Microproteins—Discovery,structure, and function

Advances in proteogenomic technologies have revealed hundreds to thousands of translated small open reading frames (sORFs) that encode microproteins in genomes across evolutionary space. While many microproteins have now been shown to play critical roles in biology and human disease, a majority of recently identified microproteins have little or no experimental evidence regarding their functionality. Computational tools have some limitations for analysis of short, poorly conserved microprotein sequences, so additional approaches are needed to determine the role of each member of this recently discovered polypeptide class. A currently underexplored avenue in the study of microproteins is structure prediction and determination, which delivers a depth of functional information. In this review, we provide a brief overview of microprotein discovery methods, then examine examples of microprotein structures (and, conversely, intrinsic disorder) that have been experimentally determined using crystallography, cryo-electron microscopy, and NMR, which provide insight into their molecular functions and mechanisms. Additionally, we discuss examples of predicted microprotein structures that have provided insight or context regarding their function. Analysis of microprotein structure at the angstrom level, and confirmation of predicted structures, therefore, has potential to identify translated microproteins that are of biological importance and to provide molecular mechanism for their in vivo roles.     

Chloroplast biogenesis — Correlation between structure and function

Chloroplast biogenesis is a multistage process leading to fully differentiated and functionally mature plastids. Complex analysis of chloroplast biogenesis was performed on the structural and functional level of its organization during the photoperiodic plant growth after initial growth of seedlings in the darkness. We correlated, at the same time intervals, the structure of etioplasts transforming into mature chloroplasts with the changes in the photosynthetic protein levels (selected core and antenna proteins of PSI and PSII) and with the function of the photosynthetic apparatus in two plant species: bean (Phaseolus vulgaris L.) and pea (Pisum sativum L). We selected these plant species since we demonstrated previously that the mature chloroplasts differ in the thylakoid organization. We showed that the protein biosynthesis as well as photosynthetic complexes formation proceeds gradually in both plants in spite of periods of darkness. We found that both steady structural differentiation of the bean chloroplast and reformation of prolamellar bodies in pea were accompanied by a gradual increase of the photochemical activity in both species. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.     

Specificity, location and function of βTrCP isoforms and their splice variants

SCF^βTrCP is the ubiquitin ligase for a wide variety of substrates and functions in many cellular processes. βTrCP, the substrate binding factor of the SCF complex, has two isoforms, produced from different genes, and several splice variants. Despite a certain level of redundancy, knock-out studies show different phenotypes indicating different preferential substrates for the two isoforms. However, until now functional differences between βTrCP1 and 2 were not studied at the endogenous protein level. We generated isoform-specific antibodies against βTrCP to characterise endogenous βTrCP isoforms and splice variants. We show that endogenous βTrCP1 and 2 localise to both nucleus and cytosol. Interestingly, we find that one splice variant of βTrCP2 localises exclusively to the nucleus and another only to the cytosol. In addition, we show that the substrate binding domain of βTrCP is the dominant localisation determinant.     

Plant pleiotropic drug resistance transporters： Transport mechanism,gene expression,and function

Pleiotropic drug resistance （PDR） transporters belonging to the ABCG subfamily of ATP-binding cassette （ABC） transporters are identified only in fungi and plants. Members of this family are expressed in plants in response to various biotic and abiotic stresses and transport a diverse array of moleculesacross membranes, Although their detailed transport mechanism is largely unknown, they play important roles in detoxification processes, preventing water loss, transport of phytohormones, and secondary metabolites. This review provides insights into transport mechanisms of plant PDR transporters, their expression profiles, and multitude functions in plants.     

Estradiol effects on the dopamine transporter – protein levels, subcellular location, and function

Background

The effects of estrogens on dopamine (DA) transport may have important implications for the increased incidence of neurological disorders in women during life stages when hormonal fluctuations are prevalent, e.g. during menarche, reproductive cycling, pregnancy, and peri-menopause.

Results

The activity of the DA transporter (DAT) was measured by the specific uptake of ³H-DA. We found that low concentrations (10^-14 to 10^-8 M) of 17β-estradiol (E₂) inhibit uptake via the DAT in PC12 cells over 30 minutes, with significant inhibition taking place due to E₂ exposure during only the last five minutes of the uptake period. Such rapid action suggests a non-genomic, membrane-initiated estrogenic response mechanism. DAT and estrogen receptor-α (ERα) were elevated in cell extracts by a 20 ng/ml 2 day NGFβ treatment, while ERβ was not. DAT, ERα and ERβ were also detectable on the plasma membrane of unpermeabilized cells by immunocytochemical staining and by a fixed cell, quantitative antibody (Ab)-based plate assay. In addition, PC12 cells contained RNA coding for the alternative membrane ER GPR30; therefore, all 3 ER subtypes are candidates for mediating the rapid nongenomic actions of E₂. At cell densities above 15,000 cells per well, the E₂-induced inhibition of transport was reversed. Uptake activity oscillated with time after a 10 nM E₂ treatment; in a slower room temperature assay, inhibition peaked at 9 min, while uptake activity increased at 3 and 20–30 min. Using an Ab recognizing the second extracellular loop of DAT (accessible only on the outside of unpermeabilized cells), our immunoassay measured membrane vs. intracellular/nonvesicular DAT; both were found to decline over a 5–60 min E₂ treatment, though immunoblot analyses demonstrated no total cellular loss of protein.

