Coherent X-Ray Diffraction Imaging of Chloroplasts from Cyanidioschyzon merolae by Using X-Ray Free Electron Laser.

Plant and Cell Physiology Advance Access published March 5, 2015

Title: Coherent X-ray diffraction imaging of chloroplasts from Cyanidioschyzon merolae by using X-ray free electron laser Running title: Coherent X-ray diffraction imaging for chloroplasts

Masayoshi Nakasako Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan. Tel; +81-45-566-1713; Fax, +81-45-566-1672; [email protected]

Subject Areas: (11) new methodology Number of black and white figures: 0 Number of color figures: 6 Number of Tables: 1 Number of supplementary material: 0

© Crown copyright 2015.

1

Downloaded from http://pcp.oxfordjournals.org/ at University of California, San Francisco on March 10, 2015

Corresponding author contact information

Title: Coherent X-ray diffraction imaging of chloroplasts from Cyanidioschyzon merolae by using X-ray free electron laser Running title: Coherent X-ray diffraction imaging for chloroplasts

Tomotaka Oroguchi1,2, Masaki Yamamoto2, Sachihiro Matsunaga3,* and Masayoshi Nakasako1,2,* 1

Department of Physics, Faculty of Science and Technology,

Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan 2

RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan 3

Department of Applied Biological Science Faculty of Science and Technology,

Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan 4

These authors contributed equally to this work.

*

Corresponding authors. E-mail: [email protected]; Fax,

+81-45-5666-1672 and [email protected]; Fax, +81-4-7124-1501. Key words: coherent X-ray diffraction imaging · chloroplast · Cyanidioschyzon merolae · fluorescence optical microscopy.

2


Yuki Takayama1,2,4, Yayoi Inui3,4, Yuki Sekiguchi1,2,4, Amane Kobayashi1,2,

Abbreviations: CXDI, coherent X-ray diffraction imaging; C. merolae, Cyanidioschyzon merolae ; EM, electron microscopy; FWHM, full-width of half maximum; FT, Fourier transformation; IFT, inverse Fourier

oversampling; OSS, oversampling smoothness; PR, phase retrieval; RH, relative humidity; XFEL, X-ray free electron laser.

3


transformation; MPCCD, multi-port CCD; OM, optical microscopy; OS,

Abstract Coherent X-ray diffraction imaging (CXDI) is a lens-less technique for visualizing the structures of non-crystalline particles with the dimensions

nanometer. We conducted cryogenic CXDI experiments at 66 K to visualize the internal structures of frozen-hydrated chloroplasts of Cyanidioschyzon merolae using X-ray free electron laser (XFEL) as a coherent X-ray source. Chloroplasts dispersed specimen disks at a number density of 7/(10×10 μm2) were flash-cooled with liquid ethane without staining, sectioning or chemical labeling. Chloroplasts are destroyed at atomic level immediately after the diffraction by XFEL pulses. Thus, diffraction patterns with good signal-to-noise ratio from single chloroplasts were selected from many diffraction patterns collected through scanning specimen disks to provide fresh specimens into irradiation area. The electron density maps of single chloroplasts projected along the direction of the incident X-ray beam were reconstructed by using the iterative phase-retrieval method and the multivariate analyses. The electron density map at a resolution of 70 nm

4


of sub-micrometer to micrometer at a resolution of several tens of

appeared as a C-shape. In addition, the fluorescence image of proteins stained with FlamingoTM dye also appeared as a C-shape as well as that of the autofluorescence from chlorophyll. The similar images suggest that

the outer membranes of chloroplasts. To statistically confirm the present results, a number of projection structures must be accumulated through high-throughput data collection in near future. Based on the results, we discuss the feasibility of XFEL-CXDI experiments in the structural analyses of cellular organelles.

5


the thylakoid membranes with an abundance of proteins distribute along

Introduction One of ultimate goals of cell biology is a seamless description of spatiotemporal hierarchies in living cells, for instance, to illustrate how

cellular level. In the last two decades, optical microscopy (OM) using fluorescent probes has significantly contributed to visualization of the spatiotemporal

dynamics

of

cellular

components

engaged

in

physiologically important events at a spatial resolution of approximately 200 nm and at a temporal resolution of several tens of millisecond (Miyawaki

2013).

Super-resolved

OM

currently

achieves

better

resolutions than 200 nm for fluorescence-labeled targets in live cell imaging (Sengupta et al. 2012). Electron microscopy (EM) has been used to illustrate cellular structures at a spatial resolution of much better than 200 nm. Because whole cellular components with the dimensions of larger than 1 μm are opaque for electrons, sectioned-specimens of cellular components are necessary for the structural investigation by using transmission EM (Gan and Jensen 2012) or freeze-fractured specimens for scanning EM (Heuser 2011). X-ray microscopy utilizing

6


external physicochemical stimuli at the molecular level propagate to the

zone plates has been developed to visualize three-dimensional structures of thick specimens at a resolution of 50 nm (McDermott et al. 2009). Recently, coherent X-ray diffraction imaging (CXDI) technique (Miao

Since 1999 (Miao et al. 1999), CXDI has been developed for visualization of the structures of non-crystalline particles with the dimensions of sub-micrometer to micrometer at resolutions of several tens of nanometers (Miao et al. 2008). In CXDI experiments, an isolated particle is irradiated by X-rays with high spatial coherence. X-rays with short wavelengths penetrate deeply into thick objects without multiple scattering, because of the weak electromagnetic interactions with atoms. CXDI visualizes whole structures of thick specimens without staining, chemical labeling and sectioning. Fraunhofer diffraction patterns of thick particles can be collected at a resolution exceeding the limit in OM. The electron density distribution of the thick particle projected along the direction of incident X-rays is reconstructed by using the iterative phase-retrieval (PR) algorithm (Fienup 1982) from the diffraction pattern alone (The details will be described in the next Theoretical background

7


et al. 2012) was applied to structural analyses of cellular components.

section.). In the last decade, several CXDI experiments at synchrotron facilities have demonstrated the potential to visualize the structures of

al. 2003a, Song et al. 2008, Nishino et al. 2009, Jiang et al. 2010). However, the experiments were conducted for dehydrated specimens at ambient temperature, where specimens are damaged by the diffusing free radicals produced in specimens by X-ray irradiation. This secondary damage is suppressed by the immobilization of radicals, when specimens are kept near liquid nitrogen temperature, thereby dramatically reducing radiation damage of specimens (Ravelli and Garman 2006, Bammes et al. 2010). To visualize the functional structures of hydrated biological specimens without radiation damage, cryogenic CXDI techniques and apparatus have been developed including the specimen preparation procedure to keep the functional structures in the frozen-hydrated state (Huang et al. 2009, Lima et al. 2009, Takayama and Nakasako 2012, Nakasako et al. 2013). The cryogenic technique provides opportunities for

8


non-crystalline biological particles with micrometer dimensions (Miao et

the structural analyses of cellular components in the frozen-hydrated state without sectioning and/or staining indispensable in EM. In addition, because CXDI visualizes electron density distribution of whole specimen,

unnecessary.

Therefore,

cryogenic

CXDI

is

suitable

for

imaging

frozen-hydrated thick specimens, although time-resolved measurement is impossible. In recent years, intense and completely coherent X-ray pulses with repetition rates of 10-100 Hz and duration of tens of femtoseconds have been available at X-ray free electron laser (XFEL) facilities. Therefore, in CXDI experiments utilizing XFEL (XFEL-CXDI), a large number of diffraction patterns can be collected in a short period of time. XFEL-CXDI has been applied to visualization of the structures of biological specimens such as a large virus (Seibert et al. 2011), a cellular organelle (Nakasako et al. 2013), and a bacterial cell (Kimura et al. 2014). The demerit of XFEL-CXDI experiments is the destruction of specimen particles at atomic level by an intense single shot (Neutze et al. 2000, Chapman et al. 2006b, Nakasako et al. 2013). For instance, the intensity of focused XFEL pulses

9


fluorescence-labeling of specific proteins used in super-resolved OM is

with the wavelength of 0.225 nm reaches 1010-11 photons/ (2×2 μm2)/pulse of 10 fs duration at the SPring-8 Angstrom Compact free electron LAser (SACLA) (Yumoto et al. 2013). However, because the

we can collect diffraction patterns from almost radiation-damage-free particles as demonstrated in recent crystal structure analysis for proteins using XFEL (Hirata et al. 2014). Since 2012, we have been studying the internal structures of some cellular organelles by using XFEL-CXDI (Nakasako et al. 2013). In the present study, we conducted cryogenic XFEL-CXDI experiments to analyze the internal structure of frozen-hydrated chloroplasts from a unicellular red alga, Cyanidioschyzon merolae (C. merolae) (Imoto et al. 2011). Here we show projected electron density distributions inside chloroplasts in the frozen-hydrated state at effective resolutions of 70 nm, and compare the density map with the distribution of proteins composing chloroplasts imaged by the fluorescence microscopy. Based on the present results, we discuss the merit of cryogenic XFEL-CXDI technique and its combinational use with the fluorescence microscopy for structural

10


destruction of specimen particles occurs after diffraction for XFEL pulses,

studies of cellular organelles.

