Genetic and virulence characterization of Flavobacterium columnare from channel catfish (Ictalurus punctatus)

Aim: To develop a method for conducting pulsed-field gel electrophoresis (PFGE) on Flavobacterium columnare, to use PFGE to characterize F. columnare channel catfish isolates, and to determine whether variation in pathogenic potential exists in F. columnare isolates from channel catfish. Methods and Results: On the basis of PFGE-derived profiles, similarity dendrograms constructed for more than 30 F. columnare isolates showed two major genetic groups with more than 60% similarity. Channel catfish fingerlings challenged with PFGE group A isolates by bath immersion had significantly higher average mortalities (>60%) than fish challenged with PFGE group B isolates (<9%). However, abrasion and skin mucus removal made channel catfish fingerlings susceptible to disease caused by group B isolates following immersion exposure. Conclusion: Our results suggest that two genetic divisions of F. columnare channel catfish isolates exist, and that isolates in PFGE group A isolates tend to be more pathogenic to immunocompetent channel catfish fingerlings than PFGE group B isolates. Significance and Impact of the Study: PFGE is a potentially useful tool for determining whether F. columnare isolates are more likely to be primary or secondary pathogens. Pathogenesis research for columnaris disease in catfish should focus on pathogenic isolates from PFGE group A.     

Use of suppressive subtractive hybridization to identify Flavobacterium columnare DNA sequences not shared with Flavobacterium johnsoniae

Aims:  To identify specific sequences in the fish pathogen Flavobacterium columnare not shared by Flavobacterium johnsoniae .
Methods and Results:  Suppressive subtractive hybridization (SSH) was used to selectively amplify and clone F. columnare -specific sequences. A highly virulent strain of F. columnare was used as tester and the type strain of F. johnsoniae was used as driver. After library construction, 192 clones were selected and sequenced. From those, 110 clones contained unique F. columnare -specific sequences that were verified using dot blot hybridization. Sequence sizes ranged from 55 to 872 bp with 45 363 bp sequenced in total.
Conclusions:  Specific F. columnare sequences representing all but one (motility related) functional categories were annotated. Several putative virulence factors were identified in F. columnare such as a collagenase, a chondroitinase, proteases, as well as drug resistance and iron transport-related genes.
Significance and Impact of the Study:  Suppressive subtractive hybridization is a cost-effective method for identifying genetic differences between Flavobacterium spp. The number of sequences available from F. columnare has been doubled.     

Chondroitin O-methyl ester: an unusual substrate for chondroitin AC lyase

Chondroitin O-methyl ester was depolymerized by chondroitin AC lyase (EC 4.2.2.5) from Flavobacterium heparinum. The major product isolated from the depolymerization reaction was found to be methyl alpha-L-threo-hex-4-enopyranosyluronate-(1-->4)-2-acetamido-2-deoxy-alpha,beta-D-galactopyranoside.     

High-resolution crystal structure of Arthrobacter aurescens chondroitin AC lyase: an enzyme-substrate complex defines the catalytic mechanism

Chondroitin lyases (EC 4.2.2.4 and EC 4.2.2.5) are glycosaminoglycan-degrading enzymes that act as eliminases. Chondroitin lyase AC from Arthrobacter aurescens (ArthroAC) is known to act on chondroitin 4-sulfate and chondroitin 6-sulfate but not on dermatan sulfate. Like other chondroitin AC lyases, it is capable of cleaving hyaluronan. We have determined the three-dimensional crystal structure of ArthroAC in its native form as well as in complex with its substrates (chondroitin 4-sulfate tetrasaccharide, CS(tetra) and hyaluronan tetrasaccharide) at resolution varying from 1.25 A to 1.9A. The primary sequence of ArthroAC has not been previously determined but it was possible to determine the amino acid sequence of this enzyme from the high-resolution electron density maps and to confirm it by mass spectrometry. The enzyme-substrate complexes were obtained by soaking the substrate into the crystals for varying lengths of time (30 seconds to ten hours) and flash-cooling the crystals. The electron density map for crystals soaked in the substrate for as short as 30 seconds showed the substrate clearly and indicated that the ring of central glucuronic acid assumes a distorted boat conformation. This structure strongly supports the lytic mechanism where Tyr242 acts as a general base that abstracts the proton from the C5 position of glucuronic acid while Asn183 and His233 neutralize the charge on the glucuronate acidic group. Comparison of this structure with that of chondroitinase AC from Flavobacterium heparinum (FlavoAC) provides an explanation for the exolytic and endolytic mode of action of ArthroAC and FlavoAC, respectively.     

