scholarly journals Structural characterization of NrnC identifies unifying features of dinucleotidases

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Justin D Lormand ◽  
Soo-Kyoung Kim ◽  
George A Walters-Marrah ◽  
Bryce A Brownfield ◽  
J Christopher Fromme ◽  
...  
Keyword(s):  
Cell Growth ◽  
Convergent Evolution ◽  
Specific Activity ◽  
Structural Features ◽  
Rna Degradation ◽  
Comparative Genomic ◽  
Quantitative Structure ◽  
Unique Role ◽  
Genomic Analyses

RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. Within the exoribonucleases, nano-RNases play a unique role as they act on the smallest breakdown products and hence catalyze the final steps in the process. We recently showed that oligoribonuclease (Orn) acts as a dedicated diribonucleotidase, defining the ultimate step in RNA degradation that is crucial for cellular fitness (Kim et al., 2019). Whether such a specific activity exists in organisms that lack Orn-type exoribonucleases remained unclear. Through quantitative structure-function analyses, we show here that NrnC-type RNases share this narrow substrate length preference with Orn. Although NrnC and Orn employ similar structural features that distinguish these two classes of dinucleotidases from other exonucleases, the key determinants for dinucleotidase activity are realized through distinct structural scaffolds. The structures, together with comparative genomic analyses of the phylogeny of DEDD-type exoribonucleases, indicate convergent evolution as the mechanism of how dinucleotidase activity emerged repeatedly in various organisms. The evolutionary pressure to maintain dinucleotidase activity further underlines the important role these analogous proteins play for cell growth.

scholarly journals Acquisition of the arginine deiminase system benefits epiparasitic Saccharibacteria and their host bacteria in a mammalian niche environment

2022 ◽  
Vol 119 (2) ◽  
pp. e2114909119
Author(s):  
Jing Tian ◽  
Daniel R. Utter ◽  
Lujia Cen ◽  
Pu-Ting Dong ◽  
Wenyuan Shi ◽  
...  
Keyword(s):  
Acid Stress ◽  
Arginine Deiminase ◽  
Oral Microbiome ◽  
Comparative Genomic ◽  
Host Bacterium ◽  
Mutualistic Interaction ◽  
Genomic Analyses ◽  
Selection For ◽  
Candidate Phyla Radiation

Saccharibacteria are a group of widespread and genetically diverse ultrasmall bacteria with highly reduced genomes that belong to the Candidate Phyla Radiation. Comparative genomic analyses suggest convergent evolution of key functions enabling the adaptation of environmental Saccharibacteria to mammalian microbiomes. Currently, our understanding of this environment-to-mammal niche transition within Saccharibacteria and their obligate episymbiotic association with host bacteria is limited. Here, we identified a complete arginine deiminase system (ADS), found in further genome streamlined mammal-associated Saccharibacteria but missing in their environmental counterparts, suggesting acquisition during environment-to-mammal niche transition. Using TM7x, the first cultured Saccharibacteria strain from the human oral microbiome and its host bacterium Actinomyces odontolyticus, we experimentally tested the function and impact of the ADS. We demonstrated that by catabolizing arginine and generating adenosine triphosphate, the ADS allows metabolically restrained TM7x to maintain higher viability and infectivity when disassociated from the host bacterium. Furthermore, the ADS protects TM7x and its host bacterium from acid stress, a condition frequently encountered within the human oral cavity due to bacterial metabolism of dietary carbohydrates. Intriguingly, with a restricted host range, TM7x forms obligate associations with Actinomyces spp. lacking the ADS but not those carrying the ADS, suggesting the acquired ADS may also contribute to partner selection for cooperative episymbiosis within a mammalian microbiome. These data present experimental characterization of a mutualistic interaction between TM7x and their host bacteria, and illustrate the benefits of acquiring a novel pathway in the transition of Saccharibacteria to mammalian microbiomes.

scholarly journals The origin of animals: an ancestral reconstruction of the unicellular-to-multicellular transition

Open Biology ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 200359
Author(s):  
Núria Ros-Rocher ◽  
Alberto Pérez-Posada ◽  
Michelle M. Leger ◽  
Iñaki Ruiz-Trillo
Keyword(s):  
Gene Regulation ◽  
Cell Communication ◽  
Regulatory Mechanisms ◽  
Comparative Genomic ◽  
Ancestral Reconstruction ◽  
Genomic Analyses ◽  
Gene Regulatory ◽  
Key Events ◽  
Early Developmental

How animals evolved from a single-celled ancestor, transitioning from a unicellular lifestyle to a coordinated multicellular entity, remains a fascinating question. Key events in this transition involved the emergence of processes related to cell adhesion, cell–cell communication and gene regulation. To understand how these capacities evolved, we need to reconstruct the features of both the last common multicellular ancestor of animals and the last unicellular ancestor of animals. In this review, we summarize recent advances in the characterization of these ancestors, inferred by comparative genomic analyses between the earliest branching animals and those radiating later, and between animals and their closest unicellular relatives. We also provide an updated hypothesis regarding the transition to animal multicellularity, which was likely gradual and involved the use of gene regulatory mechanisms in the emergence of early developmental and morphogenetic plans. Finally, we discuss some new avenues of research that will complement these studies in the coming years.

