Streptococcus agalactiae capsule polymer length and attachment is determined by the proteins CpsABCD

A group B Streptococcus indexed transposon mutant library to accelerate genetic research on an important perinatal pathogen

IMPORTANCE

Group B Streptococcus (GBS) is a significant global cause of serious infections, most of which affect pregnant women, newborns, and infants. Studying GBS genetic mutant strains is a valuable approach for learning more about how these infections are caused and is a key step toward developing more effective preventative and treatment strategies. In this resource report, we describe a newly created library of defined GBS genetic mutants, containing over 1,900 genetic variants, each with a unique disruption to its chromosome. An indexed library of this scale is unprecedented in the GBS field; it includes strains with mutations in hundreds of genes whose potential functions in human disease remain unknown. We have made this resource freely available to the broader research community through deposition in a publicly funded bacterial maintenance and distribution repository.

Long-term surveillance of group B Streptococcus strains isolated from infection and colonization in pregnant women and newborns

Introduction. Group B Streptococcus (GBS) remains the leading cause of bacterial neonatal infections worldwide, despite the spread of recommendations on vaginal screening and antibiotic prophylaxis.Hypothesis/Gap Statement. There is a need to evaluate the potential changes in GBS epidemiology over time following the introduction of such guidelines.Aim. Our aim was to perform a descriptive analysis of the epidemiological characteristics of GBS by conducting a long-term surveillance of strains isolated between 2000 and 2018, using molecular typing methods.Methodology. A total of 121 invasive strains, responsible for maternal infections (20 strains), fetal infections (8 strains) and neonatal infections (93 strains), were included in the study, representing all the invasive isolates during the period; in addition, 384 colonization strains isolated from vaginal or newborn samples were randomly selected. The 505 strains were characterized by capsular polysaccharide (CPS) type multiplex PCR assay and the clonal complex (CC) was assigned using a single nucleotide polymorphism PCR assay. Antibiotic susceptibility was also determined.Results. CPS types III (32.1 % of the strains), Ia (24.6 %) and V (19 %) were the most prevalent. The five main CCs observed were CC1 (26.3 % of the strains), CC17 (22.2 %), CC19 (16.2 %), CC23 (15.8 %) and CC10 (13.9 %). Neonatal invasive GBS diseases were predominantly due to CC17 isolates (46.3 % of the strains), which mainly express CPS type III (87.5 %), with a very high prevalence in late-onset diseases (76.2 %).Conclusion. Between 2000 and 2018, we observed a decrease in the proportion of CC1 strains, which mainly express CPS type V, and an increase in the proportion of CC23 strains, mainly expressing CPS type Ia. Conversely, there was no significant change in the proportion of strains resistant to macrolides, lincosamides or tetracyclines. The two molecular techniques used in our study provide almost as much information as classical serotyping and multilocus sequence typing, but are quicker, easy to perform, and avoid long sequencing and analysis steps.

Studying the effect of gene fusion of A and C types capsular synthesizing enzymes and anticancer sequence on inducing the expression of apoptotic BCL-2, BAX, and Caspase-3 genes by Real-time RT-PCR method

Background

Today, uterine cancer is one of the most important causes of death in the world and is one of the major problems in human health. There have been numerous reports of the effect of Streptococcus agalactiae peptide and capsular products against cancer cell lines. Objective: This study aimed to research recombinant peptide CPSA-CPSC-L-ACAN and investigate its apoptotic effect against the HeLa cell line by Real-Time-RT PCR.

Design

In this study confirmation of the recombinant fusion peptide was performed by Western blotting. The effect of cytotoxicity of different concentrations of recombinant fusion peptide against the HeLa cell line was investigated by the MTT technique. The expression of apoptotic genes including BAX, BCL-2, and Caspase-3 in comparison with the GAPDH reference gene before and after exposure to recombinant fusion peptide was measured by Real-Time RT-PCR.

Results

Recombinant fusion peptide at a concentration of 63 μg/ml destroyed 50% of the HeLa cell line in 24 h and cell treatment with this concentration increased gene expression of Caspase-3 genes by 16 times, bax by 6 times and decreased the expression of bcl-2 by 0.176 times.

Conclusions

The results showed that treatment of the HeLa cell line with recombinant fusion peptide induced an apoptotic effect. The recombinant fusion peptide could probably help the medical community as a prophylactic or therapeutic treatment for cervical cancer.

A link between STK signalling and capsular polysaccharide synthesis in Streptococcus suis

Synthesis of capsular polysaccharide (CPS), an important virulence factor of pathogenic bacteria, is modulated by the CpsBCD phosphoregulatory system in Streptococcus. Serine/threonine kinases (STKs, e.g. Stk1) can also regulate CPS synthesis, but the underlying mechanisms are unclear. Here, we identify a protein (CcpS) that is phosphorylated by Stk1 and modulates the activity of phosphatase CpsB in Streptococcus suis, thus linking Stk1 to CPS synthesis. The crystal structure of CcpS shows an intrinsically disordered region at its N-terminus, including two threonine residues that are phosphorylated by Stk1. The activity of phosphatase CpsB is inhibited when bound to non-phosphorylated CcpS. Thus, CcpS modulates the activity of phosphatase CpsB thereby altering CpsD phosphorylation, which in turn modulates the expression of the Wzx-Wzy pathway and thus CPS production.

