scholarly journals Partial Chromosome Sequence of Spiroplasma citri Reveals Extensive Viral Invasion and Important Gene Decay

2010 ◽  
Vol 76 (11) ◽  
pp. 3420-3426 ◽  
Author(s):  
Patricia Carle ◽  
Colette Saillard ◽  
Nathalie Carr�re ◽  
S�bastien Carr�re ◽  
Sybille Duret ◽  
...  
Keyword(s):  
Cell Metabolism ◽  
Atp Synthesis ◽  
Genetic Maps ◽  
Structural Element ◽  
Spiroplasma Citri ◽  
Cellular Processes ◽  
Chromosome Sequence ◽  
Dependent Protein ◽  
Coding Capacity ◽  
Gene Decay

ABSTRACT The assembly of 20,000 sequencing reads obtained from shotgun and chromosome-specific libraries of the Spiroplasma citri genome yielded 77 chromosomal contigs totaling 1,674 kbp (92%) of the 1,820-kbp chromosome. The largest chromosomal contigs were positioned on the physical and genetic maps constructed from pulsed-field gel electrophoresis and Southern blot hybridizations. Thirty-eight contigs were annotated, resulting in 1,908 predicted coding sequences (CDS) representing an overall coding density of only 74%. Cellular processes, cell metabolism, and structural-element CDS account for 29% of the coding capacity, CDS of external origin such as viruses and mobile elements account for 24% of the coding capacity, and CDS of unknown function account for 47% of the coding capacity. Among these, 21% of the CDS group into 63 paralog families. The organization of these paralogs into conserved blocks suggests that they represent potential mobile units. Phage-related sequences were particularly abundant and include plectrovirus SpV1 and SVGII3 and lambda-like SpV2 sequences. Sixty-nine copies of transposases belonging to four insertion sequence (IS) families (IS30, IS481, IS3, and ISNCY) were detected. Similarity analyses showed that 21% of chromosomal CDS were truncated compared to their bacterial orthologs. Transmembrane domains, including signal peptides, were predicted for 599 CDS, of which 58 were putative lipoproteins. S. citri has a Sec-dependent protein export pathway. Eighty-four CDS were assigned to transport, such as phosphoenolpyruvate phosphotransferase systems (PTS), the ATP binding cassette (ABC), and other transporters. Besides glycolytic and ATP synthesis pathways, it is noteworthy that S. citri possesses a nearly complete pathway for the biosynthesis of a terpenoid.

scholarly journals Research Progress of Sirtuin4 in Cancer

2021 ◽  
Vol 10 ◽  
Author(s):  
Yibing Bai ◽  
Jiani Yang ◽  
Ying Cui ◽  
Yuanfei Yao ◽  
Feng Wu ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Enzyme Activity ◽  
Energy Metabolism ◽  
Nicotinamide Adenine Dinucleotide ◽  
Enzyme Activities ◽  
Research Progress ◽  
Diverse Range ◽  
Catalytic Activities ◽  
Cellular Processes ◽  
Dependent Protein

Sirtuins (SIRTs) are members of the silent information regulator-2 family. They are a conserved family of nicotinamide adenine dinucleotide-dependent protein lysine deacylases. SIRTS are involved in intricate cellular processes. There are seven subtypes of SIRTs (1–7) in mammals. SIRT4 is located mainly in mitochondria and has various catalytic activities. These enzyme activities give it a diverse range of important biologic functions, such as energy metabolism, oxidative stress, and aging. Cancer is characterized as reprogramming of energy metabolism and redox imbalance, and SIRT4 can affect tumorigenesis. Here, we review the structure, localization, and enzyme activity of SIRT4 and its role in various neoplasms.

scholarly journals SVIP Is a Novel VCP/p97-interacting Protein Whose Expression Causes Cell Vacuolation

2003 ◽  
Vol 14 (1) ◽  
pp. 262-273 ◽  
Author(s):  
Masami Nagahama ◽  
Mie Suzuki ◽  
Yuko Hamada ◽  
Kiyotaka Hatsuzawa ◽  
Katsuko Tani ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Coiled Coil ◽  
Adaptor Proteins ◽  
Interacting Protein ◽  
Cellular Processes ◽  
Coiled Coil Region ◽  
Acid Protein ◽  
Extensive Cell ◽  
Dependent Protein ◽  
Amino Acid Protein

