The C. elegans SYS-1 protein is a bona fide beta-catenin

Utilizing the scale-invariant feature transform algorithm to align distance matrices facilitates systematic protein structure comparison

MOTIVATION

Protein structure comparison is pivotal for deriving homological relationships, elucidating protein functions, and understanding evolutionary developments. The burgeoning field of in-silico protein structure prediction now yields billions of models with near-experimental accuracy, necessitating sophisticated tools for discerning structural similarities among proteins, particularly when sequence similarity is limited.

RESULTS

In this article, we have developed the align distance matrix with scale (ADAMS) pipeline, which synergizes the distance matrix alignment method with the scale-invariant feature transform algorithm, streamlining protein structure comparison on a proteomic scale. Utilizing a computer vision-centric strategy for contrasting disparate distance matrices, ADAMS adeptly alleviates challenges associated with proteins characterized by a high degree of structural flexibility. Our findings indicate that ADAMS achieves a level of performance and accuracy on par with Foldseek, while maintaining similar speed. Crucially, ADAMS overcomes certain limitations of Foldseek in handling structurally flexible proteins, establishing it as an efficacious tool for in-depth protein structure analysis with heightened accuracy.

AVAILABILITY

ADAMS can be download and used as a python package from Python Package Index (PyPI): adams · PyPI. Source code and other materials are available from young55775/ADAMS-developing (github.com). An online server is available: Bseek Search Server (cryonet.ai).

GATA binding protein 6 regulates apoptosis in silkworms through interaction with poly (ADP-ribose) polymerase

The GATA family of genes plays various roles in crucial biological processes, such as development, cell differentiation, and disease progression. However, the roles of GATA in insects have not been thoroughly explored. In this study, a genome-wide characterization of the GATA gene family in the silkworm, Bombyx mori, was conducted, revealing lineage-specific expression profiles. Notably, GATA6 is ubiquitously expressed across various developmental stages and tissues, with predominant expression in the midgut, ovaries, and Malpighian tubules. Overexpression of GATA6 inhibits cell growth and promotes apoptosis, whereas, in contrast, knockdown of PARP mitigates the apoptotic effects driven by GATA6 overexpression. Co-immunoprecipitation (co-IP) has demonstrated that GATA6 can interact with Poly (ADP-ribose) polymerase (PARP), suggesting that GATA6 may induce cell apoptosis by activating the enzyme's activity. These findings reveal a dynamic and regulatory relationship between GATA6 and PARP, suggesting a potential role for GATA6 as a key regulator in apoptosis through its interaction with PARP. This research deepens the understanding of the diverse roles of the GATA family in insects, shedding light on new avenues for studies in sericulture and pest management.

Novel pathogenic variant in MED12 causing non-syndromic dilated cardiomyopathy

BACKGROUND

Dilated cardiomyopathy (DCM) is a major cause of sudden cardiac death and heart failure. Up to 50% of all DCM cases have a genetic background, with variants in over 250 genes reported in association with DCM. Whole-exome sequencing (WES) is a powerful tool to identify variants underlying genetic cardiomyopathies. Via WES, we sought to identify DCM causes in a family with 2 affected patients.

METHODS

WES was performed on the affected members of an Iranian family to identify the genetic etiology of DCM. The candidate variant was segregated via polymerase chain reaction and Sanger sequencing. Computational modeling and protein-protein docking were performed to survey the impact of the variant on the structure and function of the protein.

RESULTS

A novel single-nucleotide substitution (G > A) in exon 9 of MED12, c.1249G > A: p.Val417Ile, NM_005120.3, was identified. The c.1249G > A variant was validated in the family. Bioinformatic analysis and computational modeling confirmed that c.1249G > A was the pathogenic variant responsible for the DCM phenotype.

CONCLUSION

We detected a novel DCM-causing variant in MED12 using WES. The variant in MED12 may decrease binding to cyclin-dependent kinase 8 (CDK8), affect its activation, and cause alterations in calcium-handling gene expression in the heart, leading to DCM.

Exploring the roles of ZmARM gene family in maize development and abiotic stress response

Armadillo (ARM) was a gene family important to plants, with crucial roles in regulating plant growth, development, and stress responses. However, the properties and functions of ARM family members in maize had received limited attention. Therefore, this study employed bioinformatics methods to analyze the structure and evolution of ARM-repeat protein family members in maize. The maize (Zea mays L.) genome contains 56 ARM genes distributed over 10 chromosomes, and collinearity analysis indicated 12 pairs of linkage between them. Analysis of the physicochemical properties of ARM proteins showed that most of these proteins were acidic and hydrophilic. According to the number and evolutionary analysis of the ARM genes, the ARM genes in maize can be divided into eight subgroups, and the gene structure and conserved motifs showed similar compositions in each group. The findings shed light on the significant roles of 56 ZmARM domain genes in development and abiotic stress, particularly drought stress. RNA-Seq and qRT-PCR analysis revealed that drought stress exerts an influence on specific members of the ZmARM family, such as ZmARM4, ZmARM12, ZmARM34 and ZmARM36. The comprehensive profiling of these genes in the whole genome, combined with expression analysis, establishes a foundation for further exploration of plant gene function in the context of abiotic stress and reproductive development.

Crosstalk Between β-CATENIN-Mediated Cell Adhesion and the WNT Signaling Pathway

Cell adhesion and stable signaling regulation are fundamental ways of maintaining homeostasis. Among them, the Wnt/β-CATENIN signaling plays a key role in embryonic development and maintenance of body dynamic homeostasis. At the same time, the key signaling molecule β-CATENIN in the Wnt signaling can also function as a cytoskeletal linker protein to regulate tissue barriers, cell migration, and morphogenesis. Dysregulation of the balance between Wnt signaling and adherens junctions can lead to disease. How β-CATENIN maintains the independence of these two functions, or mediates the interaction and balance of these two functions, has been explored and debated for a long time. In this study, we will focus on five aspects of β-CATENIN chaperone molecules, phosphorylation of β-CATENIN and related proteins, epithelial mesenchymal transition, β-CATENIN homolog protein γ-CATENIN and disease, thus deepening the understanding of the Wnt/β-CATENIN signaling and the homeostasis between cell adhesion and further addressing related disease problems.

