It is now known that proteins associated with neurodegenerative disease can spread throughout the brain in a prionlike manner. However, the mechanisms regulating the trans-synaptic spread propagation, including the neuronal release of these proteins, remain unknown. The interaction of neurodegenerative diseaseassociated proteins with the molecular chaperone Hsc70 is well known, and we hypothesized that much like disaggregation, refolding, degradation, and even normal function, Hsc70 may dictate the extracellular fate of these proteins. Here, we show that several proteins, including TDP-43, a-synuclein, and the microtubule-associated protein tau, can be driven out of the cell by an Hsc70 cochaperone, DnaJC5. In fact, DnaJC5 overexpression induced tau release in cells, neurons, and brain tissue, but only when activity of the chaperone Hsc70 was intact and when tau was able to associate with this chaperone. Moreover, release of tau from neurons was reduced in mice lacking the DnaJC5 gene and when the complement of DnaJs in the cell was altered. These results demonstrate that the dynamics of DnaJ/Hsc70 complexes are critically involved in the release of neurodegenerative disease proteins.

To expand the understanding of aging in the model organism Caenorhabditis elegans, global quantification of metabolite and protein levels in young and aged nematodes was performed using mass spectrometry. With age there was a decreased abundance of proteins functioning in transcription termination, mRNA degradation, mRNA stability, protein synthesis, and proteasomal function. Furthermore there was altered S-adenosyl methionine metabolism as well as a decreased abundance of the S-adenosyl methionine synthetase (SAMS-1) protein. Other aging-related changes included alterations in free fatty acid levels and composition, decreased levels of ribosomal proteins, decreased levels of NADP-dependent isocitrate dehydrogenase (IDH1), a shift in the cellular redox state, an increase in sorbitol content, alterations in free amino acid levels, and indications of altered muscle function and sarcoplasmic reticulum Ca2+ homeostasis. There were also decreases in pyrimidine and purine metabolite levels, most markedly nitrogenous bases. Supplementing the culture medium with cytidine (a pyrimidine nucleoside) or hypoxanthine (a purine base) increased lifespan slightly, suggesting that aging-induced alterations in ribonucleotide metabolism affect lifespan. An age-related increase in body size, lipotoxicity from ectopic yolk lipoprotein accumulation, a decline in NAD+ levels, and mitochondrial electron transport chain dysfunction may explain many of these changes. In addition, dietary restriction in aged worms resulting from sarcopenia of the pharyngeal pump likely decreases the abundance of SAMS-1, possibly leading to decreased phosphatidylcholine levels, larger lipid droplets, and ER and mitochondrial stress. The complementary use of proteomics and metabolomics yielded unique insights into the molecular processes altered with age in C. elegans.

Microglia, the resident immune cells of the brain, have been shown to display a complex spectrum of roles that span from neurotrophic to neurotoxic depending on their activation status. Microglia can be classified into four stages of activation, M1, which most closely matches the classical (pro-inflammatory) activation stage, and the alternative activation stages M2a, M2b, and M2c. The alternative activation stages have not yet been comprehensively analyzed through unbiased, global-scale protein expression profiling. In this study, BV2 mouse immortalized microglial cells were stimulated with agonists specific for each of the four stages and total protein expression for 4644 protein groups was quantified using SILAC-based proteomic analysis. After validating induction of the various stages through a targeted cytokine assay and Western blotting of activation states, the data revealed novel insights into the similarities and differences between the various states. The data identify several protein groups whose expression in the anti-inflammatory, pro-healing activation states are altered presumably to curtail inflammatory activation through differential protein expression, in the M2a state including CD74, LYN, SQST1, TLR2, and CD14. The differential expression of these proteins promotes healing, limits phagocytosis, and limits activation of reactive nitrogen species through toll-like receptor cascades. The M2c state appears to center around the down-regulation of a key member in the formation of actin-rich phagosomes, SLP-76. In addition, the proteomic data identified a novel activation marker, DAB2, which is involved in clathrin-mediated endocytosis and is significantly different between M2a and either M1 or M2b states. Western blot analysis of mouse primary microglia stimulated with the various agonists of the classical and alternative activation states revealed a similar trend of DAB2 expression compared with BV2 cells.

