16,471 results match your criteria Biochemical Society Transactions[Journal]


Allosteric regulation of AMP-activated protein kinase by adenylate nucleotides and small-molecule drugs.

Biochem Soc Trans 2019 Apr 18. Epub 2019 Apr 18.

Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Australia

The AMP (adenosine 5'-monophosphate)-activated protein kinase (AMPK) is a key regulator of cellular and whole-body energy homeostasis that co-ordinates metabolic processes to ensure energy supply meets demand. At the cellular level, AMPK is activated by metabolic stresses that increase AMP or adenosine 5'-diphosphate (ADP) coupled with falling adenosine 5'-triphosphate (ATP) and acts to restore energy balance by choreographing a shift in metabolism in favour of energy-producing catabolic pathways while inhibiting non-essential anabolic processes. AMPK also regulates systemic energy balance and is activated by hormones and nutritional signals in the hypothalamus to control appetite and body weight. Read More

View Article

Download full-text PDF

Source
http://www.biochemsoctrans.org/lookup/doi/10.1042/BST2018062
Publisher Site
http://dx.doi.org/10.1042/BST20180625DOI Listing
April 2019
1 Read

Exploitation of the operon promoter for controlled recombinant protein production.

Biochem Soc Trans 2019 Apr 10. Epub 2019 Apr 10.

Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K.

The operon promoter is widely used as a tool to control recombinant protein production in bacteria. Here, we give a brief review of how it functions, how it is regulated, and how, based on this knowledge, a suite of promoter derivatives has been developed to give a controlled expression that is suitable for diverse biotechnology applications. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20190059DOI Listing
April 2019
2 Reads

Packaging development: how chromatin controls transcription in zebrafish embryogenesis.

Biochem Soc Trans 2019 Apr 5. Epub 2019 Apr 5.

Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 913, Dunedin, New Zealand

How developmental gene expression is activated, co-ordinated and maintained is one of the biggest questions in developmental biology. While transcription factors lead the way in directing developmental gene expression, their accessibility to the correct repertoire of genes can depend on other factors such as DNA methylation, the presence of particular histone variants and post-translational modifications of histones. Collectively, factors that modify DNA or affect its packaging and accessibility contribute to a chromatin landscape that helps to control the timely expression of developmental genes. Read More

View Article

Download full-text PDF

Source
http://www.biochemsoctrans.org/lookup/doi/10.1042/BST2018061
Publisher Site
http://dx.doi.org/10.1042/BST20180617DOI Listing
April 2019
5 Reads

Apoptotic cell-derived extracellular vesicles: structure-function relationships.

Biochem Soc Trans 2019 Apr 5. Epub 2019 Apr 5.

School of Life and Health Sciences, Aston Research Centre for Healthy Ageing, Aston University, Birmingham, U.K.

Apoptosis is an essential process for normal physiology and plays a key role in the resolution of inflammation. Clearance of apoptotic cells (ACs) involves complex signalling between phagocytic cells, ACs, and the extracellular vesicles (EVs) they produce. Here, we discuss apoptotic cell-derived extracellular vesicles (ACdEVs) and how their structure relates to their function in AC clearance and the control of inflammation, focussing on the ACdEV proteome. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180080DOI Listing
April 2019
1 Read

Imaging cell morphology and physiology using X-rays.

Biochem Soc Trans 2019 Apr 5. Epub 2019 Apr 5.

Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A.

Morphometric measurements, such as quantifying cell shape, characterizing sub-cellular organization, and probing cell-cell interactions, are fundamental in cell biology and clinical medicine. Until quite recently, the main source of morphometric data on cells has been light- and electron-based microscope images. However, many technological advances have propelled X-ray microscopy into becoming another source of high-quality morphometric information. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180036DOI Listing
April 2019
1 Read

Manipulating nitrogen regulation in diazotrophic bacteria for agronomic benefit.

Biochem Soc Trans 2019 Apr 1. Epub 2019 Apr 1.

Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich NR4 7UH, U.K.