Towards artificial methanogenesis: biosynthesis of the [Fe]-hydrogenase cofactor and characterization of the semi-synthetic hydrogenase

2017 ◽  
Vol 198 ◽  
pp. 37-58 ◽  
Author(s):  
Liping Bai ◽  
Takashi Fujishiro ◽  
Gangfeng Huang ◽  
Jürgen Koch ◽  
Atsushi Takabayashi ◽  
...  
Keyword(s):  
Sufficient Conditions ◽  
Methanogenic Archaea ◽  
Crystal Structure Analysis ◽  
Guanosine Monophosphate ◽  
Comparative Genomic ◽  
Enzymatic Reactions ◽  
Methanococcus Maripaludis ◽  
System P ◽  
Genomic Analyses

The greenhouse gas and energy carrier methane is produced on Earth mainly by methanogenic archaea. In the hydrogenotrophic methanogenic pathway the reduction of one CO2 to one methane molecule requires four molecules of H2 containing eight electrons. Four of the electrons from two H2 are supplied for reduction of an electron carrier F420, which is catalyzed by F420-reducing [NiFe]-hydrogenase under nickel-sufficient conditions. The same reaction is catalysed under nickel-limiting conditions by [Fe]-hydrogenase coupled with a reaction catalyzed by F420-dependent methylene tetrahydromethanopterin dehydrogenase. [Fe]-hydrogenase contains an iron-guanylylpyridinol (FeGP) cofactor for H2 activation at the active site. FeII of FeGP is coordinated to a pyridinol-nitrogen, an acyl-carbon, two CO and a cysteine-thiolate. We report here on comparative genomic analyses of biosynthetic genes of the FeGP cofactor, which are primarily located in a hmd-co-occurring (hcg) gene cluster. One of the gene products is HcgB which transfers the guanosine monophosphate (GMP) moiety from guanosine triphosphate (GTP) to a pyridinol precursor. Crystal structure analysis of HcgB from Methanococcus maripaludis and its complex with 6-carboxymethyl-3,5-dimethyl-4-hydroxy-2-pyridinol confirmed the physiological guanylyltransferase reaction. Furthermore, we tested the properties of semi-synthetic [Fe]-hydrogenases using the [Fe]-hydrogenase apoenzyme from several methanogenic archaea and a mimic of the FeGP cofactor. On the basis of the enzymatic reactions involved in the methanogenic pathway, we came up with an idea how the methanogenic pathway could be simplified to develop an artificial methanogenesis system.

Skeletal elements of crinoid echinoderms: High-resolution structural and microanalytical results

1983 ◽  
Vol 41 ◽  
pp. 194-195
Author(s):  
D. F. Blake ◽  
L. F. Allard ◽  
D. R. Peacor
Keyword(s):  
High Resolution ◽  
Marine Invertebrates ◽  
Sea Urchins ◽  
Structural Features ◽  
Sea Stars ◽  
High Resolution Tem ◽  
Relationship Of ◽  
The Relationship ◽  
Insight Into

Echinodermata is a phylum of marine invertebrates which has been extant since Cambrian time (c.a. 500 m.y. before the present). Modern examples of echinoderms include sea urchins, sea stars, and sea lilies (crinoids). The endoskeletons of echinoderms are composed of plates or ossicles (Fig. 1) which are with few exceptions, porous, single crystals of high-magnesian calcite. Despite their single crystal nature, fracture surfaces do not exhibit the near-perfect {10.4} cleavage characteristic of inorganic calcite. This paradoxical mix of biogenic and inorganic features has prompted much recent work on echinoderm skeletal crystallography. Furthermore, fossil echinoderm hard parts comprise a volumetrically significant portion of some marine limestones sequences. The ultrastructural and microchemical characterization of modern skeletal material should lend insight into: 1). The nature of the biogenic processes involved, for example, the relationship of Mg heterogeneity to morphological and structural features in modern echinoderm material, and 2). The nature of the diagenetic changes undergone by their ancient, fossilized counterparts. In this study, high resolution TEM (HRTEM), high voltage TEM (HVTEM), and STEM microanalysis are used to characterize tha ultrastructural and microchemical composition of skeletal elements of the modern crinoid Neocrinus blakei.

