Klebsiella serotype-13 capsular polysaccharide: primary structure and depolymerization by a bacteriophage-borne glycanase

Klebsiella pneumoniae K2 capsular polysaccharide degradation by a bacteriophage depolymerase does not require trimer formation

K2-capsular Klebsiella pneumoniae is a hypervirulent pathogen that causes fatal infections. Here, we describe a phage tailspike protein, named K2-2, that specifically depolymerizes the K2 capsular polysaccharide (CPS) of K. pneumoniae into tetrasaccharide repeating units. Nearly half of the products contained O-acetylation, which was thought crucial to the immunogenicity of CPS. The product-bound structures of this trimeric enzyme revealed intersubunit carbohydrate-binding grooves, each accommodating three tetrasaccharide units of K2 CPS. The catalytic residues and the key interactions responsible for K2 CPS recognition were identified and verified by site-directed mutagenesis. Further biophysical and functional characterization, along with the structure of a tetrameric form of K2-2, demonstrated that the formation of intersubunit catalytic center does not require trimerization, which could be nearly completely disrupted by a single-residue mutation in the C-terminal domain. Our findings regarding the assembly and catalysis of K2-2 provide cues for the development of glycoconjugate vaccines against K. pneumoniae infection.

IMPORTANCE

Generating fragments of capsular polysaccharides from pathogenic bacteria with crucial antigenic determinants for vaccine development continues to pose challenges. The significance of the C-terminal region of phage tailspike protein (TSP) in relation to its folding and trimer formation remains largely unexplored. The polysaccharide depolymerase described here demonstrates the ability to depolymerize the K2 CPS of K. pneumoniae into tetrasaccharide fragments while retaining the vital O-acetylation modification crucial for immunogenicity. By carefully characterizing the enzyme, elucidating its three-dimensional structures, conducting site-directed mutagenesis, and assessing the antimicrobial efficacy of the mutant enzymes against K2 K. pneumoniae, we offer valuable insights into the mechanism by which this enzyme recognizes and depolymerizes the K2 CPS. Our findings, particularly the discovery that trimer formation is not required for depolymerizing activity, challenge the current understanding of trimer-dependent TSP activity and highlight the catalytic mechanism of the TSP with an intersubunit catalytic center.

Exploring the enzymatic activity of depolymerase gp531 from Klebsiella pneumoniae jumbo phage RaK2

Klebsiella pneumoniae poses a major global challenge due to its virulence, multidrug resistance, and nosocomial nature. Thus, bacteriophage-derived proteins are extensively being investigated as a means to combat this bacterium. In this study, we explored the enzymatic specificity of depolymerase gp531, encoded by the jumbo bacteriophage vB_KleM_RaK2 (RaK2). We used two different methods to modify the reducing end of the oligosaccharides released during capsule hydrolysis with gp531. Subsequent acidic cleavage with TFA, followed by TLC and HPLC-MS analyses, revealed that RaK2 gp531 is a β-(1→4)-endoglucosidase. The enzyme specifically recognizes and cleaves the capsular polysaccharide (CPS) of the Klebsiella pneumoniae K54 serotype, releasing K-unit monomers (the main product), dimers, and trimers. Depolymerase gp531 remains active from 10 to 50 °C and in the pH 3-8 range, indicating its stability and versatility. Additionally, we demonstrated that gp531's activity is not affected by CPS acetylation, which is influenced by the growth conditions of the bacterial culture. Overall, our findings provide valuable insights into the enzymatic activity of the first characterized depolymerase targeting the capsule of the clinically relevant K54 serotype of K. pneumoniae.

Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation

Klebsiella species are able to colonize a wide range of environments and include worrisome nosocomial pathogens. Here, we sought to determine the abundance and infectivity of prophages of Klebsiella to understand how the interactions between induced prophages and bacteria affect population dynamics and evolution. We identified many prophages in the species, placing these taxa among the top 5% of the most polylysogenic bacteria. We selected 35 representative strains of the Klebsiella pneumoniae species complex to establish a network of induced phage-bacteria interactions. This revealed that many prophages are able to enter the lytic cycle, and subsequently kill or lysogenize closely related Klebsiella strains. Although 60% of the tested strains could produce phages that infect at least one other strain, the interaction network of all pairwise cross-infections is very sparse and mostly organized in modules corresponding to the strains' capsule serotypes. Accordingly, capsule mutants remain uninfected showing that the capsule is a key factor for successful infections. Surprisingly, experiments in which bacteria are predated by their own prophages result in accelerated loss of the capsule. Our results show that phage infectiousness defines interaction modules between small subsets of phages and bacteria in function of capsule serotype. This limits the role of prophages as competitive weapons because they can infect very few strains of the species complex. This should also restrict phage-driven gene flow across the species. Finally, the accelerated loss of the capsule in bacteria being predated by their own phages, suggests that phages drive serotype switch in nature.

