ESSENTIAL GENES!!!!

Essential Bacillus subtilis genes.

Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M, Asai K, Ashikaga S, Aymerich S, Bessieres P, Boland F, Brignell SC, Bron S, Bunai K, Chapuis J, Christiansen LC, Danchin A, Débarbouille M, Dervyn E, Deuerling E, Devine K, Devine SK, Dreesen O, Errington J, Fillinger S, Foster SJ, Fujita Y, Galizzi A, Gardan R, Eschevins C, Fukushima T, Haga K, Harwood CR, Hecker M, Hosoya D, Hullo MF, Kakeshita H, Karamata D, Kasahara Y, Kawamura F, Koga K, Koski P, Kuwana R, Imamura D, Ishimaru M, Ishikawa S, Ishio I, Le Coq D, Masson A, Mauël C, Meima R, Mellado RP, Moir A, Moriya S, Nagakawa E, Nanamiya H, Nakai S, Nygaard P, Ogura M, Ohanan T, O'Reilly M, O'Rourke M, Pragai Z, Pooley HM, Rapoport G, Rawlins JP, Rivas LA, Rivolta C, Sadaie A, Sadaie Y, Sarvas M, Sato T, Saxild HH, Scanlan E, Schumann W, Seegers JF, Sekiguchi J, Sekowska A, Séror SJ, Simon M, Stragier P, Studer R, Takamatsu H, Tanaka T, Takeuchi M, Thomaides HB, Vagner V, van Dijl JM, Watabe K, Wipat A, Yamamoto H, Yamamoto M, Yamamoto Y, Yamane K, Yata K, Yoshida K, Yoshikawa H, Zuber U, Ogasawara N. 

Abstract

To estimate the minimal gene set required to sustain bacterial life in nutritious conditions, we carried out a systematic inactivation of Bacillus subtilis genes. Among approximately 4,100 genes of the organism, only 192 were shown to be indispensable by this or previous work. Another 79 genes were predicted to be essential. The vast majority of essential genes were categorized in relatively few domains of cell metabolism, with about half involved in information processing, one-fifth involved in the synthesis of cell envelope and the determination of cell shape and division, and one-tenth related to cell energetics. Only 4% of essential genes encode unknown functions. Most essential genes are present throughout a wide range of Bacteria, and almost 70% can also be found in Archaea and Eucarya. However, essential genes related to cell envelope, shape, division, and respiration tend to be lost from bacteria with small genomes. Unexpectedly, most genes involved in the Embden-Meyerhof-Parnas pathway are essential. Identification of unknown and unexpected essential genes opens research avenues to better understanding of processes that sustain bacterial life.

Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4678-83. Epub 2003 Apr 7.

Why is this cool?

Leezle Pon is not a bacterium, but a small pox virus.

 The human genome is 3.3 billion base pairs and there are approximately 20,000 genes coded in it. Rats has a genome size of 2.75 billion base pairs that also code about 20,000 genes. This is amazing because it doesn't intuitively make sense about how an organism much smaller than humans can have a genome that codes for just about the same number of genes! Consider rice and corn. The rice genome has 340 million base pairs in it coding for about 30,000 genes. Corn has about 2.3 billion base pairs that code for about 30,000 genes. These are very different plants and their genome sizes reflect that, but the number of genes coded for does not reflect that. Both genomes code for close to the same number of genes! This inevitably leads to the question: HOW MANY GENES ARE NECESSARY FOR LIFE?!?
 That is exactly the question that these researchers set out to answer. There are some problems though. You can not mutate humans for research. You can do mice, but that is EXTREMELY EXPENSIVE. You could do plants, but that can take forever. Bacteria are inexpensive to use and easy to work with, so this research uses Bacillus subtilis to address the question. So, how did they do it?

 You would think that they would knockout one gene and tested if the organism still lived and if it did they would then knockout another and so on and so forth until they had the minimum number of genes required to maintain life in a nutrient rich environment. As it turns out, that approach is just not as easy as it sounds, so that went about a different way. They made a knockout for every gene in B. subtilis for a total of 4,100 different knockouts! Of those knockouts, only 192 genes were completely essential to maintain life.