CAF Proteins Help SOT1 Regulate the Stability of Chloroplast ndhA Transcripts

Protein-mediated RNA stabilization plays profound roles in chloroplast gene expression. Genetic studies have indicated that chloroplast ndhA transcripts, encoding a key subunit of the NADH dehydrogenase-like complex that mediates photosystem I cyclic electron transport and facilitates chlororespiration, are stabilized by PPR53 and its orthologs, but the underlying mechanisms are unclear. Here, we report that CHLOROPLAST RNA SPLICING 2 (CRS2)-ASSOCIATED FACTOR (CAF) proteins activate SUPPRESSOR OF THYLAKOID FORMATION 1 (SOT1), an ortholog of PPR53 in Arabidopsis thaliana, enhancing their affinity for the 5′ ends of ndhA transcripts to stabilize these molecules while inhibiting the RNA endonuclease activity of the SOT1 C-terminal SMR domain. In addition, we established that SOT1 improves the splicing efficiency of ndhA by facilitating the association of CAF2 with the ndhA intron, which may be due to the SOT1-mediated stability of the ndhA transcripts. Our findings shed light on the importance of PPR protein interaction partners in moderating RNA metabolism.

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Deep Profiling of the Aggregated Proteome in Alzheimer’s Disease: From Pathology to Disease Mechanisms

Proteomes ◽

10.3390/proteomes6040046 ◽

2018 ◽

Vol 6 (4) ◽

pp. 46 ◽

Cited By ~ 8

Author(s):

Brianna Lutz ◽

Junmin Peng

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Rna Splicing ◽

Protein Aggregates ◽

Small Nuclear Ribonucleoprotein ◽

Composition And Structure ◽

Underlying Mechanisms ◽

Nuclear Ribonucleoprotein ◽

Laser Capture ◽

Shed Light

Hallmarks of Alzheimer’s disease (AD), a progressive neurodegenerative disease causing dementia, include protein aggregates such as amyloid beta plaques and tau neurofibrillary tangles in a patient’s brain. Understanding the complete composition and structure of protein aggregates in AD can shed light on the as-yet unidentified underlying mechanisms of AD development and progression. Biochemical isolation of aggregates coupled with mass spectrometry (MS) provides a comprehensive proteomic analysis of aggregates in AD. Dissection of these AD-specific aggregate components, such as U1 small nuclear ribonucleoprotein complex (U1 snRNP), provides novel insights into the deregulation of RNA splicing in the disease. In this review, we summarize the methodologies of laser capture microdissection (LCM) and differential extraction to analyze the aggregated proteomes in AD samples, and discuss the derived novel insights that may contribute to AD pathogenesis.

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A PPR Protein ACM1 Is Involved in Chloroplast Gene Expression and Early Plastid Development in Arabidopsis

International Journal of Molecular Sciences ◽

10.3390/ijms22052512 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2512

Author(s):

Xinwei Wang ◽

Yaqi An ◽

Ye Li ◽

Jianwei Xiao

Keyword(s):

Fluorescent Protein ◽

Chloroplast Development ◽

Nuclear Gene ◽

Pentatricopeptide Repeat ◽

Plastid Development ◽

Chloroplast Gene Expression ◽

Knock Out ◽

Rnai Line ◽

Ppr Protein ◽

P Type

Chloroplasts cannot develop normally without the coordinated action of various proteins and signaling connections between the nucleus and the chloroplast genome. Many questions regarding these processes remain unanswered. Here, we report a novel P-type pentatricopeptide repeat (PPR) factor, named Albino Cotyledon Mutant1 (ACM1), which is encoded by a nuclear gene and involved in chloroplast development. Knock-down of ACM1 transgenic plants displayed albino cotyledons but normal true leaves, while knock-out of the ACM1 gene in seedlings was lethal. Fluorescent protein analysis showed that ACM1 was specifically localized within chloroplasts. PEP-dependent plastid transcript levels and splicing efficiency of several group II introns were seriously affected in cotyledons in the RNAi line. Furthermore, denaturing gel electrophoresis and Western blot experiments showed that the accumulation of chloroplast ribosomes was probably damaged. Collectively, our results indicate ACM1 is indispensable in early chloroplast development in Arabidopsis cotyledons.

