A Conserved Gene Structure and Expression Regulation of miR-433 and miR-127 in Mammals

MicroRNAs play essential roles in many cellular processes. However, limited information is available regarding the gene structure and transcriptional regulation of miRNAs. We explored the gene cluster encoding miR-433/127 in mammalian species using bioinformatics and in vitro “gene” expression approaches. Multiple sequence alignments (MSA) showed that the precursors of miR-433 and of miR-127 exhibited 95% and 100% similarity, respectively, in human, chimpanzee, horse, dog, monkey, rat, cow, and mouse. MSA of the promoter sequences of miR-433 and of miR-127 revealed lower sequence similarity among these mammalian species. However, the distance between miR-433 and miR-127 was strikingly similar, which was between 986 and 1007 bp and the position of transcription factor (TF) binding motifs, including estrogen related receptor response element (ERRE), was well conserved. Transient transfection assays showed that promoters of miR-433 and of miR-127 from human, rat, and dog were activated by estrogen related receptor gamma (ERRγ) and inhibited by small heterodimer partner (SHP). ChIP assays confirmed the physical association of ERRγ with the endogenous promoters of miR-433 and miR-127. In vitro over-expression of the human, rat, or dog miR-433/127 loci in cells, using an expression vector containing miR-433/127 and their promoter regions, markedly induced a differential expression of both primary and mature miR-433 and miR-127, indicating that miR-433 and miR-127 were possessed from their independent promoters. Our studies for the first time demonstrate a conserved gene structure and transcriptional regulation of miR-433 and miR-127 in mammals. The data suggest that the miR-433/127 loci may have evolved from a common gene of origin

MiR-433 and miR-127 Arise from Independent Overlapping Primary Transcripts Encoded by the miR-433-127 Locus

MicroRNAs play significant roles in development, metabolism and carcinogenesis, however, limited information is available about their primary transcripts and the transcriptional regulation of the microRNA genes. We report here the cloning of two primary miRNAs (pri-miR-433 and pri-miR-127) encoded by the miR-433-127 locus. Using both database mining and experimental methods, we isolated the full-length primary transcripts of the mouse miR-433 and miR-127 and demonstrated that they overlapped in a 5′-3′ unidirectional way. These two miRNA genes are expressed in a compact space by using overlapping coding regions. This is the first report to identify an economical structure for miR-433 and miR-127 genes, which may be a novel way of miRNA gene to maximize the genetic information in order to fit the complex physiological function of mammalian organism

Transcriptional mechanism for the paired miR-433 and miR-127 genes by nuclear receptors SHP and ERRγ

MicroRNAs (miRNAs, miRs) are genomically encoded small ∼22 nt RNA molecules that have been shown to mediate translational repression of target mRNAs involved in cellular proliferation, differentiation and death. Despite intensive studies on their physiological and pathological functions, the molecular mechanism of how miRNA gene transcription is regulated remains largely unknown. Microarray profiling revealed 21 miRNAs clustered on chromosome 12, including miR-433 and miR-127, that were co-upregulated in small heterodimer partner (SHP, NR0B2) SHP knockouts (SHP–/–) liver. Gene cloning revealed that the 3′-coding region of pri-miR-433 served as the promoter region of pri-miR-127. Estrogen related receptor (ERRγ, NR3B3) robustly activated miR-433 and miR-127 promoter reporters through ERRE, which was transrepressed by SHP. The strong elevation of miR-433 and miR-127 in Hepa-1 cells correlated with the down-regulation of SHP and up-regulation of ERRγ. Ectopic expression of ERRγ induced miR-433 and miR-127 expression, which was repressed by SHP coexpression. In contrast, knockdown ERRγ decreased miR-433 and miR-127 expression. In addition, the ERRγ agonist GSK4716 induced miR-433 and miR-127 expression both in vitro and in vivo, respectively. In summary, the coupled miR-433 and miR-127 genes were transcribed from independent promoters regulated by nuclear receptors ERRγ/SHP in a compact space by using overlapping genomic regions

