Structural basis for a novel type of cytokinin-activating protein

Seed yield as a function of cytokinin-regulated gene expression in wild Kentucky bluegrass (Poa pratensis)

BACKGROUND

Kentucky bluegrass (Poa pratensis L.) panicle development is a coordinated process of cell proliferation and differentiation with distinctive phases and architectural changes that are pivotal to determine seed yield. Cytokinin (CK) is a key factor in determining seed yield that might underpin the second "Green Revolution". However, whether there is a difference between endogenous CK content and seed yields of Kentucky bluegrass, and how CK-related genes are expressed to affect enzyme regulation and downstream seed yield in Kentucky bluegrass remains enigmatic.

RESULTS

In order to establish a potential link between CK regulation and seed yield, we dissected and characterized the Kentucky bluegrass young panicle, and determined the changes in nutrients, 6 types of endogenous CKs, and 16 genes involved in biosynthesis, activation, inactivation, re-activation and degradation of CKs during young panicle differentiation of Kentucky bluegrass. We found that high seed yield material had more meristems compared to low seed yield material. Additionally, it was found that seed-setting rate (SSR) and lipase activity at the stage of spikelet and floret primordium differentiation (S3), as well as 1000-grain weight (TGW) and zeatin-riboside (ZR) content at the stages of first bract primordium differentiation (S1) and branch primordium differentiation (S2) showed a significantly positive correlation in the two materials. And zeatin, ZR, dihydrozeatin riboside, isopentenyl adenosine and isopentenyl adenosine riboside contents were higher in seed high yield material than those in seed low yield material at S3 stage. Furthermore, the expressions of PpITP3, PpITP5, PpITP8 and PpLOG1 were positively correlated with seed yield, while the expressions of PpCKX2, PpCKX5 and PpCKX7 were negatively correlated with seed yield in Kentucky bluegrass.

CONCLUSIONS

Overall, our study established a relationship between CK and seed yield in Kentucky bluegrass. Perhaps we can increase SSR and TGW by increasing lipase activity and ZR content. Of course, using modern gene editing techniques to manipulate CK related genes such as PpITP3/5/8, PpLOG1 and PpCKX2/5/7, will be a more direct and effective method in Kentucky bluegrass, which requires further trial validation.

Suppressing a phosphohydrolase of cytokinin nucleotide enhances grain yield in rice

One-step and two-step pathways are proposed to synthesize cytokinin in plants. The one-step pathway is mediated by LONELY GUY (LOG) proteins. However, the enzyme for the two-step pathway remains to be identified. Here, we show that quantitative trait locus GY3 may boost grain yield by more than 20% through manipulating a two-step pathway. Locus GY3 encodes a LOG protein that acts as a 5'-ribonucleotide phosphohydrolase by excessively consuming the cytokinin precursors, which contrasts with the activity of canonical LOG members as phosphoribohydrolases in a one-step pathway. The residue S41 of GY3 is crucial for the dephosphorylation of iPRMP to produce iPR. A solo-LTR insertion within the promoter of GY3 suppressed its expression and resulted in a higher content of active cytokinins in young panicles. Introgression of GY302428 increased grain yield per plot by 7.4% to 16.3% in all investigated indica backgrounds, which demonstrates the great value of GY302428 in indica rice production.

The LONELY GUY gene family: from mosses to wheat, the key to the formation of active cytokinins in plants

LONELY GUY (LOG) was first identified in a screen of rice mutants with defects in meristem maintenance. In plants, LOG codes for cytokinin riboside 5'-monophosphate phosphoribohydrolase, which converts inactive cytokinin nucleotides directly to the active free bases. Many enzymes with the PGGxGTxxE motif have been misannotated as lysine decarboxylases; conversely not all enzymes containing this motif are cytokinin-specific LOGs. As LOG mutants clearly impact yield in rice, we investigated the LOG gene family in bread wheat. By interrogating the wheat (Triticum aestivum) genome database, we show that wheat has multiple LOGs. The close alignment of TaLOG1, TaLOG2 and TaLOG6 with the X-ray structures of two functional Arabidopsis thaliana LOGs allows us to infer that the wheat LOGs 1-11 are functional LOGs. Using RNA-seq data sets, we assessed TaLOG expression across 70 tissue types, their responses to various stressors, the pattern of cis-regulatory elements (CREs) and intron/exon patterns. TaLOG gene family members are expressed variously across tissue types. When the TaLOG CREs are compared with those of the cytokinin dehydrogenases (CKX) and glucosyltransferases (CGT), there is close alignment of CREs between TaLOGs and TaCKXs reflecting the key role of CKX in maintaining cytokinin homeostasis. However, we suggest that the main homeostatic mechanism controlling cytokinin levels in response to biotic and abiotic challenge resides in the CGTs, rather than LOG or CKX. However, LOG transgenics and identified mutants in rice variously impact yield, providing interesting avenues for investigation in wheat.

