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N Kyrpides

Publications and source records attributed to N Kyrpides.

14 recordsLinked to original sources
PubMed2001

Cross-talk between catalytic and regulatory elements in a DEAD motor domain is essential for SecA function.

SecA, the motor subunit of bacterial polypeptide translocase, is an RNA helicase. SecA comprises a dimerization C-terminal domain fused to an ATPase N-terminal domain containing conserved DEAD helicase motifs. We show that the N-terminal domain is organized like the motor core of DEAD proteins, encompassing two subdomains, NBD1 and IRA2. NBD1, a rigid nucleotide-binding domain, contains the minimal ATPase catalytic machinery. IRA2 binds to NBD1 and acts as an intramolecular regulator of ATP hydrolysis by controlling ADP release and optimal ATP catalysis at NBD1. IRA2 is flexible and can undergo changes in its alpha-helical content. The C-terminal domain associates with NBD1 and IRA2 and restricts IRA2 activator function. Thus, cytoplasmic SecA is maintained in the thermally stabilized ADP-bound state and unnecessary ATP hydrolysis cycles are prevented. Two DEAD family motifs in IRA2 are essential for IRA2-NBD1 binding, optimal nucleotide turnover and polypeptide translocation. We propose that translocation ligands alleviate C-terminal domain suppression, allowing IRA2 to stimulate nucleotide turnover at NBD1. DEAD motors may employ similar mechanisms to translocate different enzymes along chemically unrelated biopolymers.

Adenosine Diphosphate↗
PubMed2001

Genomes OnLine Database (GOLD): a monitor of genome projects world-wide.

GOLD is a comprehensive resource for accessing information related to completed and ongoing genome projects world-wide. The database currently provides information on 350 genome projects, of which 48 have been completely sequenced and their analysis published. GOLD was created in 1997 and since April 2000 it has been licensed to Integrated Genomics. The database is freely available through the URL: http://igweb.integratedgenomics.com/GOLD/.

Animals↗
PubMed2001

The Rhodobacter capsulatus genome.

The genome of Rhodobacter capsulatus has been completely sequenced. It consists of a single chromosome containing 3.5 Mb and a circular plasmid of 134 kb. This effort, started in 1992, began with a fine-structure restriction map of an overlapping set of cosmids that covered the genome. Cosmid sequencing led to a gapped genome that was filled by primer walking on the chromosome and by using lambda clones. Methods had to be developed to handle strong stops in the high GC (68%) inserts. Annotation was done with the ERGO system at Integrated Genomics, as was the reconstruction of the cell's metabolism. It was possible to recognize 3709 orfs of which functional assignments could be made with high confidence to 2392 (65%). Unusual features include the presence of numerous cryptic phage genomes embedded in the chromosome.

Journal Article↗
PubMed2000

WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction.

The WIT (What Is There) (http://wit.mcs.anl.gov/WIT2/) system has been designed to support comparative analysis of sequenced genomes and to generate metabolic reconstructions based on chromosomal sequences and metabolic modules from the EMP/MPW family of databases. This system contains data derived from about 40 completed or nearly completed genomes. Sequence homologies, various ORF-clustering algorithms, relative gene positions on the chromosome and placement of gene products in metabolic pathways (metabolic reconstruction) can be used for the assignment of gene functions and for development of overviews of genomes within WIT. The integration of a large number of phylogenetically diverse genomes in WIT facilitates the understanding of the physiology of different organisms.

Databases, Factual↗
PubMed1999

Universal protein families and the functional content of the last universal common ancestor.

The phylogenetic distribution of Methanococcus jannaschii proteins can provide, for the first time, an estimate of the genome content of the last common ancestor of the three domains of life. Relying on annotation and comparison with reference to the species distribution of sequence similarities results in 324 proteins forming the universal family set. This set is very well characterized and relatively small and nonredundant, containing 301 biochemical functions, of which 246 are unique. This universal function set contains mostly genes coding for energy metabolism or information processing. It appears that the Last Universal Common Ancestor was an organism with metabolic networks and genetic machinery similar to those of extant unicellular organisms.

Archaeal Proteins↗
PubMed1996

The emergence of major cellular processes in evolution.