Isolation and Characterization of Two Klebsiella pneumoniae Phages Encoding Divergent Depolymerases

The emergence of multidrug-resistant bacteria is a major global health concern. The search for new therapies has brought bacteriophages into the spotlight, and new phages are being described as possible therapeutic agents. Among the bacteria that are most extensively resistant to current antibiotics is Klebsiella pneumoniae, whose hypervariable extracellular capsule makes treatment particularly difficult. Here, we describe two new K. pneumoniae phages, πVLC5 and πVLC6, isolated from environmental samples. These phages belong to the genus Drulisvirus within the family Podoviridae. Both phages encode a similar tail spike protein with putative depolymerase activity, which is shared among other related phages and probably determines their ability to specifically infect K. pneumoniae capsular types K22 and K37. In addition, we found that phage πVLC6 also infects capsular type K13 and is capable of striping the capsules of K. pneumoniae KL2 and KL3, although the phage was not infectious in these two strains. Genome sequence analysis suggested that the extended tropism of phage πVLC6 is conferred by a second, divergent depolymerase. Phage πVLC5 encodes yet another putative depolymerase, but we found no activity of this phage against capsular types other than K22 and K37, after testing a panel of 77 reference strains. Overall, our results confirm that most phages productively infected one or few Klebsiella capsular types. This constitutes an important challenge for clinical applications.

Genomic and Biochemical Characterization of Acinetobacter Podophage Petty Reveals a Novel Lysis Mechanism and Tail-Associated Depolymerase Activity

The increased prevalence of drug-resistant, nosocomial Acinetobacter infections, particularly from pathogenic members of the Acinetobacter calcoaceticus-baumannii complex, necessitates the exploration of novel treatments such as phage therapy. In the present study, we characterized phage Petty, a novel podophage that infects multidrug-resistant Acinetobacter nosocomialis and Acinetobacter baumannii Genome analysis reveals that phage Petty is a 40,431-bp ϕKMV-like phage, with a coding density of 92.2% and a G+C content of 42.3%. Interestingly, the lysis cassette encodes a class I holin and a single-subunit endolysin, but it lacks canonical spanins to disrupt the outer membrane. Analysis of other ϕKMV-like genomes revealed that spaninless lysis cassettes are a feature of phages infecting Acinetobacter within this subfamily of bacteriophages. The observed halo surrounding Petty's large clear plaques indicated the presence of a phage-encoded depolymerase capable of degrading capsular exopolysaccharides (EPS). The product of gene 39, a putative tail fiber, was hypothesized to possess depolymerase activity based on weak homology to previously reported phage tail fibers. The 101.4-kDa protein gene product 39 (gp39) was cloned and expressed, and its activity against Acinetobacter EPS in solution was determined. The enzyme degraded purified EPS from its host strain A. nosocomialis AU0783, reducing its viscosity, and generated reducing ends in solution, indicative of hydrolase activity. Given that the accessibility to cells within a biofilm is enhanced by degradation of EPS, phages with depolymerases may have enhanced diagnostic and therapeutic potential against drug-resistant Acinetobacter strains.IMPORTANCE Bacteriophage therapy is being revisited as a treatment for difficult-to-treat infections. This is especially true for Acinetobacter infections, which are notorious for being resistant to antimicrobials. Thus, sufficient data need to be generated with regard to phages with therapeutic potential, if they are to be successfully employed clinically. In this report, we describe the isolation and characterization of phage Petty, a novel lytic podophage, and its depolymerase. To our knowledge, it is the first phage reported to be able to infect both A. baumannii and A. nosocomialis The lytic phage has potential as an alternative therapeutic agent, and the depolymerase could be used for modulating EPS both during infections and in biofilms on medical equipment, as well as for capsular typing. We also highlight the lack of predicted canonical spanins in the phage genome and confirm that, unlike the rounding of lambda lysogens lacking functional spanin genes, A. nosocomialis cells infected with phage Petty lyse by bursting. This suggests that phages like Petty employ a different mechanism to disrupt the outer membrane of Acinetobacter hosts during lysis.

