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Prokaryotic Cells (0):
Recent article
Prokaryotic Cells
Xenobiotica (41)5 2011
Abstract
We will describe the construction of a fusion protein with the SUMO-tag, its expression in Escherichia coli, and its purification followed by the removal of the SUMO-tag by a SUMO-specific protease in vitro....
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PMID: 19107426
PDF is available here.
PDF is available here.
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Abstract
We report the sequencing of 137 diverse marine isolates collected from around the world. We analysed these sequences, along with previously published marine prokaryotic genomes, in the context of marine metagenomic data, to gain insights into the ecology of the surface ocean prokaryotic picoplankton...
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PMID: 21048761
PDF is available here.
PDF is available here.
Biochemical Journal (432)1 2010
Abstract
We show that frataxin deficiency in murine liver is associated with increased basal levels of oxidative DNA base damage. Accordingly, eukaryotic V79 fibroblasts overexpressing human frataxin show decreased basal levels of these modifications, while prokaryotic Salmonella enterica serotype Typhimuriu...
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PMID: 20819074
PDF is available here.
PDF is available here.
Abstract
All complex life is composed of eukaryotic (nucleated) cells. The eukaryotic cell arose from prokaryotes just once in four billion years, and otherwise prokaryotes show no tendency to evolve greater complexity. Why not? Prokaryotic genome size is constrained by bioenergetics. The endosymbiosis that...
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PMID: 20962839
PDF is available here.
PDF is available here.
Genetika (Moskva) (46)10 2010
Abstract
The possibility is discussed that the order of genes in chromosomes is not random but determined by natural selection, i.e., is a selectively valuable character. Cases of long-term conservation of gene linkage or synteny in evolution are presented. Examples and possible mechanisms of nonrandom gene...
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PMID: 21254548
PDF is available here.
PDF is available here.
Trends in Genetics (26)9 2010
Abstract
We discuss this difference in the light of aggregation prevention, contribution to functional divergence and binding-related functions. We then address the possible underlying features that create and conserve domain repeats. Our findings provide a starting point for the identification of the fundam...
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PMID: 20643491
PDF is available here.
PDF is available here.
Abstract
In most prokaryotes and many eukaryotes, synthesis of carbamoylphosphate (CP) by carbamoylphosphate synthetase (CPSase; E.C. 6.3.5.5) and its allocation to either pyrimidine or arginine biosynthesis are highly controlled processes. Regulation at the transcriptional level occurs at either CPSase gene...
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PMID: 20451592
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1800)8 2010
Abstract
Current understanding indicates that at least two distinct mechanisms are in operation in prokaryotic ferritins. In one, the ferroxidase centre acts as a true catalytic centre in driving Fe(2+) oxidation in the cavity; in the other, the centre acts as a gated iron pore by oxidising Fe(2+) and transf...
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PMID: 20388533
PDF is available here.
PDF is available here.
Abstract
We show that the scalings of metabolic rate, population growth rate, and production efficiency with body size have changed across the evolutionary transitions. Metabolic rate scales with body mass superlinearly in prokaryotes, linearly in protists, and sublinearly in metazoans, so Kleiber's 3/4 powe...
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PMID: 20616006
PDF is available here.
PDF is available here.
Abstract
We developed a methodology for assessments of intragenomic heterogeneity of these periodic patterns and applied it in analysis of 1,025 prokaryotic chromosomes. This technique allows more detailed analysis of sequence periodicity than previous methods where sequence periodicity was assessed in an in...
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PMID: 20494989
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1804)5 2010
Abstract
Fast and accurate replication of DNA is accomplished by the interactions of multiple proteins in the dynamic DNA replisome. The DNA replisome effectively coordinates the leading and lagging strand synthesis of DNA. These complex, yet elegantly organized, molecular machines have been studied extensive...
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PMID: 19665592
PDF is available here.
PDF is available here.
Abstract
Our current understanding of the mechanism of translation is based on nearly fifty years of biochemical and biophysical studies. This mechanism, which requires the ribosome to manipulate tRNA and step repetitively along the mRNA, implies movement. High-resolution structures of the ribosome and its l...
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PMID: 20192783
PDF is available here.
PDF is available here.
