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Genetic Analysis of Signal Peptides in Amphibian Antimicrobial Secretions

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Genetic Analysis of Signal Peptides in Amphibian Antimicrobial Secretions Journal of Genetics, Vol. 97, No. 5, December 2018, pp. 1205–1212 © Indian Academy of Sciences https://doi.org/10.1007/s12041-018-1018-5 RESEARCH ARTICLE Genetic analysis of signal peptides in amphibian antimicrobial secretions L. O. PÉREZ1, N. L. CANCELARICH2, S. AGUILAR2,3,N.G.BASSO4 and M. M. MARANI2∗ 1Instituto Patagónico de Ciencias Sociales y Humanas (IPCSH), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Puerto Madryn, Argentina 2Instituto Patagónico para el Estudio de Ecosistemas Continentales (IPEEC),Puerto Madryn, Argentina 3Facultad de Ciencias Naturales, Sede Puerto Madryn, Universidad Nacional de la Patagonia San Juan Bosco, 3051 Brown Boulevard, Puerto Madryn, Argentina 4Instituto de Diversidad y Evolución Austral (IDEAus), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 2915 Brown Boulevard, Puerto Madryn, Argentina *For correspondence. E-mail: [email protected]. Received 22 February 2018; accepted 1 May 2018; published online 7 November 2018 Abstract. Amphibian secretion is an important source of bioactive molecules that naturally protect the skin against noxious microorganisms. Collectively called antimicrobial peptides (AMPs), these molecules have a wide spectrum of action, targeting viruses, bacteria and fungi. Like many membrane and secreted proteins, AMPs have cleavable signal sequences that mediate and translocate the nascent polypeptide chains into the endoplasmic reticulum. Although it is accepted that the signal peptides (SPs) are simple and interchangeable, there is neither sequence nor structure that is conserved among all gene families. They derived from a common ancestor but developed different traits as they adapt to distinct environmental pressures. The aim of this study was to provide an overview of the diversity of SPs of the frog, taking into account reported cDNA sequences and the evolutionary relationship among them. We analysed more than 2000 records that reported the relative abundance, diversity and evolutionary divergence based on the peptide signals of frog AMPs. We conclude that the physical properties of the sequence are more important than the specific peptides in AMP SPs. Since there is significant overlapping among related genera, differences in secretion from different peptide types should be regulated by additional levels, such as posttranscriptional modifications or 5-UTR sequences. Keywords. antimicrobial peptides; signal peptide; diversity. Introduction signal peptide (SP), followed by an acidic propeptide domain (16–27 residue) and a hyper-variable C-terminal Antimicrobial peptides (AMPs) are an essential part of domain containing the biologically active peptide. It is the innate immunity of organisms and display activity encoded in a single locus, spanning two exons separated against a wide range of microorganisms. Based on their by an intron that can range from several hundreds to over potential use in the pharmaceutical and biotechnology a thousand bases. The first exon encodes the SP, while industry, there has been a rise in medicinal peptide patent the second encodes the acidic region and the mature pep- applications and developmental work (Uhlig et al. 2014). tide. Depending on the genus, the whole structure could be Particularly, many amphibian species have been studied duplicated in tandem or scattered throughout the genome and more than 1000 skin-frog-derived peptides have been (Amiche et al. 1999). screened for a wide diversity of applications, demonstrat- SPs are found in the N-terminal end of secreted and ing activities such as anticancer (Wu et al. 2014), insecti- membrane protein precursors of eukaryotes and prokary- cidal (Smith et al. 2011), chemotactic (König et al. 2015), otes, and they mediate the targeting of the nascent antioxidant (Guo et al. 2014), wound healing (Gallo and polypeptide chains to the endoplasmic reticulum (ER). Huttner 1998) and protease inhibitor (Miller et al. 1989). A protein complex, the translocon, identifies the SP and AMPs typically display a tripartite structure. In modern transports the polypeptide to the ER. The SP is cleaved frogs, the N-terminal region has a 22-residue conserved in the process and the peptide is exported outside the cell 1205 1206 L. O. Pérez et al. by the secretory pathway (Lodish et al. 2000). While SPs of SP nucleotides was described with basic statistics using of different proteins share low sequence identity, they also the Poppr packages from R software (Kamvar et al. 2014). have a tripartite structure: (i) a hydrophilic N-terminus, This included the Simpson index, a common diversity (ii) a hydrophilic core and (iii) a more conserved region measure that estimates the probability that two entities that ends with cysteine (Cys) (Hon et al. 2009). In frog taken at random represent the same type in a specific AMPs, there is no certainty whether the SPs have a spe- database. We used the Shannon–Wiener index for SP cific peptidase for secretion or whether they follow an genotype variability, a measure of uncertainty