Characterization of the pits in parenchyma cells of the moso bamboo [Phyllostachys edulis (Carr.) J. Houz.] culm

AbstractPits are the main transverse channels of intercellular liquid transport in bamboo. Ramiform pits are a special type of simple pit with two or more branches. However, little is known about the morphology and physiological functions of ramiform pits. The anatomy of plants can provide important evidence for the role of cells. To better understand the ultrastructure and the structure-function relationship of ramiform pits, their characteristics need to be investigated. In this study, both qualitative and quantitative features of ramiform pits were studied using field-emission environmental scanning electron microscopy (FE-ESEM). The samples included the native structures and the replica structures obtained by resin castings. The results show that the ramiform pits have a diverse morphology that can be divided into main categories: type I (the primary branches) and type II (the secondary branches). The distribution of ramiform pits is different in ground parenchyma cells (GPCs) and vascular parenchyma cells (VPCs). The number, the pit aperture diameter and the pit canal length of ramiform pits in the VPCs were, respectively, greater (3-fold), larger (2–3-fold) and shorter (1.3-fold) than those in the GPCs.

Download Full-text

Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling

10.7287/peerj.preprints.2397v2 ◽

2017 ◽

Author(s):

Steven R Ahrendt ◽

Edgar Mauricio Medina ◽

Chia-en A Chang ◽

Jason E Stajich

Keyword(s):

Molecular Modeling ◽

Structural Characteristics ◽

Sequence Similarity ◽

Ligand Docking ◽

Binding Properties ◽

Function Relationship ◽

Relationship Of ◽

Future Work

Background. Opsin proteins are seven transmembrane receptor proteins which detect light. Opsins can be classified into two types and share little sequence identity: type 1, typically found in bacteria, and type 2, primarily characterized in metazoa. The type 2 opsins (Rhodopsins) are a subfamily of G-protein coupled receptors (GPCRs), a large and diverse class of seven transmembrane proteins and are generally restricted to metazoan lineages. Fungi use light receptors including opsins to sense the environment and transduce signals for developmental or metabolic changes. Opsins characterized in the Dikarya (Ascomycetes and Basidiomycetes) are of the type 1 bacteriorhodopsin family but the early diverging fungal lineages have not been as well surveyed. We identified by sequence similarity a rhodopsin-like GPCR in genomes of early diverging chytrids and examined the structural characteristics of this protein to assess its likelihood to be homologous to animal rhodopsins and bind similar chromophores. Methods. We used template-based structure modeling, automated ligand docking, and molecular modeling to assess the structural and binding properties of an identified opsin-like protein found in Spizellomyces punctatus, a unicellular, flagellated species belonging to Chytridiomycota, one of the earliest diverging fungal lineages. We tested if sequence and inferred structure were consistent with a solved crystal structure of a type 2 rhodopsin from the squid Todarodes pacificus. Results. Our results indicate that the Spizellomyces opsin has structural characteristics consistent with functional animal type 2 rhodopsins and is capable of maintaining a stable structure when associated with the retinaldehyde chromophore, specifically the 9-cis-retinal isomer. Together, these results support further the homology of Spizellomyces opsins to animal type 2 rhodopsins. Discussion. This represents the first test of structure/function relationship of a type 2 rhodopsin identified in early branching fungal lineages, and provides a foundation for future work exploring pathways and components of photoreception in early fungi.

Download Full-text

Investigation of Action Pattern of a Novel Chondroitin Sulfate/Dermatan Sulfate 4-O-Endosulfatase

Biochemical Journal ◽

10.1042/bcj20200657 ◽

2020 ◽

Author(s):

Wenshuang Wang ◽

Cédric Przybylski ◽

Xiaojuan Cai ◽

Chrystel Lopin-Bon ◽

Runmiao Jiao ◽

...

