1,250 results match your criteria promiscuous genes

Metagenomics and Quantitative Stable Isotope Probing Offer Insights into Metabolism of Polycyclic Aromatic Hydrocarbon Degraders in Chronically Polluted Seawater.

mSystems 2021 May 11;6(3). Epub 2021 May 11.

Department of Biological Sciences, University of Southern California, Los Angeles, California, USA

Bacterial biodegradation is a significant contributor to remineralization of polycyclic aromatic hydrocarbons (PAHs)-toxic and recalcitrant components of crude oil as well as by-products of partial combustion chronically introduced into seawater via atmospheric deposition. The Deepwater Horizon oil spill demonstrated the speed at which a seed PAH-degrading community maintained by chronic inputs responds to acute pollution. We investigated the diversity and functional potential of a similar seed community in the chronically polluted Port of Los Angeles (POLA), using stable isotope probing with naphthalene, deep-sequenced metagenomes, and carbon incorporation rate measurements at the port and in two sites in the San Pedro Channel. Read More

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Evolving origin-of-transfer sequences on staphylococcal conjugative and mobilizable plasmids-who's mimicking whom?

Nucleic Acids Res 2021 May 3. Epub 2021 May 3.

Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia.

In Staphylococcus aureus, most multiresistance plasmids lack conjugation or mobilization genes for horizontal transfer. However, most are mobilizable due to carriage of origin-of-transfer (oriT) sequences mimicking those of conjugative plasmids related to pWBG749. pWBG749-family plasmids have diverged to carry five distinct oriT subtypes and non-conjugative plasmids have been identified that contain mimics of each. Read More

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21-Hydroxypregnane 21-O-malonylation, a crucial step in cardenolide biosynthesis, can be achieved by substrate-promiscuous BAHD-type phenolic glucoside malonyltransferases from Arabidopsis thaliana and homolog proteins from Digitalis lanata.

Phytochemistry 2021 Apr 28;187:112710. Epub 2021 Apr 28.

Lehrstuhl für Pharmazeutische Biologie, Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstraße 5, 91058, Erlangen, Germany. Electronic address:

Three putative 21-hydroxypregnane 21-O-malonyltransferases (21MaT) from Digitalis lanata were partially purified. Two of them were supposed to be BAHD-type enzymes. We were unable to purify them in quantities necessary for reliable sequencing. Read More

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Origin and evolution of the zinc finger antiviral protein.

PLoS Pathog 2021 Apr 26;17(4):e1009545. Epub 2021 Apr 26.

Laboratory of Retrovirology, The Rockefeller University, New York City, New York, United States of America.

The human zinc finger antiviral protein (ZAP) recognizes RNA by binding to CpG dinucleotides. Mammalian transcriptomes are CpG-poor, and ZAP may have evolved to exploit this feature to specifically target non-self viral RNA. Phylogenetic analyses reveal that ZAP and its paralogue PARP12 share an ancestral gene that arose prior to extensive eukaryote divergence, and the ZAP lineage diverged from the PARP12 lineage in tetrapods. Read More

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Genetic characterization at the species and symbiovar level of indigenous rhizobial isolates nodulating Phaseolus vulgaris in Greece.

Sci Rep 2021 Apr 21;11(1):8674. Epub 2021 Apr 21.

Laboratory of General and Agricultural Microbiology, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, Votanikos, 11855, Athens, Greece.

Phaseolus vulgaris (L.), commonly known as bean or common bean, is considered a promiscuous legume host since it forms nodules with diverse rhizobial species and symbiovars. Most of the common bean nodulating rhizobia are mainly affiliated to the genus Rhizobium, though strains belonging to Ensifer, Pararhizobium, Mesorhizobium, Bradyrhizobium, and Burkholderia have also been reported. Read More

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Synthetic production of prenylated naringenins in yeast using promiscuous microbial prenyltransferases.

Metab Eng Commun 2021 Jun 19;12:e00169. Epub 2021 Mar 19.

Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.

