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ss rsity sti Opinion identify genes that are essential for cell viability. The era of genome sequencing and comparative genomics produced a series of estimates of the composition of a minimal cell and how it would function [3–7]. A plethora of model organisms have been investigated, including a broad spectrum of obligatory host-associated bacteria that possess near-min- imal genomes as a result of evolutionary gene erosion. These analyses led to the identification of quite similar, albeit non-identical, sets of genes [3–18] (Table 1). As a consequence, there is presently no consensus about which genes are really essential. We believe that it is safe to assume that some genes are absolutely necessary for the survival of any life form, whereas others can be omitted (at least in the laboratory environment). We focus here on the consists of less than 40 genes [7]. This number of genes identified by comparative genomics is artificially small, mainly because many essential cellular functions can be encoded by non-orthologous genes. Given that gene se- quence homologies are lower between phylogenetically unrelated organisms, the evolutionary distance between analyzed genomes can have a significant impact on the outcome of comparative genome analyses. In the first experimental study, saturation transposon mutagenesis (Figure 1b) was used in M. genitalium to identify approxi- mately 300 genes that could not be inactivated by trans- poson and thus were considered to be essential [21]. Since then this approach has been used in a broad spectrum of organisms and has led to the identification of essential gene sets of varying sizes (Table 1). This variation is probably because saturation transposon mutagenesisE-mail addresses: Juhas, M. (mario.juhas@uzh.ch, mariojuhas@googlemail.com). Essence of life: esse minimal genomes Mario Juhas1, Leo Eberl1 and John I. Gla 1Department of Microbiology, Institute of Plant Biology, Unive 2Synthetic Biology and Bioenergy group, The J. Craig Venter In Essential genes are absolutely required for cell survival. Determination of the universal minimal set of genes needed to sustain life is, therefore, expected to contrib- ute greatly to our understanding of life at its simplest level, with applications in medicine and synthetic biolo- gy. The search for the minimal genome has led to the identification of often variable gene sets. We argue here that, based on the outcome of these analyses, it is becoming increasingly evident that some genes, and the functions encoded by them, are absolutely necessary for the survival of any living entity, whereas others can be omitted. We also examine ways of determining the minimal genome and discuss possible practical applica- tions of a minimal cell. Essential genes Essential genes are, by definition, absolutely required for the survival of an organism and are therefore considered the foundation of life. Identification of the universal mini- mal set of essential genes has been the pursuit of biologists for two main purposes. With the advent of the first micro- bial genome sequences, the pharmaceutical industry hy- pothesized that genes encoding essential cellular functions would be logical targets for new antibiotics, due to their indispensability for bacterial cell survival [1]. Another group of scientists, led initially by Max Delbru¨ ck, saw the identification of essential genes as a route that could lead to an understanding of the universal principles of life [2]. The latest to take up the question of essential genes are researchers in the emerging science of synthetic biology, who aim to create a cell with a minimal genome. A wide variety of approaches have been employed to 562 0962-8924/$ – see front matter � 2011 Elsevier Ltd. All rights rese ntial genes of 2 of Zurich, CH-8057 Zurich, Switzerland tute, Rockville, MD 20850, USA biological aspects of minimal genomes and discuss func- tions encoded by essential genes that are required to support cellular life. We examine methods exploited in the search for the universal minimal genome and investi- gate reasons why they have led to such variation in the sets of genes identified. We also discuss possible practical applications of a minimal cell – in medicine for the identi- fication of novel antimicrobial targets and in synthetic biology for the creation of specialized cells with desired phenotypic traits. Experimental and computational methods to assess the minimal genome Several approaches have been employed to identify genes that are essential for cell viability. As the amount of data increased it became clear that there was variation in the sets of essential protein-coding genes identified (Table 1). One of the challenges currently is to determine which of these identified genes are really