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1.
Hairpin RNA: a secondary structure of primary importance 总被引:4,自引:0,他引:4
An RNA hairpin is an essential secondary structure of RNA. It can guide RNA folding, determine interactions in a ribozyme,
protect messenger RNA (mRNA) from degradation, serve as a recognition motif for RNA binding proteins or act as a substrate
for enzymatic reactions. In this review, we have focused on cis-acting RNA hairpins in metazoa, which regulate histone gene expression, mRNA localization and translation. We also review
evolution, mechanism of action and experimental use of trans-acting microRNAs, which are coded by short RNA hairpins. Finally, we discuss the existence and effects of long RNA hairpin
in animals. We show that several proteins previously recognized to play a role in a specific RNA stem-loop function in cis were also linked to RNA silencing pathways where a different type of hairpin acts in trans. Such overlaps indicate that the relationship between certain mechanisms that recognize different types of RNA hairpins is
closer than previously thought.
Received 21 November 2005; received after revision 3 January 2006; accepted 11 January 2006 相似文献
2.
Wittkopp PJ 《Cellular and molecular life sciences : CMLS》2005,62(16):1779-1783
Regulatory variation results from genetic changes with both cis and trans acting effects on gene expression. Here I describe the types of genetic variants that alter cis and trans regulation and discuss differences in the potential for cis and trans changes among different classes of genes. I argue that the molecular function of the protein encoded by each gene and how the gene is wired into the genomic regulatory network may influence its propensity for cis and trans regulatory changes.Received 15 February 2005; received after revision 12 April 2005; accepted 26 April 2005 相似文献
3.
Pascale Romby Emmanuelle Charpentier 《Cellular and molecular life sciences : CMLS》2010,67(2):217-237
During the last decade, RNA molecules with regulatory functions on gene expression have benefited from a renewed interest.
In bacteria, recent high throughput computational and experimental approaches have led to the discovery that 10–20% of all
genes code for RNAs with critical regulatory roles in metabolic, physiological and pathogenic processes. The trans-acting RNAs comprise the noncoding RNAs, RNAs with a short open reading frame and antisense RNAs. Many of these RNAs act
through binding to their target mRNAs while others modulate protein activity or target DNA. The cis-acting RNAs include regulatory regions of mRNAs that can respond to various signals. These RNAs often provide the missing
link between sensing changing conditions in the environment and fine-tuning the subsequent biological responses. Information
on their various functions and modes of action has been well documented for gram-negative bacteria. Here, we summarize the
current knowledge of regulatory RNAs in gram-positive bacteria. 相似文献
4.
5.
Fernández MR Porté S Crosas E Barberà N Farrés J Biosca JA Parés X 《Cellular and molecular life sciences : CMLS》2007,64(11):1419-1427
ζ-crystallins constitute a family of proteins with NADPH:quinone reductase activity found initially in mammalian lenses but
now known to be present in many other organisms and tissues. Few proteins from this family have been characterized, and their
function remains unclear. In the present work, ζ-crystallins from human and yeast (Zta1p) were expressed, purified and characterized.
Both enzymes are able to reduce ortho-quinones in the presence of NADPH but are not active with 2-alkenals. Deletion of the ZTA1 gene makes yeast more sensitive to menadione and hydrogen peroxide, suggesting a role in the oxidative stress response. The
human and yeast enzymes specifically bind to adenine-uracil rich elements (ARE) in RNA, indicating that both enzymes are ARE-binding
proteins and that this property has been conserved in ζ-crystallins throughout evolution. This supports a role for ζ-crystallins
as trans-acting factors that could regulate the turnover of certain mRNAs.
Received 21 February 2007; received after revision 16 April 2007; accepted 23 April 2007
M. R. Fernández, S. Porté: These authors contributed equally to this work. 相似文献
6.
S. Tahara S. Kasai M. Inoue J. Kawabata J. Mizutani 《Cellular and molecular life sciences : CMLS》1994,50(2):137-141
In a survey of antifungal stress compounds induced by cupric chloride we found that leaves ofChenopodium album exuded a highly fungitoxic metabolite mucondialdehyde (trans-2,trans-4-hexadienedial), which was associated with 13-oxo-9,11-tridecadienoic acids (cis-9,trans-11 andtrans-9,trans-11 isomers) presumably resulting from -scission of 13-hydroperoxy-octadecadi(tri)enoic acid. The biogenesis and role as a general defensive agent in plants are briefly discussed. 相似文献
7.
