Characterization of pACK4, a mobilizable plasmid from Staphylococcus simulans biovar staphylolyticus

Staphylococcus simulans biovar staphylolyticus, the lysostaphin-producing organism, contains five plasmids designated pACK1–pACK5. pACK4 was found to be relaxable and to share sequence similarity with a number of well-characterized mobilizable plasmids from other staphylococci. All mobilizable staphylococcal plasmids characterized to date mediate resistance to various antibiotics, but pACK4 is unique because it contains no recognizable antibiotic resistance genes. pACK4 was found to contain an origin of transfer (oriT) region that shares inverted repeat regions and the same nic site as several other mobilizable staphylococcal plasmids. The presence of this conserved oriT region suggested that pACK4 might be mobilized in the presence of a conjugative plasmid. Filter mating studies revealed that pACK4 was mobilized by the conjugative plasmid pGO1. In addition, pACK4 was found to be virtually identical to the recently described plasmid pVGA from Staphylococcus aureus, except that pVGA contains an additional region (vgaA) that confers resistance to pleuromutilin, streptogramin A, and lincosamide. The high sequence similarity among pACK4, pVGA, and several previously described mobilizable staphylococcal plasmids suggests a common origin for these plasmids.     

Deficient Beta-Mannosylation of Candida albicans Phospholipomannan Affects the Proinflammatory Response in Macrophages

Candida albicans produces a complex glycosphingolipid called phospholipomannan (PLM), which is present on the cell-wall surface of yeast and shed upon contact with host cells. The glycan moiety of PLM is composed of β-mannosides with degrees of polymerization up to 19 in C. albicans serotype A. PLM from serotype B strains displays a twofold decrease in the length of the glycan chains. In this study we compared the proinflammatory activities of PLMs purified from C. albicans serotype A and serotype B strains and from a bmt6Δ mutant of C. albicans, whose PLM is composed of short truncated oligomannosidic chain. We found that PLMs activate caspase-1 in murine macrophage cell line J774 independent of the glycan chain length although IL-1β secretion is more intense with long glycan chain. None of the tested PLMs stimulate ROS production, indicating that caspase-1 activation may occur through a ROS-independent pathway. On the other hand, only long-chain oligomannosides present on PLM from serotype A strain (PLM-A) are able to induce TNF-α production in macrophages, a property that is not affect by blocking endocytosis through latrunculin A treatment. Finally, we demonstrate that soluble and not cell surface-bound galectin-3, is able to potentiate PLM-A-induced TNF-α production in macrophages. PLMs from C. albicans serotype B and from bmt6∆ mutant are not able to induce TNF-α production and galectin-3 pretreatment does not interfere with this result. In conclusion, we show here that PLMs are able to evoke a proinflammatory state in macrophage, which is in part dependent on their glycosylation status. Long-glycan chains favor interaction with soluble galectin-3 and help amplify inflammatory response.     

Ribosome protection by ABC‐F proteins—Molecular mechanism and potential drug design

Members of the ATP‐binding cassette F (ABC‐F) proteins confer resistance to several classes of clinically important antibiotics through ribosome protection. Recent structures of two ABC‐F proteins, Pseudomonas aeruginosa MsrE and Bacillus subtilis VmlR bound to ribosome have shed light onto the ribosome protection mechanism whereby drug resistance is mediated by the antibiotic resistance domain (ARD) connecting the two ATP binding domains. ARD of the E site bound MsrE and VmlR extends toward the drug binding region within the peptidyl transferase center (PTC) and leads to conformational changes in the P site tRNA acceptor stem, the PTC, and the drug binding site causing the release of corresponding drugs. The structural similarities and differences of the MsrE and VmlR structures likely highlight an universal ribosome protection mechanism employed by antibiotic resistance (ARE) ABC‐F proteins. The variable ARD domains enable this family of proteins to adapt the protection mechanism for several classes of ribosome‐targeting drugs. ARE ABC‐F genes have been found in numerous pathogen genomes and multi‐drug resistance conferring plasmids. Collectively they mediate resistance to a broader range of antimicrobial agents than any other group of resistance proteins and play a major role in clinically significant drug resistance in pathogenic bacteria. Here, we review the recent structural and biochemical findings on these emerging resistance proteins, offering an update of the molecular basis and implications for overcoming ABC‐F conferred drug resistance.     

