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PREDAVANJA
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 Praktikum, biljni dio
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Seminari (termin seminara!!)
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tema održana u sklopu drugog kolegija!)
• Trajanje seminara – 20tak minuta
Teme seminara (biljni dio)

1. "Maternal-to-zygotic transition" (Célia Baroux, Ueli Grossniklaus)

2. Citoskelet zygote (Kimata et al. 2016)
3. Dynamics and function of DNA methylation in plants (Zhang et al. 2018)
4. Metilacija u biljaka: specificnost mehanizma "RdDM" (RNA-directed DNA
methylation) (Matzke and Moser)
5. "Stress-recovery epigenetics"( Crisp et al)
6. Mehanizmi dormancije (Nonogaki)
7. Cellular basis of growth in plants: geometry matters (Daniel Kierzkowski and Anne-
LiseRoutier-Kierzkowska)
8. Single microfilaments mediate the early steps of microtubule bundling during
preprophase band formation in onion cotyledon epidermal cells
9. Building a plant: cell fate specification in the early Arabidopsis embryo

 
1. Poglavlje 6 (M. Timmerman, Plant Development) Evolution of Leaf Shape: A Pattern
Emerges
2. Poglavlje 7 (M. Timmerman, Plant Development) Control of Tissue and Organ Growth in
Plants
3. Poglavlje 8 (M. Timmerman, Plant Development) Vascular Pattern Formation in Plants
4. Poglavlje 9 (M. Timmerman, Plant Development) Stomatal Pattering and Development
5. Poglavlje 12 (M. Timmerman, Plant Development) Sculpting the Flower; the role of
miRNAs in Flower Development
 
1."Maternal-to-zygotic transition" (Célia Baroux, Ueli
Grossniklaus)
Abstract
The maternal-to-zygotic transition (MZT) defines a developmental phase during which
the embryo progressively emancipates itself from a developmental control relying
largely on maternal information. The MZT is a functional readout of two processes:
the clearance of maternally derived information and the de novo expression of the
inherited, parental alleles enabled by zygotic genome activation (ZGA). In plants, for
many years the debate about whether the MZT exists at all focused on the ZGA alone.
However, several recent studies provide evidence for a progressive alleviation of the
maternal control over embryogenesis that is correlated with a gradual ZGA, a process
that is itself maternally controlled. Yet, several examples of zygotic genes that are
expressed and/or functionally required early in embryogenesis demonstrate a certain
flexibility in the dynamics and kinetics of the MZT among plant species and also
intraspecific hybrids.
2.Citoskelet zygote (Kimata et al. 2016)
Abstract
The asymmetric cell division of the zygote is the initial and crucial developmental step in most
multicellular organisms. In flowering plants, whether zygote polarity is inherited from the
preexisting organization in the egg cell or reestablished after fertilization has remained elusive.
How dynamically the intracellular organization is generated during zygote polarization is also
unknown. Here, we used a live-cell imaging system with Arabidopsis zygotes to visualize the
dynamics of the major elements of the cytoskeleton, microtubules (MTs), and actin filaments
(F-actins), during the entire process of zygote polarization. By combining image analysis and
pharmacological experiments using specific inhibitors of the cytoskeleton, we found features
related to zygote polarization. The preexisting alignment of MTs and F-actin in the egg cell is
lost on fertilization. Then, MTs organize into a transverse ring defining the zygote subapical
region and driving cell outgrowth in the apical direction. F-actin forms an apical cap and
longitudinal arrays and is required to position the nucleus to the apical region of the zygote,
setting the plane of the first asymmetrical division. Our findings show that, in flowering plants,
the preexisting cytoskeletal patterns in the egg cell are lost on fertilization and that the zygote
reorients the cytoskeletons to perform directional cell elongation and polar nuclear migration.
3.Dynamics and function of DNA methylation in plants
(Zhang et al. 2018)

Abstract
DNA methylation is a conserved epigenetic modification that is important for gene
regulation and genome stability. Aberrant patterns of DNA methylation can lead to plant
developmental abnormalities. A specific DNA methylation state is an outcome of dynamic
regulation by de novo methylation, maintenance of methylation and active
demethylation,which are catalysed by various enzymes that are targeted by distinct regulatory
pathways. In this Review , we discuss DNA methylation in plants, including methylating and
demethylating enzymes and regulatory factors, and the coordination of methylation and
demethylation activities by a so- called methylstat mechanism; the functions of DNA
methylation in regulating transposon silencing, gene expression and chromosome interactions;
the roles of DNA methylation in plant development; and the involvement of DNA methylation
in plant responses to biotic and abiotic stress conditions
4. Metilacija u biljaka: specificnost mehanizma "RdDM" (RNA-directed
DNA methylation) (Matzke and Moser)

