Identification of mNeonGreen as a pH-Dependent, Turn-On Fluorescent Protein Sensor for Chloride.

Chloride-sensitive fluorescent proteins generated from laboratory evolution have a characteristic tyrosine residue that interacts with a chloride ion and π-stacks with the chromophore. However, the engineered yellow-green fluorescent protein mNeonGreen lacks this interaction but still binds chloride, as seen in a recently reported crystal structure. Based on its unique coordination sphere, we were curious if chloride could influence the optical properties of mNeonGreen. Here, we present the structure-guided identification and spectroscopic characterization of mNeonGreen as a turn-on fluorescent protein sensor for chloride. Our results show that chloride binding lowers the chromophore pKa and shifts the equilibrium away from the weakly fluorescent phenol form to the highly fluorescent phenolate form, resulting in a pH-dependent, turn-on fluorescence response. Moreover, through mutagenesis, we link this sensing mechanism to a non-coordinating residue in the chloride binding pocket. This discovery sets the stage to further engineer mNeonGreen as a new fluorescent protein-based tool for imaging cellular chloride.

Nature-inspired engineering of an F-type lectin for increased binding strength.

Individual lectin-carbohydrate interactions are usually of low affinity. However, high avidity is frequently attained by the multivalent presentation of glycans on biological surfaces coupled with the occurrence of high order lectin oligomers or tandem repeats of lectin domains in the polypeptide. F-type lectins are l-fucose binding lectins with a typical sequence motif, HX(26)RXDX(4)R/K, whose residues participate in l-fucose binding. We previously reported the presence of a few eukaryotic F-type lectin domains with partial sequence duplication that results in the presence of two l-fucose-binding sequence motifs. We hypothesized that such partial sequence duplication would result in greater avidity of lectin-ligand interactions. Inspired by this example from Nature, we attempted to engineer a bacterial F-type lectin domain from Streptosporangium roseum to attain avid binding by mimicking partial duplication. The engineered lectin demonstrated 12-fold greater binding strength than the wild-type lectin to multivalent fucosylated glycoconjugates. However, the affinity to the monosaccharide l-fucose in solution was similar and partial sequence duplication did not result in an additional functional l-fucose binding site. We also cloned, expressed and purified a Branchiostoma floridae F-type lectin domain with naturally occurring partial sequence duplication and confirmed that the duplicated region with the F-type lectin sequence motif did not participate in l-fucose binding. We found that the greater binding strength of the engineered lectin from S. roseum was instead due to increased oligomerization. We believe that this Nature-inspired strategy might be useful for engineering lectins to improve binding strength in various applications.

Antibacterial activity and mechanism of action of analogues derived from the antimicrobial peptide mBjAMP1 isolated from Branchiostoma japonicum.

Objectives: The worldwide increase in antibiotic-resistant bacteria is a growing threat to public health. Antimicrobial peptides (AMPs) are potentially effective alternatives to conventional antibiotics. We therefore tested analogues of the AMP mBjAMP1 from Branchiostoma japonicum, which we produced by adding and/or replacing amino acids to increase antimicrobial activity against Gram-negative bacteria. Methods: We compared the antimicrobial activities of mBjAMP1 analogues against Gram-negative bacteria reference strains and 52 strains of Klebsiella pneumoniae isolated from patients. Antibiofilm activity and cytotoxicity were evaluated, and the mechanisms of action were then studied. Results: Analogue peptides exhibited greater antimicrobial and antibiofilm activities than mBjAMP1. In particular, the analogue IARR-Anal10 displayed not only the greatest antimicrobial and antibiofilm activities, but also no toxicity against human red blood cells or other mammalian cells. IARR-Anal10 had little or no effect on bacterial outer membrane permeability, membrane polarization or membrane integrity. Instead, it appears IARR-Anal10 binds bacterial DNA, as evidenced in DNA gel retardation assays. Thus, IARR-Anal10 likely kills bacteria through an intracellular mechanism. We also confirmed that IARR-Anal10 suppresses the virulence of K. pneumoniae to a degree similar to tigecycline, used to treat carbapenem-resistant Enterobacteriaceae infections. Notably, IARR-Anal10 did not induce development of resistance by K. pneumoniae, though both meropenem and tigecycline did so within a short time. Conclusions: These results suggest that IARR-Anal10 is a promising agent for treating infections caused by bacteria resistant to tigecycline and meropenem.