Keyword(s):

Chondroitin Sulfate ◽

Marine Bacterium ◽

Catalytic Mechanism ◽

Dermatan Sulfate ◽

Structural Characteristics ◽

Action Pattern ◽

Substrate Specificities ◽

Substrate Size ◽

Function Relationship ◽

Relationship Of

Recently, a novel CS/DS 4-O-endosulfatase was identified from a marine bacterium and its catalytic mechanism was investigated further (Wang, W., et.al (2015) J. Biol. Chem. 290, 7823-7832; Wang, S., et.al (2019) Front. Microbiol. 10:1309). In the study herein, we provide new insight about the structural characteristics of substrate which determine the activity of this enzyme. The substrate specificities of the 4-O-endosulfatase were probed by using libraries of structure-defined CS/DS oligosacccharides issued from synthetic and enzymatic sources. We found that this 4-O-endosulfatase effectively remove the 4-O-sulfate of disaccharide sequences GlcUAβ1-3GalNAc(4S) or GlcUAβ1-3GalNAc(4S,6S) in all tested hexasaccharides. The sulfated GalNac residue is resistant to the enzyme when adjacent uronic residues are sulfated as shown by the lack of enzymatic desulfation of GlcUAβ1-3GalNAc(4S) connected to a disaccharide GlcUA(2S)β1-3GalNAc(6S) in an octasaccharide. The 3-O-sulfation of GlcUA was also shown to hinder the action of this enzyme. The 4-O-endosulfatase exhibited an oriented action from the reducing to the non-reducing whatever the saturation or not of the non-reducing end. Finally, the activity of the 4-O-endosulfatase decreases with the increase of substrate size. With the deeper understanding of this novel 4-O-endosulfatase, such chondroitin sulfate (CS)/dermatan sulfate (DS) sulfatase is a useful tool for exploring the structure-function relationship of CS/DS.

Download Full-text

Exploring the binding properties and structural stability of an opsin in the chytridSpizellomyces punctatususing comparative and molecular modeling

PeerJ ◽

10.7717/peerj.3206 ◽

2017 ◽

Vol 5 ◽

pp. e3206 ◽

Cited By ~ 5

Author(s):

Steven R. Ahrendt ◽

Edgar Mauricio Medina ◽

Chia-en A. Chang ◽

Jason E. Stajich

Keyword(s):

Molecular Modeling ◽

Structural Characteristics ◽

Sequence Similarity ◽

Ligand Docking ◽

Binding Properties ◽

Function Relationship ◽

Relationship Of ◽

Future Work

BackgroundOpsin proteins are seven transmembrane receptor proteins which detect light. Opsins can be classified into two types and share little sequence identity: type 1, typically found in bacteria, and type 2, primarily characterized in metazoa. The type 2 opsins (Rhodopsins) are a subfamily of G-protein coupled receptors (GPCRs), a large and diverse class of seven transmembrane proteins and are generally restricted to metazoan lineages. Fungi use light receptors including opsins to sense the environment and transduce signals for developmental or metabolic changes. Opsins characterized in the Dikarya (Ascomycetes and Basidiomycetes) are of the type 1 bacteriorhodopsin family but the early diverging fungal lineages have not been as well surveyed. We identified by sequence similarity a rhodopsin-like GPCR in genomes of early diverging chytrids and examined the structural characteristics of this protein to assess its likelihood to be homologous to animal rhodopsins and bind similar chromophores.MethodsWe used template-based structure modeling, automated ligand docking, and molecular modeling to assess the structural and binding properties of an identified opsin-like protein found inSpizellomyces punctatus, a unicellular, flagellated species belonging to Chytridiomycota, one of the earliest diverging fungal lineages. We tested if the sequence and inferred structure were consistent with a solved crystal structure of a type 2 rhodopsin from the squidTodarodes pacificus.ResultsOur results indicate that theSpizellomycesopsin has structural characteristics consistent with functional animal type 2 rhodopsins and is capable of maintaining a stable structure when associated with the retinaldehyde chromophore, specifically the 9-cis-retinal isomer. Together, these results support further the homology ofSpizellomycesopsins to animal type 2 rhodopsins.DiscussionThis represents the first test of structure/function relationship of a type 2 rhodopsin identified in early branching fungal lineages, and provides a foundation for future work exploring pathways and components of photoreception in early fungi.