essential. Why is there such variation in the identified sets of essential genes? First, none of the methods used for their identification is flawless. An initial attempt to identify a minimal genome was performed using comparative geno- mics, assuming that genes shared between organisms are likely to be essential (Figure 1a). This analysis was stimu- lated by the availability of the first sequenced genomes of Haemophilus influenzae [19] and Mycoplasma genitalium [20] and led to the identification of approximately 250 candidate essential genes [3]. As more genome sequences became available, the number of shared genes identified by comparative genomics decreased (Table 1). As a conse- quence, it was concluded that the universal conserved core rved. doi:10.1016/j.tcb.2011.07.005 Trends in Cell Biology, October 2011, Vol. 21, No. 10 ssen counts as essential those genes that only slow down growth without arresting it. Furthermore, transposon bombard- ment is not entirely random – an analysis using two variants of the same transposon with different antibiotic resistance genes can yield slightly different essential gene sets (J. G. et al., unpublished). Recently, saturation trans- poson mutagenesis coupled with next-generation sequenc- ing has been used to facilitate high-throughput identification of essential genes (Figure 1c) [13]. Other frequently used methods include the systematic inactiva- tion of individual genes or the use of antisense RNA (Figure 1d,e) [14–18]. The use of antisense RNA is limited to those genes for which an adequate expression of the inhibitory RNA can be obtained. In addition, inactivating individual genes means that essential genes that are present in more than one copy will be missed. Experimen- tal genome reduction, based on random or targeted remov- Table 1. Essential genes identified by different methods Number of protein-coding e Organism Saccharomyces cerevisiae 878 Haemophilus influenzae 642 Acinetobacter baylyi 499 Mycoplasma pulmonis 461 Mycoplasma genitalium 381 Salmonella enterica Typhi 356 Pseudomonas aeruginosa 335 Helicobacter pylori 323 Escherichia coli 303 Staphylococcus aureus 302 Bacillus subtilis 271 Numbers of genomes compared 2 256 5 180 7 156 100 63 147 35 Opinion al of genomic segments, represents another avenue for minimal genome identification (Figure 1f). This method has led to the successful elimination of approximately 10– 30% of the Escherichia coli genome without any detectable defect in bacterial viability [22–24]. The main limitation of random genome reduction is the need for subsequent resequencing of the genome to identify the exact location of the deletion, and targeted genome reductions are cur- rently still unable to generate a minimal genome. In addition to variation due to methodological differ- ences, the organism investigated also impacts upon the outcome of the analysis. For instance, the set of essential genes of H. influenzae consists of almost twice as many genes as that of Helicobacterpylori identified by the same method (Table 1). It is therefore very likely that these variations reflect the varying environmental conditions and lifestyles of the organisms. In other words, in addition to a universal minimal genome, other important genes could also be essential for the survival of a particular organism or in a specific environment. One of the main challenges for future research is to resolve the variation in the sets of essential genes identi- fied depending on which method of analysis is employed. To address this issue, essential genes in an organism could be first identified by comparative genomics and their es- sentiality confirmed by experimental methods. Alterna- tively, genes found to be essential in one organism could be investigated in other species, preferably by different experimental methods. Currently used methods should be modified to minimize their weaknesses. For example, syn- thetic lethality screens, which use mutants to search for other mutations further attenuating viability, could be used to identify essential genes present in more than one copy [25,26]. More in-depth studies are required to determine those genes that are essential for the survival of any living organism. In the quest to find the universal core set of essential genes, researchers have also turned to organisms in which nature has reduced their genomes close to the minimum. tial genes Method of identification Ref. Single-gene-specific mutagenesis [14] Saturation transposon mutagenesis [8] Single-gene-specific mutagenesis [15] Saturation transposon mutagenesis [12] Saturation transposon mutagenesis [10] Saturation transposon mutagenesis [13] Saturation transposon mutagenesis [11] Saturation transposon mutagenesis [9] Single-gene-specific mutagenesis [16] Antisense RNA inhibition [17] Single-gene-specific