Biology subjects

Kondev, J.

Publications and source records attributed to Kondev, J..

21 records · Page 2Linked to original sources

bioRxiv2019

Length-dependent disassembly maintains four different flagellar lengths in Giardia

How flagellar length regulation is achieved in multiciliated eukaryotic cells with flagella of different equilibrium lengths is unknown. The protist Giardia lamblia is an ideal model to evaluate length regulation as it has flagella of four different lengths. Giardia axonemes have both non-membrane-bound and membrane-bound regions, but lack transition zones. Here we quantified the contributions of intraflagellar transport (IFT)-mediated assembly and kinesin-13-mediated disassembly to length control. IFT particles assemble and inject at Giardias flagellar pore complexes, which act as diffusion barriers functionally analogous to the transition zone to compartmentalize the membrane-bound regions of flagella. IFT-mediated assembly is length-independent as train size, speed, and injection frequencies are similar between flagella of different lengths. In Giardia, kinesin-13 mediates a length-dependent disassembly mechanism of length regulation to balance length-independent IFT-mediated assembly, resulting in different lengths. We anticipate that similar control mechanisms are widespread in multiciliated cells where cytoplasmic precursor pools are not limiting.

cell biology↗

bioRxiv2018

Length regulation of multiple flagella that self-assemble from a shared pool of components

Control of organelle size is a problem that has intrigued cell biologists for at least a century. The single-celled green algae Chlamydomonas reinhardtii with its two 2agella has proved to be a very useful model organism for studies of size control. Numerous experiments have identi1ed motor-driven transport of tubulin to the growing ends of microtubules at the tip of the 2agella as the key component of the machinery responsible for controlling their length. Here we consider a model of 2agellar length control whose key assumption is that proteins responsible for the intra2agellar transport (IFT) of tubulin are present in limiting amounts. We show that this limiting-pool assumption and simple reasoning based on the law of mass action leads to an inverse relationship between the rate at which a 2agellum grows and its length, which has been observed experimentally, and has been shown theoretically to provide a mechanism for length control. Experiments in which one of the two 2agella are severed have revealed the coupled nature of the growth dynamics of the two 2agella, and we extend our length-control model to two 2agella by considering different mechanisms of their coupling. We describe which coupling mechanisms are capable of reproducing the observed dynamics in severing experiments, and why some that have been proposed previously are not. Within our theoretical framework we conclude that if tubulin and IFT proteins are freely exchanged between 2agella simultaneous length control is not possible if the disassembly rate is constant. However, if disassembly depends on the concentration of IFT proteins at the tip of the 2agellum, simultaneous length control can be achieved. Finally, we make quantitative predictions for experiments that could test this model.

systems biology↗

bioRxiv2017

Regulatory mechanisms are revealed by the distribution of transcription initiation times in single microbial cells

Transcription is the dominant point of control of gene expression. Biochemical studies have revealed key molecular components of transcription and their interactions, but the dynamics of transcription initiation in cells is still poorly understood. This state of affairs is being remedied with experiments that observe transcriptional dynamics in single cells using fluorescent reporters. Quantitative information about transcription initiation dynamics can also be extracted from experiments that use electron micrographs of RNA polymerases caught in the act of transcribing a gene (Miller spreads). Inspired by these data we analyze a general stochastic model of transcription initiation and elongation, and compute the distribution of transcription initiation times. We show that different mechanisms of initiation leave distinct signatures in the distribution of initiation times that can be compared to experiments. We analyze published micrographs of RNA polymerases transcribing ribosomal RNA genes in E.coli and compare the observed distributions of inter-polymerase distances with the predictions from previously hypothesized mechanisms for the regulation of these genes. Our analysis demonstrates the potential of measuring the distribution of time intervals between initiation events as a probe for dissecting mechanisms of transcription initiation in live cells.

biophysics↗