Saturday, May 23, 2015

In yeast genetics


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“Genetics is, therefore, one of a trio of methods, the others being molecular biology/biochemistry and cell biology, which are required to understand the function of individual genes in vivo”

                         Susan L. Forsburg
Yeast geneticists half-mockingly talk about the cult of APYG: the ‘awesome power of yeast genetics’. But mocking aside, these simple, single-celled fungi have proven themselves to be the workhorses of cell biology because of the ease of their genetic manipulation. The budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe are quite different in their biology (FIG. 1), but they share a similar tool set that makes the process of gene discovery, and subsequent characterization of gene function, remarkably easy.
 Historically, S. cerevisiae has been the more popular experimental system. The first eukaryote to be transformed by plasmids, it was also the first eukaryote for which precise gene knockouts were constructed, and the first to have its genome sequenced1–3. The cell biological issues that have been explored in this ASCOMYCETE range from signal transduction to cell-cycle control, chromosome structure to secretion. The identified genes have been used as probes to uncover further pathways and to identify metazoan homologues. Despite the completion of its genome sequence several years ago1 , the roles of many of its 6,000+ genes remain unclear. The process of mutant analysis and discovery of gene function continues with the added tools of genomics4,5. By contrast, the experimental history of S. pombe involves a smaller, but growing, community. Its genome sequence is essentially complete but shares no conserved synteny (gene order) with the budding yeast in its 4,900+ genes6 . Although yeast phylogeny is still unclear, S. pombe is thus quite distinct from S. cerevisiae and filamentous fungi7–9. The fission yeast has a symmetrical pattern of cell division and has been particularly popular for studies of cell growth and division, and chromosome dynamics. Other cell biological questions have been addressed more recently, inspired by the power of a comparative approach between these two superficially similar organisms. Each of them offers unique insights as a model organism for elucidating the biology of more complex cell types10. Both yeasts are adaptable to several forms of genetic analysis that allow the identification of new genes, or the functional analysis of previously identified genes11,12. Because both can grow and divide as haploids, recessive mutations are easily recovered. However, a diploid sexual cycle exists for both, allowing facile genetic analysis, including tests of COMPLEMENTATION, RECOMBINATION and EPISTASIS. The identification of replication origin sequences allows plasmids to be maintained as free episomes, and these are easily introduced into the cell by transformation. In addition, both species have high rates of homologous recombination, allowing precise manipulation of the genome for the construction of gene disruptions and allele-specific replacements. Their nomenclature is distinct, but they benefit from similar genetic and molecular tools, which provide the basic requirements for the genetic screens described below. With the genome sequences of both species now completed, the challenge is to identify the functions associated with their genes. The classical genetic analysis described here complements the newest genomic approaches13: genetics moves from a function, defined by mutation, to identify the gene responsible, whereas genomics moves from the catalogue of genes to identify their function. The true power of genetics is its predictive value; genetic interactions predict physical interactions, and these can be tested using standard molecular and biochemical techniques. Genetics is, therefore, one of a trio of methods, the others being molecular biology/biochemistry and cell biology, which are required to understand the function of individual genes in vivo.
1. Goffeau, A. et al. Life with 6000 genes. Science 274,
546–567 (1996).
2. Beggs, J. D. Transformation of yeast by a replicating
hybrid plasmid. Nature 275, 104–109 (1978).
3. Rothstein, R. One step gene disruption in yeast. Methods
Enzymol. 101, 202–211 (1983).
4. Oliver, S. G. From gene to screen with yeast. Curr. Opin.
Genet. Dev. 7, 405–409 (1997).
5. Oliver, S. G., Winson, M. K., Kell, D. B. & Banganz, F.
Systematic functional analysis of the yeast genome.
Trends Biotechnol. 16, 373–378 (1998).
6. Sipiczki, M. Phylogenesis of fission yeasts —
contradictions surrounding the origin of a century old
genus. Antonie Van Leeuwenhoek 68, 119–149 (1995).
7. Paquin, B. et al. The fungal mitochondrial genome project:
evolution of fungal mitochondrial genomes and their gene
expression. Curr. Genet. 31, 380–395 (1997).
8. Berbee, M. L. & Taylor, J. W. Dating the evolutionary
radiations of the true fungi. Can. J. Bot. 71, 1114–1127
(1993).
9. Keogh, R. S., Seoighe, C. & Wolfe, K. H. Evolution of gene
order and chromosome number in Saccharomyces,
Kluyveromyces and related fungi. Yeast 14, 443–457
(1998).
10. Forsburg, S. L. The best yeast. Trends Genet. 15,
340–344 (1999).
Summarizes some differences in the biology of the
two yeast species.
11. Guthrie, C. & Fink, G. R. (eds) Guide to yeast genetics and
molecular biology. Methods Enzymol. 194, 1–863 (1991).
Describes more specific methods and protocols for
both yeast species.
12. Moreno, S., Klar, A. & Nurse, P. Molecular genetic analysis
of the fission yeast Schizosaccharomyces pombe.
Methods Enzymol. 194, 795–823 (1991).
13. Kumar, A. & Snyder, M. Emerging technologies in yeast
genomics. Nature Rev. Genet. 2, 302–312 (2001).
The genomics revolution complements the classical
genetics approach.


