Biology subjects

Kraemer, R.

Publications and source records attributed to Kraemer, R..

3 recordsLinked to original sources

bioRxiv2022

Osmotic stress response in BetP: How lipids and K+ team up to overcome downregulation

The trimeric betaine symporter BetP senses an osmotic upshift via its osmosensory C-terminal domain and responds rapidly with a steep increase in transport rate. Full activation requires both an elevated internal K+ concentration and a yet unknown membrane stimulus. Moreover, the molecular mechanisms of stress sensing and upregulation remain unclear. Here, we show that K+ binding to BetP in vivo is highly cooperative. Using X-ray crystallography, we identify four putative K+ interaction sites at the C-terminal domains of BetP. Single particle CryoEM on BetP reconstituted in amphipols (AMP-BetP), in the absence of K+, revealed that the three C-terminal domains are oriented symmetrically near the membrane surface, representing a new downregulated state. The presence of K+ resulted in asymmetric partial unfolding of the C-terminal domains, which was assigned as an intermediate between the downregulated state and the conformation observed in crystal structures. Attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy in 2D crystals of BetP reveal glutamate/aspartate and tyrosine responses to K+, in agreement with the identified K+ interaction sites, as well as specific unfolding events in the C-terminal domain upon activation. A rearrangement of the relative protomer orientations confers upregulation through key structural elements involved in the alternating access of BetP affecting sodium and betaine binding affinities. Although K+-specific regulation is unique to BetP we discuss unfolding/refolding of sensory domains as a unifying element in hyperosmotic stress response of osmoregulated transporters.

biophysics↗

bioRxiv2019

Immediate inhibition of sucrose uptake in Corynebacterium glutamicum in response to intracellular glucose-6-phosphate accumulation requires the ptsG encoded EII-permease

Corynebacterium glutamicum co-metabolizes most carbon sources, such as glucose and sucrose. Uptake of those sugars by the PTS involves a glucose- and a sucrose-specific permease EIIGlc (ptsG) and EIISuc (ptsS), respectively. Block of glycolysis by deletion of pgi (encodes phosphoglucoisomerase) redirects glucose-driven carbon flux towards pentose phosphate pathway. C. glutamicum {Delta}pgi grows poorly with glucose but has unaffected, good growth with sucrose. However, addition of glucose to sucrose-cultivated C. glutamicum {Delta}pgi immediately arrested growth via inhibition of the EIISuc-mediated sucrose uptake and reduction of ptsS-mRNA amounts. Kinetic analyses revealed that sucrose uptake inhibition in C. glutamicum {Delta}pgi took place within 15 s after glucose addition. We show that inhibition of PTS-mediated sucrose uptake occurs as direct response to glucose-6-P accumulation. Moreover, addition of non-PTS substrates, which are metabolized to glucose-6-P such as maltose or glucose-6-P itself (uptake was enabled by heterologously produced UhpT), led to similar growth and sucrose uptake inhibition as glucose addition. Despite EIIGlc not being involved in uptake of these substrates, negative effects on sucrose uptake after addition of maltose and glucose-6-P were absent in the EIIGlc-deficient strain C. glutamicum {Delta}pgi{Delta}ptsG. These results show that the ptsG-encoded EIIGlc is part of a novel mechanism for perception of intracellular glucose-6-P accumulation and instantaneous inhibition of EIISuc-mediated sucrose uptake in C. glutamicum. This novel mode of control of PTS activity by an early glycolytic metabolite probably allows efficient adaptation of sugar uptake to the capacity of the central metabolism during co-metabolization, which is characteristic for C. glutamicum.\n\nIMPORTANCECoordination of substrate uptake and metabolism are a prerequisite for efficient co-utilization of substrates, a trait typical for the Gram-positive C. glutamicum. Sucrose uptake via the PTS permease EIISuc in this organism immediately was inhibited in response to intracellular accumulation of the glycolysis intermediate glucose-6-phosphate. This inhibition depends exclusively on the presence but not activity of the PTS permease EIIGluc. Thus, C. glutamicum possesses a novel, immediate, and PTS-dependent way to control and coordinate both uptake and metabolization of multiple substrates by monitoring of their metabolic levels in the cell. This offers new insights and interesting concepts for a further rational engineering of this industrially important production organism and exemplifies a putative general strategy of bacteria for the coordination of sugar uptake and central metabolism.

microbiology↗

bioRxiv2018

Finding the signal in the noise of Citizen Science Observations

While many observations of species are being collected by citizen science projects worldwide, it can be challenging to identify projects collecting data that effectively monitor biodiversity. Over the past several years the allure of taking a \"Big Data\" approach has provided the opportunity to gather massive quantities of observations via the Internet, too often with insufficient information to describe how the observations were made. Information about species populations -- where and when they occur and how many of them are there -- (i.e., the signal) can be lost because insufficient information is gathered to account for the inherent biases in data collection (i.e., the noise). Here we suggest that citizen science projects that have succeeded in motivating large numbers of participants, must consider factors that influence the ecological process that affect species populations as well as the observation process that determines how observations are made. Those citizen science projects that collect sufficient contextual information describing the observation process can be used to generate increasingly accurate information about the distribution and abundance of organisms. We illustrate this using eBird as a case study, describing how this citizen science platform is able to collect vital contextual information on the observation process while maintaining a broad global constituency of participants. We highlight how eBird provides information with which to generate biodiversity indicators -- specifically distribution, abundance, and habitat associations -- across the entire annual cycle, even for populations of long distance migratory birds, a highly challenging taxon.

ecology↗