mutagenesis [18] Comparative genomics [3] Comparative genomics [4] Comparative genomics [5] Comparative genomics [6] Comparative genomics [7] Trends in Cell Biology October 2011, Vol. 21, No. 10 Essential genes in naturally occurring minimal genomes A broad spectrum of near-minimal genomes can be found in nature as a result of reductive evolution, which eliminates genes non-essential for survival in a particular environ- ment. The smallest genome identified to date is that of Hodgkinia cicadicola, a symbiont of cicadas, which is only 144 Kb in size and potentially contains 188 genes [27]. The extremely small genomes of endosymbionts usually encode only the most basic processes, suggesting that some of their genes might have been transferred into the host cell nu- cleus. The endosymbiont Wolbachia, for instance, transfers 1 Mb fragments to the nucleus of its host [28]. The genome of H. cicadicola harbors even fewer genes than some chlor- oplasts; however, comparative analyses have shown that the gene sets of endosymbionts and those of cellular orga- nelles differ significantly, because endosymbionts still har- bor genes involved in replication, transcription and translation [29]. How can endosymbionts survive despite their extremely small genomes? Phylogenetic studies show that endosym- bionts and their free-living relatives evolved from the same free-living ancestors via genome reduction [29–31]. Genome erosion is possible in endosymbionts due to the 563 Genome 1 Genome 2 Essential Key: T T T T In silico comparison of genomes mRNA Antisense RNA Monitoring growth Non-essential Essential Essential (a) (b) (c) (d) (e) (f) Suicide plasmid Monitoring growth Non-essential Essential Disruption of target gene G - Gene C - Colony T - Transposon H - Homologous sequence Cell Cell Cell Chromosome H1 H2 H1 H1 H2 H2 Suicide plasmid integration and homologous recombination Segment to be deleted Chromosome Monitoring growth Non-essential segment Essential segment Inhibition of expression Growth and sequencing of colonies T T T T Cell Illumina Insertion index Fr eq ue nc y 1 2 3 4 5 60 Essential genes Cultivation and sequencing of cells with next-generation sequencer Transposon mutant library Transposon bombardment Transposon mutant library Transposon bombardment G G G G G G G G G GG G G G G G G G G G G G G G G G G G G G G C C C C C C C C C C C C C C CC G TRENDS in Cell Biology Figure 1. Identification of essential genes. Various methods are used for the identification of essential genes. (a) Comparative genomics compares genomes in silico to identify essential genes. Genes shared among genomes are considered essential. (b) Saturation transposon mutagenesis exploits transposons for generation of whole- genome mutant libraries. Mutants are grown on selective media and sequenced to identify disrupted genes. Genes whose disruptions produce viable colonies are non- essential and the remaining genes are considered essential. (c) Saturation transposon mutagenesis in combination with next-generation sequencing has been used for high-throughput identification of essential genes. Transposon libraries are sequenced with the help of a next-generation sequencer (e.g. Illumina) and the insertion index for each gene is calculated by dividing the number of unique insertion sites for any given gene by the gene length. Genes with an insertion index close to 0 are considered to be essential. (d) Antisense RNA is used to inhibit the expression of a target gene by binding to its mRNA. If the target gene is essential, the cell will not survive. (e) Single- gene-specific mutagenesis disrupts individual genes by integration of a suicide plasmid. Lethality indicates that a disrupted gene is essential. (f) Experimental genome reduction is used to delete large segments from the chromosome by homologous recombination between flanking DNA regions and homologous sequences introduced into the cell, usually by a suicide plasmid. The deleted DNA segment is considered to be non-essential if cells without it survive. Opinion Trends in Cell Biology October 2011, Vol. 21, No. 10 564 extremely stable nutrient-rich environment provided by the host, which makes almost all the metabolic genes and genes involved in adaptation to changing environments obsolete. The bacterial endosymbionts of insects, which harbor the smallest genomes sequenced to date, are utterly dependent on the stable nutrient-rich environment provid- ed by their hosts [29]. Mycoplasmas, a group of unusual bacteria that lack a cell wall, have the smallest genomes of organisms capable of host-independent growth in laboratory media. Although Mycoplasmas possess very small genomes, they are not simple organisms. Detailed examination of the proteome, transcriptome and metabolome [32–34] of Mycoplasma pneumoniae cells revealed unexpected complexity, similar