VCP/p97 is involved in a variety of cellular processes, including membrane fusion and ubiquitin-dependent protein degradation. It has been suggested that adaptor proteins such as p47 and Ufd1p confer functional versatility to VCP/p97. To identify novel adaptors, we searched for proteins that interact specifically with VCP/p97 by using the yeast two-hybrid system, and discovered a novel VCP/p97-interacting protein named smallVCP/p97-interactingprotein (SVIP). Rat SVIP is a 76-amino acid protein that contains two putative coiled-coil regions, and potential myristoylation and palmitoylation sites at the N terminus. Binding experiments revealed that the N-terminal coiled-coil region of SVIP, and the N-terminal and subsequent ATP-binding regions (ND1 domain) of VCP/p97, interact with each other. SVIP and previously identified adaptors p47 and ufd1p interact with VCP/p97 in a mutually exclusive manner. Overexpression of full-length SVIP or a truncated mutant did not markedly affect the structure of the Golgi apparatus, but caused extensive cell vacuolation reminiscent of that seen upon the expression of VCP/p97 mutants or polyglutamine proteins in neuronal cells. The vacuoles seemed to be derived from endoplasmic reticulum membranes. These results together suggest that SVIP is a novelVCP/p97 adaptor whose function is related to the integrity of the endoplasmic reticulum.

Signalling functions for sphingolipid long-chain bases in Saccharomyces cerevisiae

2005 ◽  
Vol 33 (5) ◽  
pp. 1170-1173 ◽  
Author(s):  
K. Liu ◽  
X. Zhang ◽  
C. Sumanasekera ◽  
R.L. Lester ◽  
R.C. Dickson
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Kinase ◽  
Second Messengers ◽  
Dependent Protein Kinase ◽  
Yeast Saccharomyces Cerevisiae ◽  
Signalling Molecules ◽  
Cellular Processes ◽  
Wide Range ◽  
Dependent Protein ◽  
Long Chain

Over the past several years, studies of sphingolipid functions in the baker's yeast Saccharomyces cerevisiae have revealed that the sphingoid LCBs (long-chain bases), dihydrosphingosine and PHS (phytosphingosine), are important signalling molecules or second messengers under heat stress and during non-stressed conditions. LCBs are now recognized as regulators of AGC-type protein kinase (where AGC stands for protein kinases A, G and C) Pkh1 and Pkh2, which are homologues of mammalian phosphoinositide-dependent protein kinase 1. LCBs were previously shown to activate Pkh1 and Pkh2, which then activate the downstream protein kinase Pkc1. We have recently demonstrated that PHS stimulates Pkh1 to activate additional downstream kinases including Ypk1, Ypk2 and Sch9. We have also found that PHS acts downstream of Pkh1 and partially activates Ypk1, Ypk2 and Sch9. These kinases control a wide range of cellular processes including growth, cell wall integrity, stress resistance, endocytosis and aging. As we learn more about the cellular processes controlled by Ypk1, Ypk2 and Sch9, we will have a far greater appreciation of LCBs as second messengers.

scholarly journals Metabolic enzymes that bind RNA: yet another level of cellular regulatory network?

2006 ◽  
Vol 53 (1) ◽  
pp. 11-32 ◽  
Author(s):  
Joanna Cieśla
Keyword(s):  
Rna Binding ◽  
Regulatory Element ◽  
Cell Metabolism ◽  
Metabolic Enzymes ◽  
Wide Distribution ◽  
Eukaryotic Cell ◽  
Metabolic Enzyme ◽  
Cellular Processes ◽  
Regulatory Circuits ◽  
Regulatory Functions

Several enzymes that were originally characterized to have one defined function in intermediatory metabolism are now shown to participate in a number of other cellular processes. Multifunctional proteins may be crucial for building of the highly complex networks that maintain the function and structure in the eukaryotic cell possessing a relatively low number of protein-encoding genes. One facet of this phenomenon, on which I will focus in this review, is the interaction of metabolic enzymes with RNA. The list of such enzymes known to be associated with RNA is constantly expanding, but the most intriguing question remains unanswered: are the metabolic enzyme-RNA interactions relevant in the regulation of cell metabolism? It has been proposed that metabolic RNA-binding enzymes participate in general regulatory circuits linking a metabolic function to a regulatory mechanism, similar to the situation of the metabolic enzyme aconitase, which also functions as iron-responsive RNA-binding regulatory element. However, some authors have cautioned that some of such enzymes may merely represent "molecular fossils" of the transition from an RNA to a protein world and that the RNA-binding properties may not have a functional significance. Here I will describe enzymes that have been shown to interact with RNA (in several cases a newly discovered RNA-binding protein has been identified as a well-known metabolic enzyme) and particularly point out those whose ability to interact with RNA seems to have a proven physiological significance. I will also try to depict the molecular switch between an enzyme's metabolic and regulatory functions in cases where such a mechanism has been elucidated. For most of these enzymes relations between their enzymatic functions and RNA metabolism are unclear or seem not to exist. All these enzymes are ancient, as judged by their wide distribution, and participate in fundamental biochemical pathways.

