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Query: UMLS:C0009443 (cold)
 92,137 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Glutaminyl-tRNA synthetase generates Gln-tRNA(Gln) 10(7)-fold more efficiently than Glu-tRNA(Gln) and requires tRNA to synthesize the activated aminoacyl adenylate in the first step of the reaction. To examine the role of tRNA in amino acid activation more closely, several assays employing a tRNA analog in which the 2'-OH group at the 3'-terminal A76 nucleotide is replaced with hydrogen (tRNA(2'HGln)) were developed. These experiments revealed a 10(4)-fold reduction in kcat/Km in the presence of the analog, suggesting a direct catalytic role for tRNA in the activation reaction. The catalytic importance of the A76 2'-OH group in aminoacylation mirrors a similar role for this moiety that has recently been demonstrated during peptidyl transfer on the ribosome. Unexpectedly, tracking of Gln-AMP formation utilizing an alpha-32P-labeled ATP substrate in the presence of tRNA(2'HGln) showed that AMP accumulates 5-fold more rapidly than Gln-AMP. A cold-trapping experiment revealed that the nonenzymatic rate of Gln-AMP hydrolysis is too slow to account for the rapid AMP formation; hence, the hydrolysis of Gln-AMP to form glutamine and AMP must be directly catalyzed by the GlnRS x tRNA(2'HGln) complex. This hydrolysis of glutaminyl adenylate represents a novel reaction that is directly analogous to the pre-transfer editing hydrolysis of noncognate aminoacyl adenylates by editing synthetases such as isoleucyl-tRNA synthetase. Because glutaminyl-tRNA synthetase does not possess a spatially separate editing domain, these data demonstrate that a pre-transfer editing-like reaction can occur within the synthetic site of a class I tRNA synthetase.
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PMID:tRNA-dependent aminoacyl-adenylate hydrolysis by a nonediting class I aminoacyl-tRNA synthetase. 1584 36

Cells respond to adverse environmental conditions by synthesizing new proteins or elevating the levels of pre-existing ones that are needed to cope with the particular stress situation. We show here that Escherichia coli RNase R, a processive 3'-to5'-exoribonuclease, is dramatically increased in response to a variety of different stress conditions. Elevation of RNase R activity by as much as 10-fold was observed in response to entry into stationary phase, starvation, and cold shock, and a approximately 3-fold increase was seen during growth in minimal medium compared with rich medium. The elevation in RNase R activity was associated primarily with an increase in RNase R protein. RNase R was previously implicated in quality control of rRNA and tRNA and in the decay of mRNAs with extensive secondary structure. Its dramatic increase under multiple stress conditions suggests extensive remodeling of structured RNA in response to the altered environment.
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PMID:Elevation of RNase R in response to multiple stress conditions. 1613 21

High mutation rate in mammalian mitochondrial DNA generates a highly divergent pool of alleles even within species that have dispersed and expanded in size recently. Phylogenetic analysis of 277 human mitochondrial genomes revealed a significant (P < 0.01) excess of rRNA and nonsynonymous base substitutions among hotspots of recurrent mutation. Most hotspots involved transitions from guanine to adenine that, with thymine-to-cytosine transitions, illustrate the asymmetric bias in codon usage at synonymous sites on the heavy-strand DNA. The mitochondrion-encoded tRNAThr varied significantly more than any other tRNA gene. Threonine and valine codons were involved in 259 of the 414 amino acid replacements observed. The ratio of nonsynonymous changes from and to threonine and valine differed significantly (P = 0.003) between populations with neutral (22/58) and populations with significantly negative Tajima's D values (70/76), independent of their geographic location. In contrast to a recent suggestion that the excess of nonsilent mutations is characteristic of Arctic populations, implying their role in cold adaptation, we demonstrate that the surplus of nonsynonymous mutations is a general feature of the young branches of the phylogenetic tree, affecting also those that are found only in Africa. We introduce a new calibration method of the mutation rate of synonymous transitions to estimate the coalescent times of mtDNA haplogroups.
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PMID:The role of selection in the evolution of human mitochondrial genomes. 1617 8