to organisms with much bigger genomes such as E. coli. For example, protein interaction analysis showed that a large number of M. pneumoniae proteins were part of more than one cellular machine or protein complex. In spite of such unexpected complexity, Mycoplasmas remain among the most important models to study essential genes, mainly due to their small genomes and easy cultivation. A team at the J. Craig Venter Institute is currently removing all genes considered to be non-essential from Mycoplasma mycoides to build a synthetic version of this organism [35]. Although M. mycoides has 828 ORFs, its genome could be potentially reduced to less than 400 genes based on saturation transposon mutagenesis in M. genitalium [10]. The resulting synthetic cell will be a platform to investigate the basic functions and mechanisms of cellular life. For instance, such a synthetic cell could provide clear- er understandingof the function of a particular essential gene or key biological process, unbiased by non-essential genes. It is important to keep in mind, however, that the minimal synthetic cell constructed from the M. mycoides genome will probably also harbor some essential genes that are specific to M. mycoides. Hence, whereas the crea- tion of a synthetic cell based on information from one organism is in process, it will be a more complicated task to identify the universal minimal cell. One way to approach the problem is to compile all information on essential genes and critically assess which functions are likely to be uni- versally essential. Cellular functions encoded by essential genes Although the general consensus view held by the majority of researchers is that approximately 300 genes are re- quired to support cellular life, the exact composition of the universal minimal genome remains unknown. This number of candidate essential genes is only a rough esti- mate based on the results of previous analyses (Table 1). There is no doubt, however, that some genes are absolutely necessary for the survival of any lifeform. Analyses of the functional distribution of essential and non-essential genes show that the category of information storage and proces- sing, which involves replication, transcription and trans- lation, is strongly over-represented among the essential genes [36]. This is also true for the extremely small gen- omes of obligate endosymbionts which, although differing to a great extent among themselves, share a set of core Opinion genes [27–29,37,38]. These core genes, which are present in all analyzed organisms, even in the tiniest genomes of endosymbionts, include those involved in DNA replication, transcription and RNA processing, aminoacyl-tRNA for- mation, protein folding, as well as genes encoding transla- tion factors and ribosomal subunits [29]. In addition, genes involved in cell membrane biogenesis are among those identified by minimal genome analyses [8–18]. The cell membrane separates the protoplasm from the extracellular environment and allows compartmental- ization of biological processes, thus its essentiality for a living cell is unquestionable. Furthermore, the evolution of membrane structures is also considered to be a key step towards the emergence of life on early Earth [39]. By contrast, genes encoding a cell wall or the bacterial outer membrane are only essential for particular types of cells, and are therefore not considered to be part of the universal minimal genome. Genes involved in metabolism are gen- erally less abundant among the identified essential genes [40]. In our opinion, metabolic independence is not always a prerequisite of a ‘viable’ minimal genome because a plethora of endosymbionts lack metabolism-related genes entirely. The metabolic genes required for cell survival depend strongly on the environment because many meta- bolites can be obtained from the host. In addition to these core gene categories, analyzed minimal genomes usually harbor genes with no character- ized homologs in databases [8–18]. What cellular functions are encoded by these unknown essential genes? Owing to their indispensability for cell survival, essential genes cannot be disrupted by standard mutagenesis, and thus analyzable mutants of these unknown genes are usually lacking. This problem can be circumvented by replacement of the native promoter of the gene with one that can be easily regulated [41]. In previous analysis of the 385 M. genitalium essential candidates, no function could be ascribed to 95 genes [10]. Today that number is only 75 (J.G. et al., unpublished). Further investigation of these uncharacterized genes will provide new insights into the most fundamental biological processes essential for cell survival. Although there is variation in the sets of essential genes identified, it is becoming clear that some genes are