The phylogenetic distribution of divergently related protein families into the three domains of life (archaea, bacteria and eukaryotes) can signify the presence or absence of entire cellular processes in these domains and their ancestors. We can thus study the emergence of the major transitions during cellular evolution, and resolve some of the controversies surrounding the evolutionary status of archaea and the origins of the eukaryotic cell. In view of the ongoing projects that sequence the complete genomes of several Archaea, this work forms a testable prediction when the genome sequences become available. Using the presence of the protein families as taxonomic traits, and linking them to biochemical pathways, we are able to reason about the presence of the corresponding cellular processes in the last universal ancestor of contemporary cells. The analysis shows that metabolism was already a complex network of reactions which included amino acid, nucleotide, fatty acid, sugar and coenzyme metabolism. In addition, genetic processes such as translation are conserved and close to the original form. However, other processes such as DNA replication and repair or transcription are exceptional and seem to be associated with the structural changes that drove eukaryotes and bacteria away from their common ancestor. There are two major hypotheses in the present work: first, that archaea are probably closer to the last universal ancestor than any other extant life form, and second, that the major cellular processes were in place before the major splitting. The last universal ancestor had metabolism and translation very similar to the contemporary ones, while having an operonic genome organization and archaean-like transcription. Evidently, all cells today contain remnants of the primordial genome of the last universal ancestor.

Archaea↗
PubMed1995

A transient GCN4 mRNA destabilization follows GCN4 translational derepression.

Studies based on experimental strategies that utilized either inhibitors or structural alterations point to the existence of an inverse relationship between translation and stability of a given mRNA. In this study we have investigated the potential link between translation and stability of the yeast GCN4 mRNA whose translational rates change with respect to amino acid availability. We observed that under conditions favoring its translation, the steady state levels of the GCN4 mRNA were decreased, but this was not due to a measurable alternation in its decay rate. We have demonstrated that an extensive destabilization of this message is intimately coupled with its increased access to heavy polysomes, which occurs transiently in the process of translational derepression. This transient change in the stability is what readjusts the steady state levels of the GCN4 mRNA. This study demonstrates in vivo the existence of a mechanism of mRNA degradation that is coupled with the process of translation.

DNA-Binding Proteins↗
PubMed1995

Novel protein families in archaean genomes.

In a quest for novel functions in archaea, all archaean hypothetical open reading frames (ORFs), as annotated in the Swiss-Prot protein sequence database, were used to search the latest databases for the identification of characterized homologues. Of the 95 hypothetical archaean ORFs, 25 were found to be homologous to another hypothetical archaean ORF, while 36 were homologous to non-archaean proteins, of which as many as 30 were homologous to a characterized protein family. Thus the level of sequence similarity in this set reaches 64%, while the level of function assignment is only 32%. Of the ORFs with predicted functions, 12 homologies are reported here for the first time and represent nine new functions and one gene duplication at an acetyl-coA synthetase locus. The novel functions include components of the transcriptional and translational apparatus, such as ribosomal proteins, modification enzymes and a translation initiation factor. In addition, new enzymes are identified in archaea, such as cobyric acid synthase, dCTP deaminase and the first archaean homologues of a new subclass of ATP binding proteins found in fungi. Finally, it is shown that the putative laminin receptor family of eukaryotes and an archaean homologue belong to the previously characterized ribosomal protein family S2 from eubacteria. From the present and previous work, the major implication is that archaea seem to have a mode of expression of genetic information rather similar to eukaryotes, while eubacteria may have proceeded into unique ways of transcription and translation. In addition, with the detection of proteins in various metabolic and genetic processes in archaea, we can further predict the presence of additional proteins involved in these processes.

Animal Population Groups↗
PubMed1992

The role of IL-4 in human myeloid leukemia: stimulation of RNA synthesis and transduction of differentiation signals through an IL-4 receptor leads to functional and HLA positive HL-60 cells.