Variability of the microfloral makeup of the pathological focus in suppurative infection]

During the period of hospital treatment a change in the composition of would microflora in 145 patients was found to occur, which affected the characteristics of microflora in respect of species, types and strains. This change consisted in the appearance of new (secondary) species, variants and strains and in the disappearance of some original (primary) ones. The populations of staphylococci were found to vary in the level and spectrum of their resistance to antibiotics (resistovars) and in the degree and spectrum of their sensitivity to staphylococcal typing phages (phagovars). Changes in the populations of staphylococci were caused mainly by the cange of S. aureus or by the additional appearance of their new variants which belonged, as a rule, to phage group II, had multiple resistance to antibiotics and corresponded to the phagovars of the hospital flora. The development of hospital variants in open wounds led to an increased general level of resistance of staphylococcal populations to antibiotics.     

PLMD:An updated data resource of protein lysine modifications

Post-translational modifications(PTMs) occurring at protein lysine residues,or protein lysine modifications(PLMs),play critical roles in regulating biological processes.Due to the explosive expansion of the amount of PLM substrates and the discovery of novel PLM types,here we greatly updated our previous studies,and presented a much more integrative resource of protein lysine modification database(PLMD).In PLMD,we totally collected and integrated 284,780 modification events in 53,501 proteins across 176 eukaryotes and prokaryotes for up to 20 types of PLMs,including ubiquitination,acetylation,sumoylation,methylation,succinylation,malonylation,glutarylation,giycation,formylation,hydroxylation,butyrylation,propionylation,crotonylation,pupylation,neddylation,2-hydroxyisobutyrylation,phosphoglycerylation,carboxylation,lipoylation and biotinylation.Using the data set,a motif-based analysis was performed for each PLM type,and the results demonstrated that different PLM types preferentially recognize distinct sequence motifs for the modifications.Moreover,various PLMs synergistically orchestrate specific cellular biological processes by mutual crosstalks with each other,and we totally found 65,297 PLM events involved in 90 types of PLM co-occurrences on the same lysine residues.Finally,various options were provided for accessing the data,while original references and other annotations were also present for each PLM substrate.Taken together,we anticipated the PLMD database can serve as a useful resource for further researches of PLMs.PLMD 3.0 was implemented in PHP + MySQL and freely available at http://plmd.biocuckoo.org.     

Characterization of the Staphylococcus aureus rRNA Methyltransferase Encoded by orfX,the Gene Containing the Staphylococcal Chromosome Cassette mec (SCCmec) Insertion Site

The gene orfX is conserved among all staphylococci, and its complete sequence is maintained upon insertion of the staphylococcal chromosome cassette mec (SCCmec) genomic island, containing the gene encoding resistance to β-lactam antibiotics (mecA), into its C terminus. The function of OrfX has not been determined. We show that OrfX was constitutively produced during growth, that orfX could be inactivated without altering bacterial growth, and that insertion of SCCmec did not alter gene expression. We solved the crystal structure of OrfX at 1.7 Å and found that it belongs to the S-adenosyl-l-methionine (AdoMet)-dependent α/β-knot superfamily of SPOUT methyltransferases (MTases), with a high structural homology to YbeA, the gene product of the Escherichia coli 70 S ribosomal MTase RlmH. MTase activity was confirmed by demonstrating the OrfX-dependent methylation of the Staphylococcus aureus 70 S ribosome. When OrfX was crystallized in the presence of its AdoMet substrate, we found that each monomer of the homodimeric structure bound AdoMet in its active site. Solution studies using isothermal titration calorimetry confirmed that each monomer bound AdoMet but with different binding affinities (K_d = 52 ± 0.4 and 606 ± 2 μm). In addition, the structure shows that the AdoMet-binding pocket, formed by a deep trefoil knot, contains a bound phosphate molecule, which is the likely nucleotide methylation site. This study represents the first characterization of a staphylococcal ribosomal MTase and provides the first crystal structure of a member of the α/β-knot superfamily of SPOUT MTases in the RlmH or COG1576 family with bound AdoMet.     