abso- lutely required for the survival of any living cell. These ‘core’ essential genes, which have been identified consis- tently in all minimal genome analyses, constitute a good starting point for generation of the universal minimal genome. More work will be required, however, especially to unravel the function of unknown genes because they might pinpoint additional key gene categories indispens- able for life. More work also will be needed to characterize those genes that are essential only within a particular evolutionary lineage. These ‘accessory’ essential genes are not conserved because different solutions to the same biological problem (e.g. cell surface biosynthesis) might exist in different cell types. Consequently, there might be no single universal minimal cell because it will always be biased towards a particular evolutionary trajectory. Intriguingly, several of these accessory essential genes appear to encode proteins of unknown function (M.J. et al., unpublished). Because these genes are conserved Trends in Cell Biology October 2011, Vol. 21, No. 10 within an evolutionary clade they represent potential tar- gets for the development of antimicrobials that specifically 565 target a particular group of bacteria. Although work on the identification of the universal minimal genome is still ongoing, its potential for the development of novel drugs and for expanding our basic understanding of biology is already clear. The power of simple systems: essential genes in medicine and synthetic biology Infectious diseases are a major worldwide cause of mor- bidity and mortality. Resistance against antibiotics is rising and newspapers frequently report the emergence of new ‘superbugs’ [42–44]. In the quest for new antibiotics the pharmaceutical industry poured a huge effort into identifying essential genes in important human pathogens at the outset of the genome sequencing era [1]. Every essential gene in the model human pathogens Streptococ- cus pneumoniae and Staphylococcus aureus was consid- ered a potential target. In assembly-line fashion, high- throughput assays were developed to find compounds that block the enzymatic function of essential gene products or that bind to essential proteins of unknown function. To the chagrin of the industry, this screening failed to find new antimicrobials with clinical potential [44]. Although this failure is largely attributed to a lack of appropriate chemi- cal diversity in the compound libraries screened, it has also reinforced a view that it might be more productive to search for drugs interfering with essential genes encoding machinery, ssrA and smpB, were shown recently to be indispensable for survival and might represent excellent targets for novel antimicrobials [45]. Other recent additions to the family of novel antimicrobials include peptidomimetics blocking ostA, an essential gene of P. aeruginosa whose function is currently under investiga- tion [46], and boronic esters inhibiting the widely con- served and essential bacterial methyltransferases CcrM and MenH [47]. These examples demonstrate that investi- gation of novel essential genes can be an attractive avenue for developing novel drugs. More work is needed, however, to identify other essential genes and to distinguish be- tween universally essential genes and those indispensable for the survival of a specific group of bacteria. While the pharmaceutical industry is searching for essential genes as targets of novel drugs to kill bacteria, the emerging field of synthetic biology is looking for essen- tial genes as a way to build and study a living minimal cell. Two approaches are being employed by synthetic biolo- gists: top-down, aiming at further simplification of existing cells by removal of all non-essential genes; and bottom-up, attempting to create an artificial cell by synthesizing all of its essential components [48–50]. The major challenges at the onset of synthetic biology wereattaining fast, cheap and reliable synthesis of long DNA fragments and genomes and their ‘booting-up’ (successful expression) in the cell. First attempts to synthesize DNA were expensive and adva bori ligo e. F des Opinion Trends in Cell Biology October 2011, Vol. 21, No. 10 well-understood functions rather than to screen for novel essential targets. Despite this, there are several examples where a deep understanding of novel essential genes has, in fact, led to new antimicrobial candidates. Two components of the Helicobacter pylori trans-translational (a) (b) Synthesis of oligonucleotides In silico design of genomes Assembly of intermediates in E. coli Figure 2. Creation of synthetic minimal cells with desired phenotypic traits. Recent ‘booting-up’ in a cell, have brought us closer to the creation of a minimal cell har minimal genomes could be designed in silico before chemical synthesis of DNA o could be assembled in E.coli, followed by assembly of the genome in S. cerevisia membrane vesicle. (a) Additional genes, operons or larger DNA fragments encoding synthetic minimal cell. (b) Alternatively, additional DNA segments could be incorpora genomes. 