Compartmentalized regulation of organelle integrity in neurodegenerative diseases:lessons from the Drosophila motor neuron

Neurons are highly polarized,morphologically asymmetric,and functionally compartmentalized cells that contain long axons extending from the cell body.For this reason,their maintenance relies on spatiotemporal regulation of organelle distribution between the somatodendritic and axonal domains.Although some organelles,such as mitochondria and smooth endoplasmic reticulum,are widely distributed throughout the neuron,others are segregated to either the somatodendritic or axonal compartment.For example,Golgi outposts and acidified lysosomes are predominantly present in the somatodendritic domain and rarely distributed along the axon,whereas newly formed autophagosomes and synaptic vesicles are mainly distributed in the distal axon(Britt et al.,2016).

ATF6 aggravates apoptosis in early porcine embryonic development by regulating organelle homeostasis under high-temperature conditions

Activating transcription factor 6(ATF6),one of the three sensor proteins in the endoplasmic reticulum(ER),is an important regulator of ER stress-induced apoptosis.ATF6 resides in the ER and,upon activation,is translocated to the Golgi apparatus,where it is cleaved by site-1 protease(S1P)to generate an amino-terminal cytoplasmic fragment.Although recent studies have made progress in elucidating the regulatory mechanisms of ATF6,its function during early porcine embryonic development under high-temperature(HT)stress remains unclear.In this study,zygotes were divided into four groups:control,HT,HT+ATF6 knockdown,and HT+PF(S1P inhibitor).Results showed that HT exposure induced ER stress,which increased ATF6 protein expression and led to a decrease in the blastocyst rate.Next,ATF6 expression was knocked down in HT embryos under microinjection of ATF6 double-stranded RNA(dsRNA).Results revealed that ATF6 knockdown(ATF6-KD)attenuated the increased expression of CHOP,an ER stress marker,and Ca2+release induced by HT.In addition,ATF6-KD alleviated homeostasis dysregulation among organelles caused by HT-induced ER stress,and further reduced Golgi apparatus and mitochondrial dysfunction in HT embryos.AIFM2 is an important downstream effector of ATF6.Results showed that ATF6-KD reduced the occurrence of AIFM2-mediated embryonic apoptosis at HT.Taken together,our findings suggest that ATF6 is a crucial mediator of apoptosis during early porcine embryonic development,resulting from HT-induced ER stress and disruption of organelle homeostasis.

Development of organelle single nucleotide polymorphism (SNP) markers and their application for the identification of cytoplasmic inheritance patterns in Pyropia yezoensis (Bangiales,Rhodophyta)

The genus Pyropia contains several important cultivated species.Genetic research in nori species has mainly focused on the cell nucleus,with few studies on organelles(chloroplast and mitochondria).Due to the high copy numbers of organelles in cells,which influence the development and traits of algae,it is necessary to study their genetic mechanism.In this study,the marine red alga Pyropia yezoensis,an important economic macroalga,was selected as the study object.To investigate organelle(chloroplast and mitochondria)inheritance in P.yezoensis,the wild type RZ(maternal strain)was crossed with the red mutant HT(paternal strain)and 30 color-sectors from 11 F1 gametophytic blades were examined.The complete chloroplast and mitochondrial genomes of the red mutant(HT)were assembled for the first time.One reliable and stable single nucleotide polymorphism(SNP)loci filtrated by bioinformatics analysis was used as a molecular marker for chloroplast and mitochondrial DNA,respectively,in subsequent experiments.PCR amplification and sequence analysis showed that the haplotypes of color-sectors detected were consistent with those of the maternal parent,confirming that both chloroplast and mitochondrial genomes were inherited maternally in P.yezoensis.The inheritance pattern of organelles in P.yezoensis can be used to guide the hybridization and breeding of nori.Additionally,the organelle SNP markers developed in this study can be applied in subsequent genetic research.

