High sensitivity RNA pseudoknot prediction

Most ab initio pseudoknot predicting methods provide very few folding scenarios for a given RNA sequence and have low sensitivities. RNA researchers, in many cases, would rather sacrifice the specificity for a much higher sensitivity for pseudoknot detection. In this study, we introduce the Pseudoknot Local Motif Model and Dynamic Partner Sequence Stacking (PLMM_DPSS) algorithm which predicts all PLM model pseudoknots within an RNA sequence in a neighboring-region-interference-free fashion. The PLM model is derived from the existing Pseudobase entries. The innovative DPSS approach calculates the optimally lowest stacking energy between two partner sequences. Combined with the Mfold, PLMM_DPSS can also be used in predicting complicated pseudoknots. The test results of PLMM_DPSS, PKNOTS, iterated loop matching, pknotsRG and HotKnots with Pseudobase sequences have shown that PLMM_DPSS is the most sensitive among the five methods. PLMM_DPSS also provides manageable pseudoknot folding scenarios for further structure determination

Phosphoproteomics Analyses to Identify the Candidate Substrates and Signaling Intermediates of the Non-Receptor Tyrosine Kinase, SRMS

SRMS (Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylaton sites) is a non-receptor tyrosine kinase that belongs to the BRK family kinases (BFKs) and is evolutionarily related to the Src family kinases (SFKs). Like SFKs and BFKs, the SRMS protein comprises of two domains involved in protein-protein interactions, namely, the Src-homology 3 domain (SH3) and Src-homology 2 domain (SH2) and one catalytic kinase domain. Unlike members of the BFKs and SFKs, the biochemical and cellular role of SRMS is poorly understood primarily due to the lack of information on the substrates and signaling intermediates regulated by the kinase. Previous biochemical studies have shown that wild type SRMS is enzymatically active and leads to the tyrosine-phosphorylation of several proteins, when expressed exogenously in mammalian cells. These tyrosine-phosphorylated proteins represent the candidate cellular substrates of SRMS which are largely unknown. Further, previous studies have determined that the SRMS protein displays a characteristic punctate cytoplasmic localization pattern in mammalian cells. These SRMS cytoplasmic puncta are uncharacterized and may provide insights into the biochemical and cellular role of the kinase. Here, we utilized mass spectrometry-based quantitative label-free phosphoproteomics to (a) identify the candidate SRMS cellular substrates and (b) candidate signaling intermediates regulated by SRMS, in HEK293 cells expressing ectopic SRMS. Specifically, using a phosphotyrosine enrichment strategy we identified 663 candidate SRMS substrates and consensus substrate-motifs of SRMS. We used customized peptide arrays and performed the high-throughput validation of a subset of the identified candidate SRMS substrates. Further, we independently validated Vimentin and Sam68 as bonafide SRMS substrates. Next, using Titanium dioxide (TiO2)-based phosphopeptide enrichment columns, we identified multiple signaling intermediates of SRMS. Functional gene enrichment analyses revealed several common and unique cellular processes regulated by the candidate SRMS substrates and signaling intermediates. Overall, these studies led to the identification of a significant number of novel and biologically relevant SRMS candidate substrates and signaling intermediates, which mapped to a number of cellular and biological processes primarily involved in cell cycle regulation, apoptosis, RNA processing, DNA repair and protein synthesis. These findings provide an important resource for future mechanistic studies to investigate the cellular and physiological functions of the SRMS. Studies towards characterizing the SRMS cytoplasmic puncta showed that the SRMS punctate structures do not colocalize with some of the major cellular organelles investigated, such as the mitochondria, endoplasmic reticulum, golgi bodies and lysosomes. However, studies investigating the involvement of the SRMS domains in puncta-localization revealed that the SRMS SH2 domain partly regulates this localization pattern. These results highlight the potential role of the SRMS SH2 domain in the localization of SRMS to these cytoplasmic sites and lay important groundwork for future characterization studies

A Systems-Based Analysis of Plasmodium vivax Lifecycle Transcription from Human to Mosquito

