Assistant Professor, Section of Molecular Biology, UCSD
e-mail: niwa@ucsd.edu

We are interested in understanding how appropriate levels of organelle function are attained and regulated in coordination with cell cycle progression in eukaryotic cells. Currently, our research focuses on functions of the endoplasmic reticulum (ER), which performs essential roles in the translation, folding and further maturation of cell surface and secreted proteins, among other critical functions. The capacity of the ER to perform such functions is influenced by a variety of factors including environmental and developmental cues. Understanding how cells establish sufficient protein folding capacity to meet demand is important as mis-regulation of ER protein folding is increasingly recognized as a factor in several human diseases including cystic fibrosis, Alzheimer disease, Parkinson’s disease, type 2 diabetes, obesity, and cancer.

The ER is a specialized compartment in eukaryotic cells:
For the thousands of proteins produced by a typical eukaryotic cell, protein levels are tightly regulated at all stages of production from DNA transcription and RNA metabolism to protein translation, modification, and degradation. Broadly classed, eukaryotic proteins may be divided into two classes: (1) soluble proteins of the nucleus and cytoplasm, and (2) proteins that are secreted (e.g., hormones, growth factors, extra-cellular matrix proteins, proteolytic enzymes, antibodies) or that reside on the cell surface (e.g, receptors, adhesion molecules and channel proteins). Initial processing of proteins in this latter class occurs in the ER. During their translation, nascent linear polypeptides are transported into the ER lumen where they are subjected to (i) chaperone-assisted folding to attain proper three-dimensional configurations, (ii) post-translational modifications (e.g., disulfide bond formation, glycosylation), and (iii) complex formation by subunit assembly. In addition to these functions, the ER is also the major cellular storage depot for intracellular calcium, a critical second messenger. To meet instantaneous cellular demand in a timely manner, the capacity of the ER to perform ER-related functions is under constant surveillance. We are interested to understand how cells recognize both the need for increased ER protein folding capacity and how this recognition ultimately results in increased processing capacity. And most recently, are looking into how cells ensure that the processing capacity of ER transmitted to daughter cells during cell division (ER inheritance) will be sufficient to support daughter cell growth. Since the ER cannot be synthesized de novo, the quality of inherited ER is a critical factor. Thus, the major questions addressed by research in my lab are as follows.

How do cell recognize changes in protein folding demands in the ER?
The Unfolded Protein Response (UPR) signaling pathway plays a central role in the sensing of cellular demand for ER protein processing capacity and regulation of ER protein processing capacity. Activation of this novel pathway is initiated by the ER-transmembrane sensors IRE1, PERK, and ATF6. Using biochemical and genetic approaches, we focus on how these components sense the ER environment and how this information ultimately results in increased production of ER resident chaperons, protein folding enzymes and in the activation of other UPR effector functions. Presently, we are focusing on aspects of UPR signaling regulated through altered RNA metabolism. Recently, we discovered that transcription of ribosomal RNA (rRNA) by RNA polymerase I is rapidly repressed in response to PERK activation. Furthermore, rRNA repression during the ER stress is not mediated by mTOR pathway, a well-characterized translation regulatory pathway. Thus, we are examining (i) how information sensed by PERK at the ER membrane is transmitted to the nucleolus and (ii) on the functional significance of rRNA transcription repression. Our initial work suggests that rRNA transcription repression plays an important part for a previously un-described pathway that governs the global protein synthesis during varieties of stresses.

We also focus on the molecular mechanism of IRE1 activation.
In contrast to PERK and ATF6 that are not found in lower eukaryotes, IRE1 structure and function is highly conserved from yeast to mammalian cells. During the UPR response, IRE1 functions as a sequence specific RNase mediating the cleavage of a translation inhibitory intron from mRNA encoding a key UPR specific transcription factor. Subsequent splicing of this mRNA yields a potent transcription factor mRNA involved in up-regulation of UPR target genes. We are focusing on investigation of molecular mechanisms & steps of this IRE1 dependent splicing.

Is ER functional capacity coordinated with cell cycle progression?
A great deal of attention has been given to the coordination between cell cycle progression and nuclear events such as DNA replication and sister chromatid separation. In contrast, very little is known regarding coordination of cell cycle with extra-nuclear functions. Recently, we found that functionally stressing ER in S. cerevisiae results in cell cycle delay by stalling at cytokinesis, suggesting that cell cycle progression is coordinated with the transmission of functional ER into daughter cells. On further analyses, we have uncovered the presence of a surveillance mechanism for ER functional capacity during the cell cycle. Using biochemical, genetic and cell-based, we are investigating the components and mechanisms involved in the quality assurance inherited ER.

Maho Niwa received her Ph.D. in Biochemistry from Baylor College of Medicine and was a Jane-Coffin Childs Postdoctoral Fellow in Department of Biochemistry and Biophysics at UCSF. After joining UCSD Division of Biological Sciences, she has been named a Searle Scholar and Hellman Scholar.