• Abstract | RNA-directed DNA methylation (RdDM) is the major small

RNA-mediated epigenetic pathway in plants. RdDM requires a
specialized transcriptional machinery that comprises two plant-
specific RNA polymerases — Pol IV and Pol V — and a growing
number of accessory proteins, the functions of which in the RdDM
mechanism are only partially understood. Recent work has revealed
variations in the canonical RdDM pathway and identified factors that
recruit Pol IV and Pol V to specific target sequences. RdDM, which
transcriptionally represses a subset of transposons and genes, is
implicated in pathogen defence, stress responses and reproduction,
as well as in interallelic and intercellular communication.
 5. "Stress-recovery epigenetics"(Crisp et al)
Abstract
Plants grow in dynamic environments where they can be exposed to a multitude of stressful
factors, all of which affect their development, yield, and, ultimately, reproductive success.
Plants are adept at rapidly acclimating tostressful conditions and are able to further fortify
their defenses by retaining memories of stress to enable stronger or more rapid responses
should an environmental perturbation recur. Indeed, one mechanism that is often evoked
regarding environmental memories is epigenetics. Yet, there are relatively few examples of
such memories; neither is there a clear understanding of their duration, considering the
plethora of stresses in nature. We propose that this field would benefit from investigations
into the processes and mechanisms enabling recovery from stress. An understanding of stress
recovery could provide fresh insights into when, how, and why environmental memories
are created and regulated. Stress memories may be maladaptive, hindering recovery and
affecting development and potential yield. In some circumstances, it may be advantageous for
plants to learn to forget. Accordingly, the recovery process entails a balancing act between
resetting and memory formation. During recovery, RNA metabolism, posttranscriptional gene
silencing, and RNA-directed DNA methylation have the potential to play key roles in resetting
the epigenome and transcriptome and in altering memory. Exploration of this emerging area
of research is becoming ever more tractable with advances in genomics, phenomics, and high-
throughput sequencing methodology that will enable unprecedented profiling of high-
resolution stress recovery time series experiments and sampling of large natural populations.
 6. Mehanizmi dormancije (Nonogaki)
Seed dormancy has played a significant role in adaptation and evolution of seed plants. While
its biological significance is clear, molecular mechanisms underlying seed dormancy induction,
maintenance and alleviation still remain elusive. Intensive efforts have been made to
investigate gibberellin and abscisic acid metabolism in seeds, which greatly contributed to the
current understanding of seed dormancy mechanisms. Other mechanisms, which might be
independent of hormones, or specific to the seed dormancy pathway, are also emerging from
genetic analysis of “seed dormancy mutants.” These studies suggest that chromatin
remodeling through histone ubiquitination, methylation and acetylation, which could lead to
transcription elongation or gene silencing, may play a significant role in seed dormancy
regulation. Small interfering RNA and/or long non-coding RNA might be a trigger of epigenetic
changes at the seed dormancy or germination loci, such as DELAY OF GERMINATION1. While
new mechanisms are emerging from genetic studies of seed dormancy, novel hypotheses are
also generated from seed germination studies with high throughput gene expression analysis.
Recent studies on tissue-specific gene expression in tomato and Arabidopsis seeds, which
suggested possible “mechanosensing” in the regulatory mechanisms, advanced our
understanding of embryo-endosperm interaction and have potential to re-draw the traditional
hypotheses or integrate them into a comprehensive scheme. The progress in basic seed
science will enable knowledge translation, another frontier of research to be expanded for
food and fuel production.
7. Single microfilaments mediate the early steps of microtubule bundling
during preprophase band formation in onion cotyledon epidermal cells

