Reduced mRNA Secondary-Structure Stability Near the Start Codon Indicates Functional Genes in Prokaryotes

Keller, Thomas E.; Mis, S. David; Jia, Kevin E.; Wilke, Claus O.

doi:10.1093/gbe/evr129

Cited by 33 publications

(22 citation statements)

References 35 publications

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“…Specifically, about 86 % of genes with an SD sequence use these seven motifs. Studies have identified the −4 to +30 region of the mRNA as a region critical for ribosome binding, wherein stability has to be minimized for efficient translation initiation [ 11 , 26 – 28 ]. Although the exact distance of the RBS from the start codon is not fully ascertained in this study; it is likely that a 5-10n RBS spacer is important, as an RBS further away from the start codon could be less efficient in melting secondary structure in the critical region.…”

Section: Resultsmentioning

confidence: 99%

Distribution and diversity of ribosome binding sites in prokaryotic genomes

et al. 2015

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BackgroundProkaryotic translation initiation involves the proper docking, anchoring, and accommodation of mRNA to the 30S ribosomal subunit. Three initiation factors (IF1, IF2, and IF3) and some ribosomal proteins mediate the assembly and activation of the translation initiation complex. Although the interaction between Shine-Dalgarno (SD) sequence and its complementary sequence in the 16S rRNA is important in initiation, some genes lacking an SD ribosome binding site (RBS) are still well expressed. The objective of this study is to examine the pattern of distribution and diversity of RBS in fully sequenced bacterial genomes. The following three hypotheses were tested: SD motifs are prevalent in bacterial genomes; all previously identified SD motifs are uniformly distributed across prokaryotes; and genes with specific cluster of orthologous gene (COG) functions differ in their use of SD motifs.ResultsData for 2,458 bacterial genomes, previously generated by Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm) and currently available at the National Center for Biotechnology Information (NCBI), were analyzed. Of the total genes examined, ~77.0 % use an SD RBS, while ~23.0 % have no RBS. Majority of the genes with the most common SD motifs are distributed in a manner that is representative of their abundance for each COG functional category, while motifs 13 (5′-GGA-3′/5′-GAG-3′/5′-AGG-3′) and 27 (5′-AGGAGG-3′) appear to be predominantly used by genes for information storage and processing, and translation and ribosome biogenesis, respectively.ConclusionThese findings suggest that an SD sequence is not obligatory for translation initiation; instead, other signals, such as the RBS spacer, may have an overarching influence on translation of mRNAs. Subsequent analyses of the 5′ secondary structure of these mRNAs may provide further insight into the translation initiation mechanism.

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Section: Resultsmentioning

confidence: 99%

Distribution and diversity of ribosome binding sites in prokaryotic genomes

et al. 2015

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“…We used RT-PCR to confirm that bb0347 is actively expressed (i.e. not a pseudogene [45]–[48]) in B. burgdorferi (Fig. 1A) using primers listed in Table 1.…”

Section: Resultsmentioning

confidence: 99%

BB0347, from the Lyme Disease Spirochete Borrelia burgdorferi, Is Surface Exposed and Interacts with the CS1 Heparin-Binding Domain of Human Fibronectin

et al. 2013

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The causative agent of Lyme disease, Borrelia burgdorferi, codes for several known fibronectin-binding proteins. Fibronectin a common the target of diverse bacterial pathogens, and has been shown to be essential in allowing for the development of certain disease states. Another borrelial protein, BB0347, has sequence similarity with these other known fibronectin-binding proteins, and may be important in Lyme disease pathogenesis. Herein, we perform an initial characterization of BB0347 via the use of molecular and biochemical techniques. We found that BB0347 is expressed, produced, and presented on the outer surface of intact B. burgdorferi. We also demonstrate that BB0347 has the potential to be important in Lyme disease progression, and have begun to characterize the nature of the interaction between human fibronectin and this bacterial protein. Further work is needed to define the role of this protein in the borrelial infection process.

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“…It might interfere with the structure or stability of UppP, thereby making it less efficient as bacteriocin receptor. However, effects on mRNA secondary structures, translation regulation, or other unknown effects might also occur (Keller et al ., ). No significant change in the transcription level of uppP was observed in the two mutant strains IL3 and IL6 (Fig.…”

Section: Discussionmentioning

confidence: 99%

Sensitivity to the two‐peptide bacteriocin lactococcin G is dependent on UppP, an enzyme involved in cell‐wall synthesis

Kjos

Oppegård

Diep

et al. 2014

Molecular Microbiology

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SummaryMost bacterially produced antimicrobial peptides (bacteriocins) are thought to kill target cells by a receptor-mediated mechanism. However, for most bacteriocins the receptor is unknown. For instance, no target receptor has been identified for the two-peptide bacteriocins (class IIb), whose activity requires the combined action of two individual peptides. To identify the receptor for the class IIb bacteriocin lactococcin G, which targets strains of Lactococcus lactis, we generated 12 lactococcin G-resistant mutants and performed whole-genome sequencing to identify mutations causing the resistant phenotype. Remarkably, all had a mutation in or near the gene uppP (bacA), encoding an undecaprenyl pyrophosphate phosphatase; a membrane protein involved in peptidoglycan synthesis. Nine mutants had stop codons or frameshifts in the uppP gene, two had point mutations in putative regulatory regions and one caused an amino acid substitution in UppP. To verify the receptor function of UppP, it was shown that growth of non-sensitive Streptococcus pneumoniae could be inhibited by lactococcin G when L. lactis uppP was expressed in this bacterium. Furthermore, we show that the related class IIb bacteriocin enterocin 1071 also uses UppP as receptor. The approach used here should be broadly applicable to identify receptors for other bacteriocins as well.

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Reduced mRNA Secondary-Structure Stability Near the Start Codon Indicates Functional Genes in Prokaryotes

Cited by 33 publications

References 35 publications

Distribution and diversity of ribosome binding sites in prokaryotic genomes

Distribution and diversity of ribosome binding sites in prokaryotic genomes

BB0347, from the Lyme Disease Spirochete Borrelia burgdorferi, Is Surface Exposed and Interacts with the CS1 Heparin-Binding Domain of Human Fibronectin

Sensitivity to the two‐peptide bacteriocin lactococcin G is dependent on UppP, an enzyme involved in cell‐wall synthesis

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