A comparative in-silico analysis of autophagy proteins in ciliates.

Abstract:

:Autophagy serves as a turnover mechanism for the recycling of redundant and/or damaged macromolecules present in eukaryotic cells to re-use them under starvation conditions via a double-membrane structure known as autophagosome. A set of eukaryotic genes called autophagy-related genes (ATGs) orchestrate this highly elaborative process. The existence of these genes and the role they play in different eukaryotes are well-characterized. However, little is known of their role in some eukaryotes such as ciliates. Here, we report the computational analyses of ATG genes in five ciliate genomes to understand their diversity. Our results show that Oxytricha trifallax is the sole ciliate which has a conserved Atg12 conjugation system (Atg5-Atg12-Atg16). Interestingly, Oxytricha Atg16 protein includes WD repeats in addition to its N-terminal Atg16 domain as is the case in multicellular organisms. Additionally, phylogenetic analyses revealed that E2-like conjugating protein Atg10 is only present in Tetrahymena thermophila. We fail to find critical autophagy components Atg5, Atg7 and Atg8 in the parasitic ciliate Ichthyophthirius multifiliis. Contrary to previous reports, we also find that ciliate genomes do not encode typical Atg1 since all the candidate sequences lack an Atg1-specific C-terminal domain which is essential for Atg1 complex formation. Consistent with the absence of Atg1, ciliates also lack other members of the Atg1 complex. However, the presence of Atg6 in all ciliates examined here may rise the possibility that autophagosome formation could be operated through Atg6 in ciliates, since Atg6 has been shown as an alternative autophagy inducer. In conclusion, our results highlight that Atg proteins are partially conserved in ciliates. This may provide a better understanding for the autophagic destruction of the parental macronucleus, a developmental process also known as programmed nuclear death in ciliates.

journal_name

PeerJ

journal_title

PeerJ

authors

Aslan E,Küçükoğlu N,Arslanyolu M

doi

10.7717/peerj.2878

subject

Has Abstract

pub_date

2017-01-17 00:00:00

pages

e2878

issn

2167-8359

pii

2878

journal_volume

5

pub_type

杂志文章

相关文献

PeerJ文献大全
  • Spermatozoon ultrastructure in two monorchiid digeneans.

    abstract::Spermatological characteristics of species from two monorchiid genera, Opisthomonorchis and Paramonorcheides, have been investigated, for the first time, by means of transmission electron microscopy. The ultrastructural study reveals that the mature spermatozoon of Opisthomonorchis dinema and Paramonorcheides selaris ...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.2488

    authors: Quilichini Y,Bakhoum AJ,Justine JL,Bray RA,Bâ CT,Marchand B

    更新日期:2016-09-20 00:00:00

  • Positive affect and age as predictors of exercise compliance.

    abstract::Physical exercise is linked to individuals whose affect profiles are invariably positive and it induces anti-apoptotic and anti-excitotoxic effects, buttressing blood-brain barrier intactness in both healthy individuals and those suffering from disorders accompanying overweight and obesity. In this regard, exercise of...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.694

    authors: Garcia D,Archer T

    更新日期:2014-12-16 00:00:00

  • Forecasting biodiversity in breeding birds using best practices.

    abstract::Biodiversity forecasts are important for conservation, management, and evaluating how well current models characterize natural systems. While the number of forecasts for biodiversity is increasing, there is little information available on how well these forecasts work. Most biodiversity forecasts are not evaluated to ...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.4278

    authors: Harris DJ,Taylor SD,White EP

    更新日期:2018-02-08 00:00:00

  • Characterizing metabolic stress-induced phenotypes of Synechocystis PCC6803 with Raman spectroscopy.

    abstract:Background:During their long evolution, Synechocystis sp. PCC6803 developed a remarkable capacity to acclimate to diverse environmental conditions. In this study, Raman spectroscopy and Raman chemometrics tools (RametrixTM) were employed to investigate the phenotypic changes in response to external stressors and correl...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.8535

    authors: Tanniche I,Collakova E,Denbow C,Senger RS

    更新日期:2020-03-30 00:00:00

  • Fluctuation and diversity of Hydromedusae (Hydrozoa, Cnidaria) in a highly productive region of the Gulf of Mexico inferred from high frequency plankton sampling.

    abstract::Hydrozoa medusae undergo blooms and seasonal fluctuations; however the drivers of such fluctuations are unknown. To understand how medusa populations fluctuate in response to seasonal factors such as temperature, salinity, dissolved oxygen, and chlorophyll a, and to enhance our taxonomic knowledge of Hydrozoa in Galve...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.7848

    authors: Pruski S,Miglietta MP

    更新日期:2019-10-08 00:00:00

  • Looking upstream: enhancers of child nutritional status in post-flood rural settings.