Biochemical and Structural Aspects of Cytokinin Biosynthesis and Degradation in Bacteria

It has been known for quite some time that cytokinins, hormones typical of plants, are also produced and metabolized in bacteria. Most bacteria can only form the tRNA-bound cytokinins, but there are examples of plant-associated bacteria, both pathogenic and beneficial, that actively synthesize cytokinins to interact with their host. Similar to plants, bacteria produce diverse cytokinin metabolites, employing corresponding metabolic pathways. The identification of genes encoding the enzymes involved in cytokinin biosynthesis and metabolism facilitated their detailed characterization based on both classical enzyme assays and structural approaches. This review summarizes the present knowledge on key enzymes involved in cytokinin biosynthesis, modifications, and degradation in bacteria, and discusses their catalytic properties in relation to the presence of specific amino acid residues and protein structure.

The Hulks and the Deadpools of the Cytokinin Universe: A Dual Strategy for Cytokinin Production, Translocation, and Signal Transduction

Cytokinins are plant hormones, derivatives of adenine with a side chain at the N⁶-position. They are involved in many physiological processes. While the metabolism of trans-zeatin and isopentenyladenine, which are considered to be highly active cytokinins, has been extensively studied, there are others with less obvious functions, such as cis-zeatin, dihydrozeatin, and aromatic cytokinins, which have been comparatively neglected. To help explain this duality, we present a novel hypothesis metaphorically comparing various cytokinin forms, enzymes of CK metabolism, and their signalling and transporter functions to the comics superheroes Hulk and Deadpool. Hulk is a powerful but short-lived creation, whilst Deadpool presents a more subtle and enduring force. With this dual framework in mind, this review compares different cytokinin metabolites, and their biosynthesis, translocation, and sensing to illustrate the different mechanisms behind the two CK strategies. This is put together and applied to a plant developmental scale and, beyond plants, to interactions with organisms of other kingdoms, to highlight where future study can benefit the understanding of plant fitness and productivity.

The structure of the Moco carrier protein from Rippkaea orientalis

The molybdenum cofactor (Moco) is the prosthetic group of all molybdenum-dependent enzymes except for nitrogenase. The multistep biosynthesis pathway of Moco and its function in molybdenum-dependent enzymes are already well understood. The mechanisms of Moco transfer, storage and insertion, on the other hand, are not. In the cell, Moco is usually not found in its free form and remains bound to proteins because of its sensitivity to oxidation. The green alga Chlamydomonas reinhardtii harbors a Moco carrier protein (MCP) that binds and protects Moco but is devoid of enzymatic function. It has been speculated that this MCP acts as a means of Moco storage and transport. Here, the search for potential MCPs has been extended to the prokaryotes, and many MCPs were found in cyanobacteria. A putative MCP from Rippkaea orientalis (RoMCP) was selected for recombinant production, crystallization and structure determination. RoMCP has a Rossmann-fold topology that is characteristic of nucleotide-binding proteins and a homotetrameric quaternary structure similar to that of the MCP from C. reinhardtii. In each protomer, a positively charged crevice was identified that accommodates up to three chloride ions, hinting at a potential Moco-binding site. Computational docking experiments supported this notion and gave an impression of the RoMCP-Moco complex.

Cytokinins in Dictyostelia - A Unique Model for Studying the Functions of Signaling Agents From Species to Kingdoms

Cytokinins (CKs) are a diverse group of evolutionarily significant growth-regulating molecules. While the CK biosynthesis and signal transduction pathways are the most well-understood in plant systems, these molecules have been identified in all kingdoms of life. This review follows the recent discovery of an expanded CK profile in the social amoeba, Dictyostelium discoideum. A comprehensive review on the present knowledge of CK biosynthesis, signal transduction, and CK-small molecule interactions within members of Dictyostelia will be summarized. In doing so, the utility of social amoebae will be highlighted as a model system for studying the evolution of these hormone-like signaling agents, which will set the stage for future research in this area.

