Crystallographic Insights into the Pore Structures and Mechanisms of the EutL and EutM Shell Proteins of the Ethanolamine-Utilizing Microcompartment of Escherichia coli

The ethanolamine-utilizing bacterial microcompartment (Eut-BMC) of Escherichia coli is a polyhedral organelle that harbors specific enzymes for the catabolic degradation of ethanolamine. The compartment is composed of a proteinaceous shell structure that maintains a highly specialized environment for the biochemical reactions inside. Recent structural investigations have revealed hexagonal assemblies of shell proteins that form a tightly packed two-dimensional lattice that is likely to function as a selectively permeable protein membrane, wherein small channels are thought to permit controlled exchange of specific solutes. Here, we show with two nonisomorphous crystal structures that EutM also forms a two-dimensional protein membrane. As its architecture is highly similar to the membrane structure of EutL, it is likely that the structure represents a physiologically relevant form. Thus far, of all Eut proteins, only EutM and EutL have been shown to form such proteinaceous membranes. Despite their similar architectures, however, both proteins exhibit dramatically different pore structures. In contrast to EutL, the pore of EutM appears to be positively charged, indicating specificity for different solutes. Furthermore, we also show that the central pore structure of the EutL shell protein can be triggered to open specifically upon exposure to zinc ions, suggesting a specific gating mechanism.Bacterial microcompartments are subcellular organelles that are found in many prokaryotic organisms (10, 32). In contrast to the lipidic vesicles of many eukaryotic cells, these enclosures are entirely composed of proteins. Recent imaging by electron microscopy revealed capsid-like particles obeying 2-, 3- and 5-fold symmetries that suggest icosahedral symmetry (4, 13, 27). Shell proteins are thought to form a tightly sealed membrane structure that separates the lumen from the cytosol. Similar to the lipidic membranes of vesicles, these proteinaceous membranes have been suggested to provide a selectively permeable solute barrier, wherein specific pores maintain an optimal biochemical environment for the catabolic reactions inside (25).The ethanolamine-utilizing bacterial microcompartment (Eut-BMC) enables some bacteria to survive on ethanolamine as the sole source for carbon, nitrogen, and energy (25). It is encoded by a 17-gene-containing operon, and homologues of its genes have been identified in Escherichia coli, Salmonella enterica serovar Typhimurium, Mycobacterium tuberculosis, and Clostridium kluyveri among other prokaryotic pathogens (22). Largely based on sequence comparisons, the compartment''s outer shell was proposed to be composed of five different shell proteins: Eut-K, -L, -M, -N, and -S, all of which are fairly small proteins that typically consist of about 100 amino acids. Only EutL is about twice the size, with 216 amino acids as a result of two tandemly duplicated shell protein domains (26).To date, little is known about the composition, architecture, and function of bacterial microcompartments. Recent structural investigations of BMC particles and individual shell proteins, however, have contributed greatly to a basic understanding of BMC architecture. Electron microscopy, for example, has revealed polyhedral shell structures that are composed of a thin layer of proteins. Intriguingly, crystallizations revealed that some shell proteins also assemble into tightly packed two-dimensional arrays that may resemble the facets of the compartments (28). Within an array, these proteins typically assembled into hexamers or trimers (in the case of tandem domain proteins) that exhibited a distinct hexagonal shape. As this geometry was suggested to be of fundamental importance to the microcompartment architecture, we will here refer to it as a “tile” or “tile structure.” While it has not yet been proven directly that the assembly of proteins in the crystals is identical to that of the BMC, their almost seamless two-dimensional packing has been suggested to be of physiological relevance as it could provide an efficient barrier to prevent leakage of toxic by-products into the cytoplasm (4, 25). Overall, however, it is not understood how the various shell proteins assemble to form the polyhedral structure while maintaining an efficiently tight seal. In particular, the interactions among the shell proteins and their arrangements within facets, edges, and vertices have remained elusive.In the study presented here, we demonstrate for the first time that the shell protein EutM is also able to form tightly packed two-dimensional arrays. With two independently determined crystal structures, we show that its protein array closely resembled that of EutL and other carboxysomal proteins. As a result, we hypothesize that this assembly represents a physiologically relevant form. Both crystal forms also revealed the C-terminal tail of the protein, which is proposed to serve as a potential interaction site with other factors.Furthermore, we show that the pore structure of EutL can be triggered to open upon exposure to specific solutes. A first structure of EutL was previously determined in our laboratory, and it revealed three water-filled pores per tile (26). Interestingly, its structure consisted of two tandemly repeated shell protein domains, which assembled into an almost perfectly shaped hexagonal structure. This architectural feature was recently also found in shell proteins of other microcompartments (11, 20). Each of the pores of an EutL tile was coated with acidic residues, which indicated a possible pathway for positively charged molecules such as ethanolamine. Inspection of the structure also suggested specific metal binding sites on its surface. In order to verify this idea, we performed systematic soaking studies of the crystals with selected divalent metals. Surprisingly, we found that zinc ions bound to the protein specifically not at the suspected sites but at different sites that caused a dramatic opening of a central pore. This unprecedented observation of a specifically triggered pore opening is consistent with another previous observation (30) and may point to a mechanism for regulation of permeability.     

