Terje Dokland

Streptococcus pneumoniae is a major human respiratory pathogen. The bacterial 70S ribosome is a target of many clinically important antibiotics. The N-terminus of ribosomal protein bL27 extends into the peptidyl transferase center and contributes to the translation process. In Firmicutes, full length bL27 contains an 8-12 amino acid N-terminal extension that is absent from Gram-negative bacteria. This extension is cleaved by the protease Prp, which is absent from organisms lacking the extension. Prp-mediated cleavage of bL27 is essential in Staphylococcus aureus , and Prp has been proposed as a potential antibiotic target. Here, we show that in S. pneumoniae strain TIGR4, a Δ prp mutant remained viable, and produced ribosomes containing cleaved bL27, whereas deletion of prp was not tolerated in strain D39. These results suggested the presence of an alternate bL27-processing protease in TIGR4 that was absent from D39. Using a combination of genomics, proteomics and biochemical analyses, we identified this enzyme as the product of previously uncharacterized gene SP_1145 , encoding a protease that we named Ribosome rescue protease (Rrp). SP_1145 is carried on a mobile genetic element that is present in strain TIGR4, but absent from D39. Our findings shed light on an alternative mechanism for bL27 maturation, and indicate that some strains of S. pneumoniae harbor horizontally acquired redundant pathways for this essential ribosome processing step.

Type III CRISPR systems utilize a complex containing Cas10, additional Cas proteins and a crRNA to detect foreign transcripts. Upon detection, Cas10 synthesizes cyclic oligoadenylates (cOA), signaling molecules that coordinate interference by stimulating downstream enzymes with DNase, RNase, protease or other activities. Type III systems are among the most abundant CRISPR systems in prokaryotes and understanding the structure-function relationships that control transcript detection and cOA synthesis will advance the understanding of the broader physiological roles of these systems. Type III systems possess properties well-suited to their deployment as molecule diagnostics: specific detection and activation of a cascade of multi-turnover enzymatic reactions that can be harnessed for signal generation. We determined that Serratia marcescens Cas10-Csm (SmCas10-Csm) synthesizes predominantly cA ₃ molecules and this synthesis is sensitive to mismatches in the crRNA-target RNA duplex adjacent to Cas10. We determined the structure of SmCas10-Csm unbound and bound to target RNA identifying conformational changes associated with target binding. We demonstrate that SmCas10-Csm can distinguish between single nucleotide polymorphisms that occur in the human HBB transcript that are associated with sickle cell disease indicating an additional role for type III CRISPR systems in point-of-care diagnostics in low-resource settings.

Bacteriophages play an important role in the pathogenicity of Staphylococcus aureus , an important human pathogen. Phages are involved in generalized and specialized transduction as well as a more specific process by which they mobilize elements known as phage-inducible chromosomal islands, of which S. aureus pathogenicity islands (SaPIs) are an important group. SaPIs are mobilized at high frequency through interactions with specific “helper” bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from structural proteins supplied by the helper. Among these structural proteins is the portal protein, which forms a ring-like portal at a fivefold vertex of the capsid, through which the DNA is packaged during virion assembly and ejected upon infection of the host. We previously showed that portal protein expressed in E. coli forms tridecameric rings, while portals found in virions are always dodecamers. To understand the role of the portal in capsid assembly, DNA packaging and ejection, we have here examined this phenomenon further. We show that portals assembled at lower temperature form unclosed rings that may represent portal assembly intermediates. By analyzing portal protein deletion mutants, we demonstrate the involvement of the different functional domains in phage assembly and protein incorporation.