Reconstitution of prenylflavonoids using the flavonoid biosynthetic pathway and prenyltransferases (PTs) in microbes can be a promising attractive alternative to plant-based production or chemical synthesis. Here, we demonstrate that promiscuous microbial PTs can be a substitute for regiospecific but mostly unidentified botanical PTs. To test the prenylations of naringenin, we constructed a yeast strain capable of producing naringenin from l-phenylalanine by genomic integration of six exogenous genes encoding components of the naringenin biosynthetic pathway. Read More

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Analysis of metabolic network disruption in engineered microbial hosts due to enzyme promiscuity.

Metab Eng Commun 2021 Jun 7;12:e00170. Epub 2021 Mar 7.

Department of Computer Science, Tufts University, Medford, MA, USA.

Increasing understanding of metabolic and regulatory networks underlying microbial physiology has enabled creation of progressively more complex synthetic biological systems for biochemical, biomedical, agricultural, and environmental applications. However, despite best efforts, confounding phenotypes still emerge from unforeseen interplay between biological parts, and the design of robust and modular biological systems remains elusive. Such interactions are difficult to predict when designing synthetic systems and may manifest during experimental testing as inefficiencies that need to be overcome. Read More

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Population genomics and antimicrobial resistance dynamics of Escherichia coli in wastewater and river environments.

Commun Biol 2021 Apr 12;4(1):457. Epub 2021 Apr 12.

Antimicrobial Resistance Unit (ARU), Animal Health Department, Faculty of Veterinary Medicine and VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain.

Aquatic environments are key niches for the emergence, evolution and dissemination of antimicrobial resistance. However, the population diversity and the genetic elements that drive the dynamics of resistant bacteria in different aquatic environments are still largely unknown. The aim of this study was to understand the population genomics and evolutionary events of Escherichia coli resistant to clinically important antibiotics including aminoglycosides, in anthropogenic and natural water ecosystems. Read More

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Co-Incubation with PPARβ/δ Agonists and Antagonists Modeled Using Computational Chemistry: Effect on LPS Induced Inflammatory Markers in Pulmonary Artery.

Int J Mol Sci 2021 Mar 19;22(6). Epub 2021 Mar 19.

School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK.

Peroxisome proliferator activated receptor beta/delta (PPARβ/δ) is a nuclear receptor ubiquitously expressed in cells, whose signaling controls inflammation. There are large discrepancies in understanding the complex role of PPARβ/δ in disease, having both anti- and pro-effects on inflammation. After ligand activation, PPARβ/δ regulates genes by two different mechanisms; induction and transrepression, the effects of which are difficult to differentiate directly. Read More

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Modulation of Gene Expression in Actinobacteria by Translational Modification of Transcriptional Factors and Secondary Metabolite Biosynthetic Enzymes.

Front Microbiol 2021 16;12:630694. Epub 2021 Mar 16.

Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, Mexico.

Different types of post-translational modifications are present in bacteria that play essential roles in bacterial metabolism modulation. Nevertheless, limited information is available on these types of modifications in actinobacteria, particularly on their effects on secondary metabolite biosynthesis. Recently, phosphorylation, acetylation, or phosphopantetheneylation of transcriptional factors and key enzymes involved in secondary metabolite biosynthesis have been reported. Read More

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Refactoring the Conjugation Machinery of Promiscuous Plasmid RP4 into a Device for Conversion of Gram-Negative Isolates to Hfr Strains.

ACS Synth Biol 2021 04 22;10(4):690-697. Epub 2021 Mar 22.

Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, 28049, Spain.

Chromosomal exchange and subsequent recombination of the cognate DNA between bacteria was one of the most useful genetic tools (e.g., Hfr strains) for genetic analyses of before the genomic era. Read More

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ZFTA-translocations constitute ependymoma chromatin remodeling and transcription factors.

Cancer Discov 2021 Mar 19. Epub 2021 Mar 19.