Prediction of Monophyletic Groups Based on Gene Order and Sequence Similarity in Organelle DNA

Organelle genomics has become its own field of study. Much information can be gleaned from the study of cell organelles. The differences in the genomes of organelles, such as the mitochondrion and the chloroplast are amenable to phylogenetic and cladistic studies. These differences include the genome sequence, GC%, genome length and gene order. The conserved nature of the organelle genomes and the gene inventory of both mitochondrial and chloroplast genomes also make this easier to accomplish. This paper includes a review of existing organelle genome software. These include gene annotation and genome visualization tools as well as organelle gene databases for both mitochondrion and plastid. A new R tool, available on github, called “Organelle DNA Lineages”, or ODL, was written to compare and classify organelle genomes based on their genome sequence and gene order. The software was run on the mitochondrial genomes of a set of 51 cephalopod species, delineating ten separate monophyletic groups, including argonauts, nautiluses, octopuses, cuttlefish, and six squid groups. This new tool can help enrich and expand the field of organelle genomics.

Codon evolution in double-stranded organelle DNA: strong regulation of homonucleotides and their analog alternations

In our previous study, complete single DNA strands which were obtained from nuclei, chloroplasts and plant mitochondria obeyed Chargaff’s second parity rule, although those which were obtained from animal mitochondria deviated from the rule. On the other hand, plant mitochondria obeyed another different rule after their classification. Complete single DNA strand sequences obtained from chloroplasts, plant mitochondria, and animal mitochondria, were divided into the coding and non-coding regions. The non-coding region, which was the complementary coding region on the reverse strand, was incorporated as a coding region in the forward strand. When the nucleotide contents of the coding region or non-coding regions were plotted against the composition of the four nucleotides in the complete single DNA strand, it was determined that chloroplast and plant mitochondrial DNA obeyed Chargaff’s second parity rule in both the coding and non-coding regions. However, animal mitochondrial DNA deviated from this rule. In chloroplast and plant mitochondrial DNA, which obey Chargaff’s second parity rule, the lines of regression for G (purine) and C (pyrimidine) intersected with regression lines for A (purine) and T (pyrimidines), respectively, at around 0.250 in all cases. On the other hand, in animal mitochondrial DNA, which deviates from Chargaff’s second parity rule, only regression lines due to the content of homonucleotides or their analogs in the coding or non-coding region against those in the complete single DNA strand intersected at around 0.250 at the horizontal axis. Conversely, the intersection of the two lines of regression (G and A or C and T) against the contents of heteronucleotides or their analogs shifted from 0.25 in both coding and non-coding regions. Nucleotide alternations in chloroplasts and plant mitochondria are strictly regulated, not only by the proportion of homonucleotides and their analogs, but also by the heteronucleotides and their analogs. They are strictly regulated in animal mitochondria only by the content of homonucleotides and their analogs.

Glyphosate exposure deteriorates oocyte meiotic maturation via induction of organelle dysfunctions in pigs

Background:Recently,defects in mammalian oocytes maturation induced by environmental pollution results in the decreasing animal reproduction.Animal exposed to glyphosate is largely unavoidable because glyphosate is one of the most widely used herbicide worldwide due to its high-efficiency and broad-spectrum effects,which causes glyphosate an environmental contaminant found in soil,water and food.During the last few years,the growing and wider use of glyphosate has raised great concerns about its effects of reproductive toxicity.In this study,using porcine models,we investigated effects of glyphosate on organelle functions during oocyte meiosis.Results:The results showed glyphosate exposure disrupted porcine oocyte maturation.Expression levels of cumulus expansion-related genes were interfered,further indicating the meiotic defects.The damaging effects were mediated by destruction of mitochondrial distribution and functions,which induced ROS accumulation and oxidative stress,also indicated by the decreased mRNA expression of related antioxidant enzyme genes.We also found an interference of endoplasmic reticulum(ER)distribution,disturbance of Ca^(2+)homeostasis,as well as fluctuation of ER stress,showing with the reduced ER stress-related mRNA or protein expression,which could indicate the dysfunction of ER for protein processing and signal transduction in glyphosate-exposed oocytes.Moreover,glyphosate exposure induced the disruption of lysosome function for autophagy,showing with the decrease of LAMP2 expression and autophagy-related genes mRNA expression.Additionally,our data showed the distribution of Golgi apparatus and the functions of ribosome were disturbed after glyphosate exposure,which might affect protein synthesis and transport.Conclusions:Collectively,our study showed that exposed to glyphosate could affect animal reproduction by compromising the quality of oocytes through its wide toxic effects on organelle functions.