Most of the 250 million malaria cases outside of Africa are caused by the parasite Plasmodium vivax. Although drugs can be used to treat P. vivax malaria, drug resistance is spreading and there is no available vaccine. Because this species cannot be readily grown in the laboratory there are added challenges to understanding the function of the many hypothetical genes in the genome. We isolated transcriptional messages from parasites growing in human blood and in mosquitoes, labeled the messages and measured how their levels for different parasite growth conditions. The data for 5,419 parasite genes shows extensive changes as the parasite moves between human and mosquito and reveals highly expressed genes whose proteins might represent new therapeutic targets for experimental vaccines. We discover sets of genes that are likely to play a role in the earliest stages of hepatocyte infection. We find intriguing differences in the expression patterns of different blood stage parasites that may be related to host-response status

Actin cytoskeleton-dependent regulation of corticotropin-releasing factor receptor heteromers

Stress responses are highly nuanced and variable, but how this diversity is achieved by modulating receptor function is largely unknown. Corticotropin-releasing factor receptors (CRFRs), class B G protein–coupled receptors, are pivotal in mediating stress responses. Here we show that the two known CRFRs interact to form heteromeric complexes in HEK293 cells coexpressing both CRFRs and in vivo in mouse pancreas. Coimmunoprecipitation and mass spectrometry confirmed the presence of both CRF1R and CRF2βR, along with actin in these heteromeric complexes. Inhibition of actin filament polymerization prevented the transport of CRF2βR to the cell surface but had no effect on CRF1R. Transport of CRF1R when coexpressed with CRF2βR became actin dependent. Simultaneous stimulation of cells coexpressing CRF1R+CRF2βR with their respective high-affinity agonists, CRF+urocortin2, resulted in approximately twofold increases in peak Ca2+responses, whereas stimulation with urocortin1 that binds both receptors with 10-fold higher affinity did not. The ability of CRFRs to form heteromeric complexes in association with regulatory proteins is one mechanism to achieve diverse and nuanced function

Utilising Uracil DNA Glycosylase to detect the presence of 5-Methylcytosine

DNA is regularly subjected to endogenous and exogenous reagents that cause mutations that can be detrimental to a cell if they are not repaired. One class of enzymes responsible for DNA repair is the family of DNA glycosylases and their role is to remove damaged bases. Uracil DNA Glycosylase (UDG) is a member of this family and is highly specific, removing only uracil, an RNA base, from DNA. Uracil arises in DNA through misincorporation of deoxyuridine monophosphate (dUMP) creating an A.U base pair, or through deamination of cytosine resulting in a G.U base pair. Though UDG acts on A.U pairs, this is not it’s primarily role as A.U pairings are not mutagenic. However the G.U mispair is highly mutagenic and leads to a G.C to A.T transition on subsequent rounds of replication. UDG only reacts with uracil and has no activity at thymine since the 5-methyl group on the base is excluded from the active site. This thesis examines mutants of UDG that can cleave cytosine but not 5-methylcytosine. Methylation of cytosine at CpG sites leads to gene silencing and is an important epigenetic signal. Knowing the methylation state of cytosines will therefore be important for understanding gene control and may be beneficial for treating many diseases. The most common method for detecting cytosine methylation uses a bisulphite reaction followed by normal DNA sequencing methods. This process has several drawbacks and the aim of this work is to create an enzyme that is capable of distinguishing between5-methylcytosine and cytosine. It has been reported that mutation of a critical asparagine in UDG to an aspartate allows the enzyme to accommodate cytosine into its active site; generating a cytosine DNA glycosylase (CDG). Using the natural ability of UDG to distinguish between uracil and thymine due to the presence of the 5-methyl group, we hypothesised that the mutant enzyme should be able to discriminate between5-methylcytosine and cytosine, which differ by the presence or absence of a methyl group in the same position. E. coli and human CDGs were prepared and their ability to remove cytosine or 5-methylcytosine examined when placed in different sequence contexts. hCDG was generated through complete gene synthesis of hUDG followed by the N204D mutation. The corresponding mutation in E.coli (N123D) generates a highly cytotoxic enzyme that cannot even be cloned in pUC19. As L191 aids base flipping, mutation to alanine (L191A) renders the enzyme inactive; activity can then be rescued using a bulky synthetic nucleoside that occupies the base pair and forces the target base into an extrahelical conformation. The L191A mutation was followed by N123D to generate an expressible and functional eCDG, denoted eCYDG. We demonstrate that these mutants have cytosine glycosylase activity when the cytosine is mispaired or unpaired, but not when paired with guanine, and show no activity against5-methylcytosine in any context. The activity of these CDGs varies with the stability of the base pair, with the fastest cleavage rates being obtained with the least stable base pairs, and also varies with the local sequence context. As CDGs are able to discriminate between cytosine and 5-methylcytosine we began development of a real-time PCR assay for detection of 5-methylcytosine. This employed a hexaethylene glycol (HEG) linker opposite the target cytosine, as this produces one of the fastest cleavage rates and cannot be read by a DNA polymerase

