Reassessment of the succession of lactic acid bacteria in commercial cucumber fermentations and physiological and genomic features associated with their dominance.

A compositional re-assessment of the microbiota present in commercial cucumber fermentation using culture independent and dependent methods was conducted, with emphasis on lactic acid bacteria (LAB). Two commercial cucumber fermentation tanks were monitored by measuring pH, dissolved oxygen and temperature, and used as sources of samples for microbial plating, genomic DNA extraction and measurement of organic acids and carbohydrates by HPLC. Six additional commercial tanks were included to identify the dominant microorganisms using molecular methods. A comparative analysis of the publically available genome sequences corresponding to the LAB found in cucumber fermentations was completed to gain an understanding of genomic features possibly enabling dominance. Analyses of the microbiota suggest Lactobacillales prevail in cucumber fermentations, including in order of prevalence Lactobacillus pentosus, Lb. plantarum, Lb. brevis, Weissella spp., Pediococcus ethanolidurans, Leuconostoc spp. and Lactococcus spp. It was observed that Lb. pentosus and Lb. plantarum have comparatively larger genomes, higher gene counts, uniquely distribute the ribosomal clusters across the genome as opposed to close to the origin of replication, and possess more predicted amino acids prototrophies and selected biosynthesis related genes. It is theorized that Lb. pentosus and Lb. plantarum dominance in cucumber fermentations is the result of their genetic make-up.

Bassoon, a novel zinc-finger CAG/glutamine-repeat protein selectively localized at the active zone of presynaptic nerve terminals.

The molecular architecture of the cytomatrix of presynaptic nerve terminals is poorly understood. Here we show that Bassoon, a novel protein of >400,000 Mr, is a new component of the presynaptic cytoskeleton. The murine bassoon gene maps to chromosome 9F. A comparison with the corresponding rat cDNA identified 10 exons within its protein-coding region. The Bassoon protein is predicted to contain two double-zinc fingers, several coiled-coil domains, and a stretch of polyglutamines (24 and 11 residues in rat and mouse, respectively). In some human proteins, e.g., Huntingtin, abnormal amplification of such poly-glutamine regions causes late-onset neurodegeneration. Bassoon is highly enriched in synaptic protein preparations. In cultured hippocampal neurons, Bassoon colocalizes with the synaptic vesicle protein synaptophysin and Piccolo, a presynaptic cytomatrix component. At the ultrastructural level, Bassoon is detected in axon terminals of hippocampal neurons where it is highly concentrated in the vicinity of the active zone. Immunogold labeling of synaptosomes revealed that Bassoon is associated with material interspersed between clear synaptic vesicles, and biochemical studies suggest a tight association with cytoskeletal structures. These data indicate that Bassoon is a strong candidate to be involved in cytomatrix organization at the site of neurotransmitter release.

[Structure and chromosomal localization of human neurogranin gene]. / Struktura i khromosomnaia lokalizatsiia gena neirogranina cheloveka.

A 12.5-kb DNA fragment containing the entire human neurogranin gene (hng) was isolated from the genomic phage library using the human neurogranin (hNG) cDNA as a probe. The gene consists of four exons and three introns. The first two exons include the nucleotide sequence that encodes the complete 78-amino acid sequence of neurogranin. It is shown that the genome organization of hug is essentially similar to that of the homologous rat neurogranin gene (rng). The hng gene has several potential transcription start sites, and the promoter region is characterized by the absence of the CCAAT and TATA boxes in the proximal region upstream from the transcription start sites. The 5'-flanking region of hng has a domain with multiple AT-rich motifs, which is similar to the region present nearly at the same position in the promoter of rng. It was shown by fluorescence in situ hybridization that hng is located on chromosome 11 in the region 11q23.3-q24.1.

Evidence for synergistic and complementary roles of Bassoon and darkness in organizing the ribbon synapse.