Theoretical background of CXDI

how the electron density distribution of a non-crystalline particle is determined from its diffraction pattern (Miao et al. 1998). Here we consider the diffraction pattern of a spatially isolated non-crystalline

r particle with the electron density of ρ (r ) , which is irradiated by a coherent X-ray beam with the flux density of I 0 and the wavelength of λ (Fig. 1A). Under the Fraunhofer approximation, the diffraction intensity

()

r I S

r S

at a scattering vector

with the scattering angle of

2θ

r ( S = 2 sin θ / λ ) is written as

()

() ()

r r* r λ2 I S = I 0 re2 FS FS σ A r r r r r r F S = ρ (r ) exp 2πiS ⋅ r d 3 r = F S exp iα S

()

∫

(

( ) [ ( )]

)

(1) (2)

where re is the classical electron radius of 2.8179×10-15 m. σ is the oversampling (OS) ratio of the diffraction pattern, the details of which is described below. A is the projected area of the particle along the direction normal to the incident X-ray beam. In most CXDI experiments,

11


In this section, we briefly describe the theory of CXDI to introduce

the size of particle ranges from sub-micrometer to several micrometer.

()

r r F S is the structure factor, the Fourier transformation (FT) of ρ (r ) (Eq.

()

r (2)) and is a complex number expressed by the structure amplitude F S

()

r in diffraction experiments because only the diffraction intensity I S can

be observed. The diffraction pattern is composed of a number of intensity peaks, so-called speckles, caused by the interference of X-rays diffracted by the irradiated object (Fig. 1A). The size of each speckle is approximately comparable with the inverse of particle size. Flux density I 0 must be large

enough

to

record

the

diffraction

pattern

from

a

single

non-crystalline particle with a good signal-to-noise ratio because re is quite small (Eq. (1)). In principle, the theoretical limit of spatial resolution of the diffraction pattern is the half of X-ray wavelength as expected from the Bragg’s law, when I 0 is infinitely large. The intensity distribution of the observed diffraction pattern is limited to that intersecting a sphere with the radius of 1 λ (the Ewald sphere in Fig. 1A) (Chapman et al.

2006a).

12


()

r and the phase α S . It should be noted that the phase information is lost

In the small-angle diffraction region, where the Ewald sphere is approximated as

a

plane,

the two-dimensional

structure factor,

r FOBS (S x , S y , S z = 0 ) , is expressed as the FT of the projection of ρ (r ) along

discrete FT for ρ P (x, y ) expressed by N x × N y pixels as

FOBS (S x , S y , S z = 0) =



∑ ∑ ρ (x, y ) exp 2πi  S P

x =0

(



N x −1 N y −1



y =0

where FOBS S x , S y , S z = 0

)



x

x y  + Sy  ∆x∆y Nx N y 

(3)

is the structure amplitude of the projected

electron density ρ P (x, y ) , which is divided into N x × N y pixels by an area element ∆x∆y . To illustrate ρ P (x, y ) , this set of algebraic equations

(

regarding ρ P (x, y ) is, in principle, solved using a set of FOBS S x , S y , S z = 0

)

observed at different N x × N y points. However, in the case of objects without anomalous scatterers, the centrosymmetry in diffraction patterns, called Friedel symmetry, reduces the net structural information contained

(

in a set of FOBS S x , S y , S z = 0

)

by half as (N x × N y ) 2 . Then, to solve the

algebraic equations, the number of the observed diffraction amplitude data is requested more than the twice of (N x × N y ) 2 . To increase the

number of equations, we sample the diffraction pattern by σ x N x along

13


the direction of the incident X-ray beam, ρ P (x, y ) . Here we consider a

the direction of S x and by σ y N y along the direction of S y . When the following equation is satisfied, ρ P (x, y ) is, in principle, determined (Miao et al. 2003b).

The parameter σ is the OS ratio appearing in Eq. (1). This requirement is so-called the OS condition that defines the minimal amount of data points required to solve the algebraic equations. Therefore, diffraction patterns must be collected so as to satisfy Eq. (4). In practice, ρ P (x, y ) is determined through a numerical calculation using the iterative PR algorithm (Fig. 1B). The calculation starts with a random electron density map. After the FT of a given electron density map, the structure amplitude of the calculated structure factor is replaced by the observed structure amplitude derived by the square root of the observed intensity (Eq. (1)). Then, the electron density map is obtained through the inverse Fourier transformation (IFT) of the structure factor after the replacement. By using the constraints, the electron density map is modified for the next calculation cycle (see Eq. (5) shown below). When the OS condition is satisfied, the electron density map is, in principle,

14


(4)

σ = σ x ×σ y ≥ 2

retrieved through iterating the procedure (Fienup 1982). For instance, the hybrid-input-output (HIO) constraint (Fienup 1982) used to modify electron density map in the iterative calculation

r r r r ∈ Support and ρ ' k (r ) ≥ 0 ρ ' k (r ) r  ρ k +1 (r ) =  r r otherwise ρ k (r ) − βρ ' k (r )

(5)

r r where ρ k (r ) is the map at the beginning of the k-th cycle. ρ ' k (r ) is the IFT of the structure factor whose amplitude is derived from the observed

r r diffraction intensity and phase is calculated from ρ k (r ) . ρ k +1 (r ) is input map for next cycle. The support is the area, within which the electron density distribution of the specimen particle is to be retrieved. The electron densities outside the support are reduced with a control parameter β. In addition to this simple constraint to update electron density map, other constraints and modification methods are proposed (Elser 2003, Marchesini et al. 2003, Luke 2005, Chen et al. 2007, Martin et al. 2012a, Rodriguez et al. 2013). As seen in Fig. 1A and experimental diffraction patterns shown in the Results section, speckle diffraction patterns are composed of a lot of

15


cycle is written as

peaks and valleys appearing continuously. Thus, the continuously varying diffraction patterns can be finely sampled by an area detector to satisfy the OS ratios requested in Eq. (4). On the other hand, diffraction patterns

(Blundel and Johnson 1976). Then, the OS ratio is too small because there are no diffraction intensities between Bragg spots. Semi-periodic structures lacking perfect crystalline order may theoretically give diffraction patterns to be oversampled.

Outline of CXDI experiment Here we briefly introduce experimental conditions and limitations of CXDI experiments (Fig. 1A). To reduce scattering from air, in many cases, specimens are located in a vacuum chamber. To avoid drying in vacuum, biological specimens are kept in frozen-hydrated sate after diminishing the amount of buffer to ensure electron density contrast (Takayama and Nakasako 2012, Nakasako et al. 2013), or thin liquid chamber (Kimura et al. 2014). CXDI is usually applicable to specimen particles with the size smaller

16


from crystals of biological macromolecules are composed of Bragg spots

than the cross-section of coherent X-ray beam. In CXDI experiments using synchrotron X-ray, coherent X-ray beam is produced by the Fraunhofer diffraction from an aperture. The size of X-ray beam is

a chloroplast from spinach with the diameter of 7 μm, we used a circular aperture of 20 μmφ, which provided a coherent X-ray beam of 14 μmφ at the specimen position (Takayama and Nakasako, 2012). In contrast, the size of currently available XFEL pulses as large as 2×2 μm2 at full width of half maximum (FWHM) is fixed by the focusing mirror optics (Yumoto et al. 2013). Therefore, the sizes of specimen particles are should be less than the half of the FWHM of X-ray beam. Ideally, as in synchrotron CXDI experiments, the center of a specimen particle coincides with an X-ray beam to maximize the diffraction intensity (Jiang et al. 2010, Takayama and Nakasako, 2012). However, in XFEL-CXDI experiments, because XFEL pulses destroy specimens after diffraction, it is impossible to refine the position of specimens relative to X-ray pulses prior to data collection. In our case as described later (see the Results and Materials and Methods sections),

17


controlled by the aperture size. For instance, in our CXDI experiment for

diffraction data are collected stochastically by scanning specimen disks, on which specimen particles are randomly dispersed. Thus, the complete coincidence of specimen positions with the centers of X-ray pulses is rare.

diffraction patterns with intensity enough to be analyzed. To collect a large number of diffraction patterns with good signal-to-noise ratio, we should pay attention to the number density of dispersed specimen particles. Experimental diffraction patterns miss the very small angle-region due to the beam stop, which is used to prevent the direct beam from giving fatal damage to detectors, and the saturation of detector pixels. In addition, diffraction patterns are smeared by Poisson noise in X-ray detection. Thus, the PR calculations for experimental data are not so easy and require larger OS ratios than that expected from the theoretical consideration for ideal diffraction data as demonstrated for experimental data (Miao et al. 2003b) and simulations (Kodama and Nakasako 2011, Oroguchi and Nakasako 2013).

