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Comparative Genome Analysis of Proteases, Oligopeptide Uptake and Secretion Systems in Mycoplasma Spp

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Comparative Genome Analysis of Proteases, Oligopeptide Uptake and Secretion Systems in Mycoplasma Spp Genetics and Molecular Biology, 30, 1, 225-229 (2007) Copyright by the Brazilian Society of Genetics. Printed in Brazil www.sbg.org.br Research Article Comparative genome analysis of proteases, oligopeptide uptake and secretion systems in Mycoplasma spp Charley Christian Staats, Juliano Boldo, Leonardo Broetto, Marilene Vainstein and Augusto Schrank Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil. Abstract Mycoplasmas are very fastidious in their nutritional requirements for in vitro growth and have limited biosynthetic ca- pacity, a reflection of their reduced genomes. As a result, these bacteria depend upon external metabolites for nutri- tion and growth and have developed dependence on their hosts for survival and maintenance. Protein degradation and peptide importation play an important role in Mycoplasma spp. nutrition, and proteases can play a role in host ad- aptation and pathogenicity. Here, we present a general survey on the genes involved in protein degradation, secre- tion and importation, comparing all available Mollicute genomes. Key words: Mycoplasma, proteases, minimal genomes, secretion systems. Received: April 4, 2006; Accepted: October 5, 2006. Introduction ronmental changes, mediating functions such as quorum Mycoplasmas are considered the smallest cells capa- sensing, sporulation, pheromone transport, and chemotaxis ble of propagation in cell-free medium, and some species (Wang et al., 2004). are pathogenic to humans, animals and plants. In spite of Despite the presence of a complete set of genes re- their reduced genomes, due to significant gene loss through sponsible for essential cell activities such as replication, evolution/adaptation, mycoplasmas are a very successful transcription and translation, genes involved in post- group of organisms, as judged by their large number of spe- translational protein modifications are not readily disclosed cies and habitats (Razin et al., 1998). The `minimum cell’ by the annotation of the mycoplasma genomes. Some of life style of mycoplasmas became possible by the adoption these processes, such as protein maturation and localiza- of a parasitic mode of life, exploiting nutrients not synthe- tion, are intrinsically dependent on proteases. Microbial sized by themselves, and evolving systems to invade and to proteases may also play important roles in pathogenicity persist in their hosts (van Ham et al., 2003). and nutrition. Over the last few years, the genomes of nine Myco- Bacterial development is also dependent on the secre- plasma species were sequenced, reinforcing comparative tion of proteins with a plethora of functions. One of the ma- genome studies that allow a better understanding of their jor transport routes, the so-called Sec pathway, is con- metabolism and the relations with their hosts. Mycoplas- served in all domains of life and is the only system found in mas evolved from gram-positive bacteria and, through evo- mycoplasmas by genome surveys (Stephenson, 2005). lution, lost the cell wall and many metabolic pathways for In this work, we present a general survey on the genes the synthesis of macromolecule building blocks. Myco- involved in protein metabolism, based on the available plasmas possess no complete routes for amino acids syn- mycoplasma genomes. thesis and degradation, implying that these monomers must be acquired either from their hosts or from a culture me- Material and Methods dium, depending upon membrane transporters (Vascon- celos et al., 2005). Exogenous peptides are an important The complete genome sequences of the Mycoplasma source of amino acids. Indeed, bacteria have evolved pep- spp. used in this work were retrieved from the NCBI data tide transport systems that also assist in responses to envi- base (http://www.ncbi.nlm.nih.gov), as available in Octo- ber, 2005. Primary searches were conducted using BLAST search tools (Altschul et al., 1990), or based on annotated Send correspondence to Augusto Schrank. Centro de Biotecnolo- gia, Universidade Federal do Rio Grande do Sul, Caixa Postal genome files. The search for Opp (oligopeptide transport 15005, 91501-970 Porto Alegre, RS, Brazil. E-mail: aschrank@ genes) and secretion systems was conducted using InterPro cbiot.ufrgs.br. entries for Bacillus subtilis components (http://www.ebi. 226 Staats et al. ac.uk/interpro, Mulder et al., 2005). The classification and Table 1 - Genomic organization of Opp uptake system in mycoplasmas. analysis of proteases were done according to the MEROPS The five components are disposed in clusters or as isolated ORFs in the genome. peptidase database (http://merops.sanger.ac.uk, Rawlings