Regulatory RNAs in cyanobacteria: developmental decisions, stress responses and a plethora of chromosomally encoded cis-antisense RNAs

2011 ◽  
Vol 392 (4) ◽  
Author(s):  
Jens Georg ◽  
Wolfgang R. Hess
Keyword(s):  
Stress Responses ◽  
Carbon Fixation ◽  
Protein Biosynthesis ◽  
Oxygenic Photosynthesis ◽  
Outer Cell ◽  
Complex Species ◽  
Outer Cell Membrane ◽  
Non Coding Rnas ◽  
Regulatory Rnas ◽  
Cell Membrane Protein

Abstract Cyanobacteria are the only prokaryotes which directly convert solar energy into biomass using oxygenic photosynthesis. Therefore, these bacteria are of interest for the production of biofuels, biotechnology and are of tremendous relevance for primary carbon fixation in many ecosystems. Mechanisms controlling gene expression cannot be understood entirely without information on the numbers and functions of regulatory RNAs. In cyanobacteria, non-coding RNAs have been characterized from simple unicellular species such as Prochlorococcus up to complex species such as Anabaena. Several of these RNAs function in the control of stress responses, photosynthesis, outer cell membrane protein biosynthesis and the differentiation of cells.

scholarly journals Extensive Analysis of miRNA Trimming and Tailing Indicates that AGO1 Has a Complex Role in miRNA Turnover

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 267
Author(s):  
Axel J. Giudicatti ◽  
Ariel H. Tomassi ◽  
Pablo A. Manavella ◽  
Agustin L. Arce
Keyword(s):  
Small Rna ◽  
Stress Responses ◽  
Cellular Localization ◽  
Mirna Biogenesis ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Extensive Analysis ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Argonaute 1

MicroRNAs are small regulatory RNAs involved in several processes in plants ranging from development and stress responses to defense against pathogens. In order to accomplish their molecular functions, miRNAs are methylated and loaded into one ARGONAUTE (AGO) protein, commonly known as AGO1, to stabilize and protect the molecule and to assemble a functional RNA-induced silencing complex (RISC). A specific machinery controls miRNA turnover to ensure the silencing release of targeted-genes in given circumstances. The trimming and tailing of miRNAs are fundamental modifications related to their turnover and, hence, to their action. In order to gain a better understanding of these modifications, we analyzed Arabidopsis thaliana small RNA sequencing data from a diversity of mutants, related to miRNA biogenesis, action, and turnover, and from different cellular fractions and immunoprecipitations. Besides confirming the effects of known players in these pathways, we found increased trimming and tailing in miRNA biogenesis mutants. More importantly, our analysis allowed us to reveal the importance of ARGONAUTE 1 (AGO1) loading, slicing activity, and cellular localization in trimming and tailing of miRNAs.

scholarly journals Emerging Roles and Potential Applications of Non-Coding RNAs in Glioblastoma

2020 ◽  
Vol 21 (7) ◽  
pp. 2611 ◽  
Author(s):  
Carlos DeOcesano-Pereira ◽  
Raquel A. C. Machado ◽  
Ana Marisa Chudzinski-Tavassi ◽  
Mari Cleide Sogayar
Keyword(s):  
Cancer Type ◽  
Biological Processes ◽  
Small Nucleolar Rnas ◽  
Physiological Conditions ◽  
Master Regulators ◽  
Potential Applications ◽  
Non Coding Rnas ◽  
Regulatory Rnas ◽  
Nucleolar Rnas ◽  
Substantial Effort

Non-coding RNAs (ncRNAs) comprise a diversity of RNA species, which do not have the potential to encode proteins. Non-coding RNAs include two classes of RNAs, namely: short regulatory ncRNAs and long non-coding RNAs (lncRNAs). The short regulatory RNAs, containing up to 200 nucleotides, include small RNAs, such as microRNAs (miRNA), short interfering RNAs (siRNAs), piwi-interacting RNAs (piRNAs), and small nucleolar RNAs (snoRNAs). The lncRNAs include long antisense RNAs and long intergenic RNAs (lincRNAs). Non-coding RNAs have been implicated as master regulators of several biological processes, their expression being strictly regulated under physiological conditions. In recent years, particularly in the last decade, substantial effort has been made to investigate the function of ncRNAs in several human diseases, including cancer. Glioblastoma is the most common and aggressive type of brain cancer in adults, with deregulated expression of small and long ncRNAs having been implicated in onset, progression, invasiveness, and recurrence of this tumor. The aim of this review is to guide the reader through important aspects of miRNA and lncRNA biology, focusing on the molecular mechanism associated with the progression of this highly malignant cancer type.