Protoplasma (240)1-4 2010
Abstract
médecine/sciences (26)4 2010
Abstract
Abstract
An insect antifreeze protein gene Mpafp149 was cloned by the RT-PCR approach from the desert beetle Microdera punctipennis dzungarica. Sequence analysis revealed that this gene encoding a protein of 120 amid acids and this protein showed 65-76% homology with other insect antifreeze proteins, the ded...
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PMID: 19562508
PDF is available here.
PDF is available here.
Abstract
We here present the synthesis and application of a novel GDP-Capture Compound for the functional enrichment of GTPases, a pivotal protein family that exerts key functions in signal transduction. We present data from CCMS experiments on two biological lysates from Escherichia coli and from human-deri...
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PMID: 20026263
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1804)5 2010
Abstract
The Y-family translesion DNA polymerases enable cells to tolerate many forms of DNA damage, yet these enzymes have the potential to create genetic mutations at high rates. Although this polymerase family was defined less than a decade ago, more than 90 structures have already been determined so far....
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PMID: 20123134
PDF is available here.
PDF is available here.
Abstract
All organisms, from bacteria to humans, face the daunting task of replicating, packaging and segregating up to two metres (about 6 x 10(9) base pairs) of DNA when each cell divides. This task is carried out up to a trillion times during the development of a human from a single fertilized cell. The s...
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PMID: 20110988
PDF is available here.
PDF is available here.
Abstract
We present a whole-proteome phylogeny of prokaryotes constructed by comparing feature frequency profiles (FFPs) of whole proteomes. Features are l-mers of amino acids, and each organism is represented by a profile of frequencies of all features. The selection of feature length is critical in the FFP...
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PMID: 20018669
PDF is available here.
PDF is available here.
Abstract
We intended to evaluate in this review, and even more, to reconstruction of group specific phylogenetic tree....
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PMID: 21038699
PDF is available here.
PDF is available here.
BMC Genomics (11) 2010
Abstract
Gene duplication is a normal evolutionary process. If there is no selective advantage in keeping the duplicated gene, it is usually reduced to a pseudogene and disappears from the genome. However, some paralogs are retained. These gene products are likely to be beneficial to the organism, e.g. in ad...
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PMID: 20961426
PDF is available here.
PDF is available here.
Biochemical Journal (422)2 2009
Abstract
Pup (prokaryotic ubiquitin-like protein) from Mycobacterium tuberculosis is the first ubiquitin-like protein identified in non-eukaryotic cells. Although different ubiquitin-like proteins from eukaryotes share low sequence similarity, their 3D (three-dimensional) structures exhibit highly conserved...
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PMID: 19580545
PDF is available here.
PDF is available here.
A stochastic model for estimation of mutation rates in multiple-replication proliferation processes.
Abstract
We propose a stochastic model based on the branching process for estimation and comparison of the mutation rates in proliferation processes of cells or microbes. We assume in this model that cells or microbes (the elements of a population) are reproduced by generations and thus the model is more sui...
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PMID: 18846374
PDF is available here.
PDF is available here.
Trends in Genetics (25)7 2009
Abstract
Abstract
Infectious diseases still remain the main cause of human premature deaths, especially in developing countries. Vaccines constitute the most cost-effective tool for prophylaxis of infectious diseases. Elucidation of the complete genomes of many bacterial pathogens has provided a new blueprint for the...
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PMID: 19489702
PDF is available here.
PDF is available here.
EMBO Reports (10)6 2009
Abstract
Abstract
The work provides a simple method, based on a direct density equilibrium measurement, for the rapid in situ estimation of total lipid, hydrocarbon or biopolymer content in a variety of prokaryotic and eukaryotic samples. The method can be readily applied to live microalgae and photosynthetic bacteri...
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PMID: 19031427
PDF is available here.
PDF is available here.
Journal of Bacteriology (191)7 2009
Abstract
EMBO Reports (10)4 2009
Abstract
Plant Molecular Biology (69)5 2009
Abstract
We discuss that Dpt1 may be a bifunctional protein that couples the pyrimidine metabolism to the photosynthetic electron transport....
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PMID: 19037728
PDF is available here.
PDF is available here.
