ARTS, the unusual septin: structural and functional aspects

2011 ◽  
Vol 392 (8-9) ◽  
pp. 783-790 ◽  
Author(s):  
Yael Mandel-Gutfreund ◽  
Idit Kosti ◽  
Sarit Larisch
Keyword(s):  
Biological Activity ◽  
Intron Retention ◽  
Membrane Dynamics ◽  
Protein Isoforms ◽  
Major Protein ◽  
Cytoskeletal Reorganization ◽  
Differential Splicing ◽  
Functional Aspects ◽  
Structural And Functional Properties ◽  
Diverse Biological Activity

AbstractThe humanSeptin 4gene (Sept4) encodes two major protein isoforms; Sept4_i1 (H5/PNUTL2) and Sept4_i2/ARTS. Septins have been traditionally studied for their role in cytokinesis and their filament-forming abilities, but subsequently have been implicated in diverse functions, including membrane dynamics, cytoskeletal reorganization, vesicle trafficking, and tumorigenesis. ARTS is localized at mitochondria and promotes programmed cell death (apoptosis). These features distinguish ARTS from any other known human septin family member. This review compares the structural and functional properties of ARTS with other septins. In addition, it describes how a combination of two distinct promoters, differential splicing, and intron retention leads to the generation of two different Sept4 variants with diverse biological activity.

scholarly journals Alternative splicing takes charge of interleukin-22 and interferon lambda 4 signaling

2018 ◽  
Author(s):  
Chrissie Lim
Keyword(s):  
Alternative Splicing ◽  
Intron Retention ◽  
Protein Isoforms ◽  
Functional Domain ◽  
Type I ◽  
Protein Coding ◽  
Interleukin 22 ◽  
Interferon Lambda ◽  
Type Iii Ifn ◽  
Overexpression System

Immune responses require the tight control of dose, location, strength and duration through genetic, epigenetic or biochemical regulation. Of these, the generation of alternatively-spliced constructs increases transcriptional and proteomic diversity in post-transcriptional modification, localization and functional domain integrity. Specifically, this thesis explores how splice variation engenders profound differences in the biological functions of interleukin-22 (IL-22) binding protein (IL-22BP) and interferon lambda 4 (IFNλ4), which are both central components of distinct cytokine pathways in mucosal immunity and inflammation. IL-22BP is a soluble receptor for IL-22 that is expressed as three isoforms in humans, though the physiological relevance of the three human isoforms has remained a mystery due to the absence of this variation in mice. We present novel findings that IL-22BPi1 is inactive due to intracellular retention by its unique exon, while IL-22BPi3 is also an antagonist but with differential activity from IL-22BPi2. Importantly, while IL-22BPi3 has widespread expression in steady-state homeostatic conditions, IL-22BPi2 is the only isoform induced by inflammatory TLR2/retinoic acid stimulation, highlighting important spatiotemporal control of the two isoforms that exploit their differential activities. IFNλ4 presents a different mystery in which the protein-coding variant is genetically associated with poorer clearance, but the mechanism for this association remains unclear. We investigated several non-canonical functions proposed by the field, including intrinsic differences in activity of the three protein isoforms and their interference with antiviral activites of other type I or III interferons. Establishing an overexpression system and purifying recombinant proteins, we found that only the full-length isoform is active and exhibits similar effects to canonical type III IFN IFNλ3, without any blockade of other IFN signaling. Simultaneously, functional IFNλ4 expression is suppressed in hepatocytes and dendritic cells through preferential splicing to increase intron retention and expression of inactive isoforms. Therefore, alternative splicing in IFNλ4 is an important mechanism to control IFNλ4 bioactivity. The divergent manners in which alternative splice forms impact the activity of both IL-22BP and IFNλ4 highlight the important contributions of this process to cytokine biology and bigger implications that escape detection by genomic analyses.

scholarly journals Widespread separation of the polypyrimidine tract from 3’ AG by G tracts in association with alternative exons in metazoa and plants

2018 ◽  
Author(s):  
Hai Nguyen ◽  
Jiuyong Xie
Keyword(s):  
Alternative Splicing ◽  
Branch Point ◽  
Intron Retention ◽  
Regulatory Elements ◽  
Protein Isoforms ◽  
Model Organisms ◽  
Branch Points ◽  
Splice Sites ◽  
Polypyrimidine Tract ◽  
Whole Genome Analysis