scholarly journals β-catenin activation is not involved in sporadic parathyroid carcinomas and adenomas

2010 ◽  
Vol 17 (1) ◽  
pp. 1-6 ◽  
Author(s):  
F Cetani ◽  
E Pardi ◽  
C Banti ◽  
P Collecchi ◽  
P Viacava ◽  
...  
Keyword(s):  
Cell Membrane ◽  
Signaling Pathway ◽  
Direct Sequencing ◽  
Distant Metastases ◽  
Outer Cell ◽  
Tumor Type ◽  
Nuclear Staining ◽  
Cytoplasmic Staining ◽  
Membrane Staining ◽  
Outer Cell Membrane

Aberrant accumulation of β-catenin has been found in various types of human tumors. The aim of this study was to evaluate whether Wnt/β-catenin signaling is activated in parathyroid carcinomas and adenomas. We studied 154 parathyroid tumors (18 carcinomas (13 with distant metastases), six atypical adenomas, and 130 adenomas). Three normal parathyroid tissues were used as control. Direct sequencing of exon 3 of the CTNNB1 gene showed absence of stabilizing mutations in all the tumors. Immunostaining of β-catenin was performed in all carcinomas and in 66 adenomas (including three atypical). Normal parathyroid showed a homogeneous distinct outer cell membrane staining in the majority of cells and no nuclear staining. A weak cytoplasmic staining was observed in one case. All tumors showed negative nuclear staining. With the exception of one carcinoma, which had a negative membrane staining, all other samples showed a membrane staining which was similar to that of the normal parathyroid. β-Catenin expression was heterogeneous with a range of positive cells between 5 and 80%, independently of tumor type. Our results suggest that the Wnt/β-catenin signaling pathway is not involved in the development of parathyroid carcinomas and adenomas.

scholarly journals Cryptic oxygen cycling in anoxic marine zones

2017 ◽  
Vol 114 (31) ◽  
pp. 8319-8324 ◽  
Author(s):  
Emilio Garcia-Robledo ◽  
Cory C. Padilla ◽  
Montserrat Aldunate ◽  
Frank J. Stewart ◽  
Osvaldo Ulloa ◽  
...  
Keyword(s):  
Surface Layer ◽  
Carbon Fixation ◽  
Nitrogen Loss ◽  
Biogeochemical Cycling ◽  
Oxygenic Photosynthesis ◽  
Nitrite Oxidation ◽  
Tight Coupling ◽  
Expression Of Genes ◽  
Aerobic Processes ◽  
Oxygen Cycling

Oxygen availability drives changes in microbial diversity and biogeochemical cycling between the aerobic surface layer and the anaerobic core in nitrite-rich anoxic marine zones (AMZs), which constitute huge oxygen-depleted regions in the tropical oceans. The current paradigm is that primary production and nitrification within the oxic surface layer fuel anaerobic processes in the anoxic core of AMZs, where 30–50% of global marine nitrogen loss takes place. Here we demonstrate that oxygenic photosynthesis in the secondary chlorophyll maximum (SCM) releases significant amounts of O2to the otherwise anoxic environment. The SCM, commonly found within AMZs, was dominated by the picocyanobacteriaProchlorococcusspp. Free O2levels in this layer were, however, undetectable by conventional techniques, reflecting a tight coupling between O2production and consumption by aerobic processes under apparent anoxic conditions. Transcriptomic analysis of the microbial community in the seemingly anoxic SCM revealed the enhanced expression of genes for aerobic processes, such as nitrite oxidation. The rates of gross O2production and carbon fixation in the SCM were found to be similar to those reported for nitrite oxidation, as well as for anaerobic dissimilatory nitrate reduction and sulfate reduction, suggesting a significant effect of local oxygenic photosynthesis on Pacific AMZ biogeochemical cycling.

