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.

Genome battle: Humans vs. Chimpanzees!!!

Initial sequence of the chimpanzee genome and comparison with the human genome.

Chimpanzee Sequencing and Analysis Consortium.

Abstract

Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.

Nature. 2005 Sep 1;437(7055):69-87.

Why is this cool?

 What does it mean when people say that humans and chimpanzees are 98% genetically similar? That is the question for this paper. Well, not that question exactly, but close enough. So, the researchers sequenced the chimpanzee genome and compared it to the human genome. 

Just to make it known:

Base pairs in the human genome: 3,200,000,000

Base pairs in the chimpanzee genome: 2,900,000,000

Single base pair changes: 35,000,000

Insertion or deletions: 5,000,000

Chromosomal rearrangements: A handful.

 What do these numbers mean? Well, that is an amazing question and it has not been answered yet. But, we can some what answer from our basic knowledge of chimps and humans. The list of differences:

1. Chimps don't have the same language abilities as human.

2. Chimps are super hairy, humans not so much.

3. Arm and leg lengths in humans are different than in chimps.

4. Chimps have a bone in their penis, humans don't.

5. Humans are the only animals with psychic powers.

 Just so you know, Mandrill doesn't count for chimps because he is a human who looks like a mandrill. Mandrill's may look like all he does is look freaky, but he can secretly control women with his PHEROMONES!! Although, as far as pheromone-using-mind-controllers go, none can ever beat PURPLE MAN!!!

To villainy!

 He fell into a vat of mystery chemical and was given pheromone-based, mind-control powers and the best skin color ever: PURPLE! He has never bested anyone with the exception of Jessica Jones and that didn't even go far enough. He captured her and made her watch his debauchery? Lame. His supervillainy knows no bounds and he doesn't ever touch Jewel? Whatever. Although, outside of that one thing, Bendis made Purple Man a serious villain.

 Ok, so those two have hormone based powers, not psychic powers, but I have never heard of a psychic animals. The closest to a psychic animal was Bunicula.