Design and Validation of a Periodic Leg Movement Detector

Periodic Limb Movements (PLMs) are episodic, involuntary movements caused by fairly specific muscle contractions that occur during sleep and can be scored during nocturnal polysomnography (NPSG). Because leg movements (LM) may be accompanied by an arousal or sleep fragmentation, a high PLM index (i.e. average number of PLMs per hour) may have an effect on an individual’s overall health and wellbeing. This study presents the design and validation of the Stanford PLM automatic detector (S-PLMAD), a robust, automated leg movement detector to score PLM. NPSG studies from adult participants of the Wisconsin Sleep Cohort (WSC, n = 1,073, 2000–2004) and successive Stanford Sleep Cohort (SSC) patients (n = 760, 1999–2007) undergoing baseline NPSG were used in the design and validation of this study. The scoring algorithm of the S-PLMAD was initially based on the 2007 American Association of Sleep Medicine clinical scoring rules. It was first tested against other published algorithms using manually scored LM in the WSC. Rules were then modified to accommodate baseline noise and electrocardiography interference and to better exclude LM adjacent to respiratory events. The S-PLMAD incorporates adaptive noise cancelling of cardiac interference and noise-floor adjustable detection thresholds, removes LM secondary to sleep disordered breathing within 5 sec of respiratory events, and is robust to transient artifacts. Furthermore, it provides PLM indices for sleep (PLMS) and wake plus periodicity index and other metrics. To validate the final S-PLMAD, experts visually scored 78 studies in normal sleepers and patients with restless legs syndrome, sleep disordered breathing, rapid eye movement sleep behavior disorder, narcolepsy-cataplexy, insomnia, and delayed sleep phase syndrome. PLM indices were highly correlated between expert, visually scored PLMS and automatic scorings (r² = 0.94 in WSC and r² = 0.94 in SSC). In conclusion, The S-PLMAD is a robust and high throughput PLM detector that functions well in controls and sleep disorder patients.     

Characterization of plasmids in aminocyclitol-resistant Staphylococcus aureus: electron microscopic and restriction endonuclease analysis

Plasmid species isolated from aminocyclitol-resistant Staphylococcus aureus have been analyzed by restriction endonuclease digestion and electron microscopy. These plasmids can be divided into two interrelated groups; intergroup variability is due to the gain or loss of defined DNA sequences. Plasmids pSJ1 and pSJ24 are related to staphylococcal penicillinase plasmid pI524 which was first described over 20 years ago. Both pSJ1 and pSJ24 differ from pI524 by the acquisition of 8 and 4 kbp, respectively, and encode additional resistance to the antibiotics erythromycin and kanamycin. The gain of these resistance determinants suggests that the evolution of staphylococcal resistance plasmids parallels that observed for plasmids of gram-negative bacteria and has serious implications for the spread of antibiotic resistance among the staphylococci.     

Dependency map of proteins in the small ribosomal subunit

The assembly of the ribosome has recently become an interesting target for antibiotics in several bacteria. In this work, we extended an analytical procedure to determine native state fluctuations and contact breaking to investigate the protein stability dependence in the 30S small ribosomal subunit of Thermus thermophilus. We determined the causal influence of the presence and absence of proteins in the 30S complex on the binding free energies of other proteins. The predicted dependencies are in overall agreement with the experimentally determined assembly map for another organism, Escherichia coli. We found that the causal influences result from two distinct mechanisms: one is pure internal energy change, the other originates from the entropy change. We discuss the implications on how to target the ribosomal assembly most effectively by suggesting six proteins as targets for mutations or other hindering of their binding. Our results show that by blocking one out of this set of proteins, the association of other proteins is eventually reduced, thus reducing the translation efficiency even more. We could additionally determine the binding dependency of THX—a peptide not present in the ribosome of E. coli—and suggest its assembly path.     

