scholarly journals METTL16, Methyltransferase-Like Protein 16: Current Insights into Structure and Function

2021 ◽  
Vol 22 (4) ◽  
pp. 2176
Author(s):  
Agnieszka Ruszkowska
Keyword(s):  
Current Knowledge ◽  
Molecular Structures ◽  
Structural Basis ◽  
Small Nuclear Rna ◽  
Functional Studies ◽  
U6 Snrna ◽  
Non Coding Rna ◽  
Sam Synthetase ◽  
Lncrna Malat1 ◽  
And Function

Methyltransferase-like protein 16 (METTL16) is a human RNA methyltransferase that installs m6A marks on U6 small nuclear RNA (U6 snRNA) and S-adenosylmethionine (SAM) synthetase pre-mRNA. METTL16 also controls a significant portion of m6A epitranscriptome by regulating SAM homeostasis. Multiple molecular structures of the N-terminal methyltransferase domain of METTL16, including apo forms and complexes with S-adenosylhomocysteine (SAH) or RNA, provided the structural basis of METTL16 interaction with the coenzyme and substrates, as well as indicated autoinhibitory mechanism of the enzyme activity regulation. Very recent structural and functional studies of vertebrate-conserved regions (VCRs) indicated their crucial role in the interaction with U6 snRNA. METTL16 remains an object of intense studies, as it has been associated with numerous RNA classes, including mRNA, non-coding RNA, long non-coding RNA (lncRNA), and rRNA. Moreover, the interaction between METTL16 and oncogenic lncRNA MALAT1 indicates the existence of METTL16 features specifically recognizing RNA triple helices. Overall, the number of known human m6A methyltransferases has grown from one to five during the last five years. METTL16, CAPAM, and two rRNA methyltransferases, METTL5/TRMT112 and ZCCHC4, have joined the well-known METTL3/METTL14. This work summarizes current knowledge about METTL16 in the landscape of human m6A RNA methyltransferases.

Secondary structure of U6 small nuclear RNA: implications for spliceosome assembly

2010 ◽  
Vol 38 (4) ◽  
pp. 1099-1104 ◽  
Author(s):  
Elizabeth A. Dunn ◽  
Stephen D. Rader
Keyword(s):  
Secondary Structure ◽  
Small Nuclear Rna ◽  
Stem Loop ◽  
New Model ◽  
Rna Molecules ◽  
U6 Snrna ◽  
Small Nuclear Ribonucleoprotein ◽  
Nuclear Rna ◽  
High Level ◽  
And Function

U6 snRNA (small nuclear RNA), one of five RNA molecules that are required for the essential process of pre-mRNA splicing, is notable for its high level of sequence conservation and the important role it is thought to play in the splicing reaction. Nevertheless, the secondary structure of U6 in the free snRNP (small nuclear ribonucleoprotein) form has remained elusive, with predictions changing substantially over the years. In the present review we discuss the evidence for existing models and critically evaluate a fundamental assumption of these models, namely whether the important 3′ ISL (3′ internal stem–loop) is present in the free U6 particle, as well as in the active splicing complex. We compare existing models of free U6 with a newly proposed model lacking the 3′ ISL and evaluate the implications of the new model for the structure and function of U6's base-pairing partner U4 snRNA. Intriguingly, the new model predicts a role for U4 that was unanticipated previously, namely as an activator of U6 for assembly into the splicing machinery.

scholarly journals Invariant U2 RNA sequences bordering the branchpoint recognition region are essential for interaction with yeast SF3a and SF3b subunits.

1996 ◽  
Vol 16 (3) ◽  
pp. 818-828 ◽  
Author(s):  
D Yan ◽  
M Ares
Keyword(s):  
Yeast Cells ◽  
Small Nuclear Rna ◽  
Recognition Sequence ◽  
Rna Sequences ◽  
Synthetic Lethal ◽  
U2 Snrna ◽  
U6 Snrna ◽  
Synthetic Lethal Interactions ◽  
Protein Components ◽  
And Function