TALE and NF-Y co-occupancy marks enhancers of developmental control genes during zygotic genome activation in zebrafish [preprint]

Animal embryogenesis is initiated by maternal factors, but zygotic genome activation (ZGA) shifts control to the embryo at early blastula stages. ZGA is thought to be mediated by specialized maternally deposited transcription factors (TFs), but here we demonstrate that NF-Y and TALE – TFs with known later roles in embryogenesis – co-occupy unique genomic elements at zebrafish ZGA. We show that these elements are selectively associated with early-expressed genes involved in transcriptional regulation and possess enhancer activity in vivo. In contrast, we find that elements individually occupied by either NF-Y or TALE are associated with genes acting later in development – such that NF-Y controls a cilia gene expression program while TALE TFs control expression of hox genes. We conclude that NF-Y and TALE have a shared role at ZGA, but separate roles later during development, demonstrating that combinations of known TFs can regulate subsets of key developmental genes at vertebrate ZGA

Caracterização da ZG16p, uma lectina singular dos grânulos de zimogénio pancreáticos em mamíferos

Doutoramento em BioquímicaThe mechanisms of secretory granule biogenesis and regulated secretion of digestive enzymes in pancreatic acinar cells are still not well understood. To shed light on these processes, which are of biological and clinical importance (e.g., pancreatitis), a better molecular understanding of the components of the granule membrane, their functions and interactions is required. The application of proteomics has largely contributed to the identification of novel zymogen granule (ZG) proteins but was not yet accompanied by a better characterization of their functions. In this study we aimed at a) isolation and identification of novel membrane-associated ZG proteins; b) characterization of the biochemical properties and function of the secretory lectin ZG16p, a membrane-associated protein; c) exploring the potential of ZG16p as a new tool to label the endolysosomal compartment. First, we have performed a suborganellar proteomics approach by combining protein analysis by 2D-PAGE and identification by mass spectrometry, which has led to the identification of novel peripheral ZGM proteins with proteoglycan-binding properties (e.g., chymase, PpiB). Then, we have unveiled new molecular properties and (multiple) functions of the secretory lectin ZG16p. ZG16p is a unique mammalian lectin with glycan and proteoglycan binding properties. Here, I revealed for the first time that ZG16p is highly protease resistant by developing an enterokinase-digestion assay. In addition I revealed that ZG16p binds to a high molecular weight complex at the ZGM (which is also protease resistant) and forms highly stable dimers. In light of these findings I suggest that ZG16p is a key component of a predicted submembranous granule matrix attached to the luminal side of the ZGM that fulfils important functions during sorting and packaging of zymogens. ZG16p, may act as a linker between the matrix and aggregated zymogens due to dimer formation. Furthermore, ZG16p protease resistance might be of higher importance after secretion since it is known that ZG16p binds to pathogenic fungi in the gut. I have further investigated the role of ZG16p binding