The neurotoxins produced by various species of Clostridia are the causative agents of botulism and tetanus. The ability of the toxins, specifically those of the botulinum neurotoxin
family, to disrupt neurotransmission has been exploited for use in several medical indications and now represents the therapeutic
option of choice in a number of cases. Clostridial neurotoxins have been discovered to have a multi-domain structure that
is shared between the various proteins of the family, and it has also been determined that each domain contributes a specific
role to the holotoxin. The extensive use of recombinant expression approaches, along with solution of multiple crystallographic
structures of individual domains, has enabled researchers to explore structurefunction relationships of the toxin domains
more closely. These advances have facilitated a greater understanding of the potential use of individual domains for a wide
variety of purposes, including the development of new therapeutics.
Received 21 October 2005; received after revision 10 November 2005; accepted 16 November 2005 相似文献
8.
The elucidation of assembly pathways of multi-subunit membrane proteins is of growing interest in structural biology. In this
study, we provide an analysis of the assembly of the asymmetrically oriented PsaC subunit on the pseudo C2-symmetric Photosystem I core. Based on a comparison of the differences in the NMR solution structure of unbound PsaC with
that of the X-ray crystal structure of bound PsaC, and on a detailed analysis of the PsaC binding site surrounding the FX iron-sulfur cluster, two models can be envisioned for what are likely the last steps in the assembly of Photosystem I. Here,
we dissect both models and attempt to address heretofore unrecognized issues by proposing a mechanism that includes a thermodynamic
perspective. Experimental strategies to verify the models are proposed. In closing, the evolutionary aspects of the assembly
process will be considered, with special reference to the structural arrangement of the PsaC binding surface.
Received 22 October 2008; received after revision 17 November 2008; accepted 05 December 2008 相似文献
9.
Davies WI Zheng L Hughes S Tamai TK Turton M Halford S Foster RG Whitmore D Hankins MW 《Cellular and molecular life sciences : CMLS》2011,68(24):4115-4132
Melanopsin (OPN4) is an opsin photopigment that, in mammals, confers photosensitivity to retinal ganglion cells and regulates
circadian entrainment and pupil constriction. In non-mammalian species, two forms of opn4 exist, and are classified into mammalian-like (m) and non-mammalian-like (x) clades. However, far less is understood of the function of this photopigment family. Here we identify in zebrafish five
melanopsins (opn4m-1, opn4m-2, opn4m-3, opn4x-1 and opn4x-2), each encoding a full-length opsin G protein. All five genes are expressed in the adult retina in a largely non-overlapping
pattern, as revealed by RNA in situ hybridisation and immunocytochemistry, with at least one melanopsin form present in all
neuronal cell types, including cone photoreceptors. This raises the possibility that the teleost retina is globally light
sensitive. Electrophysiological and spectrophotometric studies demonstrate that all five zebrafish melanopsins encode a functional
photopigment with peak spectral sensitivities that range from 470 to 484 nm, with opn4m-1 and opn4m-3 displaying invertebrate-like
bistability, where the retinal chromophore interchanges between cis- and trans-isomers in a light-dependent manner and remains within the opsin binding pocket. In contrast, opn4m-2, opn4x-1 and opn4x-2
are monostable and function more like classical vertebrate-like photopigments, where the chromophore is converted from 11-cis to all-trans retinal upon absorption of a photon, hydrolysed and exits from the binding pocket of the opsin. It is thought that all melanopsins
exhibit an invertebrate-like bistability biochemistry. Our novel findings, however, reveal the presence of both invertebrate-like
and vertebrate-like forms of melanopsin in the teleost retina, and indicate that photopigment bistability is not a universal
property of the melanopsin family. The functional diversity of these teleost melanopsins, together with their widespread expression
pattern within the retina, suggests that melanopsins confer global photosensitivity to the teleost retina and might allow
for direct “fine-tuning” of retinal circuitry and physiology in the dynamic light environments found in aquatic habitats. 相似文献
10.
Control of cytoplasmic mRNA localization 总被引:1,自引:1,他引:0
11.
Su Feng Wei Chen Dan Cao Jinjun Bian Fang-Yuan Gong Wei Cheng Shun Cheng Qiang Xu Zi-Chun Hua Wu Yin 《Cellular and molecular life sciences : CMLS》2011,68(1):109-124
Increasing evidence demonstrates that Na+, K+-ATPase plays an important role in pulmonary inflammation, but the mechanism remains largely unknown. In this study, we used
cardiotonic steroids as Na+, K+-ATPase inhibitors to explore the possible involvement of Na+, K+-ATPase in pulmonary epithelial inflammation. The results demonstrated that mice after ouabain inhalation developed cyclooxygenase-2-dependent
acute lung inflammation. The in vitro experiments further confirmed that Na+, K+-ATPase inhibitors significantly stimulated cyclooxygenase-2 expression in lung epithelial cells of human or murine origin,
the process of which was participated by multiple cis-elements and trans-acting factors. Most importantly, we first described here that Na+, K+-ATPase inhibitors could evoke a significant Hu antigen R nuclear export in lung epithelial cells, which stabilized cyclooxygenase-2
mRNA by binding with a proximal AU-rich element within its 3′-untranslated region. In conclusion, HuR-mediated mRNA stabilization
opens new avenues in understanding the importance of Na+, K+-ATPase, as well as its inhibitors in inflammation. 相似文献
12.
