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1.
Cell ; 158(1): 54-68, 2014 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-24995978

RESUMO

Cells allocate substantial resources toward monitoring levels of nutrients that can be used for ATP generation by mitochondria. Among the many specialized cell types, neurons are particularly dependent on mitochondria due to their complex morphology and regional energy needs. Here, we report a molecular mechanism by which nutrient availability in the form of extracellular glucose and the enzyme O-GlcNAc Transferase (OGT), whose activity depends on glucose availability, regulates mitochondrial motility in neurons. Activation of OGT diminishes mitochondrial motility. We establish the mitochondrial motor-adaptor protein Milton as a required substrate for OGT to arrest mitochondrial motility by mapping and mutating the key O-GlcNAcylated serine residues. We find that the GlcNAcylation state of Milton is altered by extracellular glucose and that OGT alters mitochondrial motility in vivo. Our findings suggest that, by dynamically regulating Milton GlcNAcylation, OGT tailors mitochondrial dynamics in neurons based on nutrient availability.


Assuntos
Proteínas Adaptadoras de Transporte Vesicular/metabolismo , Glucose/metabolismo , Mitocôndrias/metabolismo , N-Acetilglucosaminiltransferases/metabolismo , Animais , Axônios/metabolismo , Proteínas de Transporte , Drosophila melanogaster , Técnicas de Silenciamento de Genes , Hipocampo/citologia , Hipocampo/metabolismo , Humanos , Masculino , Camundongos , Camundongos Endogâmicos C57BL , N-Acetilglucosaminiltransferases/genética , Ratos , Alinhamento de Sequência
2.
Proc Natl Acad Sci U S A ; 119(49): e2213630119, 2022 12 06.
Artigo em Inglês | MEDLINE | ID: mdl-36442121

RESUMO

In response to bacterial infection, the vertebrate host employs the metal-sequestering protein calprotectin (CP) to withhold essential transition metals, notably Zn(II), to inhibit bacterial growth. Previous studies of the impact of CP-imposed transition-metal starvation in A. baumannii identified two enzymes in the de novo biosynthesis pathway of queuosine-transfer ribonucleic acid (Q-tRNA) that become cellularly abundant, one of which is QueD2, a 6-carboxy-5,6,7,8-tetrahydropterin (6-CPH4) synthase that catalyzes the initial, committed step of the pathway. Here, we show that CP strongly disrupts Q incorporation into tRNA. As such, we compare the AbQueD2 "low-zinc" paralog with a housekeeping, obligatory Zn(II)-dependent enzyme QueD. The crystallographic structure of Zn(II)-bound AbQueD2 reveals a distinct catalytic site coordination sphere and assembly state relative to QueD and possesses a dynamic loop, immediately adjacent to the catalytic site that coordinates a second Zn(II) in the structure. One of these loop-coordinating residues is an invariant Cys18, that protects QueD2 from dissociation of the catalytic Zn(II) while maintaining flux through the Q-tRNA biosynthesis pathway in cells. We propose a "metal retention" model where Cys18 introduces coordinative plasticity into the catalytic site which slows metal release, while also enhancing the metal promiscuity such that Fe(II) becomes an active cofactor. These studies reveal a complex, multipronged evolutionary adaptation to cellular Zn(II) limitation in a key Zn(II) metalloenzyme in an important human pathogen.


Assuntos
Acinetobacter baumannii , Nucleosídeo Q , Humanos , Transcrição Gênica , RNA de Transferência/genética , Metais
3.
J Proteome Res ; 23(6): 2288-2297, 2024 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-38805445

RESUMO

In the work presented herein, a simple serial-pelleting purification strategy combined with a mass spectrometry-based proteomics analysis was developed as a means of discerning differences in extracellular vesicle (EV) populations found in bovine milk samples. A sequence of ultracentrifugation speeds was used to generate changes in the abundances of EV populations, allowing for the identification of associated proteins. A metric was developed to determine the relative abundances of proteins in large EVs (>200 nm) and small EVs (<200 nm). Of the 476 proteins consistently found in this study, 340 are associated with vesicular components. Of these, 156 were heavily enriched in large EVs, 155 shared between large and small EVs, and 29 heavily enriched in small EVs. Additionally, out of 68 proteins annotated as exosome proteins, 32 were enriched in large EVs, 27 shared between large and small EVs, 5 enriched in small EVs, and 7 were found to be nonvesicular contaminant proteins. The top correlated proteins in the small EV group were predominantly membrane-bound proteins, whereas the top correlated proteins in the large EV group were mostly cytosolic enzymes for molecular processing. This method provides a means of assessing the origins of vesicle components and provides new potential marker proteins within discrete vesicle populations.


