Cloning and analysis of thespcribosomal protein operon ofBacillus subtilis: comparison with thespcoperon ofEscherichia coli

Henkin, Tina M.; Moon, Sangook; Mattheakis, Larry; Nomura, Masayasu

doi:10.1093/nar/17.18.7469

Cited by 53 publications

(38 citation statements)

References 45 publications

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“…1). The sequence of strain JH642 is identical to the 168 sequence already published (Henkin et al, 1989), except at one nucleotide in the putative ribosome-binding site 5' to rplX. The RBS for 168 was reported as GGTGG, whereas the same region is GGAGG in JH642 and all other strains examined here.…”

Section: Nucleotide Sequence Diversitysupporting

confidence: 63%

“…Chromosomal DNA was isolated from each strain according to Rodriguez & Tait (1983). Using the published sequence of the B. subtilis 168 spc ribosomal protein operon (Henkin et al, 1989), two oligonucleotides, 5'-CTAGCTCCAGAAGTTATC-TAA-3' and 5'-CTTTTCTTTAAGGCGGTTCAT-3', were selected from the 3'-end of rplN and the complementary strand of the 5'-end of rplE, the genes preceding and following rplX, respectively. These oligonucleotides were synthesized on an Applied Biosystems 39 1 PCRMate DNA synthesizer and were used as primers for a polymerase chain reaction (PCR).…”

Section: Methodsmentioning

confidence: 99%

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DNA sequence variability at the rplX locus of Bacillus subtilis

Sharp¹,

Nolan

Cholmain

et al. 1992

Journal of General Microbiology

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The pattern and extent of DNA sequence variability at the rplXlocus (encoding r i b m a l protein L24) has been investigated in nine strains of Bacillus subtilis. Overall, there is a very low level of nucleotide diversity, even at silent sites, which is probably due to selection among synonymous codons. By analogy with Escherichia coli, there may also be some effect of the relative proximity of rplX to the chromosomal origin of replication. The small number of nucleotide substitutions are non-randomly distributed: all of the synonymous changes are in valine codons. From the sequence differences the strains can be divided into two groups, which are not coincident with their previous classification; this observation is consistent with recombination among strains.

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Section: Nucleotide Sequence Diversitysupporting

confidence: 63%

Section: Methodsmentioning

confidence: 99%

DNA sequence variability at the rplX locus of Bacillus subtilis

Sharp¹,

Nolan

Cholmain

et al. 1992

Journal of General Microbiology

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“…Sec-dependent protein secretion in the pathogenic Neisseria has been reported (18,28); however, the function of the N. meningitidis SecY protein is not known, nor has the regulation of the secY gene been examined. In E. coli, the secY gene is located in a gene cluster known as the spc operon, which includes the rplN, rplX, rplE, rpsN, rpsH, rplF, rplR, rpsE, rpmD, and rplO genes, encoding ribosomal proteins (3,19). While the structure and function of the E. coli Sec system has been well defined, the regulation of genes encompassing the E. coli Sec system are not well understood.…”

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confidence: 99%

Expression of the Iron-ActivatednspAandsecYGenes inNeisseria meningitidisGroup B by Fur-Dependent and -Independent Mechanisms

et al. 2007

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Our whole-genome microarray studies of Neisseria meningitidis MC58 previously identified a set of 153 genes whose transcription was activated during growth in iron. In this study, Fur-mediated regulation of the iron-activated nspA gene was confirmed, whereas iron-activated regulation of the secY gene was demonstrated to be Fur independent. Analysis of the Fur binding sequences in the nspA gene and an additional iron-activated and Fur-regulated gene identified a hexameric (G/T)ATAAT unit in the operator regions of these genes similar to that observed in Fur-and iron-repressed genes. These studies indicate that the expression of the ironactivated nspA and secY genes in N. meningitidis occur by Fur-dependent and -independent mechanisms, respectively.It is well established that the iron-responsive regulatory protein Fur functions as a repressor of gene transcription in several microorganisms. In its most basic state, Fur forms a dimer together with divalent cations, such as ferrous iron, and binds to a consensus sequence (the Fur box) that overlaps the promoters of iron-regulated genes to prevent their transcription. Recent studies indicate that in some organisms, Fur may also function as a positive regulator of gene transcription, together with iron (8,(9)(10)(11)(12)24), although the mechanism of iron activation by Fur is not well elucidated. Our recent studies of N. meningitidis group B, using a combination of microarray technology, computational analysis, and in vitro binding studies, revealed that a large number of genes are activated during growth in the presence of iron and that a number of these iron-activated genes have putative Fur-binding sequences to which Fur was demonstrated to bind (17). However, the biological significance of Fur binding to the operator regions of these genes has not been defined, as an N. meningitidis fur mutant had not been constructed at the time of that study.Of interest within the group of iron-activated genes under the potential control of Fur were candidate genes involved in the virulence potential of N. meningitidis, including the nspA (NMB0663) (1, 21) and secY (NMB0162) (18, 28) genes. Neisserial surface protein A (NspA) is an 18.6-kDa membrane protein of unknown function that was first described to confer protection against meningococcal infection in animal models of infection (1,21,22). NspA is highly conserved and expressed by all N. meningitidis strains tested (22,25). Recent studies indicate that conserved epitopes of the NspA protein confer protection against N. meningitidis serogroup B challenge in a mouse model of meningococcal infection (26). The N. meningitidis secY gene encodes a putative preprotein translocase (SecY) whose homolog in Escherichia coli has been studied extensively; in E. coli, it functions as an essential component of the protein translocation machinery of the cytoplasmic membrane. Sec-dependent protein secretion in the pathogenic Neisseria has been reported (18, 28); however, the function of the N. meningitidis SecY protein is not known, nor has ...

