Assessment of Frizzled 6 membrane mobility by FRAP supports G protein coupling and reveals WNT-Frizzled selectivity

The WNT receptors of the Frizzled family comprise ten mammalian isoforms, bind WNT proteins and mediate downstream signaling to regulate stem cell fate, neuronal differentiation, cell survival and more. WNT-induced signaling pathways are either β-catenin-dependent or -independent, thereby dividing the 19 mammalian WNT proteins into two groups. So far hardly any quantitative, pharmacological information is available about WNT–FZD interaction profiles, affinities or mechanisms of signaling specification through distinct WNT/FZD pairings. This lack of knowledge originates from difficulties with WNT purification and a lack of suitable assays, such as ligand binding assays and FZD activity readouts. In order to minimize this gap, we employ fluorescence recovery after photobleaching (FRAP) to investigate WNT effects on the lateral mobility of FZD₆-GFP in living cells. Pharmacological uncoupling of heterotrimeric G proteins by pertussis toxin and N-ethylmaleimide argues that changes in FZD₆ mobility are related to putative precoupling of heterotrimeric G_i/o proteins to FZD₆. We show that recombinant WNT-1, -2, 3A, -4, -5A, -7A, -9B and -10B affect FZD₆ surface mobility and thus act on this receptor. WNT-5B and WNT-11, on the other hand, have no effect on FZD₆ mobility and we conclude that they do not act through FZD₆. We introduce here a novel way to assess WNT–FZD interaction by live cell imaging allowing further mapping of WNT–FZD interactions and challenging previous experimental limitations. Increased understanding of WNT–FZD selectivity provides important insight into the biological function of this crucial signaling system with importance in developmental biology, stem cell regulation oncogenesis, and human disease.     

Molecular insights into NF2/Merlin tumor suppressor function

The FERM domain protein Merlin, encoded by the NF2 tumor suppressor gene, regulates cell proliferation in response to adhesive signaling. The growth inhibitory function of Merlin is induced by intercellular adhesion and inactivated by joint integrin/receptor tyrosine kinase signaling. Merlin contributes to the formation of cell junctions in polarized tissues, activates anti-mitogenic signaling at tight-junctions, and inhibits oncogenic gene expression. Thus, inactivation of Merlin causes uncontrolled mitogenic signaling and tumorigenesis. Merlin’s predominant tumor suppressive functions are attributable to its control of oncogenic gene expression through regulation of Hippo signaling. Notably, Merlin translocates to the nucleus where it directly inhibits the CRL4^DCAF1 E3 ubiquitin ligase, thereby suppressing inhibition of the Lats kinases. A dichotomy in NF2 function has emerged whereby Merlin acts at the cell cortex to organize cell junctions and propagate anti-mitogenic signaling, whereas it inhibits oncogenic gene expression through the inhibition of CRL4^DCAF1 and activation of Hippo signaling. The biochemical events underlying Merlin’s normal function and tumor suppressive activity will be discussed in this Review, with emphasis on recent discoveries that have greatly influenced our understanding of Merlin biology.     

G Proteins in Reverse Mode: RECEPTOR-MEDIATED GTP RELEASE INHIBITS G PROTEIN AND EFFECTOR FUNCTION*

Active G protein-coupled receptors activate heterotrimeric Gαβγ proteins by catalyzing the exchange of GDP by GTP at the Gα subunit. A paradoxical attenuation of G protein-activated inwardly rectifying potassium channels (GIRK) upon stimulation of native cells with high concentrations of agonist is known. However, a deactivation of activated G proteins by active receptors has not been experimentally studied in intact cells. We monitored GIRK currents and G_o protein activation by means of fluorescence resonance energy transfer (FRET) in parallel. The results suggested that GIRK currents were paradoxically attenuated due to an inactivation of G_o proteins by active α_2A-adrenergic receptors. To study the mechanisms, G protein activation and receptor-G protein interactions were analyzed as a function of nucleotide type and nucleotide concentrations by means of FRET, while controlling intracellular nucleotides upon permeabilization of the cell membrane. Results suggested a receptor-catalyzed dissociation of GTP from activated heterotrimeric Gαβγ. Consequently, nucleotide-free G proteins were sequestrated in heterotrimeric conformation at the active receptor, thus attenuating downstream signaling in an agonist-dependent manner.     