Eukaryotic genomes have complex spatial organization in the nucleus. The factors and the mechanisms involved in this organization
remain an enigma. Among the many proteins implicated in such a role, the ubiquitous Zn-finger protein CTCF stands out. Here
we summarize the evidence placing CTCF in the enviable position of a master organizer of the genome. CTCF can form loops in cis, and can bridge sequences located on different chromosomes in trans. The thousands of CTCF binding sites, identified in recent genome-wide localization studies, and their distribution along
the genome further support a crucial role of CTCF as a chromatin organizer.
Received 10 October 2008; received after revision 11 December 2008; accepted 16 December 2008 相似文献
13.
Mukhopadhyay A Ni L Yang CS Weiner H 《Cellular and molecular life sciences : CMLS》2005,62(16):1890-1899
Phage display was used to identify new components of the mammalian mitochondrial receptor complex using Tom20 as a binding partner. Two peptides were identified. One had partial identity (SMLTVMA) with a bacterial signal peptide from Toho-1, a periplasmic protein. The other had partial identity with a mitochondrial inner membrane glutamate carrier. The bacterial signal peptide could carry a protein into mitochondria both in vivo and in vitro. The first six residues of the sequence, SMLTVM, were necessary for import but the two adjacent arginine residues in the 30-amino-acid leader were not critical for import. The signal peptides of Escherichia coli β-lactamase and Bacillsus subtilis lipase could not carry proteins into mitochondria. Presumably, the Toho-1 leader can adopt a structure compatible for recognition by the import apparatus.Received 29 April 2005; received after revision 8 June 2005; accepted 17 June 2005 相似文献
14.
Jiuyong Xie 《Cellular and molecular life sciences : CMLS》2014,71(22):4347-4360
Cell signal-regulated alternative splicing occurs for many genes but the evolutionary origin of the regulatory components and their relationship remain unclear. This review focuses on the alternative splicing components of several systems based on the available bioinformatics data. Eight mammalian RNA elements for signal-regulated splicing were aligned among corresponding sequences from dozens of representative vertebrate species to allow for assessment of the trends in evolutionary changes. Four distinct trends were observed. Four of the elements are highly conserved in bird, reptile and fish species examined (i); two elements can be found in fish but the sequences have been changing till in marsupials or higher mammals (ii); one element is almost exclusively found in mammals with mostly the same sequence (iii); and one element can be found in birds or lower vertebrates but expanded abruptly to have variable numbers of copies in mammals (iv). All examined prototype trans-acting factors and protein kinases emerged earlier than the RNA elements but additional (paralog) factors emerged in the same or later species. Thus, after their emergence mainly in fish or mammals with pre-existing prototype trans-acting factors/kinases, half of the elements have been highly conserved from fish to humans but the other half have evolved differentially with additional trans-acting factors. Their differential evolution likely contributes to the exon- and species/class-specific control of alternative splicing and its regulation by cell signals. The evolvement of a group of mammal-specific components would help relay signals from extracellular stimuli to the splicing machinery and thus contribute to higher proteomic diversity. 相似文献
15.
Cell surface receptors bind ligands expressed on other cells (in trans) in order to communicate with neighboring cells. However, an increasing number of cell surface receptors are found to also interact with ligands expressed on the same cell (in cis). These observations raise questions regarding the biological role of such cis interactions. Specifically, it is important to know whether cis and trans binding have distinct functional effects and, if so, how a single cell discriminates between interactions in cis versus trans. Further, what are the structural features that allow certain cell surface receptors to engage ligand both on the same as well as on an apposed cell membrane? Here, we summarize known examples of receptors that display cis–trans binding and discuss the emerging diversity of biological roles played by these unconventional two-way interactions, along with their structural basis. 相似文献
16.
17.