Evolutionary conservation of molecular structure and antiviral function of a viral receptor, LGP2, in amphioxus Branchiostoma japonicum.

RIG-I-like (where RIG-I is retinoic acid inducible gene I) receptor LGP2 (where LGP2 is laboratory of genetics and physiology) is an important intracellular receptor that recognizes viral RNAs in innate immunity, but its origin and evolution remains unknown. Here we clearly demonstrate the presence of a RIG-I-like receptor, BjLGP2, in the basal chordate amphioxus. It is predominantly expressed in the hepatic caecum and hindgut, and is upregulated following challenge with poly(I:C). BjLGP2 is distributed in the cytoplasm of both grouper spleen and flounder gill (FG) cells, and the recombinant BjLGP2 interacts with poly(I:C). BjLGP2 can enhance the expression of IFN and IFN-inducible genes in FG cells upon poly(I:C) challenge. It also significantly induces the expression of the antiviral genes ifn-i and Mx as well as the signal transduction relevant genes MAVS, NF-κB, and IRF-3 in FG cells upon lymphocystis disease virus challenge. Moreover, BjLGP2 inhibits the replication of lymphocystis disease virus in FG cells and the gene transcription of Singapore grouper iridovirus in grouper spleen cells. This is the first report showing that a LGP2 protein in invertebrate species (amphioxus) is structurally conserved and plays an antiviral role similar to that of vertebrate LGP2 proteins.

Prevalence of the F-type lectin domain.

F-type lectins are fucolectins with characteristic fucose and calcium-binding sequence motifs and a unique lectin fold (the "F-type" fold). F-type lectins are phylogenetically widespread with selective distribution. Several eukaryotic F-type lectins have been biochemically and structurally characterized, and the F-type lectin domain (FLD) has also been studied in the bacterial proteins, Streptococcus mitis lectinolysin and Streptococcus pneumoniae SP2159. However, there is little knowledge about the extent of occurrence of FLDs and their domain organization, especially, in bacteria. We have now mined the extensive genomic sequence information available in the public databases with sensitive sequence search techniques in order to exhaustively survey prokaryotic and eukaryotic FLDs. We report 437 FLD sequence clusters (clustered at 80% sequence identity) from eukaryotic, eubacterial and viral proteins. Domain architectures are diverse but mostly conserved in closely related organisms, and domain organizations of bacterial FLD-containing proteins are very different from their eukaryotic counterparts, suggesting unique specialization of FLDs to suit different requirements. Several atypical phylogenetic associations hint at lateral transfer. Among eukaryotes, we observe an expansion of FLDs in terms of occurrence and domain organization diversity in the taxa Mollusca, Hemichordata and Branchiostomi, perhaps coinciding with greater emphasis on innate immune strategies in these organisms. The naturally occurring FLDs with diverse domain organizations that we have identified here will be useful for future studies aimed at creating designer molecular platforms for directing desired biological activities to fucosylated glycoconjugates in target niches.

An amphioxus gC1q protein binds human IgG and initiates the classical pathway: Implications for a C1q-mediated complement system in the basal chordate.

The origin of the classical complement pathway remains open during chordate evolution. A C1q-like member, BjC1q, was identified in the basal chordate amphioxus. It is predominantly expressed in the hepatic caecum, hindgut, and notochord, and is significantly upregulated following challenge with bacteria or lipoteichoic acid and LPS. Recombinant BjC1q and its globular head domain specifically interact with lipoteichoic acid and LPS, but BjC1q displays little lectin activity. Moreover, rBjC1q can assemble to form the high molecular weight oligomers necessary for binding to proteases C1r/C1s and for complement activation, and binds human C1r/C1s/mannan-binding lectin-associated serine protease-2 as well as amphioxus serine proteases involved in the cleavage of C4/C2, and C3 activation. Importantly, rBjC1q binds with human IgG as well as an amphioxus Ig domain containing protein, resulting in the activation of the classical complement pathway. This is the first report showing that a C1q-like protein in invertebrates is able to initiate classical pathway, raising the possibility that amphioxus possesses a C1q-mediated complement system. It also suggests a new scenario for the emergence of the classical complement pathway, in contrast to the proposal that the lectin pathway evolved into the classical pathway.