Biological nitrogen fixation (BNF) is controlled by intricate regulatory mechanisms to ensure that fixed nitrogen is readily assimilated into biomass and not released to the environment. Understanding the complex regulatory circuits that couple nitrogen fixation to ammonium assimilation is a prerequisite for engineering diazotrophic strains that can potentially supply fixed nitrogen to non-legume crops. In this review, we explore how the current knowledge of nitrogen metabolism and BNF regulation may allow strategies for genetic manipulation of diazotrophs for ammonia excretion and provide a contribution towards solving the nitrogen crisis. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180342DOI Listing
April 2019
2 Reads

Amino acid transporters in the regulation of insulin secretion and signalling.

Biochem Soc Trans 2019 Apr 1. Epub 2019 Apr 1.

Research School of Biology, Australian National University, Canberra, ACT 2601, Australia

Amino acids are increasingly recognised as modulators of nutrient disposal, including their role in regulating blood glucose through interactions with insulin signalling. More recently, cellular membrane transporters of amino acids have been shown to form a pivotal part of this regulation as they are primarily responsible for controlling cellular and circulating amino acid concentrations. The availability of amino acids regulated by transporters can amplify insulin secretion and modulate insulin signalling in various tissues. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180250DOI Listing
April 2019
1 Read

Oxysterol research: a brief review.

Biochem Soc Trans 2019 Apr 1. Epub 2019 Apr 1.

Swansea University Medical School, ILS1 Building, Singleton Park, Swansea SA2 8PP, Wales, U.K.

In the present study, we discuss the recent developments in oxysterol research. Exciting results have been reported relating to the involvement of oxysterols in the fields of neurodegenerative disease, especially in Huntington's disease, Parkinson's disease and Alzheimer's disease; in signalling and development, in particular, in relation to Hedgehog signalling; and in cancer, with a special focus on (25R)26-hydroxycholesterol. Methods for the measurement of oxysterols, essential for understanding their mechanism of action , and valuable for diagnosing rare diseases of cholesterol biosynthesis and metabolism are briefly considered. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180135DOI Listing

Protein engineering: the potential of remote mutations.

Biochem Soc Trans 2019 Mar 22. Epub 2019 Mar 22.

Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia

Engineered proteins, especially enzymes, are now commonly used in many industries owing to their catalytic power, specific binding of ligands, and properties as materials and food additives. As the number of potential uses for engineered proteins has increased, the interest in engineering or designing proteins to have greater stability, activity and specificity has increased in turn. With any rational engineering or design pursuit, the success of these endeavours relies on our fundamental understanding of the systems themselves; in the case of proteins, their structure-dynamics-function relationships. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180614DOI Listing
March 2019
1 Read

United colours of chromatin? Developmental genome organisation in flies.

Biochem Soc Trans 2019 Mar 22. Epub 2019 Mar 22.

Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart 7000, Australia

The organisation of DNA into differing forms of packaging, or chromatin, controls many of the cell fate decisions during development. Although early studies focused on individual forms of chromatin, in the last decade more holistic studies have attempted to determine a complete picture of the different forms of chromatin present within a cell. In the fruit fly, , the study of chromatin states has been aided by the use of complementary and cell-type-specific techniques that profile the marks that recruit chromatin protein binding or the proteins themselves. Read More

View Article

Download full-text PDF

Source
http://www.biochemsoctrans.org/lookup/doi/10.1042/BST2018060
Publisher Site
http://dx.doi.org/10.1042/BST20180605DOI Listing
March 2019
7 Reads

Glioblastoma heterogeneity and the tumour microenvironment: implications for preclinical research and development of new treatments.

Biochem Soc Trans 2019 Mar 22. Epub 2019 Mar 22.

Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, Australia

Glioblastoma is the deadliest form of brain cancer. Aside from inadequate treatment options, one of the main reasons glioblastoma is so lethal is the rapid growth of tumour cells coupled with continuous cell invasion into surrounding healthy brain tissue. Significant intra- and inter-tumour heterogeneity associated with differences in the corresponding tumour microenvironments contributes greatly to glioblastoma progression. Read More

View Article

Download full-text PDF

Source
http://www.biochemsoctrans.org/lookup/doi/10.1042/BST2018044
Publisher Site
http://dx.doi.org/10.1042/BST20180444DOI Listing
March 2019
6 Reads

Recruited lysosomal enzymes as major digestive enzymes in insects.

Biochem Soc Trans 2019 Mar 22. Epub 2019 Mar 22.

Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, Brazil.

The mass recruitment to the midgut contents of lysosomal proteolytic enzymes occurred in insects under three major selective pressures. Hemipteran (true bugs, aphids, and cicadas) ancestors lost their serine peptidases (SP) on adapting to feed on protein-free plant sap. When they returned to protein diets, their cathepsins L and B were recruited to replace their lost SP. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180344DOI Listing

Endothelial-to-haematopoietic transition: an update on the process of making blood.

Biochem Soc Trans 2019 Mar 22. Epub 2019 Mar 22.

MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, U.K.

The first definitive blood cells during embryogenesis are derived from endothelial cells in a highly conserved process known as endothelial-to-haematopoietic transition (EHT). This conversion involves activation of a haematopoietic transcriptional programme in a subset of endothelial cells in the major vasculature of the embryo, followed by major morphological changes that result in transitioning cells rounding up, breaking the tight junctions to neighbouring endothelial cells and adopting a haematopoietic fate. The whole process is co-ordinated by a complex interplay of key transcription factors and signalling pathways, with additional input from surrounding tissues. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180320DOI Listing

The role of the 12()-HETE/GPR31/12-HETER axis in cancer and ischemia-reperfusion injury.

Biochem Soc Trans 2019 Mar 22. Epub 2019 Mar 22.

Research and Epidemiology Unit, IDI-IRCCS, Via Monti di Creta 104, 00167 Rome, Italy

The G protein-coupled receptors (GPCRs) constitute a large superfamily of seven transmembrane-spanning receptors that are activated by several classes of ligands, including bioactive lipids. GPCRs are attractive therapeutic targets for the treatment of human diseases, as they finely regulate a wide array of cellular functions. In this minireview, we summarized what is currently known about the G protein-coupled receptor GPR31/12-HETER. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180635DOI Listing

Biological relevance of cell-in-cell in cancers.

Biochem Soc Trans 2019 Mar 8. Epub 2019 Mar 8.

Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, U.K.

Cell-in-cell (CIC) is a term used to describe the presence of one, usually living, cell inside another cell that is typically considered non-phagocytic. Examples of this include tumour cells inside tumour cells (homotypic), mesenchymal stem cells inside tumour cells (heterotypic) or immune cells inside tumour cells (heterotypic). CIC formation can occur in cell lines and in tissues and it has been most frequently observed during inflammation and in cancers. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180618DOI Listing

The multiple antibiotic resistance activator protein represses transcription of the operon.

Biochem Soc Trans 2019 Mar 8. Epub 2019 Mar 8.

Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.

In , the operon is a determinant for antibiotic resistance. Such phenotypes require the encoded transcription factor MarA that activates efflux pump expression. To better understand all genes controlled by MarA, we recently mapped binding of the regulator across the genome. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180498DOI Listing

On fitness: how do mutations shape the biology of cancer?

Authors:
Ian J Majewski

Biochem Soc Trans 2019 Mar 8. Epub 2019 Mar 8.

Division of Cancer and Haematology, The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria 3052, Australia

The theory of evolution by natural selection shapes our understanding of the living world. While natural selection has given rise to all the intricacies of life on the planet, those responsible for treating cancer have a darker view of adaptation and selection. Revolutionary changes in DNA sequencing technology have allowed us to survey the complexities that constitute the cancer genome, while advances in genetic engineering are allowing us to functionally interrogate these alterations. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180224DOI Listing
March 2019
2 Reads

Transcription in cyanobacteria: a distinctive machinery and putative mechanisms.

Biochem Soc Trans 2019 Mar 5. Epub 2019 Mar 5.

Centre for Bacterial Cell Biology, Newcastle University, Newcastle, U.K.

Transcription in cyanobacteria involves several fascinating features. Cyanobacteria comprise one of the very few groups in which no proofreading factors (Gre homologues) have been identified. Gre factors increase the efficiency of RNA cleavage, therefore helping to maintain the fidelity of the RNA transcript and assist in the resolution of stalled RNAPs to prevent genome damage. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180508DOI Listing
March 2019
1 Read

Structural studies of plasmin inhibition.

Biochem Soc Trans 2019 Mar 5. Epub 2019 Mar 5.

ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne 3800, Australia

Plasminogen (Plg) is the zymogen form of the serine protease plasmin (Plm), and it plays a crucial role in fibrinolysis as well as wound healing, immunity, tissue remodeling and inflammation. Binding to the targets via the lysine-binding sites allows for Plg activation by plasminogen activators (PAs) present on the same target. Cellular uptake of fibrin degradation products leads to apoptosis, which represents one of the pathways for cross-talk between fibrinolysis and tissue remodeling. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180211DOI Listing
March 2019
5 Reads

Caught in the act: LRRK2 in exosomes.

Biochem Soc Trans 2019 Mar 5. Epub 2019 Mar 5.

Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC 27710, U.S.A.

Mutations in the (LRRK2) gene are a frequent genetic cause of late-onset Parkinson's disease (PD) and a target for therapeutic approaches. LRRK2 protein can influence vesicle trafficking events in the cytosol, with action both in endosomal and lysosomal pathways in different types of cells. A subset of late endosomes harbor intraluminal vesicles that can be secreted into the extracellular milieu. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180467DOI Listing
March 2019
6 Reads

LRRK2 links genetic and sporadic Parkinson's disease.

Biochem Soc Trans 2019 Mar 5. Epub 2019 Mar 5.

Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bldg. 35, 35 Convent Drive, Bethesda, MD 20892-3707, U.S.A.

The past two decades in research has revealed the importance of leucine-rich repeat kinase 2 (LRRK2) in both monogenic and sporadic forms of Parkinson's disease (PD). In families, mutations in LRRK2 can cause PD with age-dependent but variable penetrance and genome-wide association studies have found variants of the gene that are risk factors for sporadic PD. Functional studies have suggested that the common mechanism that links all disease-associated variants is that they increase LRRK2 kinase activity, albeit in different ways. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180462DOI Listing
March 2019
7 Reads

Membrane trafficking in osteoclasts and implications for osteoporosis.

Biochem Soc Trans 2019 Mar 5. Epub 2019 Mar 5.

Bone Biology and Disease Laboratory, School of Biomedical Sciences, The University of Western Australia, Nedlands, Perth 6009, Western Australia

Osteoclasts are large multinucleated cells exquisitely adapted to resorb bone matrix. Like other eukaryotes, osteoclasts possess an elaborate ensemble of intracellular organelles through which solutes, proteins and other macromolecules are trafficked to their target destinations via membrane-bound intermediaries. During bone resorption, membrane trafficking must be tightly regulated to sustain the structural and functional polarity of the osteoclasts' membrane domains. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180445DOI Listing
March 2019
5 Reads

Transcriptional noise and exaptation as sources for bacterial sRNAs.

Biochem Soc Trans 2019 Mar 5. Epub 2019 Mar 5.

Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany

Understanding how new genes originate and integrate into cellular networks is key to understanding evolution. Bacteria present unique opportunities for both the natural history and experimental study of gene origins, due to their large effective population sizes, rapid generation times, and ease of genetic manipulation. Bacterial small non-coding RNAs (sRNAs), in particular, many of which operate through a simple antisense regulatory logic, may serve as tractable models for exploring processes of gene origin and adaptation. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180171DOI Listing

It's all about the T: transcription termination in archaea.

Biochem Soc Trans 2019 02 19;47(1):461-468. Epub 2019 Feb 19.

Biology II, Ulm University, 89069 Ulm, Germany

One of the most fundamental biological processes driving all life on earth is transcription. The, at first glance, relatively simple cycle is divided into three stages: initiation at the promoter site, elongation throughout the open reading frame, and finally termination and product release at the terminator. In all three processes, motifs of the template DNA and protein factors of the transcription machinery including the multisubunit polymerase itself as well as a broad range of associated transcription factors work together and mutually influence each other. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180557DOI Listing
February 2019
12 Reads

Antibiotic resistance in grass and soil.

Biochem Soc Trans 2019 02 19;47(1):477-486. Epub 2019 Feb 19.

Department of Biology, Maynooth University, Maynooth, Ireland.

