Structure and function of DnaA and the DnaA‐box in eubacteria: evolutionary relationships of bacterial replication origins

Yoshikawa, Hiroshi; Ogasawara, Nagahisa

doi:10.1111/j.1365-2958.1991.tb01967.x

Cited by 133 publications

(120 citation statements)

References 36 publications

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“…Whereas variation in rRNA and tRNA gene copy numbers may be related to the capacity to respond to changing environmental conditions (15,16), the exceptionally high copy numbers found in L. bulgaricus likely indicate that the genome has undergone a recent phase of size reduction. (17). On the opposite side of the genome, a second change in the sign of the GC skew locates the replication terminus in the region between positions 940000 and 946000 (data not shown).…”

Section: Resultsmentioning

confidence: 99%

The complete genome sequence ofLactobacillus bulgaricusreveals extensive and ongoing reductive evolution

Guchte

Penaud

Grimaldi

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

371

300

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Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) is a representative of the group of lactic acid-producing bacteria, mainly known for its worldwide application in yogurt production. The genome sequence of this bacterium has been determined and shows the signs of ongoing specialization, with a substantial number of pseudogenes and incomplete metabolic pathways and relatively few regulatory functions. Several unique features of the L. bulgaricus genome support the hypothesis that the genome is in a phase of rapid evolution. (i) Exceptionally high numbers of rRNA and tRNA genes with regard to genome size may indicate that the L. bulgaricus genome has known a recent phase of important size reduction, in agreement with the observed high frequency of gene inactivation and elimination; (ii) a much higher GC content at codon position 3 than expected on the basis of the overall GC content suggests that the composition of the genome is evolving toward a higher GC content; and (iii) the presence of a 47.5-kbp inverted repeat in the replication termination region, an extremely rare feature in bacterial genomes, may be interpreted as a transient stage in genome evolution. The results indicate the adaptation of L. bulgaricus from a plant-associated habitat to the stable protein and lactose-rich milk environment through the loss of superfluous functions and protocooperation with Streptococcus thermophilus.bulgaricus) is one of the economically most important representatives of the heterogeneous group of lactic acid bacteria, with a worldwide application in yogurt production. Yogurt has long been recognized as a nutritious, natural, and safe component of a healthy diet and is at the basis of the concept of probiotics (1, 2). A well documented health benefit of the consumption of yogurt containing live L. bulgaricus and Streptococcus thermophilus is an attenuation of lactose intolerance (3). In addition, immune modulation and diarrhea-alleviating effects have been reported (4), and both L. bulgaricus and S. thermophilus have been implicated in these effects (3,5). During yogurt fermentations protocooperation between these two bacteria results in an accelerated acidification, but the mechanisms involved are not completely understood (6).Among the lactic acid bacteria, L. bulgaricus belongs to the acidophilus complex, a group of lactobacilli related to Lactobacillus acidophilus, Lactobacillus johnsonii, and Lactobacillus gasseri, which have been used as probiotic cultures. Although within this group L. bulgaricus is considered unique because of its atypical GC content, until recently the lack of tools for genetic manipulation has severely hampered a more detailed analysis of this organism (7, 8, † †).Here we present the genome sequence of L. bulgaricus strain ATCC11842, originally isolated from bulgarian yogurt by S. OrlaJensen in 1919 (unpublished work). The analysis of this genome and comparison to other members of the acidophilus complex and S. thermophilus (9) have contributed to a more complete understanding of its p...

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Section: Resultsmentioning

confidence: 99%

The complete genome sequence ofLactobacillus bulgaricusreveals extensive and ongoing reductive evolution

Guchte

Penaud

Grimaldi

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

371

300

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“…Three sequences similar to the dnaA box, 5'-TTAT(C/ A)CA(C/A)A-3' (Yoshikawa and Ogasawara, 1991), were identified upstream of the rpmH gene.…”

Section: Resultsmentioning

confidence: 99%

Cloning, Purification and Characterization of the Protein Subunit of Ribonuclease P from the Cyanobacterium Synechocystis sp. PCC 6803

