Ribosome binding site consensus sequence of Lactobacillus delbrueckii subsp. lactis bacteriophage LL-H

Mikkonen, M

doi:10.1016/0378-1097(94)90053-1

Cited by 8 publications

(10 citation statements)

References 17 publications

(21 reference statements)

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“…The results show that the genome context of all the YdbC homologues differs, suggesting that YdbC is encoded by a monocistronic transcript. This observation is also consistent with the presence of the putative ribosomal binding site AGAAAGGA (47) located six nucleotides upstream from the start codon of the ydbC gene, and the fact that the gene downstream is transcribed in the opposite direction with respect to ydbC . A similar analysis of the genome context was also performed using PC4, SSB and PUR-α protein sequences.…”

Section: Resultssupporting

confidence: 80%

Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome

Rossi

Barbieri

Aramini

et al. 2013

Nucleic Acids Research

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Single-stranded DNA (ssDNA) binding proteins are important in basal metabolic pathways for gene transcription, recombination, DNA repair and replication in all domains of life. Their main cellular role is to stabilize melted duplex DNA and protect genomic DNA from degradation. We have uncovered the molecular function of protein domain family domain of unknown function DUF2128 (PF09901) as a novel ssDNA binding domain. This bacterial domain strongly associates into a dimer and presents a highly positively charged surface that is consistent with its function in non-specific ssDNA binding. Lactococcus lactis YdbC is a representative of DUF2128. The solution NMR structures of the 20 kDa apo-YdbC dimer and YdbC:dT19G1 complex were determined. The ssDNA-binding energetics to YdbC were characterized by isothermal titration calorimetry. YdbC shows comparable nanomolar affinities for pyrimidine and mixed oligonucleotides, and the affinity is sufficiently strong to disrupt duplex DNA. In addition, YdbC binds with lower affinity to ssRNA, making it a versatile nucleic acid-binding domain. The DUF2128 family is related to the eukaryotic nuclear protein positive cofactor 4 (PC4) family and to the PUR family both by fold similarity and molecular function.

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Section: Resultssupporting

confidence: 80%

Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome

Rossi

Barbieri

Aramini

et al. 2013

Nucleic Acids Research

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“…This sequence appears to be more than averagely conserved and is known as the Shine-Dalgarno sequence [43], [44]; (2) In Gram-negative bacteria such as organisms belonging to the former Proteobacteria division (which includes Escherichia ), an AU-rich mRNA region of 16 nucleotides long and immediately preceding the Shine-Dalgarno sequence may also attract and position ribosomes to help initiate translation of the correct, biologically active gene product [45], [46]. For E. coli , the Shine-Dalgarno sequence was determined to be a subsequence of AGGAGGU (which is the reverse complement of the 3′ end of the 16S rRNA), and the minimum AU-richness (equivalent to ribosome binding capacity) of the preceding region was arbitrarily set to 10/16.…”

Section: Methodsmentioning

confidence: 99%

Complete Nucleotide Sequence of CTX-M-15-Plasmids from Clinical Escherichia coli Isolates: Insertional Events of Transposons and Insertion Sequences

et al. 2010

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BackgroundCTX-M-producing Escherichia coli strains are regarded as major global pathogens.Methodology/Principal FindingsThe nucleotide sequence of three plasmids (pEC_B24: 73801-bp; pEC_L8: 118525-bp and pEC_L46: 144871-bp) from Escherichia coli isolates obtained from patients with urinary tract infections and one plasmid (pEC_Bactec: 92970-bp) from an Escherichia coli strain isolated from the joint of a horse with arthritis were determined. Plasmid pEC_Bactec belongs to the IncI1 group and carries two resistance genes: bla TEM-1 and bla CTX-M-15. It shares more than 90% homology with a previously published bla CTX-M-plasmid from E. coli of human origin. Plasmid pEC_B24 belongs to the IncFII group whereas plasmids pEC_L8 and pEC_L46 represent a fusion of two replicons of type FII and FIA. On the pEC_B24 backbone, two resistance genes, bla TEM-1 and bla CTX-M-15, were found. Six resistance genes, bla TEM-1, bla CTX-M-15, bla OXA-1, aac6'-lb-cr, tetA and catB4, were detected on the pEC_L8 backbone. The same antimicrobial drug resistance genes, with the exception of tetA, were also identified on the pEC_L46 backbone. Genome analysis of all 4 plasmids studied provides evidence of a seemingly frequent transposition event of the bla CTX-M-15-ISEcp1 element. This element seems to have a preferred insertion site at the tnpA gene of a bla TEM-carrying Tn3-like transposon, the latter itself being inserted by a transposition event. The IS26-composite transposon, which contains the bla OXA-1, aac6'-lb-cr and catB4 genes, was inserted into plasmids pEC_L8 and pEC_L46 by homologous recombination rather than a transposition event. Results obtained for pEC_L46 indicated that IS26 also plays an important role in structural rearrangements of the plasmid backbone and seems to facilitate the mobilisation of fragments from other plasmids.ConclusionsCollectively, these data suggests that IS26 together with ISEcp1 could play a critical role in the evolution of diverse multiresistant plasmids found in clinical Enterobacteriaceae.

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“…The ribosomebinding site sequences showed a considerable similarity to the consensus Shine-Dalgarno sequence of lactobacilli (Mikkonen et al 1994) and also complemented perfectly the 3¢-terminal sequence of 16S rDNA of L. plantarum (AJ272031; AJ271852). The G+C content of ORF3, ORF5, and ORF8 were 45.6, 46.0 and 46.5 mol%, respectively, which is close to the 44 mol% G+C content of the L. plantarum genome (Sriranganathan et al 1985).…”

Section: Complementation Of Dhpr Deficiencymentioning

confidence: 94%

Cloning of Lactobacillus plantarum IAM 12477 lysine biosynthetic genes encoding functional aspartate semialdehyde dehydrogenase, dihydrodipicolinate synthase, and dihydrodipicolinate reductase

Cahyanto

Kawasaki

Fujiyama

et al. 2005

World J Microbiol Biotechnol

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The lysine biosynthetic genes asd, dapA, and dapB, encoding aspartate semialdehyde dehydrogenase (ASADH), dihydrodipicolinate synthase (DHPS), and dihydrodipicolinate reductase (DHPR), respectively, have been cloned from Lactobacillus plantarum IAM 12477 by heterologous complementation to Escherichia coli mutants. The amino acid sequences of the cloned genes showed considerable similarities to the corresponding protein from other grampositive bacteria. We identified the amino acids that correspond to key catalytic residues of ASADH, DHPS, and DHPR and found them to be conserved in the protein from L. plantarum. ASADH, DHPS, and DHPR activity was detected in the cell extracts of E. coli mutant harboring each gene, indicating that the cloned genes were functionally expressed in E. coli. The regulation of ASADH, DHPS, and DHPR were studied in the cell extracts of both the E. coli mutant harboring the gene and L. plantarum; however, those enzymes were found not to be regulated by the end products of the pathway.

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Ribosome binding site consensus sequence of Lactobacillus delbrueckii subsp. lactis bacteriophage LL-H

Cited by 8 publications

References 17 publications

Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome

Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome

Complete Nucleotide Sequence of CTX-M-15-Plasmids from Clinical Escherichia coli Isolates: Insertional Events of Transposons and Insertion Sequences

Cloning of Lactobacillus plantarum IAM 12477 lysine biosynthetic genes encoding functional aspartate semialdehyde dehydrogenase, dihydrodipicolinate synthase, and dihydrodipicolinate reductase

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