Metagenomic analysis of the microbial community in fermented grape marc reveals that Lactobacillus fabifermentans is one of the dominant species: insights into its genome structure

Grape marc used for the production of distilled beverages undergoes prolonged storage which allows alcoholic fermentation to occur. Harsh conditions including low pH, limited oxygen and nutrients, temperature fluctuations, and high ethanol concentrations imposed by that environment create a strong selective pressure on microorganisms. A detailed characterization of the bacterial community during two time points of the fermentation process was performed using high-throughput sequencing of the V3–V6 16S rDNA hypervariable regions. The results revealed a marked reduction in the number of bacterial species after 30 days of incubation and made it possible to identify those species that are able to grow in that extreme environment. The genome sequence of Lactobacillus fabifermentans, one of the dominant species identified, was then analyzed using shotgun sequencing and comparative genomics. The results revealed that it is one of the largest genomes among the Lactobacillus sequenced and is characterized by a large number of genes involved in carbohydrate utilization and in the regulation of gene expression. The genome was shaped through a large number of gene duplication events, while lateral gene transfer contributed to a lesser extent with respect to other Lactobacillus species. According to genomic analysis, its carbohydrate utilization pattern and ability to form biofilm are the main genetic traits linked to the adaptation the species underwent permitting it to grow in fermenting grape marc.     

Short repetitive sequences in green algal mitochondrial genomes: potential roles in mitochondrial genome evolution

Current data on green algal mitochondrial genomes suggest an unexpected dichotomy within the group with respect to genome structure, organization, and sequence affiliations. The present study suggests that there is a correlation between this dichotomy on one hand and the differences in the abundance, base composition, and distribution of short repetitive sequences we observed among green algal mitochondrial genomes on the other. It is conceivable that the accumulation of GC- rich short repeated sequences in the Chlamydomonas-like but not Prototheca-like mitochondrial genomes might have triggered evolutionary events responsible for the distinct series of evolutionary changes undergone by the two green algal mitochondrial lineages. The similarity in base composition, nucleotide sequence, abundance, and mode of organization we observed between the short repetitive sequences present in Chlamydomonas-like mitochondrial genomes on one hand and fungal and vertebrate homologs on the other might extend to some of the roles that the short repetitive sequences have been shown to have in the latter. Potential involvements we propose for the short repetitive sequences in the evolution of Chlamydomonas-like mitochondrial genomes include fragmentation and scrambling of the ribosomal-RNA-coding regions, extensive gene rearrangements, coding-region deletions, surrogate origins of replication, and chromosomal linearization.      

Establishment and maintenance of nuclear position during zoospore formation in allomyces macrogynus: roles of the cytoskeleton

The involvement of the microtubule (MT) and actin microfilament (MF) cytoskeletons in establishing nuclear positions during zoosporogenesis in Allomyces macrogynus was assessed using selective cytoskeletal disrupting treatments and documented with light microscopy. These experiments were coupled with low-speed centrifugation studies to determine the degree to which cytoskeletal elements anchor nuclear position. At the onset of zoospore formation, nuclei were positioned only in cortical cytoplasmic regions of the zoosporangia (ZS). Immunofluorescence microscopy revealed that MTs primarily emanated from centrosomal regions into the surrounding cytoplasm at this stage. During delimitation of the cytoplasm into individual uninucleate zoospores, nuclei migrated from cortical regions to become distributed throughout the cytoplasm. Coincident with nuclear migrations, MTs were primarily organized at and emanated from nuclear surfaces, forming extensive perinuclear arrays. Nuclear migrations were suppressed in ZS induced to sporulate in the presence of cytochalasin D, an actin MF inhibiting compound. Disruption of MTs with nocodazole did not block nuclear migrations, although resultant nuclear spacing was irregular. Centrifugation treatments of control and drug-treated ZS demonstrated that nuclear positions were stabilized by perinuclear MT arrays. The results indicate that nuclear motility in ZS of A. macrogynus is the result of an actin-based system while perinuclear MTs arrays function to establish and fix nuclear position during zoospore formation. Copyright 1998 Academic Press.     

