The contribution of mRNA targeting to spatial protein localization in bacteria

About 30% of all bacterial proteins execute their function outside of the cytosol and must be inserted into or translocated across the cytoplasmic membrane. This requires efficient targeting systems that recognize N-terminal signal sequences in client proteins and deliver them to protein transport complexes in the membrane. While the importance of these protein transport machineries for the spatial organization of the bacterial cell is well documented in multiple studies, the contribution of mRNA targeting and localized translation to protein transport is only beginning to emerge. mRNAs can exhibit diverse subcellular localizations in the bacterial cell and can accumulate at sites where new protein is required. This is frequently observed for mRNAs encoding membrane proteins, but the physiological importance of membrane enrichment of mRNAs and the consequences it has for the insertion of the encoded protein have not been explored in detail. Here, we briefly highlight some basic concepts of signal sequence-based protein targeting and describe in more detail strategies that enable the monitoring of mRNA localization in bacterial cells and potential mechanisms that route mRNAs to particular positions within the cell. Finally, we summarize some recent developments that demonstrate that mRNA targeting and localized translation can sustain membrane protein insertion under stress conditions when the protein-targeting machinery is compromised. Thus, mRNA targeting likely acts as a back-up strategy and complements the canonical signal sequence-based protein targeting.

The role of the 5' sensing function of ribonuclease E in cyanobacteria

RNA degradation is critical for synchronising gene expression with changing conditions in prokaryotic and eukaryotic organisms. In bacteria, the preference of the central ribonucleases RNase E, RNase J and RNase Y for 5'-monophosphorylated RNAs is considered important for RNA degradation. For RNase E, the underlying mechanism is termed 5' sensing, contrasting to the alternative 'direct entry' mode, which is independent of monophosphorylated 5' ends. Cyanobacteria, such as Synechocystis sp. PCC 6803 (Synechocystis), encode RNase E and RNase J homologues. Here, we constructed a Synechocystis strain lacking the 5' sensing function of RNase E and mapped on a transcriptome-wide level 283 5'-sensing-dependent cleavage sites. These included so far unknown targets such as mRNAs encoding proteins related to energy metabolism and carbon fixation. The 5' sensing function of cyanobacterial RNase E is important for the maturation of rRNA and several tRNAs, including tRNAGluUUC. This tRNA activates glutamate for tetrapyrrole biosynthesis in plant chloroplasts and in most prokaryotes. Furthermore, we found that increased RNase activities lead to a higher copy number of the major Synechocystis plasmids pSYSA and pSYSM. These results provide a first step towards understanding the importance of the different target mechanisms of RNase E outside Escherichia coli.

mRNA targeting eliminates the need for the signal recognition particle during membrane protein insertion in bacteria

Signal-sequence-dependent protein targeting is essential for the spatiotemporal organization of eukaryotic and prokaryotic cells and is facilitated by dedicated protein targeting factors such as the signal recognition particle (SRP). However, targeting signals are not exclusively contained within proteins but can also be present within mRNAs. By in vivo and in vitro assays, we show that mRNA targeting is controlled by the nucleotide content and by secondary structures within mRNAs. mRNA binding to bacterial membranes occurs independently of soluble targeting factors but is dependent on the SecYEG translocon and YidC. Importantly, membrane insertion of proteins translated from membrane-bound mRNAs occurs independently of the SRP pathway, while the latter is strictly required for proteins translated from cytosolic mRNAs. In summary, our data indicate that mRNA targeting acts in parallel to the canonical SRP-dependent protein targeting and serves as an alternative strategy for safeguarding membrane protein insertion when the SRP pathway is compromised.

NIN-Like Proteins: Interesting Players in Rhizobia-Induced Nitrate Signaling Response During Interaction with Non-Legume Host Arabidopsis thaliana

Nitrogen is an essential macronutrient and a key cellular messenger. Plants have evolved refined molecular systems to sense the cellular nitrogen status. This is exemplified by the root nodule symbiosis between legumes and symbiotic rhizobia, where nitrate availability inhibits this mutualistic interaction. Additionally, nitrate also functions as a metabolic messenger, resulting in nitrate signaling cascades which intensively crosstalk with other physiological pathways. Nodule inception-like proteins (NLPs) are key players in nitrate signaling and regulate nitrate-dependent transcription during legume-rhizobia interactions. Nevertheless, the coordinated interplay between nitrate signaling pathways and rhizobacteria-induced responses remains to be elucidated. In our study, we investigated rhizobia-induced changes in the root system architecture of the non-legume host arabidopsis under different nitrate conditions. We demonstrate that rhizobium-induced lateral root growth and increased root hair length and density are regulated by a nitrate-related signaling pathway. Key players in this process are AtNLP4 and AtNLP5, because the corresponding mutants failed to respond to rhizobia. At the cellular level, AtNLP4 and AtNLP5 control a rhizobia-induced decrease in cell elongation rates, while additional cell divisions occurred independently of AtNLP4. In summary, our data suggest that root morphological responses to rhizobia are coordinated by a newly considered nitrate-related NLP pathway that is evolutionarily linked to regulatory circuits described in legumes.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Uncovering a novel function of the CCR4-NOT complex in phytochrome A-mediated light signalling in plants