Europium-labeled GTP as a general nonradioactive substitute for [S]GTPγS in high-throughput G protein studies

[³⁵S]GTPγS, the nonhydrolyzable radioactive GTP analog, has been a powerful tool in G protein studies and has set the standards in this field of research. However, its radioactive nature imposes clear limitations to its use in regular laboratory practice and in high-throughput experimentation. The europium-labeled GTP analog (Eu-GTP) has been used as an alternative in the analysis of G protein activation by G protein-coupled receptors in cellular membrane preparations. Here we expand the usage of Eu-GTP and show that it can be applied in other types of assays where [³⁵S]GTPγS has been previously utilized. We demonstrate the applicability of the modified Eu-GTP binding technology to analysis of heterotrimeric and monomeric G proteins of natural and recombinant sources, from different organisms, in assays with soluble proteins and membrane-containing assays of a high-throughput format. The deci-nanomolar K_D of Eu-GTP for the tested G proteins is similar to that of other fluorescent-modified GTP analogs, while the sensitivity achieved in time-resolved fluorescence analysis of Eu-GTP exceeds that of the radioactive measurements. Overall, the results of our modified Eu-GTP binding assay present Eu-GTP as a general nonradioactive alternative for G protein studies, especially attractive in high-throughput experiments.     

Two new 3D (3,8)-connected metal-organic frameworks based on zinc-triazole secondary building units and benzenetricarboxylate linkers

Two new zinc-triazole-carboxylate frameworks constructed from secondary building units (SBUs), [Zn₅(trz)₄(btc)₂(DMF)₂(H₂O)₂]·2H₂O·DMF (1) and [Zn₄(trz)₃(btc)₂(CH₃CN)(H₂O)]·5H₂O·(Bu₄N) (2), [Htrz = 1,2,4-triazole, H₃btc = 1,2,4-benzenetricarboxylate, Bu₄N = tetrabutylammonium], have been synthesized by solvothermal reactions and characterized by single-crystal X-ray diffraction analyses, X-ray power diffraction, elemental analyses, infrared spectra and thermogravimetric analyses. Both compounds 1 and 2 exhibit 3D (3,8)-connected tfz-d nets with {4³}₂{4⁶.6¹⁸.8⁴} topology symbol built from rod-shaped {[Zn₅(trz)₄]⁶⁺}_n SBUs (1) and {[Zn₄(trz)₃]⁵⁺}_n SBUs (2). In two compounds, rodlike units are connected by btc ligands via different modes. Additionally, solid state fluorescent emission spectra of two compounds show fluorescent properties at room temperature.     

ProtIdent: a web server for identifying proteases and their types by fusing functional domain and sequential evolution information

Proteases are vitally important to life cycles and have become a main target in drug development. According to their action mechanisms, proteases are classified into six types: (1) aspartic, (2) cysteine, (3) glutamic, (4) metallo, (5) serine, and (6) threonine. Given the sequence of an uncharacterized protein, can we identify whether it is a protease or non-protease? If it is, what type does it belong to? To address these problems, a 2-layer predictor, called "ProtIdent", is developed by fusing the functional domain and sequential evolution information: the first layer is for identifying the query protein as protease or non-protease; if it is a protease, the process will automatically go to the second layer to further identify it among the six types. The overall success rates in both cases by rigorous cross-validation tests were higher than 92%. ProtIdent is freely accessible to the public as a web server at http://www.csbio.sjtu.edu.cn/bioinf/Protease.     

HLA class II allele frequencies in the Lebanese population

Aims

Being one of the most polymorphic genetic systems , the Human Leukocyte Antigen system is divided into class I (HLA-A, HLA-B and HLA-C) and class II (HLA-DP, -DQ and -DR). This study is the first and largest of its kind to describe the distribution of HLA-DQB1 and HLA-DRB1 alleles in Lebanon and the region.

Methods

Respectively, 560 and 563 Lebanese individuals referred for HLA typing and possible bone marrow/kidney donation were tested for HLA-DQB1 and HLA-DRB1 alleles using the polymerase chain reaction/sequence specific priming (PCR-SSP) method.

Results

Our data were compared to that of several populations with interesting common findings between the Lebanese, Jordanian, Bahraini, Saudi, Kuwaiti, Tunisian, Korean, Japanese, Thai, Irish, Bulgarian and Polish populations.

Conclusion

These data about the Lebanese population are going to aid future researchers to study the relation of HLA-DQB1 and HLA-DRB1 alleles with major and common diseases in the Lebanese population and will add to the available international literature associated with these loci. In addition it will serve as a reference for the future national bone marrow registry program in our country. We also reviewed the literature for the described association between HLA-DRB1 and -DQB1 loci and different disease entities.     

