codexis_logoAs blog after blog comes out with end-of-year green IPO predictions, the same three companies have consistently been tapped: Solyndra (which filed for its $300 million public sale two weeks ago), Silver Spring Networks (the anointed Smart Grid leader) and Tesla Motors (because it makes the prettiest electric car of the bunch). But today, Codexis, maker of engineered microbes and catalysts for green fuel, chemical and pharmaceutical production has surprised us all, filing for a $100 million IPO.

The news is even more shocking considering that the company withdrew its previous IPO filing in September 2008, citing poor market conditions. It had originally filed in April 2008.

Codexis engineers the enzymes and microorganisms that turn feedstocks like wood chips, switchgrass, corn husk and sugar cane into ethanol. Minuscule changes in their DNA can speed conversion times and make processing more efficient. It’s a delicate science that has yet to be successfully scaled. But this could soon change.

Based in Redwood City, Calif. (down the road from both Silver Spring and Tesla), Codexis is one ambitious company. Its CEO, Alan Shaw, has talked a big game for a while now, touting the merits of drop-in fuels (fuels that will work with existing automotive technology), especially those that are biomass-based, over electric charging infrastructure and other renewable sources of energy like solar and wind. And 2010 might just be the make-it-or-break it year for this claim.

Not only are many companies launching their plug-in vehicle models, testing the viability of electric transportation infrastructure, but several Codexis competitors are also heating up on the commercial scale, including LS9, Coskata and Synthetic Genomics. Codexis has an advantage because due to its well-developed industrial chemical and pharmaceutical products, but it may have to fight for market share when it comes to fuel.

The company, which plans to trade on the Nasdaq under the symbol CDXS, says it will use the money brought in from the public sale for working capital, and perhaps to kick off an acquisition strategy to add to its output capacity.

While it saw an 84 percent increase in revenue this year, it still saw a loss. This shouldn’t hurt its chances too much, however. Battery-maker A123Systems, which broke the seal on IPOs in the cleantech sector in September, is still seeing heavy losses; and Solyndra, vying to be the first IPO in 2010 is no different.

On top of that, Codexis’ losses are obviously narrowing — falling from $38.8 million to $15.1 million in just a year. The company reported revenue of $13.4 million for the first three quarters of 2009, a small bump up from the $10.8 million it posted over the same period in 2008.

It already has an impressive roster of clients signed up, including Royal Dutch Shell, Pfizer and Merck & Co. And it appears to have more realistic plans to growing its business in new directions. Earlier this month, it announced a partnership with carbon capture provider CO2 Solution to work on enzymatic carbon capture technology. Basically, Codexis will try to engineer enzymes that can survive the inhospitable conditions of smokestacks to absorb carbon dioxide and convert it into a bicarbonate ion. This makes Codexis a contender in a whole new area of green.

The company has also been pretty fortunate in its funding. In March, Shell acquired a bigger stake in Codexis for a reported $30 million. The company has previously raised $133 million from Bio*One Capital, CMEA Capital, Pequot Capital, Chevron Technology Ventures, and Maxygen.

If Codexis successfully makes it to market next year, it will no doubt establish itself as the catalyst engineering firm to watch — potentially attracting even more attention from the big oil and gas interests like BP and Exxon.