Phosphorylation of mCRY2 at Ser557 in the Hypothalamic Suprachiasmatic Nucleus of the Mouse

Cryptochrome1 and 2 play a critical role in the molecular oscillations of the circadian clocks of central and peripheral tissues in mammals. Mouse Cryptochrome2 (mCRY2) is phosphorylated at Ser557 in the liver, in which the Ser557-phosphorylated form accumulates during the night in parallel with mCRY2 protein. Phosphorylation of mCRY2 at Ser557 allows subsequent phosphorylation at Ser553 by glycogen synthase kinase-3β (GSK-3β), resulting in efficient degradation of mCRY2 by a proteasome pathway. In the present study, we found that mCRY2 is phosphorylated at Ser557 also in the region of the mouse brain containing the suprachiasmatic nucleus (SCN), the central circadian clock tissue. Daily fluctuation of the Ser557-phosphorylation level in the SCN region suggests an important role of sequential phosphorylation of Ser557 and Ser553 in the rhythmic degradation of mCRY2 in both central and peripheral clocks of mice.     

Molecular cloning and characterization of novel splicing variants of human decay-accelerating factor

Decay-accelerating factor (DAF) is one of the complement regulatory proteins. Two isoforms of DAF have been identified in humans. In this study, we isolated novel cDNAs encoding five isoforms of DAF from the human lung, which were generated by insertion of new exonic sequences. RT-PCR revealed that all isoforms were expressed in almost all tissues tested, although the expression patterns and levels differed among the tissues. Transfection of isoform vDAF1, 2, and 3 cDNAs into CHO cells showed that these molecules are soluble forms secreted after glycosylation. Isoform vDAF4 and vDAF5 cDNAs included a part of and the entire intron 7 sequence, respectively, and the transfection of vDAF4 cDNA produced a large, glycosylated, membrane-bound form. These results suggest that more than seven isoforms of human DAF are involved in the regulation of complement activation under physiological conditions through their specific structures and localization.     

Activation of Notch1 signaling in cardiogenic mesoderm induces abnormal heart morphogenesis in mouse

Notch signaling is implicated in many developmental processes. In our current study, we have employed a transgenic strategy to investigate the role of Notch signaling during cardiac development in the mouse. Cre recombinase-mediated Notch1 (NICD1) activation in the mesodermal cell lineage leads to abnormal heart morphogenesis, which is characterized by deformities of the ventricles and atrioventricular (AV) canal. The major defects observed include impaired ventricular myocardial differentiation, the ectopic appearance of cell masses in the AV cushion, the right-shifted interventricular septum (IVS) and impaired myocardium of the AV canal. However, the fates of the endocardium and myocardium were not disrupted in NICD1-activated hearts. One of the Notch target genes, Hesr1, was found to be strongly induced in both the ventricle and the AV canal of NICD1-activated hearts. However, a knockout of the Hesr1 gene from NICD-activated hearts rescues only the abnormality of the AV myocardium. We searched for additional possible targets of NICD1 activation by GeneChip analysis and found that Wnt2, Bmp6, jagged 1 and Tnni2 are strongly upregulated in NICD1-activated hearts, and that the activation of these genes was also observed in the absence of Hesr1. Our present study thus indicates that the Notch1 signaling pathway plays a suppressive role both in AV myocardial differentiation and the maturation of the ventricular myocardium.     

