular phylogenetic analysis, we found one, five, one, and three candidate genes for CFP, GFP, RFP, and chromoprotein, respectively. The CFP and GFP genes are clustered in a ~80-kb-long genomic region, suggesting that they originated from an ancestral gene by tandem duplication. Since CFP and GFP possess the same chromophore, the gene clustering may provide the first genomic evidence for a common origin of the two proteins. Comparison between the fluorescent protein genes of closely related coral species suggests an expansion of chromoprotein genes in the A. digitifera genome, and of RFP genes in the A. millepora genome. The A. digitifera fluorescent protein genes are expressed during embryonic and larval developmental stages and in adults, suggesting that the genes play a variety of roles in coral physiology.

Fluorescent protein fusions in Candida guilliermondii

Candida guilliermondii is an emerging fungal agent of candidiasis often associated with oncology patients. This yeast also remains a promising biotechnological model for the industrial production of value-added metabolites. In the present study, we developed a recipient strain as well as a set of plasmids for construction of fluorescent protein (FP) fusions in this species. We demonstrated that C. guilliermondii phosphoglycerate kinase transcription-regulating sequences allow a constitutive expression of codon-optimized green, cyan, yellow and mCherry FP genes in C. guilliermondii cells and the fluorescence signal could be directly observed at the colony and blastospore level by epifluorescence microcopy. To illustrate differential targeting of the FPs into specified cellular compartments, we studied and validated the expected subcellular localization of various C. guilliermondii predicted proteins fused to FPs. Furthermore, co-expression experiments of various couples of FP-tagged C. guilliermondii predicted proteins in the same cell showed that the fluorescence of each FP could be detected independently, providing firm evidences that YFP/CFP and GFP/mCherry pairs can be used for dual labeling in C. guilliermondii cells. This technical advance will facilitate future studies of protein co-expression and co-localization in C. guilliermondii and will give precious help for elucidating new molecular events supporting pathogenicity, antifungal resistance and for exploring the potential of yeast metabolic engineering.

Nucleolar Follistatin Promotes Cancer Cell Survival under Glucose-deprived Conditions through Inhibiting Cellular rRNA Synthesis

Solid tumor development is frequently accompanied by energy-deficient conditions such as glucose deprivation and hypoxia. Follistatin (FST), a secretory protein originally identified from ovarian follicular fluid, has been suggested to be involved in tumor development. However, whether it plays a role in cancer cell survival under energy-deprived conditions remains elusive. In this study, we demonstrated that glucose deprivation markedly enhanced the expression and nucleolar localization of FST in HeLa cells. The nucleolar localization of FST relied on its nuclear localization signal (NLS) comprising the residues 64-87. Localization of FST to the nucleolus attenuated rRNA synthesis, a key process for cellular energy homeostasis and cell survival. Overexpression of FST delayed glucose deprivation-induced apoptosis, whereas down-regulation of FST exerted the opposite effect. These functions depended on the presence of an intact NLS because the NLS-deleted mutant of FST lost the rRNA inhibition effect and the cell protective effect. Altogether, we identified a novel nucleolar function of FST, which is of importance in the modulation of cancer cell survival in response to glucose deprivation.

Suite of novel vectors for ectopic insertion of GFP, CFP and IYFP transcriptional fusions in single copy at the amyE and bglS loci in Bacillus subtilis

We report the development of a suite of six integrative vectors for construction of single copy transcriptional fusions with the gfpmut3, cfp and iyfp reporter genes in Bacillus subtilis. The promoter fusions are constructed using the highly efficient ligation-independent cloning (LIC) technique making them suitable for high-throughput applications. The plasmids insert into the chromosome by a double cross-over event at the amyE or bglS loci and integration at each site can be verified by a plate-based screening assay. The vectors allow expression of two different promoters to be determined in the same strain using the cfp and iyfp reporter genes since CFP and iYFP are spectrally distinct and have comparable half-lives of approximately 2 h in exponentially growing B. subtilis cells. We demonstrate the versatility of these vectors by measuring expression of the tuaA and phoA operons singularly and in combination, during growth in phosphate limiting conditions.

