A Phylogenetic Analysis of Lactobacilli, Pediococcus pentosaceus and Leuconostoc mesenteroides

Stackebrandt, Erko; Fowler, Valerie J.; Woese, Carl R.

doi:10.1016/s0723-2020(83)80019-8

Cited by 46 publications

(20 citation statements)

References 25 publications

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“…The only previously established placement of m 6 A in SSU rRNA in other phylogenetic domains was in eukaryotes: X. laevis and human (11) and Rattus norvegicus (16,45), at positions analogous to that in which it occurs in H. volcanii, in the highly conserved mRNA decoding region of the SSU rRNA. Interestingly, this nearly universally conserved A (position 1500 in the E. coli numbering system) appears from the limited data available to be commonly modified in other archaea (various methanogens (17,27) and sulfur-dependent thermophiles (25)) but not in bacteria (18,24,40,41,46), yeast (11,47), or Dictyostelium discoideum (48). The extent to which the modified A at this location in archaea is specifically m 6 A (an uncommon modification in both rRNA and tRNA) remains to be determined.…”

Section: Resultsmentioning

confidence: 99%

“…Ref. 16, especially those by Woese and co-workers (17,18) of modifications in RNase T 1 fragments obtained in the course of phylogenetic cataloging, even though the structural identities of modified residues, as well as placement of the modified T 1 fragment in the RNA sequence (which predated the now common availability of rDNA sequences), were not known in many cases.…”

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confidence: 99%

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Identities and Phylogenetic Comparisons of Posttranscriptional Modifications in 16 S Ribosomal RNA from Haloferax volcanii

Kowalak¹,

Bruenger²,

Crain³

et al. 2000

Journal of Biological Chemistry

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Small subunit (16 S) rRNA from the archaeon Haloferax volcanii, for which sites of modification were previously reported, was examined using mass spectrometry. A census of all modified residues was taken by liquid chromatography/electrospray ionization-mass spectrometry analysis of a total nucleoside digest of the rRNA. Following rRNA hydrolysis by RNase T 1 , accurate molecular mass values of oligonucleotide products were measured using liquid chromatography/electrospray ionization-mass spectrometry and compared with values predicted from the corresponding gene sequence. Three modified nucleosides, distributed over four conserved sites in the decoding region of the molecule, were characterized: 3-(3-amino-3-carboxypropyl)uridine-966, N 6 -methyladenosine-1501, and N 6 ,N 6 -dimethyladenosine-1518 and -1519 (all Escherichia coli numbering). Nucleoside 3-(3-amino-3-carboxypropyl)uridine, previously unknown in rRNA, occurs at a highly conserved site of modification in all three evolutionary domains but for which no structural assignment in archaea has been previously reported. Nucleoside N 6 -methyladenosine, not previously placed in archaeal rRNAs, frequently occurs at the analogous location in eukaryotic small subunit rRNA but not in bacteria. H. volcanii small subunit rRNA appears to reflect the phenotypically low modification level in the Crenarchaeota kingdom and is the only cytoplasmic small subunit rRNA shown to lack pseudouridine.

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Section: Resultsmentioning

confidence: 99%

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confidence: 99%

Identities and Phylogenetic Comparisons of Posttranscriptional Modifications in 16 S Ribosomal RNA from Haloferax volcanii

Kowalak¹,

Bruenger²,

Crain³

et al. 2000

Journal of Biological Chemistry

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“…The pair L.pentosus and L.plantarum, which are also closely related and which belong to the subgenus L. casei together with L. casei, are only remotely related to the L.delbreuckii group (47,48 …”

Section: Evolutionary Relationship Between Lactobacillus Speciesmentioning

confidence: 99%

Divergence in codon usage ofLactobacillus species

Pouwels¹,

Leunissen

1994

Nucl Acids Res

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We have analyzed codon usage patterns of 70 sequenced genes from different Lactobacillus species. Codon usage in lactobacilli is highly biased. Both inter-species and intra-species heterogeneity of codon usage bias was observed. Codon usage in L.acidophilus is similar to that in L.helveticus, but dissimilar to that in L.bulgaricus, L.casei, L.pentosus and L.plantarum. Codon usage in the latter three organisms is not significantly different, but is different from that in L.bulgaricus. Inter-species differences in codon usage can, at least in part, be explained by differences in mutational drift. L.bulgaricus shows GC drift, whereas all other species show AT drift. L.acidophilus and L.helveticus rarely use NNG in family-box (a set of synonymous) codons, in contrast to all other species. This result may be explained by assuming that L.acidophilus and L.helveticus, but not other species examined, use a single tRNA species for translation of family-box codons. Differences in expression level of genes are positively correlated with codon usage bias. Highly expressed genes show highly biased codon usage, whereas weakly expressed genes show much less biased codon usage. Codon usage patterns at the 5'-end of Lactobacillus genes is not significantly different from that of entire genes. The GC content of codons 2-6 is significantly reduced compared with that of the remainder of the gene. The possible implications of a reduced GC content for the control of translation efficiency are discussed.

