Experimental and Theoretical Bases of Specific Affinity, a Cytoarchitecture-Based Formulation of Nutrient Collection Proposed To Supercede the Michaelis-Menten Paradigm of Microbial Kinetics

Abstract

A theory for solute uptake by whole cells was derived with a focus on the ability of oligobacteria to sequester nutrients. It provided a general relationship that was used to obtain the kinetic constants for in situ marine populations in the presence of naturally occurring substrates. In situ affinities of 0.9 to 400 liters g of cells ؊1h ؊1 found were up to 10 3 times smaller than those from a "Marinobacter arcticus " isolate, but springtime values were greatly increased by warming. Affinities of the isolate for usual polar substrates but not for hydrocarbons were diminished by ionophores. A kinetic curve or Monod plot was constructed from the best available data for cytoarchitectural components of the isolate by using the theory together with concepts and calculations from first principles. The order of effect of these components on specific affinity was membrane potential > cytoplasmic enzyme concentration > cytoplasmic enzyme affinity > permease concentration > area of the permease site > translation coefficient > porin concentration. Component balance was influential as well; a small increase in cytoplasmic enzyme concentration gave a large increase in the effect of permease concentration. The effect of permease concentration on specific affinity was large, while the effect on K m was small. These results are in contrast to the Michaelis-Menten theory as applied by Monod that has uptake kinetics dependent on the quality of the permease molecules, with K m as an independent measure of affinity. Calculations demonstrated that most oligobacteria in the environment must use multiple substrates simultaneously to attain sufficient energy and material for growth, a requirement consistent with communities largely comprising few species.The rate of nutrient transport into microorganisms is typically described by using the equations of Monod (30), formulations that are based on measurements of in vitro enzyme solutions and the theory described by Michaelis and Menten (29). Affinity for solute is usually taken as the Michaelis constant (K m ), the concentration of substrate at half the maximal rate of uptake, and taken as an inherent property of both the population (42) and its permeases (36). However, the variation of 10 10 in K m values was too great to be attributed to differences in proteins of common function and appears simply to reflect the concentration of proteins involved in substrate acquisition, metabolism, and biosynthesis. This concept was reinforced by equations that reflected the uptake rates from the number of permease molecules, the time required for each permease to translocate a molecule of substrate (6), and internal pool concentrations generated at the resulting dynamic steady-state equilibrium (5). Specific affinity for substrate S (a S ), a second-order rate constant for substrate sequestering that scales with nutrient acquisition power independently of the maximal rate (37), could thus be related to cytoarchitectural composition, including permease abundance and properties. The purpose of thi...

Photobiogeochemical cycling of carbon monoxide in the southeastern Beaufort Sea in spring and autumn

“…The present study, to our knowledge, provides the first examples of saturation and inhibition kinetics for microbial CO uptake at in situ [CO] in natural waters, as well as Hill-type kinetics. However, interpreting Hill kinetics is not straightforward (Weiss 1997) and an alternative explanation of such curve shapes based on energy limitations, which may be especially relevant in these Arctic waters, has been advanced (Button et al 2004). Because of the prevalent low [CO] in the major ocean basins, it is believed that the potential of CO as a supplemental energy source to marine microbes is limited by [CO] (Moran and Miller 2007).…”

Inherent and apparent traits in microbial nutrient uptake

“…Microbes, however, are not likely to be perfect sinks. In the case of active uptake through porters at the cell surface, only a fraction of the surface is covered by such porters (Berg & Purcell 1977, Jumars et al 1993, Button et al 2004). In the case of diffusion limitation, theoretical studies have shown that the chance of capturing a nutrient molecule is a non-linear function of the porter number, and the flux can be expressed as (Berg & Purcell 1977, Zwanzig 1990: (3) where n is the number of porters of the cell, s is the porter size (radius, m), and the factor (1 -p), where was introduced (Zwanzig 1990) to correct for interaction between porters.…”

“…But it is also redundant because α by definition (Eq. 4) is more appropriate (Healey 1980, Aksnes & Egge 1991, Button et al 2004, which suggests that affinity-based uptake models (Aksnes et al 1995, Smith et al 2009, Thingstad et al 2010) might be preferable in ecological modeling. It can be noted that affinity (α), according to Eq.…”

“…The assumption of invariant half-saturation constants for functional groups and species in models where environmental variables such as temperature are temporally and spatially heterogeneous might therefore be inappropriate (Aksnes et al 1995, Smith 2010. Another related concern is that values of K tend to vary substantially, both in experiments (Harrison et al 1989, Button et al 2004) and in models (Franks 2009). In 10 recently published ecosystem models, Franks (2009) found that variation of > 2 orders of magnitude in K was applied for similar functional groups of phytoplankton, and questioned whether the MM equation is the best representation of nutrient uptake in ecosystem models.…”

Three-Dimensional Structure of the Ultraoligotrophic Marine Bacterium “Candidatus Pelagibacter ubique”

“…The alternative explanation, i.e., that small size can make cells more competitive, assumes either that the reduced material costs of replicating drive minimization (6) or that high surface-to-volume ratios make cells more competitive for nutrients (10). For example, in some conceptual models, surface-tovolume relationships are recognized as potentially important factors influencing the balance between nutrient transport capacity and biomass (11). In one model, large cells are not competitive in dilute ecosystems because they waste energy producing metabolic enzymes that will never be pushed to process substrates at close to their turnover capacity (10).…”