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Novel Domains (novel + domain)

Distribution by Scientific Domains

Life Sciences	100%

Selected Abstracts

Novel domains of the prokaryotic two-component signal transduction systems

FEMS MICROBIOLOGY LETTERS, Issue 1 2001
Michael Y. Galperin
Abstract The archetypal two-component signal transduction systems include a sensor histidine kinase and a response regulator, which consists of a receiver CheY-like domain and a DNA-binding domain. Sequence analysis of the sensor kinases and response regulators encoded in complete bacterial and archaeal genomes revealed complex domain architectures for many of them and allowed the identification of several novel conserved domains, such as PAS, GAF, HAMP, GGDEF, EAL, and HD-GYP. All of these domains are widely represented in bacteria, including 19 copies of the GGDEF domain and 17 copies of the EAL domain encoded in the Escherichia coli genome. In contrast, these novel signaling domains are much less abundant in bacterial parasites and in archaea, with none at all found in some archaeal species. This skewed phyletic distribution suggests that the newly discovered complexity of signal transduction systems emerged early in the evolution of bacteria, with subsequent massive loss in parasites and some horizontal dissemination among archaea. Only a few proteins containing these domains have been studied experimentally, and their exact biochemical functions remain obscure; they may include transformations of novel signal molecules, such as the recently identified cyclic diguanylate. Recent experimental data provide the first direct evidence of the participation of these domains in signal transduction pathways, including regulation of virulence genes and extracellular enzyme production in the human pathogens Bordetella pertussis and Borrelia burgdorferi and the plant pathogen Xanthomonas campestris. Gene-neighborhood analysis of these new domains suggests their participation in a variety of processes, from mercury and phage resistance to maintenance of virulence plasmids. It appears that the real picture of the complexity of phosphorelay signal transduction in prokaryotes is only beginning to unfold. [source]

Identification of pseudomurein cell wall binding domains

MOLECULAR MICROBIOLOGY, Issue 6 2006
Peter J. M. Steenbakkers
Summary Methanothermobacter thermautotrophicus is a methanogenic Gram-positive microorganism with a cell wall consisting of pseudomurein. Currently, no information is available on extracellular pseudomurein biology and so far only two prophage pseudomurein autolysins, PeiW and PeiP, have been reported. In this paper we show that PeiW and PeiP contain two different N-terminal pseudomurein cell wall binding domains. This finding was used to identify a novel domain, PB007923, on the M. thermautotrophicus genome present in 10 predicted open reading frames. Three homologues were identified in the Methanosphaera stadtmanae genome. Binding studies of fusion constructs of three separate PB007923 domains to green fluorescent protein revealed that it also constituted a cell wall binding domain. Both prophage domains and the PB007923 domain bound to the cell walls of Methanothermobacter species and fluorescence microscopy showed a preference for the septal region. Domain specificities were revealed by binding studies with other pseudomurein-containing archaea. Localized binding was observed for M. stadtmanae and Methanobrevibacter species, while others stained evenly. The identification of the first pseudomurein cell wall binding domains reveals the dynamics of the pseudomurein cell wall and provides marker proteins to study the extracellular pseudomurein biology of M. thermautotrophicus and of other pseudomurein-containing archaea. [source]

Xenopus paraxis homologue shows novel domains of expression

DEVELOPMENTAL DYNAMICS, Issue 3 2004
Ronald Carpio
Abstract The paraxis gene encodes a basic helix-loop-helix transcription factor that is expressed in paraxial mesoderm and whose mutant displays an inability to form epithelial somites. Here, the molecular characterization of Xenopus paraxis is reported. paraxis is expressed in the paraxial mesoderm and somites but is down-regulated during muscle differentiation. In addition to its paraxial mesodermal expression, described in other organisms, two novel expression domains of paraxis were found: the neural tube and the head mesoderm. paraxis expression in the neural tube was compared with the expression of the neural markers Xash and Xiro1, and we concluded that paraxis is expressed in a broad band in the prospective sulcus limitans of the neural tube. Developmental Dynamics 231:609,613, 2004. © 2004 Wiley-Liss, Inc. [source]

BNR , a LINE family from Beta vulgaris, contains a RRM domain in open reading frame 1 and defines a L1 sub-clade present in diverse plant genomes

THE PLANT JOURNAL, Issue 6 2009
Tony Heitkam
Summary We characterized a novel type of plant non-LTR retrotransposons, identified as the BNR family, in sugar beet (Beta vulgaris) genomes. Although their ORF2 sequences were similar to those of previously analysed LINEs (long interspersed nuclear elements) of the L1 clade, their ORF1 sequences differ strongly from those of most plant LINEs. Two novel domains were identified, containing a conserved secondary motif, known as the RNA recognition motif (RRM). ORF1 lacks the zinc finger motif that is typical of plant LINEs, but has an RRM that is likely to have a RNA-binding function. BNR LINEs are highly diverse, and were characterized by gel-blot and fluorescent in situ hybridization, showing a widespread occurrence and clustering along chromosome arms. Insertion of BNR1 into a well-described satellite repeat was detected in two cultivars only, indicating recent activity. Database searches revealed the existence of LINE families possessing an ORF1 sequence similar to that of BNR in the genomes of higher plants such as poplar, lotus and soybean. Comparing their reverse transcriptase regions with those of other retrotransposons, these LINEs were assigned to the L1 clade, but form a distinct group, providing evidence of a major separation of L1 elements in plants. This indicates a common origin of BNR-like LINEs, suggesting that these elements form a sub-clade designated as the BNR sub-clade. [source]