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[Frontiers in Bioscience 12, 2020-2028, January 1, 2007] [Frontiers in Bioscience 12, 2020-2028, January 1, 2007] Mycoplasma genomics: tailoring the genome for minimal life requirements through reductive evolution Ahmed Fadiel1, Kenneth D. Eichenbaum2, Nermin El Semary3,Brittiny Epperson1 1Yale School of Medicine, New Haven, CT, 06511, 2Mount Sinai School of Medicine, NY, NY, 10029, 3 Department of Botany and Microbiology, Faculty of Science, University of Helwan, Cairo, Egypt TABLE OF CONTENTS 1. Abstract 2. Introduction 3. Mycoplasma genomics 3.1. Mycoplasma genome sequencing 3.2. Genome sizing and genomic redundancies 3.3. Intra- and inter-genomic rearrangements 3.4. G+C content and oligonucleotide frequencies and species-specific characteristics 4. Mycoplasma as a model for genomics research 4.1. Minimal genome with high parasitic efficiency 4.2. Codon patterns and usage 5. Developing applications of Mycoplasma research 6. Bioinformatics resources for Mycoplasma 7. Mycoplasma genomics: Future perspectives 8. Acknowledgement 9. References 1. ABSTRACT 2. INTRODUCTION Prokaryotic organisms of the genus Mycoplasma Mycoplasmas are distinct bacterial are characterized by their small body and genome size microorganisms, small in size (0.2 - 0.3 µm) and devoid of containing a 0.6 -1.35 M bp genome. The genome is noted both cell wall and motility appendages (1, 2). When for its low G+C frequency ranging from 8-40 mol%. The Mycoplasmas were initially studied, their small size permitted Mycoplasma genus stems from the class Mollicutes (for their passage through micro-filters that blocked other bacteria. soft skin), which lacks the cell walls and external motility This mistakenly led scientists to believe that Mycoplasmas appendagesoften present in other bacteria. To date, there were viruses. In the 1950 and early sixties it was established are more than 100 known species of Mycoplasma. 34 that Mycoplasmas are bacteria (3). In addition, Mycoplasmas species have been partially or completely sequenced. are characterized for their possession of the smallest known Widely known pathogenic species of Mycoplasma include: genomes and distinctively low G+C contents (4). M. pneumoniae, causing pneumonia and other respiratory Biomedically, several pathogenic Mycoplasma species were disorders, and M. genitalium, which are involved in pelvic discovered to be active in human microflora and were inflammatory disease. Because of their small genome size, associated with diseases such as AIDS, urogenital diseases and Mycoplasmas provide researchers a unique model of the cancer (2). However, the discrete mechanisms of Mycoplasma minimal genomic requirements to maintain life. As the pathogenicity are yet to be understood (5). The organism number of complete Mycoplasma genomes increase, these evades immune system response by establishing residence in organisms become more established, thus laying the white blood cells. Once in the circulation, Mycoplasma can foundation for mapping evolutionary development. This cross the blood-brain barrier and infiltrate the cerebral spinal manuscript provides an overview and update on fluid (6). Once inside the host Mycoplasma starts to compete Mycoplasma research, with particular focus on current for nutrients. In addition, the presence of Mycoplasmas in genomics. hosts’ cells might lead to DNA mutations. 2020 Mycoplasma genomics: the conundrum of minimal life requirements Like retroviruses, Mycoplasmas have the capacity Mycoplasma. S. ixodetis has 2,220 Kb in comparison to M. for cellular invasion, self-replication and the initiation of a genitalium’s 580 Kb (19, 20). The correlation between variety of immune responses (7). However, Mycoplasmas, genome size and phylogenetic rank remains a source of unlike viruses, are viable in body fluids and do not require controversy (21) prompting scientists to develop several living cell hosts for DNA replication and growth. Whereas hypotheses. One theory holds that genome reduction may viruses can demonstrate high specificity to their host organ have resulted from evolutionarily driven loss of genomic targets, the Mycoplasma pathogen has a high degree of information. It was further hypothesized that this loss may adaptability to many regions of the body. Thus, have forced the species to adopt a parasitic modality (22). Mycoplasmas can be termed "stealth pathogens" (6). The Genomic degeneration can explain the concept of reductive small genome size has made Mycoplasma ideal for evolution (23). However, in vitro studies demonstrate an genomic studies facilitating rapid and cost-effective absence of correlation between genome size and adaptation completion of the sequencing of entire bacterial genomes in non-parasitic environments (21). and producing vast quantities of relevant data. In this