NAD+ capping of RNA in Archaea and Mycobacteria

2021 ◽  
Author(s):  
Olatz Ruiz-Larrabeiti ◽  
Roberto Benoni ◽  
Viacheslav Zemlianski ◽  
Nikola Hanisakova ◽  
Marek Schwarz ◽  
...  
Keyword(s):  
Nicotinamide Adenine Dinucleotide ◽  
Mycobacterium Smegmatis ◽  
Small Rnas ◽  
Methanosarcina Barkeri ◽  
Model Organisms ◽  
Rna Modification ◽  
Essential Properties ◽  
Domains Of Life ◽  
Living Organisms ◽  
Rna Capping

Chemical modifications of RNA affect essential properties of transcripts, such as their translation, localization and stability. 5-end RNA capping with the ubiquitous redox cofactor nicotinamide adenine dinucleotide (NAD+) has been discovered in organisms ranging from bacteria to mammals. However, the hypothesis that NAD+ capping might be universal in all domains of life has not been proven yet, as information on this RNA modification is missing for Archaea. Likewise, this RNA modification has not been studied in the clinically important Mycobacterium genus. Here, we demonstrate that NAD+ capping occurs in the archaeal and mycobacterial model organisms Methanosarcina barkeri and Mycobacterium smegmatis. Moreover, we identify the NAD+-capped transcripts in M. smegmatis, showing that this modification is more prevalent in stationary phase, and revealing that mycobacterial NAD+-capped transcripts include non-coding small RNAs, such as Ms1. Furthermore, we show that mycobacterial RNA polymerase incorporates NAD+ into RNA, and that the genes of NAD+-capped transcripts are preceded by promoter elements compatible with SigA/SigF dependent expression. Taken together, our findings demonstrate that NAD+ capping exists in the archaeal domain of life, suggesting that it is universal to all living organisms, and define the NAD+-capped RNA landscape in mycobacteria, providing a basis for its future exploration.

scholarly journals Regulatory non-coding small RNAs are diverse and abundant in an extremophilic microbial community

2019 ◽  
Author(s):  
Diego R. Gelsinger ◽  
Gherman Uritskiy ◽  
Rahul Reddy ◽  
Adam Munn ◽  
Katie Farney ◽  
...  
Keyword(s):  
Small Rnas ◽  
Large Scale ◽  
Field Experiments ◽  
Target Prediction ◽  
Model Organisms ◽  
Natural Environments ◽  
Cellular Processes ◽  
Non Coding Rna ◽  
Domains Of Life ◽  
Gene Regulatory

ABSTRACTRegulatory small RNAs (sRNAs) represent a major class of regulatory molecules that play large-scale and essential roles in many cellular processes across all domains of life. Microbial sRNAs have been primarily investigated in a few model organisms and little is known about the dynamics of sRNA synthesis in natural environments, and the roles of these short transcripts at the community level. Analyzing the metatranscriptome of a model extremophilic community inhabiting halite nodules (salt rocks) from the Atacama Desert with SnapT – a new sRNA annotation pipeline – we discovered hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs. The halite sRNAs were taxonomically diverse with the majority expressed by members of the Halobacteria. We found asRNAs with expression levels negatively correlated with that of their putative overlapping target, suggesting a potential gene regulatory mechanism. A number of itsRNAs were conserved and significantly differentially expressed (FDR<5%) between 2 sampling time points allowing for stable secondary structure modeling and target prediction. This work demonstrates that metatranscriptomic field experiments link environmental variation with changes in RNA pools and have the potential to provide new insights into environmental sensing and responses in natural microbial communities through non-coding RNA mediated gene regulation.

scholarly journals Captivating Perplexities of Spinareovirinae 5′ RNA Caps

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 294
Author(s):  
Justine Kniert ◽  
Qi Feng Lin ◽  
Maya Shmulevitz
Keyword(s):  
Immune Recognition ◽  
Domains Of Life ◽  
The Many ◽  
Rna Capping ◽  
Multiple Domains ◽  
Rna Caps

RNAs with methylated cap structures are present throughout multiple domains of life. Given that cap structures play a myriad of important roles beyond translation, such as stability and immune recognition, it is not surprising that viruses have adopted RNA capping processes for their own benefit throughout co-evolution with their hosts. In fact, that RNAs are capped was first discovered in a member of the Spinareovirinae family, Cypovirus, before these findings were translated to other domains of life. This review revisits long-past knowledge and recent studies on RNA capping among members of Spinareovirinae to help elucidate the perplex processes of RNA capping and functions of RNA cap structures during Spinareovirinae infection. The review brings to light the many uncertainties that remain about the precise capping status, enzymes that facilitate specific steps of capping, and the functions of RNA caps during Spinareovirinae replication.