We examined the simultaneous incorporation of [H]thymidine and [C]leucine to obtain two independent indices of bacterial production (DNA and protein syntheses) in a single incubation. Incorporation rates of leucine estimated by the dual-label method were generally higher than those obtained by the single-label method, but the differences were small (dual/single = 1.1 +/- 0.2 [mean +/- standard deviation]) and were probably due to the presence of labeled leucyl-tRNA in the cold trichloroacetic acid-insoluble fraction. There were no significant differences in thymidine incorporation between dual- and single-label incubations (dual/ single = 1.03 +/- 0.13). Addition of the two substrates in relatively large amounts (25 nM) did not apparently increase bacterial activity during short incubations (<5 h). With the dual-label method we found that thymidine and leucine incorporation rates covaried over depth profiles of the Chesapeake Bay. Estimates of bacterial production based on thymidine and leucine differed by less than 25%. Although the need for appropriate conversion factors has not been eliminated, the dual-label approach can be used to examine the variation in bacterial production while ensuring that the observed variation in incorporation rates is due to real changes in bacterial production rather than changes in conversion factors or introduction of other artifacts.
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PMID:Estimating bacterial production in marine waters from the simultaneous incorporation of thymidine and leucine. 1634 6

We investigated the genetic structure of mitochondrial DNA (COI and 16S rRNA-tRNA(Leu(CUN))-ND1) and nuclear DNA (ITS2) variations among and within populations of Pardosa astrigera in China. Two phenotypes of males were recognized. They differed genetically also in the presence (type A) or absence (type B) of common insertions and deletions in ITS2. The concordance between mtDNA based phylogeny and the phenotypic variations of P. astrigera was weak. Haplotypes of type A did not form a monophyletic group. Instead they were found in three clades, in one of them mixed with type B haplotypes, most likely as a result of long-term and ongoing gene flow of mtDNA between the two phenotypic groups (M = 0.69). Pairwise sequence divergences of all data sets indicated that the genetic divergences between the two phenotypes fall within intraspecific range. Our results indicated that the P. astrigera populations in China consist of two sympatric lineages with male phenotypic variations. Patterns of mismatch distribution within lineages suggested long-term demographic stability in the lineage A, and growth in lineage B that expanded rapidly and recolonized from a southern refuge to the northern parts of China during the late-Pleistocene. On the basis of the estimated divergence time between the two lineages (0.18-0.41 Ma), we suggest that the dry-cold climate and the uplift of the Tibetan plateau during the mid-Pleistocene appear to have a determinating impact on the evolutionary history of P. astrigera in China.
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PMID:Incongruous nuclear and mitochondrial phylogeographic patterns in two sympatric lineages of the wolf spider Pardosa astrigera (Araneae: Lycosidae) from China. 1690 38

The thermodynamic characterization of various biological systems from psychrophiles points to a larger entropic contribution when compared to the corresponding mesophilic or (hyper) thermophilic counterparts, either at the level of the macromolecules (thermodynamic and kinetic stabilities) or of their function (ligand binding, catalytic activity). It is suggested here that in an environment characterized by a low heat content (enthalpy) and at temperatures that strongly slowdown molecular motions, the cold-adapted biological systems rely on a larger disorder to maintain macromolecular dynamics and function. Such pre-eminent involvement of entropy is observed in the experimental results and, from a macroscopic point of view, is also reflected for instance by the steric hindrances introduced by cis-unsaturated and branched lipids to maintain membrane fluidity, by the loose conformation of psychrophilic proteins or by the local destabilization of tRNA by dihydrouridine in psychrophilic bacteria.
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PMID:Life at low temperatures: is disorder the driving force? 1716 Mar 45