How Weird is The Worm? Evolution of the Developmental Gene Toolkit in Caenorhabditis elegans

Comparative developmental biology and comparative genomics are the cornerstones of evolutionary developmental biology. Decades of fruitful research using nematodes have produced detailed accounts of the developmental and genomic variation in the nematode phylum. Evolutionary developmental biologists are now utilising these data as a tool with which to interrogate the evolutionary basis for the similarities and differences observed in Nematoda. Nematodes have often seemed atypical compared to the rest of the animal kingdom-from their totally lineage-dependent mode of embryogenesis to their abandonment of key toolkit genes usually deployed by bilaterians for proper development-worms are notorious rule breakers of the bilaterian handbook. However, exploring the nature of these deviations is providing answers to some of the biggest questions about the evolution of animal development. For example, why is the evolvability of each embryonic stage not the same? Why can evolution sometimes tolerate the loss of genes involved in key developmental events? Lastly, why does natural selection act to radically diverge toolkit genes in number and sequence in certain taxa? In answering these questions, insight is not only being provided about the evolution of nematodes, but of all metazoans.

Sequential cleavage of the proteins encoded by HNOT/ALG3, the human counterpart of the Drosophila NOT and yeast ALG3 gene, results in products acting in distinct cellular compartments

This study provides first insights into the biosynthesis, structure, biochemistry and complex processing of the proteins encoded by hNOT/ALG3, the human counterpart of the Drosophila Neighbour of TID (NOT) and the yeast asparagine linked glycosylation 3 gene (ALG3), which encodes a mannosyltransferase. Unambiguous evidence that both the fly and human proteins act as mannosyltransferases has not been provided yet. Previously, we showed that hNOT/ALG3 encodes two alternatively spliced main transcripts, hNOT-1/ALG3-1 and hNOT-4/ALG3-4, and their 15 truncated derivatives that lack diverse sets of exons and/or carry point mutations that result in premature termination codons. Here we show that the truncated transcripts are not translated. The two main forms hNOT-1/ALG3-1 and -4, distinguishable by alternative exon 1, encode full-length precursors that undergo a complex posttranslational processing. To specifically detect the two full-length hNOT/ALG3 proteins and their distinct derivatives and to examine their expression profiles and cellular location we generated polyclonal antibodies against diverse parts of the putative full-length proteins. We provide experimental evidence for the N-glycosylation of the two precursors. This modification seems to be a prerequisite for their sequential cleavage resulting in derivatives destined to distinct cellular compartments and links them with the N-glycosylation machinery not as its functional component but as molecules functionally dependent on its action. We present the expression profiles and subcellular location of the two full-length proteins, their N-glycosylated forms and distinct cleavage products. Furthermore, using diverse bioinformatics tools, we characterize the properties and predict the 2D and 3D structure of the two proteins and, for comparative purposes, of their Drosophila counterpart.

Functional equivalence of germ plasm organizers

The proteins Oskar (Osk) in Drosophila and Bucky ball (Buc) in zebrafish act as germ plasm organizers. Both proteins recapitulate germ plasm activities but seem to be unique to their animal groups. Here, we discover that Osk and Buc show similar activities during germ cell specification. Drosophila Osk induces additional PGCs in zebrafish. Surprisingly, Osk and Buc do not show homologous protein motifs that would explain their related function. Nonetheless, we detect that both proteins contain stretches of intrinsically disordered regions (IDRs), which seem to be involved in protein aggregation. IDRs are known to rapidly change their sequence during evolution, which might obscure biochemical interaction motifs. Indeed, we show that Buc binds to the known Oskar interactors Vasa protein and nanos mRNA indicating conserved biochemical activities. These data provide a molecular framework for two proteins with unrelated sequence but with equivalent function to assemble a conserved core-complex nucleating germ plasm.

Multicellular organisms use gametes for their propagation. Gametes are formed from germ cells, which are specified during embryogenesis in some animals by the inheritance of RNP granules known as germ plasm. Transplantation of germ plasm induces extra germ cells, whereas germ plasm ablation leads to the loss of gametes and sterility. Therefore, germ plasm is key for germ cell formation and reproduction. However, the molecular mechanisms of germ cell specification by germ plasm in the vertebrate embryo remain an unsolved question. Proteins, which assemble the germ plasm, are known as germ plasm organizers. Here, we show that the two germ plasm organizers Oskar from the fly and Bucky ball from the fish show similar functions by using a cross species approach. Both are intrinsically disordered proteins, which rapidly changed their sequence during evolution. Moreover, both proteins still interact with conserved components of the germ cell specification pathway. These data might provide a first example of two proteins with the same biological role, but distinct sequence.

Wnt Signaling in Stem Cells and Cancer Stem Cells: A Tale of Two Coactivators

Wnt signaling in stem cells plays critical roles in development, normal adult physiology, and disease. In this chapter, we focus on the role of the Wnt signaling pathway in somatic stem cell biology and its critical role in normal tissue homeostasis and cancer. Wnt signaling can both maintain potency and initiate differentiation in somatic stem cells, depending on the cellular and environmental context. Based principally on studies from our lab, we will explain the dichotomous behavior of this signaling pathway in determining stem cell fate decisions, placing special emphasis on the interaction of β-catenin with either of the two highly homologous Kat3 coactivator proteins, CBP and p300. We will also discuss our results, both preclinical and clinical, demonstrating that small molecule modulators of the β-catenin/Kat3 coactivator interaction can be safely utilized to shift the balance between maintenance of potency and initiation of differentiation.

