WATER DEFICIT ANALYSIS IN VARIOUS CROPS

U radu se razmatra manjak vode u tlu za područje Zagreba za obradiva tla (tipa: aluvij i semiglej) te za najčešće uzgajane poljoprivredne kulture (silažni kukuruz, kupus, paprika, salata, rajčica, kukuruz, jabuka itd.). Pogodnost tala je određena FAO metodom. Klimatološke karakteristike područja s aspekta navodnjavanja određene su uporabom 20-godišnjih nizova meteoroloških podataka i pedoloških podataka te indeksa faza razvoja biljaka. Referentna evapotranspiracija (ETo) izračunata je prema metodi Penman-Montheitha. Efektivne oborine izračunate su metodom USBR iz vrijednosti srednjih mjesečnih prosječnih oborina kao i iz količine mjesečnih oborina koje su razgraničene donjim kvartilom. Bilanca vode u tlu za svaku kulturu izračunata je prema metodi Palmera. Dobiveni rezultati pokazuju da su potrebe kultura za vodom različite, a ukupni nedostatak vode ovisi o količini i sezonskom rasporedu oborina i hidropedološkim značajkama tala. Za svaku kulturu izračunat je manjak vode za višegodišnji prosjek oborina i za sušne mjesece, koji su razgraničeni donjim kvartilom količine oborine. Može se zaključiti da je navodnjavanje potrebna mjera u uzgoju navedenih kultura na navedenim tipovima tala na području Zagreba.The paper deals with water a deficit in arable soils of the Zagreb region (types: calacaric fluvisol and semigley) and for the most common agricultural crops grown (silage maize, cabbage, bell pepper, lettuce, tomato, maize, apple, etc.). Soil suitability was assessed by the FAO method. Climatological characteristics of the region, from the aspect of irrigation, were assessed using 20-year series of meteorological and pedological data, and indices of plant development stages. Reference evapotranspiration (ETo) was calculated by the Penman-Monteith method. Effective precipitation was calculated by the USBR method from the values of mean monthly average precipitation as well as from the amounts of monthly precipitation, separated by the lower quartile. Palmer’s method was used to calculate soil water balance for each crop. The results show that different crops have different water requirements, the total water deficit depending on the amount and seasonal distribution of precipitation and on the soil hydropedological characteristics. The water deficit was calculated for each crop with respect to the long-term precipitation average as well as for droughty months, separated by the lower quartile of the precipitation amount. It is concluded that irrigation is a necessary measure for the production of the studied crops on the said soil types in the Zagreb region

Binding of SGTA to Rpn13 selectively modulates protein quality control

YesRpn13 is an intrinsic ubiquitin receptor of the 26S proteasome regulatory subunit that facilitates substrate capture prior to degradation. Here we show that the C-terminal region of Rpn13 binds to the tetratricopeptide repeat (TPR) domain of SGTA, a cytosolic factor implicated in the quality control of mislocalised membrane proteins (MLPs). The overexpression of SGTA results in a substantial increase in steady-state MLP levels, consistent with an effect on proteasomal degradation. However, this effect is strongly dependent upon the interaction of SGTA with the proteasomal component Rpn13. Hence, overexpression of the SGTA-binding region of Rpn13 or point mutations within the SGTA TPR domain both inhibit SGTA binding to the proteasome and substantially reduce MLP levels. These findings suggest that SGTA can regulate the access of MLPs to the proteolytic core of the proteasome, implying that a protein quality control cycle that involves SGTA and the BAG6 complex can operate at the 19S regulatory particle. We speculate that the binding of SGTA to Rpn13 enables specific polypeptides to escape proteasomal degradation and/or selectively modulates substrate degradation.BBSRC [grant number: BB/L006510/1] and the Wellcome Trust [grant number: 092107/Z/10/Z]. K.K. was supported by the UPStream network [EU, FP7, ITN project 290257

FBXL4 ubiquitin ligase deficiency promotes mitophagy by elevating NIX levels

Selective autophagy of mitochondria, mitophagy, is linked to mitochondrial quality control and as such is critical to a healthy organism. We have used a CRISPR/Cas9 approach to screen human E3 ubiquitin ligases for influence on mitophagy under both basal cell culture conditions and upon acute mitochondrial depolarization. We identify two cullin-RING ligase substrate receptors, VHL and FBXL4, as the most profound negative regulators of basal mitophagy. We show that these converge, albeit via different mechanisms, on control of the mitophagy adaptors BNIP3 and BNIP3L/NIX. FBXL4 restricts NIX and BNIP3 levels via direct interaction and protein destabilization, while VHL acts through suppression of HIF1α-mediated transcription of BNIP3 and NIX. Depletion of NIX but not BNIP3 is sufficient to restore mitophagy levels. Our study contributes to an understanding of the aetiology of early-onset mitochondrial encephalomyopathy that is supported by analysis of a disease-associated mutation. We further show that the compound MLN4924, which globally interferes with cullin-RING ligase activity, is a strong inducer of mitophagy, thus providing a research tool in this context and a candidate therapeutic agent for conditions linked to mitochondrial dysfunction