Ribbon synapses are tonically active high-throughput synapses. The performance of the ribbon synapse is accomplished by a specialization of the cytomatrix at the active zone (CAZ) referred to as the synaptic ribbon (SR). Progress in our understanding of the structure-function relationship at the ribbon synapse has come from observations that, in photoreceptors lacking a full-size scaffolding protein Bassoon (Bsn(ΔEx4/5)), dissociation of SRs coincides with perturbed signal transfer. The aim of the present study has been to elaborate the role of Bassoon as a structural organizer of the ribbon synapse and to differentiate it with regard to the ambient lighting conditions. The ultrastructure of retinal ribbon synapses has been compared between wild-type (Wt) and Bsn(ΔEx4/5) mice adapted to light (low activity) and darkness (high activity). The results obtained suggest that Bassoon and environmental illumination synergistically and complementarily act as organizers of the ribbon synapse. Thus, light-dependent and Bassoon-independent regulation involves initial SR tethering to the membrane and a basic shape transition of ribbon material from spherical to rod-like, since darkness induces these features in Bsn(ΔEx4/5) rod spherules. However, the tight anchorage of the SR via an arciform density and the proper assembly of SRs to the full-sized horseshoe-shaped complex depend on Bassoon, as these steps fail in Bsn(ΔEx4/5) rod spherules.

Molecular organization of excitatory chemical synapses in the mammalian brain.

Chemical synapses are highly specialized cell-cell junctions designed for efficient signaling between nerve cells. Distinct cytoskeletal matrices are assembled at either side of the synaptic junction. The presynaptic cytomatrix at the active zone (CAZ) defines and organizes the site of neurotransmitter release from presynaptic nerve terminals. The postsynaptic density (PSD) tethers neurotransmitter receptors and the postsynaptic signal transduction machinery. Recent progress in the identification and characterization of novel CAZ and PSD components has revealed new insights into the molecular organization and assembly mechanisms of the synaptic neurotransmission apparatus. On the presynaptic side, Bassoon and Piccolo, two related giant proteins, are crucially involved in scaffolding the CAZ. On the postsynaptic side, two families of multidomain adaptor proteins, the MAGuKs (membrane-associated guanylate kinase homologs) and the ProSAP (proline-rich synapse-associated protein, also termed Shank) family members are thought to be major organizing molecules of the PSD.

Dipeptide uptake by adenohypophysial folliculostellate cells.

Dipeptide uptake was studied in primary cultures from rat anterior pituitaries by use of radiolabeled carnosine and the fluorescent dipeptide derivative beta-Ala-Lys-N epsilon-AMCA (AMCA is 7-amino-4-methylcoumarin-3-acetic acid). Fluorescence microscopic studies revealed that the reporter peptide specifically accumulated in the S-100 positive folliculostellate cells that do not produce any known hormone. The dipeptide derivative was taken up in unmetabolized form by an energy-dependent saturable process with apparent kinetic constants as follows: Michaelis constant, 19 microM; maximum velocity, 5.5 nmol.mg protein-1.h-1. This high-affinity transporter was strongly affected by inhibitors of sodium/proton exchangers and thus appeared to be driven by a proton gradient. Competition studies revealed that the peptide transporter exhibits broad substrate specificity with a preference for hydrophobic dipeptides. In contrast to free amino acids and the pseudotetrapeptide amastatin, tripeptides were also accepted. Compounds without an alpha- and beta-amino group, such as captopril, thiorphan, and benzylpenicillin, did not affect uptake of the reporter peptide, although they were substrates of the well-characterized intestinal and renal dipeptide transporters.

The peptide transporter PepT2 is expressed in rat brain and mediates the accumulation of the fluorescent dipeptide derivative beta-Ala-Lys-Nepsilon-AMCA in astrocytes.

