Sequence, organization, transcription and evolution of RNA polymerase subunit genes from the archaebacterial extreme halophiles Halobacterium halobium and Halococcus morrhuae

Leffers, Henrik; Gropp, Felix; Lottspeich, Friedrich; Zillig, Wolfram; Garrett, Roger A.

doi:10.1016/0022-2836(89)90519-6

Cited by 135 publications

(51 citation statements)

References 59 publications

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“…This may reflect weak binding of dodecylsulfate to the hydrophilic protein owing to the high acidic amino acid content ( Table 1). The upstream sequence of this EF-2 gene (positions 1-413 in Fig.2) is in complete agreement with the downstream sequence of two open reading frames (H-S12 and H-S7) which are similar to ribosomal proteins S12 and S7 from E. coli [14]. presence of about a 4200-nucleotide transcript initiated at the first nuclcotide of the initiation codon of H-S12, an upstream gene of H-S7, in total RNA isolated from H .…”

Section: Nucleotide Seqwmcr Annlvricsupporting

confidence: 73%

Sequence analysis of the peptide‐elongation factor EF‐2 gene, downstream from those of ribosomal proteins H‐S12 and H‐S7, from the archaebacterial extreme halophile, Halobacterium halobium

Itoh

1989

European Journal of Biochemistry

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The gene for the peptide-elongation factor 2 (EF-2) was cloned from the archaebacterial extremc halophile Halobacterium halobium and sequenced. The 101 3 nucleotides upstream from this gene was two open rcading frames similar to ribosomal proteins S12 and S7 from Escherichiu coli. Sequence alignment studies showed the halobacterial elongation factor 2 to be equivalent to eukaryotic EF-2 and eubacterial EF-G. Sequcnce similarity to the eukaryotic elongation factor was much higher than to the eubacterial factor. Conserved sequence regions were present within the factor and are likely to constitute functionally important domains. These include the sites of GTP binding and ADP ribosylation by diphtheria toxin.The concept of archaebacteria as a third kingdom of organisms is based on comparative analyses of 16s rRNA [l].Protein synthesis machinery appears to be a promising subject for phylogenetic comparisons among the three kingdoms (eubacteria, archaebacteria and eukaryotes). Archaebacteria is a newly defined phylogenetic kingdom, characterized by a mixture of eubacterial, eukaryotic and unique archaebactcrial features [2-41. The peptide-elongation factor (EF-2 in eukaryote, EF-G in eubacteria), which catalyzes the translocation of-peptidyl-tRNA and mRNA on ribosomes, is essential for protein synthesis in all organisms. The archaebacterial elongation factor has the eukaryotic feature of sensitivity against ADP ribosylation by diphtheria toxin and a high degree of structrual similarity around the ADP -riboseaccepting site [5]. To determine how archaebacterial genes are transcribed and translated, and which phylogenetic relationships are present among the three kingdoms, the gene for the elongation factor from archaebacterial Halobacterium halobium was cloned and sequenced.The results indicated EF-2 from archaebacterial Halobacterium to be more similar to the eukaryotic EF-2 than to the eubacterial EF-G and the gene for the protein to lie downstream from those of ribosomal H-S12 and H-S7. This is analogous to the ribosomal protein S12 operon in E. coli.

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Section: Nucleotide Seqwmcr Annlvricsupporting

confidence: 73%

Sequence analysis of the peptide‐elongation factor EF‐2 gene, downstream from those of ribosomal proteins H‐S12 and H‐S7, from the archaebacterial extreme halophile, Halobacterium halobium

Itoh

1989

European Journal of Biochemistry

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“…The cDNA was prepared from either primary term trophoblasts or transformed human amnion cells. H. halobium ORF139 was made by PCR from a I clone containing the genomic RNA polymerase subunit operon (Leffers et al, 1989). The full-length ; PCBP-1 and 2, Leffers et al, 1995;HBP, McKnight et al, 1992;FMRl, Verkerk et al, 1991) or gene (H. halobium ORF 139, Leffers et al, 1989), for primers that matched both PCBP-1 and, the positions are shown as: PCBP-1PCBP-2.…”

Section: Methodsmentioning

confidence: 99%

“…The protein with the highest number of repeats is the HBP protein (McKnight et al, 1992), also known as Vigilin (Schmidt et al, 1992), which consists of 14 or 15 KH domains with little or no space in between. Among the prokaryotic proteins there is one domain in the ribosomal S3 proteins (Zurawski and Zurawski, 1985;Kao et al, 1990) and one and a half in the hypothetical archae 130-139 proteins (Puehler et al, 1989;Leffers et al, 1989).…”