Evolution and diversity of cadherins and catenins

Cadherin genes encode a superfamily of conserved transmembrane proteins that share an adhesive ectodomain composed of tandem cadherin repeats. More than 100 human cadherin superfamily members have been identified, which can be classified into three families: major cadherins, protocadherins and cadherin-related proteins. These superfamily members are involved in diverse fundamental cellular processes including cell-cell adhesion, morphogenesis, cell recognition and signaling. Epithelial cadherin (E-cadherin) is the founding cadherin family member. Its cytoplasmic tail interacts with the armadillo catenins, p120 and β-catenin. Further, α-catenin links the cadherin/armadillo catenin complex to the actin filament network. Even genomes of ancestral metazoan species such as cnidarians and placozoans encode a limited number of distinct cadherins and catenins, emphasizing the conservation and functional importance of these gene families. Moreover, a large expansion of the cadherin and catenin families coincides with the emergence of vertebrates and reflects a major functional diversification in higher metazoans. Here, we revisit and review the functions, phylogenetic classifications and co-evolution of the cadherin and catenin protein families.

Wnt Signaling Polarizes C. elegans Asymmetric Cell Divisions During Development

Asymmetric cell division is a common mode of cell differentiation during the invariant lineage of the nematode, C. elegans. Beginning at the four-cell stage, and continuing throughout embryogenesis and larval development, mother cells are polarized by Wnt ligands, causing an asymmetric inheritance of key members of a Wnt/β-catenin signal transduction pathway termed the Wnt/β-catenin asymmetry pathway. The resulting daughter cells are distinct at birth with one daughter cell activating Wnt target gene expression via β-catenin activation of TCF, while the other daughter displays transcriptional repression of these target genes. Here, we seek to review the body of evidence underlying a unified model for Wnt-driven asymmetric cell division in C. elegans, identify global themes that occur during asymmetric cell division, as well as highlight tissue-specific variations. We also discuss outstanding questions that remain unanswered regarding this intriguing mode of asymmetric cell division.

Determinants in the LIN-12/Notch Intracellular Domain That Govern Its Activity and Stability During Caenorhabditis elegans Vulval Development

Upon ligand binding, the LIN-12/Notch intracellular domain is released from its transmembrane tether to function in a nuclear complex that activates transcription of target genes. During Caenorhabditis elegans vulval development, LIN-12/Notch is activated by ligand in two of six multipotential vulval precursor cells (VPCs), specifying the "secondary vulval fate" and descendants that contribute to the vulva. If LIN-12 is ectopically activated in other VPCs, they also adopt the secondary fate, dividing to produce extra vulval cells, resulting in a "Multivulva" phenotype. Here, we identify determinants in the LIN-12 intracellular domain ["LIN-12(intra)"] that govern its activity and stability during C. elegans vulval development; we assayed activity of mutant forms based on their ability to cause a Multivulva phenotype and stability using a GFP tag to visualize their accumulation. Our analysis has revealed that, while the ubiquitin ligase SEL-10/Fbw7 promotes LIN-12(intra) downregulation in VPCs, there is a distinct mechanism for downregulation of LIN-12(intra) in VPC descendants. Our analysis also revealed that LIN-12(intra) must be in the nuclear complex to be regulated appropriately in VPCs and their descendants, and that the structure or conformation of the carboxy-terminal region influences stability as well. Although activity and stability are generally well-correlated, exceptions where they are uncoupled suggest that there may be roles for the carboxy-terminal region and sel-10 that are independent of their roles in regulating LIN-12(intra) stability.

An Integrated Analysis of MicroRNA and mRNA Expression Profiles to Identify RNA Expression Signatures in Lambskin Hair Follicles in Hu Sheep

Wave patterns in lambskin hair follicles are an important factor determining the quality of sheep’s wool. Hair follicles in lambskin from Hu sheep, a breed unique to China, have 3 types of waves, designated as large, medium, and small. The quality of wool from small wave follicles is excellent, while the quality of large waves is considered poor. Because no molecular and biological studies on hair follicles of these sheep have been conducted to date, the molecular mechanisms underlying the formation of different wave patterns is currently unknown. The aim of this article was to screen the candidate microRNAs (miRNA) and genes for the development of hair follicles in Hu sheep. Two-day-old Hu lambs were selected from full-sib individuals that showed large, medium, and small waves. Integrated analysis of microRNA and mRNA expression profiles employed high-throughout sequencing technology. Approximately 13, 24, and 18 differentially expressed miRNAs were found between small and large waves, small and medium waves, and medium and large waves, respectively. A total of 54, 190, and 81 differentially expressed genes were found between small and large waves, small and medium waves, and medium and large waves, respectively, by RNA sequencing (RNA-seq) analysis. Differentially expressed genes were classified using gene ontology and pathway analyses. They were found to be mainly involved in cell differentiation, proliferation, apoptosis, growth, immune response, and ion transport, and were associated with MAPK and the Notch signaling pathway. Reverse transcription-polymerase chain reaction (RT-PCR) analyses of differentially-expressed miRNA and genes were consistent with sequencing results. Integrated analysis of miRNA and mRNA expression indicated that, compared to small waves, large waves included 4 downregulated miRNAs that had regulatory effects on 8 upregulated genes and 3 upregulated miRNAs, which in turn influenced 13 downregulated genes. Compared to small waves, medium waves included 13 downregulated miRNAs that had regulatory effects on 64 upregulated genes and 4 upregulated miRNAs, which in turn had regulatory effects on 22 downregulated genes. Compared to medium waves, large waves consisted of 13 upregulated miRNAs that had regulatory effects on 48 downregulated genes. These differentially expressed miRNAs and genes may play a significant role in forming different patterns, and provide evidence for the molecular mechanisms underlying the formation of hair follicles of varying patterns.

