Stephen M. Miller

Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri

Going Multicellular The volvocine algae include both the unicellular Chlamydomonas and the multicellular Volvox, which diverged from one another 50 to 200 million years ago. Prochnik et al. (p. 223) compared the Volvox genome with that of Chlamydomonas to identify any genomic innovations that might have been associated with the transition to multicellularity. Size changes were observed in several protein families in Volvox, but, overall, the Volvox genome and predicted proteome were highly similar to those of Chlamydomonas. Thus, biological complexity can arise without major changes in genome content or protein domains. Comparison of the Chlamydomonas and Volvox genomes show few differences, despite their divergent life histories. The multicellular green alga Volvox carteri and its morphologically diverse close relatives (the volvocine algae) are well suited for the investigation of the evolution of multicellularity and development. We sequenced the 138–mega–base pair genome of V. carteri and compared its ~14,500 predicted proteins to those of its unicellular relative Chlamydomonas reinhardtii. Despite fundamental differences in organismal complexity and life history, the two species have similar protein-coding potentials and few species-specific protein-coding gene predictions. Volvox is enriched in volvocine-algal–specific proteins, including those associated with an expanded and highly compartmentalized extracellular matrix. Our analysis shows that increases in organismal complexity can be associated with modifications of lineage-specific proteins rather than large-scale invention of protein-coding capacity.

Volvox: Simple steps to developmental complexity?

Volvox, Chlamydomonas, and their close relatives - collectively the volvocine green algae - comprise an excellent system for investigating the origins of developmental complexity. Over a relatively short period of time Volvox evolved an impressive suite of developmental traits, including asymmetric cell division, multicellularity with germ-soma division of labor, embryonic morphogenesis, and oogamy. Recent molecular genetic analyses of important developmental genes and comparative analyses of the fully sequenced Volvox and Chlamydomonas genomes have provided important insights into how these and other traits came to be. Surprisingly, the acquisition of much of the developmental innovation in this family seems to have involved relatively minor tinkering with the ancestral unicellular blueprint.

The VARL Gene Family and the Evolutionary Origins of the Master Cell-Type Regulatory Gene, regA, in Volvox carteri

Chlamydomonas reinhardtii, Volvox carteri, and their relatives in the family Volvocaceae provide an excellent opportunity for studying how multicellular organisms with differentiated cell types evolved from unicellular ancestors. While C. reinhardtii is unicellular, V. carteri is multicellular with two cell types, one of which resembles C. reinhardtii cytologically but is terminally differentiated. Maintenance of this “somatic cell” fate is controlled by RegA, a putative transcription factor. We recently showed that RegA shares a conserved region with several predicted V. carteri and C. reinhardtii proteins and that this region, the VARL domain, is likely to include a DNA-binding SAND domain. As the next step toward understanding the evolutionary origins of the regA gene, we analyzed the genome sequences of C. reinhardtii and V. carteri to identify additional genes with the potential to encode VARL domain proteins. Here we report that the VARL gene family, which consists of 12 members in C. reinhardtii and 14 in V. carteri, has experienced a complex evolutionary history in which members of the family have been both gained and lost over time, although several pairs of potentially orthologous genes can still be identified. We find that regA is part of a tandem array of four VARL genes in V. carteri but that a similar array is absent in C. reinhardtii. Most importantly, our phylogenetic analysis suggests that a proto-regA gene was present in a common unicellular ancestor of V. carteri and C. reinhardtii and that this gene was lost in the latter lineage.

Design and performance of collimated coincidence point sources for simultaneous transmission measurements in 3-D PET

The authors have implemented a simultaneous emission-transmission measurement for three-dimensional positron emission tomography (3-D PET) using a collimated coincidence point source design employing a fast, dedicated, reference detector close to the transmission source. This design reduces the effects of randoms, scatter, dead time, and sensitivity loss on the emission data compared to previous implementations. It also greatly reduces the effect of emission contamination of the transmission data compared to the use of rod sources. Here, the authors present performance characterizations of this measurement technique on both the Siemens/CTI ECAT ART and PET/SPECT tomographs. The main effect of the transmission sources on the emission measurement is an increased randoms rate, which lends to a 10-25% reduction in NECR at specific activities >2 kBq/mL in a 21-cm-diameter phantom on the PET/SPECT. Emission contamination effects on the transmission measurement are estimated to be less than 1% for up to 20 kBq/mL in a 21-cm phantom on the PET/SPECT. Both the emission and transmission NECR are dominated by the effects of randoms. Considering the effects of both emission and transmission noise on the final corrected image, it appears that 3-6 kBq/mL of emitter concentration is an optimal imaging range for simultaneous acquisitions. The authors present the first images of a normal volunteer using this system on a Siemens/CTI PET/SPECT tomograph.