Adapted from: THE ART AND DESIGN OF GENETIC SCREENS; Susan L. Forsburg; YEAST, NATURE REVIEWS | GENETICS ; VOLUME 2 | SEPTEMBER 2001 | 659-668
Macherki M E

La descrimination de la longeur de CDS //Macherki M E

L’analyse de la phylogénie nous permettre de déterminer les relations entre les groupes d’individus qui sont discriminatoire et  différents. Dans ce contexte, il est commun d’utiliser l’ADN dans la comparaison étant qu’il représente le support de l’information génétique. Avec tout les critiques qu’il entoure, la taille de génome était toujours une grandeur de base dans cette analyse. Le pourcentage en GC reste le paramètre dépendant puis qu’il est stable au nivaux de génome. Autrement, nous avons essayé d’utiliser l’ADNc dans la comparaison et non l’ADN génomique pour bien cibler la partie transcrite et non hérédité. Nous avons utilisé une méthode de permutation de Monte Carlo (n=10000) pour déterminer le moyenne  de Log de longueur exprimé en paire de base (table I)


Macherki M E:R course and applications in genomic 2014

Tentative en biologie computationnelle//Macherki M E

L’étude  de l’ADN permet de révéler plusieurs informations permettant l’identification des différents compartiments dans le  génome et entre des génomes distincts. L’information la plus commun est la fréquence d’un oligo au sein d’une séquence. Par contre cet information est non explicatif .C’est juste un indice calculé qui vari énormément au sein de la séquence. En utilisant la méthode de "DNA walk", cette fréquence suit par conséquence une loi normale puisque cette fréquence change d’un emplacement à un autre dans le génome. Nous étudions la distance entre les oligo présent dans la séquence. Nous considérons alors que les bases symbolisent un enchaînement de pièces de dominos mis l’une après l’autre. Nous avons déterminé la loi de probabilité pour ce variable discret notamment géométrique  et une corrélation entre la fréquence et la distance. Pour des buts comparatifs, nous avons essayé de stabiliser nos statistique en utilisant la méthode de karlin S. et al.et comparer les séquences des génomique après une normalisation à des prédit issu de l’approximation géométrique.
En fin, nous avons essayé de comparer  la structure eucaryote (Chr X de l’homme) et celle de procaryote (E.coli k12)en utilisant notre approximation d’indépendance telle que l’indice de rho avec deux oligos à la fois . Nous avons signalé un effet d'usage des  codons  chez E.coli (aire segmentée dans la FIG) avec des zone sur exprimées et sous exprimées consécutives tel qu’il signaler ultérieurement avec karlin et al.






Dans le chromosome X, l’effet d'usage des  codons est omis et nous reportons que les effets d’abondance( aire bleu dans la FIG indique la répression GC). Cette remarque permet de nous conclure que notre tentative peut permettre de distinguer entre une zone transcrit et non transcrit se qui permet de distinguer l’ADN eucaryote de celle procaryote facilement.