Role of Staphylococcus saprophyticus in urinary infections]

A proportion of S. saprophyticus in other coagulase-negative staphylococcal isolates from the urine of patients with urinary infections and healthy individuals has been investigated. Certain diagnostic aspect of the urinary infections with S. saprophyticus have also been considered. Hundred four coagulase-negative staphylococcal strains isolated from patients in S?upsk and Gdańsk area and 72 strains of the coagulase-negative staphylococci isolated from the urine of healthy women have been divided into 9 species, according to Kloos and Schleifers' classification. Bacteriologic tests have shown that S. saprophyticus produced 20.4% of the urinary tract infections in S?upsk area holding the second place after S. haemolyticus (27.3%). This species was the most infrequent in the urine of patients in Gdańsk area (3.3%). Its sensitivity to antibiotics did not differ from that of other coagulase-negative staphylococci. In contrast to the majority of other strains, S. saprophyticus has not been isolated from the urinary tract of healthy women and has been encountered most frequently in low bacteriuria. Test of resistance to novobiocin which is considered as a simplified identification method of this species proved to be not very precise as other species have also been resistant to this antibiotic.     

Site‐Specific Systematic Analysis of Lysine Modification Crosstalk

Research has revealed that post‐translational modifications (PTMs) that occur at lysine (PLMs) can cooperatively regulate various biological processes by crosstalk. However, the trend of the crosstalk between multiple PLMs and the properties of PLM crosstalk require additional investigation. Here, the crosstalk among acetylation, succinylation, and SUMOylation is systematically studied in a site‐specific waz. First, crosstalk between SUMOylation is detected and succinylation is found to be underexpressed, whereas succinylation tends to crosstalk with acetylation and SUMOylation on the same lysine residue while PLM crosstalk is tissue‐specific across different species. Further analysis reveals that different PLMs tend to occur crosstalk at diverse subcellular compartments and structural regions, and they participate in distinct biological processes and functions. Additionally, short‐term evolutionary analysis shows that there is no additional evolutionary pressure on PLMs crosstalk sites, as found by comparison with singly modified sites. Finally, phylogenetic classification reveals that genes with co‐occupied lysine crosstalk are more likely to have higher evolutionary similarity and possess a tendency to cluster in the specific branch. The integrated approach reported here has the potential for large‐scale prioritization of in situ crosstalk of PLM candidates and provides a profound understanding of the underlying relationship between different lysine modifications.     

Iterative Structure-Based Peptide-Like Inhibitor Design against the Botulinum Neurotoxin Serotype A

The botulinum neurotoxin serotype A light chain (BoNT/A LC) protease is the catalytic component responsible for the neuroparalysis that is characteristic of the disease state botulism. Three related peptide-like molecules (PLMs) were designed using previous information from co-crystal structures, synthesized, and assayed for in vitro inhibition against BoNT/A LC. Our results indicate these PLMS are competitive inhibitors of the BoNT/A LC protease and their K_i values are in the nM-range. A co-crystal structure for one of these inhibitors was determined and reveals that the PLM, in accord with the goals of our design strategy, simultaneously involves both ionic interactions via its P1 residue and hydrophobic contacts by means of an aromatic group in the P2′ position. The PLM adopts a helical conformation similar to previously determined co-crystal structures of PLMs, although there are also major differences to these other structures such as contacts with specific BoNT/A LC residues. Our structure further demonstrates the remarkable plasticity of the substrate binding cleft of the BoNT/A LC protease and provides a paradigm for iterative structure-based design and development of BoNT/A LC inhibitors.     

