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Publications (87)
Formins are a large, evolutionarily old family of cytoskeletal regulators whose roles include actin capping and nucleation, as well as modulation of microtubule dynamics. The plant class I formin clade is characterized by a unique domain organization, as most of its members are transmembrane proteins with possible cell wall-binding motifs exposed t...
Proteins participating in plant cell morphogenesis are often encoded by large gene families, in some cases comprising paralogs with variable (modular) domain organization, as in the case of the formin (FH2 protein) family of actin nucleators that can have also additional functions. Unravelling the phylogeny of such a complex gene family brings a nu...
The possibility of associative learning in plants is a topic of ongoing controversy. In one published study, growing pea plants were reported to associate two stimuli (airflow and light) and thereafter use one (airflow) as an indicator for the other (light), similar to dogs in Pavlov’s famous experiments. However, this observation could not be inde...
Formins are a large, evolutionarily conserved family of actin-nucleating proteins with additional roles in regulating microfilament, microtubule, and membrane dynamics. Angiosperm formins, expressed in both sporophytic and gametophytic tissues, can be divided into two subfamilies, Class I and Class II, each often exhibiting characteristic domain or...
Spatially directed cell division and expansion is important for plant growth and morphogenesis, and relies on the cooperation between the cytoskeleton and secretory pathway. The phylogenetically conserved octameric complex exocyst mediates exocytotic vesicle tethering at the plasma membrane. Unlike other exocyst subunits of land plants, the core ex...
Pollen development, pollen grain germination, and pollen tube elongation are crucial biological processes in angiosperm plants that need precise regulation to deliver sperm cells to fertilize ovules. Highly polarized secretion at a growing pollen tube tip requires the exocyst tethering complex responsible for specific targeting of secretory vesicle...
The heterooctameric vesicle-tethering complex exocyst is important for plant development, growth, and immunity. Multiple paralogs exist for most subunits of this complex; especially the membrane-interacting subunit EXO70 underwent extensive amplification in land plants, suggesting functional specialization. Despite this specialization, most Arabido...
The ARP2/3 complex and formins are the only known plant actin nucleators. Besides their actin-related functions, both systems also modulate microtubule organization and dynamics. Loss of the main housekeeping Arabidopsis thaliana Class I membrane-targeted formin FH1 (At3g25500) is known to increase cotyledon pavement cell lobing, while mutations af...
Formins are evolutionarily conserved multi-domain proteins participating in the control of both actin and microtubule dynamics. Angiosperm formins form two evolutionarily distinct families, Class I and Class II, with class-specific domain layouts. The model plant Arabidopsis thaliana has 21 formin-encoding loci, including 10 Class II members. In th...
SH3P2 (At4g34660), an Arabidopsis thaliana SH3 and Bin/amphiphysin/Rvs (BAR) domain-containing protein, was reported to have a specific role in cell plate assembly, unlike its paralogs SH3P1 (At1g31440) and SH3P3 (At4g18060). SH3P family members were also predicted to interact with formins—evolutionarily conserved actin nucleators that participate...
Pollen development, pollen grain germination and pollen tube elongation are crucial biological processes in angiosperm plants that need precise regulation to deliver sperm cells to fertilize ovules. Pollen grains undergo two major developmental switches: dehydration characterized by metabolic quiescent state, and rehydration upon pollination that l...
Localized delivery of plasma membrane and cell wall components is an essential process in all plant cells. The vesicle-tethering complex, the exocyst, an ancient eukaryotic hetero-octameric protein cellular module, assists in targeted delivery of exocytosis vesicles to specific plasma membrane domains. Analyses of Arabidopsis and later other land p...
Studying morphogenesis is unthinkable without visualizing shapes, and sharing the results of such studies critically depends on communicating image data. Despite a wealth of literature dealing with acquisition and analysis of image data, visualizing them for publication or presentation purposes remains a craft learned mainly by experience. This cha...
The cortical microtubule and actin meshworks play a central role in the shaping of plant cells. Transgenic plants expressing fluorescent protein markers specifically tagging the two main cytoskeletal systems are available, allowing noninvasive in vivo studies. Advanced microscopy techniques, in particular confocal laser scanning microscopy (CLSM),...
