Amino acid transport in bacteria

Valorization of food waste fermentation liquid into single cell protein by photosynthetic bacteria via stimulating carbon metabolic pathway and environmental behaviour

Single cell protein (SCP) production by photosynthetic bacteria (PSB) is dependent on the bioavailability of carbon source, while sufficient volatile fatty acids (VFAs) in food waste fermentation liquid might be a potential alternative. It is unclear how the fermentation liquid affects the SCP biosynthesis and the related metabolic mechanism. This work demonstrated that the SCP production could be improved effectively (2088.4 mg/L) with high conversion capacity of carbon source (0.99 mg-biomass/mg-COD) by regulating carbon source level. PSB preferred to utilize the VFAs in food waste fermentation liquid. The carbon metabolic pathways (e.g., the transformation of VFAs to acetyl-CoA, and tricarboxylic acid cycle) involved in the SCP production were enhanced under optimal condition. Moreover, optimal carbon source regulation could significantly stimulate the environmental behaviour of PSB (e.g., two-component system, quorum sensing, and ATP-binding cassette transporter) involved in adaptation to external stimulus and maintaining high bacterial activity, resulting in SCP yield promotion.

Metagenomic evidence for the microbial transformation of carboxyl-rich alicyclic molecules: A long-term macrocosm experiment

Carboxyl-rich alicyclic molecules (CRAMs) widely exist in the ocean and constitute the central part of the refractory dissolved organic matter (RDOM) pool. Although a consensus has been reached that microbial activity forms CRAMs, the detailed molecular mechanisms remain largely unexplored. To better understand the underlying genetic mechanisms driving the microbial transformation of CRAM, a long-term macrocosm experiment spanning 220 days was conducted in the Aquatron Tower Tank at Dalhousie University, Halifax, Canada, with the supply of diatom-derived DOM as a carbon source. The DOM composition, community structure, and metabolic pathways were characterised using multi-omics approaches. The addition of diatom lysate introduced a mass of labile DOM into the incubation seawater, which led to a low degradation index (I_DEG) and refractory molecular lability boundary (RMLB) on days 1 and 18. The molecular compositions of the DOM molecules in the later incubation period (from day 120 to day 220) were more similar in composition to those on day 0, suggesting a rapid turnover of phytoplankton debris by microbial communities. Taxonomically, while Alpha proteobacteria dominated during the entire incubation period, Gamma proteobacteria became more sensitive and abundant than the other bacterial groups on days 1 and 18. Recalcitrant measurements such as I_DEG and RMLB were closely related to the DOM molecules, bacterial community, and Kyoto encyclopaedia of Genes and Genomes (KEGG) modules, suggesting close associations between RDOM accumulation and microbial metabolism. KEGG modules that showed strong positive correlation with CRAMs were identified using a microbial ecological network approach. The identified KEGG modules produced the substrates, such as the acetyl-CoA or 3‑hydroxy-3-methylglutaryl-CoA, which could participate in the mevalonate pathway to generate the precursor of CRAM analogues, isopentenyl-PP, suggesting a potential generation pathway of CRAM analogues in bacteria and archaea. This study revealed the potential genetic and molecular processes involved in the microbial origin of CRAM analogues, and thus indicated a vital ecological role of bacteria and archaea in RDOM production. This study also offered new perspectives on the carbon sequestration in the ocean.

Escherichia coli K-12 Lacks a High-Affinity Assimilatory Cysteine Importer

The most direct route by which microbes might assimilate sulfur would be by importing cysteine. However, alone among the amino acids, cysteine does not have well-characterized importers. We determined that Escherichia coli can rapidly import cysteine, but in our experiments, it did so primarily through the LIV ATP-driven system that is dedicated to branched-chain amino acids. The affinity of this system for cysteine is far lower than for Leu, Ile, and Val, and so in their presence, cysteine is excluded. Thus, this transport is unlikely to be relevant in natural environments. Growth studies, transcriptomics, and transport assays failed to detect any high-affinity importer that is dedicated to cysteine assimilation. Enteric bacteria do not contain the putative cysteine importer that was identified in Campylobacter jejuni This situation is surprising, because E. coli deploys ion- and/or ATP-driven transporters that import cystine, the oxidized form of cysteine, with high affinity and specificity. We conjecture that in oxic environments, molecular oxygen oxidizes environmental cysteine to cystine, which E. coli imports. In anoxic environments where cysteine is stable, the cell chooses to assimilate hydrogen sulfide instead. Calculations suggest that this alternative is almost as economical, and it avoids the toxic effects that can result when excess cysteine enters the cell.IMPORTANCE This investigation discovered that Escherichia coli lacks a transporter dedicated to the assimilation of cysteine, an outcome that is in striking contrast to the many transporters devoted to the other 19 amino acids. We ascribe the lack of a high-affinity cysteine importer to two considerations. First, the chemical reactivity of this amino acid is unique, and its poorly controlled import can have adverse consequences for the cell. Second, our analysis suggests that the economics of biosynthesis depend sharply upon whether the cell is respiring or fermenting. In the anoxic habitats in which cysteine might be found, the value of import versus biosynthesis is strongly reduced compared to that in oxic habitats. These studies may explain why bacteria choose to synthesize rather than to import other useful biomolecules as well.