Two T7-like Bacteriophages, K5-2 and K5-4, Each Encodes Two Capsule Depolymerases: Isolation and Functional Characterization

Two Klebsiella bacteriophages K5-2 and K5-4, which are able to infect and grow on either capsular types K30/K69 and K5 or K8 and K5 of Klebsiella strains, were isolated and characterized. Each phage contained two open reading frames (ORFs), which encoded two putative capsule depolymerases, respectively. The first ORF encoded tail fiber proteins, which have K30/K69 depolymerase and K8 depolymerase activities. The second ORF encoded hypothetical proteins, which are almost identical in amino acid sequences, and have K5 depolymerase activity. Alcian blue staining of enzyme-treated capsular polysaccharides (CPS) showed that purified depolymerases can cleave purified Klebsiella CPS in vitro and liberate monosaccharaides. Capsule K5 deletion mutants were not lysed by either phage, suggesting that the capsule was essential for phage infection. Bacterial killing was observed when incubated Klebsiella strains with phages but not with purified depolymerases. Treatment with the K5-4 phage significantly increased the survival of mice infected with a K. pneumoniae K5 strain. In conclusion, two dual host-specific Klebsiella phages and their tailspikes exhibit capsule depolymerase activity were characterized. Each phage and phage-encoded depolymerase has specificity for capsular type K30/K69, K8 or K5, and could be used for the typing and treatment of K. pneumoniae infection.

Isolation of a bacteriophage specific for a new capsular type of Klebsiella pneumoniae and characterization of its polysaccharide depolymerase

BACKGROUND

Klebsiella pneumoniae is one of the major pathogens causing hospital-acquired multidrug-resistant infections. The capsular polysaccharide (CPS) is an important virulence factor of K. pneumoniae. With 78 capsular types discovered thus far, an association between capsular type and the pathogenicity of K. pneumoniae has been observed.

METHODOLOGY/PRINCIPAL FINDINGS

To investigate an initially non-typeable K. pneumoniae UTI isolate NTUH-K1790N, the cps gene region was sequenced. By NTUH-K1790N cps-PCR genotyping, serotyping and determination using a newly isolated capsular type-specific bacteriophage, we found that NTUH-K1790N and three other isolates Ca0507, Ca0421 and C1975 possessed a new capsular type, which we named KN2. Analysis of a KN2 CPS(-) mutant confirmed the role of capsule as the target recognized by the antiserum and the phage. A newly described lytic phage specific for KN2 K. pneumoniae, named 0507-KN2-1, was isolated and characterized using transmission electron microscopy. Whole-genome sequencing of 0507-KN2-1 revealed a 159 991 bp double-stranded DNA genome with a G+C content of 46.7% and at least 154 open reading frames. Based on its morphological and genomic characteristics, 0507-KN2-1 was classified as a member of the Myoviridae phage family. Further analysis of this phage revealed a 3738-bp gene encoding a putative polysaccharide depolymerase. A recombinant form of this protein was produced and assayed to confirm its enzymatic activity and specificity to KN2 capsular polysaccharides. KN2 K. pneumoniae strains exhibited greater sensitivity to this depolymerase than these did to the cognate phage, as determined by spot analysis.

CONCLUSIONS/SIGNIFICANCE

Here we report that a group of clinical strains possess a novel Klebsiella capsular type. We identified a KN2-specific phage and its polysaccharide depolymerase, which could be used for efficient capsular typing. The lytic phage and depolymerase also have potential as alternative therapeutic agents to antibiotics for treating K. pneumoniae infections, especially against antibiotic-resistant strains.

Bacterial capsular antigens. Structural patterns of capsular antigens

Structural patterns of bacterial capsular antigens including capsular polysaccharides and exoglycans are given in this review. In addition, the immunological activity of capsular antigens and their role in type specificity of bacteria are discussed.

The capsular antigen of Escherichia coli serotype O8:K102:H-

The structure of the capsular antigen of E. coli O8:K102:H- was investigated by methylation analysis, beta-elimination of the methylated polysaccharide, lithium-ethylenediamine mediated degradation, and by 1D and 2D 1H and 13C NMR spectroscopy of the lithium-degraded and native polysaccharides. The capsular antigen was shown to have the following branched pentasaccharide repeating unit: [formula: see text]

The structure of the capsular polysaccharide of Escherichia coli O9:K35:H-

The annexed structure of the capsular polysaccharide of Escherichia coli O9:K35:H- (A104a) has been determined by glycose and methylation analysis, base-catalysed degradation, and 1D and 2D NMR spectroscopy on the polysaccharide and the products obtained by bacteriophage-mediated depolymerisation. [formula: see text]