of informa- ER-independent pathway. tion (H) (Morris et al. 2014). The analysis of diversity From a practical point of view, a better understanding among individuals, genera and families was performed of the diversity of SPs would lead to a more efficient by the analysis of molecular variance (AMOVA) using screening by molecular techniques. These complement the amove.ppoppr function with the following parameters: conventional methodologies such as liquid chromatogra- positive clone correcting, distance matrix by raw pairwise phy and others that infer the peptide sequence from the distances and farthest neighbour clustering. For test sig- mature peptide (Csordas and Michl 1969). Cloning and nificance of the results, we performed a randomization test DNA sequencing allow the identification of the complete that permutes the samples (Excoffier et al. 1992). Follow- AMP pre-propeptide by directly examining the mRNA, ing which we performed discriminant analysis of principal providing unambiguous sequence assignments. A com- components (DAPC), a method specifically designed for mon practice is to perform the 3RACE amplification with genetic data to find the best discrimination of individu- primers that match the 5-UTR or the SP region (Nico- als in predefined groups to provide a visual assessment of las et al. 2003). In this case, the presence of polymorphic genetic differentiation and allele contribution. We used the regions is a concern for researchers when designing spe- ade4 package for cross-validation of DAPC using varying cific primers. Degenerate primers are required to recover numbers of principal components (PC), setting 300 as the the diversity of products at expenses of sensitivity. maximum number of PCs, training set to 0.9 of the sample In this study,we performed an overview of the SP regions and 30 repetitions. of amphibian skin AMPs. The main objective of this study was to analyse their sequences and report frequent motifs SP alignment and consensuses to provide useful information for bioprospecting AMPs. Sequence alignment was performed using the MUSCLE Materials and methods algorithm from the mass package (R) (Edgar 2004). DNA consensuses of families were obtained using the Biostrings SP dataset package (Pagès et al. 2017). The output was uploaded to the CIPRES (https://www.phylo.org/)(Miller et al. Complementary DNA sequences corresponding to 2010) portal and the best tree was built using the maxi- complete prepropeptides of skin AMPs from amphib- mum likelihood method (RAxML v8 algorithm using a ians were downloaded from the NCBI (http://www.ncbi. GTR+Gamma nucleotide substitution model) and Bom- nlm.nih.gov/pubmed/). In both cases, the words ‘cDNA’, binatoridae as the rooted branch. Analysis of records of ‘antimicrobial peptides’ and ‘frog’ were used as search key- the whole dataset was performed by maximum likelihood words. The search comprised a period that extended from analysis and the model selection was calculated by neigh- 1988 to the beginning of 2017. Curation of sequences was bour joining analysis. Graphical representation of trees performed according to the following criteria: exclusion was performed using MEGA software. of sequences that were obtained with primers that over- lapped the SP region (the source article was examined when Results available), data redundancy and incomplete sequences. Sequence alignment was performed at the nucleotide level SP dataset using the MUSCLE algorithm of the mass package of R (Edgar 2004). We compiled 2852 individual records of the AMP precursors (prepropeptides) from the NCBI nucleotide Diversity description database. After processing the genotypes that did not meet the criteria, there were 2165 sequences left (1125 geno- Total compiled and manually curated SP sequences were types). These AMPs belonged to 14 amphibian families, 32 analysed. The SP region was defined as the first 22 amino genera and 118 species. Frog families were not equally rep- acid residues that usually end with a Cys (Neobatrachia). resented. Ranidae was the largest family, comprising 86% In the case of sequence descriptions that stated otherwise of the total. A summary of the data is shown in table 1. (primitive frogs), or sequences that did not end with a Cys, The SP region of AMP prepropeptides was defined the length was based on published data (if available) or the as the first 66 nucleotides in modern frogs (Neobatra- SignalP 4.1 algorithm (Petersen et al. 2011). The variation chia). A few exceptions did not show the common Cys Signal peptide diversity from frogs 1207 Table 1. Description of SP nucleotide sequences, families and to two bases (52 and 53), near the C-terminal codon 17, species. Simpson’s index >1.2 (figure 2). On the other hand, codons 35, 38, 41 and 50 were highly conserved amongst species. Unique SP They were all located in the middle region and the triplets No. of sequences No. of Family records (DNA) species coded for hydrophobic residues. The overall diversity measured by the Shannon–Wiener Alytidae 2 2 1 (SW) index H was 6.383, with the standard error of 0.47. In Bombinatoridae 113 85 3 general, variability increased with increasing sample size Ceratophryidae 1 1 1 within each genus.
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