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At least 19 recordsLinked to original sources
PubMed2004

Evolution of the PPM-family protein phosphatases in Streptomyces: duplication of catalytic domain and lateral recruitment of additional sensory domains.

Originally identified from eukaryotes, the Mg2+- or Mn2+-dependent protein phosphatases (PPMs) are a diverse group of enzymes whose members include eukaryotic PP2C and some prokaryotic serine/threonine phosphatases. In a previous study, unexpectedly large numbers of PPMs were identified in two Streptomyces genomes. In this work, a phylogenetic analysis was performed with all the PPMs available from a wide variety of microbial sources to determine the evolutionary origin of the Streptomyces PPM proteins. Consistent with earlier hypotheses, the results suggested that the microbial PPMs were relatively recent additions from eukaryotic sources. Results also indicated that the Streptomyces PPMs were divided into two major subfamilies at an early stage of their emergence in Streptomyces genomes. The first subfamily, which contains only six Streptomyces PPMs, possesses a catalytic domain whose sequence and architecture are similar to that of eukaryotic PPMs; the second subfamily contains 89 Streptomyces PPMs that lack the 5a and 5b catalytic domain motifs, similar to the PPMs SpoIIE and RsbU of Bacillus subtilis. Significant gene duplication was observed for the PPMs in the second subfamily. In addition, more than half (54 %) of the Streptomyces PPMs from the second subfamily were found to have at least one additional sensory domain, most commonly the PAS or the GAF domain. Phylogenetic analysis showed that these domains tended to be clustered according to the putative physiological functions rather than taxonomic relationship, implying that they might have arisen as a result of domain recruitment in a late evolutionary stage. This study provides an insight into how Streptomyces spp. may have expanded their PPM-based signal transduction networks to enable them to respond to a greater range of environmental changes.

Catalytic Domain↗
PubMed2003

Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea.

Transmembrane receptors in microorganisms, such as sensory histidine kinases and methyl-accepting chemotaxis proteins, are molecular devices for monitoring environmental changes. We report here that sensory domain sharing is widespread among different classes of transmembrane receptors. We have identified two novel conserved extracellular sensory domains, named CHASE2 and CHASE3, that are found in at least four classes of transmembrane receptors: histidine kinases, adenylate cyclases, predicted diguanylate cyclases, and either serine/threonine protein kinases (CHASE2) or methyl-accepting chemotaxis proteins (CHASE3). Three other extracellular sensory domains were shared by at least two different classes of transmembrane receptors: histidine kinases and either diguanylate cyclases, adenylate cyclases, or phosphodiesterases. These observations suggest that microorganisms use similar conserved domains to sense similar environmental signals and transmit this information via different signal transduction pathways to different regulatory circuits: transcriptional regulation (histidine kinases), chemotaxis (methyl-accepting proteins), catabolite repression (adenylate cyclases), and modulation of enzyme activity (diguanylate cyclases and phosphodiesterases). The variety of signaling pathways using the CHASE-type domains indicates that these domains sense some critically important extracellular signals.

Adenylyl Cyclases↗
PubMed2004

Spiral wave dynamics under feedback control derived from a variety of sensory domains.

The dynamics of rigidly rotating spiral waves in a reaction layer with light-dependent excitability is studied by numerical integration of a reaction-diffusion equation system with a feedback control. The feedback signal is derived from sensory domains with different geometries by introducing an algorithm that computes the illumination intensity to be proportional to the average wave activity in these domains. It is shown that the shape and size of the trajectories of the spiral wave tip as well as the stability of the spiral rotation depend sensitively on the choice of the geometry of the sensory domain. The numerically observed effects are complemented by constructing a flow map based on an analysis of the feedback signal.

Journal Article↗
PubMed2003

The NMR structure of the sensory domain of the membranous two-component fumarate sensor (histidine protein kinase) DcuS of Escherichia coli.

The structure of the water-soluble, periplasmic domain of the fumarate sensor DcuS (DcuS-pd) has been determined by NMR spectroscopy in solution. DcuS is a prototype for a sensory histidine kinase with transmembrane signal transfer. DcuS belongs to the CitA family of sensors that are specific for sensing di- and tricarboxylates. The periplasmic domain is folded autonomously and shows helices at the N and the C terminus, suggesting direct linking or connection to helices in the two transmembrane regions. The structure constitutes a novel fold. The nearest structural neighbor is the Per-Arnt-Sim domain of the photoactive yellow protein that binds small molecules covalently. Residues Arg107, His110, and Arg147 are essential for fumarate sensing and are found clustered together. The structure constitutes the first periplasmic domain of a two component sensory system and is distinctly different from the aspartate sensory domain of the Tar chemotaxis sensor.