N4BP1 is dimerization-dependent linear ubiquitin reader regulating TNFR1 signalling through linear ubiquitin binding and Caspase-8-mediated processing

This article is a preprint and has not been certified by peer review.Data and material availability: All the plasmids generated in this study will be available upon request. All data is available in the main text or the supplementary materials online at: https://doi.org/10.1101/2021.11.02.466974 ..Signalling through TNFR1 modulates proinflammatory gene transcription and programmed cell death, and its impairment causes autoimmune diseases and cancer. NEDD4-binding protein 1 (N4BP1) was recently identified as a critical suppressor of proinflammatory cytokine production1, whose mode of action remained unknown. Here, we show that N4BP1 is a novel linear ubiquitin reader that negatively regulates NFκB signalling by its unique dimerizationdependent ubiquitin-binding module that we named LUBIN. Dimeric N4BP1 strategically positions two non-selective ubiquitin-binding domains to ensure exclusive recognition of linear ubiquitin. Under proinflammatory conditions, N4BP1 is recruited to the nascent TNFR1 signalling complex, where it regulates duration of proinflammatory signalling in LUBIN-dependent manner. N4BP1 deficiency accelerates TNFα-induced cell death by increasing complex II assembly. Under proapoptotic conditions, Caspase-8 mediates proteolytic processing of N4BP1 and the resulting cleavage fragment of N4BP1, which retains the ability to bind linear ubiquitin, is rapidly degraded by the 26S proteasome, accelerating apoptosis. In summary, our findings demonstrate that N4BP1 dimerization creates a unique linear ubiquitin reader that ensures timely and coordinated regulation of TNFR1-mediated inflammation and cell death.This work was supported by the Francis Crick Institute through provision of access to the MRC Biomedical NMR Centre. The Francis Crick Institute receives its core funding from Cancer Research UK (FC001029), the UK Medical Research Council (FC001029), and the Wellcome Trust (FC001029). KK was supported by the UPStream grant (EU, FP7, ITN project 290257)

N4BP1 functions as a dimerization-dependent linear ubiquitin reader which regulates TNF signalling

Data availability; Coordinates of the structure of N4BP1-CUE and the N4BP1-CUE/Ub complex have been deposited in the PDB-Dev Protein Data Bank (https://pdb-dev.wwpdb.org) under accession codes PDBDEV_00000076 and PDBDEV_00000093, respectively. Chemical shift data have been deposited in the Biological Magnetic Resonance Data Bank (https://bmrb.io) with BMRB entry ID 50688. The model of dimeric N4BP1 in complex with linear Ub2 is available in ModelArchive (modelarchive.org) with the accession code ma-2x3cw. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository [76] with the dataset identifier PXD024355. All the plasmids generated in this study will be available upon request. All data is available in the main text or the supplementary materials. All original western blot images are available in the Supplemental Material.Supplementary information is available at: https://www.nature.com/articles/s41420-024-01913-8#Sec40 .Signalling through TNFR1 modulates proinflammatory gene transcription and programmed cell death, and its impairment causes autoimmune diseases and cancer. NEDD4-binding protein 1 (N4BP1) is a critical suppressor of proinflammatory cytokine production that acts as a regulator of innate immune signalling and inflammation. However, our current understanding about the molecular properties that enable N4BP1 to exert its suppressive potential remain limited. Here, we show that N4BP1 is a novel linear ubiquitin reader that negatively regulates NFκB signalling by its unique dimerization-dependent ubiquitin-binding module that we named LUBIN. Dimeric N4BP1 strategically positions two non-selective ubiquitin-binding domains to ensure preferential recognition of linear ubiquitin. Under proinflammatory conditions, N4BP1 is recruited to the nascent TNFR1 signalling complex, where it regulates duration of proinflammatory signalling in LUBIN-dependent manner. N4BP1 deficiency accelerates TNFα-induced cell death by increasing complex II assembly. Under proapoptotic conditions, caspase-8 mediates proteolytic processing of N4BP1, resulting in rapid degradation of N4BP1 by the 26 S proteasome, and acceleration of apoptosis. In summary, our findings demonstrate that N4BP1 dimerization creates a novel type of ubiquitin reader that selectively recognises linear ubiquitin which enables the timely and coordinated regulation of TNFR1-mediated inflammation and cell death.This work was supported by the Francis Crick Institute through provision of access to the MRC Biomedical NMR Centre. The Francis Crick Institute receives its core funding from Cancer Research UK (FC001029), the UK Medical Research Council (FC001029), and the Wellcome Trust (FC001029). KK was supported by the UPStream grant (EU, FP7, ITN project 290257). BS is supported by the UK Medical Research Council (MR/X036944/1)