The Space Environment Activates Capsular Polysaccharide Production in Lacticaseibacillus rhamnosus Probio-M9 by Mutating the wze (ywqD) Gene

The study of microorganisms in outer space has focused mainly on investigating phenotypic changes in microbial pathogens induced by factors encountered in space. This study aimed to investigate the effect of space exposure on a probiotic bacterium, Lacticaseibacillus rhamnosus Probio-M9. Probio-M9 cells were exposed to space in a spaceflight. Interestingly, our results showed that a substantial proportion of space-exposed mutants (35/100) exhibited a ropy phenotype, characterized by their larger colony sizes and an acquired ability to produce capsular polysaccharide (CPS), compared with the original Probio-M9 or the ground control isolates without space exposure. Whole-genome sequencing analyses on both the Illumina and PacBio platforms revealed a skewed distribution of single nucleotide polymorphisms (12/89 [13.5%]) toward the CPS gene cluster, particularly in the wze (ywqD) gene. The wze gene encodes a putative tyrosine-protein kinase that regulates CPS expression through substrate phosphorylation. Transcriptomics analysis of two space-exposed ropy mutants revealed increased expression in the wze gene relative to a ground control isolate. Finally, we showed that the acquired ropy phenotype (CPS-producing ability) and space-induced genomic changes could be stably inherited. Our findings confirmed that the wze gene directly influences the capacity for CPS production in Probio-M9, and space mutagenesis is a potential strategy for inducing stable physiological changes in probiotics. IMPORTANCE This work investigated the effect of space exposure on a probiotic bacterium, Lacticaseibacillus rhamnosus Probio-M9. Interestingly, the space-exposed bacteria became capable of producing capsular polysaccharide (CPS). Some probiotic-derived CPSs have nutraceutical potential and bioactive properties. They also enhance the survival of probiotics through the gastrointestinal transit and ultimately strengthen the probiotic effects. Space mutagenesis seems to be a promising strategy for inducing stable changes in probiotics, and the obtained high-CPS-yielding mutants are valuable resources for future applications.

Virulence factors of Streptococcus anginosus - a molecular perspective

Streptococcus anginosus together with S. constellatus and S. intermedius constitute the Streptococcus anginosus group (SAG), until recently considered to be benign commensals of the human mucosa isolated predominantly from oral cavity, but also from upper respiratory, intestinal, and urogenital tracts. For years the virulence potential of SAG was underestimated, mainly due to complications in correct species identification and their assignment to the physiological microbiota. Still, SAG representatives have been associated with purulent infections at oral and non-oral sites resulting in abscesses formation and empyema. Also, life threatening blood infections caused by SAG have been reported. However, the understanding of SAG as potential pathogen is only fragmentary, albeit certain aspects of SAG infection seem sufficiently well described to deserve a systematic overview. In this review we summarize the current state of knowledge of the S. anginosus pathogenicity factors and their mechanisms of action.

CRISPR Contributes to Adhesion, Invasion, and Biofilm Formation in Streptococcus agalactiae by Repressing Capsular Polysaccharide Production

The clustered regularly interspaced palindromic repeat (CRISPR)-associated (Cas) system functions classically as a prokaryotic defense system against invading mobile genetic elements, such as phages, plasmids, and viruses. Our previous study revealed that CRISPR deletion caused increased transcription of capsular polysaccharide (CPS) synthesis-related genes and severely attenuated virulence in the hypervirulent piscine Streptococcus agalactiae strain GD201008-001. Here, we found that CRISPR deficiency resulted in reduced adhesion, invasion, and biofilm formation abilities in this strain by upregulating the production of CPS. However, enhanced CPS production was not responsible for the attenuated phenotype of the ΔCRISPR mutant. RNA degradation assays indicated that inhibited transcription of the cps operon by CRISPR RNA (crRNA) was not due to the base pairing of the crRNA with the cps mRNA but to the repression of the promoter activity of cpsA, which is a putative transcriptional regulator of the capsule locus. IMPORTANCE Beyond protection from invading nucleic acids, CRISPR-Cas systems have been shown to have an important role in regulating bacterial endogenous genes. In this study, we demonstrate that crRNA inhibits the transcription of the cps operon by repressing the activity of promoter PcpsA, leading to increases in the abilities of adhesion, invasion, and biofilm formation in S. agalactiae. This study highlights the regulatory role of crRNA in bacterial physiology and provides a new explanation for the mechanism of crRNA-mediated endogenous gene regulation in S. agalactiae.

The LCP Family Protein, Psr, Is Required for Cell Wall Integrity and Virulence in Streptococcus agalactiae

A robust cell envelope is the first line of protection for an infecting pathogen when encountering the immune defense of its host. In Gram-positive organisms, LytR-CpsA-Psr (LCP) family proteins play a major role in the synthesis and assembly of the cell envelope. While these proteins could be considered for potential new drug targets, not enough is known about how they function to support the integrity of the cell wall. Streptococcus agalactiae (group B streptococcus or GBS) is known to encode at least three LCP family proteins, including CpsA, LytR (BrpA) and Psr. Using strains of GBS that have mutations in two of the three LCP proteins, we were able to determine a role for these proteins in GBS cell wall integrity. The results presented here demonstrate that the absence of Psr results in a decreased growth rate, decreased viability over time, inconsistent cocci morphology and diminished cell wall integrity, as well as an increased penicillin susceptibility, decreased capsule levels and attenuation in virulence in a zebrafish model of infectious disease. A strain that is missing two of the LCP family proteins, CpsA and Psr, exhibits an increase in these defective phenotypes, indicating that CpsA and Psr are partially redundant in function.

The bacterial tyrosine kinase system CpsBCD governs the length of capsule polymers

Many pathogenic bacteria are encased in a layer of capsular polysaccharide (CPS). This layer is important for virulence by masking surface antigens, preventing opsonophagocytosis, and avoiding mucus entrapment. The bacterial tyrosine kinase (BY-kinase) regulates capsule synthesis and helps bacterial pathogens to survive different host niches. BY-kinases autophosphorylate at the C-terminal tyrosine residues upon external stimuli, but the role of phosphorylation is still unclear. Here, we report that the BY-kinase CpsCD is required for growth in Streptococcus pneumoniae Cells lacking a functional cpsC or cpsD accumulated low molecular weight CPS and lysed because of the lethal sequestration of the lipid carrier undecaprenyl phosphate, resulting in inhibition of peptidoglycan (PG) synthesis. CpsC interacts with CpsD and the polymerase CpsH. CpsD phosphorylation reduces the length of CPS polymers presumably by controlling the activity of CpsC. Finally, pulse-chase experiments reveal the spatiotemporal coordination between CPS and PG synthesis. This coordination is dependent on CpsC and CpsD. Together, our study provides evidence that BY-kinases regulate capsule polymer length by fine-tuning CpsC activity through autophosphorylation.

