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Post-Transcriptional Control in the Regulation of Polyhydroxy- Alkanoates Synthesis

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Post-Transcriptional Control in the Regulation of Polyhydroxy- Alkanoates Synthesis Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 23 August 2021 Review Post-transcriptional control in the regulation of polyhydroxy- alkanoates synthesis Alexandra Peregrina1*, João Martins-Lourenço1, Filomena Freitas 2,3, Maria A. M. Reis 2,3 and Cecília M. Arraiano1* 1 Control of Gene Expression Lab., Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal; [email protected] (J.M-L.) 2 Associate Laboratory i4HB-Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, 2829-516 Ca- parica, Portugal; [email protected] (F.F.); [email protected] (M.A.M.R.) 3 UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal * Correspondence: [email protected] (A.P.); [email protected] (C.M.A.) Abstract: The large production of non-degradable petrol-based plastics has become a major global issue due to its environ- mental pollution. Biopolymers produced by microorganisms such as polyhydroxyalkanoates (PHAs) are gaining potential as a sustainable alternative, but the high cost associated to their industrial production has been a limiting factor. Post-transcriptional regulation is a key step to control gene expression in changing environments and has been reported to play a major role in numerous cellular processes. However, limited reports are available con- cerning the regulation of PHA accumulation in bacteria, and many essential regulatory factors still need to be identified. Here, we review studies where the synthesis of PHA has been reported to be regulated at the post-transcriptional level, and we analyze the RNA-mediated networks involved. Finally, we discuss the forth- coming research on riboregulation, synthetic and metabolic engineering which could lead to improved strategies for PHAs synthesis in industrial production, thereby reducing the costs currently associated with this procedure. Keywords: Polyhydroxyalkanoates; mcl-PHA; scl-PHA; Post-transcriptional regulation; Riboregulation; Small non-coding RNAs 1. INTRODUCTION 1.1. The age of plastics Petroleum‐based plastics are pervasive appearing as cheap and easy to make but at the cost of the environ- mental toll [1,2]. Eight million tons of plastic end up in the oceans every year, where they break down into mi- cro-and nanoplastics [3,4]. Plastics have also been found falling out of the air in several mountain locations. This discovery suggests that, after the evaporation of the water, microplastics are carried around the planet in atmos- pheric winds, becoming part of the breathable air [5]. The impact of deposition of waste plastics in the land is also extremely relevant. Animals eat plastic and can get wrapped up, trapped or asphyxiated by them [6]. In addition, plastics can easily enter the food chain and have adverse consequences for humans. During their processing and consumption, they release toxic additives that were used to shape, harden or make them flexible, and these addi- tives can enter into the food chain and water supply. For instance, bisphenol A (BPA), a common precursor of widely used plastics, was found in the urine of approx. 93% of the 2,517 individual tested in a study [7]. In addition, © 2021 by the author(s). Distributed under a Creative Commons CC BY license. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 23 August 2021 these molecules could interfere with our endocrine system since they are thought to adopt hormonal functions in the human body [8]. Therefore, to break the plastic wave, bio-based and biodegradable should appear as alternatives to synthetic plastics [9,10], especially with the drastic increase in plastic pollution due to the current COVID-19 pandemic [11,12]. However, the elevated cost of industrial procedures and lack of significant large-scale production [13,14,15,16], together with the availability of appropriated carbon sources, have limited faster progress in these processes and consequently greater market penetration [17,18]. 