24_Identification of spore specific allergens from Penicillium chrysogenum
Goodman V, Müller A, Gröger-Arndt H, Schlosser D, Jehmlich N, Treudler R, Lehmann I, Simon JC, von Bergen M
Journal of integrated OMICS (2011) 1(2):272-279
The common indoor mould Penicillium chrysogenum is reported to be associated with respiratory diseases and allergic asthma. Beside the already known specific allergens stemming from mixtures of hyphae and spores the question was which allergens are specifically abundant in the airborne spores.
23_Time resolved protein-based stable isotope probing (Protein-SIP) analysis allows quantification of induced proteins in substrate shift experiments
Taubert M, Jehmlich N, Vogt C, Richnow HH, Schmidt F, von
Bergen M, Seifert J
Proteomics (2011) Jun;11(11):2265-74
In this study, Protein-SIP
is used for a fast and reliable detection of newly synthesized proteins in a substrate shift experiment.
22_Protein based stable isotope
labeling
Jehmlich N, Schmidt F, Taubert M, Seifert J, von
Bergen M, Richnow HH, Vogt C
Nature Protocols (2010) Dec;5(12):1957-66
In this article, we provide guidelines for incubating
microbial cultures with labeled substrates and a protocol for Protein-SIP.
The protocol guides readers through the proteomics pipeline, including
protein extraction, gel-free and gel-based protein separation, the
subsequent mass spectrometric analysis of peptides and the calculation of
the incorporation of stable isotopes into peptides.
21_Phylogenetic and proteomic analysis
of an anaerobic toluene-degrading community
Jehmlich N,
Kleinsteuber S, Vogt C, Benndorf D, Harms H, Schmidt F, von Bergen M,
Seifert J
Journal of Applied Microbiology (2010) Dec;109(6):1937-45
An enriched toluene-degrading community (Zz5-7) growing
in batch cultures was investigated by DNA- and protein-based analyses.
This is the first study that combines genetic and proteomic analyses to
indicate the interactions in an anaerobic toluene-degrading microbial
consortium.
20_Advanced tool for the characterization of microbial
cultures by combining cytomics and proteomics
Jehmlich N,
Hübschmann T, Gesell Salazar M, Völker U, Benndorf D, Müller S, von Bergen
M, Schmidt F
Applied Microbiology and Biotechnology (2010)
Sep;88(2):575-84
A workflow was developed to analyze successfully
microbial sorted cells by downstream analysis of proteomics. Cytometric
analysis and cell sortinng of sub-populations of interest are the
prerequisites for a successful subsequent application of
Omics-technologies. Therefore, we applied a filter device approach that
enabled a comprehensive proteomic approach by LC-MS.
19_Declining capacity of starving
Deltia acidovorans MC1 to degrade phenoxypropionate herbicides
correlates with oxidative modification of the initial
enzyme
Leibeling S, Schmidt F, Jehmlich N, von Bergen M,
Müller RH, Harms H
Environmental Science & Technology (2010)
May 15;44(10):3793-9
Starving Deltia acidovorans MC1 were found to
lose specific degradation activity, while accumulating variants of the
alpha-ketoglutarate-dependent dioxygenase RdpA, the enzyme initiating the
degradation of (RS)-2-(2,4-dichlorophenoxy)propionate. These variants
differed in their pI and originated from post-translational modification,
since there is only one rdpA gene in the genome.
18_Elucidating MTBE degradation in a
mixed consortium using a multidisciplinary approach
Bastida
F, Rosell M, Franchini A, Seifert J, Finsterbusch S, Jehmlich N, Jechalke
S, von Bergen M, Richnow HH
FEMS Microbiology Ecology (2010)
Aug;73(2):370-84
Enrichment culture (US3-M) originated from a
gasoline-impacted site in the USA has been enriched on MTBE as the sole
carbon source. The biodegrading capacity of methyl tert-butyl ether (MTBE)
was characterised using compound specific stable isotope analysis (CSIA),
clone libraries and Protein-SIP.
