A comparison of the Caulobacter NA1000 and K31 genomes reveals extensive genome rearrangements and differences in metabolic potential.

Abstract:

:The genus Caulobacter is found in a variety of habitats and is known for its ability to thrive in low-nutrient conditions. K31 is a novel Caulobacter isolate that has the ability to tolerate copper and chlorophenols, and can grow at 4 ° C with a doubling time of 40 h. K31 contains a 5.5 Mb chromosome that codes for more than 5500 proteins and two large plasmids (234 and 178 kb) that code for 438 additional proteins. A comparison of the K31 and the Caulobacter crescentus NA1000 genomes revealed extensive rearrangements of gene order, suggesting that the genomes had been randomly scrambled. However, a careful analysis revealed that the distance from the origin of replication was conserved for the majority of the genes and that many of the rearrangements involved inversions that included the origin of replication. On a finer scale, numerous small indels were observed. K31 proteins involved in essential functions shared 80-95% amino acid sequence identity with their C. crescentus homologues, while other homologue pairs tended to have lower levels of identity. In addition, the K31 chromosome contains more than 1600 genes with no homologue in NA1000.

journal_name

Open Biol

journal_title

Open biology

authors

Ash K,Brown T,Watford T,Scott LE,Stephens C,Ely B

doi

10.1098/rsob.140128

subject

Has Abstract

pub_date

2014-10-01 00:00:00

issue

10

issn

2046-2441

pii

rsob.140128

journal_volume

4

pub_type

杂志文章
  • Understanding the mammalian TRAP complex function(s).

    abstract::In eukaryotic cells, about one-third of the synthesized proteins are translocated into the endoplasmic reticulum; they are membrane or lumen resident proteins and proteins direct to the Golgi apparatus. The co-translational translocation takes place through the heterotrimeric protein-conducting channel Sec61 which is ...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.190244

    authors: Russo A

    更新日期:2020-05-01 00:00:00

  • TNF-α-induced NF-κB activation upregulates microRNA-150-3p and inhibits osteogenesis of mesenchymal stem cells by targeting β-catenin.

    abstract::Although systemic or local inflammation, commonly featured by cytokine activation, is implicated in patients with bone loss, the underlying mechanisms are still elusive. As microRNAs (miR), a class of small non-coding RNAs involved in essential physiological processes, have been found in bone cells, we aimed to invest...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.150258

    authors: Wang N,Zhou Z,Wu T,Liu W,Yin P,Pan C,Yu X

    更新日期:2016-03-01 00:00:00

  • A new role for muscle segment homeobox genes in mammalian embryonic diapause.

    abstract::Mammalian embryonic diapause is a phenomenon defined by the temporary arrest in blastocyst growth and metabolic activity within the uterus which synchronously becomes quiescent to blastocyst activation and implantation. This reproductive strategy temporally uncouples conception from parturition until environmental or ...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.130035

    authors: Cha J,Sun X,Bartos A,Fenelon J,Lefèvre P,Daikoku T,Shaw G,Maxson R,Murphy BD,Renfree MB,Dey SK

    更新日期:2013-04-24 00:00:00

  • Wnt signalling in the development of axon, dendrites and synapses.

    abstract::Wnts are a highly conserved family of secreted glycoproteins that play essential roles in the morphogenesis and body patterning during the development of metazoan species. In recent years, mounting evidence has revealed important functions of Wnt signalling in diverse aspects of neural development, including neuronal ...

    journal_title:Open biology

    pub_type: 杂志文章,评审

    doi:10.1098/rsob.180116

    authors: He CW,Liao CP,Pan CL

    更新日期:2018-10-03 00:00:00

  • A brain-derived metric for preferred kinetic stimuli.

    abstract::We here address the question of whether there is any correlation between subjective preference for simple configurations within a specific visual domain such as motion and strength of activity in visual areas in which that domain is emphasized. We prepared several distinctive patterns of dots in motion with various ch...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.120001

    authors: Zeki S,Stutters J

    更新日期:2012-02-01 00:00:00

  • Covalent ISG15 conjugation positively regulates the ubiquitin E3 ligase activity of parkin.

    abstract::Parkinson's disease (PD) is characterized by selective loss of dopaminergic neurons in the pars compacta of the substantia nigra and accumulation of ubiquitinated proteins in aggregates called Lewy bodies. Several mutated genes have been found in familial PD patients, including SNCA (α-synuclein), PARK2 (parkin), PINK...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.160193

    authors: Im E,Yoo L,Hyun M,Shin WH,Chung KC

    更新日期:2016-08-01 00:00:00

  • Short linear motif acquisition, exon formation and alternative splicing determine a pathway to diversity for NCoR-family co-repressors.

