scholarly journals Organic Matter Composition at Ocean Station Papa Affects Its Bioavailability, Bacterioplankton Growth Efficiency and the Responding Taxa

2020 ◽  
Vol 7 ◽  
Author(s):  
Brandon M. Stephens ◽  
Keri Opalk ◽  
Daniel Petras ◽  
Shuting Liu ◽  
Jacqueline Comstock ◽  
...  
Keyword(s):  
Organic Matter ◽  
Amino Acid ◽  
Microbial Community Composition ◽  
High Growth ◽  
Community Diversity ◽  
Mass Spectrometry Analysis ◽  
Removal Rates ◽  
Spectrometry Analysis ◽  
Relative Abundances ◽  
Ocean Station Papa

The bioavailability of organic matter (OM) to marine heterotrophic bacterioplankton is determined by both the chemical composition of OM and the microbial community composition. In the current study, changes in OM bioavailability were identified at Ocean Station Papa as part of the 2018 Export Processes in the Ocean from Remote Sensing (EXPORTS) field study. Removal rates of carbon (C) in controlled experiments were significantly correlated with the initial composition of total hydrolyzable amino acids, and C removal rates were high when the amino acid degradation index suggested a more labile composition. Carbon remineralization rates averaged 0.19 ± 0.08 μmol C L–1 d–1 over 6–10 days while bacterial growth efficiencies averaged 31 ± 7%. Amino acid composition and tandem mass spectrometry analysis of compound classes also revealed transformations to a more degraded OM composition during experiments. There was a log2-fold increase in the relative abundances of 16S rDNA-resolved bacterioplankton taxa in most experiments by members of the Methylophilaceae family (OM43 genus) and KI89A order. Additionally, when OM was more bioavailable, relative abundances increased by at least threefold for the classes Bacteroidetes (Flavobacteriaceae NS2b genus), Alphaproteobacteria (Rhodobacteraceae Sulfitobacter genus), and Gammaproteobacteria (Alteromonadales and Ectothiorhodospiraceae orders). Our data suggest that a diverse group of bacterioplankton was responsible for removing organic carbon and altering the OM composition to a more degraded state. Elevated community diversity, as inferred from the Shannon–Wiener H index, may have contributed to relatively high growth efficiencies by the bacterioplankton. The data presented here shed light on the interconnections between OM bioavailability and key bacterioplankton taxa for the degradation of marine OM.

The amino acid sequence of porcine intestinal calcium-binding protein

1979 ◽  
Vol 57 (6) ◽  
pp. 737-748 ◽  
Author(s):  
Theo Hofmann ◽  
Michiko Kawakami ◽  
Anthony J. W. Hitchman ◽  
Joan E. Harrison ◽  
Keith J. Dorrington
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Intestinal Mucosa ◽  
Calcium Binding ◽  
Binding Protein ◽  
Troponin C ◽  
Calcium Binding Protein ◽  
Mass Spectrometry Analysis ◽  
Spectrometry Analysis

The complete amino acid sequence of the calcium-binding protein (CaBP) from pig intestinal mucosa has been determined: Ac-Ser-Ala-Gln-Lys-Ser-Pro-Ala-Glu-Leu-Lys-Ser-Ile-Phe-Glu-Lys-Tyr-Ala-Ala-Lys-Glu-Gly-Asp-Pro-Asn-Gln-Leu-Ser-Lys-Glu-Glu-Leu-Lys-Gln-Leu-Ile-Gln-Ala-Glu-Phe-Pro-Ser-Leu-Leu-Lys-Gly-Pro-Arg-Thr-Leu-Asp-Asp-Leu-Phe-Gln-Glu-Leu-Asp-Lys-Asn-Gly-Asn-Gly-Glu-Val-Ser-Phe-Glu-Glu-Phe-Gln-Val-Leu-Val-Lys-Lys-Ile-Ser-Gln-OH. The N-terminal octapeptide sequence was determined by mass spectrometry analysis by Morris and Dell. The first 45 residues of bovine CaBP differ only in six positions from the corresponding sequence of the porcine protein, except that the sequence starts in position two of the porcine sequence. The mammalian intestinal CaBP's belong to the troponin-C superfamily on the basis of an analysis by Barker and Dayhoff.

Mass spectrometry analysis, amino acid sequence and biological activity of venom components from the Brazilian scorpion Opisthacanthus cayaporum

Toxicon ◽  
2008 ◽  
Vol 51 (8) ◽  
pp. 1499-1508 ◽  
Author(s):  
Elisabeth F. Schwartz ◽  
Thalita S. Camargos ◽  
Fernando Z. Zamudio ◽  
Luciano P. Silva ◽  
Carlos Bloch ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Biological Activity ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Mass Spectrometry Analysis ◽  
Spectrometry Analysis

scholarly journals Novel Bifunctional α-l-Arabinofuranosidase/Xylobiohydrolase (ABF3) from Penicillium purpurogenum

