Isolation and MS characterisation of recombinant human septin octameric complexes containing distinct SEPT9 isoforms
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ABSTRACT: Native human septins form heterooctameric complexes containing different SEPT9 isoforms. To enable studies of SEPT9 function, we established a protocol for the isolation of recombinant human octamers harboring distinct SEPT9 isoforms. Mass spectrometry analysis is used to assess the purity, integrity and stoichiometry of septins in the purified complex.
Project description:Septins are a family of multimeric GTP-binding proteins, which are abnormally expressed in cancer. Septin 9 (SEPT9) is an essential and ubiquitously expressed septin with multiple isoforms, which have differential expression patterns and effects in breast cancer cells. It is unknown, however, if SEPT9 isoforms associate with different molecular networks and functions. Here, we performed a proteomic screen in MCF-7 breast cancer cells to identify the interactome of GFP-SEPT9 isoforms 1, 4 and 5, which vary in the length of their N-terminus. While all three isoforms associated with SEPT2 and SEPT7, the truncated SEPT9_i4 and SEPT9_i5 interacted with septins of the SEPT6 group more promiscuously than SEPT9_i1, which bound predominately SEPT8. Spatial mapping and functional clustering of non-septin partners showed isoform-specific differences in interactions with proteins of distinct subcellular organelles (nuclei, centrosomes, cilia) and functions (signaling, degradation). Notably, the interactome of the full length SEPT9_i1 was more enriched in cytoskeletal regulators, while the truncated SEPT9_i4 and SEPT9_i5 exhibited preferential and isoform-specific interactions with nuclear and signaling factors as well as ubiquitinating enzymes. These data provide evidence for isoform-specific interactions, which arise from truncations in the N-terminal extensions of SEPT9, and point to novel roles in the pathogenesis of breast cancer.
Project description:Experimentally deciphering and understanding the interaction network of a particular protein provides often evidence for so far unknown functions. For the septins, a class of cytoskeletal proteins, targeted high-throughput approaches that aim at systematically deciphering interaction partners have not yet been performed. Septins regulate the organization of the acin cytoskeleton, vesicle transport and fusion, chromosome alignment- and segregation, and cytokinesis. SEPT9 is part of the core septin hetero-octamer in human cells which is composed of SEPT2, SEPT6, SEPT7, and SEPT9. SEPT9 has been linked to a variety of intracellular functions as well as to diseases and diverse types of cancer. We applied a quantitative proteomics approach to establish an interactome of SEPT9 in human fibroblast cells. We identified among others so far unknown interaction partners from the myosin familiy and could provide evidence that SEPT9 participates in vesicle transport from and to the plasma membrane as well as in the attachment of actin stress fibers to cellular adhesions.
Project description:Septin 9 (SEPT9), a member of the septin gene family, is strongly linked to cancer, particularly breast cancer, where genomic amplification occurs in ~11% of cases. SEPT9 is a putative oncogene as it is amplified in the form of double minute chromosomes in murine models of breast cancer, is a fusion partner of mixed lineage leukemia (MLL) gene in leukemia, and it is a known hot spot of retroviral tagging insertion. SEPT9 contributes to cytoskeleton dynamics, thus oncogenic functions have been proposed based on the broad range of cellular functions it partakes. Yet, a clear mechanism by which SEPT9 elicits tumor-promoting functions is lacking. To obtain unbiased insights on molecular signatures of SEPT9 upregulation in breast tumors, we overexpressed several of its isoforms in breast cancer cell lines. Global transcriptomic profiling supports a role of SEPT9 in invasion. Functional studies indicate that SEPT9 upregulation is sufficient to increase degradation of the extracellular matrix, while its downregulation inhibits this process. The degradation pattern is associated with focal adhesions (FA) at the cell periphery. Increased extracellular matrix digestion during epithelial–mesenchymal transition digestion is significantly associated with increased expression of matrix metalloproteinases. In SEPT9 over expressing cells, MMP3 is secreted to the media at FAs. Downregulation of SEPT9 or chemical inhibition of septin filaments assembly impairs recruitment of MMP3 to FAs. Our results indicate that SEPT9 promotes both trafficking and secretion of MMPs near FAs, thus enhancing migration and invasion of breast cancer cells.
Project description:This experiment aim was to characterize the catabolism of L-rhamnose of Clostridium beijerinckii DSM 6423 by transcriptomic analysis, generating new insights and knowledge on utilization of L-rhamnose for production of chemicals, including Isopropanol, Butanol, Ethanol (IBE) and 1,2-propandiol. These analysis on cultures grown on L-rhamnose compared to D-glucose grown cultures showed upregulation of the L-rhamnose-related clusters and genes, and lower expression of the solventogenic genes, which was reflected in the products formed.