Formins are evolutionarily conserved eukaryotic proteins engaged in actin nucleation and other aspects of cytoskeletal organization. Angiosperms have two formin clades with multiple paralogs; typical plant Class I formins are integral membrane proteins that can anchor cytoskeletal structures to membranes. For the main Arabidopsis housekeeping Class...
Reproductive isolation is an important component of species differentiation. The plastid accD gene coding for the acetyl-CoA carboxylase subunit and the nuclear bccp gene coding for the biotin carboxyl carrier protein were identified as candidate genes governing nuclear-cytoplasmic incompatibility in peas. We examined the allelic diversity in a set...
The collet (root–hypocotyl junction) region is an important plant transition zone between soil and atmospheric environments. Despite its crucial importance for plant development, little is known about how this transition zone is specified. Here we document the involvement of the exocyst complex in this process. The exocyst, an octameric tethering c...
Formins are evolutionarily conserved eukaryotic proteins engaged in actin nucleation and other aspects of cytoskeletal organization. Angiosperms have two formin clades with multiple paralogs; typical plant Class I formins are integral membrane proteins that can anchor cytoskeletal structures to membranes. For the main Arabidopsis housekeeping Class...
The extent of literature devoted to the eukaryotic cell cycle as well as the complexity of the underlying ideas, hypotheses, and models has become rather intimidating. However, our current understanding of the processes that produce (usually) two cells out of one is rooted in a relatively limited set of underlying concepts. Some of these originated...
The exocyst, an evolutionarily conserved secretory vesicle‐tethering complex, spatially controls exocytosis and membrane turnover in fungi, metazoans and plants. The exocyst subunit EXO 70 exists in multiple paralogs in land plants, forming three conserved clades with assumed distinct roles. Here we report functional analysis of the first moss exoc...
Background
Cytoskeleton can be observed in live plant cells in situ with high spatial and temporal resolution using a combination of specific fluorescent protein tag expression and advanced microscopy methods such as spinning disc confocal microscopy (SDCM) or variable angle epifluorescence microscopy (VAEM). Existing methods for quantifying cytosk...
Phylogenetic analysis has become a common step in characterization of gene and protein sequences. However, despite the availability of numerous affordable and more-or-less intuitive software tools, construction of biologically relevant, informative phylogenetic trees remains a process involving several critical steps that are inherently non-algorit...
“A developmental change is usually not a behavior.” In the light of plant biology tradition this is somewhat puzzling# hinting at the need to examine what is understood as developmental change by animal and plant biologists. Growth and production of vegetative organs may not be perceived as a “change” by plant biologists, because it is just somethi...
Development of the plant aerial organs epidermis involves a complex interplay of cytoskeletal rearrangements, membrane trafficking-dependent cell surface expansion, and intra- and intercellular signalling, resulting in a pattern of perfectly interlocking pavement cells. While recent detailed in vivo observations convincingly identify microtubules r...
Plant cell morphogenesis involves concerted rearrangements of microtubules and actin microfilaments. We previously reported
that FH1, the main housekeeping Arabidopsis thaliana Class I membrane-anchored formin, contributes to actin dynamics and microtubule stability in rhizodermis cells. Here we examine
effects of mutations affecting FH1 (At3g25500...
We usually expect the dose-response curves of biological responses to quantifiable stimuli to be simple, either monotonic or exhibiting a single maximum or minimum. Deviations are often viewed as experimental noise. However, detailed measurements in plant primary tissue cultures (stem pith explants of kale and tobacco) exposed to varying doses of s...
The cytoskeleton plays a central part in spatial organization of the plant cytoplasm, including the endomebrane system. However, the mechanisms involved are so far only partially understood. Formins (FH2 proteins), a family of evolutionarily conserved proteins sharing the FH2 domain whose dimer can nucleate actin, mediate the co-ordination between...
The budding yeast (Saccharomyces cerevisiae) can serve as a unique experimental system for functional studies of heterologous genes, allowing not only complementation of readily available yeast mutations but also generation of overexpression phenotypes and in some cases also rescue of such phenotypes. Here we summarize the main considerations that...
