Miri Krupkin

Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus.

Significance Clinical use of the currently available antibiotics is severely compromised by the increasing resistance to them, acquired by the natural bacterial capability to manipulate their genomes. Many existing antibiotics target the fundamental process of protein biosynthesis, mainly by paralyzing the ribosome. Although antibiotics’ modes of action are similar across most eubacteria, species specificity has been detected. We determined the structures of the large ribosomal subunit from Staphylococcus aureus, a pathogenic bacterial species with a known capacity to become multiresistant, and of its complexes with known antibiotic compounds, as well as with a novel potential pleuromutilin derivative. Our new insights provide unique chemical tools for enhanced distinction between pathogens and the useful benign microbiome, as well as for suggesting novel sites for potential future antibiotics. The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from Staphylococcus aureus, a versatile Gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, BC-3205. These crystal structures shed light on specific structural motifs of the S. aureus ribosome and the binding modes of the aforementioned antibiotics. Moreover, by analyzing the ribosome structure and comparing it with those of nonpathogenic bacterial models, we identified some unique internal and peripheral structural motifs that may be potential candidates for improving known antibiotics and for use in the design of selective antibiotic drugs against S. aureus.

A vestige of a prebiotic bonding machine is functioning within the contemporary ribosome

Based on the presumed capability of a prebiotic pocket-like entity to accommodate substrates whose stereochemistry enables the creation of chemical bonds, it is suggested that a universal symmetrical region identified within all contemporary ribosomes originated from an entity that we term the ‘proto-ribosome’. This ‘proto-ribosome’ could have evolved from an earlier machine that was capable of performing essential tasks in the RNA world, called here the ‘pre-proto-ribosome’, which was adapted for producing proteins.

A novel pleuromutilin antibacterial compound, its binding mode and selectivity mechanism.

The increasing appearance of pathogenic bacteria with antibiotic resistance is a global threat. Consequently, clinically available potent antibiotics that are active against multidrug resistant pathogens are becoming exceedingly scarce. Ribosomes are a main target for antibiotics, and hence are an objective for novel drug development. Lefamulin, a semi-synthetic pleuromutilin compound highly active against multi-resistant pathogens, is a promising antibiotic currently in phase III trials for the treatment of community-acquired bacterial pneumonia in adults. The crystal structure of the Staphylococcus aureus large ribosomal subunit in complex with lefamulin reveals its protein synthesis inhibition mechanism and the rationale for its potency. In addition, analysis of the bacterial and eukaryotes ribosome structures around the pleuromutilin binding pocket has elucidated the key for the drug’s selectivity.

Protoribosome by quantum kernel energy method

Significance The ribosome is essential to life as it functions as “the protein factory” that translates the genetic code into proteins. A universally conserved region around its major active site, where the nascent proteins are being created, was identified in all contemporary ribosomes. Thus, it seems to be a remnant of an entity from the prebiotic RNA world, hence called the “protoribosome.” Using quantum mechanics and crystal coordinates of this region, we aimed at answering the question of whether the putative protoribosome has properties essential to function as an evolutionary precursor to the modern ribosome. Our findings show that the necessary conditions that would characterize a practicable protoribosome, namely energetic structural stability and energetically stable attachment to substrates, are well satisfied. Experimental evidence suggests the existence of an RNA molecular prebiotic entity, called by us the “protoribosome,” which may have evolved in the RNA world before evolution of the genetic code and proteins. This vestige of the RNA world, which possesses all of the capabilities required for peptide bond formation, seems to be still functioning in the heart of all of the contemporary ribosome. Within the modern ribosome this remnant includes the peptidyl transferase center. Its highly conserved nucleotide sequence is suggestive of its robustness under diverse environmental conditions, and hence on its prebiotic origin. Its twofold pseudosymmetry suggests that this entity could have been a dimer of self-folding RNA units that formed a pocket within which two activated amino acids might be accommodated, similar to the binding mode of modern tRNA molecules that carry amino acids or peptidyl moieties. Using quantum mechanics and crystal coordinates, this work studies the question of whether the putative protoribosome has properties necessary to function as an evolutionary precursor to the modern ribosome. The quantum model used in the calculations is density functional theory–B3LYP/3–21G*, implemented using the kernel energy method to make the computations practical and efficient. It occurs that the necessary conditions that would characterize a practicable protoribosome—namely (i) energetic structural stability and (ii) energetically stable attachment to substrates—are both well satisfied.