The benefits of local depletion: The centrosome as a scaffold for ubiquitin-proteasome-mediated degradation

The centrosome is the major microtubule-organizing center in animal cells but is dispensable for proper microtubule spindle formation in many biological contexts and is thus thought to fulfill additional functions. Recent observations suggest that the centrosome acts as a scaffold for proteasomal degradation in the cell to regulate a variety of biological processes including cell fate acquisition, cell cycle control, stress response, and cell morphogenesis. Here, we review the body of studies indicating a role for the centrosome in promoting proteasomal degradation of ubiquitin-proteasome substrates and explore the functional relevance of this system in different biological contexts. We discuss a potential role for the centrosome in coordinating local degradation of proteasomal substrates, allowing cells to achieve stringent spatiotemporal control over various signaling processes.

Kat3 coactivators in somatic stem cells and cancer stem cells: biological roles, evolution, and pharmacologic manipulation

Long-lived somatic stem cells regenerate adult tissues throughout our lifetime. However, with aging, there is a significant deterioration in the function of stem and progenitor cells, which contribute to diseases of aging. The decision for a long-lived somatic stem cell to become activated and subsequently to undergo either a symmetric or an asymmetric division is a critical cellular decision process. The decision to preferentially divide symmetrically or asymmetrically may be the major fundamental intrinsic difference between normal somatic stem cells and cancer stem cells. Based upon work done primarily in our laboratory over the past 15 years, this article provides a perspective on the critical role of somatic stem cells in aging. In particular, we discuss the importance of symmetric versus asymmetric divisions in somatic stem cells and the role of the differential usage of the highly similar Kat3 coactivators, CREB-binding protein (CBP) and p300, in stem cells. We describe and propose a more complete model for the biological mechanism and roles of these two coactivators, their evolution, and unique roles and importance in stem cell biology. Finally, we discuss the potential to pharmacologically manipulate Kat3 coactivator interactions in endogenous stem cells (both normal and cancer stem cells) to potentially ameliorate the aging process and common diseases of aging.

A combined binary interaction and phenotypic map of C. elegans cell polarity proteins

The establishment of cell polarity is an essential process for the development of multicellular organisms and the functioning of cells and tissues. Here, we combine large-scale protein interaction mapping with systematic phenotypic profiling to study the network of physical interactions that underlies polarity establishment and maintenance in the nematode Caenorhabditis elegans. Using a fragment-based yeast two-hybrid strategy, we identified 439 interactions between 296 proteins, as well as the protein regions that mediate these interactions. Phenotypic profiling of the network resulted in the identification of 100 physically interacting protein pairs for which RNAi-mediated depletion caused a defect in the same polarity-related process. We demonstrate the predictive capabilities of the network by showing that the physical interaction between the RhoGAP PAC-1 and PAR-6 is required for radial polarization of the C. elegans embryo. Our network represents a valuable resource of candidate interactions that can be used to further our insight into cell polarization.

A conserved phosphorylation switch controls the interaction between cadherin and β-catenin in vitro and in vivo

In metazoan adherens junctions, β-catenin links the cytoplasmic tail of classical cadherins to the F-actin-binding protein α-catenin. Phosphorylation of a Ser/Thr-rich region in the cadherin tail dramatically enhances affinity for β-catenin and promotes cell-cell adhesion in cell culture systems, but its importance has not been demonstrated in vivo. Here, we identify a critical phosphorylated serine in the C. elegans cadherin HMR-1 required for strong binding to the β-catenin homolog HMP-2. Ablation of this phosphoserine interaction produces developmental defects that resemble full loss-of-function (Hammerhead and Humpback) phenotypes. Most metazoans possess a single gene for β-catenin, which is also a transcriptional coactivator in Wnt signaling. Nematodes and planaria, however, have a set of paralogous β-catenins; for example, C. elegans HMP-2 functions only in cell-cell adhesion, whereas SYS-1 mediates transcriptional activation through interactions with POP-1/Tcf. Our structural data define critical sequence differences responsible for the unique ligand specificities of these two proteins.

Study of Wnt2 secreted by A-549 cells in paracrine activation of β-catenin in co-cultured mesenchymal stem cells

The canonical Wnt signal pathway is a key regulator of self-renewal and cell fate determination in various types of stem cells. The total pool of β-catenin consists of two different forms: the signaling form of the protein transmits the Wnt signals from the cell membrane to the target genes, whereas the membrane β-catenin is involved in formation of cell-to-cell contact at cadherin junctions. Earlier we developed an in vitro model of epithelial differentiation of mesenchymal stem cells (MSCs) co-cultured with epithelial A-549 cells. The purpose of the present work was to study the role of Wnt2 secreted by the A-549 cells in paracrine induction of β-catenin in co-cultured MSCs. Using the somatic gene knockdown technique, we obtained A-549 cell cultures with down-regulated WNT2. The MSCs co-cultured with the control A-549 cells displayed an increase in the levels of total cellular and signaling β-catenin and transactivation of a reporter construction containing the Lef/Tcf protein family binding sites. In contrast, β-catenin was not induced in the MSCs co-cultured with the A-549 cells with down-regulated WNT2 expression, but the total protein level was increased. We suggest that Wnt2 secreted by A-549 cells induces in co-cultured MSCs the Wnt/β-catenin signaling pathway, whereas the associated increase in total β-catenin level should be due to another mechanism.