Rho plays an important role in angiotensin II-induced hypertrophic responses in cardiac myocytes

Angiotensin II (Ang II) evokes a variety of hypertrophic responses such as activation of protein kinases, reprogramming of gene expressions and an increase in protein synthesis in cardiac myocytes. In this study, we examined the role of Rho family small GTP binding proteins (G proteins) in Ang II-induced cardiac hypertrophy. Ang II strongly activated extracellular signal-regulated protein kinases (ERKs) in cardiac myocytes of neonatal rats. Although Ang II-induced activation of ERKs was completely suppressed by an Ang II type 1 receptor antagonist, CV-11974, this activation was not inhibited by the pretreatment with C3 exoenzyme, which abrogates Rho functions. Overexpression of Rho GDP dissociation inhibitor (Rho-GDI), dominant negative mutants of Rac1 (D.N.Rac1), or D.N.Cdc42 had no effects on Ang II-induced activation of transfected ERK2. The promoter activity of skeletal a-actin and c-fos genes was increased by Ang II, and the increase was partly inhibited by overexpression of Rho-GDI and the pretreatment with C3 exoenzyme. Ang II increased phenylalanine incorporation into cardiac myocytes by approximately 1.4 fold as compared with control, and this increase was also significantly suppressed by the pretreatment with C3 exoenzyme. These results suggest that the Rho family small G proteins play important roles in Ang II-induced hypertrophic responses in cardiac myocytes.     

Structural Evidence for a Sequential Release Mechanism for Activation of Heterotrimeric G Proteins

Heptahelical G-protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptors couple to heterotrimeric G proteins to relay extracellular signals to intracellular signaling networks, but the molecular mechanism underlying guanosine 5′-diphosphate (GDP) release by the G protein α-subunit is not well understood. Amino acid substitutions in the conserved α5 helix of G_i, which extends from the C-terminal region to the nucleotide-binding pocket, cause dramatic increases in basal (receptor-independent) GDP release rates. For example, mutant Gα_i1-T329A shows an 18-fold increase in basal GDP release rate and, when expressed in culture, it causes a significant decrease in forskolin-stimulated cAMP accumulation. The crystal structure of Gα_i1-T329A·GDP shows substantial conformational rearrangement of the switch I region and additional striking alterations of side chains lining the catalytic pocket that disrupt the Mg⁺² coordination sphere and dislodge bound Mg⁺². We propose a “sequential release” mechanism whereby a transient conformational change in the α5 helix alters switch I to induce GDP release. Interestingly, this mechanistic model for heterotrimeric G protein activation is similar to that suggested for the activation of the plant small G protein Rop4 by RopGEF8.     

Association of the PIK3C2G gene polymorphisms with type 2 DM in a Japanese population

The associations of five SNPs (SNPs1-5: A-5468G, A-3333G, C-1794T, C437T and T9148C) of the class II phosphoinositide 3-kinase γ-subunit (PIK3C2G) gene with type 2 diabetes were examined using a population of the Takahata Study (n (M/W): 2930 (1328/1602); age: 63.3 ± 10.2 years), a Japanese community-based study. Quantitative association study of the SNPs with HbA1c levels showed significant association for SNPs 2 and 4 (p = 0.018 and 0.004, respectively). A case-control association study of SNP 4 with diabetes by multiple logistic regression analysis showed a significant association of the genotype TT of the SNP with an odds ratio of 2.21 (p = 0.001) independently of age, gender and BMI. In the NGT subjects, serum fasting insulin levels in the at-risk genotype group of SNP 4 were significantly lower than those in the others (TT, TC, and CC, 4.9 ± 2.6, 5.4 ± 3.0, and 5.6 ± 3.4 μU/ml, respectively; p = 0.029).     

Systematic Mapping of WNT-FZD Protein Interactions Reveals Functional Selectivity by Distinct WNT-FZD Pairs

