Ribosome heterogeneity: another level of complexity in bacterial translation regulation

Byrgazov, Konstantin; Vesper, Oliver; Moll, Isabella

doi:10.1016/j.mib.2013.01.009

Cited by 113 publications

(92 citation statements)

References 52 publications

(38 reference statements)

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“…The reduced number of proteins below 32 kDa and fewer ribosomal interacting partners of NCR247 in the bacteroids were indicative for reduced amounts of ribosomal proteins and even diversification of the ribosomes, comprised of lower amounts of certain ribosomal proteins. Evidence is accumulating that ribosomal heterogeneity represents another level of complexity in bacterial translation regulation (19). Comparing the transcriptome of S. meliloti bacteria and bacteroids reveals at least 10-fold lower expression level of ribosomal protein genes in the bacteroids (SI Appendix, Fig.…”

Section: Ncr247-ribosomal Protein Interactions: Modulation Of the Bacmentioning

confidence: 99%

Medicago truncatula symbiotic peptide NCR247 contributes to bacteroid differentiation through multiple mechanisms

Farkas

Maróti

Dürgő

et al. 2014

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

149

178

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Symbiosis between rhizobia soil bacteria and legume plants results in the formation of root nodules where plant cells are fully packed with nitrogen fixing bacteria. In the host cells, the bacteria adapt to the intracellular environment and gain the ability for nitrogen fixation. Depending on the host plants, the symbiotic fate of bacteria can be either reversible or irreversible. In Medicago and related legume species, the bacteria undergo a host-directed multistep differentiation process culminating in the formation of elongated and branched polyploid bacteria with definitive loss of cell division ability. The plant factors are nodule-specific symbiotic peptides. Approximately 600 of them are nodule-specific cysteine-rich (NCR) peptides produced in the rhizobium-infected plant cells. NCRs are targeted to the endosymbionts, and concerted action of different sets of peptides governs different stages of endosymbiont maturation, whereas the symbiotic function of individual NCRs is unknown. This study focused on NCR247, a cationic peptide exhibiting in vitro antimicrobial activities. We show that NCR247 acts in those nodule cells where bacterial cell division is arrested and cell elongation begins. NCR247 penetrates the bacteria and forms complexes with many bacterial proteins. Interaction with FtsZ required for septum formation is one of the host interventions for inhibiting bacterial cell division. Complex formation with the ribosomal proteins affects translation and contributes to altered proteome and physiology of the endosymbiont. Binding to the chaperone GroEL amplifies the NCR247-modulated biological processes. We show that GroEL1 of Sinorhizobium meliloti is required for efficient infection, terminal differentiation, and nitrogen fixation.bacterial targets | antimicrobial peptides | protein interactions | translation inhibition | host peptides S ymbiosis between microbes and hosts, like legumes and various insects, often results in the formation of symbiotic organs where host cells harbor thousands of endosymbiotic bacteria. In rhizobium-legume symbiosis, rhizobia in the soil interact with their host legume and induce the formation of root nodules where bacteria reside in the host cytosol in membrane-enclosed vesicles called symbiosomes. The bacteria adapt to the endosymbiotic lifestyle in the plant cells and gain the capacity for nitrogen fixation, thereby ensuring the nitrogen need of the host plant.In addition to the physiological changes required for nitrogen fixation, in certain rhizobium-legume interactions, like in the Medicago truncatula-Sinorhizobium meliloti symbiosis, the bacteria undergo an additional remarkable differentiation process (1). The endosymbiotic bacteria called bacteroids become polyploid, noncultivable elongated, and frequently branched cells (2). This terminal bacterial differentiation is provoked by hundreds of nodule-specific cysteine-rich (NCR) host peptides that are exclusively expressed in the rhizobium-infected symbiotic cells (3).Nodule development and bacterial infection a...

