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Molecular mechanisms in fungal fatty acid synthase (FAS) assembly

The fungal fatty acid synthase (fFAS) multienzyme is a barrel-shaped 2.6 MDa complex comprising six times eight catalytic domains. Upon barrel-formation, up to several hundred kDa large polypeptides intertwine to bury about 170,000 [A]2 of protein surface. Functional, regulatory and structural data as well as evolutionary aspects of fFAS have been elucidated during the last decades. Notwithstanding a profound knowledge of this protein family, the biogenesis of the elaborate structure remained elusive. Remarkably, experimental data have recently demonstrated that fFAS self-assembles without the assistance of specific factors. Considering the infinitesimal probability that the barrel-shaped complex forms simply by domains approaching in the correct orientation, we were interested in understanding the sequence of events that have to orchestrate fFAS assembly. Here, we show that fFAS attains its quaternary structure along a pathway of successive domain-domain interactions, which is strongly related to the evolutionary development of this protein family. The knowledge on fFAS assembly may pave the way towards antifungal therapy, and further develops fFAS as biofactory in technological applications.

molecular biology

Tristetraprolin/ZFP36 regulates the turnover of autoimmune-associated HLA-DQ mRNAs

We have previously demonstrated that the expression of HLA class II genes is regulated by the binding of a ribonucleoprotein complex that affects the mRNA processing. We identified protein components of a complex binding transcripts encoding the HLA-DR molecule. Here we investigate whether the same RNA binding proteins interact with 3UTR of mRNAs encoding the HLA-DQ isotype. Specifically, we focused on the HLA-DQ2.5 molecule, expressed on the surface of antigen presenting cells, and representing the main susceptibility factor for celiac disease (CD). This molecule, encoded by HLA-DQA1*05 and HLA-DQB1*02 alleles, presents the antigenic gluten peptides to CD4+ T lymphocytes, activating the autoimmune response.\n\nHere, we identified an additional component of the RNP complex, Tristetraprolin (TTP) or ZFP36, a zinc-finger protein, widely described as a factor modulating mRNA stability. TTP shows high affinity binding to 3UTR of CD-associated HLA-DQA1*05 and HLA-DQB1*02 alleles, in contrast to lower affinity binding to HLA-DQA1*01 and HLA-DQB1*05 non-CD associated alleles. Our in silico analysis, confirmed by molecular experiments, demonstrates that TTP specifically modulates the stability of the transcripts associated with celiac disease.

molecular biology

GZMA and RASGRP1 are novel tumor suppressors that counter dissemination of Theileria annulata-transformed macrophages

Theileria annulata is a tick-transmitted apicomplexan parasite that infects and transforms bovine leukocytes into disseminating tumors that cause a disease called tropical theileriosis. Using comparative transcriptomics we identified genes transcriptionally perturbed during Theileria-induced transformation. Dataset comparisons highlighted a small set of genes associated with Theileria-transformed leukocyte dissemination. The roles of Granzyme A (GZMA) and RAS guanyl-releasing protein 1 (RASGRP1) were verified by CRISPR/Cas9-mediated knock-down. Knocking down of GZMA and RASGRP1 in attenuated macrophages led to a regain in their dissemination in Rag2/{gamma}C mice confirming their role as dissemination suppressors in vivo. We further evaluated the roles of GZMA and RASGRP1 in human B-lymphoma cells by comparing the transcriptome of 934 human cancer cell lines to that of Theileria-transformed bovine host cells. We confirmed dampened dissemination potential of human B-lymphoma cells that overexpress GZMA and RASGRP1. Our results provide evidence that GZMA and RASGRP1 have a novel tumor suppressor function in both T. annulata-infected bovine host cells and in human B-lymphomas.\n\nSummaryWe compared the transcriptomes of Theileria annulata transformed B-lymphocytes to 934 human cancer cell lines and provide functional evidence for shared tumor suppressor roles for GZMA and RASGRP1 in controlling the dissemination phenotype of both human B lymphomas and Theileria-transformed leukocytes.

