Physiological and Proteomic Adaptation of “Aromatoleum aromaticum” EbN1 to Low Growth Rates in Benzoate-Limited, Anoxic Chemostats

Abstract

؊1 ) growth rates. A positive correlation to growth rate was observed for cellular parameters (cell size, and DNA and protein contents). The free energy consumed for biomass formation steadily increased with growth rate. In contrast, the energy demand for maintenance increased only from low to med and then remained constant until high . The most comprehensive proteomic changes were observed at low compared to high . Uniformly decreased abundances of protein components of the anaerobic benzoyl coenzyme A (benzoyl-CoA) pathway, central carbon metabolism, and information processing agree with a general deceleration of benzoate metabolism and cellular processes in response to slow growth. In contrast, increased abundances were observed at low for diverse catabolic proteins and components of uptake systems in the absence of the respective substrate (aromatic or aliphatic compounds) and for proteins involved in stress responses. This potential catabolic versatility and stress defense during slow growth may be interpreted as preparation for future needs. Most terrestrial and aquatic habitats are characterized by dynamic fluctuations in the composition and concentration of nutrients, supporting heterotrophic growth of bacteria in a feastand-famine manner. In most cases, poor carbon and nutrient availabilities restrict or even arrest microbial growth (see, e.g., references 19, 27, and 33). Thus, the capacity of bacteria to cope with nutrient limitation is a key determinant for their survival and success in the environment. Substrate limitation and its longknown intimate coupling to bacterial growth rates are best studied by continuous cultivation in chemostats (for an overview, see, e.g., references 20 and 27). Constrained by a defined and constant supply of the limiting nutrient at a specific rate (dilution rate [D]), the bacterial population in a chemostat approaches a steady state characterized by a specific growth rate () and stable growth parameters (39, 45). Combining these quantities with chemostat models can describe the dynamics of bacterial populations at many levels (see, e.g., reference 25).Steady-state responses are best understood in Escherichia coli and other enterobacteria. Early physiological studies revealed a tight coupling of growth rate with the size and molecular composition of cells (7,42,61). Subsequently, growth rate-dependent global alterations in gene expression (21, 30) and proteome signatures (49, 76) were observed. An interesting outcome from these global surveys of slowly growing, carbon-limited cells was the apparently preemptive adaptation to future needs for stress resistance and multiple substrate utilization (for an overview, see reference 19).The denitrifying strain "Aromatoleum aromaticum" EbN1 is a versatile aquatic betaproteobacterium that anaerobically degrades 24 different monoaromatic compounds, including petroleum hydrocarbons (57), phenolic solvents (79), and 3-phenylpropanoids (69). With few exceptions, these aromatic substrates are channeled via specific reaction sequences i...

Assessment of Anaerobic Toluene Biodegradation Activity by bssA Transcript/Gene Ratios

“…In carbon-and energy-limited environments, constitutive expression increases an organism's capacity to react quickly to transiently available nutrients (30). For example, in what they termed "catabolic preparedness," Trautwein et al (31) recently demonstrated that Azoarcus sp. EbN1 expressed a large number of proteins involved in anaerobic hydrocarbon degradation despite the absence of their respective substrates from the growth medium.…”

Complete genome, catabolic sub‐proteomes and key‐metabolites of Desulfobacula toluolica Tol2, a marine, aromatic compound‐degrading, sulfate‐reducing bacterium

“…Membrane proteins were prepared as described by Trautwein and colleagues () and subjected to separation according to molecular mass on 25 × 30 cm, 12.5% SDS gels (Bio‐Rad, Munich, Germany). Each sample lane was divided into 15 gel slices, and each slice cut into smaller pieces (about 1 mm) prior to washing, reduction, alkylation and tryptic digest.…”

Pathways and substrate‐specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade)

“…For shotgun analysis, total protein prepared individually from three biological replicates per substrate condition was digested and subjected to nanoLC-ESI-MS/MS as described (Trautwein et al, 2012).…”