1.2. Polyhydroxyalkanoates: bio-based biodegradable plastics The word “bioplastics” has commonly been used to make a distinction from petrochemical polymers, which is partially misleading, since not all types of bioplastics are bio-based and biodegradable [16,19] (Figure 1, A). Some bioplastics are biodegradable but fully fossil-based. Their chemical structure can be degraded in a slow process catalyzed by enzymes of some aerobic and anaerobic microorganisms that are widely distributed in various eco- systems. However, they are not biodegradable in animal bodies and sometimes they remain in marine waters [16,20] (Figure 1, A, bottom-right). Others are bio-based but chemically identical to their fossil counterparts, so they are not biodegradable [16,21] (Figure 1, A, upper-left). Only bio-based and biodegradable bioplastics are more ecologically friendly and serve as the best substitute for conventional plastics (Figure 1, A, upper-right). Among them, one of the most promising class of bioplastics are the bacterial polyesters polyhydroxyalkanoates (PHAs), which are produced through industrial bacterial fermen- tation of sugar or lipids by numerous Gram‐positive and Gram‐negative bacteria [16,20]. Inside the cells, PHAs molecules aggregate to form water-insoluble granules, the carbonosomes, which are intracellular reserves of energy during starvation [22,23] (Figure 1, B). In carbonosomes there is a constant cycle of synthesis and degradation, and this bidirectional process is a great advantage in the adaptation to rapid changes in the environment [24,25]. During the last years, PHAs are being proclaimed as the best alternative to fossil-based plastic due to their good balance between biodegradability rate, material properties that range from thermoplastics to elastomers, and the possibility to be processed into different final products [9,10,26]. However, production costs of PHAs are still too high when compared to the synthetic plastics [13,14]. Although they have not yet reached industrial scale, in the last decade more cost-effective processes for production of PHA have been developed based on the use of wastes/industrial by products and less energy demanding approaches [27,28]. Once the process scale constraints are overcome, PHA will become more competitive and replace the synthetic plastics in many applications. Figure 1. Material coordinate system of plastics. A) Type of plastics. Division of plastics into four groups, according to their biodegradability and biological origin. Upper-right, PHA: polyhydroxyalkanoates-are biodegradable polymers naturally produced by numerous microorganisms Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 23 August 2021 (Modified after [16,19]). B) PHAs: bio-based biodegradable plastics. When a carbon substrate is present in excess in parallel to depletion of other nutrients essential for biomass formation, PHAs are stored in the form of cytoplasmic spherical inclusions. These PHA granules are mul- ti-complexes usually called “carbonosomes”. They contain a hydrophobic core surrounded by PHA granule-associated proteins, such as PHA synthase, PHA depolymerases, regulatory and structural proteins (Modified after [24,29.]). 1.3. Types and chemical structure of PHAs polymers PHA generally consists of (R)-hydroxy fatty acid monomer units, which contain an alkyl side chain R group that varies in carbon length from methyl (C1) [30,31] (Figure 2). These polymers are usually divided into three dif- ferent types, according to the number of carbons in the monomeric subunits [31]. Short-chain-length PHA (scl-PHA) polymers are composed of monomers containing 3 to 5 carbon atoms, whereas medium-chain-length PHA (mcl-PHA) polymers are composed of monomers containing 6 to 14 carbon atoms. The third type are the long-chain-length PHAs (lcl-PHA), with minimum 15 carbons [30,31] (Figure 2, B). Their chemical properties are different and depend on the bacterial host and the fermentation conditions used for their production, making them suitable for different purposes. Scl-PHAs are highly crystalline, which makes them relatively stiff and brittle [30,32]. However, polymers with a greater number of carbons are more flexible and elastic, resulting in increased research interests [33]. Figure 2. Chemical Structure of polyhydroxyalkanoates (PHAs). A) General structure of a PHA molecule. The ´R’ functional group rep‐ resents the alkyl side chain, and the number of repetitions of the monomeric unit is given by ‘n’. B) PHAs can be classified as scl-PHAs, mcl-PHAs and lcl-PHAs, depending on the carbon numbers in the monomeric constituents (modified after [31]). Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 23 August 2021 PHAs are classified into homopolyesters, with only one variety of monomer, and heteropolyesters, which can be subdivided into copolyesters (monomers differing in either backbones or side chains) and terpolyesters (differ- ent side chains and backbones) [29,34]. The so-called polyhydroxybutyrate (PHB) is one of the most common ho- mopolymer PHA and best studied scl-PHA, containing the shortest possible side chain with only one methyl group [35,36] (Figure 2, B). The mechanical properties of PHB are comparable to conventional fossil-based plastics like polypropylene or polyethylene [30,32], and are reaching new interest for applications in medicine, where chemical composition and product purity are crucial [37]. Other uses are food packaging
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