Development of an assay and determination of kinetic parameters for chondroitin AC lyase using defined synthetic substrates

Many techniques have been developed for the assay of polysaccharide lyases; however, none have allowed the measurement of defined and reproducible k(cat) and K(m) values due to the inhomogeneous nature of the polymeric substrates. We have designed three different substrates for chondroitin AC lyase from Flavobacterium heparinum that can be monitored by three different techniques: UV/Vis spectroscopy, fluorescence spectroscopy, and use of a fluoride ion-selective electrode. Each is a continuous assay, free from interferences caused by other components present in crude enzyme preparations, and allows meaningful and reproducible kinetic parameters to be determined. The development of these defined synthetic substrates has opened up a wide variety of mechanistic studies that can be performed to elucidate the detailed catalytic mechanism of this, and other, polysaccharide lyases. The application of these techniques, which include kinetic isotope effects and linear free energy analyses, was not possible with the previous polymeric substrates and will allow this relatively poorly understood class of polysaccharide-degrading enzymes to be studied mechanistically.     

Foliar application of l-phenylalanine and ferulic acids to pea plants: induced phenylalanine ammonia lyase activity and resistance against Erysiphe pisi

Phenylalanine ammonia lyase (PAL) activity was measured using HPLC in pea leaves following exogenous application of l-phenylalanine and ferulic acid. Treatment with different concentrations (50, 100 and 150 ppm) of l-phenylalanine caused increased activity of PAL in comparison to the control. In pea leaves treated with 50 ppm l-phenylalanine, maximum PAL activity was observed after 72 h of treatment. Application of ferulic acid first reduced PAL activity at lower concentration (50 ppm) but increased at higher concentrations of the compound (100 and 150 ppm) in pea leaves as compared to the control. Maximum PAL activity was 0.19 nM cinnamic acid/min/g fresh wt. after 24 h at 50 ppm and then increased with time. Treatment with both the compounds significantly reduced conidial germination of Erysiphe pisi on pea leaves. They were equally effective at 100 and 150 ppm in reducing conidial germination. The conidial germination on l-phenylalanine-treated leaves was 26% after 24 h and that on ferulic acid-treated leaves was 34% as compared to the control (46%). Foliar application of different concentrations of l-phenylalanine increased the level of ferulic acid in the leaves of pea plants. Maximum accumulation of ferulic acid (79.3 and 83.5 μg/g fresh wt.) was observed following the application of l-phenylalanine after 24 h and 48 h, respectively. At 50 ppm, ferulic acid accumulation in pea leaves was 35.6 and 39.4 μg/g fresh wt. and 74.3 and 86.5 μg/g fresh wt. at 100 ppm.     

Molecular and Morphological characterization of multiple nucleopolyhedrovirus from Mexico and their insecticidal activity against Spodoptera frugiperda (Lepidoptera: Noctuidae)

The fall armyworm (FAW), Spodoptera frugiperda (Lepidoptera: Noctuidae), is the most important pest of maize in many countries. Entomopathogenic viruses mainly Baculoviruses family are excellent biological control agents and therefore a viable alternative for managing this pest. The aim of this study was to determine the biological activity of eight native nucleopolyhedrovirus (NPVs) against FAW larvae. Additionally, two of the most virulent isolates (SfCH32 and SfCH15) were characterized biologically by bioassays to estimate their median lethal dose (LD₅₀) and median lethal time (LT₅₀), morphologically by scanning electron microscopy (SEM) and transmission electron microscopy (TEM) and molecularly by restriction enzymes. Three (SfCH15, SfCH18 and SfCH32) of the eight tested native nucleopolyhedrovirus isolates caused mortalities ˃98% at 168-hr post-inoculation (hpi) with a dose of 9.2 × 10⁴ OBs/larva. SfCH15 and SfCH32 isolates showed occlusion bodies (OBs) of irregular shape and size (1.02–2.24 μm). The SfCH15 and SfCH32 isolates showed similar median lethal dose (5.6 × 10²–6.4 × 10² OBs/larva). The lowest median lethal time (114.5 hpi) was observed with the SfCH15 isolate at the highest concentration (2.5 × 10⁶ OBs/larva). The DNA restriction profiles for SfCH15 and SfCH32 were different, with their genome size being ~128,000 bp and 132,000 bp, respectively. SfCH15 and SfCH32 isolates showed similar morphological characteristics and the highest virulence against fall armyworm. This study showed that native isolates were highly virulent against S. frugiperda larvae, being similar to other reported strains; however, field studies are required to confirm their insecticidal effect.     

