Potential Transmembrane Domains Research Articles

Efficient integration of transmembrane domains depends on the folding properties of the upstream sequences

The topology of most membrane proteins is defined by the successive integration of α-helical transmembrane domains at the Sec61 translocon. The translocon provides a pore for the transfer of polypeptide segments across the membrane while giving them lateral access to the lipid. For each polypeptide segment of ∼20 residues, the combined hydrophobicities of its constituent amino acids were previously shown to define the extent of membrane integration. Here, we discovered that different sequences preceding a potential transmembrane domain substantially affect its hydrophobicity requirement for integration. Rapidly folding domains, sequences that are intrinsically disordered or very short or capable of binding chaperones with high affinity, allow for efficient transmembrane integration with low-hydrophobicity thresholds for both orientations in the membrane. In contrast, long protein fragments, folding-deficient mutant domains, and artificial sequences not binding chaperones interfered with membrane integration, requiring higher hydrophobicity. We propose that the latter sequences, as they compact on their hydrophobic residues, partially folded but unable to reach a native state, expose hydrophobic surfaces that compete with the translocon for the emerging transmembrane segment, reducing integration efficiency. The results suggest that rapid folding or strong chaperone binding is required for efficient transmembrane integration.

Casein Kinase 1δ Stabilizes Mature Axons by Inhibiting Transcription Termination of Ankyrin.

After axon outgrowth and synapse formation, the nervous system transitions to a stable architecture. In C.elegans, this transition is marked by the appearance of casein kinase 1δ (CK1δ) in the nucleus. In CK1δ mutants, neurons continue to sprout growth cones into adulthood, leading to a highly ramified nervous system. Nervous system architecture in these mutants is completely restored by suppressor mutations in ten genes involved in transcription termination. CK1δ prevents termination by phosphorylating and inhibiting SSUP-72. SSUP-72 would normally remodel the C-terminal domain of RNA polymerase in anticipation of termination. The antitermination activity of CK1δ establishes the mature state of a neuron by promoting the expression of the long isoform of a single gene, the cytoskeleton protein Ankyrin.

RPW8/HR repeats control NLR activation in Arabidopsis thaliana.

In many plant species, conflicts between divergent elements of the immune system, especially nucleotide-binding oligomerization domain-like receptors (NLR), can lead to hybrid necrosis. Here, we report deleterious allele-specific interactions between an NLR and a non-NLR gene cluster, resulting in not one, but multiple hybrid necrosis cases in Arabidopsis thaliana. The NLR cluster is RESISTANCE TO PERONOSPORA PARASITICA 7 (RPP7), which can confer strain-specific resistance to oomycetes. The non-NLR cluster is RESISTANCE TO POWDERY MILDEW 8 (RPW8) / HOMOLOG OF RPW8 (HR), which can confer broad-spectrum resistance to both fungi and oomycetes. RPW8/HR proteins contain at the N-terminus a potential transmembrane domain, followed by a specific coiled-coil (CC) domain that is similar to a domain found in pore-forming toxins MLKL and HET-S from mammals and fungi. C-terminal to the CC domain is a variable number of 21- or 14-amino acid repeats, reminiscent of regulatory 21-amino acid repeats in fungal HET-S. The number of repeats in different RPW8/HR proteins along with the sequence of a short C-terminal tail predicts their ability to activate immunity in combination with specific RPP7 partners. Whether a larger or smaller number of repeats is more dangerous depends on the specific RPW8/HR autoimmune risk variant.

Cloning and characterization of UL34 gene of pseudorabies virus HB isolate

In this study, China isolate HB of pseudorabies virus (PRV) was confirmed and genotypically characterized by amplifying and sequencing of partial UL34, a conservative gene involved in the egress of nucleocapsids from the nucleus, for phylogenetic analysis. The open reading frame (orf) of UL34 of PRV HB isolate is composed of 786 nucleotides, which encoded 262 amino acids. In addition, a potential transmembrane domain (241-260 aa) and 11 potential phosphorylation sites were also found in the UL34 of PRV HB isolate. Multiple amino acids alignment indicated that UL34 proteins of PRV strains derived from different geographic origins were highly conservative, but some mutations were also found. Phylogenetic analysis based on UL34 protein indicated that PRV HB strain was evolutionarily distinct from other recent China strains sequenced so far, forming a single clade within the phylogeny. Moreover, PRV HB isolate had close evolutionary relationship with BoHV-1 and BoHV-5 within the Alphaherpesvirinae. Taken together, these results indicated that PRV strains were in the progress of evolution. This study has expanded the knowledge of genetic profiles of PRV strains.

