The recently discovered prokaryotic signal transducer HemAT, which has been described in both Archaea and Bacteria, mediates aerotactic responses. The N-terminal regions of HemAT from the archaeon Halobacterium salinarum (HemAT-Hs) and from the Gram-positive bacterium Bacillus subtilis (HemAT-Bs) contain a myoglobin-like motif, display characteristic heme-protein absorption spectra, and bind oxygen reversibly. Recombinant HemAT-Hs and HemAT-Bs shorter than 195 and 176 residues, respectively, do not bind heme effectively. Sequence homology comparisons and three-dimensional modeling predict that His-123 is the proximal heme-binding residue in HemAT from both species. The work described here used site-specific mutagenesis and spectroscopy to confirm this prediction, thereby providing direct evidence for a functional domain of prokaryotic signal transducers that bind heme in a globin fold. We postulate that this domain is part of a globin-coupled sensor (GCS) motif that exists as a two-domain transducer having no similarity to the PER-ARNT-SIM (PAS)-domain superfamily transducers. Using the GCS motif, we have identified several two-domain sensors in a variety of prokaryotes. We have cloned, expressed, and purified two potential globin-coupled sensors and performed spectral analysis on them. Both bind heme and show myoglobin-like spectra. This observation suggests that the general function of GCS-type transducers is to bind diatomic oxygen and perhaps other gaseous ligands, and to transmit a conformational signal through a linked signaling domain.proximal histidine ͉ transducer G lobins are heme-containing proteins that are involved in binding and͞or transport of diatomic oxygen. Presently, more than 700 globin sequences are known (1). It has been proposed that all globins have evolved from an ancestral redox protein of about 17 kDa that displayed the globin fold, which is characterized by the presence of eight helices, designated A through H (2). The residues absolutely conserved among all globins are the proximal histidine in the F helix (F8) and phenylalanine in the CD region (CD1) (3, 4). Highly conserved residues include the distal histidine in the E helix (E7), phenylalanine in the CD4 region, and proline at the beginning of the C helix (C2).We recently discovered heme-containing transducers in the archaeon Halobacterium salinarum (HemAT-Hs) and the Grampositive bacterium Bacillus subtilis (HemAT-Bs). These proteins bind diatomic oxygen and mediate an aerotactic response (5). The N termini of these transducers resemble myoglobin, and their C termini are homologous to the cytoplasmic signaling domain of bacterial chemoreceptors. We have also described three-dimensional homology models of the putative oxygensensing domain of HemATs (6). In these models the overall globin topology, including the orientation of the heme prosthetic group, is preserved, as is the hydrophobic core of the hemebinding pocket and the electrostatic stabilization of the CD region. Therefore, an experimental determination of the organizatio...

Kidney transplant is the reference treatment for patients with end-stage renal disease, but patients may develop long-term rejection of the graft. However, some patients do not reject the transplant, but instead are operationally tolerant state despite withdrawal of immunosuppressive treatment. In this second article we outline a microarray-based identification of key leader genes associated respectively to rejection and to operational tolerance of the kidney transplant in humans by utilizing a non/statistical bioinformatic approach based on the identification of "key genes," either as those mostly changing their expression, or having the strongest interconnections. A uniquely informative picture emerges on the genes controlling the human transplant from the detailed comparison of these findings with the traditional statistical SAM (Tusher et al. 2001 Proc Natl Acad Sci USA 98:5116-5121) analysis of the microarrays and with the clinical study carried out in the accompanying part I article.

The key genes involved in the cell cycle of human T lymphocytes were identified by iterative searches of gene-related databases, as derived also from DNA microarray experimentation, revealing and predicting interactions between those genes, assigning scores to each of the genes according to numbers of interaction for each gene weighted by significance of each interaction, and finally applying several types of clustering algorithms to genes basing on the assigned scores. All clustering algorithms applied, both hierarchical and K-means, invariably selected the same six "leader" genes involved in controlling the cell cycle of human T lymphocytes. Relations of the six genes to experimental data describing switching between stages of cell cycle of human T lymphocytes are discussed.