Phytochromes are photoreceptors regulating growth and development in plants. Using the model plant Arabidopsis, we identified a novel signalling pathway downstream of the far-red light-sensing phytochrome, phyA, that depends on the highly conserved CCR4-NOT complex. CCR4-NOT is integral to RNA metabolism in yeast and animals, but its function in plants is largely unknown. NOT9B, an Arabidopsis homologue of human CNOT9, is a component of the CCR4-NOT complex, and acts as negative regulator of phyA-specific light signalling when bound to NOT1, the scaffold protein of the complex. Light-activated phyA interacts with and displaces NOT9B from NOT1, suggesting a potential mechanism for light signalling through CCR4-NOT. ARGONAUTE 1 and proteins involved in splicing associate with NOT9B and we show that NOT9B is required for specific phyA-dependent alternative splicing events. Furthermore, association with nuclear localised ARGONAUTE 1 raises the possibility that NOT9B and CCR4-NOT are involved in phyA-modulated gene expression.

Place a seedling on a windowsill, and soon you will notice the fragile stem bending towards the glass to soak in the sun and optimize its growth. Plants can ‘sense’ light thanks to specialized photoreceptor molecules: for instance, the phytochrome A is responsible for detecting weak and ‘far-red’ light from the very edge of the visible spectrum. Once the phytochrome has been activated, this message is relayed to the rest of the plant through an intricate process that requires other molecules.

The CCR4-NOT protein complex is vital for all plants, animals and fungi, suggesting that it was already present in early life forms. Here, Schwenk et al. examine whether CCR4-NOT could have acquired a new role in plants to help them respond to far-red light.

Scanning the genetic information of the plant model Arabidopsis thaliana revealed that the gene encoding the NOT9 subunit of CCR4-NOT had been duplicated in plants during evolution. NOT9B, the protein that the new copy codes for, has a docking site that can attach to both phytochrome A and CCR4-NOT. When NOT9B binds phytochrome A, it is released from the CCR4-NOT complex: this could trigger a cascade of reactions that ultimately changes how A. thaliana responds to far-red light. Plants that had not enough or too much NOT9B were respectively more or less responsive to that type of light, showing that the duplication of the gene coding for this subunit had helped plants respond to certain types of light.

The findings by Schwenk et al. illustrate how existing structures can be repurposed during evolution to carry new roles. They also provide a deeper understanding of how plants optimize their growth, a useful piece of information in a world where most people rely on crops as their main source of nutrients.

Adverse health experiences, environmental attitudes, and pesticide usage behavior of farm operators

Water pollution from agricultural pesticides continues to be a public concern. Given that the use of such pesticides on the farm is largely governed by voluntary behavior, it is important to understand what drives farmer behavior. Health belief models in public health and social psychology argue that persons who have adverse health experiences are likely to undertake preventive behavior. An analogous hypothesis set was tested here: farmers who believe they have had adverse health experiences from pesticides are likely to have heightened concerns about pesticides and are more likely to take greater precautions in dealing with pesticides. This work is based on an original survey of a population of 2700 corn and soybean growers in Maryland, New York, and Pennsylvania using the U.S. Department of Agriculture data base. It was designed as a mail survey with telephone follow-up, and resulted in a 60 percent response rate. Farm operators report experiencing adverse health problems they believe are associated with pesticides that is equivalent to an incidence rate that is higher than the reported incidence of occupational pesticide poisonings, but similar to the reported incidence of all pesticide poisonings. Farmers who report experiencing such problems have more heightened concerns about water pollution from fertilizers and pesticides, and illness and injury from mixing, loading, and applying pesticides than farmers who have not experienced such problems. Farmers who report experiencing such problems also are more likely to report using alternative pest management practices than farmers who do not report having such problems. This implies that farmers who have had such experiences do care about the effects of application and do engage in alternative means of pest management, which at least involve the reduction in pesticide use.