Centrosome-Associated Degradation Limits β-Catenin Inheritance by Daughter Cells after Asymmetric Division

Caenorhabditis elegans embryos rapidly diversify cell fate using a modified Wnt/β-catenin signaling strategy to carry out serial asymmetric cell divisions (ACDs). Wnt-dependent ACDs rely on nuclear asymmetry of the transcriptional coactivator SYS-1/β-catenin between daughter cells to differentially activate Wnt-responsive target genes. Here, we investigate how dynamic localization of SYS-1 to mitotic centrosomes influences SYS-1 inheritance in daughter cells and cell-fate outcomes after ACD. Through yeast two-hybrid screening, we identify the centrosomal protein RSA-2 as a SYS-1 binding partner and show that localization of SYS-1 to mitotic centrosomes is dependent on RSA-2. Uncoupling SYS-1 from the centrosome by RSA-2 depletion increases SYS-1 inheritance after ACD and promotes Wnt-dependent cell fate. Photobleaching experiments reveal that centrosome-bound SYS-1 turns over rapidly. Interestingly, disruption of the proteasome leads to an increased accumulation of SYS-1 at the centrosome but disrupts its dynamic turnover. We conclude that centrosomal targeting of SYS-1 promotes its degradation during asymmetric cell division. We propose a model whereby centrosome-associated SYS-1 degradation couples negative regulation with cell-division timing to facilitate SYS-1 clearance from the mother cell at the time of asymmetric division. Based on our observations of centrosomal SYS-1 dynamics, we discuss the possibility that the centrosome may coordinate various cell-cycle-dependent processes by synchronizing mitosis and protein regulation.

β-Catenin-related protein WRM-1 is a multifunctional regulatory subunit of the LIT-1 MAPK complex

Vertebrate β-catenin has two functions, as a structural component of the adherens junction in cell adhesion and as the T-cell factor (TCF) transcriptional coactivator in canonical Wnt (wingless-related integration site) signaling. These two functions are split between three of the four β-catenin-related proteins present in the round worm Caenorhabditis elegans. The fourth β-catenin-related protein, WRM-1, exhibits neither of these functions. Instead, WRM-1 binds the MAPK loss of intestine 1 (LIT-1), and these two proteins have been shown to be essential for the transcription of Wnt target genes by phosphorylating and regulating the nuclear level of the sole worm TCF protein. We showed previously that WRM-1 binds to worm TCF and functions as the substrate-binding subunit for LIT-1. In this study, we show that phosphorylation of T220 in the activation loop is essential for LIT-1 kinase activity in vivo and in vitro. T220 can be phosphorylated either through LIT-1 autophosphorylation or directly by the upstream MAP3K MOM-4. Our data support a model in which WRM-1, which can undergo homotypic interaction, binds LIT-1 and thereby generates a kinase complex in which LIT-1 molecules are situated in a conformation enabling autophosphorylation as well as promoting phosphorylation of the T220 residue by MOM-4. In addition, we show that WRM-1 is essential for the translocation of the LIT-1 kinase complex to the nucleus, the site of its TCF substrate. To our knowledge, this is the first report of a MAP3K directly activating a MAPK by phosphorylation within the activation loop. This study should help uncover novel and as yet underappreciated functions of vertebrate β-catenin.

CACN-1/Cactin plays a role in Wnt signaling in C. elegans

Wnt signaling is tightly regulated during animal development and controls cell proliferation and differentiation. In C. elegans, activation of Wnt signaling alters the activity of the TCF/LEF transcription factor, POP-1, through activation of the Wnt/β-catenin or Wnt/β-catenin asymmetry pathways. In this study, we have identified CACN-1 as a potential regulator of POP-1 in C. elegans larval development. CACN-1/Cactin is a well-conserved protein of unknown molecular function previously implicated in the regulation of several developmental signaling pathways. Here we have used activation of POPTOP, a POP-1-responsive reporter construct, as a proxy for Wnt signaling. POPTOP requires POP-1 and SYS-1/β-catenin for activation in L4 uterine cells. RNAi depletion experiments show that CACN-1 is needed to prevent excessive activation of POPTOP and for proper levels and/or localization of POP-1. Surprisingly, high POPTOP expression correlates with increased levels of POP-1 in uterine nuclei, suggesting POPTOP may not mirror endogenous gene expression in all respects. Genetic interaction studies suggest that CACN-1 may act partially through LIT-1/NLK to alter POP-1 localization and POPTOP activation. Additionally, CACN-1 is required for proper proliferation of larval seam cells. Depletion of CACN-1 results in a loss of POP-1 asymmetry and reduction of terminal seam cell number, suggesting an adoption of the anterior, differentiated fate by the posterior daughter cells. These findings suggest CACN-1/Cactin modulates Wnt signaling during larval development.

Our evolving view of Wnt signaling in C. elegans: If two's company and three's a crowd, is four really necessary?

In this commentary, we discuss how our recent paper by Yang et al. contributes a new wrinkle to the already somewhat curious Wnt signaling pathway in C. elegans. We begin with a historical perspective on the Wnt pathway in the worm, followed by a summary of the key salient point from Yang et al., 2011, namely demonstration of mutually inhibitory binding of a β-catenin SYS-1 to the N-terminus and another β-catenin WRM-1 to the C-terminus of the TCF protein POP-1, and a plausible structural explanation for these differential binding specificities. The mutually inhibitory binding creates one population of POP-1 that is bound by WRM-1, phosphorylated by the NLK kinase and exported from the nucleus, and another bound by coactivator SYS-1 that remains in the nucleus. We speculate on the evolutionary history of the four β-catenins in C. elegans and suggest a possible link between multiple β-catenin gene duplications and the requirement to reduce nuclear POP-1 levels to activate Wnt target genes.