Proteomic analysis capsule synthesis and redox mechanisms in the intracellular survival of group B Streptococcus in fish microglia

Group B Streptococcus (GBS) causes meningitis in neonates and Nile tilapia (Oreochromis niloticus). The molecular mechanisms regulating the intracellular survival of this pathogen in the host cell are complex and crucial for the progression of infection. Thus, we propose the use of GBS-infected Nile tilapia microglia as an in vitro model system simulating infection caused by homologous bacteria in humans. We used this model to evaluate the phagocytic activity, as well as the functional aspects of the capsular proteins A, B, C, and D and the major redox enzymes, and the synergistic role of mechanisms/proteins involved in blocking phagocytic process. We observed that in the intracellular phase, GBS showed enhanced synthesis of the polysaccharide capsule and used superoxide dismutase, thioredoxin, NADH oxidase, and alkyl hydroperoxide reductase to scavenge reactive oxygen species and reactive nitrogen species produced by the host cell. Furthermore, although these virulence mechanisms were effective during the initial hours of infection, they were not able to subvert microglial responses, which partially neutralized the infection. Altogether, our findings provided important information regarding the intracellular survival mechanisms of GBS and perspectives for the production of new drugs and vaccines, through the druggability analysis of specific proteins. In conclusion, tilapia microglia serve as a potent in vitro experimental model for the study of meningitis.

Distribution of virulence determinants in Streptococcus agalactiae recovered from different clinical sources

Streptococcus agalactiae (group B Streptococcus, GBS) is a pathobiont, a member of human microbiota that can change from commensal to pathogen, causing a large spectrum of diseases. This study assessed virulence determinants of 32 GBS isolates recovered from different clinical sources associated with asymptomatic and symptomatic clinical outcomes that present distinct capsular types and antimicrobial resistance profiles. The ability of a unique strain to colonize and cause infection in different subjects was also evaluated. By PFGE analysis, it was observed that a given strain could be associated with both asymptomatic and symptomatic outcomes. Cell wall anchor proteins β and alpha C encoding genes (bac and bca, respectively) were detected in all capsular type Ib isolates. bca was more frequent among asymptomatic outcome-related isolates, as well as high expression of β-hemolysin/cytolysin (β-H/C). Symptomatic outcome-related isolates produced strong biofilm more frequently. All bacterial isolates recovered from urine were strong biofilm producers. In growth experiments, asymptomatic outcome-related isolates grew faster after 2 h until the end of the log phase. Taken together, these findings show virulence genotypic and phenotypic features of GBS from distinct sources, which may be helpful to understand their pathogenic potential and predict different clinical outcomes.

Homologous Over-Expression of Chain Length Determination Protein EpsC Increases the Molecular Weight of Exopolysaccharide in Streptococcus thermophilus 05-34

In Streptococcus thermophilus, EpsC is a polysaccharide co-polymerase which is involved in determining the chain length of EPS synthesized by the Wzx/Wzy-dependent pathway. Our previous study found that there was a positive correlation between transcription level of epsC and molecular weight of EPS in S. thermophilus 05-34. To further investigate the effects of EpsC on EPS biosynthesis, this gene was over-expressed in S. thermophilus 05-34 in this study. Reverse transcription qPCR and Western blotting confirmed the successful transcription and translation of epsC in 05-34, respectively. The yield of EPS was not affected by the over-expression of EpsC. Gas chromatography-mass spectrometry (GC-MS) showed that the monosaccharide composition was still composed of galactose and glucose in a molar ratio of 1.0:0.8, whereas high performance gel permeation chromatography (HPGPC) indicated that the molecular weight of EPS was increased from 4.62 × 10⁵ Da to 9.17 × 10⁵ Da by the over-expression of EpsC. In addition, S. thermophilus 05epsC which could produce higher molecular weight EPS improved the viscoelasticity and water-holding capacity of yogurt, but significantly reduced the level of syneresis in yogurt. In summary, these results indicated that homologous over-expression of EpsC in S. thermophilus could increase the molecular weight of EPS and improve the microrheological or physical properties of yogurt.

The surprising structural and mechanistic dichotomy of membrane-associated phosphoglycosyl transferases

Phosphoglycosyl transferases (PGTs) play a pivotal role at the inception of complex glycoconjugate biosynthesis pathways across all domains of life. PGTs promote the first membrane-committed step in the en bloc biosynthetic strategy by catalyzing the transfer of a phospho-sugar from a nucleoside diphospho-sugar to a membrane-resident polyprenol phosphate. Studies on the PGTs have been hampered because they are integral membrane proteins, and often prove to be recalcitrant to expression, purification and analysis. However, in recent years exciting new information has been derived on the structures and the mechanisms of PGTs, revealing the existence of two unique superfamilies of PGT enzymes that enact catalysis at the membrane interface. Genome neighborhood analysis shows that these superfamilies, the polytopic PGT (polyPGT) and monotopic PGT (monoPGT), may initiate different pathways within the same organism. Moreover, the same fundamental two-substrate reaction is enacted through two different chemical mechanisms with distinct modes of catalysis. This review highlights the structural and mechanistic divergence between the PGT enzyme superfamilies and how this is reflected in differences in regulation in their varied glycoconjugate biosynthesis pathways.

