GRAS transcription factors regulate cell division planes in moss overriding the default rule.

Plant cells are surrounded by a cell wall and do not migrate, which makes the regulation of cell division orientation crucial for development. Regulatory mechanisms controlling cell division orientation may have contributed to the evolution of body organization in land plants. The GRAS family of transcription factors was transferred horizontally from soil bacteria to an algal common ancestor of land plants. SHORTROOT (SHR) and SCARECROW (SCR) genes in this family regulate formative periclinal cell divisions in the roots of flowering plants, but their roles in nonflowering plants and their evolution have not been studied in relation to body organization. Here, we show that SHR cell autonomously inhibits formative periclinal cell divisions indispensable for leaf vein formation in the moss Physcomitrium patens, and SHR expression is positively and negatively regulated by SCR and the GRAS member LATERAL SUPPRESSOR, respectively. While precursor cells of a leaf vein lacking SHR usually follow the geometry rule of dividing along the division plane with the minimum surface area, SHR overrides this rule and forces cells to divide nonpericlinally. Together, these results imply that these bacterially derived GRAS transcription factors were involved in the establishment of the genetic regulatory networks modulating cell division orientation in the common ancestor of land plants and were later adapted to function in flowering plant and moss lineages for their specific body organizations.

AT-hook motif nuclear localized transcription factors function redundantly in promoting root growth through modulation of redox homeostasis.

Maintaining an optimal redox status is essential for plant growth and development, particularly when the plants are under stress. AT-hook motif nuclear localized (AHL) proteins are evolutionarily conserved transcription factors in plants. Much of our understanding about this gene family has been derived from studies on clade A members. To elucidate the functions of clade B genes, we first analyzed their spatial expression patterns using transgenic plants expressing a nuclear localized GFP under the control of their promoter sequences. AHL1, 2, 6, 7, and 10 were further functionally characterized owing to their high expression in the root apical meristem. Through mutant analyses and transgenic studies, we showed that these genes have the ability to promote root growth. Using yeast one-hybrid and dual luciferase assays, we demonstrated that AHL1, 2, 6, 7, and 10 are transcription regulators and this activity is required for their roles in root growth. Although mutants for these genes did not showed obvious defects in root growth, transgenic plants expressing their fusion proteins with the SRDX repressor motif exhibited a short-root phenotype. Through transcriptome analysis, histochemical staining and molecular genetics experiments, we found that AHL10 maintains redox homeostasis via direct regulation of glutathione transferase (GST) genes. When the transcript level of GSTF2, a top-ranked target of AHL10, was reduced by RNAi, the short-root phenotype in the AHL10-SRDX expressing plant was largely rescued. These results together suggest that AHL genes function redundantly in promoting root growth through direct regulation of redox homeostasis.

Stem-cell-expressed DEVIL-like small peptides maintain root growth under abiotic stress via abscisic acid signaling.

Stem cells are essential to plant growth and development. Through data mining, we identified five DEVIL-like (DVL) small peptide genes that are preferentially expressed in the quiescent center of Arabidopsis (Arabidopsis thaliana) root but whose functions are unknown. When overexpressed, these genes caused a dramatic decrease in root length and pleiotropic phenotypes in the shoot. No root-growth defect was observed in the single-gene mutants, but the quintuple mutant exhibited slightly longer roots than the wild type (WT). Through transcriptome analysis with DVL20-overexpressing plants, we found that many genes involved in abscisic acid (ABA) signaling were regulated by these peptides. Consistent with this finding, we demonstrated that, relative to the WT, DVL20-overexpressing plants were more tolerant whereas the quintuple mutant was more sensitive to ABA. Using RT-qPCR, we showed that ABA signaling-associated genes were affected in an opposite manner when the plants were grown in normal or ABA-containing medium. Strikingly, ectopic expression of ABA signaling genes such as PYRABACTIN RESISTANCE 1-LIKE (PYL) 4, 5, or 6 or suppression of HIGHLY ABA-INDUCED 2 (HAI2) and MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 18 (MAPKKK18) not only largely rescued the root growth defects in DVL20-overexpressing plants in normal growth condition but also conferred tolerance to ABA. Based on these results, we propose that DVL1, 2, 5, 8 and 20 function redundantly in root stem-cell maintenance under abiotic stress, and this role is achieved via ABA signaling.