Iubmb Life (61)2 2009
Abstract
I PSDs include enzymes of eukaryotic mitochondria and bacterial origin which contain the amino acid sequence LGST as a characteristic motif. Type II PSDs are found in the endomembrane system of eukaryotes and contain a typical GGST motif. These characteristic motifs are considered as autocatalytic c...
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PMID: 19165886
PDF is available here.
PDF is available here.
Abstract
We draw attention to the differences between eukaryotic and prokaryotic glycoproteins. We also focus on the main bottlenecks that may be encountered in the search for glycosylation in concrete bacterium and outline a possible work-flow for the exploration of glycoproteins in bacteria....
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PMID: 19210128
PDF is available here.
PDF is available here.
Abstract
We determined the Langmuir surface pressure/molecular area isotherms of prokaryotic lipid monolayers, as well as the phospholipid phase transitions, by employing differential scanning calorimetry on unilamellar prokaryotic liposomes (bilayers). Results. Articaine hydrochloride was foun...
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PMID: 18941950
PDF is available here.
PDF is available here.
Abstract
We discuss these guidelines and provide illustration through reference to case studies from phage lambda biology.In our experience, computational modelling is best facilitated with a large and diverse set of quantitative, in vivo data, preferably obtained from standardised measurements and expressed...
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PMID: 19381541
PDF is available here.
PDF is available here.
Abstract
Prokaryotic protein expression changes in detectable amounts due to the environmental stimuli encountered by the organism. To understand the underlying mechanisms involved it is necessary to comprehensively detect both the proteins present and their relative abundance under the growth conditions of...
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PMID: 19241026
PDF is available here.
PDF is available here.
Abstract
This paper reviews phylogeny and evolution of ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) protein which is the key enzyme of the autotrophic Kalvin-Benson cycle and the most abundant protein on the planet. It consists of several structural-functional forms which include fully functiona...
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PMID: 19899625
PDF is available here.
PDF is available here.
Abstract
Aquaglyceroporin (AQP) channels facilitate the diffusion of a wide range of neutral solutes, including water, glycerol, and other small uncharged solutes. More recently, AQPs have been shown to allow the passage of trivalent arsenic and antimony compounds. Arsenic and antimony are metalloid elements....
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PMID: 19096785
PDF is available here.
PDF is available here.
Abstract
BMC Genomics (10)1 2009
Abstract
The SD sequences for 530 prokaryote genomes have been predicted using computer calculations of the base-pairing free energy between translation initiation regions and the 16S rRNA 3' tail. Genomes with a large number of genes with the SD sequence concentrate this regulatory motif from 4 to 11 bps be...
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PMID: 19922619
PDF is available here.
PDF is available here.
BMC Genomics (10)1 2009
Abstract
Our results indicate that RR and YR-stretches are differently distributed in prokaryotic phyla. RR stretches are overrepresented in all phyla except for the Actinobacteria and beta-Proteobacteria. In contrast, YR tracts are underrepresented in all phyla except for the beta-Proteobacterial group. YR-...
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PMID: 19646265
PDF is available here.
PDF is available here.
Abstract
Abstract
Changes in elemental abundances in Earth's oceans on geological time scales are intimately linked to evolutionary processes. School of Earth and Space Exploration and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA. E-mail: anbar{at}asu.edu
PDF is available here.
PDF is available here.
Journal of Molecular Biology (383)5 2008
Abstract
We determine here the solution structure of the functionally active Smr domain of the Bcl3-binding protein (also known as Nedd4-binding protein 2), a protein with unknown function that lacks other domains present in MutS proteins. The Smr domain adopts a two-layer alpha-beta sandwich fold, which has...
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PMID: 18804481
PDF is available here.
PDF is available here.
Acta Microbiologica Sinica (48)11 2008
Abstract
We introduce the brief history', structure, function, bioinformatics research and application of this amazing immunity system in prokaryotic organism for inspiring more scientists to find their interest in this developing topic....
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PMID: 19149174
PDF is available here.
PDF is available here.
Abstract
We employed the yeast REFs and searched for their evolutionary origin in more than 500 genomes of archaea and eubacteria by the PSI-BLAST search. Our results showed that the non-membranous REFs (non-mREFs) originated exclusively from eubacterial proteins, whereas the membranous REFs (mREFs) are from...
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PMID: 18620034
PDF is available here.
