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https://www.readbyqxmd.com/read/27898036/screening-of-a-haloferax-volcanii-transposon-library-reveals-novel-motility-and-adhesion-mutants
#1
Georgio Legerme, Evan Yang, Rianne N Esquivel, Saija Kiljunen, Harri Savilahti, Mechthild Pohlschroder
Archaea, like bacteria, use type IV pili to facilitate surface adhesion. Moreover, archaeal flagella-structures required for motility-share a common ancestry with type IV pili. While the characterization of archaeal homologs of bacterial type IV pilus biosynthesis components has revealed important aspects of flagellum and pilus biosynthesis and the mechanisms regulating motility and adhesion in archaea, many questions remain. Therefore, we screened a Haloferax volcanii transposon insertion library for motility mutants using motility plates and adhesion mutants, using an adapted air-liquid interface assay...
November 26, 2016: Life
https://www.readbyqxmd.com/read/27827919/taming-prebiotic-chemistry-the-role-of-heterogeneous-and-interfacial-catalysis-in-the-emergence-of-a-prebiotic-catalytic-information-polymer-system
#2
REVIEW
Pierre-Alain Monnard
Cellular life is based on interacting polymer networks that serve as catalysts, genetic information and structural molecules. The complexity of the DNA, RNA and protein biochemistry suggests that it must have been preceded by simpler systems. The RNA world hypothesis proposes RNA as the prime candidate for such a primal system. Even though this proposition has gained currency, its investigations have highlighted several challenges with respect to bulk aqueous media: (1) the synthesis of RNA monomers is difficult; (2) efficient pathways for monomer polymerization into functional RNAs and their subsequent, sequence-specific replication remain elusive; and (3) the evolution of the RNA function towards cellular metabolism in isolation is questionable in view of the chemical mixtures expected on the early Earth...
November 4, 2016: Life
https://www.readbyqxmd.com/read/27618105/functional-annotations-of-paralogs-a-blessing-and-a-curse
#3
Rémi Zallot, Katherine J Harrison, Bryan Kolaczkowski, Valérie de Crécy-Lagard
Gene duplication followed by mutation is a classic mechanism of neofunctionalization, producing gene families with functional diversity. In some cases, a single point mutation is sufficient to change the substrate specificity and/or the chemistry performed by an enzyme, making it difficult to accurately separate enzymes with identical functions from homologs with different functions. Because sequence similarity is often used as a basis for assigning functional annotations to genes, non-isofunctional gene families pose a great challenge for genome annotation pipelines...
September 8, 2016: Life
https://www.readbyqxmd.com/read/27608044/evidence-supporting-the-uptake-and-genomic-incorporation-of-environmental-dna-in-the-ancient-asexual-bdelloid-rotifer-philodina-roseola
#4
Olaf R P Bininda-Emonds, Claus Hinz, Wilko H Ahlrichs
Increasing evidence suggests that bdelloid rotifers regularly undergo horizontal gene transfer, apparently as a surrogate mechanism of genetic exchange in the absence of true sexual reproduction, in part because of their ability to withstand desiccation. We provide empirical support for this latter hypothesis using the bdelloid Philodina roseola, which we demonstrate to readily internalize environmental DNA in contrast to a representative monogonont rotifer (Brachionus rubens), which, like other monogononts, is facultative sexual and cannot withstand desiccation...
September 6, 2016: Life
https://www.readbyqxmd.com/read/27598206/bipyrimidine-signatures-as-a-photoprotective-genome-strategy-in-g-c-rich-halophilic-archaea
#5
Daniel L Jones, Bonnie K Baxter
Halophilic archaea experience high levels of ultraviolet (UV) light in their environments and demonstrate resistance to UV irradiation. DNA repair systems and carotenoids provide UV protection but do not account for the high resistance observed. Herein, we consider genomic signatures as an additional photoprotective strategy. The predominant forms of UV-induced DNA damage are cyclobutane pyrimidine dimers, most notoriously thymine dimers (T^Ts), which form at adjacent Ts. We tested whether the high G + C content seen in halophilic archaea serves a photoprotective function through limiting T nucleotides, and thus T^T lesions...
September 2, 2016: Life
https://www.readbyqxmd.com/read/27571106/the-genetic-code-francis-crick-s-legacy-and-beyond
#6
EDITORIAL
Koji Tamura
Francis Crick (Figure 1) was born on 8 June 1916, in Northampton, England, and passed away on 28 July 2004, in La Jolla, California, USA.[...].
August 25, 2016: Life
https://www.readbyqxmd.com/read/27556494/the-use-of-a-fractional-factorial-design-to-determine-the-factors-that-impact-1-3-propanediol-production-from-glycerol-by-halanaerobium-hydrogeniformans
#7
Shivani Kalia, Jordan Trager, Oliver C Sitton, Melanie R Mormile
In recent years, biodiesel, a substitute for fossil fuels, has led to the excessive production of crude glycerol. The resulting crude glycerol can possess a high concentration of salts and an alkaline pH. Moreover, current crude glycerol purification methods are expensive, rendering this former commodity a waste product. However, Halanaerobium hydrogeniformans, a haloalkaliphilic bacterium, possesses the metabolic capability to convert glycerol into 1,3-propanediol, a valuable commodity compound, without the need for salt dilution or adjusting pH when grown on this waste...
