Cell-cycle-dependent transcriptional and translational DNA-damage response of 2 ribonucleotide reductase genes in S. cerevisiae

The ribonucleotide reductase (RNR) enzyme catalyzes an essential step in the production of deoxyribonucleotide triphosphates (dNTPs) in cells. Bulk biochemical measurements in synchronized Saccharomyces cerevisiae cells suggest that RNR mRNA production is maximal in late G1 and S phases; however, damaged DNA induces RNR transcription throughout the cell cycle. But such en masse measurements reveal neither cell-to-cell heterogeneity in responses nor direct correlations between transcript and protein expression or localization in single cells which may be central to function. We overcame these limitations by simultaneous detection of single RNR transcripts and also Rnr proteins in the same individual asynchronous S. cerevisiae cells, with and without DNA damage by methyl methanesulfonate (MMS). Surprisingly, RNR subunit mRNA levels were comparably low in both damaged and undamaged G1 cells and highly induced in damaged S/G2 cells. Transcript numbers became correlated with both protein levels and localization only upon DNA damage in a cell cycle-dependent manner. Further, we showed that the differential RNR response to DNA damage correlated with variable Mec1 kinase activity in the cell cycle in single cells. The transcription of RNR genes was found to be noisy and non-Poissonian in nature. Our results provide vital insight into cell cycle-dependent RNR regulation under conditions of genotoxic stress.Massachusetts Institute of Technology. Center for Environmental Health Sciences (deriving from NIH P30-ES002109)National Institutes of Health (U.S.) (grant R01-CA055042)National Institutes of Health (U.S.) (grant DP1-OD006422)Massachusetts Institute of Technology (CSBi Merck-MIT Fellowship

Use of Motor Abundance in Young and Older Adults during Dual-Task Treadmill Walking

Contains fulltext : 110120.pdf (publisher's version ) (Open Access)Motor abundance allows individuals to perform any task reliably while being variable in movement's particulars. The study investigated age-related differences in this feature when young adults (YA) and older adults (OA) performed challenging tasks, namely treadmill walking alone and while performing a cognitive task. A goal function for treadmill walking was first defined, i.e., maintain constant speed at each step, which led to a goal equivalent manifold (GEM) containing all combinations of step time and step length that equally satisfied the function. Given the GEM, amounts of goal-equivalent and non-goal-equivalent variability were afterwards determined and used to define an index providing information about the set of effective motor solutions relative to the GEM. The set was limited in OA compared to YA in treadmill walking alone, indicating that OA made less flexible use of motor abundance than YA. However, this differentiation between YA and OA disappeared when concurrently performing the cognitive task. It is proposed that OA might have benefited from cognitive compensation

Joint angle variability and co-variation in a reaching with a rod task

The problem at the heart of motor control is how the myriad units of the neuromotor system are coordinated to perform goal-directed movements. Although for long these numerous degrees of freedom (DOFs) were considered redundant, recent views emphasize more that the DOFs should be considered abundant, allowing flexible performance. We studied how variability in arm joints was employed to stabilize the displaced end-effector in tool use to examine how the neuromotor system flexibly exploits DOFs in the upper extremity. Participants made pointing movements with the index finger and with the index finger extended by rods of 10, 20, and 30 cm. Using the uncontrolled manifold (UCM) method, the total joint angle variance was decomposed into two parts, the joint angle variance that did not affect the position of the end-effector (VUCM) and the variance that results in a deviation of the position of the end-effector from its mean (VORT). Analyses showed that some angles depended on length of the rod in use. For all rod lengths, VUCM was larger than VORT, and this did not differ over rod lengths, demonstrating that the arm was organized into a synergy. Finally, the variation in the joint angles in the arm as well as the degree of co-variation between these angles did not differ for the rod’s tip and the hand. We concluded that synergies are formed in the arm during reaching with an extended end-effector and those synergies stabilize different parts of the arm+rod system equally

Dissociating Variability and Effort as Determinants of Coordination

When coordinating movements, the nervous system often has to decide how to distribute work across a number of redundant effectors. Here, we show that humans solve this problem by trying to minimize both the variability of motor output and the effort involved. In previous studies that investigated the temporal shape of movements, these two selective pressures, despite having very different theoretical implications, could not be distinguished; because noise in the motor system increases with the motor commands, minimization of effort or variability leads to very similar predictions. When multiple effectors with different noise and effort characteristics have to be combined, however, these two cost terms can be dissociated. Here, we measure the importance of variability and effort in coordination by studying how humans share force production between two fingers. To capture variability, we identified the coefficient of variation of the index and little fingers. For effort, we used the sum of squared forces and the sum of squared forces normalized by the maximum strength of each effector. These terms were then used to predict the optimal force distribution for a task in which participants had to produce a target total force of 4–16 N, by pressing onto two isometric transducers using different combinations of fingers. By comparing the predicted distribution across fingers to the actual distribution chosen by participants, we were able to estimate the relative importance of variability and effort of 1∶7, with the unnormalized effort being most important. Our results indicate that the nervous system uses multi-effector redundancy to minimize both the variability of the produced output and effort, although effort costs clearly outweighed variability costs

Systematic quantification of gene interactions by phenotypic array analysis

A phenotypic array method, developed for quantifying cell growth, was applied to the haploid and homozygous diploid yeast deletion strain sets. A growth index was developed to screen for non-additive interacting effects between gene deletion and induced perturbations. From a genome screen for hydroxyurea (HU) chemical-genetic interactions, 298 haploid deletion strains were selected for further analysis. The strength of interactions was quantified using a wide range of HU concentrations affecting reference strain growth. The selectivity of interaction was determined by comparison with drugs targeting other cellular processes. Bio-modules were defined as gene clusters with shared strength and selectivity of interaction profiles. The functions and connectivity of modules involved in processes such as DNA repair, protein secretion and metabolic control were inferred from their respective gene composition. The work provides an example of, and a general experimental framework for, quantitative analysis of gene interaction networks that buffer cell growth

Identification and Characterization of Alternative Promoters, Transcripts and Protein Isoforms of Zebrafish R2 Gene

Ribonucleotide reductase (RNR) is the rate-limiting enzyme in the de novo synthesis of deoxyribonucleoside triphosphates. Expression of RNR subunits is closely associated with DNA replication and repair. Mammalian RNR M2 subunit (R2) functions exclusively in DNA replication of normal cells due to its S phase-specific expression and late mitotic degradation. Herein, we demonstrate the control of R2 expression through alternative promoters, splicing and polyadenylation sites in zebrafish. Three functional R2 promoters were identified to generate six transcript variants with distinct 5′ termini. The proximal promoter contains a conserved E2F binding site and two CCAAT boxes, which are crucial for the transcription of R2 gene during cell cycle. Activity of the distal promoter can be induced by DNA damage to generate four transcript variants through alternative splicing. In addition, two novel splice variants were found to encode distinct N-truncated R2 isoforms containing residues for enzymatic activity but no KEN box essential for its proteolysis. These two N-truncated R2 isoforms remained in the cytoplasm and were able to interact with RNR M1 subunit (R1). Thus, our results suggest that multilayered mechanisms control the differential expression and function of zebrafish R2 gene during cell cycle and under genotoxic stress