tRNAdb 2009: compilation of tRNA sequences and tRNA genes

One of the first specialized collections of nucleic acid sequences in life sciences was the ‘compilation of tRNA sequences and sequences of tRNA genes’ (http://www.trna.uni-bayreuth.de). Here, an updated and completely restructured version of this compilation is presented (http://trnadb.bioinf.uni-leipzig.de). The new database, tRNAdb, is hosted and maintained in cooperation between the universities of Leipzig, Marburg, and Strasbourg. Reimplemented as a relational database, tRNAdb will be updated periodically and is searchable in a highly flexible and user-friendly way. Currently, it contains more than 12 000 tRNA genes, classified into families according to amino acid specificity. Furthermore, the implementation of the NCBI taxonomy tree facilitates phylogeny-related queries. The database provides various services including graphical representations of tRNA secondary structures, a customizable output of aligned or un-aligned sequences with a variety of individual and combinable search criteria, as well as the construction of consensus sequences for any selected set of tRNAs

Biodiversitätsmonitoring im Südtiroler Kräuteranbau = Biodiversity surveys in medicinal and aromatic plant fields in South Tyrol

Medicinal and aromatic plants in mountain regions such as South Tyrol are cultivated on small-scale farms, which are characterized by a high diversity of cultivated crop species grown on a relatively small area. This small-scale cultivation of medicinal and aromatic plants suggests that MAP fields are of high ecological value. However, research on this topic is generally lacking. In this study flower-visiting arthropods were recorded with pan traps in three herb fields during three survey events conducted in 2021. Our results indicate that medicinal and aromatic plant fields are valuable habitats for several taxa. In total 12.570 individuals were collected. Wild bees were particularly species-rich, accounting for 10 % of the regional wild bee species pool. Next to beneficial arthropods, potential pests, such as aphids were also highly abundant. However, natural enemies possibly counteracting pests were also numerous. Overall, we conclude that medicinal and aromatic plant cultivation may act as resource-rich oases for several arthropod groups, thereby promoting biodiversity also on a broader scale.Der Anbau von Arznei- und Gewürzpflanzen zeichnet sich in der Regel durch vielfältige Anbaukulturen auf relativ kleinen Flächen aus. Dies gilt insbesondere für Südtirol, wo diese Kulturen hauptsächlich von kleinen Betrieben im Berggebiet angebaut werden. Dieser kleinflächige Anbau von Arznei- und Gewürzpflanzen lässt vermuten, dass die Betriebe einen hohen ökologischen Wert haben. Es gibt wenige Studien zur Erfassung der Biodiversität im Anbau von Arznei- und Gewürzpflanzen. Daher wurden in dieser Arbeit Kräuteranbau-Betriebe als Lebensraum für blütenbesuchende Arthropoden untersucht. An drei Untersuchungsstandorten wurden im Jahr 2021 jeweils an drei Terminen Farbschalen zur Sammlung von Arthropoden verwendet. Kräuteranbau-Betriebe stellten sich als ein wertvoller Lebensraum für verschiedene Arthropoden heraus. Insgesamt wurden 12.570 Individuen mit den Farbschalen gesammelt. Insbesondere Wildbienen waren mit 10 % des regionalen Artenpools sehr artenreich. Auch potenzielle Schädlinge, wie zum Beispiel Blattläuse, waren sehr häufig anzutreffen, wobei natürliche Feinde, wie zum Beispiel Parasitoide, ebenfalls zahlreich vertreten waren. Insgesamt können Kräuteranbaubetriebe als strukturreiche Oasen für Arthropoden fungieren und sich somit auf einer breiteren Skala positiv auf die Biodiversität auswirken

A comparative analysis of two conserved motifs in bacterial poly(A) polymerase and CCA-adding enzyme

Showing a high sequence similarity, the evolutionary closely related bacterial poly(A) polymerases (PAP) and CCA-adding enzymes catalyze quite different reactions—PAP adds poly(A) tails to RNA 3′-ends, while CCA-adding enzymes synthesize the sequence CCA at the 3′-terminus of tRNAs. Here, two highly conserved structural elements of the corresponding Escherichia coli enzymes were characterized. The first element is a set of amino acids that was identified in CCA-adding enzymes as a template region determining the enzymes' specificity for CTP and ATP. The same element is also present in PAP, where it confers ATP specificity. The second investigated region corresponds to a flexible loop in CCA-adding enzymes and is involved in the incorporation of the terminal A-residue. Although, PAP seems to carry a similar flexible region, the functional relevance of this element in PAP is not known. The presented results show that the template region has an essential function in both enzymes, while the second element is surprisingly dispensable in PAP. The data support the idea that the bacterial PAP descends from CCA-adding enzymes and still carries some of the structural elements required for CCA-addition as an evolutionary relic and is now fixed in a conformation specific for A-addition

Deep Sequencing of Human Nuclear and Cytoplasmic Small RNAs Reveals an Unexpectedly Complex Subcellular Distribution of miRNAs and tRNA 3′ Trailers

