A role for codon order in translation dynamics.

The genetic code is degenerate. Each amino acid is encoded by up to six synonymous codons; the choice between these codons influences gene expression. Here, we show that in coding sequences, once a particular codon has been used, subsequent occurrences of the same amino acid do not use codons randomly, but favor codons that use the same tRNA. The effect is pronounced in rapidly induced genes, involves both frequent and rare codons and diminishes only slowly as a function of the distance between subsequent synonymous codons. Furthermore, we found that in S. cerevisiae codon correlation accelerates translation relative to the translation of synonymous yet anticorrelated sequences. The data suggest that tRNA diffusion away from the ribosome is slower than translation, and that some tRNA channeling takes place at the ribosome. They also establish that the dynamics of translation leave a significant signature at the level of the genome.

Comprehensive assessment of the regulons controlled by the FixLJ-FixK2-FixK1 cascade in Bradyrhizobium japonicum.

Symbiotic N(2) fixation in Bradyrhizobium japonicum is controlled by a complex transcription factor network. Part of it is a hierarchically arranged cascade in which the two-component regulatory system FixLJ, in response to a moderate decrease in oxygen concentration, activates the fixK(2) gene. The FixK(2) protein then activates not only a number of genes essential for microoxic respiration in symbiosis (fixNOQP and fixGHIS) but also further regulatory genes (rpoN(1), nnrR, and fixK(1)). The results of transcriptome analyses described here have led to a comprehensive and expanded definition of the FixJ, FixK(2), and FixK(1) regulons, which, respectively, consist of 26, 204, and 29 genes specifically regulated in microoxically grown cells. Most of these genes are subject to positive control. Particular attention was addressed to the FixK(2)-dependent genes, which included a bioinformatics search for putative FixK(2) binding sites on DNA (FixK(2) boxes). Using an in vitro transcription assay with RNA polymerase holoenzyme and purified FixK(2) as the activator, we validated as direct targets eight new genes. Interestingly, the adjacent but divergently oriented fixK(1) and cycS genes shared the same FixK(2) box for the activation of transcription in both directions. This recognition site may also be a direct target for the FixK(1) protein, because activation of the cycS promoter required an intact fixK(1) gene and either microoxic or anoxic, denitrifying conditions. We present evidence that cycS codes for a c-type cytochrome which is important, but not essential, for nitrate respiration. Two other, unexpected results emerged from this study: (i) specifically FixK(1) seemed to exert a negative control on genes that are normally activated by the N(2) fixation-specific transcription factor NifA, and (ii) a larger number of genes are expressed in a FixK(2)-dependent manner in endosymbiotic bacteroids than in culture-grown cells, pointing to a possible symbiosis-specific control.

New target genes controlled by the Bradyrhizobium japonicum two-component regulatory system RegSR.

RegSR-like proteins, members of the family of two-component regulatory systems, are present in a large number of proteobacteria in which they globally control gene expression mostly in a redox-responsive manner. The controlled target genes feature an enormous functional diversity. In Bradyrhizobium japonicum, the facultative root nodule symbiont of soybean, RegSR activate the transcription of the nitrogen fixation regulatory gene nifA, thus forming a RegSR-NifA cascade which is part of a complex regulatory network for gene regulation in response to changing oxygen concentrations. Whole-genome transcription profiling was performed here in order to assess the full regulatory scope of RegSR. The comparative analysis of wild-type and delta regR cells grown under oxic and microoxic conditions revealed that expression of almost 250 genes is dependent on RegR, a result that underscores the important contribution of RegR to oxygen- or redox-regulated gene expression in B. japonicum. Furthermore, transcription profiling of delta regR bacteroids compared with wild-type bacteroids revealed expression changes for about 1,200 genes in young and mature bacteroids. Incidentally, many of these were found to be induced in symbiosis when wild-type bacteroids were compared with free-living, culture-grown wild-type cells, and they appeared to encode diverse functions possibly related to symbiosis and nitrogen fixation. We demonstrated direct RegR-mediated control at promoter regions of several selected target genes by means of DNA binding experiments and in vitro transcription assays, which revealed six novel direct RegR target promoters.

Prediction of transcription factor binding sites using genetical genomics methods.

In this paper, we wanted to test whether it is possible to use genetical genomics information such as expression quantitative trait loci (eQTL) mapping results as input to a transcription factor binding site (TFBS) prediction algorithm. Furthermore, this new approach was compared to the more traditional cluster based TFBS prediction. The results of eQTL mapping are used as input to one of the top ranking TFBS prediction algorithms. Genes with observed expression profiles showing the same eQTL region are collected into eQTL groups. The promoter sequences of all the genes within the same eQTL group are used as input in the transcription factor binding site search. This approach is tested with a real data set of a recombinant inbred line population of Arabidopsis thaliana. The predicted motifs are compared to results obtained from the conventional approach of first clustering the gene expression values and then using the promoter sequences of the genes within the same cluster as input for the transcription factor binding site prediction. Our eQTL based approach produced different motifs compared to the cluster based method. Furthermore the score of the eQTL based motifs was higher than the score of the cluster based motifs. In a comparison to already predicted motifs from the AtcisDB database, the eQTL based and the cluster based method produced about the same number of hits with binding sites from AtcisDB. In conclusion, the results of this study clearly demonstrate the usefulness of eQTL to predict transcription factor binding sites.

Dissection of the Bradyrhizobium japonicum NifA+sigma54 regulon, and identification of a ferredoxin gene (fdxN) for symbiotic nitrogen fixation.