The seven-transmembrane-spanning receptors of the FZD_1–10 class are bound and activated by the WNT family of lipoglycoproteins, thereby inducing a complex network of signaling pathways. However, the specificity of the interaction between mammalian WNT and FZD proteins and the subsequent signaling cascade downstream of the different WNT-FZD pairs have not been systematically addressed to date. In this study, we determined the binding affinities of various WNTs for different members of the FZD family by using bio-layer interferometry and characterized their functional selectivity in a cell system. Using purified WNTs, we show that different FZD cysteine-rich domains prefer to bind to distinct WNTs with fast on-rates and slow off-rates. In a 32D cell-based system engineered to overexpress FZD₂, FZD₄, or FZD₅, we found that WNT-3A (but not WNT-4, -5A, or -9B) activated the WNT-β-catenin pathway through FZD_2/4/5 as measured by phosphorylation of LRP6 and β-catenin stabilization. Surprisingly, different WNT-FZD pairs showed differential effects on phosphorylation of DVL2 and DVL3, revealing a previously unappreciated DVL isoform selectivity by different WNT-FZD pairs in 32D cells. In summary, we present extensive mapping of WNT-FZD cysteine-rich domain interactions complemented by analysis of WNT-FZD pair functionality in a unique cell system expressing individual FZD isoforms. Differential WNT-FZD binding and selective functional readouts suggest that endogenous WNT ligands evolved with an intrinsic natural bias toward different downstream signaling pathways, a phenomenon that could be of great importance in the design of FZD-targeting drugs.     

C-Terminal exchange between Gα o and Gα i3 proteins differently modulates α2A-adrenoceptor activation

Chimeric G proteins, obtained by exchanging their C-terminal portion for that of a G protein from an unrelated class, drive the receptor selectivity to that corresponding to the introduced G protein domain. The _2A-adrenoceptor (_2AAR), which yielded an efficacious and weak [³⁵S]GTPS binding response by respectively G _o and G _i3 protein, was investigated in CHO-K1 cells co-expressing chimeric G proteins for which the six last C-terminal amino acids between G _o and G _i3 proteins, and reciprocally, were permuted. Activation of the chimeric G _{o / i3} protein was highly efficient whereas the G _{i3 / o} protein yielded a weak stimulation. These [³⁵S]GTPS binding responses were not different from their parental wild-type G _o and G _i3 proteins. Similar results were obtained with an _2AAR carrying a facilitating Thr³⁷³Lys mutation in a putative G protein interaction domain. These data indicate that the six terminal G _o protein amino acids do not constitute a major _2AAR interaction domain for G protein activation.     

Expression of the μ-Opioid Receptor in CHO Cells: Ability of μ-Opioid Ligands to Promote α-Azidoanilido[32P]GTP Labeling of Multiple G Protein α Subunits

Abstract: The identities of heterotrimeric G proteins that can interact with the μ-opioid receptor were investigated by α-azidoanilido[³²P]GTP labeling of α subunits in the presence of opioid agonists in Chinese hamster ovary (CHO)-MORIVA3 cells, a CHO clone that stably expressed μ-opioid receptor cDNA (MOR-1). This clone expressed 1.01 × 10⁶μ-opioid receptors per cell and had higher binding affinity and potency to inhibit adenylyl cyclase for the μ-opioid-selective ligands [d -Ala²,N-MePhe⁴,Gly-ol]-enkephalin and [N-MePhe³,d -Pro⁴]-morphiceptin, relative to the δ-selective opioid agonist [d -Pen²,d -Pen⁵]-enkephalin or the κ-selective opioid agonist U-50,488H. μ-Opioid ligands induced an increase in α-azidoanilido[³²P]GTP photoaffinity labeling of four Gα subunits in this clone, three of which were identified as G_i3α, G_i2α, and G_o2α. The same pattern of simultaneous interaction of the μ-opioid receptor with multiple Gα subunits was also observed in two other clones, one expressing about three times more and the other 10-fold fewer receptors as those expressed in CHO-MORIVA3 cells. The opioid-induced increase of labeling of these G proteins was agonist specific, concentration dependent, and blocked by naloxone and by pretreatment of these cells with pertussis toxin. A greater agonist-induced increase of α-azidoanilido[³²P]GTP incorporation into G_i2α (160–280%) and G_o2α (110–220%) than for an unknown Gα (G_?α) (60%) or G_i3α (40%) was produced by three different μ-opioid ligands tested. In addition, slight differences were also found between the ability of various μ-opioid agonists to produce half-maximal labeling (ED₅₀) of any given Gα subunit, with a rank order of G_i3α > G_o2α > G_i2α = G_?α. In any case, these results suggest that the activated μ-opioid receptor couples to four distinct G protein α subunits simultaneously.     