    abstract::Vertebrate NCoR-family co-repressors play central roles in the timing of embryo and stem cell differentiation by repressing the activity of a range of transcription factors. They interact with nuclear receptors using short linear motifs (SLiMs) termed co-repressor for nuclear receptor (CoRNR) boxes. Here, we identify ...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.150063

    authors: Short S,Peterkin T,Guille M,Patient R,Sharpe C

    更新日期:2015-08-01 00:00:00

  • Glareosin: a novel sexually dimorphic urinary lipocalin in the bank vole, Myodes glareolus.

    abstract::The urine of bank voles (Myodes glareolus) contains substantial quantities of a small protein that is expressed at much higher levels in males than females, and at higher levels in males in the breeding season. This protein was purified and completely sequenced at the protein level by mass spectrometry. Leucine/isoleu...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.170135

    authors: Loxley GM,Unsworth J,Turton MJ,Jebb A,Lilley KS,Simpson DM,Rigden DJ,Hurst JL,Beynon RJ

    更新日期:2017-09-01 00:00:00

  • Neutrophil heterogeneity in health and disease: a revitalized avenue in inflammation and immunity.

    abstract::Leucocytes form the principal cellular components of immunity and inflammation, existing as multiple subsets defined by distinct phenotypic and functional profiles. To date, this has most notably been documented for lymphocytes and monocytes. In contrast, as neutrophils are traditionally considered, to be short-lived,...

    journal_title:Open biology

    pub_type: 杂志文章,评审

    doi:10.1098/rsob.120134

    authors: Beyrau M,Bodkin JV,Nourshargh S

    更新日期:2012-11-01 00:00:00

  • Phylogeny rather than ecology or lifestyle biases the construction of Escherichia coli-Shigella genetic exchange communities.

    abstract::Genetic material can be transmitted not only vertically from parent to offspring, but also laterally (horizontally) from one bacterial lineage to another. Lateral genetic transfer is non-uniform; biases in its nature or frequency construct communities of genetic exchange. These biases have been proposed to arise from ...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.120112

    authors: Skippington E,Ragan MA

    更新日期:2012-09-01 00:00:00

  • Core regulatory circuitries in defining cancer cell identity across the malignant spectrum.

    abstract::Gene expression programmes driving cell identity are established by tightly regulated transcription factors that auto- and cross-regulate in a feed-forward manner, forming core regulatory circuitries (CRCs). CRC transcription factors create and engage super-enhancers by recruiting acetylation writers depositing permis...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.200121

    authors: Jahangiri L,Tsaprouni L,Trigg RM,Williams JA,Gkoutos GV,Turner SD,Pereira J

    更新日期:2020-07-01 00:00:00

  • Mutational analysis of dimeric linkers in peri- and cytoplasmic domains of histidine kinase DctB reveals their functional roles in signal transduction.

    abstract::Membrane-associated histidine kinases (HKs) in two-component systems respond to environmental stimuli by autophosphorylation and phospho-transfer. HK typically contains a periplasmic sensor domain that regulates the cytoplasmic kinase domain through a conserved cytoplasmic linker. How signal is transduced from the lig...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.140023

    authors: Liu J,Yang J,Wen J,Yang Y,Wei X,Zhang X,Wang YP

    更新日期:2014-06-01 00:00:00

  • Mitochondrial determinants of mammalian longevity.

    abstract::Current ageing theories are far from satisfactory because of the many determinants involved in ageing. The well-known rate-of-living theory assumes that the product (lifetime energy expenditure, LEE) of maximum lifespan (MLS) and mass-specific basal metabolic rate (msBMR) is approximately constant. Although this theor...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.170083

    authors: Kitazoe Y,Hasegawa M,Tanaka M,Futami M,Futami J

    更新日期:2017-10-01 00:00:00

  • The first cell-fate decision of mouse preimplantation embryo development: integrating cell position and polarity.

    abstract::During the first cell-fate decision of mouse preimplantation embryo development, a population of outer-residing polar cells is segregated from a second population of inner apolar cells to form two distinct cell lineages: the trophectoderm and the inner cell mass (ICM), respectively. Historically, two models have been ...

