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Identification of proteins from an Antarctic bacterium Pseudomonas syringae Lz4W

ABSTRACT: Proteins separated on 12%SDS gel, digested with trypsin after cutting the bands, the extracted Peptides were subjected to LC MS/MS on an Ion trap mass spectrometer (Finnigan LTQ from Thermo Electron Corporation).

INSTRUMENT(S): instrument model, LTQ

ORGANISM(S): Pseudomonas Sp.

SUBMITTER: Medicharla V. Jagannadham

PROVIDER: PRD000238 | Pride | 2011-03-29

REPOSITORIES: Pride

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			Action	DRS
	PRIDE_Exp_Complete_Ac_12279.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_12279.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_12280.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_12280.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_12281.pride.mgf.gz	Mgf

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Publications

Identification of outer membrane proteins from an Antarctic bacterium Pseudomonas syringae Lz4W.

Jagannadham M V MV Abou-Eladab Ehab F EF Kulkarni Heramb M HM

Molecular & cellular proteomics : MCP 20110329 6

Subcellular fractionation of proteins is a preferred method of choice for detection and identification of proteins from complex mixtures such as bacterial cells. To characterize the membrane proteins of the Antarctic bacterium Pseudomonas syringae Lz4W, the membrane fractions were prepared using three different methods, namely Triton X-100 solubilization, sucrose density gradient, and carbonate extraction methods. The proteins were separated on one-dimensional polyacrylamide gels and analyzed us ...[more]

PMID: 21447709

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Proteins of Pseudomonas syringae Lz4W

Project description:Proteins separated on 12%SDS gel, digested with trypsin after cutting the bands, the extracted Peptides were subjected to LC MS/MS on an Ion trap mass spectrometer (Finnigan LTQ from Thermo Electron Corporation).

2011-03-29 | PRD000239 | Pride

Draft Genome Sequence of the Antarctic Psychrophilic Bacterium Pseudomonas syringae Strain Lz4W.

Project description:The psychrophilic bacterium Pseudomonas syringae strain Lz4W was isolated from soil samples from Antarctica to decipher the mechanisms of low-temperature adaptation. We report here the 4.982-Mb draft genome sequence of P. syringae Lz4W. This sequence will provide insights into the genomic basis of the psychrophilicity of this bacterium.

| S-EPMC3707596 | biostudies-literature

rnr gene from the antarctic bacterium Pseudomonas syringae Lz4W, encoding a psychrophilic RNase R.

Project description:RNase R is a highly processive, hydrolytic 3'-5' exoribonuclease belonging to the RNB/RNR superfamily which plays significant roles in RNA metabolism in bacteria. The enzyme was observed to be essential for growth of the psychrophilic Antarctic bacterium Pseudomonas syringae Lz4W at a low temperature. We present results here pertaining to the biochemical properties of RNase R and the RNase R-encoding gene (rnr) locus from this bacterium. By cloning and expressing a His₆-tagged form of the P. syringae RNase R (RNase R(Ps)), we show that the enzyme is active at 0 to 4°C but exhibits optimum activity at ∼25°C. The enzyme is heat labile in nature, losing activity upon incubation at 37°C and above, a hallmark of many psychrophilic enzymes. The enzyme requires divalent cations (Mg²⁺ and Mn²⁺) for activity, and the activity is higher in 50 to 150 mM KCl when it largely remains as a monomer. On synthetic substrates, RNase R(Ps) exhibited maximum activity on poly(A) and poly(U) in preference over poly(G) and poly(C). The enzyme also degraded structured malE-malF RNA substrates. Analysis of the cleavage products shows that the enzyme, apart from releasing 5'-nucleotide monophosphates by the processive exoribonuclease activity, produces four-nucleotide end products, as opposed to two-nucleotide products, of RNA chain by Escherichia coli RNase R. Interestingly, three ribonucleotides (ATP, GTP, and CTP) inhibited the activity of RNase R(Ps) in vitro. The ability of the nonhydrolyzable ATP-γS to inhibit RNase R(Ps) activity suggests that nucleotide hydrolysis is not required for inhibition. This is the first report on the biochemical property of a psychrophilic RNase R from any bacterium.

| S-EPMC3208988 | biostudies-literature

The proteome of the outer membrane vesicles of an Antarctic bacterium Pseudomonas syringae Lz4W.

Project description:Outer membrane vesicles (OMVs) of gram-negative bacteria are released during all growth phases and play an important role in bacterial physiology. They consist of lipids, proteins, lipopolysaccharides and other molecules. The OMVs of the Antarctic bacterium Pseudomonas syringae Lz 4W were isolated and identified their proteins. The mass spectral data set deposited with PRIDE, accession number PXD 000221 is presented in this report. The proteins identified from the OMVs of P. syringae Lz4W, data of this study were published in the Journal of proteome research [1].

| S-EPMC4534585 | biostudies-literature

Cloning, sequencing, and expression of the cold-inducible hutU gene from the antarctic psychrotrophic bacterium Pseudomonas syringae.