molecular biology

ALV-J and REV synergistically activate a new oncogene of KIAA1199 via NF-κB and EGFR signaling regulated by miR-147

The tumorigenesis is the result of the accumulation of multiple oncogenes and tumor suppressor genes changes. Co-infection of avian leucosis virus subgroup J (ALV-J) and reticuloendotheliosis virus (REV), as two oncogenic retroviruses, showed synergistic pathogenic effects characterized by enhanced tumor initiation and progression. The molecular mechanism underlying synergistic effects of ALV-J and REV on the neoplasia remains unclear. Here, we found co-infection of ALV-J and REV enhanced the ability of virus infection, increased viral life cycle, maintained cell survival and enhanced tumor formation. We combined the high-throughput proteomic readout with a large-scale miRNA screening to identify which molecules are involved in the synergism. Our results revealed co-infection of ALV-J and REV activated a latent oncogene of KIAA1199 and inhibited the expression of tumor suppressor miR-147. Further, enhanced KIAA1199, down-regulated miR-147, activated NF-{kappa}B and EGFR were demonstrated in co-infected tissues and tumor. Mechanistically, we showed ALV-J and REV synergistically enhanced KIAA1199 by activation of NF-{kappa}B and EGFR signalling pathway, and the suppression of tumor suppressor miR-147 was contributed to maintain the NF-{kappa}B/KIAA1199/EGFR pathway crosstalk by targeting the 3UTR region sequences of NF-{kappa}B p50 and KIAA1199. Our results contributed to the understanding of the molecular mechanisms of viral synergistic tumorgenesis, which provided the evidence that suggested the synergistic actions of two retroviruses could result in activation of latent pro-oncogenes.\n\nAuthor summaryThe tumorigenesis is the result of the accumulation of multiple oncogenes and tumor suppressor genes changes. Co-infection with ALV-J and REV showed synergistic pathogenic effects characterized by enhanced tumor progression, however, the molecular mechanism on the neoplasia remains unclear. Our results revealed co-infection of ALV-J and REV promotes tumorigenesis by both induction of a latent oncogene of KIAA1199 and suppression of the expression of tumor suppressor miR-147. Mechanistic studies revealed that ALV-J and REV synergistically enhance KIAA1199 by activation of NF-{kappa}B and EGFR signalling pathway, and the suppression of tumor suppressor miR-147 was contributed to maintain the NF-{kappa}B/KIAA1199/EGFR pathway crosstalk by targeting the 3UTR region sequences of NF-{kappa}B p50 and KIAA1199. These results provided the evidence that suggested the synergistic actions of two retroviruses could result in activation of latent pro-oncogenes, indicating the potential preventive target and predictive factor for ALV-J and REV induced tumorigenesis.

molecular biology

Proteomics reveals ablation of placental growth factor inhibits the insulin resistance pathways in diabetic mouse retina

The underlying molecular mechanisms that placental growth factor (PlGF) mediates the early complications at non-proliferative diabetic retinopathy (DR) remain largely elusive. The objective of this study is to characterize expression profile due to PlGF ablation in the retina of diabetic mice. The quantitative label-free proteomics was carried out on retinal tissues collected from mouse strains (Akita; PlGF-/- and Akita.PlGF-/-). We have identified 3176 total proteins, and 107 were significantly different between the experimental groups, followed by gene ontology, functional pathways, and protein-protein network interaction analysis. Gnb1, Gnb2, Gnb4, Gnai2, Gnao1, Snap25, Stxbp1, Vamp2 and Gngt1 proteins are involved in insulin resistance pathways, which are down-regulated in PlGF ablation in Akita diabetics (Akita.PlGF-/- vs. Akita), up-regulation in Akita vs. C57, PlGF-/- vs. C57. Prdx6, Prdx5 (up-regulation) are known of antioxidant activity; Map2 is involved in neural protection pathways which are up-regulated in Akita.PlGF-/- vs. Akita. Our results suggest that inhibition of insulin resistance pathway and the enhancement of antioxidant defence and neural function may represent the potential mechanisms of anti-PlGF compounds in the treatment of DR.