Assuntos
Exossomos , Leite , Proteômica , Ultracentrifugação , Animais , Bovinos , Exossomos/química , Exossomos/metabolismo , Proteômica/métodos , Leite/química , Ultracentrifugação/métodos , Vesículas Extracelulares/química , Vesículas Extracelulares/metabolismo , Proteínas do Leite/análise , Proteínas do Leite/metabolismo , Proteínas do Leite/química , Espectrometria de Massas/métodos
4.
Proc Natl Acad Sci U S A ; 118(13)2021 03 30.
Artigo em Inglês | MEDLINE | ID: mdl-33753485

RESUMO

In plants, transcription of selfish genetic elements such as transposons and DNA viruses is suppressed by RNA-directed DNA methylation. This process is guided by 24-nt short-interfering RNAs (siRNAs) whose double-stranded precursors are synthesized by DNA-dependent NUCLEAR RNA POLYMERASE IV (Pol IV) and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2). Pol IV and RDR2 coimmunoprecipitate, and their activities are tightly coupled, yet the basis for their association is unknown. Here, we show that an interval near the RDR2 active site contacts the Pol IV catalytic subunit, NRPD1, the largest of Pol IV's 12 subunits. Contacts between the catalytic regions of the two enzymes suggests that RDR2 is positioned to rapidly engage the free 3' ends of Pol IV transcripts and convert these single-stranded transcripts into double-stranded RNAs (dsRNAs).


Assuntos
Proteínas de Arabidopsis/metabolismo , RNA Polimerases Dirigidas por DNA/metabolismo , RNA de Cadeia Dupla/biossíntese , RNA Polimerase Dependente de RNA/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/isolamento & purificação , Domínio Catalítico/genética , RNA Polimerases Dirigidas por DNA/genética , RNA Polimerases Dirigidas por DNA/isolamento & purificação , Simulação de Acoplamento Molecular , Mutagênese Sítio-Dirigida , RNA Polimerase Dependente de RNA/genética , RNA Polimerase Dependente de RNA/isolamento & purificação , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Técnicas do Sistema de Duplo-Híbrido
5.
Proc Natl Acad Sci U S A ; 118(9)2021 03 02.
Artigo em Inglês | MEDLINE | ID: mdl-33627406

RESUMO

Marine Synechococcus cyanobacteria owe their ubiquity in part to the wide pigment diversity of their light-harvesting complexes. In open ocean waters, cells predominantly possess sophisticated antennae with rods composed of phycocyanin and two types of phycoerythrins (PEI and PEII). Some strains are specialized for harvesting either green or blue light, while others can dynamically modify their light absorption spectrum to match the dominant ambient color. This process, called type IV chromatic acclimation (CA4), has been linked to the presence of a small genomic island occurring in two configurations (CA4-A and CA4-B). While the CA4-A process has been partially characterized, the CA4-B process has remained an enigma. Here we characterize the function of two members of the phycobilin lyase E/F clan, MpeW and MpeQ, in Synechococcus sp. strain A15-62 and demonstrate their critical role in CA4-B. While MpeW, encoded in the CA4-B island and up-regulated in green light, attaches the green light-absorbing chromophore phycoerythrobilin to cysteine-83 of the PEII α-subunit in green light, MpeQ binds phycoerythrobilin and isomerizes it into the blue light-absorbing phycourobilin at the same site in blue light, reversing the relationship of MpeZ and MpeY in the CA4-A strain RS9916. Our data thus reveal key molecular differences between the two types of chromatic acclimaters, both highly abundant but occupying distinct complementary ecological niches in the ocean. They also support an evolutionary scenario whereby CA4-B island acquisition allowed former blue light specialists to become chromatic acclimaters, while former green light specialists would have acquired this capacity by gaining a CA4-A island.


