CHEMICAL COMPOSITION OF THE BACTERIAL CELL

1. CHEMICAL COMPOSITION OF THE BACTERIAL CELL

3. Size of the “average cell” • A given strain (E. coli B/r) in steady-state growth (unchanging rate and constant average cell size and composition) under specified conditions (balanced growth) • The average cell: a rod-shaped body with diameter and length of approximately 1 and 2 μm, respectively • Total volume of an average cell: approximately 9 x 10-13 mL (0.9 femtoliters). The periplasmic space forms a full 30% of the cell volume

4. Meaning of the “average cell” • Approximately 44% along the cell cycle in age • Approximately 33% larger than when it was born (If individual cells increase in mass exponentially) • The idealized frequency distribution (relative number of cells) of cell age in a steady-state culture increasing by binary fission is given by f(x) = 21-x, where x is the age of cells measured on the scale from 0 to 1 cell generation time

5. Weight of the “average cell” • Total weight of an average cell: 9.5 x 10-13 g • Total dry weight of an average cell: 2.8 x 10-13 g • Approximately 70% of the packed cell mass is water (c.a. 90% in cells of higher organisms) • 1.05 x 1012 cells / g of wet biomass • Density of the average cell: 1.06 g/mL

7. Composition of the “average cell” • Elemental assayof dry cells: approximately 50% C, 20% O, 14% N, 8% H, 3% P, 2% K, 1% S, 0.2% Fe, 0.05% each of Ca, Mg, Cl, and a total of 0.3% trace elements including Mn, Co, Cu, Zn, Mo • Components: protein 55%, ribosomal RNA 16.7%, transfer RNA 3%, messenger RNA 0.8%, DNA 3.1%, lipids 9.1%, LPS 3.4%, peptidoglycan 2.5%, building block metabolites and vitamins 2.9%, inorganic ions 1.0% • It will contain 18,700 ribosomes and a little over 2 million molecules of protein, of which there are between 1000 and 2000 different varieties

9. Genome size of the “average cell” • Chromosomal DNA of E. coli: a ccd molecule of 4,720 kbp / approximately 1 mm long • Although considered haploid, will contain two copies of the chromosome when growing rapidly • Maximal number of protein-encoding genes: cannot possibly be more than 4,300 protein-encoding gene (average mw. of proteins is 40,000 / average mw. of an amino acid residue in protein is 110 / the average protein has 364 amino acids / the average gene size is 1.1 kbp) • The genome size of cells of the genus Mycoplasma is approximately one-fifth the size of that of E. coli

10. http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/chroms-genes-prots/genomes.htmlhttp://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/chroms-genes-prots/genomes.html

11. Minimum genome size of a cell? • Smallest Archae genome from Nanoarchaeum equtans, 0.491 Mbp: obligate symbiont lacks genes required for synthesis of lipids, amino acids, nucleotides, and vitamins, and hence must grow in close association with another organism which provides these nutrients. • Smallest Bacterial genome from Mycoplasma genitalium, 0.58 Mbp: obligate intracellular pathogen lacks genes required for amino acid biosynthesis and the peptidoglycan cell wall, genes encoding TCA cycle enzymes, and many other biosynthetic genes. • The smallest free-living organisms have a genome size over 1 Mbp.

12. http://www-micro.msb.le.ac.uk/109/Genomes.html

13. Small molecules of the “average cell” • Varieties: (1) precursors (building blocks) of macromolecules; (2) metabolic intermediates; (3) enzyme cofactors; (4) polyamines bound to DNA • Approximate number of kinds of small molecules: (1) 120 amino acids, their precursors and derivatives; (2) 100 nucleotides, their precursors and derivatives; (3) 50 fatty acids and their precursors; (4) 250 sugars, carbohydrates, and their precursors; (5) 300 quinones, polyisoprenoids, prophyrins, vitamins, other coenzymes and prosthetic groups, and their precursors

14. Study questions 1 • A newly isolated bacterial species is found to have a single chromosome with a molecular weight of 1 x 109. Estimate the maximum number of protein-encoding genes it is likely to have if a two-dimensional gel reveals that the average molecular weight of its proteins (polypeptides) is 35,000. Assume that 10% of the genome does not code for protein and that 1% codes for stable RNA species. • Ans: 1,510 (using 110 and 618 as the molecular weights of an average amino acid residue and an average nucleotide base-pair residue, respectively)

15. Study questions 2 • For the reference culture of E. coli described in Table 1, calculate the number of ribosomes in a newborn cell. • Ans: 14,060 ribosomes per newborn cell

16. A giant step toward the creation of artificial life: synthetic genome • A team led by Dr. Hamilton Smith, director of the Venter Institute's Synthetic Biology Group, has manufactured from laboratory chemicals a ring of DNA containing all the genes of Mycoplasma genitalium - the tiniest bacteria ever found. That means the team is tantalizingly close to creating an artificial form of life that could replicate itself using these machine-made genes. • The feat is described in an online edition of the journal Science released Thursday (January 24, 2008 ) by researchers at the J. Craig Venter Institute in Rockville, Md. • The secret to the success of the project was finding ways to assemble the 100 pieces of genome into subgroups, then joining the subgroups into successive larger pieces, until the entire genome could be spliced together from four lengthy chains.

17. A giant step toward the creation of artificial life: transplant of synthetic genome • In August (2007), the Venter Institute team reported that they had performed a successful transplant of a natural genome by removing the chromosome from one Mycoplasma species and implanting it into another, which began replicating copies of the first species. • The plan is to slip the synthetic chromosome inside the microscopic skin of one of the Mycoplasma bacterium, replacing its natural genome with the machine-made one and sparking the creature into a life form that can reproduce itself. • There are still several technical hurdles to pass before a similar procedure could work with the synthetic chromosome.

18. A giant step toward the creation of artificial life: impact • The work is not merely a demonstration of laboratory finesse, Venter insisted, but a step toward development of technologies that could grow fuel in bacterial vats and speed cures for diseases. "It puts a lot of power in the hands of humans," he said. • And there is the matter of bragging rights of mythological proportions. Mere mortals have yet to lay claim to creating life.

19. A giant step toward the creation of artificial life: next step • Once the laboratory produces living, replicating bacteria using this artificial chromosome, Venter scientists plan to strip away genes systematically, to find how few are truly necessary to sustain life. It is largely an academic exercise, but in the process the scientists hope to refine the tools for building living organisms from this fundamental base, and custom-design them to perform certain tasks - such as manufacturing fuel.

20. A giant step toward the creation of artificial life: biosafty and other concern • Jim Thomas, a Montreal researcher for ETC, a Canadian environmental and social justice advocacy group, said the "synthetic biology" work pursued by Venter's group is potentially dangerous and ought to be subject to government oversight. • "There are real concerns about biosafety for synthetic organisms, and this takes us a step closer to them," he said. "Because of the push toward rapid commercialization, an environmental release of a synthetic organism is inevitable. This is an ecological disaster waiting to happen." • The push to develop synthetic fuels using these bugs, he suggested, will place more stress on farmland to produce energy crops. "We are already seeing fuel versus food conflicts because of the drive to produce ethanol," he said.