scholarly journals Genomic Analysis Reveals Chromosomal Variation in Natural Populations of the Uncultured Psychrophilic ArchaeonCenarchaeum symbiosum

1998 ◽  
Vol 180 (19) ◽  
pp. 5003-5009 ◽  
Author(s):  
Christa Schleper ◽  
Edward F. DeLong ◽  
Christina M. Preston ◽  
Robert A. Feldman ◽  
Ke-Ying Wu ◽  
...  
Keyword(s):  
Large Subunit ◽  
Natural Populations ◽  
Genomic Analysis ◽  
Rrna Genes ◽  
Homologous Protein ◽  
Dna Libraries ◽  
Ribosomal Operon ◽  
Molecular Phylogenetic ◽  
Large Subunit Rrna ◽  
Genotypic Characteristics

ABSTRACT Molecular phylogenetic surveys have recently revealed an ecologically widespread crenarchaeal group that inhabits cold and temperate terrestrial and marine environments. To date these organisms have resisted isolation in pure culture, and so their phenotypic and genotypic characteristics remain largely unknown. To characterize these archaea, and to extend methodological approaches for characterizing uncultivated microorganisms, we initiated genomic analyses of the nonthermophilic crenarchaeoteCenarchaeum symbiosum found living in association with a marine sponge, Axinella mexicana. Complex DNA libraries derived from the host-symbiont population yielded several large clones containing the ribosomal operon from C. symbiosum. Unexpectedly, cloning and sequence analysis revealed the presence of two closely related variants that were consistently found in the majority of host individuals analyzed. Homologous regions from the two variants were sequenced and compared in detail. The variants exhibit >99.2% sequence identity in both small- and large-subunit rRNA genes and they contain homologous protein-encoding genes in identical order and orientation over a 28-kbp overlapping region. Our study not only indicates the potential for characterizing uncultivated prokaryotes by genome sequencing but also identifies the primary complication inherent in the approach: the widespread genomic microheterogeneity in naturally occurring prokaryotic populations.

An rRNA variable region has an evolutionarily conserved essential role despite sequence divergence

1994 ◽  
Vol 14 (6) ◽  
pp. 4203-4215
Author(s):  
R Sweeney ◽  
L Chen ◽  
M C Yao
Keyword(s):  
Large Subunit ◽  
Sequence Divergence ◽  
Variable Region ◽  
Rrna Genes ◽  
Functional Importance ◽  
Functional Feature ◽  
Tertiary Structures ◽  
Unrelated Sequence ◽  
Evolutionarily Conserved ◽  
Large Subunit Rrna

Regions extremely variable in size and sequence occur at conserved locations in eukaryotic rRNAs. The functional importance of one such region was determined by gene reconstruction and replacement in Tetrahymena thermophila. Deletion of the D8 region of the large-subunit rRNA inactivates T. thermophila rRNA genes (rDNA): transformants containing only this type of rDNA are unable to grow. Replacement with an unrelated sequence of similar size or a variable region from a different position in the rRNA also inactivated the rDNA. Mutant rRNAs resulting from such constructs were present only in precursor forms, suggesting that these rRNAs are deficient in either processing or stabilization of the mature form. Replacement with D8 regions from three other organisms restored function, even though the sequences are very different. Thus, these D8 regions share an essential functional feature that is not reflected in their primary sequences. Similar tertiary structures may be the quality these sequences share that allows them to function interchangeably.

scholarly journals Sequence and organization of large subunit rRNA genes from the extrachromosomal 35 kb circular DNA of the malaria parasitePlasmodium falciparum

1993 ◽  
Vol 21 (5) ◽  
pp. 1067-1071 ◽  
Author(s):  
M.J. Gardner ◽  
J.E. Feagin ◽  
D.J. Moore ◽  
K. Rangachari ◽  
D.H. Williamson ◽  
...  
Keyword(s):  
Large Subunit ◽  
Rrna Genes ◽  
Circular Dna ◽  
Large Subunit Rrna

scholarly journals An rRNA variable region has an evolutionarily conserved essential role despite sequence divergence.

1994 ◽  
Vol 14 (6) ◽  
pp. 4203-4215 ◽  
Author(s):  
R Sweeney ◽  
L Chen ◽  
M C Yao
Keyword(s):  
Large Subunit ◽  
Sequence Divergence ◽  
Variable Region ◽  
Rrna Genes ◽  
Functional Importance ◽  
Functional Feature ◽  
Tertiary Structures ◽  
Unrelated Sequence ◽  
Evolutionarily Conserved ◽  
Large Subunit Rrna

Regions extremely variable in size and sequence occur at conserved locations in eukaryotic rRNAs. The functional importance of one such region was determined by gene reconstruction and replacement in Tetrahymena thermophila. Deletion of the D8 region of the large-subunit rRNA inactivates T. thermophila rRNA genes (rDNA): transformants containing only this type of rDNA are unable to grow. Replacement with an unrelated sequence of similar size or a variable region from a different position in the rRNA also inactivated the rDNA. Mutant rRNAs resulting from such constructs were present only in precursor forms, suggesting that these rRNAs are deficient in either processing or stabilization of the mature form. Replacement with D8 regions from three other organisms restored function, even though the sequences are very different. Thus, these D8 regions share an essential functional feature that is not reflected in their primary sequences. Similar tertiary structures may be the quality these sequences share that allows them to function interchangeably.

