BL-11C Micro-MX: a high-flux microfocus macromolecular-crystallography beamline for micrometre-sized protein crystals at Pohang Light Source II

BL-11C, a new protein crystallography beamline, is an in-vacuum undulator-based microfocus beamline used for macromolecular crystallography at the Pohang Accelerator Laboratory and it was made available to users in June 2017. The beamline is energy tunable in the range 5.0-20 keV to support conventional single- and multi-wavelength anomalous-dispersion experiments against a wide range of heavy metals. At the standard working energy of 12.659 keV, the monochromated beam is focused to 4.1 µm (V) × 8.5 µm (H) full width at half-maximum at the sample position and the measured photon flux is 1.3 × 10¹² photons s^-1. The experimental station is equipped with a Pilatus3 6M detector, a micro-diffractometer (MD2S) incorporating a multi-axis goniometer, and a robotic sample exchanger (CATS) with a dewar capacity of 90 samples. This beamline is suitable for structural determination of weakly diffracting crystalline substances, such as biomaterials, including protein, nucleic acids and their complexes. In addition, serial crystallography experiments for determining crystal structures at room temperature are possible. Herein, the current beamline characteristics, technical information for users and some recent scientific highlights are described.

A quick and easy method to identify bacteria by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry

Concerns with water quality have increased in recent years, in part due to the more frequent contamination of water by pathogens like E. coli and L. pneumophila. Current methods for the typing of bacteria in water samples are based on culture of samples on specific media. These techniques are time-consuming, subject to the impact of interferents and do not totally meet all the requirements of prevention. There is a need for accurate and rapid identification of these microorganisms. This report deals with the detection of bacteria, more precisely of Legionella spp., and the development of an analytical strategy for a rapid and unambiguous identification of these pathogens in water from diverse origins. Therefore, a protein mass mapping using matrix-assisted laser desorption/ionisation mass spectrometry (MALDI MS) of whole bacteria combined with a home-made database of bacteria spectra is applied. A large variety of different bacteria and microorganisms is used to approach the actual composition of samples with numerous interferents. The objective is to propose a universal method for sampling preparation before MALDI MS analysis and optimised spectrometric conditions for reproducible intense peaks. Several experimental factors known to influence signal quality such as time and media of culture have been studied. The proposed method gives promising results for a sure differentiation of Legionella species and subspecies and a rapid identification of bacteria which are the most dangerous or difficult to eradicate. This method is easy to perform with an excellent reproducibility. The analytical protocol and the corresponding database were validated on samples from different origins (cooling tower, plumbing hot water).

Complete nucleotide sequence of pLD-TEX-KL, a 66-kb plasmid of Legionella dumoffii TEX-KL strain

The complete nucleotide sequence of a large (66 kb) plasmid pLD-TEX-KL of Legionella dumoffii TEX-KL strain was determined. Of the 57 predicted open reading frames (ORFs), 39 (68%) encoded proteins similar to previously known proteins, five (9%) were assigned with putative functions, three (5%) encoded conserved hypothetical proteins, and 10 (18%) had no homology to any genes present in the current open databases. The ORFs with similar functions were organized in a modular structure; thus, transfer region was identified, as well as a putative heavy-metal ion transporter system (hel). The transfer region encoded homologs of the Salmonella entrica serovar Typhi conjugative system components involved in conjugation. In addition, we also found a potential protein that was analogous to the DNA polymerase III epsilon subunit. It is rarely found that plasmid encode the DNA polymerase.

The HopX (AvrPphE) family of Pseudomonas syringae type III effectors require a catalytic triad and a novel N-terminal domain for function

Many gram-negative plant pathogenic bacteria employ type III secretion systems to deliver effector proteins directly into the host cell during infection. On susceptible hosts, type III effectors aid pathogen growth by manipulating host defense pathways. On resistant hosts, some effectors can activate specific host disease resistance (R) genes, leading to generation of rapid and effective immune responses. The biochemical basis of these processes is poorly understood. The HopX (AvrPphE) family is a widespread type III effector among phytopathogenic bacteria. We determined that HopX family members are modular proteins composed of a conserved putative cysteine-based catalytic triad and a conserved potential target/cofactor interaction domain. HopX is soluble in host cells. Putative catalytic triad residues are required for avirulence activity on resistant bean hosts and for the generation of a cell-death response in specific Arabidopsis genotypes. The putative target/cofactor interaction domain is also required for these activities. Our data suggest that specific interaction with and modification of a cytosolic host target drives HopX recognition in resistant hosts and may contribute to virulence in susceptible hosts. Surprisingly, the Legionella pneumophila genome was found to contain a protein with similarity to HopX in sequence and domain arrangement, suggesting that these proteins might also contribute to animal pathogenesis and could be delivered to plant and animal hosts by diverse secretion systems.