SummaryAt the end of introns, the polypyrimidine tract (Py) is often close to the 3’ AG in a consensus (Y)20NCAGgt in humans. Interestingly, we have found that they could also be separated by purine-rich elements including G tracts in thousands of human genes. These regulatory elements between the Py and 3’AG (REPA) mainly regulate alternative 3’ splice sites (3’SS) and intron retention. Here we show their widespread distribution and special properties across kingdoms. The purine-rich 3’SS are found in up to about 60% of the introns among more than 1000 species/lineages by whole genome analysis, and up to 18% of these introns contain the REPA G tracts in about 2.4 millions of 3’SS in total. In particular, they are significantly enriched over their 3’SS and genome backgrounds in metazoa and plants, and highly associated with alternative splicing of genes in diverse functional clusters. They are also highly enriched (3-6 folds) in the canonical as well as aberrantly used 3’ splice sites in cancer patients carrying mutations of the branch point factor SF3B1 or the 3’AG binding factor U2AF35. Moreover, the REPA G tract-harbouring 3’SS have significantly reduced occurrences of branch point (BP) motifs between the −24 and −4 positions, in particular absent from the −7 - −5 positions in several model organisms examined. The more distant branch points are associated with increased occurrences of alternative splicing in human and zebrafish. The branch points, REPA G tracts and associated 3’SS motifs appear to have emerged differentially in a phylum- or species-specific way during evolution. Thus, there is widespread separation of the Py and 3’AG by REPA G tracts, likely evolved among different species or branches of life. This special 3’SS arrangement contributes to the generation of diverse transcript or protein isoforms in biological functions or diseases through alternative or aberrant splicing.

scholarly journals The Emergence of the Metabolic Signaling of the Nucleoredoxin-like Genes during Evolution

2022 ◽  
Author(s):  
Najate Ait-Ali ◽  
Frederic Blond ◽  
Emmanuelle Clerin ◽  
Ala Morshedian ◽  
Quenol Cesar ◽  
...  
Keyword(s):  
Biological Activity ◽  
Alternative Splicing ◽  
Intron Retention ◽  
Hydra Vulgaris ◽  
Metabolic Signaling ◽  
Retinal Degenerations ◽  
Animal Phyla ◽  
Alternatively Spliced ◽  
Early Vertebrates ◽  
Rod And Cone Photoreceptors

The nucleoredoxin-like genes NXNL1 and NXNL2 were identified through the biological activity of rod-derived cone viability factors (RdCVF and RdCVF2), the alternatively spliced variants produced by intron retention, that mediate signaling between rod and cone photoreceptors by stimulating glucose uptake. These therapeutic genes for inherited retinal degenerations also produce by splicing thioredoxin-like proteins that reduce oxidized cysteines in photoreceptor proteins. The first NXNL genes date from the first animal phyla. Intron retention produces an active RdCVF protein in the tentacles of Hydra vulgaris, a species without eyes. A Scallop RdCVF protein is produced by ciliated photoreceptors of the retina and binds its receptor, BSG1. In the lamprey, a descendent of early vertebrates, RdCVF metabolic signaling between rod and cones is fully established. In the mouse, the production of BSG1 by photoreceptors is regulated by cell-specific splicing inhibition. RdCVF signaling predates photoreceptors and evolved through two alternative splicing events.

scholarly journals Assignment of a single disulphide bridge in human α2-antiplasmin: implications for the structural and functional properties

1997 ◽  
Vol 323 (3) ◽  
pp. 847-852 ◽  
Author(s):  
Søren CHRISTENSEN ◽  
Zuzana VALNICKOVA ◽  
Ida B. THØGERSEN ◽  
Eva H. N. OLSEN ◽  
Jan J. ENGHILD
Keyword(s):  
Functional Analysis ◽  
Acetic Acid ◽  
Blood Coagulation ◽  
Proteinase Inhibitors ◽  
Serine Proteinase ◽  
Thiol Groups ◽  
Disulphide Bridge ◽  
Disulphide Bonds ◽  
Functional Aspects ◽  
Structural And Functional Properties

Human α2-antiplasmin (α2AP) is a serpin involved in the regulation of blood coagulation. Most serpins, unlike smaller serine proteinase inhibitors, do not contain disulphide bridges. α2AP is an exception from this generalization and has previously been shown to contain four Cys residues organized into two disulphide bridges [Lijnen, Holmes, van Hoef, Wiman, Rodriguez and Collen (1987) Eur. J. Biochem. 166, 565–574]. However, we found that α2AP incorporates iodo[14C]acetic acid, suggesting that the protein contains reactive thiol groups. This observation prompted a re-examination of the state of the thiol groups, which revealed (i) a disulphide bridge between Cys43 and Cys116, (ii) that Cys76 is bound to a cysteinyl-glycine dipeptide, and (iii) and Cys125 exists as either a free thiol or in a mixed disulphide with another Cys residue. The disulphide identified between Cys43 and Cys116 appears to be conserved in orthologous proteins since the homologous Cys residues form disulphide bonds in bovine and possibly mouse α2AP. The conservation of this disulphide bridge suggests that it is important for functional aspects of α2AP. However, the structural and functional analysis described in this study does not support this conclusion.