Avian 3-hydroxy-3-methylglutaryl-CoA lyase: sensitivity of enzyme activity to thiol/disulfide exchange and identification of proximal reactive cysteines.

Catalysis by purified avian 3-hydroxy-3-methylglutaryl-CoA lyase is critically dependent on the reduction state of the enzyme, with less than 1% of optimal activity being observed with the air-oxidized enzyme. The enzyme is irreversibly inactivated by sulfhydryl-directed reagents with the rate of this inactivation being highly dependent upon the redox state of a critical cysteine. Methylation of reduced avian lyase with 1 mM 4-methylnitrobenzene sulfonate results in rapid inactivation of the enzyme with a k(inact) of 0.178 min-1. The oxidized enzyme is inactivated at a sixfold slower rate (k(inact) = 0.028 min-1). Inactivation of the enzyme with the reactive substrate analog 2-butynoyl-CoA shows a similar dependence upon the enzyme's redox state, with a sevenfold difference in k(inact) observed with oxidized vs. reduced forms of the enzyme. Chemical cross-linking of the reduced enzyme with stoichiometric amounts of the bifunctional reagents 1,3-dibromo-2-propanone (DBP) or N,N'-ortho-phenylene-dimaleimide (PDM) coincides with rapid inactivation. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of enzyme treated with bifunctional reagent reveals a band of twice the molecular weight of the lyase monomer, indicating that an intersubunit cross-link has been formed. Differential labeling of native and cross-linked protein with [1-14C]iodoacetate has identified as the primary cross-linking target a cysteine within the sequence VSQAACR, which maps at the carboxy-terminus of the cDNA-deduced sequence of the avian enzyme (Mitchell, G.A., et al., 1991, Am. J. Hum. Genet. 49, 101). In contrast, bacterial HMG-CoA lyase, which contains no corresponding cysteine, is not cross-linked by comparable treatment with bifunctional reagent. These results provide evidence for a potential regulatory mechanism for the eukaryotic enzyme via thiol/disulfide exchange and identify a cysteinyl residue with the reactivity and juxtaposition required for participation in disulfide formation.     

Regulation of the catalytic activity of PTP1B: roles for cell adhesion, tyrosine residue 66, and proline residues 309 and 310

The reversible phosphorylation of proteins on tyrosine residues is fundamental to a variety of intracellular signaling pathways and is controlled by the actions of protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs). While much progress has been made in understanding the regulation of PTKs, there is still relatively little known concerning the regulation of PTPs. Using immune complex phosphatase assays, we demonstrated that the enzymatic activity of the nonreceptor type PTP, PTP1B, is regulated by cell adhesion. Placing primary human foreskin fibroblasts (HFFs) in suspension leads to a distinct increase in PTP1B activity, whereas the readhesion of suspended HFFs onto fibronectin or collagen I inhibited activity. To gain insight into the mechanisms involved, we analyzed recombinant forms of PTP1B mutated at potential regulatory sites. Our results indicated that tyrosine residue 66 is essential for maintaining activity at 37 degrees C. We also found that the C-terminal region of PTP1B and localization to the endoplasmic reticulum are not required for the inhibition of activity by cell adhesion. However, analysis of PA-PTP1B, in which alanines are substituted for prolines 309 and 310, revealed an important role for these residues as the catalytic activity of this mutant did not decrease following readhesion onto collagen I. Since the binding of p130cas and Src to PTP1B is dependent upon these proline residues, we assayed the regulation of PTP1B in mouse embryo fibroblasts deficient in these proteins. We found that neither p130cas nor Src is required for the inhibition of PTP1B activity by adhesion to extracellular matrix proteins. Additionally, pretreatment with cytochalasin D did not prevent the reduction of PTP1B activity when cells adhered to collagen I, indicating that cell spreading is not required for this regulation. The control of the catalytic activity of PTP1B by cell adhesion demonstrated in this study is likely to have important implications for growth factor and insulin signaling.     