scholarly journals Regulation of Mitochondrial Dynamics by Proteolytic Processing and Protein Turnover

2017 ◽  
Author(s):  
Sumaira Ali ◽  
Gavin P. McStay
Keyword(s):  
Mitochondrial Dynamics ◽  
Mitochondrial Fission ◽  
Atp Synthesis ◽  
Proteolytic Processing ◽  
Central Metabolism ◽  
Mitochondrial Network ◽  
Mitochondrial Membranes ◽  
Cellular Processes ◽  
Homeostasis Regulation ◽  
Apoptosis And Inflammation

The mitochondrial network is a dynamic organization within eukaryotic cells that participates in a variety of essential cellular processes, such as ATP synthesis, central metabolism, apoptosis and inflammation. The mitochondrial network is balanced between rates of fusion and fission that respond to pathophysiologic signals to coordinate appropriate mitochondrial processes. Mitochondrial fusion and fission are regulated by proteins that either reside or translocate to the inner or outer mitochondrial membranes or are soluble in the inter-membrane space. Mitochondrial fission and fusion are performed by GTPases on the outer and inner mitochondrial membranes with the assistance of other mitochondrial proteins. Due to the essential nature of mitochondrial function for cellular homeostasis regulation of mitochondrial dynamics is under strict control. Some of the mechanisms used to regulate the function of these proteins are post-translational proteolysis and/or turnover and this review will discuss these mechanisms required for correct mitochondrial network organization.

scholarly journals Intrinsic OXPHOS limitations underlie cellular bioenergetics in leukemia

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Margaret A M Nelson ◽  
Kelsey L McLaughlin ◽  
James T Hagen ◽  
Hannah S Coalson ◽  
Cameron Schmidt ◽  
...  
Keyword(s):  
Cancer Biology ◽  
Atp Synthesis ◽  
Therapeutic Index ◽  
Cell Types ◽  
Mitochondrial Metabolism ◽  
Metabolic Phenotype ◽  
Hematopoietic Stem ◽  
Cellular Processes ◽  
Underlying Mechanisms ◽  
Primary Output

Typified by oxidative phosphorylation (OXPHOS), mitochondria catalyze a wide variety of cellular processes seemingly critical for malignant growth. As such, there is considerable interest in targeting mitochondrial metabolism in cancer. However, notwithstanding the few drugs targeting mutant dehydrogenase activity, nearly all hopeful 'mito-therapeutics' cannot discriminate cancerous from non-cancerous OXPHOS and thus suffer from a limited therapeutic index. The present project was based on the premise that the development of efficacious mitochondrial-targeted anti-cancer compounds requires answering two fundamental questions: 1) is mitochondrial bioenergetics in fact different between cancer and non-cancer cells? and 2) If so, what are the underlying mechanisms? Such information is particularly critical for the subset of human cancers, including acute myeloid leukemia (AML), in which alterations in mitochondrial metabolism are implicated in various aspects of cancer biology (e.g., clonal expansion and chemoresistance). Herein, we leveraged an in-house diagnostic biochemical workflow to comprehensively evaluate mitochondrial bioenergetic efficiency and capacity in various hematological cell types, with a specific focus on OXPHOS dynamics in AML. Consistent with prior reports, clonal cell expansion, characteristic of leukemia, was universally associated with a hyper-metabolic phenotype which included increases in basal and maximal glycolytic and respiratory flux. However, despite having nearly 2-fold more mitochondria per cell, clonally expanding hematopoietic stem cells, leukemic blasts, as well as chemoresistant AML were all consistently hallmarked by intrinsic limitations in oxidative ATP synthesis (i.e., OXPHOS). Remarkably, by performing experiments across a physiological span of ATP free energy (i.e, ΔGATP), we provide direct evidence that, rather than contributing to cellular ΔGATP, leukemic mitochondria are particularly poised to consume ATP. Relevant to AML biology, acute restoration of OXPHOS kinetics proved highly cytotoxic to leukemic blasts, suggesting that active OXPHOS repression supports aggressive disease dissemination in AML. Taken together, these findings argue against ATP being the primary output of mitochondria in leukemia and provide proof-of-principle that restoring, rather than disrupting, OXPHOS and/or cellular ΔGATP in cancer may represent an untapped therapeutic avenue for combatting hematological malignancy and chemoresistance.

