The role of transport processes in survival of lactic acid bacteria, Energy transduction and multidrug resistance

Lactic acid bacteria play an essential role in many food fermentation processes. They are anaerobic organisms which obtain their metabolic energy by substrate phosphorylation. In addition three secondary energy transducing processes can contribute to the generation of a proton motive force: proton/substrate symport as in lactic acid excretion, electrogenic precursor/product exchange as in malolactic and citrolactic fermentation and histidine/histamine exchange, and electrogenic uniport as in malate and citrate uptake in Leuconostoc oenos. In several of these processes additional H+ consumption occurs during metabolism leading to the generation of a pH gradient, internally alkaline. Lactic acid bacteria have also developed multidrug resistance systems. In Lactococcus lactis three toxin excretion systems have been characterized: cationic toxins can be excreted by a toxin/proton antiport system and by an ABC-transporter. This cationic ABC-transporter has surprisingly high structural an d functional analogy with the human MDR1-(P-glycoprotein). For anions an ATP-driven ABC-like excretion systems exist.     

Single vesicle tracking for studying synaptic vesicle dynamics in small central synapses

Sustained neurotransmission is driven by a continuous supply of synaptic vesicles to the release sites and modulated by synaptic vesicle dynamics. However, synaptic vesicle dynamics in synapses remain elusive because of technical limitations. Recent advances in fluorescence imaging techniques have enabled the tracking of single synaptic vesicles in small central synapses in living neurons. Single vesicle tracking has uncovered a wealth of new information about synaptic vesicle dynamics both within and outside presynaptic terminals, showing that single vesicle tracking is an effective tool for studying synaptic vesicle dynamics. Particularly, single vesicle tracking with high spatiotemporal resolution has revealed the dependence of synaptic vesicle dynamics on the location, stages of recycling, and neuronal activity. This review summarizes the recent findings from single synaptic vesicle tracking in small central synapses and their implications in synaptic transmission and pathogenic mechanisms of neurodegenerative diseases.     

A Stretch of Unpaired Purines in the Leader Region of Simian Immunodeficiency Virus (SIV) Genomic RNA is Critical for its Packaging into Virions

Simian immunodeficiency virus (SIV) is an important lentivirus used as a non-human primate model to study HIV replication, and pathogenesis of human AIDS, as well as a potential vector for human gene therapy. This study investigated the role of single-stranded purines (ssPurines) as potential genomic RNA (gRNA) packaging determinants in SIV replication. Similar ssPurines have been implicated as important motifs for gRNA packaging in many retroviruses like, HIV-1, MPMV, and MMTV by serving as Gag binding sites during virion assembly. In examining the secondary structure of the SIV 5′ leader region, as recently deduced using SHAPE methodology, we identified four specific stretches of ssPurines (I-IV) in the region that harbors major packaging determinants of SIV. The significance of these ssPurine motifs were investigated by mutational analysis coupled with a biologically relevant single round of replication assay. These analyses revealed that while ssPurine II was essential, the others (ssPurines I, III, & IV) did not significantly contribute to SIV gRNA packaging. Any mutation in the ssPurine II, such as its deletion or substitution, or other mutations that caused base pairing of ssPurine II loop resulted in near abrogation of RNA packaging, further substantiating the crucial role of ssPurine II and its looped conformation in SIV gRNA packaging. Structure prediction analysis of these mutants further corroborated the biological results and further revealed that the unpaired nature of ssPurine II is critical for its function during SIV RNA packaging perhaps by enabling it to function as a specific binding site for SIV Gag.     

The mode of speciation during a recent radiation in open-ocean phytoplankton

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Phylogeography of the banded killifish (Fundulus diaphanus): glacial races and secondary contact

Spatial patterns of morphological and genetic polymorphisms between the two banded killifish sub-species ( Fundulus diaphanus diaphanus and F. d. menona ) provide evidence that these sub-species represent distinct evolutionary lineages corresponding to glacial races of Atlantic and Mississippian origins. Individuals with intermediate phenotypes in Lake Ontario and the upper St Lawrence River probably result from secondary contacts between these races. The hybrid zone unexpectedly extends to Lake Erie and involves the introgression of the F. d. diaphanus mitochondrial genome into fish with morphology like that of F. d. menona .     

Semioticians Make Strange Bedfellows! Or, Once Again: “Is Language a Primary Modelling System?”

Like other sciences, biosemiotics also has its time-honoured archive, consisting of writings by those who have been invented and revered as ancestors of the discipline. One such example is Jakob von Uexküll. As to the people who ‘invented’ him, they are either, to paraphrase a French cliché, ‘agents du cosmopolitisme sémiotique’ like Thomas Sebeok, or de jure and de facto progenitor like Thure von Uexküll. In the archive is the special issue of Semiotica 42. 1 (1982) edited by the late Sebeok and introduced by Thure von Uexküll. It is in the opening essay that Thure von UexküIl tries to restore Jakob von Uexküll’s role as a precursor of semiotics by negotiating the Elder with Saussure and the linguistics-oriented ‘semiology’ in his wake. However, semiotic mapping, in the strictly ‘disciplinary’ sense, of Jakob von Uexküll is no easy task because he ‘knew neither Peirce nor Saussure and did not use their terminology’ (Thure von Uexküll 1982,2). Because Thure prefers to call the Elder’s science ‘general semiotics’ (Thure von Uexküll 1982), this paper begins by assessing Thure von Uexküll’s semiotic configuration of Jakob, probe into the force and limits of the linguistic analogy, revisit the already time-honoured debate on the primary and secondary modelling systems, which was made famous by the Moscow-Tartu semioticians in the early 1970s, but severely criticized by Sebeok and his followers. The paper engages Sebeok from several fronts, directed first at his relegation of the Saussurian linguistic model, then at his critique of the Primary Modelling System, and finally at his reservation about evolutionism in light of the current debate on gene/meme co-evolution. Paper presented at the Eighth Annual International Gatherings in Biosemiotics University of the Aegean, Syros, Greece, 23–28 June 2008     

