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1.
Plant Biotechnol J ; 22(1): 248-261, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-37822043

RESUMEN

Vascular wilt diseases caused by Fusarium oxysporum are a major threat to many agriculturally important crops. Genetic resistance is rare and inevitably overcome by the emergence of new races. To identify potentially durable and non-race-specific genetic resistance against Fusarium wilt diseases, we set out to identify effector targets in tomato that mediate susceptibility to the fungus. For this purpose, we used the SIX8 effector protein, an important and conserved virulence factor present in many pathogenic F. oxysporum isolates. Using protein pull-downs and yeast two-hybrid assays, SIX8 was found to interact specifically with two members of the tomato TOPLESS family: TPL1 and TPL2. Loss-of-function mutations in TPL1 strongly reduced disease susceptibility to Fusarium wilt and a tpl1;tpl2 double mutant exerted an even higher level of resistance. Similarly, Arabidopsis tpl;tpr1 mutants became significantly less diseased upon F. oxysporum inoculation as compared to wildtype plants. We conclude that TPLs encode susceptibility genes whose mutation can confer resistance to F. oxysporum.


Asunto(s)
Arabidopsis , Fusarium , Solanum lycopersicum , Arabidopsis/genética , Arabidopsis/microbiología , Solanum lycopersicum/genética , Factores de Virulencia/genética , Mutación/genética , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/microbiología
2.
Mol Plant Microbe Interact ; 37(4): 380-395, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38114195

RESUMEN

Bemisia tabaci (whitefly) is a polyphagous agroeconomic pest species complex. Two members of this species complex, Mediterranean (MED) and Middle-East-Asia Minor 1 (MEAM1), have a worldwide distribution and have been shown to manipulate plant defenses through effectors. In this study, we used three different strategies to identify three MEAM1 proteins that can act as effectors. Effector B1 was identified using a bioinformatics-driven effector-mining strategy, whereas effectors S1 and P1 were identified in the saliva of whiteflies collected from artificial diet and in phloem exudate of tomato on which nymphs were feeding, respectively. These three effectors were B. tabaci specific and able to increase whitefly fecundity when transiently expressed in tobacco plants (Nicotiana tabacum). Moreover, they reduced growth of Pseudomonas syringae pv. tabaci in Nicotiana benthamiana. All three effectors changed gene expression in planta, and B1 and S1 also changed phytohormone levels. Gene ontology and KEGG pathway enrichment analysis pinpointed plant-pathogen interaction and photosynthesis as the main enriched pathways for all three effectors. Our data thus show the discovery and validation of three new B. tabaci MEAM1 effectors that increase whitefly fecundity and modulate plant immunity. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.


Asunto(s)
Hemípteros , Nicotiana , Animales , Nicotiana/genética , Nicotiana/microbiología , Proteínas de Insectos/genética , Proteínas de Insectos/metabolismo , Solanum lycopersicum/genética , Solanum lycopersicum/microbiología , Solanum lycopersicum/parasitología , Pseudomonas syringae/fisiología , Enfermedades de las Plantas/parasitología , Enfermedades de las Plantas/microbiología , Reguladores del Crecimiento de las Plantas/metabolismo , Fertilidad/genética
3.
Nat Commun ; 14(1): 3666, 2023 06 28.
Artículo en Inglés | MEDLINE | ID: mdl-37380635

RESUMEN

Green leaf volatiles (GLVs) are short-chain oxylipins that are emitted from plants in response to stress. Previous studies have shown that oral secretions (OS) of the tobacco hornworm Manduca sexta, introduced into plant wounds during feeding, catalyze the re-arrangement of GLVs from Z-3- to E-2-isomers. This change in the volatile signal however is bittersweet for the insect as it can be used by their natural enemies, as a prey location cue. Here we show that (3Z):(2E)-hexenal isomerase (Hi-1) in M. sexta's OS catalyzes the conversion of the GLV Z-3-hexenal to E-2-hexenal. Hi-1 mutants that were raised on a GLV-free diet showed developmental disorders, indicating that Hi-1 also metabolizes other substrates important for the insect's development. Phylogenetic analysis placed Hi-1 within the GMCß-subfamily and showed that Hi-1 homologs from other lepidopterans could catalyze similar reactions. Our results indicate that Hi-1 not only modulates the plant's GLV-bouquet but also functions in insect development.