Macherki M E:R course and applications in genomic 2014



Friday, May 22, 2015

Strategies using bacteria to target tumors



The hypothesis that living bacteria may function as anticancer therapeutic agents was first advanced in the middle of the twentieth century. Due to the obstacles of hypoxia and necrosis, accessing tumor tissue with traditional treatments has proved difficult. However, bacteria may actively migrate away from the vasculature and penetrate deep into tumor tissue and accumulate (Fig. 1A). Three classes of anaerobic and facultative anaerobes have been examined for use inanticancer therapy (1,2): Bifidobacteria, facultative intracellular bacteria and strictly anaerobic bacteria. The ideal criteria for the selection of therapeutic bacteria (3,4) are as follows: Non-toxic to the host; selective for a specific type of tumor; has the ability to penetrate deeply into the tumor where ordinary treatment does not reach; non-immunogenic (does not trigger an immune response immediately but may be cleared by the host); harmless to normal tissue; able to be manipulated easily; and has a drug carrier that may be controlled. In addition to studies of bacteria designed to induce immune responses (5)and mediate antiangiogenesis therapy (6), a recent study has focused on the usage of bacterial products as anticancer agents (7). Three main strategies in bacterial cancer treatment are discussed : i) Bacteria as tumor markers; ii) Bacteria engineered to express anticancer agents (Fig. 1B); and iii) Bacteria for oncolytic therapy (Fig. 1C).



Bacteria as tumor markers


As replicating anaerobic bacteria are able to selectively target tumors, the use of these bacteria may be an innovative approach for locating tumors that is simple and direct, but practical and effective. Two types of non-bacterial material have served as tumor markers: Viral vectors, including adenovirus, adeno-associated virus, herpes simplex virus (HSV)-1, HSV amplicon, Sindbis, poliovirus replicon and lentivirus/Moloney murine leukemia virus; and non-viral vectors, such as therapeutic DNA, microRNA, short hairpin (sh)RNA, small interfering (si)RNA and oligodeoxynucleotides (ODNs) (14-16). However, anaerobic bacteria are preferable to these other two types of tumor marker due to increased mobility. Once the marker has been administered, a number of methods may be used to locate the tumor, including bioluminescence, fluorescence and magnetic resonance imaging (MRI), as well as positron emission tomography (17). Bacteria may be detected using light, MRI or positron emission tomography (18,19).


Bacteria engineered to express anticancer agents



 Bacteria exhibit the ability to manufacture and deliver specific materials; these can be artificially coupled to certain anticancer agents (Fig. 1B) (18). The most common current carriers employed ingene therapy are viral vectors, such as retrovirus, adenovirus, viral vaccines, herpes simplex virus and adeno-associated virus. Non-viral delivery systems have been gradually established with the development of technology; currently, the gene therapy field has evolved to encompass not only the delivery of therapeutic DNA, but also of microRNA, shRNA, siRNA and ODNs (4). However, non-viral gene delivery systems exhibit lower transfection potency, resulting in lowered ability to traverse the various obstacles encountered during treatment. Conversely, bacteria have great advantages in the drug carrier field. Two predominant mechanisms have been investigated: The direct expression of antitumor proteins and the transfer of eukaryotic expression vectors into infected cancer cells. In direct expression, four categories of anticancer therapies may be utilized: Proteins with physiological activity against tumors, cytotoxic agents, antiangiogenic agents or enzymes that convert the nonfunctional prodrug to an anticancer drug. In the transfer of eukaryotic expression vectors, gene-silencing shRNAs (20), cytokines and growth factors, and tumor antigens have been investigated (21). Furthermore, the number of useful agents is increasing due to new developments in combinatorial synthesis and the advent of metagenomics, which is an unlimited source of novel anticancer bacterial products. Bacterial oncolytic therapy. The employment of bacteria in oncolytic therapy is the initial treatment and most direct method to kill tumor cells. Clostridial spores are the main components in oncolytic therapy and have been thoroughly analyzed (6,22,23). Bacterial-based cancer therapies usingClostridium spores have the advantage of overcoming the obstacles of hypoxia and necrosis (24). Clostridium spp. are strictly anaerobic and only colonize areas devoid of oxygen; therefore, when Clostridium spp. are systematically injected into solid tumors, spores germinate and multiply in the hypoxic/necrotic regions. Parker et al were the first to demonstrate clostridial oncolysis and tumor regression in mouse tumors by injecting a Clostridium spore suspension into transplanted mouse sarcomas 25). However, during follow-up studies, spore treatment with wild-type Clostridium was not sufficient to eradicate solid tumors (2,8,9). Thus, genetic engineering and repetitive screens are required to enhance the tumor oncolytic capacity of Clostridium. M-55, which was isolated from a non-pathogenic Clostridium oncolyticum strain by Carey et al (10,11), broke this impasse. Since then, multitudinous recombinant Clostridium strains have been used in tumor treatment. Among these, C. histolyticium, C. tetani, C. oncolyticum, C. oncolyticum (sporogenes), C. beijer‑ inckii (acetobutylicum) and C. novyi‑NT have been the most commonly investigated (12,13).