    abstract::Background. Child undernutrition and flooding are highly prevalent public health issues in many developing countries, yet we have little understanding of preventive strategies for effective coping in these circumstances. Education has been recently highlighted as key to reduce the societal impacts of extreme weather e...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.1741

    authors: Rodriguez-Llanes JM,Ranjan-Dash S,Mukhopadhyay A,Guha-Sapir D

    更新日期:2016-03-01 00:00:00

  • The right thalamus may play an important role in anesthesia-awakening regulation in frogs.

    abstract:Background:Previous studies have shown that the mammalian thalamus is a key structure for anesthesia-induced unconsciousness and anesthesia-awakening regulation. However, both the dynamic characteristics and probable lateralization of thalamic functioning during anesthesia-awakening regulation are not fully understood,...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.4516

    authors: Fan Y,Yue X,Xue F,Brauth SE,Tang Y,Fang G

    更新日期:2018-03-15 00:00:00

  • Clinical impact of human papillomavirus in laryngeal squamous cell carcinoma: a retrospective study.

    abstract:OBJECTIVES:The purpose of this study is to determine the prevalence and clinical impact of human papillomavirus (HPV) related laryngeal squamous cell carcinoma (LSCC). METHODS:A total of 106 LSCC patients who underwent primary surgical resection with or without adjuvant radiotherapy/chemoradiotherapy were enrolled ret...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.3395

    authors: Chen WC,Chuang HC,Lin YT,Huang CC,Chien CY

    更新日期:2017-05-30 00:00:00

  • Unravelling the ontogeny of a Devonian early gnathostome, the "acanthodian" Triazeugacanthus affinis (eastern Canada).

    abstract::The study of vertebrate ontogenies has the potential to inform us of shared developmental patterns and processes among organisms. However, fossilised ontogenies of early vertebrates are extremely rare during the Palaeozoic Era. A growth series of the Late Devonian "acanthodian" Triazeugacanthus affinis, from the Migua...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.3969

    authors: Chevrinais M,Sire JY,Cloutier R

    更新日期:2017-10-27 00:00:00

  • Analysis of the light intensity dependence of the growth of Synechocystis and of the light distribution in a photobioreactor energized by 635 nm light.

    abstract::Synechocystis gathered momentum in modelling studies and biotechnological applications owing to multiple factors like fast growth, ability to fix carbon dioxide into valuable products, and the relative ease of genetic manipulation. Synechocystis physiology and metabolism, and consequently, the productivity of Synechoc...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.5256

    authors: Cordara A,Re A,Pagliano C,Van Alphen P,Pirone R,Saracco G,Branco Dos Santos F,Hellingwerf K,Vasile N

    更新日期:2018-07-27 00:00:00

  • Genome-wide characterization and expression analysis of soybean trihelix gene family.

    abstract::Trihelix transcription factors play multiple roles in plant growth, development and various stress responses. In this study, we identified 71 trihelix family genes in the soybean genome. These trihelix genes were located at 19 out of 20 soybean chromosomes unevenly and were classified into six distinct subfamilies: GT...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.8753

    authors: Liu W,Zhang Y,Li W,Lin Y,Wang C,Xu R,Zhang L

    更新日期:2020-03-13 00:00:00

  • Phylogenetic and morphologic evidence confirm the presence of a new montane cloud forest associated bird species in Mexico, the Mountain Elaenia (Elaenia frantzii; Aves: Passeriformes: Tyrannidae).

    abstract::Here we provide evidence to support an extension of the recognized distributional range of the Mountain Elaenia (Elaenia frantzii) to include southern Mexico. We collected two specimens in breeding condition in northwestern Sierra Norte de Chiapas, Mexico. Morphologic and genetic evidence support their identity as Ela...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.1598

    authors: Hanna ZR,Ortiz-Ramírez MF,Ríos-Muñoz CA,Cayetano-Rosas H,Bowie RC,Navarro-Sigüenza AG

    更新日期:2016-02-01 00:00:00

  • Survival of side grafts with scions from pure species Pinus engelmannii Carr. and the P. engelmannii × P. arizonica Engelm. var. arizonica hybrid.

    abstract::Grafting is one of the most widely used methods for vegetative propagation, particularly for multiplying trees considered important, but there has been little research done on the effect of hybridization on grafts from the genus Pinus. Sometimes hybrids show the ability to reproduce and adapt efficiently to the enviro...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.8468

    authors: Pérez-Luna A,Wehenkel C,Prieto-Ruíz JÁ,López-Upton J,Hernández-Díaz JC

    更新日期:2020-02-07 00:00:00

  • Aridity and land use negatively influence a dominant species' upper critical thermal limits.

