Is macroevolution impossible to study (Part 2)?

The plant kingdom is many things – the basis of agriculture and civilization, a natural laboratory with a stupefying capability in organic synthesis, a source of untold numbers of pharmaceuticals, antimicrobials, herbals, and other chemical playthings, a fascinating range of biological form and function, and an eminently accessible subject for studies of evolution. Along the lines of the last two bullets, one of the more interesting aspects of plants is the range of growth habits that may be adopted. Among these are two sets of contrasting characteristics – annual or perennial, and herbaceous or woody. Differences in these characteristics are among the bases for classification of plant species. For this reason, but also because accompanying morphological differences can be quite considerable, evolutionary changes that involve transitioning between these states are macroevolutionary. Thus, it stands to reason that studying the means by these characteristics evolve amounts to experimental analysis of macroevolution, and understanding the underlying mechanisms constitutes an explanation of macroevolutionary processes.

It is in this light that a recent report deserves some attention. This report, by Melzer et al., describes studies of the functioning of two regulators of flowering in the herbaceous annual Arabidopsis thaliana. These proteins, called SOC1 and FUL, had been known for some time to be involved in the regulation of flowering. Melzer et al. constructed double mutants deficient in the expression of these two proteins, with the intent of understanding the physiological significance of interactions between these two proteins, associations discovered using the so-called yeast two-hybrid assay. Amazingly, soc1 ful double mutants were dramatically different – they had a more woody growth habit, and they behaved like perennials when it comes to reproduction. The abstract from the paper follows this paragraph. The bottom line that is in keeping with the title of the essay – not only can this particular macroevolutionary process be studied experimentally, it can be understood and the corresponding macroevolutionary process recapitulated in a controlled setting.

The abstract:

Plants have evolved annual and perennial life forms as alternative strategies to adapt reproduction and survival to environmental constraints. In isolated situations, such as islands, woody perennials have evolved repeatedly from annual ancestors1. Although the molecular basis of the rapid evolution of insular woodiness is unknown, the molecular difference between perennials and annuals might be rather small, and a change between these life strategies might not require major genetic innovations2, 3. Developmental regulators can strongly affect evolutionary variation4 and genes involved in meristem transitions are good candidates for a switch in growth habit. We found that the MADS box proteins SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and FRUITFULL (FUL) not only control flowering time, but also affect determinacy of all meristems. In addition, downregulation of both proteins established phenotypes common to the lifestyle of perennial plants, suggesting their involvement in the prevention of secondary growth and longevity in annual life forms.

The citation:

Melzer S, Lens F, Gennen J, Vanneste S, Rohde A, Beeckman T. 2008. Flowering-time genes modulate meristem determinacy and growth form in Arabidopsis thaliana. Nature Genetics, published online: 9 November 2008 | doi:10.1038/ng.253

Is macroevolution impossible to study?

Once again, the Discovery Institute is playing word games with educational systems, trying to give legal protection to religion-based incompetence.  I refer, of course, to the ongoing debate about standards in Texas, and the insidious influence that the DI is wielding.

As Wesley Elsberry notes in his summary of the alleged weaknesses of evolutionary theory, an oft-repeated mantra rears its head yet again.  This ID tenet holds that macroevolution is either not possible, or cannot be observed, or cannot be studied (or any combination of the these).  Apparently, Board of Education member Ken Mercer is of the opinion that macroevolution has not been observed.

Transplastomics – a convergence of biotechnology and evolution

One of the going concerns in plant biotechnology is the matter of containment of transgenes in the field.  This concern arises from the inescapable fact that genetically-modified crop plants may, depending on the specific species involved, “disseminate” transgenes via hybridization with nearby plants (of the same species or closely-related ones).  A number of strategies have been devised to reduce or eliminate this possibility.  Among these is the approach of placing transgenes in the chloroplast genome of a recipient crop plant.  The rationale behind this approach lies in the fact that the chloroplast genome is inherited in a maternal fashion (much as are mitochondrial genomes in animals).  Consequently, pollen shed by a transplastomic plant (the jargon shorthand term for the plant that has one or more transgenes resident in the plastid genome, as opposed to the nuclear genome) should not carry or transmit the transgene, since transmission is through the female gamete.

Expressing foreign genes in the chloroplast comes with some other advantages.  Since the chloroplast is a prokaryotic genetic system, it is not “encumbered” by the presence of an elaborate and hard-to-control gene silencing system, one that affects nuclear-sited transgenes in a haphazard fashion.  This means that expression of chloroplast-situated transgenes is more consistent (and often attains higher levels) that that of similar nuclear transgenes.  The chloroplast is as well the location for some very highly-expressed proteins (plant physiology students learn early on that the chloroplast enzyme rubisco aka ribulose-1,5-bisphosphate carboxylase is the most abundant protein on earth), which means that it is feasible to attain higher protein levels in such systems than from nuclear transgenes.  (Of course, there are controls on mRNA and protein accumulation in the chloroplast, so that it is necessary to test and manipulate the specific transgene and its protein product to achieve the desired results.)

