scholarly journals A Redox-Responsive Regulator of Photosynthesis Gene Expression in the Cyanobacterium Synechocystis sp. Strain PCC 6803

2000 ◽  
Vol 182 (15) ◽  
pp. 4268-4277 ◽  
Author(s):  
Hong Li ◽  
Louis A. Sherman
Keyword(s):  
Gene Expression ◽  
Reaction Center ◽  
D1 Protein ◽  
Insertion Mutation ◽  
Mrna Levels ◽  
Related Gene ◽  
Wild Type ◽  
Unicellular Cyanobacterium ◽  
Redox Poise ◽  
Pcc 6803

ABSTRACT We have identified genes in the unicellular cyanobacteriumSynechocystis sp. strain PCC 6803 that are involved with redox control of photosynthesis and pigment-related genes. The genes,rppA (sll0797) and rppB (sll0798), represent a two-component regulatory system that controls the synthesis of photosystem II (PSII) and PSI genes, in addition to photopigment-related genes. rppA (regulator of photosynthesis- and photopigment-related gene expression) andrppB exhibit strong sequence similarity to prokaryotic response regulators and histidine kinases, respectively. In the wild type, the steady-state mRNA levels of PSII reaction center genes increased when the plastoquinone (PQ) pool was oxidized and decreased when the PQ pool was reduced, whereas transcription of the PSI reaction center genes was affected in an opposite fashion. Such results suggested that the redox poise of the PQ pool is critical for regulation of the photosystem reaction center genes. In ΔrppA, an insertion mutation of rppA, the PSII gene transcripts were highly up-regulated relative to the wild type under all redox conditions, whereas transcription of phycobilisome-related genes and PSI genes was decreased. The higher transcription of the psbA gene in ΔrppA was manifest by higher translation of the D1 protein and a concomitant increase in O2 evolution. The results demonstrated that RppA is a regulator of photosynthesis- and photopigment-related gene expression, is involved in the establishment of the appropriate stoichiometry between the photosystems, and can sense changes in the PQ redox poise.

scholarly journals Insertion of the retroposable element, jockey, near the Adh gene of Drosophila melanogaster is associated with altered gene expression

1996 ◽  
Vol 68 (3) ◽  
pp. 203-209 ◽  
Author(s):  
Lisa D. White ◽  
James W. Jacobson
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Alcohol Dehydrogenase ◽  
Insertion Mutation ◽  
Activity Levels ◽  
Mrna Levels ◽  
Wild Type ◽  
Reporter System ◽  
Wild Type Counterpart ◽  
Altered Gene

SummaryThe alcohol dehydrogenase (Adh) gene of Drosophila melanogaster is well suited to be a gene expression reporter system. Adh produces a measurable phenotype at both the enzyme and mRNA levels. We recovered a spontaneous transposable element (TE) insertion mutation near the Adh gene. The insertion is a truncated retroposable element, jockey, inserted upstream of the adult Adh enhancer region. Comparisons between the Adhjockey allele and its direct wild-type ancestral allele were made in an isogenic background (i.e. identical cis and trans factors). Differences in Adhjockey expression compared with the wild-type can be attributed solely to the presence of the jockey element. This jockey insertion results in a decrease in adult mRNA transcript levels in the Adhjockey homozygous lines relative to the wild-type counterpart and accounts for a correlated decrease in alcohol dehydrogenase (ADH) enzyme activity. The larval ADH activity levels are not detectably different.

scholarly journals Role of Sigma Factors in Controlling Global Gene Expression in Light/Dark Transitions in the Cyanobacterium Synechocystis sp. Strain PCC 6803

2007 ◽  
Vol 189 (21) ◽  
pp. 7829-7840 ◽  
Author(s):  
Tina C. Summerfield ◽  
Louis A. Sherman
Keyword(s):  
Gene Expression ◽  
Global Gene Expression ◽  
Growth Conditions ◽  
Day Length ◽  
Regulation Of Transcription ◽  
Wild Type ◽  
Protein Levels ◽  
In The Wild ◽  
Altered Gene ◽  
Pcc 6803