Pertussis toxin-sensitive heterotrimeric Gαi/o proteins mediate WNT/β-catenin and WNT/ERK1/2 signaling in mouse primary microglia stimulated with purified WNT-3A

WNT-3A is a secreted lipoglycoprotein that engages Class Frizzled receptors and LDL receptor related protein 5/6 (LRP5/6) for cellular communication. Generally, WNT-3A mediates WNT/β-catenin signaling to regulate TCF/LEF-dependent gene expression. We have previously shown that β-catenin levels are elevated in proinflammatory microglia of Alzheimer's disease patients and that WNT-3A can evoke a strong proinflammatory response in primary microglia. In order to investigate the underlying mechanisms, we focus here on the pharmacological dissection of WNT-3A-induced signaling to β-catenin and to the extracellular signal-regulated kinases 1/2 (ERK1/2) in mouse primary microglia. Both pathways are induced by WNT-3A with slightly different kinetics, suggesting that they might be pharmacologically separable. Inhibition of heterotrimeric G_αi/o proteins by pertussis toxin blocks WNT-3A-induced LRP6 phosphorylation, disheveled shift, β-catenin stabilization and phosphorylation of ERK1/2. On the other hand LRP6 blockade by Dickkopf 1 treatment abrogated the WNT/β-catenin pathway without affecting WNT/ERK1/2 signaling. In the opposite way, inhibition of βγ subunits, phospholipase C (PLC), intracellular calcium and MEK1/2, the upstream kinase of ERK1/2, blocked ERK1/2 phosphorylation but not β-catenin stabilization. In summary, the data suggest a central role of G_αi/o for both β-catenin-dependent and -independent pathways. WNT-3A-induced ERK1/2 phosphorylation is mediated by βγ subunits, PLC, intracellular calcium and MEK1/2. Furthermore, we show that cyclooxygenase 2 (COX2), a generic proinflammatory marker of microglia, is induced by WNT-3A through ERK1/2-dependent pathways arguing that β-catenin-independent signaling downstream of WNT-3A is of physiological importance for the proinflammatory regulation of microglia.     

Conservation of key members in the course of the evolution of the insulin signaling pathway

Our understanding of the evolution of the insulin signaling pathway (ISP) is still incomplete. One intriguing unanswered question is the explanation of the emergence of the glucostatic role of insulin in mammals. To find out whether this is due to the development of new sets of signaling transduction elements in these organisms, or to the establishment of new interactions between pre-existing proteins, we rebuilt putative orthologous ISPs in 17 eukaryotic organisms. Then, we computed the conservation of orthologous ISPs at different levels, from sequence similarity of orthologous proteins to co-evolution of interacting domains. We found that the emergence of glucostatic role in mammals can neither be explained by the development of new sets of signaling elements, nor by the establishment of new interactions between pre-existing proteins. The comparison of orthologous IRS molecules indicates that only in mammals have they acquired their complete functionality as efficient recruiters of effector sub-pathways.     

Prokineticin receptors interact unselectively with several G protein subtypes but bind selectively to β-arrestin 2

Prokineticin 1 (pk1) and prokineticin 2 (pk2) interact with two structurally related G-protein coupled receptors, prokineticin receptor 1 (PKR1) and prokineticin receptor 2 (PKR2). Cellular signalling studies show that the activated receptors can evoke Ca²⁺-mobilization, pertussis toxin-sensitive ERK phosphorylation, and intracellular cAMP accumulation, which suggests the partecipation of several G protein subtypes, such as G_q/11, G_i/o and G_s. However, direct interactions with these transduction proteins have not been studied yet. Here we measured by bioluminescence resonance energy transfer (BRET) the association of PKR1 and PKR2 with different heterotrimeric Gα proteins in response to pk1 and pk2 activation. Using host-cell lines carrying gene deletions of Gα_q/11 or Gα_s, and pertussis toxin treatment to abolish the receptor interactions with Gα_i/o, we determined that both receptors could couple with comparable efficiency to G_q/11 and G_i/o, but far less efficiently to G_s or other pertussis toxin-insensitive G proteins. We also used BRET methodology to assess the association of prokineticin receptors with β-arrestin isoforms. Fluorescent versions of the isoforms were transfected both in HEK293 cells and in double KO β-arrestin 1/2 mouse fibroblasts, to study receptor interaction with the reconstituted individual β-arrestins without background expression of the endogenous genes. Both receptors formed stable BRET-emitting complexes with β-arrestin 2 but not with β-arrestin 1, indicating strong selectivity for the former. In all the studied transducer interactions and in both receptors, pk2 was more potent than pk1 in promoting receptor binding to transduction proteins.     

