oalib
Search Results: 1 - 10 of 100 matches for " "
All listed articles are free for downloading (OA Articles)
Page 1 /100
Display every page Item
Viruses and Lipids  [PDF]
Akira Ono
Viruses , 2010, DOI: 10.3390/v2051236
Abstract: As obligatory intracellular pathogens, viruses exploit various cellular molecules and structures, such as cellular membranes, for their propagation. Enveloped viruses acquire lipid membranes as their outer coat through interactions with cellular membranes during morphogenesis within, and egress from, infected cells. In contrast, non-enveloped viruses typically exit cells by cell lysis, and lipid membranes are not part of the released virions. However, non-enveloped viruses also interact with lipid membranes at least during entry into target cells. Therefore, lipids, as part of cellular membranes, inevitably play some roles in life cycle of viruses. [...]
Archaeal Viruses, Not Archaeal Phages: An Archaeological Dig  [PDF]
Stephen T. Abedon,Kelly L. Murray
Archaea , 2013, DOI: 10.1155/2013/251245
Abstract: Viruses infect members of domains Bacteria, Eukarya, and Archaea. While those infecting domain Eukarya are nearly universally described as “Viruses”, those of domain Bacteria, to a substantial extent, instead are called “Bacteriophages,” or “Phages.” Should the viruses of domain Archaea therefore be dubbed “Archaeal phages,” “Archaeal viruses,” or some other construct? Here we provide documentation of published, general descriptors of the viruses of domain Archaea. Though at first the term “Phage” or equivalent was used almost exclusively in the archaeal virus literature, there has been a nearly 30-year trend away from this usage, with some persistence of “Phage” to describe “Head-and-tail” archaeal viruses, “Halophage” to describe viruses of halophilic Archaea, use of “Prophage” rather than “Provirus,” and so forth. We speculate on the root of the early 1980’s transition from “Phage” to “Virus” to describe these infectious agents, consider the timing of introduction of “Archaeal virus” (which can be viewed as analogous to “Bacterial virus”), identify numerous proposed alternatives to “Archaeal virus,” and also provide discussion of the general merits of the term, “Phage.” Altogether we identify in excess of one dozen variations on how the viruses of domain Archaea are described, and document the timing of both their introduction and use. 1. Introduction …most viruses infecting archaea have nothing in common with those infecting bacteria, although they are still considered as “bacteriophages” by many virologists, just because archaea and bacteria are both prokaryotes (without nucleus). [1] For historical reasons, bacteriophage is widely used to refer to viruses of bacteria (and sometimes even archaea). The problem with such nomenclature is that it artificially divides the virosphere into two camps, with viruses of bacteria and archaea on one hand and viruses of eukaryotes on the other. [2] Viruses are infectious agents that alternate between autonomous, encapsidated states known as virions, which are “packages of genes” [3], and unencapsidated, intracellular states known as infections [1], infected cells [3] or, more holistically, as “Virocells” or “Ribovirocells” [4, 5]. Numerous differences exist among viruses in terms of virion morphology, genome architecture, and infection strategy [6], and viruses also may be differentiated as a function of host range [7]. While it is possible to describe a virus’s host range in terms of what species or even subspecies or strains of cellular hosts it is capable of infecting, it is also possible to distinguish
Archaeal viruses—novel, diverse and enigmatic
Xu Peng,Roger A. Garrett,QunXin She
Science China Life Sciences , 2012, DOI: 10.1007/s11427-012-4325-8
Abstract: Recent research has revealed a remarkable diversity of viruses in archaeal-rich environments where spindles, spheres, filaments and rods are common, together with other exceptional morphotypes never recorded previously. Moreover, their double-stranded DNA genomes carry very few genes exhibiting homology to those of bacterial and eukaryal viruses. Studies on viral life cycles are still at a preliminary stage but important insights are being gained especially from microarray analyses of viral transcripts for a few model virus-host systems. Recently, evidence has been presented for some exceptional archaeal-specific mechanisms for extra-cellular morphological development of virions and for their cellular extrusion. Here we summarise some of the recent developments in this rapidly developing and exciting research area.