    journal_title:Open biology

    pub_type: 杂志文章,评审

    doi:10.1098/rsob.170210

    authors: Mihajlović AI,Bruce AW

    更新日期:2017-11-01 00:00:00

  • Establishment and function of chromatin modification at enhancers.

    abstract::How a single genome can give rise to distinct cell types remains a fundamental question in biology. Mammals are able to specify and maintain hundreds of cell fates by selectively activating unique subsets of their genome. This is achieved, in part, by enhancers-genetic elements that can increase transcription of both ...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.200255

    authors: Tafessu A,Banaszynski LA

    更新日期:2020-10-01 00:00:00

  • Efficiency of RNA interference is improved by knockdown of dsRNA nucleases in tephritid fruit flies.

    abstract::RNA interference (RNAi) in insects is routinely used to ascertain gene function, but also has potential as a technology to control pest species. For some insects, such as beetles, ingestion of small quantities of double-stranded RNA (dsRNA) is able to knock down a targeted gene's expression. However, in other species,...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.190198

    authors: Tayler A,Heschuk D,Giesbrecht D,Park JY,Whyard S

    更新日期:2019-12-01 00:00:00

  • Labile disulfide bonds are common at the leucocyte cell surface.

    abstract::Redox conditions change in events such as immune and platelet activation, and during viral infection, but the biochemical consequences are not well characterized. There is evidence that some disulfide bonds in membrane proteins are labile while others that are probably structurally important are not exposed at the pro...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.110010

    authors: Metcalfe C,Cresswell P,Ciaccia L,Thomas B,Barclay AN

    更新日期:2011-11-01 00:00:00

  • Sex-biased expression of microRNAs in Drosophila melanogaster.

    abstract::Most animals have separate sexes. The differential expression of gene products, in particular that of gene regulators, is underlying sexual dimorphism. Analyses of sex-biased expression have focused mostly on protein-coding genes. Several lines of evidence indicate that microRNAs, a class of major gene regulators, are...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.140024

    authors: Marco A

    更新日期:2014-04-02 00:00:00

  • IDH1 mutation promotes lung cancer cell proliferation through methylation of Fibulin-5.

    abstract::Mutation in isocitrate dehydrogenase (IDH) leads to an aberrant function of the enzyme, leading to the production of hydroxyglutarate, as well as changes in cellular metabolism, DNA methylation and histone modification. Previous studies uncovered mutations in IDH1 in several malignancies, with the most frequent mutati...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.180086

    authors: Yan B,Hu Y,Ma T,Wang Y

    更新日期:2018-10-10 00:00:00

  • Mechanism of Hsp70 specialized interactions in protein translocation and the unfolded protein response.

    abstract::Hsp70 chaperones interact with substrate proteins in a coordinated fashion that is regulated by nucleotides and enhanced by assisting cochaperones. There are numerous homologues and isoforms of Hsp70 that participate in a wide variety of cellular functions. This diversity can facilitate adaption or specialization base...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.200089

    authors: Larburu N,Adams CJ,Chen CS,Nowak PR,Ali MMU

    更新日期:2020-08-01 00:00:00

  • Rheb and mammalian target of rapamycin in mitochondrial homoeostasis.

    abstract::Mitochondrial dysfunction has been associated with various diseases, such as cancer, myopathies, neurodegeneration and obesity. Mitochondrial homoeostasis is achieved by mechanisms that adapt the number of mitochondria to that required for energy production and for the supply of metabolic intermediates necessary to su...

    journal_title:Open biology

    pub_type: 杂志文章,评审

    doi:10.1098/rsob.130185

    authors: Groenewoud MJ,Zwartkruis FJ

    更新日期:2013-12-18 00:00:00

  • Two-step phosphorylation of Ana2 by Plk4 is required for the sequential loading of Ana2 and Sas6 to initiate procentriole formation.

    abstract::The conserved process of centriole duplication requires Plk4 kinase to recruit and promote interactions between Sas6 and Sas5/Ana2/STIL (respective nomenclature of worms/flies/humans). Plk4-mediated phosphorylation of Ana2/STIL in its conserved STAN motif has been shown to promote its interaction with Sas6. However, S...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.170247

    authors: Dzhindzhev NS,Tzolovsky G,Lipinszki Z,Abdelaziz M,Debski J,Dadlez M,Glover DM

    更新日期:2017-12-01 00:00:00

  • Nonlinear ionizing radiation-induced changes in eye lens cell proliferation, cyclin D1 expression and lens shape.