review we provide a primer on genomics and informatics of The exact mechanism of Mycoplasma genome Mycoplasmas. size reduction is not completely understood. It is argued that many factors contributed to shaping the final size of 3. MYCOPLASMA GENOMICS each Mycoplasma, including the dynamic behavior of repetitive elements and integration of viral sequences and 3.1. Mycoplasma Genome Sequencing: a historical mutations (23, 24, 25, 26, 27). Variation in the spectrum of perspective Mycoplasma size and mode provide an ample opportunity With the smallest known genome sizes to explore the functional content of the genomes and the Mycoplasma offers a unique model for examining the evolutionary relationships between them (28). Small minimal requirements for establishing life. Early attempts genomic size allows for easy handling with current of deciphering Mollicutes genomes were primarily based computational capacity. Comparative studies frequently on physical mapping synthesized from genomic sequence show that most bacterial proteins are highly conserved. fragments (8, 9). Morowitz began studies to define the This facilitates functional assignment to coding regions by comprehensive cellular machinery of Mycoplasma in 1984 homology. Interestingly, the number of genes required for (10). By the early 1990s, laboratory groups at Harvard certain cellular function is often independent of genome University focused their sequencing efforts on the M. size, demonstrating that proscribed discrete protein capricolum genome. However, this initiative was curtailed functional pathways may be required for basic homeostasis. in 1995 as a result of technical limitations. To understand With more complex amino acid biosynthesis and energy genome organization and DNA repeat distribution, metabolism, the machinery for protein synthesis often researchers at the University of Heidelberg sought to increases with genome size (29). Knowledge about the sequence the pathogenic species M. pneumoniae using a function and number of genes required for maintaining cosmid library. This sequencing approach was successful basic cellular machinery, in general, would allow for in identifying approximately 90% of the organism genome composite identification of the essential gene set sufficient and spanned approximately 720 Kbp (11, 12). However, for sustaining cellular life. the exact size of the pathogen genome was not fully characterized by that time. Other studies estimated the Understanding the evolution of small, or “reduced genome size of the M. pneumoniae to contain close to 800 genomes”, may aid in defining genes essential for minimal Kbp (13, 14, 15). In 1995 a group from The Institute for cellular requirements and associated pathways. M. Genomic Research (TIGR), utilized a new shotgun genitalium possesses the smallest genome known to date sequencing technique considered a breakthrough in genome (16) and hence was selected as a model to study these technologies. This technique offered improved reliability phenomena. Comparisons between M. genitalium and other and speed in obtaining the comprehensive genome small genome pathogenic prokaryotes, such as H. sequence within 6 months (16). This technology involves influenzae, indicate a possible common source ancestry. cloning and sequencing of small sheared DNA fragments Phylogenomic studies of the two genera show that which can subsequently be arranged into contigs and separation likely occurred approximately 1.5 billion years supercontigs. This technology incorporates computational ago. In addition, comparative genome analysis shows that biology, making use of computational algorithms to both have approximately 240 genes in common (30). The assemble sequenced fragments (17). This technique has larger E. coli genome also has a similar number of subsequently facilitated the completion of close to 50 translational proteins. This indicates that strict functional complete genomes of prokaryotes including Mycoplasma, constraints imply high degrees of sequence conservation which are currently available (at www.NCBI.nlm.nih.gov). (31). On the other hand, this level of sequence conservation Mycoplasma genomes (Table 1) along with other families was reduced in other functional categories, including cell of prokaryotic genomes provide templates for comparative envelope and cytoskeletal proteins. Genes in certain genome and evolutionary analyses (18). metabolic pathways have been relegated to the set of minimal genes required for a “modern-type” cell (16, 30). 3.2. Genome sizing and genomic redundancies Some scientists further argue that M. genitalium may yet Within the class Mollicutes, Acholeplasma and contain up to double the number of genes requisite for Spiroplasma species, thought to be older on the modern life, (22) based on the finding
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