Mechanisms by Which Small RNAs Affect Bacterial Activity

2019 ◽  
Vol 98 (12) ◽  
pp. 1315-1323
Author(s):  
L. Lei ◽  
Y. Yang ◽  
Y. Yang ◽  
S. Wu ◽  
X. Ma ◽  
...  
Keyword(s):  
Stress Responses ◽  
Small Rnas ◽  
Environmental Changes ◽  
Expression Profiles ◽  
Bacterial Flora ◽  
Oral Disease ◽  
Bacterial Gene ◽  
Bacterial Physiology ◽  
Cellular Processes ◽  
Regulatory Rnas

The oral cavity contains a distinct habitat that supports diverse bacterial flora. Recent observations have provided additional evidence that sRNAs are key regulators of bacterial physiology and pathogenesis. These sRNAs have been divided into 5 functional groups: cis-encoded RNAs, trans-encoded RNAs, RNA regulators of protein activity, bacterial CRISPR (clustered regularly interspaced short palindromic repeat) RNAs, and a novel category of miRNA-size small RNAs (msRNAs). In this review, we discuss a critical group of key commensal and opportunistic oral pathogens. In general, supragingival bacterial sRNAs function synergistically to fine-tune the regulation of cellular processes and stress responses in adaptation to environmental changes. Particularly in the cariogenic bacteria Streptococcus mutans, both the antisense vicR RNA and msRNA1657 can impede the metabolism of bacterial exopolysaccharides, prevent biofilm formation, and suppress its cariogenicity. In Enterococcus faecalis, selected sRNAs control the expression of proteins involved in diverse cellular processes and stress responses. In subgingival plaques, sRNAs from periodontal pathogens can function as novel bacterial signaling molecules that mediate bacterial-human interactions in periodontal homeostasis. In Porphyromonas gingivalis, the expression profiles of putative sRNA101 and sRNA42 were found to respond to hemin availability after hemin starvation. Regarding Aggregatibacter actinomycetemcomitans (previously Actinobacillus actinomycetemcomitans), a major periodontal pathogen associated with aggressive periodontitis, the predicted sRNAs interact with several virulence genes, including those encoding leukotoxin and cytolethal distending toxin. Furthermore, in clinical isolates, these associated RNAs could be explored not only as potential biomarkers for oral disease monitoring but also as alternative types of regulators for drug design. Thus, this emerging subspecialty of bacterial regulatory RNAs could reshape our understanding of bacterial gene regulation from their key roles of endogenous regulatory RNAs to their activities in pathologic processes.

scholarly journals Non-Coding and Regulatory RNAs as Epigenetic Remodelers of Fatty Acid Homeostasis in Cancer

Cancers ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 2890
Author(s):  
Silvia Cruz-Gil ◽  
Lara P. Fernández ◽  
Ruth Sánchez-Martínez ◽  
Marta Gómez de Cedrón ◽  
Ana Ramírez de Molina
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
Cancer Cells ◽  
Noncoding Rna ◽  
De Novo ◽  
Atp Synthesis ◽  
Membrane Composition ◽  
Structural Cell ◽  
Non Coding Rnas ◽  
Regulatory Rnas

Cancer cells commonly display metabolic fluctuations. Together with the Warburg effect and the increased glutaminolysis, alterations in lipid metabolism homeostasis have been recognized as a hallmark of cancer. Highly proliferative cancer cells upregulate de novo synthesis of fatty acids (FAs) which are required to support tumor progression by exerting multiple roles including structural cell membrane composition, regulators of the intracellular redox homeostasis, ATP synthesis, intracellular cell signaling molecules, and extracellular mediators of the tumor microenvironment. Epigenetic modifications have been shown to play a crucial role in human development, but also in the initiation and progression of complex diseases. The study of epigenetic processes could help to design new integral strategies for the prevention and treatment of metabolic disorders including cancer. Herein, we first describe the main altered intracellular fatty acid processes to support cancer initiation and progression. Next, we focus on the most important regulatory and non-coding RNAs (small noncoding RNA—sncRNAs—long non-coding RNAs—lncRNAs—and other regulatory RNAs) which may target the altered fatty acids pathway in cancer.

scholarly journals Long non-coding RNAs in plants: emerging modulators of gene activity in development and stress responses