scholarly journals On the Diversification of the Translation Apparatus across Eukaryotes

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Greco Hernández ◽  
Christopher G. Proud ◽  
Thomas Preiss ◽  
Armen Parsyan
Keyword(s):  
Model Organisms ◽  
Ecological Niches ◽  
Translational Machinery ◽  
Functional Differences ◽  
Profound Knowledge ◽  
Genome Wide ◽  
Translation Apparatus ◽  
Fundamental Process ◽  
Organismal Complexity ◽  
Living Organisms

Diversity is one of the most remarkable features of living organisms. Current assessments of eukaryote biodiversity reaches 1.5 million species, but the true figure could be several times that number. Diversity is ingrained in all stages and echelons of life, namely, the occupancy of ecological niches, behavioral patterns, body plans and organismal complexity, as well as metabolic needs and genetics. In this review, we will discuss that diversity also exists in a key biochemical process, translation, across eukaryotes. Translation is a fundamental process for all forms of life, and the basic components and mechanisms of translation in eukaryotes have been largely established upon the study of traditional, so-called model organisms. By using modern genome-wide, high-throughput technologies, recent studies of many nonmodel eukaryotes have unveiled a surprising diversity in the configuration of the translation apparatus across eukaryotes, showing that this apparatus is far from being evolutionarily static. For some of the components of this machinery, functional differences between different species have also been found. The recent research reviewed in this article highlights the molecular and functional diversification the translational machinery has undergone during eukaryotic evolution. A better understanding of all aspects of organismal diversity is key to a more profound knowledge of life.

scholarly journals Archaeal cell biology: diverse functions of tubulin-like cytoskeletal proteins at the cell envelope

2018 ◽  
Vol 2 (4) ◽  
pp. 547-559 ◽  
Author(s):  
Yan Liao ◽  
Solenne Ithurbide ◽  
Roshali T. de Silva ◽  
Susanne Erdmann ◽  
Iain G. Duggin
Keyword(s):  
Cell Biology ◽  
Shape Control ◽  
Cell Envelope ◽  
Light And Electron Microscopy ◽  
Halophilic Archaea ◽  
Cytoskeletal Proteins ◽  
Model Organisms ◽  
Full Spectrum ◽  
Peptidoglycan Cell Wall ◽  
Domains Of Life

The tubulin superfamily of cytoskeletal proteins is widespread in all three domains of life — Archaea, Bacteria and Eukarya. Tubulins build the microtubules of the eukaryotic cytoskeleton, whereas members of the homologous FtsZ family construct the division ring in prokaryotes and some eukaryotic organelles. Their functions are relatively poorly understood in archaea, yet these microbes contain a remarkable diversity of tubulin superfamily proteins, including FtsZ for division, a newly described major family called CetZ that is involved in archaeal cell shape control, and several other divergent families of unclear function that are implicated in a variety of cell envelope-remodelling contexts. Archaeal model organisms, particularly halophilic archaea such as Haloferax volcanii, have sufficiently developed genetic tools and we show why their large, flattened cells that are capable of controlled differentiation are also well suited to cell biological investigations by live-cell high-resolution light and electron microscopy. As most archaea only have a glycoprotein lattice S-layer, rather than a peptidoglycan cell wall like bacteria, the activity of the tubulin-like cytoskeletal proteins at the cell envelope is expected to vary significantly, and may involve direct membrane remodelling or directed synthesis or insertion of the S-layer protein subunits. Further studies of archaeal cell biology will provide fresh insight into the evolution of cells and the principles in common to their fundamental activities across the full spectrum of cellular life.

scholarly journals The thermal limits to life on Earth

2014 ◽  
Vol 13 (2) ◽  
pp. 141-154 ◽  
Author(s):  
Andrew Clarke
Keyword(s):  
Life Cycle ◽  
Higher Plants ◽  
Temperature Limit ◽  
Current Data ◽  
High Temperature Limit ◽  
Thermal Limits ◽  
Resource Limited ◽  
Almost Everywhere ◽  
Domains Of Life ◽  
Living Organisms

