Alternative splicing in plants

2008 ◽  
Vol 36 (3) ◽  
pp. 508-510 ◽  
Author(s):  
Craig G. Simpson ◽  
Dominika Lewandowska ◽  
John Fuller ◽  
Monika Maronova ◽  
Maria Kalyna ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Reverse Transcription ◽  
Protein Function ◽  
Mrna Levels ◽  
Reverse Transcription Pcr ◽  
Multiple Genes ◽  
The Impact

The impact of AS (alternative splicing) is well-recognized in animal systems as a key regulator of gene expression and proteome complexity. In plants, AS is of growing importance as more genes are found to undergo AS, but relatively little is known about the factors regulating AS or the consequences of AS on mRNA levels and protein function. We have established an accurate and reproducible RT (reverse transcription)–PCR system to analyse AS in multiple genes. Initial studies have identified new AS events confirming that current values for the frequency of AS in plants are likely to be underestimates.

Regulation of plant gene expression by alternative splicing

2010 ◽  
Vol 38 (2) ◽  
pp. 667-671 ◽  
Author(s):  
Craig G. Simpson ◽  
Sujatha Manthri ◽  
Katarzyna Dorota Raczynska ◽  
Maria Kalyna ◽  
Dominika Lewandowska ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Protein Function ◽  
Cell Types ◽  
Splicing Factors ◽  
Mrna Levels ◽  
Sr Protein ◽  
Nonsense Mediated Decay ◽  
Cis Acting ◽  
Reverse Transcription Pcr

AS (alternative splicing) is a post-transcriptional process which regulates gene expression through increasing protein complexity and modulating mRNA transcript levels. Regulation of AS depends on interactions between trans-acting protein factors and cis-acting signals in the pre-mRNA (precursor mRNA) transcripts, termed ‘combinatorial’ control. Dynamic changes in AS patterns reflect changes in abundance, composition and activity of splicing factors in different cell types and in response to cellular or environmental cues. Whereas the SR protein family of splicing factors is well-studied in plants, relatively little is known about other factors influencing the regulation of AS or the consequences of AS on mRNA levels and protein function. To address fundamental questions on AS in plants, we are exploiting a high-resolution RT (reverse transcription)–PCR system to analyse multiple AS events simultaneously. In the present paper, we describe the current applications and development of the AS RT–PCR panel in investigating the roles of splicing factors, cap-binding proteins and nonsense-mediated decay proteins on AS, and examining the extent of AS in genes involved in the same developmental pathway or process.

scholarly journals Assessment of flhDC mRNA Levels inSerratia liquefaciens Swarm Cells

2000 ◽  
Vol 182 (10) ◽  
pp. 2680-2686 ◽  
Author(s):  
Tim Tolker-Nielsen ◽  
Allan Beck Christensen ◽  
Kim Holmstrøm ◽  
Leo Eberl ◽  
Thomas Bovbjerg Rasmussen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Differentiation ◽  
Reverse Transcription ◽  
Present Report ◽  
Maximum Level ◽  
Northern Analysis ◽  
Mrna Levels ◽  
Reverse Transcription Pcr ◽  
Serratia Liquefaciens

ABSTRACT We reported previously that artificial overexpression of theflhDC operon in liquid-grown Serratia liquefaciens resulted in the formation of filamentous, multinucleated, and hyperflagellated cells that were indistinguishable from surface-induced swarm cells (L. Eberl, G. Christiansen, S. Molin, and M. Givskov, J. Bacteriol. 178:554–559, 1996). In the present report we show by means of reporter gene measurements, Northern analysis, and in situ reverse transcription-PCR that the amount offlhDC mRNA in surface-grown swarm cells does not exceed the maximum level found in nondifferentiated, vegetative cells. This suggests that surface-induced S. liquefaciens swarm cell differentiation, although dependent on flhDC gene expression, does not occur through elevated flhDC mRNA levels.

