Thomas Okita

Okita Laboratory Website

Research Interests (Decipihering the Role of Multi-Protein Complexes)

I. RNA localization in plants

My laboratory is interested in elucidating the mechanism by which the storage protein mRNAs are targeted to specific subdomains of the cortical endoplasmic reticulum during rice endosperm development.  Our RNA localization project has identified the cis-elements (zipcodes) of the storage protein mRNAs responsible for RNA targeting and the trans-factors (RNA binding proteins or RBPs), arranged in multi-protein complexes, which recognize these zipcode sequences.  By using a combination of co-immunoprecipitation, yeast 2-hybrid, and bimolecular fluorescence complementation approaches, we have established that these zipcode RBPs comprise a larger protein interactome network. Based on the existence of multi-protein complexes containing common RBPs, we hypothesize that different combinations of RBPs are arranged in higher-order multi-protein complexes to mediate post-transcriptional regulation. Such RBP complexes confer the targeting specificity of RNAs to specific intracellular locations where they are translated, stabilized, subjected to mRNA decay, processed by RISCs, or associated with P-bodies and stress granules. Moreover, analysis of the mRNAs, which are extracellularly displaced in rice mutant lines defective in mRNA localization [5], suggests that mRNAs that code for proteins related by function, cytological location, and/or cellular fate may possibly be co-transported together as regulons.   We are testing this regulon hypothesis by employing seCLIP and RIPiT-seq technologies.

II. The multi-functional plastidial phosphorylase

Although catalyzing the same enzymatic reaction, the plastidial phosphorylase differs in structure and function from the mammalian and yeast phosphorylases.  The higher plant phosphorylase participates in starch synthesis (as opposed to the degradative role of the non-plant enzymes) and its catalytic activity is not regulated by allosterism and covalent phosphorylation as seen for the non-plant enzymes.  Moreover, the higher plant phosphorylase has an extra peptide (L80 for the rice enzyme) not present in the non-plant enzymes and it interacts with proteins of photosystem I (PS I) in addition to its assembly with other starch biosynthetic enzymes.  Our available evidence indicates that the rice L80 peptide acts as a negative regulatory element as the rice plant expressing a phosphorylase lacking the L80 peptide (Pho1ΔL80) display increased growth, productivity, and yields, the latter due, in part, to higher grain weights.  These improved traits are likely a product of enhanced starch synthesis via the elevated activity of protein complexes consisting of Pho1ΔL80 with starch synthases and branching enzymes and increased PS I activity by Pho1ΔL80 interaction with PsaC.  Present efforts are directed at identifying the L80 negative regulatory sequences and characterizing the structure-function relationships of Pho1 and Pho1ΔL80 with PsaC of PS I.

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