Recent studies in a variety of bacterial systems have revealed a number of regulatory systems in which the 5' region of a gene plays a key role in regulation of the downstream coding sequences. These RNA regions act in cis to determine if the full-length transcript will be synthesized or if the coding sequence(s) will be translated. Each class of system includes an RNA element whose structure is modulated in response to a specific regulatory signal, and the signals measured can include small molecules, small RNAs (including tRNA), and physical parameters such as temperature. Multiple sets of genes can be regulated by a particular mechanism, and multiple systems of this type, each of which responds to a specific signal, can be present in a single organism. In addition, different classes of RNA elements can be found that respond to a particular signal, indicating the existence of multiple alternate solutions to the same regulatory problem. The T box and S box systems, which respond to uncharged tRNA and S-adenosylmethionine (SAM), respectively, provide paradigms of two systems of this type.
Cold Spring Harb Symp Quant Biol 2006
PMID:Sensing metabolic signals with nascent RNA transcripts: the T box and S box riboswitches as paradigms. 1738 2

In recent years, Bacillus subtilis, the model organism for gram-positive bacteria, has been a focal point for study of posttranscriptional regulation. In this bacterium, more than 70 regulatory RNAs have been discovered that respond to intracellular proteins, tRNAs, and small-molecule metabolites. In total, these RNA elements are responsible for genetic control of more than 4.1% of the genome-coding capacity. This pool of RNA-based regulatory elements is now large enough that it has become a worthwhile endeavor to examine their general features and to extrapolate these simple observations to the remaining genome in an effort to predict how many more may remain unidentified. Furthermore, both metabolite- and tRNA-sensing regulatory RNAs are remarkably widespread throughout eubacteria, and it is therefore becoming increasingly clear that some of the observations for B. subtilis gene regulation will be generally applicable to many different species.
Cold Spring Harb Symp Quant Biol 2006
PMID:Genetic control by cis-acting regulatory RNAs in Bacillus subtilis: general principles and prospects for discovery. 1738 3

The mRNA is bound and poised in the decoding center of the small subunit of the ribosome where the genetic code is translated by the tRNAs, which recognize sense codons, and by the release factors, which recognize stop-codons. Structural and biochemical studies have identified key universally conserved nucleotides, G530, A1492, and A1493, that are important for selection of cognate tRNA species during elongation. Here, we present evidence that these same universally conserved nucleotides are also important for interactions with the release factors, but must assume a very different structure during stopcodon recognition. These data provide mechanistic insight into how the decoding center of the ribosome has evolved to recognize distinct substrates with high fidelity, which in turn regulates the downstream chemical events of peptidyl transfer and peptide release.
Cold Spring Harb Symp Quant Biol 2006
PMID:Two distinct conformations of the conserved RNA-rich decoding center of the small ribosomal subunit are recognized by tRNAs and release factors. 1738 38

Adaptation of Escherichia coli at low temperature implicates a drastic reprogramming of gene expression patterns. Mechanisms operating downstream of transcription initiation, such as control of transcription termination, mRNA stability and translatability, play a major role in controlling gene expression in the cold acclimation phase. It was previously shown that Rho-dependent transcription termination within pnp, the gene encoding polynucleotide phosphorylase (PNPase), was suppressed in pnp nonsense mutants, whereas it was restored by complementation with wild type allele. Using a tRNA gene as a reporter and the strong Rho-dependent transcription terminator t ( imm ) of bacteriophage P4 as a tester, here we show that specific sites in the 5'-untranslated region of pnp mRNA are required for PNPase-sensitive cold-induced suppression of Rho-dependent transcription termination. We suggest that suppression of Rho-dependent transcription termination within pnp and its restoration by PNPase is an autogenous regulatory circuit that modulates pnp expression during cold acclimation.
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PMID:Autogenous regulation of Escherichia coli polynucleotide phosphorylase during cold acclimation by transcription termination and antitermination. 1738 64


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