A cytokinin-activation enzyme-like gene improves grain yield under various field conditions in rice

CRISPR-edited variants at the 3'-end of OsLOGL5's coding sequence (CDS), significantly increased rice grain yield under well-watered, drought, normal nitrogen, and low nitrogen field conditions at multiple geographical locations. Cytokinins impact numerous aspects of plant growth and development. This study reports that constitutive ectopic overexpression of a rice cytokinin-activation enzyme-like gene, OsLOGL5, significantly reduced primary root growth, tiller number, and yield. Conversely, mutations at the 3'-end of OsLOGL5 CDS resulted in normal rice plant morphology but with increased grain yield under well-watered, drought, normal nitrogen, and low nitrogen field conditions at multiple geographical locations. Six gene edited variants (Edit A to F) were created and tested in the field. Edit-B and Edit-F plants increased, but Edit-D and Edit-E plants decreased, the panicle number per plant. All OsLOGL5-edited plants significantly increased seed setting rate, total grain numbers, full-filled grain numbers per panicle, and thousand seed weight under drought conditions, suggesting that OsLOGL5 is likely involved in the regulation of both seed development and grain filling processes. Our results indicate that the C-terminal end of OsLOGL5 protein plays an important role in regulating rice yield improvement under different abiotic stress conditions, and OsLOGL5 is important for rice yield enhancement and stability.

Phenotypic, Transcriptomic, and Metabolomic Signatures of Root-Specifically Overexpressed OsCKX2 in Rice

Cytokinins are crucial signaling molecules that regulate plant growth and development. OsCKX2 irreversibly degrades nucleobase cytokinins by encoding cytokinin oxidase/dehydrogenase to control grain production in rice. In this study, OsCKX2 was specifically overexpressed in roots using RCc3 promoter to investigate the effects of root-source cytokinins on the growth of rice. OsCKX2 overexpressed (OE) rice showed retarded growth with lower cytokinin levels and biomass production. Shoot-specific transcriptome analysis between OsCKX2 OE rice and wild type (WT) revealed differentially expressed genes (DEGs) associated with cell division, cell wall structure, phytohormone signaling, and assimilation and catabolism. Metabolome analysis indicated that a majority of differential primary metabolites, such as amino acids and organic acids, increased, while lipids decreased in OsCKX2 OE rice. Integration of transcriptomic and metabolomic data showed that several DEGs and differential metabolites were related to glycolysis and tricarboxylic acid cycle (TCA). To conclude, reduced cytokinin levels via root-specific overexpression of OsCKX2 resulted in developmental defects, which confirmed the importance of root-source cytokinins in plant growth and morphogenesis.

A LONELY GUY protein of Bordetella pertussis with unique features is related to oxidative stress

The Gram-negative bacterium B. pertussis is the causative agent of whooping cough. This infection is re-emerging and new features related to Bordetella pathogenesis and microbiology could be relevant to defeat it. Therefore, we focused our attention on BP1253, a predicted exported protein from B. pertussis erroneously classified as lysine decarboxylase. We showed that BP1253 shares the highly conserved motif PGGxGTxxE and the key catalytic amino-acid residues with newly structurally characterized "LONELY GUY" (LOG) proteins. Biochemical studies have confirmed that this protein functions as a cytokinin-activating enzyme since it cleaves the N-glycosidic linkage between the base and the ribose, leading to the formation of free bases, which are the active form of plant hormones called cytokinins. Remarkably, BP1253 selectively binds monophosphate nucleotides such as AMP, GMP and CMP, showing a wider variety in binding capacity compared to other LOGs. Cytokinin production studies performed with B. pertussis have revealed 6-O-methylguanine to be the physiological product of BP1253 in agreement with the higher activity of the enzyme towards GMP. 6-O-methylguanine is likely to be responsible for the increased sensitivity of B. pertussis to oxidative stress. Although BP1253 has a primary sequence resembling the hexameric type-II LOGs, the dimeric state and the presence of specific amino-acids suggests that BP1253 can be classified as a novel type-II LOG. The discovery of a LOG along with its product 6-O-methylguanine in the human pathogen B. pertussis may lead to the discovery of unexplored functions of LOGs, broadening their role beyond plants.

The Lonely Guy (LOG) Homologue SiRe_0427 from the Thermophilic Archaeon Sulfolobus islandicus REY15A Is a Phosphoribohydrolase Representing a Novel Group