Mammary microbial dysbiosis leads to the zoonosis of bovine mastitis: a One-Health perspective

Bovine mastitis is a prototypic emerging and reemerging bacterial disease that results in cut-by-cut torture to animals, public health and the global economy. Pathogenic microbes causing mastitis have overcome a series of hierarchical barriers resulting in the zoonotic transmission from bovines to humans either by proximity or remotely through milk and meat. The disease control is challenging and has been attributed to faulty surveillance systems to monitor their emergence at the human-animal interface. The complex interaction between the pathogens, the hidden pathobionts and commensals of the bovine mammary gland that create a menace during mastitis remains unexplored. Here, we review the zoonotic potential of these pathogens with a primary focus on understanding the interplay between the host immunity, mammary ecology and the shift from symbiosis to dysbiosis. We also address the pros and cons of the current management strategies and the extent of the success in implementing the One-Health approach to keep these pathogens at bay.

LytR-CpsA-Psr Glycopolymer Transferases: Essential Bricks in Gram-Positive Bacterial Cell Wall Assembly

The cell walls of Gram-positive bacteria contain a variety of glycopolymers (CWGPs), a significant proportion of which are covalently linked to the peptidoglycan (PGN) scaffolding structure. Prominent CWGPs include wall teichoic acids of Staphylococcus aureus, streptococcal capsules, mycobacterial arabinogalactan, and rhamnose-containing polysaccharides of lactic acid bacteria. CWGPs serve important roles in bacterial cellular functions, morphology, and virulence. Despite evident differences in composition, structure and underlaying biosynthesis pathways, the final ligation step of CWGPs to the PGN backbone involves a conserved class of enzymes-the LytR-CpsA-Psr (LCP) transferases. Typically, the enzymes are present in multiple copies displaying partly functional redundancy and/or preference for a distinct CWGP type. LCP enzymes require a lipid-phosphate-linked glycan precursor substrate and catalyse, with a certain degree of promiscuity, CWGP transfer to PGN of different maturation stages, according to in vitro evidence. The prototype attachment mode is that to the C6-OH of N-acetylmuramic acid residues via installation of a phosphodiester bond. In some cases, attachment proceeds to N-acetylglucosamine residues of PGN-in the case of the Streptococcus agalactiae capsule, even without involvement of a phosphate bond. A novel aspect of LCP enzymes concerns a predicted role in protein glycosylation in Actinomyces oris. Available crystal structures provide further insight into the catalytic mechanism of this biologically important class of enzymes, which are gaining attention as new targets for antibacterial drug discovery to counteract the emergence of multidrug resistant bacteria.

Genome reanalysis to decipher resistome, virulome, and attenuated characters of attenuated Streptococcus agalactiae strain HZAUSC001

Streptococcus agalactiae is a serious pathogen causing severe anthropozoonosis in a broad range of hosts, from aquatic animals to mammals, including humans. S. agalactiae HZAUSC001 was isolated from a moribund tilapia fish exhibiting classic clinical symptoms of streptococcosis in Zhanjiang, Guangdong, China. And it was identified as the etiological factor resulting in fish disease, but was notable because it exhibited attenuated virulence. Here, the genome of S. agalactiae HZAUSC001 was re-analyzed; we assessed the resistome and virulome and deciphered the attenuated characters of HZAUSC001. The S. agalactiae HZAUSC001 genome was assembled into one chromosome with a GC-content of 35.37% and 1972 predicted open reading frames (ORFs). Phylogenetic analysis indicated that it is evolutionarily similar to piscine GBS strains GD201008-001 and ZQ0910. After re-analyzing the published genomic sequence of HZAUSC001, we identified 38 virulence factor genes and one antibiotic-resistance gene. Note that three previously noted virulence genes, bca (C protein alpha-antigen), cpbA (choline-binding protein A) and esp (enterococcal surface protein), were absent in the virulence-attenuated strain S. agalactiae HZAUSC001 but present in the highly virulent strain S. agalactiae GD201008-001. We speculate that the absence of these three virulence genes may be associated with the attenuated traits of the HZAUSC001 strain. Collectively, our study supports that HZAUSC001 may be an excellent candidate for development of an attenuated vaccine, and our results contribute to further understanding of GBS epidemiology and surveillance targets.

Streptococcus agalactiae in pregnant women: serotype and antimicrobial susceptibility patterns over five years in Eastern Sicily (Italy)

Streptococcus agalactiae (also known Group B Streptococcus or GBS) represents the main pathogen responsible for early- and late-onset infections in newborns. The present study aimed to determine the antimicrobial susceptibility pattern and the capsular serotypes of GBS isolated in Eastern Sicily over 5 years, from January 2015 to December 2019. A total of 3494 GBS were isolated from vaginal swabs of pregnant women (37–39 weeks), as recommended by the Centers for Disease Control and Prevention. Capsular polysaccharide’s typing of GBS was determined by a commercial latex agglutination test containing reagents to serotypes I–IX. The antimicrobial resistance pattern of GBS was determined through the disk diffusion method (Kirby-Bauer) and the double-disk diffusion test on Mueller-Hinton agar plates supplemented with 5% defibrinated sheep blood, according to the guidelines of the Clinical and Laboratory Standards Institute. Serotypes III (1218, 34.9%) and V (1069, 30.6%) were the prevalent colonizers, followed by not typable (570, 16.3%) and serotypes Ia (548, 15.7%), Ib (47, 1.3%), II (40, 1.1%), and IV (2, 0.1%). All 3494 clinical isolates were susceptible to cefditoren and vancomycin. Resistance to penicillin, ampicillin, levofloxacin, clindamycin, and erythromycin was observed in 6 (0.2%), 5 (0.1%), 161 (4.6%), 1090 (31.2%), and 1402 (40.1%) of the strains, respectively. Most of erythromycin-resistant GBS (1090/1402) showed the cMLS_B phenotype, 276 the M phenotype, and 36 the iMLS_B phenotype. Our findings revealed a higher prevalence of serotype III and a relevant resistance rate, among GBS strains, to the most frequently used antibiotics in antenatal screening.