References:


1. Bernardes N, Chakrabarty AM and Fialho AM: Engineering
of bacterial strains and their products for cancer therapy. Appl
Microbiol Biotechnol 97: 5189-5199, 2013.
2. Xu J, Liu XS, Zhou SF and Wei MQ: Combination of immunotherapy
with anaerobic bacteria for immunogene therapy of
solid tumours. Gene Ther Mol Biol 13: 36-52, 2009.
3. Inoue M, Mukai M, Hamanaka Y, et al: Targeting hypoxic
cancer cells with a protein prodrug is effective in experimental
malignant ascites. Int J Oncol 25: 713-720, 2004.
19. Forbes NS: Profile of a bacterial tumor killer. Nat Biotechnol 24:
1484-1485, 2006.
4. Schmidt-Wolf GD and Schmidt-Wolf IG: Non-viral and hybrid
vectors in human gene therapy: an update. Trends Mol Med 9:
67-72, 2003.
5. Cebra JJ: Influences of microbiota on intestinal immune system
development. Am J Clin Nutr 69: 1046S-1051S, 1999.
6. Gardlik R, Behuliak M, Palffy R, Celec P and Li C: Gene
therapy for cancer: bacteria-mediated anti-angiogenesis
therapy. Gene Ther 18: 425-431, 2011.
7. Jain KK: Use of bacteria as anticancer agents. Expert Opin Biol
Ther 1: 291-300, 2001.
8. Gericke D and Engelbart K: Oncolysis by Clostridia.
II. Experiments on a tumor spectrum with a variety of Clostridia
in combination with heavy metal. Cancer Res 24: 217-221, 1964.

9. Dietzel F and Gericke D: Intensification of the oncolysis
by Clostridia by means of radio-frequency hyperthermy
in experiments on animals-dependence on dosage and on
intervals (author's transl). Strahlentherapie 153: 263‑266, 1977
(In German).
10. Brown JM: Tumor hypoxia in cancer therapy. Methods
Enzymol 435: 297-321, 2007.
11. Brown JM and Wilson WR: Exploiting tumour hypoxia in cancer
treatment. Nat Rev Cancer 4: 437-447, 2004.
12. Wei MQ, Mengesha A, Good D and Anné J: Bacterial targeted
tumour therapy-dawn of a new era. Cancer Lett 259: 16-27, 2008.
13. Mengesha A, Dubois L, Paesmans K, et al: Clostridia in
anti-tumour therapy. In: Clostridia: Molecular Biology in the
Post-Genomic Era. Brüggemann H and Gottschalk G (Eds).
Caister Academic Press, Norfolk, UK, pp199-214, 2009.
14. Thomas CE, Ehrhardt A and Kay MA: Progress and problems
with the use of viral vectors for gene therapy. Nat Rev Genet 4:
346-358, 2003.
15. Ji SR, Liu C, Zhang B, et al: Carbon nanotubes in cancer
diagnosis and therapy. Biochim Biophys Acta 1806: 29-35,
2010.
16. McCrudden CM and McCarthy HO: Cancer gene therapy - key
biological concepts in the design of multifunctional non-viral delivery
systems. In: Gene Therapy - Tools and Potential Applications. Martin
Molina F (ed). InTech, Rijeka, pp213‑248, 2013.
17. Ptak C and Petronis A: Epigenetics and complex disease: from
etiology to new therapeutics. Annu Rev Pharmacol Toxicol 48:
257-276, 2008.
18. Forbes NS: Engineering the perfect (bacterial) cancer therapy.
Nat Rev Cancer 10: 785-794, 2010.
19. van der Meel R, Gallagher WM, Oliveira S, et al: Recent
advances in molecular imaging biomarkers in cancer: application
of bench to bedside technologies. Drug Discov Today 15:
102-114, 2010.