Preparation of cobalt sandwich diphosphine ligand [(η-C5H4Pr)Co(η-C4(PPh2)2Ph2)] and its chelated palladium complex: Application of diphosphine ligand in the preparation of mono-substituted ferrocenylarenes

The reaction of (η⁵-C₅H₄ⁱPr)Co(PPh₃)₂ with PhCCPPh₂ furnished two isomeric cyclobutadiene-substituted Cp′CoCb diphosphines, [(η⁵-C₅H₄ⁱPr)Co(η⁴-1,2-(PPh₂)₂C₄Ph₂)] (5-cis) and [(η⁵-C₅H₄ⁱPr)Co(η⁴-1,3-(PPh₂)₂C₄Ph₂)] (5-trans). Further reaction of 5-cis with one molar equivalent of Pd(COD)Cl₂ gave palladium complex [(η⁵-C₅H₄ⁱPr)Co(η⁴-1,2-(PPh₂)₂C₄Ph₂)-PdCl₂] (6) in good yield. Both of the molecular structures of 5-cis and 6 were determined by single-crystal X-ray diffraction methods. Unexpectedly, the palladium complex 6 was found to be more efficient than the combination of the commonly used Buchwald’s ligand, biphenyl-2-yl-di-tert-butyl-phosphane, with Pd(OAc)₂ as the catalytic precursor in the Suzuki-Miyaura reaction between ferroceneboronic acid and 4-bromoaldehyde. The X-ray structural analysis and DFT study of several palladium complexes containing sandwich-type diphosphine chelating ligands revealed that the variations in bite angles are much larger than those in bite distances. The more energetically favorable conformation in the Pd(II) complexes is the one with bite angle close to 90°.     

Limonoids from the seeds of a Godavari mangrove, Xylocarpus moluccensis

Ten limonoids, named godavarins A-J (1-7, 9-11), were isolated from seeds of an Indian mangrove (Xylocarpus moluccensis) collected in the mangrove wetlands of Godavari estuary, Andhra Pradesh. Eight known limonoids, viz. xyloccensins L (8), P (12), Q (13), mexicanolide (14), 6-deoxy-3-detigloyl-swietenine acetate (15), fissinolide (16), methyl 3β-acetoxy-1-oxomeliaca-8(30),14-dienoate (17), and methyl 3β-acetoxy-1-oxomeliaca-8(9),14-dienoate (18), were also obtained. The structures of these compounds were established on the basis of spectroscopic data or comparison with data in the literature (known compounds). The stereostructure of godavarin D was confirmed by means of single-crystal X-ray analysis. Godavarins A-C are the first mexicanolide derivatives with a C₇-C₂₈ ester-linked δ-lactone ring, while godavarins D-G are further additions to the small group of limonoids with a C₁-C₂₉ oxygen bridge. Godavarin H is a phragmalin with five acetoxy groups. Two limonoids, mexicanolide and fissinolide, were found to exhibit marked antifeedant activity against the third-instar larvae of Brontispa longissima (Gestro) at a concentration of 0.5 mg/mL. The most potent compound was mexicanolide. It also showed moderate insecticidal activity.     

Proposal of Ensifer psoraleae sp. nov., Ensifer sesbaniae sp. nov., Ensifer morelense comb. nov. and Ensifer americanum comb. nov

In a survey of rhizobia associated with the native legumes in Yunnan Province, China, seven and nine strains isolated from the root nodules of Psoralea corylifolia, Sesbania cannabina and Medicago lupulina were respectively classified into the novel genomic species groups I and II in the genus Ensifer (former Sinorhizobium) based on the sequence analyses of the 16S rRNA gene. Analyses of concatenated housekeeping genes (atpD, recA and glnII) further revealed that they were distinct lineages in the genus, and group I was most similar to Ensifer terangae and Ensifer garamanticus (both with 94.2% similarity), while group II was most similar to Ensifer adhaerens (94.0%). These groups could be distinguished from closely related species by DNA–DNA relatedness, MALID-TOF MS, cellular fatty acid profiles and a series of phenotypic characters. Therefore, two novel species were proposed: Ensifer psoraleae sp. nov. (seven strains, type strain CCBAU 65732^T = LMG 26835^T = HAMBI 3286^T) and Ensifer sesbaniae sp. nov. (nine strains, type strain CCBAU 65729^T = LMG 26833^T = HAMBI 3287^T). They had a DNA G + C mol% (T_m) of 58.9 and 60.4, respectively. Both of the type strains formed effective nodules on common bean (Phaseolus vulgaris) and their hosts of origin. In addition, the previously described species Sinorhizobium morelense and Sinorhizobium americanum were renamed as Ensifer morelense comb. nov. and Ensifer americanum comb. nov. according to the accumulated data from different studies.