MicroRNAs (miRNAs) are ∼22-nt small non-coding regulatory RNAs that have generally been considered to regulate gene expression at the post-transcriptional level in the cytoplasm. However, recent studies have reported that some miRNAs localize to and function in the nucleus.To determine the number of miRNAs localized to the nucleus, we systematically investigated the subcellular distribution of small RNAs (sRNAs) by independent deep sequencing sequenced of the nuclear and cytoplasmic pools of 18- to 30-nucleotide sRNAs from human cells. We identified 339 nuclear and 324 cytoplasmic known miRNAs, 300 of which overlap, suggesting that the majority of miRNAs are imported into the nucleus. With the exception of a few miRNAs evidently enriched in the nuclear pool, such as the mir-29b, the ratio of miRNA abundances in the nuclear fraction versus in the cytoplasmic fraction vary to some extent. Moreover, our results revealed that a large number of tRNA 3′trailers are exported from the nucleus and accumulate in the cytoplasm. These tRNA 3′ trailers accumulate in a variety of cell types, implying that the biogenesis of tRNA 3′ trailers is conserved and that they have a potential functional role in vertebrate cells.Our results provide the first comprehensive view of the subcellular distribution of diverse sRNAs and new insights into the roles of miRNAs and tRNA 3′ trailers in the cell

Food-associated cues alter forebrain functional connectivity as assessed with immediate early gene and proenkephalin expression

<p>Abstract</p> <p>Background</p> <p>Cues predictive of food availability are powerful modulators of appetite as well as food-seeking and ingestive behaviors. The neurobiological underpinnings of these conditioned responses are not well understood. Monitoring regional immediate early gene expression is a method used to assess alterations in neuronal metabolism resulting from upstream intracellular and extracellular signaling. Furthermore, assessing the expression of multiple immediate early genes offers a window onto the possible sequelae of exposure to food cues, since the function of each gene differs. We used immediate early gene and proenkephalin expression as a means of assessing food cue-elicited regional activation and alterations in functional connectivity within the forebrain.</p> <p>Results</p> <p>Contextual cues associated with palatable food elicited conditioned motor activation and corticosterone release in rats. This motivational state was associated with increased transcription of the activity-regulated genes <it>homer1a</it>, <it>arc</it>, <it>zif268</it>, <it>ngfi-b </it>and c-<it>fos </it>in corticolimbic, thalamic and hypothalamic areas and of proenkephalin within striatal regions. Furthermore, the functional connectivity elicited by food cues, as assessed by an inter-regional multigene-expression correlation method, differed substantially from that elicited by neutral cues. Specifically, food cues increased cortical engagement of the striatum, and within the nucleus accumbens, shifted correlations away from the shell towards the core. Exposure to the food-associated context also induced correlated gene expression between corticostriatal networks and the basolateral amygdala, an area critical for learning and responding to the incentive value of sensory stimuli. This increased corticostriatal-amygdalar functional connectivity was absent in the control group exposed to innocuous cues.</p> <p>Conclusion</p> <p>The results implicate correlated activity between the cortex and the striatum, especially the nucleus accumbens core and the basolateral amygdala, in the generation of a conditioned motivated state that may promote excessive food intake. The upregulation of a number of genes in unique patterns within corticostriatal, thalamic, and hypothalamic networks suggests that food cues are capable of powerfully altering neuronal processing in areas mediating the integration of emotion, cognition, arousal, and the regulation of energy balance. As many of these genes play a role in plasticity, their upregulation within these circuits may also indicate the neuroanatomic and transcriptional correlates of extinction learning.</p

Control of local NGF mRNA synthesis by preformed factors rapidly released from peripheral nerves

After nerve lesion, a biphasic upregulation of nerve growth factor synthesis occurs in nonneuronal cells. Two fundamentally different regulatory principles underlie this phenomenon. A previously described tissue-extrinsic mechanism depends on macrophages invading the lesioned nerve and their secreted products, such as interleukin 1. It is responsible for the second delayed response. Here we demonstrate a novel mechanism of lesion-induced NGF regulation, which makes use exclusively of tissue-intrinsic elements. Sciatic nerve contains a potent preformed NGF-inducing activity. It is released within minutes after nerve lesion and is responsible for the first rapid NGF increase, which occurs within hours after injury. This type of regulatory mechanism may allow for matching of NGF synthesis with the severity of the lesion

Control of local NGF mRNA synthesis by preformed factors rapidly released from peripheral nerves

After nerve lesion, a biphasic upregulation of nerve growth factor synthesis occurs in nonneuronal cells. Two fundamentally different regulatory principles underlie this phenomenon. A previously described tissue-extrinsic mechanism depends on macrophages invading the lesioned nerve and their secreted products, such as interleukin 1. It is responsible for the second delayed response. Here we demonstrate a novel mechanism of lesion-induced NGF regulation, which makes use exclusively of tissue-intrinsic elements. Sciatic nerve contains a potent preformed NGF-inducing activity. It is released within minutes after nerve lesion and is responsible for the first rapid NGF increase, which occurs within hours after injury. This type of regulatory mechanism may allow for matching of NGF synthesis with the severity of the lesion

J. Mol. Biol.

All tRNA molecules carry the invariant sequence CCA at their 3'-terminus for amino acid attachment. The post-transcriptimal addition of CCA is carried out by ATP(CTP):tRNA nucleotidyltransferase, also called CCase. This enzyme catalyses a unique template-independent but sequence-specific nucleotide polymerization reaction. In order to reveal the molecular mechanism of this activity, we solved the crystal structure of human CCase by single isomorphous replacement. The structure reveals a four domain architecture with a cluster of conserved residues forming a positively charged cleft between the first two domains. Structural homology of the N-terminal CCase domain to other nucleotidyltransferases could be exploited for modeling a tRNA-substrate complex. The model places the tRNA 3'-end into the N-terminal nucleotidyltransferase site, close to a patch of conserved residues that provide the binding sites for CTP and ATP Based on our results, we introduce a corkscrew model for CCA addition that includes a fixed active site and a traveling tRNA-binding region formed by flexible parts of the protein. (C) 2003 Elsevier Science Ltd. All rights reserved