Methods for identifying one or more amino acid substitutions in a Rubisco large subunit polypeptide (variant) that confer increased Rubisco activity in a unicellular photosynthetic organism and transferring those substitutions to a Rubisco large subunit polypeptide of a higher plant cell are described herein. Methods and compositions for modulating plant productivity using the modified Rubisco large subunit polypeptide variants are provided. The Rubisco large subunit sequences are used in a variety of methods including increasing plant productivity in a plant. Transformed plants, plant cell, tissues, seed, and expression vectors are also provided.