17_Calculation of partial isotope incorporation into
peptides measured by mass spectrometry
Fetzer I, Jehmlich N,
Vogt C, Richnow HH, Seifert J, Harms H, von Bergen M, Schmidt F
BMC
Research Notes (2010) 3:178
Bioinformatical background information about our new
method is given that allows us to calculate the degrees of partial (13)C
incorporation into proteins using the characteristics of the so-called
half decimal place rule.
16_Quantitative analysis of 13C incorporation into peptides
by decimal place slope calculation
Jehmlich N, Fetzer I,
Mattow J, Thiede B, Harms H, Richnow HH, Vogt C, von Bergen M, Schmidt
F
Molecular and Cellular Proteomics (2010) Jun;9(6):1221-7
The decimal place slope calculation method was applied
for accurate and sensitive estimation of (13)C incorporation in proteins
of Pseudomonas putida ML2 labeled uniformly via the consumption of
labeled benzene present in the medium in concentrations of 0 atom, 10
atom, 25 atom, 50 atom and 100 atom percent.
15_NBDT a novel fluorescent dye for uptake studies of
toluene in bacteria
Sträuber H, Hübschmann T, Jehmlich N,
Schmidt F, von Bergen M,
Harms H, Müller S
Cytometry Part A
(2010) Feb;77(2):113-20
In this study, a fluorescently labeled toluene analogue
dye (3-(N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)-3-toluene; NBDT), flow
cytometry, and shot gun proteome analysis were used to follow toluene
uptake into bacteria in more detail.
14_Gene clusters involved in anaerobic
2-methylnaphthalene degradation of the sulfate-reducing enrichment culture
N47
Selesi D, Jehmlich N, von Bergen M, Schmidt F, Rattei T,
Tischler P, Lueders T, Meckenstock RU
Journal of Bacteriology
(2010) Jan;192(1):295-306
The work provides the first insight into the genetic
basis of anaerobic 2-methylnaphthalene metabolism and delivers
implications for understanding contaminant degradation. Proteome analysis
of 2-methylnaphthalene- grown N47 cells resulted in the identification of
putative enzymes catalyzing the anaerobic conversion of
2-methylnaphthalene to 2-naphthoyl coenzyme A (2-naphthoyl-CoA), as well
as the reductive ring cleavage of 2-naphthoyl-CoA, leading to the
formation of acetyl-CoA and CO2.
13_Octapeptide NMHRYPNQ of the celluar prion protein (PrPc)
inhibits aggregation and its a potential key for understanding prion prion
interactions
Rehders D, Claasen B, Redecke L, Buschke A,
Reibe C, Jehmlich N, von Bergen M, Betzel C, Meyer B
Journal of
Molecular Biology (2009) Sep 11;392(1):198-207
Knowledge of molecules that inhibit such contacts leads
to an understanding of the mechanism of the aggregation, and these
molecules may serve as leads for drugs against transmissible spongiform
encephalopathies. Therefore, we screened a synthetic octapeptide library
of the globular domain of the human PrP(C) for binding affinity to PrP(C).
12_Comparison of methods for
simultaneous identification of bacterial species and determination of
metabolic activity by protein-based stable isotope probing (Protein-SIP)
experiments
Jehmlich N, Schmidt F, Taubert M, von Bergen,
Richnow HH, Vogt C
Rapid Communications in Mass Spectrometry
(2009) June; 23(12): 1871-1878
The Protein-SIP concept was tested using two more
gel-free proteomic methods namely intact protein profiling (IPP) and
shotgun mass mapping (SMM). Whereas SMM revealed a higher robustness of
species identification by mass spectrometry and a higher certainty of
incorporation level calculation compared to IPP.