Subcelullar localization of proteins associated with Prune dwarf virus replication

Prune dwarf virus (PDV) is one of the most dangerous pathogens of fruit trees worldwide. One of the most important proteins required for PDV infection is replicase. (P1 protein) which anchored viral RNA and builds replication complex along with RNA depended polymerase. Despite the importance of PDV as a pathogen, our knowledge regarding tissue/cellular localization and structure of PDV P1 protein is still incomplete. The aim of this work was to localize replicase distribution in leaf tissues and cells by immunofluorescent and immunogold labeling of Nicotiana tobaccum cv Samsun and development of a 3D model of PDV replicase. In this paper we demonstrate that PDV replication, is similar to that of Alfalfa mosaic virus and is strongly connected with tonoplasts. In addition, PDV replicase and coat protein (CP) were also found to be strongly associated with membranes of endoplasmic reticulum and, indicating the potential involvement of these membrane structures in the processes related to viral infection. Bioinformatic analyzes based on 3D modeling and structure prediction revealed that P1 protein has a potential transmembrane domain which enables protein anchoring to tonoplast during replication complex assembly.

New Insights into Molecular Organization of Human Neuraminidase-1: Transmembrane Topology and Dimerization Ability.

Neuraminidase 1 (NEU1) is a lysosomal sialidase catalyzing the removal of terminal sialic acids from sialyloconjugates. A plasma membrane-bound NEU1 modulating a plethora of receptors by desialylation, has been consistently documented from the last ten years. Despite a growing interest of the scientific community to NEU1, its membrane organization is not understood and current structural and biochemical data cannot account for such membrane localization. By combining molecular biology and biochemical analyses with structural biophysics and computational approaches, we identified here two regions in human NEU1 - segments 139–159 (TM1) and 316–333 (TM2) - as potential transmembrane (TM) domains. In membrane mimicking environments, the corresponding peptides form stable α-helices and TM2 is suited for self-association. This was confirmed with full-size NEU1 by co-immunoprecipitations from membrane preparations and split-ubiquitin yeast two hybrids. The TM2 region was shown to be critical for dimerization since introduction of point mutations within TM2 leads to disruption of NEU1 dimerization and decrease of sialidase activity in membrane. In conclusion, these results bring new insights in the molecular organization of membrane-bound NEU1 and demonstrate, for the first time, the presence of two potential TM domains that may anchor NEU1 in the membrane, control its dimerization and sialidase activity.

Investigating the Role of Transmembrane Domain Cysteine Residues in the Organization of TNF Receptors

We recently showed that disulfide bond formation via cysteine residues in the transmembrane (TM) domains of the long isoform of Death Receptor 5 play a significant role in receptor homodimerization and activation. This is significant because the dominant paradigm in TNF Receptor signaling had been that receptor trimers, not dimers, are the signaling competent oligomeric state. Here, we surveyed the full TNF Receptor superfamily and found that potential TM domain disulfide bonds exist in approximately one third of the superfamily members. To investigate the broader importance of these cysteine residues and the potential for disulfide bond formation in the TNF Receptor superfamily, we studied Fas and TNF-Receptor 1 in cells. We also performed computational calculations (potential of mean force) to explore the thermodynamics of conformational changes of disulfide-bonded TM domain dimers. Additionally, we performed a bioinformatics study on transmembrane domains to further investigate the prevalence of TM domain cysteine residues and potential disulfide bonded TM dimers.

