New paradigm in ankyrin repeats: Beyond protein-protein interaction module

Islam, Zeyaul; Nagampalli, Raghavendra Sashi Krishna; Fatima, Mahvish; Ashraf, Ghulam Md

doi:10.1016/j.ijbiomac.2017.11.101

Cited by 35 publications

(31 citation statements)

References 87 publications

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“…However, most commonly, the permissivity of known eukaryotic hosts to giant viruses differs considerably according to the host strain or to the viral family or lineage, as previously described for mimiviruses, pandoraviruses, and Bodo saltans virus 32,48 . The analysis of giant virus homologs in the V. vermiformis genome showed here that the most represented sequences were those of giant viruses that grew in V. vermiformis, including faustovirus isolates and Orpheovirus IHUMI-LCC2, whereas a small proportion included genes from giant viruses isolated from Acanthamoeba spp.. Ankyrin repeats, which are associated with protein-protein interactions, were highly represented among V. vermiformis genes best matching with giant viruses 49,50 in addition to DUF4114 domains which are conserved domains that help to adapt to nutrient-depleted conditions by down-regulating protein biosynthesis 51 . Overall, the phylogenies of genes predicted to have arisen www.nature.com/scientificreports www.nature.com/scientificreports/ through lateral sequence transfer illustrate the complexity of sequence exchanges between amoebae, bacteria (including CPR), and giant viruses.…”

Section: Discussionmentioning

confidence: 83%

Vermamoeba vermiformis CDC-19 draft genome sequence reveals considerable gene trafficking including with candidate phyla radiation and giant viruses

Chelkha

Hasni

Louazani

et al. 2020

Sci Rep

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Vermamoeba vermiformis is a predominant free-living amoeba in human environments and amongst the most common amoebae that can cause severe infections in humans. it is a niche for numerous amoeba-resisting microorganisms such as bacteria and giant viruses. Differences in the susceptibility to these giant viruses have been observed. V. vermiformis and amoeba-resisting microorganisms share a sympatric lifestyle that can promote exchanges of genetic material. This work analyzed the first draft genome sequence of a V. vermiformis strain (CDC-19) through comparative genomic, transcriptomic and phylogenetic analyses. the genome of V. vermiformis is 59.5 megabase pairs in size, and 22,483 genes were predicted. A high proportion (10% (n = 2,295)) of putative genes encoded proteins showed the highest sequence homology with a bacterial sequence. the expression of these genes was demonstrated for some bacterial homologous genes. In addition, for 30 genes, we detected best BLAST hits with members of the Candidate Phyla Radiation. Moreover, 185 genes (0.8%) best matched with giant viruses, mostly those related to the subfamily Klosneuvirinae (101 genes), in particular Bodo saltans virus (69 genes). Lateral sequence transfers between V. vermiformis and amoeba-resisting microorganisms were strengthened by Sanger sequencing, transcriptomic and phylogenetic analyses. This work provides important insights and genetic data for further studies about this amoeba and its interactions with microorganisms. Amoebozoa species are widely distributed in different environments from terrestrial to aquatic ecosystems, where they can play important ecological roles 1,2. Members of the family Hartmannellidae are frequently detected along with a few other amoebae belonging to different genera of the taxon Amoebozoa 3. Vermamoeba vermiformis, a free-living amoeba of the family Hartmannellidae, formerly named Hartmannella vermiformis, was first isolated in freshwater from the Pigeon Lake, Wisconsin, and the Kankakee River, Indiana (United States) 4. V. vermiformis was thereafter commonly found in fresh surface water 5 , and also in tap water, bottled mineral water, thermal water, and recreational water environments such as fountains and swimming pools 6-8. Its density in drinking water sources and biofilms is higher than that of Acanthamoeba castellanii 9. V. vermiformis has two-stage life, switching between trophozoite and cystic form 3. Free-living amoebae (FLA) are commonly in contact with animals including humans. V. vermiformis was found to be the predominant amoeba in human environments 10,11 , and has been isolated more frequently from different hospital water systems than Acanthamoeba spp. 12. This amoeba is of special interest for human health as it is able, along with other Amoebozoa members including Acanthamoeba spp., to cause severe infections such as human keratitis 13-15. Despite its prevalence in human environments and its pathogenicity in humans, the genome of V. vermiformis had not been sequenced.

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Section: Discussionmentioning

confidence: 83%

Vermamoeba vermiformis CDC-19 draft genome sequence reveals considerable gene trafficking including with candidate phyla radiation and giant viruses

Chelkha

Hasni

Louazani

et al. 2020

Sci Rep

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“…At a molecular level, all TRPCs consist of a poreloop motif, three to four NH 2 -terminal ankyrin repeat domains (ARDs), and a COOH-terminal TRP domain (Venkatachalam and Montell, 2007). The ARD is a common protein-protein interaction module, typically consisting of 33 amino acid residues, which forms a canonical helix-loop-helix fold followed by a β-hairpin loop (Islam et al, 2018). ARDs perform crucial roles in various cellular processes, including thetranscription, signal transduction, inflammatory responses, cell development, and cell cycle (Islam et al, 2018).…”

Section: The Trpc Subfamily and Their Roles In Cnsmentioning

confidence: 99%

Novel Targets for Stroke Therapy: Special Focus on TRPC Channels and TRPC6

Liu

Chen

et al. 2020

Front. Aging Neurosci.