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“…Although a few other ribosomal determinants have been identified, r-protein gene organization and expression have not been well characterized (7-10, 20, 21). Interestingly, the organization and transcriptional regulation of r-protein operons appear to be well conserved among eubacteria; however, their regulation among evolutionary distant species remains unelucidated (15).…”

mentioning

confidence: 99%

“…In Bacillus subtilis and Thennus aquaticus, however, no structure resembling an S8 translational repressor has been identified, suggesting some different mechanism of transcriptional regulation (15,18). Immediately upstream of the spc operon in E. coli lies the S10 operon, which sequentially encodes EcoS10, EcoL3, EcoL4, EcoL23, EcoL22, EcoS19, EcoS3, EcoL16, EcoL29, and EcoS17 (33).…”

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confidence: 99%

Cloning and sequence analysis of the Chlamydia trachomatis spc ribosomal protein gene cluster

et al. 1992

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We identified and sequenced a segment of Chlamydia trachomatis chromosomal DNA that shows homology to the Escherichia coli spc and distal region of the S10 ribosomal protein (r-protein) operons. Its sequence revealed a high degree of nucleotide and operon context conservation with the E. coli r-protein genes. The C. trachomatis spc operon contains the r-protein genes for L14, L24, L5, S8, L6, L18, S5, L15, and Sec Y along with the genes for r-proteins L16, L29, and S17 of the S10 operon. The two operons are separated by a 16-bp intragenic region which contains no transcription signals. However, a putative promoter for the transcription of the spc operon was found 162 nucleotides upstream of the CtrL14e start site; it revealed significant homology to the E. coli consensus promoter sequences. Interestingly, our results indicate the absence of any structure resembling an EcoS8 regulatory target site on C. trachomatis spc mRNA in spite of significant amino acid identity between E. coli and C. trachomatis r-proteins. Also, the intrinsic aminoglycoside resistance in C. trachomatis is unlikely to be mediated by CtrL6e since E. coli expressing CtrL6e remained susceptible to gentamicin (MIC < 0.5 ,ug/ml).Chlamydia trachomatis infections represent major public health problems in both developing and industrialized countries (30). Chlamydia species have evolved a complex and unique developmental cycle which involves two distinct forms: the small (0.2 to 0.3 ,um) extracellular, rigid elementary bodies and the large (1 ,um) intracellular, fragile reticulate bodies (44). The genetics of chlamydial regulation is largely undefined, mainly because of the lack of any convenient system for gene transfer and also because of the paucity of information about the signals and machinery that govern gene expression.Ribosomes constitute the protein-synthesizing machinery of both prokaryotes and eukaryotes. The entire prokaryotic ribosome comprises three rRNAs with sedimentation coefficients of 23S, 16S, and 5S and approximately 52 ribosomal proteins (r-proteins) that are organized into 19 different operons (26,33). Earlier attempts at characterizing the rRNA from Chlamydia species have met with some success. Tamura and Iwanaga (42) identified 21S, 16S, and 4S rRNA fractions in Chlamydia psittaci; of these, 21S and 16S were more predominant forms in reticulate bodies, whereas 4S predominated in the elementary bodies. Sarov and Becker found similar rRNA species in C. trachomatis (39). On the basis of their 16S rRNA gene sequence, chlamydiae have been identified as eubacterial in origin, related peripherally to planctomyces (45). Although a few other ribosomal determinants have been identified, r-protein gene organization and expression have not been well characterized (7-10, 20, 21). Interestingly, the organization and transcriptional regulation of r-protein operons appear to be well conserved among eubacteria; however, their regulation among evolutionary distant species remains unelucidated (15).Recently, we reported the cloning and sequen...

show abstract

Cloning and analysis of thespcribosomal protein operon ofBacillus subtilis: comparison with thespcoperon ofEscherichia coli

Cited by 53 publications

References 45 publications

DNA sequence variability at the rplX locus of Bacillus subtilis

DNA sequence variability at the rplX locus of Bacillus subtilis

Expression of the Iron-ActivatednspAandsecYGenes inNeisseria meningitidisGroup B by Fur-Dependent and -Independent Mechanisms

Cloning and sequence analysis of the Chlamydia trachomatis spc ribosomal protein gene cluster

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