Spatial and temporal distribution of Patched-related protein in the Drosophila embryo

Patched-related (Ptr) encodes a protein with 12 potential transmembrane domains and a sterol-sensing domain that is closely related in predicted topology and domain organization to Patched, the canonical receptor of the Hedgehog pathway. Here we describe the production of an antibody specific for Drosophila Ptr and analyse its spatial and temporal distribution in the embryo. We find that at early developmental stages Ptr is predominantly localized at cell periphery but later on it becomes strongly and almost exclusively expressed in hemocytes. Interestingly Ptr null mutant embryos died without hatching. Our findings suggest that Ptr plays an essential function in Drosophila development, perhaps as a new receptor of embryonic hemocytes.

TAL effectors and the executor R genes.

Transcription activator-like (TAL) effectors are bacterial type III secretion proteins that function as transcription factors in plants during Xanthomonas/plant interactions, conditioning either host susceptibility and/or host resistance. Three types of TAL effector associated resistance (R) genes have been characterized—recessive, dominant non-transcriptional, and dominant TAL effector-dependent transcriptional based resistance. Here, we discuss the last type of R genes, whose functions are dependent on direct TAL effector binding to discrete effector binding elements in the promoters. Only five of the so-called executor R genes have been cloned, and commonalities are not clear. We have placed the protein products in two groups for conceptual purposes. Group 1 consists solely of the protein from pepper, BS3, which is predicted to have catalytic function on the basis of homology to a large conserved protein family. Group 2 consists of BS4C-R, XA27, XA10, and XA23, all of which are relatively short proteins from pepper or rice with multiple potential transmembrane domains. Group 2 members have low sequence similarity to proteins of unknown function in closely related species. Firm predictions await further experimentation on these interesting new members to the R gene repertoire, which have potential broad application in new strategies for disease resistance.

A Unique C-terminal Domain Allows Retention of Matrix Metalloproteinase-27 in the Endoplasmic Reticulum

Matrix metalloproteinase-27 (MMP-27) is poorly characterized. Sequence comparison suggests that a C-terminal extension (CTE) includes a potential transmembrane domain as in some membrane-type (MT)-MMPs. Having noticed that MMP-27 was barely secreted, we investigated its subcellular localization and addressed CTE contribution for MMP-27 retention. Intracellular MMP-27 was sensitive to endoglycosidase H. Subcellular fractionation and confocal microscopy evidenced retention of endogenous MMP-27 or recombinant rMMP-27 in the endoplasmic reticulum (ER) with locked exit across the intermediate compartment (ERGIC). Conversely, truncated rMMP-27 without CTE accessed downstream secretory compartments (ERGIC and Golgi) and was constitutively secreted. CTE addition to rMMP-10 (a secreted MMP) caused ER retention and blocked secretion. Addition of a PKA target sequence to the cytosolic C-terminus of transmembrane MT1-MMP/MMP-14 led to effective phosphorylation upon forskolin stimulation, but not for MMP-27, excluding transmembrane anchorage. Moreover, MMP-27 was protected from digestion by proteinase K. Finally, MT1-MMP/MMP-14 but neither endogenous nor recombinant MMP-27 partitioned in the detergent phase after Triton X-114 extraction, indicating that MMP-27 is not an integral membrane protein. In conclusion, MMP-27 is efficiently retained within the ER due to its unique CTE, which does not lead to stable membrane insertion. This could represent a novel ER retention system.

A novel marker, ARM58, confers antimony resistance to Leishmania spp.

Protozoa of the Leishmania genus cause a variety of disease forms that rank at the top of the list of neglected tropical diseases. Anti-leishmanial drugs based on pentavalent antimony have been the mainstay of therapy for over 60years and resistance against them is increasingly encountered in the field. The biochemical basis for this is poorly understood and likely diverse. No stringent correlation between genetic markers and antimony resistance has so far been shown, prompting us to use a functional cloning approach to identify markers of resistance. Using gene libraries derived from drug-resistant and drug-sensitive Leishmania braziliensis clinical isolates in a functional cloning strategy, we repeatedly selected one gene locus located on chromosome 20 whose amplification confers increased antimony (III) resistance in vitro to an otherwise sensitive L. braziliensis clone. The gene responsible for the effect encodes a previously hypothetical protein that we dubbed LbrARM58. It comprises four repeats of a domain of unknown function, DUF1935, one of them harbouring a potential trans-membrane domain. The gene is so far unique to the Leishmania genus, while a structurally related gene without antimony resistance functionality is also found in Trypanosoma spp. Overexpression of LbrARM58 also confers antimony resistance to promastigotes and intracellular amastigotes of the related species Leishmania infantum, indicating a conserved function in Old World and New World Leishmania species. Our results also show that in spite of their RNAi system, L. braziliensis promastigotes can serve as acceptor cells for episomally propagated cosmid libraries, at least for the initial stages of functional cloning efforts.