Project description:A promoter-fusion study with a Tn 5-based promoter probe vector had earlier found that the hutU gene which encodes the enzyme urocanase for the histidine utilization pathway is upregulated at a lower temperature (4 degrees C) in the Antarctic psychrotrophic bacterium Pseudomonas syringae. To examine the characteristics of the urocanase gene and its promoter elements from the psychrotroph, the complete hutU and its upstream region from P. syringae were cloned, sequenced, and analyzed in the present study. Northern blot and primer extension analyses suggested that the hutU gene is inducible upon a downshift of temperature (22 to 4 degrees C) and that there is more than one transcription initiation site. One of the initiation sites was specific to the cells grown at 4 degrees C, which was different from the common initiation sites observed at both 4 and 22 degrees C. Although no typical promoter consensus sequences were observed in the flanking region of the transcription initiation sites, there was a characteristic CAAAA sequence at the -10 position of the promoters. Additionally, the location of the transcription and translation initiation sites suggested that the hutU mRNA contains a long 5'-untranslated region, a characteristic feature of many cold-inducible genes of mesophilic bacteria. A comparison of deduced amino acid sequences of urocanase from various bacteria, including the mesophilic and psychrotrophic Pseudomonas spp., suggests that there is a high degree of similarity between the enzymes. The enzyme sequence contains a signature motif (GXGX(2)GX(10)G) of the Rossmann fold for dinucleotide (NAD(+)) binding and two conserved cysteine residues in and around the active site. The psychrotrophic enzyme, however, has an extended N-terminal end.

| S-EPMC126550 | biostudies-literature

RecD plays an essential function during growth at low temperature in the antarctic bacterium Pseudomonas syringae Lz4W.

Project description:The Antarctic psychrotrophic bacterium Pseudomonas syringae Lz4W has been used as a model system to identify genes that are required for growth at low temperature. Transposon mutagenesis was carried out to isolate mutant(s) of the bacterium that are defective for growth at 4 degrees but normal at 22 degrees . In one such cold-sensitive mutant (CS1), the transposon-disrupted gene was identified to be a homolog of the recD gene of several bacteria. Trans-complementation and freshly targeted gene disruption studies reconfirmed that the inactivation of the recD gene leads to a cold-sensitive phenotype. We cloned, sequenced, and analyzed approximately 11.2 kbp of DNA from recD and its flanking region from the bacterium. recD was the last gene of a putative recCBD operon. The RecD ORF was 694 amino acids long and 40% identical (52% similar) to the Escherichia coli protein, and it could complement the E. coli recD mutation. The recD gene of E. coli, however, could not complement the cold-sensitive phenotype of the CS1 mutant. Interestingly, the CS1 strain showed greater sensitivity toward the DNA-damaging agents, mitomycin C and UV. The inactivation of recD in P. syringae also led to cell death and accumulation of DNA fragments of approximately 25-30 kbp in size at low temperature (4 degrees ). We propose that during growth at a very low temperature the Antarctic P. syringae is subjected to DNA damage, which requires direct participation of a unique RecD function. Additional results suggest that a truncated recD encoding the N-terminal segment of (1-576) amino acids is sufficient to support growth of P. syringae at low temperature.

| S-EPMC1449786 | biostudies-literature

Bombyx mori anterior silk gland LC-MS/MS

Project description:The anterior silk gland in the silkworm plays an important role in the process of liquid fibroin to solid silk fiber .In view of this,the proteomics analysis was applied to to study the relationship between the function of proteins in the anterior silk gland and the mechanism of spinning. The anterior silk glands on the 3rd day of fifth instar were dissected.Aftter 1D SDS-PAGE ,one gel lane was cut into 10 bands and each band further sliced into small pieces was subjected to in-gel tryptic digestion for 20 hours.The digested peptides were separated by RP nanoscale capillary liquid chromatography and analyzed using a surveyor LC system (Thermo Figgigan, San Jose, CA).The eluate from the RP column was analyzed by Finnigan LTQ(Thermo Electron Corporation）linear ion trap Mass equipped with a nanospray souce in the positive ion mode. The MS analysis was performed with one full MS scan followed by three MS/MS scans on the most intense ions from the MS spectrum with the dynamic exclusion settings: repeat count 2, repeat duration 30s, exclusion duration 90s. Data were acquired in data-dependent mode using Xcalibur software.Ten raw datasets from LC-MS/MS were searched against the predicted silkworm database by Xia.et al which consists of 21312 silkworm proteins.The searching was carried out with the Turbo SEQUEST(Bioworks version 3.2, Thermo Electron).

2014-03-26 | PXD000090 | Pride

Transcriptome analysis in the Antarctic bacterium Pseudomonas extremaustralis at low temperatures

Project description:In this work we analyzed the whole transcriptome of early exponential cultures growing at 8 degree C and 30 degree C by RNA deep-sequencing technology.

2017-07-05 | E-MTAB-3453 | biostudies-arrayexpress

Transcription profiling of Arabidopsis infected with the bacterium Pseudomonas syringae

Project description:The effect of bacterial infection with Pseudomonas syringae on gene expression of Arabidopsis thaliana

2005-01-01 | E-TIGR-3 | biostudies-arrayexpress

Exoribonuclease RNase R protects Antarctic <i>Pseudomonas syringae</i> Lz4W from DNA damage and oxidative stress.

Project description:ImportanceBacterial exoribonucleases play a crucial role in RNA maturation, degradation, quality control, and turnover. In this study, we have uncovered a previously unknown role of 3'-5' exoribonuclease RNase R of Pseudomonas syringae Lz4W in DNA damage and oxidative stress response. Here, we show that neither the exoribonuclease function of RNase R nor its association with the RNA degradosome complex is essential for this function. Interestingly, in P. syringae Lz4W, hydrolytic RNase R exhibits physiological roles similar to phosphorolytic 3'-5' exoribonuclease PNPase of E. coli. Our data suggest that during the course of evolution, mesophilic E. coli and psychrotrophic P. syringae have apparently swapped these exoribonucleases to adapt to their respective environmental growth conditions.

| S-EPMC10686088 | biostudies-literature

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