Structural elucidation of the capsular polysaccharide of E. coli serotype K47

The capsular polysaccharide from Escherichia coli K47 was investigated using mainly methylation analysis and 1H and 13C NMR spectroscopy and shown to have the following repeating unit: [Formula: see text]

Primary structure of Klebsiella serotype K22 capsular polysaccharide: another glycan containing 4-O-[(S)-1-carboxyethyl]-D-glucuronic acid

The primary structure of the acidic capsular polysaccharide isolated from Klebsiella serotype K22 has been investigated using methylation analysis, hydrolysis, bacteriophage-borne enzyme degradation, and n.m.r. spectroscopy. The repeating unit comprises the chain disaccharide----3)-beta-D-Galp-(1----4)-beta-D-Glcp-(1---- substituted by 4-O-[(S)-1-carboxyethyl]-beta-D-GlcpA-(1----6)-alpha-D-Glcp-(1---- at O-4 of the galactose. The galactose carries an O-acetyl group on position 6.

Structural investigation of Klebsiella serotype K10 capsular polysaccharide

The primary structure of Klebsiella serotype K10 capsular polysaccharide has been investigated using mainly the techniques of methylation, partial hydrolysis, and 1H and 13C NMR spectroscopy. The polysaccharide was found to consist of hexasaccharide repeating units having the following structure: (formula; see text)

Studies of the primary structure of the capsular polysaccharide from Klebsiella serotype K15

The capsular polysaccharide of Klebsiella serotype K15 has been investigated mainly by methylation analysis, characterisation of the oligosaccharides obtained by partial acid hydrolysis, periodate oxidation, enzymic degradation, and 1H- and 13C-n.m.r. spectroscopy, and shown to have the hexasaccharide repeating-unit 1. The glycan does not contain any pyruvic acetal or O-acetyl substituents. (formula; see text)

Structural studies on the capsular polysaccharide of Klebsiella serotype K40

The capsular polysaccharide of Klebsiella serotype K40 contained D-mannose, D-glucuronic acid, D-galactose, and L-rhamnose in the approximate molar ratios 1:1:1:2. The primary structure of the capsular polysaccharide has been investigated mainly by methylation analysis, periodate oxidation, characterization of oligosaccharides, base degradation reaction, and 1H and 13CNMR spectroscopy. The polysaccharide does not contain any pyruvic acetal or O-acetyl substitution. It has a pentasaccharide repeating unit of the following primary structure: alpha-D-Manp 1----4 ----4)-beta-D-GlcpA-(1----2)-alpha-L-Rhap-(1----3)-beta-D-Ga lp-(1----2)-alpha- L-Rhap-(1----.

Preparation of oligosaccharides by the action of bacteriophage-borne enzymes on Klebsiella capsular polysaccharides

Depolymerization of bacterial, capsular polysaccharides by viral enzymes provides a convenient method for preparing oligosaccharides that correspond to one or more repeating unit(s) of the polysaccharide. Previous methods used for purifying bacteriophage particles, and also the procedures employed in the isolation and purification of the oligomers generated by the bacteriophage action, have been so modified as to provide a more direct route to the degradation products. Improved techniques, both for the propagation of bacteriophage and for the isolation of the oligosaccharides formed, are reported. These simplified methods make possible the use of bacteriophages as convenient "reagents" for the preparation of oligosaccharides on a gram scale. The acid- and base-labile substituents present in certain of the polysaccharides examined were seemingly unaffected by the conditions used for depolymerization. The methods are illustrated by degradation of the capsular polysaccharides from Klebsiella serotypes K17, K36, K46, K60, K63, and K74

Structural investigation of Klebsiella K-type 4 capsular polysaccharide

The capsular polysaccharide from Klebsiella K4 contains the tetrasaccharide repeating-sequence leads to 3)-alpha-D-Glcp-(1 leads to 2)-alpha-D-Glcp A-(1 leads to 3)-alpha-D-Manp-(1 leads to 3)-beta-D-Glcp-(1 leads to. P.m.r. spectroscopy and the measurement of optical rotation were used to establish the anomeric linkages in the polysaccharide and in the oligosaccharides derived by partial hydrolysis. The repeating unit also contains one 0-acetyl group.