Download Full-text

Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling

10.7287/peerj.preprints.2397v1 ◽

2016 ◽

Author(s):

Steven R Ahrendt ◽

Edgar Mauricio Medina ◽

Chia-en A Chang ◽

Jason E Stajich

Keyword(s):

Molecular Modeling ◽

Structural Characteristics ◽

Sequence Similarity ◽

Ligand Docking ◽

Binding Properties ◽

Function Relationship ◽

Relationship Of ◽

Future Work

Background. Opsin proteins are seven transmembrane receptor proteins which detect light. Opsins can be classified into two types and share little sequence identity: type 1, typically found in bacteria, and type 2, primarily characterized in metazoa. The type 2 opsins (Rhodopsins) are a subfamily of G-protein coupled receptors (GPCRs), a large and diverse class of seven transmembrane proteins and are generally restricted to metazoan lineages. Fungi use light receptors including opsins to sense the environment and transduce signals for developmental or metabolic changes. Opsins characterized in the Dikarya (Ascomycetes and Basidiomycetes) are of the type 1 bacteriorhodopsin family but the early diverging fungal lineages have not been as well surveyed. We identified by sequence similarity a rhodopsin-like GPCR in genomes of early diverging chytrids and examined the structural characteristics of this protein to assess its likelihood to be homologous to animal rhodopsins and bind similar chromophores. Methods. We used template-based structure modeling, automated ligand docking, and molecular modeling to assess the structural and binding properties of an identified opsin-like protein found in Spizellomyces punctatus, a unicellular, flagellated species belonging to Chytridiomycota, one of the earliest diverging fungal lineages. We tested if sequence and inferred structure were consistent with a solved crystal structure of a type 2 rhodopsin from the squid Todarodes pacificus. Results. Our results indicate that the Spizellomyces opsin has structural characteristics consistent with functional animal type 2 rhodopsins and is capable of maintaining a stable structure when associated with the retinaldehyde chromophore, specifically the 9-cis-retinal isomer. Together, these results support further the homology of Spizellomyces opsins to animal type 2 rhodopsins. Discussion. This represents the first test of structure/function relationship of a type 2 rhodopsin identified in early branching fungal lineages, and provides a foundation for future work exploring pathways and components of photoreception in early fungi.

Download Full-text

WOOD ANATOMY OF WOLLEMI PINE (WOLLEMIA NOBILIS, ARAUCARIACEAE)

IAWA Journal ◽

10.1163/22941932-90000309 ◽

2002 ◽

Vol 23 (4) ◽

pp. 339-357 ◽

Cited By ~ 15

Author(s):

R.D. Heady ◽

J.G. Banks ◽

P.D. Evans

Keyword(s):

Wood Anatomy ◽

Juvenile Wood ◽

Growth Ring ◽

Dry Density ◽

Anatomical Features ◽

Bordered Pits ◽

Parenchyma Cells ◽

Helical Thickenings ◽

Resin Canals ◽

First Time

The wood anatomy of the recently-discovered conifer Wollemia nobilis (Wollemi pine) is described for the first time. Its mature heartwood is light brown in colour and has an air dry density of 0.57 g /cm3. Growth ring boundaries are distinct and the transition from earlywood to latewood is gradual. Average tracheid length is ~ 3.4 mm. Bordered pits are one-, two- or three-seriate and the double and triple rows of pits are ‘alternate’. In the bordered pits there is a flat transition from torus to margo. A warty layer lines tracheid walls and pit cavity surfaces. Resin plugs are common in tracheids that are adjacent to rays. Helical thickenings and crassulae are absent. Rays are uniseriate, low, and are composed entirely of parenchyma cells whose walls are thin and unpitted. Cross-field pitting is ‘araucaroid’ and the number of pits per cross-field ranges from 3–11 (av. 7). Resin canals and axial parenchyma cells are absent. The differences between normal mature wood compared to compression and juvenile wood are consistent with those of most other conifer genera. The anatomical features of wood of W. nobilis strongly support its classification as a member of the Araucariaceae, but show no major differences that distinguish it as a monotypic genus. On the basis of its wood anatomy, it is not possible to state whether W. nobilis is more closely related to Agathis or to Araucaria.