Choice of hospital for delivery: a comparison of high-risk and low-risk women

OBJECTIVE

This article tests whether or not the factors that affect hospital choice differ for selected subgroups of the population.

DATA SOURCES

1985 California Office of Statewide Health Planning and Development (OSHPD) discharge abstracts and hospital financial data were used.

STUDY DESIGN

Models for hospital choice were estimated using McFadden's conditional logit model. Separate models were estimated for high-risk and low-risk patients, and for high-risk and low-risk women covered either by private insurance or by California Medicaid. The model included independent variables to control for quality, price, ownership, and distance to the hospital.

DATA EXTRACTION

Data covered all maternal deliveries in the San Francisco Bay Area in 1985 (N = 61,436). ICD-9 codes were used to classify patients as high-risk or low-risk. The expected payment code on the discharge abstract was used to identify insurance status.

PRINCIPAL FINDINGS

The results strongly reject the hypothesis that high-risk and low-risk women have the same choice process. Hospital quality tended to be more important for high-risk than low-risk women. These results also reject the hypothesis that factors influencing choice of hospital are the same for women covered by private insurance as for those covered by Medicaid. Further, high-risk women covered by Medicaid were less likely than high-risk women covered by private insurance to deliver in hospitals with newborn intensive care units.

CONCLUSIONS

The results show that the choice factors vary across several broadly defined subgroups of patients with a specific condition. Thus, estimates aggregating all patients may be misleading. Specifically, such estimates will understate actual patient response to quality of care indicators, since patient sensitivity to quality of care varies with the patients' risk status.

Modeling the effect of hospital charges and quality on choice

The authors apply a conditional choice model to simulate the results of patient and physician choices of hospitals for a specific surgical procedure in response to improvements in quality or changes in charges. The model includes all zip code areas and relevant hospitals in a large metropolitan area and estimates the impact on admissions at each hospital. It can be used to estimate both the impact of decisions by a given hospital and the potential responses of competitors, as well as the effects of selective contracting with hospitals by certain payors.

The economics of pesticide use and regulation

Pesticides enhance agricultural productivity, but the environmental and health side effects of their use justify government regulation, a subject of continuing societal debate. Bans on pesticide use are the principal regulatory device used in the United States. The economic impacts of such bans depend on the availability of substitutes, supply and trade conditions, and research and development. Without substitutes, pesticide bans result in reduced production levels and higher prices, a substantial loss of discretionary income to consumers, and a redistribution of income among agricultural producers. Most food safety concerns can be addressed by establishing standards and markets for pesticide-differentiated products, but worker safety and clean water concerns will require direct controls. Pesticide-use fees are shown to be more efficient than outright pesticide bans as a mechanism to obtain environmental goals.

Does quality influence choice of hospital?

In recent years, much information has been provided to the public and to physicians about hospital quality measured in terms of patient outcomes. To examine if, before these public data releases, quality influenced the attractiveness of a hospital to referring or admitting physicians and to patients, we estimated the influences of quality, charges, ownership, and distance on the choice of hospitals for patients with seven surgical procedures and five medical diagnoses in hospitals in three geographic areas in California in 1983. Greater distance and public or proprietary ownership consistently reduced the likelihood of selection while medical school affiliation increased the likelihood of selection. For five of seven surgical procedures and two of five medical diagnoses, hospitals with poorer than expected outcomes attracted significantly fewer admissions. The reverse held for two surgical procedures and one medical diagnosis. The results suggest that quality played an important role in choices among hospitals even before explicit data were widely available.

The sensitivity of conditional choice models for hospital care to estimation technique

It is plausible that distance, quality, and hospital charges all influence which hospital patients (and their referring physicians) choose. Several researchers have estimated conditional choice models that explicitly incorporate the existence of competing hospitals. To be useful for hospital administrators, health planners and insurers, however, estimates must be made for specific types of patients and include entire market areas. Data sets meeting these requirements have many combinations of hospitals and locations with zero patients. This raises computational difficulties with the linear estimation techniques used previously. In this paper, we use data on patients undergoing cardiac catheterization in several market areas to assess alternative estimation techniques. First, we estimate the conditional choice model with the two techniques used previously to transform the non-linear choice model. These involve using as a reference (1) a single hospital, or (2) the geometric mean of all the hospitals in the market. When there are many zeros, these techniques require extensive adjustments to the data which may lead to biased estimators. We then compare these results with maximum likelihood estimates. The latter results are substantively and significantly different from those using traditional techniques. More importantly, the linear estimates are much more sensitive to the proportion of zeros. We thus conclude that maximum likelihood estimates are preferable when there are many zeros.