Complete organelle genomes of Sinapis arvensis and their evolutionary implications

Sinapis arvensis,belonging to the genus Sinapis of the family Brassicaceae,has good agronomic characters that make it a valuable genetic resource for crop improvement and is a cytoplasmic source of heterologous cytoplasmic male sterility(CMS).In addition,S.arvensis has played an important role in the evolution of the six major cultivated Brassica species involved in the triangle of U.Using next-generation sequencing,we assembled and revealed the gene composition of S.arvensis cytoplasmic genome.The chloroplast genome comprises 153,590 bp,with 112 individual genes,including 4 r RNA,29 t RNA,and 79 proteincoding genes.The mitochondrial genome comprises 240,024 bp,with 54 genes,including 18 t RNA,three r RNA and 33 protein-coding genes.Genome structure and evolutionary analysis indicated that the sequences of the S.arvensis organellar genomes were more similar to those of Brassica nigra and B.carinata than to those of other Brassicaceae species.Four mitochondrial open reading frames displaying chimeric structural features and encoding hypothetical proteins with transmembrane domains may account for the infertility of Nsa CMS previously derived from somatic cell hybridization between B.napus and S.arvensis.These results will not only contribute to utilize the germplasm resource of S.arvensis,and comprehend the evolution of organelle genomes within the Brassicaceae family,but also help to identify genes conditioning the alloplasmic male sterility of Nsa CMS in B.napus.

De Novo Organelle Biogenesis in the Cyanobacterium TDX16 Released from the Green Alga <i>Haematococcus pluvialis</i>

It is believed that eukaryotes arise from prokaryotes, which means that organelles can form de novo in prokaryotes. Such events, however, had not been observed previously. Here, we report the biogenesis of organelles in the endosymbiotic cyanobacterium TDX16 (prokaryote) that was released from its senescent/necrotic host cell of green alga Haematococcus pluvialis (eukaryote). Microscopic observations showed that organelle biogenesis in TDX16 initiated with cytoplasm compartmentalization, followed by de-compartmentalization, DNA allocation, and re-compartmentalization, as such two composite organelles-the primitive chloroplast and primitive nucleus sequestering minor and major fractions of cellular DNA respectively were formed. Thereafter, the eukaryotic cytoplasmic matrix was built up from the matrix extruded from the primitive nucleus;mitochondria were assembled in and segregated from the primitive chloroplast, whereby the primitive nucleus and primitive chloroplast matured into the nucleus and chloroplast respectively. While mitochondria subsequently turned into double-membraned vacuoles after matrix degradation. Results of pigment analyses, 16S rRNA and genome sequencing revealed that TDX16 is a phycocyanin-containing cyanobacterium resembling Chroococcidiopsis thermalis, which had acquired 9,017,401 bp DNAs with 10,301 genes from its host. Accordingly, we conclude that organelle biogenesis in TDX16 is achieved by hybridizing the acquired eukaryotic DNAs with its own one and expressing the hybrid genome. The formation of organelles in cyanobacterium TDX16 is the first case of organelle biogenesis in prokaryotes observed so far, which sheds an unprecedented light on eukaryotes and their connections with prokaryotes, and thus has broad implications on biology.