The PLETHORA Homolog in Marchantia polymorpha is Essential for Meristem Maintenance, Developmental Progression, and Redox Homeostasis.

To adapt to a terrestrial habitat, the ancestors of land plants must have made several morphological and physiological modifications, such as a meristem allowing for three-dimensional growth, rhizoids for water and nutrient uptake, air pore complexes or stomata that permit air exchange, and a defense system to cope with oxidative stress that occurs frequently in a terrestrial habitat. To understand how the meristem was determined during land plant evolution, we characterized the function of the closest PLETHORA homolog in the liverwort Marchantia polymorpha, which we named MpPLT. Through a transgenic approach, we showed that MpPLT is expressed not only in the stem cells at the apical notch but also in the proliferation zone of the meristem, as well as in cells that form the air-pore complex and rhizoids. Using the CRISPR method we then created mutants for MpPLT and found that the mutants are not only defective in meristem maintenance but also compromised in air-pore complex and rhizoid development. Strikingly, at later developmental stages, numerous gemma-like structures were formed in Mpplt mutants, suggesting developmental arrest. Further experiments indicated that MpPLT promotes plant growth by regulating MpWOX, which shared a similar expression pattern to MpPLT, and genes involved in auxin and cytokinin signaling pathways. Through transcriptome analyses, we found that MpPLT also has a role in redox homeostasis and that this role is essential for plant growth. Taken together, these results suggest that MpPLT has a crucial role in liverwort growth and development and hence may have played a crucial role in early land plant evolution.

SCARECROW maintains the stem cell niche in Arabidopsis roots by ensuring telomere integrity.

Stem cells are the ultimate source of cells for various tissues and organs and thus are essential for postembryonic plant growth and development. SCARECROW (SCR) is a plant-specific transcription regulator well known for its role in stem cell renewal in plant roots, but the mechanism by which SCR exerts this function remains unclear. To address this question, we carried out a genetic screen for mutants that no longer express SCR in the stem cell niche of Arabidopsis (Arabidopsis thaliana) roots and characterized 1 of these mutants. Molecular genetics methods allowed us to pinpoint the causal mutation in this mutant in TELOMERIC PATHWAYS IN ASSOCIATION WITH STN 1 (TEN1), encoding a factor that protects telomere ends. Interestingly, TEN1 expression was dramatically reduced in the scr mutant. Telomerase and STN1 and CONSERVED TELOMERE MAINTENANCE COMPONENT 1 (CTC1), components of the same protein complex as TEN1, were also dramatically downregulated in scr. Loss of STN1, CTC1, and telomerase caused defects in root stem cells. These results together suggest that SCR maintains root stem cells by promoting expression of genes that ensure genome integrity. Supporting this conclusion, we demonstrated that the scr mutant accumulates more DNA damage than wild-type Arabidopsis and that this problem is aggravated after exposure to zeocin, a DNA damage reagent. Finally, we identified 2 previously uncharacterized motifs in TEN1 and provide evidence that a conserved amino acid residue in 1 of the motifs is indispensable for TEN1 function. SCR thus provides a connection between genome integrity and stem cell maintenance in Arabidopsis roots.

Research on the anti-aging efficacy of fermented lysate VHProbi® MixA as the functional skincare ingredient.