et al., 2004). Microorganism Clusters Scattered III Results and Discussion Mycoplasma genitalium OppBCDF -a -- Oligopeptide importing Mycoplasma pulmonis OppBCDF OppBCDF -- Mycoplasma genomes possess a diversity of ABC Mycoplasma penetrans OppBCDF OppBCDF -- transporters predicted to be involved in the uptake of sev- Mycoplasma pneumoniae OppBCDFb --- eral inorganic and organic substrates. One class of ABC Ureaplasma urealyticum OppBCDF --- transporters, the peptide/opine/nickel uptake transporter Mycoplasma OppBCDF OppCDF OppF OppF family (3.A.1.5.1), is involved in oligopeptide uptake with gallisepticum high affinity for tripeptides (Transport Classification Data- Phytoplasma sp. OppABCDF OppABCDF OppF OppA base, http://www.tcdb.org). Mycoplasma mycoides OppBCDFA OppABCDF OppF OppF The known genomic organization of the Opp operon Mycoplasma mobile OppBCDFc - OppF - in Mollicutes is shown in Table 1. Proteins encoded by this Mycoplasma OppBCDF OppBCDF -- operon are anchored in the cell membrane; they transport hyopneumoniaed oligopeptides from the extracellular milieu and represent Mycoplasma synoviae OppBCFD --- an important form of nutrition (Detmers et al., 1998). a b c Mesoplasma florum is the only species with no sequences not found. OppC also known as AmiD. OppD annotated as pgk, but con- tains the classical ATP-binding domain of the opp family. dstrains J, 7448 related to the Opp system, as far as predicted by the annota- [P], and 232. tion. The remaining genomes vary from one to two copies of the operon and also scattered single cistron copies. This mycoplasma cell membranes (Razin et al., 1998), and the distribution does not follow the division hominis/ substrate recognition function of OppA could be fulfilled pneumoniae clades. The complete Opp operon by one of these proteins. (OppABCDF) was annotated only in M. mycoides and in Phytoplasma, and is present in two copies. It is noteworthy Proteases that in one of the M. mycoides operons the cistron order is altered from ABCDF to BCDFA. Moreover, in both species Bacterial development is dependent on a plethora of there are scattered copies of single components elsewhere proteolytic activities involved in diverse functions, such as in the genome. Two copies of the incomplete operon (lack- protein homeostasis, pathogenicity and nutrient acquisi- ing OppA) are present in three species (M. pulmonis, M. tion. Mycoplasma genomes analysis revealed a complex penetrans and M. hyopneumoniae). The same incomplete distribution of these enzymes (Table 2). ATP-dependent operon is present, as single copies, in all five genomes; proteases, such as Lon and FtsH, that degrade aberrant pro- however, in M. synoviae, the cistron order is different, and teins, were found in all genomes analyzed here. Lon is a in M. mobile an extra copy of OppF is present. DNA-binding protease that degrades regulatory and abnor- The function of OppA as substrate-binding protein mal proteins and has both the proteolytic and the ATPase (oligopeptide recognition) is well recognized in bacteria domains. FtsH is a membrane protease that degrades mem- (LeDeaux et al., 1997; Detmers et al., 1998). In brane and cytoplasmic proteins. However, other important Mycoplasma hominis (genome sequence not available), proteases involved in abnormal protein degradation, such OppA functions as the P100 adherence-associated lipopro- as ClpPX and HslUV, were not annotated in five Myco- tein, and the operon is organized as OppABCDF (Henrich plasma species analyzed previously. This wider in silico et al., 1999). Therefore, an important role for OppA in survey of 12 Mollicute genomes supports the hypothesis oligopeptide uptake could be expected in other Mollicutes. outlined by Wong and Houry (2004) that the protein However, the OppA gene was found only in two Mollicute homeostatic process in these organisms has shifted through genome sequences (Table 1). This raises the question if evolution towards favoring protein degradation rather than OppA is really a necessary component of the oligopeptide protein folding. Lon-defective Escherichia coli mutants re- uptake systems in these bacteria. Nevertheless, the low main phenotypically stable when overproducing HslU and conservation of this protein could hinder its annotation. In HslV proteases, denoting a probable substrate overlapping addition, the habitat broadness of Mollicutes could result in among these proteins under certain physiological condi- strong selection/adaptation, especially for proteins tions (Wu et al., 1999). This suggests that the lack of the involved in the recognition (binding) of oligopeptides, ex- HslUV system in mycoplasmas could be surpassed by the pected to be variable in different habitats. Also, lipo- presence of Lon. FtsH is an endopeptidase, dependent on proteins are among the most prominent components of ATP and Zn2+, that degrades abnormally-folded
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