Microbial production of commodity and specialty chemicals has the potential to decrease our reliance on fossil fuels and reduce the accompanying environmental effects. The scope of traditional biomanufacturing can be greatly enhanced by constructing new-to-nature pathways toward target chemicals. Here, we outline the principles of artificial pathway design and engineering, highlight notable examples and provide an outlook on its future.

The production of commodity and specialty chemicals relies heavily on fossil fuels. The negative impact of this dependency on our environment and climate has spurred a rising demand for more sustainable methods to obtain such chemicals from renewable resources. Herein, biotransformations of these renewable resources facilitated by enzymes or (micro)organisms have gained significant attention, since they can occur under mild conditions and reduce waste. These biotransformations typically leverage natural metabolic processes, which limits the scope and production capacity of such processes. In this mini-review, we provide an overview of advancements made in the past 5 years to expand the repertoire of biotransformations in engineered microorganisms. This ranges from redesign of existing pathways driven by retrobiosynthesis and computational design to directed evolution of enzymes and de novo pathway design to unlock novel routes for the synthesis of desired chemicals. We highlight notable examples of pathway designs for the production of commodity and specialty chemicals, showcasing the potential of these approaches. Lastly, we provide an outlook on future pathway design approaches.

Autophagy is a conserved intracellular degradation system in eukaryotes, involving the sequestration of degradation targets into autophagosomes. Autophagosome formation and cargo selectivity rely on core Atg proteins and cargo receptors, respectively. In this review, I cover the 30-year history of structural studies on core Atg proteins and cargo receptors and discuss the molecular mechanisms of autophagosome formation and selective autophagy.

Autophagy is a conserved intracellular degradation system in eukaryotes, involving the sequestration of degradation targets into autophagosomes, which are subsequently delivered to lysosomes (or vacuoles in yeasts and plants) for degradation. In budding yeast, starvation-induced autophagosome formation relies on approximately 20 core Atg proteins, grouped into six functional categories: the Atg1/ULK complex, the phosphatidylinositol-3 kinase complex, the Atg9 transmembrane protein, the Atg2–Atg18/WIPI complex, the Atg8 lipidation system, and the Atg12–Atg5 conjugation system. Additionally, selective autophagy requires cargo receptors and other factors, including a fission factor, for specific sequestration. This review covers the 30-year history of structural studies on core Atg proteins and factors involved in selective autophagy, examining X-ray crystallography, NMR, and cryo-EM techniques. The molecular mechanisms of autophagy are explored based on protein structures, and future directions in the structural biology of autophagy are discussed, considering the advancements in the era of AlphaFold.

RAN binding protein 2 (RANBP2/Nup358) is a cytoplasmic filament nucleoporin involved in various cellular processes, such as nucleocytoplasmic transport and post-translational modifications. This review comprehensively discusses how dysregulation or mutation of RANBP2 contributes to human pathologies, and how the dynamic chromosomal region containing RANBP2 led to the appearance of the RGPD gene family during ape evolution.

RANBP2/Nup358 (Ran Binding Protein 2) is a nucleoporin and a key component of the nuclear pore complex. Through its multiple functions (e.g. SUMOylation, regulation of nucleocytoplasmic transport) and subcellular localizations (e.g. at the nuclear envelope, kinetochores, annulate lamellae), it is involved in many cellular processes. RANBP2 dysregulation or mutation leads to the development of human pathologies, such as Acute Necrotizing Encephalopathy 1 (ANE1), cancer, neurodegenerative diseases and it is also involved in viral infections. The chromosomal region containing the RANBP2 gene is highly dynamic, with high structural variation and recombination events that led to the appearance of a gene family called RGPD (RANBP2 and GCC2 Protein Domains), with multiple gene loss/duplication events during ape evolution. Although RGPD homoplasy and maintenance during evolution suggest they might confer an advantage to their hosts, their functions are still unknown and understudied. In this review, we discuss the appearance and importance of RANBP2 in metazoans and its function-related pathologies, caused by an alteration of its expression levels (through promotor activity, post-transcriptional or post-translational modifications), its localization or genetic mutations.

We consider the features of the nuclear lamina and NPC comparing humans, yeasts and trypanosomes. We discuss how those nuclear elements are structured in trypanosomes and how they differ from, or are conserved with other eukaryotic lineages. We also discuss the functional and evolutionary aspects of those fundamental elements of nuclear structure.

One of the remarkable features of eukaryotes is the nucleus, delimited by the nuclear envelope, a complex structure and home to the nuclear lamina and nuclear pore complex (NPC). For decades these structures were believed to be mainly architectural elements and, in the case of the NPC, simply facilitating nucleocytoplasmic trafficking. More recently the critical roles of the lamina, NPC and other nuclear envelope constituents in genome organisation, maintaining chromosomal domains and regulating gene expression have been recognised. Importantly, mutations in genes encoding lamina and NPC components lead to pathogenesis in humans, while in pathogenic protozoa disrupt the progression of normal development and expression of pathogenesis-related genes. Here we review features of the lamina and NPC across eukaryotes and discuss how these elements are structured in trypanosomes, protozoa of high medical and veterinary importance, highlighting lineage-specific and conserved aspects of nuclear organisation.

Autophagy is stimulated by starvation (amino acids and/or glucose deprivation) and growth factor limitation. In addition, mechanical forces are also positive regulators of autophagy. Growth factors and mechanical forces trigger signaling from the cell surface including from the primary cilium (PC) whereas nutrients directly act intracellularly. Many of the stimuli that control autophagy converge on the kinases mTOR and AMPK.

Macroautophagy is a lysosomal degradative pathway for intracellular macromolecules, protein aggregates and organelles. The formation of the autophagosome, a double membrane-bound structure that sequesters cargoes before their delivery to the lysosome, is regulated by several stimuli in multicellular organisms. Pioneering studies in rat liver showed the importance of amino acids, insulin and glucagon in controlling macroautophagy. Thereafter, many studies have deciphered the signaling pathways downstream of these biochemical stimuli to control autophagosome formation. Two signaling hubs have emerged: the kinase mTOR, in a complex at the surface of lysosomes which is sensitive to nutrients and hormones; and AMPK, which is sensitive to the cellular energetic status. Besides nutritional, hormonal and energetic fluctuations, many organs have to respond to mechanical forces (compression, stretching and shear stress). Recent studies have shown the importance of mechanotransduction in controlling macroautophagy. This regulation engages cell surface sensors, such as the primary cilium, in order to translate mechanical stimuli into biological responses.