Computational and Experimental Analyses of the Transmembrane Domain Dimerization of IRE1α Protein

The Inositol-requiring 1α protein (IRE1α) is a type I transmembrane protein essential for the endoplasmic reticulum (ER) unfolded protein response that promotes cell survival by reducing the level of misfolded/unfolded proteins. IRE1α consists of an N-terminal luminal domain, a single-pass transmembrane (TM) spanning segment and a cytosolic region, which contains a kinase domain and an endoribonuclease (RNase) domain. Upon ER stress, the IRE1α protein dimerizes to activate its cytoplasmic kinase and RNase domains. Dimerization by either the luminal or the cytosolic domains can enhance IRE1α enzymatic activity. Current information on the TM domain of the IRE1α protein does not exist. Therefore, we designed a model TM segment which contains the potential TM domain sequence predicted by several TM prediction servers. using circular dichroism spectroscopy, we confirmed that the model TM peptide has α-helical conformation in POPC liposome. SDS-PAGE and FRET analyses further showed that the TM peptide forms dimers and higher-order oligomers. Molecular dynamics (MD) simulations were performed to determine potential mechanism(s) wherein the TM domain of IRE1α could dimerize and regulate IRE1α activity. We arbitrarily assigned three different conformations (face-to-face, face-to-back, and back-to-back) and embedded two TM molecules in POPC bilayers for each conformation in the MD simulations. The simulations revealed that the back-to-back is the most favorable conformation for inducing dimerization of the TM peptide. In addition, the computational results predicted that the TM dimerization is mediated by the SxxLxxx sequence motif. Further mutation analyses in cells showed that the TM domain plays a key role in regulating the dimerization as well as the protein activities. The combination of computational and experimental studies provided potential insight into how the TM domain could impact the dimerization of IRE1α.

Investigation of ORF0 as a sensitive alternative diagnostic segment to detect Sugarcane yellow leaf virus

The worldwide distribution of Sugarcane yellow leaf virus (SCYLV) has led several research groups to study the function of the viral genome, the role of open reading frames (ORFs), their influence on virus accumulation and methods for diagnosis. The detection of SCYLV is usually based on the viral coat protein whether using serological and/or molecular techniques. In this study, ORF0 has been used as a diagnostic segment for SCYLV due to its highly conserved region in all SCYLV isolates. The results revealed that, ORF0 was expressed more consistently in all cultivars. In contrast, the expression of the coat protein varied. The RNA poleroviruses sequences of ORF0 were variable compared with the same segment of SCYLV populations. Analysis of the amino acid sequence of the ORF0 translation product revealed the presence of a potential transmembrane domain. The relatively high content of hydrophobic amino acids in the ORF0 protein further suggests that it may serve as a membrane anchor for the replication complex.

The Chimeric Approach Reveals That Differences in the TRPV1 Pore Domain Determine Species-specific Sensitivity to Block of Heat Activation