Assembly of Bacterial Capsular Polysaccharides and Exopolysaccharides

Polysaccharides are dominant features of most bacterial surfaces and are displayed in different formats. Many bacteria produce abundant long-chain capsular polysaccharides, which can maintain a strong association and form a capsule structure enveloping the cell and/or take the form of exopolysaccharides that are mostly secreted into the immediate environment. These polymers afford the producing bacteria protection from a wide range of physical, chemical, and biological stresses, support biofilms, and play critical roles in interactions between bacteria and their immediate environments. Their biological and physical properties also drive a variety of industrial and biomedical applications. Despite the immense variation in capsular polysaccharide and exopolysaccharide structures, patterns are evident in strategies used for their assembly and export. This review describes recent advances in understanding those strategies, based on a wealth of biochemical investigations of select prototypes, supported by complementary insight from expanding structural biology initiatives. This provides a framework to identify and distinguish new systems emanating from genomic studies.

A Diverse Repertoire of Exopolysaccharide Biosynthesis Gene Clusters in Lactobacillus Revealed by Comparative Analysis in 106 Sequenced Genomes

Production of exopolysaccharides (EPS) is one of the unique features of Lactobacillus genus. EPS not only have many physiological roles such as in stress tolerance, quorum sensing and biofilm formation, but also have numerous applications in the food and pharmaceutical industries. In this study, we identified and compared EPS biosynthesis gene clusters in 106 sequenced Lactobacillus genomes representing 27 species. Of the 146 identified clusters, only 41 showed the typical generic organization of genes as reported earlier. Hierarchical clustering showed highly varied nature of the clusters in terms of the gene composition; nonetheless, habitat-wise grouping was observed for the gene clusters from host-adapted and nomadic strains. Of the core genes required for EPS biosynthesis, epsA, B, C, D and E showed higher conservation, whereas gt, wzx and wzy showed high variability in terms of the number and composition of the protein families. Analysis of the distribution pattern of the protein families indicated a higher proportion of mutually exclusive families in clusters from host-adapted and nomadic strains, whereas those from the free-living group had very few unique families. Taken together, this analysis highlights high variability in the EPS gene clusters amongst Lactobacillus with some of their properties correlated to the habitats.

Targeted isolation and cultivation of uncultivated bacteria by reverse genomics

Most microorganisms from all taxonomic levels are uncultured. Single-cell genomes and metagenomes continue to increase the known diversity of Bacteria and Archaea, but while ‘omics can be used to infer physiological or ecological roles for species in a community, most of those hypothetical roles remain unvalidated. Here we report an approach to capture specific microorganisms from complex communities into pure cultures using genome-informed antibody engineering. We apply our reverse genomics approach to isolate and sequence single cells and to cultivate three different species-level lineages of human oral Saccharibacteria/TM7. Using our pure cultures we show that all three saccharibacteria species are epibionts of diverse Actinobacteria. We also isolate and cultivate human oral SR1 bacteria, which are members of a lineage of previously uncultured bacteria. Reverse-genomics-enabled cultivation of microorganisms can be applied to any species from any environment and has the potential to unlock the isolation, cultivation and characterization of species from as-yet-uncultured branches of the microbial tree of life.

Porphyromonas gingivalis Tyrosine Phosphatase Php1 Promotes Community Development and Pathogenicity

Protein-tyrosine phosphorylation in bacteria plays a significant role in multiple cellular functions, including those related to community development and virulence. Metal-dependent protein tyrosine phosphatases that belong to the polymerase and histindinol phosphatase (PHP) family are widespread in Gram-positive bacteria. Here, we show that Porphyromonas gingivalis, a Gram-negative periodontal pathogen, expresses a PHP protein, Php1, with divalent metal ion-dependent tyrosine phosphatase activity. Php1 tyrosine phosphatase activity was attenuated by mutation of conserved histidine residues that are important for the coordination of metal ions and by mutation of a conserved arginine residue, a key residue for catalysis in other bacterial PHPs. The php1 gene is located immediately downstream of the gene encoding the bacterial tyrosine (BY) kinase Ptk1, which was a substrate for Php1 in vitro Php1 rapidly caused the conversion of Ptk1 to a state of low tyrosine phosphorylation in the absence of discernible intermediate phosphoforms. Active Php1 was required for P. gingivalis exopolysaccharide production and for community development with the antecedent oral biofilm constituent Streptococcus gordonii under nutrient-depleted conditions. In contrast, the absence of Php1 had no effect on the ability of P. gingivalis to form monospecies biofilms. In vitro, Php1 enzymatic activity was resistant to the effects of the streptococcal secreted metabolites pABA and H2O2, which inhibited Ltp1, an enzyme in the low-molecular-weight (LMW) phosphotyrosine phosphatase family. Ptk1 reciprocally phosphorylated Php1 on tyrosine residues 159 and 161, which independently impacted phosphatase activity. Loss of Php1 rendered P. gingivalis nonvirulent in an animal model of periodontal disease. Collectively, these results demonstrate that P. gingivalis possesses active PHP and LMW tyrosine phosphatases, a unique configuration in Gram-negatives which may allow P. gingivalis to maintain phosphorylation/dephosphorylation homeostasis in multispecies communities. Moreover, Php1 contributes to the pathogenic potential of the organism.IMPORTANCE Periodontal diseases are among the most common infections of humans and are also associated with systemic inflammatory conditions. Colonization and pathogenicity of P. gingivalis are regulated by signal transduction pathways based on protein tyrosine phosphorylation and dephosphorylation. Here, we identify and characterize a novel component of the tyrosine (de)phosphorylation axis: a polymerase and histindinol phosphatase (PHP) family enzyme. This tyrosine phosphatase, designated Php1, was required for P. gingivalis community development with other oral bacteria, and in the absence of Php1 activity P. gingivalis was unable to cause disease in a mouse model of periodontitis. This work provides significant insights into the protein tyrosine (de)phosphorylation network in P. gingivalis, its adaptation to heterotypic communities, and its contribution to colonization and virulence.