Antibiotic resistance is currently one of the greatest threats to human health. The global overuse of antibiotics in human medicine and in agriculture has resulted in the proliferation and dissemination of a multitude of antibiotic resistance genes (ARGs). Despite a large proportion of antibiotics being used in agriculture, little is understood about how this may contribute to the overall antibiotic resistance crisis. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180552DOI Listing
February 2019
2 Reads

Coenzyme A: a protective thiol in bacterial antioxidant defence.

Authors:
Ivan Gout

Biochem Soc Trans 2019 02 19;47(1):469-476. Epub 2019 Feb 19.

Department of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, U.K.

Coenzyme A (CoA) is an indispensable cofactor in all living organisms. It is synthesized in an evolutionarily conserved pathway by enzymatic conjugation of cysteine, pantothenate (Vitamin B5), and ATP. This unique chemical structure allows CoA to employ its highly reactive thiol group for diverse biochemical reactions. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180415DOI Listing
February 2019
3 Reads

Engineering of receptor-binding proteins in bacteriophages and phage tail-like bacteriocins.

Biochem Soc Trans 2019 02 19;47(1):449-460. Epub 2019 Feb 19.

Department of Biotechnology, Ghent University, Ghent, Belgium

Bacteriophages and phage tail-like bacteriocins (PTLBs) rely on receptor-binding proteins (RBPs) located in tail fibers or spikes for an initial and specific interaction with susceptible bacteria. Bacteriophages kill bacteria through a lytic, replicative cycle, whereas PTLBs kill the target through membrane depolarization in a single hit mechanism. Extensive efforts in the engineering of RBPs of both phages and PTLBs have been undertaken to obtain a greater understanding of the structural organization of RBPs. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180172DOI Listing
February 2019
1 Read

The role of VPS4 in ESCRT-III polymer remodeling.

Biochem Soc Trans 2019 02 19;47(1):441-448. Epub 2019 Feb 19.

CEA, CNRS, Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, 38000 Grenoble, France

The endosomal sorting complex required for transport-III (ESCRT-III) and VPS4 catalyze a variety of membrane-remodeling processes in eukaryotes and archaea. Common to these processes is the dynamic recruitment of ESCRT-III proteins from the cytosol to the inner face of a membrane neck structure, their activation and filament formation inside or at the membrane neck and the subsequent or concomitant recruitment of the AAA-type ATPase VPS4. The dynamic assembly of ESCRT-III filaments and VPS4 on cellular membranes induces constriction of membrane necks with large diameters such as the cytokinetic midbody and necks with small diameters such as those of intraluminal vesicles or enveloped viruses. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180026DOI Listing
February 2019
1 Read

Twenty years of Mediator complex structural studies.

Biochem Soc Trans 2019 02 7;47(1):399-410. Epub 2019 Feb 7.

UMR 8576, Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), CNRS, Univ. Lille, F-59000 Lille, France.

Mediator is a large multiprotein complex conserved in all eukaryotes that plays an essential role in transcriptional regulation. Mediator comprises 25 subunits in yeast and 30 subunits in humans that form three main modules and a separable four-subunit kinase module. For nearly 20 years, because of its size and complexity, Mediator has posed a formidable challenge to structural biologists. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393861PMC
February 2019
1 Read

The role of chromosome segregation and nuclear organisation in human subfertility.

Biochem Soc Trans 2019 02 7;47(1):425-432. Epub 2019 Feb 7.

School of Biosciences, University of Kent, Canterbury, U.K.

Spermatogenesis is central to successful sexual reproduction, producing large numbers of haploid motile male gametes. Throughout this process, a series of equational and reductional chromosome segregation precedes radical repackaging of the haploid genome. Faithful chromosome segregation is thus crucial, as is an ordered spatio-temporal 'dance' of packing a large amount of chromatin into a very small space. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180231DOI Listing
February 2019
1 Read

Towards functional characterization of archaeal genomic dark matter.

Biochem Soc Trans 2019 02 1;47(1):389-398. Epub 2019 Feb 1.

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, U.S.A.

A substantial fraction of archaeal genes, from ∼30% to as much as 80%, encode 'hypothetical' proteins or genomic 'dark matter'. Archaeal genomes typically contain a higher fraction of dark matter compared with bacterial genomes, primarily, because isolation and cultivation of most archaea in the laboratory, and accordingly, experimental characterization of archaeal genes, are difficult. In the present study, we present quantitative characteristics of the archaeal genomic dark matter and discuss comparative genomic approaches for functional prediction for 'hypothetical' proteins. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180560DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393860PMC
February 2019

Emerging paradigms for PilZ domain-mediated C-di-GMP signaling.

