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UniProt release 8.8

Published October 3, 2006

Headlines

Over 1,000 rice proteins annotated

Rice (Oryza sativa) is the most important food crop in the world and part of the daily diet of over half of the human population. It is grown in 114 countries worldwide and provides 50-80% of the calory consumption in a number of Southeast Asian countries (see world rice statistics).

In the current release, over 1,000 rice entries have been completed in UniProtKB/Swiss-Prot. How?

Following the completion of the first genome sequence of the model plant Arabidopsis thaliana, in 2001 the Swiss-Prot group initiated the Plant Proteome Annotation Program, which focuses on the annotation of plant-specific proteins and protein families. Our major effort was directed towards Arabidopsis, but the completion of the Oryza sativa (cultivar Nipponbare) genome sequence by the IRGSP prompted us to broaden our focus.

Each manually annotated rice entry already contains the TIGR locus identifiers - which map each protein to the corresponding gene in the rice genome - and will soon also include RAP loci. Amongst the numerous cross-references in rice entries is the link to Gramene which gives access to comparative grass genomics. We also plan to link our entries to RAP-DB in the near future, which will provide links to genomic data and genome annotation.

We are currently concentrating on the annotation of well-characterized proteins for which experimental data are available. The function of a number of rice proteins reflects physiological trait adaptation and grain property evolution owing to centuries of selection by farmers (over 100,000 rice varieties exist throughout the world).

As an example, large areas of Southeast Asia are flooded during the monsoon season. Deepwater rice copes with this by way of rapid internode elongation (up to 25 cm/day), and expansin A4 contributes by causing the cell walls to slacken and expand.

What is more, a primary factor that decreases rice crop yield is coastal salinity and the accumulation of salts in irrigated land. Pokkali, an indica variety of lowland rice, is classified as highly tolerant, because it contains a specific potassium-sodium cotransporter (HKT2), which mediates increased potassium uptake with external sodium accumulation.

Finally, grain texture of cooked rice is essential in various food cultures. A generic classification exists between long grain, medium grain and short grain rice, where the first is separate and fluffy and the last more moist, sticky and tender. The proportion of long chain amylopectin is correlated with firmer cooked rice. A starch synthase (SSII-3), which synthesizes long chain amylopectin, is barely active in the sticky cultivar japonica Nipponbare, however, a variation of 4 amino acids leads to an increased activity in firmer indica varieties.

All rice proteins annotated in UniProtKB/Swiss-Prot are classified by chromosome locus (ordered locus name starting with "Os") and listed in the file rice.txt. In the future, we plan to manually annotate every rice gene family and to develop semi-automated annotation tools to complete rice proteome annotation.