U2 small nuclear RNA (snRNA) contains a sequence (GUAGUA) that pairs with the intron branchpoint during splicing. This sequence is contained within a longer invariant sequence of unknown secondary structure and function that extends between U2 and I and stem IIa. A part of this region has been proposed to pair with U6 in a structure called helix III. We made mutations to test the function of these nucleotides in yeast U2 snRNA. Most single base changes cause no obvious growth defects; however, several single and double mutations are lethal or conditional lethal and cause a block before the first step of splicing. We used U6 compensatory mutations to assess the contribution of helix III and found that if it forms, helix III is dispensable for splicing in Saccharomyces cerevisiae. On the other hand, mutations in known protein components of the splicing apparatus suppress or enhance the phenotypes of mutations within the invariant sequence that connect the branchpoint recognition sequence to stem IIa. Lethal mutations in the region are suppressed by Cus1-54p, a mutant yeast splicing factor homologous to a mammalian SF3b subunit. Synthetic lethal interactions show that this region collaborates with the DEAD-box protein Prp5p and the yeast SF3a subunits Prp9p, Prp11p, and Prp21p. Together, the data show that the highly conserved RNA element downstream of the branchpoint recognition sequence of U2 snRNA in yeast cells functions primarily with the proteins that make up SF3 rather than with U6 snRNA.

Biology, Management, and Conservation of Lampreys in North America

2009 ◽  
Keyword(s):  
Hormone Receptors ◽  
Current Knowledge ◽  
Reproductive Hormones ◽  
Reproductive Endocrinology ◽  
Functional Roles ◽  
Cdna Sequences ◽  
Functional Studies ◽  
Glycoprotein Hormone Receptors ◽  
Ancient Lineage ◽  
And Function

<em>Abstract</em>.—This chapter summarizes reproduction and the latest findings on reproductive endocrinology in one of the only two living representatives of the most ancient lineage of vertebrates, agnathans. Modern vertebrates are classified into two major groups, the gnathostomes (jawed vertebrates) and the agnathans (jawless vertebrates). The agnathans are classified into two groups, myxinoids (hagfishes) and petromyzonids (lampreys), while the gnathostomes constitute all the other living vertebrates, including the bony and cartilaginous fishes and the tetrapods. During the past two decades, there have been rapid advances in our knowledge of the structure and function of reproductive hormones in lamprey. Lampreys are the earliest evolved vertebrates for which there are demonstrated functional roles for two (possibly three) gonadotropin-releasing hormones (GnRHs) that act via the hypothalamic-pituitary-gonadal axis controlling reproductive processes. From our structural and functional studies, we have determined the primary amino acid and cDNA sequences of two forms of GnRH, lamprey GnRH-I and -III, one GnRH receptor, and one gonadotropin-beta (GTH-b) hormone. Since 2006, with the availability of the lamprey genome, we have identified an additional GnRH isoform (lamprey GnRH-II) and two glycoprotein hormone receptors (one gonadotropic-like and one thyrotropic-like). The high conservation of these hormones and their receptors throughout vertebrate species makes the lamprey model highly appropriate for examining the neuroendocrine system. Here, we present a summary on our current knowledge of reproductive endocrinology in these basal vertebrates.

scholarly journals Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1

2019 ◽  
Vol 48 (3) ◽  
pp. 1423-1434
Author(s):  
Yuichiro Nomura ◽  
Eric J Montemayor ◽  
Johanna M Virta ◽  
Samuel M Hayes ◽  
Samuel E Butcher
Keyword(s):  
Homo Sapiens ◽  
Structural Basis ◽  
Evolutionary Divergence ◽  
Sequence Identity ◽  
U6 Snrna ◽  
Mechanistic Insight ◽  
Substrate Analog ◽  
Cyclic Phosphate ◽  
And Function ◽  
Insight Into

Abstract U6 snRNA undergoes post-transcriptional 3′ end modification prior to incorporation into the active site of spliceosomes. The responsible exoribonuclease is Usb1, which removes nucleotides from the 3′ end of U6 and, in humans, leaves a 2′,3′ cyclic phosphate that is recognized by the Lsm2–8 complex. Saccharomycescerevisiae Usb1 has additional 2′,3′ cyclic phosphodiesterase (CPDase) activity, which converts the cyclic phosphate into a 3′ phosphate group. Here we investigate the molecular basis for the evolution of Usb1 CPDase activity. We examine the structure and function of Usb1 from Kluyveromyces marxianus, which shares 25 and 19% sequence identity to the S. cerevisiae and Homo sapiens orthologs of Usb1, respectively. We show that K. marxianus Usb1 enzyme has CPDase activity and determined its structure, free and bound to the substrate analog uridine 5′-monophosphate. We find that the origin of CPDase activity is related to a loop structure that is conserved in yeast and forms a distinct penultimate (n – 1) nucleotide binding site. These data provide structural and mechanistic insight into the evolutionary divergence of Usb1 catalysis.

scholarly journals Beyond classic editing: innovative CRISPR approaches for functional studies of long non-coding RNA