18


When specimen particles are within the FWHM of X-ray beam, they give

Results Diffraction data collection in cryogenic XFEL-CXDI experiments For

cryogenic

chloroplasts

experiments,

without

chemical

we

prepared

modification

and

sectioning according to the procedure illustrated in Fig. 2A. During the specimen preparation, isolated chloroplasts were kept under high relative humidity (99%rh) condition (Takayama and Nakasako 2012). For assisting the adhesion of chloroplasts to the carbon membranes on specimen disks, we coated the surfaces of carbon membranes with using poly-lysine. Through varying the concentration of poly-lysine solution and the number density of chloroplasts in suspension, we prepared the specimens with the average number density of dispersed chloroplasts at approximately

7/(10×10

μm2)

(Fig.

2B).

From

the

microscopic

observation (Fig. 2B), the diameters of chloroplasts ranged roughly from 1.5 to 2 μm. The chloroplasts adhering to poly-lysine were in random orientation regarding the incident X-ray beam. The thickness of the remaining buffer solution on the carbon membranes was reduced as much as possible by

19


frozen-hydrated

XFEL-CXDI

blotting and vapor diffusion as judged from the microscopic observation before flash-cooling (Fig. 2B). Thus, by the flash-cooling with liquid ethane, chloroplasts embedded in thin water films would be in

spinach with much larger diameter of 7 μm in our previous CXDI study (Takayama and Nakasako 2012). Specimen disks stored in liquid nitrogen were transferred to the cryogenic stage at 66 K inside the KOTOBUKI-1 diffraction apparatus by using a set of devices to prevent frosting and warming of specimen disks during the transfer (Figs. 2C-D) (Nakasako et al. 2013, Sekiguchi et al. 2014a). Diffraction patterns were collected by scans for specimen disks against focused X-ray pulses selected at a repetition rate of 1 Hz as done in our previous XFEL-CXDI experiments (Fig. 2E) (Nakasako et al. 2013, Takahashi et al. 2013, Sekiguchi et al. 2014b). For instance, we collected approximately 1000 single-shot diffraction patterns within 40 min in XFEL-CXDI experiments.

Statistics of collected diffraction data

20


frozen-hydrated state as successfully carried out for chloroplasts of

Figure 3A shows a diffraction pattern obtained, when an X-ray pulse hit a chloroplast particle such that the center of the X-ray pulse almost coincided with the center of the particle. The resolution of the diffraction

diffraction pattern in a small-angle region up to a resolution of r approximately 125 nm ( S of 8 μm-1) was missed due to the saturation of

detector pixels receiving very strong diffraction. At present, the PR calculations of such diffraction patterns remain very difficult even using the latest algorithm (Martin et al. 2012b, Kobayashi et al. 2014), which is robust for the lack of the small-angle region. Figures 3B-C summarizes the statistics of diffraction data in 8 scans. The diffraction intensity and the maximum resolution depended on the size of chloroplasts, the relative positions between chloroplasts and X-ray pulses, and the fluctuation in incident intensities and coherence of XFEL pulses. Diffraction patterns with the total intensity worth analyzing reaches 91% of the collected patterns (Fig. 3B). In most of those diffraction patterns, speckles recorded with the signal-to-noise ratio better than 2 per pixel were observed up to a resolution beyond 50 nm

21


r pattern reached beyond 18 nm ( S of 55 μm-1). Unfortunately, the

(Fig. 3C). However, most of the diffraction patterns with good signal-to-noise ratio were composed of small speckles with the size of 2×2 ~ 3×3 pixels (Figs. 3D and E). Although OS condition in Eq. (4) is

reconstruct correct electron density maps by applying currently available PR protocols due to missed small-angle regions and Poisson noise in diffraction patterns.

Diffraction patterns used for structural analysis Sometimes, we observed diffraction patterns with the speckle sizes of 5×5 pixels, which were suitable for PR calculations using currently available algorithm. We selected single-shot diffraction patterns which comprise speckles with the sizes of larger than 5×5 pixels and reached a r resolution of 50 nm ( S of 20 μm-1). In the case of two representative

examples shown in Figs. 4A-B, diffracted X-rays were detected up to a resolution of 29 nm with significant signal-to-noise ratio. The characteristic concentric pattern with an approximate period of 2.5 μm-1 in Fig. 4A (indicated by arrow) suggests the interference of

22


theoretically satisfied, those speckle size were practically too small to

electron density separated by approximately 400 nm. The diffraction pattern in Fig. 4B is composed of speckle peaks of ellipsoid shapes, and has no concentric patterns in contrast to those in Figs 3A and 4A. In both

direction of the incident X-ray are calculated to be in the range of 1.0-1.5 μm from the rough dimensions of speckles (see also Fig. 1A). Considering the size of the particle, the Ewald sphere is approximated as a plane up to a resolution of 11 nm according to the equation derived previously (Oroguchi and Nakasako 2013). The diffraction patterns display good Friedel symmetry with the Csym values (see the legend of Table 1) of r around 0.8 calculated around a resolution of S =16.2 μm-1 (Table 1 and

Figs. 4A-B).

Electron density distribution in chloroplasts From the diffraction patterns in Figs. 4A-B, projected electron density maps of chloroplasts were retrieved at effective resolutions of 70 nm (Table 1 and Figs. 4C-D). Here we describe the characteristics of the electron density distribution in chloroplasts.

23


diffraction patterns, the dimensions of chloroplasts projected along the

In the projected electron density map retrieved from the diffraction pattern in Fig. 4A (Fig. 4C), several high density peaks distribute in a characteristic C-shape with the dimensions of approximately 600×800

C-shape was consistent with the distance estimated from the intervals between concentrically distributing speckles (2.5 μ m-1) indicated by arrows in Fig. 4A. The projected electron density map retrieved from the diffraction pattern in Fig. 4B appeared as a rectangular shape, which was quite different from that in Fig. 4C. As schematically illustrated in the inset of Fig. 4D, the phase-retrieved map is divided into a triangle-shaped high-density region designated as α and an additional low-density region β. The quite different density maps between the two chloroplasts will be discussed in the following sections together with the structural information from fluorescence microscopy and EM.

Fluorescent imaging of a chloroplast In images obtained by using a phase-contrast OM (Fig. 5A), many

24


nm. The approximate diameter (400 nm) of the high density region in the

chloroplasts had small and dark regions at the center. This observation suggested a non-uniform distribution of chloroplast components such as thylakoid membranes which are known as protein-rich lipid bi-layers

1971). In

order

to

visualize

thylakoid

membranes,

we

performed

fluorescent imaging of autofluorescence from chlorophylls (Fig. 5B). Next, we visualized distribution of proteins stained by FlamingoTM fluorescent dye, which has been used for selectively staining of protein spots or bands separated by electrophoresis (Chakravarti et al., 2010) (Fig. 5C). Six sections at 0.2-μm step along the optical axis were acquired by confocal microscopy. Fluorescent images exhibiting the distribution of proteins and chlorophylls are very similar. While the fluorescence intensity was low near the surface of the chloroplast, the intensity became strong in approaching to the equatorial plane of the chloroplast. At the equatorial plane, the region with strong fluorescence intensity was distributed in the C-shape with the diameter of approximately 1 μm. Thus, these images

25


including much amount of chlorophylls for photosynthesis (French,

indicated that both chlorophylls and stained proteins were abundantly distributed along the marginal regions in the chloroplast.

We visualized the electron density distribution in frozen-hydrated chloroplasts from C. merolae at effective resolutions of 70 nm by XFEL-CXDI (Table 1, Figs. 2-4). We also visualized the autofluorescence of chlorophylls and the distribution of proteins stained by FlamingoTM dye inside a chloroplast by the confocal fluorescence microscopy (Fig. 5). Here we discuss the structure of chloroplasts based on all observations. Furthermore, we also discuss the application of the CXDI to the visualization of cellular components at a resolution of tens of nanometers.