Structure of anthocyanin from the blue petals of Phacelia campanularia and its blue flower color development

The dicaffeoyl anthocyanin, phacelianin, was isolated from blue petals of Phacelia campanularia. Its structure was determined to be 3-O-(6-O-(4'-O-(6-O-(4'-O-beta-d-glucopyranosyl-(E)-caffeoyl)-beta-d-glucopyranosyl)-(E)-caffeoyl)-beta-d-glucopyranosyl)-5-O-(6-O-malonyl-beta-d-glucopyranosyl)delphinidin. The CD of the blue petals of the phacelia showed a strong negative Cotton effect and that of the suspension of the colored protoplasts was the same, indicating that the chromophores of phacelianin may stack intermolecularly in an anti-clockwise stacking manner in the blue-colored vacuoles. In a weakly acidic aqueous solution, phacelianin displayed the same blue color and negative Cotton effect in CD as those of the petals. However, blue-black colored precipitates gradually formed without metal ions. A very small amount of Al(3+) or Fe(3+) may be required to stabilize the blue solution. Phacelianin may take both an inter- and intramolecular stacking form and shows the blue petal color by molecular association and the co-existence of a small amount of metal ions. We also isolated a major anthocyanin from the blue petals of Evolvulus pilosus and revised the structure identical to phacelianin.     

WRNIP1 accumulates at laser light irradiated sites rapidly via its ubiquitin-binding zinc finger domain and independently from its ATPase domain

WRNIP1 (Werner helicase-interacting protein 1) was originally identified as a protein that interacts with the Werner syndrome responsible gene product. WRNIP1 contains a ubiquitin-binding zinc-finger (UBZ) domain in the N-terminal region and two leucine zipper motifs in the C-terminal region. In addition, it possesses an ATPase domain in the middle of the molecule and the lysine residues serving as ubiquitin acceptors in the entire of the molecule. Here, we report that WRNIP1 accumulates in laser light irradiated sites very rapidly via its ubiquitin-binding zinc finger domain, which is known to bind polyubiquitin and to be involved in ubiquitination of WRNIP1 itself. The accumulation of WRNIP1 in laser light irradiated sites also required the C-terminal region containing two leucine zippers, which is reportedly involved in the oligomerization of WRNIP1. Mutated WRNIP1 with a deleted ATPase domain or with mutations in lysine residues, which serve as ubiquitin acceptors, accumulated in laser light irradiated sites, suggesting that the ATPase domain of WRNIP1 and ubiquitination of WRNIP1 are dispensable for the accumulation.     

Metabolome analysis of photosynthesis and the related primary metabolites in the leaves of transgenic rice plants with increased or decreased Rubisco content

Because the comprehensive effects on metabolism by genetic manipulation of leaf Rubisco content are unknown, metabolome analysis was carried out on transgenic rice plants with increased or decreased Rubisco content using the capillary electrophoresis-time-of-flight mass spectrometry (CE-TOFMS) technique. In RBCS-sense plants, an increase in Rubisco content did not improve light-saturated photosynthesis. Glyceraldehyde 3-phosphate and sedoheputulose 7-phosphate levels increased, but ribulose bisphosphate (RuBP), ATP and ADP levels were not affected. It is considered from these results that RuBP regeneration independent of ATP supply became a bottleneck for photosynthesis. In RBCS-antisense plants, a decline in Rubisco content decreased photosynthesis with a substantial accumulation of RuBP. ATP and ADP levels also increased and were associated with increases in the diphosphate and triphosphate compounds of other nucleosides. These results imply that a decline in Rubisco content slowed down the Calvin cycle and that the resultant excess energy of ATP was transferred to other nucleoside diphosphates and triphosphates. The levels of amino acids tended to decline in RBCS-sense plants and increase in RBCS-antisense plants, probably reflecting the demand for Rubisco synthesis. Starch and carbohydrate levels decreased only in RBCS-antisense plants. Thus, genetic manipulation of Rubisco contents widely affected C and N metabolism in rice.