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Forward Rate Bias in Developed and Developing Countries: More Risky Not Less Rational

Econometrics ◽

10.3390/econometrics8040043 ◽

2020 ◽

Vol 8 (4) ◽

pp. 43

Author(s):

Michael D. Goldberg ◽

Olesia Kozlova ◽

Deniz Ozabaci

Keyword(s):

Developing Countries ◽

Forward Rate ◽

Currency Markets ◽

Developed Country ◽

Slope Coefficient ◽

Break Points ◽

Time Periods ◽

The Stability ◽

Widespread View ◽

Shed Light

This paper examines the stability of the Bilson–Fama regression for a panel of 55 developed and developing countries. We find multiple break points for nearly every country in our panel. Subperiod estimates of the slope coefficient show a negative bias during some time periods and a positive bias during other time periods in nearly every country. The subperiod biases display two key patterns that shed light on the literature’s linear regression findings. The results point toward the importance of risk in currency markets. We find that risk is greater for developed country markets. The evidence undercuts the widespread view that currency returns are predictable or that developed country markets are less rational.

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The splicing factor XAB2 interacts with ERCC1-XPF and XPG for R-loop processing

Nature Communications ◽

10.1038/s41467-021-23505-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Evi Goulielmaki ◽

Maria Tsekrekou ◽

Nikos Batsiotos ◽

Mariana Ascensão-Ferreira ◽

Eleftheria Ledaki ◽

...

Keyword(s):

Dna Damage ◽

Rna Splicing ◽

Excision Repair ◽

Intron Retention ◽

Dna Lesions ◽

Splicing Factor ◽

Loop Formation ◽

Rna Targets ◽

Underlying Mechanisms

AbstractRNA splicing, transcription and the DNA damage response are intriguingly linked in mammals but the underlying mechanisms remain poorly understood. Using an in vivo biotinylation tagging approach in mice, we show that the splicing factor XAB2 interacts with the core spliceosome and that it binds to spliceosomal U4 and U6 snRNAs and pre-mRNAs in developing livers. XAB2 depletion leads to aberrant intron retention, R-loop formation and DNA damage in cells. Studies in illudin S-treated cells and Csbm/m developing livers reveal that transcription-blocking DNA lesions trigger the release of XAB2 from all RNA targets tested. Immunoprecipitation studies reveal that XAB2 interacts with ERCC1-XPF and XPG endonucleases outside nucleotide excision repair and that the trimeric protein complex binds RNA:DNA hybrids under conditions that favor the formation of R-loops. Thus, XAB2 functionally links the spliceosomal response to DNA damage with R-loop processing with important ramifications for transcription-coupled DNA repair disorders.

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CDKN1C mutation in Wiedemann-Beckwith syndrome patients reduces RNA splicing efficiency and identifies a splicing enhancer

American Journal of Medical Genetics ◽

10.1002/ajmg.a.30020 ◽

2004 ◽

Vol 127A (3) ◽

pp. 268-276 ◽

Cited By ~ 8

Author(s):

Jocelyne M. Lew ◽

Yan Ling Fei ◽

Kirk Aleck ◽

Benjamin J. Blencowe ◽

Rosanna Weksberg ◽

...

Keyword(s):

Rna Splicing ◽

Splicing Efficiency ◽

Splicing Enhancer

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Nonlinear Blade Stability for a Scaled Autogyro Rotor at High Advance Ratios

Journal of the American Helicopter Society ◽

10.4050/jahs.65.012005 ◽

2020 ◽

Vol 65 (1) ◽

pp. 1-19

Author(s):

Djamel Rezgui ◽

Mark H. Lowenberg

Keyword(s):