ABSTRACT We report on differential gene expression in the cyanobacterium Synechocystis sp. strain PCC 6803 after light-dark transitions in wild-type, ΔsigB, and ΔsigD strains. We also studied the effect of day length in the presence of glucose on a ΔsigB ΔsigE mutant. Our results indicated that the absence of SigB or SigD predominately altered gene expression in the dark or in the light, respectively. In the light, approximately 350 genes displayed transcript levels in the ΔsigD strain that were different from those of the wild type, with over 200 of these up-regulated in the mutant. In the dark, removal of SigB altered more than 150 genes, and the levels of 136 of these were increased in the mutant compared to those in the wild type. The removal of both SigB and SigE had a major impact on gene expression under mixotrophic growth conditions and resulted in the inability of cells to grow in the presence of glucose with 8-h light and 16-h dark cycles. Our results indicated the importance of group II σ factors in the global regulation of transcription in this organism and are best explained by using the σ cycle paradigm with the stochastic release model described previously (R. A. Mooney, S. A. Darst, and R. Landick, Mol. Cell 20:335-345, 2005). We combined our results with the total protein levels of the σ factors in the light and dark as calculated previously (S. Imamura, S. Yoshihara, S. Nakano, N. Shiozaki, A. Yamada, K. Tanaka, H. Takahashi, M. Asayama, and M. Shirai, J. Mol. Biol. 325:857-872, 2003; S. Imamura, M. Asayama, H. Takahashi, K. Tanaka, H. Takahashi, and M. Shirai, FEBS Lett. 554:357-362, 2003). Thus, we concluded that the control of global transcription is based on the amount of the various σ factors present and able to bind RNA polymerase.

The rmc locus does not affect plant interactions or defence-related gene expression when tomato (Solanum lycopersicum) is infected with the root fungal parasite, Rhizoctonia

2006 ◽  
Vol 33 (3) ◽  
pp. 289 ◽  
Author(s):  
Ling-Ling Gao ◽  
F. Andrew Smith ◽  
Sally E. Smith
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Fungal Species ◽  
Plant Interactions ◽  
Related Gene ◽  
Wild Type ◽  
Cell Layers ◽  
Almost All

A tomato mutant with reduced mycorrhizal colonisation, rmc, confers resistance to almost all arbuscular mycorrhizal (AM) fungal species tested, although there is variation in colonisation of different root cell layers by different fungi and one species of AM fungus can colonise this mutant relatively normally. These variations indicate a high degree of specificity in relation to AM colonisation. We explored the possibility of specificity or otherwise in interactions between rmc and three non-AM root-infecting fungi, Rhizoctonia solani anastomosis groups (AG) 4 and AG8, and binucleate Rhizoctonia (BNR). There were no differences between the wild type tomato 76R and rmc in the speed or extent to which these fungi infected roots or caused disease. Infection by R. solani induced high levels of defence-related gene expression in both tomato genotypes relative to non-infected plants. In contrast, with BNR the expression of these genes was not induced or induced to a much lower extent than with R. solani. The expression of defence-related genes with these two non-AM fungi was very similar in the two plant genotypes. It was different from effects observed during colonisation by AM fungi, which enhanced expression of defence-related genes in rmc compared with the wild type tomato. The specificity and molecular mechanisms of rmc in control of AM colonisation are discussed.

Effect of LCR 5′HS4 and 5′HS1 Deletions on β-Like Globin Gene Expression in β-Yac Transgenic Mice.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 1209-1209
Author(s):  
Susanna Harju ◽  
Halyna Fedosyuk ◽  
Kenneth R. Peterson
Keyword(s):  
Gene Expression ◽  
Homologous Recombination ◽  
Globin Gene ◽  
Developmental Expression ◽  
Mrna Levels ◽  
Wild Type ◽  
Rnase Protection ◽  
Transgenic Lines ◽  
Definitive Erythropoiesis ◽  
Globin Gene Expression