Hierarchically organized regulatory proteins form a complex network for expression control of symbiotic and accessory genes in the nitrogen-fixing soybean symbiont Bradyrhizobium japonicum. A genome-wide survey of regulatory interactions was made possible with the design of a custom-made gene chip. Here, we report the first use of the microarray in a comprehensive and complete characterization of the B. japonicum NifA+sigma(54) regulon which forms an important node in the entire network. Comparative transcript profiles of anaerobically grown wild-type, nifA, and rpoN (1/2) mutant cells were complemented with a position-specific frequency matrix-based search for NifA- and sigma(54)-binding sites plus a simple operon definition. One of the newly identified NifA+sigma(54)-dependent genes, fdxN, encodes a ferredoxin required for efficient symbiotic nitrogen fixation, which makes it a candidate for being a direct electron donor to nitrogenase. The fdxN gene has an unconventional, albeit functional sigma(54 )promoter with the dinucleotide GA instead of the consensus GC motif at position -12. A GC-containing mutant promoter and the atypical GA-containing promoter of the wild type were disparately activated. Expression analyses were also carried out with two other NifA+sigma(54) targets (ectC; ahpC). Incidentally, the tiling-like design of the microarray has helped to arrive at completely revised annotations of the ectC- and ahpC-upstream DNA regions, which are now compatible with promoter locations. Taken together, the approaches used here led to a substantial expansion of the NifA+sigma(54 )regulon size, culminating in a total of 65 genes for nitrogen fixation and diverse other processes.

Prediction of transcription factor binding sites using ChIP-chip and phylogenetic footprinting data.

We present an algorithm for predicting transcription factor binding sites based on ChIP-chip and phylogenetic footprinting data. Our algorithm is robust against low promoter sequence similarity and motif rearrangements, because it does not depend on multiple sequence alignments. This, in turn, allows us to incorporate information from more distant species. Representative random data sets are used to estimate the score significance. Our algorithm is fully automatic, and does not require human intervention. On a recent S. cerevisiae data set, it achieves higher accuracy than the previously best algorithms. Adaptive ChIP-chip threshold and the modular positional bias score are two general features of our algorithm that increase motif prediction accuracy and could be implemented in other algorithms as well. In addition, since our algorithm works partly orthogonally to other algorithms, combining several algorithms can increase prediction accuracy even further. Specifically, our method finds 6 motifs not found by the 2nd best algorithm.

The Iron control element, acting in positive and negative control of iron-regulated Bradyrhizobium japonicum genes, is a target for the Irr protein.

Bradyrhizobium japonicum, the nitrogen-fixing soybean symbiont, possesses a heme uptake system encoded by the gene cluster hmuVUT-hmuR-exbBD-tonB. Transcription of the divergently oriented hmuT and hmuR genes was previously found to be induced by iron limitation and to depend on a 21-bp promoter-upstream iron control element (ICE). Here, we show by deletion analysis that the full-length ICE is needed for this type of positive control. Additional genes associated with ICE-like motifs were identified in the B. japonicum genome, of which bll6680 and blr7895 code for bacterioferritin and rubrerythrin homologs, respectively. Transcription start site mapping revealed that their ICEs directly overlap with either the -10 promoter region or the transcription initiation site, suggesting an involvement of the ICE in negative control of both genes. Consistent with this inference was the observed down-regulation of both genes under iron limitation, which in the case of bll6680 was shown to require an intact ICE motif. Using a yeast one-hybrid system, we demonstrated in vivo interaction of the iron response regulator (Irr) with all three ICEs. Moreover, specific in vitro binding of purified Irr protein to the ICE motifs of bll6680 and blr7895 was shown in electrophoretic mobility shift experiments. A genome-wide survey for iron-regulated genes with a custom-made Affymetrix gene chip revealed 17 genes to be induced and 68 to be repressed under iron-replete conditions. Remarkably, ICE-like motifs are associated with a large subset of those B. japonicum genes. We propose the ICE as an important cis-acting element in B. japonicum which represents the DNA-binding site for the Irr protein and, depending on its location within promoter regions, is involved in positive or negative control of the associated iron-regulated genes.

Scoring functions for transcription factor binding site prediction.

BACKGROUND: Transcription factor binding site (TFBS) prediction is a difficult problem, which requires a good scoring function to discriminate between real binding sites and background noise. Many scoring functions have been proposed in the literature, but it is difficult to assess their relative performance, because they are implemented in different software tools using different search methods and different TFBS representations. RESULTS: Here we compare how several scoring functions perform on both real and semi-simulated data sets in a common test environment. We have also developed two new scoring functions and included them in the comparison. The data sets are from the yeast (S. cerevisiae) genome. Our new scoring function LLBG (least likely under the background model) performs best in this study. It achieves the best average rank for the correct motifs. Scoring functions based on positional bias performed quite poorly in this study. CONCLUSION: LLBG may provide an interesting alternative to current scoring functions for TFBS prediction.

Limitations of codon adaptation index and other coding DNA-based features for prediction of protein expression in Saccharomyces cerevisiae.

The relationship between codon usage and protein/mRNA expression in S. cerevisiae has been extensively studied. Recently, protein expression data for the whole yeast genome was published. We investigate which properties of coding DNA sequences can be used to predict expression levels. The new algorithm by Carbone et al. for computing dominating codon bias in a genome is evaluated. It is concluded that it works at least as well as existing methods, and eliminates the need to arbitrarily choose a set of highly expressed genes. Also, the hypothesis that information on codon pair frequencies can be used to predict expression is investigated. Our conclusion is that codon pairs do not contribute more information than do single codon frequencies. Overall correlation between predicted and actual expression data using properties of coding DNA sequences is around 0.65. Hence, while being a useful source of information, the expression levels predicted by these methods should only be used as a rule of thumb.