Asunto(s)
Líquidos Corporales , Manduca , Animales , Filogenia , Catálisis , Hojas de la Planta
4.
Microorganisms ; 10(9)2022 Aug 24.
Artículo en Inglés | MEDLINE | ID: mdl-36144297

RESUMEN

Fluorescent fusion proteins were expressed in Bacillus cereus to visualize the germinosome by introducing a plasmid that carries fluorescent fusion proteins of germinant receptor GerR subunits or germinosome scaffold protein GerD. The effects of plasmid insertion and recombinant protein expression on the spore proteome were investigated. Proteomic analysis showed that overexpression of the target proteins had negligible effects on the spore proteome. However, plasmid-bearing spores displayed dramatic abundance changes in spore proteins involved in signaling and metabolism. Our findings indicate that the introduction of a plasmid alone alters the spore protein composition dramatically, with 993 proteins significantly down-regulated and 415 proteins significantly up-regulated among 3323 identified proteins. This shows that empty vector controls are more appropriate to compare proteome changes due to plasmid-encoded genes than is the wild-type strain, when using plasmid-based genetic tools. Therefore, researchers should keep in mind that molecular cloning techniques can alter more than their intended targets in a biological system, and interpret results with this in mind.

5.
Front Cell Infect Microbiol ; 11: 790465, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34869084

RESUMEN

Candida glabrata is among the most prevalent causes of candidiasis. Unlike Candida albicans, it is not capable of changing morphology between yeast and hyphal forms but instead has developed other virulence factors. An important feature is its unprecedented large repertoire of predicted cell wall adhesins, which are thought to enable adherence to a variety of surfaces under different conditions. Here, we analyzed the wall proteome of PEU1221, a high biofilm-forming clinical strain isolated from an infected central venous catheter, under biofilm-forming conditions. This isolate shows increased incorporation of putative adhesins, including eight proteins that were not detected in walls of reference strain ATCC 2001, and of which Epa22, Awp14, and Awp2e were identified for the first time. The proteomics data suggest that cluster III adhesin Awp14 is relatively abundant in PEU1221. Phenotypic studies with awp14Δ deletion mutants showed that Awp14 is not responsible for the high biofilm formation of PEU1221 onto polystyrene. However, awp14Δ mutant cells in PEU1221 background showed a slightly diminished binding to chitin and seemed to sediment slightly slower than the parental strain suggesting implication in fungal cell-cell interactions. By structural modeling, we further demonstrate similarity between the ligand-binding domains of cluster III adhesin Awp14 and those of cluster V and VI adhesins. In conclusion, our work confirms the increased incorporation of putative adhesins, such as Awp14, in high biofilm-forming isolates, and contributes to decipher the precise role of these proteins in the establishment of C. glabrata infections.


Asunto(s)
Candida glabrata , Candidiasis , Biopelículas , Candida albicans , Candida glabrata/genética , Proteínas Fúngicas/genética , Humanos
6.
Int J Mol Sci ; 22(22)2021 Nov 19.
Artículo en Inglés | MEDLINE | ID: mdl-34830357

RESUMEN

Membrane proteins are fascinating since they play an important role in diverse cellular functions and constitute many drug targets. Membrane proteins are challenging to analyze. The spore, the most resistant form of known life, harbors a compressed inner membrane. This membrane acts not only as a barrier for undesired molecules but also as a scaffold for proteins involved in signal transduction and the transport of metabolites during spore germination and subsequent vegetative growth. In this study, we adapted a membrane enrichment method to study the membrane proteome of spores and cells of the food-borne pathogen Bacillus cereus using quantitative proteomics. Using bioinformatics filtering we identify and quantify 498 vegetative cell membrane proteins and 244 spore inner membrane proteins. Comparison of vegetative and spore membrane proteins showed there were 54 spore membrane-specific and 308 cell membrane-specific proteins. Functional characterization of these proteins showed that the cell membrane proteome has a far larger number of transporters, receptors and proteins related to cell division and motility. This was also reflected in the much higher expression level of many of these proteins in the cellular membrane for those proteins that were in common with the spore inner membrane. The spore inner membrane had specific expression of several germinant receptors and spore-specific proteins, but also seemed to show a preference towards the use of simple carbohydrates like glucose and fructose owing to only expressing transporters for these. These results show the differences in membrane proteome composition and show us the specific proteins necessary in the inner membrane of a dormant spore of this toxigenic spore-forming bacterium to survive adverse conditions.


