scholarly journals The Discovery of Vitreoscilla Hemoglobin and Early Studies on Its Biochemical Functions, the Control of Its Expression, and Its Use in Practical Applications

2021 ◽  
Vol 9 (8) ◽  
pp. 1637
Author(s):  
Dale A. Webster ◽  
Kanak L. Dikshit ◽  
Krishna R. Pagilla ◽  
Benjamin C. Stark
Keyword(s):  
Biochemical Properties ◽  
Early Years ◽  
Cell Physiology ◽  
Oxygen Binding ◽  
Biotechnological Applications ◽  
Gene Encoding ◽  
Practical Applications ◽  
Bacterial Hemoglobin ◽  
Practical Usefulness ◽  
Protein Functions

In 1986, the surprising identification of a hemoglobin (VHb) in the bacterium Vitreoscilla greatly extended the range of taxa in which this oxygen binding protein functions. Elucidation of many of its biochemical properties and relation to overall cell physiology, as well as the sequence of the gene encoding it and aspects of control of its expression were determined in the following years. In addition, during the early years following its discovery, strategies were developed to use its expression in heterologous microbial hosts to enhance processes of practical usefulness. The VHb discovery also served as the foundation for what has become the fascinatingly rich field of bacterial hemoglobins. VHb’s position as the first known bacterial hemoglobin and its extensive use in biotechnological applications, which continue today, make a review of the early studies of its properties and uses an appropriate and interesting topic thirty-five years after its discovery.

scholarly journals Structural requirements of the glucocorticoid-response unit of the carbamoyl-phosphate synthase gene

2004 ◽  
Vol 382 (2) ◽  
pp. 463-470 ◽  
Author(s):  
Onard J. L. M. SCHONEVELD ◽  
Ingrid C. GAEMERS ◽  
Atze T. DAS ◽  
Maarten HOOGENKAMP ◽  
Johan RENES ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Distal Enhancer ◽  
Carbamoyl Phosphate ◽  
Gene Encoding ◽  
Response Elements ◽  
Response Unit ◽  
Glucocorticoid Response ◽  
Protein Functions ◽  
Spatial Positioning ◽  
Phosphate Synthase

The GRU (glucocorticoid-response unit) within the distal enhancer of the gene encoding carbamoyl-phosphate synthase, which comprises REs (response elements) for the GR (glucocorticoid receptor) and the liver-enriched transcription factors FoxA (forkhead box A) and C/EBP (CCAAT/enhancer-binding protein), and a binding site for an unknown protein denoted P3, is one of the simplest GRUs described. In this study, we have established that the activity of this GRU depends strongly on the positioning and spacing of its REs. Mutation of the P3 site within the 25 bp FoxA–GR spacer eliminated GRU activity, but the requirement for P3 could be overcome by decreasing the length of this spacer to ≤12 bp, by optimizing the sequence of the REs in the GRU, and by replacing the P3 sequence with a C/EBPβ sequence. With spacers of ≤12 bp, the activity of the GRU depended on the helical orientation of the FoxA and GR REs, with highest activities observed at 2 and 12 bp respectively. Elimination of the 6 bp C/EBP–FoxA spacer also increased GRU activity 2-fold. Together, these results indicate that the spatial positioning of the transcription factors that bind to the GRU determines its activity and that the P3 complex, which binds to the DNA via a 75 kDa protein, functions to facilitate interaction between the FoxA and glucocorticoid response elements when the distance between these transcription factors means that they have difficulties contacting each other.

scholarly journals BECLIN1: Protein Structure, Function and Regulation

Cells ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1522
Author(s):  
Sharon Tran ◽  
W. Douglas Fairlie ◽  
Erinna F. Lee
Keyword(s):  
Protein Structure ◽  
Structure Function ◽  
Membrane Trafficking ◽  
Biochemical Properties ◽  
Class Iii ◽  
Form Class ◽  
Protein Interactome ◽  
Protein Functions ◽  
Phosphoinositide 3 Kinase ◽  
Shed Light

BECLIN1 is a well-established regulator of autophagy, a process essential for mammalian survival. It functions in conjunction with other proteins to form Class III Phosphoinositide 3-Kinase (PI3K) complexes to generate phosphorylated phosphatidylinositol (PtdIns), lipids essential for not only autophagy but other membrane trafficking processes. Over the years, studies have elucidated the structural, biophysical, and biochemical properties of BECLIN1, which have shed light on how this protein functions to allosterically regulate these critical processes of autophagy and membrane trafficking. Here, we review these findings and how BECLIN1’s diverse protein interactome regulates it, as well as its impact on organismal physiology.