A Survey of Protein Structures from Archaeal Viruses  [PDF]
Nikki Dellas,C. Martin Lawrence,Mark J. Young
Life , 2013, DOI: 10.3390/life3010118
Abstract: Viruses that infect the third domain of life, Archaea, are a newly emerging field of interest. To date, all characterized archaeal viruses infect archaea that thrive in extreme conditions, such as halophilic, hyperthermophilic, and methanogenic environments. Viruses in general, especially those replicating in extreme environments, contain highly mosaic genomes with open reading frames (ORFs) whose sequences are often dissimilar to all other known ORFs. It has been estimated that approximately 85% of virally encoded ORFs do not match known sequences in the nucleic acid databases, and this percentage is even higher for archaeal viruses (typically 90%–100%). This statistic suggests that either virus genomes represent a larger segment of sequence space and/or that viruses encode genes of novel fold and/or function. Because the overall three-dimensional fold of a protein evolves more slowly than its sequence, efforts have been geared toward structural characterization of proteins encoded by archaeal viruses in order to gain insight into their potential functions. In this short review, we provide multiple examples where structural characterization of archaeal viral proteins has indeed provided significant functional and evolutionary insight.
Impacts of temperature and pH on the distribution of archaeal lipids in Yunnan hot springs, China  [PDF]
Weiyan Wu,Chuanlun L. Zhang,Huanye Wang,Liu He,Wenjun Li,Hailiang Dong
Frontiers in Microbiology , 2013, DOI: 10.3389/fmicb.2013.00312
Abstract: In culture experiments and many low temperature environments, the distribution of isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs) commonly shows a strong correlation with temperature; however, this is often not the case in hot springs. We studied 26 hot springs in Yunnan, China, in order to determine whether temperature or other factors control the distribution of GDGTs in these environments. The hot springs ranged in temperature from 39.0 to 94.0°C, and in pH from 2.35 to 9.11. Water chemistry including nitrogen-, sulfur-, and iron species was also determined. Lipids from the samples were analyzed using liquid chromatography–mass spectrometry (LC–MS). Distributions of GDGTs in these hot springs were examined using cluster analysis, which resulted in two major groups. Group 1 was characterized by the lack of dominance of any individual GDGTs, while Group 2 was defined by the dominance of GDGT-0 or thaumarchaeol. Temperature was the main control on GDGT distribution in Group 1, whereas pH played an important role in the distribution of GDGTs in Group 2. However, no correlations were found between the distribution of GDGTs and any of the nitrogen-, sulfur-, or iron species. Results of this study indicate the dominance of temperature or pH control on archaeal lipid distribution, which can be better evaluated in the context of lipid classification.
Novel archaeal macrocyclic diether core membrane lipids in a methane-derived carbonate crust from a mud volcano in the Sorokin Trough, NE Black Sea  [PDF]
Alina Stadnitskaia,Marianne Baas,Michael K. Ivanov,Tjeerd C. E. Van Weering,Jaap S. Sinninghe Damsté
Archaea , 2003, DOI: 10.1155/2003/329175
Abstract: A methane-derived carbonate crust was collected from the recently discovered NIOZ mud volcano in the Sorokin Trough, NE Black Sea during the 11th Training-through-Research cruise of the R/V Professor Logachev. Among several specific bacterial and archaeal membrane lipids present in this crust, two novel macrocyclic diphytanyl glycerol diethers, containing one or two cyclopentane rings, were detected. Their structures were tentatively identified based on the interpretation of mass spectra, comparison with previously reported mass spectral data, and a hydrogenation experiment. This macrocyclic type of archaeal core membrane diether lipid has so far been identified only in the deep-sea hydrothermal vent methanogen Methanococcus jannaschii. Here, we provide the first evidence that these macrocyclic diethers can also contain internal cyclopentane rings. The molecular structure of the novel diethers resembles that of dibiphytanyl tetraethers in which biphytane chains, containing one and two pentacyclic rings, also occur. Such tetraethers were abundant in the crust. Compound-specific isotope measurements revealed δ13C values of –104 to –111‰ for these new archaeal lipids, indicating that they are derived from methanotrophic archaea acting within anaerobic methane-oxidizing consortia, which subsequently induce authigenic carbonate formation.