Asunto(s)
Bacillus cereus/genética , Proteínas Bacterianas/genética , Enfermedades Transmitidas por los Alimentos/genética , Proteoma/genética , Bacillus cereus/patogenicidad , Proteínas Bacterianas/clasificación , Membrana Celular/genética , Contaminación de Alimentos , Microbiología de Alimentos , Enfermedades Transmitidas por los Alimentos/microbiología , Humanos , Proteínas de la Membrana/clasificación , Proteínas de la Membrana/genética , Proteómica , Esporas Bacterianas/genética , Esporas Bacterianas/crecimiento & desarrollo , Esporas Bacterianas/patogenicidad
7.
Int J Mol Sci ; 22(17)2021 Aug 28.
Artículo en Inglés | MEDLINE | ID: mdl-34502250

RESUMEN

Bacillus subtilis vegetative cells switch to sporulation upon nutrient limitation. To investigate the proteome dynamics during sporulation, high-resolution time-lapse proteomics was performed in a cell population that was induced to sporulate synchronously. Here, we are the first to comprehensively investigate the changeover of sporulation regulatory proteins, coat proteins, and other proteins involved in sporulation and spore biogenesis. Protein co-expression analysis revealed four co-expressed modules (termed blue, brown, green, and yellow). Modules brown and green are upregulated during sporulation and contain proteins associated with sporulation. Module blue is negatively correlated with modules brown and green, containing ribosomal and metabolic proteins. Finally, module yellow shows co-expression with the three other modules. Notably, several proteins not belonging to any of the known transcription regulons were identified as co-expressed with modules brown and green, and might also play roles during sporulation. Finally, levels of some coat proteins, for example morphogenetic coat proteins, decreased late in sporulation.


Asunto(s)
Bacillus subtilis/metabolismo , Bacillus subtilis/fisiología , Proteoma/análisis , Proteoma/metabolismo , Esporas Bacterianas/metabolismo , Esporas Bacterianas/fisiología , Bacillus subtilis/citología , Proteínas Bacterianas/clasificación , Proteínas Bacterianas/metabolismo , Regulación Bacteriana de la Expresión Génica , Esporas Bacterianas/citología , Factores de Transcripción/metabolismo , Factores de Transcripción/fisiología
8.
Pathogens ; 10(4)2021 Apr 19.
Artículo en Inglés | MEDLINE | ID: mdl-33921809

RESUMEN

Candida parapsilosis is among the most frequent causes of candidiasis. Clinical isolates of this species show large variations in colony morphotype, ranging from round and smooth to a variety of non-smooth irregular colony shapes. A non-smooth appearance is related to increased formation of pseudohyphae, higher capacity to form biofilms on abiotic surfaces, and invading agar. Here, we present a comprehensive study of the cell wall proteome of C. parapsilosis reference strain CDC317 and seven clinical isolates under planktonic and sessile conditions. This analysis resulted in the identification of 40 wall proteins, most of them homologs of known Candida albicans cell wall proteins, such as Gas, Crh, Bgl2, Cht2, Ecm33, Sap, Sod, Plb, Pir, Pga30, Pga59, and adhesin family members. Comparative analysis of exponentially growing and stationary phase planktonic cultures of CDC317 at 30 °C and 37 °C revealed only minor variations. However, comparison of smooth isolates to non-smooth isolates with high biofilm formation capacity showed an increase in abundance and diversity of putative wall adhesins from Als, Iff/Hyr, and Hwp families in the latter. This difference depended more strongly on strain phenotype than on the growth conditions, as it was observed in planktonic as well as biofilm cells. Thus, in the set of isolates analyzed, the high biofilm formation capacity of non-smooth C. parapsilosis isolates with elongated cellular phenotypes correlates with the increased surface expression of putative wall adhesins in accordance with their proposed cellular function.