Human mitochondrial complex I assembly: A dynamic and versatile process

One can but admire the intricate way in which biomolecular structures are formed and cooperate to allow proper cellular function. A prominent example of such intricacy is the assembly of the five inner membrane embedded enzymatic complexes of the mitochondrial oxidative phosphorylation (OXPHOS) system, which involves the stepwise combination of > 80 subunits and prosthetic groups encoded by both the mitochondrial and nuclear genomes. This review will focus on the assembly of the most complicated OXPHOS structure: complex I (NADH:ubiquinone oxidoreductase, EC 1.6.5.3). Recent studies into complex I assembly in human cells have resulted in several models elucidating a thus far enigmatic process. In this review, special attention will be given to the overlap between the various assembly models proposed in different organisms. Complex I being a complicated structure, its assembly must be prone to some form of coordination. This is where chaperone proteins come into play, some of which may relate complex I assembly to processes such as apoptosis and even immunity.     

Molecular evidence for introgressive hybridization in New Zealand masked gulls

We used mitochondrial DNA (mtDNA) gene sequences and nuclear microsatellite loci to investigate the extent and outcome of hybridization between the Black-billed Gull Chroicocephalus bulleri and the Red-billed Gull Chroicocephalus novaehollandiae scopulinus in New Zealand. Six of 26 sampled Black-billed Gulls possessed mtDNA typical of Red-billed Gulls, but allele frequencies at six polymorphic microsatellites provided little evidence of mixed ancestry expected in very recent hybrids. None of the Red-billed Gulls sampled from different colonies possessed Black-billed Gull mtDNA expected in the reciprocal cross, suggesting that hybridization in the two species typically occurs between female Red-billed Gulls and Black-billed Gull males. The lack of any hybrid signal in the nuclear loci indicates that there has been extensive backcrossing with Black-billed Gulls, effectively diluting the Red-billed Gull nuclear DNA contribution. Divergence of Red-billed Gulls and Black-billed Gulls occurred approximately 250 000 years ago, indicating that unsorted ancestral polymorphism is an unlikely alternative to hybridization. Comparing demographic models within an approximate Bayesian computation (ABC) framework, we confirm that the observed patterns cannot result from incomplete lineage sorting. Using an ABC random forest approach, we determined that the most likely model explaining the data is a recent introgression scenario, whereby unidirectional gene flow is re-established following a period of strict isolation. The ability of Black-billed and Red-billed Gulls to successfully interbreed shows that despite significant differentiation (F_ST > 0.3), there has been insufficient time for the two species to develop complete reproductive isolation. The apparent one-way transfer of Red-billed Gull mtDNA into Black-billed Gulls and extensive backcrossing argues against cytoplasmic–nuclear genome incompatibilities between the two species. We hypothesize that the specific mate recognition system cued on colours of soft parts normally functions to prevent hybridization, but that it can break down under demographic conditions where there is a shortage of available mates and a surplus of females in the Red-billed Gull population. The high incidence of introgression in Black-billed Gulls conflicts with field observations that interbreeding is extremely rare.     

Requirement of the Pro-Cys-His-Arg sequence for O6-methylguanine-DNA methyltransferase activity revealed by saturation mutagenesis with negative and positive screening

O⁶-Methylguanine-DNA methyltransferase catalyzes transfer of a methyl group from O⁶-methylguanine and O⁴-methylthymine of DNA to a cysteine residue of the enzyme protein, thereby repairing the mutagenic and carcinogenic lesions in a single-step reaction. There are highly conserved amino acid sequences around the methyl-accepting cysteine site in eleven molecular species of methyltransferases. To elucidate the significance of the conserved sequence, amino acid substitutions were introduced by site-directed mutagenesis of the cloned DNA for Escherichia coli Ogt methyltransferase, and the activity and stability of mutant forms of the enzyme were examined. When cysteine-139, to which methyl transfer occurs, was replaced by other amino acids, all of the mutants showed the methyltransferase-negative phenotype. Methyltransferase-positive revertants, isolated from one of the negative mutants, had restored codons for cysteine. Thus the cysteine residue is essential for acceptance of the methyl group and is not replaceable by other amino acids. Using this negative and positive selection procedure, the analysis was extended to other residues near the acceptor site. At the histidine-140 and arginine-141 sites, all the positive revertants isolated carried codons for amino acids identical to those of the wild-type protein. At proline-138, five substitutions (serine, glutamine, threonine, histidine, and alanine) exhibited the positive phenotype but levels of methyltransferase activity in extracts of cells harboring these mutant forms were very low. This suggests that the proline residue at this site is important for maintaining the proper conformation of the protein. With valine-142 substitutions there were seven types of positive revertants, among which mutants carrying isoleucine, cysteine, leucine, and alanine showed relatively high levels of methyltransferase activity. These results indicate that the sequence Pro-Cys-His-Arg is a sine qua non for methyltransferase to exert its function.