Monthly Archives: October 2011

The Genomes of Two Thermophilic and Biomass-Degrading Fungi, Thielavia terrestris and Myceliophthora thermophila

One of the hurdles to the production of cellulosic biofuel is the economic breakdown plant biomass.  Currently, fungi used to break down plant biomass operate at, or slightly above, room temperature.  Chemical reactions at room temperature proceed slowly, are less efficient, and may be riddled with contaminating fungi which lower the efficiency of the breakdown process.  One scientific goal is to increase the heat in bioreactors with the hopes of speeding up the degradation using efficient fungal enzymes that operate at higher temperatures.

In an effort find thermostable fungal degradative enzymes, researchers have sequenced the genomes of two fungi, Thielavia terrestris and Myceliophthora thermophila, known for their ability to survive at high temperatures, namely 40oC to 75oC.  A report entitled “Comparative Genomic Analysis of the Thermophilic Biomass-Degrading Fungi Myceliophthora thermophila and Thielavia terrestris” has been published online on October 2nd in the journal Nature Biotechnology.  (Image: Myceliophthora thermophila link)

The 38.7 Mbp genome of M. thermophila and the 36.9 Mbp genome of T. terrestris are the first thermophilic eukaryotes to have their genomes sequenced, and contain seven and six complete chromosomes, respectively.  The genome of M. thermophila contains 9,110 protein-coding genes and there are 9,813 such genes in the genome of T. terrestris.  Both filamentous Ascomycetes – placed in the class Sordariomycetes and family Chaetomiaceae – have a similar level of genomic organization, barring numerous translocations and transversions.  When considering the three species with sequenced genomes in the Chaetomiaceae, large portions of the genomes, some of which are greater than 6000 contiguous genes, are shared in syntenous blocks.

Enzymes for the breakdown of plant matter – which can include a wide array of materials from agricultural and forestry waste, recycled pulp and paper products, leaves, etc. – were discovered across the genomes of both T. terrestris and M. thermophila.  These enzymes include numerous carbohydrate-active proteins (CAZymes) which include enzymes in the glycoside hydrolase, polysaccharide lyase, carbohydrate esterase, and glycosyl transferase families.  With some slight differences in regard to the breakdown of specific plant polysaccharides, such as pectin, both fungi can be categorized as general decomposers with regards to their enzyme repertoire.

The researchers then tested the expression of some enzymes identified in these newly sequenced fungal genomes, as well as comparing their diversity to well characterized enzymes from Trichoderma reesei.  Differing from T. reesei, both M. thermophila and T. terrestris have exhibited a proliferation in the GH61 enzyme family, responsible for the degradation of plant cell wall polysaccharides, as well as the GH10 and GH11 xylanase gene families.  The researchers used RNA-Seq to compare the expression of these enzymes on differing plant materials, such as alfalfa and barley straw, which represented characteristic dicot and monocot plants, respectively.  While there are noticeable differences to the degradation of plant material from dicots and monocots by both T. terrestris and M. thermophila, orthologs from both fungal genomes show similar patterns of gene expression, particularly when growing on complex plant substrates.

Research commentaries on this publication can be found here and here.

7th Annual Joint Genome Institute Users Meeting 2012

Recently announced, the Joint Genome Institute – US Department of Energy is planning to have their annual meeting in Walnut Creek, California, during the dates of March 20th to 22nd.  Registration is now open.  This should be another great meeting and includes another impressive array of speakers.

One Hundred Important Questions Facing Plant Science Research

The October issue of the journal New Phytologist contains a commentary article by a group of plant scientists who conducted a survey to identify the 100 most pressing scientific questions facing plant biologists.  The article “One Hundred Important Questions Facing Plant Science Research” is very thought provoking.

I’ve replicated the questions here for you to read and ponder.  I know the list is heavy on the text, but I think these questions are worthy of the space.  You should definitely then read their article (and supplementary commentary) and see how they have collectively addressed these questions.  They may have addressed these questions in their commentary, but these questions are far from answered and may demand many careers to answer fully.

 Most important questions relating to plants and society:

1. How do we feed our children’s children?

2. Which crops must be grown and which sacrificed, to feed the billions?

3. When and how can we simultaneously deliver increased yields and reduce the environmental impact of agriculture?

4. What are the best ways to control invasive species including plants, pests and pathogens?

5. Considering two plants obtained for the same trait, one by genetic modification and one by traditional plant breeding techniques, are there differences between those two plants that justify special regulation?

6. How can plants contribute to solving the energy crisis and ameliorating global warming?

7. How do plants contribute to the ecosystem services upon which humanity depends?

8. What new scientific approaches will be central to plant biology in the 21st Century?

9. (a) How do we ensure that society appreciates the full importance of plants? (b) How can we attract the best young minds to plant science so that they can address Grand Challenges facing humanity such as climate change, food security, and fossil fuel replacement?

10. How do we ensure that sound science informs policy decisions?

11. How can we translate our knowledge of plant science into food security?

12. Which plants have the greatest potential for use as biofuels with the least effects on biodiversity, carbon footprints and food security?

13. Can crop production move away from being dependent on oil-based technologies?

14. How can we use plant science to prevent malnutrition?

15. How can we use knowledge of plants and their properties to improve human health?

16. How do plants and plant communities (morphology, color, fragrance, sound, taste etc.) affect human well-being?

17. How can we use plants and plant science to improve the urban environment?

18. How do we encourage and enable the interdisciplinarity that is necessary to achieve the UN’s Millennium Development Goals which address poverty and the environment?

 Most important questions relating to environment and adaptation:

1. How can we test if a trait is adaptive?

2. What is the role of epigenetic processes in modulating response to the environment during the life span of an individual?