Biochem Soc Trans 2019 02 1;47(1):381-388. Epub 2019 Feb 1.

School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, S637551 Singapore

PilZ domain-containing proteins constitute a large family of bacterial signaling proteins. As a widely distributed protein domain for the binding of the second messenger c-di-GMP, the canonical PilZ domain contains a set of motifs that define the binding site for c-di-GMP and an allosteric switch for propagating local conformational changes. Here, we summarize some new insights gathered from recent studies on the commonly occurring single-domain PilZ proteins, YcgR-like proteins and PilZ domain-containing cellulose synthases. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180543DOI Listing
February 2019

The demise of catalysis, but new functions arise: pseudoenzymes as the phoenixes of the protein world.

Biochem Soc Trans 2019 02 1;47(1):371-379. Epub 2019 Feb 1.

Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, U.S.A.

Pseudoenzymes are noncatalytic homologues of enzymes and are found in most enzyme families. Although lacking catalytic activity and sometimes referred to as 'dead' enzymes, they instead resemble phoenixes because the loss of a catalytic function during evolution was associated with the development of vital new functions. They are important in regulating the activity and location of catalytically active homologues, scaffolding the assembly of signaling complexes, and regulating transcription or translation. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180473DOI Listing
February 2019

ADP-ribosylation and intracellular traffic: an emerging role for PARP enzymes.

Biochem Soc Trans 2019 02 1;47(1):357-370. Epub 2019 Feb 1.

Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy

ADP-ribosylation is an ancient and reversible post-translational modification (PTM) of proteins, in which the ADP-ribose moiety is transferred from NAD to target proteins by members of poly-ADP-ribosyl polymerase (PARP) family. The 17 members of this family have been involved in a variety of cellular functions, where their regulatory roles are exerted through the modification of specific substrates, whose identification is crucial to fully define the contribution of this PTM. Evidence of the role of the PARPs is now available both in the context of physiological processes and of cell responses to stress or starvation. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180416DOI Listing
February 2019
1 Read

Transcription initiation factor TBP: old friend new questions.

Biochem Soc Trans 2019 02 1;47(1):411-423. Epub 2019 Feb 1.

Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany

In all domains of life, the regulation of transcription by DNA-dependent RNA polymerases (RNAPs) is achieved at the level of initiation to a large extent. Whereas bacterial promoters are recognized by a σ-factor bound to the RNAP, a complex set of transcription factors that recognize specific promoter elements is employed by archaeal and eukaryotic RNAPs. These initiation factors are of particular interest since the regulation of transcription critically relies on initiation rates and thus formation of pre-initiation complexes. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180623DOI Listing
February 2019

Dissecting metabolism using zebrafish models of disease.

Biochem Soc Trans 2019 02 30;47(1):305-315. Epub 2019 Jan 30.

Peter MacCallum Cancer Centre, 305 Grattan St., Melbourne, Victoria 3000, Australia

Zebrafish () are becoming an increasingly powerful model organism to study the role of metabolism in disease. Since its inception, the zebrafish model has relied on unique attributes such as the transparency of embryos, high fecundity and conservation with higher vertebrates, to perform phenotype-driven chemical and genetic screens. In this review, we describe how zebrafish have been used to reveal novel mechanisms by which metabolism regulates embryonic development, obesity, fatty liver disease and cancer. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180335DOI Listing
February 2019
1 Read

Detecting ovarian cancer using extracellular vesicles: progress and possibilities.

Biochem Soc Trans 2019 02 30;47(1):295-304. Epub 2019 Jan 30.

Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Gipsy Lane, Headington, Oxford OX3 0BP, U.K.

Ovarian cancer (OC) is the deadliest gynecological malignancy. Most patients are diagnosed when they are already in the later stages of the disease. Earlier detection of OC dramatically improves the overall survival, but this is rarely achieved as there is a lack of clinically implemented biomarkers of early disease. Read More

View Article

Download full-text PDF

Source
http://biochemsoctrans.org/lookup/doi/10.1042/BST20180286
Publisher Site
http://dx.doi.org/10.1042/BST20180286DOI Listing
February 2019
12 Reads

Adenine nucleotides as paracrine mediators and intracellular second messengers in immunity and inflammation.