molecular biology

Yeast PAF1 complex restricts the accumulation of RNA polymerase III and counters the replication stress on the transcribed genes

Many regulatory proteins and complexes influence transcription by RNA polymerase (pol) II. In comparison, only a few regulatory proteins are known for pol III, which transcribes mostly house-keeping and non-coding genes. Yet, pol III transcription is precisely regulated under various stress conditions like starvation. We used pol III transcription complex components TFIIIC (Tfc6), pol III (Rpc128) and TFIIIB (Brf1) as baits to identify potential interactors through mass spectrometry-based proteomics. A large interactome constituting known chromatin modifiers, factors and regulators of transcription by pol I and pol II revealed the possibility of a large number of signaling cues for pol III transcription against adverse conditions. We found one of the pol II-associated factors, Paf1 complex (PAF1C) interacts with the three baits. Its occupancy on the pol III-transcribed genes is low and not correlated with pol III occupancy. Paf1 deletion leads to higher occupancy of pol III, {gamma}-H2A and DNA pol2 but no change in nucleosome positions. Genotoxins exposure causes pol III but not Paf1 loss from the genes. PAF1C promotes the pol III pausing and restricts its accumulation on the genes, which reduces the replication stress caused by the pol III barrier and transcription-replication conflict on these highly transcribed genes.

molecular biology

Tandem repeats drive variation of intrinsically disordered regions in budding yeast

Copy-number variation in tandem repeat coding regions is more prevalent in eukaryotic genomes than current literature suggests. We have reexamined the genomes of nearly 100 yeast strains looking to map regions of repeat variation. From this analysis we have identified that length variation is highly correlated to intrinsically disordered regions (IDRs). Furthermore, the majority of length variation is associated with tandem repeats. These repetitive regions are rich in homopolymeric amino acid sequences but nearly half of the variation comes from longer-repeating motifs. Comparisons of repeat copy number and sequence between strains of budding yeast as well as closely related fungi suggest selection for and conservation of IDR-related tandem repeats. In some instances, repeat variation has been demonstrated to mediate binding affinity, aggregation, and protein stability. With this analysis, we can identify proteins for which repeat variation may play conserved roles in modulating protein function.

molecular biology

LncRNA Spehd regulates hematopoietic stem cells and progenitors and is required for multilineage differentiation

Long non-coding RNAs (lncRNAs) show patterns of tissue- and cell-type-specific expression that are very similar to those of protein coding genes and consequently have the potential to control stem and progenitor cell fate decisions along a differentiation trajectory. To understand the roles that lncRNAs might play in hematopoiesis, we selected a subset of mouse lncRNAs with potentially relevant expression patterns and refined our candidate list using evidence of conserved expression in human blood lineages. For each candidate, we assessed its possible role in hematopoietic differentiation in vivo using competitive transplantation. Our studies identified two lncRNAs that were required for hematopoiesis. One of these, Spehd, showed defective multi-lineage differentiation, and its silencing yielded common myeloid progenitors deficient in their oxidative phosphorylation pathway. This effort not only suggests that lncRNAs can contribute to differentiation decisions during hematopoiesis but also provides a path toward the identification of functional lncRNAs in other differentiation hierarchies.

molecular biology

Antiviral viral compound from Streptomyces ghanaensis like strain against white spot syndrome virus (WSSV) of shrimp