August 20, 2016: Life
https://www.readbyqxmd.com/read/27548228/pressure-as-a-limiting-factor-for-life
#8
Rachael Hazael, Filip Meersman, Fumihisa Ono, Paul F McMillan
Facts concerning the stability and functioning of key biomolecular components suggest that cellular life should no longer be viable above a few thousand atmospheres (200-300 MPa). However, organisms are seen to survive in the laboratory to much higher pressures, extending into the GPa or even tens of GPa ranges. This is causing main questions to be posed concerning the survival mechanisms of simple to complex organisms. Understanding the ultimate pressure survival of organisms is critical for food sterilization and agricultural products conservation technologies...
August 17, 2016: Life
https://www.readbyqxmd.com/read/27529283/a-self-assembled-aggregate-composed-of-a-fatty-acid-membrane-and-the-building-blocks-of-biological-polymers-provides-a-first-step-in-the-emergence-of-protocells
#9
REVIEW
Roy A Black, Matthew C Blosser
We propose that the first step in the origin of cellular life on Earth was the self-assembly of fatty acids with the building blocks of RNA and protein, resulting in a stable aggregate. This scheme provides explanations for the selection and concentration of the prebiotic components of cells; the stabilization and growth of early membranes; the catalysis of biopolymer synthesis; and the co-localization of membranes, RNA and protein. In this article, we review the evidence and rationale for the formation of the proposed aggregate: (i) the well-established phenomenon of self-assembly of fatty acids to form vesicles; (ii) our published evidence that nucleobases and sugars bind to and stabilize such vesicles; and (iii) the reasons why amino acids likely do so as well...
August 11, 2016: Life
https://www.readbyqxmd.com/read/27509525/ultra-large-gene-families-a-matter-of-adaptation-or-genomic-parasites
#10
Philipp H Schiffer, Jan Gravemeyer, Martina Rauscher, Thomas Wiehe
Gene duplication is an important mechanism of molecular evolution. It offers a fast track to modification, diversification, redundancy or rescue of gene function. However, duplication may also be neutral or (slightly) deleterious, and often ends in pseudo-geneisation. Here, we investigate the phylogenetic distribution of ultra large gene families on long and short evolutionary time scales. In particular, we focus on a family of NACHT-domain and leucine-rich-repeat-containing (NLR)-genes, which we previously found in large numbers to occupy one chromosome arm of the zebrafish genome...
August 8, 2016: Life
https://www.readbyqxmd.com/read/27527219/aglm-and-vng1048g-two-haloarchaeal-udp-glucose-dehydrogenases-show-different-salt-related-behaviors
#11
Lina Kandiba, Jerry Eichler
Haloferax volcanii AglM and Halobacterium salinarum VNG1048G are UDP-glucose dehydrogenases involved in N-glycosylation in each species. Despite sharing >60% sequence identity and the ability of VNG1048G to functionally replace AglM in vivo, these proteins behaved differently as salinity changed. Whereas AglM was active in 2-4 M NaCl, VNG1048G lost much of its activity when salinity dropped below 3 M NaCl. To understand the molecular basis of this phenomenon, each protein was examined by size exclusion chromatrography in 2 M NaCl...
August 3, 2016: Life
https://www.readbyqxmd.com/read/27527218/gene-family-extension-measures-and-correlations
#12
Gon Carmi, Alexander Bolshoy
The existence of multiple copies of genes is a well-known phenomenon. A gene family is a set of sufficiently similar genes, formed by gene duplication. In earlier works conducted on a limited number of completely sequenced and annotated genomes it was found that size of gene family and size of genome are positively correlated. Additionally, it was found that several atypical microbes deviated from the observed general trend. In this study, we reexamined these associations on a larger dataset consisting of 1484 prokaryotic genomes and using several ranking approaches...
August 3, 2016: Life
https://www.readbyqxmd.com/read/27490571/a-hypothesis-life-initiated-from-two-genes-as-deduced-from-the-rna-world-hypothesis-and-the-characteristics-of-life-like-systems
#13
Kunio Kawamura
RNA played a central role in the emergence of the first life-like system on primitive Earth since RNA molecules contain both genetic information and catalytic activity. However, there are several drawbacks regarding the RNA world hypothesis. Here, I briefly discuss the feasibility of the RNA world hypothesis to deduce the RNA functions that are essential for forming a life-like system. At the same time, I have conducted a conceptual analysis of the characteristics of biosystems as a useful approach to deduce a realistic life-like system in relation to the definition of life...
