Plasmids and characteristic features.

<p>Plasmids and characteristic features.</p

Two differentially translated <i>H. volcanii</i> genes and their UTRs.

<p>(A) The lengths of the 5′- and 3′-UTRs of the <i>hp</i> and the <i>hlr</i> transcripts are tabulated. The UTRs of the genes were determined in a prior study <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004484#pone.0004484-Brenneis1" target="_blank">[22]</a>. (B) The sequences of the 5′- and 3′-UTRs of the <i>hlr</i> and the <i>hp</i> transcripts are shown. The start as well as the stop codon of the orf are also included and printed in bold. (C) Growth phase-dependent differential translational efficiencies of the <i>hlr</i> and <i>hp</i> genes. The values were obtained by isolating free, non-translated RNAs as well as polysome-bound RNAs and their genome-wide comparison with DNA microarrays <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004484#pone.0004484-Lange1" target="_blank">[7]</a>. The results were normalized to the average of all genes. The ratio of polysomal to free RNA for the <i>hlr</i> and <i>hp</i> transcripts are shown for exponentially growing and stationary phase cells.</p

The direction of translational regulation is determined by the 3′-UTRs.

<p>Using the reporter gene system different combinations of 5′- and 3′-UTRs of the <i>hlr</i> and the <i>hp</i> transcript were studied. (A) The transcript fusions are shown schematically. The DHFR enzymatic activities, the <i>dhfr</i> transcript levels and the translational efficiencies of exponential and stationary growth phases are tabulated. Three biological replicates were performed and average values with standard deviations (in parenthesis) were calculated. (B) The translational efficiencies after normalization to the control transcript without UTRs (No. 1) are shown.</p

The structure of the 5′-UTR can influence translational efficiency and translational regulation.

<p>Specific putative structure elements were stabilized and destabilized in a native 5′-UTR (compare <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004484#pone-0004484-g003" target="_blank">Figure 3</a>). Translational efficiencies of the mutated versions and the wild type were determined by using the reporter gene system. (A) The transcript fusions are shown schematically. The DHFR enzymatic activities, the <i>dhfr</i> transcript levels and the translational efficiencies of exponential and stationary growth phases are tabulated. Three biological replicates were performed and average values with standard deviations (in parenthesis) were calculated. (B) The translational efficiencies after normalization to the control transcript without UTRs (No. 1) are shown.</p

Sequences and proposed structures of native and mutated 5′-UTRs.

<p>(A) Nucleotide sequences. A putative stem loop of the native <i>hp</i> 5′-UTR was changed by <i>in vitro</i> mutagenesis. The mutated nucleotides are shown in grey and are underlined. (B) <i>In silico</i> structural analysis of the stabilized, the native, and the destabilized 5′-UTRs. The structural analysis were performed by using the mfold 3.2 program <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004484#pone.0004484-Mathews1" target="_blank">[40]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004484#pone.0004484-Zuker1" target="_blank">[41]</a>. Mutated nucleotides are indicated by a bar. The start codon of the orf is also included and marked by an arrow.</p

Transcriptome changes and cAMP oscillations in an archaeal cell cycle-2

<p><b>Copyright information:</b></p><p>Taken from "Transcriptome changes and cAMP oscillations in an archaeal cell cycle"</p><p>http://www.biomedcentral.com/1471-2121/8/21</p><p>BMC Cell Biology 2007;8():21-21.</p><p>Published online 11 Jun 2007</p><p>PMCID:PMC1906763.</p><p></p> an independent method, i.e. Northern blot analysis. They represent all clusters of co-regulated genes as well as unregulated control genes. The transcript level profiles obtained for individual genes by microarray analysis are shown on the left side (average of three biological replicates). On the right side the results of Northern blot analysis are shown (one typical experiment). Gene identifier [23] and the gene No. in Table 1 are included

Transcriptome changes and cAMP oscillations in an archaeal cell cycle-5

<p><b>Copyright information:</b></p><p>Taken from "Transcriptome changes and cAMP oscillations in an archaeal cell cycle"</p><p>http://www.biomedcentral.com/1471-2121/8/21</p><p>BMC Cell Biology 2007;8():21-21.</p><p>Published online 11 Jun 2007</p><p>PMCID:PMC1906763.</p><p></p>region around the translational start point of cluster five genes (compare Table 2). The region is shown schematically, and the numbering refers to the translational start point. Because the majority of haloarchaeal transcripts are leaderless, the transcriptional and the translational start points often nearly coincide. The basal promoter elements "transcription factor B recognition element" (BRE) and "TATA box" are indicated at positions they would have for leaderless transcripts. Gene identifiers [23] are shown to the left. The conserved motif and its direction are indicated by arrows which are drawn to scale. The sequence logo of the conserved motif of cluster five genes (generated with MEME)

Transcriptome changes and cAMP oscillations in an archaeal cell cycle-3

<p><b>Copyright information:</b></p><p>Taken from "Transcriptome changes and cAMP oscillations in an archaeal cell cycle"</p><p>http://www.biomedcentral.com/1471-2121/8/21</p><p>BMC Cell Biology 2007;8():21-21.</p><p>Published online 11 Jun 2007</p><p>PMCID:PMC1906763.</p><p></p> an independent method, i.e. Northern blot analysis. They represent all clusters of co-regulated genes as well as unregulated control genes. The transcript level profiles obtained for individual genes by microarray analysis are shown on the left side (average of three biological replicates). On the right side the results of Northern blot analysis are shown (one typical experiment). Gene identifier [23] and the gene No. in Table 1 are included

Transcriptome changes and cAMP oscillations in an archaeal cell cycle-1

<p><b>Copyright information:</b></p><p>Taken from "Transcriptome changes and cAMP oscillations in an archaeal cell cycle"</p><p>http://www.biomedcentral.com/1471-2121/8/21</p><p>BMC Cell Biology 2007;8():21-21.</p><p>Published online 11 Jun 2007</p><p>PMCID:PMC1906763.</p><p></p>usters of co-regulated genes (compare text and Table 1). The average transcription profiles of all seven clusters and the standard deviations are shown. Genes that share an identical profile of induction and repression do not necessarily share the same degree of induction/repression, therefore the transcript profiles of all genes were normalized to their highest value (= 100%) before calculation of averages and standard deviations. Gene identifiers, names, and functional classes are summarized in Table 1

Transcriptome changes and cAMP oscillations in an archaeal cell cycle-0

<p><b>Copyright information:</b></p><p>Taken from "Transcriptome changes and cAMP oscillations in an archaeal cell cycle"</p><p>http://www.biomedcentral.com/1471-2121/8/21</p><p>BMC Cell Biology 2007;8():21-21.</p><p>Published online 11 Jun 2007</p><p>PMCID:PMC1906763.</p><p></p>res using the DNA polymerase inhibitor aphidicolin. The average cell length and its standard deviation was calculated from the lengths of 50 cells that were determined microscopically with an ocular micrometer. The cell density was determined microscopically with a Neubauer counting chamber. Times of addition and removal of the inhibitor are indicated. The time of inhibitor removal was set to zero to allow a direct comparison of the times shown in this and additional Figures (2 – 6, see Additional file ). The box in this and additional Figures denotes the only time interval in which dividing cells with visible constrictions could be observed. Microscopic images of dividing cells and the intracellular DNA localization have been published previously [22]