Actinomycetes isolates collected from different environments were screened for antiviral activity against WSSV. One isolate designated as CAHSH-2 showed antiviral activity against WSSV at the concentration of 0.2 mg per shrimp. The laboratory trial of determining antiviral activity of ethyl acetate extract (EtOAcE) of CAHSH-2 against WSSV was carried out 21 times since 2014. CAHSH-2 isolate which showed antiviral activity was characterized and identified as Streptomyces ghanaensis like strain. Among the five fractions obtained from EtOAcE of potential actinomycetes isolate, F1 was found to have strong antiviral activity. The F1A and F1B sub-fractions from F1 fraction were subjected to GC-MS, FTIR, 1H and 13C NMR analyses and, the compounds identified were di-n-octyl phthalate and bis (2-methylheptyl) phthalate, respectively. Among these compounds, di-n-octyl phthalate showed strong antiviral activity against WSSV. Molecular docking studies revealed that di-n-octyl phthalate was found to have high binding affinity with VP26 and VP28 proteins of WSSV, whereas the bis (2-methylheptyl) phthalate showed low binding affinity with VP26 and VP28. The antiviral activity of EtOAcE of actinomycetes against WSSV was confirmed by PCR, RT-PCR, Western blot and ELISA. The EA extract of active isolate was found to be non-toxic to Artemia, post-larvae and adult Litopenaeus vannamei.\n\nImportanceWhite spot syndrome virus (WSSV) is an important shrimp viral pathogen and responsible for huge economic loss to shrimp culture industry worldwide including India. The global loss due to WSSV has been estimated about USD 10 billion and the loss continues at the same extent even now. Various strategies have been followed to prevent or control diseases of aquatic animals. In spite of various preventive and control strategies, WSSV has been still persisting for more than two decades. No control strategies have so far been evolved to put a break to WSSV. In this situation, an attempt was made in the present work to screen some actinomycetes isolates for antiviral activity against WSSV. Among these isolates, one isolate identified as Streptomyces ghanaensis like isolate CAHSH-2 showed activity against WSSV. This article gives the information about the antiviral compound against WSSV and the mechanism of viral inhibition.

molecular biology

Identification of Common Adulterants in Walnut Beverage Based on Plant DNA Barcode Technology

Walnut beverage is a common vegetable protein drink that is rich in proteins and has a wide consumption market. In this study, a plant DNA barcode technology was used to establish a method to identify common adulterated ingredients (peanut and soybean) in walnut beverage. In this experiment, universal primers were designed, and PCR amplification was performed. The universal primers were screened by sequencing and comparing the amplified products. Results showed that the primers rbcL-4 and matK-4 amplified walnut, peanut, sesame, soybean, and hazelnut. Peanut genomic DNA and soybean genomic DNA were added to the genomic DNA of walnut in different proportions. Primer rbcL-4 can detect 10% peanut genome DNA, and primer matK-4 can detect 10% soybean genome DNA. Calculation results of the extraction rate revealed that primer rbcL-4 can detect 8.88% peanut raw materials and primer matK-4 can detect 2.30% soybean raw materials. The combination of these two primers can be used as a universal primer for the identification of adulterated components in walnut beverage. This experiment could serve as a theoretical reference for related research and detection.

molecular biology

Rapid, specific detection and quantification of Yersinia pestis using a species-specific SNP in the ferric uptake regulator gene (furMAMA)

Yersinia pestis, the causative agent of plague, is responsible for about 700 human cases of bubonic and pneumonic plague each year. Yet the disease is far more prevalent within rodent reservoirs than in humans. One of the main means of outbreak prevention is extensive wildlife surveillance, where accurate and rapid detection is essential to prevent spillover into the human population from which, it may otherwise spread more rapidly and over larger distances. Moreover, detection and quantification of the agent aids in investigative studies to understand aspects of the pathogen such as transmission mechanics, pathology, contamination risk and more. Partially based on a previously developed assay by Gabitzsch et al. 2008 we designed a TaqMan(R) mismatch amplification mutation assay (TaqMAMA) where a primer leverages a species-specific SNP in the chromosomal single copy ferric uptake regulator gene of Yersinia pestis. The assay allows for specific, rapid detection and quantification of Yersinia pestis using only a single species-specific marker in a highly conserved virulence gene. This low-cost and simple modification of an existing assay eliminates the need for running multiple molecular markers for pathogen detection or performing time-consuming culturing and counting of colonies for quantification.

