Proteomics of marine bacteria

Schweder, Thomas; Markert, Stephanie; Hecker, Michael

doi:10.1002/elps.200800009

Cited by 27 publications

(14 citation statements)

References 135 publications

(164 reference statements)

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“…So far, only a few studies of the proteome of marine bacteria are available (42). This initial proteomic characterization of exponentially growing P. haloplanktis cells shows that the observed fast growth of this cold-adapted marine bacterium at 16°C correlates with a prevalence of the protein synthesis machinery, an efficient utilization of available amino acids, a high abundance of transport capacities, and the presence of cold acclimation and oxidative stress proteins.…”

Section: Resultsmentioning

confidence: 99%

Cytoplasmic and Periplasmic Proteomic Signatures of Exponentially Growing Cells of the Psychrophilic Bacterium Pseudoalteromonas haloplanktis TAC125

Wilmes

Kock

Glagla

et al. 2011

Appl Environ Microbiol

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The psychrophilic model bacterium Pseudoalteromonas haloplanktis is characterized by remarkably fast growth rates under low-temperature conditions in a range from 5°C to 20°C. In this study the proteome of cellular compartments, the cytoplasm and periplasm, of P. haloplanktis strain TAC125 was analyzed under exponential growth conditions at a permissive temperature of 16°C. By means of two-dimensional protein gel electrophoresis and mass spectrometry, a first inventory of the most abundant cytoplasmic and periplasmic proteins expressed in a peptone-supplemented minimal medium was established. By this approach major enzymes of the amino acid catabolism of this marine bacterium could be functionally deduced. The cytoplasmic proteome showed a predominance of amino acid degradation pathways and tricarboxylic acid (TCA) cycle enzymes but also the protein synthesis machinery. Furthermore, high levels of cold acclimation and oxidative stress proteins could be detected at this moderate growth temperature. The periplasmic proteome was characterized by a significant abundance of transporters, especially of highly expressed putative TonB-dependent receptors. This high capacity for protein synthesis, efficient amino acid utilization, and substrate transport may contribute to the fast growth rates of the copiotrophic bacterium P. haloplanktis in its natural environments.The Antarctic marine environment is characterized by low temperatures that very seldom exceed 0°C. Despite the permanent low temperatures, the surface water and the pack ice zones in this region harbor a surprisingly high level of microbial activity. The most abundant bacterial populations in sea ice samples from Antarctic coastal areas belong mainly to four phylogenetic groups: the Gram-positive branch, the Flexibacter-Bacteroides-Cytophaga phylum, and the alpha and gamma subdivisions of the proteobacteria (4). Up to 50% of the identified bacterial isolates could be assigned to the gammaproteobacteria (5). It is assumed that this group of heterotrophic bacteria plays a key role in carbon cycling in this extreme environment.A prominent, cold-adapted member of this group is the obligatory marine bacterium Pseudoalteromonas haloplanktis TAC125, which was isolated from an Antarctic coastal seawater sample (32). P. haloplanktis features remarkable metabolic versatility and has become a model organism of psychrophilic bacteria. Several cold-adapted proteins of this species have been characterized, such as aspartate aminotransferase (2), polynucleotide phosphorylase (18), DNA ligase (25), cytochrome c (15), superoxide dismutase (33), lipase (14), esterases (46), xylanase (10), cellulase (47), and alpha-amylase (21, 43). As expected, most of these enzymes possess strong catalytic activities at lower temperatures and need less activation energy than do their mesophilic or thermophilic counterparts (31). It is worth noting that, quite unexpectedly and presumably associated with the cold salt-washing process, P. haloplanktis has also been found to develop routinely on ...

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Section: Resultsmentioning

confidence: 99%

Cytoplasmic and Periplasmic Proteomic Signatures of Exponentially Growing Cells of the Psychrophilic Bacterium Pseudoalteromonas haloplanktis TAC125

Wilmes

Kock

Glagla

et al. 2011

Appl Environ Microbiol

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“…In addition, the concept of using a combination of methods to define metalloproteomes may continue to prove important. With the caveats discussed throughout the text in mind, we believe that metalloproteomics, together with other approaches including "pure" proteomics on cellular [114], sub-cellular [81], and even the metaproteomic [115] levels, will be important in enabling understanding of how biosphere and geosphere interact.…”

Section: Discussionmentioning

confidence: 98%

Protein fractionation and detection for metalloproteomics: challenges and approaches

2012

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At least one third of all proteins are thought to require a metal ion co-factor for their function. Recognition of the importance of metals in biological systems and major advances in analytical instrumentation and technology have led to the emergence of the new research area of metalloproteomics in recent years. Despite this progress, the experimental determination of in-vivo metal cofactors has remained challenging, because this requires elucidation of protein interactions with non-covalently bound metal ions. This critical review highlights current methodological approaches, focusing, in particular, on issues relating to the fractionation and separation of the metalloproteome, including recent experience with metalloproteomics for marine cyanobacteria in our laboratory. Metalloproteomics promises to deliver novel insights into fundamental biological processes in the future, but it is clear that further methodological advances are necessary to exploit the full potential of this emerging research area.

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“…However, it is possible to find many general references about proteomic tools applied to fast bacterial classification from early years (Lay 2001;Emerson, Agulto, Liu, & Liu, 2008, Dworzanski & Snyder, 2005Dworzanski et al, 2006) and applications to the study of common pathogenic seafood bacteria such as Listeria and Staphylococcus genus (Guilbaud et al, 2008;Hain et al, 2007;Ho & Reddy, 2008;Scott & Cordwell, 2009), mentioning nutrient limitations and starvation (Schweder, Markert, & Hecker, 2008) or salt concentration response as climate change consequences.…”

Section: Modificationmentioning

confidence: 99%

The role of proteomics in the study of the influence of climate change on seafood products

Piñeiro¹,

Cañas²,

Carrera³

2010

Food Research International

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a b s t r a c tThe climate change influence over the oceans has been the subject of numerous articles informs and strategies from different scientific perspectives, focused mainly in the ecological impact. The majority of the related studies have been focused in measuring or predicting the physical, chemical, geographical, sociological and economical consequences of this reality, which seems to be unstoppable, and only a few of them are devoted to detect the effects of the climate change over the quality of seafood products, wild or cultivated.The stress produced in marine organisms by the consequences of climate change is reflected at the cell molecular level, being affected the metabolite concentration, the expression of proteins and their modifications. The study of the climate change may take advantage of these molecular changes, which may be used as a source of possible biomarkers of its evolution.After the genomic age, proteomics appears as a young but robust discipline for a global study of the protein content in cells, including their identification, possible modifications, quantification of differential expression and tissue localization, being the most adequate set of methodologies to evidence protein changes in marine organisms affected by climate variations. In the last decade proteomic technologies have experienced an exponential development, but the research has been mainly applied to biomedical and human health research, being scarcely focused to the study of the marine environment. The application of the proteomics methods to study the effects of climate change over seafood, mainly from the safety point of view, is reviewed.

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Proteomics of marine bacteria

Cited by 27 publications

References 135 publications

Cytoplasmic and Periplasmic Proteomic Signatures of Exponentially Growing Cells of the Psychrophilic Bacterium Pseudoalteromonas haloplanktis TAC125

Cytoplasmic and Periplasmic Proteomic Signatures of Exponentially Growing Cells of the Psychrophilic Bacterium Pseudoalteromonas haloplanktis TAC125

Protein fractionation and detection for metalloproteomics: challenges and approaches

The role of proteomics in the study of the influence of climate change on seafood products

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