ocean science: the many shades of ocean blue
TRANSCRIPT
DOI: 10.1126/science.1092704, 1514 (2003);302 Science
Hervé Claustre and Stéphane MaritorenaThe Many Shades of Ocean Blue
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portin-β for FG nucleoporins by altering therelative positions of HEAT repeats 5 and 6 (7,8); this change also facilitates cargo release.
Crystallography has defined the interac-tion interfaces between importin-β and manyof its binding partners. FG nucleoporins bindon the outer, convex surface of importin-β toa primary site between HEAT repeats 5 and6 and to several secondary sites, includingone near the carboxyl terminus (7, 8, 15).However, the remainder of importin-β’sbinding partners interact primarily with theinner, concave face. RanGTP binds to HEATrepeats 1 to 8 at the amino terminus of im-portin-β (4), whereas the mainly helical IBBdomain binds over an extensive area of theconcave surface that encompasses HEAT re-peats 7 to 19 (3). The interface between IBBand importin-β exhibits an extended networkof interactions involving more than 40 elec-trostatic, hydrophobic, and van der Waalscontacts. Tryptophan residues (especiallytryptophan-864) in importin-β help to stabi-lize the helical conformation of the IBB do-main and so ensure specific, high-affinitybinding (16). By contrast, the NLS of PTHrP(parathyroid hormone–related protein) bindsat the importin-β amino terminus (HEAT re-peats 2 to 6) and overlaps with the RanGTPbinding site (9). This NLS adopts primarily aβ-sheet conformation, and its interaction isreminiscent of the way classic NLSs bind toimportin-α (6). Although the binding sitesfor the PTHrP-NLS and IBB domain on im-portin-β partly overlap, the molecular archi-tecture of their sites is different and both canbind to importin-β simultaneously (9).
SREBP-2 lacks a classic NLS and, as Leeet al. (10) describe, binds to importin-β via itsdimeric helix-loop-helix zipper (HLHZ) do-main. As the investigators show, the crystalstructure of the importin-β:SREBP-2 com-plex reveals a remarkable new twist in the waythat importin-β recognizes its cargo. In this
complex, the dimeric HLHZ domain isgripped primarily by the long α helices ofHEAT repeats 7 and 17 that move like chop-sticks to pick up the cargo. In contrast to theIBB domain α helix, the α helices of theHLHZ domain are perpendicular to the cen-tral axis of the importin-β superhelix. To ac-commodate this interaction, importin-βmoves the long helices of HEAT repeats 7 and17 and adopts a more twisted and open con-formation. The conformational change intro-duced in this way is dramatic, with the amino-terminal region moving by 20 Å (a rotation of22°). In contrast to the PTHrP-NLS and theIBB domain, the interaction between im-portin-β and the HLHZ domain of SREBP-2is mediated primarily by hydrophobic interac-tions; charge complementation is of less im-portance. Lee et al. also note the presence ofa possible structural repeat in the sequence ofimportin-β that offers a convenient way forimportin-β to bind to dimeric cargo proteinsand perhaps also to FG nucleoporins (15).
Overall, the remarkable conformationalvariability of importin-β:cargo complexesimplies that unbound free importin-β is flex-ible and so can adapt its shape to recognize avariety of different partners. Such flexibilityis consistent with the greater susceptibility offree versus bound importin-β to proteolysis(3). Although high-resolution structures ofdifferent binding states have not yet been ob-tained, several homologs of importin-β prob-ably also provide an analogous flexible scaf-fold that facilitates versatility in substraterecognition (14). By contrast, although im-portin-α interacts with a range of substrates,these interactions do not appear to involvemajor conformational changes, even whenthey accelerate the rate of cargo release (17).