August 2, 2016: Life
https://www.readbyqxmd.com/read/27472365/dry-wet-cycling-and-the-thermodynamics-and-kinetics-of-prebiotic-polymer-synthesis
#14
David S Ross, David Deamer
The endoergic nature of protein and nucleic acid assembly in aqueous media presents two questions that are fundamental to the understanding of life's origins: (i) how did the polymers arise in an aqueous prebiotic world; and (ii) once formed in some manner, how were they sufficiently persistent to engage in further chemistry. We propose here a quantitative resolution of these issues that evolved from recent accounts in which RNA-like polymers were produced in evaporation/rehydration cycles. The equilibrium Nm + Nn ↔ Nm+n + H₂O is endoergic by about 3...
July 26, 2016: Life
https://www.readbyqxmd.com/read/27429005/conservation-of-the-exon-intron-structure-of-long-intergenic-non-coding-rna-genes-in-eutherian-mammals
#15
Diana Chernikova, David Managadze, Galina V Glazko, Wojciech Makalowski, Igor B Rogozin
The abundance of mammalian long intergenic non-coding RNA (lincRNA) genes is high, yet their functions remain largely unknown. One possible way to study this important question is to use large-scale comparisons of various characteristics of lincRNA with those of protein-coding genes for which a large body of functional information is available. A prominent feature of mammalian protein-coding genes is the high evolutionary conservation of the exon-intron structure. Comparative analysis of putative intron positions in lincRNA genes from various mammalian genomes suggests that some lincRNA introns have been conserved for over 100 million years, thus the primary and/or secondary structure of these molecules is likely to be functionally important...
2016: Life
https://www.readbyqxmd.com/read/27420098/constructive-approaches-for-understanding-the-origin-of-self-replication-and-evolution
#16
REVIEW
Norikazu Ichihashi, Tetsuya Yomo
The mystery of the origin of life can be divided into two parts. The first part is the origin of biomolecules: under what physicochemical conditions did biomolecules such as amino acids, nucleotides, and their polymers arise? The second part of the mystery is the origin of life-specific functions such as the replication of genetic information, the reproduction of cellular structures, metabolism, and evolution. These functions require the coordination of many different kinds of biological molecules. A direct strategy to approach the second part of the mystery is the constructive approach, in which life-specific functions are recreated in a test tube from specific biological molecules...
2016: Life
https://www.readbyqxmd.com/read/27376334/the-cosmic-zoo-the-near-inevitability-of-the-evolution-of-complex-macroscopic-life
#17
William Bains, Dirk Schulze-Makuch
Life on Earth provides a unique biological record from single-cell microbes to technologically intelligent life forms. Our evolution is marked by several major steps or innovations along a path of increasing complexity from microbes to space-faring humans. Here we identify various major key innovations, and use an analytical toolset consisting of a set of models to analyse how likely each key innovation is to occur. Our conclusion is that once the origin of life is accomplished, most of the key innovations can occur rather readily...
2016: Life
https://www.readbyqxmd.com/read/27338479/the-effect-of-limited-diffusion-and-wet-dry-cycling-on-reversible-polymerization-reactions-implications-for-prebiotic-synthesis-of-nucleic-acids
#18
Paul G Higgs
A long-standing problem for the origins of life is that polymerization of many biopolymers, including nucleic acids and peptides, is thermodynamically unfavourable in aqueous solution. If bond making and breaking is reversible, monomers and very short oligomers predominate. Recent experiments have shown that wetting and drying cycles can overcome this problem and drive the formation of longer polymers. In the dry phase, bond formation is favourable, but diffusion is restricted, and bonds only form between monomers that are initially close together...
2016: Life
https://www.readbyqxmd.com/read/27338478/probing-saltern-brines-with-an-oxygen-electrode-what-can-we-learn-about-the-community-metabolism-in-hypersaline-systems
#19
REVIEW
Aharon Oren
We have explored the use of optical oxygen electrodes to study oxygenic photosynthesis and heterotrophic activities in crystallizer brines of the salterns in Eilat, Israel. Monitoring oxygen uptake rates in the dark enables the identification of organic substrates that are preferentially used by the community. Addition of glycerol (the osmotic solute synthesized by Dunaliella) or dihydroxyacetone (produced from glycerol by Salinibacter) enhanced respiration rates. Pyruvate, produced from glycerol or from some sugars by certain halophilic Archaea also stimulated community respiration...
2016: Life
https://www.readbyqxmd.com/read/27240407/effects-of-low-temperature-plasma-sterilization-on-mars-analog-soil-samples-mixed-with-deinococcus-radiodurans
#20
Janosch Schirmack, Marcel Fiebrandt, Katharina Stapelmann, Dirk Schulze-Makuch
We used Ar plasma-sterilization at a temperature below 80 °C to examine its effects on the viability of microorganisms when intermixed with tested soil. Due to a relatively low temperature, this method is not thought to affect the properties of a soil, particularly its organic component, to a significant degree. The method has previously been shown to work well on spacecraft parts. The selected microorganism for this test was Deinococcus radiodurans R1, which is known for its remarkable resistance to radiation effects...
2016: Life
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