Characterization of GRP as a functional neuropeptide in basal chordate amphioxus.

Amphioxus belongs to the subphylum cephalochordata, an extant representative of the most basal chordates, whose regulation of endocrine system remains ambiguous. Here we clearly demonstrated the existence of a functional GRP neuropeptide in amphioxus, which was able to interact with GRP receptor, activate both PKC and PKA pathways, increase gh, igf, and vegf expression. We also showed that the transcription level of amphioxus grp was affected by temperature and light, indicating the role of this gene in the regulation of energy balance and circadian rhythms. In addition, the expression of the amphioxus grp was detected in cerebral vesicle that has been proposed to be the homologous organ of vertebrate brain. These data collectively suggested that a functional GRP neuropeptide had already emerged in amphioxus, which provided insights into the evolutionary origin of GRP in chordate and the functional homology between the cerebral vesicle and vertebrate brain.

Structural Factors Enabling Successful GFP-Like Proteins with Alanine as the Third Chromophore-Forming Residue.

GFP-like proteins from lancelets (lanFPs) is a new and least studied group that already generated several outstanding biomarkers (mNeonGreen is the brightest FP to date) and has some unique features. Here, we report the study of four homologous lanFPs with GYG and GYA chromophores. Until recently, it was accepted that the third chromophore-forming residue in GFP-like proteins should be glycine, and efforts to replace it were in vain. Now, we have the first structure of a fluorescent protein with a successfully matured chromophore that has alanine as the third chromophore-forming residue. Consideration of the protein structures revealed two alternative routes of posttranslational transformation, resulting in either chromophore maturation or hydrolysis of GYG/GYA tripeptide. Both transformations are catalyzed by the same set of catalytic residues, Arg88 and Glu35-Wat-Glu211 cluster, whereas the residues in positions 62 and 102 shift the equilibrium between chromophore maturation and hydrolysis.

Immunohistochemical analysis of the distribution of molecules involved in ionic and pH regulation in the lancelet Branchiostoma floridae (Hubbs, 1922).

The aim of present work is to analyse the distribution of carbonic anhydrase II (CAII), cystic fibrosis transmembrane regulator (CFTR), vacuolar-type H+-ATPase (V-H+-ATPase), Na+/K+ ATPase, Na+/H+ exchanger (NHE) and SLC26A6 (solute carrier family 26, member 6), also known as pendrin protein, in the lancelet Branchiostoma floridae in order to go in depth in the evolution of osmoregulation and pH regulation in Chordates. In view of their phylogenetic position, lancelets may indeed provide a critical point of reference for studies on osmoregulation evolution in Chordates. The results of present work demonstrated that, except to Na+/K+ ATPase that is strongly expressed in nephridia only, all the other studied molecules are abundantly present in skin, coelomic epithelium, renal papillae and nephridia and hepatic coecum. Thus, it is possible to hypothesize that also in lancelet, as in fish, these organs are involved in pH control and ionic regulation. In the digestive tract of B. floridae, the intestine epithelium was weakly immune-reactive to all tested antibodies, while the hepatic coecum showed an intense immunoreactivity to all molecules. Since in amphioxus the hepatic coecum functions simultaneously as stomach, liver and pancreas, these immunohistochemical results proved the secretion of H+ and HCO3- ions, typical of digestive process. Colocalization studies indicated a co-expression of the studied proteins in all considered organs, excluding NHE and pendrin for renal papillae, since some renal papillae are NHE immunopositive only.

Structural and Functional Assessment of mBjAMP1, an Antimicrobial Peptide from Branchiostoma japonicum, Revealed a Novel α-Hairpinin-like Scaffold with Membrane Permeable and DNA Binding Activity.