Pascual

Vioque

1996

European Journal of Biochemistry

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The rnpA gene from the cyanobacterium Synechocystis sp. PCC 6803, which codes for the protein subunit of ribonuclease P (RNase P), has been cloned by functional complementation of an Escherichia coli mutant. This protein had previously been characterized only in proteobacteria and gram-positive bacteria. rnpA and the closely linked rpmH gene, which code for the large subunit ribosomal protein L34, have been sequenced. The Syneclzocystis 6803 L34 protein is more similar to the homologous protein from some non-green chloroplasts than to the L34 protein from other bacteria. The protein subunit of RNase P from Synechocystis 6803 has been overexpressed in E. coli and purified to homogeneity. Antibodies raised against the Synechocystis 6803 RNase P protein did not recognize the homologous protein from E. coli (C5 protein). Similarly, antibodies raised against the E. coli C5 protein did not recognize significantly the Synechocystis 6803 protein. In spite of the lack of immunological cross-reactivity and the low level of sequence identity, the E. coli and Synecfzocystis 6803 proteins are functionally interchangeable. In enzymatic assays using either an E. coli precursor tRNATy' or a Synechocystis 6803 precursor tRNAG'" as substrates, we have detected RNase P activity with holoenzymes reconstituted with the RNA subunit from E. coli and the protein subunit from Synechocystis 6803 or with the RNA subunit from Synechocystis 6803 and the protein subunit from E. coli. The relative efficiency of cleavage of the different substrates is dependent on the origin of the protein subunit used to reconstitute the holoenzyme.Keywords: ribonuclease P; Synechocystis 6803 ; protein-RNA interaction; precursor tRNA processing ; cyanobacteria.Ribonuclease P (RNase P) is an endonuclease responsible for the generation of the mature 5' end of tRNAs from precursors of tRNAs (Altman, 1989;Pace and Smith, 1990). Every cell and every cellular compartment that synthesizes tRNAs has been shown to contain an RNase P activity. The enzyme is composed of RNA and protein in most of the RNaseP activities investigated so far. In many eubacteria, the RNA component of the enzyme has been shown to be catalytically active in vitro in the absence of the protein subunit (Guerrier-Takada et al., 1983) under appropriate buffer conditions. In vivo, the protein subunit is essential. It has been proposed that the protein functions as an electrostatic shield (Reich et al., 1988) and that it also facilitates product release (Tallsjo and Kirsebom, 1993 E-mail: vioque@cica.esAbbreviations. IPTG, isopropyl thio-P-~-galactoside; C5 protein, protein subunit of Escherichia coli RNase P; M1 RNA, RNA subunit of E. coli RNase P ; pre-tRNA, precursor tRNA; RNase P, ribonuclease P; Synechocystis RNase P RNA, RNA subunit of Synechocystis 6803 RNase P; Synechocystis RNase P protein, protein subunit of Synechocysfis 6803 RNase P.Enzyme. Ribonuclease P (EC 3.1.26.5).Note. The novel nucleotide sequence data published here have been deposited with the EMBL sequence data bank and are av...

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“…DnaA binds to a nonpalindromic 9-bp consensus sequence 5Ј-T-T-A/T-T-N-C-A-C-A or a close match to it [13,16,17]. The binding eYciency of DnaA is aVected by this 9-bp consensus sequence and by the Xanking sequences [18] and involves both strands [19].…”

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confidence: 99%

Protein microarray technology and ultraviolet crosslinking combined with mass spectrometry for the analysis of protein–DNA interactions

Kersten

Possling

Blaesing

et al. 2004

Analytical Biochemistry

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To gain insights into complex biological processes, such as transcription and replication, the analysis of protein-DNA interactions and the determination of their sequence requirements are of central importance. In this study, we probed protein microarray technology and ultraviolet crosslinking combined with mass spectrometry (MS) for their practicability to study protein-DNA interactions. We chose as a model system the well-characterized interaction of bacterial replication initiator DnaA with its cognate binding site, the DnaA box. Interactions of DnaA domain 4 with a high-aYnity DnaA box (R4) and with a low-aYnity DnaA box (R3) were compared. A mutant DnaA domain 4, A440V, was included in the study. DnaA domain 4, wt, spotted onto FAST slides, revealed a strong signal only with a Cy5-labeled, double-stranded, 21-mer oligonucleotide containing DnaA box R4. No signals were obtained when applying the mutant protein. Ultraviolet crosslinking combined with nanoLC/MALDI-TOF MS located the site of interaction to a peptide spanning amino acids 433-442 of Escherichia coli DnaA. This fragment contains six residues that were identiWed as being involved in DNA binding by recently published crystal structure and nuclear magnetic resonance (NMR) analysis. In the future, the technologies applied in this study will become important tools for studying protein-DNA interactions.  2004 Elsevier Inc. All rights reserved.

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Structure and function of DnaA and the DnaA‐box in eubacteria: evolutionary relationships of bacterial replication origins

Cited by 133 publications

References 36 publications

The complete genome sequence ofLactobacillus bulgaricusreveals extensive and ongoing reductive evolution

The complete genome sequence ofLactobacillus bulgaricusreveals extensive and ongoing reductive evolution

Cloning, Purification and Characterization of the Protein Subunit of Ribonuclease P from the Cyanobacterium Synechocystis sp. PCC 6803

Protein microarray technology and ultraviolet crosslinking combined with mass spectrometry for the analysis of protein–DNA interactions

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