2 A prebiotic RNA apparatus functions within the contemporary ribosome

Ribosomes, the universal cellular machines, possess spectacular architecture accompanied by inherent mobility, allowing for their smooth performance as polymerases that translate the genetic code into proteins. The site for peptide bond formation is located within a universal internal semi-symmetrical region, which was identified within all contemporary ribosomes. The high conservation of this region implies its existence irrespective of environmental conditions and indicates that it may represent an ancient RNA molecular apparatus. Hence, we named it the “proto-ribosome”. This prebiotic pocket-like RNA entity is suggested to be capable to accommodate substrates whose stereochemistry enables the creation of chemical bonds. It could have evolved from an earlier catalytic RNA entity that we named the “pre-proto-ribosome”, presumed to be a molecular machine capable of performing various essential tasks in the RNA world, which was snatched by the amino acid invaders for producing proteins.

Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding

Significance Resistance to antibiotics poses a serious threat in contemporary medicine. Avilamycin and evernimicin, polysaccharide antibiotics belonging to the orthosomycin family, possess inhibitory activity against multidrug-resistant pathogenic strains of Enterococci, Staphylococci, and other Streptococci gram-positive bacteria by paralyzing ribosomes function in protein biosynthesis. The crystal structures of the large ribosomal subunit from the eubacteria Deinococcus radiodurans in complex with avilamycin and evernimicin revealed their binding sites at the entrance to the A-site tRNA accommodating corridor, thus illuminating the mechanisms of their translation inhibition. Analysis of the binding interactions of these antibiotics depicted the features enabling their species discrimination (namely, selectivity) and elucidated the various mechanisms by which pathogens use single mutations to acquire resistance to those drugs. Two structurally unique ribosomal antibiotics belonging to the orthosomycin family, avilamycin and evernimicin, possess activity against Enterococci, Staphylococci, and Streptococci, and other Gram-positive bacteria. Here, we describe the high-resolution crystal structures of the eubacterial large ribosomal subunit in complex with them. Their extended binding sites span the A-tRNA entrance corridor, thus inhibiting protein biosynthesis by blocking the binding site of the A-tRNA elbow, a mechanism not shared with other known antibiotics. Along with using the ribosomal components that bind and discriminate the A-tRNA—namely, ribosomal RNA (rRNA) helices H89, H91, and ribosomal proteins (rProtein) uL16—these structures revealed novel interactions with domain 2 of the CTC protein, a feature typical to various Gram-positive bacteria. Furthermore, analysis of these structures explained how single nucleotide mutations and methylations in helices H89 and H91 confer resistance to orthosomycins and revealed the sequence variations in 23S rRNA nucleotides alongside the difference in the lengths of the eukaryotic and prokaryotic α1 helix of protein uL16 that play a key role in the selectivity of those drugs. The accurate interpretation of the crystal structures that could be performed beyond that recently reported in cryo-EM models provide structural insights that may be useful for the design of novel pathogen-specific antibiotics, and for improving the potency of orthosomycins. Because both drugs are extensively metabolized in vivo, their environmental toxicity is very low, thus placing them at the frontline of drugs with reduced ecological hazards.

A Recombinant Collagen-mRNA Platform for Controllable Protein Synthesis.

We have developed a collagen–mRNA platform for controllable protein production that is intended to be less prone to the problems associated with commonly used mRNA therapy as well as with collagen skin‐healing procedures. A collagen mimic was constructed according to a recombinant method and was used as scaffold for translating mRNA chains into proteins. Cysteines were genetically inserted into the collagen chain at positions allowing efficient ribosome translation activity while minimizing mRNA misfolding and degradation. Enhanced green fluorescence protein (eGFP) mRNA bound to collagen was successfully translated by cell‐free Escherichia coli ribosomes. This system enabled an accurate control of specific protein synthesis by monitoring expression time and level. Luciferase–mRNA was also translated on collagen scaffold by eukaryotic cell extracts. Thus we have demonstrated the feasibility of controllable protein synthesis on collagen scaffolds by ribosomal machinery.

Ribosomal Antibiotics: Contemporary Challenges.

Most ribosomal antibiotics obstruct distinct ribosomal functions. In selected cases, in addition to paralyzing vital ribosomal tasks, some ribosomal antibiotics are involved in cellular regulation. Owing to the global rapid increase in the appearance of multi-drug resistance in pathogenic bacterial strains, and to the extremely slow progress in developing new antibiotics worldwide, it seems that, in addition to the traditional attempts at improving current antibiotics and the intensive screening for additional natural compounds, this field should undergo substantial conceptual revision. Here, we highlight several contemporary issues, including challenging the common preference of broad-range antibiotics; the marginal attention to alterations in the microbiome population resulting from antibiotics usage, and the insufficient awareness of ecological and environmental aspects of antibiotics usage. We also highlight recent advances in the identification of species-specific structural motifs that may be exploited for the design and the creation of novel, environmental friendly, degradable, antibiotic types, with a better distinction between pathogens and useful bacterial species in the microbiome. Thus, these studies are leading towards the design of “pathogen-specific antibiotics,” in contrast to the current preference of broad range antibiotics, partially because it requires significant efforts in speeding up the discovery of the unique species motifs as well as the clinical pathogen identification.