Section: Hagen Denmarkmentioning

confidence: 99%

“…To do this, we isolated and expressed the first three or four of the 14 or 15 KH domains from HBP (McKnight et al, 1992), the H. hulobium ORF 139 protein (Leffers et al, 1989) which contains one and a half KH domain (Fig. 3) and a construct from FMRl (Verkerk et al, 1991 ;Siomi et al, 1993b) that included at least the first and part of the second KH domain.…”

Section: Isolation and Analysis Of Additional Kh Domainsmentioning

confidence: 99%

“…3) and a construct from FMRl (Verkerk et al, 1991 ;Siomi et al, 1993b) that included at least the first and part of the second KH domain. Although we originally intended to cover both the KH domains of FMRl, it is very likely, considering a more recent sequence alignment based on the structure of a representitative member of the family (Musco et al, 1996), that Leffers et al, 1995;HBP, McKnight, et al, 1992;FMR1, Verkerk et al, 1991; H. halobiurn (Hh) ORFl39, Leffers et al, 1989). The numbering for FMRl Starts from the first Met residue (Met66 in Verkerk et al, 1991 (Musco et al, 1996) suggest that the second KH domain of FMRl is considerably larger than previous estimates and thus that the nucleic acid binding activity reported here most likely only includes the contribution from KH-domain 1 .…”

Section: Isolation and Analysis Of Additional Kh Domainsmentioning

confidence: 99%

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Characterisation of the Nucleic‐Acid‐Binding Activity of KH Domains Different Properties of Different Domains

Dejgaard

Leffers

1996

European Journal of Biochemistry

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118

114

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The KH module is a sequence motif recently identified in a number of diversified RNA-binding proteins and suggested to be the functional element responsible for RNA binding. So far, however, this hypothesis has not received direct experimental support. We have expressed the three KH-domains from heterogeneous nuclear ribonucleoprotein K (hnRNP-K), the poly(C)-binding proteins PCBP-1 and PCBP-2, the first three to four domains from the high-density binding protein HBP, the one and a half domain from the archaeon Halobacterium halobium ORF139 and one and a half domain of the fragile-X protein FMRl in Escherichia coli and analysed their nucleic-acid-binding properties in vitro. The results showed that the in vitro poly(rC)-binding activity of hnRNP-K can be assigned to KH-domain 3, whereas both domains 1 and 3 in the PCBPs bind poly(rC). In addition, all these domains exhibit binding activity towards other nucleic acids, albeit at a significantly lower level. The first KH domain from the FMRl protein binds poly(rG) and single-stranded and double-stranded DNA. The N-terminal three or four domains from HBP bind poly(rG) and, at a much lower level, single-stranded and double-stranded DNA. Thus, single KH domains are discrete and independent nucleic-acid-binding units. Moreover, different KH domains bind different nucleic acids, suggesting that KH domains are composed of a conserved, weakly nucleic-acid-binding, structure that is fine tuned, by sequence variation, resulting in sequencespecific nucleic-acid-binding entities.

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Novel RNA-binding motif: The KH module

Adinolfi¹,

Bagni

Morelli

et al. 1999

Biopolymers

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The KH motif has recently been identified in single or multiple copies in a number of RNA associated proteins. Here we review the current knowledge accumulated about the sequence, structure, and functions of the KH. The multidomain architecture of most of the KH‐containing proteins inspired an approach based on the production of peptides spanning the sequence of an isolated KH motif. Correct identification of the minimal length necessary for producing a folded peptide has had a number of important consequences for interpreting functional data. The presence of the KH motifs in fmr1, the protein responsible for the fragile X syndrome, and their possible role in the fmr1 functions are also discussed. © 1999 John Wiley & Sons, Inc. Biopoly 51: 153–164, 1999

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Sequence, organization, transcription and evolution of RNA polymerase subunit genes from the archaebacterial extreme halophiles Halobacterium halobium and Halococcus morrhuae

Cited by 135 publications

References 59 publications

Sequence analysis of the peptide‐elongation factor EF‐2 gene, downstream from those of ribosomal proteins H‐S12 and H‐S7, from the archaebacterial extreme halophile, Halobacterium halobium

Sequence analysis of the peptide‐elongation factor EF‐2 gene, downstream from those of ribosomal proteins H‐S12 and H‐S7, from the archaebacterial extreme halophile, Halobacterium halobium

Characterisation of the Nucleic‐Acid‐Binding Activity of KH Domains Different Properties of Different Domains

Novel RNA-binding motif: The KH module

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