Planta ◽  
2020 ◽  
Vol 252 (5) ◽  
Author(s):  
Li Chen ◽  
Qian-Hao Zhu ◽  
Kerstin Kaufmann
Keyword(s):  
Stress Responses ◽  
Translational Regulation ◽  
Molecular Mechanisms ◽  
Functional Characterization ◽  
Reproductive Organs ◽  
Gene Activity ◽  
Protein Coding ◽  
Wide Range ◽  
Non Coding Rnas ◽  
Coding Potential

Abstract Main conclusion Long non-coding RNAs modulate gene activity in plant development and stress responses by various molecular mechanisms. Abstract Long non-coding RNAs (lncRNAs) are transcripts larger than 200 nucleotides without protein coding potential. Computational approaches have identified numerous lncRNAs in different plant species. Research in the past decade has unveiled that plant lncRNAs participate in a wide range of biological processes, including regulation of flowering time and morphogenesis of reproductive organs, as well as abiotic and biotic stress responses. LncRNAs execute their functions by interacting with DNA, RNA and protein molecules, and by modulating the expression level of their targets through epigenetic, transcriptional, post-transcriptional or translational regulation. In this review, we summarize characteristics of plant lncRNAs, discuss recent progress on understanding of lncRNA functions, and propose an experimental framework for functional characterization.

scholarly journals The Emerging Role of Long Non-Coding RNAs in Plant Defense Against Fungal Stress

2020 ◽  
Vol 21 (8) ◽  
pp. 2659
Author(s):  
Hong Zhang ◽  
Huan Guo ◽  
Weiguo Hu ◽  
Wanquan Ji
Keyword(s):  
Stress Responses ◽  
Higher Plants ◽  
Regulatory Elements ◽  
Cellular Functions ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Resistance To Infection ◽  
Regulatory Functions ◽  
Long Non Coding Rna

Growing interest and recent evidence have identified long non-coding RNA (lncRNA) as the potential regulatory elements for eukaryotes. LncRNAs can activate various transcriptional and post-transcriptional events that impact cellular functions though multiple regulatory functions. Recently, a large number of lncRNAs have also been identified in higher plants, and an understanding of their functional role in plant resistance to infection is just emerging. Here, we focus on their identification in crop plant, and discuss their potential regulatory functions and lncRNA-miRNA-mRNA network in plant pathogen stress responses, referring to possible examples in a model plant. The knowledge gained from a deeper understanding of this colossal special group of plant lncRNAs will help in the biotechnological improvement of crops.

scholarly journals Damage of lipopolysaccharides in outer cell membrane and production of ROS-mediated stress within bacteria makes nano zinc oxide a bactericidal agent

2014 ◽  
Vol 5 (7) ◽  
pp. 857-866 ◽  
Author(s):  
Prasun Patra ◽  
Shuvrodeb Roy ◽  
Sampad Sarkar ◽  
Shouvik Mitra ◽  
Saheli Pradhan ◽  
...  
Keyword(s):  
Zinc Oxide ◽  
Cell Membrane ◽  
Outer Cell ◽  
Nano Zinc Oxide ◽  
Outer Cell Membrane ◽  
Nano Zinc ◽  
Bactericidal Agent

The dark matter rises: the expanding world of regulatory RNAs

2013 ◽  
Vol 54 ◽  
pp. 1-16 ◽  
Author(s):  
Michael B. Clark ◽  
Anupma Choudhary ◽  
Martin A. Smith ◽  
Ryan J. Taft ◽  
John S. Mattick
Keyword(s):  
Phenotypic Diversity ◽  
Rapid Progress ◽  
Major Area ◽  
Protein Coding ◽  
Diverse Range ◽  
Protein Coding Genes ◽  
Evolutionary Innovation ◽  
Non Coding Rnas ◽  
Cellular Pathways ◽  
Regulatory Rnas

The ability to sequence genomes and characterize their products has begun to reveal the central role for regulatory RNAs in biology, especially in complex organisms. It is now evident that the human genome contains not only protein-coding genes, but also tens of thousands of non–protein coding genes that express small and long ncRNAs (non-coding RNAs). Rapid progress in characterizing these ncRNAs has identified a diverse range of subclasses, which vary widely in size, sequence and mechanism-of-action, but share a common functional theme of regulating gene expression. ncRNAs play a crucial role in many cellular pathways, including the differentiation and development of cells and organs and, when mis-regulated, in a number of diseases. Increasing evidence suggests that these RNAs are a major area of evolutionary innovation and play an important role in determining phenotypic diversity in animals.

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