Evolutionary history of the poly(ADP-ribose) polymerase gene family in eukaryotes

Abstract Background The Poly(ADP-ribose)polymerase (PARP) superfamily was originally identified as enzymes that catalyze the attachment of ADP-ribose subunits to target proteins using NAD+ as a substrate. The family is characterized by the catalytic site, termed the PARP signature. While these proteins can be found in a range of eukaryotes, they have been best studied in mammals. In these organisms, PARPs have key functions in DNA repair, genome integrity and epigenetic regulation. More recently it has been found that proteins within the PARP superfamily have altered catalytic sites, and have mono(ADP-ribose) transferase (mART) activity or are enzymatically inactive. These findings suggest that the PARP signature has a broader range of functions that initially predicted. In this study, we investigate the evolutionary history of PARP genes across the eukaryotes. Results We identified in silico 236 PARP proteins from 77 species across five of the six eukaryotic supergroups. We performed extensive phylogenetic analyses of the identified PARPs. They are found in all eukaryotic supergroups for which sequence is available, but some individual lineages within supergroups have independently lost these genes. The PARP superfamily can be subdivided into six clades. Two of these clades were likely found in the last common eukaryotic ancestor. In addition, we have identified PARPs in organisms in which they have not previously been described. Conclusions Three main conclusions can be drawn from our study. First, the broad distribution and pattern of representation of PARP genes indicates that the ancestor of all extant eukaryotes encoded proteins of this type. Second, the ancestral PARP proteins had different functions and activities. One of these proteins was similar to human PARP1 and likely functioned in DNA damage response. The second of the ancestral PARPs had already evolved differences in its catalytic domain that suggest that these proteins may not have possessed poly(ADP-ribosyl)ation activity. Third, the diversity of the PARP superfamily is larger than previously documented, suggesting as more eukaryotic genomes become available, this gene family will grow in both number and type.</p

The Making of Leaves: How Small RNA Networks Modulate Leaf Development

Leaf development is a sequential process that involves initiation, determination, transition, expansion and maturation. Many coding genes and a few non-coding small RNAs (sRNAs) have been identified as being involved in leaf development. sRNAs and their interactions not only determine gene expression and regulation, but also play critical roles in leaf development through their coordination with other genetic networks and physiological pathways. In this review, we first introduce the biogenesis pathways of sRNAs, mainly microRNAs (miRNAs) and trans-acting small interfering RNAs (ta-siRNAs), and then describe the function of miRNA-transcription factors in leaf development, focusing on guidance by interactive sRNA regulatory networks

Perspectives on microRNAs and phased small interfering RNAs in Maize (Zea mays L.): Functions and big impact on agronomic traits enhancement

Small RNA (sRNA) population in plants comprises of primarily micro RNAs (miRNAs) and small interfering RNAs (siRNAs). MiRNAs play important roles in plant growth and development. The miRNA-derived secondary siRNAs are usually known as phased siRNAs, including phasiRNAs and tasiRNAs. The miRNA and phased siRNA biogenesis mechanisms are highly conserved in plants. However, their functional conservation and diversification may differ in maize. In the past two decades, lots of miRNAs and phased siRNAs have been functionally identified for curbing important maize agronomic traits, such as those related to developmental timing, plant architecture, sex determination, reproductive development, leaf morphogenesis, root development and nutrition, kernel development and tolerance to abiotic stresses. In contrast to Arabidopsis and rice, studies on maize miRNA and phased siRNA biogenesis and functions are limited, which restricts the small RNA-based fundamental and applied studies in maize. This review updates the current status of maize miRNA and phased siRNA mechanisms and provides a survey of our knowledge on miRNA and phased siRNA functions in controlling agronomic traits. Furthermore, improvement of those traits through manipulating the expression of sRNAs or their targets is discussed

The interaction between miR160 and miR165/166 in the control of leaf development and drought tolerance in Arabidopsis

MicroRNAs (miRNAs) are a class of non-coding RNAs that play important roles in plant development and abiotic stresses. To date, studies have mainly focused on the roles of individual miRNAs, however, a few have addressed the interactions among multiple miRNAs. In this study, we investigated the interplay and regulatory circuit between miR160 and miR165/166 and its effect on leaf development and drought tolerance in Arabidopsis using Short Tandem Target Mimic (STTM). By crossing STTM160 Arabidopsis with STTM165/166, we successfully generated a double mutant of miR160 and miR165/166. The double mutant plants exhibited a series of compromised phenotypes in leaf development and drought tolerance in comparison to phenotypic alterations in the single STTM lines. RNA-seq and qRT-PCR analyses suggested that the expression levels of auxin and ABA signaling genes in the STTM-directed double mutant were compromised compared to the two single mutants. Our results also suggested that miR160-directed regulation of auxin response factors (ARFs) contribute to leaf development via auxin signaling genes, whereas miR165/166- mediated HD-ZIP IIIs regulation confers drought tolerance through ABA signaling. Our studies further indicated that ARFs and HD-ZIP IIIs may play opposite roles in the regulation of leaf development and drought tolerance that can be further applied to other crops for agronomic traits improvement

The interaction between miR160 and miR165/166 in the control of leaf development and drought tolerance in Arabidopsis