Thilo Bartolm?s Caroline Hirschfeld-Ihlow Sven Jonas Michael Schaefer Reinhard Ge?ner 《Cellular and molecular life sciences : CMLS》2012,69(22):3851-3862
LI-cadherin belongs to the family of 7D-cadherins that is characterized by a low sequence similarity to classical cadherins, seven extracellular cadherin repeats (ECs), and a short cytoplasmic domain. Nevertheless, LI-cadherins mediates Ca2+-dependent cell–cell adhesion and induces an epitheloid cellular phenotype in non-polarized CHO cells. Whereas several studies suggest that classical cadherins cis-dimerize in a Ca2+-dependent manner and interact in trans by strand-swapping tryptophan 2 of EC1, little is known about the molecular interactions of LI-cadherin, which lacks tryptophan 2. We thus expressed fluorescent LI-cadherin fusion proteins in HEK293 and CHO cells, analyzed their cell–cell adhesive properties and studied their cellular distribution, cis-interaction, and lateral diffusion in the presence and absence of Ca2+. LI-cadherin highly concentrates in cell contact areas but rapidly leaves those sites upon Ca2+ depletion and redistributes evenly on the cell surface, indicating that it is only kept in the contact areas by trans-interactions. Fluorescence resonance energy transfer analysis of LI-cadherin-CFP and -YFP revealed that LI-cadherin forms cis-dimers that resist Ca2+ depletion. As determined by fluorescence redistribution after photobleaching, LI-cadherin freely diffuses in the plasma membrane as a cis-dimer (D?=?0.42?±?0.03?μm2/s). When trapped by trans-binding in cell contact areas, its diffusion coefficient decreases only threefold to D?=?0.12?±?0.01?μm2/s, revealing that, in contrast to classical and desmosomal cadherins, trans-contacts formed by LI-cadherin are highly dynamic. 相似文献
18.
Ferreri C Kratzsch S Landi L Brede O 《Cellular and molecular life sciences : CMLS》2005,62(7-8):834-847
Thiyl radicals are intermediates of enzyme- and radical-driven biochemical processes, and their potential as reactive species in the biological environment has been somehow underestimated. From organic chemistry, however, it is known that thiyl radicals isomerize the double bonds of unsaturated fatty acids to a mixture with very dominating trans isomers. Recently, this reaction has been particularly studied for biosystems, focusing on the effect of thiyl radicals on the natural all-cis double bonds of unsaturated phospholipids, which undergo a conversion to the unnatural trans form. In this paper we report briefly the role of thiyl radicals in biosystems, describe the main features of the radical-induced cis-trans isomerization process under both in vitro and in vivo conditions, and reflect on some consequences for membrane structures, lipid metabolism and enzymatic reactions.Received 29 October 2004; received after revision 3 December 2004; accepted 4 January 2005 相似文献
19.
The BAG (Bcl-2 associated athanogene) family is a multifunctional group of proteins that perform diverse functions ranging from apoptosis to tumorigenesis.
An evolutionarily conserved group, these proteins are distinguished by a common conserved region known as the BAG domain.
BAG genes have been found in yeasts, plants, and animals, and are believed to function as adapter proteins forming complexes
with signaling molecules and molecular chaperones. In humans, a role for BAG proteins has been suggested in carcinogenesis,
HIV infection, and Parkinson’s disease. These proteins are therefore potential therapeutic targets, and their expression in
cells may serve as a predictive tool for such diseases. In plants, the Arabidopsis thaliana genome contains seven homologs of the BAG family, including four with domain organization similar to animal BAGs. Three members
contain a calmodulin-binding domain possibly reflecting differences between plant and animal programmed cell death. This review
summarizes current understanding of BAG proteins in both animals and plants.
Received 21 November 2007; received after revision 17 December 2007; accepted 2 January 2008 相似文献
20.
Albert-Weissenberger C Cazalet C Buchrieser C 《Cellular and molecular life sciences : CMLS》2007,64(4):432-448
The bacterial pathogen Legionella pneumophila is found ubiquitously in fresh water environments where it replicates within protozoan hosts. When inhaled by humans it can
replicate within alveolar macrophages and cause a severe pneumonia, Legionnaires disease. Yet much needs to be learned regarding
the mechanisms that allow Legionella to modulate host functions to its advantage and the regulatory network governing its intracellular life cycle. The establishment
and publication of the complete genome sequences of three clinical L. pneumophila isolates paved the way for major breakthroughs in understanding the biology of L. pneumophila. Based on sequence analysis many new putative virulence factors have been identified foremost among them eukaryotic-like
proteins that may be implicated in many different steps of the Legionella life cycle. This review summarizes what is currently known about regulation of the Legionella life cycle and gives insight in the Legionella-specific features as deduced from genome analysis.
Received 1 September 2006; received after revision 10 October 2006; accepted 22 November 2006 相似文献