Oncology/CRUK Cambridge Institute, University of Cambridge

ZFTA (C11orf95)-a gene of unknown function-partners with a variety of transcriptional co-activators in translocations that drive supratentorial ependymoma, a frequently lethal brain tumor. Understanding the function of ZFTA is key to developing therapies that inhibit these fusion proteins. Here, using a combination of transcriptomics, chromatin immunoprecipitation-sequencing, and proteomics, we interrogated a series of deletion-mutant genes to identify a tri-partite transformation mechanism of ZFTA-containing fusions, including: spontaneous nuclear translocation, extensive chromatin binding, and SWI/SNF, SAGA and NuA4/Tip60 HAT chromatin modifier complex recruitment. Read More

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COMMD1 Exemplifies the Power of Inbred Dogs to Dissect Genetic Causes of Rare Copper-Related Disorders.

Animals (Basel) 2021 Feb 25;11(3). Epub 2021 Feb 25.

Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 108, 3584 CM Utrecht, The Netherlands.

Wilson's Disease is a rare autosomal recessive disorder in humans, often presenting with hepatic copper overload. Finding the genetic cause of a rare disease, especially if it is related to food constituents like the trace element copper, is a Herculean task. This review describes examples of how the unique population structure of in-bred dog strains led to the discovery of a novel gene and two modifier genes involved in inherited copper toxicosis. Read More

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February 2021

Underground metabolism facilitates the evolution of novel pathways for vitamin B6 biosynthesis.

Appl Microbiol Biotechnol 2021 Mar 4;105(6):2297-2305. Epub 2021 Mar 4.

FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Universitätsplatz 1, 01968, Senftenberg, Germany.

The term vitamin B6 is a designation for the vitamers pyridoxal, pyridoxamine, pyridoxine and the respective phosphate esters pyridoxal-5'-phosphate (PLP), pyridoxamine-5'-phosphate and pyridoxine-5'-phosphate. Animals and humans are unable to synthesise vitamin B6. These organisms have to take up vitamin B6 with their diet. Read More

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Beyond alcohol oxidase: the methylotrophic yeast Komagataella phaffii utilizes methanol also with its native alcohol dehydrogenase Adh2.

FEMS Yeast Res 2021 Mar;21(2)

Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria.

Methylotrophic yeasts are considered to use alcohol oxidases to assimilate methanol, different to bacteria which employ alcohol dehydrogenases with better energy conservation. The yeast Komagataella phaffii carries two genes coding for alcohol oxidase, AOX1 and AOX2. The deletion of the AOX1 leads to the MutS phenotype and the deletion of AOX1 and AOX2 to the Mut- phenotype. Read More

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Basis of specificity for a conserved and promiscuous chromatin remodeling protein.

Elife 2021 Feb 12;10. Epub 2021 Feb 12.

Institute of Molecular Biology, University of Oregon, Eugene, United States.

Eukaryotic genomes are organized dynamically through the repositioning of nucleosomes. Isw2 is an enzyme that has been previously defined as a genome-wide, nonspecific nucleosome spacing factor. Here, we show that Isw2 instead acts as an obligately targeted nucleosome remodeler in vivo through physical interactions with sequence-specific factors. Read More

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February 2021

Thymus and autoimmunity.

Semin Immunopathol 2021 Feb 3;43(1):45-64. Epub 2021 Feb 3.

Institute of Pathology, University Medical Centre Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany.

The thymus prevents autoimmune diseases through mechanisms that operate in the cortex and medulla, comprising positive and negative selection and the generation of regulatory T-cells (Tregs). Egress from the thymus through the perivascular space (PVS) to the blood is another possible checkpoint, as shown by some autoimmune/immunodeficiency syndromes. In polygenic autoimmune diseases, subtle thymic dysfunctions may compound genetic, hormonal and environmental cues. Read More

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February 2021

Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes.

Proc Natl Acad Sci U S A 2021 Feb;118(6)

Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China;

It is well established that plasmids play an important role in the dissemination of antimicrobial resistance (AMR) genes; however, little is known about the role of the underlying interactions between different plasmid categories and other mobile genetic elements (MGEs) in shaping the promiscuous spread of AMR genes. Here, we developed a tool designed for plasmid classification, AMR gene annotation, and plasmid visualization and found that most plasmid-borne AMR genes, including those localized on class 1 integrons, are enriched in conjugative plasmids. Notably, we report the discovery and characterization of a massive insertion sequence (IS)-associated AMR gene transfer network (245 combinations covering 59 AMR gene subtypes and 53 ISs) linking conjugative plasmids and phylogenetically distant pathogens, suggesting a general evolutionary mechanism for the horizontal transfer of AMR genes mediated by the interaction between conjugative plasmids and ISs. Read More

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February 2021

Analyzing the G3BP-like gene family of Arabidopsis thaliana in early turnip mosaic virus infection.

