Thermophiles terminators

We infer that it is unlikely that the thermophile terminators resemble bacterial rho-independent terminators. Moreover, this view is reinforced by examining the sequences for the bacterial terminators using a program in the GCG-software package from the University of Wisconsin. This is based on the observations of Brendel and Trifonov [125] that in addition to the inverted repeat preceding a polythymidine sequence many bacterial terminators share sequence features located both upstream and downstream from the termination site. Only one of the termination sites shown in Table 5 is predicted by this program. 

The C-terminal domain (85 amino acid residues, not completely denatured at 90 °C) of the so-called a subunit of the RNAP from the extremely thermophilic eubacterium T. thermophilus (Tt) has been expressed uniformly N/ C-labelled and structurally characterized by the NMR spectroscopy. The tertiary structure of the domain, comprising a helical turn and four helices, was found to be almost identical to that of the corresponding domain from the mesophilic E. coli, despite 32% sequence homology. The interaction of the Tt domain with a variety of DNAs at 37 °C and 50 °C was investigated by chemical shift perturbation of the NMR signals and the DNA binding site was localized. ... 

The primary structure of AspAT from Thermophilic bacillus was determined from cDNA sequence.24 Sequence information of an N-terminal portion of the native enzyme and 19 tryptic peptide fragments, recovered from HPLC, was obtained from gas phase sequencer analyses. Based on such sequence information, four oligonucleotide probes were prepared. cDNA encoding AspAT was cloned by screening restriction enzyme fragments from genomic cDNA of Thermophilic bacillus species YM-2. Amino acid sequence of Thermophilic bacillus AspAT deduced from cDNA was confirmed by the sequences made available by gas phase sequencer analysis. 

S. acidocaldarius (DSM 639) extrudes protons and synthesizes ATP while respiring endogenous substrates [65]. DCCD inhibits this ATP synthesis and the inhibitor binds to a membrane proteolipid [57]. This proteolipid (M, 34 000) can be purified using procedures for isolating DCCD-binding proteolipids [66]. Two subunits are observed after SDS-electrophoresis (M, 17 000 and 19000) but a single peptide (M, 6000) is detected when SDS-electrophoresis is carried out in the presence of 8 M urea. The amino-acid sequence from the N-terminal end of an Mr 2000 CNBr-peptide exhibits considerable homology to sequences of subunit c from the Fq of E. coli and the thermophilic bacterium, PS3 [64]. 

Analysis of the sequences located upstream of archaeal rRNA genes has shown that archaeal rRNA promoters consist of the sequence TTTA(A/T)A located 20-30 nucleotides upstream of the transcription initiation site and a weakly conserved sequence, (A/T)TG(A/C) around the transcription initiation site [40]. Transcription of the rRNA genes terminates within pyrimidine-rich regions in the extreme thermophiles [30,41], in pyrimidine-rich regions followed by a short hairpin loop in the methanogens [27,34] and in AT-rich regions preceded by a GC-rich region in the extreme... 

Transcripts of 5S rRNAs and tRNAs generally start just before and terminate immediately after single genes amongst sulfothermophiles, while these stable RNA genes are often clustered in transcriptional units in the thermophilic methanogens and other archaea. 

The reconstituted liposomes (0.055 mg of EgF, and 4 mg of thermophilic phospholipids) were first incubated in acidic medium (pH 5.5, final volume 0.25 ml) containing 10 ftmol malonate, 1 pmol ADP, and 0.1 pg valinomycin at 40 °C for 10 min. Then 0.25 ml of an alkaline medium consisting of glycylglycine (40 pmol, pH 8.5), 75 pmol KCl, 0.5 pmol MgS04, 2 pmol (6X10 cpm, sodium salt), 25 pmol glucose, and 10 units of hexokinase was added. The final pH was 8.3. The reaction was carried out at 40 °C and terminated after 5 min. 

D-alanine residue. Other polyketides which contain such an arrangement are the trienomycins [99], while similar CHC chain terminating (synthase starter) units are found in a branch of asukamycin [96], and in the eo-cyclohexyl fatty acids of certain thermophilic bacteria [100] substituted CHCs are also found as PKS starter units in the rapamycin family of polyketides (see Sect. 8). The cyclohexyl moieties of these compounds have been demonstrated to derive from the shiki-mate pathway. 

Takai M, Kamimura K, Sugio T (2001) A new iron oxidase from moderately thermophilic iron-oxidizing bacterium strain TI-1. Eur J Biochem 268 1653-1658 Takakuwa S (1976) Studies on the metabolism of a sulfur-oxidizing bacterium XI. Electron transfer and the terminal oxidase system in sulfite oxidation of Thiobacillus thiooxidans. Plant Cell Physiol 17 103-110... 

The conformation of LARFH was created by mimicking the Lac repressor C-terminal a-heUces. After energy minimization and solvent relaxation, we performed simulation in water for 10 ns. Then, the coordinates of the protein were determined (Fig. 33.2a). Sulerythrin (PDBID 1J30) contains two pairs of Fe " " and Zn " " that we disregard and remove in this simulation (Fig. 33.2b). The coordinates of IPMDH (PDBID lOSJ) are derived from T. thermophiles (Fig. 33.2c). 

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