AIMS: This study aimed to investigate the efficacy of a cream containing VHProbi® MixA for improving skin aging. METHODS AND RESULTS: In vitro studies demonstrated that the lysate produced from Lacticaseibacillus paracasei E12 (E12) exhibited immunoregulatory effects in a 3D skin model, with significant reductions in levels of interleukin (IL)-1α, IL-1ß, and IL-8 (P < 0.05) compared with the control group. In addition, the lysate of E12 mitigated the hydrogen peroxide-induced mortality of 3D skin cells and enhanced the transepithelial electrical resistance to show significant differences in comparison with control (P < 0.05), suggesting favorable antioxidant effects. The antioxidant capacity of the lysate of E12 was also confirmed using the Caenorhabditis elegans N2 model. C. elegans N2 fed the E12 strain showed a significantly higher % survival than those fed Escherichia coli OP50 (P < 0.05). Subsequently, VHProbi® MixA was formulated using the fermented lysates of E12, Lactiplantibacillus plantarum E15, and Limosilactobacillus reuteri E18. In a clinical study to ascertain if a cream containing VHProbi® MixA could improve the skin aging trends, participants were asked to use the investigational products for 60 days, and six indicators, transepidermal water loss (TEWL), hydration, elasticity, wrinkles, skin texture (roughness), and pores were measured at baseline and the endpoint of the study. A self-evaluation questionnaire analysis was also provided. TEWL, wrinkles, skin texture, and thickness of pores decreased significantly after treatment with the cream for 60 days (P < 0.01), whereas hydration and elasticity increased significantly (P < 0.01), in comparison to the baseline measurements. CONCLUSIONS: We hypothesize that the use of the cream containing VHProbi® MixA could be favorable for skin anti-aging management.

A mechanism coordinating root elongation, endodermal differentiation, redox homeostasis and stress response.

Root growth relies on both cell division and cell elongation, which occur in the meristem and elongation zones, respectively. SCARECROW (SCR) and SHORT-ROOT (SHR) are GRAS family genes essential for root growth and radial patterning in the Arabidopsis root. Previous studies showed that SCR and SHR promote root growth by suppressing cytokinin response in the meristem, but there is evidence that SCR expressed beyond the meristem is also required for root growth. Here we report a previously unknown role for SCR in promoting cell elongation. Consistent with this, we found that the scr mutant accumulated a higher level of reactive oxygen species (ROS) in the elongation zone, which is probably due to decreased expression of peroxidase gene 3, which consumes hydrogen peroxide in a reaction leading to Casparian strip formation. When the oxidative stress response was blocked in the scr mutant by mutation in ABSCISIC ACID 2 (ABA2) or when the redox status was ameliorated by the upbeat 1 (upb1) mutant, the root became significantly longer, with longer cells and a larger and more mitotically active meristem. Remarkably, however, the stem cell and radial patterning defects in the double mutants still persisted. Since ROS and peroxidases are essential for endodermal differentiation, these results suggest that SCR plays a role in coordinating cell elongation, endodermal differentiation, redox homeostasis and oxidative stress response in the root. We also provide evidence that this role of SCR is independent of SHR, even though they function similarly in other aspects of root growth and development.

Marinifilum caeruleilacunae sp. nov., isolated from Yongle Blue Hole in the South China Sea.

A Gram-stain-negative, non-motile, facultatively anaerobic and non-flagellated marine bacterium, designated JC070T was isolated from the Yongle Blue Hole in the South China Sea. The temperature, pH and NaCl ranges for growth of strain JC070T were 4-37 °C (optimum, 16 °C), pH 6.0-9.0 (optimum, pH 7.0) and 1.0 -6.0% (w/v; optimum, 3.0%). The predominant isoprenoid quinone of strain JC070T was identified as menaquinone-7. The dominant fatty acids (>10%) were iso-C15:0 (59.6%) and iso-C17:0 3-OH (17.2%). The major polar lipids were aminophospholipid, aminolipid, two unknown phospholipids and two unidentified lipids. The genomic DNA G+C content was determined to be 37.0 mol%. Based on the results of polyphasic analysis, a new species, named Marinifilum caeruleilacunae sp. nov., within the genus Marinifilum was proposed. The type strain is JC070T (= JCM 39045T=MCCC 1K03774T).