566 time-consuming. Work over the last few years has led to several advances in the synthesis of long DNA sequences and in 2008 synthesis of the first complete, 583 kb long, genome of M. genitalium was reported [51–56]. An impor- tant step towards propagation of synthetic genomes and Genome transplantation to a suitable cell Complete genome assembly in S. cerevisiae Synthesis of genes encoding the desired phenotype TRENDS in Cell Biology nces in synthetic biology, especially in the areas of genome synthesis and genome ng only specific phenotypic traits. Modifying a previously described method [35], nucleotides spanning the entire genome. Subsequently, 10 and 100 kb fragments inally, the synthetic minimal genome could be transplanted into a suitable cell or ired phenotypes, such as biofuel or antimicrobial production, could be added to the ted from the outset by in silico design of specific phenotype-encoding minimal their ‘booting-up’ was achieved when the genomic DNA from M. mycoides was transplanted into Mycoplasma capricolum to produce a viable M. mycoides cell [57]. This experiment showed that whole genomes can be successful- ly transferred between species and that they are expressed in the new host cell, thus changing one species into anoth- er. The exact mechanism by which the transplanted ge- nome takes over the host cell remains unsolved, however, and will require further investigation. Furthermore, the design and synthesis of the entire M. mycoides genome and Opinion its transplantation into a M. capricolum – generating M. mycoides cells controlled only by the synthetic chromo- some – was reported recently [35,58]. The major difference between the two experiments is that in the latter the complete genome of M. mycoides was designed in silico and synthesized in the lab before transplantation into a new cell. This achievement brings us closer to one of the key goals of synthetic biology: building a minimal cell harboring, in addition to essential genes, only genes encod- ing a desired phenotype (Figure 2). The practical applica- tions of designed minimal cells could be immense, ranging from the production of biofuels to more effective production of antimicrobials. Although two major hurdles in the synthesis of genomes and their ‘booting-up’ have been largely overcome, other challenges remain. Whereas the design, synthesis and transplantation of the M. mycoides genome is a good starting point, the de novo design of a functional minimal genome will be a major challenge in the future. Currently, minimized cells generated by experimental genome reduc- tions play a leading role in biotech applications because extensive genome deletions can improve particular cellular functions such as transformation efficiency or protein yields [24,50]. We believe that the great potential of a designed cell harboring only the minimal genome lies in its simplicity. Minimized E. coli cells still harbor many non-essential genes, and these could, by as yet unknown routes, influence the designed and desired functions of the cell. Concluding remarks Work over the past few years aimed at investigation of essential genes has provided evidence that some genes are required for the survival of any living organism. These investigations also raised a number of outstanding ques- tions for future research (Box 1). Recent high-throughput methods (e.g. saturation transposon mutagenesis coupled with next-generation sequencing) or combinations of more traditional approaches could provide answers to some of Box 1. Outstanding questions � Which genes are universally required for the survival of all living cells and which are essential only for particular cell types (prokaryotes, eukaryotes or even for different bacterial species)? � How can we minimize the weaknesses of individual methods used in a search for the universal minimal gene set? � How important is the environment of a specific cell type in determining its minimal gene set? � What are the roles in cell survival of the uncharacterized genes identified in minimal genome analyses? these questions. The search for the universal minimal genome has identified several uncharacterized genes and we believe that their investigation could offer invaluable insights into the basic functions required to sustain cellu- lar life. The exact composition of the universal minimal genome is still unknown and the role of the environment in determining cell type- or condition-specific essential genes is also unclear. 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