Assuntos
Proteínas de Bactérias/metabolismo , Complexos de Proteínas Captadores de Luz/metabolismo , Liases/metabolismo , Ficocianina/biossíntese , Ficoeritrina/biossíntese , Pigmentos Biológicos/biossíntese , Synechococcus/metabolismo , Aclimatação , Organismos Aquáticos , Proteínas de Bactérias/genética , Clonagem Molecular , Escherichia coli/genética , Escherichia coli/metabolismo , Regulação Bacteriana da Expressão Gênica , Teste de Complementação Genética , Vetores Genéticos/química , Vetores Genéticos/metabolismo , Ilhas Genômicas , Luz , Complexos de Proteínas Captadores de Luz/genética , Liases/genética , Ficobilinas/biossíntese , Ficobilinas/genética , Ficocianina/genética , Ficoeritrina/genética , Filogenia , Pigmentos Biológicos/genética , Subunidades Proteicas/genética , Subunidades Proteicas/metabolismo , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Synechococcus/classificação , Synechococcus/genética , Synechococcus/efeitos da radiação , Urobilina/análogos & derivados , Urobilina/biossíntese , Urobilina/genética
6.
Analyst ; 148(18): 4438-4446, 2023 Sep 11.
Artigo em Inglês | MEDLINE | ID: mdl-37555458

RESUMO

A one-step protocol for the automated flow synthesis of protected glycosylated amino acids is described using pumps with open-source controls in overall yields of 21-50%. The resulting glycosylated amino acids could be used directly in solid-phase peptide synthesis (SPPS) protocols to quickly produce glycopeptide standards. Access to a variety of stereoisomers of the sugar enabled the development of an LC-MS/MS protocol that can distinguish between peptides modified with carbohydrates having the same exact mass. This method could definitively identify fucose in an O-glycosylation site on the transmembrane protein, Notch1.


Assuntos
Glicopeptídeos , Açúcares , Glicopeptídeos/química , Cromatografia Líquida , Espectrometria de Massas em Tandem , Carboidratos , Aminoácidos/química
7.
Cell ; 134(5): 866-76, 2008 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-18722006

RESUMO

The nearly 600 proteases in the human genome regulate a diversity of biological processes, including programmed cell death. Comprehensive characterization of protease signaling in complex biological samples is limited by available proteomic methods. We have developed a general approach for global identification of proteolytic cleavage sites using an engineered enzyme to selectively biotinylate free protein N termini for positive enrichment of corresponding N-terminal peptides. Using this method to study apoptosis, we have sequenced 333 caspase-like cleavage sites distributed among 292 protein substrates. These sites are generally not predicted by in vitro caspase substrate specificity but can be used to predict other physiological caspase cleavage sites. Structural bioinformatic studies show that caspase cleavage sites often appear in surface-accessible loops and even occasionally in helical regions. Strikingly, we also find that a disproportionate number of caspase substrates physically interact, suggesting that these dimeric proteases target protein complexes and networks to elicit apoptosis.


Assuntos
Apoptose/efeitos dos fármacos , Caspases/metabolismo , Proteínas/análise , Proteínas/metabolismo , Proteômica , Antineoplásicos Fitogênicos/farmacologia , Caspases/química , Etoposídeo/farmacologia , Humanos , Células Jurkat , Ligação Proteica , Especificidade por Substrato
8.
Int J Mol Sci ; 24(5)2023 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-36902150

RESUMO

Calcium/calmodulin (CaM)-dependent protein kinase kinase 2 (CaMKK2) regulates bone remodeling through its effects on osteoblasts and osteoclasts. However, its role in osteocytes, the most abundant bone cell type and the master regulator of bone remodeling, remains unknown. Here we report that the conditional deletion of CaMKK2 from osteocytes using Dentine matrix protein 1 (Dmp1)-8kb-Cre mice led to enhanced bone mass only in female mice owing to a suppression of osteoclasts. Conditioned media isolated from female CaMKK2-deficient osteocytes inhibited osteoclast formation and function in in vitro assays, indicating a role for osteocyte-secreted factors. Proteomics analysis revealed significantly higher levels of extracellular calpastatin, a specific inhibitor of calcium-dependent cysteine proteases calpains, in female CaMKK2 null osteocyte conditioned media, compared to media from female control osteocytes. Further, exogenously added non-cell permeable recombinant calpastatin domain I elicited a marked, dose-dependent inhibition of female wild-type osteoclasts and depletion of calpastatin from female CaMKK2-deficient osteocyte conditioned media reversed the inhibition of matrix resorption by osteoclasts. Our findings reveal a novel role for extracellular calpastatin in regulating female osteoclast function and unravel a novel CaMKK2-mediated paracrine mechanism of osteoclast regulation by female osteocytes.