scholarly journals Codon usage is an important determinant of gene expression levels largely through its effects on transcription

2016 ◽  
Vol 113 (41) ◽  
pp. E6117-E6125 ◽  
Author(s):  
Zhipeng Zhou ◽  
Yunkun Dang ◽  
Mian Zhou ◽  
Lin Li ◽  
Chien-hung Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Codon Usage ◽  
Important Determinant ◽  
Mrna Translation ◽  
Mrna Levels ◽  
Protein Coding ◽  
Expression Levels ◽  
Highly Expressed Genes ◽  
The Impact ◽  
Gene Expression Levels

Codon usage biases are found in all eukaryotic and prokaryotic genomes, and preferred codons are more frequently used in highly expressed genes. The effects of codon usage on gene expression were previously thought to be mainly mediated by its impacts on translation. Here, we show that codon usage strongly correlates with both protein and mRNA levels genome-wide in the filamentous fungus Neurospora. Gene codon optimization also results in strong up-regulation of protein and RNA levels, suggesting that codon usage is an important determinant of gene expression. Surprisingly, we found that the impact of codon usage on gene expression results mainly from effects on transcription and is largely independent of mRNA translation and mRNA stability. Furthermore, we show that histone H3 lysine 9 trimethylation is one of the mechanisms responsible for the codon usage-mediated transcriptional silencing of some genes with nonoptimal codons. Together, these results uncovered an unexpected important role of codon usage in ORF sequences in determining transcription levels and suggest that codon biases are an adaptation of protein coding sequences to both transcription and translation machineries. Therefore, synonymous codons not only specify protein sequences and translation dynamics, but also help determine gene expression levels.

scholarly journals Use of Multiplex Reverse Transcription-PCR To Study the Expression of a Laccase Gene Family in a Basidiomycetous Fungus

2003 ◽  
Vol 69 (12) ◽  
pp. 7083-7090 ◽  
Author(s):  
Tania González ◽  
María C. Terrón ◽  
Ernesto J. Zapico ◽  
Alejandro Téllez ◽  
Susana Yagüe ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reverse Transcription ◽  
White Rot Fungi ◽  
Gene Families ◽  
Veratryl Alcohol ◽  
White Rot ◽  
Laccase Gene ◽  
Reverse Transcription Pcr ◽  
Basidiomycetous Fungus ◽  
Laccase Genes

ABSTRACT Laccases produced by white rot fungi are involved in the degradation of lignin and a broad diversity of other natural and synthetic molecules, having a great potential for biotechnological applications. They are frequently encoded by gene families, as in the basidiomycete Trametes sp. strain I-62, from which the lcc1, lcc2, and lcc3 laccase genes have been cloned and sequenced. A multiplex reverse transcription-PCR method to simultaneously study the expression of these genes was developed in this study. The assay proved to be quick, simple, highly sensitive, and reproducible and is particularly valuable when numerous samples are to be analyzed and/or if the amount of initial mRNA is limited. It was used to analyze the effect of 3,4-dimethoxybenzyl alcohol (veratryl alcohol) and two of its isomers (2,5-dimethoxybenzyl alcohol and 3,5-dimethoxybenzyl alcohol) on differential laccase gene expression in Trametes sp. strain I-62. These aromatic compounds produced different induction patterns despite their chemical similarity. We found 2,5-dimethoxybenzyl alcohol to be the best inducer of laccase activity while also producing the highest increase in gene expression; 3,5-dimethoxybenzyl alcohol was the next best inducer. Transcript amounts of each gene fluctuated dramatically in the presence of these three inducers, while the total amounts of laccase mRNAs seemed to be modulated by a coordinated regulation of the different genes.

scholarly journals Gene Transcription in Lactarius quietus-Quercus petraea Ectomycorrhizas from a Forest Soil