scholarly journals Molecular Characterization of the Gene Encoding a New AmpC β-Lactamase in a Clinical Strain of Acinetobacter Genomic Species 3

2004 ◽  
Vol 48 (4) ◽  
pp. 1374-1378 ◽  
Author(s):  
Alejandro Beceiro ◽  
Lourdes Dominguez ◽  
Anna Ribera ◽  
Jordi Vila ◽  
Francisca Molina ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Molecular Characterization ◽  
Biochemical Properties ◽  
Clinical Strain ◽  
The Novel ◽  
Gene Encoding ◽  
Genomic Species ◽  
First Time

ABSTRACT A presumptive chromosomal cephalosporinase (pI, 9.0) from a clinical strain of Acinetobacter genomic species 3 (AG3) is reported. The nucleotide sequence of this β-lactamase shows for the first time the gene encoding an AmpC enzyme in AG3. In addition, the biochemical properties of the novel AG3 AmpC β-lactamase are reported

scholarly journals Functional characterization of a loss-of-function mutant I324M of arginine vasopressin receptor 2 in X-linked nephrogenic diabetes insipidus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lixia Wang ◽  
Weihong Guo ◽  
Chunyun Fang ◽  
Wenli Feng ◽  
Yumeng Huang ◽  
...  
Keyword(s):  
Diabetes Insipidus ◽  
Arginine Vasopressin ◽  
Nephrogenic Diabetes Insipidus ◽  
Functional Characterization ◽  
Gene Mutations ◽  
Biochemical Properties ◽  
Vasopressin Receptor ◽  
Inherited Disease ◽  
Loss Of Function ◽  
Gene Encoding

AbstractX-linked nephrogenic diabetes insipidus (X-linked NDI) is a rare inherited disease mainly caused by lost-of-function mutations in human AVPR2 gene encoding arginine vasopressin receptor 2 (V2R). Our focus of the current study is on exploration of the functional and biochemical properties of Ile324Met (I324M) mutation identified in a pedigree showing as typical recessive X-linked NDI. We demonstrated that I324M mutation interfered with the conformation of complex glycosylation of V2R. Moreover, almost all of the I324M-V2R failed to express on the cell surface due to being captured by the endoplasmic reticulum control system. We further examined the signaling activity of DDAVP-medicated cAMP and ERK1/2 pathways and the results revealed that the mutant receptor lost the ability in response to DDAVP stimulation contributed to the failure of accumulation of cAMP and phosphorylated ERK1/2. Based on the characteristics of molecular defects of I324M mutant, we selected two reagents (SR49059 and alvespimycin) to determine whether the functions of I324M-V2R can be restored and we found that both compounds can significantly “rescue” I324M mutation. Our findings may provide further insights for understanding the pathogenic mechanism of AVPR2 gene mutations and may offer some implications on development of promising treatments for patients with X-linked NDI.

scholarly journals Class I Phosphoinositide 3-Kinase PIK3CA/p110α and PIK3CB/p110β Isoforms in Endometrial Cancer

2018 ◽  
Vol 19 (12) ◽  
pp. 3931 ◽  
Author(s):  
Fatemeh Mazloumi Gavgani ◽  
Victoria Smith Arnesen ◽  
Rhîan Jacobsen ◽  
Camilla Krakstad ◽  
Erling Hoivik ◽  
...  
Keyword(s):  
Endometrial Cancer ◽  
Gene Copy Number ◽  
Biochemical Properties ◽  
Class I ◽  
Gene Copy ◽  
Gene Encoding ◽  
Cellular Processes ◽  
Pi3k Signalling ◽  
Phosphoinositide 3 Kinase ◽  
Phosphatase And Tensin Homologue

The phosphoinositide 3-kinase (PI3K) signalling pathway is highly dysregulated in cancer, leading to elevated PI3K signalling and altered cellular processes that contribute to tumour development. The pathway is normally orchestrated by class I PI3K enzymes and negatively regulated by the phosphatase and tensin homologue, PTEN. Endometrial carcinomas harbour frequent alterations in components of the pathway, including changes in gene copy number and mutations, in particular in the oncogene PIK3CA, the gene encoding the PI3K catalytic subunit p110α, and the tumour suppressor PTEN. PIK3CB, encoding the other ubiquitously expressed class I isoform p110β, is less frequently altered but the few mutations identified to date are oncogenic. This isoform has received more research interest in recent years, particularly since PTEN-deficient tumours were found to be reliant on p110β activity to sustain transformation. In this review, we describe the current understanding of the common and distinct biochemical properties of the p110α and p110β isoforms, summarise their mutations and highlight how they are targeted in clinical trials in endometrial cancer.