ABSTRACT
• The preprophase band (PPB) is a cytokinetic apparatus that determines the site of cell division in
plants. It originates as a broad band of microtubules (MTs) in G2 and narrows to demarcate the
future division site during late prophase. Studies with fluorescent probes have shown that PPBs
contain F-actin during early stages of their development but become actin depleted in late
prophase. Although this suggests that actins contribute to the early stages of PPB formation, how
actins contribute to PPB-MT organization remains unsolved. To address this question, we used
electron tomography to investigate the spatial relationship between microfilaments (MFs) and
MTs at different stages of PPB assembly in onion cotyledon epidermal cells. We demonstrate that
the PPB actins observed by fluorescence microscopy correspond to short, single MFs. A majority
of the MFs are bound to MTs, with a subset forming MT-MF-MT bridging structures. During the
later stages of PPB assembly, the MF-mediated links between MTs are displaced by MT-MT linkers
as the PPB MT arrays mature into tightly packed MT bundles. On the basis of these observations,
we propose that the primary function of actins during PPB formation is to mediate the initial
bundling of the PPB MTs.
8. Building a plant: cell fate specification in
the early Arabidopsis embryo
Embryogenesis is the beginning of plant development, yet the
cell fate decisions and patterning steps that occur during this time
are reiterated during development to build the post-embryonic
architecture. In Arabidopsis, embryogenesis follows a simple and
predictable pattern, making it an ideal model with which to understand
how cellular and tissue developmental processes are controlled.
Here, we review the early stages of Arabidopsis embryogenesis,
focusing on the globular stage, during which time stem cells are first
specified and all major tissues obtain their identities.We discuss four
different aspects of development: the formation of outer versus inner
layers; the specification of vascular and ground tissues; the
determination of shoot and root domains; and the establishment of
the first stem cells.
 9. Cellular basis of growth in plants: geometry matters
(Daniel Kierzkowski and Anne-LiseRoutier-Kierzkowska)
Abstract
The growth of individual cells underlies the development of
biological forms. In plants, cells are interconnected by rigid
walls, fixing their position with respect to one another and
generating mechanical feedbacks between cells. Current
research is shedding new light on how plant growth is
controlled by physical inputs at the level of individual cells and
growing tissues. In this review, we discuss recent progress in
our understanding of the cellular basis of growth from a
biomechanical perspective. We describe the role of the cell wall
and turgor pressure in growth and highlight the oftenoverlooked
role of cell geometry in this process. It is becoming
apparent that a combination of experimental and theoretical
approaches is required to answer new emerging questions in
the biomechanics of plant morphogenesis. We summarise how
this multidisciplinary approach brings us closer to a unified
understanding of the generation of biological forms in plants.
 11. Poglavlje 6 (M. Timmerman, Plant Development) Evolution of Leaf
Shape: A Pattern Emerges

Abstract
Leaf shape is a highly variable trait. Ancestrally, all leaves are proposed to have
derived from modifications of branched shoot systems. The formation of blade,
smooth margins or serrations on the blade, or distinct leaflets that are the
characteristic features of some leaves provides an opportunity to study the
generation of morphogenesis in organs that are evolutionarily homologous and
yet developmentally distinct in patterning. Intense research in several model
species with distinct leaf morphologies has revealed a complex network of
genes that interact to pattern the leaf. Several parallels between leaf patterning
and shoot patterning exist. The plant growth hormone auxin is emerging as a
key player in the specification of both shoot and leaf patterning. The outcome of
this underlying auxin pattern may be determined by variation in the two
opposing developmental forces of differentiation and indeterminancy. The
expanded suite of genetic and physiological factors regulating leaf shape has
provided interesting insight into the mechanisms by which morphological innovation
is accomplished.
12. Poglavlje 7 (M. Timmerman, Plant Development)
Control of Tissue and Organ Growth in Plants)
Abstract
Plant organs grow to characteristic, species-specific sizes and shapes. At the
cellular level, organ growth is initially characterized by cell proliferation, which
gives way to cell expansion at later stages. Using mainly Arabidopsis thaliana
as a model species, a number of factors have been isolated in recent years that
promote or restrict organ growth, with the altered organ size being associated
with changes in cell number, in cell size, or in both. However, cells in an organ do not appear to
follow a strictly autonomous program of proliferation and
expansion, and their behavior is coordinated in at least three different respects:
normally sized organs can be formed consisting of altered numbers of cells with
compensatory changes in the size of the individual cells, suggesting that
cellular behavior is subject to organ-wide control; the growth of cells derived
from more than one clonal origin is coordinated within a plant lateral organ with
its different histological layers; and growth of cells in different regions of an
organ is coordinated to generate a reasonably flat leaf or floral organ. Organ
growth is strongly modulated by environmental factors, and the molecular basis
for this regulation is beginning to be understood. Given the complexity of organ
growth as a dynamic four-dimensional process, precise quantification of growth
parameters and mathematical modeling are increasingly used to understand
this fascinating problem of plant biology.
13. Poglavlje 8 (M. Timmerman, Plant Development) Vascular Pattern
Formation in Plants