Amino Acid Sequence↗
PubMed2003

Molecular evolution of sensory domains in cyanobacterial chemoreceptors.

Components of the chemotaxis system encoded in multiple homologous operons were identified in five cyanobacterial genomes. Analysis of phylogenetic profiles, genomic context, domain architectures and sequence identity reveal that sensory modules of chemoreceptors that detect environmental cues are the subject of frequent domain birth and death events and have accelerated rates of sequence evolution. This fact could explain a remarkable diversity of the sensing repertoire of chemotaxis receptors in microorganisms.

Bacterial Proteins↗
PubMed2003

MASE1 and MASE2: two novel integral membrane sensory domains.

Escherichia coli proteins YegE and YaiC contain N-terminal integral membrane regions, followed by the putative diguanylate cyclase (GGDEF, DUF1) domains. The membrane domains of these proteins, named MASE1 (membrane-associated sensor) and MASE2, respectively, were found in other bacterial signaling proteins, such as histidine kinases (MASE1) and an adenylate cyclase (MASE2). Although the nature of the signals sensed by MASE1 and MASE2 is still unknown, MASE1-containing receptors appear to play important roles in bacteria, including iron and/or oxygen sensing by hemerythrine-containing proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris.

Adenylyl Cyclases↗
PubMed1983

Regulation of ciliary pattern in dileptus (Ciliata). II. Formation of a cortical domain of sensory cilia from a domain of locomotor cilia.

The surface of the ciliate Dileptus contains locomotor and sensory domains. Each domain contains cilia of its own kind, arranged in a characteristic pattern. Transformation of a portion of the locomotor area into the sensory domain has been studied. Locomotor ciliary units in the transforming area undergo resorption of ciliary shafts, which are subsequently replaced by shafts of a sensory type. Anterior to each transforming ciliary unit a new one is formed, and both acquire sensory rootlets. As a result, a double-kinetosomal sensory unit emerges. A regulatory change in structure occurs over a definite area that is determined to become the sensory cortical domain.

Animals↗
PubMed2000

A model instrument for the documentation of outcome after nerve repair.

We present a new model for documentation and quantification of the functional outcome after nerve repair at the wrist or distal forearm level and a protocol that includes a numerical scoring system. The model, presented here along with validation and reliability test results, supports our hypothesis that the summarized test results reflecting specific functional limitations correlates well with the patient's opinion of the impact of the nerve injury on activities of daily living. Seventy patients with nerve repair were examined using the protocol. Analysis included 3 factors: sensory domain (sensory innervation, tactile agnosis, and finger dexterity), motor domain (motor innervation and grip strength), and pain/discomfort domain (hyperaesthesia and cold intolerance). The analysis explained 73% of the variances of the variables and the variables had a logical distribution between the factors. Analysis of internal consistency demonstrated good homogeneity. A calculated total score correlated strongly with the patients' global estimation of the impact of the injury on activities of daily living and the summary of sensory and pain/discomfort domains correlated significantly with the Medical Research Council S0-S4 scale. The presented model represents a useful new tool for evaluation of the functional outcome after nerve injury and repair.

Adolescent↗
PubMed2006

The signaling helix: a common functional theme in diverse signaling proteins.

BACKGROUND: The mechanism by which the signals are transmitted between receptor and effector domains in multi-domain signaling proteins is poorly understood. RESULTS: Using sensitive sequence analysis methods we identify a conserved helical segment of around 40 residues in a wide range of signaling proteins, including numerous sensor histidine kinases such as Sln1p, and receptor guanylyl cyclases such as the atrial natriuretic peptide receptor and nitric oxide receptors. We term this helical segment the signaling (S)-helix and present evidence that it forms a novel parallel coiled-coil element, distinct from previously known helical segments in signaling proteins, such as the Dimerization-Histidine phosphotransfer module of histidine kinases, the intra-cellular domains of the chemotaxis receptors, inter-GAF domain helical linkers and the alpha-helical HAMP module. Analysis of domain architectures allowed us to reconstruct the domain-neighborhood graph for the S-helix, which showed that the S-helix almost always occurs between two signaling domains. Several striking patterns in the domain neighborhood of the S-helix also became evident from the graph. It most often separates diverse N-terminal sensory domains from various C-terminal catalytic signaling domains such as histidine kinases, cNMP cyclase, PP2C phosphatases, NtrC-like AAA+ ATPases and diguanylate cyclases. It might also occur between two sensory domains such as PAS domains and occasionally between a DNA-binding HTH domain and a sensory domain. The sequence conservation pattern of the S-helix revealed the presence of a unique constellation of polar residues in the dimer-interface positions within the central heptad of the coiled-coil formed by the S-helix. CONCLUSION: Combining these observations with previously reported mutagenesis studies on different S-helix-containing proteins we suggest that it functions as a switch that prevents constitutive activation of linked downstream signaling domains. However, upon occurrence of specific conformational changes due to binding of ligand or other sensory inputs in a linked upstream domain it transmits the signal to the downstream domain. Thus, the S-helix represents one of the most prevalent functional themes involved in the flow of signals between modules in diverse prokaryote-type multi-domain signaling proteins. REVIEWERS: This article was reviewed by Frank Eisenhaber, Arcady Mushegian and Sandor Pongor.