Biochem Soc Trans 2019 02 23;47(1):329-337. Epub 2019 Jan 23.

Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany

Adenine nucleotides (AdNs) play important roles in immunity and inflammation. Extracellular AdNs, such as adenosine triphosphate (ATP) or nicotinamide adenine dinucleotide (NAD) and their metabolites, act as paracrine messengers by fine-tuning both pro- and anti-inflammatory processes. Moreover, intracellular AdNs derived from ATP or NAD play important roles in many cells of the immune system, including T lymphocytes, macrophages, neutrophils and others. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180419DOI Listing
February 2019

H2 influenza viruses: designing vaccines against future H2 pandemics.

Biochem Soc Trans 2019 02 15;47(1):251-264. Epub 2019 Jan 15.

Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, U.S.A.

Influenza-related pathologies affect millions of people each year and the impact of influenza on the global economy and in our everyday lives has been well documented. Influenza viruses not only infect humans but also are zoonotic pathogens that infect various avian and mammalian species, which serve as viral reservoirs. While there are several strains of influenza currently circulating in animal species, H2 influenza viruses have a unique history and are of particular concern. Read More

View Article

Download full-text PDF

Source
http://biochemsoctrans.org/lookup/doi/10.1042/BST20180602
Publisher Site
http://dx.doi.org/10.1042/BST20180602DOI Listing
February 2019
15 Reads

Initiating DNA replication: a matter of prime importance.

Authors:
Stephen D Bell

Biochem Soc Trans 2019 02 15;47(1):351-356. Epub 2019 Jan 15.

Department of Molecular and Cellular Biochemistry, Indiana University, Simon Hall MSB, 212 S Hawthorne Dr., Bloomington, IN 47405, U.S.A.

It has been known for decades that the principal replicative DNA polymerases that effect genome replication are incapable of starting DNA synthesis Rather, they require a 3'-OH group from which to extend a DNA chain. Cellular DNA replication systems exploit a dedicated, limited processivity RNA polymerase, termed primase, that synthesizes a short oligoribonucleotide primer which is then extended by a DNA polymerase. Thus, primases can initiate synthesis, proceed with primer elongation for a short distance then transfer the primer to a DNA polymerase. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180627DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393858PMC
February 2019
1 Read

An updated structural classification of replicative DNA polymerases.

Biochem Soc Trans 2019 02 15;47(1):239-249. Epub 2019 Jan 15.

Unit of Structural Dynamics of Macromolecules, CNRS UMR 3528, Pasteur Institute, 75015 Paris, France

Replicative DNA polymerases are nano-machines essential to life, which have evolved the ability to copy the genome with high fidelity and high processivity. In contrast with cellular transcriptases and ribosome machines, which evolved by accretion of complexity from a conserved catalytic core, no replicative DNA polymerase is universally conserved. Strikingly, four different families of DNA polymerases have evolved to perform DNA replication in the three domains of life. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180579DOI Listing
February 2019
2 Reads

Mechanisms of antibiotics inhibiting bacterial RNA polymerase.

Biochem Soc Trans 2019 02 15;47(1):339-350. Epub 2019 Jan 15.

Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne NE2 4AX, U.K.

Transcription, the first phase of gene expression, is performed by the multi-subunit RNA polymerase (RNAP). Bacterial RNAP is a validated target for clinical antibiotics. Many natural and synthetic compounds are now known to target RNAP, inhibiting various stages of the transcription cycle. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180499DOI Listing
February 2019
2 Reads

Structural mass spectrometry comes of age: new insight into protein structure, function and interactions.

Biochem Soc Trans 2019 02 15;47(1):317-327. Epub 2019 Jan 15.

Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France

Mass spectrometry (MS) provides an impressive array of information about the structure, function and interactions of proteins. In recent years, many new developments have been in the field of native MS and these exemplify a new coming of age of this field. In this mini review, we connect the latest methodological and instrumental developments in native MS to the new insights these have enabled. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180356DOI Listing
February 2019
1 Read

Cryo-EM in drug discovery.

