Transcript WOODS HOLE PowerPoint File - Biology Department | UNC Chapel

MUTATIONAL CHANGES IN THE AMINO
ACIDS OF RUBISCO BETWEEN ANTARCTIC
AND TEMPERATE SISTER SPECIES OF MARINE
RED ALGAE DISTRIBUTED BETWEEN THE
ANTARCTIC PENINSULA AND CHILE OR THE
FALKLAND IS. MAY HAVE BIOGEOGRAPHICAL
AND ECOLOGICAL SIGNIFICANCE
Max H. Hommersand*, Department of Biology
Chang Jun Lee, Department of Chemistry
Lee G. Pedersen, Department of Chemistry
University of North Carolina at Chapel Hill,
North Carolina, USA
*http://www.bio.unc.edu/Faculty/Hommersand/Power_Point/
COLLECTIONS
DNA SEQUENCES
Charles D. Amsler
Showe-Mei Lin
C.W. Aumack
Suzanne Fredericq
Max H. Hommersand
Paul W. Gabrielson
Showe-Mei Lin
Suzanne Fredericq
Maria Eliana Ramírez
*
= significantly different from NZ/ANT (P <0.05)
No other comparisons significant
Kruskal-Wallis One Way ANOVA on Ranks, Dunn’s method
UNCORRECTED “P” DISTANCES
0.05
*
0.04
*
0.03
*
0.02
0.01
0.00
NZ/ANT
NZ/C-F
NZ/SA
ANT/C-F
SISTER REGIONS
Box plot of uncorrected “P” distances between sister
regions calculated using 1&2 codon positions only
Polar oceanographic projection at ca. 32 Ma (Oligocene)
[from Hommersand et al.(2009) Botanica Marina 52(6): 529].
“Gigartina” skottsbergii
Galdieria sulphuraria
(Galdieria partita)
PROCEDURES
1. Maximum Likelihood (ML) phylogenetic analyses and pairwise
base distances were computed by Wilson Freshwater for sequences of
rbcL, the gene coding for the large subunit of RuBisCo, from samples from
New Zealand, South Africa, South America and the Antarctic Peninsula.
2. Ten pairs of nearest-neighbor species from Antarctica and either
Chile or the Falkland Islands were selected and compared to related
sequences from Antarctica and Galdieria partita using MacClade.
3. Sequence data were translated into Amino Acid sequences in
MacClade and the position of every Amino Acid that underwent
a change was noted together with the changes in the Amino Acids.
4. The primary structure of the large subunit of RuBisCo was constructed
as a multifile that included each of the 10 nearest-neighbor samples
and Galdieria partita plus a consensus sequence using the program
Biology WorkBench 3.2, SDSC, UCSD using Clustal W and Boxshade
routines.
Primary structure of the large subunit of red algal RuBisCo
showing amino acid changes for 10 species’ pairs
˚ orientation
Secondary structure of the large
subunit of RuBisCo
Tertiary structure of the large
subunit of RuBisCo showing the
positions of Amino Acid changes for
Myriogramme livida to M. manginii
Space filling model
Active site
Substrate
specificity
(CO2 carboxylase/
O2 oxygenase)
Conformational
change
Loop 6 stabilizer
(C terminal)
Conformational
change
0˚ orientation
Functional regions of the large subunit of RuBisCo conserved
between Galdieria partita and spinach
2 small subunits
4 large subunits
4 small subunits
4 large subunits
Galdieria partita RuBisCo, QUATERNARY STRUCTURE
8 large and 8 small subunits
Large subunit of RuBisCo
0˚ rotation
90˚ rotation
Changeable Amino acids for 10 pairs of AA: Antarctica/ So. America
blue spheres = surface AA; grayish-blue spheres = subsurface AA
Large subunit of RuBisCo
Subunit contact
sites (magenta)
180˚ rotation
270˚ rotation
Changeable Amino acids for 10 pairs of AA: Antarctica/ So. America
blue spheres = surface AA; grayish-blue spheres = subsurface AA
+charge changes
(brown)
-charge changes
(lavender)
+charge changes
(brown)
-charge changes
(lavender)
0˚ orientation
270˚ orientation
Charge changes for 10 pairs of AA: Antarctica/South America
(+changes = Lys, Arg, His; -changes = Glu, Asp)
CHARACTERISTICS OF THE ANTARCTIC OCEAN
1. Long polar nights in winter are followed by starch (floridoside) breakdown
and ice breakup in Spring with clear seawater and deep light penetration
and rapid algal growth until onset of the phytoplankton bloom in summer.
2. Red algae that lack cryoprotectants against UV damage (most) live in deep
water and photosynthesize at intensities as low as 10 µmol m-2 s-1.
3. Nitrate (30-110 µmolar) and phosphate (2 µmolar) levels are non-limiting.
4. Seawater temperatures range from 0˚ to 5˚C. Many species die in culture at
temperatures above 5˚C.
5. The pH at the Palmer station is ca. 8.1 where HCO3- predominates; even so…
6. Diffusive CO2 is the likely source of carbon at the low light intensities that
cannot support active HCO3 transport. Extracellular carbonic anhydrase
may help, though this is not established --- John Raven (pers. com.).
7. Except for periods glacial ice expansion, Antarctic conditions have
persisted over the past 14 million years --- Christian Wienke (2011).
CONCLUSIONS
1. Amino acid changes between the Antarctic Peninsula and Chile or
the Falkland Islands, including changes involving charged Amino Acids,
occur essentially at random.
2. There is no evidence for a Positive Selection for particular Amino Acid.
Changes resulting from the Antarctic environment.
3. The most likely explanation for the accumulation of relatively large
numbers of Amino Acid changes in Antarctic red algae is the absence of
Selection Pressure that might operate against their accumulation.
(Antarctica is a demanding environment for the selection of adapted red
algae, but not for a special Amino Acid composition of RuBisCo.)
4. The role of Natural Selection must not be overlooked when investigating
phylogenetic relationships or biogeographical distributions any more for
molecular and protein characters than for morphological characters.