Assuntos
Osteoclastos , Osteócitos , Animais , Feminino , Camundongos , Cálcio/metabolismo , Quinase da Proteína Quinase Dependente de Cálcio-Calmodulina/metabolismo , Meios de Cultivo Condicionados/farmacologia , Osteoclastos/metabolismo , Osteócitos/metabolismo , Caracteres Sexuais
9.
Glycobiology ; 32(3): 201-207, 2022 03 30.
Artigo em Inglês | MEDLINE | ID: mdl-34939082

RESUMO

A substantial shortcoming of large-scale datasets is often the inability to easily represent and visualize key features. This problem becomes acute when considering the increasing technical ability to profile large numbers of glycopeptides and glycans in recent studies. Here, we describe a simple, concise graphical representation intended to capture the microheterogeneity associated with glycan modification at specific sites. We illustrate this method by showing visual representations of the glycans and glycopeptides from a variety of species. The graphical representation presented allows one to easily discern the compositions of all glycans, similarities and differences of modifications found in different samples and, in the case of N-linked glycans, the initial steps in the biosynthetic pathway.


Assuntos
Proteômica , Espectrometria de Massas em Tandem , Glicopeptídeos/química , Glicosilação , Polissacarídeos/química , Proteômica/métodos , Espectrometria de Massas em Tandem/métodos
10.
J Am Chem Soc ; 144(23): 10241-10250, 2022 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-35647863

RESUMO

Using a discrete, intracellular 19F nuclear magnetic resonance (NMR) probe on transmembrane helix 6 of the neurotensin receptor 1 (NTS1), we aim to understand how ligands and transducers modulate the receptor's structural ensemble in a solution. For apo NTS1, 19F NMR spectra reveal an ensemble of at least three conformational substates (one inactive and two active-like) in equilibrium that exchange on the millisecond to second timescale. Dynamic NMR experiments reveal that these substates follow a linear three-site exchange process that is both thermodynamically and kinetically remodeled by orthosteric ligands. As previously observed in other G protein-coupled receptors (GPCRs), the full agonist is insufficient to completely stabilize the active-like state. The inactive substate is abolished upon coupling to ß-arrestin-1 (ßArr1) or the C-terminal helix of Gαq, which comprises ≳60% of the GPCR/G protein interface surface area. Whereas ßArr1 exclusively selects for pre-existing active-like substates, the Gαq peptide induces a new substate. Both transducer molecules promote substantial line broadening of active-like states, suggesting contributions from additional microsecond to millisecond exchange processes. Together, our study suggests that (i) the NTS1 allosteric activation mechanism may be alternatively dominated by induced fit or conformational selection depending on the coupled transducer, and (ii) the available static structures do not represent the entire conformational ensemble observed in a solution.


Assuntos
Receptores Acoplados a Proteínas G , Receptores de Neurotensina , Ligantes , Proteínas de Membrana , Conformação Proteica , Receptores Acoplados a Proteínas G/química , Receptores de Neurotensina/química , Receptores de Neurotensina/metabolismo , Transdutores
11.
Anal Chem ; 94(25): 8909-8918, 2022 06 28.
Artigo em Inglês | MEDLINE | ID: mdl-35699514