XFEL-CXDI experiments for frozen-hydrated chloroplasts In the present study, we efficiently collected diffraction data of frozen-hydrated chloroplasts in the XFEL-CXDI experiments (Figs. 3B-C). Because the KOTOBUKI-1 diffraction apparatus is easy to operate and stably works during 84 hours in a beam time, the efficiency in diffraction

26


Discussion

data collection mainly depends on the number density of chloroplasts on specimen disks. Specimen disks with high number densities of chloroplasts with less aggregates result in high hit rates of X-ray pulses to

Because of the low electron density contrast between chloroplasts and water, the amount of buffer is necessary to be diminished for visualizing chloroplasts clearly. Without the poly-lysine coating for the adhesion

of

chloroplasts

on

carbon

membranes,

aggregates

of

chloroplasts are easily induced by surface tension of buffer solution during the removal of the excess amount of buffer solution by blotting and vapor diffusion. Aggregates yield diffraction patterns with small OS ratio, which is fatal to retrieve the electron density map. Thus, the poly-lysine coating of carbon membranes is an indispensable step for collecting diffraction patterns from isolated single chloroplasts. Unfortunately, the number of diffraction patterns with the speckle sizes of 5×5 pixels (corresponding to the diameter of chloroplasts of 1.5 μm) is still smaller than those of chloroplasts of approximately 2 μm. Most of the diffraction patterns collected are difficult to be analyzed mainly due

27


chloroplasts in the scan measurements.

to the small OS ratio (Figs. 3D-E). Near future, for instance, we will try a longer camera distance of the two detectors to make the OS ratio larger in addition to the expansion of the sizes of detectors.

From the selected diffraction patterns recorded with good statistics in intensity and OS ratios suitable for the currently available PR algorithms, the projected electron density maps are retrieved at effective resolutions of 70 nm. This may be the highest resolution among frozen-hydrated cellular components visualized by XFEL-CXDI experiments so far. However, to statistically confirm the current results, a large number of projection structures must be accumulated through high-throughput data collection for diffraction patterns with large OS ratio in near future. The C-shaped high density region in the electron density map (Fig. 4A) is similar to the high fluorescence intensity region (Fig. 4D, E) in the chloroplast both in the shape and size. The average electron density of the central region is comparable with that of vitreous ice embedding the chloroplast. The density of vitreous ice is known to be 0.933±0.020 g/cm3

28


Structure of chloroplast

corresponding to the electron density of 0.311±0.01 e/A3 (Dubochet et al. 1982, Dubochet et al. 1988). The high electron density regions in the C-shape are probably composed of chloroplast proteins, which have the

In the preliminary CXDI study on C. melorae chloroplast (Nakasako et al. 2013), we also obtained a phase-retrieved map, which had a low-density region in the middle. The region displaying high fluorescence intensity is, of course, reflecting the high density distribution of proteins stained by the dye (Fig. 5C). Thus, based on the similarities in the dimensions and shapes, the orientation of the chloroplast against the incident X-ray pulse in Fig. 4C is close to that against the optical axis in the fluorescence microscopy observation. Dye-stained proteins in chloroplast distribute predominantly around the marginal regions rather than the center (Fig. 5C). The internal structures of chloroplasts have been visualized by applying EM to sectioned ultra-thin specimens after a heavy-atom stain and a resin-fixation (Yagisawa et al. 2009, Yoshida et al. 2010). The distributions of the high electron density regions (Fig. 4C) and the high

29


average electron density of 0.41-0.43 e/A3 (Stuhrmann and Miller 1978).

fluorescence intensity of chlorophylls (Fig. 5B) resemble the distribution of thylakoid membranes located at the marginal regions of chloroplasts observed in the EM study.

than the stroma and the envelope of chloroplasts (Kouranov and Schnell 1996, Su et al. 2010). Thus, in the frozen-hydrated chloroplast, the C-shaped object with the high electron density probably indicates that the stacked layers of thylakoid membranes predominantly distribute in the marginal regions rather than the central regions as illustrated in Fig. 6A. The thylakoid membranes would extend to more than several hundred nanometer area. The projected electron density map in Fig. 4C and images from fluorescence microscopy (Fig. 5B-C) suggest the extension of thylakoid membrane with keeping the C-shape as illustrated in Fig. 6B. In this regard, the other electron density map in Fig. 4D may be interpreted as the projection view of the stacked thylakoid membranes from the different direction from that in Fig. 4C as illustrated in Fig. 6C. The C-shaped stacks of thylakoid membranes may be advantageous for efficient photosynthesis for C. merolae, which is rotated randomly and

30


In chloroplasts, proteins are more abundant in thylakoid membranes

freely by fluid dynamic perturbation in the living medium. In a CXDI experiment for a frozen-hydrated chloroplast from spinach, the phase-retrieved projection electron density map has structural

similar with EM images of stained and sectioned chloroplast particles (Shimoni et al. 2005). In spinach, blue-light induced movements of chloroplasts and phototropism mediated by phototropins maximize the efficiency of photosynthesis (Suetsugu and Wada 2007). C. merolae is a small eukaryote evolutionally classified as the origin of eukaryote. According to the endosymbiotic theory on the evolution of eukaryote (Gray and Archibald 2012), several key organelles, such as mitochondrion and chloroplast, are originated as symbioses between separate single-celled organisms. In this regard, the structure of cyanobacterium, which has lamellar structures of thylakoid membranes in the marginal region rather than the central part (van de Meene et al. 2006), is interesting. To compare the structures of the chloroplast and whole cyanobacterium, we are planning to carry out XFEL-CXDI experiments and fluorescence microscopy for cyanobacterium in the next

31


features assignable as granum (Takayama and Nakasako 2012). That was

stage. XFEL-CXDI experiments on frozen-hydrated whole biological particles would make the structural relation among evolutionally related organelles clear.

In the present study, we demonstrated that the cryogenic CXDI experiment has potential to visualize the structures of chloroplasts with the dimension of approximately 1.0 μm at effective resolutions of 70 nm, better than the resolution limit of OM. Considering the currently available incident X-ray intensity at SACLA and the diffraction intensity given by Eq. (1), the structural analyses of cellular organelles and small living cells are suitable for experimental targets of XFEL-CXDI from biology. Thus, the CXDI for frozen-hydrated biological specimens contribute to the structural analyses of cellular components in the following three points. First, specimens supplied to CXDI experiments are in the frozen-hydrated state. Second, the resolution of diffraction patterns exceeds the limit of fluorescence microscopy. Finally, as demonstrated in the present study, that X-rays with the short wavelengths are suitable to

32


Feasibility of CXDI in cell biology

visualize the internal structure of thick objects opaque in EM. In addition, cryogenic synchrotron-CXDI experiments at synchrotron facility under the reduction of radiation damage will enable us to perform the

et al., 2009) For synthesized metal particles with dimensions of less than 1 μm, we conducted simultaneous analyses of their size distribution and the structures through collecting thousands of single-shot diffraction patterns in a few hours at SACLA (Takahashi et al. 2013, Sekiguchi et al. 2014b). For biological specimens, thousands of diffraction patterns from single specimen particles are necessary to statistically confirm structural characteristics found from single-shot diffraction patterns (Fig. 4). To perform statistical analyses at a resolution of better than 20 nm, we are now developing an apparatus for high-speed data collection at a rate of 30 Hz used in near future experiments. Toward understanding of the structures and functions of cellular organelles with hierarchical structures, CXDI introduced here would be a tool suitable to visualize whole organelles in addition to the sophisticated

33


tomographic structure analyses at a spatial resolution of ~10 nm (Howells

imaging techniques such as fluorescence microscopy, EM, X-ray microscopy, and so on. In addition to CXDI, X-ray ptychography (Rodenburg et al. 2007) , which can survey a large object by synchrotron

with far larger sizes than the limitation of coherent beam sizes. The complementary use of the CXDI together with those sophisticated and established imaging techniques will bridge the resolution gap between the cellular biology and structural biology for molecules.

Materials and Methods Isolation of chloroplasts C. merolae strain 10D-14 (Toda et al. 1998) cell culture was maintained in 2× Allen’s medium at pH 2.3 subjected to continuous light (40 W/m2) and shaking at 313 K. The cells were subcultured to yield a concentration of 1×107 cells / mL. Isolation of chloroplasts was performed as previously described (Miyagishima et al. 1999) with the following modifications. The cells were mixed with 20% (w/v) maize starch solution (final concentration) containing the protease inhibitor cocktail Complete (Roche,

34


X-ray, is available for imaging structures of specimens, such as tissues

Applied Science), and then the mixture was homogenized by a Dounce homogenizer (Wheaton Industrial) (Fujiwara et al. 2010). After adding DNase I to the lysate at a final concentration of 200 mg

at 100g for 1 min to remove starch, the lysate layered on the top of four steps gradient of Percoll in 40-mL tubes. The four gradient steps from the bottom are 6 mL of 80% (v/v), 7 mL of 60% (v/v), and 6 mL of 40% (v/v), 4 mL of 0% (v/v) Percoll dissolved in isolation medium containing 300 mM sucrose (isotonic isolation medium). Through a centrifugation at 23,000g for 50 min in a swinging-bucket rotor (SW28; Beckman Coulter), chloroplasts were concentrated in a band at the 60-80% Percoll interface. The fraction was washed with isolation medium containing 300mM sucrose by centrifugation at 500g.