    abstract::Understanding the physiological tolerances of ectotherms, such as thermal limits, is important in predicting biotic responses to climate change. However, it is even more important to examine these impacts alongside those from other landscape changes: such as the reduction of native vegetation cover, landscape fragment...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.6252

    authors: Andrew NR,Miller C,Hall G,Hemmings Z,Oliver I

    更新日期:2019-01-10 00:00:00

  • Future sea-level rise drives rocky intertidal habitat loss and benthic community change.

    abstract::The impacts of sea-level rise (SLR) are likely to be the greatest for ecosystems that exist at the land-sea interface, where small changes in sea-level could result in drastic changes in habitat availability. Rocky intertidal ecosystems possess a number of characteristics which make them highly vulnerable to changes i...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.9186

    authors: Kaplanis NJ,Edwards CB,Eynaud Y,Smith JE

    更新日期:2020-05-29 00:00:00

  • Soymilk residue (okara) as a natural immobilization carrier for Lactobacillus plantarum cells enhances soymilk fermentation, glucosidic isoflavone bioconversion, and cell survival under simulated gastric and intestinal conditions.

    abstract::Cell immobilization is an alternative to microencapsulation for the maintenance of cells in a liquid medium. However, artificial immobilization carriers are expensive and pose a high safety risk. Okara, a food-grade byproduct from soymilk production, is rich in prebiotics. Lactobacilli could provide health enhancing e...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.2701

    authors: Xiudong X,Ying W,Xiaoli L,Ying L,Jianzhong Z

    更新日期:2016-11-10 00:00:00

  • Transcriptome sequencing and comparative analysis of adult ovary and testis identify potential gonadal maintenance-related genes in Mauremys reevesii with temperature-dependent sex determination.

    abstract::Mauremys reevesii is a classical organism with temperature-dependent sex determination (TSD). Gonad development in early life has recently received considerable attention but gonadal maintenance after sex differentiation in turtles with TSD remains a mystery. In this study, we sequenced the transcriptomes for the adul...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.6557

    authors: Xiong L,Dong J,Jiang H,Zan J,Tong J,Liu J,Wang M,Nie L

    更新日期:2019-03-08 00:00:00

  • Aberrant expression of two miRNAs promotes proliferation, hepatitis B virus amplification, migration and invasion of hepatocellular carcinoma cells: evidence from bioinformatic analysis and experimental validation.

    abstract:Background:As key negative regulators of gene expression, microRNAs (miRNAs) play an important role in the onset and progression of hepatocellular carcinoma (HCC). This study aimed to identify the miRNAs involved in HCC carcinogenesis and their regulated genes. Methods:The Gene Expression Omnibus (GEO) dataset (GSE108...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.9100

    authors: Liu Y,Cao Y,Cai W,Wu L,Zhao P,Liu XG

    更新日期:2020-04-29 00:00:00

  • Efficiently detecting outlying behavior in video-game players.

    abstract::In this paper, we propose a method for automatically detecting the times during which game players exhibit specific behavior, such as when players commonly show excitement, concentration, immersion, and surprise. The proposed method detects such outlying behavior based on the game players' characteristics. These chara...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.1502

    authors: Kim YB,Kang SJ,Lee SH,Jung JY,Kam HR,Lee J,Kim YS,Lee J,Kim CH

    更新日期:2015-12-10 00:00:00

  • Vertical and horizontal distribution of Desmophyllum dianthus in Comau Fjord, Chile: a cold-water coral thriving at low pH.

    abstract::Cold-water corals provide an important habitat for a rich fauna along the continental margins and slopes. Although these azooxanthellate corals are considered particularly sensitive to ocean acidification, their responses to natural variations in pH and aragonite saturation are largely unknown due to the difficulty of...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.194

    authors: Fillinger L,Richter C

    更新日期:2013-10-29 00:00:00

  • Test re-test reliability and construct validity of the star-track test of manual dexterity.

    abstract::Objectives. We wished to determine test re-test reliability and construct validity of the star-track test of manual dexterity. Design. Test re-test reliability was examined in a controlled study. Construct validity was tested in a blinded randomized crossover study. Setting. The study was performed at a university hos...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.917

    authors: Kildebro N,Amirian I,Gögenur I,Rosenberg J

    更新日期:2015-04-23 00:00:00

  • Applied phylogeography of Cyclopia intermedia (Fabaceae) highlights the need for 'duty of care' when cultivating honeybush.