motifs in its targeting to ZG in AR42J cells, a pancreatic model system. Point mutations of the glycan and the proteoglycan binding motifs did not inhibit the targeting of ZG16p to ZG in AR42J cells. I have also demonstrated that when ZG16p is present in the cytoplasm it interacts with and modulates the endo-lysosomal compartment. Since it is known that impaired autophagy due to lysosomal malfunction is involved in the course of pancreatitis, a potential role of ZG16p in pancreatitis is discussed.Os mecanismos de biogénese dos grânulos secretores e a secreção regulada das enzimas digestivas, nas células acinares do pâncreas, ainda não são totalmente compreendidos. Para esclarecer estes processos, que são de importância biológica e clínica (ex., pancreatite), é necessário um melhor conhecimento molecular dos componentes da membrana dos grânulos, as suas funções e interações. A aplicação da proteómica contribuiu largamente para a identificação de novas proteínas dos grânulos de zimogénio (ZG) mas ainda não foi acompanhada por uma melhor caracterização das suas funções. Este estudo teve como objectivos a) o isolamento e identificação de novas proteínas associadas à membrana dos ZG; b) a caracterização das propriedades bioquímicas e da função da lectina ZG16p, uma proteína associada a membrana dos ZG; c) explorar o potencial da ZG16p como uma nova ferramenta para marcar o compartimento endolisossomal. Inicialmente, efetuamos uma abordagem proteómica ao estudo das frações dos ZG, a qual nos levou à identificação de novas proteínas periféricas da ZGM com capacidade de se ligarem a proteoglicanos (Chymase e PpiB). Depois, começamos a desvendar as propriedades moleculares e (múltiplas) funções da lectina ZG16p. A ZG16p é uma proteína única nos mamíferos com capacidade de se ligar a glicanos e a proteoglicanos. Pela primeira vez, foi revelado que a ZG16p é extremamente resistente a proteases através do desenvolvimento de um ensaio de digestão com enterokinase. Adicionalmente, demonstrei que a ZG16p se liga a um complexo de elevado peso molecular (também resistente a proteases) e forma homodímeros muito estáveis. À luz destas descobertas, nós sugerimos que a ZG16p poderá actuar como um elo de ligação aos proteoglicanos, ajudando na formação e estabilização de uma rede/estrutura (matriz submembranar) ligada ao lúmen da ZGM, que desempenhará uma função importante durante a segregação e empacotamento dos zimogénios. A ZG16p poderá atuar como um elo de ligação entre a matriz e os zimogénios agregados devido à sua capacidade para formar dímeros. Adicionalmente, a resistência da ZG16p a protéases poderá ser de maior importância após a secreção, uma vez que é sabido que a ZG16p se liga a fungos patogénicos nos intestinos. Investiguei ainda, o papel dos domínios de ligação da ZG16p na sua segregação para os ZG em células AR42J, um modelo pancreático. A mutação pontual dos motivos de ligação a glicanos e a proteoglicanos não alterou a segregação da ZG16p para os ZG. Também demonstrei que quando a ZG16p se encontra no citoplasma liga-se ao compartimento endolisossomal. Como é sabido, a desregulação da autofagia devido ao funcionamento defeituoso dos lisossomas está associado à pancreatite, por isso iremos discutir o papel potencial da ZG16p nesta doença

Nuclear FGFR1 regulates gene transcription and promotes antiestrogen resistance in ER+ breast cancer