9.
Plant Physiol ; 182(1): 361-377, 2020 01.
Artículo en Inglés | MEDLINE | ID: mdl-31570508

RESUMEN

SNF1-RELATED PROTEIN KINASES 2 (SnRK2) are important components of early osmotic and salt stress signaling pathways in plants. The Arabidopsis (Arabidopsis thaliana) SnRK2 family comprises the abscisic acid (ABA)-activated protein kinases SnRK2.2, SnRK2.3, SnRK2.6, SnRK2.7, and SnRK2.8, and the ABA-independent subclass 1 protein kinases SnRK2.1, SnRK2.4, SnRK2.5, SnRK2.9, and SnRK2.10. ABA-independent SnRK2s act at the posttranscriptional level via phosphorylation of VARICOSE (VCS), a member of the mRNA decapping complex, that catalyzes the first step of 5'mRNA decay. Here, we identified VCS and VARICOSE RELATED (VCR) as interactors and phosphorylation targets of SnRK2.5, SnRK2.6, and SnRK2.10. All three protein kinases phosphorylated Ser-645 and Ser-1156 of VCS, whereas SnRK2.6 and SnRK2.10 also phosphorylated VCS Ser-692 and Ser-680 of VCR. We showed that subclass 1 SnRK2s, VCS, and 5' EXORIBONUCLEASE 4 (XRN4) are involved in regulating root growth under control conditions as well as modulating root system architecture in response to salt stress. Our results suggest interesting patterns of redundancy within subclass 1 SnRK2 protein kinases, with SnRK2.1, SnRK2.5, and SnRK2.9 controlling root growth under nonstress conditions and SnRK2.4 and SnRK2.10 acting mostly in response to salinity. We propose that subclass 1 SnRK2s function in root development under salt stress by affecting the transcript levels of aquaporins, as well as CYP79B2, an enzyme involved in auxin biosynthesis.


Asunto(s)
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , ARN Mensajero/metabolismo , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Exorribonucleasas/genética , Exorribonucleasas/metabolismo , Fosforilación/efectos de los fármacos , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Proteínas Quinasas/genética , Proteínas Quinasas/metabolismo , Proteínas Serina-Treonina Quinasas/genética , Proteínas Serina-Treonina Quinasas/metabolismo , ARN Mensajero/genética , Sales (Química)/farmacología , Transducción de Señal/efectos de los fármacos
10.
Front Plant Sci ; 8: 1342, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28824678

RESUMEN

E-2-hexenal is a volatile compound that is commonly emitted by wounded or stressed plants. It belongs to the group of so-called green leaf volatiles (GLVs), which play an important role in transferring information to plants and insects. While most biosynthetic enzymes upstream of E-2-hexenal have been studied extensively, much less is known about the enzyme responsible for the conversion from Z-3- to E-2-hexenal. In this study we have identified two (3Z):(2E)-hexenal isomerases (HIs) from cucumber fruits by classical biochemical fractionation techniques and we were able to confirm their activity by heterologous expression. Recombinant protein of the HIs did not only convert the leaf aldehyde Z-3-hexenal to E-2-hexenal, but also (Z,Z)-3,6-nonadienal to (E,Z)-2,6-nonadienal, these last two representing major flavor volatiles of cucumber fruits. Transient expression of the cucumber HIs in Nicotiana benthamiana leaves drastically changed the GLV bouquet of damaged plants from a Z-3- to an E-2-enriched GLV profile. Furthermore, transcriptional analysis revealed that the two HIs showed distinct expression patterns. While HI-1 was specifically expressed in the flesh of cucumber fruits HI-2 was expressed in leaves as well. Interestingly, wounding of cucumber leaves caused only a slight increase in HI-2 transcript levels. These results demonstrate that cucumber HIs are responsible for the rearrangement of Z-3-aldehydes in both leaves and fruits. Future research will reveal the physiological importance of an increased conversion to E-2-aldehydes for plants and insects.