These considerations aside, the possibility of transmission of chloroplast-sited transgenes remains something of an open issue.  One matter should be familiar to readers who follow the field of human ancestry; work in this field has been complicated by the observation that mitochondrial genomes, typically assumed to be maternally-transmitted, may on occasion be inherited through the paternal gamete.  A similar concern applies to those plant species that are assumed to transmit chloroplast genomes maternally; for example, recent studies (5, 8 ) show that paternal inheritance of chloroplast-localized transgenes does occur.

Hope for school cafeterias, parents, …

…. and others who must deal with allergies to peanuts. A commodity that would be of considerable utility and value, a hypoallergenic peanut, is the goal of several laboratories. One group, consisting of labs at a USDA research unit in New Orleans and the campus of the University of Georgia in Tifton, recently published an interesting and promising approach to develop such a commodity. These researchers set out to screen wild relatives of the peanut (Arachis hypogaea L.) for variants of the principle allergen in peanuts, the seed storage protein Ara h 2.01, that did not possess the allergenic properties of the peanut protein. They used an approach called EcoTILLING (1) to screen several accessions of the wild relative Arachis duranensis for those with point mutations in the gene homologous to that encoding Ara h 2.01. In so doing, they identified several such variants, including one that had a significant reduction in IgE binding but otherwise seemed to cause a minimal structural change in the protein. This result is encouraging, as it may provide a way to replace, by standard breeding or by TILLING-assisted mutagenesis, the offending seed storage protein with one that is less allergenic.

An interesting take on poly(A) signals

One interesting facet of RNA biology is the matter of the occurrence and function of structural RNA units within RNAs inside of living cells.  Excellent examples of these are the many so-called riboswitches, motifs that bind metabolites and alter the functionalities of RNAs in which they reside.  As more and more examples of RNAs with catalytic activities become known, questions naturally arise as to whether such activities might impact RNA function in vivo.  A recent study poses just such a question for what is among the simplest of known catalytic RNAs, namely the manganese-dependent ribozyme.  This enzyme consists of little more that a GAAA-UUU complex.  These two motifs, that need not be adjacent in the RNA, are expected to occur at a high frequency in natural RNAs.  A recent report indeed finds that RNAs that possess such motifs indeed may be Mn-dependent ribozymes.  The physiological signifiance of this finding is, in my opinion, a bit of an open issue.  But the possibilities are fascinating.  The last sentence of the abstract (that follows) is especially provocative.

Protocells, the origins of life, and the RNA World

This essay is a bit less formal than many I’ve posted here, more of an indulgence than the cut-and-dried stuff I’ve been posting about polyadenylation. It is essentially a repost of an essay I posted on the old ARN boards many years ago. I’m moved to this by a recent a recent article in PNAS. The overall context is the origin of life, and some of the different arguments and perspectives that are brought to the table in ev/cre debates.

As a segue, the abstract of the PNAS article:

“Life is that which replicates and evolves. The origin of life is also the origin of evolution. A fundamental question is when do chemical kinetics become evolutionary dynamics? Here, we formulate a general mathematical theory for the origin of evolution. All known life on earth is based on biological polymers, which act as information carriers and catalysts. Therefore, any theory for the origin of life must address the emergence of such a system. We describe prelife as an alphabet of active monomers that form random polymers. Prelife is a generative system that can produce information. Prevolutionary dynamics have selection and mutation, but no replication. Life marches in with the ability of replication: Polymers act as templates for their own reproduction. Prelife is a scaffold that builds life. Yet, there is competition between life and prelife. There is a phase transition: If the effective replication rate exceeds a critical value, then life outcompetes prelife. Replication is not a prerequisite for selection, but instead, there can be selection for replication. Mutation leads to an error threshold between life and prelife.”

Reasons for optimism

A favorite blogger of mine comments on Millennials, the recent election, and the future.  Needless to say, one can see reasons for optimism.  Enjoy.

On the Origins of Life and The RNA World

On The Panda’s Thumb, Ian Musgrave has an interesting entry on the origins of life and the RNA World – it traces back to this ScienceBlogs essay.  Apropos of this, a nice publication came across my RSS feed late last week.  This study reveals that one of the chemical functionalities that catalyzes the charging of a tRNA is provided by the tRNA substrate itself.  The abstract, and brief commentary, are after the fold.  As always, enjoy.