The capsaicin-, heat-, and proton-activated ion channel TRPV1, a member of the transient receptor potential cation channel family is a polymodal nociceptor. For almost a decade, TRPV1 has been explored by the pharmaceutical industry as a potential target for example for pain conditions. Antagonists which block TRPV1 activation by capsaicin, heat, and protons were developed by a number of pharmaceutical companies. The unexpected finding of hyperthermia as an on-target side effect in clinical studies using polymodal TRPV1 antagonists has prompted companies to search for ways to circumvent hyperthermia, for example by the development of modality-selective antagonists. The significant lack of consistency of the pharmacology of many TRPV1 antagonists across different species has been a further obstacle. JYL-1421 for example was shown to block capsaicin and heat responses in human and monkey TRPV1 while it was largely ineffective in blocking heat responses in rat TRPV1. These findings suggested structural dissimilarities between different TRPV1 species relevant for small compound antagonism for example of heat activation. Using a chimeric approach (human and rat TRPV1) in combination with a novel FLIPR-based heat activation assay and patch-clamp electrophysiology we have identified the pore region as being strongly linked to the observed species differences. We demonstrate that by exchanging the pore domains JYL-1421, which is modality-selective in rat can be made modality-selective in human TRPV1 and vice-versa.

Identification and functional characterization of an ovarian aquaporin from the cockroachBlattella germanicaL. (Dictyoptera, Blattellidae)

Aquaporins (AQPs) are membrane proteins that form water channels, allowing rapid movement of water across cell membranes. AQPs have been reported in species of all life kingdoms and in almost all tissues, but little is known about them in insects. Our purpose was to explore the occurrence of AQPs in the ovary of the phylogenetically basal insect Blattella germanica (L.) and to study their possible role in fluid homeostasis during oogenesis. We isolated an ovarian AQP from B. germanica (BgAQP) that has a deduced amino acid sequence showing six potential transmembrane domains, two NPA motifs and an ar/R constriction region, which are typical features of the AQP family. Phylogenetic analyses indicated that BgAQP belongs to the PRIP group of insect AQPs, previously suggested to be water specific. However, ectopic expression of BgAQP in Xenopus laevis oocytes demonstrated that this AQP transports water and modest amounts of urea, but not glycerol, which suggests that the PRIP group of insect AQPs may have heterogeneous solute preferences. BgAQP was shown to be highly expressed in the ovary, followed by the fat body and muscle tissues, but water stress did not significantly modify the ovarian expression levels. RNA interference (RNAi) reduced BgAQP mRNA levels in the ovary but the oocytes developed normally. The absence of an apparent ovarian phenotype after BgAQP RNAi suggests that other functionally redundant AQPs that were not silenced in our experiments might exist in the ovary of B. germanica.

Expression and localization of aquaporin 1b during oocyte development in the Japanese eel (Anguilla japonica)

To elucidate the molecular mechanisms underling hydration during oocyte maturation, we characterized the structure of Japanese eel (Anguilla japonica) novel-water selective aquaporin 1 (AQP1b) that thought to be involved in oocyte hydration. The aqp1b cDNA encodes a 263 amino acid protein that includes the six potential transmembrane domains and two Asn-Pro-Ala motifs. Reverse transcription-polymerase chain reaction showed transcription of Japanese eel aqp1b in ovary and testis but not in the other tissues. In situ hybridization studies with the eel aqp1b cRNA probe revealed intense eel aqp1b signal in the oocytes at the perinucleolus stage and the signals became faint during the process of oocyte development. Light microscopic immunocytochemical analysis of ovary revealed that the Japanese eel AQP1b was expressed in the cytoplasm around the yolk globules which were located in the peripheral region of oocytes during the primary yolk globule stage; thereafter, the immunoreactivity was observed throughout the cytoplasm of oocyte as vitellogenesis progressed. The immunoreactivity became localized around the large membrane-limited yolk masses which were formed by the fusion of yolk globules during the oocyte maturation phase. These results together indicate that AQP1b, which is synthesized in the oocyte during the process of oocyte growth, is essential for mediating water uptake into eel oocytes.

Identification and characterization of two genes encoding plasma membrane H+-ATPase in Cucumis sativus L.