MicroRNAs (miRNAs) are a class of non-coding RNAs that play important roles in plant development and abiotic stresses. To date, studies have mainly focused on the roles of individual miRNAs, however, a few have addressed the interactions among multiple miRNAs. In this study, we investigated the interplay and regulatory circuit between miR160 and miR165/166 and its effect on leaf development and drought tolerance in Arabidopsis using Short Tandem Target Mimic (STTM). By crossing STTM160 Arabidopsis with STTM165/166, we successfully generated a double mutant of miR160 and miR165/166. The double mutant plants exhibited a series of compromised phenotypes in leaf development and drought tolerance in comparison to phenotypic alterations in the single STTM lines. RNA-seq and qRT-PCR analyses suggested that the expression levels of auxin and ABA signaling genes in the STTM-directed double mutant were compromised compared to the two single mutants. Our results also suggested that miR160-directed regulation of auxin response factors (ARFs) contribute to leaf development via auxin signaling genes, whereas miR165/166- mediated HD-ZIP IIIs regulation confers drought tolerance through ABA signaling. Our studies further indicated that ARFs and HD-ZIP IIIs may play opposite roles in the regulation of leaf development and drought tolerance that can be further applied to other crops for agronomic traits improvement

The miR167-OsARF12 module regulates grain filling and grain size downstream of miR159

Grain weight and quality are always determined by the grain filling. Plant miRNAs have drawn attention as key targets for regulating grain size and yield. Yet the mechanisms underlying the regulation of grain size are largely unclear due to the complex networks controlling this trait. Our earlier studies proved that the suppressed expression of miR167 (STTM/MIM167) substantially increased grain weight. In a field test, the increased yield up to 12.90%-21.94% due to the significantly enhanced grain filling rate. Biochemical and genetic analyses reveal the regulatory effects of miR159 on miR167 expression. Further analysis indicates that OsARF12 is the major mediator of miR167 in regulating rice grain filling. Expectedly, over expressing OsARF12 could resemble the phenotype of STTM/MIM167 plants with respect to grain weight and grain filling rate. Upon in-depth analysis, we found that OsARF12 activates OsCDKF;2 expressions by directly binding to the TGTCGG motif in the promoter region. Flow cytometric analysis in young panicles of plants overexpressing OsARF12 and cell number examination of cdkf;2 mutants verify that OsARF12 positively regulates grain filling and grain size by targeting OsCDKF;2. Moreover, RNA-seq result suggests that miR167-OsARF12 module is involved in the cell development process and hormone pathways. Additionally, plants overexpressing OsARF12 or cdkf;2 mutants present enhanced or reduced sensitivity to exogenous auxin and brassinosteroid (BR) treatments, confirming that OsCDKF;2 targeting by OsARF12 mediates auxin and BR signaling. Our results reveal that miR167-OsARF12 module works downstream of miR159 to regulate rice grain filling and grain size by OsCDKF;2 through controlling cell division and mediating auxin and BR signals

RCD1 and SRO1 are necessary to maintain meristematic fate in Arabidopsis thaliana

The RADICAL-INDUCED CELL DEATH1 and SIMILAR TO RCD ONE1 genes of Arabidopsis thaliana encode members of the poly(ADP-ribose) polymerase (PARP) superfamily and have pleiotropic functions in development and abiotic stress response. In order to begin to understand the developmental and molecular bases of the defects seen in rcd1-3; sro1-1 plants, this study used the root as a model. Double mutant roots are short and display abnormally organized root apical meristems. However, acquisition of most cell fates within the root is not significantly disrupted. The identity of the quiescent centre is compromised, the zone of cell division is smaller than in wild-type roots and abnormal divisions are common, suggesting that RCD1 and SRO1 are necessary to maintain cells in a division-competent state and to regulate division plane placement. In addition, differentiation of several cell types is disrupted in rcd1-3; sro1-1 roots and shoots, demonstrating that RCD1 and SRO1 are also necessary for proper cell differentiation. Based on the data shown in this article and previous work, we hypothesize that RCD1 and SRO1 are involved in redox control and, in their absence, an altered redox balance leads to abnormal development

To bloom or not to bloom: Role of micrornas in plant flowering

© 2015 The Author. During the course of their life cycles, plants undergo various morphological and physiological changes underlying juvenile-to-adult and adult-to-flowering phase transitions. To flower or not to flower is a key step of plasticity of a plant toward the start of its new life cycle. In addition to the previously revealed intrinsic genetic programs, exogenous cues, and endogenous cues, a class of small non-coding RNAs, microRNAs (miRNAs), plays a key role in plants making the decision to flower by integrating into the known flowering pathways. This review highlights the age-dependent flowering pathway with a focus on a number of timing miRNAs in determining such a key process. The contributions of other miRNAs which exist mainly outside the age pathway are also discussed. Approaches to study the flowering-determining miRNAs, their interactions, and applications are presented

Knockdown of rice microRNA166 by short tandem target mimic (STTM)

© Springer Science+Business Media LLC 2017. Small RNAs, including microRNAs (miRNAs), are abundant in plants and play key roles in controlling plant development and physiology. miRNAs regulate the expression of the target genes involved in key plant processes. Due to functional redundancy among miRNA family members in plants, an ideal approach to silence the expression of all members simultaneously, for their functional characterization, is desirable. Target mimic (TM) was the first approach to achieve this goal. Short tandem target mimic (STTM) is a potent approach complementing TM for silencing miRNAs in plants. STTMs have been successfully used in dicots to block miRNA functions. Here, we describe in detail the protocol for designing STTM construct to block miRNA functions in rice. Such approach can be applied to silence miRNAs in other monocots as well