That importin-β must bind to a remarkablerange of different proteins to carry out both itsnuclear trafficking and nuclear assembly tasksexerts extraordinary demands on molecular
recognition capabilities. Such demands aremade even more pressing by the necessity forimportin-β to bind to and release many of itspartners in a spatially and temporally definedsequence. Molecular recognition usually in-volves matching of complementary interfacesbetween interacting proteins, and it is not un-common for relatively small structural alter-ations to be present at the interface associatedwith binding, or for domains of molecules torotate around a hinge. However, the confor-mational changes observed when importin-βbinds to its partners, particularly when it bindsto SREBP-2, involve an unusually large dis-tortion. Although stacking of 19 tandemHEAT repeats generates an extensive interac-tion surface that enables importin-β to bind toa wide range of different molecules, importin-β supplements this ability with a remarkabledegree of conformational flexibility. In thisway, it is able to greatly increase its versatilityin recognizing and releasing its different bind-ing partners. As more crystal structures of im-portin-β bound to different cargo proteins be-come available, it will be fascinating to seehow the interplay of surface structure andconformational dynamics is exploited to ac-complish a variety of different tasks.
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In satellite data over the South Pacific gyre,Earth’s largest oceanic desert (see the fig-ure), Dandonneau et al. [page 1548 of this
issue (1)] have detected areas that are green-er than the surrounding deep blue waters.They suggest that these “hotspots” are not
vegetal oases, but rather result from residuesand by-products of marine life accumulatedby physical processes. This detrital materialwould be incorrectly interpreted as phyto-plankton biomass from satellite ocean colordata. The study provides further evidence thatthe current paradigm—the greener the openocean waters, the higher their phytoplanktoncontent—has its limitations.
For nearly 25 years, ocean color has beenused as a proxy for algal biomass. Empiricalalgorithms (2) for mapping the global phy-toplankton distribution from space rely on
mean statistical relationships between thechlorophyll a concentration [Chla] (a proxyfor phytoplankton biomass) and the blue-to-green (B/G) reflectance ratio (an optical in-dex for water color). The resulting [Chla]maps are used to estimate the contributionof phytoplankton to global CO2 fixation (3)and investigate long-term changes in vege-tal biomass (4).
However, there is increasing evidencethat the simple empirical relationship be-tween [Chla] and B/G ratio does not alwayshold. Which optically active componentscause these deviations, and where do theyoccur? Answers to these questions shouldshed light on regional ecosystem structureand functioning.
Phytoplankton itself is one of the firstcandidates to be examined. Marine phyto-
O C E A N S C I E N C E
The Many Shades of Ocean BlueHervé Claustre and Stéphane Maritorena
H. Claustre is at the Observatoire Océanologique deVillefranche, Laboratoire d’Océanographie deVillefranche, CNRS-INSU, 06238 Villefranche-sur-mer, France. E-mail: [email protected] S. Maritorenais at the Institute for Computational Earth SystemScience, University of California, Santa Barbara, CA93106, USA. E-mail: [email protected]
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plankton are highly diverse in shape, size,and pigmentation, a diversity reflected bytheir varying color. Thus, it might be a prioripossible to track the composition of phyto-plankton communities from space. For ex-ample, Emiliania huxleyi is covered with cal-cium carbonate plates that, when released inthe water, give it a milky turquoise color,easily captured by satellite (5). Trichodes-mium sp.’s gas vesicles and specific pigmen-tation may also allow its remote detection(6). However, apart from E. huxleyi andTrichodesmium sp., discriminating phyto-plankton types from space is difficult, be-cause detected nuances could easily be con-founded with noise.
Besides phytoplankton, colored dis-solved organic matter (CDOM) and submi-crometer detritus particles also affect theoptical properties of oceanic waters.CDOM is responsible for a large (some-times dominant) fraction of the visible bluelight absorbed by the water (7). Assess-ments of [Chla] from empirical ocean col-or algorithms can be skewed by the pres-ence of such dissolved material.
Absorption by submicrometer particlesis generally small compared to that of phy-toplankton or CDOM. However, these par-ticles are a major source of backscatteredlight in the open ocean. Underestimates of[Chla] at high latitudes have been attrib-uted to low backscattering, possibly be-cause of low concentrations of submicrom-eter particles, either detritus or living (bac-teria, viruses) (8). Conversely, a phyto-plankton bloom could rapidly be trans-formed into detrital material by viruses (9),leading to overestimates of [Chla].
Recent studies have also suggested thatfine desert dust trapped in the upper layerof the ocean might depress the B/G ratio,causing overestimates of [Chla] (10). Dustdeposition is associated with the dissolu-tion of iron, an important phytoplanktonfertilizer. Future studies aiming to assessthe impact of desert dust deposition on ma-rine biogeochemical cycles must discrimi-nate between the enhanced backscatteringdue to the dust and the increased phyto-
plankton biomass due to fertilization (11). The story becomes even more complex
with the presence of bubbles, which makethe water appear greener (12). Hence, therougher the sea state and the higher its bub-ble content, the more standard algorithmswould overestimate [Chla].