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Section: Ncr247-ribosomal Protein Interactions: Modulation Of the Bacmentioning

confidence: 99%

Medicago truncatula symbiotic peptide NCR247 contributes to bacteroid differentiation through multiple mechanisms

Farkas

Maróti

Dürgő

et al. 2014

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

149

178

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“…Each helical element comprises one or more helices connected by internal loops occurring throughout the molecule. [12][13][14][15] It is important to maintain the structure because there are segments that play essential roles in ribosome function. For instance, ribosomal proteins attach to 16S rRNA in a hierarchical order, which produces a cooperativity effect; [16][17][18][19] however, it is possible that structural variations would affect this process.…”

Section: Introductionmentioning

confidence: 99%

Size-variable zone in V3 region of 16S rRNA

et al. 2017

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The size distribution of complete 16S-rRNA sequences from the SILVA-database and nucleotide shifts that might interfere with the secondary structure of the molecules were evaluated. Overall, 513,309 sequences recorded in SILVA were used to estimate the size of hypervariable regions of the gene. Redundant sequences were treated as a single sequence to achieve a better representation of the molecular diversity. Nucleotides found in each position in 95% of the sequences were considered the consensus sequences for different size-groups (consensus95). The sizes of different regions ranged from 96.7 to 283.1 nucleotides and had similar distribution patterns, except for the V3 region, which exhibited a bimodal distribution composed of 2 main peaks of 161 and 186 nt. The alignment of Consensuses95 of fractions 161 and 186 showed a high degree of similarity and conservation, except for the central positions (gap zone), where the sequence was highly variable and several deletions were observed. Structurally, the gap zone forms the central part of helix 17 (H17), and its extension was directly reflected in the size of this helix. H17 is part of a multihelix conjunction known as the 5-way junction (5 WJ), which is indispensable for 30 S ribosome assembly. However, because a drastic variation in the sequence size of V3 region occurs at a central position in loop H17 without affecting the base of the loop, it has no apparent effect on 5 WJ. Finally, considering that these differences were detected in non-redundant sequences, it can be concluded that this is not an uncommon or isolated event and that the V3 region is possibly more likely to mutate than are other regions.

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“…I n all three domains of life, translational GTPases (trGTPases), highly conserved members of the G protein family, play diverse and central roles during protein biosynthesis (1)(2)(3). G proteins can be regarded as molecular switches that are driven by GTP hydrolysis and cycle between the active GTP-bound state and the inactive GDP-bound form.…”

mentioning

confidence: 99%

Role of a ribosomal RNA phosphate oxygen during the EF-G–triggered GTP hydrolysis

Koch

Flür

Kreutz

et al. 2015

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

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Elongation factor-catalyzed GTP hydrolysis is a key reaction during the ribosomal elongation cycle. Recent crystal structures of G proteins, such as elongation factor G (EF-G) bound to the ribosome, as well as many biochemical studies, provide evidence that the direct interaction of translational GTPases (trGTPases) with the sarcin-ricin loop (SRL) of ribosomal RNA (rRNA) is pivotal for hydrolysis. However, the precise mechanism remains elusive and is intensively debated. Based on the close proximity of the phosphate oxygen of A2662 of the SRL to the supposedly catalytic histidine of EF-G (His87), we probed this interaction by an atomic mutagenesis approach. We individually replaced either of the two nonbridging phosphate oxygens at A2662 with a methyl group by the introduction of a methylphosphonate instead of the natural phosphate in fully functional, reconstituted bacterial ribosomes. Our major finding was that only one of the two resulting diastereomers, the SP methylphosphonate, was compatible with efficient GTPase activation on EF-G. The same trend was observed for a second trGTPase, namely EF4 (LepA). In addition, we provide evidence that the negative charge of the A2662 phosphate group must be retained for uncompromised activity in GTP hydrolysis. In summary, our data strongly corroborate that the nonbridging proSP phosphate oxygen at the A2662 of the SRL is critically involved in the activation of GTP hydrolysis. A mechanistic scenario is supported in which positioning of the catalytically active, protonated His87 through electrostatic interactions with the A2662 phosphate group and H-bond networks are key features of ribosome-triggered activation of trGTPases.

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Ribosome heterogeneity: another level of complexity in bacterial translation regulation

Cited by 113 publications

References 52 publications

Medicago truncatula symbiotic peptide NCR247 contributes to bacteroid differentiation through multiple mechanisms

Medicago truncatula symbiotic peptide NCR247 contributes to bacteroid differentiation through multiple mechanisms

Size-variable zone in V3 region of 16S rRNA

Role of a ribosomal RNA phosphate oxygen during the EF-G–triggered GTP hydrolysis

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