3. Are there untapped potential benefits to developing perennial forms of currently annual crops?

4. Can we generate a step-change in C3crop yield through incorporation of a C4 or intermediate C3/C4 or crassulacean acid metabolism (CAM) mechanism?

5. How do plants regulate the proportions of storage reserves laid down in various plant parts?

6. What is the theoretical limit of productivity of crops and what are the major factors preventing this being realized?

7. What determines seed longevity and dormancy?

8. How can we control flowering time?

9. How do signaling and cross-talk between the different plant hormones operate?

10. Can we develop salt/heavy metal/drought-tolerant crops without creating invasive plants?

11. Can plants be better utilized for large-scale remediation and reclamation efforts on degraded and/or toxic land?

12. How can we translate our knowledge of plants and ecosystems into ‘clever farming’ practices?

13. Can alternatives to monoculture be found without compromising yields?

14. Can plants be bred to overcome dry land salinity or even reverse it?

15. Can we develop crops that are more resilient to climate fluctuation without yield loss?

16. Can we understand (explain and predict) the succession of plant species in any habitat, and crop varieties in any location, under climate change?

17. To what extent are the stress responses of cultivated plants appropriate for current and future environments?

18. Are endogenous plant adaption mechanisms enough to keep up with the pace of man-made environmental change?

19. How can we improve our cultivated plants to make better use of finite resources?

20. How do we grow plants in marginal environments without encouraging invasiveness?

21. How can we use the growing of crops to limit deserts spreading?

 Most important questions relating to plant species interactions:

1. What are the best ways to control invasive species including plants, pests and pathogens?

2. Can we provide a solution to intractable plant pest problems in order to meet increasingly stringent pesticide restrictions?

3. Is it desirable to eliminate all pests and diseases in cultivated plants?

4. What is the most sustainable way to control weeds?

5. How can we simultaneously eradicate hunger and conserve biodiversity?

6. How can we move nitrogen-fixing symbioses into non-legumes?

7. Why is symbiotic nitrogen fixation restricted to relatively few plant species?

8. How can the association of plants and mycorrhizal fungi be improved or extended towards better plant and ecosystem health?

9. How do plants communicate with each other?

10. How can we use our knowledge of the molecular biology of disease resistance to develop novel approaches to disease control?

11. What are the mechanisms for systemic acquired resistance to pathogens?

12. When a plant resists a pathogen, what stops the pathogen growing?

13. How do pathogens overcome plant disease resistance, and is it inevitable?

14. What are the molecular mechanisms for uptake and transport of nutrients?

15. Can we use non-host resistance to deliver more durable resistance in plants?

Most important questions relating to the understanding and utilization of plant cells:

1. How do plant cells maintain totipotency and how can we use this knowledge to improve tissue culture and regeneration?

2. How are growth and division of individual cells coordinated to form genetically programmed structures with specific shapes, sizes and compositions?

3. How do different genomes in the plant talk to one another to maintain the appropriate complement of organelles?

4. How and why did multicellularity evolve in plants?

5. How can we improve our understanding of programmed developmental gene regulation from a genome sequence?

6. How do plants integrate multiple environmental signals and respond?

7. How do plants store information on past environmental and developmental events?

8. To what extent do epigenetic changes affect heritable characteristics of plants?

9. Why are there millions of short RNAs in plants and what do they do?

10. What is the array of plant protein structures?

11. How do plant cells detect their location in the organism and develop accordingly?

12. How do plant cells restrict signaling and response to specific regions of the cell?

13. Is there a cell wall integrity surveillance system in plants?

14. How are plant cell walls assembled, and how are their strength and composition determined?

15. Can we usefully implant new synthetic biological modules in plants?

16. To what extent can plant biology become predictive?

17. What is the molecular/biochemical basis of heterosis?

18. How do we achieve high-frequency targeted homologous recombination in plants?

19. What factors control the frequency and distribution of genetic crossovers during meiosis?

20. How can we use our knowledge about photosynthesis and its optimization to better harness the energy of the sun?

21. Can we improve algae to better capture CO2and produce higher yields of oil or hydrogen for fuel?

22. How can we use our knowledge of carbon fixation at the biochemical, physiological and ecological levels to address the rising concentrations of atmospheric CO2?

23. What is the function of the phenomenal breadth of secondary metabolites?

24. How can we use plants as the chemical factories of the future?

25. How do we translate our knowledge of plant cell walls to produce food, fuel and fibre more efficiently and sustainably?

 Most important questions relating to plant diversity:

1. How much do we know about plant diversity?

2. How can we better exploit a more complete understanding of plant diversity?

3. Can we increase crop productivity without harming biodiversity?

4. Can we define objective criteria to determine when and where intensive or extensive farming practices are appropriate?

5. How do plants contribute to ecosystem services?

6. How can we ensure the long-term availability of genetic diversity within socio-economically valuable gene pools?

7. How do specific genetic differences result in the diverse phenotypes of different plant species? That is, why is an oak tree an oak tree and a wheat plant a wheat plant?

8. Which genomes should we sequence and how can we best extract meaning from the sequences?

9. What is the significance of variation in genome size?

10. What is the molecular and cellular basis of plants’ longevity and can plant life spans be manipulated?

11. Why is the range of life spans in the plant kingdom so much greater than in animals?

12. What is a plant species?

13. Why are some clades of plants more species-rich than others?

14. What is the answer to Darwin’s ‘abominable mystery’ of the rapid rise and diversification of angiosperms?

15. How has polyploidy contributed to the evolutionary success of flowering plants?

16. What are the closest fossil relatives of the flowering plants?

17. How do we best conserve phylogenetic diversity in order to maintain evolutionary potential?