AbstractLiving organisms on Earth are characterized by three necessary features: a set of internal instructions encoded in DNA (software), a suite of proteins and associated macromolecules providing a boundary and internal structure (hardware), and a flux of energy. In addition, they replicate themselves through reproduction, a process that renders evolutionary change inevitable in a resource-limited world. Temperature has a profound effect on all of these features, and yet life is sufficiently adaptable to be found almost everywhere water is liquid. The thermal limits to survival are well documented for many types of organisms, but the thermal limits to completion of the life cycle are much more difficult to establish, especially for organisms that inhabit thermally variable environments. Current data suggest that the thermal limits to completion of the life cycle differ between the three major domains of life, bacteria, archaea and eukaryotes. At the very highest temperatures only archaea are found with the current high-temperature limit for growth being 122 °C. Bacteria can grow up to 100 °C, but no eukaryote appears to be able to complete its life cycle above ∼60 °C and most not above 40 °C. The lower thermal limit for growth in bacteria, archaea, unicellular eukaryotes where ice is present appears to be set by vitrification of the cell interior, and lies at ∼−20 °C. Lichens appear to be able to grow down to ∼−10 °C. Higher plants and invertebrates living at high latitudes can survive down to ∼−70 °C, but the lower limit for completion of the life cycle in multicellular organisms appears to be ∼−2 °C.

scholarly journals Human RNA cap1 methyltransferase CMTr1 cooperates with RNA helicase DHX15 to modify RNAs with highly structured 5′ termini

2018 ◽  
Vol 373 (1762) ◽  
pp. 20180161 ◽  
Author(s):  
Diana Toczydlowska-Socha ◽  
Magdalena M. Zielinska ◽  
Malgorzata Kurkowska ◽  
Astha ◽  
Catarina F. Almeida ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rna Degradation ◽  
Rna Modification ◽  
Structure Characteristic ◽  
Helicase Activity ◽  
Theme Issue ◽  
Rna Capping ◽  
Advantageous Effect

The 5′-cap structure, characteristic for RNA polymerase II-transcribed RNAs, plays important roles in RNA metabolism. In humans, RNA cap formation includes post-transcriptional modification of the first transcribed nucleotide by RNA cap1 methyltransferase (CMTr1). Here, we report that CMTr1 activity is hindered towards RNA substrates with highly structured 5′ termini. We found that CMTr1 binds ATP-dependent RNA DHX15 helicase and that this interaction, mediated by the G-patch domain of CMTr1, has an advantageous effect on CMTr1 activity towards highly structured RNA substrates. The effect of DHX15 helicase activity is consistent with the strength of the secondary structure that has to be removed for CMTr1 to access the 5′-terminal residues in a single-stranded conformation. This is, to our knowledge, the first demonstration of the involvement of DHX15 in post-transcriptional RNA modification, and the first example of a molecular process in which DHX15 directly affects the activity of another enzyme. Our findings suggest a new mechanism underlying the regulatory role of DHX15 in the RNA capping process. RNAs with highly structured 5′ termini constitute a significant fraction of the human transcriptome. Hence, CMTr1–DHX15 cooperation is likely to be important for the metabolism of RNA polymerase II-transcribed RNAs. This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.

scholarly journals Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis

2010 ◽  
Vol 38 (12) ◽  
pp. 4067-4078 ◽  
Author(s):  
J. M. DiChiara ◽  
L. M. Contreras-Martinez ◽  
J. Livny ◽  
D. Smith ◽  
K. A. McDonough ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Mycobacterium Bovis ◽  
Mycobacterium Smegmatis ◽  
Small Rnas ◽  
Mycobacterium Bovis Bcg

scholarly journals The Alternative Route to Heme in the Methanogenic ArchaeonMethanosarcina barkeri

Archaea ◽  
2014 ◽  
Vol 2014 ◽  
pp. 1-13 ◽  
Author(s):  
Melanie Kühner ◽  
Kristin Haufschildt ◽  
Alexander Neumann ◽  
Sonja Storbeck ◽  
Judith Streif ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Feedback Regulation ◽  
Methanosarcina Barkeri ◽  
Heme Biosynthesis ◽  
Alternative Route ◽  
Activity Assay ◽  
Enzyme Activity Assay ◽  
Living Organisms