Project description:Septin proteins interact intermolecularly to form hetero-oligomeric complexes that further assemble into higher-order filaments. To investigate whether the interactions among septin proteins are affected by RID, we conducted affinity purification-mass spectrometry (AP-MS) experiments. In this regard, EGFP-tagged SEPT6 or its quadruple mutant SEPT6-4KR was co-expressed with RID-WT or RID-CA in cells and immunoprecipitated by anti-EGFP beads. The resulting co-immunoprecipitates were analyzed and compared with the vector control by label-free quantitative (LFQ) proteomics to identify and quantify septin proteins associated with SEPT6. The MS analysis showed that SEPT6 were indeed co-affinity-purified with all endogenous septin proteins that were identified, such as SEPT2, SEPT3, SEPT5, SEPT6, SEPT7, SEPT8, SEPT9, SEPT10, and SEPT11, in the absence of RID activity. More importantly, the interactions between SEPT6 and these septins were not affected by RID-WT expression. Interestingly, the SEPT6-4KR mutant could still interact and likely form heteromeric complexes with other fatty-acylated septin proteins (e.g., SEPT2, SEPT3, SEPT5, SEPT6, SEPT7, SEPT8, SEPT9, SEPT10 and SEPT11) in the presence of RID activity.
Project description:The propagation of intracellular T cell receptor (TCR) signals involved various adapter proteins that are important molecular switches to connect proteins together. The global characterization of changes in protein-protein interactions following genetic perturbations is critical to understand the reorganization of protein networks associated with the observed phenotypes. Here, by combining genome editing techniques and AP-MS analysis we determined and quantified the molecular reorganization of the SLP76 interactome resulting from the inactivation of each of the three GRB2-family adaptors. Our data define disruption context-specific and time-dependent networks that form around SLP76 after TCR stimulation, and selectively preserved or highly affected protein complexes that regulate T cell activation.
Project description:The project was initially aimed at identifying new members of the SLX4 complex as well as members of the complex that are SUMOylated in vitro. The project was also aimed at assessing whether SUMOylation may change the compositon of the complex by reducing complex association of SUMOylated partners. YFP-SLX4 complexes were immunopurified from Hela Flp-In TRex cells producing full length YFP-SLX4 using a GFP nanobody. The YFP-SLX4 pull down was used in an ex vivo/in vitro SUMO-ligation assay as described in Guervilly et al. 2015. After the SUMO-ligation reaction, beads were washed 5 times with 50 mM Tris-HCl [pH 8.0] buffer, allowing for the removal of SUMOylated proteins that associate less efficiently with SLX4, or other members of the complex. SLX4 and proteins remaining associated with SLX4 after the successive washes were eluted directly in NuPAGE LDS sample buffer (Invitrogen) for 5 min at 95˚C.
Project description:Sertoli cells (SCs), the only somatic cells within seminiferous tubules, associate intimately with developing germ cells. They not only provide physical and nutritional support but also secrete factors essential to the complex developmental processes of germ cell proliferation and differentiation. The SC transcriptome must therefore adapt rapidly during the different stages of spermatogenesis. We report comprehensive genome-wide expression profiles of pure populations of SCs isolated at 5 distinct stages of the first wave of mouse spermatogenesis, using RNA sequencing technology. We were able to reconstruct about 13 901 high-confidence, nonredundant coding and noncoding transcripts, characterized by complex alternative splicing patterns with more than 45% comprising novel isoforms of known genes. Interestingly, roughly one-fifth (2939) of these genes exhibited a dynamic expression profile reflecting the evolving role of SCs during the progression of spermatogenesis, with stage-specific expression of genes involved in biological processes such as cell cycle regulation, metabolism and energy production, retinoic acid synthesis, and blood-testis barrier biogenesis. Finally, regulatory network analysis identified the transcription factors endothelial PAS domain-containing protein 1 (EPAS1/Hif2α), aryl hydrocarbon receptor nuclear translocator (ARNT/Hif1β), and signal transducer and activator of transcription 1 (STAT1) as potential master regulators driving the SC transcriptional program. Our results highlight the plastic transcriptional landscape of SCs during the progression of spermatogenesis and provide valuable resources to better understand SC function and spermatogenesis and its related disorders, such as male infertility. Genome-wide expression profiling analysis using Illumina next-generation sequencing technology
Project description:T cell recirculation and organ entry involve diapedesis through cytoskeleton remodeling. Part of this process is controlled by guanosine exchange factors (GEFs) and GTPase activating proteins (GAPs) that promote active and inactive forms of Rho family of GTPases. Among GAPs, we identified the ARHGAP45, also known as HMHA1 (human minor histocompatibility antigen 1) and determined its interactome by affinity purification coupled to quantitative mass spectrometry (AP-MS) in Jurkat cells. This dataset contains results of AP-MS of Jurkat cells expressing One-Strep-tagged (OST) ARHGAP45 prior to and after TCR stimulation. Each AP-MS purification of OST- protein is associated with a corresponding control (WT Jurkat) at the same time point of stimulation. For each time point, three independent biological replicates were performed and each biological replicate was analyzed in duplicate by mass spectrometry.