Specimen preparation for CXDI experiments We used custom-made specimen disks of 3-mm diameter with single (Takayama and Nakasako 2012) or several pinholes (Nakasako et al. 2013). Laboratory-made carbon membranes with the thickness of

35


/ mL, the mixture was incubated on ice for 1 h. Following a centrifugation

approximately 20 nm were glued on each specimen disk. The surface of each carbon membrane was coated with poly-lysine. A 5-μL droplet of 1 mg/mL poly-lysine solution (Sigma-Aldrich) was applied on the carbon.

To avoid drying of chloroplasts, specimen preparation were carried out under a relative humidity of approximately 99% using our custom-made humidity-controlling device (Fig. 2A) (Takayama and Nakasako 2012, Nakasako et al. 2013). A 2-μL droplet of concentrated chloroplast suspension in the isolation medium containing 300 mM sucrose was set on the carbon membrane of the specimen disk. An excess amount of the buffer was removed by vapor diffusion after roughly blotting with a tip of a filter paper. The specimen disk with a diminished amount of buffer was then flash-cooled by using liquid ethane. Cooled specimen disks were stored

in

liquid nitrogen

until

XFEL-CXDI

experiments.

Cryogenic XFEL-CXDI experiment Cryogenic XFEL-CXDI experiments were carried out by using our

36


After 30-60 min, the solution was washed with distilled water.

custom-made diffraction apparatus for cryogenic XFEL-CXDI experiments named KOTOBUKI-1 (Nakasako et al. 2013) at BL3 in the SACLA (Tono et al. 2013) (Figs. 2C-D). X-ray pulses with the wavelength of 0.225 nm

(10-fs pulse) (Yumoto et al. 2013). The KOTOBUKI-1 apparatus was placed so that the specimen position was within the focal spot. The background scattering from the upstream optics were eliminated by a pair of silicon slits set at the 10-mm upstream from the focal spot. The diffraction patterns were recorded simultaneously by two multi-port CCD (MPCCD) detectors (Kameshima et al. 2014) in a tandem arrangement. The MPCCD-Octal detector composed of 8 CCD sensors (512×1024 pixels of (50×50 μm2)/sensor) was placed at approximately 1.6-m downstream from the specimen position, and recorded diffraction patterns in the resolution range of 7-210 nm. The size of the central aperture of the MPCCD-Octal detector was varied in the range of 3-9 mm (Figs. 2C-D, 3A, 3D-E and 4A-B). Diffracted X-rays passing through the central aperture was recorded by the MPCCD-Dual detector with two sensor panels. The MPCCD-Dual detector was located at 3.2-m

37


were focused to give an intensity of 1010 photons / (2×2 μm2 (FWHM)) /

downstream from the specimen, and covered the resolution range of 210-480 nm. Aluminum attenuators with various thickness of 15-100 μm were placed in front of the MPCCD-Dual detector. The direct beam was

The KOTOBUKI-1 apparatus was controlled by using the IDATEN software suite (Sekiguchi et al. 2014a). Because focused single X-ray pulse destroys particles at atomic level, a specimen disk was scanned at a step of 25-50 μm/pulse by the goniometer stage of the diffraction apparatus to supply fresh particles to the irradiation area (Fig. 2E) (Nakasako et al. 2013, Takahashi et al. 2013, Sekiguchi et al. 2014b, Xu et al. 2014). Then, X-ray pulses stochastically hit chloroplasts randomly dispersed on a specimen disk.

Data processing Diffraction patterns collected by the two MPCCD detectors were processed automatically after the finish of each scan by using the program suite G-SITENNO (Sekiguchi et al., 2014a, Sekiguchi et al. 2014b). The suite subtracts dark current of the MPCCD detectors from the

38


completely absorbed by a beam stop with the cross section of 2×2 mm2.

raw data, extracts diffraction patterns worth analyzing regarding the signal-to-noise ratio, determines the beam center positions in the two MPCCD detectors, evaluates the degrees of centrosymmetry in diffraction

preliminary examination of electron density maps, the PR calculation for a merged data is executed by the ZOCHO subprogram (Kodama and Nakasako 2011, Oroguchi and Nakasako 2013, Sekiguchi et al. 2014a) in the G-SITENNO suite. The automated data processing was performed on a cluster system composed of 960 Intel Xeon(R) CPU X5690 (3.47 GHz/core) cores at SACLA.

Reconstruction of electron density maps Further PR calculations for each selected diffraction pattern were executed on a FX10 supercomputer composed of 6144 Fujitsu SPARC64TM IXfx CPU (1.848GHz / core) cores at SACLA. To estimate the support area, we conducted 1800 independent PR calculations using the HIO algorithm r for the diffraction pattern up to S =17.5 μm-1 (corresponding to a

resolution of 57 nm). Through a multivariate analysis for the 1800

39


patterns, and merges the patterns from the two detectors. For

electron density maps, we determined a support shape of the chloroplast through averaging a selected set of maps displaying good scores of the γ (Miao et al. 2003b) and RF (Miao et al. 2006). Next, we performed 1000

algorithm (Rodriguez et al. 2013) for the determined support at a resolution of 57 nm. Again, through the multivariate analysis for the 1000 OSS-retrieved electron density maps, we selected a set of hundreds of maps (Table 1). Final PR calculations were carried out by using the OSS algorithm starting from the selected maps in the previous step. Here the resolution of the diffraction pattern was extended to 28.5 nm. Through the multivariate analyses for the OSS-retrieved electron density maps, we obtained a set of electron density maps with good scores of the γ and

RF (Table 1). Then, we obtained a final electron density map through averaging the maps in the selected set. The effective resolution of the final map (Figs. 4C-D) was estimated by using the phase-retrieval transfer function (PRTF) (Chapman et al. 2006a) applied to the set of the maps (Table 1). It should be noted that the effective resolution estimated

40


independent PR calculations using the oversampling smoothness (OSS)

by the PRTF is lower than the resolution of the diffraction pattern used for the PR calculations, due to the small fluctuations among the set of retrieved electron density maps.

utilization of multivariate analysis, used in the present study will be reported elsewhere in near future.

Fluorescence microscopy In fluorescent imaging of chloroplasts, a FV1000 confocal microscope (Olympus) was used to collect their Z-sliced fluorescent images with a step of 0.2 μm. Images were processed digitally with the ImageJ software (Schneider et al. 2012). For the observation of the autofluorescence from chlorophylls, chloroplasts in the isolation medium containing 300 mM sucrose were excited at 570 nm and acquired at 670 nm. Prior to acquiring the fluorescent images of chloroplast proteins, chloroplasts were fixed in a chilled methanol solution containing 2% (w/v) paraformaldehyde, 10% (v/v) dimethyl sulfoxide, and 1.5 mM NaOH for 5

41


The details of the structure analysis procedure, particularly the

min at 253 K. After the two steps washing with methanol, and then with a PBS solution (containing 137 mM NaCl, 2.7 mM KCl, 1 mM Na2HPO4, and 1.4 mM K2HPO4), fixed chloroplasts were stained with 1X FlamingoTM

methanol, and then with PBS, stained chloroplasts were placed on glass slides and observed. Under the irradiation by the excitation light at 485 nm, the fluorescent images were acquired at 545 nm.

Funding This study was supported by a grant for XFEL key technology and the X-ray Free Electron Laser Priority Strategy Program from the MEXT to M.N, M.Y., and S.M; Grant-in-Aid for Scientific Research on Innovative Areas [22244054 to M.N., 25120725 to M.N. and 24113723 to T.O., 26104535 to T.O., 25120726 to S.M., and 25114514 to S.M.]; Grant-in-Aid for Scientific Research (B) [26291067 To S.M.]; Grant-in-Aid for Young Scientists (B) [26800227 To T.O.]; Grant-in-Aid for Challenging Exploratory Research [24654140 To M.N.]; Grant-in-Aid for Research Activity Start-up [25891033 to Y.T.]; RIKEN Special Postdoctoral

42


fluorescent gel stain (Bio Lad). Through the two step washing with

Researchers Program to Y.T.