scholarly journals Attenuated rapid onset vasodilation with greater force production in skeletal muscle of caveolin-2−/− mice

2016 ◽  
Vol 311 (2) ◽  
pp. H415-H425 ◽  
Author(s):  
Charmain A. Fernando ◽  
Yajun Liu ◽  
Grzegorz Sowa ◽  
Steven S. Segal
Keyword(s):  
Skeletal Muscle ◽  
Contractile Function ◽  
Force Production ◽  
Gluteus Maximus ◽  
Rapid Onset ◽  
Major Protein ◽  
Contraction Duration ◽  
Structural And Functional Properties ◽  
Gluteus Maximus Muscle

Caveolin-2 (Cav2) is a major protein component of caveolae in membranes of vascular smooth muscle and endothelium, yet its absence alters the ultrastructure of skeletal muscle fibers. To gain insight into Cav2 function in skeletal muscle, we tested the hypothesis that genetic deletion of Cav2 would alter microvascular reactivity and depress contractile function of skeletal muscle in vivo. In the left gluteus maximus muscle (GM) of anesthetized Cav2−/− and wild-type (WT) male mice (age, 6 mo), microvascular responses to physiological agonists and to GM contractions were studied at 34°C. For feed arteries (FA), first- (1A), second- (2A) and third-order (3A) arterioles, respective mean diameters at rest (45, 35, 25, 12 μm) and during maximal dilation (65, 55, 45, 30 μm) were similar between groups. Cumulative dilations to ACh (10−9 to 10−5 M) and constrictions to norepinephrine (10−9 to 10−5 M) were also similar between groups, as were steady-state dilations during rhythmic twitch contractions (2 and 4 Hz; 30 s). For single tetanic contractions (100 Hz; 100, 250, and 500 ms), rapid onset vasodilation (ROV) increased with contraction duration throughout networks in GM of both groups but was reduced by nearly half in Cav2−/− mice compared with WT mice ( P < 0.05). Nevertheless, maximal force during tetanic contraction was ∼40% greater in GM of Cav2−/− vs. WT mice (152 ± 14 vs. 110 ± 3 mN per square millimeter, respectively; P < 0.05). Thus, while structural and functional properties of resistance networks are well maintained in the GM of Cav2−/− mice, diminished ROV with greater force production reveals novel physiological roles for Cav2 in skeletal muscle.

scholarly journals Genetics of alternative splicing evolution during sunflower domestication

2018 ◽  
Vol 115 (26) ◽  
pp. 6768-6773 ◽  
Author(s):  
Chris C. R. Smith ◽  
Silas Tittes ◽  
J. Paul Mendieta ◽  
Erin Collier-zans ◽  
Heather C. Rowe ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Intron Retention ◽  
Population Divergence ◽  
Evolutionary Transition ◽  
Differential Splicing ◽  
Evolutionary Transitions ◽  
Protein Coding ◽  
Standing Variation ◽  
Splice Forms ◽  
Splicing Patterns

Alternative splicing enables organisms to produce the diversity of proteins necessary for multicellular life by using relatively few protein-coding genes. Although differences in splicing have been identified among divergent taxa, the shorter-term evolution of splicing is understudied. The origins of novel splice forms, and the contributions of alternative splicing to major evolutionary transitions, are largely unknown. This study used transcriptomes of wild and domesticated sunflowers to examine splice differentiation and regulation during domestication. We identified substantial splicing divergence between wild and domesticated sunflowers, mainly in the form of intron retention. Transcripts with divergent splicing were enriched for seed-development functions, suggesting that artificial selection impacted splicing patterns. Mapping of quantitative trait loci (QTLs) associated with 144 differential splicing cases revealed primarilytrans-acting variation affecting splicing patterns. A large proportion of identified QTLs contain known spliceosome proteins and are associated with splicing variation in multiple genes. Examining a broader set of wild and domesticated sunflower genotypes revealed that most differential splicing patterns in domesticated sunflowers likely arose from standing variation in wildHelianthus annuusand gained frequency during the domestication process. However, several domesticate-associated splicing patterns appear to be introgressed from otherHelianthusspecies. These results suggest that sunflower domestication involved selection on pleiotropic regulatory alleles. More generally, our findings indicate that substantial differences in isoform abundances arose rapidly during a recent evolutionary transition and appear to contribute to adaptation and population divergence.

