Mitochondrial genome of Neuryurus rudis (Xenarthra, Cingulata); contribution to phylogeny and origin of glyptodonts.

The remarkable glyptodonts have sparked the interest of evolutionary biologists since the 19th century, in their attempts to elucidate the phylogenetic relationships among the various species of these armored giants and their relationship with other xenarthrans. In recent years, the molecular analysis of the first glyptodont has included them within the cingulates, as a special group of armadillos that lost the mobility of the bands of their armor during their evolutionary history. In this research, we obtained the mitochondrial DNA sequence of the elusive and poorly known glyptodont Neuryurus rudis, inferring its phylogenetic position with respect to the glyptodont Doedicurus sp.

Arabidopsis AGO1 N-terminal extension acts as an essential hub for PRMT5 interaction and post-translational modifications.

Plant ARGONAUTE (AGO) proteins play pivotal roles regulating gene expression through small RNA (sRNA) -guided mechanisms. Among the 10 AGO proteins in Arabidopsis thaliana, AGO1 stands out as the main effector of post-transcriptional gene silencing. Intriguingly, a specific region of AGO1, its N-terminal extension (NTE), has garnered attention in recent studies due to its involvement in diverse regulatory functions, including subcellular localization, sRNA loading and interactions with regulatory factors.

The p53 tumor suppressor regulates AKR1B1 expression, a metastasis-promoting gene in breast cancer.

Alteration of metabolism in cancer cells is a central aspect of the mechanisms that sustain aggressive traits. Aldo-keto reductase 1 B1 (AKR1B1) catalyzes the reduction of several aldehydes to alcohols consuming NADPH. Nevertheless, the ability of AKR1B1 to reduce different substrates renders difficult to comprehensively ascertain its biological role.

The Zika virus infection remodels the expression of the synaptotagmin-9 secretory protein.

The exact mechanisms involved in flaviviruses virions' release and the specific secretion of viral proteins, such as the Non Structural protein-1 (NS1), are still unclear. While these processes might involve vesicular transport to the cell membrane, NS1 from some flaviviruses was shown to participate in viral assembly and release. Here, we assessed the effect of the Zika virus (ZIKV) NS1 expression on the cellular proteome to identify trafficking-related targets that may be altered in the presence of the viral protein.

Arabidopsis mediator subunit 17 connects transcription with DNA repair after UV-B exposure.

Mediator 17 (MED17) is a subunit of the Mediator complex that regulates transcription initiation in eukaryotic organisms. In yeast and humans, MED17 also participates in DNA repair, physically interacting with proteins of the nucleotide excision DNA repair system, but this function in plants has not been investigated. We studied the role of MED17 in Arabidopsis plants exposed to UV-B radiation.

Structural basis for the Pr-Pfr long-range signaling mechanism of a full-length bacterial phytochrome at the atomic level.

Phytochromes constitute a widespread photoreceptor family that typically interconverts between two photostates called Pr (red light–absorbing) and Pfr (far-red light–absorbing). The lack of full-length structures solved at the (near-)atomic level in both pure Pr and Pfr states leaves gaps in the structural mechanisms involved in the signal transmission pathways during the photoconversion. Here, we present the crystallographic structures of three versions from the plant pathogen virulence regulator BphP bacteriophytochrome, including two full-length proteins, in the Pr and Pfr states.

Starting a new recombinant protein production project in Escherichia coli.

One of the goals in recombinant protein production in Escherichia coli is to maximize productivity. High volumetric and specific yields can be reached after careful selection of expression strains and optimization of cultivation parameters. In this chapter, we review the many tools available to make the most out of this versatile microbial cell factory.

From the notebook to recombinant protein production in Escherichia coli: Design of expression vectors and gene cloning.

Research in recombinant protein expression in microorganism hosts spans half a century. The field has evolved from mostly trial-and-error approaches to more rational strategies, including careful design of the expression vectors and the coding sequence for the protein of interest. It is important to reflect on many aspects about vector construction, such as codon usage, integration site, coding sequence mutagenesis and many others.

Structural features of the plant N-recognin ClpS1 and sequence determinants in its targets that govern substrate selection.

In the N-degron pathway of protein degradation of Escherichia coli, the N-recognin ClpS identifies substrates bearing N-terminal phenylalanine, tyrosine, tryptophan, or leucine and delivers them to the caseinolytic protease (Clp). Chloroplasts contain the Clp system, but whether chloroplastic ClpS1 adheres to the same constraints is unknown. Moreover, the structural underpinnings of substrate recognition are not completely defined.

Biochemical characterization of ClpB3, a chloroplastic disaggregase from Arabidopsis thaliana.

The first biochemical characterization of a chloroplastic disaggregase is reported (Arabidopsis thaliana ClpB3). ClpB3 oligomerizes into active hexamers that resolubilize aggregated substrates using ATP and without the aid of partners. Disaggregases from the Hsp100/Clp family are a type of molecular chaperones involved in disassembling protein aggregates.

New tools for recombinant protein production in Escherichia coli: A 5-year update.

