Transcription signals for stable RNA genes in<i>Methanococcus</i>

Wich, Günter; Hummel, H.; Jarsch, Michael; Bär, U; Böck, August

doi:10.1093/nar/14.6.2459

Cited by 117 publications

(96 citation statements)

References 35 publications

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“…The last five differences probably produce distinct base triples and/or stacking interactions in the augmented D-stem region of the globular core. Despite the unusual structure, analysis of the genomic DNA surrounding tRNA 1 Cys reveals the presence of both the A-box and B-box transcriptional initiation motifs (25). Therefore, this unusual tRNA may well be expressed in vivo.…”

Section: Differential Utilization Of Trnamentioning

confidence: 99%

Redundant Synthesis of Cysteinyl-tRNACys in Methanosarcina mazei

Hauenstein

Perona

2008

Journal of Biological Chemistry

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mazei CysRS and SepRS reveals that each enzyme prefers a distinct tRNACys isoacceptor or pair of isoacceptors. Recognition determinants distinguishing the tRNAs are shown to reside in the globular core of the molecule. Both enzymes also require the S-adenosylmethionedependent formation of m1 G37 in the anticodon loop for efficient aminoacylation. We further report a new, highly sensitive assay to measure the activity of SepCysS under anaerobic conditions. With this approach, we demonstrate that SepCysS functions as a multiple-turnover catalyst with kinetic behavior similar to bacterial selenocysteine synthase and the archaeal/ eukaryotic SepSecS enzyme. Together, these data suggest that both metabolic routes and all three tRNA Cys species in M. mazei play important roles in the cellular physiology of the organism.

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Section: Differential Utilization Of Trnamentioning

confidence: 99%

Redundant Synthesis of Cysteinyl-tRNACys in Methanosarcina mazei

Hauenstein

Perona

2008

Journal of Biological Chemistry

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“…Different classes of promoters can be distinguished in archaebacteria. Stable RNA promoters appear to be conserved even more than those of protein genes: box A of the 16s and 5s rRNA genes of Sulfolobus reads TTTATATG [41], the consensus of box A among stable rRNA genes of the phylogenetically distant archaebacterium Methanococcus vannielii [see 21 reads TTTATATA [52]. Within two sets of putative promoters in the virus-like particle SSVl of Sulfolobus sp.…”

Section: Promotersmentioning

confidence: 99%

“…Several terminators for SSVl transcripts [86] and of M . vannielii [52] and Desuljiurococcus [32] rRNA genes exhibit oligopyrimidine stretches in the vicinity of the S1-mapped termination regions, which appear to cover four to five, in the case of T1 even more nucleotides in the genome of SSV. No stem and loop structures are evident immediately upstream of the termination sites in the case of SSV1.…”

Section: Terminationmentioning

confidence: 99%

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Comparative evaluation of gene expression in archaebacteria

Zillig

Palm

Reiter

et al. 1988

European Journal of Biochemistry

111

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Gene organization, gene structure, especially regarding transcription and translation signals, and the structure of essential components of the gene expression machinery of archaebacteria are compared with those of eubacteria and eukaryotes. Many features of the genetic machinery of archaebacteria are shared either with eubacteria or with eukaryotes. For example, the translation signals including ribosome-binding sites are the same as in eubacteria, but the consensus sequence of archaebacterial promoters closely resembles that of the eukaryotic polymerase I1 promoters.Archaebacterial genes can be organized in transcription units resembling those of eubacteria. But the sequences of several protein components of the genetic machinery have strikingly more homology with those of their eukaryotic than with those of their eubacterial correspondents.The sequences of the large components of DNA-dependent RNA polymerases of archaebacteria closely resemble those of the eukaryotic RNA polymerases I1 and, somewhat less, 111. In a dendrogram calculated from percentage homology data, the eukaryotic RNA polymerase I component A shares a branching point with the eubacterial component. The implications of these findings for the origin and the evolution of the eukryotic ancestry are discussed.The comparison of sequences of rRNAs 11-61, tRNAs [7, 81, G. Piihler & F. Gropp, unpublished) and a characteristic pattern of few unique and many quasi-eubacterial or quasieukaryotic feature designs (see e.g. [l, 2, 121) indicates that archaebacteria form a monophyletic holophyletic (singlerooted, comprising all descendants) rather than a paraphyletic (not comprising all descendants) group of organisms. The possibility that eubacteria and eukaryotes might have arisen from within the archaebacteria is not entirely excluded but has become remote, because each of the unrooted phylogenetic trees derived from these data shows a significant though short distance between the lowest branching point within the archaebacteria and the trifurcation point between the three kingdoms [2, unpublished). Thus at present the major issue of comparative molecular biology is to establish the branching order in the early evolution of organisms, i.e. to determine the roots of the phylogenetic trees, a task, which in the absence of paleontological evidence appears at least difficult.The comparative molecular biology of archaebacteria has made its most remarkable progress in the fields of molecular phylogeny and molecular genetics (see [13 -171). Recent developments in our understanding of structure and function, especially expression of archaebacterial genes and genomes, and the nature of the components of the genetic machinery call for comparative evaluation. This overview discusses these new findings with an emphasis on areas in which our laboratory is directly involved.