The evolutionary origin of epithelial cell-cell adhesion mechanisms

A simple epithelium forms a barrier between the outside and the inside of an organism, and is the first organized multicellular tissue found in evolution. We examine the relationship between the evolution of epithelia and specialized cell-cell adhesion proteins comprising the classical cadherin/β-catenin/α-catenin complex (CCC). A review of the divergent functional properties of the CCC in metazoans and non-metazoans, and an updated phylogenetic coverage of the CCC using recent genomic data reveal: (1) The core CCC likely originated before the last common ancestor of unikonts and their closest bikont sister taxa. (2) Formation of the CCC may have constrained sequence evolution of the classical cadherin cytoplasmic domain and β-catenin in metazoa. (3) The α-catenin-binding domain in β-catenin appears to be the favored mutation site for disrupting β-catenin function in the CCC. (4) The ancestral function of the α/β-catenin heterodimer appears to be an actin-binding module. In some metazoan groups, more complex functions of α-catenin were gained by sequence divergence in the non-actin-binding (N-, M-) domains. (5) Allosteric regulation of α-catenin may have evolved for more complex regulation of the actin cytoskeleton.

New insights into the evolution of metazoan cadherins and catenins

E-Cadherin and β-catenin are the best studied representatives of the superfamilies of transmembrane cadherins and intracellular armadillo catenins, respectively. However, in over 600 million years of multicellular animal evolution, these two superfamilies have diversified remarkably both structurally and functionally. Although their basic building blocks, respectively, the cadherin repeat domain and the armadillo repeat domain, predate metazoans, the specific and complex domain compositions of the different family members and their functional roles in cell adhesion and signaling appear to be key features for the emergence of multicellular animal life. Basal animals such as placozoans and sponges have a limited number of distinct cadherins and catenins. The origin of vertebrates, in particular, coincided with a large increase in the number of cadherins and armadillo proteins, including modern "classical" cadherins, protocadherins, and plakophilins. Also, α-catenins increased. This chapter introduces the many different family members and describes the putative evolutionary relationships between them.

TCF/LEFs and Wnt signaling in the nucleus

T-cell factor/lymphoid enhancer factor (TCF/LEF) transcription factors are the major end point mediators of Wnt/Wingless signaling throughout metazoans. TCF/LEFs are multifunctional proteins that use their sequence-specific DNA-binding and context-dependent interactions to specify which genes will be regulated by Wnts. Much of the work to define their actions has focused on their ability to repress target gene expression when Wnt signals are absent and to recruit β-catenin to target genes for activation when Wnts are present. Recent advances have highlighted how these on/off actions are regulated by Wnt signals and stabilized β-catenin. In contrast to invertebrates, which typically contain one TCF/LEF protein that can both activate and repress Wnt targets, gene duplication and isoform complexity of the family in vertebrates have led to specialization, in which individual TCF/LEF isoforms have distinct activities.

β-catenin-dependent Wnt signaling in C. elegans: teaching an old dog a new trick

Wnt signaling is an evolutionarily ancient pathway used to regulate many events during metazoan development. Genetic results from Caenorhabditis elegans more than a dozen years ago suggested that Wnt signaling in this nematode worm might be different than in vertebrates and Drosophila: the worm had a small number of Wnts, too many β-catenins, and some Wnt pathway components functioned in an opposite manner than in other species. Work over the ensuing years has clarified that C. elegans does possess a canonical Wnt/β-catenin signaling pathway similar to that in other metazoans, but that the majority of Wnt signaling in this species may proceed via a variant Wnt/β-catenin signaling pathway that uses some new components (mitogen-activated protein kinase signaling enzymes), and in which some conserved pathway components (β-catenin, T-cell factor [TCF]) are used in new and interesting ways. This review summarizes our current understanding of the canonical and novel TCF/β-catenin-dependent signaling pathways in C. elegans.

The many faces and functions of β-catenin

β-Catenin (Armadillo in Drosophila) is a multitasking and evolutionary conserved molecule that in metazoans exerts a crucial role in a multitude of developmental and homeostatic processes. More specifically, β-catenin is an integral structural component of cadherin-based adherens junctions, and the key nuclear effector of canonical Wnt signalling in the nucleus. Imbalance in the structural and signalling properties of β-catenin often results in disease and deregulated growth connected to cancer and metastasis. Intense research into the life of β-catenin has revealed a complex picture. Here, we try to capture the state of the art: we try to summarize and make some sense of the processes that regulate β-catenin, as well as the plethora of β-catenin binding partners. One focus will be the interaction of β-catenin with different transcription factors and the potential implications of these interactions for direct cross-talk between β-catenin and non-Wnt signalling pathways.

20-hydroxyecdysone upregulates apoptotic genes and induces apoptosis in the Bombyx fat body

During insect metamorphosis, obsolete larval tissues are removed by programed cell death (PCD), mainly apoptosis and autophagy, which is directed by the molting hormone, 20-hydroxyecdysone (20E) and the 20E-triggered transcriptional cascade. Here, we investigated how 20E regulates apoptosis at the transcriptional level in the fat body of the silkworm, Bombyx mori. As detected by TdT-mediated dUTP Nick-End Labeling (TUNEL), apoptosis weakly occurred during the fourth larval molting, decreased to undetected levels during the early fifth instar, and gradually increased from day 4 of fifth instar to the wandering stage to the prepupal stage. Meanwhile, as determined by quantitative real-time PCR, eight genes involved in apoptosis, including Apaf-1, Nedd2 like1, Nedd2 like2, ICE1, ICE3, ICE5, Arp, and IAP, were highly expressed during molting and pupation, when the 20E titer is high. Injection of 20E into day 2 of fifth instar larvae significantly induced apoptosis and upregulated apoptotic genes after 6 h of treatment, and in vitro treatment of larval fat body tissues with 20E upregulated all the eight apoptotic genes. Moreover, RNAi knockdown of USP, a component of the 20E receptor complex EcR-USP, at the early-wandering stage reduced apoptosis and downregulated apoptotic genes after 24 h of treatment. Taken together, we infer that 20E upregulates apoptotic genes and thus induces apoptosis in the Bombyx fat body during larval molting and the larval-pupal transition.