Staphylococcus aureus is a major human pathogen that causes infection in a wide variety of sites within the human body. Its ability to adapt to the human host and to produce a successful infection requires precise orchestration of gene expression. While DNA-dependent RNA polymerase (RNAP) is generally well characterized, the roles of several small accessory subunits within the complex have yet to be fully explored. This is particularly true for the omega ( or RpoZ) subunit, which has been extensively studied in Gram-negative bacteria but largely neglected in Grampositive counterparts. In Escherichia coli, it has been shown that ppGpp binding, and thus control of the stringent response, is facilitated by . Interestingly, key residues that facilitate ppGpp binding by are not conserved in S. aureus, and consequently, survival under starvation conditions is unaffected by rpoZ deletion. Further to this, -lacking strains of S. aureus display structural changes in the RNAP complex, which result from increased degradation and misfolding of the ␤= subunit, alterations in ␦ and factor abundance, and a general dissociation of RNAP in the absence of . Through RNA sequencing analysis we detected a variety of transcriptional changes in the rpoZ-deficient strain, presumably as a response to the negative effects of depletion on the transcription machinery. These transcriptional changes translated to an impaired ability of the rpoZ mutant to resist stress and to fully form a biofilm. Collectively, our data underline, for the first time, the importance of for RNAP stability, function, and cellular physiology in S. aureus. IMPORTANCEIn order for bacteria to adjust to changing environments, such as within the host, the transcriptional process must be tightly controlled. Transcription is carried out by DNA-dependent RNA polymerase (RNAP). In addition to its major subunits (␣ 2 ␤␤=) a fifth, smaller subunit, , is present in all forms of life. Although this small subunit is well studied in eukaryotes and Gram-negative bacteria, only limited information is available for Gram-positive and pathogenic species. In this study, we investigated the structural and functional importance of , revealing key roles in subunit folding/stability, complex assembly, and maintenance of transcriptional integrity. Collectively, our data underline, for the first time, the importance of for RNAP function and cellular harmony in S. aureus.KEYWORDS RNA polymerase subunit omega, RpoZ, Staphylococcus aureus, gene regulation T ranscription in all forms of life is a tightly controlled process, necessitated by the essentiality of correct temporal and spatial expression of genes for survival. All transcriptional activity within a cell is maintained by the DNA-dependent RNA polymerase (RNAP). This multiprotein complex is structurally and functionally similar in distant forms of life, displaying only minor variations in composition, e.g., the presence/ absence of certain subunits (1, 2). In bacteria RNAP consists of four main subunits, i.e.,

Long-term exposure to alcohol can have profound effects on the central nervous system including pathophysiological consequences associated with neuroinflammation. Along with astroglia, microglia play an important role in the neuroinflammatory response. Using a SILAC-labeled rat microglial cell line, an expression profile of 2994 proteins was identified in ethanol-treated microglial cells, where 160 and 69 protein groups were determined to be significantly upregulated and downregulated, respectively. In addition, SILAC-based proteomic analysis of lipopolysaccharide-treated microglial cells was performed in order to generate a reference data set representing a "classical" (M1) macrophage activation response in order to compare to the differential protein expression profile of ethanol-treated microglia. On the basis of this comparison as well as other validation experiments performed in this study, ethanol appears to induce partial activation of microglia that is devoid of conventional markers that indicate an M1 phenotype. This study is the first comprehensive proteomic analysis to assess the impact of acute ethanol exposure on microglial function and will provide a significant foundation that includes novel protein markers for future work aimed to characterize the molecular mechanisms associated with ethanol-induced microglial activation and its role in neurodegeneration.

Alzheimer’s disease (AD) is the most prevalent form of dementia in the elderly. Amyloid plaque formation through aggregation of the amyloid beta peptide derived from amyloid precursor protein (APP) is considered one of the hallmark processes leading to AD pathology; however, the precise role of APP in plaque formation and AD pathogenesis is yet to be determined. Using stable isotope labeling by amino acids in cell culture (SILAC) and mass spectrometry, protein expression profiles of APP null, rat neuronal-like B103 cells were compared to B103-695 cells which express the APP isoform, APP-695. A total of 2,979 unique protein groups were identified among 3 biological replicates and significant protein expression changes were identified in a total of 100 non-redundant proteins. Some of the top biological functions associated with the differentially expressed proteins identified include cellular assembly, organization and morphology, cell cycle, lipid metabolism, protein folding, and posttranslational modifications. We report several novel biological pathways influenced by APP-695 expression in neuronal-like cells and provide additional framework for investigating altered molecular mechanisms associated with APP expression and processing and contribution to AD pathology.