Abstract
The growth of individual cells underlies the development of
biological forms. In plants, cells are interconnected by rigid
walls, fixing their position with respect to one another and
generating mechanical feedbacks between cells. Current
research is shedding new light on how plant growth is
controlled by physical inputs at the level of individual cells and
growing tissues. In this review, we discuss recent progress in
our understanding of the cellular basis of growth from a
biomechanical perspective. We describe the role of the cell wall
and turgor pressure in growth and highlight the oftenoverlooked
role of cell geometry in this process. It is becoming
apparent that a combination of experimental and theoretical
approaches is required to answer new emerging questions in
the biomechanics of plant morphogenesis. We summarise how
this multidisciplinary approach brings us closer to a unified
understanding of the generation of biological forms in plants.
14. Poglavlje 9 (M. Timmerman, Plant Development) Stomatal Pattering and
Development
Abstract
Stomata are epidermal pores used for water and gas exchange between a plant
and the atmosphere. Both the entry of carbon dioxide for photosynthesis and
the evaporation of water that drives transpiration and temperature regulation
are modulated by the activities of stomata. Each stomatal pore is surrounded by two highly specialized
cells called guard cells (GCs), and may also be associated
with neighboring subsidiary cells; this entire unit is referred to as the
stomatal complex. Generation of GCs requires stereotyped asymmetric and
symmetric cell divisions, and the pattern of stomatal complexes in the epidermis
follows a “one-cell-spacing rule” (one complex almost never touches
another one). Both stomatal formation and patterning are highly regulated by
a number of genetic components identified in the last decade, including, but not
limited to, secreted peptide ligands, plasma membrane receptors and receptorlike
kinases, a MAP kinase module, and a series of transcription factors.
This review will elaborate on the current state of knowledge about components
in signaling pathways required for cell fate and pattern, with emphasis on
(1) a family of extracellular peptide ligands and their relationship to the TOO
MANY MOUTHS receptor-like protein and/or members of the ERECTA receptorlike
kinase family, (2) three tiers of a MAP kinase module and the kinases that
confer novel regulatory effects in specific stomatal cell types, and (3) transcription
factors that generate specific stomatal cell types and the regulatory
mechanisms for modulating their activities. We will then consider two new
proteins (BASL and PAN1, from Arabidopsis and maize, respectively) that
regulate stomatal asymmetric divisions by establishing cell polarity.
 15. Poglavlje 12 (M. Timmerman, Plant Development) Sculpting
the Flower; the role of miRNAs in Flower Development

Abstract
microRNAs (miRNAs) are small approximately 21-nucleotide RNAs that function posttranscriptionally to
regulate gene activity. miRNAs function by binding to complementary sites in target genes causing mRNA
degradation and/or translational repression of the target. Since the discovery of miRNAs in plants in
2002 much has been learned about the function of these small regulatory RNAs. miRNAs function
broadly to control many aspects of plant biology and plant development. This review focuses on the role
of miRNAs in flower development. miRNAs function throughout flower development, from the earliest
stages (floral induction) to very late stages (floral organ cell type specification). miRNAs such as miR156
and miR172 play a key role in vegetative phase change and in the vegetative to reproductive transition in
both Arabidopsis and maize. miR172 in Arabidopsis and maize and miR169 in Petunia and Antirrhinum
function to control floral organ identity fate during the early stages of flower development by regulating
the spatial boundaries of expression of target genes. miR164, miR319, miR159, and miR167 function to
specify particular cell types during later stages of flower development. Although much has been learned
about the role of miRNAs in flower development in the last 8 years, many challenges remain to fully
elucidate the function of these important regulatory molecules.
LITERATURA

Marja C. P. Timmermans (ed): Current topics in

developmental biology; Cold Spring Harbor Laboratory
Cold Spring Harbor, New York, USA

V. Raghavan: Developmental Biology of Flowering Plants

Taiz, L., Zeiger, E. (2004): Plant Physiology.

Sinauer Associates, Inc., Sunderland,
Massachusetts.

Leyser O: Mechanisms in Plant development

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