Vânia Pobre

Background/Objectives: The rising prevalence of antibiotic-resistant bacteria, particularly within biofilms, presents a critical challenge in treating hospital-acquired infections. Staphylococcus aureus is a clinically significant pathogen, notorious for its ability to form biofilms that drastically reduce antimicrobial susceptibility. This study aimed to characterize the metabolic response of S. aureus in both planktonic and biofilm states to under-stand resistance mechanisms better. A key objective was to optimize methodologies for large-scale biofilm production and high-yield RNA extraction, providing a vital tool for subsequent transcriptomic analyses. Methods: To reach our goals, we investigated two strains with differing resistance profiles: a methicillin-sensitive reference strain (ATCC 6538) and a methicillin-resistant clinical isolate (MRSA pHUA585). Biofilm morphology was characterized, and the response to vancomycin was assessed. To facilitate RNA extraction, we optimized a large-scale biofilm production method using a solid membrane support on agar plates, followed by RNA purification via an enhanced phenol/chloroform protocol. Results: Our results revealed distinct biofilm architectures between the strains, with differences in thickness and the distribution of nucleic acids and polysaccharides. Vancomycin exhibited a concentration-dependent inhibitory effect on both, though the response varied, suggesting strain-specific biofilm formation mechanisms and matrix composition. Furthermore, we successfully standardized the scaled-up biofilm production and obtained high-quality RNA. However, under the conditions tested, biofilms from both strains showed low expression of the icaA gene, a key mediator of polysaccharide intercellular adhesion, potentially indicating growth condition dependencies or biofilm maturity state. Conclusions: In summary, this work establishes a methodological foundation for biofilm research and provides crucial insights into the strain-specific phenotypic and potential genetic determinants that underline antibiotic tolerance in S. aureus biofilms.

Biofilms provide an ecological advantage against many environmental stressors, such as pH and temperature, making it the most common life‐cycle stage for many bacteria. These protective characteristics make eradication of bacterial biofilms challenging. This is especially true in the health sector where biofilm formation on hospital or patient equipment, such as respirators, or catheters, can quickly become a source of anti‐microbial resistant strains. Biofilms are complex structures encased in a self‐produced polymeric matrix containing numerous components such as polysaccharides, proteins, signalling molecules, extracellular DNA and extracellular RNA. Biofilm formation is tightly controlled by several regulators, including quorum sensing (QS), cyclic diguanylate (c‐di‐GMP) and small non‐coding RNAs (sRNAs). These three regulators in particular are fundamental in all stages of biofilm formation; in addition, their pathways overlap, and the significance of their role is strain‐dependent. Currently, ribonucleases are also of interest for their potential role as biofilm regulators, and their relationships with QS, c‐di‐GMP and sRNAs have been investigated. This review article will focus on these four biofilm regulators (ribonucleases, QS, c‐di‐GMP and sRNAs) and the relationships between them.

Bacterial biofilms are defined as complex aggregates of bacteria that grow attached to surfaces or are associated with interfaces. Bacteria within biofilms are embedded in a self-produced extracellular matrix made of polysaccharides, nucleic acids, and proteins. It is recognized that bacterial biofilms are responsible for the majority of microbial infections that occur in the human body, and that biofilm-related infections are extremely difficult to treat. This is related with the fact that microbial cells in biofilms exhibit increased resistance levels to antibiotics in comparison with planktonic (free-floating) cells. In the last years, the introduction into the market of novel compounds that can overcome the resistance to antimicrobial agents associated with biofilm infection has slowed down. If this situation is not altered, millions of lives are at risk, and this will also strongly affect the world economy. As such, research into the identification and eradication of biofilms is important for the future of human health. In this sense, this article provides an overview of techniques developed to detect and imaging biofilms as well as recent strategies that can be applied to treat biofilms during the several biofilm formation steps.

Summary: Pseudomonas putida is recognized as a very promising strain for industrial application due to its high redox capacity and frequently observed tolerance towards organic solvents. In this research, we studied the metabolic and transcriptional response of P. putida KT2440 exposed to large‐scale heterogeneous mixing conditions in the form of repeated glucose shortage. Cellular responses were mimicked in an experimental setup comprising a stirred tank reactor and a connected plug flow reactor. We deciphered that a stringent response‐like transcriptional regulation programme is frequently induced, which seems to be linked to the intracellular pool of 3‐hydroxyalkanoates (3‐HA) that are known to serve as precursors for polyhydroxyalkanoates (PHA). To be precise, P. putida is endowed with a survival strategy likely to access cellular PHA, amino acids and glycogen in few seconds under glucose starvation to obtain ATP from respiration, thereby replenishing the reduced ATP levels and the adenylate energy charge. Notably, cells only need 0.4% of glucose uptake to build those 3‐HA‐based energy buffers. Concomitantly, genes that are related to amino acid catabolism and β‐oxidation are upregulated during the transient absence of glucose. Furthermore, we provide a detailed list of transcriptional short‐ and long‐term responses that increase the cellular maintenance by about 17% under the industrial‐like conditions tested.