TGA factors promote plant root growth by modulating redox homeostasis or response.

To identify novel regulators of stem cell renewal, we mined an existing but little explored cell type-specific transcriptome dataset for the Arabidopsis root. A member of the TGA family of transcription factors, TGA8, was found to be specifically expressed in the quiescent center (QC). Mutation in TGA8 caused a subtle root growth phenotype, suggesting functional redundancy with other TGA members. Using a promoter::HGFP transgenic approach, we showed that all TGA factors were expressed in the root, albeit at different levels and with distinct spatial patterns. Mutant analyses revealed that all TGA factors examined contribute to root growth by promoting stem cell renewal, meristem activity, and cell elongation. Combining transcriptome analyses, histochemical assays, and physiological tests, we demonstrated that functional redundancy exists among members of clades II and V or those in clades I and III. These two groups of TGA factors act differently, however, as their mutants responded to oxidative stress differently and quantitative reverse transcription polymerase chain reaction assays showed they regulate different sets of genes that are involved in redox homeostasis. Our study has thus uncovered a previously unrecognized broad role and a mechanistic explanation for TGA factors in root growth and development.

Ancylomarina longa sp. nov., isolated from southern Okinawa Trough sediment and emended description of the family Marinifilaceae.

A Gram-stain-negative, obligately anaerobic, non-motile, non-spore-forming, long-rod-shaped and non-flagellated bacterial strain, designated T3-2 S1-CT, was isolated from a sediment sample collected at the Okinawa Trough. Phylogenetic analyses of 16S rRNA gene sequences and the whole genome revealed that strain T3-2 S1-CT was a member of the family Marinifilaceae and exhibited less than 95.1 % sequence similarities to the closely related type strains of the family Marinifilaceae. Optimal growth occurred at pH 7.0, 28 °C and in the presence of 3 % (w/v) NaCl. The isoprenoid quinone of strain T3-2 S1-CT was identified as menaquinone-7 (MK-7) and the predominant fatty acids (>10 %) were iso-C15 : 0 (38.9 %) and anteiso-C15 : 0 (11.6 %). The major polar lipids were one phosphatidylethanolamine, one phosphatidylmonomethylethanolamine, one aminolipids, two unidentified lipids and two unidentified phospholipids. The DNA G+C content of strain T3-2 S1-CT was 35.7 mol%. On the basis of the results of polyphasic analyses, strain T3-2 S1-CT is considered to represent a novel species of the genus Ancylomarina, for which the name Ancylomarina longa sp. nov. is proposed. The type strain is T3-2 S1-CT (=KCTC 15505T=MCCC 1K01617T).

Ancylomarina psychrotolerans sp. nov., isolated from sediments of Fildes Peninsula and emended the description of genus Ancylomarina.

A Gram-stain negative, obligately anaerobic, non-motile, asporogenous long rod-shaped and non-flagellated bacterial strain, designated 4SWWS2-6T, was isolated from sediment in the intertidal zone of Fildes Peninsula, Antarctica. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 4SWWS2-6T belongs to the genus Ancylomarina and showed high sequence similarity with Ancylomarina subtilis FA102T (96.5%). Optimal growth occurred at pH 6.5, 16 °C and in the presence of 3% (w/v) NaCl. Strain 4SWWS2-6T contained menaquinone-7 (MK-7) as the major respiratory quinone and held iso-C15:0, anteiso-C15:0 and iso-C15:0 3-OH as the major cellular fatty acids. The major polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, an aminolipid, two unidentified lipids and an unidentified phospholipid. The DNA G + C content of strain 4SWWS2-6T was 37.6 mol%. On the basis of the polyphasic analyses, strain 4SWWS2-6T is considered to represent a novel species in the genus Ancylomarina, for which the name Ancylomarina psychrotolerans sp. nov. is proposed. The type strain is 4SWWS2-6T (= KCTC 15504T = MCCC 1K01618T).