TCFs and Wnt/β-catenin signaling: more than one way to throw the switch

Wnts are conserved, secreted signaling proteins that can influence cell behavior by stabilizing β-catenin. Accumulated β-catenin enters the nucleus, where it physically associates with T-cell factor (TCF) family members to regulate target gene expression in many developmental and adult tissues. Recruitment of β-catenin to Wnt response element (WRE) chromatin converts TCFs from transcriptional repressors to activators. This review will outline the complex interplay between factors contributing to TCF repression and coactivators working with β-catenin to regulate Wnt targets. In addition, three variations of the standard transcriptional switch model will be discussed. One is the Wnt/β-catenin symmetry pathway in Caenorhabditis elegans, where Wnt-mediated nuclear efflux of TCF is crucial for activation of targets. Another occurs in vertebrates, where distinct TCF family members are associated with repression and activation, and recent evidence suggests that Wnt signaling facilitates a "TCF exchange" on WRE chromatin. Finally, a "reverse switch" mechanism for target genes that are directly repressed by Wnt/β-catenin signaling occurs in Drosophila cells. The diversity of TCF regulatory mechanisms may help to explain how a small group of transcription factors can function in so many different contexts to regulate target gene expression.

Parallel duplication and partial subfunctionalization of β-catenin/armadillo during insect evolution

β-Catenin is a multifunctional scaffolding protein with roles in Wnt signaling, cell adhesion, and centrosome separation. Here, we report on independent duplications of the insect β-Catenin ortholog armadillo (arm) in the red flour beetle Tribolium castaneum and the pea aphid Acyrthosiphon pisum. Detailed sequence analysis shows that in both species, one paralog lost critical residues of the α-Catenin binding domain, which is essential for cell adhesion, and accumulated a dramatically higher number of amino acid substitutions in the central Arm repeat domain. Residues associated with aspects of Wnt signaling, however, are conserved in both paralogs. Consistent with these molecular signatures, the effects of specific and combinatorial knockdown experiments in the Tribolium embryo indicate that the duplication resulted in redundant involvement in Wnt signaling of both β-Catenin paralogs but differential inheritance of the ancestral cell adhesion and centrosome separation functions. We conclude that the duplicated pea aphid and flour beetle β-catenin genes experienced partial subfunctionalization, which appears to be evolutionarily favored. Providing first evidence of genetic separability of the cell adhesion and centrosome separation functions, the duplicated Tribolium and Acyrthosiphon arm paralogs offer new inroads for context-specific analyses of β-Catenin. Our data also revealed the conservation of a C-terminally truncated Arm isoform in both singleton and duplicated homologs, suggesting an as yet unexplored role in Wnt signaling.

Distinct and mutually inhibitory binding by two divergent β-catenins coordinates TCF levels and activity in C. elegans

Wnt target gene activation in C. elegans requires simultaneous elevation of β-catenin/SYS-1 and reduction of TCF/POP-1 nuclear levels within the same signal-responsive cell. SYS-1 binds to the conserved N-terminal β-catenin-binding domain (CBD) of POP-1 and functions as a transcriptional co-activator. Phosphorylation of POP-1 by LIT-1, the C. elegans Nemo-like kinase homolog, promotes POP-1 nuclear export and is the main mechanism by which POP-1 nuclear levels are lowered. We present a mechanism whereby SYS-1 and POP-1 nuclear levels are regulated in opposite directions, despite the fact that the two proteins physically interact. We show that the C terminus of POP-1 is essential for LIT-1 phosphorylation and is specifically bound by the diverged β-catenin WRM-1. WRM-1 does not bind to the CBD of POP-1, nor does SYS-1 bind to the C-terminal domain. Furthermore, binding of WRM-1 to the POP-1 C terminus is mutually inhibitory with SYS-1 binding at the CBD. Computer modeling provides a structural explanation for the specificity in WRM-1 and SYS-1 binding to POP-1. Finally, WRM-1 exhibits two independent and distinct molecular functions that are novel for β-catenins: WRM-1 serves both as the substrate-binding subunit and an obligate regulatory subunit for the LIT-1 kinase. Mutual inhibitory binding would result in two populations of POP-1: one bound by WRM-1 that is LIT-1 phosphorylated and exported from the nucleus, and another, bound by SYS-1, that remains in the nucleus and transcriptionally activates Wnt target genes. These studies could provide novel insights into cancers arising from aberrant Wnt activation.

The β-catenin HMP-2 functions downstream of Src in parallel with the Wnt pathway in early embryogenesis of C. elegans

The Wnt and Src pathways are widely used signal transduction pathways in development. β-catenin is utilized in both pathways, as a signal transducer and a component of the cadherin cell adhesion complex, respectively. A C. elegans β-catenin HMP-2 is involved in cell adhesion, but its signaling role has been unknown. Here, we report that in early embryogenesis HMP-2 acts as a signaling molecule in the Src signal. During early embryogenesis in C. elegans, the Wnt and Src pathways are redundantly involved in endoderm induction at the four-cell stage and spindle orientation in an ABar blastomere. RNAi experiments demonstrated that HMP-2 functions in the Src pathway, but in parallel with the Wnt pathway in these processes. HMP-2 localized at the cell boundaries and nuclei, and its localization at cell boundaries was negatively regulated by SRC-1. In addition, HMP-2 was Tyr-phosphorylated in a SRC-1-dependent manner in vivo. Taken together, we propose that HMP-2 functions downstream of the Src signaling pathway and contribute to endoderm induction and ABar spindle orientation, in parallel with the Wnt signaling pathway.