[Physicochemical factors influencing distribution of Legionella species in Japanese hot springs]

We examined the relationship between the distribution of Legionella bacteria and various physicochemical characteristics of hot springs in Japan. Legionella bacteria were isolated from 52 (49.5%) out of 105 water samples, particularly from outdoor hot springs (67.3%). The bacterial count in the water samples positive for Legionella (86.5%) ranged from 10(1) to < 10(3) cfu/100 mL. L. pneumophila serogroup (SG) 4 (27.8%) was predominant in the water samples, followed by SG 5 (12.2%). The pulsefield gel electrophoresis (PFGE) patterns of chromosomal DNA for L. pneumophila SG 4 isolated from different parts of a hot spring resort were identical. Isolation of Legionella species from hot spring waters did not occur at pH 1.8-3.3, SO4(2-): > 780 mg/L, and H2SiO3: > 146 mg/L. The hot water-recirculating systems were applied to 18 out of 20 (90%) hot spring facilities which were found positive for Legionella. These results indicate that Legionella species are widespread in hot springs throughout Japan, except for waters with a low pH and non-recirculating waters, and that a single strain of L. pneumophila SG 4 is predominant in a particular hot spring resort.

Usefulness of fatty acid composition for differentiation of Legionella species

Numerical analysis of fatty acid methyl ester (FAME) profiles of 199 isolates and 76 reference strains, belonging to all validly described species of the genus Legionella that can be cultured in laboratory media, was used to differentiate between the species of this genus. With the exception of the strains that autofluoresced red, it was possible to differentiate all the other Legionella species. The strains of the species L. bozemanii, L. dumoffii, L. feeleii, L. gormanii, L. maceachernii, L. micdadei, and L. quinlivanii did not form single clusters, showing some degree of variability in the fatty acid compositions. The strains of the blue-white autofluorescent species had very similar fatty acid compositions and were difficult to distinguish from each other. Nine isolates had fatty acid profiles unlike those of any of the validly described species and may represent different FAME groups of known species or undescribed Legionella species. The method used in this study was useful for screening and discriminating large number of isolates of Legionella species. Moreover, the results obtained can be included in a database of fatty acid profiles, leading to a more accurate automatic identification of Legionella isolates.

Legionella taurinensis sp. nov., a new species antigenically similar to Legionella spiritensis

A group of 42 Legionella-like organisms reacting specifically with Legionella spiritensis serogroup 1 antisera were collected throughout Europe by the Centre National de Référence (French National Reference Centre) for Legionella. This group of isolates differed somewhat from L. spiritensis in terms of biochemical reactions, ubiquinone content and protein profile. The latter two analyses revealed that one of these L. spiritensis-like isolates, Turin I no. 1T, was highly related, but not identical to any of the red autofluorescent species of Legionella. In fact, this strain was the first of these particular isolates recognized to emit a red autofluorescence when exposed to UV light. Profile analysis of randomly amplified polymorphic DNA established that the red autofluorescent L. spiritensis-like isolates constituted a homogeneous group distinct from Legionella rubrilucens and Legionella erythra. DNA-DNA hybridization studies involving the use of S1 nuclease confirmed that the indicated group of isolates are a new species of Legionella, for which the name Legionella taurinensis is proposed with strain Turin I no. 1T (deposited as ATCC 700508T) as the type strain.

Dam-like methylation in legionellae

The chromosomal DNA of a variety of legionellae, including clinical, environmental, and plasmid-containing strains, was examined for evidence of Dam-like methylation. It was found that Dam-like methylation was present in all the strains examined regardless of their origin or plasmid content.

