| idiomarina loihiensis sp. nov., a halophilic gamma-proteobacterium from the lō'ihi submarine volcano, hawai'i. | during an investigation of bacterial diversity at hydrothermal vents on the lō'ihi seamount, hawai'i, a novel bacterium (designated l2-tr(t)) was cultivated, which shares 99.9 % 16s rrna gene sequence similarity over 1415 nt with an uncultured eubacterium from sediment at a depth of 11 000 m in the mariana trench. the nearest cultivated neighbour of l2-tr(t), however, is idiomarina abyssalis kmm 227(t), with which it shares 98.9 % 16s rrna sequence similarity. l2-tr(t) differed from i. abyssalis ... | 2003 | 14657116 |
| genome sequence of the deep-sea gamma-proteobacterium idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. | we report the complete genome sequence of the deep-sea gamma-proteobacterium, idiomarina loihiensis, isolated recently from a hydrothermal vent at 1,300-m depth on the loihi submarine volcano, hawaii. the i. loihiensis genome comprises a single chromosome of 2,839,318 base pairs, encoding 2,640 proteins, four rrna operons, and 56 trna genes. a comparison of i. loihiensis to the genomes of other gamma-proteobacteria reveals abundance of amino acid transport and degradation enzymes, but a loss of ... | 2004 | 15596722 |
| flagellar filaments of the deep-sea bacteria idiomarina loihiensis belong to a family different from those of salmonella typhimurium. | the helical filaments of the bacterial flagella so far studied seem to be universal in the bacterial kingdom. despite the variation in flagellin molecular masses, which range from 24 kda to 62 kda in different species, there are only two forms: either the so-called normal (left-handed) or the curly (right-handed). the normal and curly helical forms are asymmetric; the two characteristic helical parameters, which are the pitch and diameter, of normal filaments are twice those of curly filaments. ... | 2005 | 16120444 |
| bioinformatic analysis of an unusual gene-enzyme relationship in the arginine biosynthetic pathway among marine gamma proteobacteria: implications concerning the formation of n-acetylated intermediates in prokaryotes. | the n-acetylation of l-glutamate is regarded as a universal metabolic strategy to commit glutamate towards arginine biosynthesis. until recently, this reaction was thought to be catalyzed by either of two enzymes: (i) the classical n-acetylglutamate synthase (nags, gene arga) first characterized in escherichia coli and pseudomonas aeruginosa several decades ago and also present in vertebrates, or (ii) the bifunctional version of ornithine acetyltransferase (oat, gene argj) present in bacteria, a ... | 2006 | 16409639 |
| solving ambiguities in contig assembly of idiomarina loihiensis l2tr chromosome by in silico analyses. | nucleotide composition analyses of bacterial genomes such as cumulative gc skew highlight the atypical, strongly asymmetric architecture of the recently published chromosome of idiomarina loihiensis l2tr, suggesting that an inversion of a 600-kb chromosomal segment occurred. the presence of 3.4-kb inverted repeated sequences at the borders of the putative rearrangement supports this hypothesis. reverting in silico this segment restores (1) a symmetric chromosome architecture; (2) the co-orientat ... | 2007 | 17442016 |
| comparing patterns of natural selection across species using selective signatures. | comparing gene expression profiles over many different conditions has led to insights that were not obvious from single experiments. in the same way, comparing patterns of natural selection across a set of ecologically distinct species may extend what can be learned from individual genome-wide surveys. toward this end, we show how variation in protein evolutionary rates, after correcting for genome-wide effects such as mutation rate and demographic factors, can be used to estimate the level and ... | 2008 | 18266472 |
| ca-mg kutnahorite and struvite production by idiomarina strains at modern seawater salinities. | the production of mg-rich carbonates by idiomarina bacteria at modern seawater salinities has been investigated. with this objective, four strains: idiomarina abyssalis (strain atcc baa-312), idiomarina baltica (strain dsm 15154), idiomarina loihiensis (strains dsm 15497 and mah1) were used. the strain i. loihiensis mah1 is a new isolate, identified in the scope of this work. the four moderately halophilic strains precipitated struvite (nh4mgpo4 x 6h2o) crystals that appear encased by small ca-m ... | 2008 | 18355891 |