Acknowledgements

performed at SACLA (proposal Nos. 2013A8043, 2013B8049, and 2014A8033). The authors thank to Dr. Koji Yonekura and his laboratory members of RIKEN for their advice for the specimen preparation.

43


We collected diffraction data in cryogenic XFEL-CXDI experiments

References Bamme, B. E., Jakana, J., Schmid, M. F. and Chiu, W. (2010) Radiation damage effects at four specimen temperatures from 4 to 100 K. J.

Blundel, T. L., and Johnson, L. N. (1976) Protein Crystallography. pp 107-150. Academic Press, London. Chakravarti, B., Fathy, P., Sindicich, M., Mallik, B. and Chakravarti, D.N. (2010) Comparison of SYPRO Ruby and Flamingo fluorescent stains for application in proteomic research. Anal. Biochem. 398:1-6. Chapman, H. N., Barty, A., Marchesini, S., Noy, A., Hau-Riege, S. P., Cui, C. et al. (2006a) High-resolution ab initio three-dimensional x-ray diffraction microscopy. J. Opt. Soc. Am. A 23: 1179-1200. Chapman, H. N., Barty, A., Bogan, M. J., Boutet, S., Frank, M., Hau-Riege, S. P. et al. (2006b) Femtosecond diffractive imaging with a soft-X-ray free-electron laser. Nature Phys. 2: 839-843. Chen, C.-C., Miao, J., Wang, C. W. and Lee, T. K. (2007) Application of optimization

technique

to

noncrystalline

x-ray

diffraction

microscopy: Guided hybrid input-output method. Phys. Rev. B 76:

44


Struct. Biol. 169: 331-341.

064113. Dubochet, J., Chang, J.-J., Freeman, R., Lepault, J., and McDowell, A.W. (1982) Frozen aqueous suspensions. Ultramicroscopy 10: 55-61.

A.W. et al. (1988) Cryo-electron microscopy of vitrified specimens. Quart. Rev. Biophys. 21: 129-228. Elser, V. (2003) Phase retrieval by iterated projections. J. Opt. Soc. Am. A 20: 40-55. Fienup, J. R. (1982) Phase retrieval algorithms: a comparison. Appl. Opt. 21: 2758-2769. French C.S. (1971) The distribution and action in photosynthesis of several

forms

of

chlorophyll.

Proc.

Natl.

Acad.

Sci.

USA

68:2893-2897. Fujiwara T, Kuroiwa H, Yagisawa F, Ohnuma M, Yoshida Y, Yoshida M et al. (2010) The coiled-coil protein VIG1 is essential for tethering vacuoles

to

mitochondria

during

vacuole

inheritance

of

Cyanidioschyzon merolae. The Plant Cell 22: 772–781. Gan, L. and Jensen, G. J. (2011) Electron tomography of cells. Q. Rev.

45


Dubochet, J., Adrian, M., Chang, J.-J., Momo, J.-C., Lepault, J., McDowell,

Biophys. 45: 27-56. Giepmans, B. N. G., Adams, S. R., Ellisman, M. H. and Tsien, R. Y. (2006) The fluorescent toolbox for assessing protein location and function.

Gray, M. W. and Archibald, J. M. (2012) Origins of mitochondria and plastids. In Genomics of Chloroplasts and Mitochondria. Edited by Bock, R. and Knoop, V. pp.1-30. Springer, Dordrecht. Heuser, J. E. (2011) The origins and evolution of freeze-etch electron microscopy. J. Electron Microsc. 60: S3-S29. Hirata, K., Shinzawa-Itoh, K., Yano, N., Takemura, S., Kato, K., Hatanaka, M. et al. (2014) Determination of damage-free crystal structure of an X-ray sensitive protein using an XFEL. Nat. Methods 11: 734-736. Howells, M. R., Beetz, T., Chapman, H. N., Cui, C., Holton, J. M., Jacobsen, C. J. et al. (2009) An assessment of the resolution limitation due to radiation-damage

in

X-ray

diffraction

microscopy.

J.

Elect.

Spectrosc. Relat. Phenom. 170: 4-12. Huang, X., Nelson, J., Kirz, J., Lima, E., Marchesini, S., Miao, H. et al.

46


Science 312: 217-224.

(2009) Soft x-ray diffraction microscopy of a frozen hydrated yeast cell. Phys. Rev. Lett. 103: 198101. Imoto, Y., Yoshida, Y., Yagisawa, F., Kuroiwa, H. and Kuroiwa, T. (2011)

cycles, as revealed by cytological observations. J. Electron Microsc. 60: S117-S136. Jiang, H., Song, C., Chen, C.-C., Xu, R., Raines, K. S., Fahimian, B. P. et al. (2010) Quantitative 3D imaging of whole, unstained cells by using X-ray diffraction microscopy. Proc. Natl. Acad. Sci. USA 107: 11234-11239. Kameshima,T., Ono, S., Kudo, T., Ozaki, K., Kirihara, Y., Kobayashi, K. et al. (2014) Development of an X-ray pixel detector with multi-port charge-coupled device for X-ray free-electron laser experiments. Rev. Sci. Instrum. 85: 033110. Kimura, T., Joti, Y., Shibuya, A., Song, C., Kim, S., Tono, K. et al. (2014) Imaging live cell in micro-liquid enclosure by X-ray laser diffraction. Nat. Commun. 5: 3052. Kobayashi, A., Sekiguchi, Y., Takayama, Y., Oroguchi T. and Nakasako, M.

47


The cell cycle, including the mitotic cycle and organelle division

(2014) Dark-field phase retrieval under the constraint of the Friedel symmetry in coherent X-ray diffraction imaging. Opt. Express 22: 27892–27909.

three-dimensional image reconstruction method in the structural analysis of noncrystalline biological macromolecules enveloped by water in coherent x-ray diffraction microscopy. Phys. Rev. E 84: 021902. Kouranov, A. and Schnell, D. J. (1996) Protein translocation at the envelope and thylakoid membranes of chloroplasts. J. Biol. Chem. 271: 31009-31012. Lima, E., Wiegart, L., Pernot, P., Howells, M., Timmins, J., Zontone, F. et al. (2009) Cryogenic x-ray diffraction microscopy for biological samples. Phys. Rev. Lett. 103: 198102. Luke, D. R. (2005) Relaxed averaged alternating reflections for diffraction imaging. Inverse Probl. 21: 37-50. Marchesini, S., He, H., Chapman, H. N., Hau-Riege, S. P., Noy, A., Howells, M. R. et al. (2003) X-ray image reconstruction from a diffraction

48


Kodama, W. and Nakasako, M. (2011) Application of a real-space

pattern alone. Phys. Rev. B 68: 140101. Martin, A. V., Wang, F., Loh, N. D., Ekeberg, T., Maia, F. R. N. C., Hantke, M. et al. (2012a) Noise-robust coherent diffractive imaging with a

Martin, A. V., Loh, N. D., Hapmton, C. Y., Sierra, R. G., Wang, F., Aquila, A. et al. (2012b) Femtosecond dark-field imaging with an X-ray free electron laser. Opt. Express 20: 13501-13512. McDermott, G., Le Gros, M. A., Knoechel, C. G., Uchida, M. and Larabell C. A. (2009) Soft X-ray tomography and cryogenic light microscopy: the cool combination in cellular imaging. Trends Cell Biol. 19: 587-595. van de Meene, A. M. L., Hohmann-Marriott, M. F., Vermaas, W. F. J. and Roberson, R. W. (2006) The three-dimensional structure of the cyanobacterium Synechocystis sp. PCC 6803. Arch. Microbiol. 184: 259-270. Miao, J. Sayre, D. and Chapman, H. N. (1998) Phase retrieval from the magnitude of the Fourier transforms of nonperiodic objects. J. Opt. Soc. Am. A 15: 1662-1669.

49


single diffraction pattern. Opt. Express 20: 16650-16661.

Miao, J., Charalambous, P., Kirz, J. and Sayre, D. (1999) Extending the methodology of X-ray crystallography to allow imaging of micrometre-sized

non-crystalline

specimens.

Nature

400:

Miao, J., Hodgson, K. O., Ishikawa, T., Larabell, C. A., LeGros, M. A. and Nishino, Y. (2003a) Imaging whole Escherichia coli bacteria by using single-particle x-ray diffraction. Proc. Natl. Acad. Sci. USA 100: 110-112. Miao, J., Ishikawa, T., Anderson, E. H. and Hodgson ,K. O. (2003b) Phase retrieval of diffraction patterns from noncrystalline samples using the oversampling method. Phys. Rev. B 67: 174104. Miao, J., Chen, C.-C., Song, C., Nishino, Y., Kohmura, Y. Ishikawa, T. et al. (2006) Three-dimensional GaN-Ga2O3 core shell structure revealed by x-ray diffraction microscopy. Phys. Rev. Lett. 97: 215503. Miao, J., Ishikawa, T., Shen, Q. and Earnest, T. (2008) Extending X-ray crystallography to allow the imaging of nanocrystalline materials, cells, and single protein complexes. Annu. Rev. Phys. Chem. 59: 387-410.