Ultrastructural identification of three types of sensory setae on copepod antennae

1995 ◽  
Vol 53 ◽  
pp. 956-957
Author(s):  
T. M. Weatherby ◽  
P.H. Lenz
Keyword(s):  
Phase Locking ◽  
Membrane Surface ◽  
Reaction Times ◽  
High Sensitivity ◽  
Structural Features ◽  
Calanoid Copepods ◽  
Marine Food Webs ◽  
Dendritic Membrane ◽  
Ultrastructural Characterization

Crustaceans, as well as other arthropods, are covered with sensory setae and hairs, including mechanoand chemosensory sensillae with a ciliary origin. Calanoid copepods are small planktonic crustaceans forming a major link in marine food webs. In conjunction with behavioral and physiological studies of the antennae of calanoids, we undertook the ultrastructural characterization of sensory setae on the antennae of Pleuromamma xiphias.Distal mechanoreceptive setae exhibit exceptional behavioral and physiological performance characteristics: high sensitivity (<10 nm displacements), fast reaction times (<1 msec latency) and phase locking to high frequencies (1-2 kHz). Unusual structural features of the mechanoreceptors are likely to be related to their physiological sensitivity. These features include a large number (up to 3000) of microtubules in each sensory cell dendrite, arising from or anchored to electron dense rods associated with the ciliary basal body microtubule doublets. The microtubules are arranged in a regular array, with bridges between and within rows. These bundles of microtubules extend far into each mechanoreceptive seta and terminate in a staggered fashion along the dendritic membrane, contacting a large membrane surface area and providing a large potential site of mechanotransduction.

Quantitative nano-characterization of heterogeneous catalysts

1995 ◽  
Vol 53 ◽  
pp. 398-399
Author(s):  
P.A. Crozier ◽  
M. Pan
Keyword(s):  
Heterogeneous Catalysts ◽  
Low Dose ◽  
Imaging Techniques ◽  
Structural Features ◽  
Catalyst Characterization ◽  
New Developments ◽  
Double Phase ◽  
Phase Systems ◽  
Dose Imaging

Heterogeneous catalysts can be of varying complexity ranging from single or double phase systems to complicated mixtures of metals and oxides with additives to help promote chemical reactions, extend the life of the catalysts, prevent poisoning etc. Although catalysis occurs on the surface of most systems, detailed descriptions of the microstructure and chemistry of catalysts can be helpful for developing an understanding of the mechanism by which a catalyst facilitates a reaction. Recent years have seen continued development and improvement of various TEM, STEM and AEM techniques for yielding information on the structure and chemistry of catalysts on the nanometer scale. Here we review some quantitative approaches to catalyst characterization that have resulted from new developments in instrumentation.HREM has been used to examine structural features of catalysts often by employing profile imaging techniques to study atomic details on the surface. Digital recording techniques employing slow-scan CCD cameras have facilitated the use of low-dose imaging in zeolite structure analysis and electron crystallography. Fig. la shows a low-dose image from SSZ-33 zeolite revealing the presence of a stacking fault.

Assays for Phospholipid-Dependent Formation of Thrombin and Xa: A Potential Method for Quantifying Lupus Anticoagulant Activity

1991 ◽  
Vol 66 (04) ◽  
pp. 453-458 ◽  
Author(s):  
John T Brandt
Keyword(s):  
Specific Activity ◽  
Anticoagulant Activity ◽  
Factor Xa ◽  
Clinical Importance ◽  
Potential Method ◽  
Quantitative Expression ◽  
Increased Risk ◽  
Apparent Association

SummaryLupus anticoagulants (LAs) are antibodies which interfere with phospholipid-dependent procoagulant reactions. Their clinical importance is due to their apparent association with an increased risk of thrombo-embolic disease. To date there have been few assays for quantifying the specific activity of these antibodies in vitro and this has hampered attempts to purify and characterize these antibodies. Methods for determining phospholipid-dependent generation of thrombin and factor Xa are described. Isolated IgG fractions from 7 of 9 patients with LAs were found to reproducibly inhibit enzyme generation in these assay systems, permitting quantitative expression of inhibitor activity. Different patterns of inhibitory activity, based on the relative inhibition of thrombin and factor Xa generation, were found, further substantiating the known heterogeneity of these antibodies. These systems may prove helpful in further purification and characterization of LAs.

Influence of Seeding Conditions on Initial Biofilm Development during the Startup of Anaerobic Fluidized Bed Reactors

1989 ◽  
Vol 21 (4-5) ◽  
pp. 157-165 ◽  
Author(s):  
F. Ehlinger ◽  
J. M. Audic ◽  
G. M. Faup
Keyword(s):  
Fluidized Bed ◽  
Future Development ◽  
Protein Concentration ◽  
Specific Activity ◽  
Fluidized Bed Reactor ◽  
Fluidized Bed Reactors ◽  
Support Material ◽  
Biofilm Development ◽  
Initial Biofilm

The characterization of the biofilm of an anaerobic fluidized-bed reactor was completed under standard conditions. The distribution of the fixed protein concentration depended on the level in the reactor. The protein concentration reached 1520 µg.g−1 of support at the top of the reactor and only 1200 µg.g−1 at the bottom after 504 hours of operation but the specific activity of the biofilm was 33×10−4 µM acetate.h−1.mg−1 proteins at the bottom and only 26×10−4 µM.h−1.mg−1 at the top. The efficiency of a fluidized bed reactor and the composition of the biofilm changed with an increase of the pH from 7 to 8.5 during the seeding of the support material. Future development of the biofilm and the specific activity of the support were affected.

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