Journal Article↗
PubMed2004

Bacterial signal transduction network in a genomic perspective.

Bacterial signalling network includes an array of numerous interacting components that monitor environmental and intracellular parameters and effect cellular response to changes in these parameters. The complexity of bacterial signalling systems makes comparative genome analysis a particularly valuable tool for their studies. Comparative studies revealed certain general trends in the organization of diverse signalling systems. These include (i) modular structure of signalling proteins; (ii) common organization of signalling components with the flow of information from N-terminal sensory domains to the C-terminal transmitter or signal output domains (N-to-C flow); (iii) use of common conserved sensory domains by different membrane receptors; (iv) ability of some organisms to respond to one environmental signal by activating several regulatory circuits; (v) abundance of intracellular signalling proteins, typically consisting of a PAS or GAF sensor domains and various output domains; (vi) importance of secondary messengers, cAMP and cyclic diguanylate; and (vii) crosstalk between components of different signalling pathways. Experimental characterization of the novel domains and domain combinations would be needed for achieving a better understanding of the mechanisms of signalling response and the intracellular hierarchy of different signalling pathways.

Adenylyl Cyclases↗
PubMed2006

MEKHLA, a novel domain with similarity to PAS domains, is fused to plant homeodomain-leucine zipper III proteins.

Homeodomain (HD) proteins play important roles in the development of plants, fungi, and animals. Here we identify a novel domain, MEKHLA, in the C terminus of HD-Leu zipper (HD-ZIP) III plant HD proteins that shares similarity with a group of bacterial proteins and a protein from the green alga Chlamydomonas reinhardtii. The group of bacterial MEKHLA proteins is found in cyanobacteria and other bacteria often found associated with plants. Phylogenetic analysis suggests that a MEKHLA protein transferred, possibly from a cyanobacterium or an early chloroplast, into the nuclear genome of an early plant in a first step, and attached itself to the C terminus of an HD-ZIP IV homeobox gene in a second step. Further position-specific iterated-BLAST searches with the bacterial MEKHLA proteins revealed a subregion within the MEKHLA domain that shares significant similarity with the PAS domain. The PAS domain is a sensory module found in many proteins through all kingdoms of life. It is involved in light, oxygen, and redox potential sensation. The fact that HD-ZIP III proteins are transcription factors that have this sensory domain attached to their C terminus uncovers a potential new signaling pathway in plants.

Amino Acid Sequence↗
PubMed2025

Specificities of chemosensory receptors in the human gut microbiota.

The human gut is rich in metabolites and harbors a complex microbial community, yet surprisingly little is known about the spectrum of chemical signals detected by the large variety of sensory receptors present in the gut microbiome. Here, we systematically mapped the ligand specificities of selected extracytoplasmic sensory domains from twenty members of the human gut microbiota, with a primary focus on the abundant and physiologically important class of Clostridia. Twenty-five metabolites from different chemical classes-including amino acids, nucleobase derivatives, amines, indole, and carboxylates-were identified as specific ligands for fifteen sensory domains from nine bacterial species, which represent all three major functional classes of transmembrane receptors: chemotaxis receptors, histidine kinases, and enzymatic sensors. We have further characterized the specificity and evolution of ligand binding to Cache superfamily sensors specific for lactate, dicarboxylic acids, and for uracil and short-chain fatty acids (SCFAs). Structural and biochemical analysis of the dCache sensor of uracil and SCFAs revealed that its two different ligand types bind at distinct sensory modules. Overall, combining experimental identification with computational analyses, we were able to assign ligands to approximately half of the Cache-type chemotaxis receptors found in the eleven gut commensal genomes from our set, with carboxylic acids representing the largest ligand class. Among these, the most commonly found ligand specificities were for lactate and formate, indicating a particular importance of these metabolites in the human gut microbiota and consistent with their observed growth-promoting effects on selected bacterial commensals.

Humans↗
PubMedDate not supplied

The minimal clinically important difference of the Carpal Tunnel Syndrome Symptom Severity Scale.