20. Xu DQ, Zhang L, Kopecko DJ, et al: Bacterial delivery of
siRNAs: a new approach to solid tumor therapy. In: siRNA and
miRNA Gene Silencing. Sioud M (ed). Springer, New York,
NY, pp1-27, 2009.
21. Patyar S, Joshi R, Byrav DS, et al: Review bacteria in cancer
therapy: a novel experimental strategy. J Biomed Sci 17: 21, 2010.
22. Barbé S, Van Mellaert L and Anné J: The use of clostridial
spores for cancer treatment. J Appl Microbiol 101: 571-578,
2006.
23. Minton NP, Mauchline ML, Lemmon MJ, et al: Chemotherapeutic
tumour targeting using clostridial spores. FEMS Microbiol
Rev 17: 357-364, 1995.
24. Umer B, Good D, Anné J, Duan W and Wei MQ: Clostridial
spores for cancer therapy: targeting solid tumour microenvironment.
J Toxicol 2012: 862764, 2012.
25. Parker RC, Plummer HC, et al: Effect of histolyticus infection
and toxin on transplantable mouse tumors. Proc Soc Exp Biol
Med 66: 461-467, 1947.


***Adapted from:LIU et al: TUMOR-TARGETING BACTERIAL THERAPY IN TREATMENT OF ORAL CANCERONCOLOGY LETTERS 8: 2359-2366, 2014


Macherki M E



Bacterial treatment for cancer

Macherki M E


"These results … are promising and support the further testing of C. novyi-NT for treatment of inoperable therapyresistant tumours in humans"


A new study by Roberts and colleagues has shown that intratumoural injection of an attenuated version of Clostridium novyi bacteria can reduce tumour volume in several preclinical animal models as well as in one human. C. novyi can induce tumour cell lysis, is very sensitive to oxygen levels and thrives in hypoxic environments, such as those often found in advanced solid tumours, but does not grow in normoxic environments, such as those typically found in normal tissue. Roberts et al. hypothesized that these characteristics would make it an ideal therapy for tumours that cannot be removed surgically, such as gliomas. The authors had previously treated tumours in mice and rabbits intravenously with an attenuated C. novyi strain (C. novyi-NT) and observed promising response rates but could not recapitulate these responses in larger canine models. As this might be due to inadequate delivery to the tumour, the authors tested intratumoural injections of C. novyi-NT, initially in a rat model of highly aggressive gliomas. Treatment of these rat brain tumours with intratumoural injections caused a significant decrease in tumour burden within 48 hours of the injection and spared surrounding normal cellsthat were only micrometres away. Although brain oedemas were commonly seen in these animals, this adverse effect was easily managed. The authors next tested this treatment in dogs, as dogs often develop spontaneous solid tumours and thus might more accurately model human tumours. Intratumoural injection of C. novyi-NT spores into a variety of solid tumours in dogs resulted in an objective response in 37.5% of all dogs (n=16). Half of the dogs that showed objective responses had long-term responses. Adverse events were related to bacterial infection and could be controlled with antibiotics. Owing to the success in the canine models, the authors set up a phase I investigational clinical trial and enrolled a patient with a late-stage metastatic retroperitoneal leiomyosarcoma. One of the metastases, located in the patient’s shoulder, was targeted for treatment with C. novyi-NT spores. The treatment reduced the tumour volume although the patient also developed adverse effects related to bacterial infection, such as fever, which was managed with antibiotics. The clinical trial is ongoing, and the authors outline several avenues of further research including determining the role of acquired immunity in the response to C. novyi-NT treatment, and whether this therapy could be combined with established chemotherapies and radiotherapies. Thus, although these results are preliminary, they are promising and support the further testing of C. novyi-NT for treatment of inoperable therapy-resistant tumours in humans.