In living organisms heme is formed from the common precursor uroporphyrinogen III by either one of two substantially different pathways. In contrast to eukaryotes and most bacteria which employ the so-called “classical” heme biosynthesis pathway, the archaea use an alternative route. In this pathway, heme is formed from uroporphyrinogen III via the intermediates precorrin-2, sirohydrochlorin, siroheme, 12,18-didecarboxysiroheme, and iron-coproporphyrin III. In this study the heme biosynthesis proteins AhbAB, AhbC, and AhbD fromMethanosarcina barkeriwere functionally characterized. Using anin vivoenzyme activity assay it was shown that AhbA and AhbB (Mbar_A1459 and Mbar_A1460) together catalyze the conversion of siroheme into 12,18-didecarboxysiroheme. The two proteins form a heterodimeric complex which might be subject to feedback regulation by the pathway end-product heme. Further, AhbC (Mbar_A1793) was shown to catalyze the formation of iron-coproporphyrin IIIin vivo. Finally, recombinant AhbD (Mbar_A1458) was produced inE. coliand purified indicating that this protein most likely contains two [4Fe-4S] clusters. Using anin vitroenzyme activity assay it was demonstrated that AhbD catalyzes the conversion of iron-coproporphyrin III into heme.

scholarly journals The Influence of Electromagnetic Pollution on Living Organisms: Historical Trends and Forecasting Changes

2015 ◽  
Vol 2015 ◽  
pp. 1-18 ◽  
Author(s):  
Grzegorz Redlarski ◽  
Bogdan Lewczuk ◽  
Arkadiusz Żak ◽  
Andrzej Koncicki ◽  
Marek Krawczuk ◽  
...  
Keyword(s):  
Electromagnetic Radiation ◽  
Electromagnetic Fields ◽  
Helix Pomatia ◽  
Scientific Research ◽  
Great Majority ◽  
Land Snail ◽  
Negative Influence ◽  
Model Organisms ◽  
Living Organisms ◽  
Electromagnetic Pollution

Current technologies have become a source of omnipresent electromagnetic pollution from generated electromagnetic fields and resulting electromagnetic radiation. In many cases this pollution is much stronger than any natural sources of electromagnetic fields or radiation. The harm caused by this pollution is still open to question since there is no clear and definitive evidence of its negative influence on humans. This is despite the fact that extremely low frequency electromagnetic fields were classified as potentially carcinogenic. For these reasons, in recent decades a significant growth can be observed in scientific research in order to understand the influence of electromagnetic radiation on living organisms. However, for this type of research the appropriate selection of relevant model organisms is of great importance. It should be noted here that the great majority of scientific research papers published in this field concerned various tests performed on mammals, practically neglecting lower organisms. In that context the objective of this paper is to systematise our knowledge in this area, in which the influence of electromagnetic radiation on lower organisms was investigated, including bacteria,E. coliandB. subtilis, nematode,Caenorhabditis elegans, land snail,Helix pomatia, common fruit fly,Drosophila melanogaster, and clawed frog,Xenopus laevis.

scholarly journals A Novel Pathway for the Biosynthesis of Heme inArchaea: Genome-Based Bioinformatic Predictions and Experimental Evidence

Archaea ◽  
2010 ◽  
Vol 2010 ◽  
pp. 1-15 ◽  
Author(s):  
Sonja Storbeck ◽  
Sarah Rolfes ◽  
Evelyne Raux-Deery ◽  
Martin J. Warren ◽  
Dieter Jahn ◽  
...  
Keyword(s):  
Experimental Verification ◽  
Biosynthetic Pathway ◽  
Gene Clusters ◽  
Methanosarcina Barkeri ◽  
Heme Biosynthesis ◽  
Alternative Route ◽  
Biological Processes ◽  
Prosthetic Group ◽  
Biosynthesis Gene ◽  
Domains Of Life

Heme is an essential prosthetic group for many proteins involved in fundamental biological processes in all three domains of life. InEukaryotaandBacteriaheme is formedviaa conserved and well-studied biosynthetic pathway. Surprisingly, inArchaeaheme biosynthesis proceedsviaan alternative route which is poorly understood. In order to formulate a working hypothesis for this novel pathway, we searched 59 completely sequenced archaeal genomes for the presence of gene clusters consisting of established heme biosynthetic genes and colocalized conserved candidate genes. Within the majority of archaeal genomes it was possible to identify such heme biosynthesis gene clusters. From this analysis we have been able to identify several novel heme biosynthesis genes that are restricted to archaea. Intriguingly, several of the encoded proteins display similarity to enzymes involved in hemed1biosynthesis. To initiate an experimental verification of our proposals twoMethanosarcina barkeriproteins predicted to catalyze the initial steps of archaeal heme biosynthesis were recombinantly produced, purified, and their predicted enzymatic functions verified.

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