A general Temperature-Guided Language model to engineer enhanced Stability and Activity in Proteins

Designing protein mutants with high stability and activity is a critical yet challenging task in protein engineering. Here, we introduce PRIME, an innovative deep learning approach for the zero-shot prediction of both protein stability and enzymatic activity. PRIME leverages temperature-guided language modelling, providing robust and precise predictions without relying on prior experimental mutagenesis data. Tested against 33 protein datasets, PRIME demonstrated superior predictive performance and generalizability compared to current state-of-the-art modelsComment: arXiv admin note: text overlap with arXiv:2304.0378

Nuclear Receptor SHP Activates miR-206 Expression via a Cascade Dual Inhibitory Mechanism

MicroRNAs play a critical role in many essential cellular functions in the mammalian species. However, limited information is available regarding the regulation of miRNAs gene transcription. Microarray profiling and real-time PCR analysis revealed a marked down-regulation of miR-206 in nuclear receptor SHP−/− mice. To understand the regulatory function of SHP with regard to miR-206 gene expression, we determined the putative transcriptional initiation site of miR-206 and also its full length primary transcript using a database mining approach and RACE. We identified the transcription factor AP1 binding sites on the miR-206 promoter and further showed that AP1 (c-Jun and c-Fos) induced miR-206 promoter transactivity and expression which was repressed by YY1. ChIP analysis confirmed the physical association of AP1 (c-Jun) and YY1 with the endogenous miR-206 promoter. In addition, we also identified nuclear receptor ERRγ (NR3B3) binding site on the YY1 promoter and showed that YY1 promoter was transactivated by ERRγ, which was inhibited by SHP (NROB2). ChIP analysis confirmed the ERRγ binding to the YY1 promoter. Forced expression of SHP and AP1 induced miR-206 expression while overexpression of ERRγ and YY1 reduced its expression. The effects of AP1, ERRγ, and YY1 on miR-206 expression were reversed by siRNA knockdown of each gene, respectively. Thus, we propose a novel cascade “dual inhibitory” mechanism governing miR-206 gene transcription by SHP: SHP inhibition of ERRγ led to decreased YY1 expression and the de-repression of YY1 on AP1 activity, ultimately leading to the activation of miR-206. This is the first report to elucidate a cascade regulatory mechanism governing miRNAs gene transcription

EbMYBP1, a R2R3-MYB transcription factor, promotes flavonoid biosynthesis in Erigeron breviscapus

Erigeron breviscapus, a traditional Chinese medicinal plant, is enriched in flavonoids that are beneficial to human health. While we know that R2R3-MYB transcription factors (TFs) are crucial to flavonoid pathway, the transcriptional regulation of flavonoid biosynthesis in E. breviscapus has not been fully elucidated. Here, EbMYBP1, a R2R3-MYB transcription factor, was uncovered as a regulator involved in the regulation of flavonoid accumulation. Transcriptome and metabolome analysis revealed that a large group of genes related to flavonoid biosynthesis were significantly changed, accompanied by significantly increased concentrations of the flavonoid in EbMYBP1-OE transgenic tobacco compared with the wild-type (WT). In vitro and in vivo investigations showed that EbMYBP1 participated in flavonoid biosynthesis, acting as a nucleus-localized transcriptional activator and activating the transcription of flavonoid-associated genes like FLS, F3H, CHS, and CHI by directly binding to their promoters. Collectively, these new findings are advancing our understanding of the transcriptional regulation that modulates the flavonoid biosynthesis

Photoproduction de monoxyde de carbone dans les écosystèmes marins : particules contre solutés