11.
Int J Mol Sci ; 17(11)2016 Oct 26.
Artículo en Inglés | MEDLINE | ID: mdl-27792189

RESUMEN

The structural maintenance of chromosomes (SMC) protein complexes shape and regulate the structure and dynamics of chromatin, thereby controlling many chromosome-based processes such as cell cycle progression, differentiation, gene transcription and DNA repair. The SMC5/6 complex is previously described to promote DNA double-strand breaks (DSBs) repair by sister chromatid recombination, and found to be essential for resolving recombination intermediates during meiotic recombination. Moreover, in budding yeast, SMC5/6 provides structural organization and topological stress relief during replication in mitotically dividing cells. Despite the essential nature of the SMC5/6 complex, the versatile mechanisms by which SMC5/6 functions and its molecular regulation in mammalian cells remain poorly understood. By using a human osteosarcoma cell line (U2OS), we show that after the CRISPR-Cas9-mediated removal of the SMC5/6 subunit NSMCE2, treatment with the topoisomerase II inhibitor etoposide triggered an increased sensitivity in cells lacking NSMCE2. In contrast, NSMCE2 appeared not essential for a proper DNA damage response or cell survival after DSB induction by ionizing irradiation (IR). Interestingly, by way of immunoprecipitations (IPs) and mass spectrometry, we found that the SMC5/6 complex physically interacts with the DNA topoisomerase II α (TOP2A). We therefore propose that the SMC5/6 complex functions in resolving TOP2A-mediated DSB-repair intermediates generated during replication.


Asunto(s)
Proteínas de Ciclo Celular/metabolismo , Roturas del ADN de Doble Cadena , Reparación del ADN , Ligasas/metabolismo , Antígenos de Neoplasias/metabolismo , Sistemas CRISPR-Cas , Proteínas de Ciclo Celular/genética , Línea Celular Tumoral , Supervivencia Celular/efectos de la radiación , Proteínas Cromosómicas no Histona , Roturas del ADN de Doble Cadena/efectos de los fármacos , Roturas del ADN de Doble Cadena/efectos de la radiación , ADN-Topoisomerasas de Tipo II/metabolismo , Proteínas de Unión al ADN/metabolismo , Etopósido/efectos adversos , Humanos , Ligasas/genética , Proteínas de Unión a Poli-ADP-Ribosa , Mapas de Interacción de Proteínas , Inhibidores de Topoisomerasa II/efectos adversos
12.
Metab Eng ; 35: 83-94, 2016 May.
Artículo en Inglés | MEDLINE | ID: mdl-26869136

RESUMEN

Retinal-based photosynthesis may contribute to the free energy conversion needed for growth of an organism carrying out oxygenic photosynthesis, like a cyanobacterium. After optimization, this may even enhance the overall efficiency of phototrophic growth of such organisms in sustainability applications. As a first step towards this, we here report on functional expression of the archetype proteorhodopsin in Synechocystis sp. PCC 6803. Upon use of the moderate-strength psbA2 promoter, holo-proteorhodopsin is expressed in this cyanobacterium, at a level of up to 10(5) molecules per cell, presumably in a hexameric quaternary structure, and with approximately equal distribution (on a protein-content basis) over the thylakoid and the cytoplasmic membrane fraction. These results also demonstrate that Synechocystis sp. PCC 6803 has the capacity to synthesize all-trans-retinal. Expressing a substantial amount of a heterologous opsin membrane protein causes a substantial growth retardation Synechocystis, as is clear from a strain expressing PROPS, a non-pumping mutant derivative of proteorhodopsin. Relative to this latter strain, proteorhodopsin expression, however, measurably stimulates its growth.


Asunto(s)
Expresión Génica , Rodopsinas Microbianas/biosíntesis , Synechocystis/metabolismo , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/genética , Rodopsinas Microbianas/genética , Synechocystis/genética
13.
J Proteome Res ; 15(2): 585-94, 2016 Feb 05.
Artículo en Inglés | MEDLINE | ID: mdl-26731423

RESUMEN

The endospore is the dormant form of Bacillus subtilis and many other Firmicutes. By sporulation, these spore formers can survive very harsh physical and chemical conditions. Yet, they need to go through germination to return to their growing form. The spore inner membrane (IM) has been shown to play an essential role in triggering the initiation of germination. In this study, we isolated the IM of bacterial spores, in parallel with the isolation of the membrane of vegetative cells. With the use of GeLC-MS/MS, over 900 proteins were identified from the B. subtilis spore IM preparations. By bioinformatics-based membrane protein predictions, ca. one-third could be predicted to be membrane-localized. A large number of unique proteins as well as proteins common to the two membrane proteomes were identified. In addition to previously known IM proteins, a number of IM proteins were newly identified, at least some of which are likely to provide new insights into IM physiology, unveiling proteins putatively involved in spore germination machinery and hence putative germination inhibition targets.