Abstract A 213 Kb human β-globin locus yeast artificial chromosome (β-YAC) was modified by homologous recombination to delete 2.9 Kb of cross-species conserved sequence similarity encompassing the LCR 5′HS4 (Δ5′HS4 β-YAC). Three transgenic mouse lines were established; each contained two intact copies of the β-globin locus as determined by long range restriction enzyme mapping (LRRM) and Southern blot hybridization analyses. Human ε-, γ- and β-globin, and mouse α- and ζ-globin mRNAs were measured by RNAse protection in hematopoietic tissues derived from staged embryos, fetuses and adult mice. No difference in the temporal pattern of globin transgene expression was observed between Δ5′HS4 β-YAC mice and wild-type β-YAC mice. In addition, quantitative per-copy human β-like globin mRNA levels were similar between Δ5′HS4 and wild-type β-YAC transgenic lines, although γ-globin gene expression was slightly increased in the fetal liver, while β-globin gene expression was slightly decreased in Δ5′HS4 β-YAC mice. These data are in contrast to data obtained from β-YAC mice containing a deletion of the 280 bp 5′HS4 core. In these mice, γ- and β-globin gene expression was significantly decreased during fetal definitive erythropoiesis and β-globin gene expression was decreased during adult definitive erythropoiesis. However, these data are consistent with the observation that deletion of the 5′HS core elements is more deleterious than large deletions of the 5′HSs. Together, the compiled deletion data supports the hypothesis that the LCR exists as a holocomplex in which the 5′HS cores form an active site and the flanking 5′HS regions constrain the holocomplex conformation. In this model, 5′HS core mutations are dominant negative, whereas larger deletions allow the LCR to fold into alternate holocomplex structures that function normally, albeit less efficiently. To complete the study on the contribution of the individual 5′HSs to LCR function, a 0.8 Kb 5′HS1 fragment was deleted in the 213 Kb β-YAC by homologous recombination. Two ΔHS1 β-YAC transgenic lines have been established; four additional founders were recently identified. Of the two lines, one contains two intact copies of the globin locus; the other contains four deleted copies, one of which extends from the LCR through just 5′ to the β-globin gene. For both lines, ε-globin gene expression was markedly reduced, approximately 5–10 fold, during primitive erythropoiesis. Developmental expression profiles and levels of the γ- and β-globin genes (in the line that contains loci including the β-globin gene) were unaffected by deletion of 5′HS1. Breeding of the remaining four founders to obtain F1 and F2 progeny for similar structure/function studies is in progress. Decreased expression of the β-globin gene is the first phenotype ascribed to a 5′HS1 mutation, suggesting that this HS does indeed have a role in LCR function.

A Targeted Resequencing Study Allows the Detection of a Common Polymorphism At Mirna-223 Binding Site in 3′Untranslated Region Which Deregulates HSP90B1 Expression in Chronic Lymphocytic Leukemia

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 1776-1776
Author(s):  
Ana E Rodríguez ◽  
Dalia Qwaider ◽  
Rocío Benito ◽  
Irena Misiewicz-Krzeminska ◽  
María Hernández-Sánchez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Binding Site ◽  
Cell Line ◽  
B Lymphocytes ◽  
Prognostic Significance ◽  
Mrna Levels ◽  
Healthy Controls ◽  
Wild Type ◽  
Single Nucleotide ◽  
Custom Made

Abstract Abstract 1776 Array-based sequence capture (Roche NimbleGen) followed by next-generation sequencing (Roche GS FLX Titanium sequencing platform) was used to analyze genetic variations in 93 genes relevant in CLL and two chromosomal regions: 13q14.3 and 17p13.1. CD19+ cells from 4 patients with CLL and 4 patients with other hematological malignancies (used as controls) were studied. A custom-made data analysis pipeline was used to annotate detected variants, including known single-nucleotide polymorphisms (SNPs), amino acid consequences, genomic location and miRNA binding sites. The enrichment assay followed by NGS allowed the detection of over 1600 variations/sample (median 1721, range 1618–1823). All putative variants were first compared with published single nucleotide polymorphism (SNP) data (dbSNP build 130) and most of the variants detected were identified as known SNPs. Overall, 10% of variants detected in each sample were variations not previously described. Interestingly, a 4bp insertion/deletion polymorphism (rs2307842) in the 3′UTR of HSP90B1, target site for miR-223, was detected. There is an increasing evidence suggesting that SNPs in the 3′UTR targeted by miRNAs (known as miRSNPs) are associated with diseases by affecting gene expression. We hypothesized that this ‘GACT’ deletion disrupts the binding site for miR-223 thereby increasing the translation of HSP90B1 and we confirmed that miR-223 regulates HSP90B1 expression by 3′UTR reporter assays. The relative luciferase activity of the construct with wild-type 3′UTR (WT-3′UTR) was significantly repressed by 31% following miR-223 transfection (p<0.05). However, the presence of rs2307842 polymorphism in 3′UTR of HSP90B1 (VAR-3′UTR) abolished this suppression, suggesting that miR-223 directly binds to this site. We also validated HSP90B1 as a target gene of miR223 by transfecting MM1S and H929 cell lines with miR-223/NC mimics and then measuring HSP90B1 expression by semi-quantitative PCR and Western blot. Exogenous expression of miR-223 downregulated the expression levels of HSP90B1 in H929 cell line (WT-3′UTR) in both mRNA (p<0.05) and protein levels. By contrast, HSP90B1 expression was not modified in MM1S cell line (VAR-3′UTR). To evaluate the clinical impact of HSP90B1 3′UTR polymorphism, we expanded the study to 109 additional patients with CLL and 32 healthy controls. Sequencing of the HSP90B1 3′UTR region was performed by pyrosequencing (PyroMark Q24 system, Qiagen). The rs2307842 was detected in 27/109 (25%) patients and 8/32 (25%) healthy controls, as expected. Overall, we did not find any significant relationship between rs2307842 and clinical characteristics of CLL patients. To gain insight into its influence on gene expression, we measured HSP90B1 mRNA levels in paired samples (tumoral and normal) from CLL patients with rs2307842 (VAR-CLLs, n=6) and wild-type (WT-CLLs, n=12). PCR results showed that B lymphocytes (tumoral fraction) from VAR-CLLs have a higher expression of HSP90B1 than B lymphocytes from WT-CLLs (P=0.002) and also from the normal cells of the same patients (VAR-CLLs) (P=0.011). However, in WT-CLLs, no changes in mRNA expression were observed between tumor and normal fractions, being HSP90B1 mRNA levels similar to the normal fraction of VAR-CLLs. Thus, rs2307842 determined HSP90B1 overexpression only in the tumor fraction of the CLL patients with the polymorphism. Downregulation of miR-223 has prognostic significance in CLL. However, there is no evidence of the pathogenetic mechanism of this miRNA in CLL patients, and no target has been proposed or validated for miR-223 in CLL until date. Thus, this work provides novel information about how the downregulation of miR-223 can be determining the poor outcome of CLL patients, maybe through upregulation of HSP90B1 expression. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Accelerated Prion Replication in, but Prolonged Survival Times of, Prion-Infected CXCR3−/− Mice