Coordination of capsule assembly and cell wall biosynthesis in Staphylococcus aureus

The Gram-positive cell wall consists of peptidoglycan functionalized with anionic glycopolymers, such as wall teichoic acid and capsular polysaccharide (CP). How the different cell wall polymers are assembled in a coordinated fashion is not fully understood. Here, we reconstitute Staphylococcus aureus CP biosynthesis and elucidate its interplay with the cell wall biosynthetic machinery. We show that the CapAB tyrosine kinase complex controls multiple enzymatic checkpoints through reversible phosphorylation to modulate the consumption of essential precursors that are also used in peptidoglycan biosynthesis. In addition, the CapA1 activator protein interacts with and cleaves lipid-linked CP precursors, releasing the essential lipid carrier undecaprenyl-phosphate. We further provide biochemical evidence that the subsequent attachment of CP is achieved by LcpC, a member of the LytR-CpsA-Psr protein family, using the peptidoglycan precursor native lipid II as acceptor substrate. The Ser/Thr kinase PknB, which can sense cellular lipid II levels, negatively controls CP synthesis. Our work sheds light on the integration of CP biosynthesis into the multi-component Gram-positive cell wall.

The Double Life of Group B Streptococcus: Asymptomatic Colonizer and Potent Pathogen

Group B streptococcus (GBS) is a β-hemolytic gram-positive bacterium that colonizes the lower genital tract of approximately 18% of women globally as an asymptomatic member of the gastrointestinal and/or vaginal flora. If established in other host niches, however, GBS is highly pathogenic. During pregnancy, ascending GBS infection from the vagina to the intrauterine space is associated with preterm birth, stillbirth, and fetal injury. In addition, vertical transmission of GBS during or after birth results in life-threatening neonatal infections, including pneumonia, sepsis, and meningitis. Although the mechanisms by which GBS traffics from the lower genital tract to vulnerable host niches are not well understood, recent advances have revealed that many of the same bacterial factors that promote asymptomatic vaginal carriage also facilitate dissemination and virulence. Furthermore, highly pathogenic GBS strains have acquired unique factors that enhance survival in invasive niches. Several host factors also exist that either subdue GBS upon vaginal colonization or alternatively permit invasive infection. This review summarizes the GBS and host factors involved in GBS's state as both an asymptomatic colonizer and an invasive pathogen. Gaining a better understanding of these mechanisms is key to overcoming the challenges associated with vaccine development and identification of novel strategies to mitigate GBS virulence.

Development of Freeze-Thaw Tolerant Lactobacillus rhamnosus GG by Adaptive Laboratory Evolution

The industrial application of microorganisms as starters or probiotics requires their preservation to assure viability and metabolic activity. Freezing is routinely used for this purpose, but the cold damage caused by ice crystal formation may result in severe decrease in microbial activity. In this study, adaptive laboratory evolution (ALE) technique was applied to a lactic acid bacterium to select tolerant strains against freezing and thawing stresses. Lactobacillus rhamnosus GG was subjected to freeze-thaw-growth (FTG) for 150 cycles with four replicates. After 150 cycles, FTG-evolved mutants showed improved fitness (survival rates), faster growth rate, and shortened lag phase than those of the ancestor. Genome sequencing analysis of two evolved mutants showed genetic variants at distant loci in six genes and one intergenic space. Loss-of-function mutations were thought to alter the structure of the microbial cell membrane (one insertion in cls), peptidoglycan (two missense mutations in dacA and murQ), and capsular polysaccharides (one missense mutation in wze), resulting in an increase in cellular fluidity. Consequently, L. rhamnosus GG was successfully evolved into stress-tolerant mutants using FTG-ALE in a concerted mode at distal loci of DNA. This study reports for the first time the functioning of dacA and murQ in freeze-thaw sensitivity of cells and demonstrates that simple treatment of ALE designed appropriately can lead to an intelligent genetic changes at multiple target genes in the host microbial cell.

Capsular Switching and ICE Transformation Occurred in Human Streptococcus agalactiae ST19 With High Pathogenicity to Fish

Although Streptococcus agalactiae (GBS) cross-infection between human and fish has been confirmed in experimental and clinical studies, the mechanisms underlying GBS cross-species infection remain largely unclear. We have found different human GBS ST19 strains exhibiting strong or weak pathogenic to fish (sGBS and wGBS). In this study, our objective was to identify the genetic elements responsible for GBS cross species infection based on genome sequence data and comparative genomics. The genomes of 11 sGBS strains and 11 wGBS strains were sequenced, and the genomic analysis was performed base on pan-genome, CRISPRs, phylogenetic reconstruction and genome comparison. The results from the pan-genome, CRISPRs analysis and phylogenetic reconstruction indicated that genomes between sGBS were more conservative than that of wGBS. The genomic differences between sGBS and wGBS were primarily in the Cps region (about 111 kb) and its adjacent ICE region (about 106 kb). The Cps region included the entire cps operon, and all sGBS were capsular polysaccharide (CPS) type V, while all wGBS were CPS type III. The ICE region of sGBS contained integrative and conjugative elements (ICE) with IQ element and erm(TR), and was very conserved, whereas the ICE region of wGBS contained ICE with mega elements and the variation was large. The capsular switching (III–V) and transformation of ICE adjacent to the Cps region occurred in human GBS ST19 with different pathogenicity to fish, which may be related to the capability of GBS cross-infection.

Progress toward a group B streptococcal vaccine

Streptococcus agalactiae (group B Streptococcus, GBS) is a leading cause of severe invasive disease in neonate, elderly, and immunocompromised patients worldwide. Despite recent advances in the diagnosis and intrapartum antibiotic prophylaxis (IAP) of GBS infections, it remains one of the most common causes of neonatal morbidity and mortality, causing serious infections. Furthermore, recent studies reported an increasing number of GBS infections in pregnant women and elderly. Although IAP is effective, it has several limitations, including increasing antimicrobial resistance and late GBS infection after negative antenatal screening. Maternal immunization is the most promising and effective countermeasure against GBS infection in neonates. However, no vaccine is available to date, but two types of vaccines, protein subunit and capsular polysaccharide conjugate vaccines, were investigated in clinical trials. Here, we provide an overview of the GBS vaccine development status and recent advances in the development of immunoassays to evaluate the GBS vaccine clinical efficacy.