Asunto(s)
Bacillus subtilis/metabolismo , Proteínas Bacterianas/metabolismo , Proteínas de la Membrana/metabolismo , Proteoma/metabolismo , Proteómica/métodos , Esporas Bacterianas/metabolismo , Proteínas Bacterianas/clasificación , Cromatografía Liquida , Electroforesis en Gel de Poliacrilamida , Proteínas de la Membrana/clasificación , Microscopía Electrónica de Transmisión , Proteoma/clasificación , Esporas Bacterianas/ultraestructura , Espectrometría de Masas en Tándem
14.
Methods Mol Biol ; 1356: 79-94, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-26519067

RESUMEN

Analysis of fungal secretomes using mass spectrometry is a useful technique in cell biology. Knowledge of the secretome of a human fungal pathogen may yield important information of host-pathogen interactions and may be useful for identifying vaccines candidates or diagnostic markers for antifungal strategies. In this chapter, with a main focus on sample preparation aspects, we describe the methodology that we apply for gel-independent batch identification and quantification of proteins that are secreted during growth in liquid cultures. Using these techniques with Candida and other yeast species, the majority of the identified proteins are classical secretory proteins and cell wall proteins containing N-terminal signal peptides for secretion, although dependent on sample preparation quality and the mass spectrometric analysis also usually, a number of nonsecretory proteins are identified.


Asunto(s)
Candida/metabolismo , Proteínas Fúngicas/metabolismo , Espectrometría de Masas , Proteoma , Proteómica , Espectrometría de Masas/métodos , Proteómica/métodos
15.
FEMS Yeast Res ; 15(8)2015 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-26546455

RESUMEN

Attachment to human host tissues or abiotic medical devices is a key step in the development of infections by Candida glabrata. The genome of this pathogenic yeast codes for a large number of adhesins, but proteomic work using reference strains has shown incorporation of only few adhesins in the cell wall. By making inventories of the wall proteomes of hyperadhesive clinical isolates and reference strain CBS138 using mass spectrometry, we describe the cell wall proteome of C. glabrata and tested the hypothesis that hyperadhesive isolates display differential incorporation of adhesins. Two clinical strains (PEU382 and PEU427) were selected, which both were hyperadhesive to polystyrene and showed high surface hydrophobicity. Cell wall proteome analysis under biofilm-forming conditions identified a core proteome of about 20 proteins present in all C. glabrata strains. In addition, 12 adhesin-like wall proteins were identified in the hyperadherent strains, including six novel adhesins (Awp8-13) of which only Awp12 was also present in CBS138. We conclude that the hyperadhesive capacity of these two clinical C. glabrata isolates is correlated with increased and differential incorporation of cell wall adhesins. Future studies should elucidate the role of the identified proteins in the establishment of C. glabrata infections.


Asunto(s)
Candida glabrata/química , Pared Celular/química , Proteínas Fúngicas/análisis , Proteoma/análisis , Candida glabrata/aislamiento & purificación , Candidiasis/microbiología , Humanos , Espectrometría de Masas , Proteómica
16.
Biotechnol Biofuels ; 8: 111, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-26246854