2008 ◽  
Vol 82 (24) ◽  
pp. 12464-12471 ◽  
Author(s):  
Constanze Riemer ◽  
Julia Schultz ◽  
Michael Burwinkel ◽  
Anja Schwarz ◽  
Simon W. F. Mok ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prion Diseases ◽  
Proteinase K ◽  
Prolonged Survival ◽  
Disease Development ◽  
Mrna Levels ◽  
Wild Type ◽  
Survival Times ◽  
Cytokines And Chemokines ◽  
Asymptomatic Stage

ABSTRACT Prion diseases have a significant inflammatory component. Glia activation, which is associated with increased production of cytokines and chemokines, may play an important role in disease development. Among the chemokines upregulated highly and early upregulated during scrapie infections are ligands of CXCR3. To gain more insight into the role of CXCR3 in a prion model, CXCR3-deficient (CXCR3−/−) mice were infected intracerebrally with scrapie strain 139A and characterized in comparison to similarly infected wild-type controls. CXCR3−/− mice showed significantly prolonged survival times of up to 30 days on average. Surprisingly, however, they displayed accelerated accumulation of misfolded proteinase K-resistant prion protein PrPSc and 20 times higher infectious prion titers than wild-type mice at the asymptomatic stage of the disease, indicating that these PrP isoforms may not be critical determinants of survival times. As demonstrated by immunohistochemistry, Western blotting, and gene expression analysis, CXCR3-deficient animals develop an excessive astrocytosis. However, microglia activation is reduced. Quantitative analysis of gliosis-associated gene expression alterations demonstrated reduced mRNA levels for a number of proinflammatory factors in CXCR3−/− compared to wild-type mice, indicating a weaker inflammatory response in the knockout mice. Taken together, this murine prion model identifies CXCR3 as disease-modifying host factor and indicates that inflammatory glial responses may act in concert with PrPSc in disease development. Moreover, the results indicate that targeting CXCR3 for treatment of prion infections could prolong survival times, but the results also raise the concern that impairment of microglial migration by ablation or inhibition of CXCR3 could result in increased accumulation of misfolded PrPSc.

scholarly journals Tight Control of Respiration by NADH Dehydrogenase ND5 Subunit Gene Expression in Mouse Mitochondria

2000 ◽  
Vol 20 (3) ◽  
pp. 805-815 ◽  
Author(s):  
Yidong Bai ◽  
Rebecca M. Shakeley ◽  
Giuseppe Attardi
Keyword(s):  
Gene Expression ◽  
Nadh Dehydrogenase ◽  
Mrna Level ◽  
Mouse Cell ◽  
Synthesis Rate ◽  
Mrna Levels ◽  
Wild Type ◽  
Normal Number ◽  
Nd5 Gene ◽  
Cell Variant

