Genetic Code of Rice


Staff member
Posted on Thu, Apr. 04, 2002

U.S., Chinese scientists set to reveal rice's genetic code

By Lisa M. Krieger
Mercury News

A small grain that feeds much of the world yields its biggest secret today when American and Chinese researchers publish the long-sought genetic code for rice.

In a feat certain to accelerate efforts to create crops with special traits, the researchers describe the blueprint for the inner workings of a plant that is a cornerstone of California agriculture and a staple for more than half the world's population.

The complete genome sequencing, the first ever of a crop plant, is also expected to help scientists better understand wheat, corn and barley. Together, these crops represent an estimated two-thirds of all calories consumed by people in developing countries, according to the U.N. Food and Agriculture Organization.

``It is a navigational aid for agriculture, something that is potentially very, very valuable to those 800 million people in the world without enough to eat,'' said Dr. Donald Kennedy, former Stanford University president and now a professor of environmental sciences and editor of the journal Science, where the paper was published.

The publication of two different rough drafts of the rice genome comes as growing populations and diminishing land have forced the world's farmers to seek greater efficiency in growing plants.

The availability of the full genome sequence can make the search for genes easier and faster and allow scientists to pose new questions. Each team studied a different strain of rice.

``The information can be leveraged for improving not just rice, but other crops as well,'' said Thomas H. Tai, research geneticist at the U.S. Department of Agriculture's Agricultural Research Service in Davis. ``And it'll help not just biotechnology, but traditional plant breeding as well.''

A team lead by Dr. Stephen Goff of the Torrey Mesa Research Institute of San Diego detailed the genome of Oryza sativa japonica. Details on japonica are free to academic and government scientists; for commercial researchers, they are offered for a fee.

The other effort, lead by Dr. Jun Yu of Beijing Genomics Institute, described the genome of indica rice. This information is freely available to everyone over the Internet.

The research will be immediately put to use identifying the multitude of varieties of rice, through a DNA fingerprinting technique similar to that used in humans.

More exciting are future plans to scan the genomes of the thousands of strains of rice from seed banks around the world, only one-quarter of which have been commercialized. Scientists will seek traits that could help unlock the genetic potential of the grain.

For centuries, plant breeders have tried to raise crop yields by breeding whole plants. It is far more efficient, they say, to find the best individual genes or groups of genes. These genes may hide not only in modern varieties, but also in wild relatives and in the old heirloom varieties that have been saved in the world's ``gene banks,'' created by farsighted plant breeders and conservationists.

One of the first targets will be the gene for cold tolerance, which permits germination of seeds in cool damp soils, say scientists. This would be a breakthrough for California's Central Valley rice farmers, who must use chilly snowmelt from the Sierras to water their seeds.

Scientists will also seek a gene that boosts the vigor of tiny seedlings. Strong seedlings are better able to compete for sun and nutrients against quick-growing weeds. If weeds pose less of a threat, herbicide use can be reduced, Tai said.

``This should allow us to breed better and stronger growing rice in the future that has less susceptibility to disease and higher quality grain -- as well as open the door to future biotech rices that may be produced,'' said Tim Johnson of the California Rice Commission.

Rice farming is a $500 million-a-year business in the state. Production is centered in the Sacramento Valley, with its warm Mediterranean climate and hard, water-holding soils.

The state's rice is of the japonica variety -- a medium-grain rice that is soft, clings together, and is slightly translucent. This makes it well-suited for Asian cuisine, paella, risotto and desserts.

But critics cautioned against a rush to alter the characteristics of rice without understanding the long-term impact on the environment.

``The gene does not define the plant. What's important is the ecological dynamics of the plant,'' said Beverly Thorpe of the Washington D.C.-based environmental group Greenpeace. While Greenpeace supports any genetic shifts that happen through conventional breeding practices, it opposes any genetic mixing-and-matching not seen in nature.

Researchers mapping the rice genome made a startling observation: The 50,000-gene sequence of the lowly rice plant is larger than humans, who have only 30,000 to 40,000 genes. But the rice genes themselves are relatively small. And they are incapable of multitasking -- a trait of human genes and the explanation for what makes us so complicated.
And rice is one of the smaller plant genomes. Supposedly animals use genes in a more complicated manner than do plants, leading to more proteins per gene. ('Course this was from an article written by a critter with a small animal genome.)
Many plants are polyploid, meaning they have multiples of their whole genome ie 4n, 6n ... where humans are 2n.