Download Full-text

Characterization of ground parenchyma cells in Moso bamboo (Phyllostachys edulis–Poaceae)

IAWA Journal ◽

10.1163/22941932-bja10076 ◽

2021 ◽

pp. 1-9

Author(s):

Caiping Lian ◽

Hong Chen ◽

Shuqin Zhang ◽

Rong Liu ◽

Zhihui Wu ◽

...

Keyword(s):

Three Dimensional ◽

Environmental Scanning Electron Microscopy ◽

Moso Bamboo ◽

Dimensional Structure ◽

Environmental Scanning ◽

Wall Thickening ◽

Phyllostachys Edulis ◽

Starch Grains ◽

Parenchyma Cells ◽

Quantitative Basis

Abstract Ground parenchyma cells play a crucial role in the growth and the mechanical properties of bamboo plants. Investigation of the morphology of ground parenchyma cells is essential for understanding the physiological functions andmechanical properties of these cells. This study aimed to characterize the anatomical structure of bamboo ground parenchyma cells and provide a qualitative and quantitative basis for the more effective utilization of bamboo. To do this, the morphology of ground parenchyma cells in Moso bamboo (Phyllostachys edulis) was studied using light microscopy and field-emission environmental scanning electron microscopy. Results show that various geometric shapes of ground parenchyma cells were observed, including nearly circular, square, long, oval, and irregular shapes. Cell walls of both long and short parenchyma cells exhibited primary wall thickening and secondary wall thickening, resulting in a primary pit field and simple pits. Most long cells were strip-shaped (L/W = 2.52), while most short cells were short and wide (L/W = 0.59). The proportion of long cells was 11 times greater than that of short cells. Most long cells were filled with starch grains, and some short cells also occasionally had starch grains. These findings allowed the first construction of the three-dimensional structure of parenchyma cells.

Download Full-text

Wood Anatomy of Trees and Shrubs from China. IV. Ulmaceae

IAWA Journal ◽

10.1163/22941932-90001299 ◽

1992 ◽

Vol 13 (4) ◽

pp. 419-453 ◽

Cited By ~ 15

Author(s):

Y. Zhong ◽

P. Baas ◽

E.A. Wheeler

Keyword(s):

Wood Anatomy ◽

Axial Parenchyma ◽

Bordered Pits ◽

Vessel Elements ◽

Parenchyma Cells ◽

First Time ◽

Trees And Shrubs

The wood anatomy of 37 species belonging to the eight genera of Ulmaceae native to China is described. The wood of Chinese Ulmaceae is characterised by mostly simple perforations (sporadic scalariform plates occur in Hemiptelea and Zelkova); altemate, non-vestured intervessel pits; relatively short vessel elements and fibres; non septate fibres with simple to minutely bordered pits confined to the radial walls; mainly paratracheal parenchyma; rays rarely higher than 1 mm. Tanniniferous tubes are reported for the first time in Ulmaceae; they are limited to the genus Pteroceltis. Other, sporadically occurring features such as perforated ray and axial parenchyma cells and perforated fibres are also reported for the first time.