Detection of bacterial DNA polymerase chain reaction products by matrix-assisted laser desorption/ionization mass spectrometry

Accurate monitoring and identification of Legionella species, the causative agents of Legionnaires' and other diseases, in environmental water sources is an important public health issue. Traditional culture methods often lack the sensitivity and specificity that can be attained using the polymerase chain reaction (PCR) to amplify targeted regions of the bacterial genome. Matrix-assisted laser desorption/ionization combined with time-of-flight (MALDI-TOF) mass spectrometry is shown to be useful for detection of 108- and 168-base PCR products specific to Legionella. A rapid purification aimed at removal of salts and unreacted primers is demonstrated. The addition of a synthetic DNA 20-mer to the MALDI sample facilitates aiming the laser at a favorable spot on the sample probe from which the PCR products can be detected.

Characterization of Legionella species by numerical analysis of whole-cell protein electrophoresis

The results of a computer-assisted whole-cell protein sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of 291 isolates and 74 reference strains belonging to all known species of the genus Legionella revealed that the majority of the species of this genus can be adequately identified by this method. The type strain of Legionella bozemanii did not cluster with the other strains of this species, and the only strain of Legionella geestiana available clustered with the strains of Legionella feeleii. When we performed a numerical analysis by omitting certain portions of the pattern containing dense bands, all of the species could be distinguished. Our results also show that the type strains of Legionella nautarum and Legionella londiniensis deposited in the National Collection of Type Cultures do not correspond to the type strains deposited in the American Type Culture Collection. We used the results of a fatty acid and ubiquinone composition analysis to complement the SDS-PAGE results for several strains whose identities as determined by indirect immunofluorescence were doubtful. Computer-assisted SDS-PAGE of whole-cell proteins can be used in the classification of Legionella species and to identify and screen large numbers of isolates for further, in-depth taxonomic studies of smaller numbers of strains.

Chemical characterization of lipopolysaccharides from Legionella feeleii, Legionella hackeliae and Legionella jordanis

Lipopolysaccharides (LPS) from Legionella feeleii serogroup 1, L. hackeliae serogroup 1 and L. jordanis were subjected to chemical analysis. All three LPS contained D-mannose, D-glucose, D-glucosamine, L-glycero-D-manno-heptose, 2-keto-3-deoxyoctonic acid and glycerol. In addition the LPS of L. feeleii was characterized by L-quinovose (tentatively identified) and L-fucosamine, L. hackeliae LPS by D-quinovosamine, D-galactosamine and D-galacturonic acid, and L. jordanis LPS by D-quinovosamine. Phosphorylated sugars were detected in all three LPS. The backbone sugar of the lipid A part was in each case 2,3-diamino-2,3-dideoxy-D-glucose substituted with a complex pattern of fatty acid, including 20-22 different amide-linked (non-branched and methyl-branched) 3-hydroxy fatty acids of chain-length ranging from 12 to 23 carbon atoms. The fatty acid patterns included also ester-linked nonhydroxylated entities and the uncommon 27-oxo-octacosanoic acid and 29-oxotriacontanoic acid. The LPS of L. hackeliae and L. jordanis also contained heptacosane-1,27-dioic and nonacosane-1,29-dioic acid, and their 2-hydroxy analogues were characteristic of L. jordanis LPS. SDS-PAGE patterns of the three LPS were distinctly different. Both L. feeleii and L. jordanis produced smooth-form LPS with characteristic ladder patterns, whereas L. hackeliae LPS were of more rough-type character.

Chemical composition of lipopolysaccharides from Legionella bozemanii and Legionella longbeachae