The HiPIP from the acidophilic Acidithiobacillus ferrooxidans is correctly processed and translocated in Escherichia coli, in spite of the periplasm pH difference between these two micro-organisms

Microbiology ◽  
2005 ◽  
Vol 151 (5) ◽  
pp. 1421-1431 ◽  
Author(s):  
Patrice Bruscella ◽  
Laure Cassagnaud ◽  
Jeanine Ratouchniak ◽  
Gaël Brasseur ◽  
Elisabeth Lojou ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Acidithiobacillus Ferrooxidans ◽  
Biochemical Properties ◽  
Gene Encoding ◽  
Iron Sulfur Cluster ◽  
E Coli ◽  
Iron Sulfur ◽  
Sulfur Protein ◽  
Tat System ◽  
Micro Organisms

The gene encoding a putative high-potential iron–sulfur protein (HiPIP) from the strictly acidophilic and chemolithoautotrophic Acidithiobacillus ferrooxidans ATCC 33020 has been cloned and sequenced. This potential HiPIP was overproduced in the periplasm of the neutrophile and heterotroph Escherichia coli. As shown by optical and EPR spectra and by electrochemical studies, the recombinant protein has all the biochemical properties of a HiPIP, indicating that the iron–sulfur cluster was correctly inserted. Translocation of this protein in the periplasm of E. coli was not detected in a ΔtatC mutant, indicating that it is dependent on the Tat system. The genetic organization of the iro locus in strains ATCC 23270 and ATCC 33020 is different from that found in strains Fe-1 and BRGM. Indeed, in A. ferrooxidans ATCC 33020 and ATCC 23270 (the type strain), iro was not located downstream from purA but was instead downstream from petC2, encoding cytochrome c 1 from the second A. ferrooxidans cytochrome bc 1 complex. These findings underline the genotypic heterogeneity within the A. ferrooxidans species. The results suggest that Iro transfers electrons from a cytochrome bc 1 complex to a terminal oxidase, as proposed for the HiPIP in photosynthetic bacteria.

scholarly journals A cellular endolysosome-modulating pore-forming protein from a toad is negatively regulated by its paralog under oxidizing conditions

2020 ◽  
Vol 295 (30) ◽  
pp. 10293-10306 ◽  
Author(s):  
Qiquan Wang ◽  
Xianling Bian ◽  
Lin Zeng ◽  
Fei Pan ◽  
Lingzhen Liu ◽  
...  
Keyword(s):  
Disulfide Bond ◽  
Cell Biology ◽  
Biochemical Properties ◽  
Bacterial Toxin ◽  
Cell Physiology ◽  
Dependent Manner ◽  
Membrane Pore ◽  
Intracellular Vesicles

Endolysosomes are key players in cell physiology, including molecular exchange, immunity, and environmental adaptation. They are the molecular targets of some pore-forming aerolysin-like proteins (ALPs) that are widely distributed in animals and plants and are functionally related to bacterial toxin aerolysins. βγ-CAT is a complex of an ALP (BmALP1) and a trefoil factor (BmTFF3) in the firebelly toad (Bombina maxima). It is the first example of a secreted endogenous pore-forming protein that modulates the biochemical properties of endolysosomes by inducing pore formation in these intracellular vesicles. Here, using a large array of biochemical and cell biology methods, we report the identification of BmALP3, a paralog of BmALP1 that lacks membrane pore-forming capacity. We noted that both BmALP3 and BmALP1 contain a conserved cysteine in their C-terminal regions. BmALP3 was readily oxidized to a disulfide bond-linked homodimer, and this homodimer then oxidized BmALP1 via disulfide bond exchange, resulting in the dissociation of βγ-CAT subunits and the elimination of biological activity. Consistent with its behavior in vitro, BmALP3 sensed environmental oxygen tension in vivo, leading to modulation of βγ-CAT activity. Interestingly, we found that this C-terminal cysteine site is well conserved in numerous vertebrate ALPs. These findings uncover the existence of a regulatory ALP (BmALP3) that modulates the activity of an active ALP (BmALP1) in a redox-dependent manner, a property that differs from those of bacterial toxin aerolysins.

scholarly journals Rem2, a new member of the Rem/Rad/Gem/Kir family of Ras-related GTPases