11_Decarboxylating and nondecarboxylating
glutaryl-coenzyme A dehydrogenases in the aromatic metabolism of obligately
anaerobic bacteria
Wischgoll S, Taubert M, Peters F, Jehmlich N,
von Bergen M, Boll M
J Bacteriol
(2009) Jul;191(13):4401-9
In anaerobic bacteria using aromatic growth substrates,
glutaryl-coenzyme A (CoA) dehydrogenases (GDHs) are involved in the catabolism
of the central intermediate benzoyl-CoA to three acetyl-CoAs and CO(2).
In this work, we studied GDHs from the strictly anaerobic, aromatic compound-degrading
organisms Geobacter metallireducens (GDH(Geo)) (Fe[III] reducing) and
Desulfococcus multivorans (GDH(Des)) (sulfate reducing).
10_Biochemical and molecular genetic characterisation of a
novel dimeric laccase with an alkaline isoelectric point produced by the
aquatic ascomycete Phoma sp. UHH 5-1-03
Junghanns C,
Böhm D, Pecyna M, Jehmlich N, Martin C, von Bergen M, Schauer F, Schlosser
D
Applied Microbiology and Biotechnology (2009)
Oct;84(6):1095-105
A laccase from the aquatic ascomycete Phoma sp.
UHH 5-1-03 (DSM 22425) was purified. Mass spectrometric analysis of the
laccase monomer yielded a molecular mass of 75.6 kDa. The enzyme possesses
an unusual alkaline isoelectric point above 8.3. The Phoma sp.
laccase undergoes pH-dependent dimerisation, with the dimer (approximately
150 kDa, as assessed by SEC) predominating in a pH range of 5.0 to 8.0.
9_Improving protein extraction and isolation methods for
investigating the metaproteome of anaerobic benzene communities within
sediments
Benndorf D, Vogt C, Jehmlich N, Schmidt Y, Thomas
H, Shevchenko A, Woffendin G, Richnow HH, von Bergen
M
Biodegradation (2009) Nov;20(6):737-50
A modified protein extraction method was developed to
analyze anoxic, slow growing benzene degrading microbial community
containing low cell numbers and low amounts of biomass. After 2-DE and MS,
proteins were identified which are involved in the anoxic degradation of
xenobiotics.
8_Phenol degradation pathway in the strictly anaerobic iron
reducing bacterium Geobacter metallireducens
GS-15
Schleinitz KM, Schmeling S, Jehmlich N, von Bergen M,
Harms H, Kleinsteuber S, Vogt C, Fuchs G
Applied and Environmental
Microbiology (2009) Jun;75(12):3912-9
We investigated phenol degradation in the strictly
anaerobic iron-reducing deltaproteobacterium Geobacter
metallireducens GS-15 using metabolite, transcriptome, proteome, and
enzyme analyses. The results showed that the initial steps of phenol
degradation are accomplished by phenylphosphate synthase (encoded by pps
genes) and phenylphosphate carboxylase (encoded by ppc genes) as known
from Thauera aromatica, but they also revealed some distinct
differences.
7_Snake venomics of the siamese russell viper (Daboia
russelli siamensis) relation to pharmacological
activities
Risch M, Georgieva D, von Bergen M, Jehmlich N,
Genov N, Arni RK, Betzel C
Journal of Proteomics (2009) March 6,
72(2):256-269
The proteome comprises toxins from six protein
families: serine proteinases, metalloproteinases, phospholipases A(2),
L-amino acid oxidases, vascular endothelial growth factors and C-type
lectin-like proteins. The venom toxin composition correlates with the
clinical manifestation of the Russell viper bite and explains
pathological effects of the venom such as coagulopathy, oedema,
hypotensive, necrotic and tissue damaging effects.
6_Purification and characterization of
active site components of the putative p-cresol methylhydroxylase membrane
complex from Geobacter metallireducens GS-15
Johannes
J, Bluschke A, Jehmlich N, von Bergen M, Boll M
Journal of
Bacteriology (2008) Oct,190(19):6493-500
The soluble components of this complex were purified
and characterized. The data obtained suggest a molecular mass of 124 +/-
15 kDa and a unique alpha alpha beta(2) subunit composition, with alpha
and alpha?representing isoforms of the flavin adenine dinucleotide
(FAD)-containing subunit and beta representing a c-type cytochrome.