High Speed ◽

Flow Speed ◽

Numerical Continuation ◽

Control Input ◽

Nonlinear Phenomenon ◽

Scaled Model ◽

Underlying Mechanisms ◽

Slowed Rotor ◽

The Stability ◽

Blade Pitch Angle

Despite current research advances in aircraft dynamics and increased interest in the slowed rotor concept for high-speed compound helicopters, the stability of autogyro rotors remains partially understood, particularly at lightly loaded conditions and high advance ratios. In autorotation, the periodic behavior of a rotor blade is a complex nonlinear phenomenon, further complicated by the fact that the rotor speed is not held constant. The aim of the analysis presented in this article is to investigate the underlying mechanisms that can lead to rotation-flap blade instability at high advance ratios for a teetering autorotating rotor. The stability analysis was conducted via wind tunnel tests of a scaled autogyro model combined with numerical continuation and bifurcation analysis. The investigation assessed the effect of varying the flow speed, blade pitch angle, and rotor shaft tilt relative to the flow on the rotor performance and blade stability. The results revealed that rotor instability in autorotation is associated with the existence of fold bifurcations, which bound the control-input and design parameter space within which the rotor can autorotate. This instability occurs at a lightly loaded condition and at advance ratios close to 1 for the scaled model. Finally, it was also revealed that the rotor inability to autorotate was driven by blade stall.

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Ab Initio Molecular Dynamics Investigations of the Speciation and Reactivity of Deep Eutectic Electrolytes in Aluminum Batteries

10.26434/chemrxiv.13720888.v2 ◽

2021 ◽

Author(s):

David Carrasco-Busturia ◽

Steen Lysgaard ◽

Piotr Jankowski ◽

Tejs Vegge ◽

Arghya Bhowmik ◽

...

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Deep Eutectic Solvents ◽

Ionic Species ◽

Electrochemical Activity ◽

Molecular Composition ◽

Ab Initio Molecular Dynamics ◽

The Stability ◽

Shed Light ◽

Battery Anode

Deep eutectic solvents (DES) have emerged as an alternative for conventional ionic liquids in aluminum batteries. Elucidating DES composition is fundamental to understand aluminum electrodeposition in the battery anode. Despite numerous experiemental efforts, the speciation of these DES remains elusive. This work shows how \textit{Ab initio} molecular dynamics (AIMD) simulations can shed light on the molecular composition of DES. For the particular example of AlCl$_{3}$:urea, one of the most popular DES, we carried out a systematic AIMD study, showing how an excess of AlCl$_{3}$ in the AlCl$_{3}$:urea mixture promotes the stability of ionic species vs neutral ones and also favors the reactivity in the system. These two facts explain the experimentally observed enhanced electrochemical activity in salt-rich DES. We also observe the transfer of simple $[$AlCl$_{x}$(urea)$_{y}]$ clusters between different species in the liquid, giving rise to free $[$AlCl$_{4}]^{-}$ units. The small size of these $[$AlCl$_{4}]^{-}$ units favors the transport of ionic species towards the anode, facilitating the electrodeposition of aluminum.

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The collapse of genetic incompatibilities in a hybridizing population

10.1101/2021.01.08.425971 ◽

2021 ◽

Author(s):

Tianzhu Xiong ◽

James L MALLET

Keyword(s):

Gene Regulation ◽

Reproductive Isolation ◽

Genetic Drift ◽

Recombination Rate ◽

Time Scale ◽

Genetic Incompatibility ◽

Genetic Process ◽

Underlying Mechanisms ◽

The Stability

Genetic incompatibility has long been considered to be a hallmark of speciation due to its role in reproductive isolation. Previous analyses of the stability of epistatic incompatibility show that it is subject to collapse upon hybridization. In the present work, we derive explicitly the distribution of the lifespan of two-locus incompatibilities, and show that genetic drift, along with recombination, is critical in determining the time scale of collapse. The first class of incompatibilities, where derived alleles separated in parental populations act antagonistically in hybrids, survive longer in smaller populations when incompatible alleles are (co)dominant and tightly linked, but collapse more quickly when they are recessive. The second class of incompatibilities, where fitness is reduced by disrupting co-evolved elements in gene regulation systems, collapse on a time scale proportional to the exponential of effective recombination rate. Overall, our result suggests that the effects of genetic drift and recombination on incompatibility's lifespan depend strongly on the underlying mechanisms of incompatibilities. As the time scale of collapse is usually shorter than the time scale of establishing a new incompatibility, the observed level of genetic incompatibilities in a particular hybridizing population may be shaped more by the collapse than by their initial accumulation. Therefore, a joint theory of accumulation-erosion of incompatibilities is in need to fully understand the genetic process under speciation with hybridization.