RESUMO

Unresolved inflammation compromises diabetic wound healing. Recently, we reported that inadequate RNA packaging in murine wound-edge keratinocyte-originated exosomes (Exoκ) leads to persistent inflammation [Zhou, X. ACS Nano 2020, 14(10), 12732-12748]. Herein, we use charge detection mass spectrometry (CDMS) to analyze intact Exoκ isolated from a 5 day old wound-edge tissue of diabetic mice and a heterozygous nondiabetic littermate control group. In CDMS, the charge (z) and mass-to-charge ratio (m/z) of individual exosome particles are measured simultaneously, enabling the direct analysis of masses in the 1-200 MDa range anticipated for exosomes. These measurements reveal a broad mass range for Exoκ from ∼10 to >100 MDa. The m and z values for these exosomes appear to fall into families (subpopulations); a statistical modeling analysis partially resolves ∼10-20 Exoκ subpopulations. Complementary proteomics, immunofluorescence, and electron microscopy studies support the CDMS results that Exoκ from diabetic and nondiabetic mice vary substantially. Subpopulations having high z (>650) and high m (>44 MDa) are more abundant in nondiabetic animals. We propose that these high m and z particles may arise from differences in cargo packaging. The veracity of this idea is discussed in light of other recent CDMS results involving genome packaging in vaccines, as well as exosome imaging experiments. Characterization of intact exosome particles based on the physical properties of m and z provides a new means of investigating wound healing and suggests that CDMS may be useful for other pathologies.


Assuntos
Diabetes Mellitus Experimental , Exossomos , Animais , Diabetes Mellitus Experimental/patologia , Exossomos/patologia , Inflamação , Queratinócitos , Espectrometria de Massas , Camundongos
12.
Proc Biol Sci ; 289(1982): 20220668, 2022 09 14.
Artigo em Inglês | MEDLINE | ID: mdl-36100021

RESUMO

Coordinating physiological and behavioural processes across the annual cycle is essential in enabling individuals to maximize fitness. While the mechanisms underlying seasonal reproduction and its associated behaviours are well characterized, fewer studies have examined the hormonal basis of non-reproductive social behaviours (e.g. aggression) on a seasonal time scale. Our previous work suggests that the pineal hormone melatonin facilitates a 'seasonal switch' in neuroendocrine regulation of aggression in male and female Siberian hamsters (Phodopus sungorus), specifically by acting on the adrenal glands to increase the production of the androgen dehydroepiandrosterone (DHEA) during the short-day (SD) photoperiods of the non-breeding season. Here, we provide evidence that the activity of 3ß-hydroxysteroid dehydrogenase/Δ5-Δ4 isomerase (3ß-HSD), a key enzyme within the steroidogenic pathway that mediates DHEA synthesis and metabolism, varies in a sex-specific and melatonin-dependent manner. Although both male and female hamsters displayed increased aggression in response to SDs and SD-like melatonin, only males showed an increase in adrenal 3ß-HSD activity. Conversely, SD and melatonin-treated females exhibited reductions in both adrenal and neural 3ß-HSD activity. Collectively, these results suggest a potential role for 3ß-HSD in modulating non-breeding aggression and, more broadly, demonstrate how distinct neuroendocrine mechanisms may underlie the same behavioural phenotype in males and females.


Assuntos
Melatonina , Phodopus , Agressão/fisiologia , Animais , Cricetinae , Desidroepiandrosterona/metabolismo , Feminino , Masculino , Melatonina/metabolismo , Phodopus/metabolismo , Estações do Ano
13.
Plant Cell ; 31(11): 2664-2681, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31727786

RESUMO

The Pseudomonas syringae effector protein AvrRpm1 activates the Arabidopsis (Arabidopsis thaliana) intracellular innate immune receptor protein RESISTANCE TO PSEUDOMONAS MACULICOLA1 (RPM1) via modification of a second Arabidopsis protein, RPM1-INTERACTING PROTEIN4 (AtRIN4). Prior work has shown that AvrRpm1 induces phosphorylation of AtRIN4, but homology modeling indicated that AvrRpm1 may be an ADP-ribosyl transferase. Here, we show that AvrRpm1 induces ADP-ribosylation of RIN4 proteins from both Arabidopsis and soybean (Glycine max) within two highly conserved nitrate-induced (NOI) domains. It also ADP ribosylates at least 10 additional Arabidopsis NOI domain-containing proteins. The ADP-ribosylation activity of AvrRpm1 is required for subsequent phosphorylation on Thr-166 of AtRIN4, an event that is necessary and sufficient for RPM1 activation. We also show that the C-terminal NOI domain of AtRIN4 interacts with the exocyst subunits EXO70B1, EXO70E1, EXO70E2, and EXO70F1. Mutation of either EXO70B1 or EXO70E2 inhibited secretion of callose induced by the bacterial flagellin-derived peptide flg22. Substitution of RIN4 Thr-166 with Asp enhanced the association of AtRIN4 with EXO70E2, which we posit inhibits its callose deposition function. Collectively, these data indicate that AvrRpm1 ADP-ribosyl transferase activity contributes to virulence by promoting phosphorylation of RIN4 Thr-166, which inhibits the secretion of defense compounds by promoting the inhibitory association of RIN4 with EXO70 proteins.plantcell;31/11/2664/FX1F1fx1.