Lipopolysaccharides (LPS) from Legionella bozemanii serogroup 1 and Legionella longbeachae serogroup 1 were subjected to chemical analyses. The lipid A part of both LPSs contained 2,3-dideoxy-2,3-diamino-D-glucose as major constituents and D-glucosamine and glycerol as minor constituents of the sugar backbone structure. Both LPSs exhibited a very complex fatty acid composition. Twenty amide-linked 3-hydroxy fatty acids were detected in LPS of L. longbeachae, whereas seventeen were encountered in LPS of L. bozemanii. Both LPSs contained nine ester-linked nonhydroxy fatty acids and the unique long-chain fatty acids 27-oxo-octacosanoic acid, 29-oxo-triacontanoic acid, heptacosane-1,27-dioic acid and nonacosane-1, 29-dioic acid. SDS-PAGE showed that L. bozemanii produced smooth-form LPS, whereas L. longbeachae LPS was mainly of the R-type. Composition analyses were in accordance with these electrophoretic patterns. D-Quinovosamine and L-fucosamine constituted 80 mol% of the polysaccharide part of L. bozemanii LPS. Other sugars identified were D-glucosamine, D-mannose, D-glucose, L-rhamnose, D-glycero-D-manno-heptose, L-glycero-D-manno-heptose, 2-keto-3-deoxy-octonic acid and glycerol. The polysaccharide chain from LPS of L. longbeachae appeared to be shorter, but composed of the same sugars except L-fucosamine. Both LPSs contained glycerol phosphate and glucosamine phosphate and L. longbeachae LPS contained in addition glucose phosphate.

Lipopolysaccharides of Legionella erythra and Legionella oakridgensis

The chemical composition of lipopolysaccharides from Legionella erythra and Legionella oakridgensis was analysed. Sodium dodecyl sulfate polyacrylamide gel electrophoresis showed both lipopolysaccharides to have a smooth-type character. The polysaccharide part of both lipopolysaccharides contained D-mannose, D-glucose, D-glycero-D-mannoheptose, L-glycero-D-manno-heptose, 2-keto-3-deoxyoctonic acid, L-fucosamine, D-glucosamine, and glucosamine phosphate. In addition, L-rhamnose, glycerol phosphate, and glucose phosphate were identified in the polysaccharide part of L. erythra lipopolysaccharide. The main sugar identified in the lipid A part of both lipopolysaccharides, 2,3-diamino-2,3-dideoxy-D-glucose, was found to be substituted with a complex fatty acid composition including at least 16 different amide-linked 3-hydroxy fatty acids. Both lipopolysaccharides contained nonhydroxy fatty acids and the uncommon 27-oxo-octacosanoic acid, 29-oxotriacontanoic acid, and 27-hydroxyoctacosanoic acid. The lipopolysaccharide of L. oakridgensis also contained 29-hydroxytriacontanoic acid. The dioic long-chain acids heptacosane-1,27-dioic acid and nonacosane-1,29-dioic acid were only present in the lipopolysaccharide of L. erythra.

Composition of 2,3-dihydroxy fatty acid-containing lipopolysaccharides from Legionella israelensis, Legionella maceachernii and Legionella micdadei

Lipopolysaccharides (LPS) from Legionella israelensis, L. maceachernii and L. micdadei were analysed for chemical composition. The main sugar of the lipid A fractions was in each case 2,3-diamino-2,3-dideoxy-D-glucose. Lipid A of L. israelensis also contained a substantial amount of D-glucosamine. In each lipid A fraction a complex fatty acid pattern was detected. This comprised at least 19 different 3-hydroxy fatty acids (amide-linked), three 2,3-dihydroxy fatty acids (amide-linked), non-hydroxy fatty acids (ester-linked) as well as long-chain (omega-1)-oxo, (omega-1)-hydroxy and (1,omega)-dioic fatty acids (ester-linked). In addition, L. maceachernii and L. micdadei contained alpha-hydroxylated long-chain (omega-1)-oxo and (1,omega)-dioic fatty acids. The polysaccharide parts of L. maceachernii and L. micdadei LPS were similar and contained mainly L-rhamnose, L-fucose, D-mannose, D-glucose, L-fucosamine, D-glucosamine, 2-keto-3-deoxy-octonic acid (Kdo) as well as the rare octose yersiniose A. The corresponding composition of L. israelensis LPS was simpler and consisted mainly of L-rhamnose and 3-amino-3,6-dideoxy-D-mannose. LPS of L. israelensis and L. micdadei contained, in addition, 2-keto-octonic acid linked to Kdo. Phosphorylated sugar constituents were detected in all three LPS, whereas ethanolamine was found only in LPS from L. maceachernii. The SDS-PAGE band pattern of L. micdadei differed from the two others in a higher proportion of the low molecular mass constituents.