Functional analyses of vertebrate TCF proteins in C. elegans embryos

In the canonical Wnt pathway, signaling results in the stabilization and increased levels of β-catenin in responding cells. β-catenin then enters the nucleus, functioning as a coactivator for the Wnt effector, TCF/LEF protein. In the absence of Wnt signaling, TCF is complexed with corepressors, together repressing Wnt target genes. In C. elegans, Wnt signaling specifies the E blastomere to become the endoderm precursor. Activation of endoderm genes in E requires not only an increase in β-catenin level, but a concomitant decrease in the nuclear level of POP-1, the sole C. elegans TCF. A decrease in nuclear POP-1 levels requires Wnt-induced phosphorylation of POP-1 and 14-3-3 protein-mediated nuclear export. Nuclear POP-1 levels remain high in the sister cell of E, MS, where POP-1 represses the expression of endoderm genes. Here we express three vertebrate TCF proteins (human TCF4, mouse LEF1 and Xenopus TCF3) in C. elegans embryos and compare their localization, repression and activation functions to POP-1. All three TCFs are localized to the nucleus in C. elegans embryos, but none undergoes Wnt-induced nuclear export. Although unable to undergo Wnt-induced nuclear export, human TCF4, but not mouse LEF1 or Xenopus TCF3, can repress endoderm genes in MS, in a manner very similar to POP-1. This repressive activity requires that human TCF4 recognizes specific promoter sequences upstream of endoderm genes and interacts with C. elegans corepressors. Domain swapping identified two regions of POP-1 that are sufficient to confer nuclear asymmetry to human TCF4 when swapped with its corresponding domains. Despite undergoing Wnt-induced nuclear export, the human TCF4/POP-1 chimeric protein continues to function as a repressor for endoderm genes in E, a result we attribute to the inability of hTCF4 to bind to C. elegans β-catenin. Our results reveal a higher degree of species specificity among TCF proteins for coactivator interactions than for corepressor interactions, and uncover a basic difference between how POP-1 and human TCF4 steady state nuclear levels are regulated.

The C. elegans SoxC protein SEM-2 opposes differentiation factors to promote a proliferative blast cell fate in the postembryonic mesoderm

The proper development of multicellular organisms requires precise regulation and coordination of cell fate specification, cell proliferation and differentiation. Abnormal regulation and coordination of these processes could lead to disease, including cancer. We have examined the function of the sole C. elegans SoxC protein, SEM-2, in the M lineage, which produces the postembryonic mesoderm. We found that SEM-2/SoxC is both necessary and sufficient to promote a proliferating blast cell fate, the sex myoblast fate, over a differentiated striated bodywall muscle fate. A number of factors control the specific expression of sem-2 in the sex myoblast precursors and their descendants. This includes direct control of sem-2 expression by a Hox-PBC complex. The crucial nature of the HOX/PBC factors in directly enhancing expression of this proliferative factor in the C. elegans M lineage suggests a possible more general link between Hox-PBC factors and SoxC proteins in regulating cell proliferation.

Armadillo-repeat protein functions: questions for little creatures

Armadillo (ARM)-repeat proteins form a large family with diverse and fundamental functions in many eukaryotes. ARM-repeat proteins have largely been characterised in multicellular organisms and much is known about how a subset of these proteins function. The structure of ARM-repeats allows proteins containing them to be functionally very versatile. Are the ARM-repeat proteins in 'little creatures' as multifunctional as their better-studied relatives? The time is now right to start analysing ARM-repeat proteins in these new systems to better understand their cell biology. Here, we review recent advances in understanding the many cellular roles of both well-known and novel ARM-repeat proteins.

A new look at TCF and beta-catenin through the lens of a divergent C. elegans Wnt pathway

The canonical Wnt/beta-catenin pathway is extensively characterized, broadly conserved, and clinically important. In this review, we describe the C. elegans Wnt/beta-catenin asymmetry pathway and suggest that some of its unusual features may have important implications for the canonical Wnt/beta-catenin pathway.

A conserved Six-Eya cassette acts downstream of Wnt signaling to direct non-myogenic versus myogenic fates in the C. elegans postembryonic mesoderm

The subdivision of mesodermal cells into muscle and non-muscle cells is crucial to animal development. In the C. elegans postembryonic mesoderm, this subdivision is a result of an asymmetric cell division that leads to the formation of striated body wall muscles and non-muscle coelomocytes. Here we report that the Six homeodomain protein CEH-34 and its cofactor Eyes Absent, EYA-1, function synergistically to promote the non-muscle fate in cells also competent to form muscles. We further show that the asymmetric expression of ceh-34 and eya-1 is regulated by a combination of 1) mesodermal intrinsic factors MAB-5, HLH-1 and FOZI-1, 2) differential POP-1 (TCF/LEF) transcriptional activity along the anterior-posterior axis, and 3) coelomocyte competence factor(s). These factors are conserved in both vertebrates and invertebrates, suggesting a conserved paradigm for mesoderm development in metazoans.

The long and the short of Wnt signaling in C. elegans

The simplicity of C. elegans makes it an outstanding system to study the role of Wnt signaling in development. Many asymmetric cell divisions in C. elegans require the Wnt/beta-catenin asymmetry pathway. Recent studies confirm that SYS-1 is a structurally and functionally divergent beta-catenin, and implicate lipids and retrograde trafficking in maintenance of WRM-1/beta-catenin asymmetry. Wnts also regulate short-range events such as spindle rotation and gastrulation, and a PCP-like pathway regulates asymmetric divisions. Long-range, cell non-autonomous Wnt signals regulate vulval induction. Both short-range and long-range Wnt signal s are regulated by recycling of MIG-14/Wntless via the retromer complex. These studies indicate that C. elegans continues to be useful for identifying new, conserved mechanisms underlying Wnt signaling in metazoans.