Assuntos
ADP Ribose Transferases/metabolismo , Proteínas de Arabidopsis/metabolismo , Proteínas de Bactérias/metabolismo , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Proteínas de Soja/metabolismo , Arabidopsis , Proteínas de Bactérias/genética , Mutagênese Sítio-Dirigida , Mutação , Fosforilação , Plantas Geneticamente Modificadas , Pseudomonas syringae/patogenicidade , Glycine max , Nicotiana/genética , Virulência
14.
Plant Cell ; 2019 Sep 23.
Artigo em Inglês | MEDLINE | ID: mdl-31548257

RESUMO

The Pseudomonas syringae effector protein AvrRpm1 activates the Arabidopsis intracellular innate immune receptor protein RPM1 via modification of a second Arabidopsis protein, RIN4. Prior work has shown that AvrRpm1 induces phosphorylation of AtRIN4, but homology modeling indicated that AvrRpm1 may be an ADP-ribosyl transferase. Here we show that AvrRpm1 induces ADP-ribosylation of RIN4 proteins from both Arabidopsis and soybean within two highly conserved nitrate-induced (NOI) domains. It also ADP-ribosylates at least ten additional Arabidopsis NOI domain-containing proteins. The ADP-ribosylation activity of AvrRpm1 is required for subsequent phosphorylation on threonine 166 of Arabidopsis RIN4, an event that is necessary and sufficient for RPM1 activation. We also show that the C-terminal NOI domain of AtRIN4 interacts with the exocyst subunits EXO70B1, EXO70E1, EXO70E2 and EXO70F1. Mutation of either EXO70B1 or EXO70E2 inhibited secretion of callose induced by the bacterial flagellin-derived peptide flg22. Substitution of RIN4 threonine 166 with aspartate enhanced the association of AtRIN4 with EXO70E2, which we posit inhibits its callose deposition function. Collectively, these data indicate that AvrRpm1 ADP-ribosyl transferase activity contributes to virulence by promoting phosphorylation of RIN4 threonine 166, which inhibits the secretion of defense compounds by promoting the inhibitory association of RIN4 with EXO70 proteins.

15.
Anal Chem ; 93(24): 8484-8492, 2021 06 22.
Artigo em Inglês | MEDLINE | ID: mdl-34101419

RESUMO

The thermal stabilities of endogenous, intact proteins and protein assemblies in complex mixtures were characterized in parallel by means of variable-temperature electrospray ionization coupled to mass spectrometry (vT-ESI-MS). The method is demonstrated by directly measuring the melting transitions of seven proteins from a mixture of proteins derived from ribosomes. A proof-of-concept measurement of a fraction of an Escherichia coli lysate is provided to extend this approach to characterize the thermal stability of a proteome. As the solution temperature is increased, proteins and protein complexes undergo structural and organizational transitions; for each species, the folded ↔ unfolded and assembled ↔ disassembled populations are monitored based on changes in vT-ESI-MS charge state distributions and masses. The robustness of the approach illustrates a step toward the proteome-wide characterization of thermal stabilities and structural transitions-the stabilitome.


Assuntos
Proteínas Ribossômicas , Espectrometria de Massas por Ionização por Electrospray , Escherichia coli , Proteoma , Temperatura
16.
Anal Chem ; 92(21): 14357-14365, 2020 11 03.
Artigo em Inglês | MEDLINE | ID: mdl-32985870

RESUMO

Exosomes represent a class of secreted biological vesicles, which have recently gained attention due to their function as intertissue and interorganism transporters of genetic materials, small molecules, lipids, and proteins. Although the protein constituents of these exosomes are often glycosylated, a large-scale characterization of the glycoproteome has not yet been completed. This study identified 3144 unique glycosylation events belonging to 378 glycoproteins and 604 unique protein sites of glycosylation. With these data, we investigated the level of glycan microheterogeneity within the urinary exosomes, finding on average 5.9 glycans per site. The glycan family abundance on individual proteins showed subtle differences, providing an additional level of molecular characterization compared to the unmodified proteome. Finally, we show protein site-specific changes in regard to the common urinary glycoprotein, uromodulin. While uromodulin is an individual case, these same site-specific analyses provide a way forward for developing diagnostic glycoprotein biomarkers with urine as a noninvasive biological fluid. This study represents an important first step in understanding the functional urinary glycoproteome.