    abstract::Elevated cataract risk after radiation exposure was established soon after the discovery of X-rays in 1895. Today, increased cataract incidence among medical imaging practitioners and after nuclear incidents has highlighted how little is still understood about the biological responses of the lens to low-dose ionizing ...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.150011

    authors: Markiewicz E,Barnard S,Haines J,Coster M,van Geel O,Wu W,Richards S,Ainsbury E,Rothkamm K,Bouffler S,Quinlan RA

    更新日期:2015-04-01 00:00:00

  • The contribution of non-essential Schizosaccharomyces pombe genes to fitness in response to altered nutrient supply and target of rapamycin activity.

    abstract::Nutrient fluctuations in the cellular environment promote changes in cell metabolism and growth to adapt cell proliferation accordingly. The target of rapamycin (TOR) signalling network plays a key role in the coordination of growth and cell proliferation with the nutrient environment and, importantly, nutrient limita...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.180015

    authors: Lie S,Banks P,Lawless C,Lydall D,Petersen J

    更新日期:2018-05-01 00:00:00

  • Spotlight on the microbes that produce heat shock protein 90-targeting antibiotics.

    abstract::Heat shock protein 90 (Hsp90) is a promising cancer drug target as a molecular chaperone critical for stabilization and activation of several of the oncoproteins that drive cancer progression. Its actions depend upon its essential ATPase, an activity fortuitously inhibited with a very high degree of selectivity by nat...

    journal_title:Open biology

    pub_type: 杂志文章,评审

    doi:10.1098/rsob.120138

    authors: Piper PW,Millson SH

    更新日期:2012-12-12 00:00:00

  • A conditional mutant of the fatty acid synthase unveils unexpected cross talks in mycobacterial lipid metabolism.

    abstract::Unlike most bacteria, mycobacteria rely on the multi-domain enzyme eukaryote-like fatty acid synthase I (FAS I) to make fatty acids de novo. These metabolites are precursors of the biosynthesis of most of the lipids present both in the complex mycobacteria cell wall and in the storage lipids inside the cell. In order ...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.160277

    authors: Cabruja M,Mondino S,Tsai YT,Lara J,Gramajo H,Gago G

    更新日期:2017-02-01 00:00:00

  • Direct interaction of avermectin with epidermal growth factor receptor mediates the penetration resistance in Drosophila larvae.

    abstract::With the widespread use of avermectins (AVMs) for managing parasitic and agricultural pests, the resistance of worms and insects to AVMs has emerged as a serious threat to human health and agriculture worldwide. The reduced penetration of AVMs is one of the main reasons for the development of the resistance to the che...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.150231

    authors: Chen LP,Wang P,Sun YJ,Wu YJ

    更新日期:2016-04-01 00:00:00

  • The interesting relationship between APOBEC3 deoxycytidine deaminases and cancer: a long road ahead.

    abstract::Cancer is considered a group of diseases characterized by uncontrolled growth and spread of abnormal cells and is propelled by somatic mutations. Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) family of enzymes are endogenous sources of somatic mutations found in multiple human cancers. Wh...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.200188

    authors: Granadillo Rodríguez M,Flath B,Chelico L

    更新日期:2020-12-01 00:00:00

  • Correlating efficacy and desensitization with GluK2 ligand-binding domain movements.

    abstract::Gating of AMPA- and kainate-selective ionotropic glutamate receptors can be defined in terms of ligand affinity, efficacy and the rate and extent of desensitization. Crucial insights into all three elements have come from structural studies of the ligand-binding domain (LBD). In particular, binding-cleft closure is as...

    journal_title:Open biology

    pub_type: 杂志文章

    doi:10.1098/rsob.130051

    authors: Nayeem N,Mayans O,Green T

    更新日期:2013-05-29 00:00:00

  • Plasticity within the αβ⁺CD4⁺ T-cell lineage: when, how and what for?

    abstract::Following thymic output, αβ⁺CD4⁺ T cells become activated in the periphery when they encounter peptide-major histocompatibility complex. A combination of cytokine and co-stimulatory signals instructs the differentiation of T cells into various lineages and subsequent expansion and contraction during an appropriate and...

    journal_title:Open biology

    pub_type: 杂志文章,评审

    doi:10.1098/rsob.120157

    authors: Coomes SM,Pelly VS,Wilson MS

    更新日期:2013-01-23 00:00:00