Streptococcus pneumoniae is one of the most important human respiratory pathogens worldwide. The increase in antibiotic resistance in S. pneumoniae and other pathogens is a significant public health concern. The streptococcal 70S ribosome is a prime target for antibiotics. Ribosomal protein L27 reaches into the peptidyl transferase center with its extended N-terminus and may be involved in the translation process. We have shown that L27 in Firmicutes, including staphylococci and streptococci, has an additional 9-12 amino acid N-terminal extension compared to Gram-negative organisms like Escherichia coli . The extension is cleaved by a protease called Prp that is absent from organisms that lack the extension. In S. aureus , Prp and the N-terminal extension of L27 are essential. Here, we have characterized the cleavage of L27 by Prp in S. pneumoniae . Prp forms dimers that efficiently cleave L27 in vitro . An inactive form of Prp (PrpC34S) binds to L27 without cleaving, whereas L27 with a mutation (F12A) of the cleavage site does not bind Prp. Overexpression of PrpC34S in vivo is detrimental to S. pneumoniae growth. Surprisingly, a S. pneumoniae Δ prp strain was viable, apparently due to cleavage of L27 by another, unknown protease. Unlike in S. aureus , a mutant strain lacking the N-terminal extension of L27 was viable, but showed impaired growth. Our study sheds light on a process that could be exploited for novel antibiotics, but emphasizes important differences between streptococci and staphylococci. HIGHLIGHTS: Ribosomal protein L27 in S. pneumoniae is N-terminally processed by Prp protease A S. pneumoniae Δ prp mutant is viable, but exhibits impaired growth Cleavage of L27 is required for viability, but the N-terminal extension is not essential In the absence of Prp, L27 is processed by another protease. There are distinct differences in the role of Prp between S. aureus and S. pneumoniae .

Tailed bacteriophages with double-stranded DNA genomes (class Caudoviricetes ) play an important role in the evolution of bacterial pathogenicity, both as carriers of genes encoding virulence factors and as the main means of horizontal transfer of mobile genetic elements (MGEs) in many bacteria, such as Staphylococcus aureus . The S. aureus pathogenicity islands (SaPIs), including SaPI1, are a type of MGEs are that carry a variable complement of genes encoding virulence factors. SaPI1 is mobilized at high frequency by “helper” bacteriophages, such as 80α, leading to packaging of the SaPI1 genome into virions made from structural proteins supplied by the helper. 80α and SaPI1 virions consist of an icosahedral head (capsid) connected via a unique vertex to a long, non-contractile tail. At one end of the tail, proteins associated with the baseplate recognize and bind to the host. At the other end, a connector or “neck” forms the interface between the tail and the head. The neck consists of several specialized proteins with specific roles in DNA packaging, phage assembly, and DNA ejection. Using cryo-electron microscopy and three-dimensional reconstruction, we have determined the high-resolution structure of the neck section of SaPI1 virions made in the presence of phage 80α, including the dodecameric portal (80α gene product (gp) 42) and head-tail-connector (gp49) proteins, the hexameric head-tail joining (gp50) and tail terminator (gp52) proteins, and the major tail protein (gp53) itself. We were also able to resolve the DNA, the tail completion protein (gp51) and the tape measure protein (gp56) inside the tail. This is the first detailed structural description of these features in a bacteriophage, providing insights into the assembly and infection process in this important group of MGEs and their helper bacteriophages.

Staphylococcus aureus is an important human pathogen, and the prevalence of antibiotic resistance is a major public health concern. The evolution of pathogenicity and resistance in S. aureus often involves acquisition of mobile genetic elements (MGEs). Bacteriophages play an especially important role, since transduction represents the main mechanism for horizontal gene transfer. S. aureus pathogenicity islands (SaPIs), including SaPI1, are MGEs that carry genes encoding virulence factors, and are mobilized at high frequency through interactions with specific “helper” bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from structural proteins supplied by the helper. Among these structural proteins is the portal protein, which forms a ring-like portal at a fivefold vertex of the capsid, through which the DNA is packaged during virion assembly and ejected upon infection of the host. We have used high- resolution cryo-electron microscopy to determine structures of the S. aureus bacteriophage 80α portal in solution and in situ in the empty and full SaPI1 virions, and show how the portal interacts with the capsid. These structures provide a basis for understanding portal and capsid assembly and the conformational changes that occur upon DNA packaging and ejection.