ABSTRACT A mouse cell variant carrying in heteroplasmic form a nonsense mutation in the mitochondrial DNA-encoded ND5 subunit of the respiratory NADH dehydrogenase has been isolated and characterized. The derivation from this mutant of a large number of cell lines containing between 4 and 100% of the normal number of wild-type ND5 genes has allowed an analysis of the genetic and functional thresholds operating in mouse mitochondria. In wild-type cells, ∼40% of the ND5 mRNA level was in excess of that required for ND5 subunit synthesis. However, in heteroplasmic cells, the functional mRNA level decreased in proportion to the number of wild-type ND5 genes over a 25-fold range, pointing to the lack of any compensatory increase in rate of transcription and/or stability of mRNA. Most strikingly, the highest ND5 synthesis rate was just sufficient to support the maximum NADH dehydrogenase-dependent respiration rate, with no upregulation of translation occurring with decreasing wild-type mRNA levels. These results indicate that, despite the large excess of genetic potential of the mammalian mitochondrial genome, respiration is tightly regulated by ND5 gene expression.

Unique Gene Expression Profiles of AML Patients with CEBPA Mutations.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 745-745
Author(s):  
Bas J. Wouters ◽  
Claudia A. Erpelinck ◽  
Peter J. Valk ◽  
Roel G. Verhaak ◽  
Bob Löwenberg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Dominant Negative ◽  
Differentially Expressed ◽  
Rank Test ◽  
Insertion Mutation ◽  
Wild Type ◽  
Unique Gene ◽  
Cebpa Mutations

Abstract The transcription factor CCAAT/enhancer binding protein alpha (C/EBPalpha) is critical for granulopoiesis. 5–10% of patients with acute myeloid leukemia (AML) carry mutations in the coding region of the CEBPA gene. In a gene expression profiling study of 285 de novo AML patients we previously identified sixteen distinct clusters of AML (Valk et al, N Engl J Med 2004). Eighteen patients (6.3%) carried mutations in CEBPA, and 17 of them were found in two clusters (clusters #4 and #15), indicating that patients with CEBPA mutations exhibit unique gene expression profiles. In cluster #15, all specimens (n=8) carried CEBPA mutations, whereas in cluster #4 CEBPA mutations were found in 9 out of 15 cases. The other 6 cases in this subgroup showed low or no CEBPA mRNA expression, and in 4 of the latter the gene appeared to be switched off by CpG-hypermethylation. We sought to understand why CEBPA mutations were found in two separate clusters, and asked whether we could identify differences between the two clusters. We found no difference when analyzing CEBPA mutation types as most specimens in both clusters carried both an N-terminal truncation and a C-terminal in-frame insertion mutation. Morphologically, specimens in cluster #4 appeared to be less differentiated as compared to patients in cluster #15 (predominant FAB-types being M1 and M2, respectively). With respect to overall survival, patients in cluster #15 tend to have a slightly worse prognosis than patients with mutations in cluster #4 (Kaplan-Meier method, log-rank test, p=0.03). Although two separate clusters were formed, we felt that genes present in expression profiles of both cluster #4 and #15 could be potentially interesting as they could be linked to defective C/EBPalpha functioning. Strikingly, out of the 22 genes differentially expressed in cluster #15, 12 were also differentially expressed in cluster #4, including CTNNA1, TUBB-5, NDFIP1, SFXN3, KIAA0746 and TENS1. Interestingly, all 12 genes were significantly downregulated, suggesting that they could be targets of wild type C/EBPalpha and/or downregulated by mutated C/EBPalpha. To test this hypothesis, we introduced either wild type or mutant CEBPA-ER into 32Dcl1, a cell line model constitutively expressing the human G-CSFR. In line with previous reports, we found that activation of C/EBPalpha by addition of beta-estradiol resulted in proliferation arrest and differentiation of these cells within two days, even in the presence of IL-3. Expression levels of the C/EBPalpha target gene CSF3R increased drastically (12-fold after 24 hours, 53-fold after 48 hours) upon stimulation with beta-estradiol as compared to unstimulated or empty vector control clones. Experiments with clones expressing a C-terminal mutant carrying an 18-nt insertion in the bZIP region showed that proliferation was only modestly inhibited and that differentiation was severely impaired both in the presence of IL-3 or G-CSF. Interestingly, no upregulation of the CSF3R gene was observed following beta-estradiol stimulation of mutant CEBPA-ER in the presence of IL-3. Moreover, activation of mutant C/EBPalpha counteracted the induction of CSF3R expression observed following G-CSF activation. These findings suggest that C-terminal C/EBPalpha mutants can have a dominant negative role in AML. Our studies demonstrate that 32Dcl1-CEBPA-ER cells provide a useful model to further elucidate the possible relationships of C/EBPalpha and C/EBPalpha mutants with differentially expressed genes identified in the gene expression studies.

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