RÉSUMÉ: Le monoxide de carbone (CO) joue un rôle important dans le cycle du carbone organique marin et dans la chimie atmosphérique. L'océan est reconnu depuis longtemps comme la principale source de CO dans l'atmosphère. Dans la couche supérieure de l'océan, le CO est produit principalement à partir de la photodégradation de la matière organique dissoute chromophorique (CDOM). Cependant, des données récentes suggèrent que la photolyse de la matière organique particulaire (POM) peut également produire une quantité importante de CO dans la colonne d'eau. Pour comprendre la contribution de la POM à la photoproduction de CO et, par conséquent, évaluer l'importance de la photodégradation de la POM dans le cycle du carbone marin, ce travail a permis, pour la première fois, de quantifier le rendement apparent quantique de la photoproduction de CO (AQY CO) à partir de la POM et du CDOM dans des écosystèmes aquatiques de climat froid (c.-à-d., le sud-est de la mer de Beaufort) et tempéré (c.-à-d, la baie du Delaware). La variation spatio-temporelle du CO dans la glace de mer de première année, un autre écosystème important de l'Arctique, a également été évaluée. En outre, les spectres AQY CO de la POM et du CDOM provenant de cultures d'algues de glace ont été déterminés. La contribution de la POM et du CDOM à la photoproduction de CO à la base de la glace de mer a également été estimée. La concentration de CO a fluctué de façon irrégulière dans la couche superficielle de la glace de mer. À la base de la glace, elle a toutefois suivi la concentration des algues, avec de faibles valeurs au début de la période d'accumulation des algues, un fort enrichissement pendant l'efflorescence et la période post-efflorescence, et un appauvrissement de nouveau pendant la fonte de la banquise. Les profils verticaux montrent une diminution de la concentration en CO de la surface vers la base de la glace au début du printemps et ces profils sont variables pendant la saison de fonte. En présence de fortes biomasses algales à la base de la glace à la mi-printemps, le CO a été fortement enrichi à la base de la glace (82,9 ± 84 nmol L-1) par rapport à la surface (16,8 ± 7 nmol L-1). De plus, la banquise côtière contenait des teneurs en CO supérieures à celles de la glace dérivante. La concentration moyenne de CO dans la glace de mer pendant la campagne d'échantillonnage a été de 13,9 ± 10 umol m-2 et la production nette de CO pendant le bloom d'algues de glace a été évaluée à 13,2 umol m-2 • La glace de mer est reconnue comme une source importante de CO atmosphérique et elle pourrait contribuer à un flux annuel vers l'atmosphère de 7.4 x 107 moles de CO dans la zone d'étude. Généralement, les AQYs CO des particules et du CDOM diminuent avec l'augmentation de la longueur d'onde, mais la forme du spectre dans le visible, en ce qui concerne les particules était supérieure et plus platte. Cette caractéristique a donné lieu à une production de CO par la lumière visible disproportionnellement élevée pour les particules. Ainsi, le ratio entre la photoproduction de CO par les particules et celle par le CDOM augmente avec la profondeur dans la zone euphotique et dans la glace de mer. Plus précisément, les spectres AQY CO des particules provenant de cultures d'algues de glace en phases de croissance exponentielles et sénescentes ont été plus élevés que ceux du CDOM des cultures, en particulier aux longues longueurs d'onde. Contrairement au CDOM , il y avait une photoproduction de CO substantielle à partir des particules aux longueurs d'ondes > 600 nm. Étant donné que le flux de photons du rayonnement solaire atteignant la couche inférieure de la glace de mer est largement dominé par la lumière visible, notamment sous un couvert de neige, on s'attend à ce que la POM joue un rôle plus important que celui de la matière organique dissoute (DOM) dans l'accumulation de CO durant le bloom d'algues de glace. Toutefois, nous estimons que la contribution relative de la DOM à l'accumulation du CO dans la glace augmente avec la progression de la fonte de la neige et de la glace. Dans le sud-est de la mer de Beaufort, l'AQY CO des particules a augmenté de l'estuaire et du plateau vers le bassin, tandis que celui du CDOM a suivi une tendance inverse. L'eau provenant du maximum profond de chlorophylle (DCM) a révélé des dominée par le rayonnement ultraviolet (UV, 290-400 nm) alors que la lumière UV et visible a joué un rôle à peu près égal dans la production de CO à partir des particules. Dans l'estuaire du Delaware, les valeurs du AQY CO ont été déterminées sur des échantillons d'eau de mer filtrée sur membranes de 0,2, 10 et 20 flm de porosité, afin d'évaluer l'effet de la taille de la matière organique sur l'efficacité de photoproduction de CO. En raison des propriétés distinctes de la matière organique le long de l'estuaire, la forme des spectres du CO AQY du CDOM et des particules a moins varié que celle obtenue lors d'études précédentes. Par conséquent, la lumière visible plutôt que l'UV a été le principal responsable de la photoproduction de CO à partir, à la fois, des particules et du CDOM dans la colonne d'eau. Les particules et le CDOM au milieu de la zone de tubidité maximum ont été plus photoréactifs que leurs homologues provenant de la terre ferme, en raison de la floculation, de l'adsorption et/ou de la désorption aux endroits où il y avait suffisamment de mélange de l'eau douce avec l'eau salée. Aucune différence significative dans la photoréactivité des particules en termes de production de CO n'a été trouvée entre les deux fractions de taille des particules le long de l'estuaire. Selon notre modèle, la contribution des particules à la photoproduction totale de CO serait supérieure à 84% à la base de la glace de mer, de 12-32% en eau libre dans le secteur sud-est de la mer de Beaufort et de 29-77% dans l'estuaire du Delaware. En outre, la contribution des particules de petite taille (<10 um) à la photoproduction totale de CO