Biochem Soc Trans 2019 02 15;47(1):281-293. Epub 2019 Jan 15.

Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K.

The impact of structural biology on drug discovery is well documented, and the workhorse technique for the past 30 years or so has been X-ray crystallography. With the advent of several technological improvements, including direct electron detectors, automation, better microscope vacuums and lenses, phase plates and improvements in computing power enabled by GPUs, it is now possible to record and analyse images of protein structures containing high-resolution information. This review, from a pharmaceutical perspective, highlights some of the most relevant and interesting protein structures for the pharmaceutical industry and shows examples of how ligand-binding sites, membrane proteins, both big and small, pseudo symmetry and complexes are being addressed by this technique. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180267DOI Listing
February 2019
3 Reads

Structure and mechanism of the ESCRT pathway AAA+ ATPase Vps4.

Biochem Soc Trans 2019 02 15;47(1):37-45. Epub 2019 Jan 15.

Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-5650, U.S.A.

The progression of ESCRT (Endosomal Sorting Complexes Required for Transport) pathways, which mediate numerous cellular membrane fission events, is driven by the enzyme Vps4. Understanding of Vps4 mechanism is, therefore, of fundamental importance in its own right and, moreover, it is highly relevant to the understanding of many related AAA+ ATPases that function in multiple facets of cell biology. Vps4 unfolds its ESCRT-III protein substrates by translocating them through its central hexameric pore, thereby driving membrane fission and recycling of ESCRT-III subunits. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393862PMC
February 2019
1 Read

The role of extracellular vesicles in cancer microenvironment and metastasis: myths and challenges.

Biochem Soc Trans 2019 02 15;47(1):273-280. Epub 2019 Jan 15.

Department of Urology, Mayo Clinic, Rochester, MN, U.S.A.

The concept of vesicles or cell debris released by cancer cells to promote metastasis is not new, but the mechanisms used to currently ascribe their impact in metastasis are of intense debate. A significant increase in reports describing the role of cancer-derived EVs in cancer metastasis has been followed by a growing amount of uncertainty behind these claims. This review will delve into the role of EVs in promoting cancer metastasis by relying on a balanced perspective that looks at challenges faced previously by extracellular vesicle biologists, current technical limitations in the field, and overlooked physiologic mechanisms that may play a confounding role. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180253DOI Listing
February 2019
1 Read

Multilayered control of chromosome replication in .

Biochem Soc Trans 2019 02 9;47(1):187-196. Epub 2019 Jan 9.

Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Quartier UNIL/Sorge, Lausanne CH 1015, Switzerland

The environmental is a classical model to study the regulation of the bacterial cell cycle. It divides asymmetrically, giving a stalked cell that immediately enters S phase and a swarmer cell that stays in the G1 phase until it differentiates into a stalked cell. Its genome consists in a single circular chromosome whose replication is tightly regulated so that it happens only in stalked cells and only once cell cycle. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393856PMC
February 2019
1 Read

Ghrelin octanoylation by ghrelin -acyltransferase: Unique protein biochemistry underlying metabolic signaling.

Authors:
James L Hougland

Biochem Soc Trans 2019 02 9;47(1):169-178. Epub 2019 Jan 9.

Department of Chemistry, Syracuse University, Syracuse, NY, U.S.A.

Ghrelin is a small peptide hormone that requires a unique post-translational modification, serine octanoylation, to bind and activate the GHS-R1a receptor. Ghrelin signaling is implicated in a variety of neurological and physiological processes, but is most well known for its roles in controlling hunger and metabolic regulation. Ghrelin octanoylation is catalyzed by ghrelin -acyltransferase (GOAT), a member of the membrane-bound -acyltransferase (MBOAT) enzyme family. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180436DOI Listing
February 2019
2 Reads

Hereditary diseases of coenzyme A thioester metabolism.

Biochem Soc Trans 2019 02 9;47(1):149-155. Epub 2019 Jan 9.

Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Montréal, QC, Canada

Coenzyme A (CoA) thioesters (acyl-CoAs) are essential intermediates of metabolism. Inborn errors of acyl-CoA metabolism include a large fraction of the classical organic acidemias. These conditions can involve liver, muscle, heart and brain, and can be fatal. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST20180423DOI Listing
February 2019
1 Read