We show that the calcium sensor, CML39, is important in various developmental processes from seeds to mature plants. This study bridges previous work on CML39 as a stress-induced gene and highlights the importance of calcium signalling in plant development. In addition to the evolutionarily-conserved Ca sensor, calmodulin (CaM), plants possess a large family of CaM-related proteins (CMLs). Using a cml39 loss-of-function mutant, we investigated the roles of CML39 in Arabidopsis and discovered a range of phenotypes across developmental stages and in different tissues. In mature plants, loss of CML39 results in shorter siliques, reduced seed number per silique, and reduced number of ovules per pistil. We also observed changes in seed development, germination, and seed coat properties in cml39 mutants in comparison to wild-type plants. Using radicle emergence as a measure of germination, cml39 mutants showed more rapid germination than wild-type plants. In marked contrast to wild-type seeds, the germination of developing, immature cml39 seeds was not sensitive to cold-stratification. In addition, germination of cml39 seeds was less sensitive than wild-type to inhibition by ABA or by treatments that impaired gibberellic acid biosynthesis. Tetrazolium red staining indicated that the seed-coat permeability of cml39 seeds is greater than that of wild-type seeds. RNA sequencing analysis of cml39 seedlings suggests that changes in chromatin modification may underlie some of the phenotypes associated with cml39 mutants, consistent with previous reports that orthologs of CML39 participate in gene silencing. Aberrant ectopic expression of transcripts for seed storage proteins in 7-day old cml39 seedlings was observed, suggesting mis-regulation of early developmental programs. Collectively, our data support a model where CML39 serves as an important Ca sensor during ovule and seed development, as well as during germination and seedling establishment.

The rotation of the earth generates dramatic daily and seasonal variation in the terrestrial environment. Plants, like other organisms, have evolved an endogenous biological oscillator to predict these daily changes in light and temperature and adjust to shifting seasonal conditions. This system must be robust to unexpected environmental challenges but can also assist plants to adjust physiology accordingly. Key features of the circadian system which contribute to achieve these are the process of entrainment, by which external cues adjust the state of the oscillator, and gating, by which the sensitivity to a stimulus is modified according to the time of day. In this way, the circadian clock is a dynamic hub which integrates physiology, metabolism and growth in the context of a plant's current environment. We provide a comprehensive summary of the molecular composition of the core oscillator in Arabidopsis and the mechanisms of entrainment and gating. In particular, we focus on phytohormone signalling, photosynthetic metabolism and defense responses as examples of core plant responses to environment that are integrated within the circadian system. We are grateful for financial support from the University of Melbourne.

Bacterial-type PEP carboxylase is highly expressed in developing sink tissues that accumulate abundant levels of malate.

Ribosome profiling (Ribo-seq) is a powerful method for the deep analysis of translation mechanisms and regulatory circuits during gene expression in plant cells. Here, we established an optimized and high resolution Ribo-seq protocol for the unicellular model alga Chlamydomonas reinhardtii (Chlamydomonas). Comparing different nuclease treatments for the extraction and sequencing of ribosome-protected fragments (RPFs) and parallel RNA-seq, provided deep insight into translational dynamics and post-transcriptional control of gene expression, thoroughly covering more than 10,000 different transcripts. Our high quality Ribo-seq protocol captures the 3-nucleotide movement of elongating ribosomes along nuclear and chloroplast transcripts. Detailed analysis of the ribosomal offsets on transcripts uncovers presumable transition states during translocation of elongating ribosomes within the 5′- and 3′- sections of transcripts and features of eukaryotic translation termination. Furthermore, drastic differences between cytosolic and chloroplast offset distributions underline the different nature of the chloroplast translation mechanism. Analyses of RPF distribution along specific transcripts revealed characteristic patterns of translation elongation exemplified for the major light harvesting complex proteins, LHCs. Moreover, our Ribo-seq data can be utilized to survey coding sequence annotations and the expression preference of alternatively spliced transcripts in Chlamydomonas. These features will be easily accessible for the research community since we attached our ribosome profiling data to the most recent Chlamydomonas reference genome.

No abstract