Sci Rep 2021 Jan 26;11(1):2187. Epub 2021 Jan 26.

Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7 B, 38124, Braunschweig, Germany.

The Arabidopsis thaliana genome encodes several genes that are known or predicted to participate in the formation of stress granules (SG). One family of genes encodes for Ras GTPase-activating protein-binding protein (G3BP)-like proteins. Seven genes were identified, of which one of the members was already shown to interact with plant virus proteins in a previous study. Read More

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January 2021

In-silico identification of subunit vaccine candidates against lung cancer-associated oncogenic viruses.

Comput Biol Med 2021 Mar 12;130:104215. Epub 2021 Jan 12.

Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India. Electronic address:

Globally, ~20% of cancer malignancies are associated with virus infections. Lung cancer is the most prevalent cancer and has a 10% 5-year survival rate when diagnosed at stage IV. Cancer vaccines and oncolytic immunotherapy are promising treatment strategies for better clinical outcomes in advanced-stage cancer patients. Read More

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Systematic Pharmacology and GEO Database Mining Revealed the Therapeutic Mechanism of Xuefu Zhuyu Decoration for Atherosclerosis Cardiovascular Disease.

Front Cardiovasc Med 2020 3;7:592201. Epub 2020 Dec 3.

Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China.

Xuefu Zhuyu decoration (XFZYD), as a traditional Chinese compound recipe, has been used to treat atherosclerosis cardiovascular disease (ASCVD) for thousands of years in China, but its effective compounds and underlying treatment molecular mechanism remains promiscuous, which severely limits its clinical application. The effective components and their targets of XFZYD were predicted and screened based on the Traditional Chinese Medicine System Pharmacology (TCMSP) database. The candidate therapeutic targets of ASCVD were screened by Pharmacogenomics Knowledgebase (PharmGKB) and Comparative Toxicogenomics Database (CTD). Read More

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December 2020

RepC_soli: a novel promiscuous plasmid type of Rhodobacteraceae mediates horizontal transfer of antibiotic resistances in the ocean.

Environ Microbiol 2021 Jan 3. Epub 2021 Jan 3.

Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Inhoffenstraße 7 B, D-38124, Germany.

Alphaproteobacteria are typically characterized by a multipartite genome organization with a chromosome, stable chromids and accessory plasmids. Extrachromosomal elements determine the lifestyle of roseobacters and their horizontal transfer was previously correlated with rapid adaptations to novel ecological niches. We characterized the distribution and biology of a novel Rhodobacteraceae-specific plasmid type that was designated RepC_soli according to its diagnostic solitary replicase. Read More

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January 2021

Bidirectional Genetic Control of Phenotypic Heterogeneity and Its Implication for Cancer Drug Resistance.

Mol Biol Evol 2021 May;38(5):1874-1887

Department of Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.

Negative genetic regulators of phenotypic heterogeneity, or phenotypic capacitors/stabilizers, elevate population average fitness by limiting deviation from the optimal phenotype and increase the efficacy of natural selection by enhancing the phenotypic differences among genotypes. Stabilizers can presumably be switched off to release phenotypic heterogeneity in the face of extreme or fluctuating environments to ensure population survival. This task could, however, also be achieved by positive genetic regulators of phenotypic heterogeneity, or "phenotypic diversifiers," as shown by recently reported evidence that a bacterial divisome factor enhances antibiotic resistance. Read More

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The Neuromodulator-Encoding Gene Is Widely Distributed in the Human Skin Microbiome.

Front Microbiol 2020 1;11:573679. Epub 2020 Dec 1.

Microbial Genetics, University of Tübingen, Tübingen, Germany.