Organelle Structures: Bridging Strategy and Technological Processes

The shifting requirements as imposed on operations ma nagement require adjusting and tailoring the organisational structure to meet ma rket demands. However, translating these requirements directly into hierarchical structure will not ensure the integration of processes across organisational un its and guarantee desirable performance. Therefore, management and management li terature wonders: · How should we connect processes to the external environment within a strategi c framework · Which organisational structures do meet performance requirements · Which choices and freedom do we have within organisational structures · How and when do we implement organisational structures That the hierarchical structure does not meet as such the performance requiremen ts nor did it relate to these became already clear during case studies performed in the ’70s. The conclusion was drawn that organisational changes should affect working processes before they proof to be viable. This required the development of new approach through empirical studies and base d on literature. This led to the development of the organelle structure. The org anelle structure should connect to the strategy and the product flow. Thereto, a decision model has been developed for revealing these relations and the practic al implication. During a number of case studies this methodology has been refined and includes t he strategic choice between variants for the organelle structure with their own performance capabilities; we distinguish about 20 variants ranging between the f unctional organisation and the product flow organisation. These ranges of choice s however can be connected to different order entry points, stemming from logist ic concepts. This extends the performance to improved lead-times and improved c ontrol. Strategic choices relate the organelle structure to external performance criteria dictated by product/market-combinations: · lead-time · quality · costs and internal choices for performance criteria: · flexibility · productivity · resource utilisation · innovative performance. Case studies reveal the drastic improvements of the performance of operations an d manufacturing. The paper will discuss a few of these implementations to demons trate the impact. They also show how one derives the hierarchical structure from the choice for the organelle structure. Organelle structures do bridge the link of an industrial company to its environm ent and the internal possibilities, dictated by characteristics of product flow and process execution. The link to the environment results in a strategic framew ork for assessment of alternatives and possibilities. Choices for organelle stru ctures depend strongly on choices on the order entry points of the hardware flow and the specification flow. The evaluation of the characteristics takes place a gainst the strategic framework ensuring competitive advantage as well as a high probability of factual implementation and performance improvement.

Structural features of the nucleotide sequences of virus and organelle genomes

The four nucleotides (bases), A, T (U), G and C in small genomes, virus DNA/RNA, organelle and plastid genomes were also arranged sophisticatedly in the structural features in a single-strand with 1) reverse-complement symmetry of base or base sequences, 2) bias of four bases, 3) multiple fractality of the distribution of each four bases depending on the distance in double logarithmic plot (power spectrum) of L (the distance of a base to the next base) vs. P (L) (the probability of the base-distribution at L), although their genomes were composed of low numbers of the four bases, and the base-symmetry was rather lower than the prokaryotic-and the eukaryotic cells. In the case of the genomic DNA composed of less than 10,000 nt, it was better than to be partitioned at 10 of the L-value, and the structural features for the biologically active genomic DNA were observed as the large genomes. As the results, the base sequences of the genomic DNA including the genomic-RNA might be universal in all genomes. In addition, the relationship between the structural features of the genome and the biological complexity was discussed.

Neurodegeneration and Mitochondria Organelle Transplantation: “A Technology That Proof of Principle Suggest Is Ready for Prime Time”

It is known that mitochondrial dysfunction is associated with neurodegenerative diseases including amyotrophic lateral sclerosis (ALS). Researchers have tested the therapeutic efficacy of many mitochondrial targeted agents;however, results have been disappointing without significant impact on disease survival. Several groups have demonstrated that mitochondrial transfer of isolated normal healthy mitochondria to defective calls can restore functional recovery. Our experience with mitochondria organelle transplantation (MOT) in cancer cells led to investigating the technology for neurodegenerative diseases (NDs), especially ALS. The rationale was that if the uptake of normal mitochondria into cancer cells inhibited proliferation and glycolysis;then MOT might be a cell-based therapy for NDs. In this communication, we will present background research on MOT in vitro and in vivo cell culture and animal models respectively. This research evidence showed proof of principle of the technology. This fact led us to try the procedure on a desperate human ALS patient.