RESUMEN

BACKGROUND: This study aimed at exploring the molecular physiological consequences of a major redirection of carbon flow in so-called cyanobacterial cell factories: quantitative whole-cell proteomics analyses were carried out on two (14)N-labelled Synechocystis mutant strains, relative to their (15)N-labelled wild-type counterpart. Each mutant strain overproduced one specific commodity product, i.e. ethanol or lactic acid, to such an extent that the majority of the incoming CO2 in the organism was directly converted into the product. RESULTS: In total, 267 proteins have been identified with a significantly up- or down-regulated expression level. In the ethanol-producing mutant, which had the highest relative direct flux of carbon-to-product (>65%), significant up-regulation of several components involved in the initial stages of CO2 fixation for cellular metabolism was detected. Also a general decrease in abundance of the protein synthesizing machinery of the cells and a specific induction of an oxidative stress response were observed in this mutant. In the lactic acid overproducing mutant, that expresses part of the heterologous l-lactate dehydrogenase from a self-replicating plasmid, specific activation of two CRISPR associated proteins, encoded on the endogenous pSYSA plasmid, was observed. RT-qPCR was used to measure, of nine of the genes identified in the proteomics studies, also the adjustment of the corresponding mRNA level. CONCLUSION: The most striking adjustments detected in the proteome of the engineered cells were dependent on the specific product formed, with, e.g. more stress caused by lactic acid- than by ethanol production. Up-regulation of the total capacity for CO2 fixation in the ethanol-producing strain was due to hierarchical- rather than metabolic regulation. Furthermore, plasmid-based expression of heterologous gene(s) may induce genetic instability. For selected, limited, number of genes a striking correlation between the respective mRNA- and the corresponding protein expression level was observed, suggesting that for the expression of these genes regulation takes place primarily at the level of gene transcription.

17.
Biochim Biophys Acta ; 1854(10 Pt A): 1269-79, 2015 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-26049081

RESUMEN

Time-series transcript- and protein-profiles were measured upon initiation of carbon catabolite repression in Escherichia coli, in order to investigate the extent of post-transcriptional control in this prototypical response. A glucose-limited chemostat culture was used as the CCR-free reference condition. Stopping the pump and simultaneously adding a pulse of glucose, that saturated the cells for at least 1h, was used to initiate the glucose response. Samples were collected and subjected to quantitative time-series analysis of both the transcriptome (using microarray analysis) and the proteome (through a combination of 15N-metabolic labeling and mass spectrometry). Changes in the transcriptome and corresponding proteome were analyzed using statistical procedures designed specifically for time-series data. By comparison of the two sets of data, a total of 96 genes were identified that are post-transcriptionally regulated. This gene list provides candidates for future in-depth investigation of the molecular mechanisms involved in post-transcriptional regulation during carbon catabolite repression in E. coli, like the involvement of small RNAs.


Asunto(s)
Proteínas de Escherichia coli/genética , Escherichia coli/genética , Regulación Bacteriana de la Expresión Génica , Glucosa/deficiencia , Proteoma , Transcriptoma , Reactores Biológicos , Escherichia coli/crecimiento & desarrollo , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , Perfilación de la Expresión Génica , Marcaje Isotópico , Análisis por Micromatrices , Anotación de Secuencia Molecular , Isótopos de Nitrógeno , Factores de Tiempo
18.
J Proteome Res ; 14(5): 2169-76, 2015 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-25853650

RESUMEN

Bacillus weihenstephanensis is a subspecies of the Bacillus cereus sensu lato group of spore-forming bacteria known to cause food spoilage or food poisoning. The key distinguishing phenotype of B. weihenstephanensis is its ability to grow below 7 °C or, from a food safety perspective, to grow and potentially produce toxins in a refrigerated environment. Comparison of the proteome profile of B. weihenstephanensis upon its exposure to different culturing conditions can reveal clues to the mechanistic basis of its psychrotolerant phenotype as well as elucidate relevant aspects of its toxigenic profile. To this end, the genome of the type strain B. weihenstephanensis WSBC 10204 was sequenced and annotated. Subsequently, the proteome profiles of cells grown at either 6 or 30 °C were compared, which revealed considerable differences and indicated several hundred (uncharacterized) proteins as being subproteome- and/or temperature-specific. In this manner, several processes were newly indicated to be dependent on growth temperature, such as varying carbon flux routes and a different role for the urea cycle. Furthermore, a possible post-translational regulatory function for acetylation was suggested. Toxin production was determined to be largely independent of growth temperature.