| polar, peritrichous, and lateral flagella belong to three distinguishable flagellar families. | the bacterial flagellum transforms its shape into several distinguishable helical shapes (polymorphs) under various environmental conditions. polymorphs of each type of flagellum stay on a circle in the pitch-diameter (p versus pid) plot, indicating that they all belong to one family. previously, we showed that the flagellar family of a marine bacterium idiomarina loihiensis (family ii) differed from the conventional flagellar family of salmonella typhimurium (family i). the pitch and diameter o ... | 2008 | 18455187 |
| characterization of a deep-sea sediment metagenomic clone that produces water-soluble melanin in escherichia coli. | to access to the microbial genetic resources of deep-sea sediment by a culture-independent approach, the sediment dna was extracted and cloned into fosmid vector (pcc1fos) generating a library of 39,600 clones with inserts of 24-45 kb. the clone fss6 producing red-brown pigment was isolated and characterized. the pigment was identified as melanin according to its physico-chemical characteristics. subcloning and sequences analyses of fss6 demonstrated that one open reading frame (orf2) was respon ... | 2009 | 18648877 |
| locked chromophore analogs reveal that photoactive yellow protein regulates biofilm formation in the deep sea bacterium idiomarina loihiensis. | idiomarina loihiensis is a heterotrophic deep sea bacterium with no known photobiology. we show that light suppresses biofilm formation in this organism. the genome of i. loihiensis encodes a single photoreceptor protein: a homologue of photoactive yellow protein (pyp), a blue light receptor with photochemistry based on trans to cis isomerization of its p-coumaric acid (pca) chromophore. the addition of trans-locked pca to i. loihiensis increases biofilm formation, whereas cis-locked pca decreas ... | 2009 | 19891493 |
| respiratory kinetics of marine bacteria exposed to decreasing oxygen concentrations. | during aerobic respiration, microorganisms consume oxygen (o2) through the use of different types of terminal oxidases which have a wide range of affinities for o2. the km values for o2 of these enzymes have been determined to be in the range of 3 to 200 nmol liter(-1). in this study, we examined the time course of development of aerobic respiratory kinetics of four marine bacterial species (dinoroseobacter shibae, roseobacter denitrificans, idiomarina loihiensis, and marinobacter daepoensis) du ... | 2016 | 26682857 |
| biosorption and biomineralization of u(vi) by the marine bacterium idiomarina loihiensis mah1: effect of background electrolyte and ph. | the main goal of this study is to compare the effects of ph, uranium concentration, and background electrolyte (seawater and naclo4 solution) on the speciation of uranium(vi) associated with the marine bacterium idiomarina loihiensis mah1. this was done at the molecular level using a multidisciplinary approach combining x-ray absorption spectroscopy (xas), time-resolved laser-induced fluorescence spectroscopy (trlfs), and high resolution transmission electron microscopy (hrtem). we showed that t ... | 2014 | 24618567 |
| molecular characterization of a new n-acetylneuraminate synthase (neub1) from idiomarina loihiensis. | n-acetylneuraminate lyase synthase (neub; e.c. 2.5.1.56) is a key enzyme in pathogenic microorganisms for producing n-acetylneuraminic acid through the irreversible condensation of n-acetylmannosamine (mannac) and phosphoenolpyruvate (pep). however, nothing is known about this enzyme in non-pathogenic bacteria. this paper describes, for the first time, one of the two putative n-acetylneuraminate synthases from the halophilic non-pathogenic gamma-proteobacterium idiomarina loihiensis neub1 (ilneu ... | 2015 | 25214154 |
| induction of apoptosis in cancer cell lines by the red sea brine pool bacterial extracts. | marine microorganisms are considered to be an important source of bioactive molecules against various diseases and have great potential to increase the number of lead molecules in clinical trials. progress in novel microbial culturing techniques as well as greater accessibility to unique oceanic habitats has placed the marine environment as a new frontier in the field of natural product drug discovery. | 2013 | 24305113 |
| assessment of bacterial community composition in response to uranium levels in sediment samples of sacred cauvery river. | global industrialization is a major cause of effluent discharge from industries up to alarming concentrations. especially, uranium concentrations in water bodies are of great concern, as its radioactivity significantly affects the persistent diversity of microbiota. recently, continuous application of pesticides in the agricultural lands and accumulation of quartz that enter the cauvery river has significantly increased the concentration of uranium (u) and other heavy metals. to perceive the imp ... | 2017 | 27812801 |