We describe complex multiple concentration dependencies for the response of isolated pith tissues to plant biologically active substances. Kale and tobacco stem pith explants were cultured on agar media containing combinations of sucrose, cytokinin [kinetin or benzyladenine (BA)] and auxin [indole-3-acetic acid (IAA) or naphthaleneacetic acid (NAA)...
Repetitive sequences present a challenge for genome sequence assembly, and highly similar segmental duplications may disappear from assembled genome sequences. Having found a surprising lack of observable phenotypic deviations and non-Mendelian segregation in Arabidopsis thaliana mutants in SEC10, a gene encoding a core subunit of the exocyst tethe...
Volatiles produced by bacterial cultures are known to induce regulatory and metabolic alterations in nearby con-specific or heterospecific bacteria, resulting in phenotypic changes including acquisition of antibiotic resistance. We observed unhindered growth of ampicillin-sensitive Serratia rubidaea and S. marcescens exposed to volatiles from dense...
The cortical microtubules, and to some extent also the actin meshwork, play a central role in the shaping of plant cells. Transgenic plants expressing fluorescent protein markers specifically tagging the two main cytoskeletal systems are available, allowing noninvasive in vivo studies. Advanced microscopy techniques, in particular confocal laser sc...
Plant Cell Morphogenesis: Methods and Protocols provides a collection of experimental techniques used in current research on the cellular aspects of plant morphogenesis. Methods and techniques include contemporary takes on classical light microscopy and histochemistry through automated microscopy applications, use of advanced optical tools, quantit...
In a recent addendum, Oren Tzfadia and Gad Galili (PSB 2014; 9:e26732) showed that several Arabidopsis exocyst subunits possess consensus Atg8-interacting motifs (AIMs), which may mediate their interaction with the autophagy-associated Atg8 protein, providing thus a mechanistic base for participation of exocyst (sub)complexes in autophagy. However,...
Formins are evolutionarily conserved eukaryotic proteins participating in actin and microtubule organization. Land plants have three formin clades, with only two – Class I and II – present in angiosperms. Class I formins are often transmembrane proteins, residing at the plasmalemma and anchoring the cortical cytoskeleton across the membrane to the...
Meaning is a central concept of (bio)semiotics. At the same time, it is also a word of everyday language. Here, on the example of the world information, we discuss the “reduction-inflation model” of evolution of a common word into a scientific concept, to return subsequently into everyday circulation with new connotations. Such may be, in the near...
Plant cell growth and morphogenesis depend on remodelling of both actin and microtubule cytoskeletons. AtFH1 (At5g25500),
the main housekeeping Arabidopsis formin, is targeted to membranes and known to nucleate and bundle actin. The effect of mutations in AtFH1 on root development
and cytoskeletal dynamics was examined. Consistent with primarily ac...
Formins (FH2 proteins) are an evolutionarily conserved family of eukaryotic proteins, sharing the common FH2 domain. While they have been, until recently, understood mainly as actin nucleators, formins are also engaged in various additional aspects of cytoskeletal organization and signaling, including, but not limited to, the crosstalk between the...
Formins (FH2 proteins) are implicated in F-actin nucleation and other aspects of cytoskeletal organization. Plants possess two formin clades, relatively well-described Class I formins and so far poorly characterized Class II formins. Comparison of Class II formin genes of two Arabidopsis species, A. thaliana and A. lyrata, indicates dynamic evoluti...
Exocyst is an evolutionarily conserved vesicle tethering complex functioning especially in the last stage of exocytosis. Homologs of its eight canonical subunits – Sec3, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70, and Exo84 – were found also in higher plants and confirmed to form complexes in vivo, and to participate in cell growth including polarized e...
Novel regulatory elements from the family of Tetratricopeptide-repeat Thioredoxin-like proteins
were identified to take part in lateral root development. Their expression pattern and mutant phenotype were recorded and bioinformatics analysis of phylogeny and distribution of genes was tested.
Objectives Lateral root initiation and growth is a central point of root system morphogenesis and subsequent plant interaction with its rhizosphere. The TTL3 gene (Tetratricopeptide-repeat Thioredoxin-Like 3, AT2G42580) was identified during the forward screening of Arabidopsis gene-trap lines searching for new genes related to lateral root initiat...