Escherichia coli, an Intestinal Microorganism, as a Biosensor for Quantification of Amino Acid Bioavailability

In animal diets optimal amino acid quantities and balance among amino acids is of great nutritional importance. Essential amino acid deficiencies have negative impacts on animal physiology, most often expressed in sub-optimal body weight gains. Over supplementation of diets with amino acids is costly and can increase the nitrogen emissions from animals. Although in vivo animal assays for quantification of amino acid bioavailability are well established, Escherichia coli-based bioassays are viable potential alternatives in terms of accuracy, cost, and time input. E. coli inhabits the gastrointestinal tract and although more abundant in colon, a relatively high titer of E. coli can also be isolated from the small intestine, where primary absorption of amino acids and peptides occur. After feed proteins are digested, liberated amino acids and small peptides are assimilated by both the small intestine and E. coli. The similar pattern of uptake is a necessary prerequisite to establish E. coli cells as accurate amino acid biosensors. In fact, amino acid transporters in both intestinal and E. coli cells are stereospecific, delivering only the respective biological l-forms. The presence of free amino- and carboxyl groups is critical for amino acid and dipeptide transport in both biological subjects. Di-, tri- and tetrapeptides can enter enterocytes; likewise only di-, tri- and tetrapeptides support E. coli growth. These similarities in addition to the well known bacterial genetics make E. coli an optimal bioassay microorganism for the assessment of nutritionally available amino acids in feeds.

Deciphering the mechanisms of intestinal imino (and amino) acid transport: The redemption of SLC36A1

The absorption of zwitterionic imino and amino acids, and related drugs, is an essential function of the small intestinal epithelium. This review focuses on the physiological roles of transporters recently identified at the molecular level, in particular SLC36A1, by identifying how they relate to the classical epithelial imino and amino acid transporters characterised in mammalian small intestine in the 1960s-1990s. SLC36A1 transports a number of D- and L-imino and amino acids, beta- and gamma-amino acids and orally-active neuromodulatory and antibacterial agents. SLC36A1 (or PAT1) functions as a proton-coupled imino and amino acid symporter in cooperation with the Na+/H+ exchanger NHE3 (SLC9A3) to produce the imino acid carrier identified in rat small intestine in the 1960s but subsequently ignored because of confusion with the IMINO transporter. However, it is the sodium/imino and amino acid cotransporter SLC6A20 which corresponds to the betaine carrier (identified in hamster, 1960s) and IMINO transporter (identified in rabbit and guinea pig, 1980s). This review summarises evidence for expression of SLC36A1 and SLC6A20 in human small intestine, highlights the differences in functional characteristics of the imino acid carrier and IMINO transporter, and explains the confusion surrounding these two distinct transport systems.

Hierarchical amino acid utilization and its influence on fermentation dynamics: rifamycin B fermentation using Amycolatopsis mediterranei S699, a case study

Background

Industrial fermentation typically uses complex nitrogen substrates which consist of mixture of amino acids. The uptake of amino acids is known to be mediated by several amino acid transporters with certain preferences. However, models to predict this preferential uptake are not available. We present the stoichiometry for the utilization of amino acids as a sole carbon and nitrogen substrate or along with glucose as an additional carbon source. In the former case, the excess nitrogen provided by the amino acids is excreted by the organism in the form of ammonia. We have developed a cybernetic model to predict the sequence and kinetics of uptake of amino acids. The model is based on the assumption that the growth on a specific substrate is dependent on key enzyme(s) responsible for the uptake and assimilation of the substrates. These enzymes may be regulated by mechanisms of nitrogen catabolite repression. The model hypothesizes that the organism is an optimal strategist and invests resources for the uptake of a substrate that are proportional to the returns.

Results

Stoichiometric coefficients and kinetic parameters of the model were estimated experimentally for Amycolatopsis mediterranei S699, a rifamycin B overproducer. The model was then used to predict the uptake kinetics in a medium containing cas amino acids. In contrast to the other amino acids, the uptake of proline was not affected by the carbon or nitrogen catabolite repression in this strain. The model accurately predicted simultaneous uptake of amino acids at low cas concentrations and sequential uptake at high cas concentrations. The simulated profile of the key enzymes implies the presence of specific transporters for small groups of amino acids.

Conclusion

The work demonstrates utility of the cybernetic model in predicting the sequence and kinetics of amino acid uptake in a case study involving Amycolatopsis mediterranei, an industrially important organism. This work also throws some light on amino acid transporters and their regulation in A. mediterranei .Further, cybernetic model based experimental strategy unravels formation and utilization of ammonia as well as its inhibitory role during amino acid uptake. Our results have implications for model based optimization and monitoring of other industrial fermentation processes involving complex nitrogen substrate.

The threonine story

L-Threonine is an essential amino acid which has recently been brought into agricultural industry for balancing the livestock feed. L-Threonine is produced by microbial synthesis using glucose or sucrose as substrates. For the process to be cost-effective, the microbial strain must be capable of threonine overproduction. This paper reviews the biochemical pathways of L-threonine synthesis in bacteria and the regulation of these pathways, the principles and the techniques of constructing high-producing strains, and the most efficient strains thus developed.