Here we describe the three-dimensional structure and antimicrobial mechanism of mBjAMP1, an antimicrobial peptide (AMP) isolated from Branchiostoma japonicum. The structure of mBjAMP1 was determined by 2D solution NMR spectroscopy and revealed a novel α-hairpinin-like scaffold stabilized by an intramolecular disulfide bond. mBjAMP1 showed effective growth inhibition and bactericidal activities against pathogenic bacteria but was not cytotoxic to mammalian cells. Antimicrobial mechanism studies using fluorescence-based experiments demonstrated that mBjAMP1 did not disrupt membrane integrity. Laser-scanning confocal microscopy indicated that mBjAMP1 is able to penetrate the bacterial cell membrane without causing membrane disruption. Moreover, gel retardation assay suggested that mBjAMP1 directly binds to bacterial DNA as an intracellular target. Collectively, mBjAMP1 may inhibit biological functions by binding to DNA or RNA after penetrating the bacterial cell membrane, thereby causing cell death. These results suggest that mBjAMP1 may present a promising template for the development of peptide-based antibiotics.

Structural analysis of the bright monomeric yellow-green fluorescent protein mNeonGreen obtained by directed evolution.

Until recently, genes coding for homologues of the autofluorescent protein GFP had only been identified in marine organisms from the phyla Cnidaria and Arthropoda. New fluorescent-protein genes have now been found in the phylum Chordata, coding for particularly bright oligomeric fluorescent proteins such as the tetrameric yellow fluorescent protein lanYFP from Branchiostoma lanceolatum. A successful monomerization attempt led to the development of the bright yellow-green fluorescent protein mNeonGreen. The structures of lanYFP and mNeonGreen have been determined and compared in order to rationalize the directed evolution process leading from a bright, tetrameric to a still bright, monomeric fluorescent protein. An unusual discolouration of crystals of mNeonGreen was observed after X-ray data collection, which was investigated using a combination of X-ray crystallography and UV-visible absorption and Raman spectroscopies, revealing the effects of specific radiation damage in the chromophore cavity. It is shown that X-rays rapidly lead to the protonation of the phenolate O atom of the chromophore and to the loss of its planarity at the methylene bridge.

A new LDLa domain-containing C-type lectin with bacterial agglutinating and binding activity in amphioxus.

Over 1200 C-type lectin gene models have been identified in amphioxus, but only a few of them have been functionally characterized. In this study, we identified a C-type lectin, BjCTL, with domain structure of LDLa-CTLD-EGF_Lam, the first such data in chordates. It was expressed mainly in the notochord and ovary in a tissue-dependent fashion. Recombinant BjCTL was characterized as a typical Ca2+-dependent carbohydrate-binding protein capable of agglutinating and binding to both Gram-negative and positive bacteria we tested. In addition, it specifically bound to insoluble lipopolysaccharide, lipoteichoic acid and peptidoglycan, which can be inhibited by galactose. We also showed that the interaction of BjCTL with the bacteria is primarily attributable to CTLD domain. Thus, BjCTL is a novel pattern recognition protein involved in lectin-mediated innate immunity.

Identification and characterization of complement factor H in Branchiostoma belcheri.

Complement factor H (CFH) is an essential regulator of the complement system and plays very important roles in animal innate immunity. Although the complement system of amphioxus has been extensively studied, the expression in amphioxus and evolution of CFH gene remain unknown. In this study, we identified and characterized an amphioxus (Branchiostoma belcheri) CFH gene (designated as AmphiCFH). Our results showed that the full-length cDNA of AmphiCFH gene consists of 1295 bp nucleotides containing an 855 bp open reading frame (ORF) that was predicted to encode a 284 amino acid protein. The putative AmphiCFH protein possessed the characteristic of the CFH protein family, including typical CCP (complement control protein) domain. Real-time PCR analysis showed that the AmphiCFH was ubiquitously and differentially expressed in five investigated tissues (intestine, gills, notochord, muscles, and hepatic cecum). The expression level of the AmphiCFH gene was induced upon lipopolysaccharide stimulation, indicating that the AmphiCFH gene might be involved in innate immunity. In addition, phylogenetic analysis showed that the AmphiCFH gene was located between that of invertebrates and vertebrates, suggesting that the AmphiCFH gene is a member of the CFH gene family. In conclusion, our findings provided an insight into animal innate immunity and evolution of the CFH gene family.