2010 ◽  
Vol 76 (15) ◽  
pp. 5247-5253 ◽  
Author(s):  
Mar�a Cristina Ravanal ◽  
Eduardo Callegari ◽  
Jaime Eyzaguirre
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
Glycosyl Hydrolase ◽  
Biochemical Properties ◽  
Amino Acid Sequences ◽  
Mass Spectrometry Analysis ◽  
Carbohydrate Binding ◽  
Penicillium Purpurogenum ◽  
Spectrometry Analysis ◽  
Amino Terminal

ABSTRACT The soft rot fungus Penicillium purpurogenum grows on a variety of natural substrates and secretes various isoforms of xylanolytic enzymes, including three arabinofuranosidases. This work describes the biochemical properties as well as the nucleotide and amino acid sequences of arabinofuranosidase 3 (ABF3). This enzyme has been purified to homogeneity. It is a glycosylated monomer with a molecular weight of 50,700 and can bind cellulose. The enzyme is active with p-nitrophenyl α-l-arabinofuranoside and p-nitrophenyl β-d-xylopyranoside with a Km of 0.65 mM and 12 mM, respectively. The enzyme is active on xylooligosaccharides, yielding products of shorter length, including xylose. However, it does not hydrolyze arabinooligosaccharides. When assayed with polymeric substrates, little arabinose is liberated from arabinan and debranched arabinan; however, it hydrolyzes arabinose and releases xylooligosaccharides from arabinoxylan. Sequencing both ABF3 cDNA and genomic DNA reveals that this gene does not contain introns and that the open reading frame is 1,380 nucleotides in length. The deduced mature protein is composed of 433 amino acids residues and has a calculated molecular weight of 47,305. The deduced amino acid sequence has been validated by mass spectrometry analysis of peptides from purified ABF3. A total of 482 bp of the promoter were sequenced; putative binding sites for transcription factors such as CreA (four), XlnR (one), and AreA (three) and two CCAAT boxes were found. The enzyme has two domains, one similar to proteins of glycosyl hydrolase family 43 at the amino-terminal end and a family 6 carbohydrate binding module at the carboxyl end. ABF3 is the first described modular family 43 enzyme from a fungal source, having both α-l-arabinofuranosidase and xylobiohydrolase functionalities.

scholarly journals Microbially mediated reduction of FeIII and AsV in Cambodian sediments amended with 13C-labelled hexadecane and kerogen

2014 ◽  
Vol 11 (5) ◽  
pp. 538 ◽  
Author(s):  
Athanasios Rizoulis ◽  
Wafa M. Al Lawati ◽  
Richard D. Pancost ◽  
David A. Polya ◽  
Bart E. van Dongen ◽  
...  
Keyword(s):  
Organic Matter ◽  
Critical Role ◽  
Stable Isotope Probing ◽  
Mass Spectrometry Analysis ◽  
Gas Chromatography Mass Spectrometry ◽  
Organic Substrates ◽  
Spectrometry Analysis ◽  
Subsurface Sediments ◽  
Extractable Organic Matter ◽  
Long Chain

Environmental context The use of groundwater with elevated concentrations of arsenic for drinking, cooking or irrigation has resulted in the worst mass poisoning in human history. This study shows that organic compounds that can be found in arsenic rich subsurface sediments may be used by indigenous microorganisms, contributing to the release of arsenic from the sediments into the groundwater. This study increases our understanding of the range of organic substrates (and their sources) that can potentially stimulate arsenic mobilisation into groundwaters. Abstract Microbial activity is generally accepted to play a critical role, with the aid of suitable organic carbon substrates, in the mobilisation of arsenic from sediments into shallow reducing groundwaters. The nature of the organic matter in natural aquifers driving the reduction of AsV to AsIII is of particular importance but is poorly understood. In this study, sediments from an arsenic rich aquifer in Cambodia were amended with two 13C-labelled organic substrates. 13C-hexadecane was used as a model for potentially bioavailable long chain n-alkanes and a 13C-kerogen analogue as a proxy for non-extractable organic matter. During anaerobic incubation for 8 weeks, significant FeIII reduction and AsIII mobilisation were observed in the biotic microcosms only, suggesting that these processes were microbially driven. Microcosms amended with 13C-hexadecane exhibited a similar extent of FeIII reduction to the non-amended microcosms, but marginally higher AsIII release. Moreover, gas chromatography–mass spectrometry analysis showed that 65% of the added 13C-hexadecane was degraded during the 8-week incubation. The degradation of 13C-hexadecane was microbially driven, as confirmed by DNA stable isotope probing (DNA-SIP). Amendment with 13C-kerogen did not enhance FeIII reduction or AsIII mobilisation, and microbial degradation of kerogen could not be confirmed conclusively by DNA-SIP fractionation or 13C incorporation in the phospholipid fatty acids. These data are, therefore, consistent with the utilisation of long chain n-alkanes (but not kerogen) as electron donors for anaerobic processes, potentially including FeIII and AsV reduction in the subsurface.

scholarly journals Regulation of Insulin Secretion by SIRT4, a Mitochondrial ADP-ribosyltransferase