5_Incorporation of carbon and nitrogen
atoms into proteins measured by protein based stable isotope probing
(Protein-SIP)
Jehmlich N, Schmidt F, Hartwich M, von Bergen
M, Richnow HH, Vogt C
Rapid Communications in Mass Spectrometry
(2008) Sep; 22(18): 2889-2897
The concept of Protein-SIP was evaluated by analysing
the metabolic incorporation of stable isotopes into the proteins of an
aerobic benzene-metabolizing microorganism (Pseudomonas putida ML2)
in a proof-of-principle approach. The substrates (12)C-benzene,
(13)C-benzene or (15)N-ammonium and (12)C-benzene were applied to monitor
the heavy stable isotope incorporation into proteins by matrix-assisted
laser ionization/desorption mass spectrometric (MALDI-MS) analysis.
4_Aromatizing cyclohex-1,5-diene-1-carbonyl-coenzyme A
oxidase: initial characterization and its role in anaerobic aromatic
metabolism
Thiele B, Rieder O, Jehmlich N, von Bergen M,
Müller M, Boll M
Journal of Biological Chemistry (2008) Jul 25;
283(30):20713-21
In extracts from anaerobically grown denitrifying
Thauera aromatica, we detected a benzoate-induced,
benzoyl-CoA-forming, 1,5-dienoyl-CoA:acceptor oxidoreductase activity.
This activity co-purified with BCR but could be partially separated from
it by hydroxyapatite chromatography. After activity staining on native
gels, a monomeric protein with a subunit molecular weight of M(r) 76,000
was identified.
3_Protein based stable isotope probing (Protein-SIP) reveals
active species within anoxic mixed cultures
Jehmlich N,
Schmidt F, von Bergen M, Richnow HH, Vogt C
ISME Journal (2008)
Nov 2(11):1122-33
Incorporation of (13)C was exclusively found in
proteins from strain EbN1 at a content of 82.6+/-2.3%, as an average
calculated from 19 proteins, demonstrating the suitability of the method
used to identify metabolic active species with specific properties within
a mixed culture.
2_Purification and characterization of a laccase from the
aquatic fungus Myrioconium sp. UHH 1-13-18-4 and analysis of the
laccase-encoding gene
Martin C, Pecyna M, Kellner H,
Jehmlich N, Junghanns C, Benndorf D, von Bergen M, Schlosser
D
Applied Microbiology and Biotechnology (2007) Dec;77(3)
613-624
An extracellular, monomeric, and glycosylated laccase
with a molecular mass of 72.7 kDa and an isoelectric point below 2.8 was
purified from CuSO(4) and vanillic acid amended liquid fungal cultures
grown in malt extract medium.
1_Detection, quantification and
identification of fungal extracellular laccases using polyclonal antibody
and mass spectrometry
Kellner H, Jehmlich N, Benndorf D,
Hoffmann R, Rühl M, Hoegger PJ, Majcherczyk A, Kües U, von Bergen M,
Buscot F
Enzyme and Microbial Technology (2007) 41:694-701
The polyclonal anti-laccase antibody LccCbr2 was raised
against peptides designed from the copper binding region 11 of fungal
laccases using in silico data obtained from GenBank database. As a
consequence, detection requires denaturation of the enzymes due to the
stable conformation of the copper binding region II. The specificity of
the antibody was shown with denatured laccase Lcc1 of Coprinopsis
cinerea and laccase of Hypholoma fasciculare.
Book Chapter
1_Stable Isotope Probing in Microbial
Molecular Ecology
Jehmlich N, Seifert J, Taubert M, Schmidt
F, von Bergen M, Richnow HH, Vogt C
American Society for
Microbiology (2010)
Editors: Colin Murrell and Andrew
Whiteley
Dr.
Nico Jehmlich | Personalized Proteomics | nico.jehmlich@uni-greifswald.de
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