Members of the generaHydrogenovibrio,Thiomicrospira, andThiomicrorhabdusfix carbon at hydrothermal vents, coastal sediments, hypersaline lakes, and other sulfidic habitats. The genome sequences of these ubiquitous and prolific chemolithoautotrophs suggest a surprising diversity of mechanisms for the uptake and fixation of dissolved inorganic carbon (DIC); these mechanisms are verified here. Carboxysomes are apparent in the transmission electron micrographs of most of these organisms but are lacking inThiomicrorhabdussp. strain Milos-T2 andThiomicrorhabdus arctica, and the inability ofThiomicrorhabdussp. strain Milos-T2 to grow under low-DIC conditions is consistent with the absence of carboxysome loci in its genome. For the remaining organisms, genes encoding potential DIC transporters from four evolutionarily distinct families (Tcr_0853 and Tcr_0854, Chr, SbtA, and SulP) are located downstream of carboxysome loci. Transporter genes collocated with carboxysome loci, as well as some homologs located elsewhere on the chromosomes, had elevated transcript levels under low-DIC conditions, as assayed by reverse transcription-quantitative PCR (qRT-PCR). DIC uptake was measureable via silicone oil centrifugation when a representative of each of the four types of transporter was expressed inEscherichia coli. The expression of these genes in the carbonic anhydrase-deficientE. colistrain EDCM636 enabled it to grow under low-DIC conditions, a result consistent with DIC transport by these proteins. The results from this study expand the range of DIC transporters within the SbtA and SulP transporter families, verify DIC uptake by transporters encoded byTcr_0853andTcr_0854and their homologs, and introduce DIC as a potential substrate for transporters from the Chr family.IMPORTANCEAutotrophic organisms take up and fix DIC, introducing carbon into the biological portion of the global carbon cycle. The mechanisms for DIC uptake and fixation by autotrophicBacteriaandArchaeaare likely to be diverse but have been well characterized only for “Cyanobacteria.” Based on genome sequences, members of the generaHydrogenovibrio,Thiomicrospira, andThiomicrorhabdushave a variety of mechanisms for DIC uptake and fixation. We verified that most of these organisms are capable of growing under low-DIC conditions, when they upregulate carboxysome loci and transporter genes collocated with these loci on their chromosomes. When these genes, which fall into four evolutionarily independent families of transporters, are expressed inE. coli, DIC transport is detected. This expansion in known DIC transporters across four families, from organisms from a variety of environments, provides insight into the ecophysiology of autotrophs, as well as a toolkit for engineering microorganisms for carbon-neutral biochemistries of industrial importance.

Tau dysfunction is common in several neurodegenerative diseases including Alzheimer’s disease (AD) and frontotemporal dementia (FTD). Affective symptoms have often been associated with aberrant tau pathology and are commonly comorbid in patients with tauopathies, indicating a connection between tau functioning and mechanisms of depression. The current study investigated depression-like behavior in Mapt−/− mice, which contain a targeted deletion of the gene coding for tau. We show that 6-month Mapt−/− mice are resistant to depressive behaviors, as evidenced by decreased immobility time in the forced swim and tail suspension tests, as well as increased escape behavior in a learned helplessness task. Since depression has also been linked to deficient adult neurogenesis, we measured neurogenesis in the hippocampal dentate gyrus and subventricular zone using 5-bromo-2-deoxyuridine (BrdU) labeling. We found that neurogenesis is increased in the dentate gyrus of 14-month-old Mapt−/− brains compared to wild type, providing a potential mechanism for their behavioral phenotypes. In addition to the hippocampus, an upregulation of proteins involved in neurogenesis was observed in the frontal cortex and amygdala of the Mapt−/− mice using proteomic mass spectrometry. All together, these findings suggest that tau may have a role in the depressive symptoms observed in many neurodegenerative diseases and identify tau as a potential molecular target for treating depression.