2007 ◽  
Vol 282 (46) ◽  
pp. 33583-33592 ◽  
Author(s):  
Nidhi Ahuja ◽  
Bjoern Schwer ◽  
Stefania Carobbio ◽  
David Waltregny ◽  
Brian J. North ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Insulin Secretion ◽  
Amino Acid ◽  
Bovine Serum Albumin ◽  
Matrix Protein ◽  
Mass Spectrometry Analysis ◽  
Carrier Proteins ◽  
Β Cells ◽  
Spectrometry Analysis ◽  
Adp Ribosyltransferase

Sirtuins are homologues of the yeast transcriptional repressor Sir2p and are conserved from bacteria to humans. We report that human SIRT4 is localized to the mitochondria. SIRT4 is a matrix protein and becomes cleaved at amino acid 28 after import into mitochondria. Mass spectrometry analysis of proteins that coimmunoprecipitate with SIRT4 identified insulindegrading enzyme and the ADP/ATP carrier proteins, ANT2 and ANT3. SIRT4 exhibits no histone deacetylase activity but functions as an efficient ADP-ribosyltransferase on histones and bovine serum albumin. SIRT4 is expressed in islets of Langerhans and colocalizes with insulin-expressing β cells. Depletion of SIRT4 from insulin-producing INS-1E cells results in increased insulin secretion in response to glucose. These observations define a new role for mitochondrial SIRT4 in the regulation of insulin secretion.

Molecular Changes in Dissolved Organic Matter After Soil Rewetting

2021 ◽  
Author(s):  
Alice Orme ◽  
Simon Benk ◽  
Markus Lange ◽  
Christian Zerfaß ◽  
Georg Pohnert ◽  
...  
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Mass Spectrometry Analysis ◽  
Microbial Decomposition ◽  
Molecular Changes ◽  
Spectrometry Analysis ◽  
Subsurface Waters ◽  
High Production ◽  
High Concentrations ◽  
Over Time

<p>The intensity and occurrence of droughts is projected to increase due to climate change. Dried soils release high concentrations of dissolved organic matter (DOM) into subsurface waters when they are rewet, the so-called rewetting peak. To more accurately predict the role of rewetting of soils after drought on the carbon cycle in a changing climate, it is important to understand the processes behind this DOM release.</p><p>The DOM rewetting peak origin is disputed between soil organic matter (SOM) from breakdown of soil particles; accumulated root exudates; and microbial release due to a change in osmotic potential through osmolytes or cell bursting. To better understand the origin of the rewetting DOM peak, we took a rewetting series of soil water samples from different vegetation types between December 2018 and April 2019 for targeted and untargeted metabolomics. Initial results using untargeted ultrahigh-resolution mass spectrometry analysis revealed a clear temporal trend, indicating that vegetation-independent molecular changes occur following rewetting. An increase in O/C and a decrease in H/C over time was observed which is attributed to microbial decomposition, supported by a decrease in m/z over time. We also observed an increase in the content of lipidic compounds (R > 0.6) following rewetting. This indicates that cells do not burst upon rewetting and, over time, microbial activity increases, suggesting that the DOM rewetting peak is caused by a lack of decomposition, rather than a high production, of organic matter.</p>

scholarly journals Cloning and Characterization of the DNA Region Responsible for Megacin A-216 Production in Bacillus megaterium 216

2008 ◽  
Vol 190 (19) ◽  
pp. 6448-6457 ◽  
Author(s):  
Antal Kiss ◽  
Gabriella Balikó ◽  
Attila Csorba ◽  
Tungalag Chuluunbaatar ◽  
Katalin F. Medzihradszky ◽  
...  
Keyword(s):  
Amino Acid ◽  
Bacillus Megaterium ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Biologically Active ◽  
Mass Spectrometry Analysis ◽  
High Sequence Similarity ◽  
Spectrometry Analysis ◽  
Acid Protein ◽  
Amino Acid Protein

ABSTRACT Upon induction, Bacillus megaterium 216 produces the bacteriocin megacin A-216, which leads to lysis of the producer cell and kills B. megaterium and a few other bacterial species. The DNA region responsible for megacinogeny was cloned in B. megaterium. The nucleotide sequence of a 5,494-bp-long subfragment was determined, and the function of the genes on this fragment was studied by generating deletions and analyzing their effects on MegA phenotypes. An open reading frame (ORF) encoding a 293-amino-acid protein was identified as the gene (megA) coding for megacin A-216. BLAST searches detected sequence similarity between megacin A-216 and proteins with phospholipase A2 activity. Purified biologically active megacin A-216 preparations contained three proteins. Mass spectrometry analysis showed that the largest protein is the full-length translation product of the megA gene, whereas the two shorter proteins are fragments of the long protein created by cleavage between Gln-185 and Val-186. The molecular masses of the three polypeptides are 32,855, 21,018, and 11,855 Da, respectively. Comparison of different megacin preparations suggests that the intact chain as well as the two combined fragments can form biologically active megacin. An ORF located next to the megA gene and encoding a 91-amino-acid protein was shown to be responsible for the relative immunity displayed by the producer strain against megacin A-216. Besides the megA gene, at least two other genes, including a gene encoding a 188-amino-acid protein sharing high sequence similarity with RNA polymerase sigma factors, were shown to be required for induction of megacin A-216 expression.

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