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Genome Biol,
2011]
Cullin proteins are molecular scaffolds that have crucial roles in the post-translational modification of cellular proteins involving ubiquitin. The mammalian cullin protein family comprises eight members (CUL1 to CUL7 and PARC), which are characterized by a cullin homology domain. CUL1 to CUL7 assemble multi-subunit Cullin-RING E3 ubiquitin ligase (CRL) complexes, the largest family of E3 ligases with more than 200 members. Although CUL7 and PARC are present only in chordates, other members of the cullin protein family are found in Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and yeast. A cullin protein tethers both a substrate-targeting unit, often through an adaptor protein, and the RING finger component in a CRL. The cullin-organized CRL thus positions a substrate close to the RING-bound E2 ubiquitin-conjugating enzyme, which catalyzes the transfer of ubiquitin to the substrate. In addition, conjugation of cullins with the ubiquitin-like molecule Nedd8 modulates activation of the corresponding CRL complex, probably through conformational regulation of the interactions between cullin's carboxy-terminal tail and CRL's RING subunit. Genetic studies in several model organisms have helped to unravel a multitude of physiological functions associated with cullin proteins and their respective CRLs. CRLs target numerous substrates and thus have an impact on a range of biological processes, including cell growth, development, signal transduction, transcriptional control, genomic integrity and tumor suppression. Moreover, mutations in CUL7 and CUL4B genes have been linked to hereditary human diseases.
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Neuron,
2002]
The DEG/ENaC ion channel family contributes to channels of striking functional diversity. Neuronally expressed family members include the C. elegans degenerins that mediate touch and are thought to be mechanically gated, and the mammalian ASICs, which are gated by protons. ASICs affect a range of sensory functions that includes perception of gentle touch, harsh touch, heat, sour taste, and pain. Family member ASIC1 is now implicated in long-term potentiation, suggesting that minute fluxes in synaptic pH may activate ASICs to enhance learning.
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Apoptosis,
2014]
The death associated protein kinases (DAPK) are a phylogenetically widespread family of calcium-regulated serine/threonine kinases, initially identified from their roles in apoptosis. Subsequent studies, principally in vertebrate cells or models, have elucidated the functions of the DAPK family in autophagy and tumor suppression. Invertebrate genetic model organisms such as Drosophila and C. elegans have revealed additional functions for DAPK and related kinases. In the nematode C. elegans, the sole DAPK family member DAPK-1 positively regulates starvation-induced autophagy. Genetic analysis in C. elegans has revealed that DAPK-1 also acts as a negative regulator of epithelial innate immune responses in the epidermis. This negative regulatory role for DAPK in innate immunity may be analogous to the roles of mammalian DAPK in inflammatory responses.
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Adv Exp Med Biol,
2010]
Trim-NHL proteins are defined by RING, B-Box and Coiled-coil protein motifs (referred to collectively as the Trim domain) coupled to an NHL domain. The C. elegans, D. melanogaster, mouse and human Trim-NHL proteins are potential and in several cases confirmed, E3 ubiquitin ligases. Current research is focused on identifying targets and pathways for Trim-NHL-mediated ubiquitination and in assessing the contribution of the NHL protein-protein interactiondomain for function and specificity. Several Trim-NHL proteins were discovered in screens for developmental genes in model organisms; mutations in one of the family members, Trim32, cause developmental disturbances in humans. In most instances, mutations that alter protein function map to the NHL domain. The NHL domain is a scaffold for the assembly of a translational repressor complex by the Brat proto-oncogene, a well-studied family member in Drosophila. The link to translational control is common to at least four Trim-NHLs that associate with miRNA pathway proteins. So far, two have been shown to repress (Mei-P26 and Lin41) and two to promote (NHL-2, Trim32) miRNA-mediated gene silencing. In this chapter we will describe structure-function relations for each of the proteins and then focus on the lessons being learned from these proteins about miRNA functions in development and in stem cell biology.