Double-strand breaks induce homologous recombinational repair of interstrand cross-links via cooperation of MSH2, ERCC1-XPF, REV3, and the Fanconi anemia pathway

DNA interstrand cross-linking agents have been widely used in chemotherapeutic treatment of cancer. The majority of interstrand cross-links (ICLs) in mammalian cells are removed via a complex process that involves the formation of double-strand breaks at replication forks, incision of the ICL, and subsequent error-free repair by homologous recombination. How double-strand breaks effect the removal of ICLs and the downstream homologous recombination process is not clear. Here, we describe a plasmid-based recombination assay in which one copy of the CFP gene is inactivated by a site-specific psoralen ICL and can be repaired by gene conversion with a mutated homologous donor sequence. We found that the homology-dependent recombination (HDR) is inhibited by the ICL. However, when we introduced a double-strand break adjacent to the site of the ICL, the removal of the ICL was enhanced and the substrate was funneled into a HDR repair pathway. This process was not dependent on the nucleotide excision repair pathway, but did require the ERCC1-XPF endonuclease and REV3. In addition, both the Fanconi anemia pathway and the mismatch repair protein MSH2 were required for the recombinational repair processing of the ICL. These results suggest that the juxtaposition of an ICL and a DSB stimulates repair of ICLs through a process requiring components of mismatch repair, ERCC1-XPF, REV3, Fanconi anemia proteins, and homologous recombination repair factors.

Expression in sugar beet of the introduced cercosporin toxin export (CFP) gene from Cercospora kikuchii, the causative organism of purple seed stain in soybean.

The Cercospora kikuchii cercosporin export gene, CFP, introduced into Beta vulgaris L. by conjugation with Rhizobium radiobacter, was stably maintained during vegetative propagation as verified by PCR using primers specific for the CFP gene. Transcriptional expression of the CFP gene in leaves was determined by RT-PCR using CFP-specific primers. CFP protein was detected using Western analysis with an affinity-purified polypeptide-specifc antibody. Analysis of the relative susceptibility of CFP-transgenic and non-transgenic sugar beet plants is planned but will probably take several years to complete.

The Neurospora crassa cfp promoter drives a carbon source-dependent expression of transgenes in filamentous fungi.

The objective of the present study was to determine the potential of promoter sequences from the cfp gene of Neurospora crassa to drive the expression of transgenes in filamentous fungi. Northern blot analyses showed that the mRNA levels of cfp were rapidly modified in response to either inducing or repressing culture conditions. The hygromycin phosphotransferase (hph) and S-adenosylmethionine synthetase (eth-1) genes were fused to a minimal cfp promoter fragment (Pcfp) and used as reporter genes. These constructs were highly expressed in transformant N. crassa strains grown in media containing glucose or sucrose and repressed in media containing ethanol or ethanol plus glucose. A gene fusion of the cfp promoter to the beta-glucuronidase gene (cfp-uidA) showed identical patterns of expression in the heterologous filamentous fungus Aspergillus nidulans. Our results show that the levels of expression of the native cfp gene, as well as reporter genes driven by cfp promoter sequences, can be rapidly modified in response to different carbon sources. These modified levels of expression are maintained by continuous growth in the presence of the corresponding carbon source. We propose that the cfp promoter can be used to control the expression of transgenes in filamentous fungi in a carbon source-dependent fashion.

Rhizobium radiobacter conjugation and callus-independent shoot regeneration used to introduce the cercosporin export gene cfp from Cercospora into sugar beet (Beta vulgaris L.).

Leaf spot disease caused by Cercospora is responsible for crop and profitability losses in sugar beet crops in the US and worldwide. The cfp gene that encodes a protein that exports phytotoxic cercosporins from Cercospora was conjugally transferred to sugar beet using Rhizobium radiobacter (Agrobacterium tumefaciens), to improve Cercospora-induced leafspot resistance. Conditions for shoot regeneration were optimized to increase regeneration/transformation efficiencies. Low-light and room-temperature conditions were favorable to sugar beet regeneration without callus when cytokinin had been added to the tissue culture medium. Using this procedure adventitious shoots from leaf pieces were obtained in a simple, one-step regeneration procedure. T7, a cfp-transgenic clone verified by PCR with gene-specific primers, is being propagated for leaf spot disease resistance evaluation.