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Stroke remains a leading cause of death, disability, and medical care burden worldwide. However, transformation from laboratory findings toward effective pharmacological interventions for clinical stroke has been unsatisfactory. Novel evidence has been gained on the underlying mechanisms and therapeutic potential related to the transient receptor potential (TRP) channels in several disorders. The TRP superfamily consists of a diverse group of Ca 2+ permeable non-selective cation channels. In particular, the members of TRP subfamilies, TRP canonical (TRPC) channels and TRPC6, have been found in different cell types in the whole body and have high levels of expression in the central nervous system (CNS). Notably, the TRPCs and TRPC6 channel have been implicated in neurite outgrowth and neuronal survival during normal development and in a range of CNS pathological conditions. Recent studies have shown that suppression of TRPC6 channel degradation prevents ischemic neuronal cell death in experimental stroke. Accumulating evidence supports the important functions of TRPC6 in brain ischemia. We have highlighted some crucial advancement that points toward an important involvement of TRPCs and TRPC6 in ischemic stroke. This review will make an overview of the TRP and TRPC channels due to their roles as targets for clinical trials and CNS disorders. Besides, the primary goal is to discuss and update the critical role of TRPC6 channels in stroke and provide a promising target for stroke prevention and therapy.

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“…One of these scaffold proteins comprises repeated proteins that are naturally used for a wide variety of protein–protein interactions. In other words, these repeat proteins act as “antibodies” in nature . The designed anykrin repeat proteins (DARPins) are composed of completely recited repeats, which usually contain 33 amino acid residues.…”

Section: Introductionmentioning

confidence: 99%

“…In other words, these repeat proteins act as "antibodies" in nature. 15,16 The designed anykrin repeat proteins (DARPins) are composed of completely recited repeats, which usually contain 33 amino acid residues. Each repeat has a single structure, which includes a beta-turn and the subsequent two antiparallel alpha helixes, and over 29 consecutive repeats that can be observed in a single protein.…”

Section: Introductionmentioning

confidence: 99%

Design and construction of a recombinant lentiviral vector with specific tropism to human epidermal growth factor‐overexpressed cancer cells: Developing a new retargeting system for lentivirus vectors

Ebrahimabadi

Shahbazi

Akbari

et al. 2019

The Journal of Gene Medicine

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Background Targeting of specific tissues and cells by viruses is one of the challenges faced by researchers. Lentiviral vectors (LVs) are one of the most promising gene delivery systems in cancer gene therapy. Therefore, we aimed to design a novel lentiviral delivery system that expresses anti‐ human epidermal growth factor 2 (HER2) designed anykrin repeat protein (DARPin) on the vector envelope to create a pseudotyped lentivirus for targeting HER2‐positive cancer cells. Methods A helper plasmid producing the viral vector envelope containing anti‐HER2 DARPin‐G3 was constructed. LV was produced by transfer vector containing green fluorescent protein (GFP) gene and helper plasmids in human embryonic kidney 293 cells. The human breast cancer cell lines SKBR3 (normal and with inhibited endocytosis) (HER2‐positive) and MDA‐MB‐231 (HER2‐negative) were transduced by the recombinant viral vector. The GFP‐based transduction rate was determined by flow cytometry and fluorescence microscopy. Results The anti‐HER2 DARPin concentration in DARPin‐LVs was significantly higher than the envelope G glycoprotein of the vesicular stomatitis virus‐LVs (non‐anti‐HER2 control) (p < 0.0001). In flow cytometry assays, the percentage of transduction by recombinant LV was significantly higher in SKBR3 cells than in SKBR3 cells with inhibited endocytosis (p = 0.0074) and MDA‐MB‐231 cells (p = 0.0037). In fluorescence microscopy assays, the percentage of transduction by new LV was significantly higher in SKBR3 cells than in SKBR3 cells with inhibited endocytosis (p = 0.0026) and MDA‐MB‐231 cells (p = 0.0014). Conclusions We constructed a new recombinant LV with a defect in cell entry directly, containing an anti‐HER2 DARPin on the vector envelope with specific tropism to HER2 receptor on HER2‐positive cancer cells. We assumed that this viral vector transduces cells via an endocytosis‐dependent process.

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New paradigm in ankyrin repeats: Beyond protein-protein interaction module

Cited by 35 publications

References 87 publications

Vermamoeba vermiformis CDC-19 draft genome sequence reveals considerable gene trafficking including with candidate phyla radiation and giant viruses

Vermamoeba vermiformis CDC-19 draft genome sequence reveals considerable gene trafficking including with candidate phyla radiation and giant viruses

Novel Targets for Stroke Therapy: Special Focus on TRPC Channels and TRPC6

Design and construction of a recombinant lentiviral vector with specific tropism to human epidermal growth factor‐overexpressed cancer cells: Developing a new retargeting system for lentivirus vectors

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