The distribution and abundance of archaeal tetraether lipids in U.S. Great Basin hot springs  [PDF]
Julienne J. Paraiso,Amanda J. Williams,Qiuyuan Huang,Yuli Wei,Paul Dijkstra,Bruce A. Hungate,Hailiang Dong,Brian P. Hedlund,Chuanlun L. Zhang
Frontiers in Microbiology , 2013, DOI: 10.3389/fmicb.2013.00247
Abstract: Isoprenoidal glycerol dialkyl glycerol tetraethers (iGDGTs) are core membrane lipids of many archaea that enhance the integrity of cytoplasmic membranes in extreme environments. We examined the iGDGT profiles and corresponding aqueous geochemistry in 40 hot spring sediment and microbial mat samples from the U.S. Great Basin with temperatures ranging from 31 to 95°C and pH ranging from 6.8 to 10.7. The absolute abundance of iGDGTs correlated negatively with pH and positively with temperature. High lipid concentrations, distinct lipid profiles, and a strong relationship between polar and core lipids in hot spring samples suggested in situ production of most iGDGTs rather than contamination from local soils. Two-way cluster analysis and non-metric multidimensional scaling (NMS) of polar iGDGTs indicated that the relative abundance of individual lipids was most strongly related to temperature (r2 = 0.546), with moderate correlations with pH (r2 = 0.359), nitrite (r2 = 0.286), oxygen (r2 = 0.259), and nitrate (r2 = 0.215). Relative abundance profiles of individual polar iGDGTs indicated potential temperature optima for iGDGT-0 (≤70°C), iGDGT-3 (≥55°C), and iGDGT-4 (≥60°C). These relationships likely reflect both physiological adaptations and community-level population shifts in response to temperature differences, such as a shift from cooler samples with more abundant methanogens to higher-temperature samples with more abundant Crenarchaeota. Crenarchaeol was widely distributed across the temperature gradient, which is consistent with other reports of abundant crenarchaeol in Great Basin hot springs and suggests a wide distribution for thermophilic ammonia-oxidizing archaea (AOA).
Shaping the Archaeal Cell Envelope  [PDF]
Albert F. Ellen,Behnam Zolghadr,Arnold M. J. Driessen,Sonja-Verena Albers
Archaea , 2010, DOI: 10.1155/2010/608243
Abstract: Although archaea have a similar cellular organization as other prokaryotes, the lipid composition of their membranes and their cell surface is unique. Here we discuss recent developments in our understanding of the archaeal protein secretion mechanisms, the assembly of macromolecular cell surface structures, and the release of S-layer-coated vesicles from the archaeal membrane. 1. The Archaeal Cell Envelope The ability of many archaea to endure extreme conditions in hostile environments intrigues researchers to study the molecular mechanisms and specific adaptations involved. Very early, it was realized that the structure of the archaeal cell envelope differs substantially from that of bacteria [1]. With the only exception of Ignicoccus which exhibits an outer membrane enclosing a huge periplasmic space [2], known archaea possess only a single membrane. This cytoplasmic membrane is enclosed by an S-layer, a two-dimensional protein crystal that fully covers the cells (see review Jarrell et al. in this issue). In contrast to bacterial ester lipids, archaeal lipids consist of repeating isoprenyl groups linked to a glycerol backbone through an ether linkage [3, 4]. These lipids typically form diether bilayer membranes similar to membranes of eukarya and bacteria. Hyperthermo-acidophiles contain tetraether lipids that consist of C40 isoprenoid acyl chains that span the membrane entirely forming a monolayer membrane [5]. These membranes are extremely proton impermeable and enable these organisms to survive under conditions that the extracellular pH is up to 4 units below that of the cytoplasm [6]. Another peculiarity is that most of the extracellular proteins of archaea are glycosylated via N- and O-glycosylation. Finally, Archaea do not produce any murein, and only some methanogenic species are known to produce pseudomurein [7]. As the archaeal cell surface is so different from that of bacteria and eukarya, unique mechanisms must exist to form and shape it. Until recently most of our knowledge of protein secretion and on the assembly of the cell surface components in archaea was obtained by comparative genomic studies. However, in recent years tremendous progress has been made in our understanding of the assembly and function of cell surface structures and both the structural and functional basis of protein translocation across the archaeal membrane. Here we will discuss these topics with an emphasis on the cell surface structures. 2. Protein Secretion 2.1. Transport of Unfolded Proteins Across the Cytoplasmic Membrane The ability to transport proteins
