The process of phase separation allows for the establishment and formation of subcompartmentalized structures, thus enabling cells to perform simultaneous processes with precise organization and low energy requirements. Chemical modifications of proteins, RNA, and lipids alter the molecular environment facilitating enzymatic reactions at higher concentrations in particular regions of the cell. In this review, we discuss the nucleolus as an example of the establishment, dynamics, and maintenance of a membraneless organelle with a high level of organization.

Fibrillarin is a highly conserved nucleolar methyltransferase responsible for ribosomal RNA methylation across evolution from Archaea to humans. It has been reported that fibrillarin is involved in the methylation of histone H2A in nucleoli and other processes, including viral progression, cellular stress, nuclear shape, and cell cycle progression. We show that fibrillarin has an additional activity as a ribonuclease. The activity is affected by phosphoinositides and phosphatidic acid and insensitive to ribonuclease inhibitors. Furthermore, the presence of phosphatidic acid releases the fibrillarin-U3 snoRNA complex. We show that the ribonuclease activity localizes to the GAR (glycine/arginine-rich) domain conserved in a small group of RNA interacting proteins. The introduction of the GAR domain occurred in evolution in the transition from archaea to eukaryotic cells. The interaction of this domain with phospholipids may allow a phase separation of this protein in nucleoli.

Horizontal gene transfer (HGT) is a well-documented strategy used by bacteria to enhance their adaptability to challenging environmental conditions. Through HGT, a group of conserved genetic elements known as mobile genetic elements (MGEs) is disseminated within bacterial communities. MGEs offer numerous advantages to the host, increasing its fitness by acquiring new functions that help bacteria contend with adverse conditions, including exposure to heavy metal and antibiotics. This study explores MGEs within microbial communities along the Yucatan coast using a metatranscriptomics approach. Prior to this research, nothing was known about the coastal Yucatan’s microbial environmental mobilome and HGT processes between these bacterial communities. This study reveals a positive correlation between MGEs and antibiotic resistance genes (ARGs) along the Yucatan coast, with higher MGEs abundance in more contaminated sites. The Proteobacteria and Firmicutes groups exhibited the highest number of MGEs. It’s important to highlight that the most abundant classes of MGEs might not be the ones most strongly linked to ARGs, as observed for the recombination/repair class. This work presents the first geographical distribution of the environmental mobilome in Yucatan Peninsula mangroves.

Physiological response to feeding is crucial for various production factors such as feed catabolism and growth. Despite growing significance in red Octopus maya aquaculture, large-scale commercial production is limited by not sufficiently knowing their nutritional needs, especially their digestive physiology. Since this species is carnivorous, one of the main feeding aspects is directed to protein digestion, but its enzymatic digestive repertoire has not been studied yet at genomic and transcriptomic levels. This study searched for protease enzymes encoded in O. maya genome and expressed in the transcriptome, allowing an initial annotation of genes involved in protein catabolism; 117 amino acid sequences related to ‘octopus digestive enzymes’ were retrieved from 66 available-species’ genomes in the NCBI database, coding for cathepsins, papilins, and metalloproteases. Homology analysis identified 36 homologous sequences from O. maya transcriptome and three from its genome. Phylogenetic analysis grouped 37 of 39 sequences into 11 of 14 main clades, offering new insights into the evolutionary relationships and functional roles of these proteases. Phylogenetic and motif analyses resulted in selecting 19 amino acid O. maya sequences using multiple sequence alignment that were used to generate three-dimensional protein models. The obtained models revealed a diverse structural architecture among 16 modelled cathepsins; however, their catalytic potential to fully clarify their role in protein hydrolysis and cellular processes remains to be determined. Foundational data provides insights into biochemistry and physiology behind O. maya protein digestion. Further complementation of these results with enzymatic characterization of the identified proteases should allow for improved diet formulation in order to foster this species aquaculture.

Protein identity and functional roles within the cell provide the landscape of proteomics and other high-throughput technologies. However, not all protein sequences are cataloged with an identity or a functional protein family. The lack of identity and functional role of a set of proteins are collectively named as the dark proteome. Key structural features are, for example, ordered sequences (with a defined structural arrangement) and disordered sequences (presenting one or more intrinsically disordered stretches). Here, we reanalyzed eight proteomic datasets and the subset of the “unknown” proteome of S. lycopersicum to describe if there is a relationship between disorder, length, and tissue-specific abundance of proteins with key structural features in the relation of ordered/disordered abundance in the protein sequences. Intriguingly, we unveil that from the S. lycopersicum proteome, the “unknown” subset represents around 10% only. We further cataloged dark proteome in terms of ordered and disordered sequences and found that proteins with disorder represent around 23% of the total “unknown” proteins. Also, we describe an amino acid composition and sequence length enrichment both, in the ordered and disordered fraction of the dark proteome. Finally, we describe that proteins within the dark proteome can be related to a specific location and abundance in an organ or tissue. An unknown protein sequence presenting a combination of specific length and degree of disorder can be explored with other biotechnological alternatives to improve responses or tolerate abiotic stress, also serving as sensors during development or ripening stages. These findings suggest an opportunity to study “protein darkness” in terms of disorder and functional associations.

Drastic changes in temperature, salinity of soils and drought are some of the most studied abiotic stressors in important crops. Plants have developed various biochemical mechanisms to counteract these conditions. Transcription factors play a significant role in regulating stress responses. Previously, in our lab, it was identified that the CpRap2.4a protein, which belongs to the AP2/ERF superfamily, is related to the response to abiotic stress from extreme temperature, and confers thermal tolerance to Carica papaya CV. This study presents a randomized experimental strategy for the analysis of the physiological and biochemical responses of Nicotiana tabacum plants subjected to heat stress, and how the foliar application of the recombinantly expressed CpRap2.4a can modulate beneficial responses. Plants subjected to heat stress present a healthier physiology, as clearly shown by biochemical parameters. Moreover, physiological parameters also suggest an improvement of heat tolerance compared with the control group. Scanning electron microscopy suggests that stomatal aperture and conductance are the key mechanisms for how recombinantly expressed CpRap2.4a can act as a regulatory player to heat stress.