The qacG gene on plasmid pST94 confers resistance to quaternary ammonium compounds in staphylococci isolated from the food industry

The 2.3 kb resistance plasmid pST94 revealed a new gene (qacG) encoding resistance to benzalkonium chloride (BC), a commonly used quaternary ammonium disinfectant, and the intercalating dye ethidium bromide (Eb) in staphylococci isolated from the food industry. The 107 amino acid QacG protein showing 69.2% identity to the staphylococcal multi-drug resistance protein Smr is a new member of the small multi-drug resistance (SMR) protein family. QacG conferred resistance via proton dependent efflux. An additional ORF on pST94 encoded a protein with extensive similarity to replication proteins of other Gram-positive bacteria. Gene constructs containing the qacG and smr gene region combined with the smr or qacG promoter, respectively, indicated that QacG is more efficient than Smr and that qacG has a weaker promoter. Resistant qacG-containing cells could be adapted to withstand higher concentrations of BC. Adapted qacG-containing cells showed increased resistance mainly to BC. In contrast, adaptation of sensitive cells showed cross-resistance development to a range of compounds. Induction of proton-dependent efflux was observed for BC-adapted staphylococci cells not containing qacG. The ability of sublethal concentrations of BC to develop cross-resistance and induce efflux mechanisms could be of practical significance; it should be considered before use of any new disinfectant and in the design of better disinfection procedures.     

Genetic manipulation of the biosynthetic process leading to phoslactomycins, potent protein phosphatase 2A inhibitors

Phoslactomycins (PLMs) represent an unusual structural class of natural products secreted by various streptomycetes, containing an α,β-unsaturated δ-lactone, an amino group, phosphate ester, conjugated diene and a cyclohexane ring. Phosphazomycins, phospholines and leustroducsins contain the same structural moieties, varying only in the acyl substituent at the C-18 hydroxyl position. These compounds possess either antifungal or antitumor activities or both. The antitumor activity of the PLM class of compounds has been attributed to a potent and selective inhibition of protein phosphatase 2A (PP2A). The cysteine-269 residue of PP2Ac-subunit has been shown to be the site of covalent modification by PLMs. In this article, we review previous work on the isolation, structure elucidation and biological activities of PLMs and related compounds and current status of our work on both PLM stability and genetic manipulation of the biosynthetic process. Our work has shown that PLM B is surprisingly stable in solution, with a pH optimum of 6. Preliminary biosynthetic studies utilizing isotopically labeled shikimic acid and cyclohexanecarboxylic acid (CHC) suggested PLM B to be a polyketide-type antibiotic synthesized using CHC as a starter unit. Using a gene (chcA) from a set of CHC-CoA biosynthesis genes from Streptomyces collinus as a probe, a 75 kb region of 29 ORFs encoding PLM biosynthesis was located in the genome of Streptomyces sp. strain HK803. Analysis and subsequent manipulation of plmS ₂ and plmR ₂ in the gene cluster has allowed for rational engineering of a strain that produces only one PLM analog, PLM B, at ninefold higher titers than the wild type strain. A strain producing PLM G (the penultimate intermediate in PLMs biosynthesis) has also been generated. Current work is aimed at selective in vitro acylation of PLM G with various carboxylic acids and a precursor-directed biosynthesis in a chcA deletion mutant with the aim of generating novel PLM analogs.     

Study of beta-lactamase activity of staphylococci from different sources

The beta-lactamase activity of staphylococci isolated from the nasopharynx and skin of children with destructive affections of the lungs and from blood of patients with cardiovascular diseases subjected to surgical operations was determined with acidometric and microbiological procedures. Interrelation between synthesis of beta-lactamase by the staphylococcal strains and their resistance to beta-lactam antibiotics was demonstrated. No correlation of the antibiotic resistance and the taxonomic position of the staphylococcal strains was observed.     

Staphylococci in orthopaedic surgical wounds.

