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N C Kyrpides

Publications and source records attributed to N C Kyrpides.

28 records · Page 2Linked to original sources
PubMed1996

Parallel origins of the nucleosome core and eukaryotic transcription from Archaea.

Computational sequence analysis of 10 available archaean histone-like proteins has shown that this family is not only divergently related to the eukaryotic core histones H2A/B, H3, and H4, but also to the central domain of subunits A and C of the CCAAT-binding factor (CBF), a transcription factor associated with eukaryotic promoters. Despite the low sequence identity, it is unambiguously shown that the core histone fold shares a common evolutionary history. Archaean histones and the two CBF families show a remarkable variability in contrast to eukaryotic core histones. Conserved residues shared between families are identified, possibly being responsible for the functional versatility of the core histone fold. The H4 subfamily is most similar to archaean proteins and may be the progenitor of the other core histones in eukaryotes. While it is not clear whether archaean histones are more actively involved in transcription regulation, the present observations link two processes, nucleosomal packing and transcription in a unique way. Both these processes, evidently hybrid in Archaea, have originated before the ermergence of the eukaryotic cell.

Amino Acid Sequence↗
PubMed1996

Methanococcus jannaschii genome: revisited.

Analysis of genomic sequences is necessarily an ongoing process. Initial gene assignments tend (wisely) to be on the conservative side (Venter, 1996). The analysis of the genome then grows in an iterative fashion as additional data and more sophisticated algorithms are brought to bear on the data. The present report is an emendation of the original gene list of Methanococcus jannaschii (Bult et al., 1996). By using a somewhat more updated database and more relaxed (and operator-intensive) pattern matching methods, we were able to add significantly to, and in a few cases amend, the gene identification table originally published by Bult et al. (1996).

Databases as Topic↗
PubMed1995

Nucleic acid-binding metabolic enzymes: living fossils of stereochemical interactions?

Recently, a series of intriguing observations expanded the list of a number of metabolic enzymes known to be associated with various forms of nucleic acids, including single- and double-stranded DNA, cognate and noncognate RNAs, and specific tRNAs. There is no clear reason why such a phenomenon should take place in contemporary cell physiology, or, further, why such a property has evolved at all. Sixteen known cases are presented in an attempt to delineate any common features of these enzymes. Apart from their ancient nature, as judged by their wide distribution and their participation in fundamental biochemical pathways, it appears that these enzymes do not share any structural or functional characteristics. Given that most of these proteins require nucleotide-based cofactors for their activity, it is proposed that they may represent genuine molecular fossils of the transition from an RNA to a protein world. Their nucleic acid-binding properties are in keeping with previously proposed hypotheses regarding the origins and evolution of nucleotide-based cofactors. The mode of interaction between these proteins and their nucleic acid substrates remains unclear, but it may represent an extended form of stereochemical interactions that have been proposed for the origins of the genetic code.

Animals↗
PubMed1994

Reverse interpretation: a hypothetical selection mechanism for adaptive mutagenesis based on autoregulated mRNA stability.

The problem of adaptive mutagenesis is examined under the assumption that selection occurs through the interaction of cognate mRNA and protein molecules, a phenomenon that has been considered to lead to differential mRNA decay (Kyrpides & Ouzounis, 1993, J. theor. Biol. 163, 373-392). Based on the stereochemical hypothesis, we speculate that the origin of this process relies on an extended form of molecular interactions. This mechanism, termed reverse interpretation, predicts the selective amplification of successful molecular forms with the capability of their immortalization through reverse transcription, in a manner that resembles, but is not equivalent to, reverse translation. Finally, we argue that the proposed mechanism conforms with the Darwinian view of evolutionary change, if variability is considered to be a property of molecular and not cellular populations.

Animals↗
PubMed1994

On the evolution of arginases and related enzymes.

Sequence analysis of the arginase/agmatine ureohydrolase family, important enzymes in arginine/agmatine metabolism and the urea cycle, reveals the similarity of arginases to formiminoglutamate hydrolase (hutG) in Klebsiella aerogenes and to a previously unidentified open reading frame adjacent to the HMf locus of the archaebacterium Methanothermus fervidus. The gene structure and distribution of these homologous proteins across primary kingdoms suggest that this family is another example of a primordial enzyme possibly present in the universal common ancestor and that can be used as phylogenetic marker.

Amino Acid Sequence↗
PubMed1993

Mechanisms of specificity in mRNA degradation: autoregulation and cognate interactions.

Autoregulation of gene expression is a common control mechanism for a large number of transcriptional units. Cases of self-regulation of the stability of various messenger RNAs (mRNAs) are re-evaluated here, and a general hypothesis for the origins and the mechanism of this process is presented. It is proposed that post-transcriptional autoregulation and mRNA stability are closely associated processes that might represent a general class of gene regulation mechanisms, with special regard to mRNA-protein cognate interactions. Generalizing from known examples, autoregulation is here considered to induce the decay of certain messenger RNAs through a yet undiscovered mechanism. Autoregulation via cognate interactions might be the vestigial process of a primitive world, where protein-nucleic acid interactions originated. The model can therefore serve as a framework to study the origins of the genetic code in particular, and gene expression in general.

Animals↗