A Large Deletion Within the Protein 4.1 Gene Associated With a Stable Truncated mRNA and an Unaltered Tissue-Specific Alternative Splicing

Blood ◽  
1998 ◽  
Vol 91 (11) ◽  
pp. 4361-4367 ◽  
Author(s):  
N. Dalla Venezia ◽  
P. Maillet ◽  
L. Morlé ◽  
L. Roda ◽  
J. Delaunay ◽  
...  
Keyword(s):  
Blood Cell ◽  
Red Blood Cell ◽  
Large Deletion ◽  
Major Protein ◽  
Differential Splicing ◽  
Tissue Specific ◽  
Protein 4.1 ◽  
Genes Encoding ◽  
Specific Alternative ◽  
Partial Deficiency

Abstract Protein 4.1 is a major protein of the red blood cell skeleton. It binds to the membrane through its 30-kD N-terminal domain and to the spectrin-actin lattice through its 10-kD domain. We describe here the molecular basis of a heterozygous hereditary elliptocytosis (HE) associated with protein 4.1 partial deficiency. The responsible allele displayed a greater than 70-kb genomic deletion, beginning within intron 1 and ending within a 1.3-kb region upstream from exon 13. This deletion encompassed both erythroid and nonerythroid translation initiation sites. It accounts for the largest deletion known in genes encoding proteins of the red blood cell membrane. The corresponding mRNA was shortened by 1727 bases, due to the absence of exons 2 to 12. Nevertheless, this mRNA was stable. It showed a similar pattern in lymphoblastoid cells as in reticulocytes. Differential splicing of exons within the undeleted region remained regulated in a tissue-specific manner. Exons 14, 15, and 17a were absent from both reticulocyte and lymphocyte mRNAs, whereas exon 16 was present in reticulocytes but absent from lymphocytes. Thus, differential splicing on a local scale was not dependent on the overall structure of protein 4.1 mRNA in this particular instance.

scholarly journals Crystal Structure of the Apo-Form of NADPH-Dependent Thioredoxin Reductase from a Methane-Producing Archaeon

Antioxidants ◽  
2018 ◽  
Vol 7 (11) ◽  
pp. 166 ◽  
Author(s):  
Rubén Buey ◽  
Ruth Schmitz ◽  
Bob Buchanan ◽  
Monica Balsera
Keyword(s):  
Crystal Structure ◽  
Redox Regulation ◽  
Nicotinamide Adenine Dinucleotide Phosphate ◽  
Thioredoxin Reductase ◽  
Binding Pocket ◽  
Major Protein ◽  
Exchange Reactions ◽  
Functional Sites ◽  
Structural And Functional Properties ◽  
Thioredoxin System

The redox regulation of proteins via reversible dithiol/disulfide exchange reactions involves the thioredoxin system, which is composed of a reductant, a thioredoxin reductase (TR), and thioredoxin (Trx). In the pyridine nucleotide-dependent Trx reduction pathway, reducing equivalents, typically from reduced nicotinamide adenine dinucleotide phosphate (NADPH), are transferred from NADPH-TR (NTR) to Trx and, in turn, to target proteins, thus resulting in the reversible modification of the structural and functional properties of the targets. NTR enzymes contain three functional sites: an NADPH binding pocket, a non-covalently bound flavin cofactor, and a redox-active disulfide in the form of CxxC. With the aim of increasing our knowledge of the thioredoxin system in archaea, we here report the high-resolution crystal structure of NTR from the methane-generating organism Methanosarcina mazei strain Gö1 (MmNTR) at 2.6 Å resolution. Based on the crystals presently described, MmNTR assumes an overall fold that is nearly identical to the archetypal fold of authentic NTRs; however, surprisingly, we observed no electron density for flavin adenine dinucleotide (FAD) despite the well-defined and conserved FAD-binding cavity in the folded module. Remarkably, the dimers of the apo-protein within the crystal were different from those observed by small angle X-ray scattering (SAXS) for the holo-protein, suggesting that the binding of the flavin cofactor does not require major protein structural rearrangements. Rather, binding results in the stabilization of essential parts of the structure, such as those involved in dimer stabilization. Altogether, this structure represents the example of an apo-form of an NTR that yields important insight into the effects of the cofactor on protein folding.

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