molecular biology

HERC2 promotes BLM and WRN to suppress G-quadruplex DNA

BLM and WRN are RecQ DNA helicases essential for genomic stability. Here we demonstrate that HERC2, a HECT E3 ligase, is critical for their functions to suppress G-quadruplex (G4) DNA. HERC2 interacts with BLM, WRN, and replication protein A (RPA) complexes during S-phase of the cell cycle. Depletion of HERC2 dissociates RPA from BLM and WRN complexes and significantly increases G4 formation. Triple depletion revealed that HERC2 has an epistatic relationship with BLM and WRN in their G4- suppressing function. In vitro, HERC2 releases RPA onto single-stranded DNA (ssDNA), rather than anchoring onto RPA-coated ssDNA. CRISPR/Cas9-mediated deletion of the catalytic ubiquitin-binding site of HERC2 causes RPA accumulation in the helicase complexes and increases G4, indicating an essential role for E3 activity in G4 suppression. Both HERC2 depletion and E3 inactivation sensitize cells to the G4-interacting compounds, telomestatin and pyridostatin. Overall, HERC2 is a master regulator of G4 suppression and affects the sensitivity of cells to G4 stabilizers.

molecular biology

The non-canonical SMC protein SmcHD1 antagonises TAD formation on the inactive X chromosome

The inactive X chromosome (Xi) in female mammals adopts an atypical higher-order chromatin structure, manifested as a global loss of local topologically associated domains (TADs), and formation of two mega-domains. In this study we demonstrate that the non-canonical SMC family protein, SmcHD1, which is important for gene silencing on Xi, contributes to this unique chromosome architecture. Specifically, allelic mapping of the transcriptome and epigenome in SmcHD1 null cells revealed the appearance of sub-megabase domains defined by gene activation, CpG hypermethylation and depletion of Polycomb-mediated H3K27me3. These domains, which correlate with sites of SmcHD1 enrichment on Xi in wild-type cells, additionally adopt features of active X chromosome higher-order chromosome architecture, including partial restoration of TAD boundaries. Xi chromosome architecture changes also occurred in an acute SmcHD1 knockout model, but in this case, independent of Xi gene de-repression. We conclude that SmcHD1 is a key factor in antagonising TAD formation on Xi.

molecular biology

Long-range chromatin interactions on the inactive X and at Hox clusters are regulated by the non-canonical SMC protein Smchd1.

The regulation of higher order chromatin structure is complex and dynamic; however we do not yet understand the full suite of mechanisms governing architecture. Here we reveal the non-canonical SMC protein Smchd1 as a novel regulator of long-range chromatin interactions, and add it to the canon of epigenetic proteins required for Hox gene regulation. The effect of losing Smchd1-dependent chromatin interactions has varying outcomes dependent on chromatin context. At autosomal targets transcriptionally sensitive to Smchd1 deletion, we find increased short-range interactions and ectopic enhancer activation. By contrast, the inactive X chromosome is transcriptionally refractive to Smchd1 ablation, despite chromosome-wide increases in short-range interactions. There we observe spreading of H3K27me3 domains into regions not normally decorated by this mark. Together these data suggest Smchd1 has the capacity to insulate the chromatin, thereby limiting access to other chromatin modifying proteins.

molecular biology

A novel amidase signature family amidase from the marine actinomycete Salinispora arenicola CNS-205

We cloned a new gene from the amidase signature (AS) family, designated am, from the marine actinomycete Salinispora arenicola CNS-205. As indicated by bioinformatics analysis and site-directed mutagenesis, the AM protein belonged to the AS family. AM was expressed, purified, and characterised in Escherichia coli BL21 (DE3), and the AM molecular mass was determined to be 51 kDa. The optimal temperature and pH were 40 {degrees}C and pH 8.0, respectively. AM exhibited a wide substrate spectrum and showed amidase, aryl acylamidase, and acyl transferase activities. AM had high activity towards aromatic and aliphatic amides. The AM substrate specificity for anilides was very narrow; only propanil could be used as an effective substrate. The extensive substrate range of AM indicates it may have broad potential applications in biosynthetic processes and biodegradation.