FGFR1 overexpression has been associated with endocrine resistance in ER+ breast cancer. We found FGFR1 localized in the nucleus of breast cancer cells in primary tumors resistant to estrogen suppression. We investigated a role of nuclear FGFR1 on gene transcription and antiestrogen resistance. Tumors from patients treated with letrozole were subjected to Ki67 and FGFR1 IHC. MCF7 cells were transduced with FGFR1(SP-)(NLS) to promote nuclear FGFR1 overexpression. FGFR1 genomic activity in ER+/FGFR1-amplified breast cancer cells ± FOXA1 siRNA or ± the FGFR tyrosine kinase inhibitor (TKI) erdafitinib was examined by ChIP-Seq and RNA-Seq. The nuclear and chromatin-bound FGFR1 interactome was investigated by Mass Spectrometry (MS). High nuclear FGFR1 expression in ER+ primary tumors positively correlated with post-letrozole Ki67 values. Nuclear FGFR1 overexpression influenced gene transcription and promoted resistance to estrogen suppression and to fulvestrant in vivo. A gene expression signature induced by nuclear FGFR1 correlated with shorter survival in the METABRIC cohort of patients treated with antiestrogens. ChIP-Seq revealed FGFR1 occupancy at transcription start sites, overlapping with active transcription histone marks. MS analysis of the nuclear FGFR1 interactome identified phosphorylated RNA-Polymerase II and FOXA1, with FOXA1 RNAi impairing FGFR1 recruitment to chromatin. Treatment with erdafitinib did not impair nuclear FGFR1 translocation and genomic activity. These data suggest nuclear FGFR1 contributes to endocrine resistance by modulating gene transcription in ER+ breast cancer. Nuclear FGFR1 activity was unaffected by FGFR TKIs, thus supporting the development of treatment strategies to inhibit nuclear FGFR1 in ER+/FGFR1 overexpressing breast cancer

Identification of the Pokeweed Antiviral Protein Interactome by Co-Immunoprecipitation-Mass Spectrometry

Ribosome-inactivating proteins (RIPs) are produced primarily by plants and are named for their enzymatic ability to depurinate ribosomal RNA. RIPs have been shown to have antiviral, antifungal, and antibacterial activity in vitro and when expressed transgenically. They are therefore of interest for their potential in human health, as both pathogenic agents and therapeutics, as well as in agriculture, to confer disease resistance in transgenic crops. However, little is known about the biological function of RIPs in their native context. Phytolacca americana, the American pokeweed, produces a RIP called pokeweed antiviral protein (PAP). The objective of this work is to investigate the role of PAP by mapping out the PAP-protein interactome; this will elucidate PAPs function by implicating the processes in which it is involved. Co-immunoprecipitation coupled with mass spectrometry was used to identify PAP protein interactors in pokeweed. Results identified protein interactions with diverse cellular functions in both the extracellular matrix, where PAP is primarily localized, and the cytoplasm, where the ribosomal target resides. One interactor was identified as a probable extracellular cysteine protease (paCP1); since this protein class has known roles in plant defense, paCP1 was chosen for further validation of its interaction with PAP using reverse co-IP. Differential expression and in silico promoter analysis demonstrated PAP and paCP1 co-expression in response to jasmonic acid, supporting the role of this interaction in defense. This work represents the first protein interactome mapping for a RIP; identification of PAP interactors in plant cells contributes to understanding PAP function and will aid in characterizing the biological role of RIPs in general

Identification of the Pokeweed Antiviral Protein Interactome by Co-Immunoprecipitation-Mass Spectrometry

Ribosome-inactivating proteins (RIPs) are produced primarily by plants and are named for their enzymatic ability to depurinate ribosomal RNA. RIPs have been shown to have antiviral, antifungal, and antibacterial activity in vitro and when expressed transgenically. They are therefore of interest for their potential in human health, as both pathogenic agents and therapeutics, as well as in agriculture, to confer disease resistance in transgenic crops. However, little is known about the biological function of RIPs in their native context. Phytolacca americana, the American pokeweed, produces a RIP called pokeweed antiviral protein (PAP). The objective of this work is to investigate the role of PAP by mapping out the PAP-protein interactome; this will elucidate PAP’s function by implicating the processes in which it is involved. Co-immunoprecipitation coupled with mass spectrometry was used to identify PAP protein interactors in pokeweed. Results identified protein interactions with diverse cellular functions in both the extracellular matrix, where PAP is primarily localized, and the cytoplasm, where the ribosomal target resides. One interactor was identified as a probable extracellular cysteine protease (paCP1); since this protein class has known roles in plant defense, paCP1 was chosen for further validation of its interaction with PAP using reverse co-IP. Differential expression and in silico promoter analysis demonstrated PAP and paCP1 co-expression in response to jasmonic acid, supporting the role of this interaction in defense. This work represents the first protein interactome mapping for a RIP; identification of PAP interactors in plant cells contributes to understanding PAP function and will aid in characterizing the biological role of RIPs in general