Activated cortical domains (ACDs) are regions of the plant cell cortex performing localized membrane turnover, delimited by concerted action of the cortical cytoskeleton and endomembrane compartments. Arabidopsis thaliana rhizodermis consists of two cell types differing by a single ACD (trichoblasts, carrying tip-growing root hairs, and hairless at...
• Polarized deposition of cell wall pectins is a key process in Arabidopsis thaliana myxospermous seed coat development. The exocyst, an octameric secretory vesicle tethering complex, has recently been shown to be involved in the regulation of cell polarity in plants. Here, we used the Arabidopsis seed coat to study the participation of the exocyst...
Bacterial bodies (colonies) can develop complex patterns of color and structure. These patterns may arise as a result of both colony-autonomous developmental and regulatory processes (self-patterning) and environmental influences, including those generated by neighbor bodies. We have studied the interplay of intra-colony signaling (self-patterning)...
The dynamic behaviour of the actin cytoskeleton in plants relies on the coordinated action of several classes of actin-binding proteins (ABPs). These ABPs include the plant-specific subfamilies of actin-nucleating formin proteins. The model plant species Arabidopsis thaliana has over 20 formin proteins, all of which contain plant-specific regions i...
In plants, exocytosis is a central mechanism of cell morphogenesis. We still know surprisingly little about some aspects of this process, starting with exocytotic vesicle formation, which may take place at the trans‐Golgi network even without coat assistance, facilitated by the local regulation of membrane lipid organization. The RabA4b guanosine t...
The concept of plant intelligence, as proposed by Anthony Trewavas, has raised considerable discussion. However, plant intelligence remains loosely defined; often it is either perceived as practically synonymous to Darwinian fitness, or reduced to a mere decorative metaphor. A more strict view can be taken, emphasizing necessary prerequisites such...
Keyhole limpet hemocyanin (KLH)-conjugated peptides are routinely used to raise polyclonal antibodies for biochemical or immunolocalization studies. Rats are suitable for producing antisera against plant antigens as they often lack non-specific response towards plant materials. We attempted to obtain rat antisera against peptides derived from sever...
The bacterium Serratia marcescens produces a plethora of multicellular shapes of different colorations on solid substrates, allowing immediate visual detection of varieties. Such a plasticity allows studies on multicellular community scale spanning two extremes, from well-elaborated individual colonies to undifferentiated cell mass.For a single str...
Shuffling of modular protein domains is an important source of evolutionary innovation. Formins are a family of actin-organizing proteins that share a conserved FH2 domain but their overall domain architecture differs dramatically between opisthokonts (metazoans and fungi) and plants. We performed a phylogenomic analysis of formins in most eukaryot...
Plant hybrid proline-rich proteins (HyPRPs) are putative cell wall proteins consisting, usually, of a repetitive proline-rich (PR) N-terminal domain and a conserved eight-cysteine motif (8 CM) C-terminal domain. Understanding the evolutionary dynamics of HyPRPs might provide not only insight into their so far elusive function, but also a model for...
The presence of a complex cytoskeletal system is a hallmark feature of eukaryotic cells, distinguishing them from their prokaryotic
(bacterial or archaeal) “cousins”. No extant prokaryote studied so far possesses obvious homologues of major cytoskeletal
proteins shared universally among eukaryotes, such as e.g., actin or tubulin. However, several p...
To understand the biological context of lipid metabolism and signalling in pollen, we have to
consider male gametophytes as organisms optimised for their role in sexual reproduction, but also
for survival in dry conditions. While our knowledge of molecular mechanisms governing pollen development
and pollen tube growth is based on the studies of afe...
The closely related proteins AtFH4 and AtFH8 represent the group Ie clade of Arabidopsis formin homologues. The subcellular localization of these proteins and their ability to affect the actin cytoskeleton were examined. AtFH4 protein activity was identified using fluorimetric techniques. Interactions between Arabidopsis profilin isoforms and AtFH4...
The actin cytoskeleton plays a central part in the dynamic organization of eukaryotic cell structure. Nucleation of actin filaments is a crucial step in the establishment of new cytoskeletal structures or modification of existing ones, providing abundant targets for regulatory processes. A substantial part of our understanding of actin nucleation d...