SCARECROW, SCR-LIKE 23 and SHORT-ROOT control bundle sheath cell fate and function in Arabidopsis thaliana.

Bundle sheath (BS) cells form a single cell layer surrounding the vascular tissue in leaves. In C3 plants, photosynthesis occurs in both the BS and mesophyll cells, but the BS cells are the major sites of photosynthesis in C4 plants, whereas the mesophyll cells are only involved in CO2 fixation. Because C4 plants are more efficient photosynthetically, introduction of the C4 mechanism into C3 plants is considered a key strategy to improve crop yield. One prerequisite for such C3-to-C4 engineering is the ability to manipulate the number and physiology of the BS cells, but the molecular basis of BS cell-fate specification remains unclear. Here we report that mutations in three GRAS family transcription factors, SHORT-ROOT (SHR), SCARECROW (SCR) and SCARECROW-LIKE 23 (SCL23), affect BS cell fate in Arabidopsis thaliana. SCR and SCL23 are expressed specifically in the BS cells and act redundantly in BS cell-fate specification, but their expression pattern and function diverge at later stages of leaf development. Using ChIP-chip experiments and sugar assays, we show that SCR is primarily involved in sugar transport whereas SCL23 functions in mineral transport. SHR is also essential for BS cell-fate specification, but it is expressed in the central vascular tissue. However, the SHR protein moves into the BS cells, where it directly regulates SCR and SCL23 expression. SHR, SCR and SCL23 homologs are present in many plant species, suggesting that this developmental pathway for BS cell-fate specification is likely to be evolutionarily conserved.

Probiotic potential of Lacticaseibacillus rhamnosus VHProbi M15 on sucralfate-induced constipation in mice.

The main objective of this study was to investigate the potential probiotic properties of Lacticaseibacillus rhamnosus VHProbi®M15 (M15). This study examined the effects of M15 on sucralfate-induced constipation in a mouse model. The BALB/c mice were randomly divided into four groups: the normal group (NOR) was without any treatment, while the constipation (CON), phenolphthalein (PHE), and probiotic (PRO) treatment groups were fed with sucralfate until the appearance of constipation symptoms. Afterward, the NOR and CON groups were given 1 ml saline orally every day until the end of the experiment; the PHE and PRO groups were given phenolphthalein or M15 suspension in 1 ml orally, respectively. Compared with the CON group, the fecal water content and intestinal peristalsis improved in the PRO group. Here, intake of M15 effectively attenuated sucralfate-induced constipation, recuperated colonic epithelial integrity, and increased serum levels of gastrointestinal excitatory neurotransmitters (motilin, gastrin, substance P). Analysis of the intestinal microbiota of mice by 16S rRNA metagenomic revealed an increase in the relative abundance of Bacteroides and a decrease in Sclerotinia, Verrucosa and Proteus in the PRO group. Compared with the CON group, the constipation-induced intestinal microecological changes were partially recovered in the PHE and PRO groups. These results demonstrate that M15 enhanced gastrointestinal transit and alleviated in mice with sucralfate-induced constipation.

SCARECROW has a SHORT-ROOT-independent role in modulating the sugar response.

Sugar is essential for all cellular activities, but at high levels it inhibits growth and development. How plants balance the tradeoffs between the need for sugars and their growth inhibitory effects is poorly understood. SHORT-ROOT (SHR) and SCARECROW (SCR) are key regulators of stem cell renewal and radial patterning in the root of Arabidopsis (Arabidopsis thaliana). Recently, we identified direct targets of SHR at the genome scale. Intriguingly, among the top-ranked list, we found a number of genes that are involved in stress responses. By chromatin immunoprecipitation-polymerase chain reaction (PCR), we showed that SHR and SCR regulate a similar but not identical set of stress response genes. Consistent with this, scr and shr were found to be hypersensitive to abscisic acid (ABA). We further showed that both mutants were hypersensitive to high levels of glucose (Glc) but responded normally to high salinity and osmoticum. The endogenous levels of sucrose, Glc, and fructose were also elevated in shr and scr. Intriguingly, although shr had sugar content and developmental defects similar to those of scr, it was much less sensitive to Glc. Chromatin immunoprecipitation-PCR and reverse transcription-PCR assays as well as transgenic studies with an ABA-INSENSITIVE2 (ABI4)-ß-glucuronidase reporter construct revealed that in root, SCR, but not SHR, repressed ABI4 and ABI5 directly and specifically in the apical meristem. When combined with abi4, scr became much more tolerant of high Glc. Finally, transgenic plants expressing ABI4 under the control of the SCR promoter manifested a short-root phenotype. These results together suggest that SCR has a SHR-independent role in mitigating the sugar response and that this role of SCR is important for root growth.