PDF is available here.
Current protocols in protein science / editorial board, John E. Coligan ... [et al.] (Chapter 19) 2008
Abstract
Native gels enable the analysis of protein complexes on a proteome-wide scale in a single experiment. The protocols described in this unit are based on separation of protein complexes by blue native polyacrylamide electrophoresis (BN-PAGE), the most versatile native gel system, and t...
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PMID: 19016435
PDF is available here.
PDF is available here.
Abstract
We have identified 2697 ELKs, most of which are encoded by multicellular strains of the phyla Proteobacteria (Myxococcales), Actinobacteria, Cyanobacteria, and Chloroflexi, and 2 Acidobacteria and 1 Planctomycetes. Astonishingly, 7 myxobacterial strains together encode 892 ELKs, with 4 of the strain...
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PMID: 18836084
PDF is available here.
PDF is available here.
Abstract
Abstract
Journal of Bacteriology (190)20 2008
Abstract
We report that ClpCP, ClpEP, and ClpXP localize in foci often near the poles of growing cells and that ClpP and the ATPase are each capable of polar localization independently of the other component. A region of ClpC containing an AAA domain was necessary and sufficient for polar localization. We al...
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PMID: 18689476
PDF is available here.
PDF is available here.
Physiological Reviews (88)4 2008
Abstract
We know about the structure of eukaryotic ion channels is based on the structure of bacterial channels, this should not be surprising given the evolutionary relatedness of all living organisms and suitability of microbial cells for structural studies of biological macromolecules in a laboratory envi...
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PMID: 18923187
PDF is available here.
PDF is available here.
Journal of Molecular Biology (381)5 2008
Abstract
We report the crystal structure of UK from Bacillus anthracis (BA1797) in complex with ATP at 2.82 A resolution. It reveals that the cofactor, in addition to binding in the active sites, also interacts with separate binding pockets located near the center of the hexameric structure. The existence of...
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PMID: 18625239
PDF is available here.
PDF is available here.
Abstract
We discuss examples of lateral gene transfer and introgressive hybridization that have resulted in the transfer or de novo origin of adaptations. The evolutionary clades in which this process has been identified include all types of organisms. However, we restrict our discussion to bacteria, fungi,...
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PMID: 18522920
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1778)9 2008
Abstract
We define the CISM family of enzymes on the basis of emerging structural and bioinformatic data, and show that the catalytic and FCP subunit architectures appear in a wide range of bacterial redox enzymes. We evaluate evolutionary events involving genes encoding the CISM catalytic subunit that resul...
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PMID: 17964535
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1779)9 2008
Abstract
We still do not understand neither what precise features define a faulty RNA, nor the molecular basis for recognition of such molecules. Nonetheless, our knowledge about the controlled degradation of both stable and labile RNAs is now converging into a unified picture that points to the poly(A) tail...
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PMID: 18657638
PDF is available here.
PDF is available here.
Abstract
We assessed them using comparative genomics in a phylogenetic context. First, we find that aerobiosis is a trait with important phylogenetic inertia but that oxygen content in proteins is not. Instead, oxygen content is close to the expected values given the nucleotide composition. Accordingly, we f...
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PMID: 18579552
PDF is available here.
PDF is available here.
Abstract
We used simulations to show that the method used previously tends to underestimate the expected number of inverted repeats. However, this bias is not large and cannot explain the excess of inverted repeats observed in real data. In contrast, our method is unbiased. When both methods are applied to b...
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PMID: 18696026
PDF is available here.
PDF is available here.
Hereditas (Beijing) (30)9 2008
Abstract
Horizontal gene transfer is the gene exchange between different organisms or different organelles, which occurs frequently in prokaryotes. Many newly identified horizontal transfer events in eukaryotes indicates that it is a common phenomenon in all organisms. This paper describes the concept of hor...
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PMID: 18779166
PDF is available here.
PDF is available here.
Abstract
We report that viral production in deep-sea benthic ecosystems worldwide is extremely high, and that viral infections are responsible for the abatement of 80% of prokaryotic heterotrophic production. Virus-induced prokaryotic mortality increases with increasing water depth, and beneath a depth of 1,...
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PMID: 18756250
PDF is available here.
PDF is available here.