***Adapted from:Isabel Lokody, Assistant Editor Nature Reviews Cancer This article is modified from the original in Nature Rev. Cancer (http://dx.doi.org/10.1038/nrc3827).



C. difficile spore ultrastructure //Paredes-Sabja, D (2014)

The overall structure and morphology of C. difficile spores is similar to what has been seen in other endospore-forming bacteria (Box 2), but the outermost layers are particularly different. Transmission electron microscopy (TEM) of C. difficile spores [19,21–23,25,34,35] revealed that the spore coat has distinctive laminations (i.e., lamellae), which are similar to those observed in B. subtilis but different from those in members of the B. cereus group (i.e., B. anthracis) (Figure 1A,B) [36,37]. It is remarkable that despite these structural similarities, only 25% of the genes encoding spore coat proteins have homologs in C. difficile, suggesting that the components that govern spore coat assembly are divergent to those defined for B. subtilis and/or the B. cereus group [11].



In members of the B. cereus group, the outermost layer is the exosporium, defined for these species as a distinguishable spore layer with hair-like projections formed in the mother cell compartment, and it does not have direct interactions with the spore coat layers that surround the cortex [38–40]. In C. difficile, the exosporium is the outermost layer. Although the C. difficile exosporium has hair-like projections, it lacks many of the B. cereus group exosporium orthologs and the frequently observed gap that separates the spore coat from the exosporium. Nevertheless, the C. difficile exosporium exhibits a conserved genetic signature to the B. cereus group, because the exosporium glycoproteins encoded by bclA1, bclA2, and bclA3 are also expressed in the mother cell (see below). The stability of the exosporium, remains a matter of controversy because several reports suggest that this layer is fragile and easily lost [21,22], or absent in spores developed during biofilm formation [39],
whereas other reports indicate that it is a reasonably stable layer that is only removed by proteases and/or sonication treatments [19,23,25,34,35]. The stability ofthe exosporium could be related to strain type or the use of proteases in purification procedures. Indeed, recent evidence indicates that proteinase K can remove the exosporium layer while leaving the spore coat intact [34]. Interestingly, the morphology of the exosporium seems to be strain-dependent (Figure 1A,B) [34,35]. C. difficile 630 spores have an electron-dense, compact exosporium layer (Figure 1A), whereas spores derived from strains R20291, M120, TL176, and TL178 have a hair-like exosporium layer reminiscent of the B. anthracis exosporium (Figure 1A,B). Interestingly, the ultrastructural organization of the exosporium surface of R20291, M120, and TL176 is identical to that of TL178 spores (Figure 1C), suggesting that the exosporium layer of C. difficile strain 630 may be an outlier among C. difficile strains.

Although the roles ofthe outermostlayers (i.e., spore coat and exosporium) on CDI and pathogenesis are unclear, recent reports have shed light on their potential functions. The C. difficile spore surface was shown to interact with unidentified surface receptor(s) of intestinal epithelium cells [25]. In vitro infection of macrophages with C. difficile spores revealed that spores become cytotoxic to macrophages possibly by disrupting the phagosomal membrane through spore surface-membrane interactions [41]. The exosporium layer was also shown to confer hydrophobicityto the spore surface affecting its adherence to inert surfaces [35]. C. difficile R20291 spores with a defective exosporium layer adhere better to Caco-2 cells than those with an intact exosporium layer suggesting a potential role in adherence to epithelial surfaces and in the transmission of CDI [23]. Removal of the exosporium layer also increases the ability of C. difficile spores to outgrow into colonies in vitro [34], raising the possibility that C. difficile spores lacking an exosporium are not only able to adhere better to colonic surfaces but also germinate more efficiently. The fraction of spores that have a firmly attached exosporium layer and the half-life of this layer in the environment remain to be determined.
               Adapted from:Clostridium difficile spore biology: sporulation, germination, and spore structural proteins,Daniel Paredes-Sabja et al.Trends in Microbiology July 2014, Vol. 22, No. 7
         

