Re: Spectral analysis of echinoderm small subunit ribosomal RNA gene sequence data.
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Animals↗
Biomedical subjects
J O McInerney
Publications and source records attributed to J O McInerney.
Replicational and transcriptional selection on codon usage in Borrelia burgdorferi.
With more than 10 fully sequenced, publicly available prokaryotic genomes, it is now becoming possible to gain useful insights into genome evolution. Before the genome era, many evolutionary processes were evaluated from limited data sets and evolutionary models were constructed on the basis of small amounts of evidence. In this paper, I show that genes on the Borrelia burgdorferi genome have two separate, distinct, and significantly different codon usages, depending on whether the gene is transcribed on the leading or lagging strand of replication. Asymmetrical replication is the major source of codon usage variation. Replicational selection is responsible for the higher number of genes on the leading strands, and transcriptional selection appears to be responsible for the enrichment of highly expressed genes on these strands. Replicational-transcriptional selection, therefore, has an influence on the codon usage of a gene. This is a new paradigm of codon selection in prokaryotes.
Borrelia burgdorferi Group↗
GCUA: general codon usage analysis.
UNLABELLED: The program General Codon Usage Analysis (GCUA) has been developed for analysing codon and amino acid usage patterns. AVAILABILITY: ftp://ftp.nhm.ac.uk/pub/gcua. Freely available for academic use, commercial users should contact the author. CONTACT: J.McInerney@nhm.ac.uk
Amino Acid Sequence↗
Sequence of the gene encoding the 16S rRNA of the beer spoilage organism Megasphaera cerevisiae.
The 16S ribosomal RNA gene from the beer-spoilage organism, Megasphaera cerevisiae was polymerase chain reaction (PCR)-amplified and sequenced. Analysis confirmed the phylogenetic position of M. cerevisiae as a sister taxon of Megasphaera elsdenii, within the obligately anaerobic, Gram-negative cocci. The sequence obtained should facilitate the development of DNA probes for early detection of this spoilage organism.
Base Sequence↗
Detection of micro-organisms in the environment.
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Archaea↗
Recovery and phylogenetic analysis of novel archaeal rRNA sequences from a deep-sea deposit feeder.
In 1992, two independent reports based on small-subunit rRNA gene (SSU rDNA) cloning revealed the presence of novel Archaea among marine bacterioplankton. Here, we report the presence of further novel Archaea SSU rDNA sequences recovered from the midgut contents of a deep-sea marine holothurian. Phylogenetic analyses show that these abyssal Archaea are a paraphyletic component of a highly divergent clade that also includes some planktonic sequences. Our data confirm that this clade is a deep-branching lineage in the tree of life.
Animals↗
Sequence analysis and evolutionary aspects of piscine alpha-1-microglobulin/bikunin mRNA transcripts.
Studies on mammalian alpha-1-microglobulin/bikunin (AMBP) protein sequences suggest the ancestral AMBP gene arose between 270 and 80 million years ago. Here we report a similar study including recently reported piscine AMBP messenger RNA sequences. The analysis implies a far earlier data for the assembly of the ancestral AMBP gene, more than 450 million years ago. Similarly, a revised date for the origin of the ancestral Kunitz-type protein is estimated at approximately 875 million years ago. Evolutionary conservation is apparent among all the AMBP amino acid sequences. This implies a common functional significance in both teleosts and mammals. However, an unusually rapid rate of evolution is observed for domain II of the piscine bikunin sequences, suggesting that this domain is no longer truly orthologous in fish.
Alpha-Globulins↗