molecular biology

Large-scale, quantitative protein assays on a high-throughput DNA sequencing chip

High-throughput DNA sequencing techniques have enabled diverse approaches for linking DNA sequence to biochemical function. In contrast, assays of protein function have substantial limitations in terms of throughput, automation, and widespread availability. We have adapted an Illumina high-throughput sequencing chip to display an immense diversity of ribosomally-translated proteins and peptides, and then carried out fluorescence-based functional assays directly on this flow cell, demonstrating that a single, widely-available high-throughput platform can perform both sequencing-by-synthesis and protein assays. We quantified the binding of the M2 anti-FLAG antibody to a library of 1.3x104 variant FLAG peptides, exploring non-additive effects of combinations of mutations and discovering a \"superFLAG\" epitope variant. We also measured the enzymatic activity of 1.56x105 molecular variants of full-length of human O6-alkylguanine-DNA alkyltransferase (SNAP-tag). This comprehensive corpus of catalytic rates linked to amino acid sequence perturbations revealed amino acid interaction networks and cooperativity, linked positive cooperativity to structural proximity, and revealed ubiquitous positively-cooperative interactions with histidine residues.

molecular biology

SUMO-based expression and purification of dermcidin-derived DCD-1L, a human antimicrobial peptide, in Escherichia coli

The dermcidin-derived peptide DCD-1L has a broad spectrum of antimicrobial activity over a wide pH range and in high salt concentrations. Thus, it offers a promising alternative to conventional antibiotics. Furthermore, it plays a role in wound healing, atopic dermatitis and acne vulgaris, indicating applications in cosmetic industries. Recently, dermcidin has been identified as a tumor marker improving cancer prognosis. Hence, large quantities of purified DCD-1L peptide are required to meet the needs of basic research and clinical trials. In the current study, we demonstrate SUMO-based heterologous DCD-1L production in Escherichia coli, followed by affinity chromatography purification. The SUMO tag is cleaved with SUMO-specific protease following purification, leaving free DCD-1L peptide without any additional amino acids. The mass of the peptide was further confirmed by MALDI-TOF-TOF analysis. Furthermore, the cleaved DCD-1L showed antimicrobial activity against the E. coli DH5 alpha test strain. The production and purification of DCD-1L using SUMO tag compare advantageously to other protocols previously described. Thus, the SUMO tag system enables large scale recombinant production of the antimicrobial peptide DCD-1L, which constitutes pharmaceutical and therapeutic potential as an alternative antibiotic.

molecular biology

X-ray structures of human ETB receptor provide mechanistic insight into receptor activation and partial activation

Endothelin receptors (ETA and ETB) are class A GPCRs activated by vasoactive peptide endothelins, and are involved in blood pressure regulation. ETB-selective signaling induces vasorelaxation, and thus selective ETB agonists are expected to be utilized for improved anti-tumour drug delivery and neuroprotection. The effectiveness of a highly ETB-selective endothelin analogue, IRL1620, has been investigated in clinical trials. Here, we report the crystal structures of human ETB receptor in complex with ETB-selective agonists, endohelin-3 and IRL1620. The 2.0 [A]-resolution structure of the endothelin-3-bound receptor revealed that the disruption of water-mediated interactions between W6.48 and D2.50, which are highly conserved among class A GPCRs, is critical for receptor activation. These hydrogen-bonding interactions are partially preserved in the IRL1620-bound structure, and a functional analysis revealed the partial agonistic effect of IRL1620. The current findings clarify the detailed molecular mechanism for the coupling between the orthosteric pocket and the G-protein binding, and the partial agonistic effect of IRL1620, thus paving the way for the design of improved agonistic drugs targeting ETB.

molecular biology