Background: Herbaspirillum seropedicae is a diazotrophic bacterium from the β-proteobacteria class that colonizes endophytically important gramineous species, promotes their growth through phytohormone-dependent stimulation and can express nif genes and fix nitrogen inside plant tissues. Due to these properties this bacterium has great potential as a commercial inoculant for agriculture. The H. seropedicae SmR1 genome is completely sequenced and annotated but despite the availability of diverse structural and functional analysis of this genome, studies involving small non-coding RNAs (sRNAs) has not yet been done. We have conducted computational prediction and RNA-seq analysis to select and confirm the expression of sRNA genes in the H. seropedicae SmR1 genome, in the presence of two nitrogen independent sources and in presence of naringenin, a flavonoid secreted by some plants. Results: This approach resulted in a set of 117 sRNAs distributed in riboswitch, cis-encoded and trans-encoded categories and among them 20 have Rfam homologs. The housekeeping sRNAs tmRNA, ssrS and 4.5S were found and we observed that a large number of sRNAs are more expressed in the nitrate condition rather than the control condition and in the presence of naringenin. Some sRNAs expression were confirmed in vitro and this work contributes to better understand the post transcriptional regulation in this bacterium. Conclusions: H. seropedicae SmR1 express sRNAs in the presence of two nitrogen sources and/or in the presence of naringenin. The functions of most of these sRNAs remains unknown but their existence in this bacterium confirms the evidence that sRNAs are involved in many different cellular activities to adapt to nutritional and environmental changes.

Pseudomonas putida is a micro-organism with great potential for industry due to its stress-endurance traits and easy manipulation of the metabolism. However, optimization is still required to improve production yields. In the last years, manipulation of bacterial small non-coding RNAs (ncRNAs) has been recognized as an effective tool to improve the production of industrial compounds. So far, very few ncRNAs are annotated in P. putida beyond the generally conserved. In the present study, P. putida was cultivated in a two-compartment scale-down bioreactor that simulates large-scale industrial bioreactors. We performed RNA-Seq of samples collected at distinct locations and time-points to predict novel and potentially important ncRNAs for the adaptation of P. putida to bioreactor stress conditions. Instead of using a purely genomic approach, we have rather identified regions of putative ncRNAs with high expression levels using two different programs (Artemis and sRNA detect). Only the regions identified with both approaches were considered for further analysis and, in total, 725 novel ncRNAs were predicted. We also found that their expression was not constant throughout the bioreactor, showing different patterns of expression with time and position. This is the first work focusing on the ncRNAs whose expression is triggered in a bioreactor environment. This information is of great importance for industry, since it provides possible targets to engineer more effective P. putida strains for large-scale production.

The transition between exponential and stationary phase is a natural phenomenon for all bacteria and requires a massive readjustment of the bacterial transcriptome. Exoribonucleases are key enzymes in the transition between the two growth phases. PNPase, RNase R and RNase II are the major degradative exoribonucleases in Escherichia coli. We analysed the whole transcriptome of exponential and stationary phases from the WT and mutants lacking these exoribonucleases (Δpnp, Δrnr, Δrnb, and ΔrnbΔrnr). When comparing the cells from exponential phase with the cells from stationary phase more than 1000 transcripts were differentially expressed, but only 491 core transcripts were common to all strains. There were some differences in the number and transcripts affected depending on the strain, suggesting that exoribonucleases influence the transition between these two growth phases differently. Interestingly, we found that the double mutant RNase II/RNase R is similar to the RNase R single mutant in exponential phase while in stationary phase it seems to be closer to the RNase II single mutant. This is the first global transcriptomic work comparing the roles of exoribonucleases in the transition between exponential and stationary phase.

Exoribonucleases are crucial for RNA degradation in Escherichia coli but the roles of RNase R and PNPase and their potential overlap in stationary phase are not well characterized. Here, we used a genome-wide approach to determine how RNase R and PNPase affect the mRNA half-lives in the stationary phase. The genome-wide mRNA half-lives were determined by a dynamic analysis of transcriptomes after transcription arrest. We have combined the analysis of mRNA half-lives with the steady-state concentrations (transcriptome) to provide an integrated overview of the in vivo activity of these exoribonucleases at the genome-scale. The values of mRNA half-lives demonstrated that the mRNAs are very stable in the stationary phase and that the deletion of RNase R or PNPase caused only a limited mRNA stabilization. Intriguingly the absence of PNPase provoked also the destabilization of many mRNAs. These changes in mRNA half-lives in the PNPase deletion strain were associated with a massive reorganization of mRNA levels and also variation in several ncRNA concentrations. Finally, the in vivo activity of the degradation machinery was found frequently saturated by mRNAs in the PNPase mutant unlike in the RNase R mutant, suggesting that the degradation activity is limited by the deletion of PNPase but not by the deletion of RNase R. This work had identified PNPase as a central player associated with mRNA degradation in stationary phase.