Assuntos
Exossomos/metabolismo , Glicoproteínas/metabolismo , Glicoproteínas/urina , Proteômica/métodos , Urina/citologia , Glicosilação , Humanos
17.
Anal Chem ; 92(4): 3285-3292, 2020 02 18.
Artigo em Inglês | MEDLINE | ID: mdl-31989813

RESUMO

The masses of particles in a bovine milk extracellular vesicle (EV) preparation enriched for exosomes were directly determined for the first time by charge detection mass spectrometry (CDMS). In CDMS, both the mass-to-charge ratio (m/z) and z are determined simultaneously for individual particles, enabling mass determinations for particles that are far beyond the mass limit (∼1.0 MDa) of conventional mass spectrometry (MS). Particle masses and charges span a wide range from m ∼ 2 to ∼90 MDa and z ∼ 50 to ∼1300 e (elementary charges) and are highly dependent upon the conditions used to extract and isolate the EVs. EV particles span a continuum of masses, reflecting the highly heterogeneous nature of these samples. However, evidence for unique populations of particles is obtained from correlation of the charges and masses. An analysis that uses a two-dimensional Gaussian model, provides evidence for six families of particles, four of which having masses in the range expected for exosomes. Complementary proteomics measurements and electron microscopy (EM) imaging are used to further characterize the EVs and confirm that these samples have been enriched in exosomes. The ability to characterize such extremely heterogeneous mixtures of large particles with rapid, sensitive, and high-resolution MS techniques is critical to ongoing analytical efforts to separate and purify exosomes and exosome subpopulations. Direct measurement of each particle's mass and charge is a new means of characterizing the physical and chemical properties of exosomes and other EVs.


Assuntos
Exossomos/química , Espectrometria de Massas/métodos , Leite/citologia , Animais , Bovinos , Cromatografia Líquida , Exossomos/metabolismo , Proteômica
18.
Proc Natl Acad Sci U S A ; 114(9): 2355-2360, 2017 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-28196888

RESUMO

Sulfide was used as an electron donor early in the evolution of photosynthesis, with many extant photosynthetic bacteria still capable of using sulfur compounds such as hydrogen sulfide (H2S) as a photosynthetic electron donor. Although enzymes involved in H2S oxidation have been characterized, mechanisms of regulation of sulfide-dependent photosynthesis have not been elucidated. In this study, we have identified a sulfide-responsive transcriptional repressor, SqrR, that functions as a master regulator of sulfide-dependent gene expression in the purple photosynthetic bacterium Rhodobacter capsulatus SqrR has three cysteine residues, two of which, C41 and C107, are conserved in SqrR homologs from other bacteria. Analysis with liquid chromatography coupled with an electrospray-interface tandem-mass spectrometer reveals that SqrR forms an intramolecular tetrasulfide bond between C41 and C107 when incubated with the sulfur donor glutathione persulfide. SqrR is oxidized in sulfide-stressed cells, and tetrasulfide-cross-linked SqrR binds more weakly to a target promoter relative to unmodified SqrR. C41S and C107S R. capsulatus SqrRs lack the ability to respond to sulfide, and constitutively repress target gene expression in cells. These results establish that SqrR is a sensor of H2S-derived reactive sulfur species that maintain sulfide homeostasis in this photosynthetic bacterium and reveal the mechanism of sulfide-dependent transcriptional derepression of genes involved in sulfide metabolism.