Two genes (CsHA2, CsHA3) homolog to the plasma membrane H+-ATPase encoding sequences have been identified in cucumber cells. The full-length cDNA of these sequences comprise an open reading frame that encodes about 950 amino acid polypeptide with several potential transmembrane domains. Both sequences share a high homology with putative plasma membrane-associated proton pumps in higher plants, ranging from 84% with that of Arabidopsis thaliana to 90% with Sesbania rostrata. Phylogenetic analysis grouped the two isoforms into one group (subfamilies II) together with Kosteletzkya virginica KVATP1, Sesbania rostrata SRHA4, tobacco PMA4 and rice OSA7. The expression of CsHA isoforms at the mRNA level showed they different organ pattern. Transcript level of CsHA2 was detected in all vegetative organs, but more abundantly in leaves than in roots, while CsHA3 expression was limited only to the roots in immature as well as in mature plants. Moreover, the RT-PCR analysis of generative organs (flowers), fruits and dry seeds revealed differential expression pattern for CsHA2 and CsHA3 suggesting that these proteins could be involved in separate physiological processes.

Properties of the TRPML3 Channel Pore and Its Stable Expansion by the Varitint-Waddler-causing Mutation

TRPML3 is a H(+)-regulated Ca(2+) channel that shuttles between intracellular compartments and the plasma membrane. The A419P mutation causes the varitint-waddler phenotype as a result of gain-of-function (GOF). The mechanism by which A419P leads to GOF is not known. Here, we show that the TRPML3 pore is dynamic when conducting Ca(2+) to change its conductance and permeability, which appears to be mediated by trapping Ca(2+) within the pore. The pore properties can be restored by strong depolarization or by conducting Na(+) through the pore. The A419P mutation results in expanded channel pore with altered permeability that limits modulation of the pore by Ca(2+). This effect is specific for the A419P mutation and is not reproduced by other GOF mutations, including A419G, H283A, and proline mutations in the fifth transmembrane domain. These findings describe a novel mode of a transient receptor potential channel behavior and suggest that pore expansion by the A419P mutation may contribute to the varitint-waddler phenotype.

Identification of a polymorphic collagen-like protein in the crustacean bacteria Pasteuria ramosa

Pasteuria ramosa is a spore-forming bacterium that infects Daphnia species. Previous results demonstrated a high specificity of host clone/parasite genotype interactions. Surface proteins of bacteria often play an important role in attachment to host cells prior to infection. We analyzed surface proteins of P. ramosa spores by two-dimensional gel electrophoresis. For the first time, we prove that two isolates selected for their differences in infectivity reveal few but clear-cut differences in protein patterns. Using internal sequencing and LC/MS/MS, we identified a collagen-like protein named Pcl1a ( Pasteuria collagen-like protein 1a). This protein, reconstructed with the help of Pasteuria genome sequences, contains three domains: a 75-amino-acid amino-terminal domain with a potential transmembrane helix domain, a central collagen-like region (CLR) containing Gly-Xaa-Yaa (GXY) repeats, and a 7-amino-acid carboxy-terminal domain. The CLR region is polymorphic among the two isolates with amino-acid substitutions and a variable number of GXY triplets. Collagen-like proteins are rare in prokaryotes, although they have been described in several pathogenic bacteria, including Bacillus cereus, Bacillus anthracis and Bacillus thuringiensis, closely related to Pasteuria species, in which they could be involved in the adherence of bacteria to host cells.

Overexpression of millet ZIP-like gene (SiPf40) affects lateral bud outgrowth in tobacco and millet

A SiPf40 gene was identified from an immature seed cDNA library of foxtail millet (Setaria italica). This gene encodes for a 29.4 KDa protein containing eight potential transmembrane domains and a highly conserved ZIP signature motif typical of ZIPs (zinc or iron transporter proteins) family. Other SiPf40 potential homologous genes have also been identified in rice, maize, wheat and Arabidopsis by Southern analysis. Expression data showed that this gene is preferentially expressed in millet hypocotyl and bud; however, a minimal level of constitutive expression could be detected in other foxtail millet tissues. Overexpression of SiPf40 gene causes extra branches in tobacco and extra tillering in millet associated with vessel enlarging and xylary fibers increasing, whereas the tiller number decreases in SiPf40 gene silenced plants. Moreover, IAA content decreased significantly in shoot apex of the transgenic tobacco overexpressing SiPf40 gene. All together, these morphological alterations indicate that SiPf40 gene is essential for lateral shoots growth.