Involvement of conservative molecular modules and cellular mechanisms in the widely diversified processes of eukaryotic cell morphogenesis leads to the intriguing question: how do similar proteins contribute to dissimilar morphogenetic outputs. Formins (FH2 proteins) play a central part in the control of actin organization and dynamics, providing a...
Review: Marcello Barbieri, The Organic Codes: An Introduction to Semantic Biology
We give a survey of epistemological and ontological approaches that have left traces in the 20th-century biology. A common motive of most of them is the effort to incorporate biology into the realm of physical sciences. However, such attempts failed, and must fail in the future, unless the criterion for what science is becomes biologically oriented...
The phospholipase D (PLD) family has been identified in plants by recent molecular studies, fostered by the emerging importance of plant PLDs in stress physiology and signal transduction. However, the presence of multiple isoforms limits the power of conventional biochemical and pharmacological approaches, and calls for a wider application of genet...
On or before Jun 10, 2016 this sequence version replaced gi:18765906, gi:18765907, gi:18765905.
Heterotrimeric and small G-proteins aresupposed to participate in tip growth of plant cells. Quantitative changes intip growth rate after introduction of non-hydrolysable guanine nucleotideanalogues (NA) into lily pollen tubes have been interpreted as support for thehypothesis that heterotrimeric G-proteins regulate tube elongation (Ma et al.,1999...
The formin family of proteins has been implicated in signaling pathways of cellular morphogenesis in both animals and fungi; in the latter case, at least, they participate in communication between the actin cytoskeleton and the cell surface. Nevertheless, they appear to be cytoplasmic or nuclear proteins, and it is not clear whether they communicat...
Rab GTPases play a central role in the control of vesicular membrane traffic. These proteins cycle between cytosolic and membrane-bound compartments in a guanine nucleotide-dependent manner, a process that is regulated by several accessory proteins. Of particular interest are the Rab guanosine nucleotide diphosphate dissociation inhibitor proteins...
Small GTPases play a central part in cell morphogenesis of both yeast and animal cells. Intracellular vesicle transport, essential for cell growth, requires the function of Rab-like GTPases, while the Rac/Cdc42-like GTPases control cytoskeletal organisation. Since relatively little is known about analogous regulation of cell morphogenesis in higher...
The yeast Ste20 protein kinase is involved in pheromone response. Mammalian homologs of Ste20 exist, but their function remains unknown. We identified a novel yeast STE20 homolog, CLA4, in a screen for mutations lethal in the absence of the G1 cyclins Cln1 and Cln2. Cla4 is involved in budding and cytokinesis and interacts with Cdc42, a GTPase requ...
Cyclin-dependent protein kinases have a central role in cell cycle regulation. In Saccharomyces cerevisiae, Cdc28 kinase and the G1 cyclins Cln1, 2 and 3 are required for DNA replication, duplication of the spindle pole body and bud emergence. These three independent processes occur simultaneously in late G1 when the cells reach a critical size, an...
A new selection method based on the use of chlorsulfuron (CS) resistance as the selection marker for protoplast fusion in industrial yeast has been introduced using the system of protoplast fusion. A petite mutant of a spontaneously CS-resistant distiller's Saccharomyces cerevisiae strain and a wild-type CS-sensitive strain of the osmotolerant yeas...
A haploid, glucoamylase-producing strain of Saccharomyces diastaticus lacking the POF gene and thus unable to produce phenolic off-flavour in beer was constructed by classical genetic techniques. Protoplast fusion was performed between this strain and a brewing polyploid Saccharomyces uvarum strain. Some clones derived from fusion products can prod...
At the exponential growth phase, nystatin-treated Saccharomyces cerevisiae cells stain with Rhodamine B if they have not previously been exposed to killer toxin produced by Kluyveromyces lactis. This finding constitutes the principle of a method for estimating the activity of this toxin.
Abstrakt. Tento příspěvek je pokusem o zmapování oblastí, kde by teoretické přístupy vypracované pro potřeby studia lidské mysli mohly přispět i k pochopení (či aspoň k úspěšnému modelování) funkce jiných projevů života. Zejména v povědomí nebiologicky zaměřených vědců přetrvává představa "neinteligentních" či "nižších" organismů jakožto víceméně d...