Download Full-text

Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling

10.7287/peerj.preprints.2397 ◽

2017 ◽

Author(s):

Steven R Ahrendt ◽

Edgar Mauricio Medina ◽

Chia-en A Chang ◽

Jason E Stajich

Keyword(s):

Molecular Modeling ◽

Structural Characteristics ◽

Sequence Similarity ◽

Ligand Docking ◽

Binding Properties ◽

Function Relationship ◽

Relationship Of ◽

Future Work

Background. Opsin proteins are seven transmembrane receptor proteins which detect light. Opsins can be classified into two types and share little sequence identity: type 1, typically found in bacteria, and type 2, primarily characterized in metazoa. The type 2 opsins (Rhodopsins) are a subfamily of G-protein coupled receptors (GPCRs), a large and diverse class of seven transmembrane proteins and are generally restricted to metazoan lineages. Fungi use light receptors including opsins to sense the environment and transduce signals for developmental or metabolic changes. Opsins characterized in the Dikarya (Ascomycetes and Basidiomycetes) are of the type 1 bacteriorhodopsin family but the early diverging fungal lineages have not been as well surveyed. We identified by sequence similarity a rhodopsin-like GPCR in genomes of early diverging chytrids and examined the structural characteristics of this protein to assess its likelihood to be homologous to animal rhodopsins and bind similar chromophores. Methods. We used template-based structure modeling, automated ligand docking, and molecular modeling to assess the structural and binding properties of an identified opsin-like protein found in Spizellomyces punctatus, a unicellular, flagellated species belonging to Chytridiomycota, one of the earliest diverging fungal lineages. We tested if sequence and inferred structure were consistent with a solved crystal structure of a type 2 rhodopsin from the squid Todarodes pacificus. Results. Our results indicate that the Spizellomyces opsin has structural characteristics consistent with functional animal type 2 rhodopsins and is capable of maintaining a stable structure when associated with the retinaldehyde chromophore, specifically the 9-cis-retinal isomer. Together, these results support further the homology of Spizellomyces opsins to animal type 2 rhodopsins. Discussion. This represents the first test of structure/function relationship of a type 2 rhodopsin identified in early branching fungal lineages, and provides a foundation for future work exploring pathways and components of photoreception in early fungi.

Download Full-text

Dosage compensation in Bombyx mori is achieved by partial repression of both Z chromosomes in males

10.1101/2021.07.18.452821 ◽

2021 ◽

Author(s):

Leah F. Rosin ◽

Yang Chen ◽

Elissa P Lei

Keyword(s):

Gene Expression ◽

Bombyx Mori ◽

Dosage Compensation ◽

Sex Chromosome ◽

Linked Gene ◽

C Elegans ◽

Males And Females ◽

Function Relationship ◽

Relationship Of ◽

First Time

Interphase chromatin is organized precisely to facilitate accurate gene expression. The structure-function relationship of chromatin is epitomized in sex chromosome dosage compensation (DC), where sex-linked gene expression is balanced between males and females via sex-specific alterations to 3D chromosome structure. Studies in ZW-bearing species suggest that DC is absent or incomplete in most lineages except butterflies and moths, where male (ZZ) chZ expression is reduced by half to equal females (ZW). However, whether one chZ is inactivated (as in mammals) or both are partially repressed (as in C. elegans) is unknown. Using Oligopaints in the silkworm, Bombyx mori, we visualize autosome and chZ organization in somatic cells from both sexes for the first time. We find that B. mori interphase chromosomes are highly compact relative to Drosophila chromosomes. Importantly, we show that in B. mori males, both chZs are similar in size and shape and are more compact than autosomes or the female chZ after DC establishment, suggesting that both male chZs are partially and equally downregulated. We also find that in the early stages of DC, the female chZ repositions toward the nuclear center concomitant with increased Z-linked gene expression, revealing the first non-sequencing-based support for Ohno's hypothesis. These studies represent the first visualization of interphase genome organization and chZ structure in Lepidoptera. We uncover striking similarities between DC in B. mori and C. elegans, despite these lineages harboring evolutionarily distinct sex chromosomes (ZW/XY), suggesting convergent evolution of DC mechanisms and a possible role for holocentricity in DC evolution.

Download Full-text