Protein-Polymer Microcapsules for PCR Technology

Protein-polymer microcapsules have attracted much attention, due to their special features and potential in biological use. How to make the most of this type of bio-abiotic hybrid material is an intriguing question. Nevertheless, several unsatisfactory technical issues significantly limited the application of these materials. For instance, introducing various biomolecules and crosslinking for the capsules remains challenging and problematic. In this report, recombinant mCherry protein was covalently linked with poly(N-isopropylacrylamide) (PNIPAAm) to form amphiphilic protein-polymer conjugates, which assembled into microcapsules. These microcapsules are thermoresistant and can be used in the polymerase chain reaction (PCR). In this setting, the reactant molecules can be readily and easily introduced into the microcapsules, and crosslinking and water-oil phase transition are not necessary. This protein-polymer microcapsule PCR system has potential in various biological applications.

Genomic characterization, phylogenetic analysis, and identification of virulence factors in Aerococcus sanguinicola and Aerococcus urinae strains isolated from infection episodes

Aerococcus sanguinicola and Aerococcus urinae are emerging pathogens in clinical settings mostly being causative agents of urinary tract infections (UTIs), urogenic sepsis and more seldomly complicated infective endocarditis (IE). Limited knowledge exists concerning the pathogenicity of these two species. Eight clinical A. sanguinicola (isolated from 2009 to 2015) and 40 clinical A. urinae (isolated from 1984 to 2015) strains from episodes of UTIs, bacteremia, and IE were whole-genome sequenced (WGS) to analyze genomic diversity and characterization of virulence genes involved in the bacterial pathogenicity. A. sanguinicola genome sizes were 2.06-2.12 Mb with 47.4-47.6% GC-contents, and 1783-1905 genes were predicted whereof 1170 were core-genes. In case of A. urinae strains, the genome sizes were 1.93-2.44 Mb with 41.6-42.6% GC-contents, and 1708-2256 genes of which 907 were core-genes. Marked differences were observed within A. urinae strains with respect to the average genome sizes, number and sequence identity of core-genes, proteome conservations, phylogenetic analysis, and putative capsular polysaccharide (CPS) loci sequences. Strains of A. sanguinicola showed high degree of homology. Phylogenetic analyses showed the 40 A. urinae strains formed two clusters according to two time periods: 1984-2004 strains and 2010-2015 strains. Genes that were homologs to virulence genes associated with bacterial adhesion and antiphagocytosis were identified by aligning A. sanguinicola and A. urinae pan- and core-genes against Virulence Factors of Bacterial Pathogens (VFDB). Bacterial adherence associated gene homologs were present in genomes of A. sanguinicola (htpB, fbpA, lmb, and ilpA) and A. urinae (htpB, lap, lmb, fbp54, and ilpA). Fifteen and 11-16 CPS gene homologs were identified in genomes of A. sanguinicola and A. urinae strains, respectively. Analysis of these genes identified one type of putative CPS locus within all A. sanguinicola strains. In A. urinae genomes, five different CPS loci types were identified with variations in CPS locus sizes, genetic content, and structural organization. In conclusion, this is the first study dealing with WGS and comparative genomics of clinical A. sanguinicola and A. urinae strains from episodes of UTIs, bacteremia, and IE. Gene homologs associated with antiphagocytosis and bacterial adherence were identified and genetic variability was observed within A. urinae genomes. These findings contribute with important knowledge and basis for future molecular and experimental pathogenicity study of UTIs, bacteremia, and IE causing A. sanguinicola and A. urinae strains.

GC-MS-Based Metabolome and Metabolite Regulation in Serum-Resistant Streptococcus agalactiae

Streptococcus agalactiae causes severe systemic infections in human and fish. In the present study, we established a pathogen-plasma interaction model by which we explored how S. agalactiae evaded serum-mediated killing. We found that S. agalactiae grew faster in the presence of yellow grouper plasma than in the absence of the plasma, indicating S. agalactiae evolved a way of evading the fish immune system. To determine the events underlying this phenotype, we applied GC-MS-based metabolomics approaches to identify differential metabolomes between S. agalactiae cultured with and without yellow grouper plasma. Through bioinformatics analysis, decreased malic acid and increased adenosine were identified as the most crucial metabolites that distinguish the two groups. Meanwhile, they presented with decreased TCA cycle and elevated purine metabolism, respectively. Finally, exogenous malic acid and adenosine were used to reprogram the plasma-resistant metabolome, leading to elevated and decreased susceptibility to the plasma, respectively. Therefore, our findings reveal for the first time that S. agalactiae utilizes a metabolic trick to respond to plasma killing as a result of serum resistance, which may be reverted or enhanced by exogenous malic acid and adenosine, respectively, suggesting that the metabolic trick can be regulated by metabolites.

Exploring the diversity of protein modifications: special bacterial phosphorylation systems

Protein modifications not only affect protein homeostasis but can also establish new cellular protein functions and are important components of complex cellular signal sensing and transduction networks. Among these post-translational modifications, protein phosphorylation represents the one that has been most thoroughly investigated. Unlike in eukarya, a large diversity of enzyme families has been shown to phosphorylate and dephosphorylate proteins on various amino acids with different chemical properties in bacteria. In this review, after a brief overview of the known bacterial phosphorylation systems, we focus on more recently discovered and less widely known kinases and phosphatases. Namely, we describe in detail tyrosine- and arginine-phosphorylation together with some examples of unusual serine-phosphorylation systems and discuss their potential role and function in bacterial physiology, and regulatory networks. Investigating these unusual bacterial kinase and phosphatases is not only important to understand their role in bacterial physiology but will help to generally understand the full potential and evolution of protein phosphorylation for signal transduction, protein modification and homeostasis in all cellular life.