Hydroxy-fatty acid profiles of Legionella species: diagnostic usefulness assessed by principal component analysis

Twenty-nine species (76 strains) of members of the genus Legionella were analyzed for their cellular hydroxylated fatty acids (OH-FAs). The individual patterns were unusually complex and included both monohydroxylated and dihydroxylated chains of unbranched or branched (iso and anteiso) types. Comparison of the strain profiles by SIMCA (Soft Independent Modelling of Class Analogy) principal component analysis revealed four main groups. Group 1 included Legionella pneumophila plus L. israelensis strains, and group 2 included L. micdadei and L. maceacherneii strains. These two closely related groups were characterized by the occurrence of di-OH-FAs and differed mainly in the amounts of 3-OH-a21:0, 3-OH-n21:0, 3-OH-n22:0, and 3-OH-a23:0. Group 3 (13 species) was distinguished by i14:0 at less than 3%, 3-OH-3-OH-n14:0 at greater than 5%, 3-OH-n15:0 at greater than 2%, and minute amounts of OH-FAs with chains longer than 21:0. Group 4 (12 species) was heterogeneous. Its main characteristics were the presence of 3-OH-n12:0 and 3-OH-n13:0, 3-OH-i14:0 at greater than 5%, as well as significant amounts of 3-OH-a21:0 and 3-OH-n21:0. The groupings obtained by OH-FA profiles were found to reflect DNA-DNA homology groupings reasonably well, and the profiles appear to be useful for differentiation of Legionella species.

Long-chain alpha-hydroxy-(omega-1)-oxo fatty acids and alpha-hydroxy-1,omega-dioic fatty acids are cell wall constituents of Legionella (L. jordanis, L. maceachernii and L. micdadei)

Four long-chain fatty acids, 2-hydroxy-27-oxo-octacosanoic acid (n28:0(2-OH,27-oxo)), 2-hydroxy-29-oxo-triacontanoic acid (n30:0(2-OH,29-oxo)), 2-hydroxy-heptacosane-1,27-dioic acid (27:0(2-OH)-dioic) and 2-hydroxy-nonacosane-1,29-dioic acid (29:0(2-OH)-dioic) were identified by GLC-MS analysis in the phenol-chloroform-petroleum ether (PCP) extracts of Legionella jordanis, L. maceachernii and L. micdadei indicating that they are constituents of lipopolysaccharide. Moreover, five long-chain fatty acids (28:0(27-OH), 28:0(27-oxo), 30:0(29-oxo), 27:0-dioic and 29:0-dioic) previously identified in L. pneumophila (Moll, H. et al., FEMS Microbiol. Lett., 97 (1992), 1-6) were also found in these species. This is to our knowledge the first report on the existence of long chain 2-hydroxylated (omega-1)-oxo fatty acids and 2-hydroxylated 1,omega-dioic fatty acids.

Legionella shakespearei sp. nov., isolated from cooling tower water

A Legionella-like organism (strain 214T [T = type strain]) was isolated from a cooling tower in Stratford-upon-Avon, England. This strain required L-cysteine and contained cellular branched-chain fatty acids that are typical of the genus Legionella. Strain 214T produced pink colonies on buffered charcoal-yeast extract agar. Ubiquinone Q-12 was the major quinone. Strain 214T was serologically distinct from other legionellae as determined by a slide agglutination test. The results of DNA hybridization studies showed that strain 214T (= ATCC 49655T) is a member of a new Legionella species, Legionella shakespearei.

Rapid identification of Legionella species from a single colony by gas-liquid chromatography with trimethylsulphonium hydroxide for transesterification

Transesterification of bacterial fatty acids to methyl esters with trimethylsulphonium hydroxide (TMSH) was compared with a conventional method for the identification of Legionella species by capillary gas chromatography. There was an extensive coincidence in the gas chromatographic profiles of bacterial fatty acid methyl esters (FAMEs) obtained by the two methods. However, the TMSH procedure needs less initial material and is much more simple and rapid. The chromatographic pattern of FAMEs obtained from a single colony is sufficient for the identification of the genus Legionella, and L. pneumophila can be clearly distinguished from other Legionella species.