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FEBS J,
2021]
The Par-3/Baz family of polarity determinants is highly conserved across metazoans, and includes C. elegans PAR-3, Drosophila Bazooka (Baz), human Par-3 (PARD3) and human Par-3-like (PARD3B). The C. elegans PAR-3 protein localises to the anterior pole of asymmetrically dividing zygotes with CDC42, atypical protein kinase C (aPKC) and PAR-6. The same C. elegans 'PAR complex' can also localise in an apical ring in epithelial cells. Drosophila Baz localises to the apical pole of asymmetrically dividing neuroblasts with Cdc42-aPKC-Par-6, while in epithelial cells localises both in an apical ring with Cdc42-aPKC-Par6 as well as with E-cadherin at adherens junctions. These apical and junctional localisations have become separated in human PARD3, which is strictly apical in many epithelia, and human PARD3B, which is strictly junctional in many epithelia. We discuss the molecular basis for this fundamental difference in localisation, as well as the possible functions of Par-3/Baz family proteins as oligomeric clustering agents at the apical domain or at adherens junctions in epithelial stem cells. The evolution of Par-3 family proteins into distinct apical PARD3 and junctional PARD3B orthologs coincides with the emergence of stratified squamous epithelia in vertebrates, where PARD3B, but not PARD3, is strongly expressed in basal layer stem cells - which lack a typical apical domain. We speculate that PARD3B may contribute to clustering of E-cadherin, signalling from adherens junctions via Src family kinases, or mitotic spindle orientation by adherens junctions in response to mechanical forces.
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Biochimica et Biophysica Acta,
2004]
Proteins belonging to the Bcl-2 family function as regulators of 'life-or-death' decisions in response to various intrinsic and extrinsic stimuli. In mammals, cell death is controlled by pro- and anti-apoptotic members of the Bcl-2 family, which function upstream of the caspase cascade. Structural and functional homologues of the Bcl-2 family proteins also exist in lower eukaryotes, such as nematodes and flies. In nematodes, an anti-apoptotic Bcl-2 family protein, CED-9, functions as a potent cell death inhibitor, and a BH3-only protein, EGL-1, acts as an inhibitor of CED-9 to facilitate the spatio-temporal regulation of programmed cell death. On the other hand, the Drosophila genome encodes two Bcl-2 family proteins, Drob-1/Debcl/dBorg-1/dBok and Buffy/dBorg-2, both of which structurally belong to the pro-apoptotic group, despite abundant similarities in the cell death mechanisms between flies and vertebrates. Drob-1 acts as a pro-apoptotic factor in vitro and in vivo, and Buffy/dBorg-2 exhibits a weak anti-apoptotic function. The ancestral role of the Bcl-2 family protein may be pro-apoptotic, and the evolution of the functions of this family of proteins may be closely linked with the contribution of mitochondria to the cell death pathway.
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Trends Biochem Sci,
2002]
A family of membrane-associated proteins related to yeast Lag1p and mammalian TRAM has been identified. The family includes the protein product of CLN8, a gene mutated in progressive epilepsy with mental retardation. Mouse CLN8 is also mutated in the mnd/mnd mouse, a model for neuronal ceroid lipofuscinoses. The identification of these homologues has potential implications for our understanding of ceramide synthesis, lipid regulation and protein translocation in the endoplasmic reticulum.
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Trends Cell Biol,
2008]
The synthesis, assembly and organisation of structural and motor proteins during muscle formation requires temporal and spatial control directed by specialized chaperones. For example, alphaB-crystallin, GimC and TRiC facilitate the assembly of sarcomeric proteins such as desmin and actin. Recent studies have demonstrated that the chaperone family of UCS proteins (UNC-45-CRO1-She4p) is required for the proper function of myosin motors. Mutations in the myosin-directed chaperone
unc-45, a founding member of this family, lead to disorganisation of striated muscle in Caenorhabditiselegans. In addition to the involvement of client-specific chaperones, myofibrillogenesis also involves ubiquitin-dependent degradation of regulatory muscle proteins. Here, we highlight the interplay between chaperone activity and protein degradation in respect to the formation and maintenance of muscle during physiological and pathological conditions.
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J Physiol Paris,
2006]
Proteins of the striatin family have been identified in all multicellular animals. They are multidomain molecules containing several protein-interacting motifs. In mammals, these proteins are principally expressed in neurons with a somato-dendritic localization and high concentration in dendritic spines. Recent reports suggest that the proteins of the striatin family are molecular scaffolds that act as links between signal transduction and vesicular trafficking.
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Lakartidningen,
2002]
Recently the complete genomic sequences for three very different multicellular organisms have been published, from one nematode (Caenorhabditis elegans), one fly (Drosophila melanogaster) and human (Homo sapiens). Of course, this means a breakthrough in many ways for biological research. Summarised in this article are the findings made using these genomic sequences regarding the protein family of nuclear receptors. This is a group of transcription factors involved in many important biological processes, i.e. regulation of cholesterol homeostasis and fertility; classical members of this protein family are, amongst others, the receptors for estradiol and progesterone.