Complete Genome Sequence of Streptococcus thermophilus VHProbi R08, Isolated from Fermented Sour Porridge.

Streptococcus thermophilus VHProbi R08 is a bacterial strain isolated from fermented sour porridge in northern China. Here, we report the complete genome sequence of VHProbi R08, which comprises 1,848,461 bp, 1,906 protein-coding genes, 57 tRNA genes, and 15 rRNA genes.

Complete Genome Sequence of Lactobacillus helveticus VHProbi Y21, Isolated from Kimchi.

The probiotic strain Lactobacillus helveticus VHProbi Y21 confers beneficial effects in the prevention and treatment of acne. Here, we report the whole-genome sequence of this bacterium, which contains a chromosome and two plasmids, with a GC content of 37.52%.

Complete Genome Sequence of Lactobacillus bulgaricus VHProbi R03, a Potential Fermentation Strain Isolated from Fermented Milk.

The Lactobacillus bulgaricus strain VHProbi R03 is a novel starter culture that was isolated from naturally fermented milk. Whole-genome sequencing-based analysis is an ideal approach to elucidate the probiotic mechanism of action of this strain. Its genome contains a circular chromosome with 1,873,403 bp, and no plasmids exist in the genome.

Complete Genome Sequence of Lacticaseibacillus paracasei Strain VHProbi O44, Isolated from Feces from a Healthy Baby.

Lacticaseibacillus paracasei strain VHProbi O44 is a Chinese commercial lactic acid bacterium with several probiotic functions. The whole genome contains a chromosome and three plasmids.

Complete genome sequence of Lactiplantibacillus plantarum strain VHProbi P06, isolated from kimchi.

Lactiplantibacillus plantarum strain VHProbi P06 is a probiotic that was isolated from kimchi soup. Here, we investigate the whole-genome sequence of this strain, which contains a chromosome and seven plasmids.

Complete genome analysis of Lactiplantibacillus plantarum VHProbi P06, a novel probiotic that resists Streptococcus pneumoniae in the upper respiratory tract.

The purpose of this study was to screen lactic acid bacteria active against Streptococcus pneumoniae and to analyze the genetic basis of their probiotic functions from the genome. We isolated a novel Lactiplantibacillus plantarum VHProbi P06 from pickles, which showed strong antibacterial activity against S. pneumoniae, adhesion to 5-8F cells, and inhibition of S. pneumoniae colonization in the respiratory tract. Genome of VHProbi P06 was analyzed, we found one class II bacteriocin synthesis gene cluster. Genome of the strain contained 42 adhesion-related protein-coding genes, and implicated three exopolysaccharide biosynthesis gene clusters with low homologous to L. plantarum WCFS1. Moreover, VHProbi P06 possessed 3 intact phage regions and 117 Carbohydrate Active Enzyme genes. By comparing the genomes of five L. plantarum, 275 unique genes were found in VHProbi P06. Finally, the gene prediction was verified, the bacteriocin PlnJK produced by P06 was identified by LC-MS/MS, and the laminar exopolysaccharide with a weight-averaged molecular of 125.37 KDa was also found. This study provides a theoretical basis for the application of VHProbi P06 to the upper respiratory tract to resist pathogenic bacteria.