Quantitative aspects of RNA silencing in metazoans

Small regulatory RNAs (microRNAs, siRNAs, and piRNAs) exhibit several unique features that clearly distinguish them from other known gene regulators. Their genomic organization, mode of action, and proposed biological functions raise specific questions. In this review, we focus on the quantitative aspect of small regulatory RNA biology. The original nature of these small RNAs accelerated the development of novel detection techniques and improved statistical methods and promoted new concepts that may unexpectedly generalize to other gene regulators. Quantification of natural phenomena is at the core of scientific practice, and the unique challenges raised by small regulatory RNAs have prompted many creative innovations by the scientific community.     

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

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.     

MicroRNAs and the regulation of cell death

Programmed cell death, or apoptosis, is ubiquitous, both during development and in the adult. Many components of the evolutionarily conserved machinery that brings about and regulates cell death have been identified, and all of these are proteins. However, in the past three years it has become clear that roughly 1% of predicted genes in animals encode small noncoding RNAs known as microRNAs, which regulate gene function. Here we review the recent identification of microRNA cell death regulators in Drosophila, hints that such regulators are also likely to exist in mammals, and more generally the approaches and tools that are now available to probe roles for noncoding RNAs in the control of cell death.     

Identification of a hormogonium polysaccharide-specific gene set conserved in filamentous cyanobacteria

Cyanobacteria comprise a phylum defined by the capacity for oxygenic photosynthesis. Members of this phylum are frequently motile as well. Strains that display gliding or twitching motility across semisolid surfaces are powered by a conserved type IV pilus system (T4P). Among the filamentous, heterocyst-forming cyanobacteria, motility is usually confined to specialized filaments known as hormogonia, and requires the deposition of an associated hormogonium polysaccharide (HPS). The genes involved in assembly and export of HPS are largely undefined, and it has been hypothesized that HPS exits the outer membrane via an atypical T4P-driven mechanism. Here, several novel hps loci, primarily encoding glycosyl transferases, are identified. Mutational analysis demonstrates that the majority of these genes are essential for both motility and production of HPS. Notably, most mutant strains accumulate wild-type cellular levels of the major pilin PilA, but not extracellular PilA, indicating dysregulation of the T4P motors, and, therefore, a regulatory interaction between HPS assembly and T4P activity. A co-occurrence analysis of Hps orthologs among cyanobacteria identified an extended set of putative Hps proteins comprising most components of a Wzx/Wzy-type polysaccharide synthesis and export system. This implies that HPS may be secreted through a more canonical pathway, rather than a T4P-mediated mechanism.     

Responses to cold shock in cyanobacteria

Acclimation of cyanobacteria to low temperatures involves induction of the expression of several families of genes. Fatty acid desaturases are responsible for maintaining the appropriate fluidity of membranes under stress conditions. RNA-binding proteins, which presumably act analogously to members of the bacterial Csp family of RNA chaperones, are involved in the maintenance of the translation under cold stress. The RNA helicase, whose expression is induced specifically by cold, might be responsible for modifying inappropriate secondary structures of RNAs induced by cold. The cold-inducible family of CIp proteins appears to be involved in the proper folding and processing of proteins. Although genes for cold-inducible proteins in cyanobacteria are heterogeneous, some common features of their untranslated regulatory regions suggest the existence of a common factor(s) that might participate in regulation of the expression of these genes under cold-stress conditions. Studies of the patterns of expression of cold-inducible genes in cyanobacteria have revealed the presence of a cold-sensing mechanism that is associated with their membrane lipids. Available information about cold-shock responses in cyanobacteria and molecular mechanisms of cold acclimation are reviewed in this article.     

Key players in regulatory RNA realm of bacteria

Precise regulation of gene expression is crucial for living cells to adapt for survival in diverse environmental conditions. Among the common cellular regulatory mechanisms, RNA-based regulators play a key role in all domains of life. Discovery of regulatory RNAs have made a paradigm shift in molecular biology as many regulatory functions of RNA have been identified beyond its canonical roles as messenger, ribosomal and transfer RNA. In the complex regulatory RNA network, riboswitches, small RNAs, and RNA thermometers can be identified as some of the key players. Herein, we review the discovery, mechanism, and potential therapeutic use of these classes of regulatory RNAs mainly found in bacteria. Being highly adaptive organisms that inhabit a broad range of ecological niches, bacteria have adopted tight and rapid-responding gene regulation mechanisms. This review aims to highlight how bacteria utilize versatile RNA structures and sequences to build a sophisticated gene regulation network.     

Paradoxes of biodiversity,phylogeny, and taxonomy of cyanobacteria

The biodiversity of cyanobacteria is paradoxical since these bacteria vary in cytological characters although are metabolically uniform. Cyanobacterial phylogeny is also paradoxical as the structural genes of rRNA are too conservative for a large phylum. On the paradoxical evolutionary tree, neighbors have strongly contrasting phenotypes, while objects with similar phenotypes demonstrate a heterological structure of 16S rDNA. The systematics of cyanobacteria is paradoxical, too, since it is logically contradictory: on the one hand, phylum BX Cyanobacteria generally is separated on molecular-biological grounds. On the other hand, in accordance with the traditional botanical algorithm used in classification of blue-green algae, this phylum is artificially subdivided into morphological groups (ultrastructural characters are taken into account only in rare cases). A unique trait of the taxonomy of cyanobacteria (with rare exceptions, e.g., Cyanobacterium stanieri) is its general nonusage of the category of species. The species epithet is replaced by a stain index (e.g., Anabaena PCC 7122).     

The role of RNAs in the regulation of virulence-gene expression

Bacterial pathogens sense their environment, and in response, virulence genes are induced or repressed through spatial and temporal regulation. They are also subjected to stress conditions, which require appropriate responses. Recent research has revealed that RNAs are key regulators in pathogens. Small RNAs regulate the translation and/or stability of mRNAs that encode virulence proteins, or proteins with roles in adaptive responses, which are triggered by environmental cues and stresses. In most cases, these small RNAs act directly on target RNAs by an antisense mechanism. Other small RNAs act indirectly, by sequestration of regulatory proteins. Direct sensing of environmental signals can occur through induced structural changes in mRNAs.     

MicroRNAs与疾病和发育

作为模式生物实验系统,线虫可用于研究控制动物发育和人类疾病遗传机制。研究发育缺陷的线虫突变体有助于在动物中发现对发育和生理过程有重要调控作用的基因。其中一些基因编码一类小RNA,如microRNA(miRNA),通过作用于特定基因信使RNA来调控其蛋白质表达。一些在线虫发育过程中有功能的miRNA在人体中也存在。它们参与调控与疾病相关的生物学过程,如癌症、糖尿病和神经退行性疾病。通过分析miRNA在临床样品、哺乳动物细胞和模式生物线虫中的表达,从而揭示miRNA调控途径在相关人类疾病中的功能。