Conclusion

Our results suggest that physiological levels of E₂ may act to sequester DAT in intracellular compartments where the transporter's second extramembrane loop is inaccessible (inside vesicles) and that rapid estrogenic actions on this differentiated neuronal cell type may be regulated via membrane ERs of several types.     

Ecosystem structure, function, and restoration success: Are they related?

A direct relationship between ecosystem structure and function has been widely accepted by restoration ecologists. According to this paradigm, ecosystem degradation and aggradation represent parallel changes in structure and function, restoration following the same path as spontaneous succession. But the existence of single bidirectional trajectories and endpoints is not supported by empirical evidence. On the contrary, multiple meta-stable states, irreversible changes and hysteresis are common in nature. These situations are better described by state-and-transition models. Merging those models into the structure–function framework may help to develop new hypotheses on ecosystem dynamics, and may provide a suitable framework for planning restoration activities. We use the relationship between ecosystem function and the effort needed to restore a degraded ecosystem (i.e. restorability) as an example. A linear relationship between ecosystem structure and function suggests that ecosystem degradation and restorability are directly related. This may not be true when multiple states, not necessarily connected, are considered. We show two case studies that support this point, and discuss the implications of the incorporation of state-and-transition models into the structure–function framework on relevant topics of restoration ecology and conservation biology, such as the choice of reference ecosystems, the evaluation of restoration actions, and the identification of priority areas for conservation and restoration.     

Cytochrome c oxidase—structure, function, and physiology of a redox-driven molecular machine

Cytochome c oxidase is the terminal member of the electron transport chains of mitochondria and many bacteria. Providing an efficient mechanism for dioxygen reduction on the one hand, it also acts as a redox-linked proton pump, coupling the free energy of water formation to the generation of a transmembrane electrochemical gradient to eventually drive ATP synthesis. The overall complexity of the mitochondrial enzyme is also reflected by its subunit structure and assembly pathway, whereas the diversity of the bacterial enzymes has fostered the notion of a large family of heme-copper terminal oxidases. Moreover, the successful elucidation of 3-D structures for both the mitochondrial and several bacterial oxidases has greatly helped in designing mutagenesis approaches to study functional aspects in these enzymes. Electronic Publication     

Thermozymes: biotechnology and structure–function relationships

Recent findings on the biochemical and molecular features of the following thermozymes are presented, based on their biotechnological use: α-amylase and amylopullulanase, used in starch processing; glucose isomerase, used in sweetener production; alcohol dehydrogenase, used in chemical synthesis; and alkaline phosphatase, used in diagnostics. The corresponding genes and recombinant proteins have been characterized in terms of sequence similarities, specific activities, thermophilicity, and unfolding kinetics. Site-directed and nested deletion mutagenesis were used to understand structure–function relationships. All these thermozymes display higher stability and activity than their counterparts currently used in the biotechnology industry. Received: January 22, 1998 / Accepted: February 16, 1998     

Starch-binding domains as CBM families–history,occurrence, structure,function and evolution

The term “starch-binding domain” (SBD) has been applied to a domain within an amylolytic enzyme that gave the enzyme the ability to bind onto raw, i.e. thermally untreated, granular starch. An SBD is a special case of a carbohydrate-binding domain, which in general, is a structurally and functionally independent protein module exhibiting no enzymatic activity but possessing potential to target the catalytic domain to the carbohydrate substrate to accommodate it and process it at the active site. As so-called families, SBDs together with other carbohydrate-binding modules (CBMs) have become an integral part of the CAZy database (http://www.cazy.org/). The first two well-described SBDs, i.e. the C-terminal Aspergillus-type and the N-terminal Rhizopus-type have been assigned the families CBM20 and CBM21, respectively. Currently, among the 85 established CBM families in CAZy, fifteen can be considered as families having SBD functional characteristics: CBM20, 21, 25, 26, 34, 41, 45, 48, 53, 58, 68, 69, 74, 82 and 83. All known SBDs, with the exception of the extra long CBM74, were recognized as a module consisting of approximately 100 residues, adopting a β-sandwich fold and possessing at least one carbohydrate-binding site. The present review aims to deliver and describe: (i) the SBD identification in different amylolytic and related enzymes (e.g., CAZy GH families) as well as in other relevant enzymes and proteins (e.g., laforin, the β-subunit of AMPK, and others); (ii) information on the position in the polypeptide chain and the number of SBD copies and their CBM family affiliation (if appropriate); (iii) structure/function studies of SBDs with a special focus on solved tertiary structures, in particular, as complexes with α-glucan ligands; and (iv) the evolutionary relationships of SBDs in a tree common to all SBD CBM families (except for the extra long CBM74). Finally, some special cases and novel potential SBDs are also introduced.     