PURPOSE: To identify the change score in the Symptom Severity Scale (SSS) of the Carpal Tunnel Syndrome (CTS) Questionnaire that is associated with an important change in clinical status. METHODS: Twenty-eight patients with CTS treated with a carpal tunnel steroid injection completed the Brigham and Women's Hospital CTS Questionnaire before steroid injections and at the 3-week follow-up visit. Satisfaction was determined by postcare review of the clinical management. To calculate the minimal clinically important difference, receiver operating characteristic curves were created. The area under the curve was calculated to determine and compare the responsiveness of the entire SSS and the pain and sensory questions in isolation. RESULTS: The SSS of the CTS Questionnaire, including its pain and sensory domain, can show a meaningful clinical improvement after carpal tunnel injection. The SSS, its sensory domain, and its pain domain were statistically better than chance. All 3 measures showed predictive ability; however, the total SSS was the most sensitive in detecting a change. The minimal clinically important difference in the score of the SSS after carpal tunnel steroid injection was found to be 1.04. CONCLUSIONS: The SSS can be used to distinguish a clinically important change after carpal tunnel injection. A decrease of 1.04 or more in the SSS score may indicate a clinically important change in a patient's state of health. TYPE OF STUDY/LEVEL OF EVIDENCE: Prognostic, Level I.

Adult↗
PubMed2003

Perceptual differences in sequential stimuli across patients with musician's and writer's cramp.

Previous research has demonstrated a relationship between the regularity of motor production and the ability to make accurate perceptual judgments. The current study investigated the temporal abilities of two groups of patients with known movement problems (musicians' and writers' cramp), some of whom have had many years of training in temporal discrimination. Patients and controls (musician and nonmusician, respectively) judged whether the last of six sequential auditory or tactile stimuli occurred earlier or later in comparison to five previously and regularly presented stimuli. In both sensory domains, patients with musicians' cramp detected the early stimulus better than controls. When detecting the onset of late stimuli, only in the auditory domain were patients worse than controls. Patients with writers' cramp, however, did not show any significant group differences in either auditory or tactile domains, suggesting that such patients are not deficient in processing sequential stimuli. In conclusion, compared to controls, patients with musician's cramp demonstrated generalized timing anomalies, occurring in the symptomatic (tactile) and the asymptomatic (auditory) sensory domains. This timing problem is likely to be a consequence of the dystonic symptoms rather than the cause.

Adult↗
PubMed2004

Different roles of the frontal and parietal regions in memory-guided saccade: a PCA approach on time course of BOLD signal changes.

Although involvement of the frontoparietal regions in visually guided saccade and visuospatial attention has been established, functional difference of the frontal and parietal regions suggested in neuropsychological observations and lesion studies in animals has not been explicitly supported by functional imaging studies. Considering a possible disadvantage of cognitive subtraction in an interregional comparison, we directly compared the time course of BOLD signal changes across regions. Normal subjects performed a modified version of a memory-guided saccade task in which saccade was performed both during encoding and execution phases. In addition, the delay period was fixed and the peripheral target was presented also during the execution phase together with distracters. Therefore, visuospatial representation was likely maintained in the sensory domain during the delay phase. A principal component analysis on the time-course data separated the 20 activated areas into three groups, which largely coincided with the cerebral lobes. The frontal group included the putative human FEF and SEF, and the parietal group PEF. The frontal and occipital groups exhibited the time course of activation with two peaks corresponding to neural responses during the encoding and execution phases, and the parietal group exhibited a single-humped activation pattern corresponding to neural activity during the delay phase. The results suggest that the frontal regions are more associated with the execution of saccade, and the parietal regions with visuospatial representation, presumably in the sensory domain.

Adolescent↗
PubMed1996

Novel phosphotransferase-encoding genes revealed by analysis of the Escherichia coli genome: a chimeric gene encoding an Enzyme I homologue that possesses a putative sensory transduction domain.

Two genes (ptsI and ptsA) that encode homologues of the energy coupling Enzyme I of the phosphoenolpyruvate-dependent sugar-transporting phosphotransferase system (PTS) have previously been identified on the Escherichia coli chromosome. We here report the presence of a third E. coli gene, designated ptsP, that encodes an Enzyme I homologue, here designated Enzyme INtr. Enzyme INtr possesses an N-terminal domain homologous to the N-terminal domains of NifA proteins [(127 amino acids (aa)] joined via two tandem flexible linkers to the C-terminal Enzyme I-like domain (578 aa). Structural features of the putative ptsP operon, including transcriptional regulatory signals, are characterized. We suggest that Enzyme INtr functions in transcriptional regulation of nitrogen-related operons together with previously described PTS proteins encoded within the rpoN operon. It may thereby provide a link between carbon and nitrogen assimilatory pathways.

Animals↗