2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Dahlia A Awwad
Keyword(s):  
Genetic Manipulation ◽  
Functional Characterization ◽  
The Novel ◽  
Functional Studies ◽  
Non Coding Rna ◽  
Rna Targeting ◽  
Potential Applications ◽  
And Function ◽  
Long Non Coding Rna

Abstract Long non-coding RNAs (lncRNAs) makeup a considerable part of the non-coding human genome and had been well-established as crucial players in an array of biological processes. In spite of their abundance and versatile roles, their functional characteristics remain largely undiscovered mainly due to the lack of suitable genetic manipulation tools. The emerging CRISPR/Cas9 technology has been widely adapted in several studies that aim to screen and identify novel lncRNAs as well as interrogate the functional properties of specific lncRNAs. However, the complexity of lncRNAs genes and the regulatory mechanisms that govern their transcription, as well as their unique functionality pose several limitations the utilization of classic CRISPR methods in lncRNAs functional studies. Here, we overview the unique characteristics of lncRNAs transcription and function and the suitability of the CRISPR toolbox for applications in functional characterization of lncRNAs. We discuss some of the novel variations to the classic CRISPR/Cas9 system that have been tailored and applied previously to study several aspects of lncRNAs functionality. Finally, we share perspectives on the potential applications of various CRISPR systems, including RNA-targeting, in the direct editing and manipulation of lncRNAs.

scholarly journals Mutational analysis of Saccharomyces cerevisiae U4 small nuclear RNA identifies functionally important domains.

1995 ◽  
Vol 15 (3) ◽  
pp. 1274-1285 ◽  
Author(s):  
J Hu ◽  
D Xu ◽  
K Schappert ◽  
Y Xu ◽  
J D Friesen
Keyword(s):  
Mutational Analysis ◽  
Current Knowledge ◽  
Rnase H ◽  
Terminal Region ◽  
Small Nuclear Rna ◽  
Stem Loop ◽  
Mutational Change ◽  
U6 Snrna ◽  
Nuclear Rna

U4 small nuclear RNA (snRNA) is essential for pre-mRNA splicing, although its role is not yet clear. On the basis of a model structure (C. Guthrie and B. Patterson, Annu. Rev. Genet. 22:387-419, 1988), the molecule can be thought of as having six domains: stem II, 5' stem-loop, stem I, central region, 3' stem-loop, and 3'-terminal region. We have carried out extensive mutagenesis of the yeast U4 snRNA gene (SNR14) and have obtained information on the effect of mutations at 105 of its 160 nucleotides. Fifteen critical residues in the U4 snRNA have been identified in four domains: stem II, the 5' stem-loop, stem I, and the 3'-terminal region. These domains have been shown previously to be insensitive to oligonucleotide-directed RNase H cleavage (Y. Xu, S. Petersen-Bjørn, and J. D. Friesen, Mol. Cell. Biol. 10:1217-1225, 1990), suggesting that they are involved in intra- or intermolecular interactions. Stem II, a region that base pairs with U6 snRNA, is the most sensitive to mutation of all U4 snRNA domains. In contrast, stem I is surprisingly insensitive to mutational change, which brings into question its role in base pairing with U6 snRNA. All mutations in the putative Sm site of U4 snRNA yield a lethal or conditional-lethal phenotype, indicating that this region is important functionally. Only two nucleotides in the 5' stem-loop are sensitive to mutation; most of this domain can tolerate point mutations or small deletions. The 3' stem-loop, while essential, is very tolerant of change. A large portion of the central domain can be removed or expanded with only minor effects on phenotype, suggesting that it has little function of its own. Analysis of conditional mutations in stem II and stem I indicates that although these single-base changes do not have a dramatic effect on U4 snRNA stability, they are defective in RNA splicing in vivo and in vitro, as well as in spliceosome assembly. These results are discussed in the context of current knowledge of the interactions involving U4 snRNA.

scholarly journals Dynamic mRNA modifications: An emerging layer of gene regulation

2015 ◽  
Vol 37 (2) ◽  
pp. 14-18 ◽  
Author(s):  
Adrian Whitehouse
Keyword(s):  
Gene Regulation ◽  
Messenger Rna ◽  
Fine Tuning ◽  
Minor Role ◽  
Small Nuclear Rna ◽  
Non Coding Rna ◽  
A Minor ◽  
And Function ◽  
Long Non Coding Rna