basée sur l'ensemble des particules a été plus grande dans l'estuaire du Delaware, car cette fraction de taille est la composante dominante des particules chromophoriques. Cette étude présente de nouvelles preuves que la photochimie des particules joue un rôle important dans le cycle du carbone océanique et des gaz traces, en particulier dans les eaux estuariennes et côtières et dans la glace de mer, des milieux où la photochimie des particules pourrait dépasser celle du CDOM. -- Mot clés: monoxyde de carbone, photoproduction, le rendement apparent quantique, CDOM, les particules, la glace de mer, la mer de Beaufort, l'estuaire du Delaware. --ABSTRACT: Carbon monoxide (CO) plays an important role in marine organic carbon cycle and in atmospheric chemistry. The ocean has long been recognized as an important source of atmospheric CO. In the upper ocean, CO is produced primarily from photodegradation of chromophoric dissolved organic matter (CDOM). However, recent evidence suggests that photolysis of particulate organic matter (POM) can also produce a significant amount of CO in the water column. To understand the contribution of POM to CO photoproduction and hence assess the importance of POM photodegradation to marine carbon cycling, this work for the first time quantified the spectrally resoived apparent quantum yields (AQYs) of CO photo production from POM, as well as from CDOM in cold (southeastern (SE) Beaufort Sea) and warm aquatic ecosystems (Delaware Bay). The spatiotemporal variation of CO concentration ([COD in first-year sea ice in the SE Beaufort Sea was also examined. CO AQY spectra of POM and CDOM harvested from ice algal cultures were determined to model the contributions of POM and CDOM to CO photoproduction in bottom sea ice. [CO] fluctuated irregularly in surface ice but followed the biomass of ice algae in bottom ice, i.e. low at the start of ice algal accumulation, highly enriched during the peakbloom and early post-bloom, and depleted again during sea ice melt. Vertical profile of CO typically decreased downward in early spring and was variable in the melting season. In the presence of high bottom ice algal biomass in mid-spring, CO was highly enriched in the bottom (82.9 ± 84 nmol L-1) relative to the surface (CO: 16.8 ± 7 nmol L-1). Furthermore, landfast ice contained higher levels of CO th an drifting ice. Cruise-mean CO inventory in sea ice was 13.9 ± 10 umol m-2, and the net production of CO during the ice algal bloom was assessed to be 13.2 mol m-2 • Sea ice is recognized as an important source of atmospheric CO and might contribute 7.4 x 10 7 moles of CO a-1 to the atmosphere in the study area. Generally, CO AQYs of both particles and CDOM decreased with wavelength but the spectral shape of the particulate AQY was flatter in the visible regime. This feature resulted in a disproportionally higher visible light-driven CO production by particles, thereby increasing the ratio of particle- to CDOM-based CO photoproduction with depth in the euphotic zone and in sea ice. Specifically, CO AQY spectra of partic1es collected from ice algal cultures at the exponential and senescent phases were higher than the corresponding CDOM samples, particularly at long wavelengths. Unlike CDOM, at λ> 600 nm, there was prolific CO photoproduction from particles collected from ice algal cultures. Given that the photon flux of solar radiation reaching the bottom sea ice is overwhelmingly dominated by the visible regime, particularly under snow coyer, POM is expected to play a far more important role than DOM in contributing to the CO accumulation during the ice algal bloom. The relative contribution from DOM, however, is estimated to increase with the progression of snow and ice melting. In the SE Beaufort Sea, CO AQY of particles augmented from the estuary and shelf to the basin while that of CDOM trended inversely. Water from the deep chlorophyll maximum (DCM) layer revealed higher CO AQYs than did surface water for both particles and CDOM. CO AQY of particles exceeded that of CDOM on the shelf and in the basin but the sequence inversed in the estuary. In terms of depth-integrated production in the euphotic zone, CO formation from CDOM was dominated by the ultraviolet (UV, 290-400 nm) radiation whereas UV and visible light played roughly equal roles in CO production from particles. In the Delaware Estuary, CO AQYs in 0.2-, 10- and 20-um filtered water samples were determined, to evaluate the size effect of organic matter on CO photoproduction efficiency. Owing to the distinct properties of organic matter along the estuary, the spectral shape of CO AQY of CDOM and particles were flatter than those in previous studies, and hence visible light, rather than UV, were the main contributor to CO photoproduction from both particles and CDOM in the water column. Both particles and CDOM in the mid-TMZ were more photoreactive than their counterparts from land, due mainly to flocculation, adsorption and/or desorption during intense mixing of fresh water with saline seawater. No significant difference in particle photoreactivity in tenns of CO production was found between the two size fractions of particles along the estuary . Modeled CO photoproduction indicated that particles could contribute more than 84% in bottom sea ice, 12-32% in open water in the SE Beaufort Sea and 29%-77 % in the Delaware Estuary to total CO photoproduction. Furthermore, small-sized particles (<10 um) accounted for more of particle-based CO photo production in the Delaware Estuary , since this size fraction is the dominant component of chromophoric particles. This study provides novel evidence that particle photochemistry is an important term in marine carbon and trace gas cycling, especially in estuarine and coastal waters and sea ice, where particle photochemistry may exceed that of CDOM. -- Keywords: carbon monoxide, photoproduction , apparent quantum yield, CDOM , particles, sea ice, Beaufort Sea, Del aware Estuary