scholarly journals Mitochondrial Calcium Regulation of Redox Signaling in Cancer

Cells ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 432 ◽  
Author(s):  
Céline Delierneux ◽  
Sana Kouba ◽  
Santhanam Shanmughapriya ◽  
Marie Potier-Cartereau ◽  
Mohamed Trebak ◽  
...  
Keyword(s):  
Metabolic Flux ◽  
Cellular Proliferation ◽  
Atp Synthesis ◽  
Redox Signaling ◽  
Mitochondrial Enzymes ◽  
Cellular Processes ◽  
Transport Chain ◽  
Atp Generation ◽  
And Function ◽  
Ca2 Channels

Calcium (Ca2+) uptake into the mitochondria shapes cellular Ca2+ signals and acts as a key effector for ATP generation. In addition, mitochondria-derived reactive oxygen species (mROS), produced as a consequence of ATP synthesis at the electron transport chain (ETC), modulate cellular signaling pathways that contribute to many cellular processes. Cancer cells modulate mitochondrial Ca2+ ([Ca2+]m) homeostasis by altering the expression and function of mitochondrial Ca2+ channels and transporters required for the uptake and extrusion of mitochondrial Ca2+. Regulated elevations in [Ca2+]m are required for the activity of several mitochondrial enzymes, and this in turn regulates metabolic flux, mitochondrial ETC function and mROS generation. Alterations in both [Ca2+]m and mROS are hallmarks of many tumors, and elevated mROS is a known driver of pro-tumorigenic redox signaling, resulting in the activation of pathways implicated in cellular proliferation, metabolic alterations and stress-adaptations. In this review, we highlight recent studies that demonstrate the interplay between [Ca2+]m and mROS signaling in cancer.

Differential proteome–metabolome profiling of YCA1-knock-out and wild type cells reveals novel metabolic pathways and cellular processes dependent on the yeast metacaspase

2015 ◽  
Vol 11 (6) ◽  
pp. 1573-1583 ◽  
Author(s):  
Maša Ždralević ◽  
Valentina Longo ◽  
Nicoletta Guaragnella ◽  
Sergio Giannattasio ◽  
Anna Maria Timperio ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Stress Response ◽  
Metabolic Pathways ◽  
Cell Metabolism ◽  
Wild Type ◽  
Knock Out ◽  
Cellular Processes ◽  
Metabolome Profiling ◽  
Metabolomic Approach

A combined proteomic and metabolomic approach revealed new non-apoptotic roles of the metacaspaseYCA1gene inSaccharomyces cerevisiae, highlighting its involvement in the cell metabolism and stress response.

scholarly journals Pseudoscaffolds and anchoring proteins: the difference is in the details

2017 ◽  
Vol 45 (2) ◽  
pp. 371-379 ◽  
Author(s):  
Stacey Aggarwal-Howarth ◽  
John D. Scott
Keyword(s):  
Atp Synthesis ◽  
Protein Protein Interaction ◽  
Cellular Processes ◽  
Signaling Dynamics ◽  
Local Environments ◽  
Anchoring Proteins ◽  
Catalytic Sites ◽  
Interaction Domains ◽  
The Difference ◽  
Second Messenger Signaling

Pseudokinases and pseudophosphatases possess the ability to bind substrates without catalyzing their modification, thereby providing a mechanism to recruit potential phosphotargets away from active enzymes. Since many of these pseudoenzymes possess other characteristics such as localization signals, separate catalytic sites, and protein–protein interaction domains, they have the capacity to influence signaling dynamics in local environments. In a similar manner, the targeting of signaling enzymes to subcellular locations by A-kinase-anchoring proteins (AKAPs) allows for precise and local control of second messenger signaling events. Here, we will discuss how pseudoenzymes form ‘pseudoscaffolds’ and compare and contrast this compartment-specific regulatory role with the signal organization properties of AKAPs. The mitochondria will be the focus of this review, as they are dynamic organelles that influence a broad range of cellular processes such as metabolism, ATP synthesis, and apoptosis.

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