Substrate specificity of the glycanase activity associated with particles of Klebsiella bacteriophage no. 6

A glycanase activity associated with the particles of Klebsiella bacteriophage No. 6 catalyses cleavage of O-beta-D-glycopyranosyl-(1 leads to 3)-4,6-O-(1-carboxyethylidene)-beta-D-mannopyranose linkages in Klebsiella serotype-6 capsular polysaccharide. Of 74 heterologous Klebsiella polysaccharides and two derivatives of the type-6 glycan, only the type-1 and type-57 polymers were additionally degraded by the phage-6 enzyme. The repeating units in the three substrates have a 1ax leads to 3eq, 1eq leads to eq-linked chain D-gluco- or D-galacto-pyranosyl residue in common (which constitutes the reducing end after glycanase action), and a carboxyl group on the next hexopyranosyl residue. Of the 72 polysaccharides not affected by the viral enzyme, at least the type-11 and type-21 glycans also contain the same homology of primary structure. This indicates that the conformation at the glycanase recognition-site also constitutes an important feature of the substrates.

Primary structure of the Escherichia coli serotype K30 capsular polysaccharide

Methylation, 1H nuclear magnetic resonance, and bacteriophage degradation results indicate that the Escherichia coli serotype K30 capsular polysaccharide consists of leads to 2)-alpha-D-Manp-(1 leads to 3)-beta-D-Galp-(1 leads to chains carrying beta-D-GlcUAp-(1 leads to 3)-alpha-D-Galp-(1 leads to branches at position 3 of the mannoses.

Structure of Klebsiella type 61 capsular polysaccharide

An aldotriouronic acid was isolated from the acid hydrolyzate of the polysaccharide from Klebsiella Type 61 (K-61), and its structure was established. Degradation of the permethylated polysaccharide with base established the identity of the sugar unit preceding the glucosyluronic acid residue. The modes of linkage and the sequence of different sugar residues were further confirmed by Smith degradation of K-61. The anomeric configurations of the different sugar residues were determined by oxidation of peracetylated native, and carboxyl-reduced, polysaccharides with chromium trioxide. The anomeric configuration of nonreducing D-galactosyl side-chains was further confirmed by enzymic degradation of K-61. Finally, gentiobiose was identified in the partial, acid hydrolyzate of K-61. Based on these results, the structure assigned the repeating unit of K-61 was as follows.

Structural studies on the capsular polysaccharide from Klebsiella serotype K64

Partial hydrolysis with acid, methylation analysis (including uronic acid degradation), Smith degradation, and p.m.r. spectroscopy have been used to determine the primary structure of the capsular polysaccharide of Klebsiella serotype K64. The hexasaccharide repeating-unit, which also contains one O-acetyl substituent, comprises a 4)-alpha-D-GlcpA-(1 leads to 3)-alpha-D-Manp-(1 leads to 3)-beta-D-Glcp-(1 leads to 4)-alpha-D-Manp-(1 leads to chain with a 4,6-O-(1-carboxyethylidene)-beta-D-glucopyranosyl and an L-rhamnosyl group attached to the 4-linked D-mannosyl residue at 0-2 and 0-3, respectively.

Structural studies of the capsular polysaccharide of Klebsiella type 33

The structure of the capsular polysaccharide from Klebsiella type 33 has been investigated. Methylation analysis, various specific degradations, graded hydrolysis with acid, and n.m.r. spectroscopy were the principal methods used. It is concluded that the polysaccharide is composed of pentasaccharide repeating-units having the following structure. (formula, see manual). The D-galactopyranosyl group, with pyruvic acid linked as a ketal to O-3 AND O-4, was degraded on treatment of the fully methylated polysaccharide with strong base. It is proposed that methyl pyruvate is eliminated, in an E2 type of reaction.

[Occurrence of pyruvic acid in capsular polysaccharides (K antigens) of klebsiellas]

The capsular polysaccharides of 77 Klebsiella K-types were analysed for the presence of pyruvic acid. One half of the polysaccharides investigated were found to contain between 1.3 and 12% of the keto acid. A comparison between the analyses performed and the calculated values from some pyruvic acid containing polysaccharides of known structure showed that there is only in 5 out of 10 cases a good correlation with a regular substitution of the oligosaccharide repeating units.

More on cross-reactions of Pneumococci and Klebsiella

Earlier studies are extended to the higher-numbered K-types of Klebsiella, several of which may now be fitted into the previously found groups. Additional correlations between chemical structure and serological specificity are given, not only among the higher K-types, but also for several which were previously uninterpretable because structures were not known at the time. K1, K5, K6, K7 and K56 are shown to form a related group, although the reasons for their cross-reactivities are not always the same.