CiteULike: mariakmejias transcription

Widespread Translational Inhibition by Plant miRNAs and siRNAs

Peter Brodersen — 2008-05-16T09:08:52-00:00

Science (15 May 2008), 1159151.

High complementarity between plant miRNAs and their mRNA targets is thought to cause silencing prevalently by endonucleolytic cleavage. We have isolated Arabidopsis mutants defective in miRNA action. Their analysis provides evidence that plant miRNA-guided silencing has a widespread translational inhibitory component that is genetically separable from endonucleolytic cleavage. We further show that the same is true of silencing mediated by short interfering (si)RNA populations. Translational repression is effected in part by the ARGONAUTE proteins AGO1 and AGO10. It also requires the activity of the microtubule-severing enzyme katanin, implicating cytoskeleton dynamics in miRNA action as recently suggested from animal studies. Also as in animals, the decapping component VCS/Ge-1 is required for translational repression by miRNAs, suggesting that the underlying mechanisms in the two kingdoms are related. 10.1126/science.1159151

Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling

Arthur Hunt — 2008-05-15T01:18:18-00:00

BMC Genomics, Vol. 9, No. 1. (2008)

BACKGROUND:The polyadenylation of mRNA is one of the critical processing steps during expression of almost all eukaryotic genes. It is tightly integrated with transcription, particularly its termination, as well as other RNA processing events, i.e. capping and splicing. The poly(A) tail protects the mRNA from unregulated degradation, and it is required for nuclear export and translation initiation. In recent years, it has been demonstrated that the polyadenylation process is also involved in the regulation of gene expression. The polyadenylation process requires two components, the cis-elements on the mRNA and a group of protein factors that recognize the cis-elements and produce the poly(A) tail. Here we report a comprehensive pairwise protein-protein interaction mapping and gene expression profiling of the mRNA polyadenylation protein machinery in Arabidopsis. RESULTS:By protein sequence homology search using human and yeast polyadenylation factors, we identified 28 proteins that may be components of Arabidopsis polyadenylation machinery. To elucidate the protein network and their functions, we first tested their protein-protein interaction profiles. Out of 320 pair-wise protein-protein interaction assays done using the yeast two-hybrid system, 56 (~17%) showed positive interactions. 15 of these interactions were further tested, and all were confirmed by co-immunoprecipitation and/or in vitro co-purification. These interactions organize into three distinct hubs involving the Arabidopsis polyadenylation factors. These hubs are centered around AtCPSF100, AtCLPS, and AtFIPS. The first two are similar to complexes seen in mammals, while the third one stands out as unique to plants. When comparing the gene expression profiles extracted from publicly available microarray datasets, some of the polyadenylation related genes showed tissue-specific expression, suggestive of potential different polyadenylation complex configurations. CONCLUSIONS:An extensive protein network was revealed for plant polyadenylation machinery, in which all predicted proteins were found to be connecting to the complex. The gene expression profiles are indicative that specialized sub-complexes may be formed to carry out targeted processing of mRNA in different developmental stages and tissue types. These results offer a roadmap for further functional characterizations of the protein factors, and for building models when testing the genetic contributions of these genes in plant growth and development.

U12 intron positions are more strongly conserved between animals and plants than U2 intron positions

Malay Basu — 2008-05-15T01:16:52-00:00

Biology Direct, Vol. 3, No. 1. (2008)

We report that the positions of minor, U12 introns are conserved in orthologous genes from human and Arabidopsis to an even greater extent than the positions of the major, U2 introns. The U12 introns, especially, conserved ones are concentrated in 5'-portions of plant and animal genes, where the U12 to U2 conversions occurs preferentially in the 3'-portions of genes. These results are compatible with the hypothesis that the high level of conservation of U12 intron positions and their persistence in genomes despite the unidirectional U12 to U2 conversion are explained by the role of the slowly excised U12 introns in down-regulation of gene expression. Reviewers: This article was reviewed by John Logsdon and Manyuan Long. For the full reviews, please go to the Reviewers' Reports section.

Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication.

Bin Cong — 2008-05-14T22:50:24-00:00

Nature genetics (11 May 2008)

Plant domestication represents an accelerated form of evolution, resulting in exaggerated changes in the tissues and organs of greatest interest to humans (for example, seeds, roots and tubers). One of the most extreme cases has been the evolution of tomato fruit. Cultivated tomato plants produce fruit as much as 1,000 times larger than those of their wild progenitors. Quantitative trait mapping studies have shown that a relatively small number of genes were involved in this dramatic transition, and these genes control two processes: cell cycle and organ number determination. The key gene in the first process has been isolated and corresponds to fw2.2, a negative regulator of cell division. However, until now, nothing was known about the molecular basis of the second process. Here, we show that the second major step in the evolution of extreme fruit size was the result of a regulatory change of a YABBY-like transcription factor (fasciated) that controls carpel number during flower and/or fruit development.

Pre-mRNA splicing: a complex picture in higher definition.

Matthew J Schellenberg — 2008-05-15T01:02:17-00:00

Trends in biochemical sciences (8 May 2008)

Intron excision from pre-mRNAs of higher eukaryotes requires a transition from splice-site recognition across short exons to organization of the spliceosome across long introns. Recently, insight into this transition has been provided and, in addition, it has been shown that an alternative splicing factor, the polypyrimidine-tract-binding protein, can exert its control on splice-site choice by blocking this key step in the assembly of the splicing machinery.

Structural evolution of multisubunit RNA polymerases.

Finn Werner — 2008-05-15T01:01:44-00:00

Trends in microbiology (9 May 2008)

Evolutionarily related multisubunit RNA polymerases (RNAPs) facilitate gene transcription throughout the three domains of life. During the past seven years an increasing number of bacterial and eukaryotic RNAP structures have been solved; however, the archaeal enzyme remained elusive. Two reports from the Murakami and Cramer laboratories have now filled this gap in our knowledge and enable us to hypothesize about the evolution of the structure and function of RNAPs.

Molecular evolution of the RNA polymerase II CTD.

Rob D Chapman — 2008-05-15T01:01:02-00:00

Trends in genetics : TIG (8 May 2008)

In higher eukaryotes, an unusual C-terminal domain (CTD) is crucial to the function of RNA polymerase II in transcription. The CTD consists of multiple heptapeptide repeats; differences in the number of repeats between organisms and their degree of conservation have intrigued researchers for two decades. Here, we review the evolution of the CTD at the molecular level. Several primitive motifs have been integrated into compound heptads that can be readily amplified. The selection of phosphorylatable residues in the heptad repeat provided the opportunity for advanced gene regulation in eukaryotes. Current findings suggest that the CTD should be considered as a collection of continuous overlapping motifs as opposed to a specific functional unit defined by a heptad.

Circadian clock function in Arabidopsis thaliana: time beyond transcription.

Paloma Más — 2008-05-15T00:59:08-00:00

Trends in cell biology (7 May 2008)

The past decade has seen a remarkable advance in our understanding of the plant circadian system, mostly in Arabidopsis thaliana. It is now well established that Arabidopsis clock genes and their protein products operate through autoregulatory feedback loops that promote rhythmic oscillations in cellular, metabolic and physiological activities. This article reviews recent studies that have provided evidence for new mechanisms of clock organization and function. These mechanisms include protein-protein interactions and the regulation of protein stability, which, together, directly connect light signalling to the Arabidopsis circadian system. Evidence of rhythmic changes in chromatin structure has also opened new and exciting ways for regulation of clock gene expression. All of these mechanisms ensure an appropriate synchronization with the environment, which is crucial for successful plant growth and development.