One reason is that the regulation of gene expression is much simpler. Instead of having a single gene with complicated regulation plants have multiple copies where each is expressed under more limited conditions. Indeed you can treat plants with chemicals like colchicine to double the number of chromosomes (I forget the details but it blocks one of the mitotic or meiotic divisions) and they are very tolerant of it.

Interestingly if you double the amount of DNA the cell cycle is effected such that the size of cells double (actually this is actually used in certain cell types in drosophila and elegans at least for making "factory cells" that are synthetic powerhouses). In many plants this leads to an increase in the size of the plant. It is not surprising that this might have even been selected for in agricultural strains.
Scilosopher, this hamster has read that human muscle cells grow in a similar manner.

Here’s an excerpt from a discussion on muscle growth.

“Neuronal activity stimulates a chain reaction (for lack of a better
description) where levels of both the mRNA (the translation of the
recipe that synthesizes the IGF-1 protein, which is the bioactive
part) and the protein are increased. Increased levels of this protein
(I stress 'increased levels' because baseline levels do not appear to
elicit the same responses) 'wake up' satellite cells, which are muscle
cell precursors in adult muscle tissue and are normally quiescent
('sleep'). They lie dormant until a signal tells them its time to
become active, proliferate, differentiate and/or fuse with existing
muscle cells, donating their DNA machinery to the cell.”

The full discussion may be found here
Muscle cells are a little different. Pre-existing cells fuse to form syncytial cells with multiple nuclei. In the cells I was speaking of the chromosomes actually remain together like the polytene chromosomes in Drosophila salivary glands. So it is a little different than polyploidy, even in that case but mainly in chromosomal organisation.

Syncytial cells are interesting too, as the different nuclei can actually run slightly different genetic programs simultaneuosly in a single cell. In nueromuscular junctions a nuclei is often associated with a given synapse and reacts to the local environment effected by synaptic signalling.

The number of mitochondria increases, as more energy is needed. Presumably muscle cells require multiple nuclei for increased protein synthesis. Wonder how other cell machinery changes due to cell specialization. In particular what would nerve cells need to support long axons? How would the cell nucleus support protein structures and machines that in cellular distances would be very, very distant? (Seems poor logistics.)
mRNAs and proteins can be localized in certain regions of the cell to increase production locally. In fact a lot of regulation in nuerons is at the level of translation to protein so the mRNAs can already be where they need to be, but not activated until needed.

Organelles are also localized to specific places. If you disrupt the cytoskeleton they drift to new locations.

Cells are very highly organized. For instance in polarized cells such as epithelial cells have apical (top) and basolateral (bottom and side) membranes which consist of different proteins constituents.

So the logistics aren't so bad.
Interesting. Always thought of mRNA being a rather fleeting substance, convey the info and then be broken up and recycled. Thought there would be enzymes to continually break up the mRNA so that protein synthesis would be controlled by the production of mRNA. Wasn’t aware mRNA could be inactivated. Seems the story always gets more complicated.

In this hamster’s simplistic view, mitochondria provided a model. Some of the genes needed to build mitochondria are in the nuclear DNA. But mitochondria also has its own DNA. Assumed that mtDNA was “operational” DNA. Thus, once the mitochondria was built, it wouldn’t require much support from the nuclear DNA. (This hamster tends to assume things would work the way a hamster would design ‘em.)

Opens up new questions. How does the mRNA get to the right places? Diffusion? Active transport? In what are they stored? (Neural transmitters are stored in vesicles.) What feedback mechanisms exist to keep the mRNA “storerooms” stocked and how do these feedback mechanisms work over long cellular distances? What local condition regulates the activation of the mRNA?

(Scilosopher, this hamster doesn’t expect answers. If the topic interests you then fine. Can’t expect you to explain everything.)
These questions are actually more along the lines of what I study than the evolution stuff.

brief sketch of the life of a mRNA:

- There are fuzzy binding sites in front of genes that mediate the assembly of protein complexes that serve to regulate the transcription, splicing, and further processing of an mRNA.