The production of proteins in sufficient amounts is key for their study or use as biotherapeutic agents. Escherichia coli is the host of choice for recombinant protein production given its fast growth, easy manipulation, and cost-effectiveness. As such, its protein production capabilities are continuously being improved.

Proteome variation of the rat liver after static cold storage assayed in an ex vivo model.

Cold storage is a common procedure for liver preservation in a transplant setting. However, during cold ischemia, the liver suffers molecular alterations that can affect its performance. Also, deleterious mechanisms set forth in the storage phase are exacerbated during reperfusion.

A Gatekeeper Residue of ClpS1 from Arabidopsis thaliana Chloroplasts Determines its Affinity Towards Substrates of the Bacterial N-End Rule.

Proteins that are to be eliminated must be proficiently recognized by proteolytic systems so that inadvertent elimination of useful proteins is avoided. One mechanism to ensure proper recognition is the presence of N-terminal degradation signals (N-degrons) that are targeted by adaptor proteins (N-recognins). The members of the caseinolytic protease S (ClpS) family of N-recognins identify targets bearing an N-terminal phenylalanine, tyrosine, tryptophan or leucine residue, and then present them to a protease system.

Dynamic regulation of Pin1 expression and function during zebrafish development.

The prolyl isomerase Pin1 plays a key role in the modulation of proline-directed phosphorylation signaling by inducing local conformational changes in phosphorylated protein substrates. Extensive studies showed different roles for Pin1 in physiological processes and pathological conditions such as cancer and neurodegenerative diseases. However, there are still several unanswered questions regarding its biological role.

Characterization of the accessory protein ClpT1 from Arabidopsis thaliana: oligomerization status and interaction with Hsp100 chaperones.

Background: The caseinolytic protease (Clp) is crucial for chloroplast biogenesis and proteostasis. The Arabidopsis Clp consists of two heptameric rings (P and R rings) assembled from nine distinct subunits. Hsp100 chaperones (ClpC1/2 and ClpD) are believed to dock to the axial pores of Clp and then transfer unfolded polypeptides destined to degradation.

Recombinant protein expression in Escherichia coli: advances and challenges.

Escherichia coli is one of the organisms of choice for the production of recombinant proteins. Its use as a cell factory is well-established and it has become the most popular expression platform. For this reason, there are many molecular tools and protocols at hand for the high-level production of heterologous proteins, such as a vast catalog of expression plasmids, a great number of engineered strains and many cultivation strategies.

Toward a unified model of the action of CLP/HSP100 chaperones in chloroplasts.

In chloroplasts, Hsp70 and Hsp100 chaperones have been long suspected to be the motors that provide the necessary energy for the import of precursor proteins destined to the organelle. The chaperones associate with the import translocon and meet the transit peptides as they emerge through the channel. After decades of active research, recent findings demonstrated that Hsp100 chaperones recognize transit peptides both in vitro and in vivo.

Chloroplastic Hsp100 chaperones ClpC2 and ClpD interact in vitro with a transit peptide only when it is located at the N-terminus of a protein.

Background: Clp/Hsp100 chaperones are involved in protein quality control. They act as independent units or in conjunction with a proteolytic core to degrade irreversibly damaged proteins. Clp chaperones from plant chloroplasts have been also implicated in the process of precursor import, along with Hsp70 chaperones.

Insights into the Clp/HSP100 chaperone system from chloroplasts of Arabidopsis thaliana.

HSP100 proteins are molecular chaperones involved in protein quality control. They assist in protein (un)folding, prevent aggregation, and are thought to participate in precursor translocation across membranes. Caseinolytic proteins ClpC and ClpD from plant chloroplasts belong to the HSP100 family.

Rare codon content affects the solubility of recombinant proteins in a codon bias-adjusted Escherichia coli strain.

Background: The expression of heterologous proteins in Escherichia coli is strongly affected by codon bias. This phenomenon occurs when the codon usage of the mRNA coding for the foreign protein differs from that of the bacterium. The ribosome pauses upon encountering a rare codon and may detach from the mRNA, thereby the yield of protein expression is reduced.

D-Mannose-binding sites are putative sperm determinants of human oocyte recognition and fertilization.

The aim of the present study was to further evaluate the participation of D-mannose in the process of human sperm-egg interaction. Zona pellucida binding competitive assays in the presence of D-mannose were carried out using discarded oocytes from IVF. Spermatozoa were capacitated and D-mannose-binding site (MBS) expression, sperm viability and follicular fluidinduced acrosome reaction (AR) were evaluated.

Doses of levonorgestrel comparable to that delivered by the levonorgestrel-releasing intrauterine system can modify the in vitro expression of zona binding sites of human spermatozoa.

Background: The levonorgestrel-releasing intrauterine system (LNG-IUS) exerts its contraceptive effect by interfering with sperm transport through the female genital tract and with ovulation. However, the possibility cannot be discarded that the device exerts a direct effect on sperm function, thus, helping prevent fertilization.

Objectives: The purpose of this study is to evaluate whether LNG at doses comparable to that measured in the uterus during the use of the LNG-IUS affects the detection of D-mannose binding sites or zona pellucida (ZP) receptors on human spermatozoa.