Archaeal Phospholipid Biosynthetic Pathway Reconstructed in Escherichia coli  [PDF]
Takeru Yokoi,Keisuke Isobe,Tohru Yoshimura,Hisashi Hemmi
Archaea , 2012, DOI: 10.1155/2012/438931
Abstract: A part of the biosynthetic pathway of archaeal membrane lipids, comprised of 4 archaeal enzymes, was reconstructed in the cells of Escherichia coli. The genes of the enzymes were cloned from a mesophilic methanogen, Methanosarcina acetivorans, and the activity of each enzyme was confirmed using recombinant proteins. In vitro radioassay showed that the 4 enzymes are sufficient to synthesize an intermediate of archaeal membrane lipid biosynthesis, that is, 2,3-di-O-geranylgeranyl-sn-glycerol-1-phosphate, from precursors that can be produced endogenously in E. coli. Introduction of the 4 genes into E. coli resulted in the production of archaeal-type lipids. Detailed liquid chromatography/electron spray ionization-mass spectrometry analyses showed that they are metabolites from the expected intermediate, that is, 2,3-di-O-geranylgeranyl-sn-glycerol and 2,3-di-O-geranylgeranyl-sn-glycerol-1-phosphoglycerol. The metabolic processes, that is, dephosphorylation and glycerol modification, are likely catalyzed by endogenous enzymes of E. coli. 1. Introduction Archaeal membrane lipids are very specific to the organisms in the domain Archaea and have structures that are distinct from those of bacterial/eukaryotic lipids [1–3]. Although they are, essentially, analogues of glycerolipids from bacteria or eukaryotes, they have specific structural features as follows: (1) hydrocarbon chains of archaeal lipids are multiply-branched isoprenoids typically derived from (all-E) geranylgeranyl diphosphate (GGPP), while linear acyl groups are general in bacterial/eukaryotic lipids; (2) the isoprenoid chains are linked with the glycerol moiety with ether bonds, while ester bonds are general in bacterial/eukaryotic lipids; (3) the glycerol moiety of archaeal lipids is derived from sn-glycerol-1-phosphate (G-1-P), which is the enantiomer of sn-glycerol-3-phosphate, the precursor for bacterial/eukaryotic glycerolipids; (4) dimerization of membrane lipids by the formation of carbon-carbon bonds between the ω-terminals of hydrocarbon chains, which generates macrocyclic structures such as caldarchaeol-type lipids with a typically 72-membered ring, is often observed in thermophilic and methanogenic archaea. These characteristics affect the properties of membranes formed with the lipids. In general, the permeability of membranes composed of archaeal lipids is lower than that of membranes that consist of bacterial/eukaryotic lipids [4, 5]. Moreover, the structural differences between archaeal and bacterial/eukaryotic lipids are believed to cause their black-and-white distribution
Archaeal Phospholipid Biosynthetic Pathway Reconstructed in Escherichia coli  [PDF]
Takeru Yokoi,Keisuke Isobe,Tohru Yoshimura,Hisashi Hemmi
Archaea , 2012, DOI: 10.1155/2012/438931
Abstract: A part of the biosynthetic pathway of archaeal membrane lipids, comprised of 4 archaeal enzymes, was reconstructed in the cells of Escherichia coli. The genes of the enzymes were cloned from a mesophilic methanogen, Methanosarcina acetivorans, and the activity of each enzyme was confirmed using recombinant proteins. In vitro radioassay showed that the 4 enzymes are sufficient to synthesize an intermediate of archaeal membrane lipid biosynthesis, that is, 2,3-di-O-geranylgeranyl-sn-glycerol-1-phosphate, from precursors that can be produced endogenously in E. coli. Introduction of the 4 genes into E. coli resulted in the production of archaeal-type lipids. Detailed liquid chromatography/electron spray ionization-mass spectrometry analyses showed that they are metabolites from the expected intermediate, that is, 2,3-di-O-geranylgeranyl-sn-glycerol and 2,3-di-O-geranylgeranyl-sn-glycerol-1-phosphoglycerol. The metabolic processes, that is, dephosphorylation and glycerol modification, are likely catalyzed by endogenous enzymes of E. coli.
Page 1 /100
Display every page Item


Home
Copyright © 2008-2017 Open Access Library. All rights reserved.