50


342-344.

Miao, J., Sandberg, R. L. and Song, C. (2012) Coherent X-ray diffraction imaging. IEEE J. Sel. Top. Quant. Electron 18: 399-410. Miyagishima S, Itoh R, Aita S, Kuroiwa H and Kuroiwa T. (1999) Isolation

synchronous culture of the unicellular red alga Cyanidioschyzon merolae. Planta 209: 371-375. Miyawaki, A. (2013) Fluorescence imaging in the last two decades. Microscopy 62: 63-68. Nakasako, M., Takayama, Y., Oroguchi, T., Sekiguchi, Y., Kobayashi, A., Shirahama, K. et al. (2013) KOTOBUKI-1 apparatus for cryogenic coherent X-ray diffraction imaging. Rev. Sci. Instrum. 84: 093705. Neutze, R., Wouts, R., van der Spoel, D., Weckert, E. and Hajdu, J. (2000) Potential for biomolecular imaging with femtosecond X-ray pulses. Nature 406: 752-757. Nishino, Y., Takahashi, Y., Imamoto, N., Ishikawa, T. and Maeshima, K. (2009) Three-dimensional visualization of a human chromosome using coherent x-ray diffraction. Phys. Rev. Lett. 102: 018101. Oroguchi, T. and Nakasako, M. (2013) Three-dimensional structure

51


of dividing chloroplasts with intact plastid-dividing rings from a

determination protocol for noncrystalline biomolecules using x-ray free-electron laser diffraction imaging. Phys. Rev. E 87: 022712. Ravelli, R. B. G. and Garman, E. F. (2006) Radiation damage in

624-629. Rodenburg, J. M., Hurst, A. C., Cullis, A. G., Dobson, B. R., Pfeiffer, F., Bunk, O., David, C., Jefimovs, K. and Johnson, I. (2007) Hard X-ray lensless imaging of extended objects. Phys. Rev. Lett. 98: 034801 Rodriguez, J., Xu, R., Chen, C.-C., Zou, Y., and Miao, J. (2013) Oversampling smoothness: an effective algorithm for phase retrieval of noisy diffraction intensities. J. Appl. Cryst. 46: 312-318. Schneider, C. A., Rasband, W. S. and Eliceiri, K. W. (2012) NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9: 671-675. Seibert, M. M., Ekeberg, T., Maia, F. R. N. C., Svenda, M., Andreasson, J., Jönsson, O. et al. (2011) Single mimivirus particles intercepted and imaged with an X-ray laser. Nature 470: 78-81. Sekiguchi, Y, Yamamoto, M., Oroguchi, T., Takayama, Y., Suzuki, S. and Nakasako, M. (2014a) IDATEN and G-SITENNO: GUI assisted

52


macromolecular cryocrystallography. Curr. Opin. Struct. Biol. 16:

software for coherent X-ray diffraction imaging experiments and data analyses at SACLA. J. Synchrotron Rad. 21: 1378-1383. Sekiguchi, Y., Oroguchi, T., Takayama, Y. and Nakasako, M. (2014b) Data

imaging using the X-ray free-electron laser SACLA. J. Synchrotron Rad. 21: 600-612. Sengupta, P., Van Engelenburg S. and Lippincott-Schwartz J. (2012) Visualizing cell structure and function with point-localization superresolution imaging. Dev. Cell 23:1092-1102. Shimoni, E., Rav-Hon, O., Ohad, I., Brumfeld, V. and Reich, Z. (2005) Three-dimensional

organization

of

higher-plant

chloroplast

thylakoid membranes revealed by electron tomography. Plant Cell 17: 2580-2586. Song, C., Jiang, H., Mancuso, A., Amirbekian, B., Peng, L., Sun, R. et al. (2008) Quantitative imaging of single, unstained viruses with coherent X rays. Phys. Rev. Lett. 101: 158101. Stuhrmann, H. B. and Miller, A. (1978) Small-angle scattering of biological structures. J. Appl. Cryst. 11: 325-345.

53


processing software suite SITENNO for coherent X-ray diffraction

Su, H.-N., Xie, B.-B., Zhang, X.-Y., Zhou, B.-C. and Zhang, Y.-Z. (2010) The supramolecular architecture, function, and regulation of thylakoid membranes in red algae: an overview. Photosynth. Res.

Suetsugu, N. and Wada, M. (2007) Chloroplast photorelocation movement mediated by phototropin family proteins in green plants. Biol. Chem. 388: 927-935. Takahashi, Y., Suzuki, A., Zettsu, N., Oroguchi, T., Takayama, Y., Sekiguchi, Y.

et

al.

(2013)

shape-controlled

Coherent

diffraction

nanoparticles

with

imaging focused

analysis hard

of

X-ray

free-electron laser pulses. Nano Lett. 13: 6028–6032. Takayama, Y. and Nakasako, M. (2012) Humidity-controlled preparation of frozen-hydrated biological samples for cryogenic coherent x-ray diffraction microscopy. Rev. Sci. Instrum. 83: 054301. Toda K, Takano H, Miyagishima S, Kuroiwa H and Kuroiwa T. (1998) Characterization of a chloroplast isoform of serine acetyltransferase from the thermo-acidiphilic red alga Cyanidioschyzone merolae. Biochim. Biophys. Acta 1403: 72–84.

54


106: 73-87.

Tono, K., Inubushi, Y., Sato, T., Togashi, T., Ohashi, H., Kimura, H. et al. (2013) Beamline for X-ray free electron laser of SACLA. J. Phys.: Conf. Ser. 425: 072006.

(2014) Single-shot three-dimensional structure determination of nanocrystals with femtosecond X-ray free electron laser pulses. Nat. Commun. 5: 4061. Yagisawa, F., Nishida, K., Yoshida, M., Ohnuma, M., Shimada, T., Fujiwara, T. et al. (2009) Identification of novel proteins in isolated polyphosphate vacuoles in the primitive red alga Cyanidioschyzon merolae. Plant J. 60: 882-893. Yoshida, Y., Kuroiwa, H., Misumi, O., Yoshida, M., Ohnuma, M., Fujiwara, T. et al. (2010) Chloroplasts divide by contraction of a bundle of nanofilaments consisting of polyglucan. Science 329: 949-953. Yumoto, H., Mimura, H., Koyama, T., Kimura, T., Matsuyama, S., Tono, K. et al. (2013) Focusing of X-ray free-electron laser pulses with reflective optics. Nat. Photon. 7: 43-47.

55


Xu, R., Jiang, H., Song, C., Rodriguez, J. A., Huang, Z., Chen, C.-C., et al.

Table 1 Statistics of diffraction patterns and PR calculations Diffraction pattern Csym

a

Fig. 4A

of diffraction pattern

Fig. 4B

0.82

0.77

1800

1800

204

363

29

18

0.262

0.168

0.035

0.012

1000

1000

154

212

0.199

0.201

0.038

0.060

154

212

47

125

0.226

0.225

0.038

0.060

76.1

67.6

HIO calculations for determining the support at 57.1 nm Number

of

selected

HIO-retrieved

maps

for

determining the support OS ratio

b c

Average R F for the selected maps Average

γ

d

for the selected maps

OSS calculations at 57. 1 nm Number of OSS calculations with the determined support Number of selected OSS-retrieved maps with good scores Average R F c for the selected maps Average

γ

d


Final OSS calculations at 28.5 nm Number of OSS calculations starting from the OSS-retrieved maps at 57.1 nm Number of selected OSS-retrieved maps with good scores Averaged RF Averaged

c


γ d for the selected maps

Effective resolution for the averaged map estimated with the PRTF a

e

(nm)

The Friedel symmetry of a diffraction pattern was evaluated using the

following correlation function: C sym = (E − O ) (E + O ) ,

[

]

E = ∑ I 0 ( x, y ) + I sym (− x, − y ) , 2

x, y

[

x, y

56

]

O = ∑ I 0 ( x, y ) − I sym (− x,− y )

2


Number of HIO calculations

where I 0 (x, y ) is the diffraction intensity in the region of interest (ROI) with 100 × 100 pixels and

I sym (− x,− y ) is the diffraction intensity of the

Friedel mate. For a diffraction pattern with ideal Friedel symmetry, the C sym value is 1. b

The OS ratio of the density model is defined as the ratio between the

number of pixels in a determined support and the number of pixels in the c

RF is defined as RF = Σ Fobs − K Fcalc / Σ Fobs , where Fcalc and Fobs

represent the structure amplitude calculated from the reconstructed electron density and observed in experiments, respectively. K is a scale factor

between

the

reconstructed

amplitudes(Miao et al. 2006). d

γ

is defined as γ =

and

r

r

∑ ρ (r ) /[(σ − 1) ∑ ρ (r )] ,

r r ∉support

r r∈support

observed

structure

r

where ρ (r ) and σ

are the electron density and OS ratio, respectively. This parameter represents the ratio of the total densities inside and outside the support (Miao et al. 2003b). e

The effective resolution of the averaged electron density map is

determined as the resolution where the PRTF value is 0.5 (Chapman et al. 2006a). PRTF is calculated with the selected electron density maps, which displayed good R F and

γ

scores.