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“…Archaebacterial RNA polymerases, which are structurally more similar to eukaryotic RNA pol II and III than to eubacterial RNA polymerases, terminate following a stretch of consecutive U residues preceded in the transcript by sequences predicted to form a hairpin structure (35,48,54). Many viral and cellular genes, transcribed by RNA pol II, contain attenuation signals early in the transcribed sequence that consist of a hairpin structure followed by a stretch of uridines in the nascent RNA (27,42).…”

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In Vitro Analysis of Elongation and Termination by Mutant RNA Polymerases with Altered Termination Behavior

Shaaban

Bobkova

Chudzik

et al. 1996

Molecular and Cellular Biology

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We have studied the in vitro elongation and termination properties of several yeast RNA polymerase III (pol III) mutant enzymes that have altered in vivo termination behavior (S. A. Shaaban, B. M. Krupp, and B. D. Hall, Mol. Cell. Biol. 15:1467-1478, 1995). The pattern of completed-transcript release was also characterized for three of the mutant enzymes. The mutations studied occupy amino acid regions 300 to 325, 455 to 521, and 1061 to 1082 of the RET1 protein (P. James, S. Whelen, and B. D. Hall, J. Biol. Chem. 266:5616-5624, 1991), the second largest subunit of yeast RNA pol III. In general, mutant enzymes which have increased termination require a longer time to traverse a template gene than does wild-type pol III; the converse holds true for most decreased-termination mutants. One increased-termination mutant (K310T I324K) was faster and two reduced termination mutants (K512N and T455I E478K) were slower than the wild-type enzyme. In most cases, these changes in overall elongation kinetics can be accounted for by a correspondingly longer or shorter dwell time at pause sites within the SUP4 tRNA Tyr gene. Of the three mutants analyzed for RNA release, one (T455I) was similar to the wild type while the two others (T455I E478K and E478K) bound the completed SUP4 pre-tRNA more avidly. The results of this study support the view that termination is a multistep pathway in which several different regions of the RET1 protein are actively involved. Region 300 to 325 likely affects a step involved in RNA release, while the Rif homology region, amino acids 455 to 521, interacts with the nascent RNA 3 end. The dual effects of several mutations on both elongation kinetics and RNA release suggest that the protein motifs affected by them have multiple roles in the steps leading to transcription termination.The two largest subunits of the DNA-dependent RNA polymerases from eubacteria, archaebacteria, and the eukaryotic nucleus are structurally similar (3, 49). Functional roles in RNA synthesis have been assigned to these subunits on the basis of affinity labeling with nucleotide substrates, DNA templates, and nascent RNA products. The binding pocket for the nucleoside triphosphate (NTP) substrate spans both subunits (18,19,40,44,55). Both subunits also seem to make up the protein surfaces that contact the DNA template (5, 16) and the nascent RNA product (6,14,20,32,45). Binding interactions between these two subunits and the DNA and RNA components of the transcription complex most likely contribute to the extreme stability and remarkable processivity of the ternary complex. At certain sequences, known as intrinsic termination sites, this stability is markedly diminished, with the result that RNA is released from the complex and RNA polymerase dissociates from the DNA. The most studied intrinsic termination sequences for Escherichia coli RNA polymerase give rise to short hairpin loops in the transcript followed by short oligo(U) sequences at the 3Ј RNA terminus (15).To terminate transcription by RNA polymerase III (pol III)...

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Transcription signals for stable RNA genes inMethanococcus

Cited by 117 publications

References 35 publications

Redundant Synthesis of Cysteinyl-tRNACys in Methanosarcina mazei

Redundant Synthesis of Cysteinyl-tRNACys in Methanosarcina mazei

Comparative evaluation of gene expression in archaebacteria

In Vitro Analysis of Elongation and Termination by Mutant RNA Polymerases with Altered Termination Behavior

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