N4BP1 functions as a dimerization-dependent linear ubiquitin reader which regulates TNF signalling

AbstractSignalling through TNFR1 modulates proinflammatory gene transcription and programmed cell death, and its impairment causes autoimmune diseases and cancer. NEDD4-binding protein 1 (N4BP1) is a critical suppressor of proinflammatory cytokine production that acts as a regulator of innate immune signalling and inflammation. However, our current understanding about the molecular properties that enable N4BP1 to exert its suppressive potential remain limited. Here, we show that N4BP1 is a novel linear ubiquitin reader that negatively regulates NFκB signalling by its unique dimerization-dependent ubiquitin-binding module that we named LUBIN. Dimeric N4BP1 strategically positions two non-selective ubiquitin-binding domains to ensure preferential recognition of linear ubiquitin. Under proinflammatory conditions, N4BP1 is recruited to the nascent TNFR1 signalling complex, where it regulates duration of proinflammatory signalling in LUBIN-dependent manner. N4BP1 deficiency accelerates TNFα-induced cell death by increasing complex II assembly. Under proapoptotic conditions, caspase-8 mediates proteolytic processing of N4BP1, resulting in rapid degradation of N4BP1 by the 26 S proteasome, and acceleration of apoptosis. In summary, our findings demonstrate that N4BP1 dimerization creates a novel type of ubiquitin reader that selectively recognises linear ubiquitin which enables the timely and coordinated regulation of TNFR1-mediated inflammation and cell death.</jats:p

The degradation of p53 and its major E3 ligase Mdm2 is differentially dependent on the proteasomal ubiquitin receptor S5a.

p53 and its major E3 ligase Mdm2 are both ubiquitinated and targeted to the proteasome for degradation. Despite the importance of this in regulating the p53 pathway, little is known about the mechanisms of proteasomal recognition of ubiquitinated p53 and Mdm2. In this study, we show that knockdown of the proteasomal ubiquitin receptor S5a/PSMD4/Rpn10 inhibits p53 protein degradation and results in the accumulation of ubiquitinated p53. Overexpression of a dominant-negative deletion of S5a lacking its ubiquitin-interacting motifs (UIM)s, but which can be incorporated into the proteasome, also causes the stabilization of p53. Furthermore, small-interferring RNA (siRNA) rescue experiments confirm that the UIMs of S5a are required for the maintenance of low p53 levels. These observations indicate that S5a participates in the recognition of ubiquitinated p53 by the proteasome. In contrast, targeting S5a has no effect on the rate of degradation of Mdm2, indicating that proteasomal recognition of Mdm2 can be mediated by an S5a-independent pathway. S5a knockdown results in an increase in the transcriptional activity of p53. The selective stabilization of p53 and not Mdm2 provides a mechanism for p53 activation. Depletion of S5a causes a p53-dependent decrease in cell proliferation, demonstrating that p53 can have a dominant role in the response to targeting S5a. This study provides evidence for alternative pathways of proteasomal recognition of p53 and Mdm2. Differences in recognition by the proteasome could provide a means to modulate the relative stability of p53 and Mdm2 in response to cellular signals. In addition, they could be exploited for p53-activating therapies. This work shows that the degradation of proteins by the proteasome can be selectively dependent on S5a in human cells, and that this selectivity can extend to an E3 ubiquitin ligase and its substrate

What is a smart device? - a conceptualisation within the paradigm of the internet of things

The Internet of Things (IoT) is an interconnected network of objects which range from simple sensors to smartphones and tablets; it is a relatively novel paradigm that has been rapidly gaining ground in the scenario of modern wireless telecommunications with an expected growth of 25 to 50 billion of connected devices for 2020 Due to the recent rise of this paradigm, authors across the literature use inconsistent terms to address the devices present in the IoT, such as mobile device, smart device, mobile technologies or mobile smart device. Based on the existing literature, this paper chooses the term smart device as a starting point towards the development of an appropriate definition for the devices present in the IoT. This investigation aims at exploring the concept and main features of smart devices as well as their role in the IoT. This paper follows a systematic approach for reviewing compendium of literature to explore the current research in this field. It has been identified smart devices as the primary objects interconnected in the network of IoT, having an essential role in this paradigm. The developed concept for defining smart device is based on three main features, namely context-awareness, autonomy and device connectivity. Other features such as mobility and userinteraction were highly mentioned in the literature, but were not considered because of the nature of the IoT as a network mainly oriented to device-to-device connectivity whether they are mobile or not and whether they interact with people or not. What emerges from this paper is a concept which can be used to homogenise the terminology used on further research in the Field of digitalisation and smart technologies