57


diffraction patterns.

Figure legend Figure 1 (A) A schematic illustration of CXDI experiment. (B) The image

PR algorithm. The details of the procedure are described in the Theoretical background section.

Figure 2 (A) A schematic illustration of specimen preparation procedure performed for the cryogenic XFEL-CXDI experiments under a controlled RH. (B) A microscopic image of chloroplasts dispersed on a carbon membrane just before flash-cooling. The photograph is taken under a safety green light. (C) A schematic illustration of our XFEL-CXDI experiments using the KOTOBUKI-1 diffraction apparatus and the two MPCCD detectors. (D) A photograph of the KOTOBUKI-1 apparatus and the two MPCCD detectors working at the experimental hutch 3 in the BL3 of SACLA on July 2014. (E) The left panel schematically illustrates the scan procedure for a specimen disk. In our XFEL-CXDI experiments, XFEL pulses were

58


reconstruction procedure from a diffraction pattern by using the iterative

provided at a repetition rate of 1 Hz. Between the pulses, a specimen disk was scanned at a speed of 25-50 μm/s. The right panel is a scanning electron microscopy image of the membrane of a specimen disk dried

(peak intensity of 1010-11 X-ray photons of 5.5 keV / (2×2 μm2) / pulse at FWHM) in one scan run. The diameter of the hole ranges approximately from 6 μm to 8 μm, depending on the beam intensity, which fluctuates pulse by pulse. Because X-ray intensity of 1010-11 X-ray photons of 5.5 keV / (2 × 2 μ m2) / pulse is enough to destroy chloroplasts and membrane, the hole is about 3 to 4 times larger than the FWHM of X-ray beam. The small particles indicated by an arrow are dried chloroplasts. The scale bar is 20 μm.

Figure 3 Diffraction patterns and a set of statistics of diffraction data obtained in scans for different specimen disks. The central aperture of the MPCCD-Octal detector was changed among scans. (A) A typical diffraction pattern of a chloroplast, the center of which nicely coincided with the peak

59


after XFEL exposure. The holes are regions destroyed by X-ray pulses

position of X-ray pulse. The resolution of the diffraction pattern is simply calculated as the inversed value of the scattering vector length. For instance, a scattering vector length of 25 μm-1 corresponds to a resolution

intensity because of the saturation of detector pixels. In panels (A), (D) and (E), the thin black lines along the vertical and horizontal directions are gaps between detector panels. (B) Frequency distribution of the total diffraction intensity summed up to a resolution of 35 μm-1 for approximately 900 diffraction patterns collected during 8 sets of 25-μm step scans, each of which covered 300×300 μm2. The black and red lines are the frequency distributions for hit and miss-hit patterns, respectively. (C) Frequency distribution of maximum resolution defined as the edge, where the signal-to-noise ratios in hit patterns are better than 2. (D, E) Typical diffraction patterns from aggregations of chloroplasts. The approximate speckle sizes are 2×2 ~ 3×3 pixels.

Figure 4

60


of 40 nm. The small-angle region of the pattern misses the diffraction

(A, B) Two representative diffraction patterns with the approximate speckle sizes of larger than 5×5 pixels obtained in scans for different specimen disks. The central aperture of the MPCCD-Octal detector was

in scans for different specimen disks. The signal-to-noise ratios of the r diffraction patterns are better than 2 in a resolution range of S =35 μm-1.

The white allows in panel (A) indicate the concentric diffraction patterns. The diffraction pattern of panel (A) missed slightly the small-angle region due to the saturation of detector pixels and the beam stop. The square at the center in the diffraction pattern of panel (B) is the shadow of the beam stop. Their electron density maps in panels (C) and (D) are retrieved at effective resolutions of 70 nm through the multivariate analysis from the diffraction patterns (A) and (B), respectively. The scale bar is 500 nm. The electron density decreases in the order of white >red > orange > yellow > green > blue > black. The statistics of the reconstruction are summarized in Table 1. The details of reconstruction procedure are described in the Materials and Methods section. The inset in panel (D) schematically illustrates the distribution of electron densities (designated as α and β).

61


set at different size between the scans. Diffraction patterns were recorded

Figure 5 (A) A phase contrast optical microscopic image of isolated chloroplasts

visualizing the autofluorescence of chlorophylls (B) and the distribution of proteins stained by FlaminogoTM dye (C) in a chloroplast. The optical sections in every 0.2-μm step are shown from the lower end (label ‘0’) to an equatorial plane (label ‘5’) of the chloroplast. The fluorescence intensity decreases in the order of white > yellow > orange > red > purple > blue > black. The image at the equatorial plane (‘5’) shows the low density of proteins around the center of chloroplasts.

Figure 6 A schematic illustration of structural model for chloroplast. The green colored sheets represent thylakoid membranes. Panels (A-C) display views along the planes of the thylakoid membranes, in an inclined orientation, and from a side of the thylakoid membrane, respectively. As discussed, the model in panel (A) is likely corresponds to the electron

62


taken under a safety green light. A set of serial Z-slice confocal images

density map of Fig. 4C and the fluorescence microscopic images of Fig. 5B-C. The side view of panel (C) likely corresponds to the electron density map of Fig. 4D.


63


76x162mm (300 x 300 DPI)


78x218mm (300 x 300 DPI)


157x207mm (300 x 300 DPI)


155x206mm (300 x 300 DPI)


75x223mm (300 x 300 DPI)


137x75mm (300 x 300 DPI)

Single-pulse enhanced coherent diffraction imaging of bacteria with an X-ray free-electron laser.

Multipurpose end-station for coherent diffraction imaging and scattering at FERMI@Elettra free-electron laser facility.

Macromolecular structures probed by combining single-shot free-electron laser diffraction with synchrotron coherent X-ray imaging.

Coherent diffraction imaging analysis of shape-controlled nanoparticles with focused hard X-ray free-electron laser pulses.

Specimen preparation for cryogenic coherent X-ray diffraction imaging of biological cells and cellular organelles by using the X-ray free-electron laser at SACLA.

Destruction-and-diffraction by X-ray free-electron laser.

Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser.

Photoelectron diffraction from laser-aligned molecules with X-ray free-electron laser pulses.

Imaging an aligned polyatomic molecule with laser-induced electron diffraction.

Laser-assisted electron diffraction for femtosecond molecular imaging.

Diffraction data of core-shell nanoparticles from an X-ray free electron laser.

Protein structure determination by single-wavelength anomalous diffraction phasing of X-ray free-electron laser data.

Coherent imaging at the diffraction limit. Erratum.

Microfluidic sorting of protein nanocrystals by size for X-ray free-electron laser diffraction.

Focus characterization at an X-ray free-electron laser by coherent scattering and speckle analysis.

Coherent imaging at the diffraction limit.

Transverse Coherence Limited Coherent Diffraction Imaging using a Molybdenum Soft X-ray Laser Pumped at Moderate Pump Energies.

Assessing Lower Limb Alignment: Comparison of Standard Knee Xray vs Long Leg View.

[Butterfly wing appearance on Xray does not always mean acute pulmonary edema: think of bronchial adenocarcinoma].

Coherent total internal reflection dark-field microscopy: label-free imaging beyond the diffraction limit.

Identification of centromere regions in chromosomes of a unicellular red alga, Cyanidioschyzon merolae.

Infrared matrix-assisted laser desorption and ionization by using a tunable mid-infrared free-electron laser.

X-ray laser-induced electron dynamics observed by femtosecond diffraction from nanocrystals of Buckminsterfullerene.

Transformation of the Cyanidioschyzon merolae chloroplast genome: prospects for understanding chloroplast function in extreme environments.