Autophosphorylation of the Bacterial Tyrosine-Kinase CpsD Connects Capsule Synthesis with the Cell Cycle in Streptococcus pneumoniae

Bacterial capsular polysaccharides (CPS) are produced by a multi-protein membrane complex, in which a particular type of tyrosine-autokinases named BY-kinases, regulate their polymerization and export. However, our understanding of the role of BY-kinases in these processes remains incomplete. In the human pathogen Streptococcus pneumoniae, the BY-kinase CpsD localizes at the division site and participates in the proper assembly of the capsule. In this study, we show that the cytoplasmic C-terminal end of the transmembrane protein CpsC is required for CpsD autophosphorylation and localization at mid-cell. Importantly, we demonstrate that the CpsC/CpsD complex captures the polysaccharide polymerase CpsH at the division site. Together with the finding that capsule is not produced at the division site in cpsD and cpsC mutants, these data show that CPS production occurs exclusively at mid-cell and is tightly dependent on CpsD interaction with CpsC. Next, we have analyzed the impact of CpsD phosphorylation on CPS production. We show that dephosphorylation of CpsD induces defective capsule production at the septum together with aberrant cell elongation and nucleoid defects. We observe that the cell division protein FtsZ assembles and localizes properly although cell constriction is impaired. DAPI staining together with localization of the histone-like protein HlpA further show that chromosome replication and/or segregation is defective suggesting that CpsD autophosphorylation interferes with these processes thus resulting in cell constriction defects and cell elongation. We show that CpsD shares structural homology with ParA-like ATPases and that it interacts with the chromosome partitioning protein ParB. Total internal reflection fluorescence microscopy imaging demonstrates that CpsD phosphorylation modulates the mobility of ParB. These data support a model in which phosphorylation of CpsD acts as a signaling system coordinating CPS synthesis with chromosome segregation to ensure that daughter cells are properly wrapped in CPS.

Bacteria utilize a multi-protein membrane complex to synthesize and export the polysaccharide capsule that conceals and covers the cell. In bacterial pathogens, the capsule protects the cell form opsonophagocytosis and complement-mediated killing. The mechanisms allowing the bacterial cell to maintain this protective capsule during cell growth and division remain unknown. The capsule assembly machinery encompasses a particular type of tyrosine-kinases found only in bacteria, which are called BY-kinases. These kinases are involved in the regulation of several cellular functions including polysaccharide capsule production. Studying the role of BY-kinase represents thus an interesting approach to decipher the mechanisms of capsule synthesis and export. Here, we study the role of the BY-kinase CpsD in the human pathogen Streptococcus pneumoniae. We show that CpsD plays a dual function in the pneumococcus. Indeed, CpsD captures the capsule assembly machinery at the site of division, but we also show that CpsD coordinates capsule production with the cell cycle by interacting with the chromosome segregation system. These features provide a simple mechanism to cover the complete surface of the pneumococcal daughter cells. This finding further opens a new view of the function of BY-kinases in the bacterial cell notably in localizing protein complexes in subcellular regions over the cell cycle.

A Vaccine Approach for the Prevention of Infections by Multidrug-resistant Enterococcus faecium

The incidence of multidrug-resistant Enterococcus faecium hospital infections has been steadily increasing. With the goal of discovering new vaccine antigens, we systematically fractionated and purified four distinct surface carbohydrates from E. faecium endocarditis isolate Tx16, shown previously to be resistant to phagocytosis in the presence of human serum. The two most abundant polysaccharides consist of novel branched heteroglycan repeating units that include signature sugars altruronic acid and legionaminic acid, respectively. A minor high molecular weight polysaccharide component was recognized as the fructose homopolymer levan, and a glucosylated lipoteichoic acid (LTA) was identified in a micellar fraction. The polysaccharides were conjugated to the CRM197 carrier protein, and the resulting glycoconjugates were used to immunize rabbits. Rabbit immune sera were evaluated for their ability to kill Tx16 in opsonophagocytic assays and in a mouse passive protection infection model. Although antibodies raised against levan failed to mediate opsonophagocytic killing, the other glycoconjugates induced effective opsonic antibodies, with the altruronic acid-containing polysaccharide antisera showing the greatest opsonophagocytic assay activity. Antibodies directed against either novel heteroglycan or the LTA reduced bacterial load in mouse liver or kidney tissue. To assess antigen prevalence, we screened a diverse collection of blood isolates (n = 101) with antibodies to the polysaccharides. LTA was detected on the surface of 80% of the strains, and antigens recognized by antibodies to the two major heteroglycans were co-expressed on 63% of these clinical isolates. Collectively, these results represent the first steps toward identifying components of a glycoconjugate vaccine to prevent E. faecium infection.

Membrane Translocation and Assembly of Sugar Polymer Precursors

Bacterial polysaccharides play an essential role in cell viability, virulence, and evasion of host defenses. Although the polysaccharides themselves are highly diverse, the pathways by which bacteria synthesize these essential polymers are conserved in both Gram-negative and Gram-positive organisms. By utilizing a lipid linker, a series of glycosyltransferases and integral membrane proteins act in concert to synthesize capsular polysaccharide, teichoic acid, and teichuronic acid. The pathways used to produce these molecules are the Wzx/Wzy-dependent, the ABC-transporter-dependent, and the synthase-dependent pathways. This chapter will cover the initiation, synthesis of the various polysaccharides on the cytoplasmic face of the membrane using nucleotide sugar precursors, and export of the nascent chain from the cytoplasm to the extracellular milieu. As microbial glycobiology is an emerging field in Gram-positive bacteria research, parallels will be drawn to the more widely studied polysaccharide biosynthesis systems in Gram-negative species in order to provide greater understanding of these biologically significant molecules.