    abstract:Background:The current cultivation and plant breeding of Honeybush tea (produced from members of Cyclopia Vent.) do not consider the genetic diversity nor structuring of wild populations. Thus, wild populations may be at risk of genetic contamination if cultivated plants are grown in the same landscape. Here, we invest...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.9818

    authors: Galuszynski NC,Potts AJ

    更新日期:2020-09-02 00:00:00

  • Taxonomic revision of the Malagasy members of the Nesomyrmex angulatus species group using the automated morphological species delineation protocol NC-PART-clustering.

    abstract::Background. Applying quantitative morphological approaches in systematics research is a promising way to discover cryptic biological diversity. Information obtained through twenty-first century science poses new challenges to taxonomy by offering the possibility of increased objectivity in independent and automated hy...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.1796

    authors: Csősz S,Fisher BL

    更新日期:2016-03-10 00:00:00

  • Bioinformatic pipelines for whole transcriptome sequencing data exploitation in leukemia patients with complex structural variants.

    abstract:Background:Extensive genome rearrangements, known as chromothripsis, have been recently identified in several cancer types. Chromothripsis leads to complex structural variants (cSVs) causing aberrant gene expression and the formation of de novo fusion genes, which can trigger cancer development, or worsen its clinical ...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.7071

    authors: Hynst J,Plevova K,Radova L,Bystry V,Pal K,Pospisilova S

    更新日期:2019-06-12 00:00:00

  • Dissociating predictability, plausibility and possibility of sentence continuations in reading: evidence from late-positivity ERPs.

    abstract::Late positive event-related potential (ERP) components occurring after the N400, traditionally linked to reanalysis due to syntactic incongruence, are increasingly considered to also reflect reanalysis and repair due to semantic difficulty. Semantic problems can have different origins, such as a mismatch of specific p...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.5717

    authors: Quante L,Bölte J,Zwitserlood P

    更新日期:2018-10-12 00:00:00

  • Utilization of maternal healthcare among adolescent mothers in urban India: evidence from DLHS-3.

    abstract::Background. Low use of maternal healthcare services is one of the reasons why maternal mortality is still considerably high among adolescents mothers in India. To increase the utilization of these services, it is necessary to identify factors that affect service utilization. To our knowledge, no national level study i...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.592

    authors: Singh A,Kumar A,Pranjali P

    更新日期:2014-11-04 00:00:00

  • Recent advances on the estimation of the thermal reaction norm for sex ratios.

    abstract::Temperature-dependent sex determination, or TSD, is a widespread phenomenon in reptiles. The shape of the relationship between constant incubation temperature and sex ratio defines the TSD pattern. The TSD pattern is considered a life-history parameter important for conservation because the wider the range of temperat...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.8451

    authors: Abreu-Grobois FA,Morales-Mérida BA,Hart CE,Guillon JM,Godfrey MH,Navarro E,Girondot M

    更新日期:2020-03-04 00:00:00

  • Assessing the growth in clinical skills using a progress clinical skills examination.

    abstract:Background:This study evaluates the generalizability of an eight-station progress clinical skills examination and assesses the growth in performance for six clinical skills domains among first- and second-year medical students over four time points during the academic year. Methods:We conducted a generalizability stud...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.9091

    authors: Laird-Fick HS,Chang C,Wang L,Parker C,Malinowski R,Emery M,Solomon DJ

    更新日期:2020-05-01 00:00:00

  • Expression of vitamin D 1α-hydroxylase in human gingival fibroblasts in vivo.

    abstract:Background:Vitamin D 1α-hydroxylase CYP27B1 is the key factor in the vitamin D pathway. Previously, we analyzed the expression of CYP27B1 in human gingival fibroblasts in vitro. In the present study, we analyzed the gingival expression of CYP27B1 in vivo. Methods:Forty-two patients with periodontitis Stage IV Grade C ...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.10279

    authors: Liu K,Han B,Hou J,Zhang J,Su J,Meng H

    更新日期:2021-01-04 00:00:00

  • Whole gut microbiome composition of damselfish and cardinalfish before and after reef settlement.

    abstract::The Pomacentridae (damselfish) and Apogonidae (cardinalfish) are among the most common fish families on coral reefs and in the aquarium trade. Members of both families undergo a pelagic larvae phase prior to settlement on the reef, where adults play key roles in benthic habitat structuring and trophic interactions. Fi...

    journal_title:PeerJ

    pub_type: 杂志文章

    doi:10.7717/peerj.2412

    authors: Parris DJ,Brooker RM,Morgan MA,Dixson DL,Stewart FJ

    更新日期:2016-08-31 00:00:00