Prochlorococcus phage ferredoxin: structural characterization and electron transfer to cyanobacterial sulfite reductases.

Marine cyanobacteria are infected by phages whose genomes encode ferredoxin (Fd) electron carriers. These Fds are thought to redirect the energy harvested from light to phage-encoded oxidoreductases that enhance viral fitness, but it is unclear how the biophysical properties and partner specificities of phage Fds relate to those of photosynthetic organisms. Here, results of a bioinformatics analysis using a sequence similarity network revealed that phage Fds are most closely related to cyanobacterial Fds that transfer electrons from photosystems to oxidoreductases involved in nutrient assimilation. Structural analysis of myovirus P-SSM2 Fd (pssm2-Fd), which infects the cyanobacterium Prochlorococcus marinus, revealed high levels of similarity to cyanobacterial Fds (root mean square deviations of ≤0.5 Å). Additionally, pssm2-Fd exhibited a low midpoint reduction potential (-336 mV versus a standard hydrogen electrode), similar to other photosynthetic Fds, although it had lower thermostability (Tm = 28 °C) than did many other Fds. When expressed in an Escherichia coli strain deficient in sulfite assimilation, pssm2-Fd complemented bacterial growth when coexpressed with a P. marinus sulfite reductase, revealing that pssm2-Fd can transfer electrons to a host protein involved in nutrient assimilation. The high levels of structural similarity with cyanobacterial Fds and reactivity with a host sulfite reductase suggest that phage Fds evolved to transfer electrons to cyanobacterially encoded oxidoreductases.

Pyridine-2,6-Dithiocarboxylic Acid and Its Metal Complexes: New Inhibitors of New Delhi Metallo ß-Lactamase-1.

Keywords: NDM-1 inhibitors; marine-derived Streptomyces sp.; carbapenem-resistant Enterobacteriaceae; metal chelators.

Large language models generate functional protein sequences across diverse families.

Deep-learning language models have shown promise in various biotechnological applications, including protein design and engineering. Here we describe ProGen, a language model that can generate protein sequences with a predictable function across large protein families, akin to generating grammatically and semantically correct natural language sentences on diverse topics. The model was trained on 280 million protein sequences from >19,000 families and is augmented with control tags specifying protein properties. ProGen can be further fine-tuned to curated sequences and tags to improve controllable generation performance of proteins from families with sufficient homologous samples. Artificial proteins fine-tuned to five distinct lysozyme families showed similar catalytic efficiencies as natural lysozymes, with sequence identity to natural proteins as low as 31.4%. ProGen is readily adapted to diverse protein families, as we demonstrate with chorismate mutase and malate dehydrogenase.

The Structure of the Arabidopsis PEX4-PEX22 Peroxin Complex-Insights Into Ubiquitination at the Peroxisomal Membrane.

Peroxisomes are eukaryotic organelles that sequester critical oxidative reactions and process the resulting reactive oxygen species into less toxic byproducts. Peroxisome function and formation are coordinated by peroxins (PEX proteins) that guide peroxisome biogenesis and division and shuttle proteins into the lumen and membrane of the organelle. Despite the importance of peroxins in plant metabolism and development, no plant peroxin structures have been reported. Here we report the X-ray crystal structure of the PEX4-PEX22 peroxin complex from the reference plant Arabidopsis thaliana. PEX4 is a ubiquitin-conjugating enzyme (UBC) that ubiquitinates proteins associated with the peroxisomal membrane, and PEX22 is a peroxisomal membrane protein that anchors PEX4 to the peroxisome and facilitates PEX4 activity. We co-expressed Arabidopsis PEX4 as a translational fusion with the soluble PEX4-interacting domain of PEX22 in E. coli. The fusion was linked via a protease recognition site, allowing us to separate PEX4 and PEX22 following purification and solve the structure of the complex. We compared the structure of the PEX4-PEX22 complex to the previously published structures of yeast orthologs. Arabidopsis PEX4 displays the typical UBC structure expected from its sequence. Although Arabidopsis PEX22 lacks notable sequence identity to yeast PEX22, it maintains a similar Rossmann fold-like structure. Several salt bridges are positioned to contribute to the specificity of PEX22 for PEX4 versus other Arabidopsis UBCs, and the long unstructured PEX22 tether would allow PEX4-mediated ubiquitination of distant peroxisomal membrane targets without dissociation from PEX22. The Arabidopsis PEX4-PEX22 structure also revealed that the residue altered in pex4-1 (P123L), a mutant previously isolated via a forward-genetic screen for peroxisomal dysfunction, is near the active site cysteine of PEX4. We demonstrated in vitro UBC activity for the PEX4-PEX22 complex and found that the pex4-1 enzyme has reduced in vitro ubiquitin-conjugating activity and altered specificity compared to PEX4. Our findings illuminate the role of PEX4 and PEX22 in peroxisome structure and function and provide tools for future exploration of ubiquitination at the peroxisome surface.