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“…The genus Sporolactobacillus differs from strain DKP and the genus Lactobacillus by spore production and from the genus Bacillus by its lack of catalase and cytochrome. The taxonomic position of Sporolactobacillus inulinus has been discussed on the basis of the results of a 16s rRNA sequence analysis (14,43,44), and despite the lack of heme proteins such as catalase and cytochrome, this organism is considered a member of the family Bacillaceae. …”

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confidence: 99%

Bacillus thermoamylovorans sp. nov., a Moderately Thermophilic and Amylolytic Bacterium

Combet-Blanc¹,

Ollivier²,

Streicher³

et al. 1995

International Journal of Systematic Bacteriology

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A moderately thermophilic, facultatively anaerobic, amylolytic bacterium was isolated from palm wine, a tropical alcoholic beverage that was sampled in Senegal. The cells were gram positive, catalase positive, non-spore forming, rod shaped, and slightly motile with peritrichous flagella. The strain which we examined did not possess cytochrome and produced L-( +)-lactate, acetate, ethanol, and formate but not hydrogen during carbohydrate fermentation. Growth occurred at pH values ranging from 5.4 to 8.5, and optimum growth occurred at around pH 7.0. The optimum temperature for growth was around 5O"C, and the upper temperature limit for growth was 58°C. The guanine-plus-cytosine content of the DNA was 38.8 k 0.2 mol%. A sequence analysis of the 16s rRNA gene revealed that the new organism is closely related phylogenetically to members of genus Bacillus. Despite the lack of spores, we propose that on the basis of phylogenetic characteristics, the new isolate should be classified as a new Bacillus species, Bacillus thermoamylovorans. The type strain is strain DKP (= Collection of Institut Pasteur CNCM 1-1378).Palm wine is the collective name of alcoholic beverages that result from spontaneous fermentation of the sap of any species of tree belonging to the large family Palmae. This traditional beverage is prepared in the tropical areas of Africa, Asia, and South America where palm trees are common (27). The sap is collected from a newly made slit at the base of an immature male inflorescence on a tree. Leaking sap is collected in a calabash, through a channel made from a plaited palm leaf (48). This method allows daily collection of about 10 liters of sap per tree (16). The sap contains about 10 to 15% (wt/vol) sucrose (12,45), amino acids (51 , and vitamins (2, 6, 38, 49).High densities of bacteria (10 to 4 X lo8 cells ml-l) and yeasts (2 x lo5 to lo8 cells m1-l) (45) give palm wine a milky flocculent appearance (29). The bacteria and yeasts isolated from palm wine belong almost exclusively to the genera Lactobacillus and Saccharomyces, respectively (30,41,45,46,51), which are both adapted to the high osmotic pressures and acidity that occur in fermented beverages (beer, grape wine, and cider) (21). Microbiological studies of palm wine have shown that the stage of fermentation markedly affects the diversity of the microflora. During the early stages of production, when the sap has a neutral pH (pH 7.0 to 7.2) and contains a high concentration of sucrose, numerous species belonging mostly to the genera Leuconostoc, Lactobacillus, Streptococcus, Saccharomyces, Schizosaccharomyces, Candida, and Rchia have been isolated from palm wine (30,41,51); a few Clostndium or Bacillus spp. and gramnegative Sewatia and Klebsiella spp. have also been isolated (30,45). This diverse microbiota ferments the sucrose within about 30 h (12,38), and this fermentation leads to acidification of the medium through the production of organic acids, mostly lactic acid. The decrease in pH results in (i) the selection of acidophilic species and (...

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A Phylogenetic Analysis of Lactobacilli, Pediococcus pentosaceus and Leuconostoc mesenteroides

Cited by 46 publications

References 25 publications

Identities and Phylogenetic Comparisons of Posttranscriptional Modifications in 16 S Ribosomal RNA from Haloferax volcanii

Identities and Phylogenetic Comparisons of Posttranscriptional Modifications in 16 S Ribosomal RNA from Haloferax volcanii

Divergence in codon usage ofLactobacillus species

Bacillus thermoamylovorans sp. nov., a Moderately Thermophilic and Amylolytic Bacterium

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