Sudoku-solving bacteria

Dec 01 2010 Published by under Biology & Environment

One of the goals of synthetic biology is to engineer bacteria into biological "machines" that can be used to produce energy, deliver drugs, or synthesize materials. If the engineered bacteria could selectively communicate with each other, would expand their possible uses.

A team of students from the University of Tokyo decided to create E. coli bacteria that could selectively communicate with each other for this year's Internationally Genetically Engineered Machine (iGEM) competition, held last November 6-8 at MIT.

Sudoku Puzzle

Sudoku Puzzle

As a proof-of-principal for their bacterial communication system, the Japanese team created microbes that could solve a Sudoku puzzle.

Sudoku puzzles are usually made from a 9x9 grid made up of nine 3x3 squares. The numerals 1 through 9 can only be used once in each row, once in each column, and once in each 3x3 square. The puzzles start out with some of the numbers already filled in, and the goal is to fill in the blanks. You can see an example of a starting grid over on the right -->

Even though a Sudoku puzzle uses numbers, it's not a math puzzle - no adding, subtracting or other number manipulation is required. It's a logic puzzle. It could work just as well with nine different pictures or nine different letters or nine different colors.

The simple logic rules of the game were an ideal way to demonstrate the ability of the modified bacteria to communicate.

The Japanese team's modified bacteria were designed to solve a 4x4 Sudoku grid.  They engineered 16 genetically different bacteria, one for each spot on the grid. Each of those strains of bacteria has the ability differentiate into one of 4 types. Each of those types can then direct "detection bacteria" to produce a corresponding fluorescent color.

Just like any Sudoku puzzle, the grid begins with some of the squares already solved, like this:

E.Coli Sudoku Puzzle

The differentiated bacteria produce signals that tell the other bacteria their type. The undifferentiated bacteria are able to detect which of the 4 types are already present in the same "row",  "column" and "block", while ignoring information from irrelevant "squares". For example, undifferentiated bacteria representing square 4 would need to detect which differentiated types were already present in squares 1-3 (the same row), squares 8, 12, and 16 (the same column), and squares 3, 7 and 8 (the same block).  They would have to ignore the bacteria in irrelevant squares 11 and 13.

Here is their video of how the system works, which is a bit clearer than my explanation:

The students already have figured out - at least theoretically - how to modify their system so that bacteria would be able to solve a 9 x 9 Sudoku grid.

But that isn't the only use of such engineered microbes. Bacteria that can differentiate between relevant and irrelevant communications could ultimately be used to design bacterial logic circuits for parallel calculation devices. Maybe someday we'll be able to use bacteria to plug away at difficult computing problems.

You  can read the technical details to learn more about the biochemistry of the system.

And if you want to test your own Sudoku skills, I recommend the daily puzzle here.

(Project via New Scientist)


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Top image: A Sudoku layout generated by the GNU programSu Doku Solver and contributed in the public domain by Lawrence Leonard Gilbert. From Wikipedia.
Bottom Image: "16 kinds of E. coli corresponding to each cell" by the UT Tokyo iGEM team, shared under a Creative Commons Attribution-ShareAlike license.

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