scholarly journals Rearranged Subtelomeric rRNA Genes in Giardia duodenalis

2005 ◽  
Vol 4 (2) ◽  
pp. 484-486 ◽  
Author(s):  
Jacqueline A. Upcroft ◽  
Mahin Abedinia ◽  
Peter Upcroft
Keyword(s):  
Large Subunit ◽  
Giardia Duodenalis ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Two Dimensional ◽  
Linear Chromosomes ◽  
Large Subunit Rrna

ABSTRACT Giardia duodenalis has linear chromosomes capped with typical eukaryotic repeats [(TAGGG) n ], subtelomeric rRNA genes, and telomere gene units. The absence of two closely associated NotI sites in the large-subunit rRNA gene was used as an indicator in hybridizations of one- and two-dimensional NotI-cleaved Giardia chromosome separations that some chromosomes carry only rearranged and, by deduction, nonfunctional rRNA genes.

scholarly journals Molecular characterization of a subgroup IE intron with wide distribution in the large subunit rRNA genes of dermatophyte fungi

2009 ◽  
Vol 47 (6) ◽  
pp. 609-617 ◽  
Author(s):  
Colin J. Jackson ◽  
Richard C. Barton ◽  
C. Graham Clark ◽  
Steven L. Kelly
Keyword(s):  
Molecular Characterization ◽  
Large Subunit ◽  
Wide Distribution ◽  
Rrna Genes ◽  
Large Subunit Rrna

Schistonchus zealandicus n. sp. (Nematoda: Aphelenchoididae) associated with Ficus macrophylla in New Zealand

Nematology ◽  
2015 ◽  
Vol 17 (1) ◽  
pp. 53-66 ◽  
Author(s):  
Zengqi Zhao ◽  
Dongmei Li ◽  
Kerrie A. Davies ◽  
Weimin Ye
Keyword(s):  
New Zealand ◽  
Large Subunit ◽  
Tail Length ◽  
Small Subunit ◽  
Rrna Genes ◽  
Lateral Field ◽  
Male Tail ◽  
Tail Tip ◽  
Large Subunit Rrna ◽  
A New Species

Schistonchus zealandicus n. sp. was recovered from the sycones of Ficus macrophylla from St Helier’s Bay, Mt Wellington, and St Johns, suburbs of Auckland, New Zealand. It is characterised by having the opening of the excretory pore located just posterior to the anterior end of the nematode but anterior to the conus level of the stylet, a short post-vulval uterine sac (10-18 μm or 0.4-0.7 vulval body diam. long), presence of two incisures in the lateral field with many broken, non-defined lines between them, rose-thorn-shaped spicule, three pairs of subventral papillae on the male tail (one pair adcloacal on the anterior lip, one pair slightly posterior to mid-tail length, and one pair close to tail tip), a distinctive mucron on the male tail, apparent biogeographical range, and its association with F. macrophylla. The absence of a lip sector disc suggests that it is close to S. altermacrophylla, S. aureus and S. laevigatus. Molecular phylogeny of near full length small subunit and D2-D3 expansion segments of the large subunit rRNA genes supports the proposal of S. zealandicus n. sp. as a new species.

scholarly journals Complex transcription from the extrachromosomal DNA encoding mitochondrial functions of Plasmodium yoelii.

1990 ◽  
Vol 10 (12) ◽  
pp. 6381-6388 ◽  
Author(s):  
K Suplick ◽  
J Morrisey ◽  
A B Vaidya
Keyword(s):  
Rna Sequencing ◽  
Large Subunit ◽  
Plasmodium Yoelii ◽  
Primer Extension ◽  
Malarial Parasite ◽  
Rrna Genes ◽  
Extrachromosomal Dna ◽  
Rna Molecules ◽  
Mitochondrial Functions ◽  
Large Subunit Rrna

All tested members of genus Plasmodium contain tandemly arrayed, transcribed, extrachromosomal DNA with a unit length of 6.0 kb. This DNA contains two open reading frames with potential to encode cytochrome c oxidase subunit I (cox1) and cytochrome b (cob) as well as fragments of rRNA genes scattered on both strands. At least 10 discrete RNA molecules transcribed during erythrocytic stages of a rodent malarial parasite, Plasmodium yoelii, were recognized by the 6.0-kb DNA probes. The RNA molecules of 1.4 and 1.1 kb were identified as encoding cox1 and cob, respectively. Primer extension and RNA sequencing were used to locate and characterize 5' ends of these two RNAs, showing that an identical 12-nucleotide sequence, 5'-TATTTTT TGTTT-3', was present at these positions. This sequence may act as a promoter or as an RNA processing signal. A stem-loop structure signifying a possible transcription termination was present at the end of the cox1 open reading frame. At least six discrete RNA molecules of less than 250 nucleotides were recognized by different fractions of the 6.0-kb DNA. The largest of these, 200 nucleotides, was also characterized by primer extension and RNA sequencing. This molecule had a high homology to portions of the large-subunit rRNA domains IV and V. Other, small RNA molecules were recognized by regions of the 6.0-kb DNA that had homology to the highly conserved peptidyltransferase domain of large-subunit rRNA. These results show that the unusual compactly organized mitochondrionlike DNA of malarial parasites is transcribed in a complex pattern.

Sign in / Sign up

Export Citation Format

Share Document