Asunto(s)
Bacillus cereus/genética , Proteínas Bacterianas/genética , Genoma Bacteriano , Procesamiento Proteico-Postraduccional , Proteoma/genética , Acetilación , Bacillus cereus/metabolismo , Proteínas Bacterianas/metabolismo , Ciclo del Carbono/fisiología , ADN Bacteriano/genética , ADN Bacteriano/metabolismo , Enterotoxinas , Microbiología de Alimentos , Isoformas de Proteínas , Proteoma/metabolismo , Análisis de Secuencia de ADN , Temperatura , Urea/metabolismo
19.
Anal Chem ; 87(10): 5387-94, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-25894977

RESUMEN

Stationary-phase-assisted modulation is used to overcome one of the limitations of contemporary comprehensive two-dimensional liquid chromatography, which arises from the combination of a first-dimension column that is typically narrow and long and a second-dimension column that is wide and short. Shallow gradients at low flow rates are applied in the first dimension, whereas fast analyses (at high flow rates) are required in the second dimension. Limitations of this approach include a low sample capacity of the first-dimension column and a high dilution of the sample in the complete system. Moreover, the relatively high flow rates used for the second dimension make direct (splitless) hyphenation to mass spectrometry difficult. In the present study we demonstrate that stationary-phase-assisted modulation can be implemented in an online comprehensive two-dimensional LC (LC × LC) setup to shift this paradigm. The proposed active modulation makes it possible to choose virtually any combination of first- and second-dimension column diameters without loss in system performance. In the current setup, a 0.30 mm internal diameter first-dimension column with a relatively high loadability is coupled to a 0.075 mm internal diameter second-dimension column. This actively modulated system is coupled to a nanoelectrospray high-resolution mass spectrometer and applied for the separation of the tryptic peptides of a six-protein mixture and for the proteome-wide analyses of yeast from Saccharomyces cerevisiae. In the latter application, about 20000 MS/MS spectra are generated within 24 h analysis time, resulting in the identification of 701 proteins.


Asunto(s)
Proteómica/métodos , Saccharomyces cerevisiae/metabolismo , Métodos Analíticos de la Preparación de la Muestra , Cromatografía Liquida , Sales (Química)/química , Espectrometría de Masas en Tándem
20.
PLoS One ; 10(3): e0122020, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-25793526

RESUMEN

Bodily secretions, including breast milk and semen, contain factors that modulate HIV-1 infection. Since anal intercourse caries one of the highest risks for HIV-1 transmission, our aim was to determine whether colorectal mucus (CM) also contains factors interfering with HIV-1 infection and replication. CM from a number of individuals was collected and tested for the capacity to bind DC-SIGN and inhibit HIV-1 cis- or trans-infection of CD4+ T-lymphocytes. To this end, a DC-SIGN binding ELISA, a gp140 trimer competition ELISA and HIV-1 capture/ transfer assays were utilized. Subsequently we aimed to identify the DC-SIGN binding component through biochemical characterization and mass spectrometry analysis. CM was shown to bind DC-SIGN and competes with HIV-1 gp140 trimer for binding. Pre-incubation of Raji-DC-SIGN cells or immature dendritic cells (iDCs) with CM potently inhibits DC-SIGN mediated trans-infection of CD4+ T-lymphocytes with CCR5 and CXCR4 using HIV-1 strains, while no effect on direct infection is observed. Preliminary biochemical characterization demonstrates that the component seems to be large (>100kDa), heat and proteinase K resistant, binds in a α1-3 mannose independent manner and is highly variant between individuals. Immunoprecipitation using DC-SIGN-Fc coated agarose beads followed by mass spectrometry indicated lactoferrin (fragments) and its receptor (intelectin-1) as candidates. Using ELISA we showed that lactoferrin levels within CM correlate with DC-SIGN binding capacity. In conclusion, CM can bind the C-type lectin DC-SIGN and block HIV-1 trans-infection of both CCR5 and CXCR4 using HIV-1 strains. Furthermore, our data indicate that lactoferrin is a DC-SIGN binding component of CM. These results indicate that CM has the potential to interfere with pathogen transmission and modulate immune responses at the colorectal mucosa.


Asunto(s)
Moléculas de Adhesión Celular/metabolismo , Colon/metabolismo , Infecciones por VIH/inmunología , VIH-1/fisiología , Lectinas Tipo C/metabolismo , Moco/metabolismo , Receptores de Superficie Celular/metabolismo , Recto/metabolismo , Linfocitos T CD4-Positivos/virología , Línea Celular Tumoral , Células Dendríticas/metabolismo , Humanos , Lactoferrina/metabolismo , Espectrometría de Masas , Unión Proteica , Multimerización de Proteína , Productos del Gen env del Virus de la Inmunodeficiencia Humana/metabolismo
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