From remotely-sensed solar-induced chlorophyll fluorescence to ecosystem structure,function, and service: Part II—Harnessing data

Although our observing capabilities of solar-induced chlorophyll fluorescence (SIF) have been growing rapidly, the quality and consistency of SIF datasets are still in an active stage of research and development. As a result, there are considerable inconsistencies among diverse SIF datasets at all scales and the widespread applications of them have led to contradictory findings. The present review is the second of the two companion reviews, and data oriented. It aims to (1) synthesize the variety, scale, and uncertainty of existing SIF datasets, (2) synthesize the diverse applications in the sector of ecology, agriculture, hydrology, climate, and socioeconomics, and (3) clarify how such data inconsistency superimposed with the theoretical complexities laid out in (Sun et al., 2023) may impact process interpretation of various applications and contribute to inconsistent findings. We emphasize that accurate interpretation of the functional relationships between SIF and other ecological indicators is contingent upon complete understanding of SIF data quality and uncertainty. Biases and uncertainties in SIF observations can significantly confound interpretation of their relationships and how such relationships respond to environmental variations. Built upon our syntheses, we summarize existing gaps and uncertainties in current SIF observations. Further, we offer our perspectives on innovations needed to help improve informing ecosystem structure, function, and service under climate change, including enhancing in-situ SIF observing capability especially in “data desert” regions, improving cross-instrument data standardization and network coordination, and advancing applications by fully harnessing theory and data.     

Infection of Plants and Plant Tissue Cultures with Cyanobacteria–Bacteria Complexes

The infection of tobacco, nightshade, rice plants, and their tissue cultures with the cyanobacteria–bacteria associative microsymbiont complexes (AMC) isolated from natural syncyanoses (the ferns Azolla pinnataand Azollasp. and the cycad Encephalartos ferox) was studied. The inoculation of the intact plants or their cuttings with AMC led to the colonization of the plant roots, stems, and leaves by cyanobacteria and their bacterial symbionts (referred to as satellite bacteria, SB). The sites of the long-term contact of plant organs with cyanobacteria were characterized by the formation of copious slime. On the roots of infected plants, one could observe the callus growth of cortical parenchyma cells and the formation of pseudonodules, in which SB cells gradually accumulated. In mixed cultures of plant callus tissues and the AMC isolated from the fernsA. pinnataand Azollasp., the callus tissue specifically influenced the growth of the AMC components, causing (depending on the plant species and strain) either their balanced growth, or their cyclic growth, or the predominant growth of one of the AMC components (either cyanobacteria or satellite bacteria). This phenomenon is proposed to be used for the dissociation of stable multicomponent natural symbiotic complexes and the selection of their particular components.     

Habitat structure, trophic structure and ecosystem function: interactive effects in a bromeliad–insect community

Although previous studies have shown that ecosystem functions are affected by either trophic structure or habitat structure, there has been little consideration of their combined effects. Such interactions may be particularly important in systems where habitat and trophic structure covary. I use the aquatic insects in bromeliads to examine the combined effects of trophic structure and habitat structure on a key ecosystem function: detrital processing. In Costa Rican bromeliads, trophic structure naturally covaries with both habitat complexity and habitat size, precluding any observational analysis of interactions between factors. I therefore designed mesocosms that allowed each factor to be manipulated separately. Increases in mesocosm complexity reduced predator (damselfly larva) efficiency, resulting in high detritivore abundances, indirectly increasing detrital processing rates. However, increased complexity also directly reduced the per capita foraging efficiency of the detritivores. Over short time periods, these trends effectively cancelled each other out in terms of detrital processing. Over longer time periods, more complex patterns emerged. Increases in mesocosm size also reduced both predator efficiency and detritivore efficiency, leading to no net effect on detrital processing. In many systems, ecosystem functions may be impacted by strong interactions between trophic structure and habitat structure, cautioning against examining either effect in isolation.