We describe the synthesis of a fluorescent dipeptide derivative, beta-Ala-Lys-Nepsilon-AMCA, which could be used as an excellent reporter molecule for studying the oligopeptide transport system in brain cell cultures. Fluorescence microscopic and immunocytochemical studies revealed that the reporter peptide specifically accumulated in astrocytes (type I and II) and O-2A progenitor cells but not in neurons or differentiated oligodendrocytes. In astroglia-rich cell culture the dipeptide derivative is taken up in unmetabolized form by an energy dependent, saturable process with apparent kinetic constants of KM = 28 microM and Vmax = 6 nmol x h(-1) x mg protein(-1) at pH 7.2. Competition studies revealed that the accumulation of beta-Ala-Lys-Nepsilon-AMCA is strongly inhibited by dipeptides and pseudopeptides such as bestatin, arphamenine A and B. The biochemical data indicated that the properties of this high-affinity oligopeptide carrier closely resemble those of the renal peptide transport system PepT2 and Northern blot analysis demonstrated that PepT2 mRNAis expressed in glial but not in neuronal cell cultures. In situ hybridization histochemistry also revealed a non-neuronal localization of PepT2 transcripts and a diffuse, widespread distribution of PepT2 signals throughout the entire rat brain. The selective accumulation of the fluorescent reporter molecule by brain cells under viable conditions may provide a useful tool for studying peptide uptake systems and other aspects of astroglial physiology.

Membrane association of presynaptic cytomatrix protein bassoon.

Components of the specialized cytomatrix at active zones of presynaptic nerve terminals are thought to be involved in organizing synaptic events such as immobilisation or translocation of synaptic vesicles and assemblingactive zone components. The 420-kDa non-transmembraneprotein Bassoon is a specific componentof the presynaptic cytomatrix that shares features with both cytoskeleton-associated and peripheral-membrane proteins. Using immunogold electron microscopy we show here that synapse associated Bassoon is distributed in a subregion of active zones. Using a biochemical assay we show that a fraction of Bassoon is membrane associated. Electron microscopy performed on the same biochemical fraction further revealed that Bassoon is associated with vesicular structures. Together these data suggest that at least a fraction of Bassoon is associated with a membraneous compartment in neurons.

The presynaptic cytomatrix protein Bassoon: sequence and chromosomal localization of the human BSN gene.

Bassoon is a novel 420-kDa protein recently identified as a component of the cytoskeleton at presynaptic neurotransmitter release sites. Analysis of the rat and mouse sequences revealed a polyglutamine stretch in the C-terminal part of the protein. Since it is known for some proteins that abnormal amplification of such polyglutamine regions can cause late-onset neurodegeneration, we cloned and localized the human BASSOON gene (BSN). Phage clones spanning most of the open reading frame and the 3' untranslated region were isolated from a human genomic library and used for chromosomal localization of BSN to chromosome 3p21 by FISH. The localization was confirmed by PCR on rodent/human somatic cell hybrids; it is consistent with the localization of the murine Bsn gene at chromosome 9F. Sequencing revealed a polyglutamine stretch of only five residues in human, and PCR amplifications from 50 individuals showed no obvious length polymorphism in this region. Analysis of the primary structure of Bassoon and comparison to previous database entries provide evidence for a newly emerging protein family.

Temporal appearance of the presynaptic cytomatrix protein bassoon during synaptogenesis.

Bassoon is a 420-kDa presynaptic cytomatrix protein potentially involved in the structural organization of neurotransmitter release sites. In this study, we have investigated a possible role for Bassoon in synaptogenesis and in defining synaptic vesicle recycling sites. We find that it is expressed at early stages of neuronal differentiation in which it is selectively sorted into axons. As synaptogenesis begins, Bassoon clusters appear along dendritic profiles simultaneously with synaptotagmin I, sites of synaptic vesicle recycling, and the acquisition of functional excitatory and inhibitory synapses. A role for Bassoon in the assembly of excitatory and inhibitory synapses is supported by the colocalization of Bassoon clusters with clusters of GKAP and AMPA receptors as well as GABA(A) receptors. These data indicate that the recruitment of Bassoon is an early step in the formation of synaptic junctions.