Semaphorin5A expression in the developing chick telencephalon.

In the present study, we analyzed the expression of Semaphorin5A (Sema5A), a gene implicated in axon guidance and many other processes of neuronal development, in the developing chick telencephalon. By using a heterologous mouse probe and in situ hybridization techniques, we showed distinct patterns of Sema5A expression within the chick telencephalon. In early development, Sema5A was present in pallial regions, mainly in the neuroepithelium and in the deep mantle of ventral and lateral pallia, and in the subpallium. As development proceeds, some ventral pallial derivatives maintained a moderate to strong Sema5A expression, whereas other lateral or dorsal pallial derivatives showed low to moderate expression of Sema5A. The overall expression of Sema5A during development in the chick telencephalon was similar to that reported in mouse. Moreover, the expression of Sema5A in mesencephalic, diencephalic, and telencephalic centers related to the tectofugal system suggests an important role of this gene in the development.

Distribution of nitric oxide-producing neurons in the developing and adult mouse amygdalar basolateral complex.

We analysed the expression of neuronal nitric oxide synthase (nNOS) in the mouse amygdalar basolateral complex (BLC) from embryonic day 15.5 to adult, using standard immunohistochemical methods. Our results indicate that each nucleus of the amygdalar basolateral complex displays a distinct nNOS expression pattern, which is established during the ontogenesis with minor changes in the adult. The basomedial nucleus (BM) exhibited the highest nNOS immunoreactivity in the basolateral complex, observable from early embryonic stages, whereas the lateral nucleus displayed the lowest level of immunoreactivity. The expression pattern for nNOS in the basolateral nucleus differed substantially from that of the lateral and basomedial nuclei, showing a slightly increase in the number of nNOS cells and neuropil staining from intermediate developmental until early postnatal stages. Two distinct types of nitrergic neurons, densely and lightly stained neurons, were observed in the developing basolateral complex. Both types of putative nitrergic neurons were unevenly distributed in the basolateral complex. On the basis of previous data regarding the colocalization between nNOS and GABA in the mouse claustrum, we suggest that nNOS expressing neurons in the basolateral amygdalar complex are both GABAergic and non-GABAergic.

Distinct types of nitric oxide-producing neurons in the developing and adult mouse claustrum.

We studied at the light and electron microscopic levels the nitric oxide-producing neurons in the mouse claustrum. Nicotinamide adenine dinucleotide phosphate (NADPH)-diaphorase histochemistry and neuronal nitric oxide synthase (nNOS) immunohistochemical staining were used to reveal putative nitrergic neurons. We also analyzed colocalization of nNOS with the inhibitory neurotransmitter gamma-aminobutyric acid (GABA) as well as the ontogenesis of the nNOS-immunoreactive neurons, providing evidence for different populations of nitrergic neurons in the mouse claustrum. The general staining pattern was similar for the histochemical and the immunohistochemical methods, resulting in neuron and neuropil staining throughout the whole claustrum. We described two populations of nitric oxide-producing neurons in the mouse claustrum on the basis of a different level of nNOS expression. Densely nNOS-stained neurons were mostly GABA immunoreactive, displayed ultrastructural features typically seen in aspiny neurons, and may originate in the subpallium; they were first seen in the claustrum at embryonic stage 17.5 and probably represent local inhibitory interneurons. Densely stained cells were found from rostral to caudal levels throughout the dorsal claustrum and the endopiriform nucleus. Lightly nNOS-stained neurons, on the other hand, were more numerous than densely stained ones, especially in the dorsal claustrum. These claustral lightly stained cells, barely observed in the NADPH-diaphorase reacted sections, were mostly non-GABAergic, and appeared earlier during ontogenesis than densely stained cells (at embryonic stages 15.5-16.5). We suggest that these neurons are probably projection neurons.