The ectopic expression of lineage markers on irrelevant cell types may be of importance in the differentiation pathway(s) of these cells. One example, that is the subject of this study, is the presence of the interleukin-4 (IL-4) receptor on the surface of the human HL-60 myeloid leukemia cell line. The presence of such a receptor, that at first seems to be a simple genetic misprogramming, has an unusual biological function: It serves as a bridge to link the B cell growth factor IL-4 in order to transduce a number of differentiation signals in this M2 acute myeloid leukemia (AML) population. Signal transduction is followed by stimulation of RNA synthesis and subsequent induction of differentiation. Daily administration of low IL-4 dose yields proliferative senescent cells that exhibit 66% of growth inhibition in a 5-day tritiated thymidine incorporation assay. These cells clearly exit from the standard M2 morphology and show more mature characteristics as assessed by the Giemsa-Wright staining technique, followed by a 2-fold increase of the monocyte-granulocyte-specific Mac-1 surface antigen. Cellular function is also affected positively since phagocytosis of latex beads increases considerably after IL-4 treatment. Finally, as reported for normal human and murine monocytes and macrophages, the receptor-ligand interaction augments the levels of the class I and class II antigenic determinants by approximately 60%. Our results suggest that ectopic expression of markers may be a "distinct" event required during a short period in the differentiation of certain hemopoietic cells leading to mature and normal phenotypes.

Cell Differentiation↗
PubMed1992

Different molecular mechanisms lead to same endpoints with different function: TNF-alpha induces non-functional CSF-1 receptors on HL-60 cells in contrast to interferon-gamma.

Tumour necrosis factor-alpha (TNF-alpha) induces differentiation on human promyelocytic leukemia cells (HL-60) as assessed by growth inhibition accompanied by reduction of c-myc levels, and expression of surface colony-stimulating factor-1 (CSF-1) receptors reported as molecular markers for acute myeloid leukemia (AML). CSF-1 receptors can be readily demonstrated by direct binding of 125I-CSF-1 and expression of v-fms whose gene product retains a complete ligand binding domain. Although the same findings have been previously demonstrated on HL-60 cells after interferon-gamma (IFN-gamma) treatment, the major difference between the two pathways of cellular differentiation is the functional state of the induced receptors: when IFN-gamma is used as differentiation agent, the cells are driven to express a high number of CSF-1 receptors and are able to respond to a CSF-1 stimulus. Such mitogenic response is not obtained when TNF-alpha is applied as inducer indicating that the newly expressed receptors are not functional. This difference may be due to different molecular mechanisms the two factors trigger in order to reach the same endpoint: the maturation of this leukemic population.

Cell Differentiation↗
PubMed1990

Evolutionary implications of duplications and Balbiani rings in Drosophila. A study of Drosophila serrata.

Drosophila serrata, a species of subgroup montium, exhibits in its salivary-gland chromosomes a high number of inverted tandem duplications and a well-formed Balbiani ring. A photographic map, the duplications, and the Balbiani ring of this species are presented. Also presented are the most prominent puffs during normal larval development and after ecdysone treatment, as well as intercalary heterochromatin regions of the above chromosomes. These data are discussed and compared with those of Drosophila auraria, another species of subgroup montium. All the inverted tandem duplications found in both species are homozygous and are not accompanied by other types of chromosomal rearrangements. These results argue in favor of the relatively old origin of these structures. The similarity of the structure and the developmental profile of the Balbiani ring 1 in both species may indicate a necessary role served by the Balbiani ring 1 and hence its selection during evolution.

Animals↗
PubMedDate not supplied

One and two-level regulation patterns affecting NF-kappa B mRNA and nuclear NF-kappa B activity after treatment with TNF-alpha, IFN-gamma and IL-4.

The transactivating nuclear factor NF-kappa B is believed to be important in the pathophysiology of many cellular systems and mainly during HIV infection. kappa B activation has also been implicated in the process of differentiation as a cell progresses to a more mature and functional stage. As induction of differentiation equals growth retardation we undertook this study in order to establish the role of NF-kappa B in cell growth and maturity. Thus we employed the well described HL-60 cellular system that expresses constitutively basal amounts of NF-kappa B and is susceptible to NF-kappa B induction by various biological or chemical agents. We also used known inducers of differentiation like TNF-alpha, IFN-gamma and IL-4 that interact via their corresponding surface receptors found on HL-60 cells. We first studied by Northern analysis the possible correlation between c-myc and NF-kappa B precursor (p105) mRNA. We witnessed that all three cytokines were able to confer proliferative senescence and down-regulate concomitantly c-myc and NF-kappa B mRNA levels, events chronologically in accord with induction of differentiation as assessed by the induction of HLA-DR surface antigens. It is known that TNF-alpha is capable of inducing nuclear kappa B activity in HL-60 as the cells progress to a more mature stage. Therefore we examined whether the other two cytokines could do the same during the time they lead the cells to a differentiated phenotype. If this was the case, nuclear activation of NF-kappa B should be obtained by the same factors.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