Assuntos
Elétrons , Regulação Bacteriana da Expressão Gênica , Sulfeto de Hidrogênio/metabolismo , Fotossíntese/genética , Proteínas Repressoras/genética , Rhodobacter capsulatus/genética , Sequência de Bases , Sítios de Ligação , Evolução Biológica , Cisteína/química , Cisteína/metabolismo , Dissulfetos/química , Transporte de Elétrons , Glutationa/análogos & derivados , Glutationa/química , Oxirredução , Regiões Promotoras Genéticas , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Proteínas Repressoras/química , Proteínas Repressoras/metabolismo , Rhodobacter capsulatus/metabolismo , Homologia Estrutural de Proteína , Enxofre/metabolismo
19.
Proc Natl Acad Sci U S A ; 113(47): 13390-13395, 2016 11 22.
Artigo em Inglês | MEDLINE | ID: mdl-27821767

RESUMO

The regulated recruitment of Cdc45 and GINS is key to activating the eukaryotic MCM(2-7) replicative helicase. We demonstrate that the homohexameric archaeal MCM helicase associates with orthologs of GINS and Cdc45 in vivo and in vitro. Association of these factors with MCM robustly stimulates the MCM helicase activity. In contrast to the situation in eukaryotes, archaeal Cdc45 and GINS form an extremely stable complex before binding MCM. Further, the archaeal GINS•Cdc45 complex contains two copies of Cdc45. Our analyses give insight into the function and evolution of the conserved core of the archaeal/eukaryotic replisome.


Assuntos
Archaea/metabolismo , Proteínas de Ciclo Celular/metabolismo , Proteínas Cromossômicas não Histona/metabolismo , Proteínas de Manutenção de Minicromossomo/metabolismo , Proteínas Arqueais/metabolismo , Evolução Molecular , Complexos Multiproteicos/química , Complexos Multiproteicos/metabolismo , Ligação Proteica
20.
J Bacteriol ; 200(23)2018 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-30201783

RESUMO

Rotary flagella propel bacteria through liquid and across semisolid environments. Flagella are composed of the basal body that constitutes the motor for rotation, the curved hook that connects to the basal body, and the flagellar filament that propels the cell. Flagellar filaments can be composed of a single flagellin protein, such as in Escherichia coli, or made up of multiple flagellins, such as in Agrobacterium tumefaciens The four distinct flagellins FlaA, FlaB, FlaC, and FlaD produced by wild-type A. tumefaciens are not redundant in function but have specific properties. FlaA and FlaB are much more abundant than FlaC and FlaD and are readily observable in mature flagellar filaments, when either FlaA or FlaB is fluorescently labeled. Cells producing FlaA with any one of the other three flagellins can generate functional filaments and thus are motile, but FlaA alone cannot constitute a functional filament. In flaA mutants that manifest swimming deficiencies, there are multiple ways by which these mutations can be phenotypically suppressed. These suppressor mutations primarily occur within or upstream of the flaB flagellin gene or in the transcription factor sciP regulating flagellin expression. The helical conformation of the flagellar filament appears to require a key asparagine residue present in FlaA and absent in other flagellins. However, FlaB can be spontaneously mutated to render helical flagella in the absence of FlaA, reflecting their overall similarity and perhaps the subtle differences in the specific functions they have evolved to fulfill.IMPORTANCE Flagellins are abundant bacterial proteins comprising the flagellar filaments that propel bacterial movement. Several members of the alphaproteobacterial group express multiple flagellins, in contrast to model systems, such as with Escherichia coli, which has one type of flagellin. The plant pathogen Agrobacterium tumefaciens has four flagellins, the abundant and readily detected FlaA and FlaB, and lower levels of FlaC and FlaD. Mutational analysis reveals that FlaA requires at least one of the other flagellins to function, as flaA mutants produce nonhelical flagella and cannot swim efficiently. Suppressor mutations can rescue this swimming defect through mutations in the remaining flagellins, including structural changes imparting helical shape to the flagella, and putative regulators. Our findings shed light on how multiple flagellins contribute to motility.


Assuntos
Agrobacterium tumefaciens/genética , Flagelina/metabolismo , Agrobacterium tumefaciens/fisiologia , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Citoesqueleto/genética , Citoesqueleto/metabolismo , Análise Mutacional de DNA , Flagelos/ultraestrutura , Flagelina/genética , Microscopia de Fluorescência , Movimento , Mutação , Fenótipo , Isoformas de Proteínas
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