- mRNA is then exported wound up in a protein complex called an mRNP. Upon export through the nuclear pore (which regulates import and export of all molecules above 30-40 kDa [kilo Daltons where a dalton ~ the weight of 1 hydrogen atom, an average amino acid is 110 daltons, and most proteins are 50 - 2000 aa]).

- Certain elements in the 3' and 5' untranslated region (UTR) are bound by proteins that can mediate the following - localized transport along the cytoskeleton by motor proteins, regulated degredation of mRNA, translational silencing (there's an interesting new twist with 21 bp complementary RNAs called siRNAs implicated in silencing transcription), translational activation, read through of stop codons, translation from internal sites caled IRESs (usually translation occurs from the first start codon).

- Translational regulation: membrane and secreted proteins actually get translated along the ER on ribosomes that are oriented such that the proteins get directly threaded into/through the membrane into the ER lumen. This localization is actually mediated by a signal in the protein as it's being translated. Cytosolic translation actually occurs in large polyribosomes which are essentially the mRNAs in a ring (formed by the 5' cap and polyA binding proteins binding eachother associated) with ribosomes doing cycles around them.

- mRNA degredation regulation: although it isn't completely understood in detail the polyA tail can serve as a timer on mRNAs and the rate at which it gets degraded can be regulated. Once it is gone the loop structure described previously is lost and this somehow leads to degredation of the rest of the mRNA. There are some non-polyadenylated RNAs which aren't destroyed like the ribosomal RNAs themselves (much of the ribosome is RNA which serves both a structural and catalytic role). There is also specific degredation not mediated through the polyA tail length.

- mRNA localization can be regulated by mRNAs binding proteins which mediate their localization. The locational cue itself can move around the cell as well. Cells can move by endocytosis of one side of the cell and moving the membrane endocytosed to the other. This makes a bit of a treadmill. Proteins needed for this process have the RNAs localized to the leading edge, but when the directional cue changes they rapidly get moved to the new location. Other examples of localized RNAs include those used to set up positional gradients in the syncytial blastoderm of Drosophila used for subdividing it into different body regions and cell types and synaptic proteins.

The cell interior is stuffed with proteins the actual process of diffusion of a protein or complex through this environment is not really clear. Most proteins are assembled into complexes and there is a cytoskeleton running throughout with vesicles and other stuff being dragged around. Proteins do move around in a fashion that can be fit by the diffusion equation, but nonspecifc randomly oriented transport could even be the main factor in this ...
Since we frequently measure how advanced and superior a species by its complexity and, implicitly, by the size of its genome, does this new research indicate that rice is a more advanced, and perhaps even a superior, species than humanity? Has rice, in fact, even developed it's own religious beliefs, which is why it is now called "converted rice"? Ugh! That was a groaner. Sorry.

But on the serious side, I've only recently started reading about this subject, and plant genetics is complex and very interesting. Fron what I understand, plants can be polyploid and even aneuploid, while in nearly all animal species polyploidy and aneuploidy are lethal. I have not found out the reason for this leathality; can anyone explain?

Plants have much simpler morphology and development than animals, which might be in part why they can handle differences in DNA content better than us.

The necessity of generating complex patterns of different cell types is sensitive to not only to relative changes in relative gene dosage (ie in annueploidy), but most likely absolute levels (ie 4n vs. 2n). The fact that development recapitulates evolution suggest that the dynamics of development are sensitive to conditions to the point important intermediate states need to be maintained or the end goal can no longer be reached.

We have more specialized and complex organs than plants, like the eye. These various organs systems must cooperatively interact to maintian overall body balance more so than plants. Generally speaking plants aren't homeostatic to nearly the same extent we are so their systems have most likely developed to be more robust to certain types of variation than ours.

We have many types of complexity elaborated to an extent not seen in plants - like extensive alternative splicing especially in the nervous system (plants have had more gene doubling and divergence events to accomodate this situation). They are most likely simpler than us. Then again all mammals (or even animals) dying out would be much less catastrophic than all plants ...