On the process of cellular division in Escherichia coli: Nucleotide sequence of the gene for penicillin-binding protein 3

Nakamura, Masataka; Maruyama, Ichiro; Soma, Masaaki; Kato, Junichi; Suzuki, Hirotoshi; Horota, Yukinori

doi:10.1007/bf00330881

Cited by 123 publications

(78 citation statements)

References 43 publications

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“…Sarkosyl solubility implies an inner membrane location for VirBi. VirB1 was predicted to reside in the periplasm or outer membrane because of the presence of a consensus export targeting signal (26); however, other signal sequence-containing proteins have been shown to target to the inner membrane (32). Possibly, VirBi is located at the periplasmic side of the inner membrane, or is exported through the inner membrane to the periplasm, and is associated with or embedded in the outer leaflet of the inner membrane as a peripheral membrane protein.…”

Section: Discussionmentioning

confidence: 99%

Subcellular localization of seven VirB proteins of Agrobacterium tumefaciens: implications for the formation of a T-DNA transport structure

1993

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Plant cell transformation by Agrobacteriwun Iwefaciens involves the transfer of a single-stranded DNAprotein complex (T-complex) from the bacterium to the plant cell. One of the least understood and important aspects of this process is how the T-complex exits the bacterium. The eleven virB gene products have been proposed to specify the DNA export channel on the basis of their predicted hydrophobicity. To determine the cellular localization of the VirB proteins, two different cell fractionation methods were employed to separate inner and outer membranes. Seven VirB-specific antibodies were used on Western blots (immunoblots) to detect the proteins in the inner and outer membranes and soluble (containing cytoplasm and periplasm) fractions. VirB5 was in both the inner membrane and cytoplasm. Six of the VwrB proteins were detected in the membrane fractions only. Three of these, VWrB8, VirB9, and VWrBlO, were present in both inner and outer membrane fractions regardless of the fractionation method used. Three additional VwrB proteins, VirBi, VWrB4, and VWrB1I, were found mainly in the inner membrane fraction by one method and were found in both inner and outer membrane fractions by a second method. These results confirm the membrane localization of seven VirB proteins and strengthen the hypothesis that VirB proteins are involved in the formation of a T-DNA export channel or gate. That most of the VwrB proteins analyzed are found in both inner and outer membrane fractions suggest that they form a complex pore structure that spans both membranes, and their relative amounts in the two membrane fractions reflect their differential sensitivity to the experimental conditions. Agrobacterium tumefaciens has the unique ability to transfer DNA to plant cells. In nature, the transfer and expression of a specific fragment of DNA (T-DNA) cause a neoplastic growth on the plant host. In the laboratory, this DNA transfer phenomenon has been exploited by using disarmed vectors to introduce new genes into plants. The T-DNA and the components necessary for packaging and transfer of the single-stranded T-DNA (T-strand) (45) are encoded by the tumor-inducing (Ti) plasmid in A. tumefaciens. The virulence (vir) region contains four operons (virA, virG, virD, and virB) that encode proteins required for virulence on all hosts (44). Three additional operons (virE, virC, and virH) encode proteins that are required only on some hosts (25,44).The transfer of DNA from the bacterium to the plant cell involves at least seven recognizable steps. Of the bacterial components necessary for DNA transfer, only the first step is thought to be mediated by chromosomally encoded functions (reviewed in reference 5). The remaining steps involve proteins that are encoded by the vir region on the Ti plasmid (reviewed in reference 59). The seven steps are as follows: (i) the bacterium binds to a specific component of the plant cell surface; (ii) a bacterial membrane protein (VirA) recognizes signals released by a wounded plant cell and transduces the signal v...

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Section: Discussionmentioning

confidence: 99%

Subcellular localization of seven VirB proteins of Agrobacterium tumefaciens: implications for the formation of a T-DNA transport structure

1993

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“…compared with those of the higher-molecular-mass PBPs 3 [21], 1A and 1B [20]. PBP 2 contained 44% polar and 56% non-polar amino acids, which is similar to the other PBPs.…”

Section: Amino Acid Composition and Codon Usagementioning

confidence: 63%

“…These sequences are essential for export and are eventually removed by processing enzymes to reveal the mature protein. However, in a number of cytoplasmic membrane proteins that have been characterized no signal sequences have been observed with the exception of PBP 3 [21], PBP 5 and PBP 6 [47] of E. coli. These PBPs are synthesized with signal sequences and are considered to be ectoproteins [48], which are anchored to the membrane by membrane-spanning segment(s) and have a substantial portion of their amino acid sequences protruding into the periplasmic space.…”

Section: Amino Acid Sequence Of Pbpmentioning

confidence: 99%

“…Codon usage in thepbpA (PBP 2) gene is shown in Table 2 compared with those in the genes for the other E. coli highermolecular-mass PBPs, pbpB for PBP 3 [21], mrcA for PBP 1A [20], and mrcB for PBP 1B [20]. Table 2 also contains the codon usages in weakly expressed E. coli genes for repressor proteins (symbol R) [49] and highly expressed E. coli genes for outer membrane proteins (symbol 0) [50-521.…”