An efficient approach for obtaining plant organelle genomes

Plant organelle(plastid and mitochondrial)genomes contain substantial information for plant evolution and adaptation.Therefore,it’s important to reveal plant whole-genome sequences including plastid and mitochondrial genomes.To decode these sequences,it is required to efficiently separate organelle genomic DNA from nucleus genome,which is difficult and laborious.In this study,an efficient procedure was established to obtain plant organelle genomes without extraction of plastid and mitochondria.Organelle DNA was extracted from three materials including Sinapis arvensis var.‘Yeyou 18’,a cytoplasmic male sterile line(Nsa CMS)and its corresponding maintainer line‘Zhongshuang 4’.DNA was sequenced by Roche 454 FLXt and Illumina Miseq platforms.Organelle genomes were assembled using the generated reads and public organelle genome sequences.This research presented a procedure that efficiently assembled organelle genomes and subsequent fill gaps by extending the consensus contig terminals.This method enabled us to assemble plant plastid and mitochondrial genomes simultaneously.The obtained organelle genomes could accelerate understanding of mitochondrial rearrangements and laid a foundation for further study of Sinapis arvensis evolution and sterility gene of Nsa CMS.

Lipid-Protein Microinclusions in the Morphological Structures of Organelle Membranes Studied by Fluorescent Confocal Microscopy

Peculiar properties of morphological structures of organelle membranes were studied by fluorescent confocal microscopy. The list of objects in our experiments was represented by mitochondria, chloroplasts and vacuoles. During this study, identification of lipid microinclusions having the form of such lipid-protein structural microformations as lipid-protein microdomains, vesicles and membrane tubular structures (cytoplasmic transvacuolar strands and nanotubes) located in organelle membranes or bound up with them was conducted. Such membrane probes as laurdan, DPH, ANS and bis-ANS were used. Comparison of fluorescence intensity of these membrane probes was conducted. This investigation of the morphological properties of lipid-protein structural microformations was accompanied with analysis of 1) the phase state and 2) dynamics of microviscosity variations in the membrane elements of isolated plant cell organelles. Distributions of laurdan fluorescence generalized polarization (GP) values for the membrane on the whole and for the intensively fluorescing membrane segments were obtained. It was discovered that the microviscosity of intensively fluorescing membrane segments essentially differed from the microviscosity of the rest part of the membrane. In conclusion, some results of the study of peculiar properties of lipid-protein structural microformations related to the structure of organelle membranes and the discoveries made in this investigation are discussed.

Mitochondrial Organelle Transplantation Is a Potential Therapeutic for Mitochondria Dysfunction in Severe Acute Respiratory Syndrome (SARS) Coronavirus Diseases

COVID-19 severe symptoms and high mortality are mainly seen in elders with age-associated diseases who have mitochondrial dysfunction. Mitochondrial dysfunction is a vulnerability and comorbidity of COVID-19. Cytokine storm, and increased serum iron and ferritin and reactive oxygen species (ROS) in COVID-19 further damage mitochondria. Amelioration of mitochondrial dysfunction may be a strategy of prevention and treatment of COVID-19. We also describe mitochondrial organelle transplantation (MOT) which has restored mitochondrial function, improved the repair of injured tissues and suppressed hyperinflammation in life-threatening sepsis. MOT is a potential therapy for severe COVID-19. Finally, we report the first case of MOT for a severe COVID-19 patient. MOT is safe and might have beneficial effect on the severe COVID-19.

ORPA:a fast and efficient phylogenetic analysis method for constructing genome-wide alignments of organelle genomes

Creating a multi-gene alignment matrix for phylogenetic analysis using organelle genomes involves aligning single-gene datasets manually,a process that can be time-consuming and prone to errors.The HomBlocks pipeline has been created to eliminate the inaccuracies arising from manual operations.The processing of a large number of sequences,however,remains a time-consuming task.To conquer this challenge,we develop a speedy and efficient method called Organelle Genomes for Phylogenetic Analysis(ORPA).ORPA can quickly generate multiple sequence alignments for whole-genome comparisons by parsing the result files of NCBI BLAST,completing the task just in 1 min.With increasing data volume,the efficiency of ORPA is even more pronounced,over 300 times faster than HomBlocks in aligning 60 high-plant chloroplast genomes.The phylogenetic tree outputs from ORPA are equivalent to HomBlocks,indicating its outstanding efficiency.Due to its speed and accuracy,ORPA can identify species-level evolutionary conflicts,providing valuable insights into evolutionary cognition.