2008 ◽  
Vol 74 (21) ◽  
pp. 6598-6605 ◽  
Author(s):  
P. E. Courty ◽  
M. Poletto ◽  
F. Duchaussoy ◽  
M. Bu�e ◽  
J. Garbaye ◽  
...  
Keyword(s):  
Gene Expression ◽  
Forest Soil ◽  
Reverse Transcription ◽  
Quercus Petraea ◽  
Primary Metabolism ◽  
Extraradical Mycelium ◽  
Root Tips ◽  
Reverse Transcription Pcr ◽  
Fungal Genes

ABSTRACT Extracting fungal mRNA from ectomycorrhizas (ECMs) and forest soil samples for monitoring in situ metabolic activities is a significant challenge when studying the role of ECMs in biogeochemical cycles. A robust, simple, rapid, and effective method was developed for extracting RNA from rhizospheric soil and ECMs by adapting previous grinding and lysis methods. The quality and yield of the extracted RNA were sufficient to be used for reverse transcription. RNA extracted from ECMs of Lactarius quietus in a 100-year-old oak stand was used to construct a cDNA library and sequence expressed sequence tags. The transcripts of many genes involved in primary metabolism and in the degradation of organic matter were found. The transcription levels of four targeted fungal genes (glutamine synthase, a general amino acid transporter, a tyrosinase, and N-acetylhexosaminidase) were measured by quantitative reverse transcription-PCR in ECMs and in the ectomycorrhizospheric soil (the soil surrounding the ECMs containing the extraradical mycelium) in forest samples. On average, levels of gene expression for the L. quietus ECM root tips were similar to those for the extraradical mycelium, although gene expression varied up to 10-fold among the samples. This study demonstrates that gene expression from ECMs and soil can be analyzed. These results provide new perspectives for investigating the role of ectomycorrhizal fungi in the functioning of forest ecosystems.

scholarly journals Dissolved Oxygen Levels Alter Gene Expression and Antigen Profiles in Borrelia burgdorferi

2004 ◽  
Vol 72 (3) ◽  
pp. 1580-1586 ◽  
Author(s):  
J. Seshu ◽  
Julie A. Boylan ◽  
Frank C. Gherardini ◽  
Jonathan T. Skare
Keyword(s):  
Gene Expression ◽  
Borrelia Burgdorferi ◽  
Dissolved Oxygen ◽  
Reverse Transcription ◽  
Host Factors ◽  
Pcr Analysis ◽  
Transcriptional Level ◽  
Environmental Signals ◽  
Reverse Transcription Pcr ◽  
Genes Encoding

ABSTRACT The Lyme disease spirochete, Borrelia burgdorferi, encounters many environmental signals as it cycles between the arthropod vector and mammalian hosts, including temperature, pH, and other host factors. To test the possibility that dissolved oxygen modulates gene expression in B. burgdorferi, spirochetes were exposed to differential levels of dissolved oxygen, and distinct alterations were observed at both the transcriptional and translational levels. Specifically NapA, a Dps/Dpr homologue involved in the oxidative stress response in other bacteria, was reduced when B. burgdorferi was grown under oxygen-limiting conditions. In contrast, several immunoreactive proteins were altered when tested with infection-derived sera from different hosts. Specifically, OspC, DbpA, and VlsE were synthesized at greater levels when cells were grown in limiting oxygen, whereas VraA was reduced. The levels of oxygen in the medium did not affect OspA production. Real-time reverse transcription-PCR analysis of RNA isolated from infectious isolates of strains B31 and cN40 indicated that the expression of ospC, dbpA, and vlsE increased while napA expression decreased under dissolved-oxygen-limiting conditions, whereas flaB was not affected. The reverse transcription-PCR results corroborated the immunoblot analyses and indicated that the increase in OspC, DbpA, and VlsE was due to regulation at the transcriptional level of the genes encoding these antigens. These results indicate that dissolved oxygen modulates gene expression in B. burgdorferi and imply that the redox environment may be an additional regulatory cue that spirochetes exploit to adapt to the disparate niches that they occupy in nature.

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