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Universal modesty in signal-burying games

10.31234/osf.io/j6a7h ◽

2018 ◽

Author(s):

Tadeg Quillien

Keyword(s):

Simple Model ◽

Evolutionary Game ◽

Costly Signaling ◽

Positive Information ◽

Probabilistic Information ◽

Signaling Dynamics ◽

The Stability ◽

Positive Traits ◽

Shed Light

Why would people hide positive information about themselves? Evolutionary game theorists have recently developed the signal-burying game as a simple model to shed light on this puzzle; they have shown that the game has an equilibrium where some agents are better off deliberately reducing the visibility of the signal by which they broadcast their positive traits. However, their explanation falls short of explaining all modesty norms, since this equilibrium also features individuals who openly brag. This leaves modesty norms that everyone adheres to in want of an explanation. Here we show that the signal-burying framework actually affords such an explanation: the game contains an equilibrium where all agents who send a signal voluntarily reduce its conspicuousness. Surprisingly, the stability of the two kinds of equilibria rely on very different principles. The equilibrium where some agents brag is stable because of costly signaling dynamics. By contrast, the universal modesty equilibrium exists because buried signals contain probabilistic information about a sender's type, and receivers make optimal use of this information. In the latter equilibrium, burying a signal can be understood as a handicap which makes the signal more honest, but honesty is not achieved through standard costly signaling dynamics.

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D-alanine metabolism via D-Ala aminotransferase by marine Gammaproteobacteria , Pseudoalteromonas sp. CF6-2

Applied and Environmental Microbiology ◽

10.1128/aem.02219-21 ◽

2021 ◽

Author(s):

Yang Yu ◽

Jie Yang ◽

Zhao-Jie Teng ◽

Li-Yuan Zheng ◽

Qi Sheng ◽

...

Keyword(s):

Amino Acid ◽

Marine Bacteria ◽

Gene Knockout ◽

Underlying Mechanism ◽

Dominant Group ◽

Seawater Samples ◽

Underlying Mechanisms ◽

Biochemical Analyses ◽

Global Oceans ◽

Shed Light

As the most abundant D-amino acid (DAA) in the ocean, D-alanine (D-Ala) is a key component of peptidoglycan in bacterial cell wall. However, the underlying mechanisms of bacterial metabolization of D-Ala through microbial food web remain largely unknown. In this study, the metabolism of D-Ala by marine bacterium Pseudoalteromonas sp. CF6-2 was investigated. Based on genomic, transcriptional and biochemical analyses combined with gene knockout, D-Ala aminotransferase was found to be indispensable for the catabolism of D-Ala in strain CF6-2. Investigation on other marine bacteria also showed that D-Ala aminotransferase gene is a reliable indicator for their ability to utilize D-Ala. Bioinformatic investigation revealed that D-Ala aminotransferase sequences are prevalent in genomes of marine bacteria and metagenomes, especially in seawater samples, and Gammaproteobacteria represents the predominant group containing D-Ala aminotransferase. Thus, Gammaproteobacteria is likely the dominant group to utilize D-Ala via D-Ala aminotransferase to drive the recycling and mineralization of D-Ala in the ocean. IMPORTANCE As the most abundant D-amino acid in the ocean, D-Ala is a component of marine DON (Dissolved organic nitrogen) pool. However, the underlying mechanism of bacterial metabolization of D-Ala to drive the recycling and mineralization of D-Ala in the ocean is still largely unknown. The results in this study showed that D-Ala aminotransferase is specific and indispensable for D-Ala catabolism in marine bacteria, and that marine bacteria containing D-Ala aminotransferase genes are predominantly Gammaproteobacteria widely distributed in global oceans. This study reveals marine D-Ala utilizing bacteria and the mechanism of their metabolization of D-Ala. The results shed light on the mechanisms of recycling and mineralization of D-Ala driven by bacteria in the ocean, which are helpful in understanding oceanic microbial-mediated nitrogen cycle.

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