Present empirical models are not wellsuited to capture the impact of these opti-cally active components. Furthermore,ocean color algorithms have been estab-lished from data collected mostly in theNorthern Hemisphere, with few data pointsfrom very oligotrophic areas. They mighttherefore not represent the SouthernHemisphere well, particularly the centralpart of the gyres, which also experiencelower dust deposition. Semianalytical algo-rithms must be developed that explicitly
take into account the various sub-stances that affect ocean color
in both hemispheres (7, 13).Further in situ investi-
gations in the SouthernHemisphere are alsoneeded, especially in re-mote areas such as theSouth Pacific gyre in-vestigated by Dandon-
neau et al. (1) (see thefigure). This vast oceanic
biome is the most olig-otrophic water body on Earth,
yet its optical and biogeochemicalproperties remain largely unexplored. In
the South Pacific gyre, new types of nuancesbetween [Chla] and ocean color might be ob-served, helping to explain the various shadesof ocean blue.
References 1. Y. Dandonneau et al., Science 302, 1548 (2003).
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3. D. Antoine et al., Global Biogeochem. Cycles 10, 57
(1996).
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(15), 10.1029/2002GL014689 (2002).
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6. A. Subramaniam et al., Deep Sea Res. II 49, 107
(2002).
7. D. A. Siegel et al., J. Geophys. Res. 107, 3228 (2002).
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26301 (2000).
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Research Conference, Honolulu, Hawaii, 15 to 20
February 2004.
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10.1029/2001GL014056 (2002).
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13. H. Loisel, D. Stramski, Appl. Opt. 39, 3001 (2000).
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Successful immune responses dependon the regulation of many genes toguide the biological effects of T and B
lymphocytes. To accomplish this, variousincoming signals must be integrated andthen distributed to a diverse set of gene ex-pression outputs. The transcription factorNF-κB serves as a key signal integrator inthis process in ways that no one could haveimagined when it was first identified as aDNA binding factor (1, 2). On page 1581 ofthis issue and in the most recent issue ofImmunity, the laboratories of Dixit andMak, respectively, reveal that a mouse pro-
tein called MALT1/Paracaspase (MPC) is acrucial regulator of NF-κB activity in Band T cells (3, 4).
Numerous cytokines, chemical media-tors, and cell surface receptors, includingthe antigen receptors of B and T lympho-cytes, activate NF-κB. Nuclear NF-κB canbind to and regulate the DNA control ele-ments of a wide variety of immune re-sponse genes [reviewed in (5)]. The center-piece of the NF-κB pathway is the IκB ki-nase (IKK) complex (6). IKK is formedfrom three subunits (IKKα, IKKβ, andIKKγ/NEMO) that transduce diverse up-stream signals into the phosphorylation anddegradation of IκB, the inhibitory bindingpartner that restrains NF-κB in the cyto-plasm. When IκB is degraded, NF-κB is
I M M U N O L O G Y
The Paracaspase ConnectionLi Yu and Michael J. Lenardo
www.sciencemag.org SCIENCE VOL 302 28 NOVEMBER 2003
Colors of an oceanic desert.The central South
Pacific gyre is Earth’s largest oceanic
desert. SeaWiFS satellite images re-
veal its consistently low [Chla]
(deep blue and purple). How-
ever, some nuances in the
blue color of these waters
can be detected (1). Only
20% of available measure-
ments (white symbols) for
ocean color algorithms de-
velopment have been collect-
ed in the Southern Hemisphere
(and less than 2% in the South
Pacific between 0° and 60°S).
60°
45°
30°
15°
0–30°–90° –45°
South Pacific gyre
–135°180°135°90°45°
–15°
–30°
–45°
–60°–75°
10.001.00
Chl a [mg m–3]0.100.01
P E R S P E C T I V E S
The authors are in the Laboratory of Immunology,National Institute of Allergy and Infectious Diseases,Bethesda, MD 20892, USA. E-mail: [email protected]