Lonely Guy (LOG) proteins are important enzymes in cellular organisms, which catalyze the final step in the production of biologically active cytokinins via dephosphoribosylation. LOG proteins are vital enzymes in plants for the activation of cytokinin precursors, which is crucial for plant growth and development. In fungi and bacteria, LOGs are implicated in pathogenic or nonpathogenic interactions with their plant hosts. However, LOGs have also been identified in the human pathogen Mycobacterium tuberculosis, and the accumulation of cytokinin-degraded products, aldehydes, within bacterial cells is lethal to the bacterium in the presence of nitric oxide, suggesting diverse roles of LOGs in various species. In this study, we conducted biochemical and genetic analysis of a LOG homologue, SiRe_0427, from the hyperthermophilic archaeon Sulfolobus islandicus REY15A. The protein possessed the LOG motif GGGxGTxxE and exhibited phosphoribohydrolase activity on adenosine-5-monophosphate (AMP), similar to LOGs from eukaryotes and bacteria. Alanine mutants at either catalytic residues or substrate binding sites lost their activity, resembling other known LOGs. SiRe_0427 is probably a homotetramer, as revealed by size exclusion chromatography and chemical cross-linking. We found that the gene encoding SiRe_0427 could be knocked out; however, the Δsire_0427 strain exhibited no apparent difference in growth compared to the wild type, nor did it show any difference in sensitivity to UV irradiation under our laboratory growth conditions. Overall, these findings indicate that archaeal LOG homologue is active as a phosphoribohydrolase.IMPORTANCE Lonely Guy (LOG) is an essential enzyme for the final biosynthesis of cytokinins, which regulate almost every aspect of growth and development in plants. LOG protein was originally discovered 12 years ago in a strain of Oryza sativa with a distinct floral phenotype of a single stamen. Recently, the presence of LOG homologues has been reported in Mycobacterium tuberculosis, an obligate human pathogen. To date, active LOG proteins have been reported in plants, pathogenic and nonpathogenic fungi, and bacteria, but there have been no experimental reports of LOG protein from archaea. In the current work, we report the identification of a LOG homologue active on AMP from Sulfolobus islandicus REY15A, a thermophilic archaeon. The protein likely forms a tetramer in solution and represents a novel evolutionary lineage. The results presented here expand our knowledge regarding proteins with phosphoribohydrolase activities and open an avenue for studying signal transduction networks of archaea and potential applications of LOG enzymes in agriculture and industry.

A Novel Subfamily of Bacterial AAT-Fold Basic Amino Acid Decarboxylases and Functional Characterization of Its First Representative: Pseudomonas aeruginosa LdcA

Polyamines are small amino-acid derived polycations capable of binding negatively charged macromolecules. Bacterial polyamines are structurally and functionally diverse, and are mainly produced biosynthetically by pyridoxal-5-phosphate-dependent amino acid decarboxylases referred to as Lysine-Arginine-Ornithine decarboxylases (LAOdcs). In a phylogenetically limited group of bacteria, LAOdcs are also induced in response to acid stress. Here, we performed an exhaustive phylogenetic analysis of the AAT-fold LAOdcs which showcased the ancient nature of their short forms in Cyanobacteria and Firmicutes, and emergence of distinct subfamilies of long LAOdcs in Proteobacteria. We identified a novel subfamily of lysine decarboxylases, LdcA, ancestral in Betaproteobacteria and Pseudomonadaceae. We analyzed the expression of LdcA from Pseudomonas aeruginosa, and uncovered its role, intimately linked to cadaverine (Cad) production, in promoting growth and reducing persistence of this multidrug resistant human pathogen during carbenicillin treatment. Finally, we documented a certain redundancy in the function of the three main polyamines—Cad, putrescine (Put), and spermidine (Spd)—in P. aeruginosa by demonstrating the link between their intracellular level, as well as the capacity of Put and Spd to complement the growth phenotype of the ldcA mutant.

Structural insight into molecular mechanism of cytokinin activating protein from Pseudomonas aeruginosa PAO1

Cytokinin (CK)-activating enzyme, called LOG, is a phosphoribohydrolase that hydrolyzes nucleotides into nucleobases and phosphoriboses. This reaction is a fascinating target for regulation of cellular active CK. However, misannotation of LOG as a lysine decarboxylase and the lack of detailed catalytic and substrate-binding mechanisms have prevented studies of LOG at a protein-level. In this study, we determined the crystal structure of PA4923 from Pseudomonas aeruginosa PAO1. The overall structure of PA4923 resembles those of type-I LOGs, and it exhibited phosphoribohydrolase activity against AMP. These observations indicated that PA4923 functions as an LOG. We also determined the PaLOG structure in complex with AMP and elucidated the detailed binding mode of LOG against the AMP substrate. Interestingly, PaLOG undergoes an open/closed conformational change upon binding AMP, during which the Glu74 residue located on the β3-β4 connecting loop flips 180° and moves 13 Å towards the AMP molecule. Structural and amino acid sequence comparisons of LOGs suggest that this conformational change upon substrate binding might be a common phenomenon in LOGs. In addition, based on our structural studies and the reported catalytic mechanism of nucleoside hydrolases, we proposed a catalytic mechanism for LOG in which an oxocarbenium ion-like transition state is formed.

The Cytokinin-Activating LOG-Family Proteins Are Not Lysine Decarboxylases

A conserved PGGxGTxxE motif misleads the cytokinin (CK) converting LONELY GUY enzymes to be wrongly annotated as lysine decarboxylases (LDCs). However, so far PGGxGTxxE motif-containing LDCs do not show any LDC activity. Instead, they show phosphoribohydrolase activity by converting inactive CK nucleotides into active free-base forms to invoke CK responses.