Production of Chromophoric Dissolved Organic Matter (CDOM) in Laboratory Cultures of Arctic Sea Ice Algae

Chromophoric dissolved organic matter (CDOM) is highly enriched in bottom sea ice in the Arctic during ice algal blooms, giving rise to multifaceted ecological implications in both the sea ice and the underlying seawater. We conducted laboratory culture incubations to assess the potential role of ice algae in the accumulation of CDOM in Arctic sea ice. Non-axenic monocultures of Attheya septentrionalis and Nitzschia frigida and a natural ice algal assemblage (NIAA) were grown at 4 &#176;C in an f/2 medium under cool white fluorescent light. Culture samples were collected several days apart throughout the exponential, stationary, and senescent phases, and analyzed for CDOM absorbance, chlorophyll a, and bacterial cell abundance. The cultures displayed apparent specific growth rates of algal and bacterial cells comparable to those in the field. Accumulations of CDOM were observed in all cultures during the time-course incubations, with the senescent phase showing the largest accumulations and the highest production rates. The senescent-phase production rate for NIAA was ~40% higher than that for A. septentrionalis. The chlorophyll a-normalized CDOM production rates in the cultures are comparable to those reported for Arctic first-year sea ice. The absorption spectra of CDOM in the cultures exhibited characteristic short-ultraviolet shoulders similar to those previously identified in sea ice. This study demonstrates that ice algal-derived CDOM can account for the springtime accumulation of CDOM in Arctic sea ice