NEW INSIGHTS INTO THE ROLES OF MOLECULAR CHAPERONES IN CHLAMYDOMONAS AND VOLVOX

The unicellular green alga Chlamydomonas reinhardtii has been used as a model organism for many decades, mainly to study photosynthesis and flagella/cilia. Only recently, Chlamydomonas has received much attention because of its ability to produce hydrogen and nonpolar lipids that have promise as biofuels. The best-studied multicellular cousin of Chlamydomonas reinhardtii is Volvox carteri, whose life cycle comprises events that have clear parallels in higher plants and/or animals, making it an excellent system in which to study fundamental developmental processes. Molecular chaperones are proteins that guide other cellular proteins through their life cycle. They assist in de novo folding of nascent chains, mediate assembly and disassembly of protein complexes, facilitate protein transport across membranes, disassemble protein aggregates, fold denatured proteins back to the native state, and transfer unfoldable proteins to proteolytic degradation. Hence, molecular chaperones regulate protein function under all growth conditions and play important roles in many basic cellular and developmental processes. The aim of this chapter is to describe recent advances toward understanding molecular chaperone biology in Chlamydomonas and Volvox.

Current advances in molecular, biochemical, and computational modeling analysis of microalgal triacylglycerol biosynthesis.

Triacylglycerols (TAGs) are highly reduced energy storage molecules ideal for biodiesel production. Microalgal TAG biosynthesis has been studied extensively in recent years, both at the molecular level and systems level through experimental studies and computational modeling. However, discussions of the strategies and products of the experimental and modeling approaches are rarely integrated and summarized together in a way that promotes collaboration among modelers and biologists in this field. In this review, we outline advances toward understanding the cellular and molecular factors regulating TAG biosynthesis in unicellular microalgae with an emphasis on recent studies on rate-limiting steps in fatty acid and TAG synthesis, while also highlighting new insights obtained from the integration of multi-omics datasets with mathematical models. Computational methodologies such as kinetic modeling, metabolic flux analysis, and new variants of flux balance analysis are explained in detail. We discuss how these methods have been used to simulate algae growth and lipid metabolism in response to changing culture conditions and how they have been used in conjunction with experimental validations. Since emerging evidence indicates that TAG synthesis in microalgae operates through coordinated crosstalk between multiple pathways in diverse subcellular destinations including the endoplasmic reticulum and plastids, we discuss new experimental studies and models that incorporate these findings for discovering key regulatory checkpoints. Finally, we describe tools for genetic manipulation of microalgae and their potential for future rational algal strain design. This comprehensive review explores the potential synergistic impact of pathway analysis, computational approaches, and molecular genetic manipulation strategies on improving TAG production in microalgae.

Functional analysis of the Volvox carteri asymmetric division protein GlsA.

The Zuotin-family J protein chaperone GlsA is essential for the asymmetric divisions that establish germ and somatic cell initials during embryogenesis in the green alga Volvox carteri, but it is not known on what cellular process GlsA acts to carry out this function. Most GlsA protein is nuclear, and GlsA possesses two SANT domains, suggesting that GlsA may function as a transcriptional regulator. On the other hand, close homologs from yeast and mice are ribosome-associated factors that regulate translation fidelity, implying GlsA might also regulate translation. Here we set out to gain additional evidence regarding the function of GlsA, specifically with respect to its possible involvement in transcription and translation. We found that like zuotin mutants, glsA mutants are ultrasensitive to both cold and to the ribosome-binding aminoglycoside antibiotic paromomycin, so some fraction of GlsA is likely to be ribosome associated. We also found that GlsA co-immunoprecipitates with histones and that this interaction is dependent on the presence of intact SANT domains. Through rescue experiments using transgenes that encode GlsA variants, we determined that the growth and asymmetric division defects of the glsA mutant are separable-a GlsA variant that rescued the growth defects did not completely rescue the asymmetric division phenotype. Considered in total, our results suggest that GlsA acts both at the level of translation and transcription, but the function that is essential for tolerance to paromomycin and cold is not sufficient for asymmetric cell division.

EFFECT OF HISTONE DEACETYLASE INHIBITORS ON TUBULIN ACETYLATION AND DEVELOPMENT IN VOLVOX CARTERI (VOLVOCALES)1

Volvox carteri f. nagariensis (Iyengar) possesses several thousand cells of just two types, gonida and somatic cells, that are set apart by asymmetric cell division. Because the division apparatus contains microtubules enriched in acetylated α‐tubulin, we wished to know whether acetylated tubulin plays any role in regulating division symmetry. Two different human histone deacetylases (HDACs) have been shown to deacetylate tubulin in vivo, thereby regulating cell motility. Here we set out to determine: (1) whether HDAC inhibitors that increase tubulin acetylation in animal cells have the same effect in V. carteri, (2) whether increasing acetylated tubulin affects microtubule stability, and (3) whether increasing acetylated tubulin affects division symmetry. Embryos exposed to two HDAC inhibitors, trichostatin A (TSA) and tubacin, accrued dramatically higher levels of acetylated tubulin (and more acetylated microtubules) and were significantly more sensitive to colchicine than controls. However, while TSA‐treated embryos cleaved aberrantly to produce adults with abnormal morphology, tubacin‐treated embryos developed normally. We conclude that increasing tubulin acetylation subtly alters microtubule stability, but does not appear to affect cell division in V. carteri.