Identification and characterization of a novel neural cell adhesion molecule (NCAM)-associated protein from quail myoblasts: relationship to myotube formation and induction of neurite-like protrusions

Abstract We identified a novel neural cell adhesion molecule (NCAM)-associated protein, myo genesis-related and N CAM- a ssociated p rotein (MYONAP), the expression of which increases during the formation of myotubes in quail myoblasts transformed with a temperature-sensitive mutant of Rous sarcoma virus (QM-RSV cells). MYONAP shares homology with PL48 in human cytotrophoblasts and KIAA0386 in human brain. Excess expression of MYONAP in presumptive QM-RSV myoblasts induced long protrusions like neurites in cooperation with microtubules. Suppression of MYONAP by antisense cDNA prevented myotubes from forming in spite of the expression of myogenin, creatine kinase, and myosin, and rendered myoblast membranes resistant to fusion. Yeast two-hybrid screening showed that MYONAP interacted with NCAM specifically. Deletion of the NCAM-associated domain resulted in a loss of the function that induces neurite-like protrusions to form and disturbed the elongation of microtubules. The results suggested that MYONAP influenced the functions of microtubules and was involved in the formation of myotubes via its interaction with NCAM.     

Application of MM/PBSA colony free energy to loop decoy discrimination: toward correlation between energy and root mean square deviation

Accurate free energy estimation is needed in many predictive tasks. The molecular mechanics/Poisson-Boltzmann solvent accessible surface area (MM/PBSA) approach has proven to be accurate. However, the correlation between the estimated free energy and the distance (e.g., root mean square deviation [RMSD]) from the most stable conformation is hindered by the strong free energy dependence on minor conformational variations. In this paper, a protocol for MM/PBSA free energy estimation is designed and tested on several loop decoy sets. We show that further integration of MM/PBSA free energy estimator with the colony energy approach makes the correlation between the free energy and RMSD from the native structure apparent, for the test sets on which it could be applied. Our results suggest that (1) the MM/PBSA free energy estimator is able to detect native-like structures for most decoy sets, and (2) application of the colony energy approach greatly hampers the MM/energy strong dependence on minor conformational changes.     

Characterization of macrophage cell line A640-BB-2: A640-BB-2 resembles peritoneal exudate macrophages in cell morphology,tumor cell recognition,responsiveness to immunomodulator OK-432 and lysosomal enzyme activity

Characteristics of mouse macrophage (MP) cell lines A640-BB-2, J774.1 and P388D1 and mouse peritoneal exudate MPs were studied and compared in cell morphology, ability to recognize tumor cells in the presence and absence of OK-432 known to activate MPs, and in lysosomal enzyme activity. In A640-BB-2 cells and exudate MPs, cell surfaces showed a few ridge-like processes and microvilli; spontaneous cytotoxicity was moderate against tumor target L929, and little or absent against targets SV3T3, B-16 and U937; and lysosomal enzyme activity of nonspecific esterase, acid phosphatase, and -glucuronidase was high. After culture in the presence of OK-432, A640-BB-2 cells and exudate MPs showed more extensive spreading with larger surface areas and with increased numbers of ridge-like processes and microvilli, and their cytotoxicity against target L929 became more extensive. The stable soluble factor did not participate in the mechanism of cytotoxicity against target L929 mediated by A640-BB-2 cells and exudate MPs. J774.1 and P388D1 cells were different from exudate MPs in cell morphology and ability to recognize tumor cells when cultured either with or without OK-432, and in lysosomal enzyme activity. A640-BB-2 cells seem to be useful in studying MP-tumor cell interaction and MP activation, and in detecting the trace biological activating factor of MPs.Abbreviations DEM Dulbecco's modified Eagle's medium - MP macrophage - PBS phosphate-buffered saline - SEM scanning electron microscopy     

Chemical characterization and antimicrobial activity of rhizome essential oils of very closely allied Zingiberaceae species endemic to Borneo: Alpinia ligulata K. Schum. and Alpinia nieuwenhuizii Val

Two poorly studied, morphologically allied Alpinia species endemic to Borneo, viz., A. ligulata and A. nieuwenhuizii, were investigated here for their rhizome essential oil. The oil compositions and antimicrobial activities were compared with those of A. galanga, a better known plant. A fair number of compounds were identified in the oils by GC‐FID and GC/MS analyses, with large differences in the oil composition between the three species. The rhizome oil of A. galanga was rich in 1,8‐cineole (29.8%), while those of A. ligulata and A. nieuwenhuizii were both found to be extremely rich in (E)‐methyl cinnamate (36.4 and 67.8%, resp.). The three oils were screened for their antimicrobial activity against three Gram‐positive and three Gram‐negative bacteria and two fungal species. The efficiency of growth inhibition of Staphylococcus aureus var. aureus was found to decline in the order of A. nieuwenhuizii>A. ligulata ～ A. galanga, while that of Escherichia coli decreased in the order of A. galanga>A. nieuwenhuzii ～ A. ligulata. Only the A. galanga oil inhibited the other bacteria and the fungi tested.