Micro/nanoelectrode-based electrochemical methodology for single cell and organelle analysis

Cells are the basic unit of life.Electrochemical analysis of single cells/organelles is essential for uncovering the molecular mechanisms of physiological and pathological processes that are difficult to elucidate on a larger scale.This paper provides an overview of the commonly used fabrication methods for micro/nanoelectrodes applied in the investigations of single cells/organelles as well as the corresponding electrochemical measurements over the last four years including extracellular measurement,combination of extra and intracellular measurement,intracellular reactive oxygen species and reactive nitrogen species(ROS/RNS)measurement,and isolated organelles measurement.

Phase-separated bienzyme compartmentalization as artificial intracellular membraneless organelles for cell repair

Implanting artificial organelles in living cells is capable of correcting cellular dysfunctionalities for cell repair and biomedical applications. In this work, phase-separated bienzyme-loaded coacervate microdroplets are established as a model of artificial membraneless organelles in endothelial dysfunctional cells for the cascade enzymatic production of nitric oxide(NO) with a purpose of correcting cellular NO deficiency. We prepared the coacervate microdroplets via liquid-liquid phase separation of oppositely charged polyelectrolytes, in which glucose oxidase/horseradish peroxidase-mediated cascade reaction was compartmented. After the coacervate microdroplets were implanted in NO-deficient dysfunctional cells, the compartments maintained a phase-separated liquid droplet structure, which facilitated a significant enhancement of NO production in the dysfunctional cells. The recovery of NO production was further exploited to inhibit clot formation in blood plasma located in the cell suspension. This demonstrated a proof-of-concept design of artificial organelles in dysfunctional cells for cell repair and anticoagulation-related medical applications. Our results demonstrate an approach for the construction of coacervate droplets through phase separation for the generation of artificial membraneless organelles, which can be designed to provide an array of functionalities in living organisms that have the potential to be used in the field of cell engineering and medical therapy.

Intracellular organelle networks： Understanding their organization and communication through systems-level modeling and analysis

BACKGROUND： Membrane-bound intracellular organelles are biochemically distinct compartments used by eukaryotic cells for serving specialized physiological functions and organizing their internal environment. Recent studies revealed surprisingly extensive communication between these organelles and highlighted the network nature of their organization and communication. Since organization and communication of the organelles are carried out at the systems level through their networks, systems-level studies are essential for understanding the underlying mechanisms. METHODS： We reviewed recent studies that used systems-level quantitative modeling and analysis to understand organization and communication of intracellular organelle networks. RESULTS： We first review modeling and analysis studies on how fusion/fission and degradation/biogenesis, two essential and closely related classes of activities of individual organelles, collectively mediate the dynamic organization of their networks. We then turn to another important aspect of the dynamic organization of the organelle networks, namely how organelles are physically connected within their networks, a property referred to as the topology of the networks in mathematics, and summarize some of their distinct properties. Lastly, we briefly review modeling and analysis studies that aim to understand communication between different organelle networks, focusing on cellular calcium homeostasis as an example. We conclude with a brief discussion of future directions for research in this area. CONCLUSIONS： Together, the reviewed studies provide critical insights into how diverse activities of individual organelles collectively mediate the organization and communication of their networks. They demonstrate the essential role of systems- level modeling and analysis in understanding complex behavior of such networks.

The lipid droplet： A conserved cellular organelle

The lipid droplet （LD） is a unique multi-functional orga- nelle that contains a neutral lipid core covered with a phospholipid monolayer membrane. The LDs have been found in almost all organisms from bacteria to humans with similar shape. Several conserved functions of LDs have been revealed by recent studies, including lipid metabolism and trafficking, as well as nucleic acid binding and protection. We summarized these findings and proposed a hypothesis that the LD is a conserved organelle.

Organelle Extensions in Plant Cells

Cell walls lock each cell in a specific position within the supraorganization of a plant. Despite its fixed location, each cell must be able to sense alterations in its immediate environment and respond rapidly to ensure the optimal functioning, continued growth and development, and eventual longterm survival of the plant.