Section: Amino Acid Composition and Codon Usagementioning

confidence: 99%

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Nucleotide sequence of the pbpA gene and characteristics of the deduced amino acid sequence of penicillin‐binding protein 2 of Escherichia coli K12

Asoh

Matsuzawa

Ishino

et al. 1986

European Journal of Biochemistry

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We have determined the nucleotide sequence of the pbpA gene encoding penicillin-binding protein (PBP) 2 of Escherichia coli. The coding region for PBP 2 was 1899 base pairs in length and was preceded by a possible promoter sequence and two open reading frames. The primary structure of PBP 2, deduced from the nucleotide sequence, comprised 633 amino acid residues. The relative molecular mass was calculated to be 70867. The deduced sequence agreed with the NH2-terminal sequence of PBP 2 purified from membranes, suggesting that PBP 2 has no signal peptide. The hydropathy profile suggested that the NH,-terminal hydrophobic region (a stretch of 25 non-ionic amino acids) may anchor PBP 2 in the cytoplasmic membrane as an ectoprotein. There were nine homologous segments in the amino acid sequence of PBP 2 when compared with PBP 3 of E. coli. The active-site serine residue of PBP 2 was predicted to be Ser-330. Around this putative active-site serine residue was found the conserved sequence of Ser-Xaa-Xaa-Lys, which has been identified in all of the other E. coli PBPs so far studied (PBPs lA, lB, 3, 5 and 6) and class A and class C B-lactamases. In the higher-molecular-mass PBPs 1 A, lB, 2 and 3, Ser-Xaa-Xaa-Lys-Pro was conserved. In the putative peptidoglycan transpeptidase domain there were six amino acid residues, which are common only in the PBPs of higher molecular mass.In Escherichia coli seven penicillin-binding proteins (PBPs) have been found in the cytoplasmic membrane [l -41. Among them, the higher-molecular-mass PBPs (PBP 1 A, PBP lB, PBP 2, and PBP 3 ) are important for completion of cell cycle of E. coli; PBP 1A and PBP 1 B are responsible for cell elongation [2, 3, 51, PBP 2 for the determination of rod shape of the cell [31,32], 3 [31, 331 and 5 [34] were obtained, and analyses of the peptides confirmed that the predicted active-site sequences were correct. The active-site serine regions of the higher-molecular-mass PBPs display a high sequence homology with each other [31].In this report we present the nucleotide sequence of the pbpA gene encoding PBP 2 of E. coli and the deduced amino acid sequence of this protein. These results prove the homology of the penicillin-binding sites of the higher-molecularmass PBPs of E. coli. Thus, the hypothesis of Tipper and Strominger [35] for the mechanism of the covalent binding of penicillin in all of the essential PBPs of E. coli has been verified.

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“…First, there is an ORF encoding for the penicillin-binding protein 2B (PBP2), which has transglycosylase activities to catalyze the formation of the beta 1-4 glycosidic links from the lipid-bound precursors to the nascent end of the peptidoglycan strand, and which is responsible for bulk peptidoglycan synthesis in other bacteria (Vollmer and Bertsche, 2008). The second gene encodes for a peptidoglycan synthetase (FtsI or PBP3), whose homolog in Escherichia coli is essential for the septum formation of the murein sacculus and synthesis of cross-linked peptidoglycan from the lipid intermediates (Nakamura et al, 1983).…”

Section: Resultsmentioning

confidence: 99%

Functional genomic analysis of an uncultured δ-proteobacterium in the sponge Cymbastela concentrica

2010

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Marine sponges are ancient, sessile, filter-feeding metazoans, which represent a significant component of the benthic communities throughout the world. Sponges harbor a remarkable diversity of bacteria, however, little is known about the functional properties of such bacterial symbionts. In this study, we present the genomic and functional characterization of an uncultured d-proteobacterium associated with the sponge Cymbastela concentrica. We show that this organism represents a novel phylogenetic clade and propose that it lives in association with a cyanobacterium. We also provide an overview of the predicted functional and ecological properties of this d-proteobacterium, and discuss its complex interactions with surrounding cells and milieu, including traits of cell attachment, nutrient transport and protein-protein interactions.

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On the process of cellular division in Escherichia coli: Nucleotide sequence of the gene for penicillin-binding protein 3

Cited by 123 publications

References 43 publications

Subcellular localization of seven VirB proteins of Agrobacterium tumefaciens: implications for the formation of a T-DNA transport structure

Subcellular localization of seven VirB proteins of Agrobacterium tumefaciens: implications for the formation of a T-DNA transport structure

Nucleotide sequence of the pbpA gene and characteristics of the deduced amino acid sequence of penicillin‐binding protein 2 of Escherichia coli K12

Functional genomic analysis of an uncultured δ-proteobacterium in the sponge Cymbastela concentrica

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