                                                                            Macherki M E

The Sporulation Process and Its Regulation in B. subtilis//de Hoon et al.2010

The genetically competent, non-pathogenic soil bacterium B. subtilis is the prevalent model system for studies of sporulation. A significant amount of detailed molecular data has been gathered over the years to characterize the mechanism of endospore formation — in particular, the regulation of the different sporulation stages.
Morphological Stages of Sporulation and Formation of Protective Structures
 In rich medium, B. subtilis cells divide by binary fission approximately every 30 minutes. By contrast, deterioration of environmental conditions triggers sporulation, a developmental process that takes about 8 to 10 hours. Thus, endospore formation represents a formidable investment of time and energy and is considered to be a survival pathway of last resort, as B. subtilis cells only commit to sporulation after they failed to deal with starvation in other ways, such as cannibalism or establishment of a genetically competent state [14–16]. The successive morphological stages of sporulation have been defined using electron microscopy [17,18] (Figure 1). Sporulation begins with an asymmetric cell division and results in the generation of two cell types, a forespore (the smaller compartment, also called the prespore) and a mother cell. The two cells experience distinct fates, because the mother cell ultimately lyses by a programmed cell death mechanism, whereas the forespore matures as a spore. Shortly after asymmetric division, two parallel programs of gene expression are established in each compartment under the control of transcription factors that are activated in a cell-specific manner. In addition to regulatory interactions within the forespore and mother cell, precise inter-compartmental signaling is required to control the spatial and temporal progression of the developmental process. Sporulation commences only after a round of DNA replication has been completed, in order to ensure that two chromosome copies are available in the predivisional cell [19]. The two chromosomes are oriented with their origin of replication anchored at one cell pole and their origin-distal region at mid-cell [20]. After asymmetric division, only about onethird of the forespore chromosome (i.e. the origin-proximalregion) is captured in the small chamber of the dividing cell. A DNA translocase, SpoIIIE, located at the center of the polar septum, is necessary to pull the rest of this chromosome into the forespore [21–23]. The other chromosome is localized entirely inside the mother cell. Following asymmetric division, the next morphological stage of sporulation is the engulfment of the forespore by the mother cell. This process is analogous to phagocytosis and is driven by mother cell proteins that facilitate membrane migration around the forespore by enzymatic removal of the peptidoglycan [24,25]. After completion of engulfment, the forespore, now entirely surrounded by its inner and outer membranes, is a free protoplast in the mother cell cytoplasm. Next, a series of protective structures is assembled around the spore core. The cortex, a modified peptidoglycan, is synthesized between the two forespore membranes [26]. Simultaneously, at least 70 individual coat proteins are synthesized in the mother cell to encase the spore in a multi-layered structure, with the crust as the outermost layer [27,28]. Finally, the mother cell lyses to release the mature spore. Fully formed spores, recognized as the most resistant form of life on the planet [29], protect the bacterial genome against heat, desiccation, radiation, and oxidation. In addition, spore formation might be an efficient way to escape predation from higher organisms [30,31]. As soon as environmental conditions become favorable for vegetative growth, however, it is critical that B. subtilis quickly exits from the dormant state. This process is referred to as spore germination [32] and is triggered by the presence of nutrients in the environment. The nutrients are sensed by specific spore membrane receptors and, within minutes, the spore core rehydrates, the cortex is hydrolyzed, and the coat is shed. Ultimately, DNA replication is initiated and the first cell division soon follows.



Adapted from:
Hierarchical Evolution of the Bacterial Review Sporulation Network,de Hoon et al.Current Biology 20, R735–R745, September 14, 2010 ª2010 Elsevier Ltd All rights reserved DOI 10.1016/j.cub.2010.06.031

Macherki M.E