From 50 infected surgical wounds of orthopaedic patients, 43 (86%) staphylococcal strains were isolated. 34 of all these staphylococci belonged to Staphylococcus aureus species (i.e. 68 % of all isolates from surgical wounds; 79% of staphylococcal isolates); 9 were coagulase-negative staphylococci (i.e. 21% of all isolates from surgical wounds; 18% of staphylococcal isolates). Among microorganisms isolated from the wounds we also found 2 (4%) of the Enterobacteriaceae family; 2 (4%) of the Pseudomonas genus; 3 (6%) of the Streptococcus genus. Thus, orthopaedic surgical wounds were infected by staphylococci (mainly S. aureus) more frequently than by other micro-organisms. All the staphylococcal strains were screened for methicillin resistance by agar disk diffusion testing and for the presence of mecA gene responsible for methicillin resistance by PCR. 32% of the S. aureus and 33% of the S. epidermidis strains resulted methicillin resistant and mecA-positive. The data confirm the diffusion of methicillin resistant S. aureus in surgical site infections and shows that the so-called "new pathogens", i.e. S. epidermidis and other coagulase-negative staphylococci, also exhibit a frequent and hazardous methicillin-resisting ability.     

Phagocytosis of chloramine B sensitive and resistant staphylococci isolated from healthy persons and patients

Phagocytic reaction with respect to antibiotic and chloramine B sensitive and resistant staphylococci isolated from healthy persons and patients, air and stock of medical institutions was studied on albino mice. It was shown that the staphylococcal isolates included strains simultaneously sensitive to antibiotics and chloramine, sensitive to antibiotics and resistant to chloramine, resistant to antibiotics and sensitive to chloramine and simultaneously resistant to antibiotics and chloramine. Activity, intensity and completeness of phagocytosis by leucocytes from mouse abdominal cavity exudates with respect to the staphylococcal strains sensitive to antibiotics and resistant to chloramine, resistant to antibiotics and sensitive to chloramine and simultaneously resistant to antibiotics and chloramine were lower than the values of the phagocytic reaction with respect to the isolates simultaneously sensitive to antibiotics and chloramine. This suggested that not only antibiotic resistance of microbes but also their resistance to disinfectants could be referred to complicating factors of hospital infections.     

医院感染葡萄球菌菌种变迁与耐药性近况

目的：了解近9年来医院感染葡萄球菌菌种的变迁与近3年来葡萄球菌药状况。方法：1993年1月至2001年12月我院传染病科等13科室住院病人的各种标本采用血琼脂培养,所分离的葡萄球菌采用美国DADE公司生产的MICROSCAN WALKAY-40全自动微生物分析仪鉴定到种及其亚种。药敏试验药物有青霉素、苯唑西林、氨苄西林、哌拉西林、阿莫西林／克拉维酸（阿莫仙）、头孢唑啉、头孢噻肟、头孢哌酮／舒巴坦（舒普深）、庆大霉素、复方新诺明、环丙沙星、氧氟沙星、利福平、万古霉素、红霉素、林可霉素、四环素、伊米配能／西司他丁（泰能）共18种。采用液体稀释法测定每株葡萄球菌对受试药物的最小抑菌浓度（MIC）,操作按说明书进行。质控菌ATCC25923。依据新近NCCLS标准判读结果。结果：1993年至1998年分离的葡萄球菌中,金黄色葡萄球菌（金葡萄）占71.43%,凝固酶阴性葡萄球菌（CNS）占28.57%,包括表皮葡萄球菌（表葡菌）、腐生葡萄球菌、里昂葡萄球菌和头状葡萄球菌4种。1999年至2001年分离的424株葡萄球菌中,金葡菌仅占29.01%,CNS增至13种,占70.995,以表葡菌、溶血葡萄球菌、松鼠葡萄球菌为主。近3年来分离的各种葡萄球菌甲氧西林耐药率在73.03%-100%之间,除对舒普深、复方新诺明、利福平和万古霉素较敏感外,对其余抗菌药物的耐药率均超过60％,以金葡菌、溶血葡萄球菌、松鼠葡萄球菌的耐药率为最高。MRS耐药率普遍高于MSS,且均呈多重耐药。5.42%(23/424)菌株万古霉素MIC＞16mg/L,除1株为MSCNS外,其余22株均为MRS。结论：3年来医院感染葡萄球菌菌种构成比发生了显著变化,以CNS为主。对抗菌药物呈多重耐药,部分菌株对万古霉素敏感性降低,应予警惕。