More than 100 different types of chemical modifications are found in cellular RNAs, including ribosomal RNA (rRNA), transfer RNA (tRNA), messenger RNA (mRNA), long non-coding RNA (lncRNA) and small nuclear RNA (snRNA). Internal modifications of mRNA were first observed in the 1970s, but, until recently, the role of these mRNA modifications has been a largely neglected field. A long-standing view was that mRNA modifications were static and unalterable, having a minor role in fine-tuning the structure and function of mRNAs. However, recent exciting discoveries now suggest that certain mRNA modifications are dynamic and, in some cases, reversible. Therefore they may have critical regulatory roles in gene expression, analogous to those which dynamically regulate DNA and protein modifications. As such, understanding the scope and mechanisms of these dynamic mRNA modifications represents an emerging layer of gene regulation at the RNA level, termed epitranscriptomics or RNA epigenetics.

scholarly journals Epigenetic modifications in neuropathic pain

2021 ◽  
Vol 17 ◽  
pp. 174480692110567
Author(s):  
Danzhi Luo ◽  
Xiaohong Li ◽  
Simin Tang ◽  
Fuhu Song ◽  
Wenjun Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Neuropathic Pain ◽  
Current Knowledge ◽  
Epigenetic Modifications ◽  
Rna Modification ◽  
Common Symptom ◽  
Non Coding Rna ◽  
And Function ◽  
Somatosensory Nervous System

Neuropathic pain (NP) is a common symptom in many diseases of the somatosensory nervous system, which severely affects the patient’s quality of life. Epigenetics are heritable alterations in gene expression that do not cause permanent changes in the DNA sequence. Epigenetic modifications can affect gene expression and function and can also mediate crosstalk between genes and the environment. Increasing evidence shows that epigenetic modifications, including DNA methylation, histone modification, non-coding RNA, and RNA modification, are involved in the development and maintenance of NP. In this review, we focus on the current knowledge of epigenetic modifications in the development and maintenance of NP. Then, we illustrate different facets of epigenetic modifications that regulate gene expression and their crosstalk. Finally, we discuss the burgeoning evidence supporting the potential of emerging epigenetic therapies, which has been valuable in understanding mechanisms and offers novel and potent targets for NP therapy.

Structure and functional mechanism of porins

1996 ◽  
Vol 76 (4) ◽  
pp. 1073-1088 ◽  
Author(s):  
B. K. Jap ◽  
P. J. Walian
Keyword(s):  
Molecular Mechanisms ◽  
Transmembrane Protein ◽  
Molecular Structures ◽  
Functional Studies ◽  
Wide Range ◽  
Voltage Dependent ◽  
High Resolution Structure ◽  
And Function ◽  
Protein Channels ◽  
Bacterial Porins

Cellular organisms such as gram-negative bacteria are enclosed by a dual lipid bilayer system. The outer membranes of the dual bilayer envelopes predominantly contain large numbers of water-filled transmembrane protein channels known as porins. The recent availability of the molecular structures of several bacterial porins has provided the opportunity for comparing the results of a wide range of functional studies with the atomic level structural details of these membrane channels. Taken together, the structure and function data present the most comprehensive set of boundary conditions available for the evaluation of theory and models predicting the characteristics of solute transport through membrane protein channels. In this paper, we review the high-resolution structure data from the bacterial porins, as well as recent theoretical studies, in the context of biophysical and biochemical observations and discuss the molecular mechanisms responsible for the transport of solutes through porin channels. Particular emphasis has been placed on the features and roles of common structural elements, channel sterics and electrostatics, and voltage-dependent gating. A model for water-coordinated transport, providing a qualitative view of the porin transport mechanism, is also described.

scholarly journals Structure and function of stator units of the bacterial flagellar motor

2020 ◽  
Author(s):  
Mònica Santiveri ◽  
Aritz Roa-Eguiara ◽  
Caroline Kühne ◽  
Navish Wadhwa ◽  
Howard C. Berg ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Mechanistic Model ◽  
Structural Data ◽  
Structural Basis ◽  
Flagellar Motor ◽  
Functional Studies ◽  
Torque Generation ◽  
Bacterial Flagellar Motor ◽  
And Function ◽  
Key Residues

AbstractMany bacteria use the flagellum for locomotion and chemotaxis. Its bi-directional rotation is driven by the membrane-embedded motor, which uses energy from the transmembrane ion gradient to generate torque at the interface between stator units and rotor. The structural organization of the stator unit (MotAB), its conformational changes upon ion transport and how these changes power rotation of the flagellum, remain unknown. Here we present ~3 Å-resolution cryo-electron microscopy reconstructions of the stator unit in different functional states. We show that the stator unit consists of a dimer of MotB surrounded by a pentamer of MotA. Combining structural data with mutagenesis and functional studies, we identify key residues involved in torque generation and present a mechanistic model for motor function and switching of rotational direction.One Sentence SummaryStructural basis of torque generation in the bidirectional bacterial flagellar motor

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