Mycorrhizae from Denali National Park and Preserve,Alaska

 Roots of 40 taxa of higher plants (Pteridophyta, Spermatophyta) from two alpine study sites in Denali National Park and Preserve in central Alaska were examined for their mycorrhizal colonization. We observed ectomycorrhizae on six species: Betula nana, Salix reticulata, Salix polaris, Salix arctica, Polygonum viviparum, and Dryas octopetala. Seven taxa, Cassiope tetragona, Empetrum nigrum, Ledum palustre subsp. decumbens, Ledum palustre subsp. groenlandicum, Loiseleuria procumbens, Vaccinium uliginosum and Vaccinium vitis–idaea (all Ericales), had ericoid mycorrhizae. One species, Arctostaphylos alpina, formed a typical arbutoid mycorrhiza. Two species (Sibbaldia procumbens and Aconitum delphinifolium) showed well-developed VA mycorrhizae, whereas three species of plants (Lycopodium clavatum, Silene acaulis and Oxytropis scammaniana) had vesicles, but no arbuscules. The roots of 11 other plants (Lycopodium clavatum, Lycopodium selago, Silene acaulis, Gentiana algida, Lupinus arcticus, Oxytropis scammaniana, Pedicularis langsdorffii, Pedicularis capitata, Pedicularis verticillata, Artemisia sp. and Carex bigelowii) had a variety of intracellular colonizations which are referred to as dark septate fungi. No mycorrhizae were found on 12 other plants: Equisetum arvense, Equisetum variegatum, Lycopodium alpinum, Polygonum bistorta, Saxifraga hieracifolia, Saxifraga hirculus, Astragalus alpinus, Pedicularis kanei, Petasites frigidus, Carex podocarpa, Carex microchaeta and Poa arctica. A possible ecological role of dark septate fungi is discussed. Accepted: 4 August 1995     

Limited proteolysis of a disulfide-linked apoA-I dimer in reconstituted HDL

The apolipoprotein A-I(Milano) (apoA-I(M)) is a molecular variant of apoA-I characterized by the Arg(173)-->Cys substitution, leading to the formation of homodimers A-I(M)/A-I(M). Upon interaction with palmitoyloleoylphosphatidylcholine, A-I(M)/A-I(M) forms only two species of reconstituted HDL (rHDL) particles, with diameters of 7.8 and 12.5 nm. We used limited proteolysis to analyze the conformation of A-I(M)/A-I(M) in the two rHDL particles, in comparison with that of apoA-I in rHDL of similar size. ApoA-I in the small, 7.8-nm rHDL is degraded to a greater extent (50% after 6 h) than in the large rHDL (<10% degraded after 6 h). The protease susceptibility of A-I(M)/A-I(M) in small and large rHDL is instead remarkably the same, with A-I(M)/A-I(M) being much more sensitive to proteolytic digestion (50% degraded after 10 min) than apoA-I. The identification of the proteolytic fragments by immunoblotting, N-terminal sequencing, and molecular mass determination, shows that the N-terminus of both proteins is resistant to proteolysis, with six cleavage sites located in the central and carboxy-terminal portions of the molecules. Cleavage in the middle of apoA-I occurs at distinct sites in 7.8-nm (Lys(118)) and 12.7-nm (Arg(123)) rHDL, indicating a different conformation in small and large rHDL particles. The A-I(M)/A-I(M) instead adopts a unique and identical conformation in small and large rHDL, with the carboxy-terminal portion of the molecule being remarkably more accessible to the proteases than in apoA-I. This suggests the presence of a novel carboxy-terminal domain in A-I(M)/A-I(M), not organized in a compact structure and not shared by wild-type apoA-I, which may account for the unique functional properties of A-I(M)/A-I(M).