Search results for "regulator"
showing 10 items of 1009 documents
Network motif-based analysis of regulatory patterns in paralogous gene pairs
2020
Current high-throughput experimental techniques make it feasible to infer gene regulatory interactions at the whole-genome level with reasonably good accuracy. Such experimentally inferred regulatory networks have become available for a number of simpler model organisms such as S. cerevisiae, and others. The availability of such networks provides an opportunity to compare gene regulatory processes at the whole genome level, and in particular, to assess similarity of regulatory interactions for homologous gene pairs either from the same or from different species. We present here a new technique for analyzing the regulatory interaction neighborhoods of paralogous gene pairs. Our central focu…
Stimulus Perception in Bacterial Signal-Transducing Histidine Kinases
2006
SUMMARY Two-component signal-transducing systems are ubiquitously distributed communication interfaces in bacteria. They consist of a histidine kinase that senses a specific environmental stimulus and a cognate response regulator that mediates the cellular response, mostly through differential expression of target genes. Histidine kinases are typically transmembrane proteins harboring at least two domains: an input (or sensor) domain and a cytoplasmic transmitter (or kinase) domain. They can be identified and classified by virtue of their conserved cytoplasmic kinase domains. In contrast, the sensor domains are highly variable, reflecting the plethora of different signals and modes of sens…
Structural and Functional Characterization of Autophosphorylation in Bacterial Histidine Kinases
2019
Autophosphorylation of histidine kinases (HK) is the first step for signal transduction in bacterial two-component signalling systems. As HKs dimerize, the His residue is phosphorylated in cis or trans depending on whether the ATP molecule used in the reaction is bound to the same or the neighboring subunit, respectively. The cis or trans autophosphorylation results from an alternative directionality in the connection between helices α1 and α2 in the HK DHp domain, in such a way that α2 could be oriented almost 90° counterclockwise or clockwise with respect to α1. Sequence and length variability of this connection appears to lie behind the different directionality and is implicated in partn…
Illuminating a Phytochrome Paradigm – a Light-Activated Phosphatase in Two-Component Signaling Uncovered
2020
ABSTRACTBacterial phytochrome photoreceptors usually belong to two-component signaling systems which transmit environmental stimuli to a response regulator through a histidine kinase domain. Phytochromes switch between red light-absorbing and far-red light-absorbing states. Despite exhibiting extensive structural responses during this transition, the model bacteriophytochrome fromDeinococcus radiodurans(DrBphP) lacks detectable kinase activity. Here, we resolve this long-standing conundrum by comparatively analyzing the interactions and output activities of DrBphP and a bacteriophytochrome fromAgrobacterium fabrum(AgP1). Whereas AgP1 acts as a conventional histidine kinase, we identify DrBp…
Sensing of O 2 and nitrate by bacteria: alternative strategies for transcriptional regulation of nitrate respiration by O 2 and nitrate
2020
Many bacteria are able to use O2 and nitrate as alternative electron acceptors for respiration. Strategies for regulation in response to O2 and nitrate can vary considerably. In the paradigmatic system of E. coli (and γ-proteobacteria), regulation by O2 and nitrate is established by the O2 -sensor FNR and the two-component system NarX-NarL (for nitrate regulation). Expression of narGHJI is regulated by the binding of FNR and NarL to the promoter. A similar strategy by individual regulation in response to O2 and nitrate is verified in many genera by the use of various types of regulators. Otherwise, in the soil bacteria Bacillus subtilis (Firmicutes) and Streptomyces (Actinobacteria), nitrat…
Control of the bifunctional O 2 ‐sensor kinase NreB of Staphylococcus carnosus by the nitrate sensor NreA: Switching from kinase to phosphatase state
2019
The NreB-NreC two-component system of Staphylococcus carnosus for O2 sensing cooperates with the accessory nitrate sensor NreA in the NreA-NreB-NreC system for coordinated sensing and regulation of nitrate respiration by O2 and nitrate. ApoNreA (NreA in the absence of nitrate) interacts with NreB and inhibits NreB autophosphorylation (and activation). NreB contains the phosphatase motif DxxxQ. The present study shows that NreB on its own was inactive for the dephosphorylation of the phosphorylated response regulator NreC (NreC-P), but co-incubation with NreB and NreA stimulated NreC-P dephosphorylation. Either the presence of NreA · NO 3 - instead of apoNreA or mutation of the phosphatase m…
1H, 13C, and 15N NMR chemical shift assignment of the complex formed by the first EPEC EspF repeat and N-WASP GTPase binding domain
2021
AbstractLEE-encoded effector EspF (EspF) is an effector protein part of enteropathogenic Escherichia coli’s (EPEC’s) arsenal for intestinal infection. This intrinsically disordered protein contains three highly conserved repeats which together compose over half of the protein’s complete amino acid sequence. EPEC uses EspF to hijack host proteins in order to promote infection. In the attack EspF is translocated, together with other effector proteins, to host cell via type III secretion system. Inside host EspF stimulates actin polymerization by interacting with Neural Wiskott-Aldrich syndrome protein (N-WASP), a regulator in actin polymerization machinery. It is presumed that EspF acts by di…
Old sleeping Sicilian beauty: seed germination in the palaeoendemic Petagnaea gussonei (Spreng.) Rauschert (Saniculoideae, Apiaceae).
2015
Petagnaea gussonei (Apiaceae) is a perennial herbaceous species endemic to northeast Sicily (Nebrodi Mountains). It is considered a remnant of the Sicilian Tertiary flora, and is endangered according to the Red List. There is no information in the literature about the germinability of its seeds, even though seed production is know to occur. The aim of this study was to obtain data to better understand seed germination of this species and its biological implications. Thus, several approaches were employed: vitality analyses, gibberellic acid supply, germination and soil microbial flora analyses via end-point and qPCR. The results suggest that seed germination occurs after ca. 1.5 years at a …
Sequence of a sea urchin hsp70 gene and its 5' flanking region.
1990
We report the nucleotide sequence of a 4470-bp fragment derived from a sea urchin genomic clone containing part of a heat-shock protein 70 (Hsp70)-encoding gene. This fragment, named hsp70 gene II, contains 1271 bp of the flanking region and 3299 bp of structural gene sequence interrupted by five introns and encoding the N-terminal 371 amino acids (aa) of the protein. The 5' flanking region contains a putative TATA element, two CCAAT boxes, four heat-shock consensus sequence elements (hse) and one consensus sequence for binding of Sp1. Remarkable homologies were observed for deduced aa sequence and intron-exon organization between hsp70 gene II and rat hsc73 gene.
pH Feedback Lifecycles Programmed by Enzymatic Logic Gates Using Common Foods as Fuels
2021
Abstract Artificial temporal signaling systems, which mimic living out‐of‐equilibrium conditions, have made large progress. However, systems programmed by enzymatic reaction networks in multicomponent and unknown environments, and using biocompatible components remain a challenge. Herein, we demonstrate an approach to program temporal pH signals by enzymatic logic gates. They are realized by an enzymatic disaccharide‐to‐monosaccharide‐to‐sugar acid reaction cascade catalyzed by two metabolic chains: invertase‐glucose oxidase and β‐galactosidase‐glucose oxidase, respectively. Lifetimes of the transient pH signal can be programmed from less than 15 min to more than 1 day. We study enzymatic k…