Trace amines (TA) are endogenously produced in mammals, have a low concentration in the central nervous system (CNS), but trigger a variety of neurological effects and intervene in host cell communication. It emerged that neurotransmitters and TA are produced also by the microbiota. As it has been shown that TA contribute to wound healing, we examined the skin microbiome of probands using shotgun metagenomics. Read More

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December 2020

The Methyltransferase DOT1L Controls Activation and Lineage Integrity in CD4 T Cells during Infection and Inflammation.

Cell Rep 2020 12;33(11):108505

Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton VIC 3800, Australia. Electronic address:

CD4 T helper (Th) cell differentiation is controlled by lineage-specific expression of transcription factors and effector proteins, as well as silencing of lineage-promiscuous genes. Lysine methyltransferases (KMTs) comprise a major class of epigenetic enzymes that are emerging as important regulators of Th cell biology. Here, we show that the KMT DOT1L regulates Th cell function and lineage integrity. Read More

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December 2020

Like Wings of a Bird: Functional Divergence and Complementarity between HLA-A and HLA-B Molecules.

Mol Biol Evol 2021 04;38(4):1580-1594

Laboratory of Anthropology, Genetics and Peopling History (AGP Lab), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.

Human leukocyte antigen (HLA) genes are among the most polymorphic of our genome, as a likely consequence of balancing selection related to their central role in adaptive immunity. HLA-A and HLA-B genes were recently suggested to evolve through a model of joint divergent asymmetric selection conferring all human populations, including those with severe loss of diversity, an equivalent immune potential. However, the mechanisms by which these two genes might undergo joint evolution while displaying very distinct allelic profiles in populations are still unknown. Read More

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Recent development and new insight of diversification and symbiosis specificity of legume rhizobia: mechanism and application.

J Appl Microbiol 2020 Dec 10. Epub 2020 Dec 10.

College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, P. R. China.

Currently, symbiotic rhizobia (sl., rhizobium) refer to the soil bacteria in α- and β-Proteobacteria that can induce root and/or stem nodules on some legumes and a few of nonlegumes. In the nodules, rhizobia convert the inert dinitrogen gas (N ) into ammonia (NH ) and supply them as nitrogen nutrient to the host plant. Read More

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December 2020

TGFβ promotes widespread enhancer chromatin opening and operates on genomic regulatory domains.

Nat Commun 2020 12 3;11(1):6196. Epub 2020 Dec 3.

Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Avenida Americo Vespucio 24, 41092, Seville, Spain.

The Transforming Growth Factor-β (TGFβ) signaling pathway controls transcription by regulating enhancer activity. How TGFβ-regulated enhancers are selected and what chromatin changes are associated with TGFβ-dependent enhancers regulation are still unclear. Here we report that TGFβ treatment triggers fast and widespread increase in chromatin accessibility in about 80% of the enhancers of normal mouse mammary epithelial-gland cells, irrespective of whether they are activated, repressed or not regulated by TGFβ. Read More

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December 2020

Plasmid replication-associated single-strand-specific methyltransferases.

Nucleic Acids Res 2020 12;48(22):12858-12873

New England Biolabs Inc., 240 County Road, Ipswich, MA, USA.

Analysis of genomic DNA from pathogenic strains of Burkholderia cenocepacia J2315 and Escherichia coli O104:H4 revealed the presence of two unusual MTase genes. Both are plasmid-borne ORFs, carried by pBCA072 for B. cenocepacia J2315 and pESBL for E. Read More

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December 2020

Expansion of the evolutionarily conserved network of J-domain proteins in the Arabidopsis mitochondrial import complex.

Plant Mol Biol 2021 Mar 18;105(4-5):385-403. Epub 2020 Nov 18.

Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Room Number 117 AB3, IISER Bhopal, Bhopal Bypass Road, Bhopal, MP, 462066, India.

Key Message: We report that discriminate interaction between the expanded mitochondrial chaperone network and variability in their expression might determine their functional specificities and impart robustness to mitochondrial import processes in plants. Mitochondrial Hsp70 (mtHsp70), the central component of the pre-sequence associated motor (PAM) complex, is crucial for the import of proteins to the mitochondrial matrix. Activity of mtHsp70 is regulated by a heterodimeric complex of two J-domain proteins (JDPs), Pam18 and Pam16. Read More

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