2000 ◽  
Vol 347 (1) ◽  
pp. 223-231 ◽  
Author(s):  
Brian S. FINLIN ◽  
Haipeng SHAO ◽  
Keiko KADONO-OKUDA ◽  
Nan GUO ◽  
Douglas A. ANDRES
Keyword(s):  
Cellular Localization ◽  
Biochemical Characterization ◽  
Fluorescent Protein ◽  
Dissociation Constants ◽  
Intrinsic Rate ◽  
Biochemical Properties ◽  
Cell Physiology ◽  
Gtp Binding ◽  
C Terminus ◽  
Green Fluorescent

Here we report the molecular cloning and biochemical characterization of Rem2 (for Rem, ad and G-related 2), a novel GTP-binding protein identified on the basis of its homology with the Rem, Rad, Gem and Kir (RGK) family of Ras-related small GTP-binding proteins. Rem2 mRNA was detected in rat brain and kidney, making it the first member of the RGK family to be expressed at relatively high levels in neuronal tissues. Recombinant Rem2 binds GTP saturably and exhibits a low intrinsic rate of GTP hydrolysis. Surprisingly, the guanine nucleotide dissociation constants for both Rem2 and Rem are significantly different than the majority of the Ras-related GTPases, displaying higher dissociation rates for GTP than GDP. Localization studies with green fluorescent protein (GFP)-tagged recombinant protein fusions indicate that Rem2 has a punctate, plasma membrane localization. Deletion of the C-terminal seven amino acid residues that are conserved in all RGK family members did not affect the cellular distribution of the GFP fusion protein, whereas a larger deletion, including much of the polybasic region of the Rem2 C-terminus, resulted in its redistribution to the cytosol. Thus Rem2 is a GTPase of the RGK family with distinctive biochemical properties and possessing a novel cellular localization signal, consistent with its having a unique role in cell physiology.

scholarly journals Quantifying the closeness to a set of random curves via the mean marginal likelihood

2020 ◽  
Author(s):  
Cédric Rommel ◽  
Joseph Frédéric Bonnans ◽  
Baptiste Gregorutti ◽  
Pierre Martinon
Keyword(s):  
Marginal Likelihood ◽  
Marginal Density ◽  
Random Curves ◽  
Practical Applications ◽  
Random Functions ◽  
Practical Usefulness ◽  
Class Of Estimators ◽  
The Mean ◽  
Multivariate Density ◽  
Aircraft Trajectories

In this paper, we tackle the problem of quantifying the closeness of a newly observed curve to a given sample of random functions, supposed to have been sampled from the same distribution. We define a probabilistic criterion for such a purpose, based on the marginal density functions of an underlying random process. For practical applications, a class of estimators based on the aggregation of multivariate density estimators is introduced and proved to be consistent. We illustrate the effectiveness of our estimators, as well as the practical usefulness of the proposed criterion, by applying our method to a dataset of real aircraft trajectories.

scholarly journals Proanthocyanidins: Oligomeric Structures with Unique Biochemical Properties and Great Therapeutic Promise

2012 ◽  
Vol 7 (3) ◽  
pp. 1934578X1200700 ◽  
Author(s):  
Zhanjie Xu ◽  
Peng Du ◽  
Peter Meiser ◽  
Claus Jacob
Keyword(s):  
Protein Interactions ◽  
Biological Activities ◽  
Antioxidant Properties ◽  
Chemical Properties ◽  
Cancer Chemoprevention ◽  
Biochemical Properties ◽  
Synthetic Methods ◽  
Practical Applications ◽  
Wide Range ◽  
Physical And Chemical

Proanthocyanidins represent a unique class of oligomeric and polymeric secondary metabolites found ubiquitously and in considerable amounts in plants and some algae. These substances exhibit a range of rather surprising physical and chemical properties which, once applied to living organisms, are translated into a multitude of biological activities. The latter include antioxidant properties, cancer chemoprevention, anti-inflammatory and anti-diabetic effects as well as some exceptional, yet highly interesting activities, such as anti-nutritional and antimicrobial activity. Despite the wide range of activities and possible medical/agricultural applications of proanthocyanidins, many questions still remain, including issues related to bioavailability, metabolism and the precise biochemical, extra- and intracellular targets and mode(s) of action of these highly potent materials. Among the various physical and chemical interactions of such substances, strong binding to proteins appears to form the basis of many of their biological activities. Once easy-to-use synthetic methods to produce appropriate quantities of pure proanthocyanidins are available, it will be possible to identify the prime biological targets of these oligomers, study oligomer-protein interactions in more detail and develop possible practical applications in medicine and agriculture.

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